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#include "../lib/trees_impl.hpp"
#include <algorithm>
#include <fstream>
#include <terraces/advanced.hpp>
#include <terraces/bitmatrix.hpp>
#include <terraces/errors.hpp>
#include <terraces/parser.hpp>
#include <terraces/terraces.h>
missingData* initializeMissingData(size_t numberOfSpecies, size_t numberOfPartitions,
const char** speciesNames) {
auto data = new missingData;
data->numberOfSpecies = numberOfSpecies;
data->numberOfPartitions = numberOfPartitions;
data->allocatedNameArray = false; // TODO What is this entry?
data->speciesNames = speciesNames;
data->missingDataMatrix = new unsigned char[numberOfSpecies * numberOfPartitions]();
return data;
}
void freeMissingData(missingData* m) {
delete[] m->missingDataMatrix;
delete m;
}
void setDataMatrix(missingData* m, size_t speciesNumber, size_t partitionNumber,
unsigned char value) {
m->missingDataMatrix[speciesNumber * m->numberOfPartitions + partitionNumber] = value;
}
unsigned char getDataMatrix(const missingData* m, size_t speciesNumber, size_t partitionNumber) {
return m->missingDataMatrix[speciesNumber * m->numberOfPartitions + partitionNumber];
}
void copyDataMatrix(const unsigned char* matrix, missingData* m) {
std::copy_n(matrix, m->numberOfSpecies * m->numberOfPartitions, m->missingDataMatrix);
}
CHECK_RESULT int terraceAnalysis(missingData* m, const char* newickTreeString, const int ta_outspec,
const char* allTreesOnTerraceFile, mpz_t terraceSize) {
// check ta_outspec
auto detect = bool(ta_outspec & TA_DETECT);
auto count = bool(ta_outspec & TA_COUNT);
auto enumerate = bool(ta_outspec & TA_ENUMERATE);
auto compress = bool(ta_outspec & TA_ENUMERATE_COMPRESS);
auto force_comprehensive = bool(ta_outspec & TA_UPPER_BOUND);
bool invalid1 = detect && (count || enumerate); // cannot detect and count at the same time
bool invalid2 = compress && !enumerate; // cannot compress if we don't enumerate
if (invalid1 || invalid2) {
return TERRACE_FLAG_CONFLICT_ERROR;
}
// check input sizes
if (m->numberOfPartitions < 2) {
return TERRACE_NUM_PARTITIONS_ERROR;
}
if (m->numberOfSpecies < 4) {
return TERRACE_NUM_SPECIES_ERROR;
}
// copy missing data matrix
terraces::bitmatrix matrix{m->numberOfSpecies, m->numberOfPartitions};
for (size_t row = 0; row < m->numberOfSpecies; ++row) {
size_t rowcount = 0;
for (size_t col = 0; col < m->numberOfPartitions; ++col) {
auto val = m->missingDataMatrix[row * m->numberOfPartitions + col];
if (val != 0 && val != 1) {
return TERRACE_MATRIX_ERROR;
}
matrix.set(row, col, val);
rowcount += val;
}
if (rowcount == 0) {
return TERRACE_SPECIES_WITHOUT_PARTITION_ERROR;
}
}
// copy names
terraces::name_map names;
terraces::index_map name_index;
for (size_t spec_i = 0; spec_i < m->numberOfSpecies; ++spec_i) {
names.emplace_back(m->speciesNames[spec_i]);
if (!name_index.insert({names.back(), spec_i}).second) {
return TERRACE_SPECIES_ERROR;
}
}
// parse newick tree
terraces::tree tree;
try {
tree = terraces::parse_nwk(newickTreeString, name_index);
} catch (const terraces::bad_input_error& err) {
switch (err.type()) {
case terraces::bad_input_error_type::nwk_multifurcating:
return TERRACE_TREE_NOT_BINARY_ERROR;
case terraces::bad_input_error_type::nwk_taxon_duplicate:
return TERRACE_SPECIES_ERROR;
default:
return TERRACE_NEWICK_ERROR;
}
}
if (terraces::num_leaves_from_nodes(tree.size()) != m->numberOfSpecies) {
return TERRACE_SPECIES_ERROR;
}
// prepare data
if (force_comprehensive) {
matrix = terraces::maximum_comprehensive_columnset(matrix);
}
terraces::supertree_data data;
try {
data = terraces::create_supertree_data(tree, matrix);
} catch (const terraces::bad_input_error&) {
return TERRACE_INTERNAL_ERROR;
} catch (const terraces::no_usable_root_error&) {
return TERRACE_NO_ROOT_SPECIES_ERROR;
}
// enumerate terrace
if (detect) {
auto lb = terraces::fast_count_terrace(data);
mpz_set_ui(terraceSize, lb);
} else if (count && !enumerate) {
try {
auto size = terraces::count_terrace_bigint(data);
mpz_set(terraceSize, size.value().get_mpz_t());
} catch (const terraces::tree_count_overflow_error&) {
return TERRACE_SPLIT_COUNT_OVERFLOW_ERROR;
}
} else {
auto ofs = std::ofstream{allTreesOnTerraceFile};
if (not ofs.is_open()) {
return TERRACE_OUTPUT_FILE_ERROR;
}
mpz_class size;
try {
if (compress) {
size = terraces::print_terrace_compressed(data, names, ofs).value();
} else {
size = terraces::print_terrace(data, names, ofs).value();
}
if (count) {
mpz_set(terraceSize, size.get_mpz_t());
}
} catch (std::ifstream::failure&) {
return TERRACE_OUTPUT_FILE_ERROR;
} catch (const terraces::tree_count_overflow_error&) {
return TERRACE_SPLIT_COUNT_OVERFLOW_ERROR;
}
}
return TERRACE_SUCCESS;
}
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