jcampconverter - npm Package Compare versions

Comparing version 2.10.0 to 2.10.2

History.md

@@ -0,1 +1,5 @@
+## [2.10.2](https://github.com/cheminfo-js/jcampconverter/compare/v2.10.1...v2.10.2) (2018-11-23)
+
+
+
 <a name="2.9.1"></a>
@@ -2,0 +6,0 @@ ## [2.9.1](https://github.com/cheminfo-js/jcampconverter/compare/v2.9.0...v2.9.1) (2017-10-19)

package.json

 {
   "name": "jcampconverter",
-  "version": "2.10.0",
+  "version": "2.10.2",
   "description": "Parse and convert JCAMP data",
@@ -39,3 +39,3 @@ "main": "./src/index.js",
     "benchmark": "^2.1.4",
-    "cheminfo-tools": "^1.20.2",
+    "cheminfo-tools": "^1.22.4",
     "codecov": "^2.3.1",
@@ -42,0 +42,0 @@ "eslint": "^4.19.1",

src/index.js

@@ -95,4 +95,10 @@ 'use strict';
           if (infos[0].indexOf('++') > 0) {
-            var firstVariable = infos[0].replace(/.*\(([a-zA-Z0-9]+)\+\+.*/, '$1');
-            var secondVariable = infos[0].replace(/.*\.\.([a-zA-Z0-9]+).*/, '$1');
+            var firstVariable = infos[0].replace(
+              /.*\(([a-zA-Z0-9]+)\+\+.*/,
+              '$1'
+            );
+            var secondVariable = infos[0].replace(
+              /.*\.\.([a-zA-Z0-9]+).*/,
+              '$1'
+            );
             xIndex = ntuples.symbol.indexOf(firstVariable);
@@ -106,8 +112,16 @@ yIndex = ntuples.symbol.indexOf(secondVariable);
           if (ntuples.first) {
-            if (ntuples.first.length > xIndex) spectrum.firstX = ntuples.first[xIndex];
-            if (ntuples.first.length > yIndex) spectrum.firstY = ntuples.first[yIndex];
+            if (ntuples.first.length > xIndex) {
+              spectrum.firstX = ntuples.first[xIndex];
+            }
+            if (ntuples.first.length > yIndex) {
+              spectrum.firstY = ntuples.first[yIndex];
+            }
           }
           if (ntuples.last) {
-            if (ntuples.last.length > xIndex) spectrum.lastX = ntuples.last[xIndex];
-            if (ntuples.last.length > yIndex) spectrum.lastY = ntuples.last[yIndex];
+            if (ntuples.last.length > xIndex) {
+              spectrum.lastX = ntuples.last[xIndex];
+            }
+            if (ntuples.last.length > yIndex) {
+              spectrum.lastY = ntuples.last[yIndex];
+            }
           }
@@ -118,8 +132,16 @@ if (ntuples.vardim && ntuples.vardim.length > xIndex) {
           if (ntuples.factor) {
-            if (ntuples.factor.length > xIndex) spectrum.xFactor = ntuples.factor[xIndex];
-            if (ntuples.factor.length > yIndex) spectrum.yFactor = ntuples.factor[yIndex];
+            if (ntuples.factor.length > xIndex) {
+              spectrum.xFactor = ntuples.factor[xIndex];
+            }
+            if (ntuples.factor.length > yIndex) {
+              spectrum.yFactor = ntuples.factor[yIndex];
+            }
           }
           if (ntuples.units) {
-            if (ntuples.units.length > xIndex) spectrum.xUnit = ntuples.units[xIndex];
-            if (ntuples.units.length > yIndex) spectrum.yUnit = ntuples.units[yIndex];
+            if (ntuples.units.length > xIndex) {
+              spectrum.xUnit = ntuples.units[xIndex];
+            }
+            if (ntuples.units.length > yIndex) {
+              spectrum.yUnit = ntuples.units[yIndex];
+            }
           }
@@ -129,5 +151,9 @@ spectrum.datatable = infos[0];
             dataLabel = 'PEAKTABLE';
-          } else if (infos[1] && (infos[1].indexOf('XYDATA') || infos[0].indexOf('++') > 0)) {
+          } else if (
+            infos[1] &&
+            (infos[1].indexOf('XYDATA') || infos[0].indexOf('++') > 0)
+          ) {
             dataLabel = 'XYDATA';
-            spectrum.deltaX = (spectrum.lastX - spectrum.firstX) / (spectrum.nbPoints - 1);
+            spectrum.deltaX =
+              (spectrum.lastX - spectrum.firstX) / (spectrum.nbPoints - 1);
           }
@@ -143,3 +169,4 @@ }
             if (!spectrum.deltaX) {
-              spectrum.deltaX = (spectrum.lastX - spectrum.firstX) / (spectrum.nbPoints - 1);
+              spectrum.deltaX =
+                (spectrum.lastX - spectrum.firstX) / (spectrum.nbPoints - 1);
             }
@@ -164,3 +191,2 @@ fastParseXYData(spectrum, dataValue, result);
 
-
       if (dataLabel === 'TITLE') {
@@ -198,13 +224,21 @@ spectrum.title = dataValue;
       } else if (dataLabel === '.OBSERVEFREQUENCY' || dataLabel === '$SFO1') {
-        if (!spectrum.observeFrequency) spectrum.observeFrequency = parseFloat(dataValue);
+        if (!spectrum.observeFrequency) {
+          spectrum.observeFrequency = parseFloat(dataValue);
+        }
       } else if (dataLabel === '.OBSERVENUCLEUS') {
-        if (!spectrum.xType) result.xType = dataValue.replace(/[^a-zA-Z0-9]/g, '');
+        if (!spectrum.xType) {
+          result.xType = dataValue.replace(/[^a-zA-Z0-9]/g, '');
+        }
       } else if (dataLabel === '$SFO2') {
-        if (!result.indirectFrequency) result.indirectFrequency = parseFloat(dataValue);
-      } else if (dataLabel === '$OFFSET') { // OFFSET for Bruker spectra
+        if (!result.indirectFrequency) {
+          result.indirectFrequency = parseFloat(dataValue);
+        }
+      } else if (dataLabel === '$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
         // if we activate this part it does not work for ACD specmanager
@@ -301,3 +335,4 @@ //         } else if (dataLabel=='.SHIFTREFERENCE') {   // OFFSET FOR Bruker Spectra
 
-    if (options.xy && wantXY) { // the spectraData should not be a oneD array but an object with x and y
+    if (options.xy && wantXY) {
+      // the spectraData should not be a oneD array but an object with x and y
       if (spectra.length > 0) {
@@ -349,3 +384,2 @@ for (i = 0; i < spectra.length; i++) {
 
-
   function convertMSFieldToLabel(value) {
@@ -389,6 +423,11 @@ return value.toLowerCase().replace(/[^a-z0-9]/g, '');
       for (var j = 0; j < existingGCMSFields.length; j++) {
-        chromatogram.series[existingGCMSFields[j]].data[i] = parseFloat(spectrum[existingGCMSFields[j]]);
+        chromatogram.series[existingGCMSFields[j]].data[i] = parseFloat(
+          spectrum[existingGCMSFields[j]]
+        );
       }
       if (spectrum.data) {
-        chromatogram.series.ms.data[i] = [spectrum.data[0].x, spectrum.data[0].y];
+        chromatogram.series.ms.data[i] = [
+          spectrum.data[0].x,
+          spectrum.data[0].y
+        ];
       }
@@ -478,3 +517,2 @@ }
 
-
   function generateContourLines(zData, options) {
@@ -512,11 +550,14 @@ var noise = zData.noise;
     var lineZValue;
-    for (var level = 0; level < iter; level++) { // multiply by 2 for positif and negatif
+    for (var level = 0; level < iter; level++) {
+      // multiply by 2 for positif and negatif
       var contourLevel = {};
       contourLevels[level] = contourLevel;
       var side = level % 2;
-      var factor = (maxZ - options.noiseMultiplier * noise) * Math.exp((level >> 1) - options.nbContourLevels);
+      var factor =
+        (maxZ - options.noiseMultiplier * noise) *
+        Math.exp((level >> 1) - options.nbContourLevels);
       if (side === 0) {
         lineZValue = factor + options.noiseMultiplier * noise;
       } else {
-        lineZValue = (0 - factor) - options.noiseMultiplier * noise;
+        lineZValue = 0 - factor - options.noiseMultiplier * noise;
       }
@@ -538,6 +579,6 @@ var lines = [];
 
-          isOver0 = (povarHeight0 > lineZValue);
-          isOver1 = (povarHeight1 > lineZValue);
-          isOver2 = (povarHeight2 > lineZValue);
-          isOver3 = (povarHeight3 > lineZValue);
+          isOver0 = povarHeight0 > lineZValue;
+          isOver1 = povarHeight1 > lineZValue;
+          isOver2 = povarHeight2 > lineZValue;
+          isOver3 = povarHeight3 > lineZValue;
 
@@ -548,6 +589,10 @@ // Example povar0 is over the plane and povar1 and
           if (isOver0 !== isOver1 && isOver0 !== isOver2) {
-            pAx = povar + (lineZValue - povarHeight0) / (povarHeight1 - povarHeight0);
+            pAx =
+              povar +
+              (lineZValue - povarHeight0) / (povarHeight1 - povarHeight0);
             pAy = iSubSpectra;
             pBx = povar;
-            pBy = iSubSpectra + (lineZValue - povarHeight0) / (povarHeight2 - povarHeight0);
+            pBy =
+              iSubSpectra +
+              (lineZValue - povarHeight0) / (povarHeight2 - povarHeight0);
             lines.push(pAx * dx + x0);
@@ -561,4 +606,10 @@ lines.push(pAy * dy + y0);
             pAx = povar + 1;
-            pAy = iSubSpectra + 1 - (lineZValue - povarHeight3) / (povarHeight1 - povarHeight3);
-            pBx = povar + 1 - (lineZValue - povarHeight3) / (povarHeight2 - povarHeight3);
+            pAy =
+              iSubSpectra +
+              1 -
+              (lineZValue - povarHeight3) / (povarHeight1 - povarHeight3);
+            pBx =
+              povar +
+              1 -
+              (lineZValue - povarHeight3) / (povarHeight2 - povarHeight3);
             pBy = iSubSpectra + 1;
@@ -572,6 +623,18 @@ lines.push(pAx * dx + x0);
           if (isOver1 !== isOver2) {
-            pAx = (povar + 1 - (lineZValue - povarHeight1) / (povarHeight2 - povarHeight1)) * dx + x0;
-            pAy = (iSubSpectra + (lineZValue - povarHeight1) / (povarHeight2 - povarHeight1)) * dy + y0;
+            pAx =
+              (povar +
+                1 -
+                (lineZValue - povarHeight1) / (povarHeight2 - povarHeight1)) *
+                dx +
+              x0;
+            pAy =
+              (iSubSpectra +
+                (lineZValue - povarHeight1) / (povarHeight2 - povarHeight1)) *
+                dy +
+              y0;
             if (isOver1 !== isOver0) {
-              pBx = povar + 1 - (lineZValue - povarHeight1) / (povarHeight0 - povarHeight1);
+              pBx =
+                povar +
+                1 -
+                (lineZValue - povarHeight1) / (povarHeight0 - povarHeight1);
               pBy = iSubSpectra;
@@ -585,3 +648,6 @@ lines.push(pAx);
               pBx = povar;
-              pBy = iSubSpectra + 1 - (lineZValue - povarHeight2) / (povarHeight0 - povarHeight2);
+              pBy =
+                iSubSpectra +
+                1 -
+                (lineZValue - povarHeight2) / (povarHeight0 - povarHeight2);
               lines.push(pAx);
@@ -594,3 +660,5 @@ lines.push(pAy);
               pBx = povar + 1;
-              pBy = iSubSpectra + (lineZValue - povarHeight1) / (povarHeight3 - povarHeight1);
+              pBy =
+                iSubSpectra +
+                (lineZValue - povarHeight1) / (povarHeight3 - povarHeight1);
               lines.push(pAx);
@@ -602,3 +670,5 @@ lines.push(pAy);
             if (isOver2 !== isOver3) {
-              pBx = povar + (lineZValue - povarHeight2) / (povarHeight3 - povarHeight2);
+              pBx =
+                povar +
+                (lineZValue - povarHeight2) / (povarHeight3 - povarHeight2);
               pBy = iSubSpectra + 1;
@@ -632,3 +702,2 @@ lines.push(pAx);
 
-
     spectrum.isXYdata = true;
@@ -639,3 +708,2 @@ // TODO to be improved using 2 array {x:[], y:[]}
 
-
     var currentX = spectrum.firstX;
@@ -682,3 +750,4 @@ var currentY = spectrum.firstY;
         // it is a number that is either new or we continue
-        if (ascii <= 57 && ascii >= 48) { // a number
+        if (ascii <= 57 && ascii >= 48) {
+          // a number
           inValue = true;
@@ -691,3 +760,4 @@ if (decimalPosition > 0) {
           }
-        } else if (ascii === 44 || ascii === 46) { // a "," or "."
+        } else if (ascii === 44 || ascii === 46) {
+          // a "," or "."
           inValue = true;
@@ -710,3 +780,3 @@ decimalPosition++;
                 if (isDifference) {
-                  lastDifference = isNegative ? (0 - currentValue) : currentValue;
+                  lastDifference = isNegative ? 0 - currentValue : currentValue;
                   isLastDifference = true;
@@ -720,3 +790,3 @@ isDifference = false;
                   } else {
-                    currentY = isNegative ? (0 - currentValue) : currentValue;
+                    currentY = isNegative ? 0 - currentValue : currentValue;
                   }
@@ -737,9 +807,8 @@ currentData.push(currentX);
           // positive SQZ digits @ A B C D E F G H I (ascii 64-73)
-          if ((ascii < 74) && (ascii > 63)) {
+          if (ascii < 74 && ascii > 63) {
             inValue = true;
             isLastDifference = false;
             currentValue = ascii - 64;
-          } else
-          // negative SQZ digits a b c d e f g h i (ascii 97-105)
-          if ((ascii > 96) && (ascii < 106)) {
+          } else if (ascii > 96 && ascii < 106) {
+            // negative SQZ digits a b c d e f g h i (ascii 97-105)
             inValue = true;
@@ -749,21 +818,18 @@ isLastDifference = false;
             isNegative = true;
-          } else
-          // DUP digits S T U V W X Y Z s (ascii 83-90, 115)
-          if (ascii === 115) {
+          } else if (ascii === 115) {
+            // DUP digits S T U V W X Y Z s (ascii 83-90, 115)
             inValue = true;
             isDuplicate = true;
             currentValue = 9;
-          } else if ((ascii > 82) && (ascii < 91)) {
+          } else if (ascii > 82 && ascii < 91) {
             inValue = true;
             isDuplicate = true;
             currentValue = ascii - 82;
-          } else
-          // positive DIF digits % J K L M N O P Q R (ascii 37, 74-82)
-          if ((ascii > 73) && (ascii < 83)) {
+          } else if (ascii > 73 && ascii < 83) {
+            // positive DIF digits % J K L M N O P Q R (ascii 37, 74-82)
             inValue = true;
             isDifference = true;
             currentValue = ascii - 73;
-          } else
-          // negative DIF digits j k l m n o p q r (ascii 106-114)
-          if ((ascii > 105) && (ascii < 115)) {
+          } else if (ascii > 105 && ascii < 115) {
+            // negative DIF digits j k l m n o p q r (ascii 106-114)
             inValue = true;
@@ -773,10 +839,8 @@ isDifference = true;
             isNegative = true;
-          } else
-          // $ sign, we need to check the next one
-          if (ascii === 36 && value.charCodeAt(i + 1) === 36) {
+          } else if (ascii === 36 && value.charCodeAt(i + 1) === 36) {
+            // $ sign, we need to check the next one
             inValue = true;
             inComment = true;
-          } else
-          // positive DIF digits % J K L M N O P Q R (ascii 37, 74-82)
-          if (ascii === 37) {
+          } else if (ascii === 37) {
+            // positive DIF digits % J K L M N O P Q R (ascii 37, 74-82)
             inValue = true;
@@ -786,6 +850,11 @@ isDifference = true;
             isNegative = false;
-          } else if (ascii === 45) { // a "-"
+          } else if (ascii === 45) {
+            // a "-"
             // check if after there is a number, decimal or comma
             var ascii2 = value.charCodeAt(i + 1);
-            if ((ascii2 >= 48 && ascii2 <= 57) || ascii2 === 44 || ascii2 === 46) {
+            if (
+              (ascii2 >= 48 && ascii2 <= 57) ||
+              ascii2 === 44 ||
+              ascii2 === 46
+            ) {
               inValue = true;
@@ -819,3 +888,6 @@ if (!newLine) isLastDifference = false;
     for (i = 1, ii = lines.length; i < ii; i++) {
-      values = lines[i].trim().replace(removeCommentRegExp, '').split(peakTableSplitRegExp);
+      values = lines[i]
+        .trim()
+        .replace(removeCommentRegExp, '')
+        .split(peakTableSplitRegExp);
       if (values.length % 2 === 0) {
@@ -833,3 +905,2 @@ for (j = 0, jj = values.length; j < jj; j = j + 2) {
 
-
   return convert;
@@ -862,7 +933,9 @@ }
     stamps[stamp] = resolve;
-    worker.postMessage(JSON.stringify({
-      stamp: stamp,
-      input: input,
-      options: options
-    }));
+    worker.postMessage(
+      JSON.stringify({
+        stamp: stamp,
+        input: input,
+        options: options
+      })
+    );
   });
@@ -872,3 +945,8 @@ }
 function createWorker() {
-  var workerURL = URL.createObjectURL(new Blob([`var getConverter =${getConverter.toString()};var convert = getConverter(); onmessage = function (event) { var data = JSON.parse(event.data); postMessage(JSON.stringify({stamp: data.stamp, output: convert(data.input, data.options)})); };`], { type: 'application/javascript' }));
+  var workerURL = URL.createObjectURL(
+    new Blob(
+      [`var getConverter =${getConverter.toString()};var convert = getConverter(); onmessage = function (event) { var data = JSON.parse(event.data); postMessage(JSON.stringify({stamp: data.stamp, output: convert(data.input, data.options)})); };`],
+      { type: 'application/javascript' }
+    )
+  );
   worker = new Worker(workerURL);
@@ -886,5 +964,3 @@ URL.revokeObjectURL(workerURL);
 function createTree(jcamp, options = {}) {
-  const {
-    flatten = false
-  } = options;
+  const { flatten = false } = options;
   if (typeof jcamp !== 'string') {
@@ -894,8 +970,9 @@ throw new TypeError('the JCAMP should be a string');
 
-  var lines = jcamp.split(/[\r\n]+/);
-  var flat = [];
-  var stack = [];
-  var result = [];
-  var current;
-  var ntupleLevel = 0;
+  let lines = jcamp.split(/[\r\n]+/);
+  let flat = [];
+  let stack = [];
+  let result = [];
+  let current;
+  let ntupleLevel = 0;
+
   for (var i = 0; i < lines.length; i++) {
@@ -909,4 +986,12 @@ var line = lines[i];
     if (line.substring(0, 7) === '##TITLE') {
+      let title = [line.substring(8).trim()];
+      for (let j = i + 1; j < lines.length; j++) {
+        if (lines[j].startsWith('##')) {
+          break;
+        } else {
+          title.push(lines[j].trim());
+        }
+      }
       stack.push({
-        title: line.substring(8).trim(),
+        title: title.join('\n'),
         jcamp: `${line}\n`,
@@ -943,3 +1028,5 @@ children: []
   if (flatten) {
-    flat.forEach( (entry) => {entry.children=undefined;});
+    flat.forEach((entry) => {
+      entry.children = undefined;
+    });
     return flat;
@@ -946,0 +1033,0 @@ } else {

New alerts

License Policy Violation

License

This package is not allowed per your license policy. Review the package's license to ensure compliance.

Found 1 instance in 1 package

Fixed alerts

License Policy Violation

License

This package is not allowed per your license policy. Review the package's license to ensure compliance.

Found 1 instance in 1 package

Improved metrics

Total package byte prevSize

41921

increased by3.48%

Lines of code

931

increased by11.1%

No dependency changes