import { Sequence } from './SeqNode';
import { Aligner } from './Aligner';
import { GapsParams, AlignmentResult } from './types';
/**
 * Generic temporal sequence aligner
 *
 * Implements the method reported in:
 *     `Syed et al. Temporal Needleman-Wunsch <http://ieeexplore.ieee.org/document/7344785/>`__
 *
 * Currently, it supports linear gap penalty but extends/adapts the notation in the original paper to support all alignment paths
 *
 * @todo
 *     extend it to affine gap penalty
 * @param alignType defining type of alignment.
 *                 There are four alignment types:
 *                     - `global` (i.e. Needleman-Wunsch or more precisely a variant of David Sankoff algorithm
 *                                      see  Sankoff, D. (1972). "Matching sequences under deletion-insertion constraints".
 *                                           Proceedings of the National Academy of Sciences of the United States of America. 69 (1): 4–6
 *                                 )
 *                     - `local` (i.e. Smith-Waterman algorithm)
 *                     - `semi-global` alignment
 *                     - `end-gap-free` alignment
 */
export declare class TemporalAligner<LabelType> extends Aligner<LabelType> {
    align(seq1: Sequence<LabelType>, seq2: Sequence<LabelType>, gaps_params: GapsParams): void;
    private initTransitionTable;
    retrieveAlignments(): AlignmentResult<LabelType>;
}