Struct NcbiFileTaxonomy

pub struct NcbiFileTaxonomy { /* private fields */ }

Implementations

impl NcbiFileTaxonomy

pub fn from_ncbi_files( nodes_filename: &str, names_filename: &str, ) -> Result<NcbiFileTaxonomy, NcbiTaxonomyError>

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 = NcbiFileTaxonomy::from_ncbi_files("data/nodes.dmp", "data/names.dmp");

pub fn save_to_sqlite( &self, db_url: Option<&str>, ) -> Result<SqliteConnection, ToSqliteError>

pub fn get_node_by_id(&self, id: i32) -> Option<&NodeId>

get_node_by_id

get a NodeId from a numeric NCBI Taxonomy ID

pub fn traversal(&self, from: i32) -> Option<Traverse<'_, i32>>

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<i32>

get_id_by_node

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

Trait Implementations

impl Debug for NcbiFileTaxonomy

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

Formats the value using the given formatter.

impl NcbiTaxonomy for NcbiFileTaxonomy

fn contains_id(&self, id: i32) -> bool

contains_id

check whether the taxonomy contains a (number) ID

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

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

fn is_descendant_taxid(&self, taxid: i32, ancestor_taxid: i32) -> bool

is_descendant_taxid

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

fn get_name_by_id(&self, id: i32) -> Option<String>

get_name_by_id

get the scientific name associated with a given NCBI Taxonomy ID

fn get_lineage(&self, name: &str) -> Option<Vec<i32>>

get_lineage

get the list of IDs of a taxon and its parents (up to the root)

fn get_distance_to_common_ancestor_taxid( &self, taxid1: i32, taxid2: i32, only_canonical: bool, ) -> Option<(i32, i32)>

get_distance_to_common_ancestor_id

get the distance (in steps in the tree) between taxid1 and the common ancestor with taxid2

fn get_distance_to_common_ancestor( &self, name1: &str, name2: &str, only_canonical: bool, ) -> Option<(i32, String)>

get_distance_to_common_ancestor

find the distance in the tree between name1 and name2

fn get_id_by_name(&self, name: &str) -> Option<i32>