ncbi.hpp File Reference

#include "genesis/taxonomy/taxon.hpp"
#include "genesis/taxonomy/taxonomy.hpp"
#include "genesis/utils/formats/csv/reader.hpp"
#include <string>
#include <unordered_map>

Go to the source code of this file.

Classes
struct	NcbiName
struct	NcbiNode

Namespaces
	genesis
	Container namespace for all symbols of genesis in order to keep them separate when used as a library.
	genesis::taxonomy

Typedefs
using	NcbiNameLookup = std::unordered_map< std::string, NcbiName >
using	NcbiNodeLookup = std::unordered_map< std::string, NcbiNode >

Functions
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)
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)
Taxonomy	convert_ncbi_tables (NcbiNodeLookup const &nodes, NcbiNameLookup const &names)
Taxonomy	read_ncbi_taxonomy (std::string const &node_file, std::string const &name_file)