siafun/lib/smith-waterman.d.ts

A collection of structure induction algorithms

export declare enum TRACES {
    NONE = 0,
    DIAGONAL = 1,
    UP = 2,
    LEFT = 3
}
export interface SmithWatermanResult {
    scoreMatrix: number[][];
    traceMatrix: number[][];
}
export declare const GAP_SCORE = -5;
export declare class SmithWaterman {
    private similarityTreshold;
    private matchScore;
    private mismatchScore;
    private gapScore;
    constructor(similarityTreshold?: any);
    run(seq1: number[][], seq2: number[][], ignoredPoints?: Set<string>): SmithWatermanResult;
    private internalRun;
    private isSimilar;
    private intersect;
}