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#include <terraces/advanced.hpp>
#include <terraces/errors.hpp>
#include <terraces/parser.hpp>
#include <terraces/rooting.hpp>
#include <terraces/simple.hpp>
#include <fstream>
#include <sstream>
#include "io_utils.hpp"
#include "utils.hpp"
namespace terraces {
namespace simple {
using utils::open_ifstream;
using utils::read_file_full;
using utils::read_ifstream_full;
namespace {
std::pair<supertree_data, name_map> parse_data(const std::string& nwk_string,
std::istream& matrix_stream, bool force) {
auto occ_data = parse_bitmatrix(matrix_stream);
auto tree = parse_nwk(nwk_string, occ_data.indices);
if (force) {
occ_data.matrix = maximum_comprehensive_columnset(occ_data.matrix);
}
auto data = create_supertree_data(tree, occ_data.matrix);
return {data, occ_data.names};
}
} // anonymous namespace
bool is_on_terrace(const std::string& nwk_string, std::istream& matrix_stream, bool force) {
return check_terrace(parse_data(nwk_string, matrix_stream, force).first);
}
bool is_on_terrace(std::istream& nwk_stream, std::istream& matrix_stream, bool force) {
return is_on_terrace(read_ifstream_full(nwk_stream), matrix_stream, force);
}
bool is_on_terrace(std::istream& nwk_stream, const std::string& matrix_string, bool force) {
auto matrix_stream = std::istringstream{matrix_string};
return is_on_terrace(read_ifstream_full(nwk_stream), matrix_stream, force);
}
bool is_on_terrace(const std::string& nwk_string, const std::string& matrix_string, bool force) {
auto matrix_stream = std::istringstream{matrix_string};
return is_on_terrace(nwk_string, matrix_stream, force);
}
bool is_on_terrace_from_file(const std::string& nwk_filename, const std::string& matrix_filename,
bool force) {
auto nwk_string = read_file_full(nwk_filename);
auto matrix_stream = open_ifstream(matrix_filename);
return is_on_terrace(nwk_string, matrix_stream, force);
}
index get_terrace_size(const std::string& nwk_string, std::istream& matrix_stream, bool force) {
return count_terrace(parse_data(nwk_string, matrix_stream, force).first);
}
index get_terrace_size(std::istream& nwk_stream, std::istream& matrix_stream, bool force) {
return get_terrace_size(read_ifstream_full(nwk_stream), matrix_stream, force);
}
index get_terrace_size(std::istream& nwk_stream, const std::string& matrix_string, bool force) {
auto matrix_stream = std::istringstream{matrix_string};
return get_terrace_size(read_ifstream_full(nwk_stream), matrix_stream, force);
}
index get_terrace_size(const std::string& nwk_string, const std::string& matrix_string,
bool force) {
auto matrix_stream = std::istringstream{matrix_string};
return get_terrace_size(nwk_string, matrix_stream, force);
}
index get_terrace_size_from_file(const std::string& nwk_filename,
const std::string& matrix_filename, bool force) {
auto nwk_string = read_file_full(nwk_filename);
auto matrix_stream = open_ifstream(matrix_filename);
return get_terrace_size(nwk_string, matrix_stream, force);
}
big_integer get_terrace_size_bigint(const std::string& nwk_string, std::istream& matrix_stream,
bool force) {
return count_terrace_bigint(parse_data(nwk_string, matrix_stream, force).first);
}
big_integer get_terrace_size_bigint(std::istream& nwk_stream, std::istream& matrix_stream,
bool force) {
return get_terrace_size_bigint(read_ifstream_full(nwk_stream), matrix_stream, force);
}
big_integer get_terrace_size_bigint(std::istream& nwk_stream, const std::string& matrix_string,
bool force) {
auto matrix_stream = std::istringstream{matrix_string};
return get_terrace_size_bigint(read_ifstream_full(nwk_stream), matrix_stream, force);
}
big_integer get_terrace_size_bigint(const std::string& nwk_string, const std::string& matrix_string,
bool force) {
auto matrix_stream = std::istringstream{matrix_string};
return get_terrace_size_bigint(nwk_string, matrix_stream, force);
}
big_integer get_terrace_size_bigint_from_file(const std::string& nwk_filename,
const std::string& matrix_filename, bool force) {
auto nwk_string = read_file_full(nwk_filename);
auto matrix_stream = open_ifstream(matrix_filename);
return get_terrace_size_bigint(nwk_string, matrix_stream, force);
}
big_integer print_terrace(const std::string& nwk_string, std::istream& matrix_stream,
std::ostream& output, bool force) {
auto data = parse_data(nwk_string, matrix_stream, force);
return print_terrace(data.first, data.second, output);
}
big_integer print_terrace(std::istream& nwk_stream, const std::string& matrix_string,
std::ostream& out, bool force) {
auto matrix_stream = std::istringstream{matrix_string};
return print_terrace(read_ifstream_full(nwk_stream), matrix_stream, out, force);
}
big_integer print_terrace(std::istream& nwk_stream, std::istream& matrix_stream, std::ostream& out,
bool force) {
return print_terrace(read_ifstream_full(nwk_stream), matrix_stream, out, force);
}
big_integer print_terrace(const std::string& nwk_string, const std::string& matrix_string,
std::ostream& output, bool force) {
auto matrix_stream = std::istringstream{matrix_string};
return print_terrace(nwk_string, matrix_stream, output, force);
}
big_integer print_terrace_from_file(const std::string& nwk_filename,
const std::string& matrix_filename, std::ostream& output,
bool force) {
auto nwk_string = read_file_full(nwk_filename);
auto matrix_stream = open_ifstream(matrix_filename);
return print_terrace(nwk_string, matrix_stream, output, force);
}
big_integer print_terrace_compressed(const std::string& nwk_string, std::istream& matrix_stream,
std::ostream& output, bool force) {
auto data = parse_data(nwk_string, matrix_stream, force);
return print_terrace_compressed(data.first, data.second, output);
}
big_integer print_terrace_compressed(std::istream& nwk_stream, const std::string& matrix_string,
std::ostream& out, bool force) {
auto matrix_stream = std::istringstream{matrix_string};
return print_terrace_compressed(read_ifstream_full(nwk_stream), matrix_stream, out, force);
}
big_integer print_terrace_compressed(std::istream& nwk_stream, std::istream& matrix_stream,
std::ostream& out, bool force) {
return print_terrace_compressed(read_ifstream_full(nwk_stream), matrix_stream, out, force);
}
big_integer print_terrace_compressed(const std::string& nwk_string,
const std::string& matrix_string, std::ostream& output,
bool force) {
auto matrix_stream = std::istringstream{matrix_string};
return print_terrace_compressed(nwk_string, matrix_stream, output, force);
}
big_integer print_terrace_compressed_from_file(const std::string& nwk_filename,
const std::string& matrix_filename,
std::ostream& output, bool force) {
auto nwk_string = read_file_full(nwk_filename);
auto matrix_stream = open_ifstream(matrix_filename);
return print_terrace_compressed(nwk_string, matrix_stream, output, force);
}
} // namespace simple
} // namespace terraces
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