Struct MultipleAlignment 

pub struct MultipleAlignment {
    pub sequences: Vec<Vec<u8>>,
    pub names: Vec<String>,
    pub score: f64,
    pub step_trace: Vec<StepTrace>,
    pub guide_tree: Option<Topology>,
    pub first_pass_sequences: Option<Vec<Vec<u8>>>,
    pub distance_matrix: Option<DistanceMatrix>,
}

Fields

sequences: Vec<Vec<u8>>

names: Vec<String>

score: f64

step_trace: Vec<StepTrace>

Per-merge-step trace: one entry per progressive merge. Each entry is (clus1_size, clus2_size, width_after_merge, score) matching C’s RDBG step clus1 clus2 width score debug line. Used for regression tests that assert byte-level parity with C on a per-step basis; harmless to ignore.

guide_tree: Option<Topology>

Final progressive guide tree, kept around so callers can serialize it for --treeout (mltaln9.c::loadtree and the various fixed_musclesupg_*_treeout variants). Populated by the engine when alignment completes; None for paths that don’t track it (e.g. tests building an MultipleAlignment directly).

first_pass_sequences: Option<Vec<Vec<u8>>>

Aligned MSA after the FIRST retree pass, BEFORE the final pass rebuilds the guide tree and re-aligns. C MAFFT’s --parttree runs splittbfast twice and feeds CALL 1’s output (pre_1) to CALL 2 — both for --reorder and --treeout. We stash pre_1 here so the CLI can replay CALL 2’s tree generation on the right input.

distance_matrix: Option<DistanceMatrix>

Pairwise distance matrix used by the engine for guide-tree construction. Populated when the engine knows callers will need it — currently --distout (writes <input>.hat2) and --scoreout (computes the unweighted SP score). None for paths that skip it (PartTree, –treein with a user-supplied tree, tests building a MultipleAlignment directly).

Implementations

impl MultipleAlignment

pub fn width(&self) -> usize

pub fn nseq(&self) -> usize

Trait Implementations

impl Clone for MultipleAlignment

fn clone(&self) -> MultipleAlignment

Returns a duplicate of the value.

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

Performs copy-assignment from source.

impl Debug for MultipleAlignment

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

Formats the value using the given formatter.