source: tags/ms_r16q3/EDIT4/ED4_root.cxx

Last change on this file was 15288, checked in by westram, 8 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 NULL;
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{
318    ED4_multi_species_manager *main_multi_man = middle_area_man->get_multi_species_manager();
319    main_multi_man->deselect_all_species_and_SAI();
320
321    main_multi_man = top_area_man->get_multi_species_manager();
322    main_multi_man->deselect_all_species_and_SAI();
323
324    ED4_setBlocktype(ED4_BT_NOBLOCK);
325
326    return ED4_R_OK;
327}
328
329void ED4_root::remove_from_selected(ED4_species_name_terminal *name_term) { // @@@ change param to ED4_species_manager ?
330    if (name_term) {
331        if ((selected_objects->has_elem(name_term->selection_info))) {
332            selected_objects->remove_elem(name_term->selection_info);
333
334            delete name_term->selection_info;
335            name_term->selection_info    = NULL;
336            name_term->containing_species_manager()->set_selected(false);
337            name_term->dragged = false; // @@@ caller shall do this
338
339#ifdef DEBUG
340            GBDATA *gbd = name_term->get_species_pointer();
341
342            if (gbd) {
343                GB_transaction ta(gbd);
344                printf("removed term '%s'\n", GB_read_char_pntr(gbd));
345            }
346            else {
347                ED4_species_manager *spec_man = name_term->get_parent(LEV_SPECIES)->to_species_manager();
348
349                if (spec_man->is_consensus_manager()) {
350                    printf("removed consensus '%s'\n", name_term->id);
351                }
352                else {
353                    printf("removed unknown term '%s'\n", name_term->id ? name_term->id : "NULL");
354                }
355            }
356#endif
357
358            name_term->request_refresh();
359            ED4_sequence_terminal *seq_term = name_term->corresponding_sequence_terminal();
360            if (seq_term) seq_term->request_refresh();
361
362            // ProtView: Refresh corresponding orf terminals
363            if (alignment_type == GB_AT_DNA) {
364                PV_CallBackFunction(this->aw_root);
365            }
366
367            ED4_multi_species_manager *multi_man = name_term->get_parent(LEV_MULTI_SPECIES)->to_multi_species_manager();
368            multi_man->invalidate_species_counters();
369        }
370    }
371}
372
373void ED4_root::announce_useraction_in(AW_window *aww) {
374    for (ED4_window *win = first_window; win; win = win->next) {
375        if (win->aww == aww) {
376            most_recently_used_window = win;
377        }
378    }
379}
380
381ED4_returncode ED4_root::add_to_selected(ED4_species_name_terminal *name_term) { // @@@ change param to ED4_species_manager ?
382    if (!name_term || !name_term->has_property(PROP_SELECTABLE)) {   // check if object exists and may be selected
383        return (ED4_R_IMPOSSIBLE);
384    }
385
386    if (!(selected_objects->has_elem(name_term->selection_info))) {     // object is really new to our list => calculate current extension and append it
387        ED4_selection_entry *sel_info = new ED4_selection_entry;
388        name_term->selection_info     = sel_info;
389
390        if (name_term->has_property(PROP_IS_HANDLE)) { // object is a handle for an object up in the hierarchy => search it
391            ED4_level  mlevel     = name_term->spec.handled_level;
392            ED4_base  *tmp_object = name_term;
393
394            while ((tmp_object != NULL) && !(tmp_object->spec.level & mlevel)) {
395                tmp_object = tmp_object->parent;
396            }
397
398            if (!tmp_object) return (ED4_R_WARNING); // no target level found
399
400            sel_info->actual_width  = tmp_object->extension.size[WIDTH];
401            sel_info->actual_height = tmp_object->extension.size[HEIGHT];
402        }
403        else // selected object is no handle => take it directly
404        {
405            sel_info->actual_width  = name_term->extension.size[WIDTH];
406            sel_info->actual_height = name_term->extension.size[HEIGHT];
407        }
408
409        sel_info->drag_old_x  = 0;
410        sel_info->drag_old_y  = 0;
411        sel_info->drag_off_x  = 0;
412        sel_info->drag_off_y  = 0;
413        sel_info->old_event_y = 0;
414
415        sel_info->object = name_term;
416
417        selected_objects->prepend_elem(sel_info);
418
419        name_term->containing_species_manager()->set_selected(true);
420
421#ifdef DEBUG
422        GBDATA *gbd = name_term->get_species_pointer();
423
424        if (gbd) {
425            printf("added term '%s'\n", GB_read_char_pntr(gbd));
426        }
427        else {
428            ED4_species_manager *spec_man = name_term->get_parent(LEV_SPECIES)->to_species_manager();
429            if (spec_man->is_consensus_manager()) {
430                printf("added consensus '%s'\n", name_term->id);
431            }
432            else {
433                printf("added unknown term '%s'\n", name_term->id ? name_term->id : "NULL");
434            }
435        }
436#endif
437
438        name_term->request_refresh();
439        ED4_sequence_terminal *seq_term = name_term->corresponding_sequence_terminal();
440        if (seq_term) seq_term->request_refresh();
441
442        // ProtView: Refresh corresponding orf terminals
443        if (alignment_type == GB_AT_DNA) {
444            PV_CallBackFunction(this->aw_root);
445        }
446
447        ED4_multi_species_manager *multi_man = name_term->get_parent(LEV_MULTI_SPECIES)->to_multi_species_manager();
448        multi_man->invalidate_species_counters();
449
450        return (ED4_R_OK);
451    }
452
453    return (ED4_R_IMPOSSIBLE);
454}
455
456void ED4_root::resize_all_requesting_childs() {
457    while (main_manager->update_info.resize) {
458        main_manager->resize_requested_children();
459    }
460}
461
462static ARB_ERROR change_char_table_length(ED4_base *base, int new_length) {
463    if (base->is_abstract_group_manager()) {
464        ED4_abstract_group_manager *group_man = base->to_abstract_group_manager();
465        group_man->table().change_table_length(new_length);
466    }
467    return NULL;
468}
469
470void ED4_alignment_length_changed(GBDATA *gb_alignment_len, GB_CB_TYPE IF_ASSERTION_USED(gbtype)) // callback from database
471{
472    e4_assert(gbtype==GB_CB_CHANGED);
473    int new_length = GB_read_int(gb_alignment_len);
474
475#if defined(DEBUG) && 1
476    printf("alignment_length_changed from %i to %i\n", MAXSEQUENCECHARACTERLENGTH, new_length);
477#endif
478
479    if (MAXSEQUENCECHARACTERLENGTH!=new_length) { // otherwise we already did this (i.e. we were called by changed_by_database)
480        bool was_increased = new_length>MAXSEQUENCECHARACTERLENGTH;
481
482        MAXSEQUENCECHARACTERLENGTH = new_length;
483
484        {
485            const char *err = ED4_ROOT->helix->init(GLOBAL_gb_main); // reload helix
486            aw_message_if(err);
487        }
488        {
489            const char *err = ED4_ROOT->ecoli_ref->init(GLOBAL_gb_main); // reload ecoli
490            aw_message_if(err);
491        }
492
493        if (ED4_ROOT->alignment_type == GB_AT_AA) {
494            // TODO: is this needed here?
495            const char *err = ED4_pfold_set_SAI(&ED4_ROOT->protstruct, GLOBAL_gb_main, ED4_ROOT->alignment_name, &ED4_ROOT->protstruct_len); // reload protstruct
496            aw_message_if(err);
497        }
498
499        if (was_increased) {
500            ED4_ROOT->main_manager->route_down_hierarchy(makeED4_route_cb(change_char_table_length, new_length)).expect_no_error();
501            ED4_ROOT->root_group_man->remap()->mark_compile_needed_force();
502        }
503    }
504}
505
506ARB_ERROR ED4_root::init_alignment() {
507    GB_transaction ta(GLOBAL_gb_main);
508
509    alignment_name = GBT_get_default_alignment(GLOBAL_gb_main);
510    alignment_type = GBT_get_alignment_type(GLOBAL_gb_main, alignment_name);
511    if (alignment_type==GB_AT_UNKNOWN) {
512        return GBS_global_string("You have to select a valid alignment before you can start ARB_EDIT4\n(%s)", GB_await_error());
513    }
514
515    GBDATA *gb_alignment = GBT_get_alignment(GLOBAL_gb_main, alignment_name);
516    if (!gb_alignment) {
517        return GBS_global_string("You can't edit without an existing alignment\n(%s)", GB_await_error());
518    }
519
520    GBDATA *gb_alignment_len = GB_search(gb_alignment, "alignment_len", GB_FIND);
521    int alignment_length = GB_read_int(gb_alignment_len);
522    MAXSEQUENCECHARACTERLENGTH = alignment_length;
523
524    GB_add_callback(gb_alignment_len, GB_CB_CHANGED, makeDatabaseCallback(ED4_alignment_length_changed));
525
526    aw_root->awar_string(AWAR_EDITOR_ALIGNMENT, alignment_name);
527
528    return NULL;
529}
530
531void ED4_root::recalc_font_group() {
532    int font_GC[] = {
533        ED4_G_SEQUENCES,
534        ED4_G_STANDARD,
535        ED4_G_FLAG_INFO,
536    };
537
538    font_group.unregisterAll();
539    for (unsigned i = 0; i<ARRAY_ELEMS(font_GC); ++i) {
540        ED4_MostRecentWinContext context;
541        font_group.registerFont(current_device(), font_GC[i]);
542    }
543}
544
545static ARB_ERROR force_group_update(ED4_base *base) {
546    if (base->is_multi_species_manager()) {
547        base->to_multi_species_manager()->update_requested_by_child();
548    }
549    return NULL;
550}
551
552ED4_returncode ED4_root::create_hierarchy(const char *area_string_middle, const char *area_string_top) {
553    // creates internal hierarchy of editor
554
555    long total_no_of_groups  = 0;
556    long total_no_of_species = 0;
557    {
558        // count species and related info (e.g. helix) displayed in the top region (a == 0)
559        // count no of species and sais including groups in middle region (a == 1)
560
561        const char *area_string[2] = { area_string_top, area_string_middle };
562        for (int a = 0; a<2; ++a) {
563            long group_count;
564            long species_count;
565            database->calc_no_of_all(area_string[a], &group_count, &species_count);
566
567            total_no_of_groups  += group_count;
568            total_no_of_species += species_count;
569        }
570    }
571
572    SmartPtr<arb_progress> startup_progress = new arb_progress("EDIT4 startup");
573
574    GB_push_transaction(GLOBAL_gb_main);
575
576    ecoli_ref = new BI_ecoli_ref;
577    ecoli_ref->init(GLOBAL_gb_main);
578
579    // [former position of ali-init-code]
580
581    main_manager   = new ED4_main_manager("Main_Manager", 0, 0, NULL); // build a test hierarchy
582    root_group_man = new ED4_root_group_manager("Root_Group_Manager", 0, 0, main_manager);
583   
584    main_manager->append_member(root_group_man);
585
586    ED4_device_manager *device_manager = new ED4_device_manager("Device_Manager", 0, 0, root_group_man);
587    root_group_man->append_member(device_manager);
588
589    {
590        int col_stat_term_height = 50; // @@@ Hoehe des ColumnStatistics Terminals ausrechnen
591
592        ref_terminals.init(
593            new ED4_sequence_info_terminal("Reference_Sequence_Info_Terminal",         MAXINFO_WIDTH, TERMINAL_HEIGHT,       NULL),
594            new ED4_sequence_terminal     ("Reference_Sequence_Terminal",              300,           TERMINAL_HEIGHT,       NULL, false),
595            new ED4_sequence_info_terminal("Reference_ColumnStatistics_Info_Terminal", MAXINFO_WIDTH, col_stat_term_height, NULL),
596            new ED4_columnStat_terminal   ("Reference_ColumnStatistics_Terminal",      300,           col_stat_term_height, NULL)
597            );
598    }
599
600    {
601        arb_progress species_progress("Loading species", total_no_of_species);
602
603        // ********** Top Area beginning **********
604
605        ED4_multi_species_manager *top_multi_species_manager;
606        ED4_spacer_terminal       *top_spacer_terminal;
607        ED4_spacer_terminal       *top_mid_spacer_terminal;
608        ED4_spacer_terminal       *top_multi_spacer_terminal_beg;
609        ED4_line_terminal         *top_mid_line_terminal;
610        {
611            ED4_area_manager *top_area_manager = new ED4_area_manager("Top_Area_Manager", 0, 0, device_manager);
612            device_manager->append_member(top_area_manager);
613            top_area_man = top_area_manager;
614
615            top_spacer_terminal = new ED4_spacer_terminal("Top_Spacer", false, 100, 10, top_area_manager);
616            top_area_manager->append_member(top_spacer_terminal);
617
618            top_multi_species_manager = new ED4_multi_species_manager("Top_MultiSpecies_Manager", 0, 0, top_area_manager);
619            top_area_manager->append_member(top_multi_species_manager);
620
621            top_multi_spacer_terminal_beg = new ED4_spacer_terminal("Top_Left_Spacer", false, 0, 3, top_multi_species_manager);
622            top_multi_species_manager->append_member(top_multi_spacer_terminal_beg);
623
624            reference = new ED4_reference(GLOBAL_gb_main);
625
626            int index = 0;
627            database->scan_string(top_multi_species_manager, ref_terminals, area_string_top, &index, species_progress);
628            GB_pop_transaction(GLOBAL_gb_main);
629
630            const int TOP_MID_LINE_HEIGHT   = 3;
631            int       TOP_MID_SPACER_HEIGHT = font_group.get_max_height()-TOP_MID_LINE_HEIGHT;
632
633            top_mid_line_terminal = new ED4_line_terminal("Top_Mid_Line_Terminal", 0, TOP_MID_LINE_HEIGHT, device_manager);    // width will be set below
634            device_manager->append_member(top_mid_line_terminal);
635
636            top_mid_spacer_terminal = new ED4_spacer_terminal("Top_Middle_Spacer", true, 880, TOP_MID_SPACER_HEIGHT, device_manager);
637            device_manager->append_member(top_mid_spacer_terminal);
638
639            // needed to avoid text-clipping problems:
640            main_manager->set_top_middle_spacer_terminal(top_mid_spacer_terminal);
641            main_manager->set_top_middle_line_terminal(top_mid_line_terminal);
642        }
643
644        // ********** Middle Area beginning **********
645
646        ED4_area_manager          *middle_area_manager;
647        ED4_tree_terminal         *tree_terminal;
648        ED4_multi_species_manager *mid_multi_species_manager;
649        ED4_spacer_terminal       *mid_multi_spacer_terminal_beg;
650        ED4_line_terminal         *mid_bot_line_terminal;
651        ED4_spacer_terminal       *total_bottom_spacer;
652        {
653            middle_area_manager = new ED4_area_manager("Middle_Area_Manager", 0, 0, device_manager);
654            device_manager->append_member(middle_area_manager);
655            middle_area_man = middle_area_manager;
656
657            tree_terminal = new ED4_tree_terminal("Tree", 2, 0, middle_area_manager);
658            middle_area_manager->append_member(tree_terminal);
659
660            mid_multi_species_manager = new ED4_multi_species_manager("Middle_MultiSpecies_Manager", 0, 0, middle_area_manager);
661            middle_area_manager->append_member(mid_multi_species_manager);
662
663            mid_multi_spacer_terminal_beg = new ED4_spacer_terminal("Mid_Multi_Spacer_Terminal_Beg", false, 0, 3, mid_multi_species_manager);
664            mid_multi_species_manager->append_member(mid_multi_spacer_terminal_beg);
665
666            scroll_links.link_for_ver_slider = middle_area_manager;
667
668            {
669                GB_transaction ta(GLOBAL_gb_main);
670                int index  = 0;
671                database->scan_string(mid_multi_species_manager, ref_terminals, area_string_middle, &index, species_progress);
672            }
673
674            {
675                ED4_spacer_terminal *mid_bot_spacer_terminal = new ED4_spacer_terminal("Middle_Bot_Spacer_Terminal", false, 880, 10, device_manager);
676                device_manager->append_member(mid_bot_spacer_terminal);
677            }
678
679            mid_bot_line_terminal = new ED4_line_terminal("Mid_Bot_Line_Terminal", 0, 3, device_manager);    // width will be set below
680            device_manager->append_member(mid_bot_line_terminal);
681
682            total_bottom_spacer = new ED4_spacer_terminal("Total_Bottom_Spacer_terminal", false, 0, 10000, device_manager);
683            total_bottom_spacer->clr_property(PROP_DYNA_RESIZE);
684            device_manager->append_member(total_bottom_spacer);
685        }
686
687        if (scroll_links.link_for_hor_slider) {
688            const long ext_width    = long(scroll_links.link_for_hor_slider->extension.size[WIDTH]);
689            const long spacer_width = ext_width + MAXNAME_WIDTH + SEQUENCE_INFO_WIDTH;
690            const long line_width   = spacer_width + TREE_TERMINAL_WIDTH;
691
692            top_multi_spacer_terminal_beg->extension.size[WIDTH] = spacer_width;
693            mid_multi_spacer_terminal_beg->extension.size[WIDTH] = spacer_width;
694            total_bottom_spacer->extension.size[WIDTH]           = spacer_width;
695
696            top_mid_line_terminal->extension.size[WIDTH] = line_width;
697            mid_bot_line_terminal->extension.size[WIDTH] = line_width;
698
699        }
700
701        tree_terminal->set_links(NULL, mid_multi_species_manager);                          // set links
702        top_spacer_terminal->set_links(tree_terminal, top_multi_species_manager);
703        top_mid_spacer_terminal->set_links(middle_area_manager, NULL);
704        total_bottom_spacer->set_links(mid_bot_line_terminal, 0);
705
706        species_progress.done();
707    }
708
709    first_window->update_window_coords();
710    resize_all_requesting_childs();
711
712    main_manager->route_down_hierarchy(makeED4_route_cb(force_group_update)).expect_no_error();
713
714    if (!scroll_links.link_for_hor_slider) { // happens when no species AND no SAI has data
715        startup_progress->done();
716        startup_progress.SetNull(); // make progress disappear (otherwise prompter below is often behind progress window)
717        GB_pop_transaction(GLOBAL_gb_main);
718       
719        aw_popup_ok(GBS_global_string("No species/SAI contains data in '%s'\nARB_EDIT4 will terminate", alignment_name));
720        ED4_exit();
721    }
722
723    // build consensi
724    {
725        arb_progress consensi_progress("Initializing consensi", total_no_of_species+total_no_of_groups+1); // 1 is root_group_man
726
727        root_group_man->create_consensus(root_group_man, &consensi_progress);
728        e4_assert(root_group_man->table().ok());
729        consensi_progress.done(); // if there is a "top"-group, progress increment is one to low
730    }
731
732    root_group_man->remap()->mark_compile_needed_force();
733    root_group_man->update_remap();
734
735    // calc size and display:
736
737    resize_all_requesting_childs();
738
739    e4_assert(main_manager);
740
741    {
742        ED4_base *x_link      = scroll_links.link_for_hor_slider;
743        ED4_base *y_link      = scroll_links.link_for_ver_slider;
744        ED4_base *width_link  = x_link;
745        ED4_base *height_link = y_link;
746
747        ED4_window *win = first_window;
748        while (win) {
749            win->set_scrolled_rectangle(x_link, y_link, width_link, height_link);
750            win->aww->show();
751            win->update_scrolled_rectangle();
752            win = win->next;
753        }
754    }
755
756    ED4_request_relayout();
757    ED4_finish_and_show_notFoundMessage();
758
759#if defined(DEBUG) && 0
760    // dump created hierarchy:
761    puts("---------------------------------------- [main_manager dump start]");
762    main_manager->dump(1);
763    puts("---------------------------------------- [main_manager dump end]");
764#endif
765
766    return ED4_R_OK;
767}
768
769ED4_returncode ED4_root::get_area_rectangle(AW_screen_area *rect, AW_pos x, AW_pos y) {
770    // returns win-coordinates of area (defined by folding lines) which contains position x/y
771    int                    x1, x2, y1, y2;
772    const AW_screen_area&  area_rect = current_device()->get_area_size();
773
774    x1 = area_rect.l;
775    for (const ED4_folding_line *flv=current_ed4w()->get_vertical_folding(); ; flv = flv->get_next()) {
776        if (flv) {
777            x2 = int(flv->get_pos()); // @@@ use AW_INT ?
778        }
779        else {
780            x2 = area_rect.r;
781            if (x1==x2) {
782                break;
783            }
784        }
785
786        y1 = area_rect.t;
787        for (const ED4_folding_line *flh=current_ed4w()->get_horizontal_folding(); ; flh = flh->get_next()) {
788            if (flh) {
789                y2 = int(flh->get_pos()); // @@@ use AW_INT ?
790            }
791            else {
792                y2 = area_rect.b;
793                if (y1==y2) {
794                    break;
795                }
796            }
797
798            if (x1<=x && x<=x2 && y1<=y && y<=y2) {
799                rect->t = y1;
800                rect->b = y2;
801                rect->l = x1;
802                rect->r = x2;
803                return ED4_R_OK;
804            }
805            y1 = y2;
806            if (!flh) break;
807        }
808        x1 = x2;
809        if (!flv) break;
810    }
811    return ED4_R_IMPOSSIBLE; // no area contains x/y :-(
812}
813
814void ED4_root::copy_window_struct(ED4_window *source,   ED4_window *destination)
815{
816    destination->slider_pos_horizontal  = source->slider_pos_horizontal;
817    destination->slider_pos_vertical    = source->slider_pos_vertical;
818    destination->coords         = source->coords;
819}
820
821
822static void reload_helix_cb() { 
823    const char *err = ED4_ROOT->helix->init(GLOBAL_gb_main);
824    if (err) aw_message(err);
825    ED4_request_full_refresh();
826}
827
828
829static void reload_ecoli_cb() {
830    const char *err = ED4_ROOT->ecoli_ref->init(GLOBAL_gb_main);
831    if (err) aw_message(err);
832    ED4_request_full_refresh();
833}
834
835// ---------------------------------------
836//      recursion through all species
837
838DECLARE_CBTYPE_FVV_AND_BUILDERS(ED4_Species_Callback, ARB_ERROR, GBDATA *); // generates makeED4_Species_Callback
839
840static ARB_ERROR do_sth_with_species(ED4_base *base, const ED4_Species_Callback *cb) {
841    ARB_ERROR error = NULL;
842
843    if (base->is_species_manager()) {
844        ED4_species_manager       *species_manager       = base->to_species_manager();
845        ED4_species_name_terminal *species_name_terminal = species_manager->search_spec_child_rek(LEV_SPECIES_NAME)->to_species_name_terminal();
846
847        if (species_name_terminal->get_species_pointer()) {
848            char *species_name = GB_read_as_string(species_name_terminal->get_species_pointer());
849
850            e4_assert(species_name);
851            GBDATA *species = GBT_find_species(GLOBAL_gb_main, species_name);
852
853            error = species
854                ? (*cb)(species)
855                : GB_append_exportedError(GBS_global_string("can't find species '%s'", species_name));
856
857            free(species_name);
858        }
859    }
860
861    return error;
862}
863
864
865static ARB_ERROR ED4_with_all_loaded_species(const ED4_Species_Callback& cb) {
866    return ED4_ROOT->root_group_man->route_down_hierarchy(makeED4_route_cb(do_sth_with_species, &cb));
867}
868
869static bool is_named(ED4_base *base, const char *wanted_name) {
870    ED4_species_name_terminal *name_term = base->to_species_name_terminal();
871    GBDATA                    *gbd       = name_term->get_species_pointer();
872    if (gbd) {
873        const char *name = GB_read_char_pntr(gbd);
874        e4_assert(name);
875
876        return strcmp(name, wanted_name) == 0;
877    }
878    return false;
879}
880
881static bool is_species_named(ED4_base *base, const char *species_name) {
882    return base->inside_species_seq_manager() && is_named(base, species_name);
883}
884
885static bool is_SAI_named(ED4_base *base, const char *sai_name) {
886    return base->inside_SAI_manager() && is_named(base, sai_name);
887}
888
889ED4_species_name_terminal *ED4_find_species_or_SAI_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() : NULL;
892}
893ED4_species_name_terminal *ED4_find_species_name_terminal(const char *species_name) {
894    ED4_base *base = ED4_ROOT->root_group_man->find_first_that(LEV_SPECIES_NAME, makeED4_basePredicate(is_species_named, species_name));
895    return base ? base->to_species_name_terminal() : NULL;
896}
897ED4_species_name_terminal *ED4_find_SAI_name_terminal(const char *sai_name) {
898    ED4_base *base = ED4_ROOT->root_group_man->find_first_that(LEV_SPECIES_NAME, makeED4_basePredicate(is_SAI_named, sai_name));
899    return base ? base->to_species_name_terminal() : NULL;
900}
901
902static char *get_group_consensus(const char *species_name, PosRange range) {
903    ED4_species_name_terminal *name_term = ED4_find_species_name_terminal(species_name);
904    char *consensus = 0;
905
906    if (name_term) {
907        ED4_abstract_group_manager *group_man = name_term->get_parent(ED4_level(LEV_GROUP|LEV_ROOTGROUP))->to_abstract_group_manager();
908        if (group_man) {
909            consensus = group_man->build_consensus_string(range);
910        }
911    }
912
913    return consensus;
914}
915
916static bool get_selected_range(PosRange& range) {
917    ED4_selected_elem *listElem = ED4_ROOT->selected_objects->head();
918    if (listElem) {
919        ED4_sequence_terminal *seqTerm = listElem->elem()->object->corresponding_sequence_terminal();
920        return ED4_get_selected_range(seqTerm, range);
921    }
922    return false;
923}
924
925static ED4_selected_elem *curr_aligner_elem = 0;
926
927static GBDATA *get_next_selected_species() {
928    if (!curr_aligner_elem) return 0;
929
930    ED4_species_manager *specMan = curr_aligner_elem->elem()->object->containing_species_manager();
931    curr_aligner_elem = curr_aligner_elem->next();
932    return specMan->get_species_pointer();
933}
934
935static GBDATA *get_first_selected_species(int *total_no_of_selected_species)
936{
937    int selected = ED4_ROOT->selected_objects->size();
938
939    if (total_no_of_selected_species) {
940        *total_no_of_selected_species = selected;
941    }
942
943    if (selected) {
944        curr_aligner_elem = ED4_ROOT->selected_objects->head();
945    }
946    else {
947        curr_aligner_elem = 0;
948    }
949
950    return get_next_selected_species();
951}
952
953static ARB_ERROR ED4_delete_temp_entries(GBDATA *species, GB_CSTR alignment_name) {
954    return FastAligner_delete_temp_entries(species, alignment_name);
955}
956
957static void ED4_remove_faligner_entries() {
958    ARB_ERROR error = GB_begin_transaction(GLOBAL_gb_main);
959    if (!error) error = ED4_with_all_loaded_species(makeED4_Species_Callback(ED4_delete_temp_entries, ED4_ROOT->alignment_name));
960    GB_end_transaction_show_error(GLOBAL_gb_main, error, aw_message);
961}
962
963static void toggle_helix_for_SAI(AW_window *aww) {
964    ED4_LocalWinContext  uses(aww);
965    ED4_cursor          *cursor = &current_cursor();
966
967    if (cursor->in_SAI_terminal()) {
968        ED4_sequence_terminal      *sai_term      = cursor->owner_of_cursor->to_sequence_terminal();
969        ED4_sequence_info_terminal *sai_info_term = sai_term->parent->search_spec_child_rek(LEV_SEQUENCE_INFO)->to_sequence_info_terminal();
970
971        GBDATA         *gb_sai_data = sai_info_term->data();
972        GB_transaction  ta(gb_sai_data);
973
974        GBDATA *gb_sai      = GB_get_grandfather(gb_sai_data);
975        GBDATA *gb_disp_sec = GB_searchOrCreate_int(gb_sai, "showsec", 0);
976
977        bool show_sec = 1-bool(GB_read_int(gb_disp_sec));
978        GB_ERROR error = GB_write_int(gb_disp_sec, show_sec);
979        if (!error) {
980            sai_term->set_secstruct_display(show_sec);
981            sai_term->request_refresh();
982        }
983        if (error) aw_message(error);
984    }
985    else {
986        aw_message("Please select an SAI");
987    }
988}
989
990static void title_mode_changed(AW_root *aw_root, AW_window *aww) {
991    int title_mode = aw_root->awar(AWAR_EDIT_TITLE_MODE)->read_int();
992
993    if (title_mode==0) {
994        aww->set_info_area_height(57);
995    }
996    else {
997        aww->set_info_area_height(170);
998    }
999}
1000
1001static void ED4_undo_redo(AW_window *aww, GB_UNDO_TYPE undo_type) {
1002    ED4_LocalWinContext uses(aww);
1003    GB_ERROR error = GB_undo(GLOBAL_gb_main, undo_type);
1004
1005    if (error) {
1006        aw_message(error);
1007    }
1008    else {
1009        GB_begin_transaction(GLOBAL_gb_main);
1010        GB_commit_transaction(GLOBAL_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{
1018    AW_window_simple *aws = new AW_window_simple;
1019
1020    aws->init(root, "ZOOM_ERR_MSG", "Errors and warnings");
1021    aws->load_xfig("edit4/message.fig");
1022
1023    aws->callback(AW_POPDOWN);
1024    aws->at("hide");
1025    aws->create_button("HIDE", "HIDE");
1026
1027    aws->callback(aw_clear_message_cb);
1028    aws->at("clear");
1029    aws->create_button("CLEAR", "CLEAR");
1030
1031    aws->at("errortext");
1032    aws->create_text_field(AWAR_ERROR_MESSAGES);
1033
1034    return (AW_window *)aws;
1035}
1036
1037
1038static char *cat(char *toBuf, const char *s1, const char *s2)
1039{
1040    char *buf = toBuf;
1041
1042    while ((*buf++=*s1++)!=0) ;
1043    buf--;
1044    while ((*buf++=*s2++)!=0) ;
1045
1046    return toBuf;
1047}
1048
1049static void insert_search_fields(AW_window_menu_modes *awmm,
1050                                 const char *label_prefix, const char *macro_prefix,
1051                                 const char *pattern_awar_name, const char *show_awar_name,
1052                                 int short_form, ED4_SearchPositionType type, ED4_window *ed4w)
1053{
1054    char buf[200];
1055
1056    if (!short_form) {
1057        awmm->at(cat(buf, label_prefix, "search"));
1058        awmm->create_input_field(pattern_awar_name, 30);
1059    }
1060
1061    awmm->at(cat(buf, label_prefix, "n"));
1062    awmm->help_text("e4_search.hlp");
1063    awmm->callback(makeWindowCallback(ED4_search_cb, ED4_encodeSearchDescriptor(+1, type), ed4w));
1064    awmm->create_button(cat(buf, macro_prefix, "_SEARCH_NEXT"), "#edit/next.xpm");
1065
1066    awmm->at(cat(buf, label_prefix, "l"));
1067    awmm->help_text("e4_search.hlp");
1068    awmm->callback(makeWindowCallback(ED4_search_cb, ED4_encodeSearchDescriptor(-1, type), ed4w));
1069    awmm->create_button(cat(buf, macro_prefix, "_SEARCH_LAST"), "#edit/last.xpm");
1070
1071    awmm->at(cat(buf, label_prefix, "d"));
1072    awmm->help_text("e4_search.hlp");
1073    awmm->callback(makeWindowCallback(ED4_popup_search_window, type));
1074    awmm->create_button(cat(buf, macro_prefix, "_SEARCH_DETAIL"), "#edit/detail.xpm");
1075
1076    awmm->at(cat(buf, label_prefix, "s"));
1077    awmm->create_toggle(show_awar_name);
1078}
1079
1080static void ED4_set_protection(AW_window *aww, int wanted_protection) {
1081    ED4_LocalWinContext uses(aww);
1082    ED4_cursor *cursor = &current_cursor();
1083    GB_ERROR    error  = 0;
1084
1085    if (cursor->owner_of_cursor) {
1086        ED4_sequence_terminal      *seq_term      = cursor->owner_of_cursor->to_sequence_terminal();
1087        ED4_sequence_info_terminal *seq_info_term = seq_term->parent->search_spec_child_rek(LEV_SEQUENCE_INFO)->to_sequence_info_terminal();
1088        GBDATA                     *gbd           = seq_info_term->data();
1089
1090        GB_push_transaction(gbd);
1091
1092        GB_push_my_security(gbd);
1093        error = GB_write_security_write(gbd, wanted_protection);
1094        GB_pop_my_security(gbd);
1095
1096        error = GB_end_transaction(gbd, error);
1097    }
1098    else {
1099        error = "No species selected";
1100    }
1101
1102    if (error) aw_message(error);
1103}
1104
1105enum MenuSelectType {
1106    ED4_MS_NONE,
1107    ED4_MS_ALL,
1108    ED4_MS_INVERT,
1109    ED4_MS_INVERT_GROUP,
1110    ED4_MS_UNMARK_ALL,
1111    ED4_MS_MARK_SELECTED,
1112    ED4_MS_UNMARK_SELECTED,
1113    ED4_MS_SELECT_MARKED,
1114    ED4_MS_DESELECT_MARKED,
1115    ED4_MS_TOGGLE_BLOCKTYPE
1116};
1117
1118static void ED4_menu_select(AW_window *aww, MenuSelectType select) {
1119    GB_transaction             ta(GLOBAL_gb_main);
1120    ED4_multi_species_manager *middle_multi_man = ED4_ROOT->middle_area_man->get_multi_species_manager();
1121
1122    e4_assert(middle_multi_man);
1123
1124    switch (select) {
1125        case ED4_MS_NONE: {
1126            if (ED4_getBlocktype()!=ED4_BT_NOBLOCK) {
1127                ED4_ROOT->deselect_all();
1128            }
1129            break;
1130        }
1131        case ED4_MS_ALL: {
1132            middle_multi_man->select_all(true); // only species
1133            ED4_correctBlocktypeAfterSelection();
1134            break;
1135        }
1136        case ED4_MS_INVERT: {
1137            middle_multi_man->invert_selection_of_all_species();
1138            ED4_correctBlocktypeAfterSelection();
1139            break;
1140        }
1141        case ED4_MS_SELECT_MARKED: {
1142            middle_multi_man->marked_species_select(true);
1143            ED4_correctBlocktypeAfterSelection();
1144            break;
1145        }
1146        case ED4_MS_DESELECT_MARKED: {
1147            middle_multi_man->marked_species_select(false);
1148            ED4_correctBlocktypeAfterSelection();
1149            break;
1150        }
1151        case ED4_MS_UNMARK_ALL: {
1152            GBT_mark_all(GLOBAL_gb_main, 0);
1153            break;
1154        }
1155        case ED4_MS_MARK_SELECTED: {
1156            middle_multi_man->selected_species_mark(true);
1157            ED4_correctBlocktypeAfterSelection();
1158            break;
1159        }
1160        case ED4_MS_UNMARK_SELECTED: {
1161            middle_multi_man->selected_species_mark(false);
1162            ED4_correctBlocktypeAfterSelection();
1163            break;
1164        }
1165        case ED4_MS_INVERT_GROUP: {
1166            ED4_cursor *cursor = &ED4_ROOT->first_window->get_matching_ed4w(aww)->cursor;
1167            int done = 0;
1168
1169            if (cursor->owner_of_cursor) {
1170                ED4_multi_species_manager *multi_man = cursor->owner_of_cursor->get_parent(LEV_MULTI_SPECIES)->to_multi_species_manager();
1171
1172                multi_man->invert_selection_of_all_species();
1173                ED4_correctBlocktypeAfterSelection();
1174                done = 1;
1175            }
1176
1177            if (!done) {
1178                aw_message("Place cursor into group");
1179            }
1180            break;
1181        }
1182        case ED4_MS_TOGGLE_BLOCKTYPE: {
1183            ED4_toggle_block_type();
1184            break;
1185        }
1186        default: {
1187            e4_assert(0);
1188            break;
1189        }
1190    }
1191
1192    ED4_request_full_refresh();
1193}
1194
1195static void ED4_menu_perform_block_operation(AW_window *, ED4_blockoperation_type type) {
1196    ED4_perform_block_operation(type);
1197}
1198
1199static void modes_cb(AW_window*, ED4_species_mode smode) {
1200    ED4_ROOT->species_mode = smode;
1201    for (ED4_window *win = ED4_ROOT->first_window; win; win = win->next) {
1202        win->aww->select_mode(smode);
1203    }
1204    if (smode == ED4_SM_INFO) {
1205        AWT_trigger_remote_action(NULL, GLOBAL_gb_main, "ARB_NT:species_info");
1206    }
1207}
1208
1209void ED4_no_dangerous_modes() {
1210    if (ED4_ROOT->species_mode == ED4_SM_KILL) {
1211        modes_cb(NULL, ED4_SM_MOVE);
1212    }
1213}
1214
1215static char *get_helix_string(GBDATA *gb_main, const char *alignment_name) {
1216    GB_transaction ta(gb_main);
1217
1218    char   *helix_string = 0;
1219    char   *helix_name   = GBT_get_default_helix(gb_main);
1220    GBDATA *gb_helix_con = GBT_find_SAI(gb_main, helix_name);
1221    if (gb_helix_con) {
1222        GBDATA *gb_helix = GBT_find_sequence(gb_helix_con, alignment_name);
1223        if (gb_helix) helix_string = GB_read_string(gb_helix);
1224    }
1225    free(helix_name);
1226
1227    return helix_string;
1228}
1229
1230const AlignDataAccess *ED4_get_aligner_data_access() {
1231    static SmartPtr<AlignDataAccess> aliDataAccess;
1232
1233    if (aliDataAccess.isNull()) {
1234        aliDataAccess = new AlignDataAccess(GLOBAL_gb_main,
1235                                            ED4_ROOT->alignment_name,
1236                                            true, ED4_trigger_instant_refresh, // perform refresh
1237                                            get_group_consensus,               // aligner fetches consensus of group of species via this function
1238                                            get_selected_range,                // aligner fetches column range of selection via this function
1239                                            get_first_selected_species,        // aligner fetches first and..
1240                                            get_next_selected_species,         // .. following selected species via these functions
1241                                            get_helix_string);                 // used by island_hopping (if configured to use sec-structure)
1242    }
1243
1244    return aliDataAccess.isSet() ? &*aliDataAccess : NULL;
1245}
1246
1247static AW_window *ED4_create_faligner_window(AW_root *awr, const AlignDataAccess *data_access) {
1248#if defined(DEBUG)
1249    static const AlignDataAccess *last_data_access = NULL;
1250
1251    e4_assert(!last_data_access || (last_data_access == data_access)); // there shall be only one AlignDataAccess
1252    last_data_access = data_access;
1253#endif
1254
1255    static AW_window *aws = NULL;
1256    if (!aws) aws = FastAligner_create_window(awr, data_access);
1257    return aws;
1258}
1259
1260static void ED4_save_properties(AW_window *aw, int mode) {
1261    AW_save_specific_properties(aw, ED4_propertyName(mode));
1262}
1263
1264void ED4_popup_gc_window(AW_window *awp, AW_gc_manager *gcman) {
1265    typedef std::map<AW_gc_manager*, AW_window*> gcwin;
1266    static gcwin win;
1267
1268    gcwin::iterator found = win.find(gcman);
1269
1270    AW_window *aww = NULL;
1271    if (found == win.end()) {
1272        aww        = AW_create_gc_window(awp->get_root(), gcman);
1273        win[gcman] = aww;
1274    }
1275    else {
1276        aww = win[gcman];
1277    }
1278    aww->activate();
1279}
1280
1281static void gc_change_cb(GcChange whatChanged) {
1282    if (whatChanged == GC_FONT_CHANGED) {
1283        ED4_resize_all_extensions();
1284    }
1285    ED4_request_full_instant_refresh();
1286}
1287
1288ED4_returncode ED4_root::generate_window(AW_device **device, ED4_window **new_window) {
1289    {
1290        ED4_window *ed4w = first_window;
1291
1292        while (ed4w) { // before creating a window look for a hidden window
1293            if (ed4w->is_hidden) {
1294                ed4w->aww->show();
1295                ed4w->is_hidden = false;
1296                return ED4_R_BREAK;
1297            }
1298            ed4w = ed4w->next;
1299        }
1300    }
1301
1302    if (ED4_window::no_of_windows == MAXWINDOWS)                            // no more than 5 windows allowed
1303    {
1304        aw_message(GBS_global_string("Restricted to %i windows", MAXWINDOWS));
1305        return ED4_R_BREAK;
1306    }
1307
1308    AW_window_menu_modes *awmm = new AW_window_menu_modes;
1309    {
1310        int   winNum   = ED4_window::no_of_windows+1;
1311        char *winName  = winNum>1 ? GBS_global_string_copy("ARB_EDIT4_%i", winNum) : ARB_strdup("ARB_EDIT4");
1312        char *winTitle = GBS_global_string_copy("ARB_EDIT4 *%d* [%s]", winNum, alignment_name);
1313
1314        awmm->init(aw_root, winName, winTitle, 800, 450);
1315
1316        free(winTitle);
1317        free(winName);
1318    }
1319
1320    *device     = awmm->get_device(AW_MIDDLE_AREA); // points to Middle Area device
1321    *new_window = ED4_window::insert_window(awmm);   // append to window list
1322
1323    e4_assert(ED4_window::no_of_windows >= 1);
1324    bool clone = ED4_window::no_of_windows>1;
1325    if (!clone) {                                   // this is the first window
1326        AW_init_color_group_defaults("arb_edit4");
1327    }
1328    else { // additional edit windows
1329        copy_window_struct(first_window, *new_window);
1330    }
1331
1332    ED4_LocalWinContext uses(*new_window);
1333
1334    // each window has its own gc-manager
1335    gc_manager = AW_manage_GC(awmm,
1336                              "ARB_EDIT4",                   // but all gc-managers use the same colors
1337                              *device,
1338                              ED4_G_DRAG,
1339                              AW_GCM_DATA_AREA,
1340                              makeGcChangedCallback(gc_change_cb), // callback triggering refresh on gc-change
1341
1342                              "#f8f8f8",
1343                              "STANDARD$black",              // standard color showing species/group info (name, ...)
1344                              "FlagInfo$#DDD",
1345                              "#SEQUENCES (0)$#505050",      // default color for sequences (color 0)
1346
1347                              "+-HELIX (1)$#8E0000",  "+-COLOR 2$#0000dd",    "-COLOR 3$#00AA55",
1348                              "+-COLOR 4$#80f",       "+-COLOR 5$#c0a020",    "-COLOR 6$grey",
1349                              "+-COLOR 7$#ff0000",    "+-COLOR 8$#44aaff",    "-COLOR 9$#ffaa00",
1350
1351                              "+-CURSOR$#FF0080",     "+-MARKED$#f4f8e0",     "-SELECTED$#FFFF80",
1352
1353                              "+-RANGE 0$#FFFFFF",    "+-RANGE 1$#F0F0F0",    "-RANGE 2$#E0E0E0",
1354                              "+-RANGE 3$#D8D8D8",    "+-RANGE 4$#D0D0D0",    "-RANGE 5$#C8C8C8",
1355                              "+-RANGE 6$#C0C0C0",    "+-RANGE 7$#B8B8B8",    "-RANGE 8$#B0B0B0",
1356                              "-RANGE 9$#A0A0A0",
1357
1358                              // colors used to Paint search patterns
1359                              // (do not change the names of these gcs)
1360                              "+-User1$#B8E2F8",      "+-User2$#B8E2F8",      "-Probe$#B8E2F8", // see also SEC_graphic::init_devices
1361                              "+-Primer(l)$#A9FE54",  "+-Primer(r)$#A9FE54",  "-Primer(g)$#A9FE54",
1362                              "+-Sig(l)$#DBB0FF",     "+-Sig(r)$#DBB0FF",     "-Sig(g)$#DBB0FF",
1363
1364                              "+-MISMATCHES$#FF9AFF", "+-Flag$#7c7ce3",       "-FlagFill$#aacef1",
1365
1366                              "&color_groups", // use color groups
1367
1368                              NULL);
1369
1370    // since the gc-managers of all EDIT4-windows point to the same window properties,
1371    // changing fonts and colors is always done on first gc-manager
1372    static AW_gc_manager *first_gc_manager = 0;
1373    if (!first_gc_manager) first_gc_manager = gc_manager;
1374
1375    // --------------
1376    //      File
1377
1378#if defined(DEBUG)
1379    AWT_create_debug_menu(awmm);
1380#endif // DEBUG
1381
1382    awmm->create_menu("File", "F", AWM_ALL);
1383
1384    awmm->insert_menu_topic("new_win", "New Editor Window", "N", 0, AWM_ALL, ED4_new_editor_window);
1385    awmm->sep______________();
1386    awmm->insert_menu_topic("save_config",                    "Save configuration",        "S", "species_configs_saveload.hlp", AWM_ALL, makeWindowCallback(ED4_saveConfiguration, false));
1387    awmm->insert_menu_topic(awmm->local_id("save_config_as"), "Save configuration as ...", "a", "species_configs_saveload.hlp", AWM_ALL, ED4_create_saveConfigurationAs_window);
1388    awmm->insert_menu_topic(awmm->local_id("load_config"),    "Load configuration ...",    "L", "species_configs_saveload.hlp", AWM_ALL, ED4_create_loadConfiguration_window);
1389    awmm->insert_menu_topic("reload_config",                  "Reload configuration",      "R", "species_configs_saveload.hlp", AWM_ALL, ED4_reloadConfiguration);
1390    insert_macro_menu_entry(awmm, true);
1391    awmm->sep______________();
1392    // keep the following entries in sync with ../NTREE/NT_extern.cxx@common_save_menu_entries
1393    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"));
1394    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"));
1395#if defined(DEBUG)
1396    awmm->sep______________();
1397    awmm->insert_menu_topic("deb1", "[DEBUG] remote: invalid app", "D", NULL, AWM_ALL, makeWindowCallback(AWT_trigger_remote_action, GLOBAL_gb_main, "ARB_NTREE:aljdlaisjdlad"));
1398    awmm->insert_menu_topic("deb2", "[DEBUG] remote: invalid cmd", "E", NULL, AWM_ALL, makeWindowCallback(AWT_trigger_remote_action, GLOBAL_gb_main, "ARB_NT:aljdlaisjdlad"));
1399#endif
1400    awmm->sep______________();
1401    GDE_load_menu(awmm, AWM_ALL, "Print");
1402    awmm->sep______________();
1403
1404    if (clone) awmm->insert_menu_topic("close", "CLOSE", "C", 0, AWM_ALL, ED4_quit_editor);
1405    else       awmm->insert_menu_topic("quit",   "QUIT",  "Q", 0, AWM_ALL, ED4_quit_editor);
1406
1407    // ----------------
1408    //      Create
1409
1410    awmm->create_menu("Create", "C", AWM_ALL);
1411    awmm->insert_menu_topic(awmm->local_id("create_species"),                "Create new species",                "n", 0, AWM_ALL, makeCreateWindowCallback(ED4_create_new_seq_window, CREATE_NEW_SPECIES));
1412    awmm->insert_menu_topic(awmm->local_id("create_species_from_consensus"), "Create new species from consensus", "u", 0, AWM_ALL, makeCreateWindowCallback(ED4_create_new_seq_window, CREATE_FROM_CONSENSUS));
1413    awmm->insert_menu_topic(awmm->local_id("copy_species"),                  "Copy current species",              "C", 0, AWM_ALL, makeCreateWindowCallback(ED4_create_new_seq_window, COPY_SPECIES));
1414    awmm->sep______________();
1415    awmm->insert_menu_topic("create_group",           "Create new Group (from selected)", "G", 0, AWM_ALL, makeWindowCallback(group_species_cb, false));
1416    awmm->insert_menu_topic("create_groups_by_field", "Create new groups using Field",    "F", 0, AWM_ALL, makeWindowCallback(group_species_cb, true));
1417
1418    // --------------
1419    //      Edit
1420
1421    awmm->create_menu("Edit", "E", AWM_ALL);
1422    awmm->insert_menu_topic("refresh",                  "Refresh [Ctrl-L]",           "f", 0,                    AWM_ALL, makeWindowCallback(ED4_request_full_refresh));
1423    awmm->insert_menu_topic("load_current",             "Load current species [GET]", "G", "e4_get_species.hlp", AWM_ALL, makeWindowCallback(ED4_get_and_jump_to_current));
1424    awmm->insert_menu_topic("load_marked",              "Load marked species",        "m", "e4_get_species.hlp", AWM_ALL, makeWindowCallback(ED4_get_marked_from_menu));
1425    awmm->insert_menu_topic(awmm->local_id("load_SAI"), "Load SAI ...",               "L", "e4_get_species.hlp", AWM_ALL, ED4_create_loadSAI_window);
1426    awmm->sep______________();
1427    awmm->insert_menu_topic("refresh_ecoli",       "Reload Ecoli sequence",        "E", "ecoliref.hlp", AWM_ALL, makeWindowCallback(reload_ecoli_cb));
1428    awmm->insert_menu_topic("refresh_helix",       "Reload Helix",                 "H", "helix.hlp",    AWM_ALL, makeWindowCallback(reload_helix_cb));
1429    awmm->insert_menu_topic("helix_jump_opposite", "Jump helix opposite [Ctrl-J]", "J", 0,              AWM_ALL, ED4_helix_jump_opposite);
1430    awmm->sep______________();
1431
1432    awmm->insert_sub_menu("Set protection of current ", "p");
1433    {
1434        char macro[] = "to_0",
1435            topic[] = ".. to 0",
1436            hotkey[] = "0";
1437
1438        for (char i='0'; i<='6'; i++) {
1439            macro[3] = topic[6] = hotkey[0] = i;
1440            awmm->insert_menu_topic(macro, topic, hotkey, "security.hlp", AWM_ALL, makeWindowCallback(ED4_set_protection, i-'0'));
1441        }
1442    }
1443    awmm->close_sub_menu();
1444
1445    awmm->sep______________();
1446    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()));
1447    awmm->insert_menu_topic("fast_align_set_ref",             "Set aligner reference [Ctrl-R]",     "R", "faligner.hlp",     AWM_ALL,            RootAsWindowCallback::simple(FastAligner_set_reference_species));
1448    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);
1449    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()));
1450    awmm->insert_menu_topic("del_ali_tmp",                    "Remove all aligner Entries",         "v", 0,                  AWM_ALL,            makeWindowCallback(ED4_remove_faligner_entries));
1451    awmm->sep______________();
1452    awmm->insert_menu_topic("missing_bases", "Dot potentially missing bases", "D", "missbase.hlp", AWM_EXP, ED4_popup_dot_missing_bases_window);
1453
1454    if (alignment_type == GB_AT_RNA) { // if the database contains valid alignment of rRNA sequences
1455        awmm->sep______________();
1456        awmm->insert_menu_topic("sec_edit", "Edit secondary structure", "c", "arb_secedit.hlp", AWM_ALL, makeWindowCallback(ED4_start_plugin, GLOBAL_gb_main, "SECEDIT"));
1457#if defined(ARB_OPENGL)
1458        awmm->insert_menu_topic("rna3d", "View 3D molecule", "3", "rna3d_general.hlp", AWM_ALL, makeWindowCallback(ED4_start_plugin, GLOBAL_gb_main, "RNA3D"));
1459#endif // ARB_OPENGL
1460#if defined(DEBUG)
1461        awmm->insert_menu_topic("noplugin", "DEBUG: call unknown plugin", "u", 0, AWM_ALL, makeWindowCallback(ED4_start_plugin, GLOBAL_gb_main, "testplugin"));
1462#endif // DEBUG
1463    }
1464
1465    // --------------
1466    //      View
1467
1468    awmm->create_menu("View", "V", AWM_ALL);
1469    awmm->insert_sub_menu("Search", "S");
1470    {
1471        int         s;
1472        const char *hotkeys  = "12Poiclrg";
1473        char        hotkey[] = "_";
1474
1475        e4_assert(strlen(hotkeys) == SEARCH_PATTERNS);
1476
1477        for (s=0; s<SEARCH_PATTERNS; s++) {
1478            ED4_SearchPositionType type = ED4_SearchPositionType(s);
1479            const char *id = ED4_SearchPositionTypeId[type];
1480            int len = strlen(id);
1481            char *macro_name = GB_give_buffer(2*(len+8));
1482            char *menu_entry_name = macro_name+(len+8);
1483
1484#ifndef NDEBUG
1485            memset(macro_name, 0, 2*(len+8)); // to avoid memchk-warning
1486#endif
1487            sprintf(macro_name, "%s_SEARCH", id);
1488            char *p = macro_name;
1489            while (1) {
1490                char c = *p++;
1491                if (!c) break;
1492                p[-1] = toupper(c);
1493            }
1494            sprintf(menu_entry_name, "%s Search", id);
1495
1496            hotkey[0] = hotkeys[s];
1497            awmm->insert_menu_topic(awmm->local_id(macro_name), menu_entry_name, hotkey, "e4_search.hlp", AWM_ALL, makeWindowCallback(ED4_popup_search_window, type));
1498        }
1499    }
1500    awmm->close_sub_menu();
1501    awmm->sep______________();
1502    awmm->insert_sub_menu("Cursor position ", "p");
1503    awmm->insert_menu_topic("store_curpos",   "Store cursor position",    "S", 0, AWM_ALL, ED4_store_curpos);
1504    awmm->insert_menu_topic("restore_curpos", "Restore cursor position ", "R", 0, AWM_ALL, ED4_restore_curpos);
1505    awmm->insert_menu_topic("clear_curpos",   "Clear stored positions",   "C", 0, AWM_ALL, makeWindowCallback(ED4_clear_stored_curpos));
1506    awmm->close_sub_menu();
1507
1508    awmm->sep______________();
1509    awmm->insert_menu_topic("change_cursor",             "Change cursor type",   "t", 0,              AWM_ALL, ED4_change_cursor);
1510    awmm->insert_menu_topic(awmm->local_id("view_diff"), "View differences ...", "V", "viewdiff.hlp", AWM_ALL, ED4_create_viewDifferences_window);
1511    awmm->sep______________();
1512    awmm->insert_menu_topic("enable_col_stat",  "Activate column statistics", "A", "st_ml.hlp", AWM_EXP, ED4_activate_col_stat);
1513    awmm->insert_menu_topic("disable_col_stat", "Disable column statistics",  "i", "st_ml.hlp", AWM_EXP, ED4_disable_col_stat);
1514    awmm->insert_menu_topic("detail_col_stat",  "Toggle detailed Col.-Stat.", "C", "st_ml.hlp", AWM_EXP, ED4_toggle_detailed_column_stats);
1515    awmm->insert_menu_topic("dcs_threshold",    "Set threshold for D.c.s.",   "f", "st_ml.hlp", AWM_EXP, makeWindowCallback(ED4_set_col_stat_threshold));
1516    awmm->sep______________();
1517    awmm->insert_menu_topic(awmm->local_id("visualize_SAI"), "Visualize SAIs",                "z", "visualizeSAI.hlp",   AWM_ALL, ED4_createVisualizeSAI_window);
1518    awmm->insert_menu_topic("toggle_saisec",                 "Toggle secondary info for SAI", "o", "toggle_secinfo.hlp", AWM_ALL, toggle_helix_for_SAI);
1519
1520    // Enable ProteinViewer only for DNA sequence type
1521    if (alignment_type == GB_AT_DNA) {
1522        awmm->insert_menu_topic(awmm->local_id("Protein_Viewer"), "Protein Viewer", "w", "proteinViewer.hlp", AWM_ALL, ED4_CreateProteinViewer_window);
1523    }
1524
1525    // ---------------
1526    //      Block
1527
1528    awmm->create_menu("Block", "B", AWM_ALL);
1529
1530    awmm->insert_menu_topic("select_marked",   "Select marked species",   "e", "e4_block.hlp", AWM_ALL, makeWindowCallback(ED4_menu_select, ED4_MS_SELECT_MARKED));
1531    awmm->insert_menu_topic("deselect_marked", "Deselect marked species", "k", "e4_block.hlp", AWM_ALL, makeWindowCallback(ED4_menu_select, ED4_MS_DESELECT_MARKED));
1532    awmm->insert_menu_topic("select_all",      "Select all species",      "S", "e4_block.hlp", AWM_ALL, makeWindowCallback(ED4_menu_select, ED4_MS_ALL));
1533    awmm->insert_menu_topic("deselect_all",    "Deselect all",            "D", "e4_block.hlp", AWM_ALL, makeWindowCallback(ED4_menu_select, ED4_MS_NONE));
1534    awmm->sep______________();
1535    awmm->insert_menu_topic("mark_selected",   "Mark selected species",   "M", "e4_block.hlp", AWM_ALL, makeWindowCallback(ED4_menu_select, ED4_MS_MARK_SELECTED));
1536    awmm->insert_menu_topic("unmark_selected", "Unmark selected species", "n", "e4_block.hlp", AWM_ALL, makeWindowCallback(ED4_menu_select, ED4_MS_UNMARK_SELECTED));
1537    awmm->insert_menu_topic("unmark_all",      "Unmark all species",      "U", "e4_block.hlp", AWM_ALL, makeWindowCallback(ED4_menu_select, ED4_MS_UNMARK_ALL));
1538    awmm->sep______________();
1539    awmm->insert_menu_topic("invert_all",   "Invert selected species", "I", "e4_block.hlp", AWM_ALL, makeWindowCallback(ED4_menu_select, ED4_MS_INVERT));
1540    awmm->insert_menu_topic("invert_group", "Invert group",            "g", "e4_block.hlp", AWM_ALL, makeWindowCallback(ED4_menu_select, ED4_MS_INVERT_GROUP));
1541    awmm->sep______________();
1542    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));
1543    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));
1544    awmm->sep______________();
1545    awmm->insert_menu_topic("reverse",            "Reverse selection ",    "v", "e4_block.hlp", AWM_ALL, makeWindowCallback(ED4_menu_perform_block_operation, ED4_BO_REVERSE));
1546    awmm->insert_menu_topic("complement",         "Complement selection ", "o", "e4_block.hlp", AWM_ALL, makeWindowCallback(ED4_menu_perform_block_operation, ED4_BO_COMPLEMENT));
1547    awmm->insert_menu_topic("reverse_complement", "Reverse complement",    "t", "e4_block.hlp", AWM_ALL, makeWindowCallback(ED4_menu_perform_block_operation, ED4_BO_REVERSE_COMPLEMENT));
1548    awmm->sep______________();
1549    awmm->insert_menu_topic("unalignBlockLeft",   "Unalign block left",   "a", "e4_block.hlp", AWM_ALL, makeWindowCallback(ED4_menu_perform_block_operation, ED4_BO_UNALIGN_LEFT));
1550    awmm->insert_menu_topic("unalignBlockCenter", "Unalign block center", "c", "e4_block.hlp", AWM_ALL, makeWindowCallback(ED4_menu_perform_block_operation, ED4_BO_UNALIGN_CENTER));
1551    awmm->insert_menu_topic("unalignBlockRight",  "Unalign block right",  "b", "e4_block.hlp", AWM_ALL, makeWindowCallback(ED4_menu_perform_block_operation, ED4_BO_UNALIGN_RIGHT));
1552    awmm->sep______________();
1553    awmm->insert_menu_topic(awmm->local_id("replace"), "Search & Replace ", "h", "e4_replace.hlp", AWM_ALL, ED4_create_replace_window);
1554    awmm->insert_menu_topic(awmm->local_id("setsai"),  "Modify SAI ",       "y", "e4_modsai.hlp",  AWM_ALL, ED4_create_modsai_window);
1555    awmm->sep______________();
1556    awmm->insert_menu_topic("toggle_block_type", "Exchange: Line<->Column", "x", "e4_block.hlp", AWM_ALL, makeWindowCallback(ED4_menu_select, ED4_MS_TOGGLE_BLOCKTYPE));
1557    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));
1558    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));
1559
1560    // --------------------
1561    //      Properties
1562
1563    awmm->create_menu("Properties", "P", AWM_ALL);
1564
1565#ifdef ARB_MOTIF
1566    awmm->insert_menu_topic(awmm->local_id("props_frame"), "Frame settings ...", "F", 0, AWM_ALL, AW_preset_window);
1567#endif
1568
1569    awmm->insert_menu_topic(awmm->local_id("props_options"),   "Editor Options ",       "O", "e4_options.hlp",   AWM_ALL, ED4_create_editor_options_window);
1570    awmm->insert_menu_topic(awmm->local_id("props_consensus"), "Consensus Definition ", "u", "e4_consensus.hlp", AWM_ALL, ED4_create_consensus_definition_window);
1571    awmm->sep______________();
1572
1573    awmm->insert_menu_topic("props_data",                       "Change Colors & Fonts ", "C", 0,                     AWM_ALL, makeWindowCallback      (ED4_popup_gc_window,          first_gc_manager));
1574    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));
1575
1576    awmm->sep______________();
1577
1578    awmm->insert_menu_topic(awmm->local_id("props_nds"),     "Select visible info (NDS) ", "D", "ed4_nds.hlp",   AWM_ALL, ED4_create_nds_window);
1579    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));
1580    {
1581        static WindowCallback reqRelCb = makeWindowCallback(ED4_request_relayout);
1582        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));
1583        else                            awmm->insert_menu_topic(awmm->local_id("props_helix_sym"), "Helix Settings ",         "H", "helixsym.hlp",    AWM_ALL, makeCreateWindowCallback(create_helix_props_window,     &reqRelCb));
1584    }
1585    awmm->insert_menu_topic(awmm->local_id("props_key_map"), "Key Mappings ",              "K", "nekey_map.hlp", AWM_ALL, create_key_map_window);
1586
1587    awmm->sep______________();
1588    AW_insert_common_property_menu_entries(awmm);
1589    awmm->sep______________();
1590    awmm->insert_sub_menu("Save properties ...", "a");
1591    {
1592        static const char * const tag[] = { "save_alispecific_props", "save_alitype_props", "save_props" };
1593        static const char * const entry_type[] = { "alignment specific ", "ali-type specific ", "" };
1594
1595        // check what is the default mode
1596        int default_mode = -1;
1597        for (int mode = 0; mode <= 2; ++mode) {
1598            if (strcmp(GB_path_in_arbprop(ED4_propertyName(mode)), db_name) == 0) {
1599                default_mode = mode;
1600                break;
1601            }
1602        }
1603        if (default_mode == -1) default_mode = 2; // no properties yet -> use 'edit4.arb'
1604
1605        const char *entry = GBS_global_string("Save loaded Properties (%s)", ED4_propertyName(default_mode));
1606        awmm->insert_menu_topic("save_loaded_props", entry, "l", "e4_defaults.hlp", AWM_ALL, makeWindowCallback(ED4_save_properties, default_mode));
1607        awmm->sep______________();
1608
1609        for (int mode = 2; mode >= 0; --mode) {
1610            char hotkey[] = "x";
1611            hotkey[0]     = "Pta"[mode];
1612            entry         = GBS_global_string("Save %sProperties (%s)", entry_type[mode], ED4_propertyName(mode));
1613            awmm->insert_menu_topic(tag[mode], entry, hotkey, "e4_defaults.hlp", AWM_ALL, makeWindowCallback(ED4_save_properties, mode));
1614        }
1615    }
1616    awmm->close_sub_menu();
1617
1618    awmm->insert_help_topic("ARB_EDIT4 help",     "E", "e4.hlp", AWM_ALL, makeHelpCallback("e4.hlp"));
1619
1620    // ----------------------------------------------------------------------------------------------------
1621
1622    aw_root->awar_int(AWAR_EDIT_TITLE_MODE)->add_callback(makeRootCallback(title_mode_changed, static_cast<AW_window*>(awmm)));
1623    awmm->set_bottom_area_height(0);   // No bottom area
1624
1625    awmm->auto_space(5, -2);
1626    awmm->shadow_width(3);
1627
1628    int db_pathx, db_pathy;
1629    awmm->get_at_position(&db_pathx, &db_pathy);
1630
1631    awmm->shadow_width(1);
1632    awmm->load_xfig("edit4/editmenu.fig", false);
1633
1634    // --------------------------
1635    //      help /quit /fold
1636
1637    awmm->button_length(0);
1638
1639    awmm->at("quit");
1640    awmm->callback(ED4_quit_editor);
1641    awmm->help_text("quit.hlp");
1642
1643    if (clone) {
1644        awmm->create_button("CLOSE", "#close.xpm");
1645#if defined(ARB_GTK)
1646        awmm->set_close_action("CLOSE");
1647#endif
1648    }
1649    else {
1650        awmm->create_button("QUIT", "#quit.xpm");
1651#if defined(ARB_GTK)
1652        awmm->set_close_action("QUIT");
1653#endif
1654    }
1655
1656    awmm->at("help");
1657    awmm->callback(AW_help_entry_pressed);
1658    awmm->help_text("e4.hlp");
1659    awmm->create_button("HELP", "#help.xpm");
1660
1661    awmm->at("fold");
1662    awmm->help_text("e4.hlp");
1663    awmm->create_toggle(AWAR_EDIT_TITLE_MODE, "#more.xpm", "#less.xpm");
1664
1665    // -------------------
1666    //      positions
1667
1668    awmm->button_length(0);
1669
1670    awmm->at("posTxt");     awmm->create_button(0, "Position");
1671
1672    awmm->button_length(6+1);
1673
1674    awmm->at("ecoliTxt");   awmm->create_button(0, ED4_AWAR_NDS_ECOLI_NAME, 0, "+");
1675
1676    awmm->button_length(0);
1677
1678    awmm->at("baseTxt");    awmm->create_button(0, "Base");
1679    awmm->at("iupacTxt");   awmm->create_button(0, "IUPAC");
1680    awmm->at("helixnrTxt"); awmm->create_button(0, "Helix#");
1681
1682    awmm->at("pos");
1683    awmm->callback(makeWindowCallback(ED4_jump_to_cursor_position, current_ed4w()->awar_path_for_cursor, ED4_POS_SEQUENCE)); // @@@ used as INPUTFIELD_CB (see #559)
1684    awmm->create_input_field(current_ed4w()->awar_path_for_cursor, 7);
1685
1686    awmm->at("ecoli");
1687    awmm->callback(makeWindowCallback(ED4_jump_to_cursor_position, current_ed4w()->awar_path_for_Ecoli, ED4_POS_ECOLI)); // @@@ used as INPUTFIELD_CB (see #559)
1688    awmm->create_input_field(current_ed4w()->awar_path_for_Ecoli, 6);
1689
1690    awmm->at("base");
1691    awmm->callback(makeWindowCallback(ED4_jump_to_cursor_position, current_ed4w()->awar_path_for_basePos, ED4_POS_BASE)); // @@@ used as INPUTFIELD_CB (see #559)
1692    awmm->create_input_field(current_ed4w()->awar_path_for_basePos, 6);
1693
1694    awmm->at("iupac");
1695    awmm->callback(makeWindowCallback(ED4_set_iupac, current_ed4w()->awar_path_for_IUPAC)); // @@@ used as INPUTFIELD_CB (see #559)
1696    awmm->create_input_field(current_ed4w()->awar_path_for_IUPAC, 4);
1697
1698    awmm->at("helixnr");
1699    awmm->callback(makeWindowCallback(ED4_set_helixnr, current_ed4w()->awar_path_for_helixNr)); // @@@ used as INPUTFIELD_CB (see #559)
1700    awmm->create_input_field(current_ed4w()->awar_path_for_helixNr, 5);
1701
1702    // ----------------------------
1703    //      jump/get/undo/redo
1704
1705    awmm->button_length(4);
1706
1707    awmm->at("jump");
1708    awmm->callback(ED4_jump_to_current_species);
1709    awmm->help_text("e4_get_species.hlp");
1710    awmm->create_button("JUMP", "Jump");
1711
1712    awmm->at("get");
1713    awmm->callback(makeWindowCallback(ED4_get_and_jump_to_current));
1714    awmm->help_text("e4_get_species.hlp");
1715    awmm->create_button("GET", "Get");
1716
1717    awmm->button_length(0);
1718
1719    awmm->at("undo");
1720    awmm->callback(makeWindowCallback(ED4_undo_redo, GB_UNDO_UNDO));
1721    awmm->help_text("undo.hlp");
1722    awmm->create_button("UNDO", "#undo.xpm");
1723
1724    awmm->at("redo");
1725    awmm->callback(makeWindowCallback(ED4_undo_redo, GB_UNDO_REDO));
1726    awmm->help_text("undo.hlp");
1727    awmm->create_button("REDO", "#redo.xpm");
1728
1729    // --------------------------
1730    //      aligner / SAIviz
1731
1732    awmm->button_length(7);
1733
1734    awmm->at("aligner");
1735    awmm->callback(makeCreateWindowCallback(ED4_create_faligner_window, ED4_get_aligner_data_access()));
1736    awmm->help_text("faligner.hlp");
1737    awmm->create_button("ALIGNER", "Aligner");
1738
1739    awmm->at("saiviz");
1740    awmm->callback(ED4_createVisualizeSAI_window);
1741    awmm->help_text("visualizeSAI.hlp");
1742    awmm->create_button("SAIVIZ", "SAIviz");
1743
1744    // -------------------------------------------
1745    //      align/insert/protection/direction
1746
1747    awmm->button_length(0);
1748
1749    awmm->at("protect");
1750    awmm->create_option_menu(AWAR_EDIT_SECURITY_LEVEL, true);
1751    awmm->insert_option("0", 0, 0);
1752    awmm->insert_option("1", 0, 1);
1753    awmm->insert_option("2", 0, 2);
1754    awmm->insert_option("3", 0, 3);
1755    awmm->insert_option("4", 0, 4);
1756    awmm->insert_option("5", 0, 5);
1757    awmm->insert_default_option("6", 0, 6);
1758    awmm->update_option_menu();
1759
1760    // draw protection icon AFTER protection!!
1761    awmm->at("pico");
1762    awmm->create_button(NULL, "#protect.xpm");
1763
1764    // draw align/edit-button AFTER protection!!
1765    awmm->at("edit");
1766    awmm->create_toggle(AWAR_EDIT_MODE, "#edit/align.xpm", "#edit/editseq.xpm", 7);
1767
1768    awmm->at("insert");
1769    awmm->create_text_toggle(AWAR_INSERT_MODE, "Replace", "Insert", 7);
1770
1771    awmm->at("direct");
1772    awmm->create_toggle(AWAR_EDIT_RIGHTWARD, "#edit/3to5.xpm", "#edit/5to3.xpm", 7);
1773
1774    // -------------------------
1775    //      secedit / rna3d
1776
1777    int xoffset = 0;
1778
1779    if (alignment_type == GB_AT_RNA) { // if the database contains valid alignment of rRNA sequences
1780        // add buttons for RNA3D and SECEDIT plugins
1781
1782        awmm->button_length(0);
1783
1784        awmm->at("secedit");
1785        awmm->callback(makeWindowCallback(ED4_start_plugin, GLOBAL_gb_main, "SECEDIT"));
1786        awmm->help_text("arb_secedit.hlp");
1787        awmm->create_button("SECEDIT", "#edit/secedit.xpm");
1788
1789#if defined(ARB_OPENGL)
1790        awmm->at("rna3d");
1791        awmm->callback(makeWindowCallback(ED4_start_plugin, GLOBAL_gb_main, "RNA3D"));
1792        awmm->help_text("rna3d_general.hlp");
1793        awmm->create_button("RNA3D", "#edit/rna3d.xpm");
1794#endif // ARB_OPENGL
1795    }
1796    else {
1797        awmm->at("secedit");
1798        int xsecedit = awmm->get_at_xposition();
1799        awmm->at("zoom");
1800        int xzoom    = awmm->get_at_xposition();
1801        xoffset      = xsecedit-xzoom; // shift message stuff to the left by xoffset
1802    }
1803
1804    {
1805        int x, y;
1806
1807        awmm->at("zoom");
1808        if (xoffset) { awmm->get_at_position(&x, &y); awmm->at(x+xoffset, y); }
1809        awmm->callback(ED4_zoom_message_window);
1810        awmm->create_button("ZOOM", "#edit/zoom.xpm");
1811
1812        awmm->at("clear");
1813        if (xoffset) { awmm->get_at_position(&x, &y); awmm->at(x+xoffset, y); }
1814        awmm->callback(aw_clear_message_cb);
1815        awmm->create_button("CLEAR", "#edit/clear.xpm");
1816
1817        awmm->at("errortext");
1818        if (xoffset) { awmm->get_at_position(&x, &y); awmm->at(x+xoffset, y); }
1819        aw_root->awar_string(AWAR_ERROR_MESSAGES, "This is ARB Edit4 [Build " ARB_VERSION "]");
1820        awmm->create_text_field(AWAR_ERROR_MESSAGES);
1821        aw_set_local_message();
1822    }
1823
1824    // ---------------------
1825    //      'more' area
1826
1827    awmm->at("cons");
1828    awmm->create_toggle(ED4_AWAR_CONSENSUS_SHOW, "#edit/nocons.xpm", "#edit/cons.xpm");
1829
1830    awmm->at("num");
1831    awmm->create_toggle(ED4_AWAR_DIGITS_AS_REPEAT, "#edit/norepeat.xpm", "#edit/repeat.xpm");
1832
1833    awmm->at("key");
1834    awmm->create_toggle("key_mapping/enable", "#edit/nokeymap.xpm", "#edit/keymap.xpm");
1835
1836    // search
1837
1838    awmm->button_length(0);
1839#define INSERT_SEARCH_FIELDS(Short, label_prefix, prefix)       \
1840    insert_search_fields(awmm,                                  \
1841                         #label_prefix,                         \
1842                         #prefix,                               \
1843                         ED4_AWAR_##prefix##_SEARCH_PATTERN,    \
1844                         ED4_AWAR_##prefix##_SEARCH_SHOW,       \
1845                         Short,                                 \
1846                         ED4_##prefix##_PATTERN,                \
1847                         current_ed4w()                         \
1848        )
1849
1850    INSERT_SEARCH_FIELDS(0, u1, USER1);
1851    INSERT_SEARCH_FIELDS(0, u2, USER2);
1852    INSERT_SEARCH_FIELDS(0, pro, PROBE);
1853    INSERT_SEARCH_FIELDS(1, pri1, PRIMER1);
1854    INSERT_SEARCH_FIELDS(1, pri2, PRIMER2);
1855    INSERT_SEARCH_FIELDS(1, pri3, PRIMER3);
1856    INSERT_SEARCH_FIELDS(1, sig1, SIG1);
1857    INSERT_SEARCH_FIELDS(1, sig2, SIG2);
1858    INSERT_SEARCH_FIELDS(1, sig3, SIG3);
1859
1860#undef INSERT_SEARCH_FIELDS
1861
1862    awmm->at("alast");
1863    awmm->callback(makeWindowCallback(ED4_search_cb, ED4_encodeSearchDescriptor(-1, ED4_ANY_PATTERN), current_ed4w()));
1864    awmm->create_button("ALL_SEARCH_LAST", "#edit/last.xpm");
1865
1866    awmm->at("anext");
1867    awmm->callback(makeWindowCallback(ED4_search_cb, ED4_encodeSearchDescriptor(+1, ED4_ANY_PATTERN), current_ed4w()));
1868    awmm->create_button("ALL_SEARCH_NEXT", "#edit/next.xpm");
1869
1870    title_mode_changed(aw_root, awmm);
1871
1872    // Buttons at left window border
1873
1874    awmm->create_mode("edit/arrow.xpm", "e4_mode.hlp", AWM_ALL, makeWindowCallback(modes_cb, ED4_SM_MOVE));
1875    awmm->create_mode("edit/kill.xpm",  "e4_mode.hlp", AWM_ALL, makeWindowCallback(modes_cb, ED4_SM_KILL));
1876    awmm->create_mode("edit/mark.xpm",  "e4_mode.hlp", AWM_ALL, makeWindowCallback(modes_cb, ED4_SM_MARK));
1877    awmm->create_mode("mode_info.xpm",  "e4_mode.hlp", AWM_ALL, makeWindowCallback(modes_cb, ED4_SM_INFO));
1878
1879    FastAligner_create_variables(awmm->get_root(), props_db);
1880
1881#if defined(DEBUG)
1882    AWT_check_action_ids(awmm->get_root(), "");
1883#endif
1884
1885    announce_useraction_in(awmm);
1886
1887    return (ED4_R_OK);
1888}
1889
1890AW_window *ED4_root::create_first_window() {
1891    // Note: other windows are generated by generate_window
1892    AW_device  *device     = NULL;
1893    ED4_window *new_window = NULL;
1894
1895    generate_window(&device, &new_window);
1896
1897    ED4_LocalWinContext uses(new_window);
1898
1899    ED4_calc_terminal_extentions(); // (Note: done again later, but otherwise variables are used uninitialized);
1900
1901    DRAW                    = 1;
1902    move_cursor             = 0;
1903    max_seq_terminal_length = 0;
1904
1905    ED4_init_notFoundMessage();
1906
1907    return new_window->aww;
1908}
1909
1910ED4_index ED4_root::pixel2pos(AW_pos click_x) {
1911    // 'click_x' is the x-offset into the terminal in pixels
1912    // returns the x-offset into the terminal in base positions (clipped to max. allowed position)
1913
1914    int       length_of_char = font_group.get_width(ED4_G_SEQUENCES);
1915    ED4_index scr_pos        = int((click_x-CHARACTEROFFSET) / length_of_char);
1916    int       max_scrpos     = root_group_man->remap()->get_max_screen_pos();
1917
1918    if (scr_pos>max_scrpos) scr_pos = max_scrpos;
1919
1920    return scr_pos;
1921}
1922
1923static char *detectProperties() {
1924    char *propname = NULL;
1925
1926    // check if edit4_?na.arb / edit4_ali_???.arb exist in $ARB_PROP
1927    for (int mode = 0; !propname && mode <= 1; ++mode) { 
1928        const char *fullprop = GB_path_in_arbprop(ED4_propertyName(mode));
1929        if (GB_is_regularfile(fullprop)) {
1930            freedup(propname, fullprop);
1931        }
1932    }
1933
1934    // if not, use 'mode 2', i.e. "edit4.arb"
1935    // (no full path, we want to load default from arb_defaults)
1936    if (!propname) propname = ARB_strdup(ED4_propertyName(2));
1937
1938    return propname;
1939}
1940
1941ED4_root::ED4_root(int* argc, char*** argv)
1942    : most_recently_used_window(0),
1943      cons_param(NULL),
1944      db_name(detectProperties()),
1945      aw_root(AWT_create_root(db_name, "ARB_EDIT4", need_macro_ability(), argc, argv)),
1946      props_db(AW_ROOT_DEFAULT),
1947      first_window(0),
1948      main_manager(0),
1949      middle_area_man(0),
1950      top_area_man(0),
1951      root_group_man(0),
1952      database(0),
1953      selected_objects(new ED4_selected_list), 
1954      folding_action(0),
1955      species_mode(ED4_SM_MOVE),
1956      ecoli_ref(0),
1957      alignment_name(0),
1958      alignment_type(GB_AT_UNKNOWN),
1959      reference(0),
1960      sequence_colors(0),
1961      gc_manager(0),
1962      st_ml(0),
1963      helix(0),
1964      helix_spacing(0),
1965      helix_add_spacing(0),
1966      terminal_add_spacing(0),
1967      protstruct(0),
1968      protstruct_len(0),
1969      edk(0),
1970      edit_string(0),
1971      column_stat_activated(false),
1972      column_stat_initialized(false),
1973      visualizeSAI(false),
1974      visualizeSAI_allSpecies(false),
1975      loadable_SAIs(LSAI_UNUSED),
1976      temp_gc(0)
1977{}
1978
1979
1980ED4_root::~ED4_root() {
1981    delete aw_root;
1982    delete first_window;
1983    delete reference; // needs to be deleted before main_manager (to ensure reference callbacks are removed)
1984    delete main_manager; // also deletes middle_area_man + top_area_man
1985    delete database;
1986    delete ecoli_ref;
1987    delete selected_objects;
1988    delete helix;
1989    delete sequence_colors;
1990    delete edk;
1991    STAT_destroy_ST_ML(st_ml);
1992
1993    free(protstruct);
1994    free(db_name);
1995    free(alignment_name);
1996}
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