jcampconverter 8.2.0 → 8.2.4

package/lib/index.js

@@ -1,1213 +1,8 @@
-'use strict';
-
-Object.defineProperty(exports, '__esModule', { value: true });
-
-var ensureString = require('ensure-string');
-var dynamicTyping = require('dynamic-typing');
-var getMedian = require('ml-array-median');
-var nmrProcessing = require('nmr-processing');
-
-function _interopDefaultLegacy (e) { return e && typeof e === 'object' && 'default' in e ? e : { 'default': e }; }
-
-var getMedian__default = /*#__PURE__*/_interopDefaultLegacy(getMedian);
-
-/**
- * Parse the jcamp to extract the structure as a tree
- * @param {string|ArrayBuffer jcamp
- * @param {object} [options={}]
- * @param {boolean} [options.flatten=false]
- * @returns
- */
-function createTree(jcamp, options = {}) {
-  jcamp = ensureString.ensureString(jcamp);
-  const { flatten = false } = options;
-  if (typeof jcamp !== 'string') {
-    throw new TypeError('the JCAMP should be a string');
-  }
-
-  let lines = jcamp.split(/[\r\n]+/);
-  let flat = [];
-  let stack = [];
-  let result = [];
-  let current;
-  let ntupleLevel = 0;
-
-  let spaces = jcamp.includes('## ');
-
-  for (let i = 0; i < lines.length; i++) {
-    let line = lines[i];
-    let labelLine = spaces ? line.replace(/ /g, '') : line;
-
-    if (labelLine.substring(0, 9) === '##NTUPLES') {
-      ntupleLevel++;
-    }
-
-    if (labelLine.substring(0, 7) === '##TITLE') {
-      let title = [labelLine.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: title.join('\n'),
-        jcamp: `${line}\n`,
-        children: [],
-      });
-      current = stack[stack.length - 1];
-      flat.push(current);
-    } else if (labelLine.substring(0, 5) === '##END' && ntupleLevel === 0) {
-      current.jcamp += `${line}\n`;
-      let finished = stack.pop();
-      if (stack.length !== 0) {
-        current = stack[stack.length - 1];
-        current.children.push(finished);
-      } else {
-        current = undefined;
-        result.push(finished);
-      }
-    } else if (current && current.jcamp) {
-      current.jcamp += `${line}\n`;
-      let match = labelLine.match(/^##(.*?)=(.+)/);
-      if (match) {
-        let canonicDataLabel = match[1].replace(/[ _-]/g, '').toUpperCase();
-        if (canonicDataLabel === 'DATATYPE') {
-          current.dataType = match[2].trim();
-        }
-      }
-    }
-
-    if (labelLine.substring(0, 5) === '##END' && ntupleLevel > 0) {
-      ntupleLevel--;
-    }
-  }
-  if (flatten) {
-    flat.forEach((entry) => {
-      entry.children = undefined;
-    });
-    return flat;
-  } else {
-    return result;
-  }
-}
-
-const GC_MS_FIELDS = ['TIC', '.RIC', 'SCANNUMBER'];
-
-function complexChromatogram(result) {
-  let spectra = result.spectra;
-  let length = spectra.length;
-  let chromatogram = {
-    times: new Array(length),
-    series: {
-      ms: {
-        dimension: 2,
-        data: new Array(length),
-      },
-    },
-  };
-
-  let existingGCMSFields = [];
-  for (let i = 0; i < GC_MS_FIELDS.length; i++) {
-    let label = convertMSFieldToLabel(GC_MS_FIELDS[i]);
-    if (spectra[0][label]) {
-      existingGCMSFields.push(label);
-      chromatogram.series[label] = {
-        dimension: 1,
-        data: new Array(length),
-      };
-    }
-  }
-
-  for (let i = 0; i < length; i++) {
-    let spectrum = spectra[i];
-    chromatogram.times[i] = spectrum.pageValue;
-    for (let j = 0; j < existingGCMSFields.length; j++) {
-      chromatogram.series[existingGCMSFields[j]].data[i] = parseFloat(
-        spectrum[existingGCMSFields[j]],
-      );
-    }
-    if (spectrum.data) {
-      chromatogram.series.ms.data[i] = [spectrum.data.x, spectrum.data.y];
-    }
-  }
-  result.chromatogram = chromatogram;
-}
-
-function isMSField(canonicDataLabel) {
-  return GC_MS_FIELDS.indexOf(canonicDataLabel) !== -1;
-}
-
-function convertMSFieldToLabel(value) {
-  return value.toLowerCase().replace(/[^a-z0-9]/g, '');
-}
-
-function convertToFloatArray(stringArray) {
-  let floatArray = [];
-  for (let i = 0; i < stringArray.length; i++) {
-    floatArray.push(parseFloat(stringArray[i]));
-  }
-  return floatArray;
-}
-
-function fastParseXYData(spectrum, value) {
-  // TODO need to deal with result
-  //  console.log(value);
-  // we check if deltaX is defined otherwise we calculate it
-
-  let yFactor = spectrum.yFactor;
-  let deltaX = spectrum.deltaX;
-
-  spectrum.isXYdata = true;
-  let currentData = { x: [], y: [] };
-  spectrum.data = currentData;
-
-  let currentX = spectrum.firstX;
-  let currentY = spectrum.firstY;
-
-  // we skip the first line
-  //
-  let endLine = false;
-  let ascii;
-  let i = 0;
-  for (; i < value.length; i++) {
-    ascii = value.charCodeAt(i);
-    if (ascii === 13 || ascii === 10) {
-      endLine = true;
-    } else {
-      if (endLine) break;
-    }
-  }
-
-  // we proceed taking the i after the first line
-  let newLine = true;
-  let isDifference = false;
-  let isLastDifference = false;
-  let lastDifference = 0;
-  let isDuplicate = false;
-  let inComment = false;
-  let currentValue = 0; // can be a difference or a duplicate
-  let lastValue = 0; // must be the real last value
-  let isNegative = false;
-  let inValue = false;
-  let skipFirstValue = false;
-  let decimalPosition = 0;
-  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) {
-                lastDifference = isNegative ? 0 - currentValue : currentValue;
-                isLastDifference = true;
-                isDifference = false;
-              } else if (!isDuplicate) {
-                lastValue = isNegative ? 0 - currentValue : currentValue;
-              }
-              let duplicate = isDuplicate ? currentValue - 1 : 1;
-              for (let j = 0; j < duplicate; j++) {
-                if (isLastDifference) {
-                  currentY += lastDifference;
-                } else {
-                  currentY = lastValue;
-                }
-                currentData.x.push(currentX);
-                currentData.y.push(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 if (ascii > 96 && ascii < 106) {
-          // negative SQZ digits a b c d e f g h i (ascii 97-105)
-          inValue = true;
-          isLastDifference = false;
-          currentValue = ascii - 96;
-          isNegative = true;
-        } 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) {
-          inValue = true;
-          isDuplicate = true;
-          currentValue = ascii - 82;
-        } 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 if (ascii > 105 && ascii < 115) {
-          // negative DIF digits j k l m n o p q r (ascii 106-114)
-          inValue = true;
-          isDifference = true;
-          currentValue = ascii - 105;
-          isNegative = true;
-        } else if (ascii === 36 && value.charCodeAt(i + 1) === 36) {
-          // $ sign, we need to check the next one
-          inValue = true;
-          inComment = true;
-        } else if (ascii === 37) {
-          // positive DIF digits % J K L M N O P Q R (ascii 37, 74-82)
-          inValue = true;
-          isDifference = true;
-          currentValue = 0;
-          isNegative = false;
-        } else if (ascii === 45) {
-          // a "-"
-          // check if after there is a number, decimal or comma
-          let ascii2 = value.charCodeAt(i + 1);
-          if (
-            (ascii2 >= 48 && ascii2 <= 57) ||
-            ascii2 === 44 ||
-            ascii2 === 46
-          ) {
-            inValue = true;
-            if (!newLine) 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
-      }
-    }
-  }
-}
-
-const removeCommentRegExp = /\$\$.*/;
-const peakTableSplitRegExp = /[,\t ]+/;
-
-function parsePeakTable(spectrum, value, result) {
-  spectrum.isPeaktable = true;
-
-  if (!spectrum.variables || Object.keys(spectrum.variables) === 2) {
-    parseXY(spectrum, value, result);
-  } else {
-    parseXYZ(spectrum, value, result);
-  }
-
-  // we will add the data in the variables
-  if (spectrum.variables) {
-    for (let key in spectrum.variables) {
-      spectrum.variables[key].data = spectrum.data[key];
-    }
-  }
-}
-
-function parseXY(spectrum, value, result) {
-  let currentData = { x: [], y: [] };
-  spectrum.data = currentData;
-
-  // counts for around 20% of the time
-  let lines = value.split(/,? *,?[;\r\n]+ */);
-
-  for (let i = 1; i < lines.length; i++) {
-    let values = lines[i]
-      .trim()
-      .replace(removeCommentRegExp, '')
-      .split(peakTableSplitRegExp);
-    if (values.length % 2 === 0) {
-      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
-        currentData.x.push(parseFloat(values[j]) * spectrum.xFactor);
-        currentData.y.push(parseFloat(values[j + 1]) * spectrum.yFactor);
-      }
-    } else {
-      result.logs.push(`Format error: ${values}`);
-    }
-  }
-}
-
-function parseXYZ(spectrum, value, result) {
-  let currentData = {};
-  let variables = Object.keys(spectrum.variables);
-  let numberOfVariables = variables.length;
-  variables.forEach((variable) => (currentData[variable] = []));
-  spectrum.data = currentData;
-
-  // counts for around 20% of the time
-  let lines = value.split(/,? *,?[;\r\n]+ */);
-
-  for (let i = 1; i < lines.length; i++) {
-    let values = lines[i]
-      .trim()
-      .replace(removeCommentRegExp, '')
-      .split(peakTableSplitRegExp);
-    if (values.length % numberOfVariables === 0) {
-      for (let j = 0; j < values.length; j++) {
-        // todo should try to find a xFactor (y, ...)
-        currentData[variables[j % numberOfVariables]].push(
-          parseFloat(values[j]),
-        );
-      }
-    } else {
-      result.logs.push(`Format error: ${values}`);
-    }
-  }
-}
-
-function parseXYA(spectrum, value) {
-  let removeSymbolRegExp = /(\(+|\)+|<+|>+|\s+)/g;
-
-  spectrum.isXYAdata = true;
-  let values;
-  let currentData = { x: [], y: [] };
-  spectrum.data = currentData;
-
-  let lines = value.split(/,? *,?[;\r\n]+ */);
-
-  for (let i = 1; i < lines.length; i++) {
-    values = lines[i].trim().replace(removeSymbolRegExp, '').split(',');
-    currentData.x.push(parseFloat(values[0]));
-    currentData.y.push(parseFloat(values[1]));
-  }
-}
-
-function convertTo3DZ(spectra) {
-  let minZ = spectra[0].data.y[0];
-  let maxZ = minZ;
-  let ySize = spectra.length;
-  let xSize = spectra[0].data.x.length;
-
-  let z = new Array(ySize);
-  for (let i = 0; i < ySize; i++) {
-    z[i] = spectra[i].data.y;
-    for (let j = 0; j < xSize; j++) {
-      let value = z[i][j];
-      if (value < minZ) minZ = value;
-      if (value > maxZ) maxZ = value;
-    }
-  }
-
-  const firstX = spectra[0].data.x[0];
-  const lastX = spectra[0].data.x[spectra[0].data.x.length - 1]; // has to be -2 because it is a 1D array [x,y,x,y,...]
-  const firstY = spectra[0].pageValue;
-  const lastY = spectra[ySize - 1].pageValue;
-
-  // Because the min / max value are the only information about the matrix if we invert
-  // min and max we need to invert the array
-  if (firstX > lastX) {
-    for (let spectrum of z) {
-      spectrum.reverse();
-    }
-  }
-  if (firstY > lastY) {
-    z.reverse();
-  }
-
-  const medians = [];
-  for (let i = 0; i < z.length; i++) {
-    const row = Float64Array.from(z[i]);
-    for (let i = 0; i < row.length; i++) {
-      if (row[i] < 0) row[i] = -row[i];
-    }
-    medians.push(getMedian__default['default'](row));
-  }
-  const median = getMedian__default['default'](medians);
-
-  return {
-    z: z,
-    minX: Math.min(firstX, lastX),
-    maxX: Math.max(firstX, lastX),
-    minY: Math.min(firstY, lastY),
-    maxY: Math.max(firstY, lastY),
-    minZ: minZ,
-    maxZ: maxZ,
-    noise: median,
-  };
-}
-
-function generateContourLines(zData, options) {
-  let noise = zData.noise;
-  let z = zData.z;
-  let povarHeight0, povarHeight1, povarHeight2, povarHeight3;
-  let isOver0, isOver1, isOver2, isOver3;
-  let nbSubSpectra = z.length;
-  let nbPovars = z[0].length;
-  let pAx, pAy, pBx, pBy;
-
-  let x0 = zData.minX;
-  let xN = zData.maxX;
-  let dx = (xN - x0) / (nbPovars - 1);
-  let y0 = zData.minY;
-  let yN = zData.maxY;
-  let dy = (yN - y0) / (nbSubSpectra - 1);
-  let minZ = zData.minZ;
-  let maxZ = zData.maxZ;
-
-  // System.out.prvarln('y0 '+y0+' yN '+yN);
-  // -------------------------
-  // Povars attribution
-  //
-  // 0----1
-  // |  / |
-  // | /  |
-  // 2----3
-  //
-  // ---------------------d------
-
-  let iter = options.nbContourLevels * 2;
-  let contourLevels = new Array(iter);
-  let lineZValue;
-  for (let level = 0; level < iter; level++) {
-    // multiply by 2 for positif and negatif
-    let contourLevel = {};
-    contourLevels[level] = contourLevel;
-    let side = level % 2;
-    let 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;
-    }
-    let lines = [];
-    contourLevel.zValue = lineZValue;
-    contourLevel.lines = lines;
-
-    if (lineZValue <= minZ || lineZValue >= maxZ) continue;
-
-    for (let iSubSpectra = 0; iSubSpectra < nbSubSpectra - 1; iSubSpectra++) {
-      let subSpectra = z[iSubSpectra];
-      let subSpectraAfter = z[iSubSpectra + 1];
-      for (let povar = 0; povar < nbPovars - 1; povar++) {
-        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 (isOver0 !== isOver1 && isOver0 !== isOver2) {
-          pAx =
-            povar + (lineZValue - povarHeight0) / (povarHeight1 - povarHeight0);
-          pAy = iSubSpectra;
-          pBx = povar;
-          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);
-        }
-        // remove push does not help !!!!
-        if (isOver3 !== isOver1 && isOver3 !== isOver2) {
-          pAx = povar + 1;
-          pAy =
-            iSubSpectra +
-            1 -
-            (lineZValue - povarHeight3) / (povarHeight1 - povarHeight3);
-          pBx =
-            povar +
-            1 -
-            (lineZValue - povarHeight3) / (povarHeight2 - povarHeight3);
-          pBy = iSubSpectra + 1;
-          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 (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);
-            lines.push(pAy);
-            lines.push(pBx * dx + x0);
-            lines.push(pBy * dy + y0);
-          }
-          if (isOver2 !== isOver0) {
-            pBx = povar;
-            pBy =
-              iSubSpectra +
-              1 -
-              (lineZValue - povarHeight2) / (povarHeight0 - povarHeight2);
-            lines.push(pAx);
-            lines.push(pAy);
-            lines.push(pBx * dx + x0);
-            lines.push(pBy * dy + y0);
-          }
-          if (isOver1 !== isOver3) {
-            pBx = povar + 1;
-            pBy =
-              iSubSpectra +
-              (lineZValue - povarHeight1) / (povarHeight3 - povarHeight1);
-            lines.push(pAx);
-            lines.push(pAy);
-            lines.push(pBx * dx + x0);
-            lines.push(pBy * dy + y0);
-          }
-          if (isOver2 !== isOver3) {
-            pBx =
-              povar +
-              (lineZValue - povarHeight2) / (povarHeight3 - povarHeight2);
-            pBy = iSubSpectra + 1;
-            lines.push(pAx);
-            lines.push(pAy);
-            lines.push(pBx * dx + x0);
-            lines.push(pBy * dy + y0);
-          }
-        }
-      }
-    }
-  }
-
-  return {
-    minX: zData.minX,
-    maxX: zData.maxX,
-    minY: zData.minY,
-    maxY: zData.maxY,
-    segments: contourLevels,
-  };
-}
-
-function add2D(result, options) {
-  let zData = convertTo3DZ(result.spectra);
-  if (!options.noContour) {
-    result.contourLines = generateContourLines(zData, options);
-    delete zData.z;
-  }
-  result.minMax = zData;
-}
-
-function postProcessingNMR(entriesFlat) {
-  // specific NMR functions
-
-  for (let entry of entriesFlat) {
-    let observeFrequency = 0;
-    let shiftOffsetVal = 0;
-    for (let spectrum of entry.spectra) {
-      if (entry.ntuples && entry.ntuples.symbol) {
-        if (!observeFrequency && spectrum.observeFrequency) {
-          observeFrequency = spectrum.observeFrequency;
-        }
-        if (!shiftOffsetVal && spectrum.shiftOffsetVal) {
-          shiftOffsetVal = spectrum.shiftOffsetVal;
-        }
-      } else {
-        observeFrequency = spectrum.observeFrequency;
-        shiftOffsetVal = spectrum.shiftOffsetVal;
-      }
-
-      if (observeFrequency) {
-        if (spectrum.xUnits && spectrum.xUnits.toUpperCase().includes('HZ')) {
-          spectrum.xUnits = 'PPM';
-          spectrum.xFactor = spectrum.xFactor / observeFrequency;
-          spectrum.firstX = spectrum.firstX / observeFrequency;
-          spectrum.lastX = spectrum.lastX / observeFrequency;
-          spectrum.deltaX = spectrum.deltaX / observeFrequency;
-          for (let i = 0; i < spectrum.data.x.length; i++) {
-            spectrum.data.x[i] /= observeFrequency;
-          }
-        }
-      }
-      if (shiftOffsetVal) {
-        let shift = spectrum.firstX - shiftOffsetVal;
-        spectrum.firstX = spectrum.firstX - shift;
-        spectrum.lastX = spectrum.lastX - shift;
-        for (let i = 0; i < spectrum.data.x.length; i++) {
-          spectrum.data.x[i] -= shift;
-        }
-      }
-
-      // we will check if some nucleus are missing ...
-      if (entry.ntuples && entry.ntuples.nucleus && entry.ntuples.symbol) {
-        for (let i = 0; i < entry.ntuples.nucleus.length; i++) {
-          let symbol = entry.ntuples.symbol[i];
-          let nucleus = entry.ntuples.nucleus[i];
-          if (symbol.startsWith('F') && !nucleus) {
-            if (symbol === 'F1') {
-              // if F1 is defined we will use F2
-              if (entry.tmp.$NUC2) {
-                entry.ntuples.nucleus[i] = entry.tmp.$NUC2;
-              } else {
-                let f2index = entry.ntuples.symbol.indexOf('F2');
-                if (f2index && entry.ntuples.nucleus[f2index]) {
-                  entry.ntuples.nucleus[i] = entry.ntuples.nucleus[f2index];
-                }
-              }
-            }
-            if (symbol === 'F2') entry.ntuples.nucleus[i] = entry.tmp.$NUC1;
-          }
-          if (symbol === 'F2') {
-            entry.yType = entry.ntuples.nucleus[0];
-          }
-        }
-      }
-
-      if (
-        observeFrequency &&
-        entry.ntuples &&
-        entry.ntuples.symbol &&
-        entry.ntuples.nucleus
-      ) {
-        let unit = '';
-        let pageSymbolIndex = entry.ntuples.symbol.indexOf(spectrum.pageSymbol);
-        if (entry.ntuples.units && entry.ntuples.units[pageSymbolIndex]) {
-          unit = entry.ntuples.units[pageSymbolIndex];
-        }
-        if (unit !== 'PPM') {
-          if (pageSymbolIndex !== 0) {
-            throw Error('Not sure about this ntuples format');
-          }
-
-          let ratio0 = nmrProcessing.gyromagneticRatio[entry.ntuples.nucleus[0]];
-          let ratio1 = nmrProcessing.gyromagneticRatio[entry.ntuples.nucleus[1]];
-          if (!ratio0 || !ratio1) {
-            throw Error('Problem with determination of gyromagnetic ratio');
-          }
-          let ratio = (ratio0 / ratio1) * observeFrequency;
-          spectrum.pageValue /= ratio;
-        }
-      }
-    }
-  }
-}
-
-function profiling(result, action, options) {
-  if (result.profiling) {
-    result.profiling.push({
-      action,
-      time: Date.now() - options.start,
-    });
-  }
-}
-
-function simpleChromatogram(result) {
-  let data = result.spectra[0].data;
-  result.chromatogram = {
-    times: data.x.slice(),
-    series: {
-      intensity: {
-        dimension: 1,
-        data: data.y.slice(),
-      },
-    },
-  };
-}
-
-function postProcessing(entriesFlat, result, options) {
-  // converting Hz to ppm
-  postProcessingNMR(entriesFlat);
-
-  for (let entry of entriesFlat) {
-    if (Object.keys(entry.ntuples).length > 0) {
-      let newNtuples = [];
-      let keys = Object.keys(entry.ntuples);
-      for (let i = 0; i < keys.length; i++) {
-        let key = keys[i];
-        let values = entry.ntuples[key];
-        for (let j = 0; j < values.length; j++) {
-          if (!newNtuples[j]) newNtuples[j] = {};
-          newNtuples[j][key] = values[j];
-        }
-      }
-      entry.ntuples = newNtuples;
-    }
-
-    if (entry.twoD && options.wantXY) {
-      add2D(entry, options);
-
-      profiling(result, 'Finished countour plot calculation', options);
-
-      if (!options.keepSpectra) {
-        delete entry.spectra;
-      }
-    }
-
-    // maybe it is a GC (HPLC) / MS. In this case we add a new format
-    if (options.chromatogram) {
-      if (entry.spectra.length > 1) {
-        complexChromatogram(entry);
-      } else {
-        simpleChromatogram(entry);
-      }
-      profiling(result, 'Finished chromatogram calculation', options);
-    }
-
-    delete entry.tmp;
-  }
-}
-
-function prepareNtuplesDatatable(currentEntry, spectrum, kind) {
-  let xIndex = -1;
-  let yIndex = -1;
-  let firstVariable = '';
-  let secondVariable = '';
-  if (kind.indexOf('++') > 0) {
-    firstVariable = kind.replace(/.*\(([a-zA-Z0-9]+)\+\+.*/, '$1');
-    secondVariable = kind.replace(/.*\.\.([a-zA-Z0-9]+).*/, '$1');
-  } else {
-    kind = kind.replace(/[^a-zA-Z]/g, '');
-    firstVariable = kind.charAt(0);
-    secondVariable = kind.charAt(1);
-    spectrum.variables = {};
-    for (let symbol of kind) {
-      let lowerCaseSymbol = symbol.toLowerCase();
-      let index = currentEntry.ntuples.symbol.indexOf(symbol);
-      if (index === -1) throw Error(`Symbol undefined: ${symbol}`);
-      spectrum.variables[lowerCaseSymbol] = {};
-      for (let key in currentEntry.ntuples) {
-        if (currentEntry.ntuples[key][index]) {
-          spectrum.variables[lowerCaseSymbol][key.replace(/^var/, '')] =
-            currentEntry.ntuples[key][index];
-        }
-      }
-    }
-  }
-  xIndex = currentEntry.ntuples.symbol.indexOf(firstVariable);
-  yIndex = currentEntry.ntuples.symbol.indexOf(secondVariable);
-
-  if (xIndex === -1) xIndex = 0;
-  if (yIndex === -1) yIndex = 0;
-
-  if (currentEntry.ntuples.first) {
-    if (currentEntry.ntuples.first.length > xIndex) {
-      spectrum.firstX = currentEntry.ntuples.first[xIndex];
-    }
-    if (currentEntry.ntuples.first.length > yIndex) {
-      spectrum.firstY = currentEntry.ntuples.first[yIndex];
-    }
-  }
-  if (currentEntry.ntuples.last) {
-    if (currentEntry.ntuples.last.length > xIndex) {
-      spectrum.lastX = currentEntry.ntuples.last[xIndex];
-    }
-    if (currentEntry.ntuples.last.length > yIndex) {
-      spectrum.lastY = currentEntry.ntuples.last[yIndex];
-    }
-  }
-  if (
-    currentEntry.ntuples.vardim &&
-    currentEntry.ntuples.vardim.length > xIndex
-  ) {
-    spectrum.nbPoints = currentEntry.ntuples.vardim[xIndex];
-  }
-  if (currentEntry.ntuples.factor) {
-    if (currentEntry.ntuples.factor.length > xIndex) {
-      spectrum.xFactor = currentEntry.ntuples.factor[xIndex];
-    }
-    if (currentEntry.ntuples.factor.length > yIndex) {
-      spectrum.yFactor = currentEntry.ntuples.factor[yIndex];
-    }
-  }
-  if (currentEntry.ntuples.units) {
-    if (currentEntry.ntuples.units.length > xIndex) {
-      if (
-        currentEntry.ntuples.varname &&
-        currentEntry.ntuples.varname[xIndex]
-      ) {
-        spectrum.xUnits = `${currentEntry.ntuples.varname[xIndex]} [${currentEntry.ntuples.units[xIndex]}]`;
-      } else {
-        spectrum.xUnits = currentEntry.ntuples.units[xIndex];
-      }
-    }
-    if (currentEntry.ntuples.units.length > yIndex) {
-      if (
-        currentEntry.ntuples.varname &&
-        currentEntry.ntuples.varname[yIndex]
-      ) {
-        spectrum.yUnits = `${currentEntry.ntuples.varname[yIndex]} [${currentEntry.ntuples.units[yIndex]}]`;
-      } else {
-        spectrum.yUnits = currentEntry.ntuples.units[yIndex];
-      }
-    }
-  }
-}
-
-function prepareSpectrum(spectrum) {
-  if (!spectrum.xFactor) spectrum.xFactor = 1;
-  if (!spectrum.yFactor) spectrum.yFactor = 1;
-}
-
-// the following RegExp can only be used for XYdata, some peakTables have values with a "E-5" ...
-const ntuplesSeparatorRegExp = /[ \t]*,[ \t]*/;
-
-class Spectrum {}
-
-const defaultOptions = {
-  keepRecordsRegExp: /^$/,
-  canonicDataLabels: true,
-  canonicMetadataLabels: false,
-  dynamicTyping: true,
-  withoutXY: false,
-  chromatogram: false,
-  keepSpectra: false,
-  noContour: false,
-  nbContourLevels: 7,
-  noiseMultiplier: 5,
-  profiling: false,
-};
-
-/**
- *
- * @param {string|ArrayBuffer} jcamp
- * @param {object} [options]
- * @param {number} [options.keepRecordsRegExp=/^$/] By default we don't keep meta information
- * @param {number} [options.canonicDataLabels=true] Canonize the Labels (uppercase without symbol)
- * @param {number} [options.canonicMetadataLabels=false] Canonize the metadata Labels (uppercase without symbol)
- * @param {number} [options.dynamicTyping=false] Convert numbers to Number
- * @param {number} [options.withoutXY=false] Remove the XY data
- * @param {number} [options.chromatogram=false] Special post-processing for GC / HPLC / MS
- * @param {number} [options.keepSpectra=false] Force to keep the spectra in case of 2D
- * @param {number} [options.noContour=false] Don't calculate countour in case of 2D
- * @param {number} [options.nbContourLevels=7] Number of positive / negative contour levels to calculate
- * @param {number} [options.noiseMultiplier=5] Define for 2D the level as 5 times the median as default
- * @param {number} [options.profiling=false] Add profiling information
- */
-
-function convert(jcamp, options = {}) {
-  jcamp = ensureString.ensureString(jcamp);
-  options = { ...defaultOptions, ...options };
-  options.wantXY = !options.withoutXY;
-  options.start = Date.now();
-
-  let entriesFlat = [];
-
-  let result = {
-    profiling: options.profiling ? [] : false,
-    logs: [],
-    entries: [],
-  };
-
-  let tmpResult = { children: [] };
-  let currentEntry = tmpResult;
-  let parentsStack = [];
-
-  let spectrum = new Spectrum();
-
-  if (typeof jcamp !== 'string') {
-    throw new TypeError('the JCAMP should be a string');
-  }
-
-  profiling(result, 'Before split to LDRS', options);
-
-  let ldrs = jcamp.replace(/[\r\n]+##/g, '\n##').split('\n##');
-
-  profiling(result, 'Split to LDRS', options);
-
-  if (ldrs[0]) ldrs[0] = ldrs[0].replace(/^[\r\n ]*##/, '');
-
-  for (let ldr of ldrs) {
-    // This is a new LDR
-    let position = ldr.indexOf('=');
-    let dataLabel = position > 0 ? ldr.substring(0, position) : ldr;
-    let dataValue = position > 0 ? ldr.substring(position + 1).trim() : '';
-
-    let canonicDataLabel = dataLabel.replace(/[_ -]/g, '').toUpperCase();
-
-    if (canonicDataLabel === 'DATATABLE') {
-      let endLine = dataValue.indexOf('\n');
-      if (endLine === -1) endLine = dataValue.indexOf('\r');
-      if (endLine > 0) {
-        // ##DATA TABLE= (X++(I..I)), XYDATA
-        // We need to find the variables
-
-        let infos = dataValue.substring(0, endLine).split(/[ ,;\t]+/);
-        prepareNtuplesDatatable(currentEntry, spectrum, infos[0]);
-
-        spectrum.datatable = infos[0];
-        if (infos[1] && infos[1].indexOf('PEAKS') > -1) {
-          canonicDataLabel = 'PEAKTABLE';
-        } else if (
-          infos[1] &&
-          (infos[1].indexOf('XYDATA') || infos[0].indexOf('++') > 0)
-        ) {
-          canonicDataLabel = 'XYDATA';
-          spectrum.deltaX =
-            (spectrum.lastX - spectrum.firstX) / (spectrum.nbPoints - 1);
-        }
-      }
-    }
-
-    if (canonicDataLabel === 'XYDATA') {
-      if (options.wantXY) {
-        prepareSpectrum(spectrum);
-        // well apparently we should still consider it is a PEAK TABLE if there are no '++' after
-        if (dataValue.match(/.*\+\+.*/)) {
-          // ex: (X++(Y..Y))
-          spectrum.deltaX =
-            (spectrum.lastX - spectrum.firstX) / (spectrum.nbPoints - 1);
-
-          fastParseXYData(spectrum, dataValue);
-        } else {
-          parsePeakTable(spectrum, dataValue, result);
-        }
-        currentEntry.spectra.push(spectrum);
-        spectrum = new Spectrum();
-      }
-      continue;
-    } else if (canonicDataLabel === 'PEAKTABLE') {
-      if (options.wantXY) {
-        prepareSpectrum(spectrum);
-        parsePeakTable(spectrum, dataValue, result);
-        currentEntry.spectra.push(spectrum);
-        spectrum = new Spectrum();
-      }
-      continue;
-    }
-    if (canonicDataLabel === 'PEAKASSIGNMENTS') {
-      if (options.wantXY) {
-        if (dataValue.match(/.*(XYA).*/)) {
-          // ex: (XYA)
-          parseXYA(spectrum, dataValue);
-        }
-        currentEntry.spectra.push(spectrum);
-        spectrum = new Spectrum();
-      }
-      continue;
-    }
-
-    if (canonicDataLabel === 'TITLE') {
-      let parentEntry = currentEntry;
-      if (!parentEntry.children) {
-        parentEntry.children = [];
-      }
-      currentEntry = {
-        spectra: [],
-        ntuples: {},
-        info: {},
-        meta: {},
-        tmp: {}, // tmp information we need to keep for postprocessing
-      };
-      parentEntry.children.push(currentEntry);
-      parentsStack.push(parentEntry);
-      entriesFlat.push(currentEntry);
-      currentEntry.title = dataValue;
-    } else if (canonicDataLabel === 'DATATYPE') {
-      currentEntry.dataType = dataValue;
-      if (dataValue.match(/(^nd|\snd\s)/i)) {
-        currentEntry.twoD = true;
-      }
-    } else if (canonicDataLabel === 'NTUPLES') {
-      if (dataValue.match(/(^nd|\snd\s)/i)) {
-        currentEntry.twoD = true;
-      }
-    } else if (canonicDataLabel === 'DATACLASS') {
-      currentEntry.dataClass = dataValue;
-    } else if (canonicDataLabel === 'XUNITS') {
-      spectrum.xUnits = dataValue;
-    } else if (canonicDataLabel === 'YUNITS') {
-      spectrum.yUnits = dataValue;
-    } else if (canonicDataLabel === 'FIRSTX') {
-      spectrum.firstX = parseFloat(dataValue);
-    } else if (canonicDataLabel === 'LASTX') {
-      spectrum.lastX = parseFloat(dataValue);
-    } else if (canonicDataLabel === 'FIRSTY') {
-      spectrum.firstY = parseFloat(dataValue);
-    } else if (canonicDataLabel === 'LASTY') {
-      spectrum.lastY = parseFloat(dataValue);
-    } else if (canonicDataLabel === 'NPOINTS') {
-      spectrum.nbPoints = parseFloat(dataValue);
-    } else if (canonicDataLabel === 'XFACTOR') {
-      spectrum.xFactor = parseFloat(dataValue);
-    } else if (canonicDataLabel === 'YFACTOR') {
-      spectrum.yFactor = parseFloat(dataValue);
-    } else if (canonicDataLabel === 'MAXX') {
-      spectrum.maxX = parseFloat(dataValue);
-    } else if (canonicDataLabel === 'MINX') {
-      spectrum.minX = parseFloat(dataValue);
-    } else if (canonicDataLabel === 'MAXY') {
-      spectrum.maxY = parseFloat(dataValue);
-    } else if (canonicDataLabel === 'MINY') {
-      spectrum.minY = parseFloat(dataValue);
-    } else if (canonicDataLabel === 'DELTAX') {
-      spectrum.deltaX = parseFloat(dataValue);
-    } else if (
-      canonicDataLabel === '.OBSERVEFREQUENCY' ||
-      canonicDataLabel === '$SFO1'
-    ) {
-      if (!spectrum.observeFrequency) {
-        spectrum.observeFrequency = parseFloat(dataValue);
-      }
-    } else if (canonicDataLabel === '.OBSERVENUCLEUS') {
-      if (!spectrum.xType) {
-        currentEntry.xType = dataValue.replace(/[^a-zA-Z0-9]/g, '');
-      }
-    } else if (canonicDataLabel === '$OFFSET') {
-      // OFFSET for Bruker spectra
-      currentEntry.shiftOffsetNum = 0;
-      if (!spectrum.shiftOffsetVal) {
-        spectrum.shiftOffsetVal = parseFloat(dataValue);
-      }
-    } else if (canonicDataLabel === '$REFERENCEPOINT') ; else if (canonicDataLabel === 'VARNAME') {
-      currentEntry.ntuples.varname = dataValue.split(ntuplesSeparatorRegExp);
-    } else if (canonicDataLabel === 'SYMBOL') {
-      currentEntry.ntuples.symbol = dataValue.split(ntuplesSeparatorRegExp);
-    } else if (canonicDataLabel === 'VARTYPE') {
-      currentEntry.ntuples.vartype = dataValue.split(ntuplesSeparatorRegExp);
-    } else if (canonicDataLabel === 'VARFORM') {
-      currentEntry.ntuples.varform = dataValue.split(ntuplesSeparatorRegExp);
-    } else if (canonicDataLabel === 'VARDIM') {
-      currentEntry.ntuples.vardim = convertToFloatArray(
-        dataValue.split(ntuplesSeparatorRegExp),
-      );
-    } else if (canonicDataLabel === 'UNITS') {
-      currentEntry.ntuples.units = dataValue.split(ntuplesSeparatorRegExp);
-    } else if (canonicDataLabel === 'FACTOR') {
-      currentEntry.ntuples.factor = convertToFloatArray(
-        dataValue.split(ntuplesSeparatorRegExp),
-      );
-    } else if (canonicDataLabel === 'FIRST') {
-      currentEntry.ntuples.first = convertToFloatArray(
-        dataValue.split(ntuplesSeparatorRegExp),
-      );
-    } else if (canonicDataLabel === 'LAST') {
-      currentEntry.ntuples.last = convertToFloatArray(
-        dataValue.split(ntuplesSeparatorRegExp),
-      );
-    } else if (canonicDataLabel === 'MIN') {
-      currentEntry.ntuples.min = convertToFloatArray(
-        dataValue.split(ntuplesSeparatorRegExp),
-      );
-    } else if (canonicDataLabel === 'MAX') {
-      currentEntry.ntuples.max = convertToFloatArray(
-        dataValue.split(ntuplesSeparatorRegExp),
-      );
-    } else if (canonicDataLabel === '.NUCLEUS') {
-      if (currentEntry.ntuples) {
-        currentEntry.ntuples.nucleus = dataValue.split(ntuplesSeparatorRegExp);
-      }
-    } else if (canonicDataLabel === 'PAGE') {
-      spectrum.page = dataValue.trim();
-      spectrum.pageValue = parseFloat(dataValue.replace(/^.*=/, ''));
-      spectrum.pageSymbol = spectrum.page.replace(/[=].*/, '');
-    } else if (canonicDataLabel === 'RETENTIONTIME') {
-      spectrum.pageValue = parseFloat(dataValue);
-    } else if (isMSField(canonicDataLabel)) {
-      spectrum[convertMSFieldToLabel(canonicDataLabel)] = dataValue;
-    } else if (canonicDataLabel === 'SAMPLEDESCRIPTION') {
-      spectrum.sampleDescription = dataValue;
-    } else if (canonicDataLabel.startsWith('$NUC')) {
-      if (!currentEntry.tmp[canonicDataLabel] && !dataValue.includes('off')) {
-        currentEntry.tmp[canonicDataLabel] = dataValue.replace(/[<>]/g, '');
-      }
-    } else if (canonicDataLabel === 'END') {
-      currentEntry = parentsStack.pop();
-    }
-
-    if (
-      currentEntry &&
-      currentEntry.info &&
-      currentEntry.meta &&
-      canonicDataLabel.match(options.keepRecordsRegExp)
-    ) {
-      let value = dataValue.trim();
-      let target, label;
-      if (dataLabel.startsWith('$')) {
-        label = options.canonicMetadataLabels
-          ? canonicDataLabel.substring(1)
-          : dataLabel.substring(1);
-        target = currentEntry.meta;
-      } else {
-        label = options.canonicDataLabels ? canonicDataLabel : dataLabel;
-        target = currentEntry.info;
-      }
-
-      if (options.dynamicTyping) {
-        value = dynamicTyping.parseString(value);
-      }
-      if (target[label]) {
-        if (!Array.isArray(target[label])) {
-          target[label] = [target[label]];
-        }
-        target[label].push(value);
-      } else {
-        target[label] = value;
-      }
-    }
-  }
-
-  profiling(result, 'Finished parsing', options);
-
-  postProcessing(entriesFlat, result, options);
-
-  profiling(result, 'Total time', options);
-
-  /*
-  if (result.children && result.children.length>0) {
-    result = { ...result, ...result.children[0] };
-  }
-  */
-  result.entries = tmpResult.children;
-  result.flatten = entriesFlat;
-
-  return result;
-}
-
-exports.convert = convert;
-exports.createTree = createTree;
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.convert = exports.createTree = void 0;
+var createTree_1 = require("./createTree");
+Object.defineProperty(exports, "createTree", { enumerable: true, get: function () { return createTree_1.createTree; } });
+var convert_1 = require("./convert");
+Object.defineProperty(exports, "convert", { enumerable: true, get: function () { return convert_1.convert; } });
+//# sourceMappingURL=index.js.map