sam.c

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/*
 * This program is free software: you can redistribute it and/or modify
 * it under the terms of the GNU General Public License as published by
 * the Free Software Foundation, either version 3 of the License, or
 * (at your option) any later version.
 *
 * This program is distributed in the hope that it will be useful,
 * but WITHOUT ANY WARRANTY; without even the implied warranty of
 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
 * GNU General Public License for more details.
 *
 * You should have received a copy of the GNU General Public License
 * along with this program.  If not, see <http://www.gnu.org/licenses/>.
 */
 
#include "sam.h"
#include "utils.h"
 
#define MU_EPSILON 0.0005 
#define N_RATES (10) 
 
static const double mrates[N_RATES] = { 0.0005, 0.001, 0.002, 0.003, 0.005,
                                        0.01,   0.015, 0.02,  0.05,  0.1 };
 
void
sam_init(double *mu, const int N, const int *type)
{
    for (int i = 0; i < N; ++i) {
        switch (type[i]) {
            case SAM_LOG_NORMAL:
            case SAM_UNIFORM:
                mu[i] = rand_uniform(MU_EPSILON, 1);
                break;
            case SAM_RATE_SELECT:
                mu[i] = mrates[rand_uniform_int(0, N_RATES)];
                break;
            default:
                printf("sam_init(): invalid sam function: %d\n", type[i]);
                exit(EXIT_FAILURE);
        }
    }
}
 
void
sam_adapt(double *mu, const int N, const int *type)
{
    for (int i = 0; i < N; ++i) {
        switch (type[i]) {
            case SAM_LOG_NORMAL:
                mu[i] *= exp(rand_normal(0, 1));
                mu[i] = clamp(mu[i], MU_EPSILON, 1);
                break;
            case SAM_RATE_SELECT:
                if (rand_uniform(0, 1) < 0.1) {
                    mu[i] = mrates[rand_uniform_int(0, N_RATES)];
                }
                break;
            case SAM_UNIFORM:
                if (rand_uniform(0, 1) < 0.1) {
                    mu[i] = rand_uniform(MU_EPSILON, 1);
                }
                break;
            default:
                printf("sam_adapt(): invalid sam function: %d\n", type[i]);
                exit(EXIT_FAILURE);
        }
    }
}
 
void
sam_json_import(double *mu, const int N, const cJSON *json)
{
    const cJSON *item = cJSON_GetObjectItem(json, "mutation");
    if (item != NULL && cJSON_IsArray(item)) {
        if (cJSON_GetArraySize(item) != N) {
            printf("Import error: mutation length mismatch\n");
            exit(EXIT_FAILURE);
        }
        for (int i = 0; i < N; ++i) {
            const cJSON *item_i = cJSON_GetArrayItem(item, i);
            if (item_i->valuedouble < 0 || item_i->valuedouble > 1) {
                printf("Import error: mutation value out of bounds\n");
                exit(EXIT_FAILURE);
            }
            mu[i] = item_i->valuedouble;
        }
    }
}