import * as DG from 'datagrok-api/dg';
import { CandidateType, ISeqGraphInfo, ISeqSplitted, MonomerFreqs, SeqColStats, SeqSplittedBase, SplitterFunc } from './types';
import { ALPHABET } from './consts';
import { SeqPalette } from '../../seq-palettes';
import { ISeqHelper } from '../seq-helper';
import { HelmType, PolymerType } from '../../helm/types';
export declare class StringListSeqSplitted implements ISeqSplitted {
    private readonly mList;
    private readonly gapOriginalMonomer;
    get length(): number;
    get graphInfo(): ISeqGraphInfo | undefined;
    isGap(posIdx: number): boolean;
    /** @param {number} posIdx monomer position 0-based index */
    getCanonical(posIdx: number): string;
    getOriginal(posIdx: number): string;
    getCanonicalRegion(start: number, end: number): string[];
    getOriginalRegion(start: number, end: number): string[];
    get gapOriginal(): string;
    constructor(mList: SeqSplittedBase, gapOriginalMonomer: string);
}
/** Same as string list splitted, but for helm will also encode the graph info, and define a getter for it
 *
 */
export declare class HelmSplitted extends StringListSeqSplitted {
    protected mListSeparated: string[][];
    private readonly connections;
    private polymerTypes;
    constructor(mListSeparated: string[][], // list of lists of monomers (separated by | in helm notation
    connections: string, // string part of helm defining connections between monomers
    polymerTypes: PolymerType[], // polymer types for each disjoint sequence part
    gapOriginalMonomer: string);
    protected _graphInfo: ISeqGraphInfo | undefined;
    get graphInfo(): ISeqGraphInfo;
    protected parseConnections(): ISeqGraphInfo;
}
/** Gets canonical monomers for original ones with cyclization marks */
export declare class BilnSeqSplitted extends HelmSplitted {
    getCanonical(posIdx: number): string;
    getOriginal(posIdx: number): string;
    constructor(seqListSplit: string[][], gapOriginalMonomer: string);
    protected parseConnections(): ISeqGraphInfo;
}
export declare class FastaSimpleSeqSplitted implements ISeqSplitted {
    private readonly seqS;
    get length(): number;
    isGap(posIdx: number): boolean;
    getCanonical(posIdx: number): string;
    getOriginal(posIdx: number): string;
    getCanonicalRegion(start: number, end: number): string[];
    getOriginalRegion(start: number, end: number): string[];
    get gapOriginal(): string;
    constructor(seqS: string);
}
/** Stats of sequences with specified splitter func, returns { freq, sameLength }.
 * @param {DG.Column} seqCol
 * @param {number} minLength
 * @param {SplitterFunc} splitter
 * @return { SeqColStats }, sameLength: boolean } stats of column sequences
 */
export declare function getStatsForCol(seqCol: DG.Column<string>, minLength: number, splitter: SplitterFunc): SeqColStats;
/** Split sequence for single character monomers, square brackets multichar monomer names or gap symbol.
 * @param seq object with sequence
 * @param getMonomer Source of the {@link seq} string
 * @return {string[]} array of monomers
 */
export declare const splitterAsFasta: SplitterFunc;
export declare const splitterAsFastaSimple: SplitterFunc;
/** Gets method to split sequence by separator
 * @param separator Monomer separator
 * @param limit
 * @return {SplitterFunc}
 */
export declare function getSplitterWithSeparator(separator: string, limit?: number | undefined): SplitterFunc;
export declare const RNA_HELM_TRIPLET_MONOMER_REG: RegExp;
export declare const RNA_HELM_TERMINAL_PHOSPHATELESS_MONOMER_REG: RegExp;
/** Splits Helm string to monomers, but does not replace monomer names to other notation (e.g. for RNA).
 * Only for linear polymers, does not split RNA for ribose and phosphate monomers.
 * EG byciclic helm: PEPTIDE1{F}|PEPTIDE2{[dI].[Trp_Ome].[Asp_OMe].[Cys_Bn].[meG].[Phe_3Cl].[dD].T.[dI].T.[dK].[aG].[3Pal].[xiIle].[meD].[Ala_tBu]}|PEPTIDE3{L.[Pro_4Me3OH].S.[NMe2Abz].Q.[3Pal].[xiIle].[D-Hyp].[Ala_tBu].[dI].[Trp_Ome].[Asp_OMe].N.[meG].[Phe_34diCl].[Phe_34diCl]}$PEPTIDE2,PEPTIDE2,16:R2-1:R1|PEPTIDE3,PEPTIDE3,16:R2-1:R1|PEPTIDE3,PEPTIDE2,10:R3-1:R3|PEPTIDE1,PEPTIDE2,1:R2-9:R3$$$V2.0
 * Also should support smiles in monomer names, like: PEPTIDE1{[ac].L.N.[*N[C@H](C(=O)*)Cc1ccc(cc1)OP(=O)(O)O |$_R1;;;;;_R2;;;;;;;;;;;;$|].I.D.L.D.L.V.[am]}$$$$
 * @param {string} seq Source string of HELM notation
 * @param {ISeqSource} src Source of the {@link seq} string
 * @return {string[]}
 */
export declare const splitterAsHelm: SplitterFunc;
export declare function splitterAsBiln(seq: string): ISeqSplitted;
/** Func type to shorten a {@link monomerLabel} with length {@link limit} */
export type MonomerToShortFunc = (monomerLabel: string, limit: number) => string;
/** Get splitter method to split sequences to monomers (required for MacromoleculeDifferenceCellRenderer)
 * @param {string} units
 * @param {string} separator
 * @param limit
 * @return {SplitterFunc}
 */
export declare function getSplitter(units: string, separator: string, limit?: number | undefined): SplitterFunc;
/** Convert long monomer names to short ones */
export declare function monomerToShort(amino: string, maxLengthOfMonomer: number): string;
/** */
export declare function getAlphabet(alphabet: ALPHABET): Set<string>;
/** Calculate similarity in current sequence and alphabet.
 * @param {MonomerFreqs} freq
 * @param {Set<string>} alphabet
 * @param {string} gapSymbol
 * @return {number} Cosine similarity
 */
export declare function getAlphabetSimilarity(freq: MonomerFreqs, alphabet: Set<string>, gapSymbol?: string): number;
/** From detectMacromolecule */
export declare function detectAlphabet(freq: MonomerFreqs, candidates: CandidateType[], gapSymbol?: string): string;
export declare function detectHelmAlphabet(freq: MonomerFreqs, candidates: CandidateType[], gapSymbol?: string): string;
/** Selects a suitable palette based on column data
 * @param {DG.Column} seqCol Column to look for a palette
 * @param {number}  minLength minimum length of sequence to detect palette (empty strings are allowed)
 * @return {SeqPalette} Palette corresponding to the alphabet of the sequences in the column
 */
export declare function pickUpPalette(seqCol: DG.Column, seqHelper: ISeqHelper, minLength?: number): SeqPalette;
export declare function getPaletteByType(paletteType: string): SeqPalette;
export declare function pickUpSeqCol(df: DG.DataFrame): DG.Column<string> | null;
export declare function polymerTypeToHelmType(pt: PolymerType): HelmType;
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