import { RcsbFvRowConfigInterface } from "@rcsb/rcsb-saguaro/lib/RcsbFv/RcsbFvConfig/RcsbFvConfigInterface";
export interface PairwiseAlignmentInterface {
    querySequence: string;
    targetSequence: string;
    queryAlignment: string;
    targetAlignment: string;
    queryBegin: number;
    queryEnd: number;
    targetBegin: number;
    targetEnd: number;
    targetId: string;
    queryId: string;
    sequenceId: number;
    isQueryExternal: boolean;
    isTargetExternal: boolean;
    pairwiseView?: boolean;
}
export declare class PairwiseAlignmentBuilder {
    private querySequence;
    private targetSequence;
    private queryAlignment;
    private targetAlignment;
    private readonly queryBegin;
    private readonly targetBegin;
    private readonly alignmentLength;
    private readonly targetId;
    private readonly queryId;
    private sequenceId;
    private readonly isQueryExternal;
    private readonly isTargetExternal;
    private readonly pairwiseView;
    constructor(paI: PairwiseAlignmentInterface);
    getLength(): number;
    buildReferenceAlignment(): Array<RcsbFvRowConfigInterface>;
    buildPairwiseAlignment(): Array<RcsbFvRowConfigInterface>;
    private addBlockTerminalTags;
}