jcampconverter - npm Package Compare versions

Comparing version 9.0.2 to 9.0.3

lib-esm/convert.js

@@ -179,3 +179,3 @@ import { parseString } from 'dynamic-typing';
             if (options.wantXY) {
-                if (dataValue.match(/.*(XYA).*/)) {
+                if (dataValue.match(/.*([^A-Z]*).*/)) {
                     // ex: (XYA)
@@ -182,0 +182,0 @@ parseXYA(spectrum, dataValue);

lib-esm/parse/parseXYA.js

@@ -0,14 +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

lib/convert.js

@@ -185,3 +185,3 @@ "use strict";
             if (options.wantXY) {
-                if (dataValue.match(/.*(XYA).*/)) {
+                if (dataValue.match(/.*([^A-Z]*).*/)) {
                     // ex: (XYA)
@@ -188,0 +188,0 @@ (0, parseXYA_1.default)(spectrum, dataValue);

lib/parse/parseXYA.js

 "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);
+        }
     }
@@ -15,0 +49,0 @@ }

package.json

 {
   "name": "jcampconverter",
-  "version": "9.0.2",
+  "version": "9.0.3",
   "description": "Parse and convert JCAMP data",
@@ -47,22 +47,24 @@ "main": "lib/index.js",
   "devDependencies": {
-    "@types/jest": "^28.1.1",
+    "@types/jest": "^29.1.1",
+    "@vitest/coverage-c8": "^0.23.4",
     "benchmark": "^2.1.4",
-    "c8": "^7.11.3",
+    "c8": "^7.12.0",
     "cheminfo-build": "^1.1.11",
-    "eslint": "^8.17.0",
-    "eslint-config-cheminfo-typescript": "^11.0.1",
+    "eslint": "^8.24.0",
+    "eslint-config-cheminfo-typescript": "^11.1.0",
     "esm": "^3.2.25",
     "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",
-    "typescript": "^4.7.3",
-    "vitest": "^0.14.1"
+    "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"
   }
 }

README.md

@@ -99,5 +99,5 @@ # JCAMP converter
 [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

src/convert.js

@@ -202,3 +202,3 @@ import { parseString } from 'dynamic-typing';
       if (options.wantXY) {
-        if (dataValue.match(/.*(XYA).*/)) {
+        if (dataValue.match(/.*([^A-Z]*).*/)) {
           // ex: (XYA)
@@ -205,0 +205,0 @@ parseXYA(spectrum, dataValue);

src/parse/parseXYA.js

@@ -0,16 +1,50 @@
+/*
+(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);
+    }
   }
 }

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Improved metrics

Total package byte prevSize

259563

increased by2.01%

Lines of code

4307

increased by2.43%

Worsened metrics

Dependency count

5

increased by25%

Dev dependency count

14

increased by7.69%

Dependency changes

• + Addedml-spectra-processing@^11.12.0

• + Addedbinary-search@1.3.6(transitive)

• + Addedd3-array@0.7.1(transitive)

• + Addeddynamic-typing@1.0.1(transitive)

• + Addedfft.js@4.0.4(transitive)

• + Addedml-array-max@1.2.4(transitive)

• + Addedml-array-min@1.2.3(transitive)

• + Addedml-array-rescale@1.3.7(transitive)

• + Addedml-matrix@6.12.0(transitive)

• + Addedml-spectra-processing@11.17.0(transitive)

• + Addedml-xsadd@2.0.0(transitive)

• + Addedspline-interpolator@1.0.0(transitive)

• - Removeddynamic-typing@0.1.3(transitive)

• Updateddynamic-typing@^1.0.0