isotopic-distribution - npm Package Compare versions

Comparing version 1.4.15 to 1.4.16

package.json

 {
   "name": "isotopic-distribution",
-  "version": "1.4.15",
+  "version": "1.4.16",
   "description": "Calculate the isotopic distribution of a molecular formula",
-  "main": "src/index.js",
+  "main": "lib/index.js",
+  "module": "src/index.js",
   "files": [
-    "src"
+    "src",
+    "lib"
   ],
@@ -19,8 +21,8 @@ "repository": {
   },
-  "homepage": "https://github.com/cheminfo/mass-tools/tree/master/packages/isotopic-distribution#readme",
+  "homepage": "https://github.com/cheminfo/mass-tools/tree/main/packages/isotopic-distribution#readme",
   "dependencies": {
-    "chemical-elements": "^1.2.3",
-    "mf-parser": "^1.4.7",
-    "mf-utilities": "^1.4.1",
-    "spectrum-generator": "^8.0.1"
+    "chemical-elements": "^1.2.4",
+    "mf-parser": "^1.4.8",
+    "mf-utilities": "^1.4.2",
+    "spectrum-generator": "^8.0.6"
   },
@@ -30,3 +32,3 @@ "devDependencies": {
   },
-  "gitHead": "09dc5f380182d586410e390df190c8d27101fc3e"
+  "gitHead": "bd2c06e05f2196c5f9c6ff011cf3ef41e1b6a0f9"
 }

README.md

@@ -15,5 +15,5 @@ # isotopic-distribution
 ```js
-import library from 'isotopic-distribution';
+const { IsotopicDistribution } = require('isotopic-distribution');
 
-const result = library(args);
+const isotopicDistribution = new IsotopicDistribution('C10H20');
 // result is ...
@@ -20,0 +20,0 @@ ```

src/__tests__/append.test.js

@@ -1,5 +0,3 @@
-'use strict';
+import { Distribution } from '../Distribution.js';
 
-const Distribution = require('../Distribution.js');
-
 describe('test distribution append', () => {
@@ -6,0 +4,0 @@ it('should append one distribution to another', () => {

src/__tests__/closestPointX.test.js

@@ -1,20 +0,16 @@
-'use strict';
+import { Distribution } from '../Distribution.js';
 
-const Distribution = require('../Distribution.js');
+test('distribution closestPointX', () => {
+  let distribution = new Distribution();
+  distribution.push({ x: 1, y: 2 });
+  distribution.push({ x: 2, y: 3 });
+  distribution.push({ x: 3, y: 3 });
+  distribution.push({ x: 4, y: 3 });
 
-describe('test distribution closestPointX', () => {
-  it('should yield the right point', () => {
-    let dist = new Distribution();
-    dist.push({ x: 1, y: 2 });
-    dist.push({ x: 2, y: 3 });
-    dist.push({ x: 3, y: 3 });
-    dist.push({ x: 4, y: 3 });
-
-    expect(dist.closestPointX(2)).toStrictEqual({ x: 2, y: 3 });
-    expect(dist.closestPointX(0)).toStrictEqual({ x: 1, y: 2 });
-    expect(dist.closestPointX(2.1)).toStrictEqual({ x: 2, y: 3 });
-    expect(dist.closestPointX(1.9)).toStrictEqual({ x: 2, y: 3 });
-    expect(dist.closestPointX(5.1)).toStrictEqual({ x: 4, y: 3 });
-    expect(dist.closestPointX(4.9)).toStrictEqual({ x: 4, y: 3 });
-  });
+  expect(distribution.closestPointX(2)).toStrictEqual({ x: 2, y: 3 });
+  expect(distribution.closestPointX(0)).toStrictEqual({ x: 1, y: 2 });
+  expect(distribution.closestPointX(2.1)).toStrictEqual({ x: 2, y: 3 });
+  expect(distribution.closestPointX(1.9)).toStrictEqual({ x: 2, y: 3 });
+  expect(distribution.closestPointX(5.1)).toStrictEqual({ x: 4, y: 3 });
+  expect(distribution.closestPointX(4.9)).toStrictEqual({ x: 4, y: 3 });
 });

src/__tests__/getGaussian.test.js

@@ -1,5 +0,3 @@
-'use strict';
+import { IsotopicDistribution } from '../IsotopicDistribution.js';
 
-const IsotopicDistribution = require('../IsotopicDistribution.js');
-
 describe('test isotopicDistribution', () => {
@@ -6,0 +4,0 @@ it('create distribution of C1 with default options', () => {

src/__tests__/isotopicDistribution.exact.test.js

@@ -1,9 +0,7 @@
-'use strict';
+import { toBeDeepCloseTo } from 'jest-matcher-deep-close-to';
 
-const { toBeDeepCloseTo } = require('jest-matcher-deep-close-to');
+import { IsotopicDistribution } from '..';
 
 expect.extend({ toBeDeepCloseTo });
 
-const IsotopicDistribution = require('../IsotopicDistribution.js');
-
 describe('isotopicDistribution with composition', () => {
@@ -10,0 +8,0 @@ it('CN', () => {

src/__tests__/isotopicDistribution.test.js

@@ -1,5 +0,3 @@
-'use strict';
+import { IsotopicDistribution } from '..';
 
-const IsotopicDistribution = require('../IsotopicDistribution.js');
-
 describe('test isotopicDistribution', () => {
@@ -6,0 +4,0 @@ it('create distribution of CH0', () => {

src/__tests__/multiply.test.js

@@ -1,5 +0,3 @@
-'use strict';
+import { Distribution } from '../Distribution.js';
 
-const Distribution = require('../Distribution.js');
-
 describe('test distribution multiply', () => {
@@ -6,0 +4,0 @@ it('should yield the product', () => {

src/__tests__/normalize.test.js

@@ -1,13 +0,11 @@
-'use strict';
+import { Distribution } from '../Distribution.js';
 
-const Distribution = require('../Distribution.js');
-
 describe('test distribution normalize', () => {
   it('should yield the product', () => {
-    let dist = new Distribution();
-    dist.push({ x: 1, y: 2 });
-    dist.push({ x: 2, y: 3 });
-    dist.normalize();
+    let distribution = new Distribution();
+    distribution.push({ x: 1, y: 2 });
+    distribution.push({ x: 2, y: 3 });
+    distribution.normalize();
 
-    expect(dist.array).toStrictEqual([
+    expect(distribution.array).toStrictEqual([
       { x: 1, y: 0.4 },
@@ -14,0 +12,0 @@ { x: 2, y: 0.6 },

src/__tests__/power.test.js

@@ -1,12 +0,10 @@
-'use strict';
+import { Distribution } from '../Distribution.js';
 
-const Distribution = require('../Distribution.js');
-
 describe('test distribution power', () => {
   it('power 2', () => {
-    let dist = new Distribution();
-    dist.push({ x: 1, y: 2 });
-    dist.push({ x: 2, y: 3 });
-    dist.power(2);
-    expect(dist.array).toStrictEqual([
+    let distribution = new Distribution();
+    distribution.push({ x: 1, y: 2 });
+    distribution.push({ x: 2, y: 3 });
+    distribution.power(2);
+    expect(distribution.array).toStrictEqual([
       { x: 2, y: 4 },
@@ -19,14 +17,14 @@ { x: 3, y: 12 },
   it('power 3 - 1 peak', () => {
-    let dist = new Distribution();
-    dist.push({ x: 1, y: 1 });
-    dist.power(3);
-    expect(dist.array).toStrictEqual([{ x: 3, y: 1 }]);
+    let distribution = new Distribution();
+    distribution.push({ x: 1, y: 1 });
+    distribution.power(3);
+    expect(distribution.array).toStrictEqual([{ x: 3, y: 1 }]);
   });
 
   it('power 3 - 2 peaks', () => {
-    let dist = new Distribution();
-    dist.push({ x: 1, y: 1 });
-    dist.push({ x: 2, y: 1 });
-    dist.power(3);
-    expect(dist.array).toStrictEqual([
+    let distribution = new Distribution();
+    distribution.push({ x: 1, y: 1 });
+    distribution.push({ x: 2, y: 1 });
+    distribution.power(3);
+    expect(distribution.array).toStrictEqual([
       { x: 3, y: 1 },
@@ -40,16 +38,16 @@ { x: 4, y: 3 },
   it('power 1000 - 2 peaks', () => {
-    let dist = new Distribution();
-    dist.push({ x: 1, y: 1 });
-    dist.push({ x: 2, y: 1 });
-    dist.power(1000);
-    expect(dist.array).toHaveLength(1001);
-    expect(dist.array[1]).toStrictEqual({ x: 1001, y: 1000 });
+    let distribution = new Distribution();
+    distribution.push({ x: 1, y: 1 });
+    distribution.push({ x: 2, y: 1 });
+    distribution.power(1000);
+    expect(distribution.array).toHaveLength(1001);
+    expect(distribution.array[1]).toStrictEqual({ x: 1001, y: 1000 });
   });
 
   it('power 100000 - 10 peaks', () => {
-    let dist = new Distribution();
-    dist.push({ x: 1, y: 0.5 });
-    dist.push({ x: 2, y: 0.5 });
-    dist.power(100000);
-    let sum = dist.array.reduce((s, a) => s + a.y, 0);
+    let distribution = new Distribution();
+    distribution.push({ x: 1, y: 0.5 });
+    distribution.push({ x: 2, y: 0.5 });
+    distribution.power(100000);
+    let sum = distribution.array.reduce((s, a) => s + a.y, 0);
     expect(sum).toBeGreaterThan(0.99);
@@ -56,0 +54,0 @@ expect(sum).toBeLessThan(1);

src/__tests__/square.test.js

@@ -1,12 +0,10 @@
-'use strict';
+import { Distribution } from '../Distribution.js';
 
-const Distribution = require('../Distribution.js');
-
 describe('test array-object-xy square', () => {
   it('should yield the product', () => {
-    let dist = new Distribution();
-    dist.push({ x: 1, y: 2 });
-    dist.push({ x: 2, y: 3 });
-    dist.square();
-    expect(dist.array).toStrictEqual([
+    let distribution = new Distribution();
+    distribution.push({ x: 1, y: 2 });
+    distribution.push({ x: 2, y: 3 });
+    distribution.square();
+    expect(distribution.array).toStrictEqual([
       { x: 2, y: 4 },
@@ -13,0 +11,0 @@ { x: 3, y: 12 },

src/__tests__/topY.test.js

@@ -1,15 +0,13 @@
-'use strict';
+import { Distribution } from '../Distribution.js';
 
-const Distribution = require('../Distribution.js');
-
 describe('test distribution topY', () => {
   it('create array', () => {
-    let dist = new Distribution();
-    dist.push({ x: 1, y: 2 });
-    dist.push({ x: 2, y: 3 });
-    dist.push({ x: 2, y: 1 });
-    dist.push({ x: 2, y: 4 });
-    dist.topY(2);
+    let distribution = new Distribution();
+    distribution.push({ x: 1, y: 2 });
+    distribution.push({ x: 2, y: 3 });
+    distribution.push({ x: 2, y: 1 });
+    distribution.push({ x: 2, y: 4 });
+    distribution.topY(2);
 
-    expect(dist.array).toStrictEqual([
+    expect(distribution.array).toStrictEqual([
       { x: 2, y: 4 },
@@ -16,0 +14,0 @@ { x: 2, y: 3 },

src/Distribution.js

@@ -1,4 +0,10 @@
-'use strict';
+import { closestPointX } from './utils/closestPointX.js';
+import { joinX } from './utils/joinX.js';
+import { multiply } from './utils/multiply.js';
+import { power } from './utils/power.js';
 
-class Distribution {
+/**
+ * Internal class to deal with isotopic distribution calculations
+ */
+export class Distribution {
   constructor(array) {
@@ -47,58 +53,109 @@ if (Array.isArray(array)) {
   }
-}
 
-Distribution.prototype.multiplyY = function multiplyY(value) {
-  this.array.forEach((item) => (item.y *= value));
-};
+  multiplyY(value) {
+    this.array.forEach((item) => (item.y *= value));
+  }
 
-Distribution.prototype.setArray = function setArray(array) {
-  this.array = array;
-  this.xSorted = false;
-  this.ySorted = false;
-};
+  setArray(array) {
+    this.array = array;
+    this.xSorted = false;
+    this.ySorted = false;
+  }
 
-Distribution.prototype.move = function move(other) {
-  this.xSorted = other.xSorted;
-  this.ySorted = other.ySorted;
-  this.array = other.array;
-};
+  move(other) {
+    this.xSorted = other.xSorted;
+    this.ySorted = other.ySorted;
+    this.array = other.array;
+  }
 
-Distribution.prototype.copy = function copy() {
-  let distCopy = new this.constructor();
-  distCopy.xSorted = this.xSorted;
-  distCopy.ySorted = this.ySorted;
-  distCopy.array = JSON.parse(JSON.stringify(this.array));
-  return distCopy;
-};
+  push(point) {
+    this.array.push(point);
 
-Distribution.prototype.push = function push(point) {
-  this.array.push(point);
+    this.xSorted = false;
+    this.ySorted = false;
+  }
 
-  this.xSorted = false;
-  this.ySorted = false;
-};
+  sortX() {
+    this.ySorted = false;
+    if (this.xSorted) return this;
+    this.array.sort((a, b) => a.x - b.x);
+    this.xSorted = true;
+    return this;
+  }
 
-/**
- * Appen another distribution to the current distribution
- * @param {*} distribution
- */
-Distribution.prototype.append = function append(distribution) {
-  for (let item of distribution.array) {
-    this.array.push(item);
+  sortY() {
+    this.xSorted = false;
+    if (this.ySorted) return this;
+    this.array.sort((a, b) => b.y - a.y);
+    this.ySorted = true;
+    return this;
   }
-  this.xSorted = false;
-  this.ySorted = false;
-};
 
-Distribution.prototype.sortX = require('./utils/sortX.js');
-Distribution.prototype.sortY = require('./utils/sortY.js');
-Distribution.prototype.joinX = require('./utils/joinX.js');
-Distribution.prototype.topY = require('./utils/topY.js');
-Distribution.prototype.maxToOne = require('./utils/maxToOne.js');
-Distribution.prototype.multiply = require('./utils/multiply.js');
-Distribution.prototype.square = require('./utils/square.js');
-Distribution.prototype.power = require('./utils/power.js');
-Distribution.prototype.normalize = require('./utils/normalize.js');
-Distribution.prototype.closestPointX = require('./utils/closestPointX.js');
+  normalize() {
+    let sum = 0;
+    for (let item of this.array) {
+      sum += item.y;
+    }
+    for (let item of this.array) {
+      item.y /= sum;
+    }
+    return this;
+  }
 
-module.exports = Distribution;
+  topY(limit) {
+    if (!limit) return this;
+    if (this.array.length <= limit) return this;
+    this.sortY();
+    this.array.splice(limit);
+    return this;
+  }
+
+  square(options = {}) {
+    return this.multiply(this, options);
+  }
+
+  multiply(b, options) {
+    return multiply(this, b, options);
+  }
+
+  power(p, options) {
+    return power(this, p, options);
+  }
+
+  copy() {
+    let distCopy = new Distribution();
+    distCopy.xSorted = this.xSorted;
+    distCopy.ySorted = this.ySorted;
+    distCopy.array = JSON.parse(JSON.stringify(this.array));
+    return distCopy;
+  }
+
+  maxToOne() {
+    if (this.array.length === 0) return this;
+    let currentMax = this.array[0].y;
+    for (let item of this.array) {
+      if (item.y > currentMax) currentMax = item.y;
+    }
+    for (let item of this.array) {
+      item.y /= currentMax;
+    }
+    return this;
+  }
+
+  joinX(threshold) {
+    return joinX(this, threshold);
+  }
+
+  append(distribution) {
+    for (let item of distribution.array) {
+      this.array.push(item);
+    }
+    this.xSorted = false;
+    this.ySorted = false;
+  }
+
+  closestPointX(target) {
+    this.sortX();
+    return closestPointX(this.array, target);
+  }
+}

src/index.js

@@ -1,5 +0,1 @@
-'use strict';
-
-const IsotopicDistribution = require('./IsotopicDistribution');
-
-module.exports = IsotopicDistribution;
+export * from './IsotopicDistribution';

src/IsotopicDistribution.js

@@ -1,12 +0,9 @@
-'use strict';
+import { ELECTRON_MASS } from 'chemical-elements';
+import { MF } from 'mf-parser';
+import { preprocessIonizations, getMsInfo } from 'mf-utilities';
+import { SpectrumGenerator } from 'spectrum-generator';
 
-const ELECTRON_MASS = require('chemical-elements').ELECTRON_MASS;
-const MF = require('mf-parser').MF;
-const getMsInfo = require('mf-utilities/src/getMsInfo');
-const preprocessIonizations = require('mf-utilities/src/preprocessIonizations');
-const SpectrumGenerator = require('spectrum-generator').SpectrumGenerator;
+import { Distribution } from './Distribution';
+import { getDerivedCompositionInfo } from './utils/getDerivedCompositionInfo';
 
-const Distribution = require('./Distribution');
-const getDerivedCompositionInfo = require('./utils/getDerivedCompositionInfo');
-
 const MINIMAL_FWHM = 1e-8;
@@ -21,3 +18,6 @@
 
-class IsotopicDistribution {
+/**
+ * A class that allows to manage isotopic distribution
+ */
+export class IsotopicDistribution {
   /**
@@ -340,3 +340,1 @@ * Class that manage isotopic distribution
 }
-
-module.exports = IsotopicDistribution;

src/utils/__tests__/getDerivedCompositionInfo.test.js

@@ -1,5 +0,3 @@
-'use strict';
+const { getDerivedCompositionInfo } = require('../getDerivedCompositionInfo');
 
-const getDerivedCompositionInfo = require('../getDerivedCompositionInfo');
-
 test('getDerivedCompositionInfo', () => {
@@ -6,0 +4,0 @@ const data = {

src/utils/closestPointX.js

@@ -1,32 +0,25 @@
-'use strict';
-
-module.exports = function closestPointX(target) {
-  this.sortX();
-
+export function closestPointX(array, target) {
   let low = 0;
-  let high = this.array.length - 1;
+  let high = array.length - 1;
   let middle = 0;
   while (high - low > 1) {
     middle = low + ((high - low) >> 1);
-    if (this.array[middle].x < target) {
+    if (array[middle].x < target) {
       low = middle;
-    } else if (this.array[middle].x > target) {
+    } else if (array[middle].x > target) {
       high = middle;
     } else {
-      return this.array[middle];
+      return array[middle];
     }
   }
 
-  if (low < this.array.length - 1) {
-    if (
-      Math.abs(target - this.array[low].x) <
-      Math.abs(this.array[low + 1].x - target)
-    ) {
-      return this.array[low];
+  if (low < array.length - 1) {
+    if (Math.abs(target - array[low].x) < Math.abs(array[low + 1].x - target)) {
+      return array[low];
     } else {
-      return this.array[low + 1];
+      return array[low + 1];
     }
   } else {
-    return this.array[low];
+    return array[low];
   }
-};
+}

src/utils/getDerivedCompositionInfo.js

@@ -1,7 +0,5 @@
-'use strict';
+import { stableIsotopesObject } from 'chemical-elements';
+import { subscript, superscript } from 'mf-parser';
 
-const { stableIsotopesObject } = require('chemical-elements');
-const { subscript, superscript } = require('mf-parser');
-
-function getDerivedCompositionInfo(composition) {
+export function getDerivedCompositionInfo(composition) {
   const shortComposition = {};
@@ -33,3 +31,1 @@ let label = '';
 }
-
-module.exports = getDerivedCompositionInfo;

src/utils/joinX.js

@@ -1,3 +0,1 @@
-'use strict';
-
 /**
@@ -7,10 +5,10 @@ * Join x values if there are similar
 
-module.exports = function joinX(threshold = Number.EPSILON) {
+export function joinX(self, threshold = Number.EPSILON) {
   // when we join we will use the center of mass
-  if (this.array.length === 0) return [];
-  this.sortX();
-  let current = this.array[0];
+  if (self.array.length === 0) return [];
+  self.sortX();
+  let current = self.array[0];
   let result = [current];
-  for (let i = 1; i < this.array.length; i++) {
-    const item = this.array[i];
+  for (let i = 1; i < self.array.length; i++) {
+    const item = self.array[i];
     if (item.x - current.x <= threshold) {
@@ -30,5 +28,5 @@ // weighted sum
   }
-  this.array = result;
-  this.ySorted = false;
-  return this;
-};
+  self.array = result;
+  self.ySorted = false;
+  return self;
+}

src/utils/maxToOne.js

@@ -1,3 +0,1 @@
-'use strict';
-
 /**
@@ -7,3 +5,3 @@ * Sum of Y to 1
 
-module.exports = function maxToOne() {
+export function maxToOne() {
   if (this.array.length === 0) return this;
@@ -18,2 +16,2 @@ let currentMax = this.array[0].y;
   return this;
-};
+}

src/utils/multiply.js

@@ -1,11 +0,9 @@
-'use strict';
-
-module.exports = function multiply(b, options = {}) {
+export function multiply(a, b, options = {}) {
   const { minY = 1e-8, maxLines = 5000, deltaX = 1e-2 } = options;
-  const result = new this.constructor();
+  const result = new a.constructor();
 
-  this.sortY();
+  a.sortY();
   b.sortY();
 
-  for (let entryA of this.array) {
+  for (let entryA of a.array) {
     for (let entryB of b.array) {
@@ -29,5 +27,5 @@ let y = entryA.y * entryB.y;
   result.topY(maxLines);
-  this.move(result);
-  return this;
-};
+  a.move(result);
+  return a;
+}
 
@@ -34,0 +32,0 @@ function calculateComposition(entryA, entryB) {

src/utils/power.js

@@ -1,17 +0,15 @@
-'use strict';
-
 // https://en.wikipedia.org/wiki/Exponentiation_by_squaring
 
-module.exports = function power(p, options = {}) {
+export function power(a, p, options = {}) {
   if (p <= 0) throw new Error('power must be larger than 0');
-  if (p === 1) return this;
+  if (p === 1) return a;
   if (p === 2) {
-    return this.square();
+    return a.square();
   }
 
   p--;
-  let base = this.copy(); // linear time
+  let base = a.copy(); // linear time
   while (p !== 0) {
     if ((p & 1) !== 0) {
-      this.multiply(base, options); // executed <= log2(p) times
+      a.multiply(base, options); // executed <= log2(p) times
     }
@@ -22,3 +20,3 @@ p >>= 1;
 
-  return this;
-};
+  return a;
+}

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Improved metrics

Total package byte prevSize

68129

increased by34.6%

Lines of code

1936

increased by40.29%

Worsened metrics

Number of package files

26

decreased by-13.33%

Dependency changes

• Updatedchemical-elements@^1.2.4

• Updatedmf-parser@^1.4.8

• Updatedmf-utilities@^1.4.2

• Updatedspectrum-generator@^8.0.6