import { PolymerEntityInstanceTranslate, TranslateContextInterface } from "../../RcsbUtils/PolymerEntityInstanceTranslate";
import { AlignedRegion, SequenceReference, TargetAlignment } from "@rcsb/rcsb-api-tools/build/RcsbGraphQL/Types/Borrego/GqlTypes";
import { RcsbFvLink, RcsbFvRowConfigInterface, RcsbFvTrackDataElementInterface } from "@rcsb/rcsb-saguaro";
import { AlignedObservedRegion } from "./SequenceCollector";
import { AlignmentCollectConfig } from "./SequenceCollectorInterface";
export interface BuildAlignementsInterface {
    targetAlignmentList: Array<TargetAlignment>;
    queryId: string;
    querySequence: string;
    filterByTargetContains?: string;
    to: SequenceReference;
    from: SequenceReference;
    excludeAlignmentLinks?: boolean;
    fitTitleWidth?: boolean;
}
interface BuildSequenceDataInterface extends TranslateContextInterface {
    sequenceData: Array<RcsbFvTrackDataElementInterface>;
    sequence: string;
    begin: number;
    oriBegin: number;
}
export declare class SequenceCollectorHelper {
    private entityInstanceTranslator;
    buildAlignments(alignmentData: BuildAlignementsInterface, dynamicDisplayFlag: boolean, tagObservedRegions: (region: AlignedRegion, commonContext: TranslateContextInterface) => Array<AlignedObservedRegion>): {
        alignments: Array<RcsbFvRowConfigInterface>;
        targets: Array<string>;
    };
    buildSequenceData(config: BuildSequenceDataInterface, isQuerySequence?: boolean): Array<RcsbFvTrackDataElementInterface>;
    buildSequenceRowTitle(requestConfig: AlignmentCollectConfig): string | RcsbFvLink;
    buildAlignmentRowTitle(targetAlignment: TargetAlignment, alignmentData: BuildAlignementsInterface): string | RcsbFvLink;
    addAuthorResIds(e: RcsbFvTrackDataElementInterface, alignmentContext: TranslateContextInterface): RcsbFvTrackDataElementInterface;
    buildInstanceId(targetId: string): string;
    setPolymerEntityInstanceTranslator(p: PolymerEntityInstanceTranslate): void;
}
export {};
