jcampconverter - npm Package Compare versions

Comparing version 2.3.0 to 2.4.3

bower.json

 {
   "name": "jcampconverter",
-  "version": "2.3.0",
+  "version": "2.4.3",
   "main": [
@@ -5,0 +5,0 @@ "dist/jcampconverter.js",

package.json

 {
   "name": "jcampconverter",
-  "version": "2.3.0",
+  "version": "2.4.3",
   "description": "Parse and convert JCAMP data",
@@ -13,3 +13,5 @@ "main": "./src/index.js",
     "build": "cheminfo build --root JcampConverter",
-    "benchmark": "node benchmark/benchmark.js"
+    "benchmark": "node benchmark/benchmark.js",
+    "deopt": "node --trace-opt --trace-deopt --code-comments debug/deoptimize.js > deopt.log",
+    "hydra": "node --trace-hydrogen --trace-phase=Z --trace-deopt --code-comments --hydrogen-track-positions --redirect-code-traces --redirect-code-traces-to=code.asm debug/deoptimize.js"
   },
@@ -31,3 +33,3 @@ "repository": {
   "devDependencies": {
-    "benchmark": "^1.0.0",
+    "benchmark": "^2.1.0",
     "cheminfo-tools": "^1.0.2",
@@ -34,0 +36,0 @@ "mocha": "^2.2.5",

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 xyDataSplitRegExp = /[,\t \+-]*(?=[^\d,\t \.])|[ \t]+(?=[\d+\.-])/;
-    var removeCommentRegExp = /\$\$.*/;
-    var peakTableSplitRegExp = /[,\t ]+/;
     var ntuplesSeparator = /[, \t]{1,}/;
-    var DEBUG = false;
 
@@ -35,3 +34,3 @@ var GC_MS_FIELDS = ['TIC', '.RIC', 'SCANNUMBER'];
 
-        var start = new Date();
+        var start = Date.now();
 
@@ -56,7 +55,7 @@ var ntuples = {},
 
-        if (result.profiling) result.profiling.push({action: 'Before split to LDRS', time: new Date() - 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: new Date() - start});
+        if (result.profiling) result.profiling.push({action: 'Split to LDRS', time: Date.now() - start});
 
@@ -221,3 +220,10 @@ if (ldrs[0]) ldrs[0] = ldrs[0].replace(/^[\r\n ]*##/, '');
                 if (dataValue.match(/.*\+\+.*/)) {
-                    parseXYData(spectrum, dataValue, result);
+                    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);
+                    }
                 } else {
@@ -244,3 +250,3 @@ parsePeakTable(spectrum, dataValue, result);
 
-        if (result.profiling) result.profiling.push({action: 'Finished parsing', time: new Date() - start});
+        if (result.profiling) result.profiling.push({action: 'Finished parsing', time: Date.now() - start});
 
@@ -265,3 +271,3 @@ if (Object.keys(ntuples).length>0) {
                 action: 'Finished countour plot calculation',
-                time: new Date() - start
+                time: Date.now() - start
             });
@@ -308,3 +314,3 @@ if (!options.keepSpectra) {
                 action: 'Finished GCMS calculation',
-                time: new Date() - start
+                time: Date.now() - start
             });
@@ -314,3 +320,3 @@ }
         if (result.profiling) {
-            result.profiling.push({action: 'Total time', time: new Date() - start});
+            result.profiling.push({action: 'Total time', time: Date.now() - start});
         }
@@ -418,151 +424,4 @@
 
-    function parsePeakTable(spectrum, value, result) {
-        spectrum.isPeaktable=true;
-        var i, ii, j, jj, values;
-        var currentData = [];
-        spectrum.data = [currentData];
 
-        // counts for around 20% of the time
-        var lines = value.split(/,? *,?[;\r\n]+ */);
 
-        var k = 0;
-        for (i = 1, ii = lines.length; i < ii; i++) {
-            values = lines[i].trim().replace(removeCommentRegExp, '').split(peakTableSplitRegExp);
-            if (values.length % 2 === 0) {
-                for (j = 0, jj = values.length; j < jj; j = j + 2) {
-                    // takes around 40% of the time to add and parse the 2 values nearly exclusively because of parseFloat
-                    currentData[k++] = (parseFloat(values[j]) * spectrum.xFactor);
-                    currentData[k++] = (parseFloat(values[j + 1]) * spectrum.yFactor);
-                }
-            } else {
-                result.logs.push('Format error: ' + values);
-            }
-        }
-    }
-
-    function parseXYData(spectrum, value, result) {
-        // we check if deltaX is defined otherwise we calculate it
-        if (!spectrum.deltaX) {
-            spectrum.deltaX = (spectrum.lastX - spectrum.firstX) / (spectrum.nbPoints - 1);
-        }
-
-        spectrum.isXYdata=true;
-
-        var currentData = [];
-        spectrum.data = [currentData];
-
-        var currentX = spectrum.firstX;
-        var currentY = spectrum.firstY;
-        var lines = value.split(/[\r\n]+/);
-        var lastDif, values, ascii, expectedY;
-        values = [];
-        for (var i = 1, ii = lines.length; i < ii; i++) {
-            //var previousValues=JSON.parse(JSON.stringify(values));
-            values = lines[i].trim().replace(removeCommentRegExp, '').split(xyDataSplitRegExp);
-            if (values.length > 0) {
-                if (DEBUG) {
-                    if (!spectrum.firstPoint) {
-                        spectrum.firstPoint = parseFloat(values[0]);
-                    }
-                    var expectedCurrentX = parseFloat(values[0] - spectrum.firstPoint) * spectrum.xFactor + spectrum.firstX;
-                    if ((lastDif || lastDif === 0)) {
-                        expectedCurrentX += spectrum.deltaX;
-                    }
-                    result.logs.push('Checking X value: currentX: ' + currentX + ' - expectedCurrentX: ' + expectedCurrentX);
-                }
-                for (var j = 1, jj = values.length; j < jj; j++) {
-                    if (j === 1 && (lastDif || lastDif === 0)) {
-                        lastDif = null; // at the beginning of each line there should be the full value X / Y so the diff is always undefined
-                        // we could check if we have the expected Y value
-                        ascii = values[j].charCodeAt(0);
-
-                        if (false) { // this code is just to check the jcamp DIFDUP and the next line repeat of Y value
-                            // + - . 0 1 2 3 4 5 6 7 8 9
-                            if ((ascii === 43) || (ascii === 45) || (ascii === 46) || ((ascii > 47) && (ascii < 58))) {
-                                expectedY = parseFloat(values[j]);
-                            } else
-                            // positive SQZ digits @ A B C D E F G H I (ascii 64-73)
-                            if ((ascii > 63) && (ascii < 74)) {
-                                // we could use parseInt but parseFloat is faster at least in Chrome
-                                expectedY = parseFloat(String.fromCharCode(ascii - 16) + values[j].substring(1));
-                            } else
-                            // negative SQZ digits a b c d e f g h i (ascii 97-105)
-                            if ((ascii > 96) && (ascii < 106)) {
-                                // we could use parseInt but parseFloat is faster at least in Chrome
-                                expectedY = -parseFloat(String.fromCharCode(ascii - 48) + values[j].substring(1));
-                            }
-                            if (expectedY !== currentY) {
-                                result.logs.push('Y value check error: Found: ' + expectedY + ' - Current: ' + currentY);
-                                result.logs.push('Previous values: ' + previousValues.length);
-                                result.logs.push(previousValues);
-                            }
-                        }
-                    } else {
-                        if (values[j].length > 0) {
-                            ascii = values[j].charCodeAt(0);
-                            // + - . 0 1 2 3 4 5 6 7 8 9
-                            if ((ascii === 43) || (ascii === 45) || (ascii === 46) || ((ascii > 47) && (ascii < 58))) {
-                                lastDif = null;
-                                currentY = parseFloat(values[j]);
-                                currentData.push(currentX, currentY * spectrum.yFactor);;
-                                currentX += spectrum.deltaX;
-                            } else
-                            // positive SQZ digits @ A B C D E F G H I (ascii 64-73)
-                            if ((ascii > 63) && (ascii < 74)) {
-                                lastDif = null;
-                                currentY = parseFloat(String.fromCharCode(ascii - 16) + values[j].substring(1));
-                                currentData.push(currentX, currentY * spectrum.yFactor);;
-                                currentX += spectrum.deltaX;
-                            } else
-                            // negative SQZ digits a b c d e f g h i (ascii 97-105)
-                            if ((ascii > 96) && (ascii < 106)) {
-                                lastDif = null;
-                                currentY = -parseFloat(String.fromCharCode(ascii - 48) + values[j].substring(1));
-                                currentData.push(currentX, currentY * spectrum.yFactor);;
-                                currentX += spectrum.deltaX;
-                            } else
-
-
-
-                            // DUP digits S T U V W X Y Z s (ascii 83-90, 115)
-                            if (((ascii > 82) && (ascii < 91)) || (ascii === 115)) {
-                                var dup = parseFloat(String.fromCharCode(ascii - 34) + values[j].substring(1)) - 1;
-                                if (ascii === 115) {
-                                    dup = parseFloat('9' + values[j].substring(1)) - 1;
-                                }
-                                for (var l = 0; l < dup; l++) {
-                                    if (lastDif) {
-                                        currentY = currentY + lastDif;
-                                    }
-                                    currentData.push(currentX, currentY * spectrum.yFactor);;
-                                    currentX += spectrum.deltaX;
-                                }
-                            } else
-                            // positive DIF digits % J K L M N O P Q R (ascii 37, 74-82)
-                            if (ascii === 37) {
-                                lastDif = parseFloat('0' + values[j].substring(1));
-                                currentY += lastDif;
-                                currentData.push(currentX, currentY * spectrum.yFactor);;
-                                currentX += spectrum.deltaX;
-                            } else if ((ascii > 73) && (ascii < 83)) {
-                                lastDif = parseFloat(String.fromCharCode(ascii - 25) + values[j].substring(1));
-                                currentY += lastDif;
-                                currentData.push(currentX, currentY * spectrum.yFactor);;
-                                currentX += spectrum.deltaX;
-                            } else
-                            // negative DIF digits j k l m n o p q r (ascii 106-114)
-                            if ((ascii > 105) && (ascii < 115)) {
-                                lastDif = -parseFloat(String.fromCharCode(ascii - 57) + values[j].substring(1));
-                                currentY += lastDif;
-                                currentData.push(currentX, currentY * spectrum.yFactor);;
-                                currentX += spectrum.deltaX;
-                            }
-                        }
-                    }
-                }
-            }
-        }
-
-    }
-
     function convertTo3DZ(spectra) {
@@ -577,8 +436,10 @@ var noise = 0;
             z[i] = new Array(xSize);
+            var xVector=spectra[i].data[0];
             for (var j = 0; j < xSize; j++) {
-                z[i][j] = spectra[i].data[0][j * 2 + 1];
-                if (z[i][j] < minZ) minZ = spectra[i].data[0][j * 2 + 1];
-                if (z[i][j] > maxZ) maxZ = spectra[i].data[0][j * 2 + 1];
+                var value = xVector[j * 2 + 1];
+                z[i][j] = value;
+                if (value < minZ) minZ = value;
+                if (value > maxZ) maxZ = value;
                 if (i !== 0 && j !== 0) {
-                    noise += Math.abs(z[i][j] - z[i][j - 1]) + Math.abs(z[i][j] - z[i - 1][j]);
+                    noise += Math.abs(value - z[i][j - 1]) + Math.abs(value - z[i - 1][j]);
                 }
@@ -590,3 +451,3 @@ }
             minX: spectra[0].data[0][0],
-            maxX: spectra[0].data[0][spectra[0].data[0].length - 2],
+            maxX: spectra[0].data[0][spectra[0].data[0].length - 2], // has to be -2 because it is a 1D array [x,y,x,y,...]
             minY: spectra[0].pageValue,
@@ -610,3 +471,3 @@ maxY: spectra[ySize - 1].pageValue,
     function generateContourLines(zData, options) {
-        //console.time('generateContourLines');
+        // console.time('generateContourLines');
         var noise = zData.noise;
@@ -616,4 +477,4 @@ var z = zData.z;
         var nbLevels = 7;
-        var povarHeight = new Float32Array(4);
-        var isOver = [];
+        var povarHeight0, povarHeight1, povarHeight2, povarHeight3;
+        var isOver0, isOver1, isOver2, isOver3;
         var nbSubSpectra = z.length;
@@ -646,3 +507,3 @@ var nbPovars = z[0].length;
             var contourLevel = {};
-            contourLevels.push(contourLevel);
+            contourLevels[level]=contourLevel;
             var side = level % 2;
@@ -661,52 +522,56 @@ if (side === 0) {
             for (var iSubSpectra = 0; iSubSpectra < nbSubSpectra - 1; iSubSpectra++) {
+                var subSpectra = z[iSubSpectra];
+                var subSpectraAfter = z[iSubSpectra + 1];
                 for (var povar = 0; povar < nbPovars - 1; povar++) {
-                    povarHeight[0] = z[iSubSpectra][povar];
-                    povarHeight[1] = z[iSubSpectra][povar + 1];
-                    povarHeight[2] = z[(iSubSpectra + 1)][povar];
-                    povarHeight[3] = z[(iSubSpectra + 1)][(povar + 1)];
-
-                    for (var i = 0; i < 4; i++) {
-                        isOver[i] = (povarHeight[i] > lineZValue);
-                    }
-
+                    povarHeight0 = subSpectra[povar];
+                    povarHeight1 = subSpectra[povar + 1];
+                    povarHeight2 = subSpectraAfter[povar];
+                    povarHeight3 = subSpectraAfter[povar + 1];
+                    
+                    isOver0 = (povarHeight0 > lineZValue);
+                    isOver1 = (povarHeight1 > lineZValue);
+                    isOver2 = (povarHeight2 > lineZValue);
+                    isOver3 = (povarHeight3 > lineZValue);
+                    
                     // Example povar0 is over the plane and povar1 and
                     // povar2 are below, we find the varersections and add
                     // the segment
-                    if (isOver[0] !== isOver[1] && isOver[0] !== isOver[2]) {
-                        pAx = povar + (lineZValue - povarHeight[0]) / (povarHeight[1] - povarHeight[0]);
+                    if (isOver0 !== isOver1 && isOver0 !== isOver2) {
+                        pAx = povar + (lineZValue - povarHeight0) / (povarHeight1 - povarHeight0);
                         pAy = iSubSpectra;
                         pBx = povar;
-                        pBy = iSubSpectra + (lineZValue - povarHeight[0]) / (povarHeight[2] - povarHeight[0]);
-                        lines.push(pAx * dx + x0, pAy * dy + y0, pBx * dx + x0, pBy * dy + y0);
+                        pBy = iSubSpectra + (lineZValue - povarHeight0) / (povarHeight2 - povarHeight0);
+                        lines.push(pAx * dx + x0); lines.push(pAy * dy + y0); lines.push(pBx * dx + x0); lines.push(pBy * dy + y0);
                     }
-                    if (isOver[3] !== isOver[1] && isOver[3] !== isOver[2]) {
+                    // remove push does not help !!!!
+                    if (isOver3 !== isOver1 && isOver3 !== isOver2) {
                         pAx = povar + 1;
-                        pAy = iSubSpectra + 1 - (lineZValue - povarHeight[3]) / (povarHeight[1] - povarHeight[3]);
-                        pBx = povar + 1 - (lineZValue - povarHeight[3]) / (povarHeight[2] - povarHeight[3]);
+                        pAy = iSubSpectra + 1 - (lineZValue - povarHeight3) / (povarHeight1 - povarHeight3);
+                        pBx = povar + 1 - (lineZValue - povarHeight3) / (povarHeight2 - povarHeight3);
                         pBy = iSubSpectra + 1;
-                        lines.push(pAx * dx + x0, pAy * dy + y0, pBx * dx + x0, pBy * dy + y0);
+                        lines.push(pAx * dx + x0); lines.push(pAy * dy + y0); lines.push(pBx * dx + x0); lines.push(pBy * dy + y0);
                     }
                     // test around the diagonal
-                    if (isOver[1] !== isOver[2]) {
-                        pAx = povar + 1 - (lineZValue - povarHeight[1]) / (povarHeight[2] - povarHeight[1]);
-                        pAy = iSubSpectra + (lineZValue - povarHeight[1]) / (povarHeight[2] - povarHeight[1]);
-                        if (isOver[1] !== isOver[0]) {
-                            pBx = povar + 1 - (lineZValue - povarHeight[1]) / (povarHeight[0] - povarHeight[1]);
+                    if (isOver1 !== isOver2) {
+                        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);
                             pBy = iSubSpectra;
-                            lines.push(pAx * dx + x0, pAy * dy + y0, pBx * dx + x0, pBy * dy + y0);
+                            lines.push(pAx); lines.push(pAy); lines.push(pBx * dx + x0); lines.push(pBy * dy + y0);
                         }
-                        if (isOver[2] !== isOver[0]) {
+                        if (isOver2 !== isOver0) {
                             pBx = povar;
-                            pBy = iSubSpectra + 1 - (lineZValue - povarHeight[2]) / (povarHeight[0] - povarHeight[2]);
-                            lines.push(pAx * dx + x0, pAy * dy + y0, pBx * dx + x0, pBy * dy + y0);
+                            pBy = iSubSpectra + 1 - (lineZValue - povarHeight2) / (povarHeight0 - povarHeight2);
+                            lines.push(pAx); lines.push(pAy); lines.push(pBx * dx + x0); lines.push(pBy * dy + y0);
                         }
-                        if (isOver[1] !== isOver[3]) {
+                        if (isOver1 !== isOver3) {
                             pBx = povar + 1;
-                            pBy = iSubSpectra + (lineZValue - povarHeight[1]) / (povarHeight[3] - povarHeight[1]);
-                            lines.push(pAx * dx + x0, pAy * dy + y0, pBx * dx + x0, pBy * dy + y0);
+                            pBy = iSubSpectra + (lineZValue - povarHeight1) / (povarHeight3 - povarHeight1);
+                            lines.push(pAx); lines.push(pAy); lines.push(pBx * dx + x0); lines.push(pBy * dy + y0);
                         }
-                        if (isOver[2] !== isOver[3]) {
-                            pBx = povar + (lineZValue - povarHeight[2]) / (povarHeight[3] - povarHeight[2]);
+                        if (isOver2 !== isOver3) {
+                            pBx = povar + (lineZValue - povarHeight2) / (povarHeight3 - povarHeight2);
                             pBy = iSubSpectra + 1;
-                            lines.push(pAx * dx + x0, pAy * dy + y0, pBx * dx + x0, pBy * dy + y0);
+                            lines.push(pAx); lines.push(pAy); lines.push(pBx * dx + x0); lines.push(pBy * dy + y0);
                         }
@@ -759,2 +624,214 @@ }
 
+    function fastParseXYData(spectrum, value) {
+        // TODO need to deal with result
+        //  console.log(value);
+        // we check if deltaX is defined otherwise we calculate it
+
+        var yFactor = spectrum.yFactor;
+        var deltaX = spectrum.deltaX;
+        
+
+        spectrum.isXYdata = true;
+        // TODO to be improved using 2 array {x:[], y:[]}
+        var currentData = [];
+        var currentPosition = 0;
+        spectrum.data = [currentData];
+
+
+        var currentX = spectrum.firstX;
+        var currentY = spectrum.firstY;
+
+        // we skip the first line
+        //
+        var endLine = false;
+        for (var i = 0; i < value.length; i++) {
+            var ascii = value.charCodeAt(i);
+            if (ascii === 13 || ascii === 10) {
+                endLine = true;
+            } else {
+                if (endLine) break;
+            }
+        }
+
+        // we proceed taking the i after the first line
+        var newLine = true;
+        var isDifference=false;
+        var isLastDifference=false;
+        var lastDifference=0;
+        var isDuplicate=false;
+        var inComment = false;
+        var currentValue = 0;
+        var isNegative = false;
+        var inValue=false;
+        var skipFirstValue=false;
+        var decimalPosition = 0;
+        var ascii;
+        for (; i <= value.length; i++) {
+            if (i===value.length) ascii=13;
+            else ascii = value.charCodeAt(i);
+            if (inComment) {
+                // we should ignore the text if we are after $$
+                if (ascii === 13 || ascii === 10) {
+                    newLine = true;
+                    inComment = false;
+                }
+            } else {
+                // when is it a new value ?
+                // when it is not a digit, . or comma
+                // it is a number that is either new or we continue
+                if ( ascii <= 57 && ascii >= 48) { // a number
+                    inValue=true;
+                    if (decimalPosition > 0) {
+                        currentValue += (ascii - 48) / Math.pow(10, decimalPosition++);
+                    } else {
+                        currentValue *= 10;
+                        currentValue += ascii - 48;
+                    }
+                } else if (ascii === 44 || ascii === 46) { // a "," or "."
+                    inValue=true;
+                    decimalPosition++;
+                } else {
+                    if (inValue) {
+                        // need to process the previous value
+                        if (newLine) {
+                            newLine = false; // we don't check the X value
+                            // console.log("NEW LINE",isDifference, lastDifference);
+                            // if new line and lastDifference, the first value is just a check !
+                            // that we don't check ...
+                            if (isLastDifference) skipFirstValue=true;
+                        } else {
+                            // need to deal with duplicate and differences
+                            if (skipFirstValue) {
+                                skipFirstValue=false;
+                            } else {
+                                if (isDifference) {
+                                    if (currentValue===0) lastDifference=0;
+                                    else lastDifference=isNegative ? -currentValue : currentValue;
+                                    isLastDifference=true;
+                                    isDifference=false;
+                                }
+                                var duplicate=isDuplicate ? currentValue - 1 : 1;
+                                for (var j=0; j<duplicate; j++) {
+                                    if (isLastDifference) {
+                                        currentY += lastDifference;
+                                    } else {
+                                        if (currentValue===0) currentY=0;
+                                        else currentY = isNegative ? -currentValue : currentValue;
+                                    }
+
+                                    //  console.log("Separator",isNegative ?
+                                    //          -currentValue : currentValue,
+                                    //      "isDiff", isDifference, "isDup", isDuplicate,
+                                    //      "lastDif", lastDifference, "dup:", duplicate, "y", currentY);
+
+                                    // push is slightly slower ... (we loose 10%)
+                                    currentData[currentPosition++]=currentX;
+                                    currentData[currentPosition++]=currentY * yFactor;
+                                    currentX += deltaX;
+                                }
+                            }
+                        }
+                        isNegative=false;
+                        currentValue=0;
+                        decimalPosition=0;
+                        inValue=false;
+                        isDuplicate=false;
+                    }
+
+                    // positive SQZ digits @ A B C D E F G H I (ascii 64-73)
+                    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)) {
+                        inValue=true;
+                        isLastDifference=false;
+                        currentValue=ascii-96;
+                        isNegative=true;
+                    } else
+                    // DUP digits S T U V W X Y Z s (ascii 83-90, 115)
+                    if (ascii===115) {
+                        inValue=true;
+                        isDuplicate=true;
+                        currentValue=9;
+                    } 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)) {
+                        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)) {
+                        inValue=true;
+                        isDifference=true;
+                        currentValue=ascii-105;
+                        isNegative=true;
+                    } else
+                    // $ sign, we need to check the next one
+                    if (ascii === 36 && value.charCodeAt(i + 1) === 36) {
+                        inValue=true;
+                        inComment = true;
+                    } else
+                    // positive DIF digits % J K L M N O P Q R (ascii 37, 74-82)
+                    if (ascii === 37) {
+                        inValue=true;
+                        isDifference=true;
+                        currentValue=0;
+                        isNegative=false;
+                    } 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) {
+                            inValue=true;
+                            isLastDifference=false;
+                            isNegative = true;
+                        }
+                    } else if (ascii === 13 || ascii === 10) {
+                        newLine = true;
+                        inComment = false;
+                    }
+                    // and now analyse the details ... space or tabulation
+                    // if "+" we just don't care
+                }
+            }
+        }
+    }
+
+    function parsePeakTable(spectrum, value, result) {
+        var removeCommentRegExp = /\$\$.*/;
+        var peakTableSplitRegExp = /[,\t ]+/;
+        
+        spectrum.isPeaktable=true;
+        var i, ii, j, jj, values;
+        var currentData = [];
+        spectrum.data = [currentData];
+
+        // counts for around 20% of the time
+        var lines = value.split(/,? *,?[;\r\n]+ */);
+
+        var k = 0;
+        for (i = 1, ii = lines.length; i < ii; i++) {
+            values = lines[i].trim().replace(removeCommentRegExp, '').split(peakTableSplitRegExp);
+            if (values.length % 2 === 0) {
+                for (j = 0, jj = values.length; j < jj; j = j + 2) {
+                    // takes around 40% of the time to add and parse the 2 values nearly exclusively because of parseFloat
+                    currentData[k++] = (parseFloat(values[j]) * spectrum.xFactor);
+                    currentData[k++] = (parseFloat(values[j + 1]) * spectrum.yFactor);
+                }
+            } else {
+                result.logs.push('Format error: ' + values);
+            }
+        }
+    }
+
+
+
     return convert;
@@ -788,3 +865,3 @@
         stamps[stamp] = resolve;
-        worker.postMessage({stamp: stamp, input: input, options: options});
+        worker.postMessage(JSON.stringify({stamp: stamp, input: input, options: options}));
     });
@@ -795,3 +872,3 @@ }
     var workerURL = URL.createObjectURL(new Blob([
-        'var getConverter =' + getConverter.toString() + ';var convert = getConverter(); onmessage = function (event) { postMessage({stamp: event.data.stamp, output: convert(event.data.input, event.data.options)}); };'
+        'var getConverter =' + getConverter.toString() + ';var convert = getConverter(); onmessage = function (event) { var data = JSON.parse(event.data); postMessage(JSON.stringify({stamp: event.data.stamp, output: convert(data.input, data.options)})); };'
     ], {type: 'application/javascript'}));
@@ -801,5 +878,6 @@ worker = new Worker(workerURL);
     worker.addEventListener('message', function (event) {
-        var stamp = event.data.stamp;
+        var data = JSON.parse(event.data);
+        var stamp = data.stamp;
         if (stamps[stamp]) {
-            stamps[stamp](event.data.output);
+            stamps[stamp](data.output);
         }
@@ -806,0 +884,0 @@ });

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

57504

increased by45.25%

Number of package files

14

increased by55.56%

Lines of code

1189

increased by59.81%

Worsened metrics

Number of low supply chain risk alerts

2

increased by100%

No dependency changes