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#include <terraces/parser.hpp>
#include <algorithm>
#include <array>
#include <stack>
#include <stdexcept>
#include <utility>
#include <vector>
#include <terraces/errors.hpp>
#include "trees_impl.hpp"
#include "utils.hpp"
namespace terraces {
// non-public parsing-utilities:
namespace parsing {
enum class token_type { lparen, rparen, name, seperator, eof };
struct token {
token_type type;
std::string name;
token(token_type type, std::string name = "") : type{type}, name{std::move(name)} {}
};
struct parser_state {
index parent;
index self;
parser_state(index parent, index self) : parent{parent}, self{self} {}
};
using parser_stack = std::stack<parser_state, std::vector<parser_state>>;
template <typename Iterator>
token next_token(Iterator& it, Iterator end) {
constexpr static std::array<char, 3> special_tokens{{'(', ')', ','}};
it = utils::skip_ws(it, end);
if (it == end) {
return {token_type::eof};
}
if (*it != '\'') {
switch (*it) {
case '(':
++it;
return {token_type::lparen};
case ')':
++it;
return {token_type::rparen};
case ',':
++it;
return {token_type::seperator};
}
} else {
++it;
const auto name_begin = it;
it = std::find(it, end, '\'');
const auto name_end = it;
utils::ensure<bad_input_error>(name_end != end,
bad_input_error_type::nwk_mismatched_quotes,
std::string{name_begin, name_end});
++it;
return {token_type::name, {name_begin, name_end}};
}
const auto name_begin = it;
it = std::find_first_of(it, end, special_tokens.begin(), special_tokens.end());
const auto name_end = utils::reverse_skip_ws(name_begin, std::find(name_begin, it, ':'));
return {token_type::name, {name_begin, name_end}};
}
template <typename NameCallback>
tree parse_nwk_impl(const std::string& input, NameCallback cb) {
auto ret = tree{};
auto stack = parsing::parser_stack{};
auto it = input.begin();
const auto end = input.end();
bool unrooted = false;
ret.emplace_back(none, none, none, none);
auto state = parsing::parser_state{none, 0};
for (auto token = parsing::next_token(it, end); token.type != parsing::token_type::eof;
token = parsing::next_token(it, end)) {
switch (token.type) {
case parsing::token_type::lparen: {
const auto parent = state.self;
const auto self = ret.size();
// Inner node names must come AFTER the closing parentheses!
utils::ensure<bad_input_error>(ret[state.self].taxon() == none,
bad_input_error_type::nwk_malformed);
stack.push(state);
state = parsing::parser_state{parent, self};
ret.emplace_back(parent, none, none, none);
ret[parent].lchild() = self;
break;
}
case parsing::token_type::seperator: {
const auto parent = state.parent;
if (ret[parent].rchild() != none) {
// (*,old,new)root, state = {root,old}
// -> (*,(old,new)aux)root
utils::ensure<bad_input_error>(
parent == 0, bad_input_error_type::nwk_multifurcating);
unrooted = true;
auto old_node = state.self;
auto aux_node = ret.size();
auto new_node = ret.size() + 1;
assert(ret[0].rchild() == state.self);
ret.emplace_back(0, old_node, new_node, none);
ret.emplace_back(aux_node, none, none, none);
ret[0].rchild() = aux_node;
ret[old_node].parent() = aux_node;
stack.push({0, aux_node});
state.parent = aux_node;
state.self = new_node;
} else {
state.self = ret.size();
ret.emplace_back(parent, none, none, none);
ret[parent].rchild() = state.self;
}
// no need to update state as the tree is binary to
// begin with, which means that we will now go up a level
break;
}
case parsing::token_type::rparen: {
utils::ensure<bad_input_error>(
not stack.empty(),
bad_input_error_type::nwk_mismatched_parentheses);
utils::ensure<bad_input_error>(ret[state.parent].rchild() != none,
bad_input_error_type::nwk_malformed);
state = stack.top();
stack.pop();
break;
}
case parsing::token_type::name: {
cb(ret[state.self], token.name);
break;
}
case parsing::token_type::eof:
default: { throw std::logic_error{"dafuq?"}; }
}
}
if (unrooted) {
utils::ensure<bad_input_error>(!stack.empty(),
bad_input_error_type::nwk_mismatched_parentheses);
stack.pop();
}
utils::ensure<bad_input_error>(stack.empty(),
bad_input_error_type::nwk_mismatched_parentheses);
return ret;
}
} // namespace parsing
tree parse_nwk(const std::string& input, const index_map& taxa) {
std::vector<bool> found_taxon(taxa.size(), false);
return parsing::parse_nwk_impl(input, [&](node& n, const std::string& name) {
if (is_leaf(n)) {
auto it = taxa.find(name);
utils::ensure<bad_input_error>(
it != taxa.end(), bad_input_error_type::nwk_taxon_unknown, name);
auto taxon_id = (*it).second;
utils::ensure<bad_input_error>(!found_taxon[taxon_id],
bad_input_error_type::nwk_taxon_duplicate,
name);
found_taxon[taxon_id] = true;
n.taxon() = taxon_id;
}
});
}
named_tree parse_new_nwk(const std::string& input) {
name_map names;
index_map indices;
auto t = parsing::parse_nwk_impl(input, [&](node& n, const std::string& name) {
if (is_leaf(n)) {
auto ret = indices.insert({name, names.size()});
utils::ensure<bad_input_error>(
ret.second, bad_input_error_type::nwk_taxon_duplicate, name);
n.taxon() = names.size();
names.emplace_back(name);
}
});
return {t, names, indices};
}
occurrence_data parse_bitmatrix(std::istream& input) {
index cols{};
index rows{};
input >> rows >> cols >> std::ws;
bitmatrix mat{rows, cols};
name_map names;
index_map indices;
std::string line{};
while (std::getline(input, line)) {
if (line.empty()) {
continue;
}
auto it = line.begin();
auto end = line.end();
auto taxon_id = names.size();
// fill matrix
for (index i = 0; i < cols; ++i) {
it = utils::skip_ws(it, end);
utils::ensure<bad_input_error>(
it != end, bad_input_error_type::bitmatrix_size_invalid, line);
auto c = *it++;
utils::ensure<bad_input_error>(c == '1' || c == '0',
bad_input_error_type::bitmatrix_malformed);
if (c == '1') {
mat.set(taxon_id, i, true);
}
}
// read taxon name
it = utils::skip_ws(it, end);
utils::ensure<bad_input_error>(it != end,
bad_input_error_type::bitmatrix_name_empty, line);
auto taxon_name = std::string{it, end};
auto was_inserted = indices.insert({taxon_name, names.size()}).second;
utils::ensure<bad_input_error>(
was_inserted, bad_input_error_type::bitmatrix_name_duplicate, taxon_name);
names.emplace_back(std::move(taxon_name));
}
utils::ensure<bad_input_error>(rows == names.size(),
bad_input_error_type::bitmatrix_size_invalid);
return {mat, names, indices};
}
} // namespace terraces
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