ms-spectrum - npm Package Compare versions

Comparing version 1.6.15 to 1.6.16

package.json

 {
   "name": "ms-spectrum",
-  "version": "1.6.15",
+  "version": "1.6.16",
   "description": "A mass spectrum",
-  "main": "src/index.js",
+  "main": "lib/index.js",
+  "module": "src/index.js",
   "files": [
-    "src"
+    "src",
+    "lib"
   ],
@@ -19,21 +21,18 @@ "repository": {
   },
-  "homepage": "https://github.com/cheminfo/mass-tools/tree/master/packages/emdb#readme",
+  "homepage": "https://github.com/cheminfo/mass-tools/tree/main/packages/emdb#readme",
   "dependencies": {
-    "emdb": "^1.13.2",
+    "emdb": "^1.13.3",
     "is-any-array": "^2.0.0",
-    "mf-parser": "^1.4.7",
-    "ml-array-max": "^1.2.4",
-    "ml-array-min": "^1.2.3",
-    "ml-array-normed": "^1.3.7",
-    "ml-gsd": "^10.2.0",
+    "mf-parser": "^1.4.8",
+    "ml-gsd": "^12.1.2",
     "ml-regression-power": "^2.0.0",
-    "ml-spectra-processing": "^11.1.0",
-    "peaks-similarity": "^2.3.1",
-    "xy-parser": "^5.0.2"
+    "ml-spectra-processing": "^11.14.0",
+    "peaks-similarity": "^3.1.1",
+    "xy-parser": "^5.0.3"
   },
   "devDependencies": {
     "jest-matcher-deep-close-to": "^3.0.2",
-    "spectrum-generator": "^8.0.1"
+    "spectrum-generator": "^8.0.6"
   },
-  "gitHead": "09dc5f380182d586410e390df190c8d27101fc3e"
+  "gitHead": "bd2c06e05f2196c5f9c6ff011cf3ef41e1b6a0f9"
 }

src/__tests__/appendPeaksCharge.test.js

@@ -1,5 +0,3 @@
-'use strict';
+import { appendPeaksCharge } from '../appendPeaksCharge';
 
-const appendPeaksCharge = require('../appendPeaksCharge');
-
 describe('test appendPeaksCharge', () => {
@@ -6,0 +4,0 @@ it('custom options', () => {

src/__tests__/getBestPeaks.test.js

@@ -1,5 +0,3 @@
-'use strict';
+import { getBestPeaks } from '../getBestPeaks';
 
-const getBestPeaks = require('../getBestPeaks');
-
 describe('test getBestPeaks', () => {
@@ -6,0 +4,0 @@ let peaks = [

src/__tests__/getFragmentPeaks.test.js

@@ -1,5 +0,3 @@
-'use strict';
+import { getFragmentPeaks } from '../getFragmentPeaks';
 
-const getFragmentPeaks = require('../getFragmentPeaks');
-
 describe('test getFragmentPeaks', () => {
@@ -6,0 +4,0 @@ let peaks = [

src/__tests__/getMassRemainder.test.js

@@ -1,5 +0,3 @@
-'use strict';
+import { getMassRemainder } from '../getMassRemainder';
 
-const getMassRemainder = require('../getMassRemainder');
-
 describe('test getMassRemainder', () => {
@@ -6,0 +4,0 @@ let spectrum = {

src/__tests__/getPeakChargeBySimilarity.test.js

@@ -1,6 +0,4 @@
-'use strict';
+import { Spectrum } from '../Spectrum';
+import { getPeakChargeBySimilarity } from '../getPeakChargeBySimilarity';
 
-const Spectrum = require('../Spectrum');
-const getPeakChargeBySimilarity = require('../getPeakChargeBySimilarity');
-
 describe('test getPeakChargeBySimilarity', () => {
@@ -7,0 +5,0 @@ let data = {

src/__tests__/getPeaks.test.js

@@ -1,5 +0,3 @@
-'use strict';
+import { getPeaks } from '../getPeaks';
 
-const getPeaks = require('../getPeaks');
-
 describe('test getPeaks', () => {
@@ -6,0 +4,0 @@ let peaks = [

src/__tests__/isContinuous.test.js

@@ -1,10 +0,8 @@
-'use strict';
+import { readFileSync } from 'fs';
+import { join } from 'path';
 
-const { readFileSync } = require('fs');
-const { join } = require('path');
+import { parseXY } from 'xy-parser';
 
-const { parseXY } = require('xy-parser');
+import { isContinuous } from '../isContinuous';
 
-const isContinuous = require('../isContinuous');
-
 describe('test isContinuous', () => {
@@ -11,0 +9,0 @@ it('to small', () => {

src/__tests__/peaksWidth.test.js

@@ -1,5 +0,3 @@
-'use strict';
+import { peaksWidth } from '../peaksWidth';
 
-const peaksWidth = require('../peaksWidth');
-
 describe('test test peakWidth', () => {
@@ -6,0 +4,0 @@ it('five peaks', () => {

src/__tests__/Spectrum.appendPeaksCharge.test.js

@@ -1,8 +0,6 @@
-'use strict';
+import { readFileSync } from 'fs';
+import { join } from 'path';
 
-const { readFileSync } = require('fs');
-const { join } = require('path');
+import { fromText } from '../Spectrum';
 
-const Spectrum = require('../Spectrum');
-
 describe('test appendPeakCharge on Spectrum', () => {
@@ -14,3 +12,3 @@ let chargedText = readFileSync(
   it('multicharged', () => {
-    let spectrum = Spectrum.fromText(chargedText);
+    let spectrum = fromText(chargedText);
     let peaks = spectrum.peakPicking();
@@ -17,0 +15,0 @@ peaks = peaks.filter((peak) => peak.y > 1000);

src/__tests__/Spectrum.fromPeaks.test.js

@@ -1,5 +0,3 @@
-'use strict';
+import { fromPeaks } from '../Spectrum';
 
-const Spectrum = require('../Spectrum');
-
 test('Spectrum fromPeaks', () => {
@@ -39,5 +37,5 @@ const peaks = [
 
-  const spectrum = Spectrum.fromPeaks(peaks);
+  const spectrum = fromPeaks(peaks);
 
   expect(Object.keys(spectrum.data)).toStrictEqual(['x', 'y', 'composition']);
 });

src/__tests__/Spectrum.jsgraph.test.js

@@ -1,5 +0,3 @@
-'use strict';
+import { JsGraph } from '..';
 
-const Spectrum = require('../Spectrum');
-
 describe('test Spectrum JSGraph', () => {
@@ -15,3 +13,3 @@ it('getAnnotation', async () => {
     ];
-    let annotations = await Spectrum.JsGraph.getPeaksAnnotation(peaks);
+    let annotations = await JsGraph.getPeaksAnnotation(peaks);
 
@@ -18,0 +16,0 @@ expect(annotations).toHaveLength(3);

src/__tests__/Spectrum.peakPicking.test.js

@@ -1,12 +0,10 @@
-'use strict';
+import { readFileSync } from 'fs';
+import { join } from 'path';
 
-const { readFileSync } = require('fs');
-const { join } = require('path');
+import { fromText } from '../Spectrum';
 
-const Spectrum = require('../Spectrum');
-
 describe('peakPicking on Spectrum', () => {
   let chargedText = readFileSync(join(__dirname, 'data/lowres2.txt'), 'utf8');
   it('lowres2', () => {
-    let spectrum = Spectrum.fromText(chargedText);
+    let spectrum = fromText(chargedText);
     let peaks = spectrum.peakPicking();
@@ -13,0 +11,0 @@

src/__tests__/Spectrum.test.js

@@ -1,9 +0,6 @@
-/* eslint-disable jest/no-if */
-'use strict';
+import { toBeDeepCloseTo } from 'jest-matcher-deep-close-to';
+import { generateSpectrum } from 'spectrum-generator';
 
-const { toBeDeepCloseTo } = require('jest-matcher-deep-close-to');
-const generateSpectrum = require('spectrum-generator').generateSpectrum;
+import { Spectrum, fromText } from '../Spectrum';
 
-const Spectrum = require('../Spectrum');
-
 expect.extend({ toBeDeepCloseTo });
@@ -14,3 +11,3 @@
     expect(() => {
-      Spectrum(1);
+      new Spectrum(1);
     }).toThrow('Spectrum data must be an object');
@@ -26,3 +23,6 @@ });
       new Spectrum({ x: [1, 2, 3, 4], y: [1, 1, 1, 1] }).normedY().data,
-    ).toStrictEqual({ x: [1, 2, 3, 4], y: [0.25, 0.25, 0.25, 0.25] });
+    ).toStrictEqual({
+      x: [1, 2, 3, 4],
+      y: Float64Array.from([0.25, 0.25, 0.25, 0.25]),
+    });
   });
@@ -89,3 +89,3 @@
 
-  it('gsd realtop', () => {
+  it('peak picking and same y value', () => {
     const peaks = [{ x: 5, y: 10000, width: 0.2 }];
@@ -107,10 +107,10 @@
   });
+});
 
-  it('fromText', () => {
-    let spectrum = Spectrum.fromText(`Title of spectrum
+test('fromText', () => {
+  let spectrum = fromText(`Title of spectrum
     1 2
     2 3
     3 4`);
-    expect(spectrum.data).toStrictEqual({ x: [1, 2, 3], y: [2, 3, 4] });
-  });
+  expect(spectrum.data).toStrictEqual({ x: [1, 2, 3], y: [2, 3, 4] });
 });

src/appendPeaksCharge.js

@@ -1,3 +0,1 @@
-'use strict';
-
 /**
@@ -14,3 +12,3 @@ * @param {object}   [options={}]
 
-function appendPeaksCharge(peaks, options = {}) {
+export function appendPeaksCharge(peaks, options = {}) {
   let {
@@ -140,3 +138,1 @@ precision = 100,
 }
-
-module.exports = appendPeaksCharge;

src/getBestPeaks.js

@@ -1,8 +0,3 @@
-'use strict';
+import { xyObjectMaxXPoint, xyObjectMinXPoint } from 'ml-spectra-processing';
 
-const {
-  xyObjectMaxXPoint,
-  xyObjectMinXPoint,
-} = require('ml-spectra-processing');
-
 /**
@@ -25,3 +20,3 @@ * Filter the array by taking the higher peaks and only
 
-function getBestPeaks(peaks, options = {}) {
+export function getBestPeaks(peaks, options = {}) {
   const {
@@ -98,3 +93,1 @@ searchMonoisotopicRatio = 0,
 }
-
-module.exports = getBestPeaks;

src/getFragmentPeaks.js

@@ -1,7 +0,6 @@
-'use strict';
+import { EMDB } from 'emdb';
+import { MF } from 'mf-parser';
 
-const { MF } = require('mf-parser');
+import { getPeaks } from './getPeaks.js';
 
-const getPeaks = require('./getPeaks.js');
-
 /**
@@ -21,4 +20,4 @@ * Filter the array of peaks
 
-async function getFragmentPeaks(peaks, mf, options = {}) {
-  const emdb = new (require('emdb'))();
+export async function getFragmentPeaks(peaks, mf, options = {}) {
+  const emdb = new EMDB();
 
@@ -44,3 +43,1 @@ const { ionizations = '', precision } = options;
 }
-
-module.exports = getFragmentPeaks;

src/getMassRemainder.js

@@ -1,5 +0,3 @@
-'use strict';
+import { xySortX, xyJoinX } from 'ml-spectra-processing';
 
-const { xySortX, xyJoinX } = require('ml-spectra-processing');
-
 /**
@@ -13,3 +11,3 @@ * Remove an integer number of time the specifiedd monoisotopic mass
  */
-function getMassRemainder(spectrum, mass, options = {}) {
+export function getMassRemainder(spectrum, mass, options = {}) {
   const { delta = 0.001 } = options;
@@ -25,3 +23,1 @@ const x = spectrum.x.slice();
 }
-
-module.exports = getMassRemainder;

src/getPeakChargeBySimilarity.js

@@ -1,5 +0,3 @@
-'use strict';
+import { Comparator } from 'peaks-similarity';
 
-const Similarity = require('peaks-similarity');
-
 /**
@@ -21,3 +19,3 @@ * @param {object}   [options={}]
 
-function getPeakChargeBySimilarity(spectrum, targetMass, options = {}) {
+export function getPeakChargeBySimilarity(spectrum, targetMass, options = {}) {
   let { similarity = {}, minCharge = 1, maxCharge = 10 } = options;
@@ -42,3 +40,3 @@ let { zone = {}, widthFunction } = similarity;
   let experimentalData = spectrum.data;
-  let similarityProcessor = new Similarity(similarity);
+  let similarityProcessor = new Comparator(similarity);
   similarityProcessor.setPeaks1([experimentalData.x, experimentalData.y]);
@@ -97,3 +95,1 @@
 }
-
-module.exports = getPeakChargeBySimilarity;

src/getPeaks.js

@@ -1,8 +0,6 @@
-'use strict';
-
-const {
+import {
   xyObjectMaxXPoint,
   xyObjectMinXPoint,
   xyObjectSumY,
-} = require('ml-spectra-processing');
+} from 'ml-spectra-processing';
 
@@ -21,3 +19,3 @@ /**
 
-function getPeaks(peaks, options = {}) {
+export function getPeaks(peaks, options = {}) {
   const {
@@ -54,3 +52,1 @@ from = xyObjectMinXPoint(peaks).x,
 }
-
-module.exports = getPeaks;

src/index.js

@@ -1,6 +0,5 @@
-'use strict';
+export * from './Spectrum.js';
+export * from './getPeaks.js';
+export * from './getBestPeaks.js';
 
-module.exports.Spectrum = require('./Spectrum');
-
-module.exports.getPeaks = require('./getPeaks');
-module.exports.getBestPeaks = require('./getBestPeaks');
+export * from './jsgraph/index.js';

src/isContinuous.js

@@ -1,4 +0,2 @@
-'use strict';
-
-const max = require('ml-array-max/lib/index');
+import { xMaxValue } from 'ml-spectra-processing';
 /**
@@ -17,3 +15,3 @@ * When a spectrum is continous ?
 
-function isContinuous(spectrum, options = {}) {
+export function isContinuous(spectrum, options = {}) {
   const {
@@ -24,3 +22,3 @@ minLength = 100,
   } = options;
-  const minHeight = max(spectrum.data.y) * relativeHeightThreshold;
+  const minHeight = xMaxValue(spectrum.data.y) * relativeHeightThreshold;
   const minRadio = 1 / maxDeltaRatio;
@@ -66,3 +64,1 @@ const maxRatio = 1 * maxDeltaRatio;
 }
-
-module.exports = isContinuous;

src/jsgraph/__tests__/getPeaksAnnotation.test.js

@@ -1,5 +0,3 @@
-'use strict';
+import { getPeaksAnnotation } from '../getPeaksAnnotation';
 
-const getPeaksAnnotation = require('../getPeaksAnnotation');
-
 describe('test getPeaksAnnotation', () => {
@@ -6,0 +4,0 @@ let peaks = [

src/jsgraph/getPeaksAnnotation.js

@@ -1,2 +0,2 @@
-'use strict';
+import { EMDB } from 'emdb';
 
@@ -20,6 +20,6 @@ /**
 
-async function getPeaksAnnotation(bestPeaks, options = {}) {
-  const emdb = new (require('emdb'))();
+export async function getPeaksAnnotation(bestPeaks, options = {}) {
+  const emdb = new EMDB();
 
-  options = Object.assign({ limit: 5, precision: 100 }, options);
+  options = { limit: 5, precision: 100, ...options };
 
@@ -133,6 +133,7 @@ let {
           // neutral loss
-          let currentMfPrefs = Object.assign({}, mfPrefs, {
+          let currentMfPrefs = {
+            ...mfPrefs,
             allowNeutral: true,
             ionizations: '',
-          });
+          };
           // we need to deal with the precision and increase it
@@ -196,3 +197,1 @@ currentMfPrefs.precision =
 }
-
-module.exports = getPeaksAnnotation;

src/jsgraph/index.js

@@ -1,5 +0,5 @@
-'use strict';
+import { getPeaksAnnotation } from './getPeaksAnnotation.js';
 
-module.exports = {
-  getPeaksAnnotation: require('./getPeaksAnnotation'),
+export const JsGraph = {
+  getPeaksAnnotation,
 };

src/peakPicking.js

@@ -1,8 +0,6 @@
-'use strict';
+import { gsd } from 'ml-gsd';
+import { xyEnsureGrowingX } from 'ml-spectra-processing';
 
-const gsd = require('ml-gsd').gsd;
-const { xyEnsureGrowingX } = require('ml-spectra-processing');
+import { appendPeaksCharge } from './appendPeaksCharge';
 
-const appendPeaksCharge = require('./appendPeaksCharge');
-
 /**
@@ -21,3 +19,3 @@ * Filter the array of peaks
 
-function peakPicking(spectrum, options = {}) {
+export function peakPicking(spectrum, options = {}) {
   const { charge: chargeOptions = {} } = options;
@@ -69,3 +67,1 @@ if (!spectrum.peaks || spectrum.peaks.length === 0) {
 }
-
-module.exports = peakPicking;

src/peaksWidth.js

@@ -1,8 +0,5 @@
-'use strict';
+import Regression from 'ml-regression-power';
+import { xMaxValue, xMinValue } from 'ml-spectra-processing';
 
-const max = require('ml-array-max/lib/index');
-const min = require('ml-array-min/lib/index');
-const Regression = require('ml-regression-power/lib/index.js');
-
-function peaksWidth(peaks) {
+export function peaksWidth(peaks) {
   let xs = peaks.map((peak) => peak.x);
@@ -25,4 +22,4 @@ let widths = peaks.map((peak) => peak.width);
 
-  let from = min(xs);
-  let to = max(xs);
+  let from = xMinValue(xs);
+  let to = xMaxValue(xs);
 
@@ -49,3 +46,1 @@ let regressionChart = { x: [], y: [] };
 }
-
-module.exports = peaksWidth;

src/Spectrum.js

@@ -1,150 +0,145 @@
-'use strict';
+import { isAnyArray } from 'is-any-array';
+import { xMaxValue, xNormed } from 'ml-spectra-processing';
+import { parseXY } from 'xy-parser';
 
-const { isAnyArray } = require('is-any-array');
-const max = require('ml-array-max/lib/index.js');
-const normed = require('ml-array-normed/lib/index.js');
-const { parseXY } = require('xy-parser');
+import { getBestPeaks } from './getBestPeaks';
+import { getFragmentPeaks } from './getFragmentPeaks';
+import { getMassRemainder } from './getMassRemainder';
+import { getPeakChargeBySimilarity } from './getPeakChargeBySimilarity';
+import { getPeaks } from './getPeaks';
+import { isContinuous } from './isContinuous';
+import { peakPicking } from './peakPicking';
+import { peaksWidth } from './peaksWidth';
 
-const getBestPeaks = require('./getBestPeaks');
-const getFragmentPeaks = require('./getFragmentPeaks');
-const getMassRemainder = require('./getMassRemainder');
-const getPeakChargeBySimilarity = require('./getPeakChargeBySimilarity');
-const getPeaks = require('./getPeaks');
-const isContinuous = require('./isContinuous');
-const peakPicking = require('./peakPicking');
-const peaksWidth = require('./peaksWidth');
+/**
+ * Class dealing with mass spectra and peak picking
+ */
+export class Spectrum {
+  constructor(data = { x: [], y: [] }) {
+    if (
+      typeof data !== 'object' ||
+      !isAnyArray(data.x) ||
+      !isAnyArray(data.y)
+    ) {
+      throw new TypeError('Spectrum data must be an object with x:[], y:[]');
+    }
+    this.data = {}; // we make a copy so that we can add new properties
+    for (let key in data) {
+      this.data[key] = data[key];
+    }
+    Object.defineProperty(this.data, 'xOriginal', {
+      enumerable: false,
+      writable: true,
+    });
+    this.cache = {};
+    this.peaks = [];
+  }
 
-function Spectrum(data = { x: [], y: [] }) {
-  if (typeof data !== 'object' || !isAnyArray(data.x) || !isAnyArray(data.y)) {
-    throw new TypeError('Spectrum data must be an object with x:[], y:[]');
+  maxY() {
+    return xMaxValue(this.data.y);
   }
-  this.data = {}; // we make a copy so that we can add new properties
-  for (let key in data) {
-    this.data[key] = data[key];
+
+  sumY() {
+    if (!this.cache.sumY) {
+      this.cache.sumY = this.data.y.reduce(
+        (previous, current) => previous + current,
+        0,
+      );
+    }
+    return this.cache.sumY;
   }
-  Object.defineProperty(this.data, 'xOriginal', {
-    enumerable: false,
-    writable: true,
-  });
-  this.cache = {};
-  this.peaks = [];
-}
 
-Spectrum.fromPeaks = function fromPeaks(peaks) {
-  if (peaks.length === 0) return new Spectrum();
-  const data = {};
-  for (let key of Object.keys(peaks[0])) {
-    data[key] = peaks.map((peak) => peak[key]);
+  scaleY(intensity = 1) {
+    let basePeak = this.maxY() / intensity;
+    this.data.y = this.data.y.map((y) => y / basePeak);
+    return this;
   }
-  return new Spectrum(data);
-};
 
-Spectrum.fromText = function fromText(text) {
-  const data = parseXY(text);
-  return new Spectrum(data);
-};
+  rescaleX(callback) {
+    this.ensureOriginalX();
 
-Spectrum.prototype.maxY = function maxY() {
-  return max(this.data.y);
-};
+    for (let i = 0; i < this.data.x.length; i++) {
+      this.data.x[i] = callback(this.data.xOriginal[i]);
+    }
 
-Spectrum.prototype.sumY = function sumY() {
-  if (!this.cache.sumY) {
-    this.cache.sumY = this.data.y.reduce(
-      (previous, current) => previous + current,
-      0,
-    );
+    return this;
   }
-  return this.cache.sumY;
-};
 
-Spectrum.prototype.scaleY = function scaleY(intensity = 1) {
-  let basePeak = this.maxY() / intensity;
-  this.data.y = this.data.y.map((y) => y / basePeak);
-  return this;
-};
+  ensureOriginalX() {
+    if (!this.data.xOriginal) {
+      this.data.xOriginal = this.data.x.slice(0);
+    }
+  }
 
-Spectrum.prototype.rescaleX = function rescaleX(callback) {
-  this.ensureOriginalX();
+  normedY(total = 1) {
+    this.data.y = xNormed(this.data.y);
+    if (total !== 1) {
+      this.data.y = this.data.y.map((y) => y * total);
+    }
+    return this;
+  }
 
-  for (let i = 0; i < this.data.x.length; i++) {
-    this.data.x[i] = callback(this.data.xOriginal[i]);
+  peakPicking() {
+    peakPicking(this);
+    return this.peaks;
   }
 
-  return this;
-};
-
-Spectrum.prototype.ensureOriginalX = function ensureOriginalX() {
-  if (!this.data.xOriginal) {
-    this.data.xOriginal = this.data.x.slice(0);
+  peaksWidth() {
+    peakPicking(this);
+    return peaksWidth(this.peaks);
   }
-};
 
-Spectrum.prototype.normedY = function normedY(total = 1) {
-  this.data.y = normed(this.data.y);
-  if (total !== 1) {
-    this.data.y = this.data.y.map((y) => y * total);
+  getBestPeaks(options) {
+    peakPicking(this);
+    return getBestPeaks(this.peaks, options);
   }
-  return this;
-};
 
-Spectrum.prototype.peakPicking = function peakPickingFct() {
-  peakPicking(this);
-  return this.peaks;
-};
-
-Spectrum.prototype.peaksWidth = function peaksWidthFct() {
-  peakPicking(this);
-  return peaksWidth(this.peaks);
-};
-
-Spectrum.prototype.getBestPeaks = function getBestPeaksFct(options) {
-  peakPicking(this);
-  return getBestPeaks(this.peaks, options);
-};
-
-Spectrum.prototype.getPeakChargeBySimilarity =
-  function getPeakChargeBySimilarityFct(targetMass, options) {
+  getPeakChargeBySimilarity(targetMass, options) {
     return getPeakChargeBySimilarity(this, targetMass, options);
-  };
+  }
 
-Spectrum.prototype.getPeaks = function getPeaksFct(options) {
-  peakPicking(this);
-  return getPeaks(this.peaks, options);
-};
+  getPeaks(options) {
+    peakPicking(this);
+    return getPeaks(this.peaks, options);
+  }
 
-/**
- * Returns also peaks possible for a specific molecular formula
- * @example
- *  const spectrum = new Spectrum({x:[], y:[]})
- *  await spectrum.getFragmentPeaks();
- * @param {string} mf
- * @param {object} options
- * @returns
- */
-Spectrum.prototype.getFragmentPeaks = function getFragmentPeaksFct(
-  mf,
-  options,
-) {
-  peakPicking(this);
-  return getFragmentPeaks(this.peaks, mf, options);
-};
+  /**
+   * Returns also peaks possible for a specific molecular formula
+   * @example
+   *  const spectrum = new Spectrum({x:[], y:[]})
+   *  await spectrum.getFragmentPeaks();
+   * @param {string} mf
+   * @param {object} options
+   * @returns
+   */
+  getFragmentPeaksFct(mf, options) {
+    peakPicking(this);
+    return getFragmentPeaks(this.peaks, mf, options);
+  }
 
-Spectrum.prototype.isContinuous = function isContinuousFct() {
-  return isContinuous(this);
-};
+  isContinuous() {
+    return isContinuous(this);
+  }
 
-/**
- * Remove an integer number of time the specifiedd monoisotopic mass
- * Mass remainder analysis (MARA): https://doi.org/10.1021/acs.analchem.7b04730
- */
-Spectrum.prototype.getMassRemainder = function getMassRemainderFct(
-  mass,
-  options = {},
-) {
-  return getMassRemainder(this.data, mass, options);
-};
+  /**
+   * Remove an integer number of time the specifiedd monoisotopic mass
+   * Mass remainder analysis (MARA): https://doi.org/10.1021/acs.analchem.7b04730
+   */
+  getMassRemainderFct(mass, options = {}) {
+    return getMassRemainder(this.data, mass, options);
+  }
+}
 
-Spectrum.JsGraph = Spectrum.prototype.JsGraph = require('./jsgraph/index');
+export function fromPeaks(peaks) {
+  if (peaks.length === 0) return new Spectrum();
+  const data = {};
+  for (let key of Object.keys(peaks[0])) {
+    data[key] = peaks.map((peak) => peak[key]);
+  }
+  return new Spectrum(data);
+}
 
-module.exports = Spectrum;
+export function fromText(text) {
+  const data = parseXY(text);
+  return new Spectrum(data);
+}

No alert changes

Improved metrics

Total package byte prevSize

5360156

increased by0.49%

Dependency count

8

decreased by-27.27%

Number of package files

38

increased by2.7%

Lines of code

2253

increased by55.81%

Worsened metrics

Number of medium supply chain risk alerts

2

increased by100%

Dependency changes

• + Added@lukeed/csprng@1.1.0(transitive)

• + Added@lukeed/uuid@2.0.1(transitive)

• + Addedml-direct@1.0.0(transitive)

• + Addedml-gsd@12.1.8(transitive)

• + Addedml-savitzky-golay-generalized@4.2.0(transitive)

• + Addedml-spectra-fitting@4.2.4(transitive)

• + Addedpeaks-similarity@3.1.1(transitive)

• - Removedml-array-max@^1.2.4

• - Removedml-array-min@^1.2.3

• - Removedml-array-normed@^1.3.7

• Updatedemdb@^1.13.3

• Updatedmf-parser@^1.4.8

• Updatedml-gsd@^12.1.2

• Updatedml-spectra-processing@^11.14.0

• Updatedpeaks-similarity@^3.1.1

• Updatedxy-parser@^5.0.3