IMPATOM_BEGIN_NAMESPACE
BondGraph::BondGraph(Hierarchy bd)
: sc_(get_as<kernel::Particles>(get_leaves(bd))) {
for (unsigned int i = 0; i < sc_.size(); ++i) {
if (!Bonded::get_is_setup(sc_[i])) {
Bonded::setup_particle(sc_[i]);
}
}
}
IMPATOM_BEGIN_NAMESPACE
double get_resolution(Model* m, ParticleIndex pi) {
double min = std::numeric_limits<double>::max();
IMP_FOREACH(Hierarchy l, get_leaves(Hierarchy(m, pi))) {
double cur = core::XYZR(l).get_radius();
IMP_USAGE_CHECK(cur > 0, "Particle " << l << " has an invalid radius");
min = std::min(min, cur);
}
void get_leaves(TreeNode *root, ItemSetNode **list)
{
if (root == NULL)
return;
ItemSetNode *l;
for (l = root->item_sets; l != NULL; l = l->next)
{
if ((float)l->data->count / TXNS >= MIN_SUPPORT)
{
append_to_list(list, l->data);
}
}
get_leaves(root->left,list);
get_leaves(root->middle, list);
get_leaves(root->right, list);
}
algebra::Sphere3D get_bounding_sphere(const Hierarchy &h) {
kernel::ParticlesTemp rep = get_leaves(h);
algebra::Sphere3Ds ss;
for (unsigned int i = 0; i < rep.size(); ++i) {
core::XYZR xyzr = core::XYZR::decorate_particle(rep[i]);
if (xyzr) {
ss.push_back(xyzr.get_sphere());
} else if (core::XYZ::get_is_setup(rep[i])) {
ss.push_back(algebra::Sphere3D(core::XYZ(rep[i]).get_coordinates(), 0));
}
}
return algebra::get_enclosing_sphere(ss);
}
core::RigidBody setup_as_rigid_body(Hierarchy h) {
IMP_USAGE_CHECK(h.get_is_valid(true),
"Invalid hierarchy passed to setup_as_rigid_body");
IMP_WARN("create_rigid_body should be used instead of setup_as_rigid_body"
<< " as the former allows one to get volumes correct at coarser"
<< " levels of detail.");
core::RigidBody rbd = core::RigidBody::setup_particle(h, get_leaves(h));
rbd.set_coordinates_are_optimized(true);
kernel::ParticlesTemp internal = core::get_internal(h);
for (unsigned int i = 0; i < internal.size(); ++i) {
if (internal[i] != h) {
core::RigidMembers leaves(get_leaves(Hierarchy(internal[i])));
if (!leaves.empty()) {
algebra::ReferenceFrame3D rf = core::get_initial_reference_frame(
get_as<kernel::ParticlesTemp>(leaves));
core::RigidBody::setup_particle(internal[i], rf);
}
}
}
IMP_INTERNAL_CHECK(h.get_is_valid(true), "Invalid hierarchy produced");
return rbd;
}
algebra::BoundingBox3D get_bounding_box(const Hierarchy &h) {
ParticlesTemp rep= get_leaves(h);
algebra::BoundingBox3D bb;
for (unsigned int i=0; i< rep.size(); ++i) {
core::XYZR xyzr= core::XYZR::decorate_particle(rep[i]);
if (xyzr) {
bb+= algebra::get_bounding_box(xyzr.get_sphere());
} else if (core::XYZ::particle_is_instance(rep[i])) {
bb+= algebra::BoundingBox3D(core::XYZ(rep[i]).get_coordinates());
}
}
IMP_LOG(VERBOSE, "Bounding box is " << bb << std::endl);
return bb;
}
IMP::core::RigidBody create_compatible_rigid_body(Hierarchy h,
Hierarchy reference) {
ParticlesTemp hl= get_leaves(h);
ParticlesTemp rl= get_leaves(reference);
algebra::Transformation3D tr
= algebra::get_transformation_aligning_first_to_second(rl, hl);
algebra::Transformation3D rtr
= core::RigidMember(reference).get_rigid_body().\
get_reference_frame().get_transformation_to();
algebra::Transformation3D rbtr= tr*rtr;
Particle *rbp= new Particle(h->get_model());
rbp->set_name(h->get_name()+" rigid body");
ParticlesTemp all = rb_process(h);
core::RigidBody rbd
= core::RigidBody::setup_particle(rbp, algebra::ReferenceFrame3D(rbtr));
for (unsigned int i=0; i< all.size(); ++i) {
rbd.add_member(all[i]);
}
rbd.set_coordinates_are_optimized(true);
IMP_INTERNAL_CHECK(h.get_is_valid(true), "Invalid hierarchy produced");
return rbd;
}
ItemSetNode *get_frequent_itemsets(TreeNode *root)
{
FILE *fp = fopen(DATA_FILE, "r");
char *line = NULL;
while ((line = read_line(fp)) != NULL && *line != '\0')
{
traverse_tree(root, line);
free(line);
}
fclose(fp);
ItemSetNode *tmp = NULL;
get_leaves(root, &tmp);
return tmp;
}
/** Dump an entire forest to a DBMS.
*
* FIXME: This should really be using something like ODBC, but ROSE is only configured to use specific DBMS like SQLite3
* or MySQL. Therefore, since we don't need to do any queries, we'll just generate straight SQL as text (the sqlite3x API
* converts all numeric values to text anyway, so there's not really any additional slowdown or loss of precision).
* Therefore, the @p user_name and @p password arguments are unused, and @p server_name is the name of the file to which
* the SQL statements are written. */
void dump(const std::string &server_name, const std::string &user_name, const std::string &password) {
std::ofstream dbc(server_name.c_str());
renumber_vertices();
dump_outputsets(dbc);
dump_inputsets(dbc);
Vertices leaves = get_leaves();
size_t leafnum = 0;
for (Vertices::const_iterator vi=leaves.begin(); vi!=leaves.end(); ++vi, ++leafnum) {
Vertex *vertex = *vi;
const Functions &functions = vertex->get_functions();
dbc <<"insert into simsets (id) values (" <<leafnum <<");\n";
for (Functions::const_iterator fi=functions.begin(); fi!=functions.end(); ++fi)
dbc <<"insert into functions (entry_va, simset_id) values (" <<(*fi)->get_entry_va() <<", " <<leafnum <<");\n";
for (Vertex *v=vertex; v; v=v->parent)
dbc <<"insert into inoutpairs (simset_id, inputset_id, outputset_id) values ("
<<leafnum <<", " <<v->get_level() <<", " <<v->id <<");\n";
}
}
void Interpreter::Helper::interpret(
const ParseTree::child_pointer_type &node,
tree_set &output)
{
ParseTreeMatcher::match_list_type matches;
helper_key[0] = node;
interpreter.parse_tree_matcher.find(helper_key, matches);
# ifdef DEBUG
std::cout << "MATCHED RULES:" << std::endl;
for(ParseTreeMatcher::match_list_type::const_iterator
i = matches.begin(), n = matches.end(); i != n; ++i)
{
i->first->print(interpreter.symbol_info, std::cout);
std::cout << std::endl;
}
# endif
typedef std::vector<tree_set> result_list_type;
typedef std::vector<ParseTree::child_list_type> alternation_list_type;
result_list_type sub_results;
TranslationTree::child_list_type translation_leaves;
alternation_list_type alternations;
for(ParseTreeMatcher::match_list_type::const_iterator
i = matches.begin(), n = matches.end(); i != n; ++i)
{
sub_results.clear();
translation_leaves.clear();
/* TODO A potential optimization is to precomute the list of
leaf nodes in each translation tree. */
get_leaves(i->first->translation, translation_leaves);
for(TranslationTree::child_list_type::const_iterator
j = translation_leaves.begin(), m = translation_leaves.end(); j != m; ++j)
{
assert((*j)->donor_index != TranslationTree::NO_DONOR);
assert(0 <= (*j)->donor_index && (*j)->donor_index < (int) i->second.size());
sub_results.push_back(tree_set());
interpret(
ParseTree::child_pointer_type(
new ParseTree(
(*j)->symbol,
i->second[(*j)->donor_index]->children)),
sub_results.back());
}
/* XXX Do note that since we are re-using references when
generating alternations of the sub-results, the parse trees
generated can share subtrees and therefore form a DAG. So, we
can use this as a justification for using shared pointers as
the pointer type for ParseTree. For TranslationTree, however,
it is not important. */
alternations.clear();
algorithm::generate_alternations(
sub_results.begin(), sub_results.end(), alternations);
for(alternation_list_type::const_iterator
j = alternations.begin(), m = alternations.end(); j != m; ++j)
{
ParseTree::child_list_type::const_iterator subroot_iter = j->begin();
output.push_back(attach_leaves(i->first->translation, subroot_iter));
}
}
/* Record any parse trees which did not have any matches. */
if(output.empty()) {
unmatched.push_back(node);
}
}
void setup_as_approximation(Hierarchy h, double resolution) {
setup_as_approximation_internal(h, get_leaves(h), resolution);
}