mf-parser - npm Package Compare versions

Comparing version 3.2.0 to 3.2.1

package.json

 {
   "name": "mf-parser",
-  "version": "3.2.0",
+  "version": "3.2.1",
   "description": "Parse a molecular formula",
-  "main": "lib/index.js",
+  "main": "lib/src/index.js",
   "module": "src/index.js",
@@ -23,6 +23,5 @@ "files": [
   "dependencies": {
-    "atom-sorter": "^2.1.0",
-    "chemical-elements": "^2.1.0",
-    "chemical-groups": "^2.2.0",
-    "mf-utilities": "^3.2.0"
+    "atom-sorter": "^2.1.1",
+    "chemical-elements": "^2.1.1",
+    "chemical-groups": "^2.2.1"
   },
@@ -32,3 +31,3 @@ "devDependencies": {
   },
-  "gitHead": "28dae91d3b42556a23097ee08acfe4061f276ed0"
+  "gitHead": "838f98a30846d4b1721b8ed7aa94a55e854d7521"
 }

src/ensureCase.js

 import { elementsObject } from 'chemical-elements';
 
-const elements = Object.keys(elementsObject).sort(
-  (a, b) => b.length - a.length,
+const elements = new Set(
+  Object.keys(elementsObject).sort((a, b) => b.length - a.length),
 );
@@ -15,2 +15,3 @@
   for (let i = 0; i < mf.length; i++) {
+    // eslint-disable-next-line unicorn/prefer-code-point
     if (mf.charCodeAt(i) > 64 && mf.charCodeAt(i) < 91) {
@@ -20,3 +21,3 @@ return mf;
   }
-  let parts = mf.replace(/([a-z]*)([^a-z]*)/g, '$1 $2 ').split(/ +/);
+  let parts = mf.replaceAll(/([a-z]*)([^a-z]*)/g, '$1 $2 ').split(/ +/);
   for (let i = 0; i < parts.length; i++) {
@@ -28,3 +29,3 @@ if (parts[i].match(/^[a-z]$/)) {
       for (let j = 0; j < parts[i].length; j++) {
-        let two = parts[i].substr(j, 2);
+        let two = parts[i].slice(j, j + 2);
         let one = parts[i].charAt(j).toUpperCase();
@@ -39,6 +40,6 @@ if (
           two = two.charAt(0).toUpperCase() + two.charAt(1);
-          if (elements.includes(two)) {
+          if (elements.has(two)) {
             newPart += two;
             j++;
-          } else if (elements.includes(one)) {
+          } else if (elements.has(one)) {
             newPart += one;
@@ -45,0 +46,0 @@ } else {

src/MF.js

@@ -15,2 +15,6 @@ import { ensureCase } from './ensureCase';
 
+/** @typedef {import('./util/getIsotopesInfo.types').IsotopesInfo} IsotopesInfo */
+/** @typedef {import('./util/getInfo.types').PartInfo} PartInfo */
+/** @typedef {import('./util/getInfo.types').PartInfoWithParts} PartInfoWithParts */
+
 /**
@@ -70,2 +74,3 @@ * Class allowing to deal with molecular formula and derived information
    * @param {string} [options.msemFieldName='observedMonoisotopicMass'] name of the observed monoisotopic mass field
+   * @returns {PartInfo|PartInfoWithParts}
    */
@@ -105,2 +110,3 @@ getInfo(options = {}) {
    * Returns an array with each atom and isotopic composition
+   * @returns {IsotopesInfo}
    */
@@ -107,0 +113,0 @@ getIsotopesInfo(options = {}) {

src/parse.js

@@ -0,1 +1,3 @@
+/* eslint-disable unicorn/prefer-code-point */
+
 import { Kind } from './Kind';
@@ -21,7 +23,4 @@ import { parseCharge } from './util/parseCharge';
     while (this.i < mf.length) {
-      if (
-        this.result.length > 0 &&
-        this.result[this.result.length - 1].kind !== Kind.TEXT
-      ) {
-        lastKind = this.result[this.result.length - 1].kind;
+      if (this.result.length > 0 && this.result.at(-1).kind !== Kind.TEXT) {
+        lastKind = this.result.at(-1).kind;
       }
@@ -56,3 +55,3 @@ let char = mf.charAt(this.i);
           }
-          this.result[this.result.length - 1].value = value.from;
+          this.result.at(-1).value = value.from;
         } else if (value.to) {
@@ -115,3 +114,3 @@ this.result.push({
         if (lastKind === Kind.ATOM) {
-          let lastResult = this.result[this.result.length - 1];
+          let lastResult = this.result.at(-1);
           lastResult.kind = Kind.ISOTOPE_RATIO;
@@ -147,3 +146,3 @@ lastResult.value = {
           kind: Kind.COMMENT,
-          value: this.mf.substring(this.i + 1),
+          value: this.mf.slice(this.i + 1),
         });
@@ -196,4 +195,4 @@ break;
       return {
-        from: parseNumberWithDivision(number.substr(0, indexOfDash)),
-        to: parseNumberWithDivision(number.substr(indexOfDash + 1)),
+        from: parseNumberWithDivision(number.slice(0, indexOfDash)),
+        to: parseNumberWithDivision(number.slice(indexOfDash + 1)),
       };
@@ -223,4 +222,4 @@ }
 
-    let atom = substring.replace(/[^a-zA-Z]/g, '');
-    let isotope = Number(substring.replace(/[^0-9]/g, ''));
+    let atom = substring.replaceAll(/[^A-Za-z]/g, '');
+    let isotope = Number(substring.replaceAll(/\D/g, ''));
     return { atom, isotope };
@@ -241,4 +240,4 @@ }
     } while (ascii !== 125 && this.i <= this.mf.length); // closing curly bracket
-    if (substring.match(/^[0-9,]+$/)) {
-      return substring.split(',').map((a) => Number(a));
+    if (substring.match(/^[\d,]+$/)) {
+      return substring.split(',').map(Number);
     }
@@ -260,4 +259,4 @@ throw new MFError(
     } while (ascii !== 41 && this.i <= this.mf.length); // closing parenthesis
-    if (substring.match(/^\([0-9+-]+$/)) {
-      return parseCharge(substring.substring(1));
+    if (substring.match(/^\([\d+-]+$/)) {
+      return parseCharge(substring.slice(1));
     } else {
@@ -264,0 +263,0 @@ this.i = begin;

src/util/capitalizeMF.js

@@ -11,3 +11,3 @@ import { elementsObject } from 'chemical-elements';
 export function capitalizeMF(mf) {
-  if (!mf.match(/^[0-9a-zA-Z ]+/)) return mf;
+  if (!mf.match(/^[\d A-Za-z]+/)) return mf;
   if (isMF(mf)) return mf;
@@ -18,3 +18,3 @@ let oldMF = mf
     .replace(/cd/, ' C D ')
-    .replace(/([0-9])([a-zA-Z])/, '$1 $2');
+    .replace(/(\d)([A-Za-z])/, '$1 $2');
   let newMF = '';
@@ -25,4 +25,4 @@ let parts = oldMF.split(/ +/);
     if (parts[i] === '') continue;
-    let label = parts[i].replace(/[0-9]*$/, '');
-    let number = parts[i].replace(/^[a-zA-Z]*/, '');
+    let label = parts[i].replace(/\d*$/, '');
+    let number = parts[i].replace(/^[A-Za-z]*/, '');
 
@@ -47,3 +47,3 @@ let casedLabel = getCasedLabel(label);
   let casedLabel =
-    label.substr(0, 1).toUpperCase() + label.substr(1).toLowerCase();
+    label.slice(0, 1).toUpperCase() + label.slice(1).toLowerCase();
   if (elementsObject[label]) return casedLabel;
@@ -55,16 +55,16 @@ if (groupsObject[label]) return casedLabel;
     .toLowerCase()
-    .replace(/cl/g, 'Cl')
-    .replace(/br/g, 'Br')
-    .replace(/na/g, 'Na')
-    .replace(/li/g, 'Li')
-    .replace(/si/g, 'Si')
-    .replace(/cr/g, 'Cr')
-    .replace(/c/g, 'C')
-    .replace(/o/g, 'O')
-    .replace(/n/g, 'N')
-    .replace(/h/g, 'H')
-    .replace(/k/g, 'K')
-    .replace(/s/g, 'S');
+    .replaceAll('cl', 'Cl')
+    .replaceAll('br', 'Br')
+    .replaceAll('na', 'Na')
+    .replaceAll('li', 'Li')
+    .replaceAll('si', 'Si')
+    .replaceAll('cr', 'Cr')
+    .replaceAll('c', 'C')
+    .replaceAll('o', 'O')
+    .replaceAll('n', 'N')
+    .replaceAll('h', 'H')
+    .replaceAll('k', 'K')
+    .replaceAll('s', 'S');
   if (isMF(newLabel)) return newLabel;
   return label;
 }

src/util/flatten.js

@@ -129,3 +129,5 @@ export function flatten(parsed, options = {}) {
     if (mfs.length > limit) {
-      throw Error(`MF.flatten generates too many fragments (over ${limit})`);
+      throw new Error(
+        `MF.flatten generates too many fragments (over ${limit})`,
+      );
     }
@@ -132,0 +134,0 @@ }

src/util/getEA.js

@@ -46,3 +46,3 @@ import {
             element = groups[line.value];
-            if (!element) throw Error(`Unknown element: ${line.value}`);
+            if (!element) throw new Error(`Unknown element: ${line.value}`);
             // need to explode group ????
@@ -72,5 +72,5 @@ }
 
-  eas.forEach((ea) => {
+  for (const ea of eas) {
     ea.ratio = ea.mass / sum;
-  });
+  }
   return eas;
@@ -77,0 +77,0 @@ }

src/util/getElements.js

@@ -30,5 +30,5 @@ import { elementsObject, elementsAndIsotopesObject } from 'chemical-elements';
           }
-          let isotope = element.isotopes.filter(
+          let isotope = element.isotopes.find(
             (a) => a.nominal === line.value.isotope,
-          )[0];
+          );
           if (!isotope) {
@@ -35,0 +35,0 @@ throw new Error(`isotope unknown: ${line.value.isotope} - ${line}`);

src/util/getInfo.js

@@ -15,2 +15,5 @@ import {
 
+/** @typedef {import('./getInfo.types').PartInfo} PartInfo */
+/** @typedef {import('./getInfo.types').PartInfoWithParts} PartInfoWithParts */
+
 /**
@@ -20,2 +23,3 @@ *
  * @param {*} [options={}]
+ * @returns {object|PartInfo|PartInfoWithParts}
  */
@@ -72,2 +76,3 @@ export function getInfo(parts, options = {}) {
 
+  /** @type {PartInfo} */
   let currentPart = {
@@ -95,3 +100,3 @@ mass: 0,
           element = groups[line.value];
-          if (!element) throw Error(`Unknown element: ${line.value}`);
+          if (!element) throw new Error(`Unknown element: ${line.value}`);
           if (!customUnsaturations[line.value]) {
@@ -98,0 +103,0 @@ customUnsaturations[line.value] = element.unsaturation;

src/util/getIsotopesInfo.js

@@ -8,6 +8,8 @@ import {
 
+/** @typedef {import('./getIsotopesInfo.types').IsotopesInfo} IsotopesInfo
+
 /**
  *
  * @param {*} parts
- * @param {*} options
+ * @returns {[]|IsotopesInfo}
  */
@@ -23,3 +25,7 @@ export function getIsotopesInfo(parts) {
 
+/**
+ * @returns {IsotopesInfo}
+ */
 function getProcessedPart(part) {
+  /** @type {IsotopesInfo} */
   let result = {
@@ -34,3 +40,7 @@ charge: 0,
         if (!isotope) {
-          throw Error('unknown isotope:', line.value.atom, line.value.isotope);
+          throw new Error(
+            'unknown isotope:',
+            line.value.atom,
+            line.value.isotope,
+          );
         }
@@ -37,0 +47,0 @@ result.isotopes.push({

src/util/isMF.js

@@ -5,4 +5,4 @@ import { elementsObject } from 'chemical-elements';
 export function isMF(mf) {
-  let tmpMF = mf.replace(/[^a-zA-Z]/g, '');
-  let parts = tmpMF.replace(/([A-Za-z])(?=[A-Z])/g, '$1 ').split(' ');
+  let tmpMF = mf.replaceAll(/[^A-Za-z]/g, '');
+  let parts = tmpMF.replaceAll(/([A-Za-z])(?=[A-Z])/g, '$1 ').split(' ');
   for (let i = 0; i < parts.length; i++) {
@@ -9,0 +9,0 @@ if (!elementsObject[parts[i]] && !groupsObject[parts[i]]) {

src/util/parseCharge.js

 /**
- * Parse a string to extract the charge
+ * Parse a string to extract the charge.
  * The charge may be in the form --, +++, +3, -2, 4+, 2-
@@ -8,3 +8,3 @@ * @param {*} charge
 export function parseCharge(charge) {
-  charge = charge.replace(/[()]/g, '');
+  charge = charge.replaceAll(/[()]/g, '');
   let chargeNumber = 0;
@@ -16,5 +16,6 @@ if (charge.match(/^[+-]+$/)) {
     }
-  } else if (charge.match(/^[0-9]+[+-]$/)) {
+  } else if (charge.match(/^\d+[+-]$/)) {
     chargeNumber = Number(
-      charge.charAt(charge.length - 1) + charge.substring(0, charge.length - 1),
+      // eslint-disable-next-line unicorn/prefer-at
+      charge.charAt(charge.length - 1) + charge.slice(0, -1),
     );
@@ -21,0 +22,0 @@ } else {

src/util/partToAtoms.js

 import { Kind } from '../Kind.js';
 
+/** @typedef {Record<string, number>} AtomsMap */
+
 /**
- * Convert a MF part to an array of atoms
+ * Convert a MF part to a map of atoms
  * This procedure will suppress the isotopes !
  * This is mainly used to make queries
+ * @returns {AtomsMap}
  */
-
 export function partToAtoms(part) {
-  let atoms = {};
+  /** @type {AtomsMap} */
+  const atoms = {};
   for (let line of part) {
@@ -12,0 +15,0 @@ switch (line.kind) {

src/util/toHtml.js

@@ -15,10 +15,8 @@ import { Format } from '../Format';
       case Format.SUPERIMPOSE:
-        html.push(`<span style="${Style.SUPERIMPOSE}">`);
         html.push(
+          `<span style="${Style.SUPERIMPOSE}">`,
           `<sup style="${Style.SUPERIMPOSE_SUP_SUB}">${line.over}</sup>`,
-        );
-        html.push(
           `<sub style="${Style.SUPERIMPOSE_SUP_SUB}">${line.under}</sub>`,
+          '</span>',
         );
-        html.push('</span>');
         break;
@@ -25,0 +23,0 @@ default:

src/util/toParts.js

@@ -112,3 +112,3 @@ import { atomSorter } from 'atom-sorter';
     // just applies to the previous element
-    currentPart.lines[currentPart.lines.length - 1].multiplier *= value;
+    currentPart.lines.at(-1).multiplier *= value;
   }
@@ -146,3 +146,3 @@ }
     }
-    if (expanded) part.lines = part.lines.filter((a) => a);
+    if (expanded) part.lines = part.lines.filter(Boolean);
   }
@@ -167,4 +167,3 @@ }
         } else {
-          result[result.length - 1].value +=
-            key.value.value * key.value.multiplier;
+          result.at(-1).value += key.value.value * key.value.multiplier;
         }
@@ -174,3 +173,3 @@ } else if (currentKey !== key.key) {
       } else {
-        result[result.length - 1].multiplier += key.value.multiplier;
+        result.at(-1).multiplier += key.value.multiplier;
       }
@@ -177,0 +176,0 @@ currentKey = key.key;

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Fixed alerts

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Improved metrics

Total package byte prevSize

157576

increased by33.72%

Dependency count

3

decreased by-25%

Number of package files

91

increased by8.33%

Lines of code

3733

increased by3.09%

Worsened metrics

Number of medium supply chain risk alerts

2

increased by100%

Dependency changes

• - Removedmf-utilities@^3.2.0

• - Removedmf-parser@3.3.0(transitive)

• - Removedmf-utilities@3.3.4(transitive)

• Updatedatom-sorter@^2.1.1

• Updatedchemical-elements@^2.1.1

• Updatedchemical-groups@^2.2.1