SEC_main.cxx

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// =============================================================== //
//                                                                 //
//   File      : SEC_main.cxx                                      //
//   Purpose   : main part of SECEDIT                              //
//                                                                 //
//   Institute of Microbiology (Technical University Munich)       //
//   http://www.arb-home.de/                                       //
//                                                                 //
// =============================================================== //

#include "SEC_root.hxx"
#include "SEC_graphic.hxx"
#include "SEC_helix.hxx"
#include "SEC_drawn_pos.hxx"
#include "SEC_toggle.hxx"

#include <BufferedFileReader.h>

#include <aw_awars.hxx>
#include <aw_preset.hxx>
#include <aw_file.hxx>
#include <aw_msg.hxx>
#include <aw_root.hxx>
#include <aw_question.hxx>

#include <mode_text.h>

#include <arb_file.h>
#include <awt_config_manager.hxx>
#include <ad_cb_prot.h>

#ifndef sec_assert // happens in NDEBUG mode
#define sec_assert(cond) arb_assert(cond)
#endif

void SEC_root::invalidate_base_positions() {
    if (root_loop) {
        SEC_base_part *start_part = root_loop->get_fixpoint_strand();
        SEC_base_part *part       = start_part;

        do {
            part->get_region()->invalidate_base_count();
            part = part->next();
        }
        while (part != start_part);
    }
}

// ------------------------------------------------------
//      auto-scrolling (triggered by structure self)

void SEC_root::nail_position(size_t absPos) {
    if (drawnPositions) {
        nailedAbsPos = absPos;
        drawnAbsPos  = *drawnPositions->drawn_at(absPos);
    }
}

void SEC_root::nail_cursor() { // re-position on cursor
    if (cursorAbsPos >= 0) {
        if (drawnPositions && !drawnPositions->empty()) {
            size_t abs;
            drawnAbsPos  = drawnPositions->drawn_after(cursorAbsPos-1, &abs);
            nailedAbsPos = abs;
        }
    }
}

void SEC_root::add_autoscroll(const Vector& scroll) {
    if (autoscroll) *autoscroll += scroll;
    else autoscroll              = new Vector(scroll);
}

bool SEC_root::perform_autoscroll() {
    bool        scrolled = false;
    AWT_canvas *canvas   = db->canvas();

    if (canvas && (nailedAbsPos != -1 || autoscroll)) {
        AW_device *device = canvas->aww->get_device(AW_MIDDLE_AREA);

        if (nailedAbsPos != -1) {
            {
                int     absPos = nailedAbsPos;
                Vector *scroll = autoscroll;

                // avoid endless recursion:
                nailedAbsPos = -1;
                autoscroll   = NULp;

                // @@@ make the refresh invisible

                {
                    // hack: we may be inside or outside sync_DB_model_and_view() here (be permissive about flags here)
                    LocallyModify<int> allow_flag_modify(canvas->gfx->exports.get_modifying_flag_ref(), -1);
                    canvas->gfx->exports.update_display_as_requested(canvas, true);
                }

                nailedAbsPos = absPos;
                autoscroll   = scroll;
            }
            const Position *newPos = drawnPositions->drawn_at(nailedAbsPos);
            if (newPos) {
                Vector old2new(drawnAbsPos, *newPos);
#if defined(DEBUG) && 0
                printf("drawnAbsPos=%.2f/%.2f newPos=%.2f/%.2f old2new=%.2f/%.2f\n",
                       drawnAbsPos.xpos(), drawnAbsPos.ypos(),
                       newPos->xpos(), newPos->ypos(),
                       old2new.x(), old2new.y());
#endif // DEBUG
                add_autoscroll(old2new);
            }
            nailedAbsPos = -1;
        }
        if (autoscroll) {
            canvas->init_device(device); // loads correct zoom
            Vector screen_scroll = device->transform(*autoscroll);

#if defined(DEBUG) && 0
            printf("autoscroll=%.2f/%.2f screen_scroll=%.2f/%.2f\n",
                   autoscroll->x(), autoscroll->y(),
                   screen_scroll.x(), screen_scroll.y());
#endif // DEBUG

            delete autoscroll;
            autoscroll = NULp;

            device->clear(-1);
            {
                // hack: we may be inside sync_DB_model_and_view() here, but scroll() instanciates an AWT_auto_refresh. Permit!
                LocallyModify<int> allow_flag_modify(canvas->gfx->exports.get_modifying_flag_ref(), 0);
                canvas->scroll(screen_scroll);
            }
            scrolled = true;
        }
    }
    return scrolled;
}
// --------------------------------------------------------------------------------

void SEC_root::position_cursor(bool toCenter, bool evenIfVisible) {
    // centers the cursor in display (or scrolls it into view)
    // if 'evenIfVisible' is true, always do it, otherwise only if not (fully) visible

    const LineVector& cursorLine = get_last_drawed_cursor_position();
    sec_assert(cursorLine.valid());

    AWT_canvas *scr    = db->canvas();
    AW_device  *device = scr->aww->get_device(AW_MIDDLE_AREA);

    Rectangle cursor(device->transform(cursorLine));
    Rectangle screen(device->get_area_size(), INCLUSIVE_OUTLINE);

    if (evenIfVisible || !screen.contains(cursor)) {
        if (!toCenter) {
            if (perform_autoscroll()) {
                cursor = Rectangle(device->transform(cursorLine));
                if (!screen.contains(cursor)) {
                    toCenter = true;
                }
            }
            else { // if autoscroll didn't work
                toCenter = true; // center cursor
            }
        }

        if (toCenter) {
            AWT_auto_refresh allowed_on(scr);
            Vector           scroll(cursor.centroid(), screen.centroid());

#if defined(DEBUG) && 1
            printf("Auto-scroll: scroll = (%f, %f) [Center cursor]\n", scroll.x(), scroll.y());
#endif
            scr->scroll(-scroll);
            scr->request_refresh();
        }
    }
}

static void SEC_toggle_cb(AW_window*, const SEC_db_interface *db) {
    AWT_auto_refresh allowed_on(db->canvas());
    GB_ERROR error = db->structure()->next();
    if (error) aw_message(error);
    db->canvas()->request_refresh();
}

static void SEC_center_cb(AW_window *, SEC_root *root) {
    root->position_cursor(true, true);
}

static void SEC_fit_window_cb(AW_window*, const SEC_db_interface *db) {
    AWT_auto_refresh allowed_on(db->canvas());
    db->canvas()->request_zoom_reset();
}

static void sec_mode_event(AW_window *aws, SEC_root *sec_root, AWT_COMMAND_MODE mode) {
    const char *text = NULp;
    switch (mode) {
        case AWT_MODE_ZOOM: text = MODE_TEXT_STANDARD_ZOOMMODE(); break;

        case AWT_MODE_EDIT:   text = MODE_TEXT_1BUTTON("CONSTRAINT", "modify constraint");       break;
        case AWT_MODE_CURSOR: text = MODE_TEXT_1BUTTON("SET CURSOR", "set cursor in ARB_EDIT4"); break;

        case AWT_MODE_FOLD:    text = MODE_TEXT_2BUTTONS("FOLD",       "fold helix",                              "unfold helix");                  break;
        case AWT_MODE_SETROOT: text = MODE_TEXT_2BUTTONS("SET ROOT",   "set logical center of structure",         "reset angles on sub-structure"); break;
        case AWT_MODE_ROTATE:  text = MODE_TEXT_2BUTTONS("ROTATE",     "rotate helix/loop",                       "same w/o substructure");         break;
        case AWT_MODE_STRETCH: text = MODE_TEXT_2BUTTONS("STRETCH",    "click and drag to stretch helices/loops", "reset");                         break;
        case AWT_MODE_PINFO:   text = MODE_TEXT_2BUTTONS("PROBE INFO", "display PROBE information",               "undisplay");                     break;

        default: text = no_mode_text_defined(); break;
    }

    sec_root->set_show_constraints((mode == AWT_MODE_STRETCH || mode == AWT_MODE_EDIT)
                                   ? SEC_ANY_TYPE
                                   : SEC_NO_TYPE);

    sec_assert(strlen(text) < AWAR_FOOTER_MAX_LEN); // text too long!

    aws->get_root()->awar(AWAR_FOOTER)->write_string(text);

    AWT_canvas       *scr = sec_root->get_db()->canvas();
    AWT_auto_refresh  allowed_on(scr);
    scr->set_mode(mode);
    scr->request_refresh();
}

static void SEC_undo_cb(AW_window *, const SEC_db_interface *db, GB_UNDO_TYPE undo_type) {
    GBDATA   *gb_main = db->gbmain();
    GB_ERROR  error   = GB_undo(gb_main, undo_type);
    if (error) {
        aw_message(error);
    }
    else {
        GB_begin_transaction(gb_main);
        GB_commit_transaction(gb_main);
        AWT_auto_refresh allowed_on(db->canvas());
        db->canvas()->request_refresh();
    }
}

// --------------------------------------------------------------------------------

#define ASS       "ARB secondary structure v1" // don't change version here!
#define ASS_START "[" ASS "]"
#define ASS_EOS   "[end of structure]"
#define ASS_EOF   "[end of " ASS "]"

static void export_structure_to_file(AW_window *, const SEC_db_interface *db) {
    GB_ERROR  error    = NULp;
    SEC_root *sec_root = db->secroot();

    if (!sec_root->get_root_loop()) {
        error = "Please select a species (to display structure once) before saving";
    }
    else {
        AW_root *aw_root  = db->awroot();
        char    *filename = aw_root->awar(AWAR_SECEDIT_SAVEDIR"/file_name")->read_string();
        FILE    *out      = fopen(filename, "wt");

        if (out) {

            fputs(ASS_START, out); fputc('\n', out);

            char *strct = sec_root->buildStructureString();
            fputs(strct, out);
            delete [] strct;

            fputs(ASS_EOS, out); fputc('\n', out);

            const XString& xstr     = sec_root->get_xString();
            const char    *x_string = xstr.get_x_string();

            sec_assert(xstr.get_x_string_length() == strlen(x_string));

            char *foldInfo = SEC_xstring_to_foldedHelixList(x_string, xstr.get_x_string_length(), sec_root->get_helixDef(), error);
            if (foldInfo) {
                fprintf(out, "foldedHelices=%s\n", foldInfo);
                free(foldInfo);
            }

            fputs(ASS_EOF, out); fputc('\n', out);
            fclose(out);

            if (error) GB_unlink_or_warn(filename, &error);
        }
        else {
            error = GB_export_errorf("Can't write secondary structure to '%s'", filename);
        }

        free(filename);
    }
    if (error) aw_message(error);
}

inline GB_ERROR expectedError(const char *expected) {
    return GBS_global_string("expected '%s'", expected);
}
inline GB_ERROR expectContent(LineReader& file, const char *expected) {
    GB_ERROR error = NULp;
    string   line;
    if (!file.getLine(line) || line != expected) {
        error = expectedError(expected);
    }
    return error;
}

static string scanToken(LineReader& file, string& rest, GB_ERROR& error) {
    string line;
    string token;

    sec_assert(!error);

    if (file.getLine(line)) {
        size_t equal = line.find('=');

        if (equal == string::npos) {
            error = "Expected '='";
        }
        else {
            token = line.substr(0, equal);
            rest  = line.substr(equal+1);
        }
    }
    else {
        error = "Unexpected EOF";
    }
    return token;
}

static GB_ERROR expectToken(LineReader& file, const char *token, string& content) {
    GB_ERROR error      = NULp;
    string   foundToken = scanToken(file, content, error);
    if (foundToken != token) error = expectedError(token);
    return error;
}

static void import_structure_from_file(AW_window *, const SEC_db_interface *db) {
    GB_ERROR  error = NULp;
    SEC_root *root  = db->secroot();

    if (!root->has_xString()) {
        error = "Please select a species in EDIT4";
    }
    else {
        char        *filename = db->awroot()->awar(AWAR_SECEDIT_SAVEDIR"/file_name")->read_string();
        FILE        *in       = fopen(filename, "rt"); // closed by FileBuffer

        if (!in) {
            error = GB_export_errorf("Can't open file '%s'", filename);
        }
        else {
            BufferedFileReader file(filename, in);
            error = expectContent(file, ASS_START);

            string structure;
            while (!error) {
                string line;
                if (!file.getLine(line)) error = expectedError(ASS_EOS);
                else {
                    if (line == ASS_EOS) break;
                    structure += line + "\n";
                }
            }

            char *x_string = NULp;
            if (!error) {
                string content;
                string token = scanToken(file, content, error);

                if (!error) {
                    // we already have an existing xstring, use it's length for new xstring
                    size_t xlength = root->get_xString().getLength();

                    if (token == "foldedHelices") { // new version
                        x_string = SEC_foldedHelixList_to_xstring(content.c_str(), xlength, root->get_helixDef(), error); // sets error
                    }
                    else if (token == "no of helices") { // old version
                        int saved_helices = atoi(content.c_str());

                        error             = expectToken(file, "length of xstring", content); // ignore, using curr value
                        if (!error) error = expectToken(file, "xstring_rel_helix", content);
                        if (!error) {
                            int helices_in_db;
                            x_string = old_decode_xstring_rel_helix(content.c_str(), xlength, root->get_helixDef(), &helices_in_db);
                            if (helices_in_db != saved_helices) {
                                error = GBS_global_string("Number of helices does not match (file=%i, db=%i).\n"
                                                          "Saving the structure again from another DB with correct number of helices will work around this restriction.",
                                                          saved_helices, helices_in_db);
                            }
                        }
                    }
                    else {
                        error = "Expected 'foldedHelices' or 'no of helices'";
                    }
                }
                if (!error) error = expectContent(file, ASS_EOF);
            }

            if (error) {
                error = GBS_static_string(file.lineError(error).c_str());
            }
            else {
                AWT_auto_refresh allowed_on(db->canvas());
                db->graphic()->write_data_to_db(structure.c_str(), x_string);
                db->canvas()->request_refresh();
            }
            free(x_string);
        }
        free(filename);
    }
    if (error) aw_message(error);
}

#undef ASS
#undef ASS_START
#undef ASS_EOS
#undef ASS_EOF

static AW_window *SEC_importExport(AW_root *root, bool export_to_file, const SEC_db_interface *db) {
    AW_window_simple *aws = new AW_window_simple;

    if (export_to_file) aws->init(root, "export_secondary_structure", "Export secondary structure to ...");
    else                aws->init(root, "import_secondary_structure", "Import secondary structure from ...");

    aws->load_xfig("sec_imexport.fig");

    aws->at("close");
    aws->callback(AW_POPDOWN);
    aws->create_button("CLOSE", "CLOSE", "C");

    aws->at("help");
    aws->callback(makeHelpCallback("sec_imexport.hlp"));
    aws->create_button("HELP", "HELP", "H");

    AW_create_standard_fileselection(aws, AWAR_SECEDIT_SAVEDIR);

    aws->at("save");
    if (export_to_file) {
        aws->callback(makeWindowCallback(export_structure_to_file, db));
        aws->create_button("EXPORT", "EXPORT", "E");
    }
    else {
        aws->callback(makeWindowCallback(import_structure_from_file, db));
        aws->create_button("IMPORT", "IMPORT", "I");
    }

    return aws;
}

static void SEC_rename_structure(AW_window*, const SEC_db_interface *db) {
    SEC_structure_toggler *structure = db->structure();

    char *new_name = aw_input("Rename structure", "New name", structure->name());
    if (new_name) {
        structure->setName(new_name);
        free(new_name);
        AWT_auto_refresh allowed_on(db->canvas());
        db->canvas()->request_refresh();
    }
}

static void SEC_new_structure(AW_window*, const SEC_db_interface *db) {
    SEC_structure_toggler *structure = db->structure();

    if (!structure) {
        db->init_toggler();
        structure = db->structure();
        sec_assert(structure);
    }

    GB_ERROR error = NULp;
    bool     done  = false;

    switch (aw_question(NULp, "Create new structure?", "Default bone,Copy current,Abort")) {
        case 0:                 // default bone
            error = structure->copyTo("Default");
            if (!error) {
                db->secroot()->create_default_bone();
                db->graphic()->save_to_DB(NULp, NULp);
                done = true;
            }
            break;

        case 1:                 // copy current
            error = structure->copyTo(GBS_global_string("%s(copy)", structure->name()));
            done  = !error;
            break;

        case 2:                 // abort
            break;
    }

    if (done) {
        {
            AWT_auto_refresh allowed_on(db->canvas());
            db->canvas()->request_zoom_reset();
        }
        SEC_rename_structure(NULp, db);
    }
}

static void SEC_delete_structure(AW_window*, const SEC_db_interface *db) {
    SEC_structure_toggler *structure = db->structure();

    if (structure->getCount()>1) {
        if (aw_ask_sure("delete_sec_structure", GBS_global_string("Are you sure to delete structure '%s'?", structure->name()))) {
            AWT_auto_refresh allowed_on(db->canvas());
            GB_ERROR error = structure->remove();
            if (error) aw_message(error);
            db->canvas()->request_refresh();
        }
    }
    else {
        aw_message("You cannot delete the last structure");
    }
}

enum SyncColors {
    COLOR_SYNC_SEARCH = 1,
    COLOR_SYNC_RANGE  = 2,
    COLOR_SYNC_REST   = 4,

    COLOR_SYNC_ALL = (COLOR_SYNC_SEARCH|COLOR_SYNC_RANGE|COLOR_SYNC_REST),
};

static void SEC_sync_colors(AW_window *aww, SyncColors which) {
    // overwrites color settings with those from EDIT4

    if (which & COLOR_SYNC_SEARCH) {
        AW_copy_GC_colors(aww->get_root(), "ARB_EDIT4", "ARB_SECEDIT",
                          "User1",   "User2",   "Probe",
                          "Primerl", "Primerr", "Primerg",
                          "Sigl",    "Sigr",    "Sigg",
                          "MISMATCHES",
                          NULp);
    }
    if (which & COLOR_SYNC_RANGE) {
        AW_copy_GC_colors(aww->get_root(), "ARB_EDIT4", "ARB_SECEDIT",
                          "RANGE_0", "RANGE_1", "RANGE_2",
                          "RANGE_3", "RANGE_4", "RANGE_5",
                          "RANGE_6", "RANGE_7", "RANGE_8",
                          "RANGE_9",
                          NULp);
    }
    if (which & COLOR_SYNC_REST) {
        AW_copy_GC_colors(aww->get_root(), "ARB_EDIT4", "ARB_SECEDIT",
                          "CURSOR",
                          NULp);
    }
}

static AW_window *SEC_create_bonddef_window(AW_root *awr) {
    AW_window_simple *aws = new AW_window_simple;

    aws->reset_layout("20230616");
    aws->init(awr, "SEC_BONDDEF", "Bond definitions");
    aws->load_xfig("sec_bonddef.fig");

    aws->at("close");
    aws->callback(AW_POPDOWN);
    aws->create_button("CLOSE", "CLOSE", "C");

    aws->callback(makeHelpCallback("sec_bonddef.hlp"));
    aws->at("help");
    aws->create_button("HELP", "HELP", "H");

    aws->label_length(24);

    aws->at("edit4");
    aws->label("Helix symbols\n"
               "defined in EDIT4:");
    aws->create_input_field(AWAR_SECEDIT_BOND_SYMBOLS_EDIT4, 30);

    aws->at("translate");
    aws->label("Translate into\n"
               "for display in SECEDIT:");
    aws->create_input_field(AWAR_SECEDIT_BOND_SYMBOLS_TRANS, 30);

    return aws;
}

static AWT_config_mapping_def secedit_display_config_mapping[] = {
    { AWAR_SECEDIT_HIDE_BASES,        "hidebases" },
    { AWAR_SECEDIT_DIST_BETW_STRANDS, "stranddist" },
    { AWAR_SECEDIT_SHOW_BONDS,        "showbonds" },

    { AWAR_SECEDIT_BOND_SYMBOLS_EDIT4, "bondsymbol_edit4" },
    { AWAR_SECEDIT_BOND_SYMBOLS_TRANS, "bondsymbol_trans" },

    { AWAR_SECEDIT_BOND_THICKNESS,     "bondthickness" },
    { AWAR_SECEDIT_SHOW_CURPOS,        "showposition" },
    { AWAR_SECEDIT_SHOW_HELIX_NRS,     "showhelixnrs" },
    { AWAR_SECEDIT_SHOW_ECOLI_POS,     "showecolipos" },
    { AWAR_SECEDIT_DISPLAY_SEARCH,     "showsearch" },
    { AWAR_SECEDIT_DISPLAY_SAI,        "showsai" },
    { AWAR_SECEDIT_DISPPOS_BINDING,    "disppos_helix" },
    { AWAR_SECEDIT_DISPPOS_ECOLI,      "disppos_ecoli" },
    { AWAR_SECEDIT_SHOW_STR_SKELETON,  "skeleton" },
    { AWAR_SECEDIT_SKELETON_THICKNESS, "skeleton_thickness" },

    { NULp, NULp }
};

static AW_window *SEC_create_display_window(AW_root *awr) {
    AW_window_simple *aws = new AW_window_simple;

    const int SCALED_TEXT_COLUMNS = 7;
    const int SCALER_WIDTH        = 200;

    aws->auto_space(5, 5);

    aws->init(awr, "SEC_DISPLAY_OPTS", "Display options");
    aws->load_xfig("sec_display.fig");

    aws->at("close");
    aws->callback(AW_POPDOWN);
    aws->create_button("CLOSE", "CLOSE", "C");

    aws->callback(makeHelpCallback("sec_display.hlp"));
    aws->at("help");
    aws->create_button("HELP", "HELP", "H");

    // ----------------------------------------

    aws->at("bases");
    aws->label("Display bases              :");
    aws->create_inverse_toggle(AWAR_SECEDIT_HIDE_BASES);

    aws->at("strand_dist");
    aws->label("Distance between strands   :");
    aws->create_input_field_with_scaler(AWAR_SECEDIT_DIST_BETW_STRANDS, SCALED_TEXT_COLUMNS, SCALER_WIDTH, AW_SCALER_EXP_LOWER);

    aws->at("bonds");
    aws->label("Display bonds");
    aws->create_option_menu(AWAR_SECEDIT_SHOW_BONDS);
    aws->insert_option("None",       "n", SHOW_NO_BONDS);
    aws->insert_option("Helix",      "h", SHOW_HELIX_BONDS);
    aws->insert_option("+Non-helix", "o", SHOW_NHELIX_BONDS);
    aws->update_option_menu();

    aws->at("bonddef");
    aws->callback(makeCreateWindowCallback(SEC_create_bonddef_window));
    aws->create_button("sec_bonddef", "Define");

    aws->at("bondThickness");
    aws->label("Bond thickness             :");
    aws->create_input_field_with_scaler(AWAR_SECEDIT_BOND_THICKNESS, SCALED_TEXT_COLUMNS, SCALER_WIDTH, AW_SCALER_EXP_LOWER);

    // ----------------------------------------

    aws->at("cursor");
    aws->label("Annotate cursor            :");
    aws->create_option_menu(AWAR_SECEDIT_SHOW_CURPOS);
    aws->insert_option("None",     "n", SHOW_NO_CURPOS);
    aws->insert_option("Absolute", "a", SHOW_ABS_CURPOS);
    aws->insert_option("Ecoli",    "e", SHOW_ECOLI_CURPOS);
    aws->insert_option("Base",     "b", SHOW_BASE_CURPOS);
    aws->update_option_menu();

    aws->at("helixNrs");
    aws->label("Annotate helices           :");
    aws->create_toggle(AWAR_SECEDIT_SHOW_HELIX_NRS);

    aws->at("ecoli");
    aws->label("Annotate ecoli positions   :");
    aws->create_toggle(AWAR_SECEDIT_SHOW_ECOLI_POS);

    aws->at("search");
    aws->label("Visualize search results   :");
    aws->create_toggle(AWAR_SECEDIT_DISPLAY_SEARCH);

    aws->at("sai");
    aws->label("Visualize SAI              :");
    aws->create_toggle(AWAR_SECEDIT_DISPLAY_SAI);

    // ----------------------------------------

    aws->at("binding");
    aws->label("Binding helix positions    :");
    aws->create_toggle(AWAR_SECEDIT_DISPPOS_BINDING);

    aws->at("ecoli2");
    aws->label("Ecoli base positions       :");
    aws->create_toggle(AWAR_SECEDIT_DISPPOS_ECOLI);

    // ----------------------------------------

    aws->at("strSkeleton");
    aws->label("Display structure skeleton :");
    aws->create_toggle(AWAR_SECEDIT_SHOW_STR_SKELETON);

    aws->at("skelThickness");
    aws->label("Skeleton thickness         :");
    aws->create_input_field_with_scaler(AWAR_SECEDIT_SKELETON_THICKNESS, SCALED_TEXT_COLUMNS, SCALER_WIDTH, AW_SCALER_EXP_LOWER);

#ifdef DEBUG
    aws->at("show_debug");
    aws->label("Show debug info:");
    aws->create_toggle(AWAR_SECEDIT_SHOW_DEBUG);
#endif

    static AWT_predefined_config secedit_display_predef_config[] = {
        { "*bonds_arb7", "Translation of helix symbols\n(from ARB_EDIT4 -> ARB_SECEDIT)\nSimulates bond display used up to arb 7.0", "bondsymbol_edit4='#~-=';bondsymbol_trans=' -.o'" },
        { NULp, NULp, NULp }
    };

    aws->at("config");
    AWT_insert_config_manager(aws, AW_ROOT_DEFAULT, "secedit_display", secedit_display_config_mapping, NULp, secedit_display_predef_config);

    return aws;
}

static void SEC_exit(GBDATA *, SEC_root *sec_root) {
    // @@@ use popdown callback for SEC_exit and valgrind open/close/open secedit
    delete sec_root;
}

static AW_window *SEC_create_gc_window(AW_root *awr, AW_gc_manager *gcman) {
    return AW_create_gc_window_named(awr, gcman, "SECEDIT_COLOR_DEF2", "SECEDIT colors and fonts");
}

AW_window *start_SECEDIT_plugin(ED4_plugin_host& host) {
    AW_root *awr     = host.get_application_root();
    GBDATA  *gb_main = host.get_database();

    SEC_graphic *gfx  = new SEC_graphic(awr, gb_main); // never freed
    SEC_root    *root = gfx->sec_root;

    AW_window_menu_modes *awm = new AW_window_menu_modes;
    awm->init(awr, "ARB_SECEDIT", "ARB_SECEDIT: Secondary structure editor", 200, 200);

    AWT_canvas *scr = new AWT_canvas(gb_main, awm, awm->get_window_id(), gfx);
    {
        AWT_auto_refresh allowed_on(scr);
        root->init(gfx, scr, host);
        scr->request_resize();
    }
    scr->set_mode(AWT_MODE_ZOOM); // Default-Mode

    const SEC_db_interface *db = root->get_db();

    GB_atclose_callback(gb_main, makeDatabaseCallback(SEC_exit, root));

    awm->create_menu("File", "F", AWM_ALL);

    awm->insert_menu_topic("secedit_new",    "New structure",    "N", NULp, AWM_ALL, makeWindowCallback(SEC_new_structure,    db));
    awm->insert_menu_topic("secedit_rename", "Rename structure", "R", NULp, AWM_ALL, makeWindowCallback(SEC_rename_structure, db));
    awm->insert_menu_topic("secedit_delete", "Delete structure", "D", NULp, AWM_ALL, makeWindowCallback(SEC_delete_structure, db));
    awm->sep______________();
    awm->insert_menu_topic("secedit_import", "Load structure", "L", "secedit_imexport.hlp", AWM_ALL, makeCreateWindowCallback(SEC_importExport, false, db));
    awm->insert_menu_topic("secedit_export", "Save structure", "S", "secedit_imexport.hlp", AWM_ALL, makeCreateWindowCallback(SEC_importExport, true, db));
    awm->sep______________();
    awm->insert_menu_topic("secStruct2xfig", "Export structure to XFIG", "X", "tree2file.hlp", AWM_ALL, makeWindowCallback(AWT_popup_sec_export_window, scr));
    awm->insert_menu_topic("print_secedit",  "Print Structure",          "P", "tree2prt.hlp",  AWM_ALL, makeWindowCallback(AWT_popup_print_window,      scr));
    awm->sep______________();

    awm->insert_menu_topic("close", "Close", "C", "quit.hlp", AWM_ALL, AW_POPDOWN);

    awm->create_menu("Properties", "P", AWM_ALL);
    awm->insert_menu_topic("sec_display", "Display options", "D", "sec_display.hlp", AWM_ALL, SEC_create_display_window);
    awm->sep______________();
    awm->insert_menu_topic("props_secedit", "Change Colors and Fonts", "C", "color_props.hlp", AWM_ALL, makeCreateWindowCallback(SEC_create_gc_window, scr->gc_manager));
    awm->sep______________();
    awm->insert_menu_topic("sync_search_colors", "Sync search colors with EDIT4", "s", "sync_colors.hlp", AWM_ALL, makeWindowCallback(SEC_sync_colors, COLOR_SYNC_SEARCH));
    awm->insert_menu_topic("sync_range_colors",  "Sync range colors with EDIT4",  "r", "sync_colors.hlp", AWM_ALL, makeWindowCallback(SEC_sync_colors, COLOR_SYNC_RANGE));
    awm->insert_menu_topic("sync_other_colors",  "Sync other colors with EDIT4",  "o", "sync_colors.hlp", AWM_ALL, makeWindowCallback(SEC_sync_colors, COLOR_SYNC_REST));
    awm->insert_menu_topic("sync_all_colors",    "Sync all colors with EDIT4",    "a", "sync_colors.hlp", AWM_ALL, makeWindowCallback(SEC_sync_colors, COLOR_SYNC_ALL));
    awm->sep______________();
    awm->insert_menu_topic("sec_save_props",    "How to save properties",   "p", "savedef.hlp", AWM_ALL, makeHelpCallback("sec_props.hlp"));

    awm->create_mode("mode_zoom.xpm",    "sec_mode.hlp", AWM_ALL, makeWindowCallback(sec_mode_event, root, AWT_MODE_ZOOM));
    awm->create_mode("mode_fold.xpm",    "sec_mode.hlp", AWM_ALL, makeWindowCallback(sec_mode_event, root, AWT_MODE_FOLD));
    awm->create_mode("mode_setroot.xpm", "sec_mode.hlp", AWM_ALL, makeWindowCallback(sec_mode_event, root, AWT_MODE_SETROOT));
    awm->create_mode("mode_rotate.xpm",  "sec_mode.hlp", AWM_ALL, makeWindowCallback(sec_mode_event, root, AWT_MODE_ROTATE));
    awm->create_mode("mode_stretch.xpm", "sec_mode.hlp", AWM_ALL, makeWindowCallback(sec_mode_event, root, AWT_MODE_STRETCH));
    awm->create_mode("mode_edit.xpm",    "sec_mode.hlp", AWM_ALL, makeWindowCallback(sec_mode_event, root, AWT_MODE_EDIT));
    awm->create_mode("mode_cursor.xpm",  "sec_mode.hlp", AWM_ALL, makeWindowCallback(sec_mode_event, root, AWT_MODE_CURSOR));
    awm->create_mode("mode_pinfo.xpm",   "sec_mode.hlp", AWM_ALL, makeWindowCallback(sec_mode_event, root, AWT_MODE_PINFO));

    awm->set_info_area_height(250);
    awm->at(5, 2);
    awm->auto_space(0, -2);

    awm->button_length(0);
    awm->help_text("quit.hlp");
    awm->callback(AW_POPDOWN);
    awm->create_button("Close", "#quit.xpm"); // use quit button, cause users regard secedit as separate program

    awm->callback(AW_help_entry_pressed);
    awm->help_text("arb_secedit.hlp");
    awm->create_button("HELP", "#help.xpm");

    awm->callback(makeWindowCallback(SEC_undo_cb, db, GB_UNDO_UNDO));
    awm->help_text("undo.hlp");
    awm->create_button("Undo", "#undo.xpm");

    awm->callback(makeWindowCallback(SEC_undo_cb, db, GB_UNDO_REDO));
    awm->help_text("undo.hlp");
    awm->create_button("Redo", "#redo.xpm");

    awm->callback(makeWindowCallback(SEC_toggle_cb, db));
    awm->help_text("sec_main.hlp");
    awm->create_button("Toggle", "Toggle");

    awm->callback(makeWindowCallback(SEC_center_cb, root));
    awm->help_text("sec_main.hlp");
    awm->create_button("Center", "Center");

    awm->callback(makeWindowCallback(SEC_fit_window_cb, db));
    awm->help_text("sec_main.hlp");
    awm->create_button("fitWindow", "Fit");

    awm->at_newline();

    {
        SmartPtr<AW_at_storage> maxSize(AW_at_storage::make(awm, AW_AT_MAXSIZE));

        awm->button_length(AWAR_FOOTER_MAX_LEN);
        awm->create_button(NULp, AWAR_FOOTER);
        awm->at_newline();
        awm->restore_at_from(*maxSize);
    }

    awm->set_info_area_height(awm->get_at_yposition());

    return awm;
}