import { SequenceAlignments } from "@rcsb/rcsb-api-tools/lib/RcsbGraphQL/Types/Borrego/GqlTypes";
import { Alignment } from "./alignment-response";
import { InstanceSequenceInterface } from "@rcsb/rcsb-saguaro-app/lib/RcsbCollectTools/DataCollectors/MultipleInstanceSequencesCollector";
type AlignmentRefType = (number | undefined)[];
export declare class AlignmentReference {
    private alignmentRefMap;
    private refId;
    private readonly alignmentRefGaps;
    private readonly memberRefList;
    private readonly alignmentMap;
    init(result: Alignment): Promise<void>;
    addAlignment(id: string, alignment: AlignmentRefType, target: AlignmentRefType): void;
    buildAlignments(): SequenceAlignments;
    addUniqueAlignmentId(result: Alignment, alignmentIndex: number, pairIndex?: 0 | 1): string;
    getAlignmentEntry(alignmentId: string): {
        entryId: string;
        instanceId: string;
        sequence: string;
        alignmentIndex: number;
        pairIndex: number;
        alignmentId: string;
    };
    getSequences(): Promise<InstanceSequenceInterface[]>;
    private addRef;
    private addEnd;
    private addBeg;
    private addGap;
    private extendGap;
}
export {};