mf-finder - npm Package Compare versions

Comparing version 1.4.2 to 1.5.0

package.json

 {
   "name": "mf-finder",
-  "version": "1.4.2",
+  "version": "1.5.0",
   "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",
-    "lib"
+    "src"
   ],
@@ -22,11 +20,11 @@ "repository": {
   },
-  "homepage": "https://github.com/cheminfo/mass-tools/tree/main/packages/mf-finder#readme",
+  "homepage": "https://github.com/cheminfo/mass-tools/tree/master/packages/mf-finder#readme",
   "dependencies": {
-    "atom-sorter": "^1.1.11",
-    "chemical-elements": "^1.2.4",
-    "mf-matcher": "^1.2.8",
-    "mf-parser": "^1.4.8",
-    "mf-utilities": "^1.4.2"
+    "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"
   },
-  "gitHead": "bd2c06e05f2196c5f9c6ff011cf3ef41e1b6a0f9"
+  "gitHead": "ade929b07af4e2f0f8b3fe1aaf0df70c50f4b2db"
 }

src/__tests__/mfFinder.test.js

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

src/__tests__/TargetMassCache.test.js

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

src/index.js

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

src/TargetMassCache.js

@@ -1,3 +0,5 @@
-import { ELECTRON_MASS } from 'chemical-elements';
+'use strict';
 
+const ELECTRON_MASS = require('chemical-elements/src/constants').ELECTRON_MASS;
+
 /**
@@ -7,70 +9,73 @@ * returns all the possible neutral mass for a defined experimental (targetMass) mass
 
-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 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 {};
 
-    if (!possibilities || possibilities.length === 0) return;
+  let firstPossibility = possibilities[0];
+  let currentMinCharge = Math.max(
+    minCharge,
+    firstPossibility.minCharge + charge,
+  );
+  let currentMaxCharge = Math.min(
+    maxCharge,
+    firstPossibility.maxCharge + charge,
+  );
 
-    let firstPossibility = possibilities[0];
-    let currentMinCharge = Math.max(
-      minCharge,
-      firstPossibility.minCharge + charge,
-    );
-    let currentMaxCharge = Math.min(
-      maxCharge,
-      firstPossibility.maxCharge + charge,
-    );
+  this.minCharge = currentMinCharge;
+  this.maxCharge = currentMaxCharge;
 
-    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;
-        }
+  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 =
-          (targetMass - range) * Math.abs(currentCharge) +
-          ELECTRON_MASS * currentCharge;
-        maxMass =
-          (targetMass + range) * Math.abs(currentCharge) +
-          ELECTRON_MASS * currentCharge;
+        minMass = Number.MAX_SAFE_INTEGER;
+        maxMass = Number.MIN_SAFE_INTEGER;
       }
-
-      this.data.push({
-        charge: currentCharge,
-        minMass,
-        maxMass,
-      });
+    } else {
+      minMass =
+        (targetMass - range) * Math.abs(currentCharge) +
+        ELECTRON_MASS * currentCharge;
+      maxMass =
+        (targetMass + range) * Math.abs(currentCharge) +
+        ELECTRON_MASS * currentCharge;
     }
-  }
 
-  getMinMass(charge) {
-    return this.data[charge - this.minCharge]
-      ? this.data[charge - this.minCharge].minMass
-      : Number.MAX_SAFE_INTEGER;
+    this.data.push({
+      charge: currentCharge,
+      minMass,
+      maxMass,
+    });
   }
+};
 
-  getMaxMass(charge) {
-    return this.data[charge - this.minCharge]
-      ? this.data[charge - this.minCharge].maxMass
-      : Number.MIN_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;
+};

No alert changes

Worsened metrics

Total package byte prevSize

33945

decreased by-30.16%

Number of package files

7

decreased by-12.5%

Lines of code

974

decreased by-29.62%

Dependency changes

• Updatedatom-sorter@^1.2.0

• Updatedchemical-elements@^1.3.0

• Updatedmf-matcher@^1.3.0

• Updatedmf-parser@^1.5.0

• Updatedmf-utilities@^1.5.0