Struct ncbitaxonomy::NcbiTaxonomy

pub struct NcbiTaxonomy { /* fields omitted */ }

Methods

impl NcbiTaxonomy

pub fn from_ncbi_files(
    nodes_filename: &str,
    names_filename: &str
) -> Result<NcbiTaxonomy, Error>

from_ncbi_files

Reads the nodes.dmp file and names.dmp file from the NCBI Taxonomy database to generate a NcbiTaxonomy structure

Examples

use ncbitaxonomy::*;

let taxonomy = NcbiTaxonomy::from_ncbi_files("data/nodes.dmp", "data/names.dmp");

pub fn contains_id(&self, id: u32) -> bool

contains_id

check whether the taxonomy contains a (number) ID

pub fn contains_name(&self, name: &str) -> bool

contains_name

check whether the taxonomy contains a node with the specified name

note: the name used is what is reported as a the 'scientific name' in the NCBI Taxonomy database. synonyms are currently not supported

pub fn is_descendant(&self, name: &str, ancestor_name: &str) -> bool

is_descendant

check if a certain named node is a descendant of another named named

pub fn is_descendant_taxid(&self, taxid: u32, ancestor_taxid: u32) -> bool

is_descendant

check if a certain node with taxid is a descendant of another taxid

pub fn get_node_by_id(&self, id: u32) -> Option<&NodeId>

get_node_by_id

get a NodeId from a numeric NCBI Taxonomy ID

pub fn traversal(&self, from: u32) -> Option<Traverse<u32>>

traversal

traverse the tree nodes (in depth first order) from the node with a given NCBI Taxonomy ID

pub fn get_id_by_node(&self, node_id: NodeId) -> Option<u32>

get_id_by_node

get the NCBI Taxonomy ID held by the node with a given NodeId

pub fn get_name_by_id(&self, id: u32) -> Option<&String>

get_name_by_id

get the scientific name associated with a given NCBI Taxonomy ID

Trait Implementations

impl Debug for NcbiTaxonomy

fn fmt(&self, f: &mut Formatter) -> Result

Formats the value using the given formatter.