nucleotide - npm Package Compare versions

Comparing version 1.2.25 to 1.3.0

package.json

@@ -11,9 +11,7 @@ {
   "description": "Deal with nucleotides and molecular formula",
-  "main": "lib/index.js",
-  "module": "src/index.js",
+  "main": "src/index.js",
   "files": [
-    "src",
-    "lib"
+    "src"
   ],
-  "homepage": "https://github.com/cheminfo/mass-tools/tree/main/packages/nucleotide#readme",
+  "homepage": "https://github.com/cheminfo/mass-tools/tree/master/packages/nucleotide#readme",
   "keywords": [],
@@ -26,11 +24,11 @@ "license": "MIT",
   },
-  "version": "1.2.25",
+  "version": "1.3.0",
   "devDependencies": {
-    "mf-parser": "^1.4.8"
+    "mf-parser": "^1.5.0"
   },
   "dependencies": {
-    "chemical-groups": "^1.2.2",
-    "mf-utilities": "^1.4.2"
+    "chemical-groups": "^1.3.0",
+    "mf-utilities": "^1.5.0"
   },
-  "gitHead": "bd2c06e05f2196c5f9c6ff011cf3ef41e1b6a0f9"
+  "gitHead": "ade929b07af4e2f0f8b3fe1aaf0df70c50f4b2db"
 }

src/__tests__/addFiveTermBaseLoss.test.js

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

src/__tests__/addThreeTermBaseLoss.test.js

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

src/__tests__/baseLoss.test.js

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

src/__tests__/baseLossExhaustive.test.js

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

src/__tests__/ensureUppercaseSequence.test.js

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

src/__tests__/furanThreeTerm.test.js

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

src/__tests__/generateFragments.internal.test.js

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

src/__tests__/generateFragments.test.js

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

src/__tests__/sequenceToMF.test.js

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

src/addFiveTerm.js

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

src/addFiveTermBaseLoss.js

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

src/addInternalTerm.js

@@ -1,6 +0,8 @@
-import { furanThreeTerm } from './furanThreeTerm.js';
+'use strict';
 
+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
 
-export function addInternalTerm(mfs, internal, ter3, ter5, options = {}) {
+function addInternalTerm(mfs, internal, ter3, ter5, options = {}) {
   if (options.aw) {
@@ -28,1 +30,3 @@ // without base loss
 }
+
+module.exports = addInternalTerm;

src/addThreeTerm.js

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

src/addThreeTermBaseLoss.js

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

src/baseLoss.js

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

src/baseLossExhaustive.js

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

src/ensureUppercaseSequence.js

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

src/furanThreeTerm.js

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

src/generateFragments.js

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

src/index.js

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

src/sequenceToMF.js

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

No alert changes

Worsened metrics

Total package byte prevSize

32816

decreased by-26.72%

Number of package files

25

decreased by-3.85%

Lines of code

871

decreased by-29.59%

Dependency changes

• Updatedchemical-groups@^1.3.0

• Updatedmf-utilities@^1.5.0