npm - jcampconverter - Versions diffs - 9.0.1 → 9.0.3 - Mend

jcampconverter 9.0.1 → 9.0.3

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.

Files changed (30) hide show

package/README.md +2 -2
package/lib/2d/convertTo3DZ.js +3 -3
package/lib/2d/convertTo3DZ.js.map +1 -1
package/lib/convert.d.ts +2 -0
package/lib/convert.d.ts.map +1 -1
package/lib/convert.js +2 -1
package/lib/convert.js.map +1 -1
package/lib/parse/fastParseXYData.d.ts.map +1 -1
package/lib/parse/fastParseXYData.js +4 -3
package/lib/parse/fastParseXYData.js.map +1 -1
package/lib/parse/parseXYA.d.ts.map +1 -1
package/lib/parse/parseXYA.js +41 -7
package/lib/parse/parseXYA.js.map +1 -1
package/lib-esm/2d/convertTo3DZ.js +3 -3
package/lib-esm/2d/convertTo3DZ.js.map +1 -1
package/lib-esm/convert.d.ts +2 -0
package/lib-esm/convert.d.ts.map +1 -1
package/lib-esm/convert.js +2 -1
package/lib-esm/convert.js.map +1 -1
package/lib-esm/parse/fastParseXYData.d.ts.map +1 -1
package/lib-esm/parse/fastParseXYData.js +4 -3
package/lib-esm/parse/fastParseXYData.js.map +1 -1
package/lib-esm/parse/parseXYA.d.ts.map +1 -1
package/lib-esm/parse/parseXYA.js +41 -7
package/lib-esm/parse/parseXYA.js.map +1 -1
package/package.json +15 -21
package/src/2d/convertTo3DZ.js +3 -3
package/src/convert.js +2 -1
package/src/parse/fastParseXYData.js +4 -2
package/src/parse/parseXYA.js +42 -8

package/README.md CHANGED Viewed

@@ -16,7 +16,7 @@ Parse and convert JCAMP data
 [![build status][ci-image]][ci-url]
 [![Test coverage][codecov-image]][codecov-url]
 [![npm download][download-image]][download-url]
-[![DOI](https://www.zenodo.org/badge/22728620.svg)](https://www.zenodo.org/badge/latestdoi/22728620)
+[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.5091526.svg)](https://doi.org/10.5281/zenodo.5091526)
 </h3>
@@ -96,7 +96,7 @@ npm run benchmark
 [npm-url]: https://npmjs.org/package/jcampconverter
 [codecov-image]: https://img.shields.io/codecov/c/github/cheminfo/jcampconverter.svg
 [codecov-url]: https://codecov.io/gh/cheminfo/jcampconverter
-[ci-image]: https://github.com/cheminfo/jcampconverter/workflows/Node.js%20CI/badge.svg?branch=master
+[ci-image]: https://github.com/cheminfo/jcampconverter/workflows/Node.js%20CI/badge.svg?branch=main
 [ci-url]: https://github.com/cheminfo/jcampconverter/actions?query=workflow%3A%22Node.js+CI%22
 [download-image]: https://img.shields.io/npm/dm/jcampconverter.svg
 [download-url]: https://npmjs.org/package/jcampconverter

package/lib/2d/convertTo3DZ.js CHANGED Viewed

@@ -45,13 +45,13 @@ function convertTo3DZ(spectra) {
     }
     const median = (0, ml_array_median_1.default)(medians);
     return {
-        z: 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,
+        minZ,
+        maxZ,
         noise: median,
     };
 }

package/lib/2d/convertTo3DZ.js.map CHANGED Viewed

	@@ -1 +1 @@
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1	+ {"version":3,"file":"convertTo3DZ.js","sourceRoot":"","sources":["../../src/2d/convertTo3DZ.js"],"names":[],"mappings":";;;;;AAAA,sEAAwC;AAExC,SAAwB,YAAY,CAAC,OAAO;IAC1C,IAAI,IAAI,GAAG,OAAO,CAAC,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC;IAChC,IAAI,IAAI,GAAG,IAAI,CAAC;IAChB,IAAI,KAAK,GAAG,OAAO,CAAC,MAAM,CAAC;IAC3B,IAAI,KAAK,GAAG,OAAO,CAAC,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,MAAM,CAAC;IAErC,IAAI,CAAC,GAAG,IAAI,KAAK,CAAC,KAAK,CAAC,CAAC;IACzB,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,KAAK,EAAE,CAAC,EAAE,EAAE;QAC9B,CAAC,CAAC,CAAC,CAAC,GAAG,OAAO,CAAC,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC;QACzB,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,KAAK,EAAE,CAAC,EAAE,EAAE;YAC9B,IAAI,KAAK,GAAG,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC;YACpB,IAAI,KAAK,GAAG,IAAI;gBAAE,IAAI,GAAG,KAAK,CAAC;YAC/B,IAAI,KAAK,GAAG,IAAI;gBAAE,IAAI,GAAG,KAAK,CAAC;SAChC;KACF;IAED,MAAM,MAAM,GAAG,OAAO,CAAC,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC;IACpC,MAAM,KAAK,GAAG,OAAO,CAAC,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,OAAO,CAAC,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,MAAM,GAAG,CAAC,CAAC,CAAC,CAAC,sDAAsD;IACrH,MAAM,MAAM,GAAG,OAAO,CAAC,CAAC,CAAC,CAAC,SAAS,CAAC;IACpC,MAAM,KAAK,GAAG,OAAO,CAAC,KAAK,GAAG,CAAC,CAAC,CAAC,SAAS,CAAC;IAE3C,qFAAqF;IACrF,0CAA0C;IAC1C,IAAI,MAAM,GAAG,KAAK,EAAE;QAClB,KAAK,IAAI,QAAQ,IAAI,CAAC,EAAE;YACtB,QAAQ,CAAC,OAAO,EAAE,CAAC;SACpB;KACF;IACD,IAAI,MAAM,GAAG,KAAK,EAAE;QAClB,CAAC,CAAC,OAAO,EAAE,CAAC;KACb;IAED,MAAM,OAAO,GAAG,EAAE,CAAC;IACnB,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,CAAC,CAAC,MAAM,EAAE,CAAC,EAAE,EAAE;QACjC,MAAM,GAAG,GAAG,YAAY,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC;QACpC,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,GAAG,CAAC,MAAM,EAAE,CAAC,EAAE,EAAE;YACnC,IAAI,GAAG,CAAC,CAAC,CAAC,GAAG,CAAC;gBAAE,GAAG,CAAC,CAAC,CAAC,GAAG,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC;SAClC;QACD,OAAO,CAAC,IAAI,CAAC,IAAA,yBAAS,EAAC,GAAG,CAAC,CAAC,CAAC;KAC9B;IACD,MAAM,MAAM,GAAG,IAAA,yBAAS,EAAC,OAAO,CAAC,CAAC;IAElC,OAAO;QACL,CAAC;QACD,IAAI,EAAE,IAAI,CAAC,GAAG,CAAC,MAAM,EAAE,KAAK,CAAC;QAC7B,IAAI,EAAE,IAAI,CAAC,GAAG,CAAC,MAAM,EAAE,KAAK,CAAC;QAC7B,IAAI,EAAE,IAAI,CAAC,GAAG,CAAC,MAAM,EAAE,KAAK,CAAC;QAC7B,IAAI,EAAE,IAAI,CAAC,GAAG,CAAC,MAAM,EAAE,KAAK,CAAC;QAC7B,IAAI;QACJ,IAAI;QACJ,KAAK,EAAE,MAAM;KACd,CAAC;AACJ,CAAC;AApDD,+BAoDC"}

package/lib/convert.d.ts CHANGED Viewed

@@ -45,6 +45,7 @@
  * @property {Spectrum[]} spectra
  * @property {Ntuples} ntuples
  * @property {object} meta
+ * @property {object} info
  * @property {object} tmp
  * @property {string} [title]
  * @property {string} [dataType]
@@ -132,6 +133,7 @@ export type Entry = {
     spectra: Spectrum[];
     ntuples: Ntuples;
     meta: object;
+    info: object;
     tmp: object;
     title?: string | undefined;
     dataType?: string | undefined;

package/lib/convert.d.ts.map CHANGED Viewed

	@@ -1 +1 @@
1	- {"version":3,"file":"convert.d.ts","sourceRoot":"","sources":["../src/convert.js"],"names":[],"mappings":"AA8BA;;;;;;;;;;;;;;GAcG;AAEH;;;;;;;;;;;;;;;GAeG;AAEH;;;;;;;;;GASG;AAEH~~;;;;;;;;;;;GAWG~~;AAEH;;;;;;;GAOG;AAEH;;;;;;GAMG;AAEH,+BALW,MAAM,GAAC,WAAW,GAAC,UAAU,yCAE3B,aAAa,CAmSzB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;~~uBAxUa~~,OAAO,MAAM,EAAE,GAAG,CAAC;;aAanB,QAAQ,EAAE;aACV,OAAO;UACP,MAAM;SACN,MAAM;;;;;;;eAUL,MAAM,EAAE,GAAG,OAAO;UAClB,MAAM,EAAE;aACR,MAAM,EAAE;aACR,KAAK,EAAE"}
1	+ {"version":3,"file":"convert.d.ts","sourceRoot":"","sources":["../src/convert.js"],"names":[],"mappings":"AA8BA;;;;;;;;;;;;;;GAcG;AAEH;;;;;;;;;;;;;;;GAeG;AAEH;;;;;;;;;GASG;AAEH;;;;;;;;;;;;GAYG;AAEH;;;;;;;GAOG;AAEH;;;;;;GAMG;AAEH,+BALW,MAAM,GAAC,WAAW,GAAC,UAAU,yCAE3B,aAAa,CAmSzB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;uBAzUa,OAAO,MAAM,EAAE,GAAG,CAAC;;aAanB,QAAQ,EAAE;aACV,OAAO;UACP,MAAM;UACN,MAAM;SACN,MAAM;;;;;;;eAUL,MAAM,EAAE,GAAG,OAAO;UAClB,MAAM,EAAE;aACR,MAAM,EAAE;aACR,KAAK,EAAE"}

package/lib/convert.js CHANGED Viewed

@@ -77,6 +77,7 @@ const defaultOptions = {
  * @property {Spectrum[]} spectra
  * @property {Ntuples} ntuples
  * @property {object} meta
+ * @property {object} info
  * @property {object} tmp
  * @property {string} [title]
  * @property {string} [dataType]
@@ -181,7 +182,7 @@ function convert(jcamp, options = {}) {
         }
         if (canonicDataLabel === 'PEAKASSIGNMENTS') {
             if (options.wantXY) {
-                if (dataValue.match(/.*(XYA).*/)) {
+                if (dataValue.match(/.*([^A-Z]*).*/)) {
                     // ex: (XYA)
                     (0, parseXYA_1.default)(spectrum, dataValue);
                 }

package/lib/convert.js.map CHANGED Viewed

	@@ -1 +1 @@
1	- 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package/lib/parse/fastParseXYData.d.ts.map CHANGED Viewed

	@@ -1 +1 @@
1	- {"version":3,"file":"fastParseXYData.d.ts","sourceRoot":"","sources":["../../src/parse/fastParseXYData.js"],"names":[],"mappings":"AAAA,~~yEA4KC~~"}
1	+ {"version":3,"file":"fastParseXYData.d.ts","sourceRoot":"","sources":["../../src/parse/fastParseXYData.js"],"names":[],"mappings":"AAAA,yEA8KC"}

package/lib/parse/fastParseXYData.js CHANGED Viewed

@@ -21,9 +21,8 @@ function fastParseXYData(spectrum, value) {
         if (ascii === 13 || ascii === 10) {
             endLine = true;
         }
-        else {
-            if (endLine)
-                break;
+        else if (endLine) {
+            break;
         }
     }
     // we proceed taking the i after the first line
@@ -55,6 +54,7 @@ function fastParseXYData(spectrum, value) {
             // 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;
@@ -84,6 +84,7 @@ function fastParseXYData(spectrum, value) {
                     }
                     else {
                         // need to deal with duplicate and differences
+                        // eslint-disable-next-line no-lonely-if
                         if (skipFirstValue) {
                             skipFirstValue = false;
                         }

package/lib/parse/fastParseXYData.js.map CHANGED Viewed

	@@ -1 +1 @@
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package/lib/parse/parseXYA.d.ts.map CHANGED Viewed

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

package/lib/parse/parseXYA.js CHANGED Viewed

@@ -1,16 +1,50 @@
 "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) {
-    let removeSymbolRegExp = /(\(+|\)+|<+|>+|\s+)/g;
     spectrum.isXYAdata = true;
-    let values;
-    let currentData = { x: [], y: [] };
+    const currentData = {};
     spectrum.data = currentData;
-    let lines = value.split(/,? *,?[;\r\n]+ */);
+    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++) {
-        values = lines[i].trim().replace(removeSymbolRegExp, '').split(',');
-        currentData.x.push(Number(values[0]));
-        currentData.y.push(Number(values[1]));
+        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;

package/lib/parse/parseXYA.js.map CHANGED Viewed

	@@ -1 +1 @@
1	- {"version":3,"file":"parseXYA.js","sourceRoot":"","sources":["../../src/parse/parseXYA.js"],"names":[],"mappings":";;~~AAAA~~,SAAwB,QAAQ,CAAC,QAAQ,EAAE,KAAK;IAC9C,IAAI,~~kBAAkB~~,GAAG,~~sBAAsB~~,CAAC;~~IAEhD~~,QAAQ,CAAC,~~SAAS~~,GAAG,~~IAAI~~,CAAC;~~IAC1B~~,IAAI,~~MAAM~~,CAAC;~~IACX~~,~~IAAI~~,~~WAAW~~,GAAG,~~EAAE~~,CAAC,~~EAAE~~,~~EAAE~~,~~EAAE~~,CAAC,~~EAAE~~,EAAE,~~EAAE~~,CAAC;~~IACnC~~,~~QAAQ~~,CAAC,~~IAAI~~,GAAG,~~WAAW~~,CAAC~~;IAE5B~~,~~IAAI~~,~~KAAK~~,~~GAAG~~,~~KAAK,~~CAAC,~~KAAK~~,CAAC,~~kBAAkB~~,CAAC,CAAC;~~IAE5C~~,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,KAAK,CAAC,MAAM,EAAE,CAAC,EAAE,EAAE;QACrC,MAAM,GAAG,KAAK,CAAC,CAAC,CAAC,CAAC,~~IAAI~~,EAAE,CAAC,OAAO,CAAC,~~kBAAkB~~,~~EAAE~~,EAAE,CAAC,CAAC,KAAK,CAAC,GAAG,CAAC,CAAC;~~QACpE~~,~~WAAW~~,CAAC,CAAC,CAAC,IAAI,CAAC,MAAM,~~CAAC~~,MAAM,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC;~~QACtC~~,WAAW,CAAC,CAAC,CAAC,~~IAAI~~,CAAC,~~MAAM~~,CAAC,~~MAAM~~,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC;~~KACvC~~;AACH,CAAC;~~AAfD~~,~~2BAeC~~"}
1	+ {"version":3,"file":"parseXYA.js","sourceRoot":"","sources":["../../src/parse/parseXYA.js"],"names":[],"mappings":";AAAA;;;;;;;;;;;;GAYG;;AAEH,SAAwB,QAAQ,CAAC,QAAQ,EAAE,KAAK;IAC9C,QAAQ,CAAC,SAAS,GAAG,IAAI,CAAC;IAC1B,MAAM,WAAW,GAAG,EAAE,CAAC;IACvB,QAAQ,CAAC,IAAI,GAAG,WAAW,CAAC;IAE5B,IAAI,KAAK,GAAG,KAAK,CAAC,KAAK,CAAC,OAAO,CAAC,CAAC;IACjC,MAAM,SAAS,GAAG,KAAK,CAAC,CAAC,CAAC;SACvB,OAAO,CAAC,iBAAiB,EAAE,IAAI,CAAC;SAChC,KAAK,CAAC,EAAE,CAAC;SACT,GAAG,CAAC,CAAC,QAAQ,EAAE,EAAE,CAAC,QAAQ,CAAC,WAAW,EAAE,CAAC,CAAC;IAE7C,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,KAAK,CAAC,MAAM,EAAE,CAAC,EAAE,EAAE;QACrC,MAAM,MAAM,GAAG,KAAK,CAAC,CAAC,CAAC,CAAC,OAAO,CAAC,YAAY,EAAE,IAAI,CAAC,CAAC,KAAK,CAAC,OAAO,CAAC,CAAC;QACnE,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,SAAS,CAAC,MAAM,EAAE,CAAC,EAAE,EAAE;YACzC,IAAI,KAAK,GAAG,MAAM,CAAC,CAAC,CAAC,CAAC;YACtB,QAAQ,SAAS,CAAC,CAAC,CAAC,EAAE;gBACpB,KAAK,GAAG,CAAC;gBACT,KAAK,GAAG,CAAC;gBACT,KAAK,GAAG;oBACN,KAAK,GAAG,MAAM,CAAC,UAAU,CAAC,KAAK,CAAC,CAAC;oBACjC,MAAM;gBACR,KAAK,GAAG;oBACN,KAAK,GAAG,KAAK,CAAC,OAAO,CAAC,UAAU,EAAE,IAAI,CAAC,CAAC;oBACxC,MAAM;gBACR,KAAK,GAAG;oBACN,MAAM;gBACR;oBACE,SAAS;aACZ;YACD,IAAI,CAAC,WAAW,CAAC,SAAS,CAAC,CAAC,CAAC,CAAC,EAAE;gBAC9B,WAAW,CAAC,SAAS,CAAC,CAAC,CAAC,CAAC,GAAG,EAAE,CAAC;aAChC;YACD,WAAW,CAAC,SAAS,CAAC,CAAC,CAAC,CAAC,CAAC,IAAI,CAAC,KAAK,CAAC,CAAC;SACvC;KACF;AACH,CAAC;AAnCD,2BAmCC"}

package/lib-esm/2d/convertTo3DZ.js CHANGED Viewed

@@ -40,13 +40,13 @@ export default function convertTo3DZ(spectra) {
     }
     const median = getMedian(medians);
     return {
-        z: 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,
+        minZ,
+        maxZ,
         noise: median,
     };
 }

package/lib-esm/2d/convertTo3DZ.js.map CHANGED Viewed

	@@ -1 +1 @@
1	- {"version":3,"file":"convertTo3DZ.js","sourceRoot":"","sources":["../../src/2d/convertTo3DZ.js"],"names":[],"mappings":"AAAA,OAAO,SAAS,MAAM,iBAAiB,CAAC;AAExC,MAAM,CAAC,OAAO,UAAU,YAAY,CAAC,OAAO;IAC1C,IAAI,IAAI,GAAG,OAAO,CAAC,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC;IAChC,IAAI,IAAI,GAAG,IAAI,CAAC;IAChB,IAAI,KAAK,GAAG,OAAO,CAAC,MAAM,CAAC;IAC3B,IAAI,KAAK,GAAG,OAAO,CAAC,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,MAAM,CAAC;IAErC,IAAI,CAAC,GAAG,IAAI,KAAK,CAAC,KAAK,CAAC,CAAC;IACzB,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,KAAK,EAAE,CAAC,EAAE,EAAE;QAC9B,CAAC,CAAC,CAAC,CAAC,GAAG,OAAO,CAAC,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC;QACzB,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,KAAK,EAAE,CAAC,EAAE,EAAE;YAC9B,IAAI,KAAK,GAAG,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC;YACpB,IAAI,KAAK,GAAG,IAAI;gBAAE,IAAI,GAAG,KAAK,CAAC;YAC/B,IAAI,KAAK,GAAG,IAAI;gBAAE,IAAI,GAAG,KAAK,CAAC;SAChC;KACF;IAED,MAAM,MAAM,GAAG,OAAO,CAAC,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC;IACpC,MAAM,KAAK,GAAG,OAAO,CAAC,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,OAAO,CAAC,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,MAAM,GAAG,CAAC,CAAC,CAAC,CAAC,sDAAsD;IACrH,MAAM,MAAM,GAAG,OAAO,CAAC,CAAC,CAAC,CAAC,SAAS,CAAC;IACpC,MAAM,KAAK,GAAG,OAAO,CAAC,KAAK,GAAG,CAAC,CAAC,CAAC,SAAS,CAAC;IAE3C,qFAAqF;IACrF,0CAA0C;IAC1C,IAAI,MAAM,GAAG,KAAK,EAAE;QAClB,KAAK,IAAI,QAAQ,IAAI,CAAC,EAAE;YACtB,QAAQ,CAAC,OAAO,EAAE,CAAC;SACpB;KACF;IACD,IAAI,MAAM,GAAG,KAAK,EAAE;QAClB,CAAC,CAAC,OAAO,EAAE,CAAC;KACb;IAED,MAAM,OAAO,GAAG,EAAE,CAAC;IACnB,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,CAAC,CAAC,MAAM,EAAE,CAAC,EAAE,EAAE;QACjC,MAAM,GAAG,GAAG,YAAY,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC;QACpC,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,GAAG,CAAC,MAAM,EAAE,CAAC,EAAE,EAAE;YACnC,IAAI,GAAG,CAAC,CAAC,CAAC,GAAG,CAAC;gBAAE,GAAG,CAAC,CAAC,CAAC,GAAG,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC;SAClC;QACD,OAAO,CAAC,IAAI,CAAC,SAAS,CAAC,GAAG,CAAC,CAAC,CAAC;KAC9B;IACD,MAAM,MAAM,GAAG,SAAS,CAAC,OAAO,CAAC,CAAC;IAElC,OAAO;QACL,CAAC~~,EAAE,CAAC~~;~~QACJ~~,IAAI,EAAE,IAAI,CAAC,GAAG,CAAC,MAAM,EAAE,KAAK,CAAC;QAC7B,IAAI,EAAE,IAAI,CAAC,GAAG,CAAC,MAAM,EAAE,KAAK,CAAC;QAC7B,IAAI,EAAE,IAAI,CAAC,GAAG,CAAC,MAAM,EAAE,KAAK,CAAC;QAC7B,IAAI,EAAE,IAAI,CAAC,GAAG,CAAC,MAAM,EAAE,KAAK,CAAC;QAC7B,IAAI~~,EAAE,IAAI~~;~~QACV~~,IAAI~~,EAAE,IAAI~~;~~QACV~~,KAAK,EAAE,MAAM;KACd,CAAC;AACJ,CAAC"}
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package/lib-esm/convert.d.ts CHANGED Viewed

@@ -45,6 +45,7 @@
  * @property {Spectrum[]} spectra
  * @property {Ntuples} ntuples
  * @property {object} meta
+ * @property {object} info
  * @property {object} tmp
  * @property {string} [title]
  * @property {string} [dataType]
@@ -132,6 +133,7 @@ export type Entry = {
     spectra: Spectrum[];
     ntuples: Ntuples;
     meta: object;
+    info: object;
     tmp: object;
     title?: string | undefined;
     dataType?: string | undefined;

package/lib-esm/convert.d.ts.map CHANGED Viewed

	@@ -1 +1 @@
1	- {"version":3,"file":"convert.d.ts","sourceRoot":"","sources":["../src/convert.js"],"names":[],"mappings":"AA8BA;;;;;;;;;;;;;;GAcG;AAEH;;;;;;;;;;;;;;;GAeG;AAEH;;;;;;;;;GASG;AAEH~~;;;;;;;;;;;GAWG~~;AAEH;;;;;;;GAOG;AAEH;;;;;;GAMG;AAEH,+BALW,MAAM,GAAC,WAAW,GAAC,UAAU,yCAE3B,aAAa,CAmSzB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;~~uBAxUa~~,OAAO,MAAM,EAAE,GAAG,CAAC;;aAanB,QAAQ,EAAE;aACV,OAAO;UACP,MAAM;SACN,MAAM;;;;;;;eAUL,MAAM,EAAE,GAAG,OAAO;UAClB,MAAM,EAAE;aACR,MAAM,EAAE;aACR,KAAK,EAAE"}
1	+ {"version":3,"file":"convert.d.ts","sourceRoot":"","sources":["../src/convert.js"],"names":[],"mappings":"AA8BA;;;;;;;;;;;;;;GAcG;AAEH;;;;;;;;;;;;;;;GAeG;AAEH;;;;;;;;;GASG;AAEH;;;;;;;;;;;;GAYG;AAEH;;;;;;;GAOG;AAEH;;;;;;GAMG;AAEH,+BALW,MAAM,GAAC,WAAW,GAAC,UAAU,yCAE3B,aAAa,CAmSzB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;uBAzUa,OAAO,MAAM,EAAE,GAAG,CAAC;;aAanB,QAAQ,EAAE;aACV,OAAO;UACP,MAAM;UACN,MAAM;SACN,MAAM;;;;;;;eAUL,MAAM,EAAE,GAAG,OAAO;UAClB,MAAM,EAAE;aACR,MAAM,EAAE;aACR,KAAK,EAAE"}

package/lib-esm/convert.js CHANGED Viewed

@@ -71,6 +71,7 @@ const defaultOptions = {
  * @property {Spectrum[]} spectra
  * @property {Ntuples} ntuples
  * @property {object} meta
+ * @property {object} info
  * @property {object} tmp
  * @property {string} [title]
  * @property {string} [dataType]
@@ -175,7 +176,7 @@ export function convert(jcamp, options = {}) {
         }
         if (canonicDataLabel === 'PEAKASSIGNMENTS') {
             if (options.wantXY) {
-                if (dataValue.match(/.*(XYA).*/)) {
+                if (dataValue.match(/.*([^A-Z]*).*/)) {
                     // ex: (XYA)
                     parseXYA(spectrum, dataValue);
                 }

package/lib-esm/convert.js.map CHANGED Viewed

	@@ -1 +1 @@
1	- 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package/lib-esm/parse/fastParseXYData.d.ts.map CHANGED Viewed

	@@ -1 +1 @@
1	- {"version":3,"file":"fastParseXYData.d.ts","sourceRoot":"","sources":["../../src/parse/fastParseXYData.js"],"names":[],"mappings":"AAAA,~~yEA4KC~~"}
1	+ {"version":3,"file":"fastParseXYData.d.ts","sourceRoot":"","sources":["../../src/parse/fastParseXYData.js"],"names":[],"mappings":"AAAA,yEA8KC"}

package/lib-esm/parse/fastParseXYData.js CHANGED Viewed

@@ -19,9 +19,8 @@ export default function fastParseXYData(spectrum, value) {
         if (ascii === 13 || ascii === 10) {
             endLine = true;
         }
-        else {
-            if (endLine)
-                break;
+        else if (endLine) {
+            break;
         }
     }
     // we proceed taking the i after the first line
@@ -53,6 +52,7 @@ export default function fastParseXYData(spectrum, value) {
             // 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;
@@ -82,6 +82,7 @@ export default function fastParseXYData(spectrum, value) {
                     }
                     else {
                         // need to deal with duplicate and differences
+                        // eslint-disable-next-line no-lonely-if
                         if (skipFirstValue) {
                             skipFirstValue = false;
                         }

package/lib-esm/parse/fastParseXYData.js.map CHANGED Viewed

	@@ -1 +1 @@
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package/lib-esm/parse/parseXYA.d.ts.map CHANGED Viewed

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

package/lib-esm/parse/parseXYA.js CHANGED Viewed

@@ -1,14 +1,48 @@
+/*
+(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.
+ */
 export default function parseXYA(spectrum, value) {
-    let removeSymbolRegExp = /(\(+|\)+|<+|>+|\s+)/g;
     spectrum.isXYAdata = true;
-    let values;
-    let currentData = { x: [], y: [] };
+    const currentData = {};
     spectrum.data = currentData;
-    let lines = value.split(/,? *,?[;\r\n]+ */);
+    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++) {
-        values = lines[i].trim().replace(removeSymbolRegExp, '').split(',');
-        currentData.x.push(Number(values[0]));
-        currentData.y.push(Number(values[1]));
+        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);
+        }
     }
 }
 //# sourceMappingURL=parseXYA.js.map

package/lib-esm/parse/parseXYA.js.map CHANGED Viewed

	@@ -1 +1 @@
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package/package.json CHANGED Viewed

@@ -1,6 +1,6 @@
 {
   "name": "jcampconverter",
-  "version": "9.0.1",
+  "version": "9.0.3",
   "description": "Parse and convert JCAMP data",
   "main": "lib/index.js",
   "module": "lib-esm/index.js",
@@ -10,13 +10,6 @@
     "src",
     "lib-esm"
   ],
-  "prettier": {
-    "arrowParens": "always",
-    "semi": true,
-    "singleQuote": true,
-    "tabWidth": 2,
-    "trailingComma": "all"
-  },
   "scripts": {
     "build": "cheminfo-build --entry src/index.js --root JcampConverter",
     "check-types": "tsc --noEmit",
@@ -27,9 +20,8 @@
     "prepack": "npm run tsc",
     "prettier": "prettier --check src",
     "prettier-write": "prettier --write src",
-    "test": "npm run test-coverage && npm run eslint && npm run prettier && npm run check-types",
-    "test-coverage": "jest --coverage",
-    "test-only": "jest",
+    "test": "npm run test-only && npm run eslint && npm run prettier && npm run check-types",
+    "test-only": "vitest run --globals --coverage",
     "tsc": "npm run clean && npm run tsc-cjs && npm run tsc-esm",
     "tsc-cjs": "tsc --project tsconfig.cjs.json",
     "tsc-esm": "tsc --project tsconfig.esm.json",
@@ -52,24 +44,26 @@
   },
   "homepage": "https://github.com/cheminfo/jcampconverter#readme",
   "devDependencies": {
-    "@types/jest": "^27.5.0",
+    "@types/jest": "^29.1.1",
+    "@vitest/coverage-c8": "^0.23.4",
     "benchmark": "^2.1.4",
+    "c8": "^7.12.0",
     "cheminfo-build": "^1.1.11",
-    "eslint": "^8.14.0",
-    "eslint-config-cheminfo-typescript": "^10.4.0",
+    "eslint": "^8.24.0",
+    "eslint-config-cheminfo-typescript": "^11.1.0",
     "esm": "^3.2.25",
-    "jest": "^28.0.3",
     "jest-matcher-deep-close-to": "^3.0.2",
-    "jscpd": "^3.4.5",
-    "prettier": "^2.6.2",
+    "jscpd": "^3.5.0",
+    "prettier": "^2.7.1",
     "rimraf": "^3.0.2",
-    "ts-jest": "^28.0.1",
-    "typescript": "^4.6.4"
+    "typescript": "^4.8.4",
+    "vitest": "^0.23.4"
   },
   "dependencies": {
-    "dynamic-typing": "^0.1.3",
+    "dynamic-typing": "^1.0.0",
     "ensure-string": "^1.2.0",
     "gyromagnetic-ratio": "^1.0.0",
-    "ml-array-median": "^1.1.6"
+    "ml-array-median": "^1.1.6",
+    "ml-spectra-processing": "^11.12.0"
   }
 }

package/src/2d/convertTo3DZ.js CHANGED Viewed

@@ -43,13 +43,13 @@ export default function convertTo3DZ(spectra) {
   const median = getMedian(medians);
   return {
-    z: 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,
+    minZ,
+    maxZ,
     noise: median,
   };
 }

package/src/convert.js CHANGED Viewed

@@ -78,6 +78,7 @@ const defaultOptions = {
  * @property {Spectrum[]} spectra
  * @property {Ntuples} ntuples
  * @property {object} meta
+ * @property {object} info
  * @property {object} tmp
  * @property {string} [title]
  * @property {string} [dataType]
@@ -198,7 +199,7 @@ export function convert(jcamp, options = {}) {
     }
     if (canonicDataLabel === 'PEAKASSIGNMENTS') {
       if (options.wantXY) {
-        if (dataValue.match(/.*(XYA).*/)) {
+        if (dataValue.match(/.*([^A-Z]*).*/)) {
           // ex: (XYA)
           parseXYA(spectrum, dataValue);
         }

package/src/parse/fastParseXYData.js CHANGED Viewed

@@ -22,8 +22,8 @@ export default function fastParseXYData(spectrum, value) {
     ascii = value.charCodeAt(i);
     if (ascii === 13 || ascii === 10) {
       endLine = true;
-    } else {
-      if (endLine) break;
+    } else if (endLine) {
+      break;
     }
   }
@@ -53,6 +53,7 @@ export default function fastParseXYData(spectrum, value) {
       // 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;
@@ -77,6 +78,7 @@ export default function fastParseXYData(spectrum, value) {
             if (isLastDifference) skipFirstValue = true;
           } else {
             // need to deal with duplicate and differences
+            // eslint-disable-next-line no-lonely-if
             if (skipFirstValue) {
               skipFirstValue = false;
             } else {

package/src/parse/parseXYA.js CHANGED Viewed

@@ -1,16 +1,50 @@
-export default function parseXYA(spectrum, value) {
-  let removeSymbolRegExp = /(\(+|\)+|<+|>+|\s+)/g;
+/*
+(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.
+ */
+export default function parseXYA(spectrum, value) {
   spectrum.isXYAdata = true;
-  let values;
-  let currentData = { x: [], y: [] };
+  const currentData = {};
   spectrum.data = currentData;
-  let lines = value.split(/,? *,?[;\r\n]+ */);
+  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++) {
-    values = lines[i].trim().replace(removeSymbolRegExp, '').split(',');
-    currentData.x.push(Number(values[0]));
-    currentData.y.push(Number(values[1]));
+    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);
+    }
   }
 }