import { AlignedRegions } from "@rcsb/rcsb-api-tools/lib/RcsbGraphQL/Types/Borrego/GqlTypes";
export declare namespace AlignmentMapper {
    function mapRangeToRegionList(range: {
        begin: number;
        end: number;
    }, regionList: AlignedRegions[], pointer: "query" | "target"): {
        begin: number;
        end: number;
    }[] | undefined;
    function mapRangeToRegion(range: {
        begin: number;
        end: number;
    }, region: AlignedRegions, pointer: "query" | "target"): {
        begin: number;
        end: number;
    } | undefined;
    function mapPointToRegion(p: number, region: AlignedRegions, pointer: "query" | "target"): number | undefined;
    function areIntersectingRegions(regionA: AlignedRegions, regionB: AlignedRegions, pointer: "query" | "target"): boolean;
    function getAllQueryIntersections(regionListA: AlignedRegions[], regionListB: AlignedRegions[]): [{
        query_begin: number;
        query_end: number;
    }, {
        query_begin: number;
        query_end: number;
    }][];
    function getAllTargetIntersections(regionListA: AlignedRegions[], regionListB: AlignedRegions[]): [{
        target_begin: number;
        target_end: number;
    }, {
        target_begin: number;
        target_end: number;
    }][];
    function getQueryIntersection(regionA: AlignedRegions, regionB: AlignedRegions): [{
        query_begin: number;
        query_end: number;
    }, {
        query_begin: number;
        query_end: number;
    }];
    function getTargetIntersection(regionA: AlignedRegions, regionB: AlignedRegions): [{
        target_begin: number;
        target_end: number;
    }, {
        target_begin: number;
        target_end: number;
    }];
    function range(start: number, stop: number, step?: number): number[];
    function swapQueryAndTarget(region: AlignedRegions): AlignedRegions;
}