void
tree_addendum_rep::notify_var_join (tree& ref, tree t, int offset) {
// cout << "Notify var join " << ref << ", " << t << ", " << offset << "\n";
(void) ref; (void) offset;
(void) set_tree (t);
// cout << "position -> " << obtain_position (observer (this)) << "\n";
}
void
tree_addendum_rep::notify_detach (tree& ref, tree closest, bool right) {
// cout << "Notify detach " << ref << ", " << closest <<", "<< right << "\n";
(void) right; (void) ref;
(void) set_tree (closest);
// cout << "position -> " << obtain_position (observer (this)) << "\n";
}
void
tree_addendum_rep::notify_var_split (tree& ref, tree t1, tree t2) {
// cout << "Notify var split " << ref << ", " << t1 << ", " << t2 << "\n";
(void) t2; (void) ref;
(void) set_tree (t1); // always at the left
// cout << "position -> " << obtain_position (observer (this)) << "\n";
}
int main(int argc, char const *argv[])
{
std::string FILE="/homes/kgori/scratch/basic_pll/GGPS1.phy";
std::string PART="/homes/kgori/scratch/basic_pll/GGPS1.partitions.txt";
std::string TREE="/homes/kgori/scratch/basic_pll/GGPS1.tree";
auto inst = make_unique<pll>(FILE, PART, TREE, 1, 123);
std::cout << inst->get_likelihood() << std::endl;
std::cout << inst->get_partition_name(0) << std::endl;
std::cout << inst->get_model_name(0) << std::endl;
std::cout << inst->get_epsilon() << std::endl;
std::cout << inst->get_alpha(0) << std::endl;
std::cout << inst->get_number_of_partitions() << std::endl;
std::cout << inst->get_tree() << std::endl;
std::cout << inst->get_frac_change() << std::endl;
inst->set_tree("((Ptro:0.00147084048849247711,Ppan:0.00106294370976534763):0.00444598321816729036,(Cjac:0.05157798212603657839,(Csab:0.00440006365327790666,(Mmul:0.00652936575529242547,Panu:0.00101047194512476272):0.00381049900890796569):0.01359968787254225639):0.01375788728353777995,Hsap:0.00674547067186638278):0.0;");
inst->set_epsilon(0.001);
inst->set_alpha(2, 0, true);
auto ef = inst->get_empirical_frequencies();
inst->optimise(true, true, true, true);
inst->optimise_tree_search(true);
std::cout << inst->get_likelihood() << std::endl;
std::cout << inst->get_tree() << std::endl;
return 0;
}
void get_args (char *argv[])
{
FILE *fp, *ofp = NULL;
fp = fopen(argv[2], "r");
if (fp == NULL) {
fprintf(stderr, "Can't open input file %s!\n",
"data.txt");
exit(1);
}
ofp = fopen("bin/proto_tree.txt", "w");
if (ofp == NULL) {
fprintf(stderr, "Can't open output file %s!\n",
"proto_tree.txt");
exit(1);
}
Tree *T = set_tree (argv);
read_data(fp, ofp, T);
if(fclose(fp) != 0 || fclose(ofp) != 0)
{
printf("\nError closing files.\n");
}
/* free_tree(T, T->head->child[R]); */
}
void
tree_addendum_rep::notify_assign (tree& ref, tree t) {
// cout << "Notify assign " << ref << ", " << t << "\n";
(void) ref; (void) set_tree (t);
// cout << "position -> " << obtain_position (observer (this)) << "\n";
}
void
tree_addendum_rep::notify_remove_node (tree& ref, int pos) {
// cout << "Notify remove node " << ref << ", " << pos << "\n";
(void) set_tree (ref[pos]);
// cout << "position -> " << obtain_position (observer (this)) << "\n";
}
static PetscErrorCode gsi_via_bit_mask(gs_id *gs)
{
PetscInt i, nel, *elms;
PetscInt t1;
PetscInt **reduce;
PetscInt *map;
PetscErrorCode ierr;
PetscFunctionBegin;
/* totally local removes ... ct_bits == 0 */
get_ngh_buf(gs);
if (gs->level)
{set_pairwise(gs);}
if (gs->max_left_over)
{set_tree(gs);}
/* intersection local and pairwise/tree? */
gs->num_local_total = gs->num_local;
gs->gop_local_reduce = gs->local_reduce;
gs->num_gop_local_reduce = gs->num_local_reduce;
map = gs->companion;
/* is there any local compression */
if (!gs->num_local) {
gs->local_strength = NONE;
gs->num_local_gop = 0;
} else {
/* ok find intersection */
map = gs->companion;
reduce = gs->local_reduce;
for (i=0, t1=0; i<gs->num_local; i++, reduce++)
{
if ((ivec_binary_search(**reduce,gs->pw_elm_list,gs->len_pw_list)>=0)
||
ivec_binary_search(**reduce,gs->tree_map_in,gs->tree_map_sz)>=0)
{
t1++;
if (gs->num_local_reduce[i]<=0) SETERRQ(PETSC_ERR_PLIB,"nobody in list?");
gs->num_local_reduce[i] *= -1;
}
**reduce=map[**reduce];
}
/* intersection is empty */
if (!t1)
{
gs->local_strength = FULL;
gs->num_local_gop = 0;
}
/* intersection not empty */
else
{
gs->local_strength = PARTIAL;
ierr = SMI_sort((void*)gs->num_local_reduce, (void*)gs->local_reduce, gs->num_local + 1, SORT_INT_PTR);CHKERRQ(ierr);
gs->num_local_gop = t1;
gs->num_local_total = gs->num_local;
gs->num_local -= t1;
gs->gop_local_reduce = gs->local_reduce;
gs->num_gop_local_reduce = gs->num_local_reduce;
for (i=0; i<t1; i++)
{
if (gs->num_gop_local_reduce[i]>=0) SETERRQ(PETSC_ERR_PLIB,"they aren't negative?");
gs->num_gop_local_reduce[i] *= -1;
gs->local_reduce++;
gs->num_local_reduce++;
}
gs->local_reduce++;
gs->num_local_reduce++;
}
}
elms = gs->pw_elm_list;
nel = gs->len_pw_list;
for (i=0; i<nel; i++)
{elms[i] = map[elms[i]];}
elms = gs->tree_map_in;
nel = gs->tree_map_sz;
for (i=0; i<nel; i++)
{elms[i] = map[elms[i]];}
/* clean up */
free((void*) gs->local_elms);
free((void*) gs->companion);
free((void*) gs->elms);
free((void*) gs->ngh_buf);
gs->local_elms = gs->companion = gs->elms = gs->ngh_buf = NULL;
PetscFunctionReturn(0);
}
