mf-finder - npm Package Compare versions

Comparing version 1.5.0 to 2.0.0

package.json

 {
   "name": "mf-finder",
-  "version": "1.5.0",
+  "version": "2.0.0",
   "description": "Find a molecular formula from a monoisotopic mass",
-  "main": "src/index.js",
   "types": "mfFinder.d.ts",
+  "main": "lib/index.js",
+  "module": "src/index.js",
   "files": [
-    "src"
+    "src",
+    "lib"
   ],
@@ -20,11 +22,11 @@ "repository": {
   },
-  "homepage": "https://github.com/cheminfo/mass-tools/tree/master/packages/mf-finder#readme",
+  "homepage": "https://github.com/cheminfo/mass-tools/tree/main/packages/mf-finder#readme",
   "dependencies": {
-    "atom-sorter": "^1.2.0",
-    "chemical-elements": "^1.3.0",
-    "mf-matcher": "^1.3.0",
-    "mf-parser": "^1.5.0",
-    "mf-utilities": "^1.5.0"
+    "atom-sorter": "^2.0.0",
+    "chemical-elements": "^2.0.0",
+    "mf-matcher": "^2.0.0",
+    "mf-parser": "^2.0.0",
+    "mf-utilities": "^2.0.0"
   },
-  "gitHead": "ade929b07af4e2f0f8b3fe1aaf0df70c50f4b2db"
+  "gitHead": "c6ebfbd64c711f8839a02a43c5708e71a379885b"
 }

src/__tests__/mfFinder.test.js

@@ -1,5 +0,3 @@
-'use strict';
+import { findMFs } from '..';
 
-const findMFs = require('..');
-
 describe('test mf-finder', () => {
@@ -6,0 +4,0 @@ it('basic case', async () => {

src/__tests__/TargetMassCache.test.js

@@ -1,7 +0,5 @@
-'use strict';
+import { preprocessRanges } from 'mf-utilities';
 
-const preprocessRanges = require('mf-utilities/src/preprocessRanges');
+import { TargetMassCache } from '../TargetMassCache';
 
-const TargetMassCache = require('../TargetMassCache');
-
 describe('TargetMassCache', () => {
@@ -8,0 +6,0 @@ it('the result with one atom', () => {

src/index.js

@@ -1,13 +0,11 @@
-'use strict';
+import { atomSorter } from 'atom-sorter';
+import { msemMatcher } from 'mf-matcher';
+import {
+  preprocessIonizations,
+  preprocessRanges,
+  getMsInfo,
+} from 'mf-utilities';
 
-const matcher = require('mf-matcher').msem;
-const atomSorter = require('atom-sorter');
-const getMsInfo = require('mf-utilities/src/getMsInfo');
-const preprocessIonizations = require('mf-utilities/src/preprocessIonizations');
-const preprocessRanges = require('mf-utilities/src/preprocessRanges');
+import { TargetMassCache } from './TargetMassCache';
 
-const TargetMassCache = require('./TargetMassCache');
-
-let targetMassCache;
-
 /**
@@ -36,3 +34,3 @@ * @param {number}        targetMass - Monoisotopic mass
 
-module.exports = async function mfFinder(targetMass, options = {}) {
+export async function findMFs(targetMass, options = {}) {
   const {
@@ -51,3 +49,3 @@ filter = {},
   } = options;
-
+  let targetMassCache;
   const {
@@ -59,3 +57,3 @@ minCharge = Number.MIN_SAFE_INTEGER,
 
-  let filterUnsaturation = unsaturation ? true : false;
+  let filterUnsaturation = !!unsaturation;
   // we calculate not the real unsaturation but the one before dividing by 2 + 1
@@ -106,7 +104,6 @@ let fakeMinUnsaturation =
     if (possibilities.length === 0) return { mfs: [] };
-    targetMassCache = new TargetMassCache(
-      targetMass,
-      possibilities,
-      Object.assign({}, options, { charge: ionization.charge }),
-    );
+    targetMassCache = new TargetMassCache(targetMass, possibilities, {
+      ...options,
+      ...{ charge: ionization.charge },
+    });
 
@@ -121,3 +118,3 @@ let theEnd = false;
 
-    initializePossibilities(possibilities, currentIonization);
+    initializePossibilities(possibilities, currentIonization, targetMassCache);
 
@@ -174,3 +171,3 @@ //  if (DEBUG) console.log('possibilities', possibilities.map((a) => `${a.mf + a.originalMinCount}-${a.originalMaxCount}`));
         if (advancedFilter) {
-          isValid = matcher(newResult, advancedFilter) !== false;
+          isValid = msemMatcher(newResult, advancedFilter) !== false;
         }
@@ -203,2 +200,3 @@ if (isValid) {
               possibilities[currentPosition - 1],
+              targetMassCache,
             );
@@ -226,3 +224,3 @@ } else {
   return result;
-};
+}
 
@@ -252,6 +250,4 @@ /**
           continue;
-        } else {
-          if (current.currentCounts[i] < bestCounts[i]) {
-            continue next;
-          }
+        } else if (current.currentCounts[i] < bestCounts[i]) {
+          continue next;
         }
@@ -304,8 +300,6 @@ }
           result.mf += `${possibility.mf}`;
+        } else if (possibility.mf.match(/^\([^()]*\)$/)) {
+          result.mf += `${possibility.mf}${possibility.currentCount}`;
         } else {
-          if (possibility.mf.match(/^\([^()]*\)$/)) {
-            result.mf += `${possibility.mf}${possibility.currentCount}`;
-          } else {
-            result.mf += `(${possibility.mf})${possibility.currentCount}`;
-          }
+          result.mf += `(${possibility.mf})${possibility.currentCount}`;
         }
@@ -339,3 +333,3 @@ if (result.groups[possibility.mf]) {
 
-function setCurrentMinMax(currentAtom, previousAtom) {
+function setCurrentMinMax(currentAtom, previousAtom, targetMassCache) {
   // the current min max can only be optimize if the charge will not change anymore
@@ -374,7 +368,11 @@ if (currentAtom.innerCharge === true || currentAtom.charge !== 0) {
 
-function initializePossibilities(possibilities, currentIonization) {
+function initializePossibilities(
+  possibilities,
+  currentIonization,
+  targetMassCache,
+) {
   for (let i = 0; i < possibilities.length; i++) {
     if (i === 0) {
       updateCurrentAtom(possibilities[i], currentIonization);
-      setCurrentMinMax(possibilities[i], currentIonization);
+      setCurrentMinMax(possibilities[i], currentIonization, targetMassCache);
     } else {
@@ -381,0 +379,0 @@ updateCurrentAtom(possibilities[i], possibilities[i - 1]);

src/TargetMassCache.js

@@ -1,5 +0,3 @@
-'use strict';
+import { ELECTRON_MASS } from 'chemical-elements';
 
-const ELECTRON_MASS = require('chemical-elements/src/constants').ELECTRON_MASS;
-
 /**
@@ -9,73 +7,70 @@ * returns all the possible neutral mass for a defined experimental (targetMass) mass
 
-let TargetMassCache = function TargetMassCache(
-  targetMass,
-  possibilities,
-  options = {},
-) {
-  const {
-    allowNeutral = false, // msem because em in this case !
-    minCharge = Number.MIN_SAFE_INTEGER,
-    maxCharge = Number.MAX_SAFE_INTEGER,
-    charge = 0,
-    precision = 100,
-  } = options;
-  if (!possibilities || possibilities.length === 0) return {};
+export class TargetMassCache {
+  constructor(targetMass, possibilities, options = {}) {
+    const {
+      allowNeutral = false, // msem because em in this case !
+      minCharge = Number.MIN_SAFE_INTEGER,
+      maxCharge = Number.MAX_SAFE_INTEGER,
+      charge = 0,
+      precision = 100,
+    } = options;
 
-  let firstPossibility = possibilities[0];
-  let currentMinCharge = Math.max(
-    minCharge,
-    firstPossibility.minCharge + charge,
-  );
-  let currentMaxCharge = Math.min(
-    maxCharge,
-    firstPossibility.maxCharge + charge,
-  );
+    if (!possibilities || possibilities.length === 0) return;
 
-  this.minCharge = currentMinCharge;
-  this.maxCharge = currentMaxCharge;
+    let firstPossibility = possibilities[0];
+    let currentMinCharge = Math.max(
+      minCharge,
+      firstPossibility.minCharge + charge,
+    );
+    let currentMaxCharge = Math.min(
+      maxCharge,
+      firstPossibility.maxCharge + charge,
+    );
 
-  let size = this.maxCharge - this.minCharge + 1;
-  this.data = [];
-  let minMass = 0;
-  let maxMass = 0;
-  let range = (targetMass * precision) / 1e6;
-  for (let i = 0; i < size; i++) {
-    let currentCharge = i + this.minCharge;
-    if (currentCharge === 0) {
-      if (allowNeutral) {
-        minMass = targetMass - range;
-        maxMass = targetMass + range;
+    this.minCharge = currentMinCharge;
+    this.maxCharge = currentMaxCharge;
+
+    let size = this.maxCharge - this.minCharge + 1;
+    this.data = [];
+    let minMass = 0;
+    let maxMass = 0;
+    let range = (targetMass * precision) / 1e6;
+    for (let i = 0; i < size; i++) {
+      let currentCharge = i + this.minCharge;
+      if (currentCharge === 0) {
+        if (allowNeutral) {
+          minMass = targetMass - range;
+          maxMass = targetMass + range;
+        } else {
+          minMass = Number.MAX_SAFE_INTEGER;
+          maxMass = Number.MIN_SAFE_INTEGER;
+        }
       } else {
-        minMass = Number.MAX_SAFE_INTEGER;
-        maxMass = Number.MIN_SAFE_INTEGER;
+        minMass =
+          (targetMass - range) * Math.abs(currentCharge) +
+          ELECTRON_MASS * currentCharge;
+        maxMass =
+          (targetMass + range) * Math.abs(currentCharge) +
+          ELECTRON_MASS * currentCharge;
       }
-    } else {
-      minMass =
-        (targetMass - range) * Math.abs(currentCharge) +
-        ELECTRON_MASS * currentCharge;
-      maxMass =
-        (targetMass + range) * Math.abs(currentCharge) +
-        ELECTRON_MASS * currentCharge;
+
+      this.data.push({
+        charge: currentCharge,
+        minMass,
+        maxMass,
+      });
     }
+  }
 
-    this.data.push({
-      charge: currentCharge,
-      minMass,
-      maxMass,
-    });
+  getMinMass(charge) {
+    return this.data[charge - this.minCharge]
+      ? this.data[charge - this.minCharge].minMass
+      : Number.MAX_SAFE_INTEGER;
   }
-};
 
-module.exports = TargetMassCache;
-
-TargetMassCache.prototype.getMinMass = function getMinMass(charge) {
-  return this.data[charge - this.minCharge]
-    ? this.data[charge - this.minCharge].minMass
-    : Number.MAX_SAFE_INTEGER;
-};
-
-TargetMassCache.prototype.getMaxMass = function getMaxMass(charge) {
-  return this.data[charge - this.minCharge]
-    ? this.data[charge - this.minCharge].maxMass
-    : Number.MIN_SAFE_INTEGER;
-};
+  getMaxMass(charge) {
+    return this.data[charge - this.minCharge]
+      ? this.data[charge - this.minCharge].maxMass
+      : Number.MIN_SAFE_INTEGER;
+  }
+}

No alert changes

Improved metrics

Total package byte prevSize

48600

increased by43.17%

Number of package files

8

increased by14.29%

Lines of code

1384

increased by42.09%

Dependency changes

• + Addedatom-sorter@2.2.0(transitive)

• + Addedchemical-elements@2.2.0(transitive)

• + Addedchemical-groups@2.2.2(transitive)

• + Addedmf-matcher@2.1.1(transitive)

• + Addedmf-parser@2.3.1(transitive)

• + Addedmf-utilities@2.0.5(transitive)

• + Addedml-spectra-processing@12.11.0(transitive)

• - Removedatom-sorter@1.2.0(transitive)

• - Removedchemical-elements@1.3.0(transitive)

• - Removedchemical-groups@1.3.0(transitive)

• - Removedmf-matcher@1.3.0(transitive)

• - Removedmf-parser@1.5.0(transitive)

• - Removedmf-utilities@1.5.0(transitive)

• - Removedml-spectra-processing@11.17.0(transitive)

• - Removedpapaparse@5.5.1(transitive)

• Updatedatom-sorter@^2.0.0

• Updatedchemical-elements@^2.0.0

• Updatedmf-matcher@^2.0.0

• Updatedmf-parser@^2.0.0

• Updatedmf-utilities@^2.0.0