isotopic-distribution - npm Package Compare versions

Comparing version 3.2.0 to 3.2.1

package.json

 {
   "name": "isotopic-distribution",
-  "version": "3.2.0",
+  "version": "3.2.1",
   "description": "Calculate the isotopic distribution of a molecular formula",
-  "main": "lib/index.js",
+  "main": "lib/src/index.js",
   "module": "src/index.js",
@@ -23,5 +23,5 @@ "files": [
   "dependencies": {
-    "chemical-elements": "^2.1.0",
-    "mf-parser": "^3.2.0",
-    "mf-utilities": "^3.2.0",
+    "chemical-elements": "^2.1.1",
+    "mf-parser": "^3.2.1",
+    "mf-utilities": "^3.2.1",
     "spectrum-generator": "^8.0.11"
@@ -32,3 +32,3 @@ },
   },
-  "gitHead": "28dae91d3b42556a23097ee08acfe4061f276ed0"
+  "gitHead": "838f98a30846d4b1721b8ed7aa94a55e854d7521"
 }

src/Distribution.js

@@ -33,3 +33,3 @@ import { closestPointX } from './utils/closestPointX.js';
   get sumY() {
-    if (!isNaN(this.cache.sumY)) return this.cache.sumY;
+    if (!Number.isNaN(this.cache.sumY)) return this.cache.sumY;
     let sumY = 0;
@@ -45,3 +45,3 @@ for (let item of this.array) {
   get minX() {
-    if (!isNaN(this.cache.minX)) return this.cache.minX;
+    if (!Number.isNaN(this.cache.minX)) return this.cache.minX;
     let minX = Number.POSITIVE_INFINITY;
@@ -59,3 +59,3 @@ for (let item of this.array) {
   get maxX() {
-    if (!isNaN(this.cache.maxX)) return this.cache.maxX;
+    if (!Number.isNaN(this.cache.maxX)) return this.cache.maxX;
     let maxX = Number.NEGATIVE_INFINITY;
@@ -73,3 +73,3 @@ for (let item of this.array) {
   get minY() {
-    if (!isNaN(this.cache.minY)) return this.cache.minY;
+    if (!Number.isNaN(this.cache.minY)) return this.cache.minY;
     let minY = Number.POSITIVE_INFINITY;
@@ -87,3 +87,3 @@ for (let item of this.array) {
   get maxY() {
-    if (!isNaN(this.cache.maxY)) return this.cache.maxY;
+    if (!Number.isNaN(this.cache.maxY)) return this.cache.maxY;
     let maxY = Number.NEGATIVE_INFINITY;
@@ -116,4 +116,4 @@ for (let item of this.array) {
 
-  push(point) {
-    this.array.push(point);
+  push(...points) {
+    this.array.push(...points);
     this.emptyCache();
@@ -195,3 +195,3 @@ }
     distCopy.cache = { ...this.cache };
-    distCopy.array = JSON.parse(JSON.stringify(this.array));
+    distCopy.array = structuredClone(this.array);
     return distCopy;
@@ -231,8 +231,8 @@ }
     ySorted: false,
-    minX: NaN,
-    maxX: NaN,
-    minY: NaN,
-    maxY: NaN,
-    sumY: NaN,
+    minX: Number.NaN,
+    maxX: Number.NaN,
+    minY: Number.NaN,
+    maxY: Number.NaN,
+    sumY: Number.NaN,
   };
 }

src/IsotopicDistribution.js

@@ -11,9 +11,9 @@ import { ELECTRON_MASS } from 'chemical-elements';
 
-/**
- * An object containing two arrays
- * @typedef {object} XY
- * @property {number[]} x - The x array
- * @property {number[]} y - The y array
- */
+/** @typedef {import('mf-parser').IsotopesInfo} IsotopesInfo */
+/** @typedef {import('mf-parser').PartInfo} PartInfo */
 
+/** @typedef {import('./IsotopicDistribution.types').XY} XY */
+/** @typedef {import('./IsotopicDistribution.types').IsotopicDistributionPart} IsotopicDistributionPart */
+/** @typedef {import('./IsotopicDistribution.types').IsotopicDistributionOptions} IsotopicDistributionOptions */
+
 /**
@@ -24,15 +24,6 @@ * A class that allows to manage isotopic distribution
   /**
-   * Class that manage isotopic distribution
-   * @param {string|array} value - Molecular formula or an array of parts
-   * @param {object} [options={}]
-   * @param {string} [options.ionizations=''] - string containing a comma separated list of modifications
-   * @param {number} [options.fwhm=0.01] - Amount of Dalton under which 2 peaks are joined
-   * @param {number} [options.maxLines=5000] - Maximal number of lines during calculations
-   * @param {number} [options.minY=1e-8] - Minimal signal height during calculations
-   * @param {boolean} [options.ensureCase=false] - Ensure uppercase / lowercase
-   * @param {number} [options.threshold] - We can filter the result based on the relative height of the peaks
-   * @param {number} [options.limit] - We may define the maximum number of peaks to keep
-   * @param {boolean} [options.allowNeutral=true] - Should we keep the distribution if the molecule has no charge
+   * Class that manages isotopic distribution
+   * @param {string|Array<any>} value - Molecular formula or an array of parts.
+   * @param {IsotopicDistributionOptions} [options]
    */
-
   constructor(value, options = {}) {
@@ -42,3 +33,3 @@ this.threshold = options.threshold;
     if (Array.isArray(value)) {
-      this.parts = JSON.parse(JSON.stringify(value));
+      this.parts = structuredClone(value);
       for (let part of this.parts) {
@@ -53,4 +44,5 @@ part.confidence = 0;
       let mfInfo = mf.getInfo();
-      let ionizations = preprocessIonizations(options.ionizations);
-      let parts = mfInfo.parts || [mfInfo];
+      const ionizations = preprocessIonizations(options.ionizations);
+      /** @type {PartInfo} */
+      const parts = 'parts' in mfInfo ? mfInfo.parts : [mfInfo];
       this.parts = [];
@@ -60,3 +52,3 @@ for (let partOriginal of parts) {
         for (const ionization of ionizations) {
-          let part = JSON.parse(JSON.stringify(partOriginal));
+          let part = structuredClone(partOriginal);
           part.em = part.monoisotopicMass; // TODO: To remove !!! we change the name !?
@@ -87,2 +79,5 @@ part.isotopesInfo = new MF(
 
+  /**
+   * @returns {Array<IsotopicDistributionPart>}
+   */
   getParts() {
@@ -120,5 +115,3 @@ return this.parts;
           if (isotope.number > 0) {
-            const newDistribution = JSON.parse(
-              JSON.stringify(isotope.distribution),
-            );
+            const newDistribution = structuredClone(isotope.distribution);
             if (this.fwhm === MINIMAL_FWHM) {
@@ -143,5 +136,5 @@ // add composition
         if (charge) {
-          totalDistribution.array.forEach((e) => {
+          for (const e of totalDistribution.array) {
             e.x = (e.x - ELECTRON_MASS * charge) / absoluteCharge;
-          });
+          }
         }
@@ -152,4 +145,3 @@
           part.fromX = totalDistribution.array[0].x;
-          part.toX =
-            totalDistribution.array[totalDistribution.array.length - 1].x;
+          part.toX = totalDistribution.array.at(-1).x;
         }
@@ -285,3 +277,3 @@
       // we need to copy the array because we prefer no side effects
-      peaks = JSON.parse(JSON.stringify(peaks));
+      peaks = structuredClone(peaks);
       for (const peak of peaks) {
@@ -341,6 +333,8 @@ peak.y = peak.y / factor;
    * @param {object} [options={}]
-   * @param {number} [options.gaussianWidth=10]
+   * @param {number} [options.gaussianWidth=10] // how good should look the gaussian ? By default we take 10 times the fwhm as number of points
    * @param {number} [options.threshold=0.00001] // minimal height to return point
    * @param {number} [options.maxLength=1e6] // minimal height to return point
    * @param {number} [options.maxValue] // rescale Y to reach maxValue
+   * @param {number} [options.from] // minimal x value, default to the first point - 2
+   * @param {number} [options.to] // maximal x value, default to the last point + 2
    * @param {function} [options.peakWidthFct=(mz)=>(this.fwhm)]
@@ -362,6 +356,6 @@ * @return {XY} isotopic distribution as an object containing 2 properties: x:[] and y:[]
     const from = Math.floor(options.from || points[0].x - 2);
-    const to = Math.ceil(options.to || points[points.length - 1].x + 2);
+    const to = Math.ceil(options.to || points.at(-1).x + 2);
     const nbPoints = Math.round(((to - from) * gaussianWidth) / this.fwhm + 1);
     if (nbPoints > maxLength) {
-      throw Error(
+      throw new Error(
         `Number of points is over the maxLength: ${nbPoints}>${maxLength}`,
@@ -368,0 +362,0 @@ );

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95695

increased by70.9%

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Dependency changes

• Updatedchemical-elements@^2.1.1

• Updatedmf-parser@^3.2.1

• Updatedmf-utilities@^3.2.1