jcampconverter - npm Package Compare versions

Comparing version 2.7.0 to 2.8.0

package.json

 {
   "name": "jcampconverter",
-  "version": "2.7.0",
+  "version": "2.8.0",
   "description": "Parse and convert JCAMP data",
   "main": "./src/index.js",
-  "directories": {
-    "lib": "src",
-    "test": "test"
-  },
   "files": [
@@ -14,3 +10,7 @@ "src"
   "scripts": {
-    "test": "mocha --require should --reporter mocha-better-spec-reporter --recursive",
+    "eslint": "eslint src test",
+    "eslint-fix": "npm run eslint -- --fix",
+    "test": "run-s testonly eslint",
+    "test-travis": "eslint src && jest --coverage && codecov",
+    "testonly": "jest",
     "build": "cheminfo build --root JcampConverter",
@@ -34,10 +34,16 @@ "benchmark": "node benchmark/benchmark.js",
   },
-  "homepage": "https://github.com/cheminfo-js/jcampconverter",
+  "homepage": "https://github.com/cheminfo-js/jcampconverter#readme",
+  "jest": {
+    "testEnvironment": "node"
+  },
   "devDependencies": {
-    "benchmark": "^2.1.0",
-    "cheminfo-tools": "^1.0.2",
-    "mocha": "^2.2.5",
-    "mocha-better-spec-reporter": "^2.1.1",
-    "should": "^7.0.2"
+    "benchmark": "^2.1.4",
+    "cheminfo-tools": "^1.19.2",
+    "codecov": "^2.3.0",
+    "eslint": "^4.4.1",
+    "eslint-config-cheminfo": "^1.8.0",
+    "eslint-plugin-no-only-tests": "^2.0.0",
+    "jest": "^20.0.4",
+    "npm-run-all": "^4.0.2"
   }
 }

README.md

@@ -5,6 +5,8 @@ # JCAMP converter
   [![build status][travis-image]][travis-url]
+  [![Test coverage][codecov-image]][codecov-url]
+  [![David deps][david-image]][david-url]
   [![npm download][download-image]][download-url]
+  
+Parse and convert JCAMP data
 
-Parse and convert JCAMP data.
-
 ## Installation
@@ -38,3 +40,3 @@
 * withoutXY - do not parse XYDATA or PEAKTABLE fields. Useful to only extract metadata fields (combine this option with `keepRecordsRegExp`)
-* newGCMS - use the new GC/MS data format output (default: false)
+* chromatogram - use the new GC/MS data format output (default: false)
 
@@ -85,3 +87,3 @@ 2D NMR options:
 
-  [MIT](./LICENSE)
+[MIT](./LICENSE)
 
@@ -92,3 +94,7 @@ [npm-image]: https://img.shields.io/npm/v/jcampconverter.svg?style=flat-square
 [travis-url]: https://travis-ci.org/cheminfo-js/jcampconverter
+[codecov-image]: https://img.shields.io/codecov/c/github/cheminfo-js/jcampconverter.svg?style=flat-square
+[codecov-url]: https://codecov.io/gh/cheminfo-js/jcampconverter
+[david-image]: https://img.shields.io/david/cheminfo-js/jcampconverter.svg?style=flat-square
+[david-url]: https://david-dm.org/cheminfo-js/jcampconverter
 [download-image]: https://img.shields.io/npm/dm/jcampconverter.svg?style=flat-square
 [download-url]: https://www.npmjs.com/package/jcampconverter

src/index.js

 'use strict';
 
-var parseXYDataRegExp = require('./parseXYData.js');
-
-
 function getConverter() {
-
     // the following RegExp can only be used for XYdata, some peakTables have values with a "E-5" ...
-    var ntuplesSeparator = /[, \t]{1,}/;
+    const ntuplesSeparator = /[, \t]+/;
+    const GC_MS_FIELDS = ['TIC', '.RIC', 'SCANNUMBER'];
 
-    var GC_MS_FIELDS = ['TIC', '.RIC', 'SCANNUMBER'];
-
     function convertToFloatArray(stringArray) {
@@ -21,12 +16,19 @@ var l = stringArray.length;
     }
-    
-    function Spectrum() {
-        
-    }
 
+    class Spectrum {}
+
+    const defaultOptions = {
+        keepRecordsRegExp: /^$/,
+        xy: false,
+        withoutXY: false,
+        chromatogram: false,
+        keepSpectra: false,
+        noContour: false,
+        nbContourLevels: 7,
+        noiseMultiplier: 5
+    };
+
     function convert(jcamp, options) {
-        options = options || {};
+        options = Object.assign({}, defaultOptions, options);
 
-        var keepRecordsRegExp = /^$/;
-        if (options.keepRecordsRegExp) keepRecordsRegExp = options.keepRecordsRegExp;
         var wantXY = !options.withoutXY;
@@ -36,8 +38,5 @@
 
-        var ntuples = {},
-            ldr,
-            dataLabel,
-            dataValue,
-            ldrs,
-            i, ii, position, endLine, infos;
+        var ntuples = {};
+        var ldr, dataLabel, dataValue, ldrs;
+        var i, ii, j, position, endLine, infos;
 
@@ -52,16 +51,21 @@ var result = {};
 
-        if (!(typeof jcamp === 'string')) return result;
-        // console.time('start');
+        if (!(typeof jcamp === 'string')) {
+            throw new TypeError('the JCAMP should be a string');
+        }
 
-        if (result.profiling) result.profiling.push({
-            action: 'Before split to LDRS',
-            time: Date.now() - start
-        });
+        if (result.profiling) {
+            result.profiling.push({
+                action: 'Before split to LDRS',
+                time: Date.now() - start
+            });
+        }
 
         ldrs = jcamp.split(/[\r\n]+##/);
 
-        if (result.profiling) result.profiling.push({
-            action: 'Split to LDRS',
-            time: Date.now() - start
-        });
+        if (result.profiling) {
+            result.profiling.push({
+                action: 'Split to LDRS',
+                time: Date.now() - start
+            });
+        }
 
@@ -137,10 +141,6 @@ if (ldrs[0]) ldrs[0] = ldrs[0].replace(/^[\r\n ]*##/, '');
                     if (dataValue.match(/.*\+\+.*/)) {
-                        if (options.fastParse === false) {
-                            parseXYDataRegExp(spectrum, dataValue, result);
-                        } else {
-                            if (!spectrum.deltaX) {
-                                spectrum.deltaX = (spectrum.lastX - spectrum.firstX) / (spectrum.nbPoints - 1);
-                            }
-                            fastParseXYData(spectrum, dataValue, result);
+                        if (!spectrum.deltaX) {
+                            spectrum.deltaX = (spectrum.lastX - spectrum.firstX) / (spectrum.nbPoints - 1);
                         }
+                        fastParseXYData(spectrum, dataValue, result);
                     } else {
@@ -202,6 +202,6 @@ parsePeakTable(spectrum, dataValue, result);
 
-            } else if (dataLabel === '$OFFSET') {   // OFFSET for Bruker spectra
+            } else if (dataLabel === '$OFFSET') { // OFFSET for Bruker spectra
                 result.shiftOffsetNum = 0;
-                if (!result.shiftOffsetVal)  result.shiftOffsetVal = parseFloat(dataValue);
-            } else if (dataLabel === '$REFERENCEPOINT') {   // OFFSET for Varian spectra
+                if (!result.shiftOffsetVal) result.shiftOffsetVal = parseFloat(dataValue);
+            } else if (dataLabel === '$REFERENCEPOINT') { // OFFSET for Varian spectra
 
@@ -243,3 +243,3 @@
                 spectrum.pageValue = parseFloat(dataValue.replace(/^.*=/, ''));
-                spectrum.pageSymbol = spectrum.page.replace(/=.*/, '');
+                spectrum.pageSymbol = spectrum.page.replace(/[=].*/, '');
                 var pageSymbolIndex = ntuples.symbol.indexOf(spectrum.pageSymbol);
@@ -258,3 +258,3 @@ var unit = '';
             }
-            if (dataLabel.match(keepRecordsRegExp)) {
+            if (dataLabel.match(options.keepRecordsRegExp)) {
                 result.info[dataLabel] = dataValue.trim();
@@ -264,6 +264,8 @@ }
 
-        if (result.profiling) result.profiling.push({
-            action: 'Finished parsing',
-            time: Date.now() - start
-        });
+        if (result.profiling) {
+            result.profiling.push({
+                action: 'Finished parsing',
+                time: Date.now() - start
+            });
+        }
 
@@ -273,6 +275,6 @@ if (Object.keys(ntuples).length > 0) {
             var keys = Object.keys(ntuples);
-            for (var i = 0; i < keys.length; i++) {
+            for (i = 0; i < keys.length; i++) {
                 var key = keys[i];
                 var values = ntuples[key];
-                for (var j = 0; j < values.length; j++) {
+                for (j = 0; j < values.length; j++) {
                     if (!newNtuples[j]) newNtuples[j] = {};
@@ -287,6 +289,8 @@ newNtuples[j][key] = values[j];
             add2D(result, options);
-            if (result.profiling) result.profiling.push({
-                action: 'Finished countour plot calculation',
-                time: Date.now() - start
-            });
+            if (result.profiling) {
+                result.profiling.push({
+                    action: 'Finished countour plot calculation',
+                    time: Date.now() - start
+                });
+            }
             if (!options.keepSpectra) {
@@ -297,4 +301,3 @@ delete result.spectra;
 
-        var isGCMS = (spectra.length > 1 && (!spectra[0].dataType || spectra[0].dataType.match(/.*mass.*/i)));
-        if (isGCMS && options.newGCMS) {
+        if (options.chromatogram) {
             options.xy = true;
@@ -305,6 +308,6 @@ }
             if (spectra.length > 0) {
-                for (var i = 0; i < spectra.length; i++) {
-                    var spectrum = spectra[i];
+                for (i = 0; i < spectra.length; i++) {
+                    spectrum = spectra[i];
                     if (spectrum.data.length > 0) {
-                        for (var j = 0; j < spectrum.data.length; j++) {
+                        for (j = 0; j < spectrum.data.length; j++) {
                             var data = spectrum.data[j];
@@ -329,12 +332,14 @@ var newData = {
         // maybe it is a GC (HPLC) / MS. In this case we add a new format
-        if (isGCMS && wantXY) {
-            if (options.newGCMS) {
-                addNewGCMS(result);
+        if (options.chromatogram) {
+            if (result.spectra.length > 1) {
+                complexChromatogram(result);
             } else {
-                addGCMS(result);
+                simpleChromatogram(result);
             }
-            if (result.profiling) result.profiling.push({
-                action: 'Finished GCMS calculation',
-                time: Date.now() - start
-            });
+            if (result.profiling) {
+                result.profiling.push({
+                    action: 'Finished chromatogram calculation',
+                    time: Date.now() - start
+                });
+            }
         }
@@ -361,12 +366,13 @@
 
-    function addNewGCMS(result) {
+    function complexChromatogram(result) {
         var spectra = result.spectra;
         var length = spectra.length;
-        var gcms = {
+        var chromatogram = {
             times: new Array(length),
-            series: [{
-                name: 'ms',
-                dimension: 2,
-                data: new Array(length)
-            }]
+            series: {
+                ms: {
+                    dimension: 2,
+                    data: new Array(length)
+                }
+            }
         };
@@ -380,7 +386,6 @@
                 existingGCMSFields.push(label);
-                gcms.series.push({
-                    name: label,
+                chromatogram.series[label] = {
                     dimension: 1,
                     data: new Array(length)
-                });
+                };
             }
@@ -391,41 +396,25 @@ }
             var spectrum = spectra[i];
-            gcms.times[i] = spectrum.pageValue;
+            chromatogram.times[i] = spectrum.pageValue;
             for (var j = 0; j < existingGCMSFields.length; j++) {
-                gcms.series[j + 1].data[i] = parseFloat(spectrum[existingGCMSFields[j]]);
+                chromatogram.series[existingGCMSFields[j]].data[i] = parseFloat(spectrum[existingGCMSFields[j]]);
             }
             if (spectrum.data) {
-                gcms.series[0].data[i] = [spectrum.data[0].x, spectrum.data[0].y];
+                chromatogram.series.ms.data[i] = [spectrum.data[0].x, spectrum.data[0].y];
             }
 
         }
-        result.gcms = gcms;
+        result.chromatogram = chromatogram;
     }
 
-    function addGCMS(result) {
-        var spectra = result.spectra;
-        var existingGCMSFields = [];
-        var i;
-        for (i = 0; i < GC_MS_FIELDS.length; i++) {
-            var label = convertMSFieldToLabel(GC_MS_FIELDS[i]);
-            if (spectra[0][label]) {
-                existingGCMSFields.push(label);
+    function simpleChromatogram(result) {
+        var data = result.spectra[0].data[0];
+        result.chromatogram = {
+            times: data.x.slice(),
+            series: {
+                intensity: {
+                    dimension: 1,
+                    data: data.y.slice()
+                }
             }
-        }
-        if (existingGCMSFields.length === 0) return;
-        var gcms = {};
-        gcms.gc = {};
-        gcms.ms = [];
-        for (i = 0; i < existingGCMSFields.length; i++) {
-            gcms.gc[existingGCMSFields[i]] = [];
-        }
-        for (i = 0; i < spectra.length; i++) {
-            var spectrum = spectra[i];
-            for (var j = 0; j < existingGCMSFields.length; j++) {
-                gcms.gc[existingGCMSFields[j]].push(spectrum.pageValue);
-                gcms.gc[existingGCMSFields[j]].push(parseFloat(spectrum[existingGCMSFields[j]]));
-            }
-            if (spectrum.data) gcms.ms[i] = spectrum.data[0];
-
-        }
-        result.gcms = gcms;
+        };
     }
@@ -504,4 +493,2 @@
         var z = zData.z;
-        var nbLevels = options.nbContourLevels || 7;
-        var noiseMultiplier = options.noiseMultiplier === undefined ? 5 : options.noiseMultiplier;
         var povarHeight0, povarHeight1, povarHeight2, povarHeight3;
@@ -533,3 +520,3 @@ var isOver0, isOver1, isOver2, isOver3;
 
-        var iter = nbLevels * 2;
+        var iter = options.nbContourLevels * 2;
         var contourLevels = new Array(iter);
@@ -541,7 +528,7 @@ var lineZValue;
             var side = level % 2;
-            var factor = (maxZ - noiseMultiplier * noise) * Math.exp((level >> 1) - nbLevels);
+            var factor = (maxZ - options.noiseMultiplier * noise) * Math.exp((level >> 1) - options.nbContourLevels);
             if (side === 0) {
-                lineZValue = factor + noiseMultiplier * noise;
+                lineZValue = factor + options.noiseMultiplier * noise;
             } else {
-                lineZValue = (0 - factor) - noiseMultiplier * noise;
+                lineZValue = (0 - factor) - options.noiseMultiplier * noise;
             }
@@ -663,4 +650,5 @@ var lines = [];
         var endLine = false;
+        var ascii;
         for (var i = 0; i < value.length; i++) {
-            var ascii = value.charCodeAt(i);
+            ascii = value.charCodeAt(i);
             if (ascii === 13 || ascii === 10) {
@@ -685,3 +673,2 @@ endLine = true;
         var decimalPosition = 0;
-        var ascii;
         for (; i <= value.length; i++) {
@@ -861,4 +848,4 @@ if (i === value.length) ascii = 13;
 
-var stamps = {},
-    worker;
+var stamps = {};
+var worker;
 
@@ -865,0 +852,0 @@ function postToWorker(input, options) {

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Improved metrics

Number of lines in readme file

97

increased by6.59%

Worsened metrics

Total package byte prevSize

40375

decreased by-16.73%

Dev dependency count

8

increased by60%

Number of package files

4

decreased by-20%

Lines of code

781

decreased by-15.38%

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