1 #ifndef GENESIS_TAXONOMY_FORMATS_NCBI_H_ 2 #define GENESIS_TAXONOMY_FORMATS_NCBI_H_ 39 #include <unordered_map> 69 size_t tax_id_pos = 0,
70 size_t parent_tax_id_pos = 1,
76 size_t tax_id_pos = 0,
78 size_t name_class_pos = 3,
79 std::string
const& name_class_filter =
"scientific name" 92 #endif // include guard
Container namespace for all symbols of genesis in order to keep them separate when used as a library...
Store a Taxonomy, i.e., a nested hierarchy of Taxa.
std::unordered_map< std::string, NcbiName > NcbiNameLookup
Taxonomy read_ncbi_taxonomy(std::string const &node_file, std::string const &name_file)
Store a Taxon, i.e., an element in a Taxonomy, with its name, rank, ID and sub-taxa.
NcbiNodeLookup convert_ncbi_node_table(utils::CsvReader::Table const &node_table, size_t tax_id_pos, size_t parent_tax_id_pos, size_t rank_pos)
std::unordered_map< std::string, NcbiNode > NcbiNodeLookup
NcbiNameLookup convert_ncbi_name_table(utils::CsvReader::Table const &name_table, size_t tax_id_pos, size_t name_pos, size_t name_class_pos, std::string const &name_class_filter)
std::string parent_tax_id
Taxonomy convert_ncbi_tables(NcbiNodeLookup const &nodes, NcbiNameLookup const &names)
std::vector< Line > Table