nucleotide - npm Package Compare versions

Comparing version 3.1.0 to 3.1.1

package.json

@@ -8,6 +8,5 @@ {
   },
-  "bundleDependencies": false,
   "deprecated": false,
   "description": "Deal with nucleotides and molecular formula",
-  "main": "lib/index.js",
+  "main": "lib/src/index.js",
   "module": "src/index.js",
@@ -26,11 +25,11 @@ "files": [
   },
-  "version": "3.1.0",
+  "version": "3.1.1",
   "devDependencies": {
-    "mf-parser": "^3.2.0"
+    "mf-parser": "^3.2.1"
   },
   "dependencies": {
-    "chemical-groups": "^2.2.0",
-    "mf-utilities": "^3.2.0"
+    "chemical-groups": "^2.2.1",
+    "mf-utilities": "^3.2.1"
   },
-  "gitHead": "28dae91d3b42556a23097ee08acfe4061f276ed0"
+  "gitHead": "838f98a30846d4b1721b8ed7aa94a55e854d7521"
 }

src/addFiveTermBaseLoss.js

@@ -7,3 +7,3 @@ import { baseLoss } from './baseLoss.js';
 
-  loss.forEach((mf) => {
+  for (const mf of loss) {
     if (options.a) {
@@ -21,3 +21,3 @@ mfs.push(`${mf}`.replace('$', `O-1H-1$a${i} `));
     }
-  });
+  }
 }

src/addThreeTermBaseLoss.js

@@ -7,3 +7,3 @@ import { baseLoss } from './baseLoss.js';
 
-  loss.forEach((mf) => {
+  for (const mf of loss) {
     if (options.w) {
@@ -21,3 +21,3 @@ mfs.push(`HO${mf}`.replace('$', `$w${i} `));
     }
-  });
+  }
 }

src/baseLoss.js

 import { mfDiff } from 'mf-utilities';
 
 const mfLosses = {};
-['Amp', 'Tmp', 'Cmp', 'Gmp', 'Ump'].forEach((nucleotide) => {
+for (const nucleotide of ['Amp', 'Tmp', 'Cmp', 'Gmp', 'Ump']) {
   mfLosses[nucleotide] = {
@@ -9,5 +9,5 @@ code: nucleotide.charAt(0),
   };
-});
+}
 
-['Damp', 'Dtmp', 'Dcmp', 'Dgmp', 'Dump'].forEach((nucleotide) => {
+for (const nucleotide of ['Damp', 'Dtmp', 'Dcmp', 'Dgmp', 'Dump']) {
   mfLosses[nucleotide] = {
@@ -17,3 +17,3 @@ code: nucleotide.charAt(1).toUpperCase(),
   };
-});
+}
 
@@ -20,0 +20,0 @@ export function baseLoss(nucleotide) {

src/baseLossExhaustive.js

@@ -5,4 +5,4 @@ export function baseLossExhaustive(nucleotide) {
   let parts = nucleotide
-    .replace(/ /g, '')
-    .replace(/([a-zA-Z0-9)])(?=[A-Z])/g, '$1 ')
+    .replaceAll(' ', '')
+    .replaceAll(/([\d)A-Za-z])(?=[A-Z])/g, '$1 ')
     .split(/ /);
@@ -13,6 +13,6 @@ let counter = 0;
     let middle = '';
-    if (part.match(/^D[atcgu]mp$/)) {
+    if (part.match(/^D[acgtu]mp$/)) {
       middle = 'Drmp';
       counter++;
-    } else if (part.match(/^[ATCGU]mp$/)) {
+    } else if (part.match(/^[ACGTU]mp$/)) {
       middle = 'Rmp';
@@ -19,0 +19,0 @@ counter++;

src/furanThreeTerm.js

 export function furanThreeTerm(nucleotide) {
   // last residue should become a furan
   let parts = nucleotide
-    .replace(/ /g, '')
-    .replace(/([a-z)0-9])([A-Z][a-z](?=[a-z]))/g, '$1 $2')
+    .replaceAll(' ', '')
+    .replaceAll(/([\d)a-z])([A-Z][a-z](?=[a-z]))/g, '$1 $2')
     .split(/ /);
   let last = parts.pop();
-  if (!last.match(/D[atcg]mp(.*)$/)) {
+  if (!last.match(/D[acgt]mp(.*)$/)) {
     // eslint-disable-next-line no-console
@@ -15,3 +15,3 @@ console.warn(
   }
-  return parts.join('') + last.replace(/D[atcg]mp(.*)$/, 'Furp');
+  return parts.join('') + last.replace(/D[acgt]mp(.*)$/, 'Furp');
 }

src/generateFragments.js

@@ -33,3 +33,3 @@ import { addFiveTerm } from './addFiveTerm';
   let mfparts = mf
-    .replace(/([a-z)0-9])([A-Z][a-z](?=[a-z]))/g, '$1 $2')
+    .replaceAll(/([\d)a-z])([A-Z][a-z](?=[a-z]))/g, '$1 $2')
     .split(/ /);
@@ -45,8 +45,5 @@
 
-  if (mfparts[mfparts.length - 1].includes('(')) {
-    threeTerm += mfparts[mfparts.length - 1].replace(/^[^()]*/, '');
-    mfparts[mfparts.length - 1] = mfparts[mfparts.length - 1].replace(
-      /\(.*/,
-      '',
-    );
+  if (mfparts.at(-1).includes('(')) {
+    threeTerm += mfparts.at(-1).replace(/^[^()]*/, '');
+    mfparts[mfparts.length - 1] = mfparts.at(-1).replace(/\(.*/, '');
   }
@@ -53,0 +50,0 @@

src/sequenceToMF.js

@@ -32,3 +32,3 @@ import { groups } from 'chemical-groups';
   let { kind, circular, fivePrime = 'monophosphate' } = options;
-  fivePrime = fivePrime.replace(/[^a-zA-Z]/g, '').toLowerCase();
+  fivePrime = fivePrime.replaceAll(/[^A-Za-z]/g, '').toLowerCase();
 
@@ -43,3 +43,3 @@ if (!kind) {
 
-  kind = kind.replace(/[^A-Za-z]/g, '').toLowerCase();
+  kind = kind.replaceAll(/[^A-Za-z]/g, '').toLowerCase();
 
@@ -98,3 +98,3 @@ if (sequence.includes('(') && kind === 'dsdna') {
 
-    currentSymbol = currentSymbol.replace(/[ \t\r\n]/, '');
+    currentSymbol = currentSymbol.replace(/[\t\n\r ]/, '');
     if (!currentSymbol) continue;
@@ -122,4 +122,4 @@
   if (!circular) {
-    results.forEach((result) => result.unshift(fivePrimeTerminal));
-    results.forEach((result) => result.push(threePrimeTerminal));
+    for (const result of results) result.unshift(fivePrimeTerminal);
+    for (const result of results) result.push(threePrimeTerminal);
   }
@@ -144,41 +144,31 @@
 
-groups
-  .filter((group) => group.kind === 'DNA')
-  .forEach((group) => {
-    if (group.oneLetter) {
-      desoxyNucleotides.alcohol[group.oneLetter] = group.symbol;
-    }
-  });
+for (const group of groups.filter(({ kind }) => kind === 'DNA')) {
+  if (group.oneLetter) {
+    desoxyNucleotides.alcohol[group.oneLetter] = group.symbol;
+  }
+}
 
-groups
-  .filter((group) => group.kind === 'DNAp')
-  .forEach((group) => {
-    if (group.oneLetter) {
-      desoxyNucleotides.monophosphate[group.oneLetter] = group.symbol;
-    }
-  });
+for (const group of groups.filter(({ kind }) => kind === 'DNAp')) {
+  if (group.oneLetter) {
+    desoxyNucleotides.monophosphate[group.oneLetter] = group.symbol;
+  }
+}
 
-groups
-  .filter((group) => group.kind === 'NucleotideP')
-  .forEach((group) => {
-    if (group.oneLetter) {
-      desoxyNucleotides.monophosphate[group.oneLetter] = group.symbol;
-    }
-  });
+for (const group of groups.filter(({ kind }) => kind === 'NucleotideP')) {
+  if (group.oneLetter) {
+    desoxyNucleotides.monophosphate[group.oneLetter] = group.symbol;
+  }
+}
 
-groups
-  .filter((group) => group.kind === 'DNApp')
-  .forEach((group) => {
-    if (group.oneLetter) {
-      desoxyNucleotides.diphosphate[group.oneLetter] = group.symbol;
-    }
-  });
+for (const group of groups.filter(({ kind }) => kind === 'DNApp')) {
+  if (group.oneLetter) {
+    desoxyNucleotides.diphosphate[group.oneLetter] = group.symbol;
+  }
+}
 
-groups
-  .filter((group) => group.kind === 'DNAppp')
-  .forEach((group) => {
-    if (group.oneLetter) {
-      desoxyNucleotides.triphosphate[group.oneLetter] = group.symbol;
-    }
-  });
+for (const group of groups.filter(({ kind }) => kind === 'DNAppp')) {
+  if (group.oneLetter) {
+    desoxyNucleotides.triphosphate[group.oneLetter] = group.symbol;
+  }
+}
 
@@ -192,40 +182,30 @@ const oxyNucleotides = {
 
-groups
-  .filter((group) => group.kind === 'RNA')
-  .forEach((group) => {
-    if (group.oneLetter) {
-      oxyNucleotides.alcohol[group.oneLetter] = group.symbol;
-    }
-  });
+for (const group of groups.filter(({ kind }) => kind === 'RNA')) {
+  if (group.oneLetter) {
+    oxyNucleotides.alcohol[group.oneLetter] = group.symbol;
+  }
+}
 
-groups
-  .filter((group) => group.kind === 'RNAp')
-  .forEach((group) => {
-    if (group.oneLetter) {
-      oxyNucleotides.monophosphate[group.oneLetter] = group.symbol;
-    }
-  });
+for (const group of groups.filter(({ kind }) => kind === 'RNAp')) {
+  if (group.oneLetter) {
+    oxyNucleotides.monophosphate[group.oneLetter] = group.symbol;
+  }
+}
 
-groups
-  .filter((group) => group.kind === 'NucleotideP')
-  .forEach((group) => {
-    if (group.oneLetter) {
-      oxyNucleotides.monophosphate[group.oneLetter] = group.symbol;
-    }
-  });
+for (const group of groups.filter(({ kind }) => kind === 'NucleotideP')) {
+  if (group.oneLetter) {
+    oxyNucleotides.monophosphate[group.oneLetter] = group.symbol;
+  }
+}
 
-groups
-  .filter((group) => group.kind === 'RNApp')
-  .forEach((group) => {
-    if (group.oneLetter) {
-      oxyNucleotides.diphosphate[group.oneLetter] = group.symbol;
-    }
-  });
+for (const group of groups.filter(({ kind }) => kind === 'RNApp')) {
+  if (group.oneLetter) {
+    oxyNucleotides.diphosphate[group.oneLetter] = group.symbol;
+  }
+}
 
-groups
-  .filter((group) => group.kind === 'RNAppp')
-  .forEach((group) => {
-    if (group.oneLetter) {
-      oxyNucleotides.triphosphate[group.oneLetter] = group.symbol;
-    }
-  });
+for (const group of groups.filter(({ kind }) => kind === 'RNAppp')) {
+  if (group.oneLetter) {
+    oxyNucleotides.triphosphate[group.oneLetter] = group.symbol;
+  }
+}

New alerts

Major refactor

Supply chain risk

Package has recently undergone a major refactor. It may be unstable or indicate significant internal changes. Use caution when updating to versions that include significant changes.

Found 1 instance in 1 package

New author

Supply chain risk

A new npm collaborator published a version of the package for the first time. New collaborators are usually benign additions to a project, but do indicate a change to the security surface area of a package.

Found 1 instance in 1 package

Fixed alerts

Major refactor

Supply chain risk

Package has recently undergone a major refactor. It may be unstable or indicate significant internal changes. Use caution when updating to versions that include significant changes.

Found 1 instance in 1 package

Improved metrics

Total package byte prevSize

66723

increased by89.82%

Number of package files

40

increased by2.56%

Worsened metrics

Lines of code

916

decreased by-4.28%

Number of medium supply chain risk alerts

2

increased by100%

Dependency changes

• Updatedchemical-groups@^2.2.1

• Updatedmf-utilities@^3.2.1