source: tags/old_import_filter/NTREE/ad_ali.cxx

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

#include "NT_local.h"
#include <insdel.h>
#include <awt_sel_boxes.hxx>
#include <aw_window.hxx>
#include <aw_root.hxx>
#include <aw_question.hxx>
#include <aw_awar.hxx>
#include <aw_msg.hxx>
#include <arbdbt.h>


static void alignment_vars_callback(AW_root *aw_root)
{
    GB_push_transaction(GLOBAL.gb_main);
    char    *use = aw_root->awar("presets/use")->read_string();
    GBDATA *ali_cont = GBT_get_alignment(GLOBAL.gb_main, use);
    if (!ali_cont) {
        GB_clear_error();
        aw_root->awar("presets/alignment_name")->unmap();
        aw_root->awar("presets/alignment_type")->unmap();
        aw_root->awar("presets/alignment_len")->unmap();
        aw_root->awar("presets/alignment_rem")->unmap();
        aw_root->awar("presets/aligned")->unmap();
        aw_root->awar("presets/auto_format")->unmap();
        aw_root->awar("presets/security")->unmap();
    }
    else {
        GBDATA *ali_name        = GB_search(ali_cont, "alignment_name",           GB_STRING);
        GBDATA *ali_len         = GB_search(ali_cont, "alignment_len",            GB_INT);
        GBDATA *ali_aligned     = GB_search(ali_cont, "aligned",                  GB_INT);
        GBDATA *ali_auto_format = GB_search(ali_cont, "auto_format",              GB_INT);
        GBDATA *ali_type        = GB_search(ali_cont, "alignment_type",           GB_STRING);
        GBDATA *ali_security    = GB_search(ali_cont, "alignment_write_security", GB_INT);
        GBDATA *ali_rem         = GB_search(ali_cont, "alignment_rem",            GB_STRING);

        aw_root->awar("presets/alignment_name")->map(ali_name);
        aw_root->awar("presets/alignment_type")->map(ali_type);
        aw_root->awar("presets/alignment_len") ->map(ali_len);
        aw_root->awar("presets/alignment_rem") ->map(ali_rem);
        aw_root->awar("presets/aligned")       ->map(ali_aligned);
        aw_root->awar("presets/auto_format")   ->map(ali_auto_format);
        aw_root->awar("presets/security")      ->map(ali_security);
    }
    GB_pop_transaction(GLOBAL.gb_main);
    free(use);
}

void NT_create_alignment_vars(AW_root *aw_root, AW_default aw_def)
{
    aw_root->awar_string("presets/use", "",     aw_def);
    GB_push_transaction(GLOBAL.gb_main);

    GBDATA *use = GB_search(GLOBAL.gb_main, "presets/use", GB_STRING);
    aw_root->awar("presets/use")->map(use);

    aw_root->awar_string("presets/alignment_name", "",   aw_def) ->set_srt(GBT_ALI_AWAR_SRT);
    aw_root->awar_string("presets/alignment_dest", "",   aw_def) ->set_srt(GBT_ALI_AWAR_SRT);

    aw_root->awar_string("presets/alignment_type", "", aw_def);
    aw_root->awar_string("presets/alignment_rem");
    aw_root->awar_int("presets/alignment_len", 0, aw_def);
    aw_root->awar_int("presets/aligned", 0, aw_def);
    aw_root->awar_int("presets/auto_format", 0, aw_def);
    aw_root->awar_int("presets/security", 0, aw_def);

    aw_root->awar("presets/use")->add_callback(alignment_vars_callback);
    alignment_vars_callback(aw_root);
    GB_pop_transaction(GLOBAL.gb_main);
}

static void ad_al_delete_cb(AW_window *aww) {
    if (aw_ask_sure("delete_ali_data", "Are you sure to delete all data belonging to this alignment")) {
        char           *source = aww->get_root()->awar("presets/use")->read_string();
        GB_transaction  ta(GLOBAL.gb_main);
        GB_ERROR        error  = GBT_rename_alignment(GLOBAL.gb_main, source, 0, 0, 1);

        if (error) {
            error = ta.close(error);
            aw_message(error);
        }
        free(source);
    }
}


static void ed_al_check_auto_format(AW_window *aww) {
    AW_root *awr = aww->get_root();
    char    *use = awr->awar("presets/use")->read_string();
    if (strcmp(use, "ali_genom") == 0) {
        awr->awar("presets/auto_format")->write_int(2); // ali_genom is always forced to "skip"
    }
}

static void ed_al_check_len_cb(AW_window *aww)
{
    char *error = 0;
    char *use = aww->get_root()->awar("presets/use")->read_string();
    GB_begin_transaction(GLOBAL.gb_main);
    if (!error) error = (char *)GBT_check_data(GLOBAL.gb_main, use);
    GB_commit_transaction(GLOBAL.gb_main);
    if (error) aw_message(error);
    free(use);
}

static void ed_al_align_cb(AW_window *aww) {
    char     *use = aww->get_root()->awar("presets/use")->read_string();
    GB_begin_transaction(GLOBAL.gb_main);
    GB_ERROR  err = ARB_format_alignment(GLOBAL.gb_main, use);
    GB_commit_transaction(GLOBAL.gb_main);
    if (err) aw_message(err);
    free(use);
    ed_al_check_len_cb(aww);
}

static void aa_copy_delete_rename(AW_window *aww, AW_CL copy, AW_CL dele) {
    char *source = aww->get_root()->awar("presets/use")->read_string();
    char *dest   = aww->get_root()->awar("presets/alignment_dest")->read_string();

    GB_ERROR error    = GB_begin_transaction(GLOBAL.gb_main);
    if (!error) error = GBT_rename_alignment(GLOBAL.gb_main, source, dest, (int)copy, (int)dele);
    if (!error) {
        char *nfield = GBS_global_string_copy("%s/data", dest);
        error        = GBT_add_new_changekey(GLOBAL.gb_main, nfield, GB_STRING);
        free(nfield);
    }

    error = GB_end_transaction(GLOBAL.gb_main, error);
    aww->hide_or_notify(error);

    free(source);
    free(dest);
}

static AW_window *create_alignment_copy_window(AW_root *root)
{
    AW_window_simple *aws = new AW_window_simple;
    aws->init(root, "COPY_ALIGNMENT", "ALIGNMENT COPY");
    aws->load_xfig("ad_al_si.fig");

    aws->callback((AW_CB0)AW_POPDOWN);
    aws->at("close");
    aws->create_button("CLOSE", "CLOSE", "C");

    aws->at("label");
    aws->create_autosize_button(0, "Please enter the new name\nof the alignment");

    aws->at("input");
    aws->create_input_field("presets/alignment_dest", 15);

    aws->at("ok");
    aws->callback(aa_copy_delete_rename, 1, 0);
    aws->create_button("GO", "GO", "G");

    return (AW_window *)aws;
}
static AW_window *create_alignment_rename_window(AW_root *root)
{
    AW_window_simple *aws = new AW_window_simple;
    aws->init(root, "RENAME_ALIGNMENT", "ALIGNMENT RENAME");
    aws->load_xfig("ad_al_si.fig");

    aws->callback((AW_CB0)AW_POPDOWN);
    aws->at("close");
    aws->create_button("CLOSE", "CLOSE", "C");

    aws->at("label");
    aws->create_autosize_button(0, "Please enter the name\nof the new alignment");

    aws->at("input");
    aws->create_input_field("presets/alignment_dest", 15);

    aws->at("ok");
    aws->callback(aa_copy_delete_rename, 1, 1);
    aws->create_button("GO", "GO", "G");

    return (AW_window *)aws;
}

static void aa_create_alignment(AW_window *aww) {
    GB_ERROR  error = GB_begin_transaction(GLOBAL.gb_main);
    if (!error) {
        char   *name             = aww->get_root()->awar("presets/alignment_dest")->read_string();
        GBDATA *gb_alignment     = GBT_create_alignment(GLOBAL.gb_main, name, 0, 0, 0, "dna");
        if (!gb_alignment) error = GB_await_error();
        else {
            char *nfield = GBS_global_string_copy("%s/data", name);
            error        = GBT_add_new_changekey(GLOBAL.gb_main, nfield, GB_STRING);
            free(nfield);
        }
        free(name);
    }
    GB_end_transaction_show_error(GLOBAL.gb_main, error, aw_message);
}

static AW_window *create_alignment_create_window(AW_root *root)
{
    AW_window_simple *aws = new AW_window_simple;
    aws->init(root, "CREATE_ALIGNMENT", "ALIGNMENT CREATE");
    aws->load_xfig("ad_al_si.fig");

    aws->callback((AW_CB0)AW_POPDOWN);
    aws->at("close");
    aws->create_button("CLOSE", "CLOSE", "C");

    aws->at("label");
    aws->create_autosize_button(0, "Please enter the new name\nof the alignment");

    aws->at("input");
    aws->create_input_field("presets/alignment_dest", 15);

    aws->at("ok");
    aws->callback(aa_create_alignment);
    aws->create_button("GO", "GO", "G");

    return (AW_window *)aws;
}

AW_window *NT_create_alignment_window(AW_root *root, AW_CL popmedown)
{
    // if popmedown points to a window, that window is popped down

    static AW_window_simple *aws = 0;

    AW_window *aw_popmedown = (AW_window*)popmedown;
    if (aw_popmedown) aw_popmedown->hide();

    if (aws) return aws; // do not duplicate

    aws = new AW_window_simple;

    aws->init(root, "INFO_OF_ALIGNMENT", "ALIGNMENT INFORMATION");
    aws->load_xfig("ad_align.fig");

    aws->callback((AW_CB0)AW_POPDOWN);
    aws->at("close");
    aws->create_button("CLOSE", "CLOSE", "C");

    aws->callback(AW_POPUP_HELP, (AW_CL)"ad_align.hlp");
    aws->at("help");
    aws->create_button("HELP", "HELP", "H");

    aws->button_length(13);

    aws->at("delete");
    aws->callback(ad_al_delete_cb);
    aws->create_button("DELETE", "DELETE", "D");

    aws->at("rename");
    aws->callback(AW_POPUP, (AW_CL)create_alignment_rename_window, 0);
    aws->create_button("RENAME", "RENAME", "R");

    aws->at("create");
    aws->callback(AW_POPUP, (AW_CL)create_alignment_create_window, 0);
    aws->create_button("CREATE", "CREATE", "N");

    aws->at("copy");
    aws->callback(AW_POPUP, (AW_CL)create_alignment_copy_window, 0);
    aws->create_button("COPY", "COPY", "C");

    aws->at("check_len");
    aws->callback(ed_al_check_len_cb);
    aws->create_button("CHECK_LEN", "CHECK LEN", "L");

    aws->at("align");
    aws->callback(ed_al_align_cb);
    aws->create_button("FORMAT", "FORMAT", "F");

    aws->at("list");
    awt_create_selection_list_on_alignments(GLOBAL.gb_main, (AW_window *)aws, "presets/use", "*=");

    aws->at("aligned");
    aws->create_option_menu("presets/aligned");
    aws->callback(ed_al_check_len_cb);
    aws->insert_default_option("not formatted", "n", 0);
    aws->callback(ed_al_align_cb);
    aws->insert_option("formatted", "j", 1);
    aws->update_option_menu();

    aws->at("auto_format");
    aws->create_option_menu("presets/auto_format");
    aws->callback(ed_al_check_auto_format);
    aws->insert_default_option("ask", "a", 0);
    aws->callback(ed_al_check_auto_format);
    aws->insert_option("always", "", 1);
    aws->callback(ed_al_check_auto_format);
    aws->insert_option("never", "", 2);
    aws->update_option_menu();

    aws->at("len");
    aws->create_input_field("presets/alignment_len", 7);

    aws->at("type");
    aws->create_option_menu("presets/alignment_type");
    aws->insert_option("dna", "d", "dna");
    aws->insert_option("rna", "r", "rna");
    aws->insert_option("pro", "p", "ami");
    aws->insert_default_option("???", "?", "usr");
    aws->update_option_menu();

    aws->at("security");
    aws->create_option_menu("presets/security");
    aws->callback(ed_al_check_len_cb);
    aws->insert_option("0", "0", 0);
    aws->callback(ed_al_check_len_cb);
    aws->insert_option("1", "1", 1);
    aws->callback(ed_al_check_len_cb);
    aws->insert_option("2", "2", 2);
    aws->callback(ed_al_check_len_cb);
    aws->insert_option("3", "3", 3);
    aws->callback(ed_al_check_len_cb);
    aws->insert_option("4", "4", 4);
    aws->callback(ed_al_check_len_cb);
    aws->insert_option("5", "5", 5);
    aws->callback(ed_al_check_len_cb);
    aws->insert_default_option("6", "6", 6);
    aws->update_option_menu();

    aws->at("rem");
    aws->create_text_field("presets/alignment_rem");

    return aws;
}