emdb - npm Package Compare versions

Comparing version 0.6.3 to 0.6.4

package.json

 {
-    "name": "emdb",
-    "version": "0.6.3",
-    "description": "Database manager for exact mass query",
-    "browser": {
-        "./src/util/fetchArrayBuffer.js": "./src/util/fetchArrayBufferBrowser.js"
-    },
-    "main": "src/index.js",
-    "files": [
-        "src"
-    ],
-    "repository": {
-        "type": "git",
-        "url": "git+https://github.com/cheminfo-js/molecular-formula.git"
-    },
-    "keywords": [],
-    "author": "Luc Patiny",
-    "license": "MIT",
-    "bugs": {
-        "url": "https://github.com/cheminfo-js/molecular-formula/issues"
-    },
-    "homepage": "https://github.com/cheminfo-js/molecular-formula/tree/master/packages/emdb#readme",
-    "dependencies": {
-        "isotopic-distribution": "^0.6.3",
-        "jszip": "^3.1.5",
-        "mf-finder": "^0.6.3",
-        "mf-from-google-sheet": "^0.6.3",
-        "mf-generator": "^0.6.3",
-        "mf-matcher": "^0.6.3",
-        "mf-parser": "^0.6.3",
-        "mf-utilities": "^0.6.3",
-        "nucleotide": "^0.6.2",
-        "peaks-similarity": "^2.3.0",
-        "peptide": "^1.6.1",
-        "request-promise-native": "^1.0.5"
-    }
+  "name": "emdb",
+  "version": "0.6.4",
+  "description": "Database manager for exact mass query",
+  "browser": {
+    "./src/util/fetchArrayBuffer.js": "./src/util/fetchArrayBufferBrowser.js",
+    "./src/util/fetchJSON.js": "./src/util/fetchJSONBrowser.js"
+  },
+  "main": "src/index.js",
+  "files": [
+    "src"
+  ],
+  "repository": {
+    "type": "git",
+    "url": "git+https://github.com/cheminfo-js/molecular-formula.git"
+  },
+  "keywords": [],
+  "author": "Luc Patiny",
+  "license": "MIT",
+  "bugs": {
+    "url": "https://github.com/cheminfo-js/molecular-formula/issues"
+  },
+  "homepage": "https://github.com/cheminfo-js/molecular-formula/tree/master/packages/emdb#readme",
+  "dependencies": {
+    "isotopic-distribution": "^0.6.4",
+    "jszip": "^3.1.5",
+    "mf-finder": "^0.6.4",
+    "mf-from-google-sheet": "^0.6.4",
+    "mf-generator": "^0.6.4",
+    "mf-matcher": "^0.6.4",
+    "mf-parser": "^0.6.4",
+    "mf-utilities": "^0.6.4",
+    "nucleotide": "^0.6.4",
+    "peaks-similarity": "^2.3.0",
+    "peptide": "^1.6.1",
+    "request-promise-native": "^1.0.5"
+  }
 }

src/__tests__/DBManager.js

@@ -5,24 +5,23 @@ 'use strict';
 
+jest.setTimeout(30000);
+
 test('test DBManager contaminants and knapSack', async () => {
-    let dbManager = new DBManager();
+  let dbManager = new DBManager();
 
-    await dbManager.loadContaminants();
-    await dbManager.loadKnapSack();
+  await dbManager.loadContaminants();
+  await dbManager.loadKnapSack();
 
-    expect(dbManager.listDatabases()).toEqual(['contaminants', 'knapSack']);
-    expect(dbManager.get('contaminants').length).toBeGreaterThan(1000);
-
+  expect(dbManager.listDatabases()).toEqual(['contaminants', 'knapSack']);
+  expect(dbManager.get('contaminants').length).toBeGreaterThan(1000);
 });
 
 test('test DBManager fromMonoisotopicMass', () => {
-    let dbManager = new DBManager();
+  let dbManager = new DBManager();
 
-    dbManager.fromMonoisotopicMass(300, {
-        ionizations: 'H+,Na+'
-    });
+  dbManager.fromMonoisotopicMass(300, {
+    ionizations: 'H+,Na+'
+  });
 
-    expect(dbManager.listDatabases()).toEqual(['monoisotopic']);
-    expect(dbManager.get('monoisotopic').length).toBeGreaterThan(100);
-
-
+  expect(dbManager.listDatabases()).toEqual(['monoisotopic']);
+  expect(dbManager.get('monoisotopic').length).toBeGreaterThan(100);
 });

src/__tests__/fromPeptidicSequence.js

@@ -5,22 +5,22 @@ 'use strict';
 
-test('test fromArray', () => {
-    let dbManager = new DBManager();
-    dbManager.fromPeptidicSequence('AAKK', {
-        allowNeutralLoss: false,
-        protonation: false,
-        protonationPH: 7,
-        ionizations: 'H+,Na+',
-        fragmentation: {
-            a: true
-        },
-        filter: {
-            minMSEM: 100,
-            maxMSEM: 300,
-            targetMass: 150, // just to test, this is useless with precision 1e6
-            precision: 1e6
-        },
-    });
+test('test fromPeptidicSequence', () => {
+  let dbManager = new DBManager();
+  dbManager.fromPeptidicSequence('AAKK', {
+    allowNeutralLoss: false,
+    protonation: false,
+    protonationPH: 7,
+    ionizations: 'H+,Na+',
+    fragmentation: {
+      a: true
+    },
+    filter: {
+      minMSEM: 100,
+      maxMSEM: 300,
+      targetMass: 150, // just to test, this is useless with precision 1e6
+      precision: 1e6
+    }
+  });
 
-    expect(dbManager.databases.peptidic).toHaveLength(2);
-    expect(dbManager.databases.peptidic).toMatchSnapshot();
+  expect(dbManager.databases.peptidic).toHaveLength(2);
+  expect(dbManager.databases.peptidic).toMatchSnapshot();
 });

src/__tests__/loadKnapSack.js

@@ -5,13 +5,13 @@ 'use strict';
 
+jest.setTimeout(30000);
 test('test loadKnapSack', async () => {
+  let data = await loadKnapSack();
 
-    let data = await loadKnapSack();
+  expect(data.length).toBeGreaterThan(40000);
 
-    expect(data.length).toBeGreaterThan(40000);
-
-    let first = data[0];
-    expect(first.mf).toBe('H3N');
-    expect(first.em).toBeGreaterThan(0);
-    expect(first.charge).toBe(0);
-    expect(first.msem).toBeUndefined();
+  let first = data[0];
+  expect(first.mf).toBe('H3N');
+  expect(first.em).toBeGreaterThan(0);
+  expect(first.charge).toBe(0);
+  expect(first.msem).toBeUndefined();
 });

src/fromPeptidicSequence.js

@@ -9,4 +9,10 @@ '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 {object} [options={}]
+ * @param {string} [options.ionizations='']
+ * @param {array} [options.mfsArray=[]]
+ *  * @param {boolean} [options.protonation=false]
+ * @param {number} [options.protonationPH=7]
+ * @param {boolean} [options.allowNeutralLoss=false]
  * @param {object} [options.digestion={}] Object defining options for digestion
- * @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 {number} [options.digestion.minMissed=0] Minimal number of allowed missed cleavage
@@ -49,49 +55,49 @@ * @param {number} [options.digestion.maxMissed=0] Maximal number of allowed missed cleavage
 module.exports = function fromPeptidicSequence(sequence, options = {}) {
-    const {
-        digestion = {},
-        mfsArray = [],
-        allowNeutralLoss = false,
-        protonation = false,
-        protonationPH = 7,
-        fragmentation = {},
-        filter = {},
-        ionizations = ''
-    } = options;
+  const {
+    digestion = {},
+    mfsArray = [],
+    allowNeutralLoss = false,
+    protonation = false,
+    protonationPH = 7,
+    fragmentation = {},
+    filter = {},
+    ionizations = ''
+  } = options;
 
-    sequence = peptide.convertAASequence(sequence);
+  sequence = peptide.convertAASequence(sequence);
 
-    let fragmentsArray = [sequence];
-    // do we also have some digest fragments ?
-    if (digestion.enzyme) {
-        var digests = peptide.digestPeptide(sequence, digestion);
-        if (options.protonation) {
-            digests = peptide.chargePeptide(digests, {
-                pH: options.protonationPH
-            });
-        }
-        fragmentsArray = fragmentsArray.concat(digests);
+  let fragmentsArray = [sequence];
+  // do we also have some digest fragments ?
+  if (digestion.enzyme) {
+    var digests = peptide.digestPeptide(sequence, digestion);
+    if (options.protonation) {
+      digests = peptide.chargePeptide(digests, {
+        pH: options.protonationPH
+      });
     }
+    fragmentsArray = fragmentsArray.concat(digests);
+  }
 
-    // allow neutral loss
-    if (allowNeutralLoss) {
-        sequence = peptide.allowNeutralLoss(sequence);
-    }
+  // allow neutral loss
+  if (allowNeutralLoss) {
+    sequence = peptide.allowNeutralLoss(sequence);
+  }
 
-    // apply protonation
-    if (protonation) {
-        sequence = peptide.chargePeptide(sequence, { pH: protonationPH });
-    }
+  // apply protonation
+  if (protonation) {
+    sequence = peptide.chargePeptide(sequence, { pH: protonationPH });
+  }
 
-    // calculate fragmentation
-    var fragments = peptide.generatePeptideFragments(sequence, fragmentation);
-    fragmentsArray = fragmentsArray.concat(fragments);
+  // calculate fragmentation
+  var fragments = peptide.generatePeptideFragments(sequence, fragmentation);
+  fragmentsArray = fragmentsArray.concat(fragments);
 
-    mfsArray.push(fragmentsArray);
+  mfsArray.push(fragmentsArray);
 
-    let combined = combineMFs(mfsArray, {
-        ionizations,
-        filter: filter
-    });
+  let combined = combineMFs(mfsArray, {
+    ionizations,
+    filter: filter
+  });
 
-    return combined;
+  return combined;
 };

src/index.js

@@ -8,10 +8,10 @@ 'use strict';
 function DBManager() {
-    this.databases = {};
-    this.experimentalSpectrum = undefined;
+  this.databases = {};
+  this.experimentalSpectrum = undefined;
 }
 
 DBManager.prototype.setExperimentalSpectrum = function setExperimentalSpectrum(
-    experimentalSpectrum
+  experimentalSpectrum
 ) {
-    this.experimentalSpectrum = experimentalSpectrum;
+  this.experimentalSpectrum = experimentalSpectrum;
 };
@@ -24,5 +24,5 @@
 DBManager.prototype.loadKnapSack = async function loadKnapSack(options = {}) {
-    const { databaseName = 'knapSack', forceReload = false } = options;
-    if (this.databases[databaseName] && !forceReload) return;
-    this.databases[databaseName] = await loadKnapSackPromise();
+  const { databaseName = 'knapSack', forceReload = false } = options;
+  if (this.databases[databaseName] && !forceReload) return;
+  this.databases[databaseName] = await loadKnapSackPromise();
 };
@@ -35,11 +35,11 @@
 DBManager.prototype.loadCommercials = async function loadCommercials(
-    options = {}
+  options = {}
 ) {
-    const { databaseName = 'commercials', forceReload = false } = options;
-    if (this.databases[databaseName] && !forceReload) return;
-    this.databases[databaseName] = await loadCommercialsPromise();
+  const { databaseName = 'commercials', forceReload = false } = options;
+  if (this.databases[databaseName] && !forceReload) return;
+  this.databases[databaseName] = await loadCommercialsPromise();
 };
 
 DBManager.prototype.get = function get(databaseName) {
-    return this.databases[databaseName];
+  return this.databases[databaseName];
 };
@@ -53,7 +53,7 @@
 DBManager.prototype.loadContaminants = async function loadContaminants(
-    options = {}
+  options = {}
 ) {
-    const { databaseName = 'contaminants', forceReload = false } = options;
-    if (this.databases[databaseName] && !forceReload) return;
-    this.databases[databaseName] = await loadGoogleSheetPromise();
+  const { databaseName = 'contaminants', forceReload = false } = options;
+  if (this.databases[databaseName] && !forceReload) return;
+  this.databases[databaseName] = await loadGoogleSheetPromise();
 };
@@ -68,41 +68,52 @@
 DBManager.prototype.loadGoogleSheet = async function loadGoogleSheet(
-    options = {}
+  options = {}
 ) {
-    const { databaseName = 'sheet', forceReload = false } = options;
-    if (this.databases[databaseName] && !forceReload) return;
-    this.databases[databaseName] = await loadGoogleSheetPromise();
+  const { databaseName = 'sheet', forceReload = false } = options;
+  if (this.databases[databaseName] && !forceReload) return;
+  this.databases[databaseName] = await loadGoogleSheetPromise();
 };
 
 DBManager.prototype.loadTest = function loadTest() {
-    this.fromArray(['C1-100'], { databaseName: 'test', ionizations: '+' });
+  this.fromArray(['C1-100'], { databaseName: 'test', ionizations: '+' });
 };
 
 DBManager.prototype.fromMonoisotopicMass = function fromMonoisotopicMass(
-    mass,
-    options = {}
+  mass,
+  options = {}
 ) {
-    const { databaseName = 'monoisotopic' } = options;
-    let result = require('./fromMonoisotopicMass')(mass, options);
-    this.databases[databaseName] = result.mfs;
-    return result;
+  const { databaseName = 'monoisotopic' } = options;
+  let result = require('./fromMonoisotopicMass')(mass, options);
+  this.databases[databaseName] = result.mfs;
+  return result;
 };
 
 DBManager.prototype.fromArray = function fromArray(sequence, options = {}) {
-    const { databaseName = 'generated' } = options;
-    this.databases[databaseName] = require('./fromArray')(sequence, options);
+  const { databaseName = 'generated' } = options;
+  this.databases[databaseName] = require('./fromArray')(sequence, options);
 };
 
 DBManager.prototype.fromPeptidicSequence = function fromPeptidicSequence(
+  sequence,
+  options = {}
+) {
+  const { databaseName = 'peptidic' } = options;
+  this.databases[databaseName] = require('./fromPeptidicSequence')(
     sequence,
-    options = {}
+    options
+  );
+};
+
+DBManager.prototype.fromNucleicSequence = function fromNucleicSequence(
+  sequence,
+  options = {}
 ) {
-    const { databaseName = 'peptidic' } = options;
-    this.databases[databaseName] = require('./fromPeptidicSequence')(
-        sequence,
-        options
-    );
+  const { databaseName = 'nucleic' } = options;
+  this.databases[databaseName] = require('./fromNucleicSequence')(
+    sequence,
+    options
+  );
 };
 
 DBManager.prototype.listDatabases = function listDatabases() {
-    return Object.keys(this.databases).sort();
+  return Object.keys(this.databases).sort();
 };
@@ -115,9 +126,2 @@
 
-DBManager.Util = {
-    IsotopicDistribution: require('isotopic-distribution'),
-    MF: require('mf-parser').MF,
-    Peptide: require('peptide'),
-    Nucleotide: require('nucleotide')
-};
-
 module.exports = DBManager;

src/searchPubchem.js

@@ -52,8 +52,9 @@ 'use strict';
             } catch (e) {
-                console.warn(e+'');
+                console.warn(`${e}`);
             }
         }
     }
-
+    // because we can combine many ionizations we should resort the data
+    mfs.sort((a, b) => a.ms.ppm - b.ms.ppm);
     return mfs;
 };

No alert changes

Improved metrics

Total package byte prevSize

100702

increased by14.6%

Lines of code

1017

increased by8.19%

Dependency changes

• Updatedisotopic-distribution@^0.6.4

• Updatedmf-finder@^0.6.4

• Updatedmf-from-google-sheet@^0.6.4

• Updatedmf-generator@^0.6.4

• Updatedmf-matcher@^0.6.4

• Updatedmf-parser@^0.6.4

• Updatedmf-utilities@^0.6.4

• Updatednucleotide@^0.6.4