Alignment

class Alignment(values)

An alignment between two related sequences.

Consider this alignment between two strings:

|it's| |aligned!|
|    \ \        |
|it is| |aligned|

An alignment stores all the indices that are known to correspond between the original and modified sequences. For the above example, it would be

let a = new Alignment([
    [0, 0],
    [4, 5],
    [5, 6],
    [13, 13],
]);

Alignments can be used to answer questions like, “what’s the smallest range of the original sequence that is guaranteed to contain this part of the modified sequence?” For example, the range (0, 5) (“it is”) is known to match the range (0, 4) (“it’s”) of the original sequence.

console.log(a.original_bounds(0, 5));
// [0, 4]

Results may be imprecise if the alignment is too course to match the exact inputs:

console.log(a.original_bounds(0, 2));
// [0, 4]

A more granular alignment like this:

|i|t|'s| |a|l|i|g|n|e|d|!|
| | |  \ \ \ \ \ \ \ \ \ /
|i|t| is| |a|l|i|g|n|e|d|

a = new Alignment([
    [0, 0], [1, 1], [2, 2], [4, 5], [5, 6], [6, 7], [7, 8],
    [8, 9], [9, 10], [10, 11], [11, 12], [12, 13], [13, 13],
]);

Can be more precise:

console.log(a.original_bounds(0, 2));
// [0, 2]

Create a new Alignment.

Arguments

values (Iterable) – The pairs of indices to align. Each element should be a pair destructurable as [x, y], where x is the original sequence position and y is the modified sequence position.

Alignment.length

type: number

The number of entries in this alignment.

Alignment.values

type: readonly BiIndex[]

The pairs of aligned indices in this alignment.

Alignment.compose(other)

Arguments

other (Alignment()) –

Returns

Alignment – An alignment equivalent to applying this first, then other.

Alignment.concat(...others)

Concatenate this alignment together with one or more others.

Arguments

others (Alignment[]()) –

Returns

Alignment –

Alignment.equals(other)

Arguments

other (Alignment()) –

Returns

boolean – Whether this alignment is the same as other.

Alignment.inverse()

Returns: Alignment – The inverse of this alignment, from the modified to the original sequence.

Alignment.modifiedBounds()

Returns: Bounds – The bounds of the modified sequence.

Alignment.originalBounds()

Returns: Bounds – The bounds of the original sequence.

Alignment.shift(deltaO, deltaM)

Shift this alignment.

Arguments

deltaO (number()) – The distance to shift the original sequence.
deltaM (number()) – The distance to shift the modified sequence.

Returns

Alignment – An alignment with all the positions shifted by the given amounts.

Alignment.slice(start, end)

Extract a slice of this alignment.

Arguments

start (number()) – The position to start from.
end (number()) – The position to end at.

Returns

Alignment – The requested slice as a new Alignment.

Alignment.sliceByModified(start, end)

Slice this alignment by a span of the modified sequence.

Arguments

start (number()) – The start of the span in the modified sequence.
end (number()) – The end of the span in the modified sequence.

Returns

Alignment – The requested slice of this alignment.

Alignment.sliceByOriginal(start, end)

Slice this alignment by a span of the original sequence.

Arguments

start (number()) – The start of the span in the original sequence.
end (number()) – The end of the span in the original sequence.

Returns

Alignment – The requested slice of this alignment.

Alignment.identity(size)

Create an identity alignment of the given size, which maps all intervals to themselves.

Arguments

size (number()) – The size of the sequences to align.

Returns

Alignment – The identity alignment for the bounds [0, size].

Alignment.infer(original, modified, costFn)

Infer the alignment between two sequences with the lowest edit distance.

Warning: this operation has time complexity O(N*M), where N and M are the lengths of the original and modified sequences, and so should only be used for relatively short sequences.

Arguments

original (Iterable) – The original sequence.
modified (Iterable) – The modified sequence.
costFn (CostFn) – A function returning the cost of performing an edit. costFn(a, b) returns the cost of replacing a with b. costFn(a, undefined) returns the cost of deleting a, and costFn(undefined, b) returns the cost of inserting b. By default, all operations have cost 1 except replacing identical elements, which has cost 0.

Returns

Alignment – The inferred alignment.