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#include <terraces/advanced.hpp>
#include <terraces/clamped_uint.hpp>
#include <terraces/errors.hpp>
#include <terraces/rooting.hpp>
#include <terraces/subtree_extraction.hpp>
#include "multitree_iterator.hpp"
#include "supertree_enumerator.hpp"
#include "supertree_variants.hpp"
#include "supertree_variants_multitree.hpp"
namespace terraces {
supertree_data create_supertree_data(const tree& tree, const bitmatrix& data) {
auto root = find_comprehensive_taxon(data);
utils::ensure<bad_input_error>(data.rows() == num_leaves_from_nodes(tree.size()),
bad_input_error_type::tree_mismatching_size);
utils::ensure<no_usable_root_error>(root != none, "No comprehensive taxon found");
auto rerooted_tree = tree;
reroot_at_taxon_inplace(rerooted_tree, root);
auto trees = subtrees(rerooted_tree, data);
auto constraints = compute_constraints(trees);
deduplicate_constraints(constraints);
auto num_leaves = data.rows();
utils::ensure<bad_input_error>(num_leaves >= 4, bad_input_error_type::nwk_tree_trivial);
return {constraints, num_leaves, root};
}
index_t find_comprehensive_taxon(const bitmatrix& data) {
for (index_t i = 0; i < data.rows(); ++i) {
bool comp = true;
for (index_t j = 0; j < data.cols(); ++j) {
comp &= data.get(i, j);
}
if (comp) {
return i;
}
}
return none;
}
bitmatrix maximum_comprehensive_columnset(const bitmatrix& data) {
std::vector<index_t> row_counts(data.rows(), 0u);
for (index_t i = 0; i < data.rows(); ++i) {
for (index_t j = 0; j < data.cols(); ++j) {
row_counts[i] += data.get(i, j) ? 1u : 0u;
}
}
auto it = std::max_element(row_counts.begin(), row_counts.end());
index_t comp_row = static_cast<index_t>(std::distance(row_counts.begin(), it));
std::vector<index_t> columns;
for (index_t j = 0; j < data.cols(); ++j) {
if (data.get(comp_row, j)) {
columns.push_back(j);
}
}
return data.get_cols(columns);
}
index_t fast_count_terrace(const supertree_data& data) {
tree_enumerator<variants::check_callback> enumerator{{}};
try {
return enumerator.run(data.num_leaves, data.constraints, data.root);
} catch (terraces::tree_count_overflow_error&) {
return std::numeric_limits<index_t>::max();
}
}
bool check_terrace(const supertree_data& data) { return fast_count_terrace(data) > 1; }
index_t count_terrace(const supertree_data& data, execution_limits limits, bool& terminated_early) {
tree_enumerator<variants::timeout_decorator<variants::clamped_count_callback>> enumerator{
{limits.time_limit_seconds}};
try {
auto result = enumerator.run(data.num_leaves, data.constraints, data.root).value();
terminated_early = enumerator.callback().has_timed_out();
return result;
} catch (terraces::tree_count_overflow_error&) {
return std::numeric_limits<index_t>::max();
}
}
big_integer count_terrace_bigint(const supertree_data& data, execution_limits limits,
bool& terminated_early) {
tree_enumerator<variants::timeout_decorator<variants::count_callback<big_integer>>>
enumerator{{limits.time_limit_seconds}};
auto result = enumerator.run(data.num_leaves, data.constraints, data.root);
terminated_early = enumerator.callback().has_timed_out();
return result;
}
using limited_multitree_callback =
variants::timeout_decorator<variants::memory_limited_multitree_callback>;
big_integer print_terrace_compressed(const supertree_data& data, const name_map& names,
std::ostream& output, execution_limits limits,
bool& terminated_early) {
tree_enumerator<limited_multitree_callback> enumerator{
limited_multitree_callback{limits.time_limit_seconds, limits.mem_limit_bytes}};
auto result = enumerator.run(data.num_leaves, data.constraints, data.root);
terminated_early = enumerator.callback().has_timed_out() ||
enumerator.callback().has_hit_memory_limit();
output << as_newick(result, names);
return result->num_trees;
}
big_integer print_terrace(const supertree_data& data, const name_map& names, std::ostream& output,
execution_limits limits, bool& terminated_early) {
tree_enumerator<limited_multitree_callback> enumerator{
limited_multitree_callback{limits.time_limit_seconds, limits.mem_limit_bytes}};
auto result = enumerator.run(data.num_leaves, data.constraints, data.root);
terminated_early = enumerator.callback().has_timed_out() ||
enumerator.callback().has_hit_memory_limit();
if (!terminated_early) {
multitree_iterator mit{result};
do {
output << as_newick(mit.tree(), names) << '\n';
} while (mit.next());
}
return result->num_trees;
}
void enumerate_terrace(const supertree_data& data, std::function<void(const tree&)> callback,
execution_limits limits, bool& terminated_early) {
tree_enumerator<limited_multitree_callback> enumerator{
limited_multitree_callback{limits.time_limit_seconds, limits.mem_limit_bytes}};
auto result = enumerator.run(data.num_leaves, data.constraints, data.root);
terminated_early = enumerator.callback().has_timed_out() ||
enumerator.callback().has_hit_memory_limit();
if (!terminated_early) {
multitree_iterator mit{result};
do {
callback(mit.tree());
} while (mit.next());
}
}
index_t count_terrace(const supertree_data& data) {
execution_limits limits{};
bool tmp;
return count_terrace(data, limits, tmp);
}
big_integer count_terrace_bigint(const supertree_data& data) {
execution_limits limits{};
bool tmp;
return count_terrace_bigint(data, limits, tmp);
}
big_integer print_terrace_compressed(const supertree_data& data, const name_map& names,
std::ostream& output) {
execution_limits limits{};
bool tmp;
return print_terrace_compressed(data, names, output, limits, tmp);
}
big_integer print_terrace(const supertree_data& data, const name_map& names, std::ostream& output) {
execution_limits limits{};
bool tmp;
return print_terrace(data, names, output, limits, tmp);
}
void enumerate_terrace(const supertree_data& data, std::function<void(const tree&)> callback) {
execution_limits limits{};
bool tmp;
return enumerate_terrace(data, std::move(callback), limits, tmp);
}
} // namespace terraces
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