sequaljs/dist/modification.d.ts

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

import { BaseBlock } from "./base_block";
/**
 * Represents a value in a ProForma modification string.
 */
export 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[];
    charge: string | null;
    chargeValue: number | null;
    /**
     * Initializes a PipeValue object.
     *
     * @param value - The value of the pipe value.
     * @param valueType - The type of the pipe value.
     * @param originalValue - The original value of the pipe value.
     */
    constructor(value: string, valueType: string, originalValue?: string | null);
    /**
     * Extracts properties from the value.
     * @private
     */
    private _extractProperties;
    /**
     * Returns a string representation of the pipe value.
     * @returns The string representation.
     */
    toString(): string;
    /**
     * Gets the type of the pipe value.
     */
    get type(): string;
    /**
     * Sets the type of the pipe value.
     * @param value - The new type.
     */
    set type(value: string);
    /**
     * Assigns a type to the pipe value.
     * @param value - The type to assign.
     */
    assignType(value: string): void;
}
/**
 * Represents the value of a modification.
 */
export declare class ModificationValue {
    private static KNOWN_SOURCES;
    private _primaryValue;
    private _source;
    private _mass;
    private _pipeValues;
    /**
     * Initializes a ModificationValue object.
     *
     * @param value - The value of the modification.
     * @param mass - The mass of the modification.
     */
    constructor(value: string, mass?: number | null);
    /**
     * Validates a glycan string.
     *
     * @param glycan - The glycan string to validate.
     * @returns True if the glycan is valid, false otherwise.
     */
    static validateGlycan(glycan: string): boolean;
    /**
     * Validates a formula string.
     *
     * @param formula - The formula string to validate.
     * @returns True if the formula is valid, false otherwise.
     */
    static validateFormula(formula: string): boolean;
    /**
     * Gets the localization score of the modification.
     */
    get localizationScore(): number | null;
    /**
     * Parses the value of the modification.
     * @param value - The value to parse.
     * @private
     */
    private _parseValue;
    /**
     * Processes the primary value of the modification.
     * @param value - The primary value to process.
     * @private
     */
    private _processPrimaryValue;
    /**
     * Validates a glycan string.
     * @param glycan - The glycan string to validate.
     * @returns True if the glycan is valid, false otherwise.
     * @private
     */
    private static _validateGlycan;
    /**
     * Validates a custom monosaccharide formula.
     * @param formula - The formula to validate.
     * @returns True if the formula is valid, false otherwise.
     * @private
     */
    private static _validateCustomMonosaccharide;
    /**
     * Validates a formula string.
     * @param formula - The formula to validate.
     * @returns True if the formula is valid, false otherwise.
     * @private
     */
    private static _validateFormula;
    /**
     * Processes a pipe component of the modification.
     * @param component - The pipe component to process.
     * @private
     */
    private _processPipeComponent;
    /**
     * Gets the source of the modification.
     */
    get source(): string | null;
    /**
     * Gets the primary value of the modification.
     */
    get primaryValue(): string;
    /**
     * Gets the mass of the modification.
     */
    get mass(): number | null;
    /**
     * Gets the pipe values of the modification.
     */
    get pipeValues(): PipeValue[];
    /**
     * Gets the info tags of the modification.
     */
    get infoTags(): string[];
    /**
     * Gets the synonyms of the modification.
     */
    get synonyms(): string[];
    /**
     * Gets the observed mass of the modification.
     */
    get observedMass(): number | null;
    /**
     * Gets the ambiguity group of the modification.
     */
    get ambiguityGroup(): string | null;
    /**
     * Checks if the modification is an ambiguity reference.
     */
    get isAmbiguityRef(): boolean;
    /**
     * Checks if the modification is a crosslink reference.
     */
    get isCrosslinkRef(): boolean;
    /**
     * Checks if the modification is a branch reference.
     */
    get isBranchRef(): boolean;
    /**
     * Checks if the modification is a branch.
     */
    get isBranch(): boolean;
    /**
     * Gets the crosslink ID of the modification.
     */
    get crossLinkId(): string | null;
}
/**
 * Represents a modification to a sequence.
 */
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;
    private _isIonType;
    private _positionConstraint;
    private _limitPerPosition;
    private _colocalizeKnown;
    private _colocalizeUnknown;
    /**
     * Initializes a Modification object.
     *
     * @param value - The value of the modification.
     * @param position - The position of the modification in the sequence.
     * @param regexPattern - The regex pattern for the modification.
     * @param fullName - The full name of the modification.
     * @param modType - The type of the modification.
     * @param labile - Whether the modification is labile.
     * @param labilNumber - The labile number of the modification.
     * @param mass - The mass of the modification.
     * @param allFilled - Whether all positions of the modification are filled.
     * @param crosslinkId - The crosslink ID of the modification.
     * @param isCrosslinkRef - Whether the modification is a crosslink reference.
     * @param isBranchRef - Whether the modification is a branch reference.
     * @param isBranch - Whether the modification is a branch.
     * @param ambiguityGroup - The ambiguity group of the modification.
     * @param isAmbiguityRef - Whether the modification is an ambiguity reference.
     * @param inRange - Whether the modification is in a range.
     * @param rangeStart - The start of the range.
     * @param rangeEnd - The end of the range.
     * @param localizationScore - The localization score of the modification.
     * @param modValue - The modification value.
     * @param isIonType - Whether the modification is an ion type.
     * @param positionConstraint - The position constraint of the modification.
     * @param limitPerPosition - The limit per position of the modification.
     * @param colocalizeKnown - Whether to colocalize known modifications.
     * @param colocalizeUnknown - Whether to colocalize unknown modifications.
     */
    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, isIonType?: boolean, positionConstraint?: string[], limitPerPosition?: number, colocalizeKnown?: boolean, colocalizeUnknown?: boolean);
    /**
     * Gets the value of the modification.
     */
    get value(): string;
    /**
     * Sets the value of the modification.
     * @param val - The new value.
     */
    set value(val: string);
    /**
     * Gets the mass of the modification.
     */
    get mass(): number;
    /**
     * Sets the mass of the modification.
     * @param val - The new mass.
     */
    set mass(val: number);
    /**
     * Gets the observed mass of the modification.
     */
    get observedMass(): number | null;
    /**
     * Gets the ambiguity group of the modification.
     */
    get ambiguityGroup(): string | null;
    /**
     * Checks if the modification is an ambiguity reference.
     */
    get isAmbiguityRef(): boolean;
    /**
     * Gets the synonyms of the modification.
     */
    get synonyms(): string[];
    /**
     * Gets the modification value.
     */
    get modValue(): ModificationValue;
    /**
     * Sets the modification value.
     * @param val - The new modification value.
     */
    set modValue(val: ModificationValue);
    /**
     * Gets the info tags of the modification.
     */
    get infoTags(): string[];
    /**
     * Gets the crosslink ID of the modification.
     */
    get crosslinkId(): string | null;
    /**
     * Checks if the modification is a crosslink reference.
     */
    get isCrosslinkRef(): boolean;
    /**
     * Gets the source of the modification.
     */
    get source(): string | null;
    /**
     * Gets the original value of the modification.
     */
    get originalValue(): string;
    /**
     * Gets the regex pattern of the modification.
     */
    get regex(): RegExp | null;
    /**
     * Gets the type of the modification.
     */
    get modType(): string;
    /**
     * Checks if the modification is labile.
     */
    get labile(): boolean;
    /**
     * Gets the labile number of the modification.
     */
    get labileNumber(): number;
    /**
     * Gets the full name of the modification.
     */
    get fullName(): string | null;
    /**
     * Checks if all positions of the modification are filled.
     */
    get allFilled(): boolean;
    /**
     * Checks if the modification is an ion type.
     */
    get isIonType(): boolean;
    /**
     * Gets the position constraint of the modification.
     */
    getPositionConstraint(): string[] | null;
    /**
     * Gets the limit per position of the modification.
     */
    getLimitPerPosition(): number | null;
    /**
     * Checks if to colocalize known modifications.
     */
    getColocalizeKnown(): boolean;
    /**
     * Checks if to colocalize unknown modifications.
     */
    getColocalizeUnknown(): boolean;
    /**
     * Finds the positions of the modification in a sequence.
     *
     * @param seq - The sequence to search in.
     * @yields The start and end positions of the modification.
     */
    findPositions(seq: string): Generator<[number, number], void, unknown>;
    /**
     * Converts the modification to a dictionary representation.
     * @returns A dictionary containing the modification's attributes.
     */
    toDict(): Record<string, any>;
    /**
     * Checks if two modifications are equal.
     * @param other - The other modification to compare with.
     * @returns True if the modifications are equal, false otherwise.
     */
    equals(other: any): boolean;
    /**
     * Generates a hash for the modification.
     * @returns The hash code.
     */
    hashCode(): number;
    /**
     * Returns a string representation of the modification.
     * @returns The string representation.
     */
    toString(): string;
    /**
     * Validates a glycan string.
     *
     * @param glycan - The glycan string to validate.
     * @returns True if the glycan is valid, false otherwise.
     */
    static validateGlycan(glycan: string): boolean;
    /**
     * Validates a formula string.
     *
     * @param formula - The formula string to validate.
     * @returns True if the formula is valid, false otherwise.
     */
    static validateFormula(formula: string): boolean;
    /**
     * Checks if a modification is an ion type modification.
     *
     * @param modStr - The modification string to check.
     * @returns True if the modification is an ion type modification, false otherwise.
     */
    static isIonTypeModification(modStr: string): boolean;
    /**
     * Checks if the modification is a branch reference.
     */
    get isBranchRef(): boolean;
    /**
     * Checks if the modification is a branch.
     */
    get isBranch(): boolean;
    /**
     * Converts the modification to a ProForma string.
     * @returns The ProForma string.
     */
    toProforma(): string;
    /**
     * Checks if the modification has an ambiguity.
     */
    get hasAmbiguity(): boolean;
}
/**
 * Represents a global modification to a sequence.
 */
export declare class GlobalModification extends Modification {
    targetResidues: string[] | null;
    globalModType: string;
    /**
     * Initializes a GlobalModification object.
     *
     * @param value - The value of the modification.
     * @param target_residues - The target residues of the modification.
     * @param mod_type - The type of the modification.
     * @param positionConstraint - The position constraint of the modification.
     * @param limitPerPosition - The limit per position of the modification.
     * @param colocalizeKnown - Whether to colocalize known modifications.
     * @param colocalizeUnknown - Whether to colocalize unknown modifications.
     */
    constructor(value: string, target_residues?: string[] | null, mod_type?: string, positionConstraint?: string[], limitPerPosition?: number, colocalizeKnown?: boolean, colocalizeUnknown?: boolean);
    /**
     * Converts the modification to a ProForma string.
     * @returns The ProForma string.
     */
    toProforma(): string;
    /**
     * Returns a string representation of the modification.
     * @returns The string representation.
     */
    toString(): string;
}
/**
 * Represents a map of modifications in a sequence.
 */
export declare class ModificationMap {
    seq: string;
    ignorePositions: Set<number>;
    modDictByName: Record<string, Modification>;
    modPositionDict: Record<string, number[]>;
    positionToMods: Map<number, Modification[]>;
    /**
     * Initializes a ModificationMap object.
     *
     * @param seq - The sequence.
     * @param mods - The modifications in the sequence.
     * @param ignore_positions - The positions to ignore in the sequence.
     * @param parse_position - Whether to parse the position of the modifications.
     * @param mod_position_dict - A dictionary of modification positions.
     */
    constructor(seq: string, mods?: Modification[], ignore_positions?: Set<number>, parse_position?: boolean, mod_position_dict?: Record<string, number[]>);
    /**
     * Builds the mappings for the modifications.
     * @param mods - The modifications to build the mappings for.
     * @param parse_position - Whether to parse the position of the modifications.
     * @private
     */
    _buildMappings(mods: Modification[], parse_position: boolean): void;
    /**
     * Gets the positions of a modification.
     *
     * @param mod_name - The name of the modification.
     * @returns The positions of the modification.
     */
    getModPositions(mod_name: string): number[] | null;
    /**
     * Gets a modification by name.
     *
     * @param mod_name - The name of the modification.
     * @returns The modification.
     */
    getMod(mod_name: string): Modification | null;
    /**
     * Gets the modifications at a specific position.
     *
     * @param position - The position to get the modifications from.
     * @returns The modifications at the specified position.
     */
    getModsAtPosition(position: number): Modification[];
    /**
     * Checks if a modification exists at a specific position.
     *
     * @param position - The position to check.
     * @param mod_name - The name of the modification.
     * @returns True if the modification exists at the specified position, false otherwise.
     */
    hasModAtPosition(position: number, mod_name?: string): boolean;
    /**
     * Converts the modification map to a dictionary representation.
     * @returns A dictionary containing the modification map's attributes.
     */
    toDict(): Record<string, any>;
}
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