source: branches/alilink/EDIT4/ED4_root.cxx

Last change on this file was 18126, checked in by westram, 6 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(GLOBAL_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(GLOBAL_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        {
482            const char *err = ED4_ROOT->helix->init(GLOBAL_gb_main); // reload helix
483            aw_message_if(err);
484        }
485        {
486            const char *err = ED4_ROOT->ecoli_ref->init(GLOBAL_gb_main); // reload ecoli
487            aw_message_if(err);
488        }
489
490        if (ED4_ROOT->alignment_type == GB_AT_AA) {
491            // TODO: is this needed here?
492            const char *err = ED4_pfold_set_SAI(&ED4_ROOT->protstruct, GLOBAL_gb_main, ED4_ROOT->alignment_name, &ED4_ROOT->protstruct_len); // reload protstruct
493            aw_message_if(err);
494        }
495
496        if (was_increased) {
497            ED4_ROOT->main_manager->route_down_hierarchy(makeED4_route_cb(change_char_table_length, new_length)).expect_no_error();
498            ED4_ROOT->root_group_man->remap()->mark_compile_needed_force();
499        }
500    }
501}
502
503ARB_ERROR ED4_root::init_alignment() {
504    GB_transaction ta(GLOBAL_gb_main);
505
506    alignment_name = GBT_get_default_alignment(GLOBAL_gb_main);
507    alignment_type = GBT_get_alignment_type(GLOBAL_gb_main, alignment_name);
508    if (alignment_type==GB_AT_UNKNOWN) {
509        return GBS_global_string("You have to select a valid alignment before you can start ARB_EDIT4\n(%s)", GB_await_error());
510    }
511
512    GBDATA *gb_alignment = GBT_get_alignment(GLOBAL_gb_main, alignment_name);
513    if (!gb_alignment) {
514        return GBS_global_string("You can't edit without an existing alignment\n(%s)", GB_await_error());
515    }
516
517    GBDATA *gb_alignment_len = GB_search(gb_alignment, "alignment_len", GB_FIND);
518    int alignment_length = GB_read_int(gb_alignment_len);
519    MAXSEQUENCECHARACTERLENGTH = alignment_length;
520
521    GB_add_callback(gb_alignment_len, GB_CB_CHANGED, makeDatabaseCallback(ED4_alignment_length_changed));
522
523    aw_root->awar_string(AWAR_EDITOR_ALIGNMENT, alignment_name);
524
525    return NULp;
526}
527
528void ED4_root::recalc_font_group() {
529    int font_GC[] = {
530        ED4_G_SEQUENCES,
531        ED4_G_STANDARD,
532        ED4_G_FLAG_INFO,
533    };
534
535    font_group.unregisterAll();
536    for (unsigned i = 0; i<ARRAY_ELEMS(font_GC); ++i) {
537        ED4_MostRecentWinContext context;
538        font_group.registerFont(current_device(), font_GC[i]);
539    }
540}
541
542static ARB_ERROR force_group_update(ED4_base *base) {
543    if (base->is_multi_species_manager()) {
544        base->to_multi_species_manager()->update_requested_by_child();
545    }
546    return NULp;
547}
548
549ED4_returncode ED4_root::create_hierarchy(const char *area_string_middle, const char *area_string_top) {
550    // creates internal hierarchy of editor
551
552    long total_no_of_groups  = 0;
553    long total_no_of_species = 0;
554    {
555        // count species and related info (e.g. helix) displayed in the top region (a == 0)
556        // count no of species and sais including groups in middle region (a == 1)
557
558        const char *area_string[2] = { area_string_top, area_string_middle };
559        for (int a = 0; a<2; ++a) {
560            long group_count;
561            long species_count;
562            database->calc_no_of_all(area_string[a], &group_count, &species_count);
563
564            total_no_of_groups  += group_count;
565            total_no_of_species += species_count;
566        }
567    }
568
569    SmartPtr<arb_progress> startup_progress = new arb_progress("EDIT4 startup");
570
571    GB_push_transaction(GLOBAL_gb_main);
572
573    ecoli_ref = new BI_ecoli_ref;
574    ecoli_ref->init(GLOBAL_gb_main);
575
576    // [former position of ali-init-code]
577
578    main_manager   = new ED4_main_manager("Main_Manager", 0, 0, NULp); // build a test hierarchy
579    root_group_man = new ED4_root_group_manager("Root_Group_Manager", 0, 0, main_manager);
580   
581    main_manager->append_member(root_group_man);
582
583    ED4_device_manager *device_manager = new ED4_device_manager("Device_Manager", 0, 0, root_group_man);
584    root_group_man->append_member(device_manager);
585
586    {
587        int col_stat_term_height = 50; // @@@ Hoehe des ColumnStatistics Terminals ausrechnen
588
589        ref_terminals.init(
590            new ED4_sequence_info_terminal("Reference_Sequence_Info_Terminal",         MAXINFO_WIDTH, TERMINAL_HEIGHT,       NULp),
591            new ED4_sequence_terminal     ("Reference_Sequence_Terminal",              300,           TERMINAL_HEIGHT,       NULp, false),
592            new ED4_sequence_info_terminal("Reference_ColumnStatistics_Info_Terminal", MAXINFO_WIDTH, col_stat_term_height, NULp),
593            new ED4_columnStat_terminal   ("Reference_ColumnStatistics_Terminal",      300,           col_stat_term_height, NULp)
594            );
595    }
596
597    {
598        arb_progress species_progress("Loading species", total_no_of_species);
599
600        // ********** Top Area beginning **********
601
602        ED4_multi_species_manager *top_multi_species_manager;
603        ED4_spacer_terminal       *top_spacer_terminal;
604        ED4_spacer_terminal       *top_mid_spacer_terminal;
605        ED4_spacer_terminal       *top_multi_spacer_terminal_beg;
606        ED4_line_terminal         *top_mid_line_terminal;
607        {
608            ED4_area_manager *top_area_manager = new ED4_area_manager("Top_Area_Manager", 0, 0, device_manager);
609            device_manager->append_member(top_area_manager);
610            top_area_man = top_area_manager;
611
612            top_spacer_terminal = new ED4_spacer_terminal("Top_Spacer", false, 100, 10, top_area_manager);
613            top_area_manager->append_member(top_spacer_terminal);
614
615            top_multi_species_manager = new ED4_multi_species_manager("Top_MultiSpecies_Manager", 0, 0, top_area_manager);
616            top_area_manager->append_member(top_multi_species_manager);
617
618            top_multi_spacer_terminal_beg = new ED4_spacer_terminal("Top_Left_Spacer", false, 0, 3, top_multi_species_manager);
619            top_multi_species_manager->append_member(top_multi_spacer_terminal_beg);
620
621            reference = new ED4_reference(GLOBAL_gb_main);
622
623            int index = 0;
624            database->scan_string(top_multi_species_manager, ref_terminals, area_string_top, &index, species_progress);
625            GB_pop_transaction(GLOBAL_gb_main);
626
627            const int TOP_MID_LINE_HEIGHT   = 3;
628            int       TOP_MID_SPACER_HEIGHT = font_group.get_max_height()-TOP_MID_LINE_HEIGHT;
629
630            top_mid_line_terminal = new ED4_line_terminal("Top_Mid_Line_Terminal", 0, TOP_MID_LINE_HEIGHT, device_manager);    // width will be set below
631            device_manager->append_member(top_mid_line_terminal);
632
633            top_mid_spacer_terminal = new ED4_spacer_terminal("Top_Middle_Spacer", true, 880, TOP_MID_SPACER_HEIGHT, device_manager);
634            device_manager->append_member(top_mid_spacer_terminal);
635
636            // needed to avoid text-clipping problems:
637            main_manager->set_top_middle_spacer_terminal(top_mid_spacer_terminal);
638            main_manager->set_top_middle_line_terminal(top_mid_line_terminal);
639        }
640
641        // ********** Middle Area beginning **********
642
643        ED4_area_manager          *middle_area_manager;
644        ED4_tree_terminal         *tree_terminal;
645        ED4_multi_species_manager *mid_multi_species_manager;
646        ED4_spacer_terminal       *mid_multi_spacer_terminal_beg;
647        ED4_line_terminal         *mid_bot_line_terminal;
648        ED4_spacer_terminal       *total_bottom_spacer;
649        {
650            middle_area_manager = new ED4_area_manager("Middle_Area_Manager", 0, 0, device_manager);
651            device_manager->append_member(middle_area_manager);
652            middle_area_man = middle_area_manager;
653
654            tree_terminal = new ED4_tree_terminal("Tree", 2, 0, middle_area_manager);
655            middle_area_manager->append_member(tree_terminal);
656
657            mid_multi_species_manager = new ED4_multi_species_manager("Middle_MultiSpecies_Manager", 0, 0, middle_area_manager);
658            middle_area_manager->append_member(mid_multi_species_manager);
659
660            mid_multi_spacer_terminal_beg = new ED4_spacer_terminal("Mid_Multi_Spacer_Terminal_Beg", false, 0, 3, mid_multi_species_manager);
661            mid_multi_species_manager->append_member(mid_multi_spacer_terminal_beg);
662
663            scroll_links.link_for_ver_slider = middle_area_manager;
664
665            {
666                GB_transaction ta(GLOBAL_gb_main);
667                int index  = 0;
668                database->scan_string(mid_multi_species_manager, ref_terminals, area_string_middle, &index, species_progress);
669            }
670
671            {
672                ED4_spacer_terminal *mid_bot_spacer_terminal = new ED4_spacer_terminal("Middle_Bot_Spacer_Terminal", false, 880, 10, device_manager);
673                device_manager->append_member(mid_bot_spacer_terminal);
674            }
675
676            mid_bot_line_terminal = new ED4_line_terminal("Mid_Bot_Line_Terminal", 0, 3, device_manager);    // width will be set below
677            device_manager->append_member(mid_bot_line_terminal);
678
679            total_bottom_spacer = new ED4_spacer_terminal("Total_Bottom_Spacer_terminal", false, 0, 10000, device_manager);
680            total_bottom_spacer->clr_property(PROP_DYNA_RESIZE);
681            device_manager->append_member(total_bottom_spacer);
682        }
683
684        if (scroll_links.link_for_hor_slider) {
685            const long ext_width    = long(scroll_links.link_for_hor_slider->extension.size[WIDTH]);
686            const long spacer_width = ext_width + MAXNAME_WIDTH + SEQUENCE_INFO_WIDTH;
687            const long line_width   = spacer_width + TREE_TERMINAL_WIDTH;
688
689            top_multi_spacer_terminal_beg->extension.size[WIDTH] = spacer_width;
690            mid_multi_spacer_terminal_beg->extension.size[WIDTH] = spacer_width;
691            total_bottom_spacer->extension.size[WIDTH]           = spacer_width;
692
693            top_mid_line_terminal->extension.size[WIDTH] = line_width;
694            mid_bot_line_terminal->extension.size[WIDTH] = line_width;
695
696        }
697
698        tree_terminal->set_links(NULp, mid_multi_species_manager);                          // set links
699        top_spacer_terminal->set_links(tree_terminal, top_multi_species_manager);
700        top_mid_spacer_terminal->set_links(middle_area_manager, NULp);
701        total_bottom_spacer->set_links(mid_bot_line_terminal, NULp);
702
703        species_progress.done();
704    }
705
706    first_window->update_window_coords();
707    resize_all_requesting_childs();
708
709    main_manager->route_down_hierarchy(makeED4_route_cb(force_group_update)).expect_no_error();
710
711    if (!scroll_links.link_for_hor_slider) { // happens when no species AND no SAI has data
712        startup_progress->done();
713        startup_progress.setNull(); // make progress disappear (otherwise prompter below is often behind progress window)
714        GB_pop_transaction(GLOBAL_gb_main);
715       
716        aw_popup_ok(GBS_global_string("No species/SAI contains data in '%s'\nARB_EDIT4 will terminate", alignment_name));
717        ED4_exit();
718    }
719
720    // build consensi
721    {
722        arb_progress consensi_progress("Initializing consensi", total_no_of_species+total_no_of_groups+1); // 1 is root_group_man
723
724        root_group_man->create_consensus(root_group_man, &consensi_progress);
725        e4_assert(root_group_man->table().ok());
726        consensi_progress.done(); // if there is a "top"-group, progress increment is one to low
727    }
728
729    root_group_man->remap()->mark_compile_needed_force();
730    root_group_man->update_remap();
731
732    // calc size and display:
733
734    resize_all_requesting_childs();
735
736    e4_assert(main_manager);
737
738    {
739        ED4_base *x_link      = scroll_links.link_for_hor_slider;
740        ED4_base *y_link      = scroll_links.link_for_ver_slider;
741        ED4_base *width_link  = x_link;
742        ED4_base *height_link = y_link;
743
744        ED4_window *win = first_window;
745        while (win) {
746            win->set_scrolled_rectangle(x_link, y_link, width_link, height_link);
747            win->aww->show();
748            win->update_scrolled_rectangle();
749            win = win->next;
750        }
751    }
752
753    ED4_request_relayout();
754    ED4_finish_and_show_notFoundMessage();
755
756#if defined(DEBUG) && 0
757    // dump created hierarchy:
758    puts("---------------------------------------- [main_manager dump start]");
759    main_manager->dump(1);
760    puts("---------------------------------------- [main_manager dump end]");
761#endif
762
763    return ED4_R_OK;
764}
765
766ED4_returncode ED4_root::get_area_rectangle(AW_screen_area *rect, AW_pos x, AW_pos y) {
767    // returns win-coordinates of area (defined by folding lines) which contains position x/y
768    int                    x1, x2, y1, y2;
769    const AW_screen_area&  area_rect = current_device()->get_area_size();
770
771    x1 = area_rect.l;
772    for (const ED4_folding_line *flv=current_ed4w()->get_vertical_folding(); ; flv = flv->get_next()) {
773        if (flv) {
774            x2 = int(flv->get_pos()); // @@@ use AW_INT ?
775        }
776        else {
777            x2 = area_rect.r;
778            if (x1==x2) {
779                break;
780            }
781        }
782
783        y1 = area_rect.t;
784        for (const ED4_folding_line *flh=current_ed4w()->get_horizontal_folding(); ; flh = flh->get_next()) {
785            if (flh) {
786                y2 = int(flh->get_pos()); // @@@ use AW_INT ?
787            }
788            else {
789                y2 = area_rect.b;
790                if (y1==y2) {
791                    break;
792                }
793            }
794
795            if (x1<=x && x<=x2 && y1<=y && y<=y2) {
796                rect->t = y1;
797                rect->b = y2;
798                rect->l = x1;
799                rect->r = x2;
800                return ED4_R_OK;
801            }
802            y1 = y2;
803            if (!flh) break;
804        }
805        x1 = x2;
806        if (!flv) break;
807    }
808    return ED4_R_IMPOSSIBLE; // no area contains x/y :-(
809}
810
811void ED4_root::copy_window_struct(ED4_window *source, ED4_window *destination) {
812    destination->slider_pos_horizontal  = source->slider_pos_horizontal;
813    destination->slider_pos_vertical    = source->slider_pos_vertical;
814    destination->coords         = source->coords;
815}
816
817
818static void reload_helix_cb() { 
819    const char *err = ED4_ROOT->helix->init(GLOBAL_gb_main);
820    if (err) aw_message(err);
821    ED4_request_full_refresh();
822}
823
824
825static void reload_ecoli_cb() {
826    const char *err = ED4_ROOT->ecoli_ref->init(GLOBAL_gb_main);
827    if (err) aw_message(err);
828    ED4_request_full_refresh();
829}
830
831// ---------------------------------------
832//      recursion through all species
833
834DECLARE_CBTYPE_FVV_AND_BUILDERS(ED4_Species_Callback, ARB_ERROR, GBDATA *); // generates makeED4_Species_Callback
835
836static ARB_ERROR do_sth_with_species(ED4_base *base, const ED4_Species_Callback *cb) {
837    ARB_ERROR error = NULp;
838
839    if (base->is_species_manager()) {
840        ED4_species_manager       *species_manager       = base->to_species_manager();
841        ED4_species_name_terminal *species_name_terminal = species_manager->search_spec_child_rek(LEV_SPECIES_NAME)->to_species_name_terminal();
842
843        if (species_name_terminal->get_species_pointer()) {
844            char *species_name = GB_read_as_string(species_name_terminal->get_species_pointer());
845
846            e4_assert(species_name);
847            GBDATA *species = GBT_find_species(GLOBAL_gb_main, species_name);
848
849            error = species
850                ? (*cb)(species)
851                : GB_append_exportedError(GBS_global_string("can't find species '%s'", species_name));
852
853            free(species_name);
854        }
855    }
856
857    return error;
858}
859
860
861static ARB_ERROR ED4_with_all_loaded_species(const ED4_Species_Callback& cb) {
862    return ED4_ROOT->root_group_man->route_down_hierarchy(makeED4_route_cb(do_sth_with_species, &cb));
863}
864
865static bool is_named(ED4_base *base, const char *wanted_name) {
866    ED4_species_name_terminal *name_term = base->to_species_name_terminal();
867    GBDATA                    *gbd       = name_term->get_species_pointer();
868    if (gbd) {
869        const char *name = GB_read_char_pntr(gbd);
870        e4_assert(name);
871
872        return strcmp(name, wanted_name) == 0;
873    }
874    return false;
875}
876
877static bool is_species_named(ED4_base *base, const char *species_name) {
878    return base->inside_species_seq_manager() && is_named(base, species_name);
879}
880
881static bool is_SAI_named(ED4_base *base, const char *sai_name) {
882    return base->inside_SAI_manager() && is_named(base, sai_name);
883}
884
885ED4_species_name_terminal *ED4_find_species_or_SAI_name_terminal(const char *species_name) {
886    ED4_base *base = ED4_ROOT->root_group_man->find_first_that(LEV_SPECIES_NAME, makeED4_basePredicate(is_species_named, species_name));
887    return base ? base->to_species_name_terminal() : NULp;
888}
889ED4_species_name_terminal *ED4_find_species_name_terminal(const char *species_name) {
890    ED4_base *base = ED4_ROOT->root_group_man->find_first_that(LEV_SPECIES_NAME, makeED4_basePredicate(is_species_named, species_name));
891    return base ? base->to_species_name_terminal() : NULp;
892}
893ED4_species_name_terminal *ED4_find_SAI_name_terminal(const char *sai_name) {
894    ED4_base *base = ED4_ROOT->root_group_man->find_first_that(LEV_SPECIES_NAME, makeED4_basePredicate(is_SAI_named, sai_name));
895    return base ? base->to_species_name_terminal() : NULp;
896}
897
898static char *get_group_consensus(const char *species_name, PosRange range) {
899    ED4_species_name_terminal *name_term = ED4_find_species_name_terminal(species_name);
900    char *consensus = NULp;
901
902    if (name_term) {
903        ED4_abstract_group_manager *group_man = name_term->get_parent(ED4_level(LEV_GROUP|LEV_ROOTGROUP))->to_abstract_group_manager();
904        if (group_man) {
905            consensus = group_man->build_consensus_string(range);
906        }
907    }
908
909    return consensus;
910}
911
912static bool get_selected_range(PosRange& range) {
913    ED4_selected_elem *listElem = ED4_ROOT->selected_objects->head();
914    if (listElem) {
915        ED4_sequence_terminal *seqTerm = listElem->elem()->object->corresponding_sequence_terminal();
916        return ED4_get_selected_range(seqTerm, range);
917    }
918    return false;
919}
920
921static ED4_selected_elem *curr_aligner_elem = NULp;
922
923static GBDATA *get_next_selected_species() {
924    if (!curr_aligner_elem) return NULp;
925
926    ED4_species_manager *specMan = curr_aligner_elem->elem()->object->containing_species_manager();
927    curr_aligner_elem = curr_aligner_elem->next();
928    return specMan->get_species_pointer();
929}
930
931static GBDATA *get_first_selected_species(int *total_no_of_selected_species) {
932    int selected = ED4_ROOT->selected_objects->size();
933
934    if (total_no_of_selected_species) {
935        *total_no_of_selected_species = selected;
936    }
937
938    if (selected) {
939        curr_aligner_elem = ED4_ROOT->selected_objects->head();
940    }
941    else {
942        curr_aligner_elem = NULp;
943    }
944
945    return get_next_selected_species();
946}
947
948static ARB_ERROR ED4_delete_temp_entries(GBDATA *species, GB_CSTR alignment_name) {
949    return FastAligner_delete_temp_entries(species, alignment_name);
950}
951
952static void ED4_remove_faligner_entries() {
953    ARB_ERROR error = GB_begin_transaction(GLOBAL_gb_main);
954    if (!error) error = ED4_with_all_loaded_species(makeED4_Species_Callback(ED4_delete_temp_entries, ED4_ROOT->alignment_name));
955    GB_end_transaction_show_error(GLOBAL_gb_main, error, aw_message);
956}
957
958static void toggle_helix_for_SAI(AW_window *aww) {
959    ED4_LocalWinContext  uses(aww);
960    ED4_cursor          *cursor = &current_cursor();
961
962    if (cursor->in_SAI_terminal()) {
963        ED4_sequence_terminal      *sai_term      = cursor->owner_of_cursor->to_sequence_terminal();
964        ED4_sequence_info_terminal *sai_info_term = sai_term->parent->search_spec_child_rek(LEV_SEQUENCE_INFO)->to_sequence_info_terminal();
965
966        GBDATA         *gb_sai_data = sai_info_term->data();
967        GB_transaction  ta(gb_sai_data);
968
969        GBDATA *gb_sai      = GB_get_grandfather(gb_sai_data);
970        GBDATA *gb_disp_sec = GB_searchOrCreate_int(gb_sai, "showsec", 0);
971
972        bool show_sec = 1-bool(GB_read_int(gb_disp_sec));
973        GB_ERROR error = GB_write_int(gb_disp_sec, show_sec);
974        if (!error) {
975            sai_term->set_secstruct_display(show_sec);
976            sai_term->request_refresh();
977        }
978        if (error) aw_message(error);
979    }
980    else {
981        aw_message("Please select an SAI");
982    }
983}
984
985static void title_mode_changed(AW_root *aw_root, AW_window *aww) {
986    int title_mode = aw_root->awar(AWAR_EDIT_TITLE_MODE)->read_int();
987
988    if (title_mode==0) {
989        aww->set_info_area_height(57);
990    }
991    else {
992        aww->set_info_area_height(170);
993    }
994}
995
996static void ED4_undo_redo(AW_window *aww, GB_UNDO_TYPE undo_type) {
997    ED4_LocalWinContext uses(aww);
998    GB_ERROR error = GB_undo(GLOBAL_gb_main, undo_type);
999
1000    if (error) {
1001        aw_message(error);
1002    }
1003    else {
1004        GB_begin_transaction(GLOBAL_gb_main);
1005        GB_commit_transaction(GLOBAL_gb_main);
1006        ED4_cursor *cursor = &current_cursor();
1007        if (cursor->owner_of_cursor) cursor->owner_of_cursor->request_refresh();
1008    }
1009}
1010
1011static AW_window *ED4_zoom_message_window(AW_root *root) {
1012    AW_window_simple *aws = new AW_window_simple;
1013
1014    aws->init(root, "ZOOM_ERR_MSG", "Errors and warnings");
1015    aws->load_xfig("edit4/message.fig");
1016
1017    aws->callback(AW_POPDOWN);
1018    aws->at("hide");
1019    aws->create_button("HIDE", "HIDE");
1020
1021    aws->callback(aw_clear_message_cb);
1022    aws->at("clear");
1023    aws->create_button("CLEAR", "CLEAR");
1024
1025    aws->at("errortext");
1026    aws->create_text_field(AWAR_ERROR_MESSAGES);
1027
1028    return aws;
1029}
1030
1031
1032static char *cat(char *toBuf, const char *s1, const char *s2) {
1033    char *buf = toBuf;
1034
1035    while ((*buf++=*s1++)!=0) ;
1036    buf--;
1037    while ((*buf++=*s2++)!=0) ;
1038
1039    return toBuf;
1040}
1041
1042static void insert_search_fields(AW_window_menu_modes *awmm,
1043                                 const char *label_prefix, const char *macro_prefix,
1044                                 const char *pattern_awar_name, const char *show_awar_name,
1045                                 int short_form, ED4_SearchPositionType type, ED4_window *ed4w)
1046{
1047    char buf[200];
1048
1049    if (!short_form) {
1050        awmm->at(cat(buf, label_prefix, "search"));
1051        awmm->create_input_field(pattern_awar_name, 30);
1052    }
1053
1054    awmm->at(cat(buf, label_prefix, "n"));
1055    awmm->help_text("e4_search.hlp");
1056    awmm->callback(makeWindowCallback(ED4_search_cb, ED4_encodeSearchDescriptor(+1, type), ed4w));
1057    awmm->create_button(cat(buf, macro_prefix, "_SEARCH_NEXT"), "#edit/next.xpm");
1058
1059    awmm->at(cat(buf, label_prefix, "l"));
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_LAST"), "#edit/last.xpm");
1063
1064    awmm->at(cat(buf, label_prefix, "d"));
1065    awmm->help_text("e4_search.hlp");
1066    awmm->callback(makeWindowCallback(ED4_popup_search_window, type));
1067    awmm->create_button(cat(buf, macro_prefix, "_SEARCH_DETAIL"), "#edit/detail.xpm");
1068
1069    awmm->at(cat(buf, label_prefix, "s"));
1070    awmm->create_toggle(show_awar_name);
1071}
1072
1073static void ED4_set_protection(AW_window *aww, int wanted_protection) {
1074    ED4_LocalWinContext uses(aww);
1075    ED4_cursor *cursor = &current_cursor();
1076    GB_ERROR    error  = NULp;
1077
1078    if (cursor->owner_of_cursor) {
1079        ED4_sequence_terminal      *seq_term      = cursor->owner_of_cursor->to_sequence_terminal();
1080        ED4_sequence_info_terminal *seq_info_term = seq_term->parent->search_spec_child_rek(LEV_SEQUENCE_INFO)->to_sequence_info_terminal();
1081        GBDATA                     *gbd           = seq_info_term->data();
1082
1083        GB_transaction      ta(gbd);
1084        GB_topSecurityLevel unsecured(gbd);
1085
1086        error = GB_write_security_write(gbd, wanted_protection);
1087        error = ta.close(error);
1088    }
1089    else {
1090        error = "No species selected";
1091    }
1092
1093    if (error) aw_message(error);
1094}
1095
1096enum MenuSelectType { // @@@ rename -> MenuHighlightType
1097    ED4_MS_NONE,
1098    ED4_MS_ALL,
1099    ED4_MS_INVERT,
1100    ED4_MS_INVERT_GROUP,
1101    ED4_MS_UNMARK_ALL,
1102    ED4_MS_MARK_SELECTED,
1103    ED4_MS_UNMARK_SELECTED,
1104    ED4_MS_SELECT_MARKED,
1105    ED4_MS_DESELECT_MARKED,
1106    ED4_MS_TOGGLE_BLOCKTYPE
1107};
1108
1109static void ED4_menu_highlight(AW_window *aww, MenuSelectType select) { // @@@ rename select -> hilight
1110    GB_transaction             ta(GLOBAL_gb_main);
1111    ED4_multi_species_manager *middle_multi_man = ED4_ROOT->middle_area_man->get_multi_species_manager();
1112
1113    e4_assert(middle_multi_man);
1114
1115    switch (select) {
1116        case ED4_MS_NONE: {
1117            if (ED4_getBlocktype()!=ED4_BT_NOBLOCK) {
1118                ED4_ROOT->deselect_all();
1119            }
1120            break;
1121        }
1122        case ED4_MS_ALL: {
1123            middle_multi_man->select_all(true); // only species
1124            ED4_correctBlocktypeAfterSelection();
1125            break;
1126        }
1127        case ED4_MS_INVERT: {
1128            middle_multi_man->invert_selection_of_all_species();
1129            ED4_correctBlocktypeAfterSelection();
1130            break;
1131        }
1132        case ED4_MS_SELECT_MARKED: {
1133            middle_multi_man->marked_species_select(true);
1134            ED4_correctBlocktypeAfterSelection();
1135            break;
1136        }
1137        case ED4_MS_DESELECT_MARKED: {
1138            middle_multi_man->marked_species_select(false);
1139            ED4_correctBlocktypeAfterSelection();
1140            break;
1141        }
1142        case ED4_MS_UNMARK_ALL: {
1143            GBT_mark_all(GLOBAL_gb_main, 0);
1144            break;
1145        }
1146        case ED4_MS_MARK_SELECTED: {
1147            middle_multi_man->selected_species_mark(true);
1148            ED4_correctBlocktypeAfterSelection();
1149            break;
1150        }
1151        case ED4_MS_UNMARK_SELECTED: {
1152            middle_multi_man->selected_species_mark(false);
1153            ED4_correctBlocktypeAfterSelection();
1154            break;
1155        }
1156        case ED4_MS_INVERT_GROUP: {
1157            ED4_cursor *cursor = &ED4_ROOT->first_window->get_matching_ed4w(aww)->cursor;
1158            int done = 0;
1159
1160            if (cursor->owner_of_cursor) {
1161                ED4_multi_species_manager *multi_man = cursor->owner_of_cursor->get_parent(LEV_MULTI_SPECIES)->to_multi_species_manager();
1162
1163                multi_man->invert_selection_of_all_species();
1164                ED4_correctBlocktypeAfterSelection();
1165                done = 1;
1166            }
1167
1168            if (!done) {
1169                aw_message("Place cursor into group");
1170            }
1171            break;
1172        }
1173        case ED4_MS_TOGGLE_BLOCKTYPE: {
1174            ED4_toggle_block_type();
1175            break;
1176        }
1177        default: {
1178            e4_assert(0);
1179            break;
1180        }
1181    }
1182
1183    ED4_request_full_refresh();
1184}
1185
1186static void ED4_menu_perform_block_operation(AW_window *, ED4_blockoperation_type type) {
1187    ED4_perform_block_operation(type);
1188}
1189
1190static void modes_cb(AW_window*, ED4_species_mode smode) {
1191    ED4_ROOT->species_mode = smode;
1192    for (ED4_window *win = ED4_ROOT->first_window; win; win = win->next) {
1193        win->aww->select_mode(smode);
1194    }
1195    if (smode == ED4_SM_INFO) {
1196        AWT_trigger_remote_action(NULp, GLOBAL_gb_main, "ARB_NT:species_info");
1197    }
1198}
1199
1200void ED4_no_dangerous_modes() {
1201    if (ED4_ROOT->species_mode == ED4_SM_KILL) {
1202        modes_cb(NULp, ED4_SM_MOVE);
1203    }
1204}
1205
1206static char *get_helix_string(GBDATA *gb_main, const char *alignment_name) {
1207    GB_transaction ta(gb_main);
1208
1209    char   *helix_string = NULp;
1210    char   *helix_name   = GBT_get_default_helix(gb_main);
1211    GBDATA *gb_helix_con = GBT_find_SAI(gb_main, helix_name);
1212    if (gb_helix_con) {
1213        GBDATA *gb_helix = GBT_find_sequence(gb_helix_con, alignment_name);
1214        if (gb_helix) helix_string = GB_read_string(gb_helix);
1215    }
1216    free(helix_name);
1217
1218    return helix_string;
1219}
1220
1221const AlignDataAccess *ED4_get_aligner_data_access() {
1222    static SmartPtr<AlignDataAccess> aliDataAccess;
1223
1224    if (aliDataAccess.isNull()) {
1225        aliDataAccess = new AlignDataAccess(GLOBAL_gb_main,
1226                                            ED4_ROOT->alignment_name,
1227                                            true, ED4_trigger_instant_refresh, // perform refresh
1228                                            get_group_consensus,               // aligner fetches consensus of group of species via this function
1229                                            get_selected_range,                // aligner fetches column range of selection via this function
1230                                            get_first_selected_species,        // aligner fetches first and..
1231                                            get_next_selected_species,         // .. following selected species via these functions
1232                                            get_helix_string);                 // used by island_hopping (if configured to use sec-structure)
1233    }
1234
1235    return aliDataAccess.content();
1236}
1237
1238static AW_window *ED4_create_faligner_window(AW_root *awr, const AlignDataAccess *data_access) {
1239#if defined(DEBUG)
1240    static const AlignDataAccess *last_data_access = NULp;
1241
1242    e4_assert(!last_data_access || (last_data_access == data_access)); // there shall be only one AlignDataAccess
1243    last_data_access = data_access;
1244#endif
1245
1246    static AW_window *aws = NULp;
1247    if (!aws) aws = FastAligner_create_window(awr, data_access);
1248    return aws;
1249}
1250
1251static void ED4_save_properties(AW_window *aw, int mode) {
1252    AW_save_specific_properties(aw, ED4_propertyName(mode));
1253}
1254
1255void ED4_popup_gc_window(AW_window *awp, AW_gc_manager *gcman) {
1256    typedef std::map<AW_gc_manager*, AW_window*> gcwin;
1257    static gcwin win;
1258
1259    gcwin::iterator found = win.find(gcman);
1260
1261    AW_window *aww = NULp;
1262    if (found == win.end()) {
1263        aww        = AW_create_gc_window(awp->get_root(), gcman);
1264        win[gcman] = aww;
1265    }
1266    else {
1267        aww = win[gcman];
1268    }
1269    aww->activate();
1270}
1271
1272static void gc_change_cb(GcChange whatChanged) {
1273    if (whatChanged == GC_FONT_CHANGED) {
1274        ED4_resize_all_extensions();
1275    }
1276    ED4_request_full_instant_refresh();
1277}
1278
1279ED4_returncode ED4_root::generate_window(AW_device **device, ED4_window **new_window) {
1280    {
1281        ED4_window *ed4w = first_window;
1282
1283        while (ed4w) { // before creating a window look for a hidden window
1284            if (ed4w->is_hidden) {
1285                ed4w->aww->show();
1286                ed4w->is_hidden = false;
1287                return ED4_R_BREAK;
1288            }
1289            ed4w = ed4w->next;
1290        }
1291    }
1292
1293    if (ED4_window::no_of_windows == MAXWINDOWS) { // no more than 5 windows allowed
1294        aw_message(GBS_global_string("Restricted to %i windows", MAXWINDOWS));
1295        return ED4_R_BREAK;
1296    }
1297
1298    AW_window_menu_modes *awmm = new AW_window_menu_modes;
1299    {
1300        int   winNum   = ED4_window::no_of_windows+1;
1301        char *winName  = winNum>1 ? GBS_global_string_copy("ARB_EDIT4_%i", winNum) : ARB_strdup("ARB_EDIT4");
1302        char *winTitle = GBS_global_string_copy("ARB_EDIT4 *%d* [%s]", winNum, alignment_name);
1303
1304        awmm->init(aw_root, winName, winTitle, 800, 450);
1305
1306        free(winTitle);
1307        free(winName);
1308    }
1309
1310    *device     = awmm->get_device(AW_MIDDLE_AREA); // points to Middle Area device
1311    *new_window = ED4_window::insert_window(awmm);   // append to window list
1312
1313    e4_assert(ED4_window::no_of_windows >= 1);
1314    bool clone = ED4_window::no_of_windows>1;
1315    if (!clone) {                                   // this is the first window
1316        AW_init_color_group_defaults("arb_edit4");
1317    }
1318    else { // additional edit windows
1319        copy_window_struct(first_window, *new_window);
1320    }
1321
1322    ED4_LocalWinContext uses(*new_window);
1323
1324    // each window has its own gc-manager
1325    gc_manager = AW_manage_GC(awmm,
1326                              "ARB_EDIT4",                   // but all gc-managers use the same colors
1327                              *device,
1328                              ED4_G_DRAG,
1329                              AW_GCM_DATA_AREA,
1330                              makeGcChangedCallback(gc_change_cb), // callback triggering refresh on gc-change
1331
1332                              "#f8f8f8",
1333                              "STANDARD$black",              // standard color showing species/group info (name, ...)
1334                              "FlagInfo$#DDD",
1335                              "#SEQUENCES (0)$#505050",      // default color for sequences (color 0)
1336
1337                              "+-HELIX (1)$#8E0000",  "+-COLOR 2$#0000dd",    "-COLOR 3$#00AA55",
1338                              "+-COLOR 4$#80f",       "+-COLOR 5$#c0a020",    "-COLOR 6$grey",
1339                              "+-COLOR 7$#ff0000",    "+-COLOR 8$#44aaff",    "-COLOR 9$#ffaa00",
1340
1341                              "+-CURSOR$#FF0080",     "+-MARKED$#f4f8e0",     "-SELECTED$#FFFF80",
1342
1343                              "+-RANGE 0$#FFFFFF",    "+-RANGE 1$#F0F0F0",    "-RANGE 2$#E0E0E0",
1344                              "+-RANGE 3$#D8D8D8",    "+-RANGE 4$#D0D0D0",    "-RANGE 5$#C8C8C8",
1345                              "+-RANGE 6$#C0C0C0",    "+-RANGE 7$#B8B8B8",    "-RANGE 8$#B0B0B0",
1346                              "-RANGE 9$#A0A0A0",
1347
1348                              // colors used to Paint search patterns
1349                              // (do not change the names of these gcs)
1350                              "+-User1$#B8E2F8",      "+-User2$#B8E2F8",      "-Probe$#B8E2F8", // see also SEC_graphic::init_devices
1351                              "+-Primer(l)$#A9FE54",  "+-Primer(r)$#A9FE54",  "-Primer(g)$#A9FE54",
1352                              "+-Sig(l)$#DBB0FF",     "+-Sig(r)$#DBB0FF",     "-Sig(g)$#DBB0FF",
1353
1354                              "+-MISMATCHES$#FF9AFF", "+-Flag$#7c7ce3",       "-FlagFill$#aacef1",
1355
1356                              "&color_groups", // use color groups
1357
1358                              NULp);
1359
1360    // since the gc-managers of all EDIT4-windows point to the same window properties,
1361    // changing fonts and colors is always done on first gc-manager
1362    static AW_gc_manager *first_gc_manager = NULp;
1363    if (!first_gc_manager) first_gc_manager = gc_manager;
1364
1365    // --------------
1366    //      File
1367
1368#if defined(DEBUG)
1369    AWT_create_debug_menu(awmm);
1370#endif // DEBUG
1371
1372    awmm->create_menu("File", "F", AWM_ALL);
1373
1374    awmm->insert_menu_topic("new_win", "New Editor Window", "N", NULp, AWM_ALL, ED4_new_editor_window);
1375    awmm->sep______________();
1376    awmm->insert_menu_topic("save_config",                    "Save configuration",        "S", "species_configs_saveload.hlp", AWM_ALL, makeWindowCallback(ED4_saveConfiguration, false));
1377    awmm->insert_menu_topic(awmm->local_id("save_config_as"), "Save configuration as ...", "a", "species_configs_saveload.hlp", AWM_ALL, ED4_create_saveConfigurationAs_window);
1378    awmm->insert_menu_topic(awmm->local_id("load_config"),    "Load configuration ...",    "L", "species_configs_saveload.hlp", AWM_ALL, ED4_create_loadConfiguration_window);
1379    awmm->insert_menu_topic("reload_config",                  "Reload configuration",      "R", "species_configs_saveload.hlp", AWM_ALL, ED4_reloadConfiguration);
1380    insert_macro_menu_entry(awmm, true);
1381    awmm->sep______________();
1382    // keep the following entries in sync with ../NTREE/NT_extern.cxx@common_save_menu_entries
1383    awmm->insert_menu_topic("save_changes", "Quicksave changes",          "c", "save.hlp", AWM_ALL, makeWindowCallback(AWT_trigger_remote_action, GLOBAL_gb_main, "ARB_NT:save_changes"));
1384    awmm->insert_menu_topic("save_all_as",  "Save whole database as ...", "w", "save.hlp", AWM_ALL, makeWindowCallback(AWT_trigger_remote_action, GLOBAL_gb_main, "ARB_NT:save_all_as"));
1385#if defined(DEBUG)
1386    awmm->sep______________();
1387    awmm->insert_menu_topic("deb1", "[DEBUG] remote: invalid app", "D", NULp, AWM_ALL, makeWindowCallback(AWT_trigger_remote_action, GLOBAL_gb_main, "ARB_NTREE:aljdlaisjdlad"));
1388    awmm->insert_menu_topic("deb2", "[DEBUG] remote: invalid cmd", "E", NULp, AWM_ALL, makeWindowCallback(AWT_trigger_remote_action, GLOBAL_gb_main, "ARB_NT:aljdlaisjdlad"));
1389#endif
1390    awmm->sep______________();
1391    GDE_load_menu(awmm, AWM_ALL, "Print");
1392    awmm->sep______________();
1393
1394    if (clone) awmm->insert_menu_topic("close", "CLOSE", "C", NULp, AWM_ALL, ED4_quit_editor);
1395    else       awmm->insert_menu_topic("quit",  "QUIT",  "Q", NULp, AWM_ALL, ED4_quit_editor);
1396
1397    // ----------------
1398    //      Create
1399
1400    awmm->create_menu("Create", "C", AWM_ALL);
1401    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));
1402    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));
1403    awmm->insert_menu_topic(awmm->local_id("copy_species"),                  "Copy current species",              "C", NULp, AWM_ALL, makeCreateWindowCallback(ED4_create_new_seq_window, COPY_SPECIES));
1404    awmm->sep______________();
1405    awmm->insert_menu_topic("create_group",           "Create new Group (from selected)", "G", NULp, AWM_ALL, makeWindowCallback(group_species_cb, false));
1406    awmm->insert_menu_topic("create_groups_by_field", "Create new groups using Field",    "F", NULp, AWM_ALL, makeWindowCallback(group_species_cb, true));
1407
1408    // --------------
1409    //      Edit
1410
1411    awmm->create_menu("Edit", "E", AWM_ALL);
1412    awmm->insert_menu_topic("refresh",                  "Refresh [Ctrl-L]",           "f", NULp,                 AWM_ALL, makeWindowCallback(ED4_request_full_refresh));
1413    awmm->insert_menu_topic("load_current",             "Load current species [GET]", "G", "e4_get_species.hlp", AWM_ALL, makeWindowCallback(ED4_get_and_jump_to_current));
1414    awmm->insert_menu_topic("load_marked",              "Load marked species",        "m", "e4_get_species.hlp", AWM_ALL, makeWindowCallback(ED4_get_marked_from_menu));
1415    awmm->insert_menu_topic(awmm->local_id("load_SAI"), "Load SAI ...",               "L", "e4_get_species.hlp", AWM_ALL, ED4_create_loadSAI_window);
1416    awmm->sep______________();
1417    awmm->insert_menu_topic("refresh_ecoli",       "Reload Ecoli sequence",        "E", "ecoliref.hlp", AWM_ALL, makeWindowCallback(reload_ecoli_cb));
1418    awmm->insert_menu_topic("refresh_helix",       "Reload Helix",                 "H", "helix.hlp",    AWM_ALL, makeWindowCallback(reload_helix_cb));
1419    awmm->insert_menu_topic("helix_jump_opposite", "Jump helix opposite [Ctrl-J]", "J", NULp,           AWM_ALL, ED4_helix_jump_opposite);
1420    awmm->sep______________();
1421
1422    awmm->insert_sub_menu("Set protection of current ", "p");
1423    {
1424        char macro[] = "to_0",
1425            topic[] = ".. to 0",
1426            hotkey[] = "0";
1427
1428        for (char i='0'; i<='6'; i++) {
1429            macro[3] = topic[6] = hotkey[0] = i;
1430            awmm->insert_menu_topic(macro, topic, hotkey, "security.hlp", AWM_ALL, makeWindowCallback(ED4_set_protection, i-'0'));
1431        }
1432    }
1433    awmm->close_sub_menu();
1434
1435    awmm->sep______________();
1436    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()));
1437    awmm->insert_menu_topic("fast_align_set_ref",             "Set aligner reference [Ctrl-R]",     "R", "faligner.hlp",     AWM_ALL,            RootAsWindowCallback::simple(FastAligner_set_reference_species));
1438    awmm->insert_menu_topic(awmm->local_id("align_sequence"), "Old aligner from ARB_EDIT [broken]", "O", "ne_align_seq.hlp", AWM_DISABLED,       create_naligner_window);
1439    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()));
1440    awmm->insert_menu_topic("del_ali_tmp",                    "Remove all aligner Entries",         "v", NULp,               AWM_ALL,            makeWindowCallback(ED4_remove_faligner_entries));
1441    awmm->sep______________();
1442    awmm->insert_menu_topic("missing_bases", "Dot potentially missing bases", "D", "missbase.hlp", AWM_EXP, ED4_popup_dot_missing_bases_window);
1443
1444    if (alignment_type == GB_AT_RNA) { // if the database contains valid alignment of rRNA sequences
1445        awmm->sep______________();
1446        awmm->insert_menu_topic("sec_edit", "Edit secondary structure", "c", "arb_secedit.hlp", AWM_ALL, makeWindowCallback(ED4_start_plugin, GLOBAL_gb_main, "SECEDIT"));
1447#if defined(ARB_OPENGL)
1448        awmm->insert_menu_topic("rna3d", "View 3D molecule", "3", "rna3d_general.hlp", AWM_ALL, makeWindowCallback(ED4_start_plugin, GLOBAL_gb_main, "RNA3D"));
1449#endif // ARB_OPENGL
1450#if defined(DEBUG)
1451        awmm->insert_menu_topic("noplugin", "DEBUG: call unknown plugin", "u", NULp, AWM_ALL, makeWindowCallback(ED4_start_plugin, GLOBAL_gb_main, "testplugin"));
1452#endif // DEBUG
1453    }
1454
1455    // --------------
1456    //      View
1457
1458    awmm->create_menu("View", "V", AWM_ALL);
1459    awmm->insert_sub_menu("Search", "S");
1460    {
1461        int         s;
1462        const char *hotkeys  = "12Poiclrg";
1463        char        hotkey[] = "_";
1464
1465        e4_assert(strlen(hotkeys) == SEARCH_PATTERNS);
1466
1467        for (s=0; s<SEARCH_PATTERNS; s++) {
1468            ED4_SearchPositionType type = ED4_SearchPositionType(s);
1469            const char *id = ED4_SearchPositionTypeId[type];
1470            int len = strlen(id);
1471            char *macro_name = GB_give_buffer(2*(len+8));
1472            char *menu_entry_name = macro_name+(len+8);
1473
1474#ifndef NDEBUG
1475            memset(macro_name, 0, 2*(len+8)); // to avoid memchk-warning
1476#endif
1477            sprintf(macro_name, "%s_SEARCH", id);
1478            char *p = macro_name;
1479            while (1) {
1480                char c = *p++;
1481                if (!c) break;
1482                p[-1] = toupper(c);
1483            }
1484            sprintf(menu_entry_name, "%s Search", id);
1485
1486            hotkey[0] = hotkeys[s];
1487            awmm->insert_menu_topic(awmm->local_id(macro_name), menu_entry_name, hotkey, "e4_search.hlp", AWM_ALL, makeWindowCallback(ED4_popup_search_window, type));
1488        }
1489    }
1490    awmm->close_sub_menu();
1491    awmm->sep______________();
1492    awmm->insert_sub_menu("Cursor position ", "p");
1493    awmm->insert_menu_topic("store_curpos",   "Store cursor position",    "S", NULp, AWM_ALL, ED4_store_curpos);
1494    awmm->insert_menu_topic("restore_curpos", "Restore cursor position ", "R", NULp, AWM_ALL, ED4_restore_curpos);
1495    awmm->insert_menu_topic("clear_curpos",   "Clear stored positions",   "C", NULp, AWM_ALL, makeWindowCallback(ED4_clear_stored_curpos));
1496    awmm->close_sub_menu();
1497
1498    awmm->sep______________();
1499    awmm->insert_menu_topic("change_cursor",             "Change cursor type",   "t", NULp,           AWM_ALL, ED4_change_cursor);
1500    awmm->insert_menu_topic(awmm->local_id("view_diff"), "View differences ...", "V", "viewdiff.hlp", AWM_ALL, ED4_create_viewDifferences_window);
1501    awmm->sep______________();
1502    awmm->insert_menu_topic("enable_col_stat",  "Activate column statistics", "A", "st_ml.hlp", AWM_EXP, ED4_activate_col_stat);
1503    awmm->insert_menu_topic("disable_col_stat", "Disable column statistics",  "i", "st_ml.hlp", AWM_EXP, ED4_disable_col_stat);
1504    awmm->insert_menu_topic("detail_col_stat",  "Toggle detailed Col.-Stat.", "C", "st_ml.hlp", AWM_EXP, ED4_toggle_detailed_column_stats);
1505    awmm->insert_menu_topic("dcs_threshold",    "Set threshold for D.c.s.",   "f", "st_ml.hlp", AWM_EXP, makeWindowCallback(ED4_set_col_stat_threshold));
1506    awmm->sep______________();
1507    awmm->insert_menu_topic(awmm->local_id("visualize_SAI"), "Visualize SAIs",                "z", "visualizeSAI.hlp",   AWM_ALL, ED4_createVisualizeSAI_window);
1508    awmm->insert_menu_topic("toggle_saisec",                 "Toggle secondary info for SAI", "o", "toggle_secinfo.hlp", AWM_ALL, toggle_helix_for_SAI);
1509
1510    // Enable ProteinViewer only for DNA sequence type
1511    if (alignment_type == GB_AT_DNA) {
1512        awmm->insert_menu_topic(awmm->local_id("Protein_Viewer"), "Protein Viewer", "w", "proteinViewer.hlp", AWM_ALL, ED4_CreateProteinViewer_window);
1513    }
1514
1515    // ---------------
1516    //      Block
1517
1518    awmm->create_menu("Block", "B", AWM_ALL);
1519
1520    awmm->insert_menu_topic("select_marked",   "Highlight marked species",    "e", "e4_block.hlp", AWM_ALL, makeWindowCallback(ED4_menu_highlight, ED4_MS_SELECT_MARKED));
1521    awmm->insert_menu_topic("deselect_marked", "De-highlight marked species", "k", "e4_block.hlp", AWM_ALL, makeWindowCallback(ED4_menu_highlight, ED4_MS_DESELECT_MARKED));
1522    awmm->insert_menu_topic("select_all",      "Highlight all species",       "s", "e4_block.hlp", AWM_ALL, makeWindowCallback(ED4_menu_highlight, ED4_MS_ALL));
1523    awmm->insert_menu_topic("deselect_all",    "De-highlight all species",    "D", "e4_block.hlp", AWM_ALL, makeWindowCallback(ED4_menu_highlight, ED4_MS_NONE));
1524    awmm->sep______________();
1525    awmm->insert_menu_topic("mark_selected",   "Mark highlighted species",   "M", "e4_block.hlp", AWM_ALL, makeWindowCallback(ED4_menu_highlight, ED4_MS_MARK_SELECTED));
1526    awmm->insert_menu_topic("unmark_selected", "Unmark highlighted species", "n", "e4_block.hlp", AWM_ALL, makeWindowCallback(ED4_menu_highlight, ED4_MS_UNMARK_SELECTED));
1527    awmm->insert_menu_topic("unmark_all",      "Unmark all species",         "U", "e4_block.hlp", AWM_ALL, makeWindowCallback(ED4_menu_highlight, ED4_MS_UNMARK_ALL));
1528    awmm->sep______________();
1529    awmm->insert_menu_topic("invert_all",   "Invert highlighted species", "I", "e4_block.hlp", AWM_ALL, makeWindowCallback(ED4_menu_highlight, ED4_MS_INVERT));
1530    awmm->insert_menu_topic("invert_group", "Invert group",               "g", "e4_block.hlp", AWM_ALL, makeWindowCallback(ED4_menu_highlight, ED4_MS_INVERT_GROUP));
1531    awmm->sep______________();
1532    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));
1533    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));
1534    awmm->sep______________();
1535    awmm->insert_menu_topic("reverse",            "Reverse highlighted ",    "v", "e4_block.hlp", AWM_ALL, makeWindowCallback(ED4_menu_perform_block_operation, ED4_BO_REVERSE));
1536    awmm->insert_menu_topic("complement",         "Complement highlighted ", "o", "e4_block.hlp", AWM_ALL, makeWindowCallback(ED4_menu_perform_block_operation, ED4_BO_COMPLEMENT));
1537    awmm->insert_menu_topic("reverse_complement", "Reverse complement",      "t", "e4_block.hlp", AWM_ALL, makeWindowCallback(ED4_menu_perform_block_operation, ED4_BO_REVERSE_COMPLEMENT));
1538    awmm->sep______________();
1539    awmm->insert_menu_topic("unalignBlockLeft",   "Unalign block left",   "a", "e4_block.hlp", AWM_ALL, makeWindowCallback(ED4_menu_perform_block_operation, ED4_BO_UNALIGN_LEFT));
1540    awmm->insert_menu_topic("unalignBlockCenter", "Unalign block center", "c", "e4_block.hlp", AWM_ALL, makeWindowCallback(ED4_menu_perform_block_operation, ED4_BO_UNALIGN_CENTER));
1541    awmm->insert_menu_topic("unalignBlockRight",  "Unalign block right",  "b", "e4_block.hlp", AWM_ALL, makeWindowCallback(ED4_menu_perform_block_operation, ED4_BO_UNALIGN_RIGHT));
1542    awmm->sep______________();
1543    awmm->insert_menu_topic(awmm->local_id("replace"), "Search & Replace ", "h", "e4_replace.hlp", AWM_ALL, ED4_create_replace_window);
1544    awmm->insert_menu_topic(awmm->local_id("setsai"),  "Modify SAI ",       "y", "e4_modsai.hlp",  AWM_ALL, ED4_create_modsai_window);
1545    awmm->sep______________();
1546    awmm->insert_menu_topic("toggle_block_type", "Exchange: Line<->Column", "x", "e4_block.hlp", AWM_ALL, makeWindowCallback(ED4_menu_highlight, ED4_MS_TOGGLE_BLOCKTYPE));
1547    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));
1548    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));
1549
1550    // --------------------
1551    //      Properties
1552
1553    awmm->create_menu("Properties", "P", AWM_ALL);
1554
1555    awmm->insert_menu_topic(awmm->local_id("props_frame"),     "Frame settings ...",    "g", NULp,               AWM_ALL, AW_preset_window);
1556    awmm->insert_menu_topic(awmm->local_id("props_options"),   "Editor Options ",       "O", "e4_options.hlp",   AWM_ALL, ED4_create_editor_options_window);
1557    awmm->insert_menu_topic(awmm->local_id("props_consensus"), "Consensus Definition ", "u", "e4_consensus.hlp", AWM_ALL, ED4_create_consensus_definition_window);
1558    awmm->sep______________();
1559
1560    awmm->insert_menu_topic("props_data",                       "Change Colors & Fonts ", "C", NULp,                  AWM_ALL, makeWindowCallback      (ED4_popup_gc_window,          first_gc_manager));
1561    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));
1562
1563    awmm->sep______________();
1564
1565    awmm->insert_menu_topic(awmm->local_id("props_nds"),     "Select visible info (NDS) ", "D", "ed4_nds.hlp",   AWM_ALL, ED4_create_nds_window);
1566    awmm->insert_menu_topic(awmm->local_id("props_flags"),   "Select species flags",       "f", "ed4_flags.hlp", AWM_ALL, makeCreateWindowCallback(ED4_configure_species_flags, GLOBAL_gb_main));
1567    {
1568        static WindowCallback reqRelCb = makeWindowCallback(ED4_request_relayout);
1569        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));
1570        else                            awmm->insert_menu_topic(awmm->local_id("props_helix_sym"), "Helix Settings ",         "H", "helixsym.hlp",    AWM_ALL, makeCreateWindowCallback(create_helix_props_window,     &reqRelCb));
1571    }
1572    awmm->insert_menu_topic(awmm->local_id("props_key_map"), "Key Mappings ",              "K", "nekey_map.hlp", AWM_ALL, create_key_map_window);
1573
1574    awmm->sep______________();
1575    AW_insert_common_property_menu_entries(awmm);
1576    awmm->sep______________();
1577    awmm->insert_sub_menu("Save properties ...", "a");
1578    {
1579        static const char * const tag[] = { "save_alispecific_props", "save_alitype_props", "save_props" };
1580        static const char * const entry_type[] = { "alignment specific ", "ali-type specific ", "" };
1581
1582        // check what is the default mode
1583        int default_mode = -1;
1584        for (int mode = 0; mode <= 2; ++mode) {
1585            if (strcmp(GB_path_in_arbprop(ED4_propertyName(mode)), db_name) == 0) {
1586                default_mode = mode;
1587                break;
1588            }
1589        }
1590        if (default_mode == -1) default_mode = 2; // no properties yet -> use 'edit4.arb'
1591
1592        const char *entry = GBS_global_string("Save loaded Properties (%s)", ED4_propertyName(default_mode));
1593        awmm->insert_menu_topic("save_loaded_props", entry, "l", "e4_defaults.hlp", AWM_ALL, makeWindowCallback(ED4_save_properties, default_mode));
1594        awmm->sep______________();
1595
1596        for (int mode = 2; mode >= 0; --mode) {
1597            char hotkey[] = "x";
1598            hotkey[0]     = "Pta"[mode];
1599            entry         = GBS_global_string("Save %sProperties (%s)", entry_type[mode], ED4_propertyName(mode));
1600            awmm->insert_menu_topic(tag[mode], entry, hotkey, "e4_defaults.hlp", AWM_ALL, makeWindowCallback(ED4_save_properties, mode));
1601        }
1602    }
1603    awmm->close_sub_menu();
1604
1605    awmm->insert_help_topic("ARB_EDIT4 help",     "E", "e4.hlp", AWM_ALL, makeHelpCallback("e4.hlp"));
1606
1607    // ----------------------------------------------------------------------------------------------------
1608
1609    aw_root->awar_int(AWAR_EDIT_TITLE_MODE)->add_callback(makeRootCallback(title_mode_changed, static_cast<AW_window*>(awmm)));
1610    awmm->set_bottom_area_height(0);   // No bottom area
1611
1612    awmm->auto_space(5, -2);
1613    awmm->shadow_width(3);
1614
1615    int db_pathx, db_pathy;
1616    awmm->get_at_position(&db_pathx, &db_pathy);
1617
1618    awmm->shadow_width(1);
1619    awmm->load_xfig("edit4/editmenu.fig", false);
1620
1621    // --------------------------
1622    //      help /quit /fold
1623
1624    awmm->button_length(0);
1625
1626    awmm->at("quit");
1627    awmm->callback(ED4_quit_editor);
1628    awmm->help_text("quit.hlp");
1629
1630    if (clone) awmm->create_button("CLOSE", "#close.xpm");
1631    else       awmm->create_button("QUIT",  "#quit.xpm");
1632
1633    awmm->at("help");
1634    awmm->callback(AW_help_entry_pressed);
1635    awmm->help_text("e4.hlp");
1636    awmm->create_button("HELP", "#help.xpm");
1637
1638    awmm->at("fold");
1639    awmm->help_text("e4.hlp");
1640    awmm->create_toggle(AWAR_EDIT_TITLE_MODE, "#more.xpm", "#less.xpm");
1641
1642    // -------------------
1643    //      positions
1644
1645    awmm->button_length(0);
1646
1647    awmm->at("posTxt");     awmm->create_button(NULp, "Position");
1648
1649    awmm->button_length(6+1);
1650
1651    awmm->at("ecoliTxt");   awmm->create_button(NULp, ED4_AWAR_NDS_ECOLI_NAME, NULp, "+");
1652
1653    awmm->button_length(0);
1654
1655    awmm->at("baseTxt");    awmm->create_button(NULp, "Base");
1656    awmm->at("iupacTxt");   awmm->create_button(NULp, "IUPAC");
1657    awmm->at("helixnrTxt"); awmm->create_button(NULp, "Helix#");
1658
1659    awmm->at("pos");
1660    awmm->callback(makeWindowCallback(ED4_jump_to_cursor_position, current_ed4w()->awar_path_for_cursor, ED4_POS_SEQUENCE)); // @@@ used as INPUTFIELD_CB (see #559)
1661    awmm->create_input_field(current_ed4w()->awar_path_for_cursor, 7);
1662
1663    awmm->at("ecoli");
1664    awmm->callback(makeWindowCallback(ED4_jump_to_cursor_position, current_ed4w()->awar_path_for_Ecoli, ED4_POS_ECOLI)); // @@@ used as INPUTFIELD_CB (see #559)
1665    awmm->create_input_field(current_ed4w()->awar_path_for_Ecoli, 6);
1666
1667    awmm->at("base");
1668    awmm->callback(makeWindowCallback(ED4_jump_to_cursor_position, current_ed4w()->awar_path_for_basePos, ED4_POS_BASE)); // @@@ used as INPUTFIELD_CB (see #559)
1669    awmm->create_input_field(current_ed4w()->awar_path_for_basePos, 6);
1670
1671    awmm->at("iupac");
1672    awmm->callback(makeWindowCallback(ED4_set_iupac, current_ed4w()->awar_path_for_IUPAC)); // @@@ used as INPUTFIELD_CB (see #559)
1673    awmm->create_input_field(current_ed4w()->awar_path_for_IUPAC, 4);
1674
1675    awmm->at("helixnr");
1676    awmm->callback(makeWindowCallback(ED4_set_helixnr, current_ed4w()->awar_path_for_helixNr)); // @@@ used as INPUTFIELD_CB (see #559)
1677    awmm->create_input_field(current_ed4w()->awar_path_for_helixNr, 5);
1678
1679    // ----------------------------
1680    //      jump/get/undo/redo
1681
1682    awmm->button_length(4);
1683
1684    awmm->at("jump");
1685    awmm->callback(ED4_jump_to_current_species);
1686    awmm->help_text("e4_get_species.hlp");
1687    awmm->create_button("JUMP", "Jump");
1688
1689    awmm->at("get");
1690    awmm->callback(makeWindowCallback(ED4_get_and_jump_to_current));
1691    awmm->help_text("e4_get_species.hlp");
1692    awmm->create_button("GET", "Get");
1693
1694    awmm->button_length(0);
1695
1696    awmm->at("undo");
1697    awmm->callback(makeWindowCallback(ED4_undo_redo, GB_UNDO_UNDO));
1698    awmm->help_text("undo.hlp");
1699    awmm->create_button("UNDO", "#undo.xpm");
1700
1701    awmm->at("redo");
1702    awmm->callback(makeWindowCallback(ED4_undo_redo, GB_UNDO_REDO));
1703    awmm->help_text("undo.hlp");
1704    awmm->create_button("REDO", "#redo.xpm");
1705
1706    // --------------------------
1707    //      aligner / SAIviz
1708
1709    awmm->button_length(7);
1710
1711    awmm->at("aligner");
1712    awmm->callback(makeCreateWindowCallback(ED4_create_faligner_window, ED4_get_aligner_data_access()));
1713    awmm->help_text("faligner.hlp");
1714    awmm->create_button("ALIGNER", "Aligner");
1715
1716    awmm->at("saiviz");
1717    awmm->callback(ED4_createVisualizeSAI_window);
1718    awmm->help_text("visualizeSAI.hlp");
1719    awmm->create_button("SAIVIZ", "SAIviz");
1720
1721    // -------------------------------------------
1722    //      align/insert/protection/direction
1723
1724    awmm->button_length(0);
1725
1726    awmm->at("protect");
1727    awmm->create_option_menu(AWAR_EDIT_SECURITY_LEVEL, true);
1728    awmm->insert_option        ("0", NULp, 0);
1729    awmm->insert_option        ("1", NULp, 1);
1730    awmm->insert_option        ("2", NULp, 2);
1731    awmm->insert_option        ("3", NULp, 3);
1732    awmm->insert_option        ("4", NULp, 4);
1733    awmm->insert_option        ("5", NULp, 5);
1734    awmm->insert_default_option("6", NULp, 6);
1735    awmm->update_option_menu();
1736
1737    // draw protection icon AFTER protection!!
1738    awmm->at("pico");
1739    awmm->create_button(NULp, "#protect.xpm");
1740
1741    // draw align/edit-button AFTER protection!!
1742    awmm->at("edit");
1743    awmm->create_toggle(AWAR_EDIT_MODE, "#edit/align.xpm", "#edit/editseq.xpm", 7);
1744
1745    awmm->at("insert");
1746    awmm->create_text_toggle(AWAR_INSERT_MODE, "Replace", "Insert", 7);
1747
1748    awmm->at("direct");
1749    awmm->create_toggle(AWAR_EDIT_RIGHTWARD, "#edit/3to5.xpm", "#edit/5to3.xpm", 7);
1750
1751    // -------------------------
1752    //      secedit / rna3d
1753
1754    int xoffset = 0;
1755
1756    if (alignment_type == GB_AT_RNA) { // if the database contains valid alignment of rRNA sequences
1757        // add buttons for RNA3D and SECEDIT plugins
1758
1759        awmm->button_length(0);
1760
1761        awmm->at("secedit");
1762        awmm->callback(makeWindowCallback(ED4_start_plugin, GLOBAL_gb_main, "SECEDIT"));
1763        awmm->help_text("arb_secedit.hlp");
1764        awmm->create_button("SECEDIT", "#edit/secedit.xpm");
1765
1766#if defined(ARB_OPENGL)
1767        awmm->at("rna3d");
1768        awmm->callback(makeWindowCallback(ED4_start_plugin, GLOBAL_gb_main, "RNA3D"));
1769        awmm->help_text("rna3d_general.hlp");
1770        awmm->create_button("RNA3D", "#edit/rna3d.xpm");
1771#endif // ARB_OPENGL
1772    }
1773    else {
1774        awmm->at("secedit");
1775        int xsecedit = awmm->get_at_xposition();
1776        awmm->at("zoom");
1777        int xzoom    = awmm->get_at_xposition();
1778        xoffset      = xsecedit-xzoom; // shift message stuff to the left by xoffset
1779    }
1780
1781    {
1782        int x, y;
1783
1784        awmm->at("zoom");
1785        if (xoffset) { awmm->get_at_position(&x, &y); awmm->at(x+xoffset, y); }
1786        awmm->callback(ED4_zoom_message_window);
1787        awmm->create_button("ZOOM", "#edit/zoom.xpm");
1788
1789        awmm->at("clear");
1790        if (xoffset) { awmm->get_at_position(&x, &y); awmm->at(x+xoffset, y); }
1791        awmm->callback(aw_clear_message_cb);
1792        awmm->create_button("CLEAR", "#edit/clear.xpm");
1793
1794        awmm->at("errortext");
1795        if (xoffset) { awmm->get_at_position(&x, &y); awmm->at(x+xoffset, y); }
1796        aw_root->awar_string(AWAR_ERROR_MESSAGES, "This is ARB Edit4 [Build " ARB_VERSION "]");
1797        awmm->create_text_field(AWAR_ERROR_MESSAGES);
1798        aw_set_local_message();
1799    }
1800
1801    // ---------------------
1802    //      'more' area
1803
1804    awmm->at("cons");
1805    awmm->create_toggle(ED4_AWAR_CONSENSUS_SHOW, "#edit/nocons.xpm", "#edit/cons.xpm");
1806
1807    awmm->at("num");
1808    awmm->create_toggle(ED4_AWAR_DIGITS_AS_REPEAT, "#edit/norepeat.xpm", "#edit/repeat.xpm");
1809
1810    awmm->at("key");
1811    awmm->create_toggle("key_mapping/enable", "#edit/nokeymap.xpm", "#edit/keymap.xpm");
1812
1813    // search
1814
1815    awmm->button_length(0);
1816#define INSERT_SEARCH_FIELDS(Short, label_prefix, prefix)       \
1817    insert_search_fields(awmm,                                  \
1818                         #label_prefix,                         \
1819                         #prefix,                               \
1820                         ED4_AWAR_##prefix##_SEARCH_PATTERN,    \
1821                         ED4_AWAR_##prefix##_SEARCH_SHOW,       \
1822                         Short,                                 \
1823                         ED4_##prefix##_PATTERN,                \
1824                         current_ed4w()                         \
1825        )
1826
1827    INSERT_SEARCH_FIELDS(0, u1, USER1);
1828    INSERT_SEARCH_FIELDS(0, u2, USER2);
1829    INSERT_SEARCH_FIELDS(0, pro, PROBE);
1830    INSERT_SEARCH_FIELDS(1, pri1, PRIMER1);
1831    INSERT_SEARCH_FIELDS(1, pri2, PRIMER2);
1832    INSERT_SEARCH_FIELDS(1, pri3, PRIMER3);
1833    INSERT_SEARCH_FIELDS(1, sig1, SIG1);
1834    INSERT_SEARCH_FIELDS(1, sig2, SIG2);
1835    INSERT_SEARCH_FIELDS(1, sig3, SIG3);
1836
1837#undef INSERT_SEARCH_FIELDS
1838
1839    awmm->at("alast");
1840    awmm->callback(makeWindowCallback(ED4_search_cb, ED4_encodeSearchDescriptor(-1, ED4_ANY_PATTERN), current_ed4w()));
1841    awmm->create_button("ALL_SEARCH_LAST", "#edit/last.xpm");
1842
1843    awmm->at("anext");
1844    awmm->callback(makeWindowCallback(ED4_search_cb, ED4_encodeSearchDescriptor(+1, ED4_ANY_PATTERN), current_ed4w()));
1845    awmm->create_button("ALL_SEARCH_NEXT", "#edit/next.xpm");
1846
1847    title_mode_changed(aw_root, awmm);
1848
1849    // Buttons at left window border
1850
1851    awmm->create_mode("edit/arrow.xpm", "e4_mode.hlp", AWM_ALL, makeWindowCallback(modes_cb, ED4_SM_MOVE));
1852    awmm->create_mode("edit/kill.xpm",  "e4_mode.hlp", AWM_ALL, makeWindowCallback(modes_cb, ED4_SM_KILL));
1853    awmm->create_mode("edit/mark.xpm",  "e4_mode.hlp", AWM_ALL, makeWindowCallback(modes_cb, ED4_SM_MARK));
1854    awmm->create_mode("mode_info.xpm",  "e4_mode.hlp", AWM_ALL, makeWindowCallback(modes_cb, ED4_SM_INFO));
1855
1856    FastAligner_create_variables(awmm->get_root(), props_db);
1857
1858#if defined(DEBUG)
1859    AWT_check_action_ids(awmm->get_root(), "");
1860#endif
1861
1862    announce_useraction_in(awmm);
1863
1864    return ED4_R_OK;
1865}
1866
1867AW_window *ED4_root::create_first_window() {
1868    // Note: other windows are generated by generate_window
1869    AW_device  *device     = NULp;
1870    ED4_window *new_window = NULp;
1871
1872    generate_window(&device, &new_window);
1873
1874    ED4_LocalWinContext uses(new_window);
1875
1876    ED4_calc_terminal_extentions(); // (Note: done again later, but otherwise variables are used uninitialized);
1877
1878    DRAW                    = 1;
1879    move_cursor             = 0;
1880    max_seq_terminal_length = 0;
1881
1882    ED4_init_notFoundMessage();
1883
1884    return new_window->aww;
1885}
1886
1887ED4_index ED4_root::pixel2pos(AW_pos click_x) {
1888    // 'click_x' is the x-offset into the terminal in pixels
1889    // returns the x-offset into the terminal in base positions (clipped to max. allowed position)
1890
1891    int       length_of_char = font_group.get_width(ED4_G_SEQUENCES);
1892    ED4_index scr_pos        = int((click_x-CHARACTEROFFSET) / length_of_char);
1893    int       max_scrpos     = root_group_man->remap()->get_max_screen_pos();
1894
1895    if (scr_pos>max_scrpos) scr_pos = max_scrpos;
1896
1897    return scr_pos;
1898}
1899
1900static char *detectProperties() {
1901    char *propname = NULp;
1902
1903    // check if edit4_?na.arb / edit4_ali_???.arb exist in $ARB_PROP
1904    for (int mode = 0; !propname && mode <= 1; ++mode) { 
1905        const char *fullprop = GB_path_in_arbprop(ED4_propertyName(mode));
1906        if (GB_is_regularfile(fullprop)) {
1907            freedup(propname, fullprop);
1908        }
1909    }
1910
1911    // if not, use 'mode 2', i.e. "edit4.arb"
1912    // (no full path, we want to load default from arb_defaults)
1913    if (!propname) propname = ARB_strdup(ED4_propertyName(2));
1914
1915    return propname;
1916}
1917
1918ED4_root::ED4_root(int* argc, char*** argv)
1919    : most_recently_used_window(NULp),
1920      cons_param(NULp),
1921      db_name(detectProperties()),
1922      aw_root(AWT_create_root(db_name, "ARB_EDIT4", need_macro_ability(), argc, argv)),
1923      props_db(AW_ROOT_DEFAULT),
1924      first_window(NULp),
1925      main_manager(NULp),
1926      middle_area_man(NULp),
1927      top_area_man(NULp),
1928      root_group_man(NULp),
1929      database(NULp),
1930      selected_objects(new ED4_selected_list), 
1931      folding_action(false),
1932      species_mode(ED4_SM_MOVE),
1933      ecoli_ref(NULp),
1934      alignment_name(NULp),
1935      alignment_type(GB_AT_UNKNOWN),
1936      reference(NULp),
1937      sequence_colors(NULp),
1938      gc_manager(NULp),
1939      st_ml(NULp),
1940      helix(NULp),
1941      helix_spacing(0),
1942      helix_add_spacing(0),
1943      terminal_add_spacing(0),
1944      protstruct(NULp),
1945      protstruct_len(0),
1946      edk(NULp),
1947      edit_string(NULp),
1948      column_stat_activated(false),
1949      column_stat_initialized(false),
1950      visualizeSAI(false),
1951      visualizeSAI_allSpecies(false),
1952      loadable_SAIs(LSAI_UNUSED),
1953      temp_gc(0)
1954{}
1955
1956
1957ED4_root::~ED4_root() {
1958    delete aw_root;
1959    delete first_window;
1960    delete reference; // needs to be deleted before main_manager (to ensure reference callbacks are removed)
1961    delete main_manager; // also deletes middle_area_man + top_area_man
1962    delete database;
1963    delete ecoli_ref;
1964    delete selected_objects;
1965    delete helix;
1966    delete sequence_colors;
1967    delete edk;
1968    STAT_destroy_ST_ML(st_ml);
1969
1970    free(protstruct);
1971    free(db_name);
1972    free(alignment_name);
1973}
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