void unit_unpack_array(UNUSED(void **state))
{
array params;
init_unpack_array(MSGPACK_OBJECT_NIL);
assert_int_equal(0, unpack_params(&deserialized, ¶ms));
init_unpack_array(MSGPACK_OBJECT_ARRAY);
assert_int_equal(0, unpack_params(&deserialized, ¶ms));
init_unpack_array(MSGPACK_OBJECT_FLOAT);
assert_int_equal(0, unpack_params(&deserialized, ¶ms));
init_unpack_array(MSGPACK_OBJECT_MAP);
assert_int_equal(0, unpack_params(&deserialized, ¶ms));
init_unpack_array(MSGPACK_OBJECT_POSITIVE_INTEGER);
assert_int_equal(0, unpack_params(&deserialized, ¶ms));
}
/* estimate free parameters */
double bd_estimate_transitions(BDPhyloHmm *bdphmm, MSA *msa) {
int i, nparams = 0;
Vector *params, *lb, *ub;
double retval;
if (bdphmm->phmm->forward == NULL) {
bdphmm->phmm->forward = smalloc(bdphmm->phmm->hmm->nstates *
sizeof(double*));
for (i = 0; i < bdphmm->phmm->hmm->nstates; i++)
bdphmm->phmm->forward[i] = smalloc(bdphmm->phmm->alloc_len *
sizeof(double));
}
if (bdphmm->estim_omega) nparams++;
if (bdphmm->estim_gamma) nparams++;
if (bdphmm->estim_phi) nparams++;
params = vec_new(nparams);
lb = vec_new(nparams);
ub = vec_new(nparams);
vec_set_all(lb, 1e-6);
nparams = 0;
if (bdphmm->estim_omega) {
vec_set(params, nparams, 1/bdphmm->mu);
vec_set(ub, nparams++, INFTY);
}
if (bdphmm->estim_gamma) {
vec_set(params, nparams, bdphmm->nu / (bdphmm->mu + bdphmm->nu));
vec_set(ub, nparams++, 0.5 /* 1-1e-6 */);
}
if (bdphmm->estim_phi) {
vec_set(params, nparams, bdphmm->phi);
vec_set(ub, nparams++, 0.7 /* 1-1e-6 */);
}
opt_bfgs(lnl_wrapper, params, bdphmm, &retval, lb, ub, stderr, NULL,
OPT_HIGH_PREC, NULL, NULL);
unpack_params(params, bdphmm);
vec_free(params);
vec_free(lb);
vec_free(ub);
return retval;
}
int message_deserialize_error_response(struct message_response *res,
msgpack_object *obj, struct api_error *api_error)
{
msgpack_object *type, *msgid, *params;
uint64_t tmp_msgid;
if (!api_error)
return (-1);
if (!res || !obj) {
error_set(api_error, API_ERROR_TYPE_VALIDATION, "Error");
return (-1);
}
/* type */
if (obj->via.array.ptr[0].type != MSGPACK_OBJECT_POSITIVE_INTEGER) {
error_set(api_error, API_ERROR_TYPE_VALIDATION, "type field has wrong type");
return (-1);
}
type = &obj->via.array.ptr[0];
if (!type) {
error_set(api_error, API_ERROR_TYPE_VALIDATION, "unpack type failed");
return (-1);
}
if (unpack_uint(type) != MESSAGE_TYPE_RESPONSE) {
error_set(api_error, API_ERROR_TYPE_VALIDATION, "type must be 1");
return (-1);
}
/* message id */
msgid = &obj->via.array.ptr[1];
if (!msgid || msgid->type != MSGPACK_OBJECT_POSITIVE_INTEGER) {
error_set(api_error, API_ERROR_TYPE_VALIDATION, "illegal msgid");
return (-1);
}
tmp_msgid = unpack_uint(msgid);
if (tmp_msgid >= UINT32_MAX) {
error_set(api_error, API_ERROR_TYPE_VALIDATION, "invalid msgid");
return (-1);
}
res->msgid = (uint32_t)tmp_msgid;
/* params */
if (obj->via.array.ptr[2].type != MSGPACK_OBJECT_ARRAY) {
error_set(api_error, API_ERROR_TYPE_VALIDATION, "params field has wrong type");
return (-1);
}
params = &obj->via.array.ptr[2];
if (!params) {
error_set(api_error, API_ERROR_TYPE_VALIDATION, "unpack params failed");
return (-1);
}
if (unpack_params(params, &res->params) == -1) {
error_set(api_error, API_ERROR_TYPE_VALIDATION, "Error unpacking params");
return (-1);
}
/* nil */
if (obj->via.array.ptr[3].type != MSGPACK_OBJECT_NIL) {
free_params(res->params);
error_set(api_error, API_ERROR_TYPE_VALIDATION, "nil field has wrong type");
return (-1);
}
return (0);
}
int message_deserialize_request(struct message_request *req,
msgpack_object *obj, struct api_error *api_error)
{
msgpack_object *type, *msgid, *method, *params;
uint64_t tmp_type;
uint64_t tmp_msgid;
if (!api_error)
return (-1);
if (!req || !obj) {
error_set(api_error, API_ERROR_TYPE_VALIDATION, "Error");
return (-1);
}
/* type */
if (obj->via.array.ptr[0].type != MSGPACK_OBJECT_POSITIVE_INTEGER) {
error_set(api_error, API_ERROR_TYPE_VALIDATION, "type field has wrong type");
return (-1);
}
type = &obj->via.array.ptr[0];
if (!type) {
error_set(api_error, API_ERROR_TYPE_VALIDATION, "unpack type failed");
return (-1);
}
tmp_type = unpack_uint(type);
if (tmp_type != MESSAGE_TYPE_REQUEST) {
error_set(api_error, API_ERROR_TYPE_VALIDATION, "type must be 0 or 1");
return (-1);
}
/* message id */
msgid = &obj->via.array.ptr[1];
if (!msgid || msgid->type != MSGPACK_OBJECT_POSITIVE_INTEGER) {
error_set(api_error, API_ERROR_TYPE_VALIDATION, "illegal msgid");
return (-1);
}
tmp_msgid = unpack_uint(msgid);
if (tmp_msgid >= UINT32_MAX) {
error_set(api_error, API_ERROR_TYPE_VALIDATION, "invalid msgid");
return (-1);
}
req->msgid = (uint32_t)tmp_msgid;
/* method */
if (obj->via.array.ptr[2].type != MSGPACK_OBJECT_STR) {
error_set(api_error, API_ERROR_TYPE_VALIDATION, "method field has wrong type");
return (-1);
}
method = &obj->via.array.ptr[2];
if (!method) {
error_set(api_error, API_ERROR_TYPE_VALIDATION, "unpack method failed");
return (-1);
}
req->method = unpack_string(method);
if (!req->method.str) {
error_set(api_error, API_ERROR_TYPE_VALIDATION, "Error unpacking method");
return (-1);
}
/* params */
if (obj->via.array.ptr[3].type != MSGPACK_OBJECT_ARRAY) {
free_string(req->method);
error_set(api_error, API_ERROR_TYPE_VALIDATION, "params field has wrong type");
return (-1);
}
params = &obj->via.array.ptr[3];
if (!params) {
free_string(req->method);
error_set(api_error, API_ERROR_TYPE_VALIDATION, "unpack params failed");
return (-1);
}
if (unpack_params(params, &req->params) == -1) {
free_string(req->method);
error_set(api_error, API_ERROR_TYPE_VALIDATION, "Error unpacking params");
return (-1);
}
return (0);
}
double lnl_wrapper(Vector *params, void *data) {
BDPhyloHmm *bdphmm = data;
unpack_params(params, data);
return -hmm_forward(bdphmm->phmm->hmm, bdphmm->phmm->emissions,
bdphmm->phmm->alloc_len, bdphmm->phmm->forward);
}
