jcampconverter 9.2.0 → 9.2.2

package/lib/parse/fastParseXYData.js

@@ -1,193 +0,0 @@
-"use strict";
-Object.defineProperty(exports, "__esModule", { value: true });
-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
-            // eslint-disable-next-line no-lonely-if
-            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
-                        // eslint-disable-next-line no-lonely-if
-                        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
-            }
-        }
-    }
-}
-exports.default = fastParseXYData;
-//# sourceMappingURL=fastParseXYData.js.map

package/lib/parse/fastParseXYData.js.map

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package/lib/parse/parsePeakTable.d.ts

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

package/lib/parse/parsePeakTable.d.ts.map

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

package/lib/parse/parsePeakTable.js

@@ -1,67 +0,0 @@
-"use strict";
-Object.defineProperty(exports, "__esModule", { value: true });
-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];
-        }
-    }
-}
-exports.default = parsePeakTable;
-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 Number
-                currentData.x.push(Number(values[j]) * spectrum.xFactor);
-                currentData.y.push(Number(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(Number(values[j]));
-            }
-        }
-        else {
-            result.logs.push(`Format error: ${values}`);
-        }
-    }
-}
-//# sourceMappingURL=parsePeakTable.js.map

package/lib/parse/parsePeakTable.js.map

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

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

package/lib/parse/parseXYA.d.ts.map

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

package/lib/parse/parseXYA.js

@@ -1,51 +0,0 @@
-"use strict";
-/*
-(5.4.4) ##РЕАК ASSIGNMENTS= (STRING). List
-of peak assignments for components or functional groups
-in the forms ##РЕАК ASSIGNMENTS= (ХУА),
-(XYW А), (ХУМА), (XYMW А). Each entry is surrounded Ьу parentheses and starts а new line. У, W (peak
-width), and М (multiplicity) values are optional. The
-symbol А stands for а string detailing the assignment
-and must Ье enclosed Ьу angle brackets. If the peak width
-value is included, then the function used to calculate the
-peak width must Ье detailed in а $$ comment on the
-line(s) below ##PEAKASSIGNMENTS=. Priority OPTIONAL. N.B.: ##РЕАК ASSIGNMENTS= is the preferred method of transmitting peak information when
-the assignments are known.
- */
-Object.defineProperty(exports, "__esModule", { value: true });
-function parseXYA(spectrum, value) {
-    spectrum.isXYAdata = true;
-    const currentData = {};
-    spectrum.data = currentData;
-    let lines = value.split(/\r?\n/);
-    const variables = lines[0]
-        .replace(/^.*?([A-Z]+).*$/, '$1')
-        .split('')
-        .map((variable) => variable.toLowerCase());
-    for (let i = 1; i < lines.length; i++) {
-        const fields = lines[i].replace(/^\((.*)\)$/, '$1').split(/ *, */);
-        for (let j = 0; j < variables.length; j++) {
-            let value = fields[j];
-            switch (variables[j]) {
-                case 'x':
-                case 'y':
-                case 'w':
-                    value = Number.parseFloat(value);
-                    break;
-                case 'a':
-                    value = value.replace(/^<(.*)>$/, '$1');
-                    break;
-                case 'm':
-                    break;
-                default:
-                    continue;
-            }
-            if (!currentData[variables[j]]) {
-                currentData[variables[j]] = [];
-            }
-            currentData[variables[j]].push(value);
-        }
-    }
-}
-exports.default = parseXYA;
-//# sourceMappingURL=parseXYA.js.map

package/lib/parse/parseXYA.js.map

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

@@ -1,2 +0,0 @@
-export default function postProcessing(entriesFlat: any, result: any, options: any): void;
-//# sourceMappingURL=postProcessing.d.ts.map

package/lib/postProcessing.d.ts.map

@@ -1 +0,0 @@
-{"version":3,"file":"postProcessing.d.ts","sourceRoot":"","sources":["../src/postProcessing.js"],"names":[],"mappings":"AAQA,0FA2CC"}

package/lib/postProcessing.js

@@ -1,93 +0,0 @@
-"use strict";
-var __importDefault = (this && this.__importDefault) || function (mod) {
-    return (mod && mod.__esModule) ? mod : { "default": mod };
-};
-Object.defineProperty(exports, "__esModule", { value: true });
-const dynamic_typing_1 = require("dynamic-typing");
-const add2D_1 = __importDefault(require("./2d/add2D"));
-const complexChromatogram_1 = require("./complexChromatogram");
-const postProcessingNMR_1 = __importDefault(require("./postProcessingNMR"));
-const profiling_1 = __importDefault(require("./profiling"));
-const simpleChromatogram_1 = __importDefault(require("./simpleChromatogram"));
-function postProcessing(entriesFlat, result, options) {
-    // converting Hz to ppm
-    (0, postProcessingNMR_1.default)(entriesFlat);
-    createArray(entriesFlat, options);
-    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) {
-            (0, add2D_1.default)(entry, options);
-            (0, profiling_1.default)(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) {
-                (0, complexChromatogram_1.complexChromatogram)(entry);
-            }
-            else {
-                (0, simpleChromatogram_1.default)(entry);
-            }
-            (0, profiling_1.default)(result, 'Finished chromatogram calculation', options);
-        }
-        delete entry.tmp;
-    }
-}
-exports.default = postProcessing;
-function createArray(entriesFlat, options) {
-    for (const entry of entriesFlat) {
-        for (const key in entry.meta) {
-            const value = entry.meta[key];
-            if (typeof value === 'string') {
-                if (value[0] === '{') {
-                    // could be an array
-                    if (value[value.length - 1] === '}') {
-                        const array = value
-                            .slice(1, -1)
-                            .split(/[,; ]+/)
-                            .filter((e) => e);
-                        for (let i = 0; i < array.length; i++) {
-                            entry.meta[key + String(i)] = options.dynamicTyping
-                                ? (0, dynamic_typing_1.parseString)(array[i])
-                                : array[i];
-                        }
-                    }
-                }
-                else if (value[0] === '(') {
-                    const lines = value.split(/\r?\n/);
-                    const regexp = /^\((?<from>\d+)\.\.(?<to>\d+)\)$/;
-                    if (regexp.test(lines[0])) {
-                        // parsing  '(0..63)'
-                        const [from, to] = lines[0].match(regexp).slice(1).map(Number);
-                        const array = lines
-                            .slice(1)
-                            .join(' ')
-                            .split(/[,; ]+/)
-                            .filter((e) => e);
-                        for (let i = from; i <= to; i++) {
-                            entry.meta[key + String(i)] = options.dynamicTyping
-                                ? (0, dynamic_typing_1.parseString)(array[i - from])
-                                : array[i - from];
-                        }
-                    }
-                }
-            }
-        }
-    }
-}
-//# sourceMappingURL=postProcessing.js.map

package/lib/postProcessing.js.map

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

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

package/lib/postProcessingNMR.d.ts.map

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

package/lib/postProcessingNMR.js

@@ -1,95 +0,0 @@
-"use strict";
-Object.defineProperty(exports, "__esModule", { value: true });
-const gyromagnetic_ratio_1 = require("gyromagnetic-ratio");
-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 && spectrum.xUnits.toLowerCase().includes('ppm')) {
-                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.match(/^[F|T]/) && !nucleus) {
-                        if (symbol.match(/[F|T]1/)) {
-                            // 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(symbol.replace(/^([F|T]).*/, '$12'));
-                                if (f2index && entry.ntuples.nucleus[f2index]) {
-                                    entry.ntuples.nucleus[i] = entry.ntuples.nucleus[f2index];
-                                }
-                            }
-                        }
-                        if (symbol.match(/[F|T]2/)) {
-                            entry.ntuples.nucleus[i] = entry.tmp.$NUC1;
-                        }
-                    }
-                    if (symbol.match(/[F|T]2/)) {
-                        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 = gyromagnetic_ratio_1.gyromagneticRatio[entry.ntuples.nucleus[0]];
-                    let ratio1 = gyromagnetic_ratio_1.gyromagneticRatio[entry.ntuples.nucleus[1]];
-                    if (!ratio0 || !ratio1) {
-                        throw Error('Problem with determination of gyromagnetic ratio');
-                    }
-                    let ratio = (ratio0 / ratio1) * observeFrequency;
-                    spectrum.pageValue /= ratio;
-                }
-            }
-        }
-    }
-}
-exports.default = postProcessingNMR;
-//# sourceMappingURL=postProcessingNMR.js.map

package/lib/postProcessingNMR.js.map

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package/lib/prepareNtuplesDatatable.d.ts

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

package/lib/prepareNtuplesDatatable.d.ts.map

@@ -1 +0,0 @@
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