graph_aligner_gui.cxx

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// =============================================================== //
//                                                                 //
//   File      : graph_aligner_gui.cxx                             //
//   Purpose   :                                                   //
//                                                                 //
//   Coded by Elmar Pruesse in October 2008                        //
//   Institute of Microbiology (Technical University Munich)       //
//   http://www.arb-home.de/                                       //
//                                                                 //
// =============================================================== //

#include "graph_aligner_gui.hxx"

#include "ed4_defs.hxx"

// need to use AlignDataAccess defined here to get selected species
#include <fast_aligner.hxx>

#include <aw_awars.hxx>
#include <aw_global_awars.hxx>
#include <aw_msg.hxx>
#include <aw_root.hxx>
#include <awt_sel_boxes.hxx>
#include <awt_config_manager.hxx>
#include <xcmd.hxx>
#include <servercntrl.h>
#include <PT_com.h>
#include <client.h>
#include <arbdbt.h>
#include <arb_strbuf.h>
#include <arb_misc.h>
#include <arb_file.h>

#include <sys/types.h>
#include <sys/wait.h>

#include <unistd.h>

#include <string>
#include <sstream>
#include <iostream>
#include <vector>

using std::cerr;
using std::cout;
using std::endl;

#define ga_assert(cond) arb_assert(cond)

#define GA_AWAR_ROOT "sina/"
#define GA_AWAR_TEMP "tmp/" GA_AWAR_ROOT

#define GA_AWAR_CMD            GA_AWAR_ROOT "cmd"
#define GA_AWAR_TGT            GA_AWAR_ROOT "target"
#define GA_AWAR_SAI            GA_AWAR_ROOT "sai"
#define GA_AWAR_ALIGNMENT      GA_AWAR_ROOT "alignment"
#define GA_AWAR_PROTECTION     GA_AWAR_ROOT "protection"
#define GA_AWAR_TURN_CHECK     GA_AWAR_ROOT "turncheck"
#define GA_AWAR_REALIGN        GA_AWAR_ROOT "realign"
#define GA_AWAR_MATCH_SCORE    GA_AWAR_ROOT "match_score"
#define GA_AWAR_MISMATCH_SCORE GA_AWAR_ROOT "mismatch_score"
#define GA_AWAR_GAP_PEN        GA_AWAR_ROOT "gap_pen"
#define GA_AWAR_GAP_EXT        GA_AWAR_ROOT "gap_ext"
#define GA_AWAR_ADVANCED       GA_AWAR_ROOT "advanced"
#define GA_AWAR_FS_MIN         GA_AWAR_ROOT "fs_min"
#define GA_AWAR_FS_MAX         GA_AWAR_ROOT "fs_max"
#define GA_AWAR_FS_MSC         GA_AWAR_ROOT "fs_msc"
#define GA_AWAR_MIN_FULL       GA_AWAR_ROOT "min_full"
#define GA_AWAR_FULL_MINLEN    GA_AWAR_ROOT "full_minlen"
#define GA_AWAR_OVERHANG       GA_AWAR_ROOT "overhang"
#define GA_AWAR_THREADS        GA_AWAR_ROOT "threads"
#define GA_AWAR_QSIZE          GA_AWAR_ROOT "qsize"
#define GA_AWAR_KMER_LEN       GA_AWAR_ROOT "kmer_len"
#define GA_AWAR_KMER_MM        GA_AWAR_ROOT "kmer_mm"
#define GA_AWAR_MIN_LEN        GA_AWAR_ROOT "min_len"
#define GA_AWAR_WEIGHT         GA_AWAR_ROOT "weight"
#define GA_AWAR_INSERT         GA_AWAR_ROOT "insert"
#define GA_AWAR_LOWERCASE      GA_AWAR_ROOT "lowercase"
#define GA_AWAR_AUTOFILTER     GA_AWAR_ROOT "autofilter"
#define GA_AWAR_KMER_NOREL     GA_AWAR_ROOT "kmer_norel"
#define GA_AWAR_KMER_NOFAST    GA_AWAR_ROOT "kmer_nofast"
#define GA_AWAR_SHOW_DIST      GA_AWAR_ROOT "show_dist"
#define GA_AWAR_SHOW_DIFF      GA_AWAR_ROOT "show_diff"
#define GA_AWAR_COLOR          GA_AWAR_ROOT "color"
#define GA_AWAR_GENE_START     GA_AWAR_ROOT "gene_start"
#define GA_AWAR_GENE_END       GA_AWAR_ROOT "gene_end"
#define GA_AWAR_FS_COVER_GENE  GA_AWAR_ROOT "fs_cover_gene"
#define GA_AWAR_USED_RELS      GA_AWAR_ROOT "write_used_rels"
#define GA_AWAR_CALC_IDENTITY  GA_AWAR_ROOT "calc_idty"
#define GA_AWAR_NOWARN_START   GA_AWAR_ROOT "nowarn_start"
#define GA_AWAR_REFDB_MODE     GA_AWAR_ROOT "refdb_mode"
#define GA_AWAR_REFDB          GA_AWAR_ROOT "refdb"
#define GA_AWAR_REFDB_SELECT   GA_AWAR_TEMP "refdb"

enum RefDbMode {
    REF_EXPLICIT,  // use explicitly specified database
    REF_LAST_SAVE, // use last saved state of loaded database
    REF_CURRENT,   // use current state of loaded database
};

static void refDbModeChanged_cb(AW_root *root) {
    RefDbMode  mode       = RefDbMode(root->awar(GA_AWAR_REFDB_MODE)->read_int());
    AW_awar   *awar_refdb = root->awar(GA_AWAR_REFDB);

    switch (mode) {
        case REF_EXPLICIT: {
            const char *refdb = awar_refdb->read_char_pntr();
            if (!GB_is_readablefile(refdb)) {
                const char *refdb_sel = root->awar(GA_AWAR_REFDB_SELECT)->read_char_pntr();
                if (GB_is_readablefile(refdb_sel)) {
                    awar_refdb->write_string(refdb_sel);
                }
                else {
                    aw_message("Please select a reference database");
                }
            }
            break;
        }
        case REF_LAST_SAVE: {
            const char *db_name = root->awar(AWAR_SAVED_DB_PATH)->read_char_pntr();
            if (db_name[0] == 0) { // happens when editor runs standalone
                aw_message("Failed to detect name of current database - please select manually");
            }
            awar_refdb->write_string(db_name);
            break;
        }
        case REF_CURRENT: {
            awar_refdb->write_string(":");
            break;
        }
    }
}

static void newRefDbSelected_cb(AW_root *root) {
    const char *refdb_sel = root->awar(GA_AWAR_REFDB_SELECT)->read_char_pntr();

    if (GB_is_readablefile(refdb_sel)) {
        root->awar(GA_AWAR_REFDB_MODE)->write_int(REF_EXPLICIT);
        root->awar(GA_AWAR_REFDB)->write_string(refdb_sel);
    }
    else {
        root->awar(GA_AWAR_REFDB_MODE)->write_int(REF_CURRENT);
    }
}

void create_sina_variables(AW_root *root, AW_default db1) {
    const char *sinaCmd = "arb_sina.sh";
    root->awar_string(GA_AWAR_CMD,            sinaCmd,  db1);
    root->awar_int   (GA_AWAR_TGT,            2,        db1);
    root->awar_int   (AWAR_PT_SERVER,         0,        db1);
    root->awar_string(GA_AWAR_SAI,            "",       db1);
    root->awar_int   (GA_AWAR_PROTECTION,     0,        db1);
    root->awar_int   (GA_AWAR_TURN_CHECK,     1,        db1);
    root->awar_int   (GA_AWAR_REALIGN,        1,        db1);
    root->awar_float (GA_AWAR_GAP_PEN,        5.0,      db1);
    root->awar_float (GA_AWAR_GAP_EXT,        2.0,      db1);
    root->awar_float (GA_AWAR_MATCH_SCORE,    2.0,      db1);
    root->awar_float (GA_AWAR_MISMATCH_SCORE, -1.0,     db1);
    root->awar_int   (GA_AWAR_ADVANCED,       0,        db1);
    root->awar_int   (GA_AWAR_FS_MIN,         40,       db1);
    root->awar_int   (GA_AWAR_FS_MAX,         40,       db1);
    root->awar_float (GA_AWAR_FS_MSC,         .7,       db1);
    root->awar_int   (GA_AWAR_MIN_FULL,       1,        db1);
    root->awar_int   (GA_AWAR_FULL_MINLEN,    1400,     db1);
    root->awar_string(GA_AWAR_OVERHANG,       "attach", db1);
    root->awar_int   (GA_AWAR_THREADS,        1,        db1);
    root->awar_int   (GA_AWAR_QSIZE,          1,        db1);
    root->awar_int   (GA_AWAR_KMER_LEN,       10,       db1);
    root->awar_int   (GA_AWAR_KMER_MM,        0,        db1);
    root->awar_int   (GA_AWAR_MIN_LEN,        150,      db1);
    root->awar_float (GA_AWAR_WEIGHT,         1,        db1);
    root->awar_string(GA_AWAR_INSERT,         "shift",  db1);
    root->awar_string(GA_AWAR_LOWERCASE,      "none",   db1);
    root->awar_string(GA_AWAR_AUTOFILTER,     "",       db1);
    root->awar_int   (GA_AWAR_KMER_NOREL,     0,        db1);
    root->awar_int   (GA_AWAR_KMER_NOFAST,    0,        db1);
    root->awar_int   (GA_AWAR_SHOW_DIST,      0,        db1);
    root->awar_int   (GA_AWAR_SHOW_DIFF,      0,        db1);
    root->awar_int   (GA_AWAR_COLOR,          1,        db1);
    root->awar_int   (GA_AWAR_GENE_START,     0,        db1);
    root->awar_int   (GA_AWAR_GENE_END,       0,        db1);
    root->awar_int   (GA_AWAR_FS_COVER_GENE,  0,        db1);
    root->awar_int   (GA_AWAR_USED_RELS,      0,        db1);
    root->awar_int   (GA_AWAR_CALC_IDENTITY,  0,        db1);
    root->awar_int   (GA_AWAR_NOWARN_START,   0,        db1);

    AW_awar *awar_mode = root->awar_int     (GA_AWAR_REFDB_MODE,   REF_CURRENT, db1);
    root->awar_string                       (GA_AWAR_REFDB,        ":",         db1);
    AW_awar *awar_select = root->awar_string(GA_AWAR_REFDB_SELECT, "",          db1);

    awar_mode->add_callback(makeRootCallback(refDbModeChanged_cb));
    awar_select->add_callback(makeRootCallback(newRefDbSelected_cb));
}

enum SinaArbInterfaceVersion {
    ARB_5_99,
    ARB_7_1,
};
const SinaArbInterfaceVersion NO_INTERFACE = SinaArbInterfaceVersion(-1);

struct sina_arb_interface_def {
    SinaArbInterfaceVersion  version;
    const char              *id; // as define by SINA
};

static sina_arb_interface_def supported_sina_versions[] = {
    // order matters: first supported version will be used.

    { ARB_7_1, "ARB7.1" },   // only defined in patched version delivered with arb
    { ARB_5_99, "ARB5.99" }, // supported at least by sina 1.3 up to 1.7.2

    { NO_INTERFACE, "<none>" }, // version=sentinel
};

static const char *get_interface_id(SinaArbInterfaceVersion version) {
    for (int v = 0; ; ++v) {
        const sina_arb_interface_def& sina_interface = supported_sina_versions[v];
        if (sina_interface.version == version) {
            return sina_interface.id;
        }
    }
    return get_interface_id(NO_INTERFACE);
}

static SinaArbInterfaceVersion used_sina_interface = NO_INTERFACE;

static GB_ERROR detect_sina_version(AW_root *awr) {
    const char  *sinaName          = awr->awar(GA_AWAR_CMD)->read_char_pntr();
    char        *sina              = ARB_executable(sinaName, GB_getenv("PATH"));
    const char  *fail_reason       = NULp;
    std::string  tested_interfaces = "";

    used_sina_interface = NO_INTERFACE;

    if (sina) {
        if (ARB_path_contains_unwanted_chars(sina)) {
            char *description = GBS_global_string_copy("the sina executable derived from\n"
                                                       "- gui property '%s' and\n"
                                                       "- environment variable PATH", sinaName);
            ARB_warn_about_unwanted_chars(sina, description);
            free(description);
        }

        for (int v = 0; ; ++v) {
            const sina_arb_interface_def& sina_interface = supported_sina_versions[v];

            if (sina_interface.version == NO_INTERFACE) {
                if (fail_reason) fail_reason = GBS_global_string("%s (this ARB supports these interface versions: %s)", fail_reason, tested_interfaces.c_str());
                break;
            }

            int exitstatus = system(GBS_global_string("%s --has-cli-vers %s", sina, sina_interface.id));
            exitstatus     = WEXITSTATUS(exitstatus);

            if (exitstatus == EXIT_FAILURE) {
                fail_reason = "Incompatible SINA and ARB versions";

                if (!tested_interfaces.empty()) tested_interfaces += ' ';
                tested_interfaces                                 += sina_interface.id;
            }
            else {
                if (exitstatus == EXIT_SUCCESS) {
                    used_sina_interface = sina_interface.version;
                    fail_reason         = NULp;

                    fprintf(stdout, "Using SINA-ARB interface version '%s'%s\n", sina_interface.id, v>0 ? " (old)" : "");
                }
                else {
                    fail_reason = GBS_global_string("Could not execute SINA binary '%s' (exitstatus was %i)",
                                                    sinaName, exitstatus);
                }
                break; // either found compatible version or failed completely -> stop
            }
        }

        free(sina);
    }
    else {
        fail_reason = GBS_global_string("'%s' not found", sinaName);
    }

    return fail_reason;
}

AW_active sina_mask(AW_root *awr) {
    GB_ERROR fail_reason = detect_sina_version(awr);

    if (fail_reason) {
        fprintf(stderr, "Note: SINA (SILVA Aligner) disabled (Reason: %s)\n", fail_reason);
    }

    return fail_reason ? AWM_DISABLED : AWM_ALL;
}

inline const char *stream2static(const std::stringstream& str) {
    return GBS_static_string(str.str().c_str());
}

inline const char *empty_as_none(const char *sainame) {
    // see http://bugs.arb-home.de/ticket/519
    if (sainame && !sainame[0]) sainame = "none";
    return sainame;
}

static void sina_start(AW_window *window, const AlignDataAccess *data_access) {
    cerr << "Starting SINA..." << endl;

    AW_root  *root     = window->get_root();
    GB_ERROR  gb_error = NULp;

    // make string from pt server selection
    const char *pt_server = NULp;
    {
        int pt = root->awar(AWAR_PT_SERVER)->read_int();
        if (pt == -1) { // do NOT use ptserver (aka "use sina internal family search")
            if (used_sina_interface == ARB_5_99) {
                gb_error = "internal SINA family search is not available with your SINA version";
            }
        }
        else {
            std::stringstream ptnam;
            ptnam << "ARB_PT_SERVER" << pt;

            pt_server = GBS_read_arb_tcp(ptnam.str().c_str());
            if (!pt_server) {
                gb_error = GBS_global_string("Unable to find definition for chosen PT-server\n(Reason: %s)", GB_await_error());
            }
            else {
                const char *pt_db = pt_server + strlen(pt_server) + 1;
                pt_db += strlen(pt_db)+3;

                // start pt server if necessary
                gb_error = arb_look_and_start_server(AISC_MAGIC_NUMBER, ptnam.str().c_str());
                if (gb_error) {
                    std::stringstream tmp;
                    tmp << "Cannot contact PT server. Aborting" << endl
                        << " ID: \"" << tmp.str().c_str()
                        << "\" PORT: \"" << pt_server
                        << "\" DB: \"" << pt_db  << endl
                        << "\" GBERROR: \"" << gb_error << "\"" << endl;
                    gb_error = stream2static(tmp);
                }
            }
        }
    }

    if (!gb_error) {
        // create temporary file
        char* tmpfile;
        FILE* tmpfile_F;
        {
            char* tmpfile_tpl = GB_unique_filename("sina_select", "tmp");
            tmpfile_F         = GB_fopen_tempfile(tmpfile_tpl, "w", &tmpfile);
            free(tmpfile_tpl);
        }

        if (!tmpfile_F) {
            std::stringstream tmp;
            tmp << "Error: Unable to create temporary file \"" << tmpfile << "\"!";
            gb_error = stream2static(tmp);
        }
        else {
            GB_remove_on_exit(tmpfile);
            GBDATA *gb_main = data_access->gb_main;

            std::vector<std::string> spec_names;
            switch (root->awar(GA_AWAR_TGT)->read_int()) {
                case 0: { // current
                    char *spec_name = root->awar(AWAR_SPECIES_NAME)->read_string();
                    if (spec_name) {
                        fwrite(spec_name, strlen(spec_name), 1, tmpfile_F);
                        fwrite("\n", 1, 1, tmpfile_F);
                    }
                    else {
                        gb_error = "Unable to get name of currently active species";
                    }
                    free(spec_name);
                    break;
                }
                case 1: { // selected
                    GB_begin_transaction(gb_main);
                    int num_selected = 0;
                    for (GBDATA *gb_spec = data_access->get_first_selected_species(&num_selected);
                         gb_spec;
                         gb_spec = data_access->get_next_selected_species())
                    {
                        GBDATA *gbd_name = GB_find(gb_spec, "name", SEARCH_CHILD);
                        if (gbd_name) {
                            const char *str = GB_read_char_pntr(gbd_name);
                            fwrite(str, strlen(str), 1, tmpfile_F);
                            fwrite("\n", 1, 1, tmpfile_F);
                        }
                    }
                    GB_commit_transaction(gb_main);
                    break;
                }
                case 2: { // marked
                    GB_begin_transaction(gb_main);
                    for (GBDATA *gb_spec = GBT_first_marked_species(gb_main);
                         gb_spec; gb_spec = GBT_next_marked_species(gb_spec)) {
                        GBDATA *gbd_name = GB_find(gb_spec, "name", SEARCH_CHILD);
                        if (gbd_name) {
                            const char *str = GB_read_char_pntr(gbd_name);
                            fwrite(str, strlen(str), 1, tmpfile_F);
                            fwrite("\n", 1, 1, tmpfile_F);
                        }
                    }
                    GB_commit_transaction(gb_main);
                    break;
                }
            }
            fclose(tmpfile_F);

            if (!gb_error) {
                // build command line
                GBS_strstruct cl(2000);

                cl.cat(root->awar(GA_AWAR_CMD)->read_char_pntr());
                cl.cat(" -i :");

                switch (used_sina_interface) {
                    case ARB_5_99: cl.cat(" --ptdb :"); break;
                    case ARB_7_1:
                        cl.cat(" --out :");
                        cl.cat(" --db "); cl.cat(root->awar(GA_AWAR_REFDB)->read_char_pntr());
                        if (root->awar(GA_AWAR_NOWARN_START)->read_int()) cl.cat(" --dont-expect-start");
                        if (root->awar(GA_AWAR_CALC_IDENTITY)->read_int()) cl.cat(" --calc-idty");
                        cl.cat(" --default-alignment "); cl.cat(data_access->alignment_name.c_str()); // always use alignment used in editor
                        break;
                }

                if (pt_server) {
                    cl.cat(" --ptport ");             cl.cat(pt_server);
                    if (used_sina_interface == ARB_7_1) {
                        cl.cat(" --fs-engine ");      cl.cat("pt-server");
                    }
                }
                else { // use sina internal search
                    ga_assert(used_sina_interface == ARB_7_1);
                    cl.cat(" --fs-engine ");          cl.cat("internal");
                }

                cl.cat(" --turn ");               cl.cat(root->awar(GA_AWAR_TURN_CHECK)->read_int() ? "all" : "none");
                cl.cat(" --overhang ");           cl.cat(root->awar(GA_AWAR_OVERHANG)->read_char_pntr());
                cl.cat(" --filter ");             cl.cat(empty_as_none(root->awar(GA_AWAR_SAI)->read_char_pntr()));
                cl.cat(" --fs-min ");             cl.putlong(root->awar(GA_AWAR_FS_MIN)->read_int());
                cl.cat(" --fs-msc ");             cl.putfloat(root->awar(GA_AWAR_FS_MSC)->read_float());
                cl.cat(" --fs-max ");             cl.putlong(root->awar(GA_AWAR_FS_MAX)->read_int());
                cl.cat(" --fs-req 1");            // hardcoded to 1 - uses stricter requirement for full-length sequences
                cl.cat(" --fs-req-full ");        cl.putlong(root->awar(GA_AWAR_MIN_FULL)->read_int());
                cl.cat(" --fs-full-len ");        cl.putlong(root->awar(GA_AWAR_FULL_MINLEN)->read_int());
                cl.cat(" --fs-kmer-len ");        cl.putlong(root->awar(GA_AWAR_KMER_LEN)->read_int());
                cl.cat(" --fs-kmer-mm ");         cl.putlong(root->awar(GA_AWAR_KMER_MM)->read_int()); // @@@ only with ptserver -> document + add 2 gui
                cl.cat(" --fs-min-len ");         cl.putlong(root->awar(GA_AWAR_MIN_LEN)->read_int());
                cl.cat(" --fs-weight ");          cl.putfloat(root->awar(GA_AWAR_WEIGHT)->read_float());
                cl.cat(" --pen-gap ");            cl.putfloat(root->awar(GA_AWAR_GAP_PEN)->read_float());
                cl.cat(" --pen-gapext ");         cl.putfloat(root->awar(GA_AWAR_GAP_EXT)->read_float());
                cl.cat(" --match-score ");        cl.putfloat(root->awar(GA_AWAR_MATCH_SCORE)->read_float());
                cl.cat(" --mismatch-score ");     cl.putfloat(root->awar(GA_AWAR_MISMATCH_SCORE)->read_float());
                cl.cat(" --prot-level ");         cl.putlong(root->awar(GA_AWAR_PROTECTION)->read_int());
                cl.cat(" --select-file ");        cl.cat(tmpfile);
                cl.cat(" --insertion ");          cl.cat(root->awar(GA_AWAR_INSERT)->read_char_pntr());
                cl.cat(" --lowercase ");          cl.cat(root->awar(GA_AWAR_LOWERCASE)->read_char_pntr());
                cl.cat(" --auto-filter-field ");  cl.cat_sQuoted(root->awar(GA_AWAR_AUTOFILTER)->read_char_pntr()); // note: default value passed to sina 1.3 was 'none' (w/o quotes)
                cl.cat(" --gene-start ");         cl.putlong(root->awar(GA_AWAR_GENE_START)->read_int());
                cl.cat(" --gene-end ");           cl.putlong(root->awar(GA_AWAR_GENE_END)->read_int());
                cl.cat(" --fs-cover-gene ");      cl.putlong(root->awar(GA_AWAR_FS_COVER_GENE)->read_int());


                if (root->awar(GA_AWAR_KMER_NOREL)->read_int())  cl.cat(" --fs-kmer-norel ");
                if (root->awar(GA_AWAR_KMER_NOFAST)->read_int()) cl.cat(" --fs-kmer-no-fast ");
                if (root->awar(GA_AWAR_SHOW_DIST)->read_int())   cl.cat(" --show-dist ");
                if (root->awar(GA_AWAR_SHOW_DIFF)->read_int())   cl.cat(" --show-diff ");
                if (root->awar(GA_AWAR_COLOR)->read_int())       cl.cat(" --color");
                if (root->awar(GA_AWAR_REALIGN)->read_int())     cl.cat(" --realign");
                if (root->awar(GA_AWAR_USED_RELS)->read_int())   cl.cat(" --write-used-rels");

                gb_error = ARB_system(cl.get_data(), XCmdType(XCMD_SERVSYNC_WAIT_ON_ERROR, gb_main));
            }

            if (!gb_error) aw_message("SINA finished aligning.");
        }
        free(tmpfile);
    }

    aw_message_if(gb_error);
}



static char* filter_posvar_SAI_for_ali(GBDATA *gb_extended, const char *ali_name) {
    char   *result   = NULp;
    char   *typePath = GBS_global_string_copy("%s/_TYPE", ali_name);
    GBDATA *gbd      = GB_search(gb_extended, typePath, GB_FIND);
    if (gbd) {
        const char* type = GB_read_char_pntr(gbd);
        if (type && strncmp("PV", type, 2) == 0) {
            gbd    = GB_find(gb_extended, "name", SEARCH_CHILD);
            result = GB_read_string(gbd);
        }
    }
    free(typePath);
    return result;
}

static AWT_config_mapping_def sina_config_mapping[] = {
    // both
    { GA_AWAR_TGT,         "target" },
    { GA_AWAR_OVERHANG,    "overhang" },
    { GA_AWAR_INSERT,      "insertions" },
    { GA_AWAR_LOWERCASE,   "lowercase" },
    { GA_AWAR_WEIGHT,      "weight" },
    { GA_AWAR_FULL_MINLEN, "fullminlen" },

    // advanced only
    { GA_AWAR_SAI,            "sai" },
    { GA_AWAR_AUTOFILTER,     "autofilter" },
    { GA_AWAR_TURN_CHECK,     "turncheck" },
    { GA_AWAR_REALIGN,        "realign" },
    { GA_AWAR_GAP_PEN,        "gappen" },
    { GA_AWAR_GAP_EXT,        "gapext" },
    { GA_AWAR_MATCH_SCORE,    "matchscore" },
    { GA_AWAR_MISMATCH_SCORE, "mismatchscore" },
    { GA_AWAR_FS_MIN,         "fs_min" },
    { GA_AWAR_FS_MSC,         "fs_minscore" },
    { GA_AWAR_FS_MAX,         "fs_min" },
    { GA_AWAR_MIN_FULL,       "minfull" },
    { GA_AWAR_KMER_LEN,       "kmerlen" },
    { GA_AWAR_KMER_MM,        "kmermm" },
    { GA_AWAR_MIN_LEN,        "refminlen" },
    { GA_AWAR_GENE_START,     "genestart" },
    { GA_AWAR_GENE_END,       "geneend" },
    { GA_AWAR_FS_COVER_GENE,  "fs_covergene" },
    { GA_AWAR_USED_RELS,      "write_used_rels" },
    { GA_AWAR_CALC_IDENTITY,  "calc_identity" },
    { GA_AWAR_KMER_NOFAST,    "kmernofast" },
    { GA_AWAR_KMER_NOREL,     "kmernorel" },

    // both
    { GA_AWAR_SHOW_DIFF, "showdiff" },
    { GA_AWAR_COLOR,     "color" },
    { GA_AWAR_SHOW_DIST, "showdist" },

    { NULp, NULp }
};

static void accept_selected_ref_db(AW_window *aww, const char * const *awar_filename) {
    AW_root *root     = aww->get_root();
    char    *filename = root->awar(*awar_filename)->read_string();

    if (GB_is_readablefile(filename)) {
        AW_awar *awar_refdb_sel = root->awar(GA_AWAR_REFDB_SELECT);
        awar_refdb_sel->write_string(filename);
        aww->hide();
    }

    free(filename);
}

static AW_window *create_ref_db_selection_window(AW_root *aw_root) {
    static char *awar_name = NULp; // do not free, bound to callback
    return awt_create_load_box(aw_root,
                               "Select",
                               "SINA reference database",
                               ".", "arb", &awar_name,
                               makeWindowCallback(accept_selected_ref_db,  (const char*const*)&awar_name));
}


static void sina_select_ref_db(AW_window *aww) {
    static AW_window *aw_ref_db_selection = NULL;

    if (!aw_ref_db_selection) {
        AW_root *root = aww->get_root();
        aw_ref_db_selection = create_ref_db_selection_window(root);
    }

    aw_ref_db_selection->activate();
}


static SinaArbInterfaceVersion gui_sina_interface = NO_INTERFACE; // interface used in GUI

static void sina_cmd_changed_cb(AW_root *awr) {
    GB_ERROR fail_reason = detect_sina_version(awr);

    if (fail_reason) {
        aw_message(fail_reason);
    }
    else {
        if (used_sina_interface != gui_sina_interface) {
            aw_message("The GUI does not match the used sina version!\n"
                       "Please save properties and restart the editor.");
        }
        aw_message(GBS_global_string("Using sina-arb interface '%s'", get_interface_id(used_sina_interface)));
    }
}

static AW_window_simple* new_sina_simple(AW_root *root, const AlignDataAccess *alignData, bool adv) {
    const int         hgap = 10;
    AW_window_simple *aws  = new AW_window_simple;

    if (gui_sina_interface == NO_INTERFACE) {
        gui_sina_interface = used_sina_interface;
        root->awar(GA_AWAR_CMD)->add_callback(sina_cmd_changed_cb);
    }

    aws->reset_layout("20220422");
    aws->init(root, adv ? "XSINA" : "SINA", "SINA (SILVA Incremental Aligner)");

    aws->button_length(12);
    aws->at(10, 10);
    aws->auto_space(5, 5);

    int closex, closey; aws->get_at_position(&closex, &closey);

    aws->callback(AW_POPDOWN);
    aws->create_button("CLOSE", "CLOSE", "O");

    int closex2 = aws->get_at_xposition();

    if (gui_sina_interface == NO_INTERFACE) {
        // happens when no sina detected + menu entry is triggered via macro // @@@ would be nice to globally avoid callbacks for inactive menu entries

        aws->at_newline();
        aws->label_length(0);
        aws->label("SINA command\nError: Failed to find or identify sina version!");
        aws->create_input_field(GA_AWAR_CMD, 20);

        return aws;
    }

    aws->at_shift(10, 0);
    aws->label_length(0);
    aws->label("Show advanced options");
    aws->create_toggle(GA_AWAR_ADVANCED);

    bool cbInstalled = false;
    if (!cbInstalled) {
        root->awar(GA_AWAR_ADVANCED)->add_callback(makeRootCallback(show_sina_window, alignData));
        cbInstalled = true;
    }

    aws->at_newline();
    aws->at_shift(0, hgap);
    int y_col2 = aws->get_at_yposition();
    aws->label_length(15);
    aws->create_toggle_field(GA_AWAR_TGT, "Align what?");
    aws->insert_toggle("Current Species:", "C", 0);
    aws->insert_toggle("Selected Species", "S", 1);
    aws->insert_default_toggle("Marked Species", "M", 2);
    aws->update_toggle_field();

    aws->at_shift(0, 3);
    aws->create_input_field(AWAR_SPECIES_NAME, 20);

    aws->at_newline();
    aws->at_shift(0, hgap);
    aws->button_length(24);
    if (used_sina_interface == ARB_5_99) {
        aws->label("PT Server:");
    }
    else {
        aws->label_length(20);
        aws->label("PT Server\n"
                   "undefined => sina kmer");
    }
    awt_create_PTSERVER_selection_button(aws, AWAR_PT_SERVER);

    aws->label_length(0);

    if (gui_sina_interface == ARB_7_1) {
        aws->at_newline();
        aws->create_toggle_field(GA_AWAR_REFDB_MODE, "Reference database");
        aws->insert_toggle("Explicit as ", "E", REF_EXPLICIT);
        aws->insert_toggle("Last saved", "s", REF_LAST_SAVE);
        aws->insert_default_toggle("Current", "C", REF_CURRENT);
        aws->update_toggle_field();

        aws->at_shift(0, 3);
        aws->callback(makeWindowCallback(sina_select_ref_db));
        aws->create_autosize_button("selected", "selected", "s");

        aws->at_newline();
        aws->create_input_field(GA_AWAR_REFDB, 40);
    }

    aws->at_newline();
    aws->label("Overhang placement");
    aws->create_option_menu(GA_AWAR_OVERHANG);
    aws->insert_option("keep attached", NULp, "attach");
    aws->insert_option("move to edge",  NULp, "edge");
    aws->insert_option("remove",        NULp, "remove");
    aws->update_option_menu();

    aws->at_newline();
    aws->label("Handling of unmappable insertions");
    aws->create_option_menu(GA_AWAR_INSERT);
    aws->insert_option("Shift surrounding bases",    NULp, "shift");
    aws->insert_option("Forbid during DP alignment", NULp, "forbid");
    aws->insert_option("Delete bases",               NULp, "remove");
    aws->update_option_menu();

    int x_col2 = aws->get_at_xposition();

    aws->at_newline();
    aws->label("Character Case");
    aws->create_option_menu(GA_AWAR_LOWERCASE);
    aws->insert_option("Do not modify",                      NULp, "original");
    aws->insert_option("Show unaligned bases as lower case", NULp, "unaligned");
    aws->insert_option("Uppercase all",                      NULp, "none");
    aws->update_option_menu();

    aws->at_newline();
    aws->label("Family conservation weight (0-1)");
    aws->create_input_field(GA_AWAR_WEIGHT, 3);

    aws->at_newline();
    aws->label("Size of full-length sequences");
    aws->create_input_field(GA_AWAR_FULL_MINLEN, 5);

    aws->at_newline();
    aws->label_length(17);
    aws->label("Protection Level");
    aws->create_option_menu(GA_AWAR_PROTECTION);
    aws->insert_option("0", NULp, 0);
    aws->insert_option("1", NULp, 1);
    aws->insert_option("2", NULp, 2);
    aws->insert_option("3", NULp, 3);
    aws->insert_option("4", NULp, 4);
    aws->insert_option("5", NULp, 5);
    aws->insert_option("6", NULp, 6);
    aws->update_option_menu();

    aws->at_newline();

    aws->label_length(21);
    aws->label("Show changed sections");
    aws->create_toggle(GA_AWAR_SHOW_DIFF);
    aws->label_length(11);
    aws->label("color bases");
    aws->create_toggle(GA_AWAR_COLOR);

    aws->at_newline();
    aws->label_length(21);
    aws->label("Show statistics");
    aws->create_toggle(GA_AWAR_SHOW_DIST);

    aws->at_newline();

    int startx, starty; aws->get_at_position(&startx, &starty);

    aws->button_length(12);
    aws->at(closex, starty);
    aws->callback(makeWindowCallback(sina_start, alignData));
    aws->highlight();
    aws->create_button("Start", "Start", "S");

    aws->at(closex2+200, starty-10);
    AWT_insert_config_manager(aws, AW_ROOT_DEFAULT, "sina", sina_config_mapping);

    if (adv) {
        aws->at(x_col2, y_col2);
        aws->auto_space(5, 5); // resets position for at_newline

        aws->label_length(0);
        aws->label("Pos. Var.:");
        awt_create_SAI_selection_button(alignData->gb_main, aws, GA_AWAR_SAI, makeSaiSelectionlistFilterCallback(filter_posvar_SAI_for_ali, alignData->alignment_name.c_str()));

        aws->at_newline();
        aws->label("Field used for automatic\nfilter selection");
        aws->create_input_field(GA_AWAR_AUTOFILTER, 20);

        aws->at_newline();
        aws->label("Turn check"); aws->create_toggle(GA_AWAR_TURN_CHECK);
        aws->label("Realign"); aws->create_toggle(GA_AWAR_REALIGN);

        aws->at_newline();
        aws->at_shift(0, hgap);

        aws->label("Gap insertion/extension penalties");
        aws->create_input_field(GA_AWAR_GAP_PEN, 5);
        aws->create_input_field(GA_AWAR_GAP_EXT, 5);

        aws->at_newline();
        aws->label("Match score");
        aws->create_input_field(GA_AWAR_MATCH_SCORE, 3);
        aws->label("Mismatch score");
        aws->create_input_field(GA_AWAR_MISMATCH_SCORE, 3);

        aws->at_newline();
        aws->label("Family search min/min_score/max");
        aws->create_input_field(GA_AWAR_FS_MIN, 3);
        aws->create_input_field(GA_AWAR_FS_MSC, 3);
        aws->create_input_field(GA_AWAR_FS_MAX, 3);

        aws->at_newline();
        aws->label("Minimal number of full length sequences");
        aws->create_input_field(GA_AWAR_MIN_FULL, 3);

        aws->at_newline();
        aws->label("Family search oligo length / mismatches");
        aws->create_input_field(GA_AWAR_KMER_LEN, 3);
        aws->create_input_field(GA_AWAR_KMER_MM, 3);

        aws->at_newline();
        aws->label("Minimal reference sequence length");
        aws->create_input_field(GA_AWAR_MIN_LEN, 5);

        aws->at_newline();
        aws->label("Alignment bounds: start");
        aws->create_input_field(GA_AWAR_GENE_START, 6);
        aws->label("end");
        aws->create_input_field(GA_AWAR_GENE_END, 6);

        aws->at_newline();
        aws->label("Number of references required to touch bounds");
        aws->create_input_field(GA_AWAR_FS_COVER_GENE, 3);

        aws->at_newline();
        aws->label("Save used references in 'used_rels'");
        aws->create_toggle(GA_AWAR_USED_RELS);

        aws->at_newline();
        aws->label("Store highest identity in 'align_ident_slv'");
        aws->create_toggle(GA_AWAR_CALC_IDENTITY);

        aws->at_newline();
        aws->label("Disable fast search");
        aws->create_toggle(GA_AWAR_KMER_NOFAST);

        aws->at_newline();
        aws->label("Score search results by absolute oligo match count");
        aws->create_toggle(GA_AWAR_KMER_NOREL);

        if (gui_sina_interface == ARB_7_1) {
            aws->at_newline();
            aws->label("Suppress warnings about missing 'start' field");
            aws->create_toggle(GA_AWAR_NOWARN_START);
        }

        aws->at_newline();
        aws->label("SINA command");
        aws->create_input_field(GA_AWAR_CMD, 20);
    }

    int winx, winy; aws->get_window_size(winx, winy);

    aws->button_length(12);
    aws->at(winx-closex2+5, closey);
    aws->callback(makeHelpCallback("sina_main.hlp"));
    aws->create_button("HELP", "HELP");

    return aws;
}

void show_sina_window(UNFIXED, const AlignDataAccess *alignData) {
    AW_root *root = AW_root::SINGLETON;

    static AW_window_simple *ga_aws     = NULp;
    static AW_window_simple *ga_aws_adv = NULp;

    if (root->awar(GA_AWAR_ADVANCED)->read_int()) {
        if (!ga_aws_adv) ga_aws_adv = new_sina_simple(root, alignData, true);
        ga_aws_adv->show();

        if (ga_aws) ga_aws->hide();
    }
    else {
        if (!ga_aws) ga_aws = new_sina_simple(root, alignData, false);
        ga_aws->show();

        if (ga_aws_adv) ga_aws_adv->hide();
    }

    static bool refdb_mode_refreshed = false;
    if (!refdb_mode_refreshed) {
        AW_awar *awar_mode         = root->awar(GA_AWAR_REFDB_MODE);
        if (awar_mode->read_int() != REF_EXPLICIT) awar_mode->touch(); // trigger callback
        refdb_mode_refreshed       = true;
    }
}