[−][src]Trait ncbitaxonomy::NcbiTaxonomy

pub trait NcbiTaxonomy {
    fn contains_id(&self, taxid: i32) -> bool;

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

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

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

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

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

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

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

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

Required methods

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

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

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

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

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

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

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

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

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

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Implementors

impl NcbiTaxonomy for NcbiFileTaxonomy[src]

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

contains_id

check whether the taxonomy contains a (number) ID

fn contains_name(&self, name: &str) -> bool[src]

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[src]

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[src]

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>[src]

get_name_by_id

get the scientific name associated with a given NCBI Taxonomy ID

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

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)>[src]

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)>[src]

get_distance_to_common_ancestor

find the distance in the tree between name1 and name2

impl NcbiTaxonomy for NcbiSqliteTaxonomy[src]

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