sequaljs/dist/modification.d.ts

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

import { BaseBlock } from "./base_block";
declare class PipeValue {
    static SYNONYM: string;
    static INFO_TAG: string;
    static MASS: string;
    static OBSERVED_MASS: string;
    static CROSSLINK: string;
    static BRANCH: string;
    static AMBIGUITY: string;
    static GLYCAN: string;
    static GAP: string;
    static FORMULA: string;
    value: string;
    private _type;
    crosslinkId: string | null;
    isBranch: boolean;
    isBranchRef: boolean;
    isCrosslinkRef: boolean;
    ambiguityGroup: string | null;
    isAmbiguityRef: boolean;
    localizationScore: number | null;
    source: string | null;
    originalValue: string | null;
    mass: number | null;
    observedMass: number | null;
    isValidGlycan: boolean;
    isValidFormula: boolean;
    assignedTypes: string[];
    constructor(value: string, valueType: string, originalValue?: string | null);
    private _extractProperties;
    toString(): string;
    get type(): string;
    set type(value: string);
    assignType(value: string): void;
}
export declare class ModificationValue {
    private static KNOWN_SOURCES;
    private _primaryValue;
    private _source;
    private _mass;
    private _pipeValues;
    constructor(value: string, mass?: number | null);
    static validateGlycan(glycan: string): boolean;
    static validateFormula(formula: string): boolean;
    get localizationScore(): number | null;
    private _parseValue;
    private _processPrimaryValue;
    private static _validateGlycan;
    private static _validateFormula;
    private _processPipeComponent;
    get source(): string | null;
    get primaryValue(): string;
    get mass(): number | null;
    get pipeValues(): PipeValue[];
    get infoTags(): string[];
    get synonyms(): string[];
    get observedMass(): number | null;
    get ambiguityGroup(): string | null;
    get isAmbiguityRef(): boolean;
    get isCrosslinkRef(): boolean;
    get isBranchRef(): boolean;
    get isBranch(): boolean;
    get crossLinkId(): string | null;
}
export declare class Modification extends BaseBlock {
    static readonly KNOWN_SOURCES: Set<string>;
    private _source;
    private _originalValue;
    private _crosslinkId;
    private _isCrosslinkRef;
    private _isBranchRef;
    private _isBranch;
    private _isAmbiguityRef;
    private _ambiguityGroup;
    private _regex;
    private _modType;
    private _labile;
    private _labileNumber;
    private _fullName;
    private _allFilled;
    private _modValue;
    inRange: boolean;
    rangeStart: number | null;
    rangeEnd: number | null;
    localizationScore: number | null;
    constructor(value: string, position?: number, regexPattern?: string, fullName?: string, modType?: string, labile?: boolean, labilNumber?: number, mass?: number, allFilled?: boolean, crosslinkId?: string, isCrosslinkRef?: boolean, isBranchRef?: boolean, isBranch?: boolean, ambiguityGroup?: string, isAmbiguityRef?: boolean, inRange?: boolean, rangeStart?: number, rangeEnd?: number, localizationScore?: number, modValue?: ModificationValue);
    get value(): string;
    set value(val: string);
    get mass(): number;
    set mass(val: number);
    get observedMass(): number | null;
    get ambiguityGroup(): string | null;
    get isAmbiguityRef(): boolean;
    get synonyms(): string[];
    get modValue(): ModificationValue;
    set modValue(val: ModificationValue);
    get infoTags(): string[];
    get crosslinkId(): string | null;
    get isCrosslinkRef(): boolean;
    get source(): string | null;
    get originalValue(): string;
    get regex(): RegExp | null;
    get modType(): string;
    get labile(): boolean;
    get labileNumber(): number;
    get fullName(): string | null;
    get allFilled(): boolean;
    findPositions(seq: string): Generator<[number, number], void, unknown>;
    toDict(): Record<string, any>;
    equals(other: any): boolean;
    hashCode(): number;
    toString(): string;
    static validateGlycan(glycan: string): boolean;
    static validateFormula(formula: string): boolean;
    get isBranchRef(): boolean;
    get isBranch(): boolean;
    toProforma(): string;
    get hasAmbiguity(): boolean;
}
export declare class GlobalModification extends Modification {
    targetResidues: string[] | null;
    globalModType: string;
    constructor(value: string, target_residues?: string[] | null, mod_type?: string);
    toProforma(): string;
    toString(): string;
}
export declare class ModificationMap {
    seq: string;
    ignorePositions: Set<number>;
    modDictByName: Record<string, Modification>;
    modPositionDict: Record<string, number[]>;
    positionToMods: Map<number, Modification[]>;
    constructor(seq: string, mods?: Modification[], ignore_positions?: Set<number>, parse_position?: boolean, mod_position_dict?: Record<string, number[]>);
    _buildMappings(mods: Modification[], parse_position: boolean): void;
    getModPositions(mod_name: string): number[] | null;
    getMod(mod_name: string): Modification | null;
    getModsAtPosition(position: number): Modification[];
    hasModAtPosition(position: number, mod_name?: string): boolean;
    toDict(): Record<string, any>;
}
export {};
//# sourceMappingURL=modification.d.ts.map