jcampconverter 8.2.2 → 8.2.5

package/lib-esm/convert.js

@@ -0,0 +1,384 @@
+import { parseString } from 'dynamic-typing';
+import { ensureString } from 'ensure-string';
+import { isMSField, convertMSFieldToLabel } from './complexChromatogram';
+import convertToFloatArray from './convertToFloatArray';
+import fastParseXYData from './parse/fastParseXYData';
+import parsePeakTable from './parse/parsePeakTable';
+import parseXYA from './parse/parseXYA';
+import postProcessing from './postProcessing';
+import prepareNtuplesDatatable from './prepareNtuplesDatatable';
+import prepareSpectrum from './prepareSpectrum';
+import profiling from './profiling';
+// the following RegExp can only be used for XYdata, some peakTables have values with a "E-5" ...
+const ntuplesSeparatorRegExp = /[ \t]*,[ \t]*/;
+const defaultOptions = {
+    keepRecordsRegExp: /^$/,
+    canonicDataLabels: true,
+    canonicMetadataLabels: false,
+    dynamicTyping: true,
+    withoutXY: false,
+    chromatogram: false,
+    keepSpectra: false,
+    noContour: false,
+    nbContourLevels: 7,
+    noiseMultiplier: 5,
+    profiling: false,
+};
+/**
+ *
+ * @typedef {object} ConvertOptions
+ * @property {RegExp} [options.keepRecordsRegExp=/^$/] - By default we don't keep meta information.
+ * @property {boolean} [options.canonicDataLabels=true] - Canonize the Labels (uppercase without symbol).
+ * @property {boolean} [options.canonicMetadataLabels=false] - Canonize the metadata Labels (uppercase without symbol).
+ * @property {boolean} [options.dynamicTyping=false] - Convert numbers to Number.
+ * @property {boolean} [options.withoutXY=false] - Remove the XY data.
+ * @property {boolean} [options.chromatogram=false] - Special post-processing for GC / HPLC / MS.
+ * @property {boolean} [options.keepSpectra=false] - Force to keep the spectra in case of 2D.
+ * @property {boolean} [options.noContour=false] - Don't calculate countour in case of 2D.
+ * @property {number} [options.nbContourLevels=7] - Number of positive / negative contour levels to calculate.
+ * @property {number} [options.noiseMultiplier=5] - Define for 2D the level as 5 times the median as default.
+ * @property {boolean} [options.profiling=false] - Add profiling information.
+ */
+/**
+ *
+ * @typedef {object} Ntuples
+ * @property {string[]} [varname]
+ * @property {string[]} [symbol]
+ * @property {string[]} [vartype]
+ * @property {string[]} [varform]
+ * @property {number[]} [vardim]
+ * @property {string[]} [units]
+ * @property {number[]} [factor]
+ * @property {number[]} [first]
+ * @property {number[]} [last]
+ * @property {number[]} [min]
+ * @property {number[]} [max]
+ * @property {string[]} [nucleus]
+ */
+/**
+ * @typedef { Record<string, any> } Spectrum
+ * @property {Record<string, number[]>} [data]
+ * @property {number} [firstX]
+ * @property {number} [lastX]
+ * @property {number} [deltaX]
+ * @property {number} [yFactor]
+ * @property {number} [xFactor]
+ * @property {number} [nbPoints]
+ */
+/**
+ *
+ * @typedef {object} Entry
+ * @property {Spectrum[]} spectra
+ * @property {Ntuples} ntuples
+ * @property {object} meta
+ * @property {object} tmp
+ * @property {string} [title]
+ * @property {string} [dataType]
+ * @property {string} [dataClass]
+ * @property {boolean} [twoD]
+ */
+/**
+ *
+ * @typedef { object } ConvertResult
+ * @property { object[] | boolean } profiling
+ * @property { string[] } logs
+ * @property { object[] } entries
+ * @property { Entry[] } flatten
+ */
+/**
+ * Parse a jcamp.
+ *
+ * @param {string|ArrayBuffer|Uint8Array} jcamp
+ * @param {ConvertOptions} [options]
+ * @returns {ConvertResult}
+ */
+export function convert(jcamp, options = {}) {
+    jcamp = 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 = {};
+    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, result);
+                }
+                else {
+                    parsePeakTable(spectrum, dataValue, result);
+                }
+                currentEntry.spectra.push(spectrum);
+                spectrum = {};
+            }
+            continue;
+        }
+        else if (canonicDataLabel === 'PEAKTABLE') {
+            if (options.wantXY) {
+                prepareSpectrum(spectrum);
+                parsePeakTable(spectrum, dataValue, result);
+                currentEntry.spectra.push(spectrum);
+                spectrum = {};
+            }
+            continue;
+        }
+        if (canonicDataLabel === 'PEAKASSIGNMENTS') {
+            if (options.wantXY) {
+                if (dataValue.match(/.*(XYA).*/)) {
+                    // ex: (XYA)
+                    parseXYA(spectrum, dataValue);
+                }
+                currentEntry.spectra.push(spectrum);
+                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 = Number(dataValue);
+        }
+        else if (canonicDataLabel === 'LASTX') {
+            spectrum.lastX = Number(dataValue);
+        }
+        else if (canonicDataLabel === 'FIRSTY') {
+            spectrum.firstY = Number(dataValue);
+        }
+        else if (canonicDataLabel === 'LASTY') {
+            spectrum.lastY = Number(dataValue);
+        }
+        else if (canonicDataLabel === 'NPOINTS') {
+            spectrum.nbPoints = Number(dataValue);
+        }
+        else if (canonicDataLabel === 'XFACTOR') {
+            spectrum.xFactor = Number(dataValue);
+        }
+        else if (canonicDataLabel === 'YFACTOR') {
+            spectrum.yFactor = Number(dataValue);
+        }
+        else if (canonicDataLabel === 'MAXX') {
+            spectrum.maxX = Number(dataValue);
+        }
+        else if (canonicDataLabel === 'MINX') {
+            spectrum.minX = Number(dataValue);
+        }
+        else if (canonicDataLabel === 'MAXY') {
+            spectrum.maxY = Number(dataValue);
+        }
+        else if (canonicDataLabel === 'MINY') {
+            spectrum.minY = Number(dataValue);
+        }
+        else if (canonicDataLabel === 'DELTAX') {
+            spectrum.deltaX = Number(dataValue);
+        }
+        else if (canonicDataLabel === '.OBSERVEFREQUENCY' ||
+            canonicDataLabel === '$SFO1') {
+            if (!spectrum.observeFrequency) {
+                spectrum.observeFrequency = Number(dataValue);
+            }
+        }
+        else if (canonicDataLabel === '.OBSERVENUCLEUS') {
+            if (!spectrum.xType) {
+                currentEntry.xType = dataValue.replace(/[^a-zA-Z0-9]/g, '');
+            }
+        }
+        else if (canonicDataLabel === '$OFFSET') {
+            // OFFSET for Bruker spectra
+            currentEntry.shiftOffsetNum = 0;
+            if (!spectrum.shiftOffsetVal) {
+                spectrum.shiftOffsetVal = Number(dataValue);
+            }
+        }
+        else if (canonicDataLabel === '$REFERENCEPOINT') {
+            // OFFSET for Varian spectra
+            // if we activate this part it does not work for ACD specmanager
+            //         } else if (canonicDataLabel=='.SHIFTREFERENCE') {   // OFFSET FOR Bruker Spectra
+            //                 var parts = dataValue.split(/ *, */);
+            //                 currentEntry.shiftOffsetNum = parseInt(parts[2].trim());
+            //                 spectrum.shiftOffsetVal = Number(parts[3].trim());
+        }
+        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 = Number(dataValue.replace(/^.*=/, ''));
+            spectrum.pageSymbol = spectrum.page.replace(/[=].*/, '');
+        }
+        else if (canonicDataLabel === 'RETENTIONTIME') {
+            spectrum.pageValue = Number(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 = 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;
+}
+//# sourceMappingURL=convert.js.map

package/lib-esm/convert.js.map

@@ -0,0 +1 @@
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package/lib-esm/convertToFloatArray.d.ts

@@ -0,0 +1,2 @@
+export default function convertToFloatArray(stringArray: any): number[];
+//# sourceMappingURL=convertToFloatArray.d.ts.map

package/lib-esm/convertToFloatArray.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"convertToFloatArray.d.ts","sourceRoot":"","sources":["../src/convertToFloatArray.js"],"names":[],"mappings":"AAAA,wEAMC"}

package/lib-esm/convertToFloatArray.js

@@ -0,0 +1,8 @@
+export default function convertToFloatArray(stringArray) {
+    let floatArray = [];
+    for (let i = 0; i < stringArray.length; i++) {
+        floatArray.push(Number(stringArray[i]));
+    }
+    return floatArray;
+}
+//# sourceMappingURL=convertToFloatArray.js.map

package/lib-esm/convertToFloatArray.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"convertToFloatArray.js","sourceRoot":"","sources":["../src/convertToFloatArray.js"],"names":[],"mappings":"AAAA,MAAM,CAAC,OAAO,UAAU,mBAAmB,CAAC,WAAW;IACrD,IAAI,UAAU,GAAG,EAAE,CAAC;IACpB,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,WAAW,CAAC,MAAM,EAAE,CAAC,EAAE,EAAE;QAC3C,UAAU,CAAC,IAAI,CAAC,MAAM,CAAC,WAAW,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC;KACzC;IACD,OAAO,UAAU,CAAC;AACpB,CAAC"}

package/lib-esm/createTree.d.ts

@@ -0,0 +1,29 @@
+/**
+ *
+ * @typedef {object} CreateTreeOptions
+ * @property {boolean} [flatten=false]
+ */
+/**
+ *
+ * @typedef {object} Tree
+ * @property {string} title
+ * @property {string} jcamp
+ * @property {Tree[]} [children]
+ */
+/**
+ * Parse the jcamp to extract the structure as a tree.
+ *
+ * @param {string|ArrayBuffer|Uint8Array} jcamp
+ * @param {CreateTreeOptions} [options={}]
+ * @returns {Tree[]}
+ */
+export function createTree(jcamp: string | ArrayBuffer | Uint8Array, options?: CreateTreeOptions | undefined): Tree[];
+export type CreateTreeOptions = {
+    flatten?: boolean | undefined;
+};
+export type Tree = {
+    title: string;
+    jcamp: string;
+    children?: Tree[] | undefined;
+};
+//# sourceMappingURL=createTree.d.ts.map

package/lib-esm/createTree.d.ts.map

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package/lib-esm/createTree.js

@@ -0,0 +1,94 @@
+import { ensureString } from 'ensure-string';
+/**
+ *
+ * @typedef {object} CreateTreeOptions
+ * @property {boolean} [flatten=false]
+ */
+/**
+ *
+ * @typedef {object} Tree
+ * @property {string} title
+ * @property {string} jcamp
+ * @property {Tree[]} [children]
+ */
+/**
+ * Parse the jcamp to extract the structure as a tree.
+ *
+ * @param {string|ArrayBuffer|Uint8Array} jcamp
+ * @param {CreateTreeOptions} [options={}]
+ * @returns {Tree[]}
+ */
+export function createTree(jcamp, options = {}) {
+    jcamp = 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;
+    }
+}
+//# sourceMappingURL=createTree.js.map

package/lib-esm/createTree.js.map

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package/lib-esm/index.d.ts

@@ -0,0 +1,3 @@
+export { createTree } from "./createTree";
+export { convert } from "./convert";
+//# sourceMappingURL=index.d.ts.map

package/lib-esm/index.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"index.d.ts","sourceRoot":"","sources":["../src/index.js"],"names":[],"mappings":""}

package/lib-esm/index.js

@@ -0,0 +1,3 @@
+export { createTree } from './createTree';
+export { convert } from './convert';
+//# sourceMappingURL=index.js.map

package/lib-esm/index.js.map

@@ -0,0 +1 @@
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package/lib-esm/parse/fastParseXYData.d.ts

@@ -0,0 +1,2 @@
+export default function fastParseXYData(spectrum: any, value: any): void;
+//# sourceMappingURL=fastParseXYData.d.ts.map

package/lib-esm/parse/fastParseXYData.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"fastParseXYData.d.ts","sourceRoot":"","sources":["../../src/parse/fastParseXYData.js"],"names":[],"mappings":"AAAA,yEA4KC"}