sequaljs/dist/proforma.d.ts

JavaScript/TypeScript library for parsing and manipulating ProForma peptide sequence notation

import { GlobalModification, Modification } from './modification';
/**
 * Represents a sequence ambiguity in a ProForma string.
 */
export declare class SequenceAmbiguity {
    value: string;
    position: number;
    /**
     * Initializes a SequenceAmbiguity object.
     *
     * @param value - The value of the sequence ambiguity.
     * @param position - The position of the sequence ambiguity.
     */
    constructor(value: string, position: number);
    /**
     * Returns a string representation of the sequence ambiguity.
     * @returns The string representation.
     */
    toString(): string;
}
/**
 * A parser for ProForma 2.1 strings.
 */
export declare class ProFormaParser {
    static readonly MASS_SHIFT_PATTERN: RegExp;
    static readonly CROSSLINK_PATTERN: RegExp;
    static readonly CROSSLINK_REF_PATTERN: RegExp;
    static readonly BRANCH_PATTERN: RegExp;
    static readonly BRANCH_REF_PATTERN: RegExp;
    /**
     * Parses a ProForma string.
     *
     * @param proformaStr - The ProForma string to parse.
     * @returns A tuple containing the base sequence, modifications, global modifications, sequence ambiguities, charge information, peptidoform name, peptidoform ion name, and compound ion name.
     */
    static parse(proformaStr: string): [string, Record<number, Modification[]>, GlobalModification[], SequenceAmbiguity[], [number | null, string | null], string | null, string | null, string | null];
    /**
     * Finds the matching closing parenthesis for an opening parenthesis at a given position.
     *
     * @param str - The string to search in.
     * @param startPos - The position of the opening parenthesis.
     * @returns The position of the matching closing parenthesis, or -1 if not found.
     * @private
     */
    static _findBalancedParen(str: string, startPos: number): number;
    /**
     * Finds the matching closing angle bracket for an opening angle bracket at a given position.
     *
     * @param str - The string to search in.
     * @param startPos - The position of the opening angle bracket.
     * @returns The position of the matching closing angle bracket, or -1 if not found.
     * @private
     */
    static _findBalancedAngleBracket(str: string, startPos: number): number;
    /**
     * Finds the matching closing curly brace for an opening curly brace at a given position.
     *
     * @param str - The string to search in.
     * @param startPos - The position of the opening curly brace.
     * @returns The position of the matching closing curly brace, or -1 if not found.
     * @private
     */
    static _findBalancedCurlyBrace(str: string, startPos: number): number;
    /**
     * Creates a modification object from a modification string.
     *
     * @param modStr - The modification string.
     * @param options - The options for creating the modification.
     * @returns The modification object.
     * @private
     */
    static _createModification(modStr: string, options?: {
        isTerminal?: boolean;
        isAmbiguous?: boolean;
        isLabile?: boolean;
        isUnknownPosition?: boolean;
        crosslinkId?: string;
        isCrosslinkRef?: boolean;
        isBranch?: boolean;
        isBranchRef?: boolean;
        isGap?: boolean;
        inRange?: boolean;
        rangeStart?: number;
        rangeEnd?: number;
    }): Modification;
    /**
     * Parses the charge information from a ProForma string.
     *
     * @param proformaStr - The ProForma string to parse.
     * @returns A tuple containing the ProForma string without the charge information, the charge value, and the ionic species.
     */
    static parseChargeInfo(proformaStr: string): [string, number | null, string | null];
}
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