jcampconverter 9.2.0 → 9.2.2
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- package/jcampconverter.cjs +8 -0
- package/{lib/convert.d.ts → jcampconverter.d.ts} +222 -182
- package/jcampconverter.mjs +8 -0
- package/package.json +27 -19
- package/lib/2d/add2D.d.ts +0 -2
- package/lib/2d/add2D.d.ts.map +0 -1
- package/lib/2d/add2D.js +0 -17
- package/lib/2d/add2D.js.map +0 -1
- package/lib/2d/convertTo3DZ.d.ts +0 -11
- package/lib/2d/convertTo3DZ.d.ts.map +0 -1
- package/lib/2d/convertTo3DZ.js +0 -59
- package/lib/2d/convertTo3DZ.js.map +0 -1
- package/lib/2d/generateContourLines.d.ts +0 -8
- package/lib/2d/generateContourLines.d.ts.map +0 -1
- package/lib/2d/generateContourLines.js +0 -163
- package/lib/2d/generateContourLines.js.map +0 -1
- package/lib/complexChromatogram.d.ts +0 -4
- package/lib/complexChromatogram.d.ts.map +0 -1
- package/lib/complexChromatogram.js +0 -49
- package/lib/complexChromatogram.js.map +0 -1
- package/lib/convert.d.ts.map +0 -1
- package/lib/convert.js +0 -412
- package/lib/convert.js.map +0 -1
- package/lib/convertToFloatArray.d.ts +0 -2
- package/lib/convertToFloatArray.d.ts.map +0 -1
- package/lib/convertToFloatArray.js +0 -11
- package/lib/convertToFloatArray.js.map +0 -1
- package/lib/createTree.d.ts +0 -29
- package/lib/createTree.d.ts.map +0 -1
- package/lib/createTree.js +0 -101
- package/lib/createTree.js.map +0 -1
- package/lib/index.d.ts +0 -3
- package/lib/index.d.ts.map +0 -1
- package/lib/index.js +0 -8
- package/lib/index.js.map +0 -1
- package/lib/parse/fastParseXYData.d.ts +0 -2
- package/lib/parse/fastParseXYData.d.ts.map +0 -1
- package/lib/parse/fastParseXYData.js +0 -193
- package/lib/parse/fastParseXYData.js.map +0 -1
- package/lib/parse/parsePeakTable.d.ts +0 -2
- package/lib/parse/parsePeakTable.d.ts.map +0 -1
- package/lib/parse/parsePeakTable.js +0 -67
- package/lib/parse/parsePeakTable.js.map +0 -1
- package/lib/parse/parseXYA.d.ts +0 -2
- package/lib/parse/parseXYA.d.ts.map +0 -1
- package/lib/parse/parseXYA.js +0 -51
- package/lib/parse/parseXYA.js.map +0 -1
- package/lib/postProcessing.d.ts +0 -2
- package/lib/postProcessing.d.ts.map +0 -1
- package/lib/postProcessing.js +0 -93
- package/lib/postProcessing.js.map +0 -1
- package/lib/postProcessingNMR.d.ts +0 -2
- package/lib/postProcessingNMR.d.ts.map +0 -1
- package/lib/postProcessingNMR.js +0 -95
- package/lib/postProcessingNMR.js.map +0 -1
- package/lib/prepareNtuplesDatatable.d.ts +0 -2
- package/lib/prepareNtuplesDatatable.d.ts.map +0 -1
- package/lib/prepareNtuplesDatatable.js +0 -87
- package/lib/prepareNtuplesDatatable.js.map +0 -1
- package/lib/prepareSpectrum.d.ts +0 -2
- package/lib/prepareSpectrum.d.ts.map +0 -1
- package/lib/prepareSpectrum.js +0 -10
- package/lib/prepareSpectrum.js.map +0 -1
- package/lib/profiling.d.ts +0 -2
- package/lib/profiling.d.ts.map +0 -1
- package/lib/profiling.js +0 -13
- package/lib/profiling.js.map +0 -1
- package/lib/simpleChromatogram.d.ts +0 -2
- package/lib/simpleChromatogram.d.ts.map +0 -1
- package/lib/simpleChromatogram.js +0 -16
- package/lib/simpleChromatogram.js.map +0 -1
- package/lib-esm/2d/add2D.d.ts +0 -2
- package/lib-esm/2d/add2D.d.ts.map +0 -1
- package/lib-esm/2d/add2D.js +0 -11
- package/lib-esm/2d/add2D.js.map +0 -1
- package/lib-esm/2d/convertTo3DZ.d.ts +0 -11
- package/lib-esm/2d/convertTo3DZ.d.ts.map +0 -1
- package/lib-esm/2d/convertTo3DZ.js +0 -53
- package/lib-esm/2d/convertTo3DZ.js.map +0 -1
- package/lib-esm/2d/generateContourLines.d.ts +0 -8
- package/lib-esm/2d/generateContourLines.d.ts.map +0 -1
- package/lib-esm/2d/generateContourLines.js +0 -160
- package/lib-esm/2d/generateContourLines.js.map +0 -1
- package/lib-esm/complexChromatogram.d.ts +0 -4
- package/lib-esm/complexChromatogram.d.ts.map +0 -1
- package/lib-esm/complexChromatogram.js +0 -43
- package/lib-esm/complexChromatogram.js.map +0 -1
- package/lib-esm/convert.d.ts +0 -182
- package/lib-esm/convert.d.ts.map +0 -1
- package/lib-esm/convert.js +0 -405
- package/lib-esm/convert.js.map +0 -1
- package/lib-esm/convertToFloatArray.d.ts +0 -2
- package/lib-esm/convertToFloatArray.d.ts.map +0 -1
- package/lib-esm/convertToFloatArray.js +0 -8
- package/lib-esm/convertToFloatArray.js.map +0 -1
- package/lib-esm/createTree.d.ts +0 -29
- package/lib-esm/createTree.d.ts.map +0 -1
- package/lib-esm/createTree.js +0 -97
- package/lib-esm/createTree.js.map +0 -1
- package/lib-esm/index.d.ts +0 -3
- package/lib-esm/index.d.ts.map +0 -1
- package/lib-esm/index.js +0 -3
- package/lib-esm/index.js.map +0 -1
- package/lib-esm/parse/fastParseXYData.d.ts +0 -2
- package/lib-esm/parse/fastParseXYData.d.ts.map +0 -1
- package/lib-esm/parse/fastParseXYData.js +0 -190
- package/lib-esm/parse/fastParseXYData.js.map +0 -1
- package/lib-esm/parse/parsePeakTable.d.ts +0 -2
- package/lib-esm/parse/parsePeakTable.d.ts.map +0 -1
- package/lib-esm/parse/parsePeakTable.js +0 -64
- package/lib-esm/parse/parsePeakTable.js.map +0 -1
- package/lib-esm/parse/parseXYA.d.ts +0 -2
- package/lib-esm/parse/parseXYA.d.ts.map +0 -1
- package/lib-esm/parse/parseXYA.js +0 -48
- package/lib-esm/parse/parseXYA.js.map +0 -1
- package/lib-esm/postProcessing.d.ts +0 -2
- package/lib-esm/postProcessing.d.ts.map +0 -1
- package/lib-esm/postProcessing.js +0 -87
- package/lib-esm/postProcessing.js.map +0 -1
- package/lib-esm/postProcessingNMR.d.ts +0 -2
- package/lib-esm/postProcessingNMR.d.ts.map +0 -1
- package/lib-esm/postProcessingNMR.js +0 -92
- package/lib-esm/postProcessingNMR.js.map +0 -1
- package/lib-esm/prepareNtuplesDatatable.d.ts +0 -2
- package/lib-esm/prepareNtuplesDatatable.d.ts.map +0 -1
- package/lib-esm/prepareNtuplesDatatable.js +0 -84
- package/lib-esm/prepareNtuplesDatatable.js.map +0 -1
- package/lib-esm/prepareSpectrum.d.ts +0 -2
- package/lib-esm/prepareSpectrum.d.ts.map +0 -1
- package/lib-esm/prepareSpectrum.js +0 -7
- package/lib-esm/prepareSpectrum.js.map +0 -1
- package/lib-esm/profiling.d.ts +0 -2
- package/lib-esm/profiling.d.ts.map +0 -1
- package/lib-esm/profiling.js +0 -10
- package/lib-esm/profiling.js.map +0 -1
- package/lib-esm/simpleChromatogram.d.ts +0 -2
- package/lib-esm/simpleChromatogram.d.ts.map +0 -1
- package/lib-esm/simpleChromatogram.js +0 -13
- package/lib-esm/simpleChromatogram.js.map +0 -1
- package/src/2d/add2D.js +0 -11
- package/src/2d/convertTo3DZ.js +0 -55
- package/src/2d/generateContourLines.js +0 -166
- package/src/complexChromatogram.js +0 -49
- package/src/convert.js +0 -412
- package/src/convertToFloatArray.js +0 -7
- package/src/createTree.js +0 -100
- package/src/index.js +0 -2
- package/src/parse/fastParseXYData.js +0 -175
- package/src/parse/parsePeakTable.js +0 -69
- package/src/parse/parseXYA.js +0 -50
- package/src/postProcessing.js +0 -93
- package/src/postProcessingNMR.js +0 -99
- package/src/prepareNtuplesDatatable.js +0 -85
- package/src/prepareSpectrum.js +0 -4
- package/src/profiling.js +0 -9
- package/src/simpleChromatogram.js +0 -12
package/lib/convert.js
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var __importDefault = (this && this.__importDefault) || function (mod) {
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return (mod && mod.__esModule) ? mod : { "default": mod };
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};
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Object.defineProperty(exports, "__esModule", { value: true });
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exports.convert = void 0;
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const dynamic_typing_1 = require("dynamic-typing");
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const ensure_string_1 = require("ensure-string");
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const complexChromatogram_1 = require("./complexChromatogram");
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const convertToFloatArray_1 = __importDefault(require("./convertToFloatArray"));
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const fastParseXYData_1 = __importDefault(require("./parse/fastParseXYData"));
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const parsePeakTable_1 = __importDefault(require("./parse/parsePeakTable"));
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const parseXYA_1 = __importDefault(require("./parse/parseXYA"));
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const postProcessing_1 = __importDefault(require("./postProcessing"));
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const prepareNtuplesDatatable_1 = __importDefault(require("./prepareNtuplesDatatable"));
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const prepareSpectrum_1 = __importDefault(require("./prepareSpectrum"));
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const profiling_1 = __importDefault(require("./profiling"));
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// the following RegExp can only be used for XYdata, some peakTables have values with a "E-5" ...
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const ntuplesSeparatorRegExp = /[ \t]*,[ \t]*/;
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const defaultOptions = {
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keepRecordsRegExp: /^$/,
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canonicDataLabels: true,
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canonicMetadataLabels: false,
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dynamicTyping: true,
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withoutXY: false,
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chromatogram: false,
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keepSpectra: false,
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noContour: false,
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nbContourLevels: 7,
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noiseMultiplier: 5,
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profiling: false,
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};
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/**
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* Conversion options
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* @typedef {object} ConvertOptions
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* @property {RegExp} [keepRecordsRegExp=/^$/] - By default we don't keep meta information.
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* @property {boolean} [canonicDataLabels=true] - Canonize the Labels (uppercase without symbol).
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* @property {boolean} [canonicMetadataLabels=false] - Canonize the metadata Labels (uppercase without symbol).
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* @property {boolean} [dynamicTyping=false] - Convert numbers to Number.
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* @property {boolean} [withoutXY=false] - Remove the XY data.
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* @property {boolean} [chromatogram=false] - Special post-processing for GC / HPLC / MS.
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* @property {boolean} [keepSpectra=false] - Force to keep the spectra in case of 2D.
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* @property {boolean} [noContour=false] - Don't calculate countour in case of 2D.
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* @property {number} [nbContourLevels=7] - Number of positive / negative contour levels to calculate.
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* @property {number} [noiseMultiplier=5] - Define for 2D the level as 5 times the median as default.
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* @property {import('cheminfo-types').Logger} [logger] - A logger like 'pino'
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* @property {boolean} [profiling=false] - Add profiling information.
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*/
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/**
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*
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* @typedef {object} Ntuples
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* @property {number[]} [vardim]
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* @property {number[]} [factor]
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* @property {number[]} [last]
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/**
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* @property {Record<string, number[]>} [data]
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* @property {number} [firstX] - first X value
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* @property {number} [lastX] - last X value
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* @property {number} [deltaX] - distance between 2 consecutive x axis values
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* @property {number} [yFactor] - y axis scaling factor
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* @property {number} [xFactor] - x axis scaling factor
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* @property {number} [nbPoints] - Number of points
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*/
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*
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* @property {Spectrum[]} spectra
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* @property {Ntuples} ntuples
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*/
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*
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/**
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* Parse a jcamp.
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* The data can be provide as a string or array buffer. In this later case
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* we will convert it first to a string before parsing.
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* @param {string|ArrayBuffer|Uint8Array} jcamp
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* @returns {ConvertResult}
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*/
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function convert(jcamp, options = {}) {
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jcamp = (0, ensure_string_1.ensureString)(jcamp);
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options = { ...defaultOptions, ...options };
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options.logger?.debug('Starting jcamp conversion');
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options.wantXY = !options.withoutXY;
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options.start = Date.now();
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let entriesFlat = [];
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let result = {
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profiling: options.profiling ? [] : false,
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logs: [],
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entries: [],
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};
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let tmpResult = { children: [] };
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let currentEntry = tmpResult;
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let parentsStack = [];
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let spectrum = {};
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if (typeof jcamp !== 'string') {
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throw new TypeError('the JCAMP should be a string');
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}
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(0, profiling_1.default)(result, 'Before split to LDRS', options);
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let ldrs = jcamp.replace(/[\r\n]+##/g, '\n##').split('\n##');
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(0, profiling_1.default)(result, 'Split to LDRS', options);
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if (ldrs[0])
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ldrs[0] = ldrs[0].replace(/^[\r\n ]*##/, '');
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for (let ldr of ldrs) {
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// This is a new LDR
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let dataLabel = position > 0 ? ldr.substring(0, position) : ldr;
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let dataValue = position > 0 ? ldr.substring(position + 1).trim() : '';
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let canonicDataLabel = dataLabel.replace(/[_ -]/g, '').toUpperCase();
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let infos = dataValue.substring(0, endLine).split(/[ ,;\t]+/);
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(0, prepareNtuplesDatatable_1.default)(currentEntry, spectrum, infos[0]);
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spectrum.datatable = infos[0];
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if (infos[1] && infos[1].indexOf('PEAKS') > -1) {
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canonicDataLabel = 'PEAKTABLE';
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}
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else if (infos[1] &&
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(infos[1].indexOf('XYDATA') || infos[0].indexOf('++') > 0)) {
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canonicDataLabel = 'XYDATA';
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spectrum.deltaX =
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(spectrum.lastX - spectrum.firstX) / (spectrum.nbPoints - 1);
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}
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}
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}
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}
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if (canonicDataLabel === 'XYDATA') {
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if (options.wantXY) {
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(0, prepareSpectrum_1.default)(spectrum);
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// well apparently we should still consider it is a PEAK TABLE if there are no '++' after
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if (dataValue.match(/.*\+\+.*/)) {
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// ex: (X++(Y..Y))
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if (spectrum.nbPoints) {
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-
spectrum.deltaX =
|
|
178
|
-
(spectrum.lastX - spectrum.firstX) / (spectrum.nbPoints - 1);
|
|
179
|
-
}
|
|
180
|
-
(0, fastParseXYData_1.default)(spectrum, dataValue, result);
|
|
181
|
-
}
|
|
182
|
-
else {
|
|
183
|
-
(0, parsePeakTable_1.default)(spectrum, dataValue, result);
|
|
184
|
-
}
|
|
185
|
-
currentEntry.spectra.push(spectrum);
|
|
186
|
-
spectrum = {};
|
|
187
|
-
}
|
|
188
|
-
continue;
|
|
189
|
-
}
|
|
190
|
-
else if (canonicDataLabel === 'PEAKTABLE') {
|
|
191
|
-
if (options.wantXY) {
|
|
192
|
-
(0, prepareSpectrum_1.default)(spectrum);
|
|
193
|
-
(0, parsePeakTable_1.default)(spectrum, dataValue, result);
|
|
194
|
-
currentEntry.spectra.push(spectrum);
|
|
195
|
-
spectrum = {};
|
|
196
|
-
}
|
|
197
|
-
continue;
|
|
198
|
-
}
|
|
199
|
-
if (canonicDataLabel === 'PEAKASSIGNMENTS') {
|
|
200
|
-
if (options.wantXY) {
|
|
201
|
-
if (dataValue.match(/.*([^A-Z]*).*/)) {
|
|
202
|
-
// ex: (XYA)
|
|
203
|
-
(0, parseXYA_1.default)(spectrum, dataValue);
|
|
204
|
-
}
|
|
205
|
-
currentEntry.spectra.push(spectrum);
|
|
206
|
-
spectrum = {};
|
|
207
|
-
}
|
|
208
|
-
continue;
|
|
209
|
-
}
|
|
210
|
-
if (canonicDataLabel === 'TITLE') {
|
|
211
|
-
let parentEntry = currentEntry;
|
|
212
|
-
if (!parentEntry.children) {
|
|
213
|
-
parentEntry.children = [];
|
|
214
|
-
}
|
|
215
|
-
currentEntry = {
|
|
216
|
-
spectra: [],
|
|
217
|
-
ntuples: {},
|
|
218
|
-
info: {},
|
|
219
|
-
meta: {},
|
|
220
|
-
tmp: {}, // tmp information we need to keep for postprocessing
|
|
221
|
-
};
|
|
222
|
-
parentEntry.children.push(currentEntry);
|
|
223
|
-
parentsStack.push(parentEntry);
|
|
224
|
-
entriesFlat.push(currentEntry);
|
|
225
|
-
currentEntry.title = dataValue;
|
|
226
|
-
}
|
|
227
|
-
else if (canonicDataLabel === 'DATATYPE') {
|
|
228
|
-
currentEntry.dataType = dataValue;
|
|
229
|
-
if (dataValue.match(/(^nd|\snd\s)/i)) {
|
|
230
|
-
currentEntry.twoD = true;
|
|
231
|
-
}
|
|
232
|
-
}
|
|
233
|
-
else if (canonicDataLabel === 'NTUPLES') {
|
|
234
|
-
if (dataValue.match(/(^nd|\snd\s)/i)) {
|
|
235
|
-
currentEntry.twoD = true;
|
|
236
|
-
}
|
|
237
|
-
}
|
|
238
|
-
else if (canonicDataLabel === 'DATACLASS') {
|
|
239
|
-
currentEntry.dataClass = dataValue;
|
|
240
|
-
}
|
|
241
|
-
else if (canonicDataLabel === 'XUNITS') {
|
|
242
|
-
spectrum.xUnits = dataValue;
|
|
243
|
-
}
|
|
244
|
-
else if (canonicDataLabel === 'YUNITS') {
|
|
245
|
-
spectrum.yUnits = dataValue;
|
|
246
|
-
}
|
|
247
|
-
else if (canonicDataLabel === 'FIRSTX') {
|
|
248
|
-
spectrum.firstX = Number(dataValue);
|
|
249
|
-
}
|
|
250
|
-
else if (canonicDataLabel === 'LASTX') {
|
|
251
|
-
spectrum.lastX = Number(dataValue);
|
|
252
|
-
}
|
|
253
|
-
else if (canonicDataLabel === 'FIRSTY') {
|
|
254
|
-
spectrum.firstY = Number(dataValue);
|
|
255
|
-
}
|
|
256
|
-
else if (canonicDataLabel === 'LASTY') {
|
|
257
|
-
spectrum.lastY = Number(dataValue);
|
|
258
|
-
}
|
|
259
|
-
else if (canonicDataLabel === 'NPOINTS') {
|
|
260
|
-
spectrum.nbPoints = Number(dataValue);
|
|
261
|
-
}
|
|
262
|
-
else if (canonicDataLabel === 'XFACTOR') {
|
|
263
|
-
spectrum.xFactor = Number(dataValue);
|
|
264
|
-
}
|
|
265
|
-
else if (canonicDataLabel === 'YFACTOR') {
|
|
266
|
-
spectrum.yFactor = Number(dataValue);
|
|
267
|
-
}
|
|
268
|
-
else if (canonicDataLabel === 'MAXX') {
|
|
269
|
-
spectrum.maxX = Number(dataValue);
|
|
270
|
-
}
|
|
271
|
-
else if (canonicDataLabel === 'MINX') {
|
|
272
|
-
spectrum.minX = Number(dataValue);
|
|
273
|
-
}
|
|
274
|
-
else if (canonicDataLabel === 'MAXY') {
|
|
275
|
-
spectrum.maxY = Number(dataValue);
|
|
276
|
-
}
|
|
277
|
-
else if (canonicDataLabel === 'MINY') {
|
|
278
|
-
spectrum.minY = Number(dataValue);
|
|
279
|
-
}
|
|
280
|
-
else if (canonicDataLabel === 'DELTAX') {
|
|
281
|
-
spectrum.deltaX = Number(dataValue);
|
|
282
|
-
}
|
|
283
|
-
else if (canonicDataLabel === '.OBSERVEFREQUENCY' ||
|
|
284
|
-
canonicDataLabel === '$SFO1') {
|
|
285
|
-
if (!spectrum.observeFrequency) {
|
|
286
|
-
spectrum.observeFrequency = Number(dataValue);
|
|
287
|
-
}
|
|
288
|
-
}
|
|
289
|
-
else if (canonicDataLabel === '.OBSERVENUCLEUS') {
|
|
290
|
-
if (!spectrum.xType) {
|
|
291
|
-
currentEntry.xType = dataValue.replace(/[^a-zA-Z0-9]/g, '');
|
|
292
|
-
}
|
|
293
|
-
}
|
|
294
|
-
else if (canonicDataLabel === '$OFFSET') {
|
|
295
|
-
// OFFSET for Bruker spectra
|
|
296
|
-
currentEntry.shiftOffsetNum = 0;
|
|
297
|
-
if (!spectrum.shiftOffsetVal) {
|
|
298
|
-
spectrum.shiftOffsetVal = Number(dataValue);
|
|
299
|
-
}
|
|
300
|
-
}
|
|
301
|
-
else if (canonicDataLabel === '$REFERENCEPOINT') {
|
|
302
|
-
// OFFSET for Varian spectra
|
|
303
|
-
// if we activate this part it does not work for ACD specmanager
|
|
304
|
-
// } else if (canonicDataLabel=='.SHIFTREFERENCE') { // OFFSET FOR Bruker Spectra
|
|
305
|
-
// var parts = dataValue.split(/ *, */);
|
|
306
|
-
// currentEntry.shiftOffsetNum = parseInt(parts[2].trim());
|
|
307
|
-
// spectrum.shiftOffsetVal = Number(parts[3].trim());
|
|
308
|
-
}
|
|
309
|
-
else if (canonicDataLabel === 'VARNAME') {
|
|
310
|
-
currentEntry.ntuples.varname = dataValue.split(ntuplesSeparatorRegExp);
|
|
311
|
-
}
|
|
312
|
-
else if (canonicDataLabel === 'SYMBOL') {
|
|
313
|
-
currentEntry.ntuples.symbol = dataValue.split(ntuplesSeparatorRegExp);
|
|
314
|
-
}
|
|
315
|
-
else if (canonicDataLabel === 'VARTYPE') {
|
|
316
|
-
currentEntry.ntuples.vartype = dataValue.split(ntuplesSeparatorRegExp);
|
|
317
|
-
}
|
|
318
|
-
else if (canonicDataLabel === 'VARFORM') {
|
|
319
|
-
currentEntry.ntuples.varform = dataValue.split(ntuplesSeparatorRegExp);
|
|
320
|
-
}
|
|
321
|
-
else if (canonicDataLabel === 'VARDIM') {
|
|
322
|
-
currentEntry.ntuples.vardim = (0, convertToFloatArray_1.default)(dataValue.split(ntuplesSeparatorRegExp));
|
|
323
|
-
}
|
|
324
|
-
else if (canonicDataLabel === 'UNITS') {
|
|
325
|
-
currentEntry.ntuples.units = dataValue.split(ntuplesSeparatorRegExp);
|
|
326
|
-
}
|
|
327
|
-
else if (canonicDataLabel === 'FACTOR') {
|
|
328
|
-
currentEntry.ntuples.factor = (0, convertToFloatArray_1.default)(dataValue.split(ntuplesSeparatorRegExp));
|
|
329
|
-
}
|
|
330
|
-
else if (canonicDataLabel === 'FIRST') {
|
|
331
|
-
currentEntry.ntuples.first = (0, convertToFloatArray_1.default)(dataValue.split(ntuplesSeparatorRegExp));
|
|
332
|
-
}
|
|
333
|
-
else if (canonicDataLabel === 'LAST') {
|
|
334
|
-
currentEntry.ntuples.last = (0, convertToFloatArray_1.default)(dataValue.split(ntuplesSeparatorRegExp));
|
|
335
|
-
}
|
|
336
|
-
else if (canonicDataLabel === 'MIN') {
|
|
337
|
-
currentEntry.ntuples.min = (0, convertToFloatArray_1.default)(dataValue.split(ntuplesSeparatorRegExp));
|
|
338
|
-
}
|
|
339
|
-
else if (canonicDataLabel === 'MAX') {
|
|
340
|
-
currentEntry.ntuples.max = (0, convertToFloatArray_1.default)(dataValue.split(ntuplesSeparatorRegExp));
|
|
341
|
-
}
|
|
342
|
-
else if (canonicDataLabel === '.NUCLEUS') {
|
|
343
|
-
if (currentEntry.ntuples) {
|
|
344
|
-
currentEntry.ntuples.nucleus = dataValue.split(ntuplesSeparatorRegExp);
|
|
345
|
-
}
|
|
346
|
-
}
|
|
347
|
-
else if (canonicDataLabel === 'PAGE') {
|
|
348
|
-
spectrum.page = dataValue.trim();
|
|
349
|
-
spectrum.pageValue = Number(dataValue.replace(/^.*=/, ''));
|
|
350
|
-
spectrum.pageSymbol = spectrum.page.replace(/[=].*/, '');
|
|
351
|
-
}
|
|
352
|
-
else if (canonicDataLabel === 'RETENTIONTIME') {
|
|
353
|
-
spectrum.pageValue = Number(dataValue);
|
|
354
|
-
}
|
|
355
|
-
else if ((0, complexChromatogram_1.isMSField)(canonicDataLabel)) {
|
|
356
|
-
spectrum[(0, complexChromatogram_1.convertMSFieldToLabel)(canonicDataLabel)] = dataValue;
|
|
357
|
-
}
|
|
358
|
-
else if (canonicDataLabel === 'SAMPLEDESCRIPTION') {
|
|
359
|
-
spectrum.sampleDescription = dataValue;
|
|
360
|
-
}
|
|
361
|
-
else if (canonicDataLabel.startsWith('$NUC')) {
|
|
362
|
-
if (!currentEntry.tmp[canonicDataLabel] && !dataValue.includes('off')) {
|
|
363
|
-
currentEntry.tmp[canonicDataLabel] = dataValue.replace(/[<>]/g, '');
|
|
364
|
-
}
|
|
365
|
-
}
|
|
366
|
-
else if (canonicDataLabel === 'END') {
|
|
367
|
-
currentEntry = parentsStack.pop();
|
|
368
|
-
}
|
|
369
|
-
if (currentEntry &&
|
|
370
|
-
currentEntry.info &&
|
|
371
|
-
currentEntry.meta &&
|
|
372
|
-
canonicDataLabel.match(options.keepRecordsRegExp)) {
|
|
373
|
-
let value = dataValue.trim();
|
|
374
|
-
let target, label;
|
|
375
|
-
if (dataLabel.startsWith('$')) {
|
|
376
|
-
label = options.canonicMetadataLabels
|
|
377
|
-
? canonicDataLabel.substring(1)
|
|
378
|
-
: dataLabel.substring(1);
|
|
379
|
-
target = currentEntry.meta;
|
|
380
|
-
}
|
|
381
|
-
else {
|
|
382
|
-
label = options.canonicDataLabels ? canonicDataLabel : dataLabel;
|
|
383
|
-
target = currentEntry.info;
|
|
384
|
-
}
|
|
385
|
-
if (options.dynamicTyping) {
|
|
386
|
-
value = (0, dynamic_typing_1.parseString)(value);
|
|
387
|
-
}
|
|
388
|
-
if (target[label]) {
|
|
389
|
-
if (!Array.isArray(target[label])) {
|
|
390
|
-
target[label] = [target[label]];
|
|
391
|
-
}
|
|
392
|
-
target[label].push(value);
|
|
393
|
-
}
|
|
394
|
-
else {
|
|
395
|
-
target[label] = value;
|
|
396
|
-
}
|
|
397
|
-
}
|
|
398
|
-
}
|
|
399
|
-
(0, profiling_1.default)(result, 'Finished parsing', options);
|
|
400
|
-
(0, postProcessing_1.default)(entriesFlat, result, options);
|
|
401
|
-
(0, profiling_1.default)(result, 'Total time', options);
|
|
402
|
-
/*
|
|
403
|
-
if (result.children && result.children.length>0) {
|
|
404
|
-
result = { ...result, ...result.children[0] };
|
|
405
|
-
}
|
|
406
|
-
*/
|
|
407
|
-
result.entries = tmpResult.children;
|
|
408
|
-
result.flatten = entriesFlat;
|
|
409
|
-
return result;
|
|
410
|
-
}
|
|
411
|
-
exports.convert = convert;
|
|
412
|
-
//# sourceMappingURL=convert.js.map
|
package/lib/convert.js.map
DELETED
|
@@ -1 +0,0 @@
|
|
|
1
|
-
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@@ -1 +0,0 @@
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1
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-
{"version":3,"file":"convertToFloatArray.d.ts","sourceRoot":"","sources":["../src/convertToFloatArray.js"],"names":[],"mappings":"AAAA,wEAMC"}
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@@ -1,11 +0,0 @@
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1
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-
"use strict";
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2
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-
Object.defineProperty(exports, "__esModule", { value: true });
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3
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-
function convertToFloatArray(stringArray) {
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4
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let floatArray = [];
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5
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-
for (let i = 0; i < stringArray.length; i++) {
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6
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floatArray.push(Number(stringArray[i]));
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7
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}
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8
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return floatArray;
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9
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}
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10
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-
exports.default = convertToFloatArray;
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11
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//# sourceMappingURL=convertToFloatArray.js.map
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@@ -1 +0,0 @@
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1
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-
{"version":3,"file":"convertToFloatArray.js","sourceRoot":"","sources":["../src/convertToFloatArray.js"],"names":[],"mappings":";;AAAA,SAAwB,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;AAND,sCAMC"}
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package/lib/createTree.d.ts
DELETED
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@@ -1,29 +0,0 @@
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1
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-
/**
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2
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-
*
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3
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export function createTree(jcamp: string | ArrayBuffer | Uint8Array, options?: CreateTreeOptions | undefined): Tree[];
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export type CreateTreeOptions = {
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export type Tree = {
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jcamp: string;
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{"version":3,"file":"createTree.d.ts","sourceRoot":"","sources":["../src/createTree.js"],"names":[],"mappings":"AAEA;;;;GAIG;AAEH;;;;;;GAMG;AAEH;;;;;;GAMG;AACH,kCAJW,MAAM,GAAC,WAAW,GAAC,UAAU,4CAE3B,IAAI,EAAE,CA8ElB;;;;;WAxFa,MAAM;WACN,MAAM"}
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|
-
function createTree(jcamp, options = {}) {
|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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ntupleLevel++;
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|
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|
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stack.push({
|
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|
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|
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|
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|
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|
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|
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57
|
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|
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current = stack[stack.length - 1];
|
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|
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flat.push(current);
|
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|
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}
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|
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else if (labelLine.substring(0, 5) === '##END' && ntupleLevel === 0) {
|
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current.jcamp += `${line}\n`;
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|
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let finished = stack.pop();
|
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|
-
if (stack.length !== 0) {
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current.children.push(finished);
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|
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else {
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current = undefined;
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|
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}
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|
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|
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else if (current && current.jcamp) {
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current.jcamp += `${line}\n`;
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|
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|
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if (match) {
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|
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let canonicDataLabel = match[1].replace(/[ _-]/g, '').toUpperCase();
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|
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if (canonicDataLabel === 'DATATYPE') {
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|
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current.dataType = match[2].trim();
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|
-
}
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|
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if (canonicDataLabel === 'DATACLASS') {
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current.dataClass = match[2].trim();
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|
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}
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|
-
}
|
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85
|
-
}
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|
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if (labelLine.substring(0, 5) === '##END' && ntupleLevel > 0) {
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|
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ntupleLevel--;
|
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|
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}
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|
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}
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|
-
if (flatten) {
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|
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|
-
flat.forEach((entry) => {
|
|
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|
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|
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|
-
});
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|
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return flat;
|
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|
-
}
|
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|
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else {
|
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|
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return result;
|
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|
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}
|
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|
-
}
|
|
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|
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exports.createTree = createTree;
|
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|
package/lib/createTree.js.map
DELETED
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|
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|
package/lib/index.d.ts
DELETED
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DELETED
|
@@ -1 +0,0 @@
|
|
|
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|
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{"version":3,"file":"index.d.ts","sourceRoot":"","sources":["../src/index.js"],"names":[],"mappings":""}
|
package/lib/index.js
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|
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|
|
|
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|
-
"use strict";
|
|
2
|
-
Object.defineProperty(exports, "__esModule", { value: true });
|
|
3
|
-
exports.convert = exports.createTree = void 0;
|
|
4
|
-
var createTree_1 = require("./createTree");
|
|
5
|
-
Object.defineProperty(exports, "createTree", { enumerable: true, get: function () { return createTree_1.createTree; } });
|
|
6
|
-
var convert_1 = require("./convert");
|
|
7
|
-
Object.defineProperty(exports, "convert", { enumerable: true, get: function () { return convert_1.convert; } });
|
|
8
|
-
//# sourceMappingURL=index.js.map
|
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|
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|
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|
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{"version":3,"file":"index.js","sourceRoot":"","sources":["../src/index.js"],"names":[],"mappings":";;;AAAA,2CAA0C;AAAjC,wGAAA,UAAU,OAAA;AACnB,qCAAoC;AAA3B,kGAAA,OAAO,OAAA"}
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|
@@ -1 +0,0 @@
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|
|
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|
-
{"version":3,"file":"fastParseXYData.d.ts","sourceRoot":"","sources":["../../src/parse/fastParseXYData.js"],"names":[],"mappings":"AAAA,yEA8KC"}
|