mafft_types/
local_hom.rs

1/// A single local homology region between two sequences.
2///
3/// Replaces the C `LocalHom` linked-list node with a plain struct.
4/// Collections of these are stored in a `Vec` rather than a linked list.
5#[derive(Debug, Clone, PartialEq)]
6pub struct HomologyRegion {
7    /// Start position in sequence 1.
8    pub start1: i32,
9    /// End position in sequence 1.
10    pub end1: i32,
11    /// Start position in sequence 2.
12    pub start2: i32,
13    /// End position in sequence 2.
14    pub end2: i32,
15    /// Optimal alignment score for this region.
16    pub opt: f64,
17    /// Overlap in amino acids.
18    pub overlapaa: i32,
19    /// Whether this region was extended.
20    pub extended: bool,
21    /// Importance weight (used in consistency scoring).
22    pub importance: f64,
23    /// Reverse importance weight.
24    pub rimportance: f64,
25    /// 'k' (keep) or 'h' (homolog) classification.
26    pub korh: u8,
27    /// Remaining count.
28    pub nokori: i32,
29}
30
31impl Default for HomologyRegion {
32    fn default() -> Self {
33        Self {
34            start1: 0,
35            end1: 0,
36            start2: 0,
37            end2: 0,
38            opt: 0.0,
39            overlapaa: 0,
40            extended: false,
41            importance: 0.0,
42            rimportance: 0.0,
43            korh: b'h',
44            nokori: 0,
45        }
46    }
47}
48
49/// Table of pairwise local homology information.
50///
51/// Replaces the C `LocalHom **localhomtable` (njob x njob linked lists)
52/// with a flat map keyed by sequence pair indices.
53#[derive(Debug, Clone, Default)]
54pub struct LocalHomologyTable {
55    /// Number of sequences.
56    pub nseq: usize,
57    /// Homology regions for each pair (i, j) where i < j.
58    /// Indexed as `regions[i * nseq + j]`.
59    entries: Vec<Vec<HomologyRegion>>,
60}
61
62impl LocalHomologyTable {
63    pub fn new(nseq: usize) -> Self {
64        Self {
65            nseq,
66            entries: vec![Vec::new(); nseq * nseq],
67        }
68    }
69
70    /// Get homology regions between sequences i and j.
71    pub fn get(&self, i: usize, j: usize) -> &[HomologyRegion] {
72        &self.entries[i * self.nseq + j]
73    }
74
75    /// Get mutable homology regions between sequences i and j.
76    pub fn get_mut(&mut self, i: usize, j: usize) -> &mut Vec<HomologyRegion> {
77        &mut self.entries[i * self.nseq + j]
78    }
79
80    /// Add a homology region between sequences i and j.
81    pub fn push(&mut self, i: usize, j: usize, region: HomologyRegion) {
82        self.entries[i * self.nseq + j].push(region);
83    }
84}
85
mafft_types/local_hom.rs

mafft_types/
local_hom.rs
