import { SequenceAlignments } from "@rcsb/rcsb-api-tools/lib/RcsbGraphQL/Types/Borrego/GqlTypes";
type AlignmentRefType = (number | undefined)[];
export declare class AlignmentReference {
    private readonly alignmentRefMap;
    private readonly refId;
    private readonly alignmentRefGaps;
    private readonly memberRefList;
    constructor(refId: string, targetId: string, alignment: AlignmentRefType, target: AlignmentRefType);
    addAlignment(id: string, alignment: AlignmentRefType, target: AlignmentRefType): void;
    buildAlignments(): SequenceAlignments;
    private addRef;
    private addEnd;
    private addBeg;
    private addGap;
    private extendGap;
}
export {};