Crate seqalign

Sequence alignment

This crate implements commonly-used sequence alignment methods based on edit operations. There are multiple crates available to compute edit distances. However, to my knowledge there was no crate that supports all of the following seqalign features:

• Works on slices of any type.
• Can return both the edit distance and the edit script/alignment.
• Can be extended with new measures.

Example

use seqalign::Align;
use seqalign::measures::LevenshteinDamerau;

let incorrect = &['t', 'p', 'y', 'o'];
let correct = &['t', 'y', 'p', 'o', 's'];

let measure = LevenshteinDamerau::new(1, 1, 1, 1);
let alignment = measure.align(incorrect, correct);

// Get the edit distance
assert_eq!(2, alignment.distance());

// Get the edit script.
use seqalign::measures::LevenshteinDamerauOp;
use seqalign::op::IndexedOperation;

assert_eq!(vec![
    IndexedOperation::new(LevenshteinDamerauOp::Match, 0, 0),
    IndexedOperation::new(LevenshteinDamerauOp::Transpose(1), 1, 1),
    IndexedOperation::new(LevenshteinDamerauOp::Match, 3, 3),
    IndexedOperation::new(LevenshteinDamerauOp::Insert(1), 4, 4)
  ], alignment.edit_script());

Modules

measures	Sequence distance measures.
op	Edit operations.

Structs

Alignment	Edit distance cost matrix.
SeqPair	A pairing of two sequences.

Traits

Align	Trait enabling alignment of all Measures.
Measure	Trait for edit distance measures.