ali_global.cxx

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

#include "ali_global.hxx"

#define EXCLUSIVE_FLAG_DEFAULT             1
#define MARK_FAMILY_FLAG_DEFAULT           0
#define MARK_EXTENSION_FLAG_DEFAULT        0
#define FIND_FAMILY_MODE_DEFAULT           1
#define MAX_FAMILY_SIZE_DEFAULT            10
#define MIN_FAMILY_SIZE_DEFAULT            5
#define MIN_WEIGHT_DEFAULT                 0.7
#define EXT_MAX_WEIGHT_DEFAULT             0.2
#define MULTI_GAP_FACTOR_DEFAULT           0.1
#define INSERT_FACTOR_DEFAULT              2.0;
#define MULTI_INSERT_FACTOR_DEFAULT        0.5;
#define COST_LOW_DEFAULT                   0.25
#define COST_MIDDLE_DEFAULT                0.5
#define COST_HIGH_DEFAULT                  0.8
#define MAX_COST_OF_SUB_PERCENT_DEFAULT    0.5
#define MAX_COST_OF_HELIX                  2.0
#define ERROR_COUNT_DEFAULT                2
#define MAX_NUMBER_OF_MAPS_DEFAULT         10 // 100
#define MAX_NUMBER_OF_MAPS_ALIGNER_DEFAULT 2
#define INTERVAL_BORDER_DEFAULT            5
#define INTERVAL_CENTER_DEFAULT            5

// ACHTUNG: muss noch durch parameter belegbar sein
#define MATCHES_MIN_DEFAULT          1000
#define PERCENT_MIN_DEFAULT          0.75
#define FAM_LIST_MAX_DEFAULT         5
#define EXT_LIST_MAX_DEFAULT         10
#define USE_SPECIFIED_FAMILY_DEFAULT NULp


static double default_substitute_matrix[5][5] = {
    // a    c    g    u    -
    { 0.0, 3.0, 1.0, 3.0, 5.0 }, // a
    { 3.0, 0.0, 3.0, 1.0, 5.0 }, // c
    { 1.0, 3.0, 0.0, 3.0, 5.0 }, // g
    { 3.0, 1.0, 3.0, 0.0, 5.0 }, // u
    { 5.0, 5.0, 5.0, 5.0, 0.0 } // -
};

static double default_binding_matrix[5][5] = {
    // a    c    g    u    -
    { 9.9, 9.9, 2.0, 0.9, 9.9 }, // a
    { 9.9, 9.9, 0.6, 9.9, 9.9 }, // c
    { 2.0, 0.6, 5.0, 1.1, 9.9 }, // g
    { 0.9, 9.9, 1.1, 9.9, 9.9 }, // u
    { 9.9, 9.9, 9.9, 9.9, 0.0 } // -
};


void ALI_GLOBAL::init(int *argc, const char *argv[]) {
    int kill, i, h, j, ret;
    const char *pos;
    arb_params *params;
    float fl;

    params = arb_trace_argv(argc, argv);

    prog_name = argv[0];
    species_name = params->species_name;
    default_file = params->default_file;
    db_server = params->db_server;

    // Set the defaults

    for (i = 0; i < 5; i++)
        for (j = 0; j < 5; j++) {
            prof_context.substitute_matrix[i][j] = default_substitute_matrix[i][j];
            prof_context.binding_matrix[i][j] = default_binding_matrix[i][j];
        }

    cost_low = COST_LOW_DEFAULT;
    cost_middle = COST_MIDDLE_DEFAULT;
    cost_high = COST_HIGH_DEFAULT;
    preali_context.max_number_of_maps = MAX_NUMBER_OF_MAPS_DEFAULT;
    preali_context.max_number_of_maps_aligner =
        MAX_NUMBER_OF_MAPS_ALIGNER_DEFAULT;
    preali_context.interval_border = INTERVAL_BORDER_DEFAULT;
    preali_context.interval_center = INTERVAL_CENTER_DEFAULT;
    preali_context.max_cost_of_sub_percent = MAX_COST_OF_SUB_PERCENT_DEFAULT;
    preali_context.max_cost_of_helix = MAX_COST_OF_HELIX;
    preali_context.error_count = ERROR_COUNT_DEFAULT;
    mark_species_flag = 0;

    prof_context.find_family_mode = FIND_FAMILY_MODE_DEFAULT;
    prof_context.exclusive_flag = EXCLUSIVE_FLAG_DEFAULT;
    prof_context.mark_family_flag = MARK_FAMILY_FLAG_DEFAULT;
    prof_context.mark_family_extension_flag = MARK_EXTENSION_FLAG_DEFAULT;
    prof_context.max_family_size = MAX_FAMILY_SIZE_DEFAULT;
    prof_context.min_family_size = MIN_FAMILY_SIZE_DEFAULT;
    prof_context.min_weight = MIN_WEIGHT_DEFAULT;
    prof_context.ext_max_weight = EXT_MAX_WEIGHT_DEFAULT;
    prof_context.multi_gap_factor = MULTI_GAP_FACTOR_DEFAULT;
    prof_context.insert_factor = INSERT_FACTOR_DEFAULT;
    prof_context.multi_insert_factor = MULTI_INSERT_FACTOR_DEFAULT;

    pt_context.matches_min = MATCHES_MIN_DEFAULT;
    pt_context.percent_min = PERCENT_MIN_DEFAULT;
    pt_context.fam_list_max = FAM_LIST_MAX_DEFAULT;
    pt_context.ext_list_max = EXT_LIST_MAX_DEFAULT;
    pt_context.use_specified_family = USE_SPECIFIED_FAMILY_DEFAULT;

    // evaluate the parameters

    for (i = 1; i < *argc;) {
        kill = 0;
        if (strcmp("-nx", argv[i]) == 0 && kill == 0) {
            prof_context.exclusive_flag = 0;
            kill = i;
        }
        if (strncmp("-f", argv[i], 2) == 0 && kill == 0) {
            pt_context.use_specified_family = ARB_strdup(argv[i] + 2);
            kill = i;
        }
        if (strcmp("-ms", argv[i]) == 0 && kill == 0) {
            mark_species_flag = 1;
            kill = i;
        }
        if (strcmp("-mf", argv[i]) == 0 && kill == 0) {
            prof_context.mark_family_flag = 1;
            kill = i;
        }
        if (strcmp("-mfe", argv[i]) == 0 && kill == 0) {
            prof_context.mark_family_extension_flag = 1;
            kill = i;
        }
        if (strncmp("-mgf", argv[i], 4) == 0 && kill == 0) {
            kill = i;
            pos = argv[i] + 4;
            ret = sscanf(pos, "%f", &prof_context.multi_gap_factor);
            if (ret != 1) {
                ali_warning("Wrong format for -mgf");
                break;
            }
        }
        if (strncmp("-if", argv[i], 3) == 0 && kill == 0) {
            kill = i;
            pos = argv[i] + 3;
            ret = sscanf(pos, "%f", &prof_context.insert_factor);
            if (ret != 1) {
                ali_warning("Wrong format for -if");
                break;
            }
        }
        if (strncmp("-mif", argv[i], 4) == 0 && kill == 0) {
            kill = i;
            pos = argv[i] + 4;
            ret = sscanf(pos, "%f", &prof_context.multi_insert_factor);
            if (ret != 1) {
                ali_warning("Wrong format for -mif");
                break;
            }
        }
        if (strcmp("-m", argv[i]) == 0 && kill == 0) {
            mark_species_flag = 1;
            prof_context.mark_family_flag = 1;
            kill = i;
        }
        if (strncmp("-msub", argv[i], 5) == 0 && kill == 0) {
            kill = i;
            pos = argv[i] + 5;
            for (h = 0; h < 5; h++)
                for (j = 0; j < 5; j++) {
                    ret = sscanf(pos, "%f", &fl);
                    if (ret != 1) {
                        ali_warning("wrong format for -msub");
                        break;
                    }
                    else
                        prof_context.substitute_matrix[h][j] = (double) fl;
                    pos = strchr(pos, ',');
                    if ((h != 4 || j != 4) && !pos) {
                        ali_warning("Not enought values for -msub");
                        break;
                    }
                    pos++;
                }
        }
        if (strncmp("-mbind", argv[i], 6) == 0 && kill == 0) {
            kill = i;
            pos = argv[i] + 6;
            for (h = 0; h < 5; h++)
                for (j = 0; j < 5; j++) {
                    ret = sscanf(pos, "%f", &fl);
                    if (ret != 1) {
                        ali_warning("Wrong format for -mbind");
                        break;
                    }
                    else
                        prof_context.binding_matrix[h][j] = (double) fl;
                    pos = strchr(pos, ',');
                    if ((h != 4 || j != 4) && !pos) {
                        ali_warning("Not enought values for -mbind");
                        break;
                    }
                    pos++;
                }
        }
        if (strncmp("-maxf", argv[i], 5) == 0 && kill == 0) {
            kill = i;
            pos = argv[i] + 5;
            ret = sscanf(pos, "%d", &prof_context.max_family_size);
            if (ret != 1) {
                ali_warning("Wrong format for -maxf");
                break;
            }
        }
        if (strncmp("-minf", argv[i], 5) == 0 && kill == 0) {
            kill = i;
            pos = argv[i] + 5;
            ret = sscanf(pos, "%d", &prof_context.min_family_size);
            if (ret != 1) {
                ali_warning("Wrong format for -minf");
                break;
            }
        }
        if (strncmp("-minw", argv[i], 5) == 0 && kill == 0) {
            kill = i;
            pos = argv[i] + 5;
            ret = sscanf(pos, "%f", &prof_context.min_weight);
            if (ret != 1) {
                ali_warning("Wrong format for -minw");
                break;
            }
        }
        if (strncmp("-maxew", argv[i], 6) == 0 && kill == 0) {
            kill = i;
            pos = argv[i] + 6;
            ret = sscanf(pos, "%f", &prof_context.ext_max_weight);
            if (ret != 1) {
                ali_warning("Wrong format for -minw");
                break;
            }
        }

        // ACHTUNG: Unused BEGIN
        if (strncmp("-cl", argv[i], 3) == 0 && kill == 0) {
            kill = i;
            pos = argv[i] + 3;
            ret = sscanf(pos, "%f", &cost_low);
            if (ret != 1) {
                ali_warning("Wrong format for -cl");
                break;
            }
        }
        if (strncmp("-cm", argv[i], 3) == 0 && kill == 0) {
            kill = i;
            pos = argv[i] + 3;
            ret = sscanf(pos, "%f", &cost_middle);
            if (ret != 1) {
                ali_warning("Wrong format for -cm");
                break;
            }
        }
        if (strncmp("-ch", argv[i], 3) == 0 && kill == 0) {
            kill = i;
            pos = argv[i] + 3;
            ret = sscanf(pos, "%f", &cost_high);
            if (ret != 1) {
                ali_warning("Wrong format for -ch");
                break;
            }
        }
        // ACHTUNG: Unused END

        if (strncmp("-csub", argv[i], 5) == 0 && kill == 0) {
            kill = i;
            pos = argv[i] + 5;
            ret = sscanf(pos, "%f", &preali_context.max_cost_of_sub_percent);
            if (ret != 1) {
                ali_warning("Wrong format for -csub");
                break;
            }
        }
        if (strncmp("-chel", argv[i], 5) == 0 && kill == 0) {
            kill = i;
            pos = argv[i] + 5;
            ret = sscanf(pos, "%f", &preali_context.max_cost_of_helix);
            if (ret != 1) {
                ali_warning("Wrong format for -chel");
                break;
            }
        }
        if (strncmp("-mma", argv[i], 4) == 0 && kill == 0) {
            kill = i;
            pos = argv[i] + 4;
            ret = sscanf(pos, "%ld", &preali_context.max_number_of_maps_aligner);
            if (ret != 1) {
                ali_warning("Wrong format for -mma");
                break;
            }
        }
        if (strncmp("-mm", argv[i], 3) == 0 && kill == 0) {
            kill = i;
            pos = argv[i] + 3;
            ret = sscanf(pos, "%ld", &preali_context.max_number_of_maps);
            if (ret != 1) {
                ali_warning("Wrong format for -mm");
                break;
            }
        }
        if (strncmp("-ec", argv[i], 3) == 0 && kill == 0) {
            kill = i;
            pos = argv[i] + 3;
            ret = sscanf(pos, "%ld", &preali_context.error_count);
            if (ret != 1) {
                ali_warning("Wrong format for -ec");
                break;
            }
        }
        if (strncmp("-ib", argv[i], 3) == 0 && kill == 0) {
            kill = i;
            pos = argv[i] + 3;
            ret = sscanf(pos, "%d", &preali_context.interval_border);
            if (ret != 1) {
                ali_warning("Wrong format for -ib");
                break;
            }
        }
        if (strncmp("-ic", argv[i], 3) == 0 && kill == 0) {
            kill = i;
            pos = argv[i] + 3;
            ret = sscanf(pos, "%d", &preali_context.interval_center);
            if (ret != 1) {
                ali_warning("Wrong format for -ic");
                break;
            }
        }

        if (kill > 0) {
            for (i++; i < *argc; i++)
                argv[i-1] = argv[i];
            (*argc)--;
            i = kill;
        }
        else
            i++;
    }

    // Check for consistency

    if (prof_context.min_family_size > prof_context.max_family_size) {
        ali_warning("minf <= maxf");
    }

    if (prof_context.ext_max_weight < 0 || prof_context.ext_max_weight > 1.0) {
        ali_warning("0 <= maxew <= 1.0");
    }

    if (prof_context.min_weight < 0 || prof_context.min_weight > 1.0) {
        ali_warning("0 <=  minw <= 1.0");
    }

    if (cost_low > cost_middle || cost_middle > cost_high ||
        cost_low < 0 || cost_high > 1.0) {
        ali_warning("0 <= cl <= cm <= ch <= 1.0");
    }

    // Open Database and Pt server

    ali_message("Connecting to Database server");
    if (arbdb.open(db_server) != 0) {
        ali_error("Can't connect to Database server");
    }
    ali_message("Connection established");
    prof_context.arbdb = &arbdb;

    pt_context.servername = params->pt_server;
    pt_context.gb_main = arbdb.gb_main;

    pt = new ALI_PT(&pt_context);

    prof_context.pt = pt;
}