nj 0.0.18

Neighbor-Joining phylogenetic tree inference. Auto-detects DNA/protein, supports multiple substitution models and bootstrap.
Documentation 
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67

//! Public configuration types shared between the core library, Python bindings,
//! and WASM bindings.
//!
//! Both [`SequenceObject`] and [`NJConfig`] implement `Serialize`/`Deserialize`
//! so they can be round-tripped through JSON (WASM), Python dicts (`serde-pyobject`),
//! and TypeScript via the generated `lib_types.ts` type definitions.

pub use crate::models::SubstitutionModel;
pub use crate::msa::MSA;
use serde::{Deserialize, Serialize};

/// A single sequence in a multiple sequence alignment.
///
/// Both fields are plain `String`s so that the struct can be constructed
/// from any source (FASTA parser, JSON, Python dict) without encoding overhead.
/// The actual byte-level encoding into typed symbols is deferred to
/// [`crate::msa::MSA::push`].
#[derive(Clone, Debug, ts_rs::TS, Serialize, Deserialize)]
#[ts(export, export_to = "../../wasm/types/lib_types.ts")]
pub struct SequenceObject {
    /// Sequence name, e.g. the FASTA header without the leading `>`.
    pub identifier: String,
    /// Raw sequence string, e.g. `"ACGT"` or `"ARND"`. Gap characters (`-`)
    /// are preserved and handled by the substitution models.
    pub sequence: String,
}

impl SequenceObject {
    /// Returns the length of the sequence in bytes (not symbols).
    pub fn len(&self) -> usize {
        self.sequence.len()
    }
}

/// Configuration for distance-only computation (no NJ, no bootstrap).
///
/// Pass a `DistConfig` to [`crate::distance_matrix`] or [`crate::average_distance`].
/// The alphabet (DNA vs. protein) is auto-detected from the sequences;
/// [`substitution_model`](DistConfig::substitution_model) must be compatible with
/// that alphabet or an error is returned.
#[derive(Serialize, Deserialize, ts_rs::TS, Clone, Debug)]
#[ts(export, export_to = "../../wasm/types/lib_types.ts")]
pub struct DistConfig {
    /// The aligned sequences. All sequences must have the same length.
    pub msa: Vec<SequenceObject>,
    /// Substitution model used to compute pairwise distances.
    pub substitution_model: SubstitutionModel,
}

/// Full configuration for a single Neighbor-Joining run.
///
/// Pass an `NJConfig` to [`crate::nj`] to run the algorithm and receive a
/// Newick string. The alphabet (DNA vs. protein) is auto-detected from the
/// sequences; [`substitution_model`](NJConfig::substitution_model) must be
/// compatible with that alphabet or an error is returned.
#[derive(Serialize, Deserialize, ts_rs::TS, Clone, Debug)]
#[ts(export, export_to = "../../wasm/types/lib_types.ts")]
pub struct NJConfig {
    /// The aligned sequences to build the tree from. All sequences must have
    /// the same length.
    pub msa: Vec<SequenceObject>,
    /// Number of bootstrap replicates used to compute support values on
    /// internal nodes. Set to `0` to skip bootstrapping entirely.
    pub n_bootstrap_samples: usize,
    /// Substitution model used to compute pairwise distances.
    pub substitution_model: SubstitutionModel,
}