emdb - npm Package Compare versions

Comparing version 1.5.0 to 1.6.0

package.json

 {
   "name": "emdb",
-  "version": "1.5.0",
+  "version": "1.6.0",
   "description": "Database manager for exact mass query",
@@ -26,5 +26,5 @@ "main": "src/index.js",
     "jszip": "^3.7.1",
-    "mf-finder": "^1.2.0",
-    "mf-from-google-sheet": "^1.1.24",
-    "mf-generator": "^1.3.12",
+    "mf-finder": "^1.2.1",
+    "mf-from-google-sheet": "^1.1.25",
+    "mf-generator": "^1.3.13",
     "mf-matcher": "^1.1.19",
@@ -36,3 +36,3 @@ "mf-parser": "^1.4.0",
     "ml-regression-theil-sen": "^2.0.0",
-    "ms-spectrum": "^1.4.6",
+    "ms-spectrum": "^1.4.7",
     "nucleotide": "^1.2.14",
@@ -42,3 +42,3 @@ "peaks-similarity": "^2.3.1",
   },
-  "gitHead": "0ccc601b2ba051652963fad05479902943d7feaf"
+  "gitHead": "0b932f49c82fd9fb2ef0804c1430b1499426ef95"
 }

src/__tests__/DBManager.test.js

@@ -15,6 +15,6 @@ 'use strict';
 
-test('DBManager fromMonoisotopicMass', () => {
+test('DBManager fromMonoisotopicMass', async () => {
   let dbManager = new DBManager();
 
-  dbManager.fromMonoisotopicMass(300, { ionizations: 'H+,Na+' });
+  await dbManager.fromMonoisotopicMass(300, { ionizations: 'H+,Na+' });
 
@@ -21,0 +21,0 @@ expect(dbManager.listDatabases()).toStrictEqual(['monoisotopic']);

src/__tests__/loadTest.test.js

@@ -5,6 +5,6 @@ 'use strict';
 
-test('loadTest', () => {
+test('loadTest', async () => {
   let dbManager = new DBManager();
-  dbManager.loadTest();
+  await dbManager.loadTest();
   expect(dbManager.databases.test).toMatchSnapshot();
 });

src/__tests__/searchSimilarity.ethylbenzene.test.js

@@ -13,5 +13,5 @@ 'use strict';
   let experimental = loadEthylbenzene();
-  it('should find one result with bad distribution', () => {
+  it('should find one result with bad distribution', async () => {
     let dbManager = new DBManager();
-    dbManager.fromMonoisotopicMass(106.077, {
+    await dbManager.fromMonoisotopicMass(106.077, {
       ionizations: 'Na+,K+,(H+),(H+)2,(H+)3,+',
@@ -32,3 +32,3 @@ ranges: 'C0-100 H0-100 N0-100 O0-100',
 
-    let results = dbManager.searchSimilarity({
+    let results = await dbManager.searchSimilarity({
       filter: {},
@@ -35,0 +35,0 @@ similarity: {

src/__tests__/searchSimilarity.peptide.test.js

@@ -19,5 +19,5 @@ /* eslint-disable import/no-extraneous-dependencies */
 
-  it('should find one result with bad distribution', () => {
+  it('should find one result with bad distribution', async () => {
     let dbManager = new DBManager();
-    dbManager.fromPeptidicSequence(
+    await dbManager.fromPeptidicSequence(
       //    'KKK',
@@ -38,3 +38,3 @@ 'MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQ',
 
-    let results = dbManager.searchSimilarity({
+    let results = await dbManager.searchSimilarity({
       filter: {},
@@ -101,5 +101,5 @@ similarity: {
 
-  it('should find one result with bad distribution and string fucntion', () => {
+  it('should find one result with bad distribution and string fucntion', async () => {
     let dbManager = new DBManager();
-    dbManager.fromPeptidicSequence(
+    await dbManager.fromPeptidicSequence(
       'MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQ',
@@ -119,3 +119,3 @@ {
 
-    let results = dbManager.searchSimilarity({
+    let results = await dbManager.searchSimilarity({
       filter: {},
@@ -122,0 +122,0 @@ similarity: {

src/__tests__/searchSimilarity.test.js

@@ -6,7 +6,7 @@ 'use strict';
 describe('test searchSimilarity', () => {
-  it('should find one result with bad distribution', () => {
+  it('should find one result with bad distribution', async () => {
     let dbManager = new DBManager();
-    dbManager.loadNeutralTest({ maxC: 10 });
+    await dbManager.loadNeutralTest({ maxC: 10 });
     dbManager.setExperimentalSpectrum({ x: [41, 121], y: [1, 1] });
-    let results = dbManager.searchSimilarity({
+    let results = await dbManager.searchSimilarity({
       ionizations: 'H+,(H+)2,(H+)3', // useless because the test database has already ionizations
@@ -32,7 +32,7 @@ filter: {},
 
-  it('should find one result with callback', () => {
+  it('should find one result with callback', async () => {
     let dbManager = new DBManager();
-    dbManager.loadNeutralTest({ maxC: 10 });
+    await dbManager.loadNeutralTest({ maxC: 10 });
     dbManager.setExperimentalSpectrum({ x: [41, 121], y: [1, 1] });
-    let results = dbManager.searchSimilarity({
+    let results = await dbManager.searchSimilarity({
       ionizations: 'H+,(H+)2,(H+)3', // useless because the test database has already ionizations
@@ -47,7 +47,7 @@ filter: {
 
-  it('should find one result with wrong callback', () => {
+  it('should find one result with wrong callback', async () => {
     let dbManager = new DBManager();
-    dbManager.loadNeutralTest({ maxC: 10 });
+    await dbManager.loadNeutralTest({ maxC: 10 });
     dbManager.setExperimentalSpectrum({ x: [41, 121], y: [1, 1] });
-    let results = dbManager.searchSimilarity({
+    let results = await dbManager.searchSimilarity({
       ionizations: 'H+,(H+)2,(H+)3', // useless because the test database has already ionizations
@@ -62,7 +62,7 @@ filter: {
 
-  it('should find one result with perfect match (small zone)', () => {
+  it('should find one result with perfect match (small zone)', async () => {
     let dbManager = new DBManager();
-    dbManager.loadTest();
+    await dbManager.loadTest();
     dbManager.setExperimentalSpectrum({ x: [120], y: [1] });
-    let results = dbManager.searchSimilarity({
+    let results = await dbManager.searchSimilarity({
       ionizations: '+',
@@ -84,7 +84,7 @@ filter: {},
 
-  it('should find one result with bad distribution, small zone, small width', () => {
+  it('should find one result with bad distribution, small zone, small width', async () => {
     let dbManager = new DBManager();
-    dbManager.loadTest();
+    await dbManager.loadTest();
     dbManager.setExperimentalSpectrum({ x: [120, 121], y: [1, 1] });
-    let results = dbManager.searchSimilarity({
+    let results = await dbManager.searchSimilarity({
       ionizations: '+',
@@ -109,7 +109,7 @@ filter: {
 
-  it('should find no result because of filter', () => {
+  it('should find no result because of filter', async () => {
     let dbManager = new DBManager();
-    dbManager.loadTest();
+    await dbManager.loadTest();
     dbManager.setExperimentalSpectrum({ x: [120, 121], y: [1, 1] });
-    let results = dbManager.searchSimilarity({
+    let results = await dbManager.searchSimilarity({
       ionizations: '+',
@@ -124,7 +124,7 @@ filter: {
 
-  it('should find one result with bad bad distribution, large window', () => {
+  it('should find one result with bad bad distribution, large window', async () => {
     let dbManager = new DBManager();
-    dbManager.loadTest();
+    await dbManager.loadTest();
     dbManager.setExperimentalSpectrum({ x: [120], y: [1] });
-    let results = dbManager.searchSimilarity({
+    let results = await dbManager.searchSimilarity({
       ionizations: '+',
@@ -148,7 +148,7 @@ filter: {
 
-  it('should find one result with bad bad distribution, large window huge width', () => {
+  it('should find one result with bad bad distribution, large window huge width', async () => {
     let dbManager = new DBManager();
-    dbManager.loadTest();
+    await dbManager.loadTest();
     dbManager.setExperimentalSpectrum({ x: [120], y: [1] });
-    let results = dbManager.searchSimilarity({
+    let results = await dbManager.searchSimilarity({
       ionizations: '+',
@@ -172,7 +172,7 @@ filter: {
 
-  it('should find one result with overlap', () => {
+  it('should find one result with overlap', async () => {
     let dbManager = new DBManager();
-    dbManager.loadTest();
+    await dbManager.loadTest();
     dbManager.setExperimentalSpectrum({ x: [120], y: [1] });
-    let results = dbManager.searchSimilarity({
+    let results = await dbManager.searchSimilarity({
       ionizations: '+',
@@ -196,7 +196,7 @@ filter: {
 
-  it('should find one result with good distribution', () => {
+  it('should find one result with good distribution', async () => {
     let dbManager = new DBManager();
-    dbManager.loadTest();
+    await dbManager.loadTest();
     dbManager.setExperimentalSpectrum({ x: [120, 121], y: [1, 0.11] });
-    let results = dbManager.searchSimilarity({
+    let results = await dbManager.searchSimilarity({
       ionizations: '+',
@@ -203,0 +203,0 @@ filter: {

src/from/__tests__/fromArray.test.js

@@ -6,11 +6,11 @@ 'use strict';
 describe('fromArray', () => {
-  it('using an array of string', () => {
+  it('using an array of string', async () => {
     let dbManager = new DBManager();
-    dbManager.fromArray(['C.N', 'N.O']);
+    await dbManager.fromArray(['C.N', 'N.O']);
     expect(dbManager.databases.generated).toHaveLength(4);
   });
 
-  it('with ranges and group', () => {
+  it('with ranges and group', async () => {
     let dbManager = new DBManager();
-    dbManager.fromArray(['(CH2)0-2N0-1', 'O0-1']);
+    await dbManager.fromArray(['(CH2)0-2N0-1', 'O0-1']);
     expect(dbManager.databases.generated).toHaveLength(12);
@@ -34,5 +34,5 @@ let mfs = dbManager.databases.generated.map((entry) => entry.mf).sort();
 
-  it('with callback filter', () => {
+  it('with callback filter', async () => {
     let dbManager = new DBManager();
-    dbManager.fromArray(['C0-100', 'H0-100'], {
+    await dbManager.fromArray(['C0-100', 'H0-100'], {
       filter: {
@@ -45,5 +45,5 @@ callback: (entry) => entry.atoms.C === entry.atoms.H,
 
-  it('using an array or array', () => {
+  it('using an array or array', async () => {
     let dbManager = new DBManager();
-    dbManager.fromArray(['C.N', ['Cl0-1', 'Br0-1']]);
+    await dbManager.fromArray(['C.N', ['Cl0-1', 'Br0-1']]);
     let result = dbManager
@@ -50,0 +50,0 @@ .get('generated')

src/from/__tests__/fromMonoisotopicMass.test.js

@@ -5,5 +5,5 @@ 'use strict';
 
-test('fromMonoisotopicMass', () => {
+test('fromMonoisotopicMass', async () => {
   let dbManager = new DBManager();
-  dbManager.fromMonoisotopicMass(120, {
+  await dbManager.fromMonoisotopicMass(120, {
     allowNeutral: true,
@@ -14,5 +14,5 @@ });
 
-test('fromMonoisotopicMass string', () => {
+test('fromMonoisotopicMass string', async () => {
   let dbManager = new DBManager();
-  dbManager.fromMonoisotopicMass('120,60', {
+  await dbManager.fromMonoisotopicMass('120,60', {
     allowNeutral: true,
@@ -23,5 +23,5 @@ });
 
-test('fromMonoisotopicMass array', () => {
+test('fromMonoisotopicMass array', async () => {
   let dbManager = new DBManager();
-  dbManager.fromMonoisotopicMass([60, 120], {
+  await dbManager.fromMonoisotopicMass([60, 120], {
     allowNeutral: true,
@@ -32,5 +32,5 @@ });
 
-test('fromMonoisotopicMass with ionizations', () => {
+test('fromMonoisotopicMass with ionizations', async () => {
   let dbManager = new DBManager();
-  dbManager.fromMonoisotopicMass(120, {
+  await dbManager.fromMonoisotopicMass(120, {
     allowNeutral: false,
@@ -43,5 +43,5 @@ ionizations: ', H+, K+',
 
-test('fromMonoisotopicMass large database', () => {
+test('fromMonoisotopicMass large database', async () => {
   let dbManager = new DBManager();
-  dbManager.fromMonoisotopicMass(1000, {
+  await dbManager.fromMonoisotopicMass(1000, {
     ranges: 'C0-100 H0-100 N0-100 O0-100',
@@ -48,0 +48,0 @@ filter: {

src/from/__tests__/fromNucleicSequence.test.js

@@ -11,5 +11,5 @@ /* eslint-disable import/no-extraneous-dependencies */
 describe('fromNucleicSequence', () => {
-  it('fromNucleicSequence', () => {
+  it('fromNucleicSequence', async () => {
     let dbManager = new DBManager();
-    dbManager.fromNucleicSequence('AAA', {
+    await dbManager.fromNucleicSequence('AAA', {
       ionizations: 'H+,Na+',
@@ -40,5 +40,5 @@ fragmentation: {
 
-  it('fromNucleicSequence ds-DNA', () => {
+  it('fromNucleicSequence ds-DNA', async () => {
     let dbManager = new DBManager();
-    dbManager.fromNucleicSequence('AAA', {
+    await dbManager.fromNucleicSequence('AAA', {
       ionizations: 'H+,Na+',
@@ -59,5 +59,5 @@ fragmentation: {
 
-  it('TACGTGCCAATAC internal fragment', () => {
+  it('TACGTGCCAATAC internal fragment', async () => {
     let dbManager = new DBManager();
-    dbManager.fromNucleicSequence('TACGTGCCAATAC', {
+    await dbManager.fromNucleicSequence('TACGTGCCAATAC', {
       ionizations: '(H+)-5',
@@ -94,5 +94,5 @@ fragmentation: {
 
-  it('TACGTGCCAATAC callback', () => {
+  it('TACGTGCCAATAC callback', async () => {
     let dbManager = new DBManager();
-    dbManager.fromNucleicSequence('TACGTGCCAATAC', {
+    await dbManager.fromNucleicSequence('TACGTGCCAATAC', {
       ionizations: '(H+)-5',
@@ -116,5 +116,5 @@ fragmentation: {
 
-  it('AGGCAG fragment', () => {
+  it('AGGCAG fragment', async () => {
     let dbManager = new DBManager();
-    dbManager.fromNucleicSequence('AGGCAG', {
+    await dbManager.fromNucleicSequence('AGGCAG', {
       ionizations: '(H+)-',
@@ -133,5 +133,5 @@ fragmentation: {
 
-  it('AGG with d-h2o and base loss', () => {
+  it('AGG with d-h2o and base loss', async () => {
     let dbManager = new DBManager();
-    dbManager.fromNucleicSequence('AGG', {
+    await dbManager.fromNucleicSequence('AGG', {
       ionizations: '(H+)-1',
@@ -152,5 +152,5 @@ fragmentation: {
 
-  it('HODamDamDamDamDamH', () => {
+  it('HODamDamDamDamDamH', async () => {
     let dbManager = new DBManager();
-    dbManager.fromNucleicSequence('HODamDamDamDamDamH', {
+    await dbManager.fromNucleicSequence('HODamDamDamDamDamH', {
       ionizations: '(H+)-',
@@ -157,0 +157,0 @@ fragmentation: {

src/from/__tests__/fromPeptidicSequence.test.js

@@ -6,5 +6,5 @@ 'use strict';
 describe('fromPeptidicSequence', () => {
-  it('AAKK', () => {
+  it('AAKK', async () => {
     let dbManager = new DBManager();
-    dbManager.fromPeptidicSequence('AAKK', {
+    await dbManager.fromPeptidicSequence('AAKK', {
       allowNeutralLoss: false,
@@ -33,5 +33,5 @@ protonation: false,
 
-  it('AAKK with callback', () => {
+  it('AAKK with callback', async () => {
     let dbManager = new DBManager();
-    dbManager.fromPeptidicSequence('AAKK', {
+    await dbManager.fromPeptidicSequence('AAKK', {
       allowNeutralLoss: false,
@@ -59,5 +59,5 @@ protonation: false,
 
-  it('AAKKKKKKKKKKKKKKKKKK allowNeutralLoss', () => {
+  it('AAKKKKKKKKKKKKKKKKKK allowNeutralLoss', async () => {
     let dbManager = new DBManager();
-    dbManager.fromPeptidicSequence('AAKKKKKKKKKKKKKKKKKK', {
+    await dbManager.fromPeptidicSequence('AAKKKKKKKKKKKKKKKKKK', {
       allowNeutralLoss: true,
@@ -87,5 +87,5 @@ protonation: false,
 
-  it('AAKKKKKKKKKKKKKKKKKK filter callback', () => {
+  it('AAKKKKKKKKKKKKKKKKKK filter callback', async () => {
     let dbManager = new DBManager();
-    dbManager.fromPeptidicSequence('AAKKKKKKKKKKKKKKKKKK', {
+    await dbManager.fromPeptidicSequence('AAKKKKKKKKKKKKKKKKKK', {
       ionizations: 'H+,Na+',
@@ -103,5 +103,5 @@ fragmentation: {
 
-  it('AAKKKKKK allowNeutralLoss limit: 1000', () => {
+  it('AAKKKKKK allowNeutralLoss limit: 1000', async () => {
     let dbManager = new DBManager();
-    expect(() => {
+    await expect(
       dbManager.fromPeptidicSequence('AAKKKKKKKKK', {
@@ -116,2 +116,3 @@ allowNeutralLoss: true,
         },
+
         filter: {
@@ -123,9 +124,11 @@ minMSEM: 100,
         },
-      });
-    }).toThrow('processRange generates to many fragments (over 100)');
+      }),
+    ).rejects.toMatchInlineSnapshot(
+      `[Error: processRange generates to many fragments (over 100)]`,
+    );
   });
 
-  it('Linked AA(H-1#1)AA,GG(H-1#1)GG', () => {
+  it('Linked AA(H-1#1)AA,GG(H-1#1)GG', async () => {
     let dbManager = new DBManager();
-    dbManager.fromPeptidicSequence('AA(H-1#1)AA,GG(H-1#2)GG', {
+    await dbManager.fromPeptidicSequence('AA(H-1#1)AA,GG(H-1#2)GG', {
       links: { filter: true },
@@ -145,5 +148,5 @@ mfsArray: ['#1C6H4#2'],
 
-  it('Optional linked AA(H-1#1)A,GG(H-1#1)G', () => {
+  it('Optional linked AA(H-1#1)A,GG(H-1#1)G', async () => {
     let dbManager = new DBManager();
-    dbManager.fromPeptidicSequence('AA(H-1#1)A,GG(H-1#2)G', {
+    await dbManager.fromPeptidicSequence('AA(H-1#1)A,GG(H-1#2)G', {
       links: { filter: true },
@@ -150,0 +153,0 @@ mfsArray: ['#1C6H4#2,'],

src/from/__tests__/fromRange.test.js

@@ -6,17 +6,17 @@ 'use strict';
 describe('fromRange', () => {
-  it('no filter', () => {
+  it('no filter', async () => {
     let dbManager = new DBManager();
-    dbManager.fromRange('C1-10, H1-10; Cl0-1 Br0-1');
+    await dbManager.fromRange('C1-10, H1-10; Cl0-1 Br0-1');
     expect(dbManager.databases.generated).toHaveLength(80);
   });
 
-  it('with charge', () => {
+  it('with charge', async () => {
     let dbManager = new DBManager();
-    dbManager.fromRange('C1-10 H1-10 (-)');
+    await dbManager.fromRange('C1-10 H1-10 (-)');
     expect(dbManager.databases.generated[0].charge).toBe(-1);
   });
 
-  it('Filter callback', () => {
+  it('Filter callback', async () => {
     let dbManager = new DBManager();
-    dbManager.fromRange('C0-4 H0-4', {
+    await dbManager.fromRange('C0-4 H0-4', {
       filter: {
@@ -23,0 +23,0 @@ callback: (entry) => entry.atoms.C - entry.atoms.H === 0,

src/from/fromArray.js

@@ -8,10 +8,11 @@ 'use strict';
  * @param {array} mfsArray - Array of string or Array of array containing the parts to combine
- * @param {obejct} [options={}]
+ * @param {object} [options={}]
  * @param {boolean} [options.estimate=false] - estimate the number of MF without filters
  * @param {string} [options.databaseName='generated']
+ * @param {function} [options.onStep] - Callback to do after each step
  * @param {number} [options.limit=10000000] - Maximum number of results
- * @param {boolean} [canonizeMF=true] - Canonize molecular formula
- * @param {boolean} [uniqueMFs=true] - Force canonization and make MF unique
- * @param {string} [ionizations=''] - Comma separated list of ionizations (to charge the molecule)
- * @param {number} [options.filter={}]
+ * @param {boolean} [options.canonizeMF=true] - Canonize molecular formula
+ * @param {boolean} [options.uniqueMFs=true] - Force canonization and make MF unique
+ * @param {string} [options.ionizations=''] - Comma separated list of ionizations (to charge the molecule)
+ * @param {object} [options.filter={}]
  * @param {number} [options.filter.minMass=0] - Minimal monoisotopic mass
@@ -26,7 +27,7 @@ * @param {number} [options.filter.maxMass=+Infinity] - Maximal monoisotopic mass
  *
- * @param {number} [options.filter.unsaturation={}]
+ * @param {object} [options.filter.unsaturation={}]
  * @param {number} [options.filter.unsaturation.min=-Infinity] - Minimal unsaturation
  * @param {number} [options.filter.unsaturation.max=+Infinity] - Maximal unsaturation
- * @param {number} [options.filter.unsaturation.onlyInteger=false] - Integer unsaturation
- * @param {number} [options.filter.unsaturation.onlyNonInteger=false] - Non integer unsaturation
+ * @param {boolean} [options.filter.unsaturation.onlyInteger=false] - Integer unsaturation
+ * @param {boolean} [options.filter.unsaturation.onlyNonInteger=false] - Non integer unsaturation
  * @param {object} [options.filter.atoms] - object of atom:{min, max}
@@ -71,4 +72,4 @@ * @param {function} [options.filter.callback] - a function to filter the MF
 
-module.exports = function fromArray(mfsArray, options = {}) {
+module.exports = async function fromArray(mfsArray, options = {}) {
   return generateMFs(mfsArray, options);
 };

src/from/fromMonoisotopicMass.js

@@ -10,2 +10,3 @@ 'use strict';
  * @param {number}    [options.maxIterations=10000000] - Maximum number of iterations
+ * @param {function} [options.onStep] - Callback to do after each step
  * @param {number}    [options.limit=1000] - Maximum number of results
@@ -25,5 +26,6 @@ * @param {string}    [options.ionizations=''] - string containing a comma separated list of modifications
  * @param {function}  [options.filter.callback] - a function to filter the MF
+ * @returns {Promise}
  */
 
-module.exports = function fromMonoisotopicMass(masses, options = {}) {
+module.exports = async function fromMonoisotopicMass(masses, options = {}) {
   if (typeof masses === 'string') {
@@ -35,3 +37,6 @@ masses = masses.split(/[ ,;\r\n\t]/).map(Number);
   }
-  let results = masses.map((mass) => findMFs(mass, options));
+  let results = [];
+  for (let mass of masses) {
+    results.push(await findMFs(mass, options));
+  }
   return {
@@ -38,0 +43,0 @@ mfs: results.map((entry) => entry.mfs).flat(),

src/from/fromNucleicSequence.js

@@ -10,6 +10,7 @@ 'use strict';
  *
- * @param {string} [sequence] Sequence as a string of 1 letter or 3 letters code. Could also be a correct molecular formula respecting uppercase, lowercase
+ * @param {string} [sequencesString] Sequence as a string of 1 letter or 3 letters code. Could also be a correct molecular formula respecting uppercase, lowercase
  * @param {object} [options={}]
- * @param {boolean}       [options.estimate=false] - estimate the number of MF without filters
- * @param {number}         [options.limit=100000]
+ * @param {boolean} [options.estimate=false] - estimate the number of MF without filters
+ * @param {function} [options.onStep] - Callback to do after each step
+ * @param {number} [options.limit=100000]
  * @param {string} [options.ionizations='']
@@ -43,10 +44,14 @@ * @param {object} [options.info={}]
  * @param {number} [options.filter.maxCharge=+Infinity] - Maximal charge
- * @param {number} [options.filter.unsaturation={}]
+ * @param {object} [options.filter.unsaturation={}]
  * @param {number} [options.filter.unsaturation.min=-Infinity] - Minimal unsaturation
  * @param {number} [options.filter.unsaturation.max=+Infinity] - Maximal unsaturation
- * @param {number} [options.filter.unsaturation.onlyInteger=false] - Integer unsaturation
- * @param {number} [options.filter.unsaturation.onlyNonInteger=false] - Non integer unsaturation
+ * @param {boolean} [options.filter.unsaturation.onlyInteger=false] - Integer unsaturation
+ * @param {boolean} [options.filter.unsaturation.onlyNonInteger=false] - Non integer unsaturation
+ * @returns {Promise}
  */
 
-module.exports = function fromNucleicSequence(sequencesString, options = {}) {
+module.exports = async function fromNucleicSequence(
+  sequencesString,
+  options = {},
+) {
   const {
@@ -63,3 +68,2 @@ mfsArray = [],
   let sequences = nucleotide.sequenceToMF(sequencesString, info).split('.');
-
   let fragmentsArray = sequences.slice();
@@ -83,3 +87,3 @@
 
-  let combined = combineMFs(mfsArray, {
+  let combined = await combineMFs(mfsArray, {
     ionizations,
@@ -86,0 +90,0 @@ filter,

src/from/fromPeptidicSequence.js

@@ -15,2 +15,3 @@ 'use strict';
  * @param {string}         [options.ionizations='']
+ * @param {function} [options.onStep] - Callback to do after each step
  * @param {array}          [options.mfsArray=[]]
@@ -54,11 +55,12 @@ * @param {boolean}        [options.protonation=false]
  * @param {number}         [options.filter.maxCharge=+Infinity] - Maximal charge
- * @param {number}         [options.filter.unsaturation={}]
+ * @param {object}         [options.filter.unsaturation={}]
  * @param {number}         [options.filter.unsaturation.min=-Infinity] - Minimal unsaturation
  * @param {number}         [options.filter.unsaturation.max=+Infinity] - Maximal unsaturation
- * @param {number}         [options.filter.unsaturation.onlyInteger=false] - Integer unsaturation
- * @param {number}         [options.filter.unsaturation.onlyNonInteger=false] - Non integer unsaturation
+ * @param {boolean}         [options.filter.unsaturation.onlyInteger=false] - Integer unsaturation
+ * @param {boolean}         [options.filter.unsaturation.onlyNonInteger=false] - Non integer unsaturation
  * @param {function}       [options.filter.callback] - a function to filter the MF
+ * @returns {Promise}
  */
 
-module.exports = function fromPeptidicSequence(sequences, options = {}) {
+module.exports = async function fromPeptidicSequence(sequences, options = {}) {
   const {
@@ -100,3 +102,3 @@ digestion = {},
 
-  let combined = generateMFs(mfsArrayUnlinked, {
+  let combined = await generateMFs(mfsArrayUnlinked, {
     ionizations,
@@ -111,3 +113,3 @@ filter,
     combined.push(
-      ...generateMFs(mfsArrayLinked, {
+      ...(await generateMFs(mfsArrayLinked, {
         ionizations,
@@ -118,3 +120,3 @@ filter,
         links,
-      }),
+      })),
     );
@@ -121,0 +123,0 @@ }

src/from/fromRange.js

@@ -7,11 +7,12 @@ 'use strict';
  * Generates a database 'generated' from an array of molecular formula
- * @param {string} range - a string representing the range to search
+ * @param {string} rangesString - a string representing the range to search
  * @param {object} [options={}]
  * @param {boolean} [options.estimate=false] - estimate the number of MF without filters
+ * @param {function} [options.onStep] - Callback to do after each step
  * @param {string} [options.databaseName='generated']
  * @param {number} [options.limit=100000] - Maximum number of results
- * @param {boolean} [canonizeMF=true] - Canonize molecular formula
- * @param {boolean} [uniqueMFs=true] - Force canonization and make MF unique
- * @param {string} [ionizations=''] - Comma separated list of ionizations (to charge the molecule)
- * @param {number} [options.filter={}]
+ * @param {boolean} [options.canonizeMF=true] - Canonize molecular formula
+ * @param {boolean} [options.uniqueMFs=true] - Force canonization and make MF unique
+ * @param {string} [options.ionizations=''] - Comma separated list of ionizations (to charge the molecule)
+ * @param {object} [options.filter={}]
  * @param {number} [options.filter.minMass=0] - Minimal monoisotopic mass
@@ -26,13 +27,12 @@ * @param {number} [options.filter.maxMass=+Infinity] - Maximal monoisotopic mass
  *
- * @param {number} [options.filter.unsaturation={}]
+ * @param {object} [options.filter.unsaturation={}]
  * @param {number} [options.filter.unsaturation.min=-Infinity] - Minimal unsaturation
  * @param {number} [options.filter.unsaturation.max=+Infinity] - Maximal unsaturation
- * @param {number} [options.filter.unsaturation.onlyInteger=false] - Integer unsaturation
- * @param {number} [options.filter.unsaturation.onlyNonInteger=false] - Non integer unsaturation
+ * @param {boolean} [options.filter.unsaturation.onlyInteger=false] - Integer unsaturation
+ * @param {boolean} [options.filter.unsaturation.onlyNonInteger=false] - Non integer unsaturation
  * @param {function} [options.filter.callback] - a function to filter the MF
  * @param {object} [options.filter.atoms] - object of atom:{min, max}
  *
+ * @returns {Promise} - list of possible molecular formula
  *
- * @returns {array} - list of possible molecular formula
- *
  * @example
@@ -46,3 +46,3 @@ * const EMDB = require('emdb');
 
-module.exports = function fromRange(rangesString, options = {}) {
+module.exports = async function fromRange(rangesString, options = {}) {
   let ranges = rangesString.split(/ *[;\r\n] */);
@@ -49,0 +49,0 @@ for (let i = 0; i < ranges.length; i++) {

src/index.js

@@ -86,12 +86,14 @@ 'use strict';
 
-DBManager.prototype.loadTest = function loadTest() {
-  this.fromArray(['C1-100'], { databaseName: 'test', ionizations: '+' });
+DBManager.prototype.loadTest = async function loadTest() {
+  await this.fromArray(['C1-100'], { databaseName: 'test', ionizations: '+' });
 };
 
-DBManager.prototype.loadNeutralTest = function loadNeutralTest(options = {}) {
+DBManager.prototype.loadNeutralTest = async function loadNeutralTest(
+  options = {},
+) {
   const { maxC = 100 } = options;
-  this.fromArray([`C1-${maxC}`], { databaseName: 'test' });
+  await this.fromArray([`C1-${maxC}`], { databaseName: 'test' });
 };
 
-DBManager.prototype.fromMonoisotopicMass = function fromMonoisotopicMass(
+DBManager.prototype.fromMonoisotopicMass = async function fromMonoisotopicMass(
   mass,
@@ -101,3 +103,3 @@ options = {},
   const { databaseName = 'monoisotopic', append = false } = options;
-  let result = require('./from/fromMonoisotopicMass')(mass, options);
+  let result = await require('./from/fromMonoisotopicMass')(mass, options);
   replaceOrAppend(this, databaseName, result.mfs, append);
@@ -107,5 +109,8 @@ return result;
 
-DBManager.prototype.fromArray = function fromArray(sequence, options = {}) {
+DBManager.prototype.fromArray = async function fromArray(
+  sequence,
+  options = {},
+) {
   const { databaseName = 'generated', append = false, estimate } = options;
-  const results = require('./from/fromArray')(sequence, options);
+  const results = await require('./from/fromArray')(sequence, options);
   if (estimate) return results;
@@ -115,5 +120,8 @@ replaceOrAppend(this, databaseName, results, append);
 
-DBManager.prototype.fromRange = function fromRange(sequence, options = {}) {
+DBManager.prototype.fromRange = async function fromRange(
+  sequence,
+  options = {},
+) {
   const { databaseName = 'generated', append = false, estimate } = options;
-  const results = require('./from/fromRange')(sequence, options);
+  const results = await require('./from/fromRange')(sequence, options);
   if (estimate) return results;
@@ -123,3 +131,3 @@ replaceOrAppend(this, databaseName, results, append);
 
-DBManager.prototype.fromPeptidicSequence = function fromPeptidicSequence(
+DBManager.prototype.fromPeptidicSequence = async function fromPeptidicSequence(
   sequence,
@@ -129,3 +137,6 @@ options = {},
   const { databaseName = 'peptidic', append = false, estimate } = options;
-  const results = require('./from/fromPeptidicSequence')(sequence, options);
+  const results = await require('./from/fromPeptidicSequence')(
+    sequence,
+    options,
+  );
   if (estimate) return results;
@@ -135,3 +146,24 @@ replaceOrAppend(this, databaseName, results, append);
 
-DBManager.prototype.fromNucleicSequence = function fromNucleicSequence(
+/**
+ *
+ * @param {string} databaseName
+ * @param {object} [options={}]
+ * @param {number} [options.precision=100]
+ * @param {string} [options.ionizations='']
+ * @returns
+ */
+DBManager.prototype.appendFragmentsInfo = async function appendFragmentsInfo(
+  databaseName,
+  options = {},
+) {
+  const database = this.databases[databaseName];
+  await require('./append/appendFragmentsInfo')(
+    this.experimentalSpectrum,
+    database,
+    options,
+  );
+  return database;
+};
+
+DBManager.prototype.fromNucleicSequence = async function fromNucleicSequence(
   sequence,
@@ -141,3 +173,6 @@ options = {},
   const { databaseName = 'nucleic', append = false, estimate } = options;
-  const results = require('./from/fromNucleicSequence')(sequence, options);
+  const results = await require('./from/fromNucleicSequence')(
+    sequence,
+    options,
+  );
   if (estimate) return results;
@@ -144,0 +179,0 @@ replaceOrAppend(this, databaseName, results, append);

src/searchMSEM.js

@@ -12,20 +12,20 @@ 'use strict';
 * @param {boolean}  [options.flatten=false] - should we return the array as a flat result
+* @param {string}   [options.ionizations] - list the allowed ionizations possibilities
 * @param {object}   [options.filter={}]
-* @param {string}   [options.ionizations] - list the allowed ionizations possibilities
- * @param {number}         [options.filter.targetMass] - Target mass, allows to calculate error and filter results
- * @param {Array<number>}  [options.filter.targetMasses] - Target masses: SORTED array of numbers
- * @param {Array<number>}  [options.filter.targetIntensities] - Target intensities: SORTED array of numbers
- * @param {number}         [options.filter.minEM=0] - Minimal monoisotopic mass
- * @param {number}         [options.filter.maxEM=+Infinity] - Maximal monoisotopic mass
- * @param {number}         [options.filter.minMSEM=0] - Minimal monoisotopic mass observed by mass
- * @param {number}         [options.filter.maxMSEM=+Infinity] - Maximal monoisotopic mass observed by mass
- * @param {number}         [options.filter.minCharge=-Infinity] - Minimal charge
- * @param {number}         [options.filter.maxCharge=+Infinity] - Maximal charge
- * @param {object}         [options.filter.unsaturation={}}]
- * @param {number}         [options.filter.unsaturation.min=-Infinity] - Minimal unsaturation
- * @param {number}         [options.filter.unsaturation.max=+Infinity] - Maximal unsaturation
- * @param {number}         [options.filter.unsaturation.onlyInteger=false] - Integer unsaturation
- * @param {number}         [options.filter.unsaturation.onlyNonInteger=false] - Non integer unsaturation
- * @param {object}         [options.filter.callback] - a function to filter the MF
- * @param {object}         [options.filter.atoms] - object of atom:{min, max}
+* @param {number}         [options.filter.targetMass] - Target mass, allows to calculate error and filter results
+* @param {Array<number>}  [options.filter.targetMasses] - Target masses: SORTED array of numbers
+* @param {Array<number>}  [options.filter.targetIntensities] - Target intensities: SORTED array of numbers
+* @param {number}         [options.filter.minEM=0] - Minimal monoisotopic mass
+* @param {number}         [options.filter.maxEM=+Infinity] - Maximal monoisotopic mass
+* @param {number}         [options.filter.minMSEM=0] - Minimal monoisotopic mass observed by mass
+* @param {number}         [options.filter.maxMSEM=+Infinity] - Maximal monoisotopic mass observed by mass
+* @param {number}         [options.filter.minCharge=-Infinity] - Minimal charge
+* @param {number}         [options.filter.maxCharge=+Infinity] - Maximal charge
+* @param {object}         [options.filter.unsaturation={}]
+* @param {number}         [options.filter.unsaturation.min=-Infinity] - Minimal unsaturation
+* @param {number}         [options.filter.unsaturation.max=+Infinity] - Maximal unsaturation
+* @param {number}         [options.filter.unsaturation.onlyInteger=false] - Integer unsaturation
+* @param {number}         [options.filter.unsaturation.onlyNonInteger=false] - Non integer unsaturation
+* @param {object}         [options.filter.callback] - a function to filter the MF
+* @param {object}         [options.filter.atoms] - object of atom:{min, max}
 */
@@ -32,0 +32,0 @@

src/searchSimilarity.js

@@ -10,2 +10,3 @@ 'use strict';
 * @param {boolean}  [options.flatten] - should we return the array as a flat result
+* @param {function} [options.onStep] - Callback to do after each step
 * @param {string}   [options.ionizations=''] - Comma separated list of ionizations (to charge the molecule)
@@ -20,7 +21,7 @@ * @param {object}   [options.minSimilarity=0.5] - min similarity value
 * @param {number}   [options.filter.maxCharge=+Infinity] - Maximal charge
-* @param {object}   [options.filter.unsaturation={}}]
+* @param {object}   [options.filter.unsaturation={}]
 * @param {number}   [options.filter.unsaturation.min=-Infinity] - Minimal unsaturation
 * @param {number}   [options.filter.unsaturation.max=+Infinity] - Maximal unsaturation
-* @param {number}   [options.filter.unsaturation.onlyInteger=false] - Integer unsaturation
-* @param {number}   [options.filter.unsaturation.onlyNonInteger=false] - Non integer unsaturation
+* @param {boolean}   [options.filter.unsaturation.onlyInteger=false] - Integer unsaturation
+* @param {boolean}   [options.filter.unsaturation.onlyNonInteger=false] - Non integer unsaturation
 * @param {object}   [options.filter.atoms] - object of atom:{min, max}
@@ -36,6 +37,7 @@ * @param {object}   [options.filter.callback] - a function to filter the MF
 * @param {object}   [options.similarity.common]
+* @returns {Promise}
 */
 
-module.exports = function searchSimilarity(options = {}) {
-  const { similarity = {}, minSimilarity = 0.5, filter = {} } = options;
+module.exports = async function searchSimilarity(options = {}) {
+  const { similarity = {}, minSimilarity = 0.5, filter = {}, onStep } = options;
 
@@ -91,3 +93,5 @@ let width = {
 
-  for (let entry of flatEntries) {
+  for (let i = 0; i < flatEntries.length; i++) {
+    const entry = flatEntries[i];
+    if (onStep) await onStep(i);
     let isotopicDistribution = new IsotopicDistribution(entry.mf, {
@@ -94,0 +98,0 @@ allowNeutral: false,

No alert changes

Improved metrics

Total package byte prevSize

1252071

increased by0.39%

Number of package files

48

increased by4.35%

Lines of code

2157

increased by7.37%

Worsened metrics

Number of low supply chain risk alerts

3

increased by50%

Dependency changes

• Updatedmf-finder@^1.2.1

• Updatedmf-from-google-sheet@^1.1.25

• Updatedmf-generator@^1.3.13

• Updatedms-spectrum@^1.4.7