import * as DG from 'datagrok-api/dg';
import { MmDistanceFunctionsNames } from '@datagrok-libraries/ml/src/macromolecule-distance-functions';
import { ISeqSplitted, SeqColStats, SplitterFunc } from './types';
import { NOTATION } from './consts';
import { HelmType } from '../../helm/types';
import { CellRendererBackBase } from '../cell-renderer-back-base';
export declare const SeqTemps: {
    /** Column's temp slot name for a SeqHandler object */
    seqHandler: string;
    notationProvider: string;
};
export type ConvertFunc = (src: string) => string;
export type JoinerFunc = (src: ISeqSplitted) => string;
export declare class SeqValueBase extends DG.SemanticValue<string> {
    private rowIdx;
    private seqHandler;
    get value(): string;
    set value(v: string);
    get helm(): string;
    isDna(): boolean;
    isRna(): boolean;
    isNaturalPeptide(): boolean;
    isHelm(): boolean;
    constructor(rowIdx: number, seqHandler: ISeqHandler);
    getSplitted(): ISeqSplitted;
    getSplittedWithSugarsAndPhosphates(): ISeqSplitted;
}
export interface ISeqHandler {
    get column(): DG.Column<string>;
    get refinerPromise(): Promise<void>;
    get alphabet(): string;
    get notation(): NOTATION;
    get separator(): string | undefined;
    get aligned(): string;
    get units(): string;
    get defaultBiotype(): HelmType;
    get maxLength(): number;
    get length(): number;
    get defaultGapOriginal(): string;
    get stats(): SeqColStats;
    get splitter(): SplitterFunc;
    get joiner(): JoinerFunc;
    get posList(): string[];
    get isCanonicalAlphabet(): boolean;
    isFasta(): boolean;
    isMsa(): boolean;
    isHelm(): boolean;
    isSeparator(): boolean;
    getSplitted(rowIdx: number, limit?: number): ISeqSplitted;
    getValue(rowIdx: number, options?: any): SeqValueBase;
    getHelm(rowIdx: number): string;
    getMonomerAtPosition(rowIdx: number, position: number, canonical: boolean): string;
    getMonomersAtPosition(position: number, canonical: boolean): string[];
    getAlphabetSize(): number;
    getAlphabetIsMultichar(): boolean;
    getNewColumnFromList(name: string, seqList: string[]): DG.Column<string>;
    convert(tgtNotation: NOTATION, tgtSeparator?: string): DG.Column<string>;
    convertHelmToFastaSeparator(srcSeq: string, tgtNotation: string, tgtSeparator?: string, tgtGapOriginal?: string): string;
    getRegion(startIdx: number | null, endIdx: number | null, name: string): DG.Column<string>;
    getJoiner(opts?: {
        notation: NOTATION;
        separator?: string;
    }): JoinerFunc;
    getDistanceFunctionName(): MmDistanceFunctionsNames;
    getConverter(tgtUnits: NOTATION, tgtSeparator?: string): ConvertFunc;
    getRendererBack(gridCol: DG.GridColumn | null, tableCol: DG.Column<string>): CellRendererBackBase<string> | null;
}
//# sourceMappingURL=seq-handler.d.ts.map