jcampconverter - npm Package Compare versions

Comparing version 2.10.2 to 2.11.0

package.json

 {
   "name": "jcampconverter",
-  "version": "2.10.2",
+  "version": "2.11.0",
   "description": "Parse and convert JCAMP data",
@@ -12,5 +12,5 @@ "main": "./src/index.js",
     "eslint-fix": "npm run eslint -- --fix",
-    "test": "run-s testonly eslint",
-    "test-travis": "eslint src && jest --coverage && codecov",
-    "testonly": "jest",
+    "test": "run-s test-only eslint",
+    "test-travis": "eslint src && jest --coverage",
+    "test-only": "jest",
     "build": "cheminfo build --root JcampConverter --no-source-map",
@@ -41,11 +41,10 @@ "benchmark": "node benchmark/benchmark.js",
     "cheminfo-tools": "^1.22.4",
-    "codecov": "^2.3.1",
-    "eslint": "^4.19.1",
-    "eslint-config-cheminfo": "^1.18.0",
-    "eslint-plugin-import": "^2.14.0",
-    "eslint-plugin-jest": "^21.21.0",
+    "eslint": "^5.12.1",
+    "eslint-config-cheminfo": "^1.20.0",
+    "eslint-plugin-import": "^2.15.0",
+    "eslint-plugin-jest": "^22.1.3",
     "eslint-plugin-no-only-tests": "^2.0.1",
-    "jest": "^21.2.1",
+    "jest": "^23.6.0",
     "npm-run-all": "^4.1.3"
   }
 }

src/index.js

@@ -9,6 +9,5 @@ 'use strict';
   function convertToFloatArray(stringArray) {
-    var l = stringArray.length;
-    var floatArray = new Array(l);
-    for (var i = 0; i < l; i++) {
-      floatArray[i] = parseFloat(stringArray[i]);
+    var floatArray = [];
+    for (let i = 0; i < stringArray.length; i++) {
+      floatArray.push(parseFloat(stringArray[i]));
     }
@@ -28,3 +27,4 @@ return floatArray;
     nbContourLevels: 7,
-    noiseMultiplier: 5
+    noiseMultiplier: 5,
+    profiling: false
   };
@@ -41,6 +41,6 @@
     var ldr, dataLabel, dataValue, ldrs;
-    var i, ii, j, position, endLine, infos;
+    var position, endLine, infos;
 
     var result = {};
-    result.profiling = [];
+    result.profiling = options.profiling ? [] : false;
     result.logs = [];
@@ -74,3 +74,3 @@ var spectra = [];
 
-    for (i = 0, ii = ldrs.length; i < ii; i++) {
+    for (let i = 0; i < ldrs.length; i++) {
       ldr = ldrs[i];
@@ -168,2 +168,3 @@ // This is a new LDR
           if (dataValue.match(/.*\+\+.*/)) {
+            // ex: (X++(Y..Y))
             if (!spectrum.deltaX) {
@@ -190,2 +191,13 @@ spectrum.deltaX =
       }
+      if (dataLabel === 'PEAKASSIGNMENTS') {
+        if (wantXY) {
+          if (dataValue.match(/.*(XYA).*/)) {
+            // ex: (XYA)
+            parseXYA(spectrum, dataValue);
+          }
+          spectra.push(spectrum);
+          spectrum = new Spectrum();
+        }
+        continue;
+      }
 
@@ -221,2 +233,10 @@ if (dataLabel === 'TITLE') {
         spectrum.yFactor = parseFloat(dataValue);
+      } else if (dataLabel === 'MAXX') {
+        spectrum.maxX = parseFloat(dataValue);
+      } else if (dataLabel === 'MINX') {
+        spectrum.minX = parseFloat(dataValue);
+      } else if (dataLabel === 'MAXY') {
+        spectrum.maxY = parseFloat(dataValue);
+      } else if (dataLabel === 'MINY') {
+        spectrum.minY = parseFloat(dataValue);
       } else if (dataLabel === 'DELTAX') {
@@ -239,4 +259,4 @@ spectrum.deltaX = parseFloat(dataValue);
         result.shiftOffsetNum = 0;
-        if (!result.shiftOffsetVal) {
-          result.shiftOffsetVal = parseFloat(dataValue);
+        if (!spectrum.shiftOffsetVal) {
+          spectrum.shiftOffsetVal = parseFloat(dataValue);
         }
@@ -249,3 +269,3 @@ } else if (dataLabel === '$REFERENCEPOINT') {
         //                 result.shiftOffsetNum = parseInt(parts[2].trim());
-        //                 result.shiftOffsetVal = parseFloat(parts[3].trim());
+        //                 spectrum.shiftOffsetVal = parseFloat(parts[3].trim());
       } else if (dataLabel === 'VARNAME') {
@@ -293,2 +313,4 @@ ntuples.varname = dataValue.split(ntuplesSeparator);
         spectrum[convertMSFieldToLabel(dataLabel)] = dataValue;
+      } else if (dataLabel === 'SAMPLEDESCRIPTION') {
+        spectrum.sampleDescription = dataValue;
       }
@@ -310,6 +332,6 @@ if (dataLabel.match(options.keepRecordsRegExp)) {
       var keys = Object.keys(ntuples);
-      for (i = 0; i < keys.length; i++) {
+      for (let i = 0; i < keys.length; i++) {
         var key = keys[i];
         var values = ntuples[key];
-        for (j = 0; j < values.length; j++) {
+        for (let j = 0; j < values.length; j++) {
           if (!newNtuples[j]) newNtuples[j] = {};
@@ -342,6 +364,6 @@ newNtuples[j][key] = values[j];
       if (spectra.length > 0) {
-        for (i = 0; i < spectra.length; i++) {
+        for (let i = 0; i < spectra.length; i++) {
           spectrum = spectra[i];
           if (spectrum.data.length > 0) {
-            for (j = 0; j < spectrum.data.length; j++) {
+            for (let j = 0; j < spectrum.data.length; j++) {
               var data = spectrum.data[j];
@@ -409,5 +431,4 @@ var newData = {
 
-    var i;
     var existingGCMSFields = [];
-    for (i = 0; i < GC_MS_FIELDS.length; i++) {
+    for (let i = 0; i < GC_MS_FIELDS.length; i++) {
       var label = convertMSFieldToLabel(GC_MS_FIELDS[i]);
@@ -423,6 +444,6 @@ if (spectra[0][label]) {
 
-    for (i = 0; i < length; i++) {
+    for (let i = 0; i < length; i++) {
       var spectrum = spectra[i];
       chromatogram.times[i] = spectrum.pageValue;
-      for (var j = 0; j < existingGCMSFields.length; j++) {
+      for (let j = 0; j < existingGCMSFields.length; j++) {
         chromatogram.series[existingGCMSFields[j]].data[i] = parseFloat(
@@ -467,4 +488,4 @@ spectrum[existingGCMSFields[j]]
     }
-    if (result.shiftOffsetVal) {
-      var shift = spectrum.firstX - result.shiftOffsetVal;
+    if (spectrum.shiftOffsetVal) {
+      var shift = spectrum.firstX - spectrum.shiftOffsetVal;
       spectrum.firstX = spectrum.firstX - shift;
@@ -491,6 +512,6 @@ spectrum.lastX = spectrum.lastX - shift;
     var z = new Array(ySize);
-    for (var i = 0; i < ySize; i++) {
+    for (let i = 0; i < ySize; i++) {
       z[i] = new Array(xSize);
       var xVector = spectra[i].data[0];
-      for (var j = 0; j < xSize; j++) {
+      for (let j = 0; j < xSize; j++) {
         var value = xVector[j * 2 + 1];
@@ -711,3 +732,4 @@ z[i][j] = value;
     var ascii;
-    for (var i = 0; i < value.length; i++) {
+    let i = 0;
+    for (; i < value.length; i++) {
       ascii = value.charCodeAt(i);
@@ -863,2 +885,22 @@ if (ascii === 13 || ascii === 10) {
 
+  function parseXYA(spectrum, value) {
+    var removeSymbolRegExp = /(\(+|\)+|<+|>+|\s+)/g;
+
+    spectrum.isXYAdata = true;
+    var values;
+    var currentData = [];
+    spectrum.data = [currentData];
+
+    var lines = value.split(/,? *,?[;\r\n]+ */);
+
+    for (let i = 1; i < lines.length; i++) {
+      values = lines[i]
+        .trim()
+        .replace(removeSymbolRegExp, '')
+        .split(',');
+      currentData.push(parseFloat(values[0]));
+      currentData.push(parseFloat(values[1]));
+    }
+  }
+
   function parsePeakTable(spectrum, value, result) {
@@ -869,3 +911,3 @@ var removeCommentRegExp = /\$\$.*/;
     spectrum.isPeaktable = true;
-    var i, ii, j, jj, values;
+    var values;
     var currentData = [];
@@ -877,3 +919,3 @@ spectrum.data = [currentData];
 
-    for (i = 1, ii = lines.length; i < ii; i++) {
+    for (let i = 1; i < lines.length; i++) {
       values = lines[i]
@@ -884,3 +926,3 @@ .trim()
       if (values.length % 2 === 0) {
-        for (j = 0, jj = values.length; j < jj; j = j + 2) {
+        for (let j = 0; j < values.length; j = j + 2) {
           // takes around 40% of the time to add and parse the 2 values nearly exclusively because of parseFloat
@@ -887,0 +929,0 @@ currentData.push(parseFloat(values[j]) * spectrum.xFactor);

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Improved metrics

Total package byte prevSize

43191

increased by3.03%

Dev dependency count

9

decreased by-10%

Lines of code

969

increased by4.08%

No dependency changes