import { LitElement } from 'lit';
/**
 * The object describing a Variant Collection.
 */
export type VariantCollection = {
    name: string;
    collectionName: string;
    synopsis: string;
};
/**
 * Encoding for allele genotype display: VCF (e.g. 0/0, 1/1) or HapMap (e.g. TT, CC).
 */
export type AlleleEncoding = 'vcf' | 'hap';
/**
 * One variant from the alleles API with genotypes per sample.
 */
export type AlleleVariant = {
    position: number;
    ref: string;
    alt: string;
    genotypes: Record<string, string>;
};
/**
 * Response from the /vcf/alleles/ API.
 */
export type AlleleVariantsResponse = {
    region: {
        chromosome: string;
        start: number;
        end: number;
    };
    encoding: AlleleEncoding;
    samples: string[];
    invalid_samples?: string[];
    variant_count: number;
    variants: AlleleVariant[];
};
/**
 * Data needed to search for genes to get coordinates.
 */
export type AlleleLocationSearchFunction = (identifier: string, abortSignal?: AbortSignal) => Promise<{
    chromosome: string;
    start: number;
    end: number;
}>;
/**
 * Data needed to search for variants.
 */
export type AlleleVariantSearchFunction = (params: {
    collection: string;
    fileName: string;
    chromosome: string;
    start: number;
    end: number;
    strains?: string[];
    encoding?: AlleleEncoding;
}, abortSignal?: AbortSignal) => Promise<AlleleVariantsResponse>;
/**
 * Function to fetch strains for a collection.
 */
export type AlleleStrainSearchFunction = (params: {
    collection: string;
    fileName: string;
}, abortSignal?: AbortSignal) => Promise<{
    identifier: string;
}[]>;
export declare class LisAlleleSearchElement extends LitElement {
    /** @ignore */
    static styles: import("lit").CSSResult;
    /** @ignore */
    createRenderRoot(): this;
    connectedCallback(): void;
    /**
     * The list of available variant collections.
     */
    collections: VariantCollection[];
    /**
     * The list of available chromosome identifiers for region search.
     */
    chromosomes: string[];
    /**
     * The name of the collection to select by default.
     */
    preSelectedCollection?: string;
    /**
     * Function to resolve a gene name to coordinates.
     */
    locationSearchFunction: AlleleLocationSearchFunction;
    /**
     * Function to fetch variants.
     */
    variantSearchFunction: AlleleVariantSearchFunction;
    /**
     * Function to fetch strains.
     */
    strainSearchFunction: AlleleStrainSearchFunction;
    private selectedCollectionIdx;
    private strainMode;
    private availableStrains;
    private selectedStrains;
    private strainFilter;
    /** Display encoding: hap or vcf. Default hap. */
    private encoding;
    private searchResults;
    private searchedRegion;
    private searchedTerm;
    private cancelPromiseController;
    private _strainLoadingRef;
    private _modalRef;
    private _resultsLoadingRef;
    willUpdate(changedProperties: Map<string, unknown>): void;
    private _onCollectionChange;
    private _onStrainModeChange;
    private _onStrainFilter;
    private _onStrainSelect;
    private _onEncodingChange;
    private _fetchStrains;
    private _onSearchLocation;
    private _onSearchRegion;
    private _performVariantSearch;
    private _toggleModal;
    render(): import("lit-html").TemplateResult<1>;
    private _renderAlleleVariantsTable;
    private _renderStrainSelector;
}
declare global {
    interface HTMLElementTagNameMap {
        'lis-allele-search-element': LisAlleleSearchElement;
    }
}
//# sourceMappingURL=lis-allele-search-element.d.ts.map