/* Loads a boolean parameter */
int load_builtin_param_bool(const char * name, void * engine_val, short int flags,
int init_val, const char * alt_name) {
param_t * param;
value_t iv, ub, lb;
iv.int_val = init_val;
ub.int_val = TRUE;
lb.int_val = FALSE;
param = create_param(name, P_TYPE_BOOL, flags, engine_val, NULL, iv, ub, lb);
if (param == NULL) {
return OUTOFMEM_ERROR;
}
if (insert_builtin_param(param) < 0) {
free_param(param);
return ERROR;
}
if (alt_name != NULL) {
insert_param_alt_name(param, alt_name);
}
return SUCCESS;
}
/* Creates a user defined parameter */
param_t * create_user_param(char * name) {
param_t * param;
value_t iv;
value_t ub;
value_t lb;
double * engine_val;
/* Set initial values to default */
iv.double_val = DEFAULT_DOUBLE_IV;
ub.double_val = DEFAULT_DOUBLE_UB;
lb.double_val = DEFAULT_DOUBLE_LB;
/* Argument checks */
if (name == NULL)
return NULL;
/* Allocate space for the engine variable */
if ((engine_val = (double*)malloc(sizeof(double))) == NULL)
return NULL;
(*engine_val) = iv.double_val; /* set some default init value */
/* Create the new user parameter */
if ((param = create_param(name, P_TYPE_DOUBLE, P_FLAG_USERDEF, engine_val, NULL, iv, ub, lb)) == NULL) {
free(engine_val);
return NULL;
}
if (PARAM_DEBUG) printf("create_param: \"%s\" initialized\n", param->name);
/* Return the instantiated parameter */
return param;
}
int main(){
const int N=5, L=10;
int i,j;
double alpha=0.5, tau=2.0;
/* create a list of sequences */
struct list_dnaseq * test = create_list_dnaseq(N, L);
for(i=0;i<N;i++){
for(j=0;j<L;j++){
if(i*j % 5 ==0) test->list[i]->seq[j] = 'a';
else if(i*j % 3 ==0)test->list[i]->seq[j] = 't';
else if(i*j % 2 ==0)test->list[i]->seq[j] = 'g';
else test->list[i]->seq[j] = 'c';
}
}
for(i=5;i<L;i++)
test->list[0]->seq[i] = '-';
for(i=0;i<5;i++)
test->list[N-1]->seq[i] = '-';
print_list_dnaseq(test);
/* COMPUTE DISTANCES */
struct dna_dist *distinfo = compute_dna_distances(test);
print_dna_dist(distinfo);
/* COMPUTE LIKELIHOOD */
struct param *par = create_param();
double out=0, nu1 = 0.01, nu2=0.02, t_vec[5]={0.0, 10.0, 12.0, 50.0, 100.0}, T;
int count=0;
par->weightNaGen = 0.001; /* near zero if no data */
for(i=0;i<N-1;i++){
for(j=i+1;j<N;j++){
T = t_vec[i]>t_vec[j] ? t_vec[i] - t_vec[j] : t_vec[j]-t_vec[i];
printf("\npair %d <-> %d:",i+1,j+1);
printf("\nnb transi %d:", get_transi(distinfo,i,j));
printf(" (esperance: %.1f)", T*nu1*get_nbcommon(distinfo,i,j));
printf("\nnb transv %d:", get_transv(distinfo,i,j));
printf(" (esperance: %.1f)", T*nu2*get_nbcommon(distinfo,i,j));
out = compute_genlike(i, j, t_vec[i], t_vec[j], nu1, nu2, alpha, tau, distinfo, par);
printf("\npseudo-likelihood %d <-> %d: %.5f\n",i+1,j+1, out);
}
}
printf("\n");
/* free and return */
free_list_dnaseq(test);
free_dna_dist(distinfo);
free_param(par);
return 0;
}
/* Loads a double parameter into the builtin database */
int load_builtin_param_double(const char * name, void * engine_val, void * matrix, short int flags,
double init_val, double upper_bound, double lower_bound, const char * alt_name) {
param_t * param = NULL;
value_t iv, ub, lb;
iv.double_val = init_val;
ub.double_val = upper_bound;
lb.double_val = lower_bound;
/* Create new parameter of type double */
if (PARAM_DEBUG == 2) {
printf("load_builtin_param_double: (name \"%s\") (alt_name = \"%s\") ", name, alt_name);
fflush(stdout);
}
if ((param = create_param(name, P_TYPE_DOUBLE, flags, engine_val, matrix, iv, ub, lb)) == NULL) {
return OUTOFMEM_ERROR;
}
if (PARAM_DEBUG == 2) {
printf("created...");
fflush(stdout);
}
/* Insert the paremeter into the database */
if (insert_builtin_param(param) < 0) {
free_param(param);
return ERROR;
}
if (PARAM_DEBUG == 2) {
printf("inserted...");
fflush(stdout);
}
/* If this parameter has an alternate name, insert it into the database as link */
if (alt_name != NULL) {
insert_param_alt_name(param, alt_name);
if (PARAM_DEBUG == 2) {
printf("alt_name inserted...");
fflush(stdout);
}
}
if (PARAM_DEBUG == 2) printf("finished\n");
/* Finished, return success */
return SUCCESS;
}
/* Creates a new parameter of type bool */
param_t * new_param_bool(const char * name, short int flags, void * engine_val,
int upper_bound, int lower_bound, int init_val) {
param_t * param;
value_t iv, ub, lb;
iv.bool_val = init_val;
ub.bool_val = upper_bound;
lb.bool_val = lower_bound;
if ((param = create_param(name, P_TYPE_BOOL, flags, engine_val, NULL, iv, ub, lb)) == NULL)
return NULL;
/* Finished, return success */
return param;
}
/* Loads a double parameter into the builtin database */
param_t * new_param_double(const char * name, short int flags, void * engine_val, void * matrix,
double upper_bound, double lower_bound, double init_val) {
param_t * param;
value_t iv, ub, lb;
iv.double_val = init_val;
ub.double_val = upper_bound;
lb.double_val = lower_bound;
if ((param = create_param(name, P_TYPE_DOUBLE, flags, engine_val, matrix,iv, ub, lb)) == NULL)
return NULL;
/* Finished, return success */
return param;
}
