TreeCallbacks.cxx

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

#include "TreeCallbacks.hxx"

#include <aw_color_groups.hxx>
#include <aw_awars.hxx>
#include <aw_advice.hxx>
#include <aw_msg.hxx>
#include <aw_root.hxx>
#include <arb_strbuf.h>
#include <mode_text.h>

#include <cctype>
#include <gb_aci.h>

using namespace AW;

// AISC_MKPT_PROMOTE:#ifndef TREEDISPLAY_HXX
// AISC_MKPT_PROMOTE:#include <TreeDisplay.hxx>
// AISC_MKPT_PROMOTE:#endif

void nt_mode_event(UNFIXED, TREE_canvas *ntw, AWT_COMMAND_MODE mode) {
    const char *text;

    switch (mode) {
        case AWT_MODE_ZOOM:  text = MODE_TEXT_STANDARD_ZOOMMODE(); break;
        case AWT_MODE_EMPTY: text = MODE_TEXT_PLACEHOLDER();       break;

        case AWT_MODE_SELECT: text = MODE_TEXT_1BUTTON("SELECT", "select species or open/close group");                  break;
        case AWT_MODE_INFO:   text = MODE_TEXT_1BUTTON("INFO",   "click for info");                                      break;
        case AWT_MODE_WWW:    text = MODE_TEXT_1BUTTON("WEB",    "Launch node dependent URL (see <Properties/WWW...>)"); break;

        case AWT_MODE_SWAP:       text= MODE_TEXT_2BUTTONS("SWAP",         "swap child branches",        "flip whole subtree");          break;
        case AWT_MODE_MARK:       text= MODE_TEXT_2BUTTONS("MARK",         "mark subtree",               "unmark subtree");              break;
        case AWT_MODE_GROUP:      text= MODE_TEXT_2BUTTONS("GROUP",        "fold/unfold group",          "create/rename/destroy group"); break;
        case AWT_MODE_NNI:        text= MODE_TEXT_2BUTTONS("OPTI(NNI)",    "once",                       "repeated");                    break;
        case AWT_MODE_KERNINGHAN: text= MODE_TEXT_2BUTTONS("OPTI(KL)",     "once",                       "repeated");                    break;
        case AWT_MODE_OPTIMIZE:   text= MODE_TEXT_2BUTTONS("OPTI(NNI&KL)", "once",                       "repeated");                    break;
        case AWT_MODE_SETROOT:    text= MODE_TEXT_2BUTTONS("REROOT",       "set root to clicked branch", "search optimal root");         break;

        case AWT_MODE_ROTATE: text = MODE_TEXT_1BUTTON_KEYS("ROTATE", "drag branch to rotate",         KEYINFO_ABORT_AND_RESET); break;
        case AWT_MODE_SPREAD: text = MODE_TEXT_1BUTTON_KEYS("SPREAD", "drag branch to spread subtree", KEYINFO_ABORT_AND_RESET); break;

        case AWT_MODE_LENGTH:    text = MODE_TEXT_2BUTTONS_KEYS("LENGTH",       "drag branch/ruler", "use discrete lengths", KEYINFO_ABORT_AND_RESET); break;
        case AWT_MODE_MULTIFURC: text = MODE_TEXT_2BUTTONS_KEYS("MULTIFURC",    "drag branch",       "use discrete lengths", KEYINFO_ABORT_AND_RESET); break;
        case AWT_MODE_LINE:      text = MODE_TEXT_2BUTTONS_KEYS("LINE",         "drag branch/ruler", "whole subtree",        KEYINFO_ABORT_AND_RESET); break;
        case AWT_MODE_MOVE:      text = MODE_TEXT_2BUTTONS_KEYS("MOVE",         "drag branch/ruler", "move groupinfo only",  KEYINFO_ABORT);           break;
        case AWT_MODE_LZOOM:     text = MODE_TEXT_2BUTTONS_KEYS("LOGICAL ZOOM", "show only subtree", "go up one step",       KEYINFO_RESET);           break;

        default: text = no_mode_text_defined(); break;
    }

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

    ntw->awr->awar(AWAR_FOOTER)->write_string(text);
    ntw->set_mode(mode);
}

// ---------------------------------------
//      Basic mark/unmark callbacks :

#define MARK_MODE_LOWER_BITS (1|2)
#define MARK_MODE_UPPER_BITS (4|8|16)

#define COUNTING_MARKED(mode) (((mode)&MARK_MODE_LOWER_BITS) == 3)

static void show_count(GBDATA *gb_main, int mark_mode, int tree_mode, long count) {
    // tree_mode: 0=none, 1=intree, 2=!intree
    if (COUNTING_MARKED(mark_mode)) { // if counting
        GBS_strstruct buf(200);

        switch (count) {
            case 0: buf.cat("There are NO"); break;
            case 1: buf.cat("There is 1"); break;
            default: buf.nprintf(100, "There are %li", count); break;
        }

        buf.cat(" marked");
        switch (mark_mode&MARK_MODE_UPPER_BITS) {
            case 0:    // all sequences
                buf.cat(" species");
                break;
            case 4:    // full sequences only
                buf.cat(" full-sequence species");
                break;
            case 8:    // partial sequences only
                buf.cat(" partial-sequence species");
                break;
            case 16: { // species with data in alignment only
                char *ali = GBT_get_default_alignment(gb_main);
                gb_assert(ali); // no caller calls 'show_count' in that case!
                buf.nprintf(100, " species with data in '%s'", ali);
                free(ali);
                break;
            }
            default:
                td_assert(0); // illegal mode
                break;
        }
        switch (tree_mode) {
            case 0: // all species
                break;
            case 1: // tree member
                buf.cat(" inside the tree");
                break;
            case 2: // tree non-members
                buf.cat(" outside the tree");
                break;
        }
        buf.put('.');

        if ((mark_mode&MARK_MODE_UPPER_BITS) == 0 && tree_mode == 0) { // traditional count all marked
            static bool hintShown = false;
            if (!hintShown) {
                buf.cat("\n(The number of species is displayed in the top area as well)");
                hintShown = true;
            }
        }

        aw_message(buf.get_data());
    }
}

static bool species_has_alignment(GBDATA *gb_species, void *cd_use) {
    return GBT_find_sequence(gb_species, (const char*)cd_use);
}

static bool sequence_is_partial(GBDATA *gb_species, void *cd_partial) {
    long wanted  = (long)cd_partial;
    td_assert(wanted == 0 || wanted == 1);
    bool partial = GBT_is_partial(gb_species, 0, false);

    return partial == wanted;
}

void NT_mark_all_cb(UNFIXED, TREE_canvas *ntw, int mark_mode) {
    // Bits 0 and 1 of mark_mode:
    //
    // mark_mode&3  == 0 -> unmark
    // mark_mode&3  == 1 -> mark
    // mark_mode&3  == 2 -> toggle mark
    // mark_mode&3  == 3 -> count marked
    //
    // Bits 2 .. 4 of mark_mode:
    //
    // mark_mode&12 == 4 -> affect only full sequences
    // mark_mode&12 == 8 -> affect only partial sequences
    // mark_mode&12 == 16 -> affect only species with data in current alignment
    // else -> affect all sequences

    AWT_auto_refresh allowed_on(ntw);
    GB_transaction   ta(ntw->gb_main);

    GB_ERROR error = NULp;
    long     count = 0;
    switch (mark_mode&MARK_MODE_UPPER_BITS) {
        case 0:                  // all sequences
            count = GBT_mark_all(ntw->gb_main, mark_mode&MARK_MODE_LOWER_BITS);
            break;
        case 4:                  // full sequences only
            count = GBT_mark_all_that(ntw->gb_main, mark_mode&MARK_MODE_LOWER_BITS, sequence_is_partial, (void*)NULp);
            break;
        case 8:                  // partial sequences only
            count = GBT_mark_all_that(ntw->gb_main, mark_mode&MARK_MODE_LOWER_BITS, sequence_is_partial, (void*)1);
            break;
        case 16: {               // species with data in alignment only
            char *ali = GBT_get_default_alignment(ntw->gb_main);
            if (!ali) {
                error = GB_await_error();
            }
            else {
                count = GBT_mark_all_that(ntw->gb_main, mark_mode&MARK_MODE_LOWER_BITS, species_has_alignment, (void*)ali);
                free(ali);
            }
            break;
        }
        default:
            td_assert(0); // illegal mode
            break;
    }

    if (error) {
        aw_message(error);
    }
    else if (COUNTING_MARKED(mark_mode)) {
        show_count(ntw->gb_main, mark_mode, 0, count);
    }
    else {
        ntw->request_structure_update(); // includes refresh etc
    }
}

static void mark_tree_cb(UNFIXED, TREE_canvas *ntw, int mark_mode) {
    GB_transaction    ta(ntw->gb_main);
    AWT_auto_refresh  allowed_on(ntw);
    AWT_graphic_tree *gtree     = AWT_TREE(ntw);
    AP_tree          *tree_root = gtree->get_root_node();

    GB_ERROR error = NULp;
    long     count = 0;
    switch (mark_mode&MARK_MODE_UPPER_BITS) {
        case 0:                  // all sequences
            count = gtree->mark_species_in_tree(tree_root, mark_mode&MARK_MODE_LOWER_BITS);
            break;
        case 4:                  // full sequences only
            count = gtree->mark_species_in_tree_that(tree_root, mark_mode&MARK_MODE_LOWER_BITS, sequence_is_partial, (void*)NULp);
            break;
        case 8:                  // partial sequences only
            count = gtree->mark_species_in_tree_that(tree_root, mark_mode&MARK_MODE_LOWER_BITS, sequence_is_partial, (void*)1);
            break;
        case 16: {               // species with data in alignment only
            char *ali = GBT_get_default_alignment(ntw->gb_main);
            if (!ali) {
                error = GB_await_error();
            }
            else {
                count = gtree->mark_species_in_tree_that(tree_root, mark_mode&MARK_MODE_LOWER_BITS, species_has_alignment, (void*)ali);
                free(ali);
            }
            break;
        }
        default:
            td_assert(0); // illegal mode
            break;
    }

    if (error) {
        aw_message(error);
    }
    else if (COUNTING_MARKED(mark_mode)) {
        show_count(ntw->gb_main, mark_mode, 1, count);
    }
    else {
        ntw->request_structure_update(); // includes refresh etc
    }
}

struct mark_nontree_cb_data {
    int      mark_mode_upper_bits;
    char    *ali;               // current alignment (only if mark_mode_upper_bits == 16)
    GB_HASH *hash;
};

static bool are_not_in_tree(GBDATA *gb_species, void *cb_data) {
    struct mark_nontree_cb_data *data = (mark_nontree_cb_data*)cb_data;
    bool mark_me = false;

    if (GBS_read_hash(data->hash, GBT_get_name_or_description(gb_species)) == (long)gb_species) { // species is not in tree!
        switch (data->mark_mode_upper_bits) {
            case 0:             // all sequences
                mark_me = true;
                break;
            case 4:             // full sequences only
                mark_me = sequence_is_partial(gb_species, (void*)NULp);
                break;
            case 8:             // partial sequences only
                mark_me = sequence_is_partial(gb_species, (void*)1);
                break;
            case 16:            // species with data in alignment only
                mark_me = species_has_alignment(gb_species, data->ali);
                break;
            default:
                td_assert(0); // illegal mode
                break;
        }
    }

    return mark_me;
}

static void mark_nontree_cb(UNFIXED, TREE_canvas *ntw, int mark_mode) {
    AWT_graphic_tree            *gtree = AWT_TREE(ntw);
    GB_transaction               ta(ntw->gb_main);
    struct mark_nontree_cb_data  cd;
    AWT_auto_refresh             allowed_on(ntw);

    if ((mark_mode&MARK_MODE_LOWER_BITS) == 0) {                // unmark is much faster
        cd.hash = GBT_create_marked_species_hash(ntw->gb_main); // because it only hashes marked species
    }
    else {
        cd.hash = GBT_create_species_hash(ntw->gb_main); // for mark we have to hash ALL species
    }

    NT_remove_species_in_tree_from_hash(gtree->get_root_node(), cd.hash);

    cd.mark_mode_upper_bits = mark_mode&MARK_MODE_UPPER_BITS;

    GB_ERROR error = NULp;
    if (cd.mark_mode_upper_bits == 16) {
        cd.ali = GBT_get_default_alignment(ntw->gb_main);
        if (!cd.ali) error = GB_await_error();
    }
    else {
        cd.ali = NULp;
    }

    long count = 0;
    if (!error) {
        count = GBT_mark_all_that(ntw->gb_main, mark_mode&MARK_MODE_LOWER_BITS, are_not_in_tree, (void*)&cd);
    }
    free(cd.ali);

    if (error) {
        aw_message(error);
    }
    else if (COUNTING_MARKED(mark_mode)) {
        show_count(ntw->gb_main, mark_mode, 2, count);
    }
    else {
        ntw->request_refresh(); // does only affect display of NDS list (if tree shown -> never changes; i.e. no structure update needed)
    }
}

static char *create_mark_menu_entry(const char *attrib, const char *entry_template) {
    char *entry = NULp;
    if (attrib) {
        bool append = attrib[0] == '-'; // if attrib starts with '-' then append (otherwise prepend)
        if (append) ++attrib; // skip '-'

        if (append) {
            char *spaced_attrib = GBS_global_string_copy(" %s", attrib);
            entry               = GBS_global_string_copy(entry_template, "", spaced_attrib);
            free(spaced_attrib);
        }
        else {
            char *spaced_attrib = GBS_global_string_copy("%s ", attrib);
            entry               = GBS_global_string_copy(entry_template, spaced_attrib, "");

            if (islower(entry[0])) entry[0] = toupper(entry[0]); // Caps prepended lowercase 'attrib'

            free(spaced_attrib);
        }
    }
    else {
        entry = GBS_global_string_copy(entry_template, "", "");
    }
    return entry;
}
static char *create_mark_menu_id(const char *attrib, const char *id_suffix) {
    char *id = NULp;
    if (attrib) {
        id = GBS_global_string_copy("%s_%s", attrib[0] == '-' ? attrib+1 : attrib, id_suffix);
    }
    else {
        id = strdup(id_suffix);
    }
    return id;
}

static void insert_mark_topic(AW_window_menu_modes *awm, AW_active mask, const char *attrib, const char *id_suffix, const char *entry_template,
                              const char *hotkey, const char *helpfile, const WindowCallback& wcb)
{
    char *entry = create_mark_menu_entry(attrib, entry_template);
    char *id    = create_mark_menu_id(attrib, id_suffix);

    awm->insert_menu_topic(id, entry, hotkey, helpfile, mask, wcb);

    free(id);
    free(entry);
}

static void insert_mark_topics(AW_window_menu_modes *awm, AW_active mask, TREE_canvas *ntw, int affect, const char *attrib) {
    td_assert(affect == (affect&MARK_MODE_UPPER_BITS)); // only bits 2 .. 4 are allowed

    insert_mark_topic(awm, mask, attrib, "count_marked","Count marks of all %sSpecies%s",  "C", "sp_mark.hlp", makeWindowCallback(NT_mark_all_cb, ntw, 3+affect));
    awm->sep______________();
    insert_mark_topic(awm, mask, attrib, "mark_all",    "Mark all %sSpecies%s",            "M", "sp_mark.hlp", makeWindowCallback(NT_mark_all_cb, ntw, 1+affect));
    insert_mark_topic(awm, mask, attrib, "unmark_all",  "Unmark all %sSpecies%s",          "U", "sp_mark.hlp", makeWindowCallback(NT_mark_all_cb, ntw, 0+affect));
    insert_mark_topic(awm, mask, attrib, "swap_marked", "Invert marks of all %sSpecies%s", "I", "sp_mark.hlp", makeWindowCallback(NT_mark_all_cb, ntw, 2+affect));
    awm->sep______________();

    char *label = create_mark_menu_entry(attrib, "%sSpecies%s in Tree");

    awm->insert_sub_menu(label, "T");
    insert_mark_topic(awm, mask, attrib, "count_marked_tree","Count marks of %sSpecies%s in Tree",  "C", "sp_mark.hlp", makeWindowCallback(mark_tree_cb, ntw, 3+affect));
    awm->sep______________();
    insert_mark_topic(awm, mask, attrib, "mark_tree",        "Mark %sSpecies%s in Tree",            "M", "sp_mark.hlp", makeWindowCallback(mark_tree_cb, ntw, 1+affect));
    insert_mark_topic(awm, mask, attrib, "unmark_tree",      "Unmark %sSpecies%s in Tree",          "U", "sp_mark.hlp", makeWindowCallback(mark_tree_cb, ntw, 0+affect));
    insert_mark_topic(awm, mask, attrib, "swap_marked_tree", "Invert marks of %sSpecies%s in Tree", "I", "sp_mark.hlp", makeWindowCallback(mark_tree_cb, ntw, 2+affect));
    awm->close_sub_menu();

    freeset(label, create_mark_menu_entry(attrib, "%sSpecies%s NOT in Tree"));

    awm->insert_sub_menu(label, "N");
    insert_mark_topic(awm, mask, attrib, "count_marked_nontree","Count marks of %sSpecies%s NOT in Tree",  "C", "sp_mark.hlp", makeWindowCallback(mark_nontree_cb, ntw, 3+affect));
    awm->sep______________();
    insert_mark_topic(awm, mask, attrib, "mark_nontree",        "Mark %sSpecies%s NOT in Tree",            "M", "sp_mark.hlp", makeWindowCallback(mark_nontree_cb, ntw, 1+affect));
    insert_mark_topic(awm, mask, attrib, "unmark_nontree",      "Unmark %sSpecies%s NOT in Tree",          "U", "sp_mark.hlp", makeWindowCallback(mark_nontree_cb, ntw, 0+affect));
    insert_mark_topic(awm, mask, attrib, "swap_marked_nontree", "Invert marks of %sSpecies%s NOT in Tree", "I", "sp_mark.hlp", makeWindowCallback(mark_nontree_cb, ntw, 2+affect));
    awm->close_sub_menu();

    free(label);
}

void NT_insert_mark_submenus(AW_window_menu_modes *awm, TREE_canvas *ntw, int insert_as_submenu) {
    if (insert_as_submenu) {
        awm->insert_sub_menu("Mark species", "M");
    }

    {
        insert_mark_topics(awm, AWM_ALL, ntw, 0, NULp);
        awm->sep______________();

        awm->insert_sub_menu("Complete sequences", "o");
        insert_mark_topics(awm, AWM_EXP, ntw, 4, "complete");
        awm->close_sub_menu();

        awm->insert_sub_menu("Partial sequences", "P");
        insert_mark_topics(awm, AWM_EXP, ntw, 8, "partial");
        awm->close_sub_menu();

        awm->insert_sub_menu("Current Alignment", "A");
        insert_mark_topics(awm, AWM_EXP, ntw, 16, "-with data");
        awm->close_sub_menu();
    }

    if (insert_as_submenu) {
        awm->close_sub_menu();
    }
}

// ----------------------------------------
//      Automated collapse/expand tree

static void group_and_refold_tree(TREE_canvas *ntw, CollapseMode mode, int color_group) {
    GB_transaction    ta(ntw->gb_main);
    AWT_auto_refresh  allowed_on(ntw);
    AWT_graphic_tree *agt       = AWT_TREE(ntw);
    AP_tree          *root_node = agt->get_root_node();

    agt->group_tree(root_node, mode, color_group);

    agt->fast_sync_changed_folding(root_node);
}

static void collapse_all_cb     (UNFIXED, TREE_canvas *ntw) { group_and_refold_tree(ntw, COLLAPSE_ALL,      0); }
static void collapse_terminal_cb(UNFIXED, TREE_canvas *ntw) { group_and_refold_tree(ntw, COLLAPSE_TERMINAL, 0); }
static void expand_unmarked_cb  (UNFIXED, TREE_canvas *ntw) { group_and_refold_tree(ntw, EXPAND_UNMARKED,   0); }
static void expand_all_cb       (UNFIXED, TREE_canvas *ntw) { group_and_refold_tree(ntw, EXPAND_ALL,        0); }
void NT_expand_marked_cb        (UNFIXED, TREE_canvas *ntw) { group_and_refold_tree(ntw, EXPAND_MARKED,     0); }
static void expand_zombies_cb   (UNFIXED, TREE_canvas *ntw) { group_and_refold_tree(ntw, EXPAND_ZOMBIES,    0); }

static void expand_color_cb(UNFIXED, TREE_canvas *ntw, int colornum) { group_and_refold_tree(ntw, EXPAND_COLOR, colornum); }

static void insert_color_collapse_submenu(AW_window_menu_modes *awm, TREE_canvas *ntree_canvas) {
    const int MAXLABEL = 31;
    const int MAXENTRY = AW_COLOR_GROUP_NAME_LEN+10;

    td_assert(ntree_canvas);

    awm->insert_sub_menu("Expand color ...", "o");

    char        label_buf[MAXLABEL+1];
    char        entry_buf[MAXENTRY+1];
    char hotkey[]       = "x";
    const char *hotkeys = "AN1234567890BC"+1;

    for (int i = -1; i <= AW_COLOR_GROUPS; ++i) {
        hotkey[0]                       = hotkeys[i];
        if (hotkey[0] == ' ') hotkey[0] = 0;

        if (i) {
            if (i<0) {
                strcpy(label_buf, "tree_group_not_any_color");
                strcpy(entry_buf, "Any color group");
            }
            else {
                sprintf(label_buf, "tree_group_not_color_%i", i);

                char   *color_group_name = AW_get_color_group_name(awm->get_root(), i);
                size_t  len              = strlen(color_group_name);
                if (len>AW_COLOR_GROUP_NAME_LEN) {
                    color_group_name[AW_COLOR_GROUP_NAME_LEN] = 0; // truncate overlong colorgroup names
                }
                sprintf(entry_buf, "%s group '%s'", hotkey, color_group_name);
                free(color_group_name);
            }
        }
        else {
            strcpy(label_buf, "tree_group_not_no_color");
            strcpy(entry_buf, "No color group");
        }

        awm->insert_menu_topic(awm->local_id(label_buf), entry_buf, hotkey, "tree_group.hlp", AWM_ALL, makeWindowCallback(expand_color_cb, ntree_canvas, i));
    }

    awm->close_sub_menu();
}

void NT_insert_collapse_submenu(AW_window_menu_modes *awm, TREE_canvas *ntw) {
    awm->insert_sub_menu("Collapse/expand groups",         "d");
    {
        const char *grouphelp = "tree_group.hlp";
        awm->insert_menu_topic(awm->local_id("tree_group_all"),         "Collapse all",      "C", grouphelp, AWM_ALL, makeWindowCallback(collapse_all_cb,      ntw));
        awm->insert_menu_topic(awm->local_id("tree_group_term_groups"), "Collapse terminal", "t", grouphelp, AWM_ALL, makeWindowCallback(collapse_terminal_cb, ntw));
        awm->sep______________();
        awm->insert_menu_topic(awm->local_id("tree_ungroup_all"),       "Expand all",        "E", grouphelp, AWM_ALL, makeWindowCallback(expand_all_cb,        ntw));
        awm->insert_menu_topic(awm->local_id("tree_group_not_marked"),  "Expand marked",     "m", grouphelp, AWM_ALL, makeWindowCallback(NT_expand_marked_cb,  ntw));
        awm->insert_menu_topic(awm->local_id("tree_ungroup_unmarked"),  "Expand unmarked",   "u", grouphelp, AWM_ALL, makeWindowCallback(expand_unmarked_cb,   ntw));
        awm->insert_menu_topic(awm->local_id("tree_ungroup_zombies"),   "Expand zombies",    "z", grouphelp, AWM_ALL, makeWindowCallback(expand_zombies_cb,    ntw));
        awm->sep______________();
        insert_color_collapse_submenu(awm, ntw);
    }
    awm->close_sub_menu();
}

// ------------------------
//      tree sorting :

GB_ERROR NT_with_displayed_tree_do(TREE_canvas *ntw, bool (*displayed_tree_cb)(TreeNode *tree, GB_ERROR& error)) {
    // 'displayed_tree_cb' has to return true if tree was changed and needs to be saved

    GB_transaction   ta(ntw->gb_main);
    AWT_auto_refresh allowed_on(ntw);

    GB_ERROR error = NULp;
    if (displayed_tree_cb(AWT_TREE(ntw)->get_root_node(), error)) {
        ntw->request_save_and_zoom_reset();
    }
    return error;
}

void NT_resort_tree_cb(UNFIXED, TREE_canvas *ntw, TreeOrder order) {
    GB_transaction   ta(ntw->gb_main);
    AWT_auto_refresh allowed_on(ntw);

    AWT_TREE(ntw)->reorderTree(order);
    ntw->request_save_and_zoom_reset();
}

void NT_reset_lzoom_cb(UNFIXED, TREE_canvas *ntw) {
    GB_transaction    ta(ntw->gb_main);
    AWT_auto_refresh  allowed_on(ntw);
    AWT_graphic_tree *agt = AWT_TREE(ntw);

    agt->set_logical_root_to(agt->get_root_node());
    ntw->request_zoom_reset();
}

void NT_reset_pzoom_cb(UNFIXED, TREE_canvas *ntw) {
    GB_transaction   ta(ntw->gb_main);
    AWT_auto_refresh allowed_on(ntw);
    ntw->request_zoom_reset();
}

void NT_set_tree_style(UNFIXED, TREE_canvas *ntw, AP_tree_display_style style) {
    {
        AWT_auto_refresh allowed_on(ntw);
        AWT_TREE(ntw)->set_tree_style(style, ntw);
        ntw->request_zoom_reset();
    }
    TREE_auto_jump_cb(NULp, ntw, AP_JUMP_REASON_STYLE);
}

void NT_reinit_treetype(UNFIXED, TREE_canvas *ntw) {
    NT_set_tree_style(NULp, ntw, AWT_TREE(ntw)->get_tree_style());
}

void NT_remove_leafs(UNFIXED, TREE_canvas *ntw, AWT_RemoveType mode) {
    GB_transaction    ta(ntw->gb_main);
    AWT_auto_refresh  allowed_on(ntw);

    AP_tree *root_node = AWT_TREE(ntw)->get_root_node();
    if (root_node) {
        AWT_TREE(ntw)->get_tree_root()->remove_leafs(mode);
        ntw->request_save_and_zoom_reset();
    }
    else {
        aw_message("Got no tree");
    }
}

void NT_remove_bootstrap(UNFIXED, TREE_canvas *ntw) { // delete all bootstrap values
    GB_transaction   ta(ntw->gb_main);
    AWT_auto_refresh allowed_on(ntw);

    AP_tree *root_node = AWT_TREE(ntw)->get_root_node();
    if (root_node) {
        root_node->remove_bootstrap();
        ntw->request_save_and_zoom_reset();
    }
    else {
        aw_message("Got no tree");
    }
}

void NT_edit_bootstrap(UNFIXED, TREE_canvas *ntw) { // edit bootstrap values
    GB_transaction   ta(ntw->gb_main);
    AWT_auto_refresh allowed_on(ntw);

    AP_tree *root_node = AWT_TREE(ntw)->get_root_node();
    if (root_node) {
        char *aci = aw_input("Enter ACI to apply to all branch remarks:");
        if (aci) {
            char *tree_name = ntw->get_awar_tree()->read_string();

            GBL_env      env(ntw->gb_main, tree_name);
            GBL_call_env callEnv(NULp, env); // do not pass any species (will only be applied to inner branches)

            GB_ERROR error = root_node->apply_aci_to_remarks(aci, callEnv);
            ntw->request_save_and_zoom_reset();

            error = ta.close(error);
            if (error) aw_message(error);

            free(tree_name);
        }
    }
    else {
        aw_message("Got no tree");
    }
}

void NT_reset_branchlengths(UNFIXED, TREE_canvas *ntw) { // set all branchlengths to tree_defaults::LENGTH
    GB_transaction   ta(ntw->gb_main);
    AWT_auto_refresh allowed_on(ntw);

    AP_tree *root_node = AWT_TREE(ntw)->get_root_node();
    if (root_node) {
        root_node->reset_branchlengths();
        ntw->request_save_and_zoom_reset();
    }
    else {
        aw_message("Got no tree");
    }
}

void NT_multifurcate_tree(TREE_canvas *ntw, const TreeNode::multifurc_limits& below) {
    GB_transaction   ta(ntw->gb_main);
    AWT_auto_refresh allowed_on(ntw);

    TreeNode *tree = AWT_TREE(ntw)->get_root_node();
    if (tree) {
        tree->multifurcate_whole_tree(below);
        ntw->request_save_and_zoom_reset();
    }
    else {
        aw_message("Got no tree");
    }
}

void NT_move_boot_branch(UNFIXED, TREE_canvas *ntw, int direction) { // copy branchlengths to bootstraps (or vice versa)
    GB_transaction   ta(ntw->gb_main);
    AWT_auto_refresh allowed_on(ntw);

    AP_tree *root_node = AWT_TREE(ntw)->get_root_node();
    if (root_node) {
        if (direction == 0) root_node->bootstrap2branchlen();
        else                root_node->branchlen2bootstrap();

        ntw->request_save_and_zoom_reset();

        char *adviceText = GBS_global_string_copy("Please note, that you just overwrote your existing %s.",
                                                  direction ? "bootstrap values" : "branchlengths");
        AW_advice(adviceText, AW_ADVICE_TOGGLE_AND_HELP, NULp, "tbl_boot2len.hlp");
        free(adviceText);
    }
    else {
        aw_message("Got no tree");
    }
}

void NT_scale_tree(UNFIXED, TREE_canvas *ntw) { // scale branchlengths
    char *answer = aw_input("Enter scale factor", "Scale branchlengths by factor:", "100");
    if (answer) {
        double   factor    = atof(answer);
        AP_tree *root_node = AWT_TREE(ntw)->get_root_node();

        if (root_node) {
            GB_transaction   ta(ntw->gb_main);
            AWT_auto_refresh allowed_on(ntw);
            root_node->scale_branchlengths(factor);
            ntw->request_save_and_zoom_reset();
        }
        else {
            aw_message("Got no tree");
        }
        free(answer);
    }
}

inline AP_tree *common_ancestor(AP_tree *t1, AP_tree *t2) {
    return DOWNCAST(AP_tree*, t1->ancestor_common_with(t2));
}

void NT_jump_cb(UNFIXED, TREE_canvas *ntw, AP_tree_jump_type jumpType) {
    if (jumpType == AP_DONT_JUMP) return;

    AW_window        *aww   = ntw->aww;
    AWT_graphic_tree *gtree = AWT_TREE(ntw);

    GB_transaction   ta(ntw->gb_main);
    AWT_auto_refresh allowed_on(ntw);

    AW_root    *aw_root  = aww->get_root();
    const char *name     = aw_root->awar(AWAR_SPECIES_NAME)->read_char_pntr();
    GBDATA     *gb_group = gtree->get_selected_group().get_group_data();

    char *msg      = NULp;
    bool  verboose = jumpType & AP_JUMP_BE_VERBOOSE;

    if (name[0] || gb_group) {
        AP_tree *found         = NULp;
        bool     is_tree       = is_tree_style(gtree->get_tree_style());
        bool     jump_to_group = gb_group && is_tree; // @@@ prefer group atm

        if (is_tree) {
            if (gtree && gtree->get_logical_root()) {
                if (jump_to_group) {
                    found = gtree->locate_selected_group(gtree->get_logical_root());
                    td_assert(found && found->is_clade());
                }
                else {
                    found = gtree->get_logical_root()->findLeafNamed(name);
                }

                if (!found && gtree->is_logically_zoomed()) {
                    if (jump_to_group) {
                        found = gtree->locate_selected_group(gtree->get_root_node());
                    }
                    else {
                        found = gtree->get_root_node()->findLeafNamed(name);
                    }

                    if (found) { // species/group is invisible because it is outside logically zoomed tree
                        if (jumpType & AP_JUMP_LOGICAL_UNZOOM) {
                            gtree->set_logical_root_to(common_ancestor(found, gtree->get_logical_root()));
                            ntw->request_resize();
                        }
                        else {
                            if (verboose) {
                                if (jump_to_group) {
                                    msg = GBS_global_string_copy("Group '%s' is outside logical zoomed subtree", gtree->get_selected_group().get_name());
                                }
                                else {
                                    msg = GBS_global_string_copy("Species '%s' is outside logical zoomed subtree", name);
                                }
                            }

                            found = NULp;
                        }
                    }
                }

                if (found && !(jumpType&AP_JUMP_AUTO_UNFOLD) && found->is_inside_folded_group()) {
                    found = NULp; // => just undo auto-unfolding
                }
                gtree->auto_unfold(found);
            }
        }

        if (found || !is_tree) {
            bool is_IRS  = gtree->get_tree_style() == AP_TREE_IRS;
            bool repeat  = is_IRS;
            bool do_jump = true;

            ntw->sync_DB_model_and_view(false); // sync w/o refresh

            while (do_jump) {
                do_jump = false;

                AW_device_size *device = aww->get_size_device(AW_MIDDLE_AREA);
                device->set_filter(AW_SIZE|AW_SIZE_UNSCALED);
                device->reset();
                ntw->init_device(device);
                ntw->gfx->show(device);

                const AW_screen_area& screen = device->get_area_size();

                const Position& cursor = jump_to_group ? gtree->get_group_cursor() : gtree->get_cursor();
                if (are_distinct(Origin, cursor)) {
                    Position S = device->transform(cursor);

                    int scroll_x = 0;
                    int scroll_y = 0;

                    bool do_vcenter = jumpType & AP_JUMP_FORCE_VCENTER;
                    bool do_hcenter = jumpType & AP_JUMP_FORCE_HCENTER;

                    if (!do_vcenter) {
                        if (is_IRS) {
                            // attempt to center IRS tree vertically often fails (too complicated to predict)
                            // => force into center-half of screen to reduce error rate
                            int border = screen.b/10;
                            do_vcenter = S.ypos()<border || S.ypos()>(screen.b-border);
                        }
                        else {
                            do_vcenter = S.ypos()<0.0 || S.ypos()>screen.b; // center if outside viewport
                        }
                    }

                    if (do_vcenter) {
                        scroll_y = (int)(S.ypos() - screen.b*(is_IRS ? .6 : .5)); // position a bit below vertical center for IRS tree

                        if (!scroll_y && (jumpType & AP_JUMP_ALLOW_HCENTER)) { // allow horizontal centering if vertical has no effect
                            do_hcenter = true;
                        }
                    }

                    if (do_hcenter) {
                        scroll_x = (int) (S.xpos() - screen.r * (is_tree ? .5 : .02));
                    }
                    else { // keep visible
                        if (S.xpos()<0.0) {
                            double relPos = 0;
                            switch (gtree->get_tree_style()) {
                                case AP_TREE_NORMAL:
                                case AP_TREE_IRS:      relPos = .1; break;
                                case AP_TREE_RADIAL:   relPos = .5; break;
                                case AP_LIST_NDS:
                                case AP_LIST_SIMPLE:   relPos = .02; break;
                            }
                            scroll_x = (int)(S.xpos() - screen.r * relPos);
                        }
                        else if (S.xpos()>screen.r) {
                            scroll_x = (int)(S.xpos() - screen.r * .5);
                        }
                    }

                    if (scroll_x || scroll_y) ntw->scroll(scroll_x, scroll_y);
                    if (repeat) {
                        // reposition jump in IRS tree (reduces jump failure rate)
                        repeat  = false;
                        do_jump = true;
                    }
                }
                else {
                    td_assert(!is_tree); // jumped-to position should have been found
                    if (verboose) msg = GBS_global_string_copy("Species '%s' is no member of this list", name);
                }
            }
        }

        if (!found && is_tree && verboose && !msg) {
            td_assert(!jump_to_group); // need special handling
            msg = GBS_global_string_copy("Species '%s' is no member of this %s", name, gtree->get_tree_style() == AP_LIST_NDS ? "list" : "tree");
        }

    }
    else { // select "no species" and "no group"
        gtree->auto_unfold(NULp); // undo auto-unfolding
        if (verboose) {
            msg = strdup("Neither species nor group selected");
        }
    }

    if (gtree) gtree->exports.request_refresh(); // always do refresh to show change of selected species

    if (msg) {
        td_assert(verboose);
        aw_message(msg);
        free(msg);
    }
}

void TREE_auto_jump_cb(UNFIXED, TREE_canvas *ntw, AP_tree_jump_reason cause) {
    AWT_auto_refresh allowed_on(ntw);

    bool tree_change = cause == AP_JUMP_REASON_TREE || cause == AP_JUMP_REASON_STYLE;

    const char        *awar_name = tree_change ? AWAR_DTREE_AUTO_JUMP_TREE : AWAR_DTREE_AUTO_JUMP;
    AW_root           *awr       = ntw->aww->get_root();
    AP_tree_jump_type  jump_type = AP_tree_jump_type(awr->awar(awar_name)->read_int());

    if (jump_type == AP_DONT_JUMP) {
        ntw->request_refresh();
    }
    else {
        bool auto_unfold           = awr->awar(AWAR_DTREE_AUTO_UNFOLD)->read_int();
        if (auto_unfold) jump_type = AP_tree_jump_type(jump_type|AP_JUMP_AUTO_UNFOLD);
        NT_jump_cb(NULp, ntw, jump_type);
    }
}

void NT_reload_tree_event(AW_root *, TREE_canvas *ntw, bool unzoom_and_expose) {
    GB_push_transaction(ntw->gb_main);

    {
        AWT_auto_refresh update(ntw);

        AWT_graphic_tree *agt   = ntw->get_graphic_tree();
        AP_tree_root     *troot = agt->get_tree_root();

        if (!troot->get_gb_tree()) { // happens at initial startup (=first load) and after a shown tree gets renamed
            // forget all about old tree
            agt->forget_auto_unfolded();
            agt->deselect_group();
        }
        else {
            agt->auto_unfold(NULp);     // undo auto-unfolding before tree-change (otherwise temp. unfolding remains saved in DB)
        }
        update.suppress_update_and_refresh(); // suppress update (speed)
    }

    char     *tree_name = ntw->get_awar_tree()->read_string();
    GB_ERROR  error     = ntw->gfx->load_from_DB(ntw->gb_main, tree_name);
    if (error) {
        aw_message(error);
    }
    else {
        int zombies, duplicates;
        DOWNCAST(AWT_graphic_tree*, ntw->gfx)->get_zombies_and_duplicates(zombies, duplicates);

        if (zombies || duplicates) {
            const char *msg = NULp;
            if (duplicates) {
                if (zombies) msg = GBS_global_string("%i zombie%s and %i duplicate%s", zombies, plural(zombies), duplicates, plural(duplicates));
                else msg         = GBS_global_string("%i duplicate%s", duplicates, plural(duplicates));
            }
            else {
                td_assert(zombies);
                msg = GBS_global_string("%i zombie%s", zombies, plural(zombies));
            }
            aw_message(GBS_global_string("%s in '%s'", msg, tree_name));
        }
    }
    free(tree_name);
    if (unzoom_and_expose) {
        AWT_auto_refresh allowed_on(ntw);
        ntw->request_zoom_reset();
    }
    GB_pop_transaction(ntw->gb_main);
}

static void tree_recompute_cb(UNFIXED, AWT_canvas *ntw) {
    AWT_auto_refresh allowed_on(ntw);
    ntw->request_structure_update();
}

void TREE_GC_changed_cb(GcChange whatChanged, AWT_canvas *ntw) {
    AWT_auto_refresh allowed_on(ntw);

    if (whatChanged == GC_COLOR_GROUP_USE_CHANGED) {
        tree_recompute_cb(NULp, ntw);
    }
    else {
        AWT_GC_changed_cb(whatChanged, ntw);
    }
}

void NT_remove_species_in_tree_from_hash(AP_tree *tree, GB_HASH *hash) {
    if (!tree) return;
    if (tree->is_leaf() && tree->name) {
        GBS_write_hash(hash, tree->name, 0); // delete species in hash table
    }
    else {
        NT_remove_species_in_tree_from_hash(tree->get_leftson(), hash);
        NT_remove_species_in_tree_from_hash(tree->get_rightson(), hash);
    }
}