Crate mafft_core 

Core MAFFT alignment engine.

Orchestrates the full alignment pipeline:

1. Progressive alignment following a guide tree.
2. Iterative refinement with score-based acceptance.
3. Adding sequences to existing alignments.

Ports the C TreeDependentIteration() from tditeration.c, progressive alignment from disttbfast.c/tbfast.c, and addonetip() from addfunctions.c.

Re-exports

pub use progressive::progressive_align;

pub use progressive::progressive_align_partial;

pub use progressive::progressive_align_unweighted;

pub use progressive::progressive_align_with_weights_override;

pub use progressive::MultipleAlignment;

pub use progressive::StepTrace;

Modules

adjust_direction

Port of C MAFFT’s --adjustdirection strand-detection preprocessing.

external

progressive

Structs

MafftEngine

The main MAFFT alignment engine.

RefinementParams

Parameters controlling iterative refinement.

Enums

AlignmentMode

Alignment mode (strategy).

Functions

add_sequences

Add new sequences to an existing alignment.

add_sequences_keeplength

Add sequences while preserving the existing alignment’s column structure (--add --keeplength). After running the standard add_sequences, deletes any columns that exist only because of new-sequence insertions, restoring the existing alignment to its original width. Columns where ANY new sequence had a residue but ALL existing sequences had gaps get the new-sequence residue dropped (truncated at that position).

add_sequences_keeplength_with_map

Like add_sequences_keeplength but also returns the per-added- sequence list of dropped insertion runs ((start_in_addbk_0based, run_length) pairs). Used by --mapout / --compactmapout.

dndpre_offset_shift

Matrix shift applied when rebuilding the refinement-tree distances the way C’s dndpre does, for the modes that have no pairlocalalign step (FFT-NS-i and friends).

iterative_refine

Iteratively refine a multiple alignment.

pair_penalty_scales

Scale factors turning the pair-phase ppenalty-style integers (lgop * 1000, …) into DP units: (gap_scale, offset_scale).