bioseq-ts/lib/BioSeqSet.d.ts

Biological Sequence in Javascript, written in Typescript.

import { BioSeq } from './BioSeq';
declare type IPartition = [number, number];
declare class BioSeqSet {
    /**
     * Contains the list of BioSeq Objects
     *
     * @private
     * @type {BioSeq[]}
     * @memberof BioSeqSet
     */
    private readonly set;
    private readonly hash;
    private hashString;
    /**
     * Contains the partition table of the set
     *
     * @private
     * @type {IPartition[]}
     * @memberof BioSeqSet
     */
    private partitionTable;
    constructor(set?: BioSeq[], partitionTable?: IPartition[]);
    /**
     * Creates a unique identifier based on the content of the dataset
     *
     * @returns {string}
     * @memberof BioSeqSet
     */
    getHash(): string;
    /**
     * Returns the set of BioSeqs.
     *
     * @returns
     * @memberof BioSeqSet
     */
    getBioSeqs(): BioSeq[];
    /**
     * Returns the partition of the set
     *
     * @returns
     * @memberof BioSeqSet
     */
    getPartitions(): IPartition[];
    /**
     * Concatenate the sequences of two BioSeqSets. Keep header of the current set.
     *
     * @param {BioSeqSet} newset
     * @memberof BioSeqSet
     */
    concatSequences(newBioSeqSet: BioSeqSet): BioSeqSet;
    /**
     * Return the length of the longest sequence in the set (with or without gaps).
     *
     * @param {boolean} [gapless=false]
     * @returns {number}
     * @memberof BioSeqSet
     */
    maxLength(gapless?: boolean): number;
    /**
     * Returns a boolean if all sequences are aligned, or if they all have the same length
     *
     * @returns {boolean}
     * @memberof BioSeqSet
     */
    isAligned(): boolean;
    /**
     * Returns the partition of the dataset. [start, end]
     *
     * @private
     * @returns
     * @memberof BioSeqSet
     */
    private calcPartitionTable;
    /**
     * Minimal sanity check to see if it is a valid partition table
     *
     * @private
     * @param {IPartition[]} partitionTable
     * @returns {boolean}
     * @memberof BioSeqSet
     */
    private isValidPartitionTable;
}
export { BioSeqSet };