Struct taxonomy::GeneralTaxonomy

pub struct GeneralTaxonomy { /* fields omitted */ }

A concrete implementation of the Taxonomy trait suitable for interconversions of different formats.

Methods

impl GeneralTaxonomy

pub fn new(
    tax_ids: Vec<String>,
    parent_ids: Vec<usize>,
    names: Option<Vec<String>>,
    ranks: Option<Vec<Option<TaxRank>>>,
    dists: Option<Vec<f32>>
) -> Self

Initializer for a new Taxonomy.

All Vecs must be the same length or initialization will fail.

pub fn from_internal_id(&self, tax_id: usize) -> Result<&str>

Given an internal tax_id (an array position) return the corresponding external tax_id (e.g. a NCBI taxonomy ID).

Because the Taxonomy train is implemented for internal IDs also, the can be used to speed up some operations by avoiding a string lookup.

pub fn to_internal_id(&self, tax_id: &str) -> Result<usize>

Given an external tax_id (e.g. a NCBI taxonomy ID) return the corresponding internal tax_id (the position of that tax node in the internal array).

Because the Taxonomy train is implemented for internal IDs also, the can be used to speed up some operations by avoiding a string lookup.

Trait Implementations

impl<'s> Taxonomy<'s, usize, f32> for GeneralTaxonomy

This is the implementation for "internal" tax ID lookup; these IDs are arbitrary (they're positions of the tax nodes in the internal array) and not linked at all to the "external" (e.g. NCBI) IDs. Using these IDs directly can lead to a decent speed up without having to build indicies.

fn root(&self) -> usize

Returns the root node of the entire tree.

fn children(&self, tax_id: usize) -> Result<Vec<usize>>

Returns a Vec of all the child IDs of the given tax_id.

fn parent(&self, tax_id: usize) -> Result<Option<(usize, f32)>>

Returns the parent of the given taxonomic node and the distance to said parent. The parent of the root node should always be None.

fn len(&self) -> usize

Returns the number of nodes in the taxonomy

fn name(&self, tax_id: usize) -> Result<&str>

Returns the name of the tax_id provided.

fn rank(&self, tax_id: usize) -> Result<Option<TaxRank>>

Returns the taxonomic rank of the tax_id provided.

fn lineage(&'t self, tax_id: T) -> Result<Vec<T>>

Returns a Vec of taxonomy nodes from the one provided back to root.

fn parent_at_rank(&'t self, tax_id: T, rank: TaxRank) -> Result<Option<(T, D)>>

Returns the parent at a given taxonomic rank (note this may not be the immediate parent). This also returns the distance to that parent.

fn lca(&'t self, id1: T, id2: T) -> Result<T>

Returns the first common parent between two nodes. E.g. for the tree:

fn traverse(&'t self, node: T) -> Result<TaxonomyIterator<'t, T, D>> where
    Self: Sized, 

Generates an iterator that traces over the entire taxonomic tree. During preorder traversal, it returns (T, true) and during postorder traversal it returns (T, false)

fn is_empty(&'t self) -> bool where
    Self: Sized, 

Convenience function for determining if there are any nodes at all in the taxonomy. This should almost always be implemented for performance reasons.

impl<'s> Taxonomy<'s, &'s str, f32> for GeneralTaxonomy

This is the implementation for &str taxonomy access for a more end-user understandable (but slightly slower) workflow.

fn root(&'s self) -> &'s str

Returns the root node of the entire tree.

fn children(&self, tax_id: &str) -> Result<Vec<&str>>

Returns a Vec of all the child IDs of the given tax_id.

fn parent(&self, tax_id: &str) -> Result<Option<(&str, f32)>>

Returns the parent of the given taxonomic node and the distance to said parent. The parent of the root node should always be None.

fn len(&self) -> usize

Returns the number of nodes in the taxonomy

fn name(&self, tax_id: &str) -> Result<&str>

Returns the name of the tax_id provided.

fn rank(&self, tax_id: &str) -> Result<Option<TaxRank>>

Returns the taxonomic rank of the tax_id provided.

fn lineage(&'t self, tax_id: T) -> Result<Vec<T>>

Returns a Vec of taxonomy nodes from the one provided back to root.

fn parent_at_rank(&'t self, tax_id: T, rank: TaxRank) -> Result<Option<(T, D)>>

Returns the parent at a given taxonomic rank (note this may not be the immediate parent). This also returns the distance to that parent.

fn lca(&'t self, id1: T, id2: T) -> Result<T>

Returns the first common parent between two nodes. E.g. for the tree:

fn traverse(&'t self, node: T) -> Result<TaxonomyIterator<'t, T, D>> where
    Self: Sized, 

Generates an iterator that traces over the entire taxonomic tree. During preorder traversal, it returns (T, true) and during postorder traversal it returns (T, false)

fn is_empty(&'t self) -> bool where
    Self: Sized, 

Convenience function for determining if there are any nodes at all in the taxonomy. This should almost always be implemented for performance reasons.

impl Clone for GeneralTaxonomy

fn clone(&self) -> GeneralTaxonomy

Returns a copy of the value.

fn clone_from(&mut self, source: &Self)

Performs copy-assignment from source.

impl Debug for GeneralTaxonomy

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

Formats the value using the given formatter.

impl Serialize for GeneralTaxonomy

fn serialize<__S>(&self, __serializer: __S) -> Result<__S::Ok, __S::Error> where
    __S: Serializer, 

Serialize this value into the given Serde serializer.

impl<'de> Deserialize<'de> for GeneralTaxonomy

fn deserialize<__D>(__deserializer: __D) -> Result<Self, __D::Error> where
    __D: Deserializer<'de>, 

Deserialize this value from the given Serde deserializer.