chromatography - npm Package Compare versions

Comparing version 3.10.0 to 3.11.0

lib/index.js

@@ -8,3 +8,3 @@ 'use strict';
 var mlGsd = require('ml-gsd');
-var max = _interopDefault(require('ml-array-max'));
+var arrayMax = _interopDefault(require('ml-array-max'));
 var IsotopicDistribution = _interopDefault(require('isotopic-distribution'));
@@ -295,3 +295,3 @@ var binarySearch = _interopDefault(require('binary-search'));
     if (massSpectrum[1].length > 0) {
-      bpc.push(max(massSpectrum[1]));
+      bpc.push(arrayMax(massSpectrum[1]));
     } else {
@@ -792,3 +792,3 @@ bpc.push(0);
 
-  let max$$1 = -1;
+  let max = -1;
   let massList = new Array(massXYObject.x.length);
@@ -801,4 +801,4 @@ for (let i = 0; i < massXYObject.x.length; ++i) {
 
-    if (massXYObject.y[i] > max$$1) {
-      max$$1 = massXYObject.y[i];
+    if (massXYObject.y[i] > max) {
+      max = massXYObject.y[i];
     }
@@ -808,4 +808,4 @@ }
   // filters based in thresholdFactor
-  max$$1 *= thresholdFactor;
-  let filteredList = massList.filter((val) => val.y > max$$1);
+  max *= thresholdFactor;
+  let filteredList = massList.filter((val) => val.y > max);
 
@@ -1121,5 +1121,3 @@ // filters based in maxNumberPeaks
 function meanFilter(chromatogram, serieName, options = {}) {
-  const {
-    factor = 2
-  } = options;
+  const { factor = 2 } = options;
 
@@ -1136,4 +1134,5 @@ var serie = chromatogram.getSerie(serieName);
 function applyFilter(serie, factor) {
+  var filtered = [[], []];
+  if (serie[1].length === 0) return filtered;
   const meanIntensity = factor * arrayMean(serie[1]);
-  var filtered = [[], []];
   for (var i = 0; i < serie[0].length; i++) {
@@ -1166,3 +1165,3 @@ if (serie[1][i] > meanIntensity) {
   try {
-    basePeak = max(serie[1]);
+    basePeak = arrayMax(serie[1]);
   } catch (e) {
@@ -1717,3 +1716,3 @@ basePeak = 0;
   for (let i = 0; i < sample.peaks.length; ++i) {
-    let max$$1 = { similarity: -3 };
+    let max = { similarity: -3 };
     let biggerCounter = 0;
@@ -1723,4 +1722,4 @@ for (let j = 0; j < reference.peaks.length; ++j) {
 
-      if (sim > options.similarityThreshold && sim > max$$1.similarity) {
-        max$$1 = {
+      if (sim > options.similarityThreshold && sim > max.similarity) {
+        max = {
           similarity: sim,
@@ -1736,5 +1735,5 @@ chrom1: reference.peaks[j],
     if (biggerCounter === 1) {
-      similarityPeaks.chrom1[similarLen] = max$$1.chrom1;
-      similarityPeaks.chrom2[similarLen] = max$$1.chrom2;
-      similarityPeaks.similarity[similarLen++] = max$$1.similarity;
+      similarityPeaks.chrom1[similarLen] = max.chrom1;
+      similarityPeaks.chrom2[similarLen] = max.chrom2;
+      similarityPeaks.similarity[similarLen++] = max.similarity;
     }
@@ -1741,0 +1740,0 @@ }

package.json

 {
   "name": "chromatography",
-  "version": "3.10.0",
+  "version": "3.11.0",
   "description": "Tools for storing, search and analize GC/MS spectra",
@@ -39,34 +39,34 @@ "main": "lib/index.js",
   "devDependencies": {
-    "babel-jest": "^21.2.0",
-    "babel-loader": "^7.1.2",
-    "babel-plugin-transform-es2015-modules-commonjs": "^6.26.0",
-    "babel-preset-env": "^1.6.1",
+    "babel-jest": "^24.5.0",
+    "babel-loader": "^8.0.5",
+    "babel-plugin-transform-es2015-modules-commonjs": "^6.26.2",
+    "babel-preset-env": "^1.7.0",
     "cheminfo-tools": "^1.22.4",
-    "codecov": "^3.0.0",
-    "documentation": "^8.1.2",
-    "eslint": "^5.9.0",
-    "eslint-config-cheminfo": "^1.15.1",
-    "eslint-plugin-import": "^2.8.0",
-    "eslint-plugin-jest": "^21.27.2",
-    "eslint-plugin-no-only-tests": "^2.0.0",
-    "jest": "^23.5.0",
-    "jest-matcher-deep-close-to": "^1.2.1",
-    "npm-run-all": "^4.1.2",
-    "rollup": "^0.52.3"
+    "codecov": "^3.2.0",
+    "documentation": "^9.3.1",
+    "eslint": "^5.15.1",
+    "eslint-config-cheminfo": "^1.20.0",
+    "eslint-plugin-import": "^2.16.0",
+    "eslint-plugin-jest": "^22.3.2",
+    "eslint-plugin-no-only-tests": "^2.1.0",
+    "jest": "^24.5.0",
+    "jest-matcher-deep-close-to": "^1.3.0",
+    "npm-run-all": "^4.1.5",
+    "rollup": "^1.6.0"
   },
   "dependencies": {
-    "binary-search": "^1.3.3",
-    "isotopic-distribution": "^0.6.4",
-    "jcampconverter": "^2.9.2",
-    "mf-parser": "^0.6.4",
-    "ml-array-max": "^1.1.0",
-    "ml-array-mean": "^1.1.0",
-    "ml-gsd": "^2.0.3",
-    "ml-regression-polynomial": "^1.0.2",
+    "binary-search": "^1.3.5",
+    "isotopic-distribution": "^0.9.1",
+    "jcampconverter": "^3.0.0",
+    "mf-parser": "^0.9.1",
+    "ml-array-max": "^1.1.1",
+    "ml-array-mean": "^1.1.1",
+    "ml-gsd": "^2.0.5",
+    "ml-regression-polynomial": "^1.0.3",
     "mzdata": "^1.1.0",
     "mzmjs": "^0.2.0",
-    "netcdf-gcms": "^1.2.3",
+    "netcdf-gcms": "^1.3.1",
     "num-sort": "^1.0.0",
-    "xy-parser": "^2.2.0"
+    "xy-parser": "^2.2.2"
   }
 }

src/filter/meanFilter.js

@@ -6,5 +6,3 @@ import arrayMean from 'ml-array-mean';
 export function meanFilter(chromatogram, serieName, options = {}) {
-  const {
-    factor = 2
-  } = options;
+  const { factor = 2 } = options;
 
@@ -21,4 +19,5 @@ var serie = chromatogram.getSerie(serieName);
 function applyFilter(serie, factor) {
+  var filtered = [[], []];
+  if (serie[1].length === 0) return filtered;
   const meanIntensity = factor * arrayMean(serie[1]);
-  var filtered = [[], []];
   for (var i = 0; i < serie[0].length; i++) {
@@ -25,0 +24,0 @@ if (serie[1][i] > meanIntensity) {

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Improved metrics

Total package byte prevSize

126522

increased by0.05%

Worsened metrics

Lines of code

3366

decreased by-0.06%

Dependency changes

• + Addedatom-sorter@0.9.1(transitive)

• + Addedchemical-elements@0.9.1(transitive)

• + Addedchemical-groups@0.9.1(transitive)

• + Addedisotopic-distribution@0.9.1(transitive)

• + Addedjcampconverter@3.0.4(transitive)

• + Addedmf-parser@0.9.1(transitive)

• + Addedmf-utilities@0.9.1(transitive)

• - Removedatom-sorter@0.6.4(transitive)

• - Removedchemical-elements@0.6.4(transitive)

• - Removedchemical-groups@0.6.4(transitive)

• - Removedisotopic-distribution@0.6.4(transitive)

• - Removedjcampconverter@2.11.0(transitive)

• - Removedmf-parser@0.6.4(transitive)

• - Removedmf-utilities@0.6.4(transitive)

• Updatedbinary-search@^1.3.5

• Updatedisotopic-distribution@^0.9.1

• Updatedjcampconverter@^3.0.0

• Updatedmf-parser@^0.9.1

• Updatedml-array-max@^1.1.1

• Updatedml-array-mean@^1.1.1

• Updatedml-gsd@^2.0.5

• Updatedml-regression-polynomial@^1.0.3

• Updatednetcdf-gcms@^1.3.1

• Updatedxy-parser@^2.2.2