nucleotide - npm Package Compare versions

Comparing version 1.3.0 to 2.0.0

package.json

@@ -11,7 +11,9 @@ {
   "description": "Deal with nucleotides and molecular formula",
-  "main": "src/index.js",
+  "main": "lib/index.js",
+  "module": "src/index.js",
   "files": [
-    "src"
+    "src",
+    "lib"
   ],
-  "homepage": "https://github.com/cheminfo/mass-tools/tree/master/packages/nucleotide#readme",
+  "homepage": "https://github.com/cheminfo/mass-tools/tree/main/packages/nucleotide#readme",
   "keywords": [],
@@ -24,11 +26,11 @@ "license": "MIT",
   },
-  "version": "1.3.0",
+  "version": "2.0.0",
   "devDependencies": {
-    "mf-parser": "^1.5.0"
+    "mf-parser": "^2.0.0"
   },
   "dependencies": {
-    "chemical-groups": "^1.3.0",
-    "mf-utilities": "^1.5.0"
+    "chemical-groups": "^2.0.0",
+    "mf-utilities": "^2.0.0"
   },
-  "gitHead": "ade929b07af4e2f0f8b3fe1aaf0df70c50f4b2db"
+  "gitHead": "c6ebfbd64c711f8839a02a43c5708e71a379885b"
 }

src/__tests__/addFiveTermBaseLoss.test.js

@@ -1,5 +0,3 @@
-'use strict';
+import { generateFragments } from '../generateFragments';
 
-const generateFragments = require('../generateFragments');
-
 describe('addFiveTermBaseLoss', () => {
@@ -6,0 +4,0 @@ it('nucleotide to sequence of HODampDtmpDcmpH', () => {

src/__tests__/addThreeTermBaseLoss.test.js

@@ -1,5 +0,3 @@
-'use strict';
+import { generateFragments } from '../generateFragments';
 
-const generateFragments = require('../generateFragments');
-
 describe('addFiveTermBaseLoss', () => {
@@ -6,0 +4,0 @@ it('nucleotide to sequence of HODampDtmpDcmpH', () => {

src/__tests__/baseLoss.test.js

@@ -1,5 +0,3 @@
-'use strict';
+import { baseLoss } from '..';
 
-const { baseLoss } = require('..');
-
 describe('baseLoss', () => {
@@ -6,0 +4,0 @@ it('Base loss of HAlaDampDtmpDcmpDcmpOH', () => {

src/__tests__/baseLossExhaustive.test.js

@@ -1,5 +0,3 @@
-'use strict';
+import { baseLossExhaustive } from '../baseLossExhaustive';
 
-const baseLossExhaustive = require('../baseLossExhaustive');
-
 describe('test base loss', () => {
@@ -6,0 +4,0 @@ it('Base loss of HAlaDampDtmpDcmpDcmpOH', () => {

src/__tests__/ensureUppercaseSequence.test.js

@@ -1,5 +0,3 @@
-'use strict';
+import { ensureUppercaseSequence } from '../ensureUppercaseSequence';
 
-const ensureUppercaseSequence = require('../ensureUppercaseSequence');
-
 describe('ensureUppercaseSequence', () => {
@@ -6,0 +4,0 @@ it('aattccgg', () => {

src/__tests__/furanThreeTerm.test.js

@@ -1,7 +0,5 @@
-'use strict';
+import { MF } from 'mf-parser';
 
-const { MF } = require('mf-parser');
+import { furanThreeTerm } from '..';
 
-const { furanThreeTerm } = require('..');
-
 describe('test nucleotide', () => {
@@ -8,0 +6,0 @@ it('remove base of three terminal of HDampDtmpDcmp', () => {

src/__tests__/generateFragments.internal.test.js

@@ -1,5 +0,3 @@
-'use strict';
+import { generateFragments } from '..';
 
-const { generateFragments } = require('..');
-
 describe('test generate internal fragments', () => {
@@ -6,0 +4,0 @@ it('nucleotide HODampDtmpDcmpDgmpDampH internal abw fragments', () => {

src/__tests__/generateFragments.test.js

@@ -1,5 +0,3 @@
-'use strict';
+import { generateFragments } from '..';
 
-const { generateFragments } = require('..');
-
 describe('test generate fragments', () => {
@@ -6,0 +4,0 @@ it('nucleotide to sequence of HODampDtmpDcmpH', () => {

src/__tests__/sequenceToMF.test.js

@@ -1,7 +0,5 @@
-'use strict';
+import { MF } from 'mf-parser';
 
-const MF = require('mf-parser').MF;
+import { sequenceToMF } from '../sequenceToMF.js';
 
-const sequenceToMF = require('../sequenceToMF');
-
 describe('sequenceToMF', () => {
@@ -8,0 +6,0 @@ it('emtpy string', () => {

src/addFiveTerm.js

@@ -1,6 +0,4 @@
-'use strict';
+import { furanThreeTerm } from './furanThreeTerm.js';
 
-const furanThreeTerm = require('./furanThreeTerm');
-
-function addFiveTerm(mfs, fiveTerm, i, options) {
+export function addFiveTerm(mfs, fiveTerm, i, options) {
   if (options.a) mfs.push(`${fiveTerm}O-1H-1$a${i}`); // neutral ok
@@ -13,3 +11,1 @@ if (options.ab && i > 1) mfs.push(`${furanThreeTerm(fiveTerm)}$a${i}-B`); // A minus base
 }
-
-module.exports = addFiveTerm;

src/addFiveTermBaseLoss.js

@@ -1,6 +0,4 @@
-'use strict';
+import { baseLoss } from './baseLoss.js';
 
-const baseLoss = require('./baseLoss');
-
-function addFiveTermBaseLoss(mfs, fiveTerm, i, options) {
+export function addFiveTermBaseLoss(mfs, fiveTerm, i, options) {
   if (!options.abcdBaseLoss) return;
@@ -24,3 +22,1 @@ let loss = baseLoss(fiveTerm);
 }
-
-module.exports = addFiveTermBaseLoss;

src/addInternalTerm.js

@@ -1,8 +0,6 @@
-'use strict';
+import { furanThreeTerm } from './furanThreeTerm.js';
 
-const furanThreeTerm = require('./furanThreeTerm');
-
 // https://books.google.ch/books?id=B57e37bJjqAC&pg=PA172&lpg=PA172&dq=oligonucleotide+b+fragmentation&source=bl&ots=mRr29Pexx2&sig=1NUQcWV-wuj6o9q81my86AVoRto&hl=fr&sa=X&ved=2ahUKEwjI5M3yn-7fAhUJMewKHQR6Bcs4ChDoATADegQIBhAB#v=onepage&q=oligonucleotide%20b%20fragmentation&f=false
 
-function addInternalTerm(mfs, internal, ter3, ter5, options = {}) {
+export function addInternalTerm(mfs, internal, ter3, ter5, options = {}) {
   if (options.aw) {
@@ -30,3 +28,1 @@ // without base loss
 }
-
-module.exports = addInternalTerm;

src/addThreeTerm.js

@@ -1,4 +0,2 @@
-'use strict';
-
-function addThreeTerm(mfs, threeTerm, i, options) {
+export function addThreeTerm(mfs, threeTerm, i, options) {
   if (options.w) mfs.push(`HO${threeTerm}$w${i}`); // neutral ok
@@ -10,3 +8,1 @@ if (options.x) mfs.push(`H-1${threeTerm}$x${i}`); // neutral ok
 }
-
-module.exports = addThreeTerm;

src/addThreeTermBaseLoss.js

@@ -1,6 +0,4 @@
-'use strict';
+import { baseLoss } from './baseLoss.js';
 
-const baseLoss = require('./baseLoss');
-
-function addThreeTermBaseLoss(mfs, threeTerm, i, options) {
+export function addThreeTermBaseLoss(mfs, threeTerm, i, options) {
   if (!options.wxyzBaseLoss) return;
@@ -24,3 +22,1 @@ let loss = baseLoss(threeTerm);
 }
-
-module.exports = addThreeTermBaseLoss;

src/baseLoss.js

@@ -1,5 +0,3 @@
-'use strict';
+import { mfDiff } from 'mf-utilities';
 
-const mfDiff = require('mf-utilities/src/mfDiff');
-
 const mfLosses = {};
@@ -20,3 +18,3 @@ ['Amp', 'Tmp', 'Cmp', 'Gmp', 'Ump'].forEach((nucleotide) => {
 
-function baseLoss(nucleotide) {
+export function baseLoss(nucleotide) {
   // any residue can loose a base
@@ -34,3 +32,1 @@ let results = [];
 }
-
-module.exports = baseLoss;

src/baseLossExhaustive.js

@@ -1,4 +0,2 @@
-'use strict';
-
-function baseLossExhaustive(nucleotide) {
+export function baseLossExhaustive(nucleotide) {
   // any residue can loose a base
@@ -31,3 +29,1 @@ let results = [];
 }
-
-module.exports = baseLossExhaustive;

src/ensureUppercaseSequence.js

@@ -1,3 +0,1 @@
-'use strict';
-
 /**
@@ -8,3 +6,3 @@ * Ensure that the sequence is in uppercase taking into account possible modifications
 
-function ensureUppercaseSequence(sequence) {
+export function ensureUppercaseSequence(sequence) {
   let parenthesisCounter = 0;
@@ -35,3 +33,1 @@ let parts = [];
 }
-
-module.exports = ensureUppercaseSequence;

src/furanThreeTerm.js

@@ -1,4 +0,2 @@
-'use strict';
-
-function furanThreeTerm(nucleotide) {
+export function furanThreeTerm(nucleotide) {
   // last residue should become a furan
@@ -19,3 +17,1 @@ let parts = nucleotide
 }
-
-module.exports = furanThreeTerm;

src/generateFragments.js

@@ -1,10 +0,8 @@
-'use strict';
+import { addFiveTerm } from './addFiveTerm';
+import { addFiveTermBaseLoss } from './addFiveTermBaseLoss';
+import { addInternalTerm } from './addInternalTerm';
+import { addThreeTerm } from './addThreeTerm';
+import { addThreeTermBaseLoss } from './addThreeTermBaseLoss';
 
-const addFiveTerm = require('./addFiveTerm');
-const addFiveTermBaseLoss = require('./addFiveTermBaseLoss');
-const addInternalTerm = require('./addInternalTerm');
-const addThreeTerm = require('./addThreeTerm');
-const addThreeTermBaseLoss = require('./addThreeTermBaseLoss');
-
-module.exports = function generateFragments(mf, options) {
+export function generateFragments(mf, options) {
   if (options === undefined) {
@@ -75,2 +73,2 @@ options = {
   return mfs;
-};
+}

src/index.js

@@ -1,8 +0,4 @@
-'use strict';
-
-module.exports = {
-  sequenceToMF: require('./sequenceToMF'),
-  generateFragments: require('./generateFragments'),
-  furanThreeTerm: require('./furanThreeTerm'),
-  baseLoss: require('./baseLoss'),
-};
+export * from './sequenceToMF.js';
+export * from './generateFragments.js';
+export * from './furanThreeTerm.js';
+export * from './baseLoss.js';

src/sequenceToMF.js

@@ -1,7 +0,5 @@
-'use strict';
+import { groups } from 'chemical-groups';
 
-const { groups } = require('chemical-groups');
+import { ensureUppercaseSequence } from './ensureUppercaseSequence';
 
-const ensureUppercaseSequence = require('./ensureUppercaseSequence');
-
 /**
@@ -16,3 +14,3 @@ * Convert a nucleic sequence to a MF
 
-function sequenceToMF(sequence, options = {}) {
+export function sequenceToMF(sequence, options = {}) {
   let fivePrimeTerminal = 'HO';
@@ -129,4 +127,2 @@ let threePrimeTerminal = 'H';
 
-module.exports = sequenceToMF;
-
 const complementary = {
@@ -133,0 +129,0 @@ A: 'T',

No alert changes

Improved metrics

Total package byte prevSize

44781

increased by36.46%

Number of package files

26

increased by4%

Lines of code

1237

increased by42.02%

Dependency changes

• + Addedatom-sorter@2.2.0(transitive)

• + Addedchemical-elements@2.2.0(transitive)

• + Addedchemical-groups@2.2.2(transitive)

• + Addedmf-parser@2.3.1(transitive)

• + Addedmf-utilities@2.0.5(transitive)

• - Removedatom-sorter@1.2.0(transitive)

• - Removedchemical-elements@1.3.0(transitive)

• - Removedchemical-groups@1.3.0(transitive)

• - Removedmf-parser@1.5.0(transitive)

• - Removedmf-utilities@1.5.0(transitive)

• - Removedpapaparse@5.5.0(transitive)

• Updatedchemical-groups@^2.0.0

• Updatedmf-utilities@^2.0.0