Struct hpo::similarity::GroupSimilarity

pub struct GroupSimilarity<T, C> { /* private fields */ }

calculate the Similarity score between two HpoSets

Note

It is recommended to use the HpoSet::similarity method instead of creating a GroupSimilarity struct yourself.

Examples

Using the preferred way

use hpo::term::InformationContentKind;
use hpo::{Ontology, HpoSet};
use hpo::term::HpoGroup;
use hpo::similarity::{Builtins, StandardCombiner};

fn set1(ontology: &Ontology) -> HpoSet {
// ...
}

fn set2(ontology: &Ontology) -> HpoSet {
// ...
}

let ontology = Ontology::from_binary("tests/example.hpo").unwrap();
let set_1 = set1(&ontology);
let set_2 = set2(&ontology);

let similarity = set_1.similarity(
    &set_2,
    Builtins::GraphIc(InformationContentKind::Omim),
    StandardCombiner::default()
);

assert_eq!(similarity, 0.8177036);

Using GroupSimilarity directly

use hpo::term::InformationContentKind;
use hpo::{Ontology, HpoSet};
use hpo::term::HpoGroup;
use hpo::similarity::{Builtins, GroupSimilarity, StandardCombiner};

fn set1(ontology: &Ontology) -> HpoSet {
// ...
}

fn set2(ontology: &Ontology) -> HpoSet {
// ...
}

let ontology = Ontology::from_binary("tests/example.hpo").unwrap();
let set_1 = set1(&ontology);
let set_2 = set2(&ontology);


let sim = GroupSimilarity::new(
    StandardCombiner::FunSimAvg,
    Builtins::GraphIc(InformationContentKind::Omim)
);

assert_eq!(sim.calculate(&set_1, &set_2), 0.8177036);

Implementations

impl<T: Similarity, C: SimilarityCombiner> GroupSimilarity<T, C>

pub fn new(combiner: C, similarity: T) -> Self

Examples

use hpo::similarity::GraphIc;
use hpo::term::InformationContentKind;
use hpo::similarity::{GroupSimilarity, StandardCombiner};

// use Omim-based InformationContent for similarity calculation
let graphic = GraphIc::new(InformationContentKind::Omim);

// use the funSimAvg algorithm to combine the similarity scores
let combiner = StandardCombiner::FunSimAvg;

let sim = GroupSimilarity::new(combiner, graphic);

pub fn calculate(&self, a: &HpoSet<'_>, b: &HpoSet<'_>) -> f32

calculates the similarity between two sets of terms

Trait Implementations

impl Default for GroupSimilarity<GraphIc, StandardCombiner>

fn default() -> Self

Returns the “default value” for a type.