nucleotide/lib/src/generateFragments.js

Deal with nucleotides and molecular formula

"use strict";
Object.defineProperty(exports, "__esModule", { value: true });
exports.generateFragments = generateFragments;
const addFiveTerm_1 = require("./addFiveTerm");
const addFiveTermBaseLoss_1 = require("./addFiveTermBaseLoss");
const addInternalTerm_1 = require("./addInternalTerm");
const addThreeTerm_1 = require("./addThreeTerm");
const addThreeTermBaseLoss_1 = require("./addThreeTermBaseLoss");
function generateFragments(mf, options) {
    if (options === undefined) {
        options = {
            a: false,
            ab: false,
            b: false,
            c: false,
            d: false,
            dh2o: false,
            w: false,
            x: false,
            y: false,
            z: false,
            zch2: false,
            aw: false,
            bw: false,
            abw: false,
            aby: false,
            abcdBaseLoss: false,
            wxyzBaseLoss: false,
        };
    }
    let mfs = [];
    // need to allow 0-9 to deal with neutral loss
    let mfparts = mf
        .replaceAll(/([\d)a-z])([A-Z][a-z](?=[a-z]))/g, '$1 $2')
        .split(/ /);
    let fiveTerm = '';
    let threeTerm = '';
    if (mfparts[0].startsWith('(')) {
        fiveTerm += mfparts[0];
        mfparts = mfparts.splice(1);
    }
    if (mfparts.at(-1).includes('(')) {
        threeTerm += mfparts.at(-1).replace(/^[^()]*/, '');
        mfparts[mfparts.length - 1] = mfparts.at(-1).replace(/\(.*/, '');
    }
    for (let ter5 = 1; ter5 < mfparts.length; ter5++) {
        fiveTerm += mfparts[ter5 - 1];
        threeTerm = mfparts[mfparts.length - ter5] + threeTerm;
        (0, addFiveTerm_1.addFiveTerm)(mfs, fiveTerm, ter5, options);
        (0, addFiveTermBaseLoss_1.addFiveTermBaseLoss)(mfs, fiveTerm, ter5, options);
        (0, addThreeTerm_1.addThreeTerm)(mfs, threeTerm, ter5, options);
        (0, addThreeTermBaseLoss_1.addThreeTermBaseLoss)(mfs, threeTerm, ter5, options);
    }
    for (let i = 1; i < mfparts.length - 1; i++) {
        let internal = '';
        for (let j = i; j < mfparts.length - 1; j++) {
            internal += mfparts[j];
            if (j > i) {
                (0, addInternalTerm_1.addInternalTerm)(mfs, internal, mfparts.length - i, j + 1, options);
            }
        }
    }
    return mfs;
}
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