jcampconverter 9.1.0 → 9.2.0

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Files changed (18) hide show
  1. package/README.md +1 -3
  2. package/lib/convert.d.ts +26 -2
  3. package/lib/convert.d.ts.map +1 -1
  4. package/lib/convert.js +14 -1
  5. package/lib/convert.js.map +1 -1
  6. package/lib/postProcessing.d.ts.map +1 -1
  7. package/lib/postProcessing.js +43 -0
  8. package/lib/postProcessing.js.map +1 -1
  9. package/lib-esm/convert.d.ts +26 -2
  10. package/lib-esm/convert.d.ts.map +1 -1
  11. package/lib-esm/convert.js +14 -1
  12. package/lib-esm/convert.js.map +1 -1
  13. package/lib-esm/postProcessing.d.ts.map +1 -1
  14. package/lib-esm/postProcessing.js +43 -0
  15. package/lib-esm/postProcessing.js.map +1 -1
  16. package/package.json +15 -14
  17. package/src/convert.js +15 -2
  18. package/src/postProcessing.js +45 -0
package/README.md CHANGED
@@ -4,12 +4,10 @@
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  [![npm download][download-image]][download-url]
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  [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.5091526.svg)](https://doi.org/10.5281/zenodo.5091526)
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-
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  # JCAMP-DX converter
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  Parse and convert JCAMP-DX data
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-
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  ## Installation
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  ### Node JS
@@ -29,7 +27,7 @@ Returns an object with information about the converted file and uncompressed spe
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  **Arguments**
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- - `jcamp` - String or ArrayBuffer containing the JCAMP data
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+ - `jcamp` - String or ArrayBuffer containing the JCAMP-DX data
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  - `options` - Object with options to pass to the converter
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  **Options**
package/lib/convert.d.ts CHANGED
@@ -11,7 +11,7 @@
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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('@types/pino').Logger} [logger] - A logger like 'pino'
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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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  * @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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+ *
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+ * @typedef {object} MinMax
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+ * @property {number[][]} [z]
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+ * @property {number} minX
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+ * @property {number} maxX
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+ * @property {number} minY
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+ * @property {number} maxY
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+ * @property {number} minZ
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+ * @property {number} maxZ
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+ * @property {number} median
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+ */
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  /**
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  *
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  * @typedef {object} Entry
@@ -52,6 +64,7 @@
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  * @property {string} [dataType]
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  * @property {string} [dataClass]
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  * @property {boolean} [twoD]
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+ * @property {MinMax} [minMax]
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  */
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  /**
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  *
@@ -117,7 +130,7 @@ export type ConvertOptions = {
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  /**
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  * - A logger like 'pino'
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  */
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- logger?: any;
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+ logger?: import("cheminfo-types").Logger | undefined;
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  /**
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  * - Add profiling information.
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  */
@@ -138,6 +151,16 @@ export type Ntuples = {
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  nucleus?: string[] | undefined;
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  };
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  export type Spectrum = Record<string, any>;
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+ export type MinMax = {
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+ z?: number[][] | undefined;
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+ minX: number;
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+ maxX: number;
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+ minY: number;
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+ maxY: number;
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+ minZ: number;
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+ maxZ: number;
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+ median: number;
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+ };
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  export type Entry = {
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  spectra: Spectrum[];
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  ntuples: Ntuples;
@@ -148,6 +171,7 @@ export type Entry = {
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  dataType?: string | undefined;
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  dataClass?: string | undefined;
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  twoD?: boolean | undefined;
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+ minMax?: MinMax | undefined;
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  };
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  export type ConvertResult = {
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  profiling: object[] | boolean;
package/lib/convert.d.ts.map CHANGED
@@ -1 +1 @@
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+ {"version":3,"file":"convert.d.ts","sourceRoot":"","sources":["../src/convert.js"],"names":[],"mappings":"AA8BA;;;;;;;;;;;;;;;GAeG;AAEH;;;;;;;;;;;;;;;GAeG;AAEH;;;;;;;;;GASG;AAEH;;;;;;;;;;;GAWG;AAEH;;;;;;;;;;;;;GAaG;AAEH;;;;;;;GAOG;AAEH;;;;;;;GAOG;AACH,+BAJW,MAAM,GAAC,WAAW,GAAC,UAAU,yCAE3B,aAAa,CAqSzB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;uBA1Va,OAAO,MAAM,EAAE,GAAG,CAAC;;;UAcnB,MAAM;UACN,MAAM;UACN,MAAM;UACN,MAAM;UACN,MAAM;UACN,MAAM;YACN,MAAM;;;aAMN,QAAQ,EAAE;aACV,OAAO;UACP,MAAM;UACN,MAAM;SACN,MAAM;;;;;;;;eAWL,MAAM,EAAE,GAAG,OAAO;UAClB,MAAM,EAAE;aACR,MAAM,EAAE;aACR,KAAK,EAAE"}
package/lib/convert.js CHANGED
@@ -43,7 +43,7 @@ const defaultOptions = {
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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('@types/pino').Logger} [logger] - A logger like 'pino'
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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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  /**
@@ -72,6 +72,18 @@ const defaultOptions = {
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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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+ *
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+ * @typedef {object} MinMax
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+ * @property {number[][]} [z]
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+ * @property {number} minX
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+ * @property {number} maxX
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+ * @property {number} minY
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+ * @property {number} maxY
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+ * @property {number} minZ
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+ * @property {number} maxZ
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+ * @property {number} median
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+ */
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  /**
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  *
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  * @typedef {object} Entry
@@ -84,6 +96,7 @@ const defaultOptions = {
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  * @property {string} [dataType]
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  * @property {string} [dataClass]
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  * @property {boolean} [twoD]
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+ * @property {MinMax} [minMax]
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  */
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  /**
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  *
package/lib/convert.js.map CHANGED
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package/lib/postProcessing.d.ts.map CHANGED
@@ -1 +1 @@
1
- {"version":3,"file":"postProcessing.d.ts","sourceRoot":"","sources":["../src/postProcessing.js"],"names":[],"mappings":"AAMA,0FAyCC"}
1
+ {"version":3,"file":"postProcessing.d.ts","sourceRoot":"","sources":["../src/postProcessing.js"],"names":[],"mappings":"AAQA,0FA2CC"}
package/lib/postProcessing.js CHANGED
@@ -3,6 +3,7 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
3
3
  return (mod && mod.__esModule) ? mod : { "default": mod };
4
4
  };
5
5
  Object.defineProperty(exports, "__esModule", { value: true });
6
+ const dynamic_typing_1 = require("dynamic-typing");
6
7
  const add2D_1 = __importDefault(require("./2d/add2D"));
7
8
  const complexChromatogram_1 = require("./complexChromatogram");
8
9
  const postProcessingNMR_1 = __importDefault(require("./postProcessingNMR"));
@@ -11,6 +12,7 @@ const simpleChromatogram_1 = __importDefault(require("./simpleChromatogram"));
11
12
  function postProcessing(entriesFlat, result, options) {
12
13
  // converting Hz to ppm
13
14
  (0, postProcessingNMR_1.default)(entriesFlat);
15
+ createArray(entriesFlat, options);
14
16
  for (let entry of entriesFlat) {
15
17
  if (Object.keys(entry.ntuples).length > 0) {
16
18
  let newNtuples = [];
@@ -47,4 +49,45 @@ function postProcessing(entriesFlat, result, options) {
47
49
  }
48
50
  }
49
51
  exports.default = postProcessing;
52
+ function createArray(entriesFlat, options) {
53
+ for (const entry of entriesFlat) {
54
+ for (const key in entry.meta) {
55
+ const value = entry.meta[key];
56
+ if (typeof value === 'string') {
57
+ if (value[0] === '{') {
58
+ // could be an array
59
+ if (value[value.length - 1] === '}') {
60
+ const array = value
61
+ .slice(1, -1)
62
+ .split(/[,; ]+/)
63
+ .filter((e) => e);
64
+ for (let i = 0; i < array.length; i++) {
65
+ entry.meta[key + String(i)] = options.dynamicTyping
66
+ ? (0, dynamic_typing_1.parseString)(array[i])
67
+ : array[i];
68
+ }
69
+ }
70
+ }
71
+ else if (value[0] === '(') {
72
+ const lines = value.split(/\r?\n/);
73
+ const regexp = /^\((?<from>\d+)\.\.(?<to>\d+)\)$/;
74
+ if (regexp.test(lines[0])) {
75
+ // parsing '(0..63)'
76
+ const [from, to] = lines[0].match(regexp).slice(1).map(Number);
77
+ const array = lines
78
+ .slice(1)
79
+ .join(' ')
80
+ .split(/[,; ]+/)
81
+ .filter((e) => e);
82
+ for (let i = from; i <= to; i++) {
83
+ entry.meta[key + String(i)] = options.dynamicTyping
84
+ ? (0, dynamic_typing_1.parseString)(array[i - from])
85
+ : array[i - from];
86
+ }
87
+ }
88
+ }
89
+ }
90
+ }
91
+ }
92
+ }
50
93
  //# sourceMappingURL=postProcessing.js.map
package/lib/postProcessing.js.map CHANGED
@@ -1 +1 @@
1
- {"version":3,"file":"postProcessing.js","sourceRoot":"","sources":["../src/postProcessing.js"],"names":[],"mappings":";;;;;AAAA,uDAA+B;AAC/B,+DAA4D;AAC5D,4EAAoD;AACpD,4DAAoC;AACpC,8EAAsD;AAEtD,SAAwB,cAAc,CAAC,WAAW,EAAE,MAAM,EAAE,OAAO;IACjE,uBAAuB;IACvB,IAAA,2BAAiB,EAAC,WAAW,CAAC,CAAC;IAE/B,KAAK,IAAI,KAAK,IAAI,WAAW,EAAE;QAC7B,IAAI,MAAM,CAAC,IAAI,CAAC,KAAK,CAAC,OAAO,CAAC,CAAC,MAAM,GAAG,CAAC,EAAE;YACzC,IAAI,UAAU,GAAG,EAAE,CAAC;YACpB,IAAI,IAAI,GAAG,MAAM,CAAC,IAAI,CAAC,KAAK,CAAC,OAAO,CAAC,CAAC;YACtC,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,IAAI,CAAC,MAAM,EAAE,CAAC,EAAE,EAAE;gBACpC,IAAI,GAAG,GAAG,IAAI,CAAC,CAAC,CAAC,CAAC;gBAClB,IAAI,MAAM,GAAG,KAAK,CAAC,OAAO,CAAC,GAAG,CAAC,CAAC;gBAChC,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,MAAM,CAAC,MAAM,EAAE,CAAC,EAAE,EAAE;oBACtC,IAAI,CAAC,UAAU,CAAC,CAAC,CAAC;wBAAE,UAAU,CAAC,CAAC,CAAC,GAAG,EAAE,CAAC;oBACvC,UAAU,CAAC,CAAC,CAAC,CAAC,GAAG,CAAC,GAAG,MAAM,CAAC,CAAC,CAAC,CAAC;iBAChC;aACF;YACD,KAAK,CAAC,OAAO,GAAG,UAAU,CAAC;SAC5B;QAED,IAAI,KAAK,CAAC,IAAI,IAAI,OAAO,CAAC,MAAM,EAAE;YAChC,IAAA,eAAK,EAAC,KAAK,EAAE,OAAO,CAAC,CAAC;YAEtB,IAAA,mBAAS,EAAC,MAAM,EAAE,oCAAoC,EAAE,OAAO,CAAC,CAAC;YAEjE,IAAI,CAAC,OAAO,CAAC,WAAW,EAAE;gBACxB,OAAO,KAAK,CAAC,OAAO,CAAC;aACtB;SACF;QAED,iEAAiE;QACjE,IAAI,OAAO,CAAC,YAAY,EAAE;YACxB,IAAI,KAAK,CAAC,OAAO,CAAC,MAAM,GAAG,CAAC,EAAE;gBAC5B,IAAA,yCAAmB,EAAC,KAAK,CAAC,CAAC;aAC5B;iBAAM;gBACL,IAAA,4BAAkB,EAAC,KAAK,CAAC,CAAC;aAC3B;YACD,IAAA,mBAAS,EAAC,MAAM,EAAE,mCAAmC,EAAE,OAAO,CAAC,CAAC;SACjE;QAED,OAAO,KAAK,CAAC,GAAG,CAAC;KAClB;AACH,CAAC;AAzCD,iCAyCC"}
1
+ {"version":3,"file":"postProcessing.js","sourceRoot":"","sources":["../src/postProcessing.js"],"names":[],"mappings":";;;;;AAAA,mDAA6C;AAE7C,uDAA+B;AAC/B,+DAA4D;AAC5D,4EAAoD;AACpD,4DAAoC;AACpC,8EAAsD;AAEtD,SAAwB,cAAc,CAAC,WAAW,EAAE,MAAM,EAAE,OAAO;IACjE,uBAAuB;IACvB,IAAA,2BAAiB,EAAC,WAAW,CAAC,CAAC;IAE/B,WAAW,CAAC,WAAW,EAAE,OAAO,CAAC,CAAC;IAElC,KAAK,IAAI,KAAK,IAAI,WAAW,EAAE;QAC7B,IAAI,MAAM,CAAC,IAAI,CAAC,KAAK,CAAC,OAAO,CAAC,CAAC,MAAM,GAAG,CAAC,EAAE;YACzC,IAAI,UAAU,GAAG,EAAE,CAAC;YACpB,IAAI,IAAI,GAAG,MAAM,CAAC,IAAI,CAAC,KAAK,CAAC,OAAO,CAAC,CAAC;YACtC,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,IAAI,CAAC,MAAM,EAAE,CAAC,EAAE,EAAE;gBACpC,IAAI,GAAG,GAAG,IAAI,CAAC,CAAC,CAAC,CAAC;gBAClB,IAAI,MAAM,GAAG,KAAK,CAAC,OAAO,CAAC,GAAG,CAAC,CAAC;gBAChC,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,MAAM,CAAC,MAAM,EAAE,CAAC,EAAE,EAAE;oBACtC,IAAI,CAAC,UAAU,CAAC,CAAC,CAAC;wBAAE,UAAU,CAAC,CAAC,CAAC,GAAG,EAAE,CAAC;oBACvC,UAAU,CAAC,CAAC,CAAC,CAAC,GAAG,CAAC,GAAG,MAAM,CAAC,CAAC,CAAC,CAAC;iBAChC;aACF;YACD,KAAK,CAAC,OAAO,GAAG,UAAU,CAAC;SAC5B;QAED,IAAI,KAAK,CAAC,IAAI,IAAI,OAAO,CAAC,MAAM,EAAE;YAChC,IAAA,eAAK,EAAC,KAAK,EAAE,OAAO,CAAC,CAAC;YAEtB,IAAA,mBAAS,EAAC,MAAM,EAAE,oCAAoC,EAAE,OAAO,CAAC,CAAC;YAEjE,IAAI,CAAC,OAAO,CAAC,WAAW,EAAE;gBACxB,OAAO,KAAK,CAAC,OAAO,CAAC;aACtB;SACF;QAED,iEAAiE;QACjE,IAAI,OAAO,CAAC,YAAY,EAAE;YACxB,IAAI,KAAK,CAAC,OAAO,CAAC,MAAM,GAAG,CAAC,EAAE;gBAC5B,IAAA,yCAAmB,EAAC,KAAK,CAAC,CAAC;aAC5B;iBAAM;gBACL,IAAA,4BAAkB,EAAC,KAAK,CAAC,CAAC;aAC3B;YACD,IAAA,mBAAS,EAAC,MAAM,EAAE,mCAAmC,EAAE,OAAO,CAAC,CAAC;SACjE;QAED,OAAO,KAAK,CAAC,GAAG,CAAC;KAClB;AACH,CAAC;AA3CD,iCA2CC;AAED,SAAS,WAAW,CAAC,WAAW,EAAE,OAAO;IACvC,KAAK,MAAM,KAAK,IAAI,WAAW,EAAE;QAC/B,KAAK,MAAM,GAAG,IAAI,KAAK,CAAC,IAAI,EAAE;YAC5B,MAAM,KAAK,GAAG,KAAK,CAAC,IAAI,CAAC,GAAG,CAAC,CAAC;YAC9B,IAAI,OAAO,KAAK,KAAK,QAAQ,EAAE;gBAC7B,IAAI,KAAK,CAAC,CAAC,CAAC,KAAK,GAAG,EAAE;oBACpB,oBAAoB;oBACpB,IAAI,KAAK,CAAC,KAAK,CAAC,MAAM,GAAG,CAAC,CAAC,KAAK,GAAG,EAAE;wBACnC,MAAM,KAAK,GAAG,KAAK;6BAChB,KAAK,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC;6BACZ,KAAK,CAAC,QAAQ,CAAC;6BACf,MAAM,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,CAAC,CAAC,CAAC;wBACpB,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,KAAK,CAAC,MAAM,EAAE,CAAC,EAAE,EAAE;4BACrC,KAAK,CAAC,IAAI,CAAC,GAAG,GAAG,MAAM,CAAC,CAAC,CAAC,CAAC,GAAG,OAAO,CAAC,aAAa;gCACjD,CAAC,CAAC,IAAA,4BAAW,EAAC,KAAK,CAAC,CAAC,CAAC,CAAC;gCACvB,CAAC,CAAC,KAAK,CAAC,CAAC,CAAC,CAAC;yBACd;qBACF;iBACF;qBAAM,IAAI,KAAK,CAAC,CAAC,CAAC,KAAK,GAAG,EAAE;oBAC3B,MAAM,KAAK,GAAG,KAAK,CAAC,KAAK,CAAC,OAAO,CAAC,CAAC;oBACnC,MAAM,MAAM,GAAG,kCAAkC,CAAC;oBAClD,IAAI,MAAM,CAAC,IAAI,CAAC,KAAK,CAAC,CAAC,CAAC,CAAC,EAAE;wBACzB,qBAAqB;wBACrB,MAAM,CAAC,IAAI,EAAE,EAAE,CAAC,GAAG,KAAK,CAAC,CAAC,CAAC,CAAC,KAAK,CAAC,MAAM,CAAC,CAAC,KAAK,CAAC,CAAC,CAAC,CAAC,GAAG,CAAC,MAAM,CAAC,CAAC;wBAC/D,MAAM,KAAK,GAAG,KAAK;6BAChB,KAAK,CAAC,CAAC,CAAC;6BACR,IAAI,CAAC,GAAG,CAAC;6BACT,KAAK,CAAC,QAAQ,CAAC;6BACf,MAAM,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,CAAC,CAAC,CAAC;wBACpB,KAAK,IAAI,CAAC,GAAG,IAAI,EAAE,CAAC,IAAI,EAAE,EAAE,CAAC,EAAE,EAAE;4BAC/B,KAAK,CAAC,IAAI,CAAC,GAAG,GAAG,MAAM,CAAC,CAAC,CAAC,CAAC,GAAG,OAAO,CAAC,aAAa;gCACjD,CAAC,CAAC,IAAA,4BAAW,EAAC,KAAK,CAAC,CAAC,GAAG,IAAI,CAAC,CAAC;gCAC9B,CAAC,CAAC,KAAK,CAAC,CAAC,GAAG,IAAI,CAAC,CAAC;yBACrB;qBACF;iBACF;aACF;SACF;KACF;AACH,CAAC"}
package/lib-esm/convert.d.ts CHANGED
@@ -11,7 +11,7 @@
11
11
  * @property {boolean} [noContour=false] - Don't calculate countour in case of 2D.
12
12
  * @property {number} [nbContourLevels=7] - Number of positive / negative contour levels to calculate.
13
13
  * @property {number} [noiseMultiplier=5] - Define for 2D the level as 5 times the median as default.
14
- * @property {import('@types/pino').Logger} [logger] - A logger like 'pino'
14
+ * @property {import('cheminfo-types').Logger} [logger] - A logger like 'pino'
15
15
  * @property {boolean} [profiling=false] - Add profiling information.
16
16
  */
17
17
  /**
@@ -40,6 +40,18 @@
40
40
  * @property {number} [xFactor] - x axis scaling factor
41
41
  * @property {number} [nbPoints] - Number of points
42
42
  */
43
+ /**
44
+ *
45
+ * @typedef {object} MinMax
46
+ * @property {number[][]} [z]
47
+ * @property {number} minX
48
+ * @property {number} maxX
49
+ * @property {number} minY
50
+ * @property {number} maxY
51
+ * @property {number} minZ
52
+ * @property {number} maxZ
53
+ * @property {number} median
54
+ */
43
55
  /**
44
56
  *
45
57
  * @typedef {object} Entry
@@ -52,6 +64,7 @@
52
64
  * @property {string} [dataType]
53
65
  * @property {string} [dataClass]
54
66
  * @property {boolean} [twoD]
67
+ * @property {MinMax} [minMax]
55
68
  */
56
69
  /**
57
70
  *
@@ -117,7 +130,7 @@ export type ConvertOptions = {
117
130
  /**
118
131
  * - A logger like 'pino'
119
132
  */
120
- logger?: any;
133
+ logger?: import("cheminfo-types").Logger | undefined;
121
134
  /**
122
135
  * - Add profiling information.
123
136
  */
@@ -138,6 +151,16 @@ export type Ntuples = {
138
151
  nucleus?: string[] | undefined;
139
152
  };
140
153
  export type Spectrum = Record<string, any>;
154
+ export type MinMax = {
155
+ z?: number[][] | undefined;
156
+ minX: number;
157
+ maxX: number;
158
+ minY: number;
159
+ maxY: number;
160
+ minZ: number;
161
+ maxZ: number;
162
+ median: number;
163
+ };
141
164
  export type Entry = {
142
165
  spectra: Spectrum[];
143
166
  ntuples: Ntuples;
@@ -148,6 +171,7 @@ export type Entry = {
148
171
  dataType?: string | undefined;
149
172
  dataClass?: string | undefined;
150
173
  twoD?: boolean | undefined;
174
+ minMax?: MinMax | undefined;
151
175
  };
152
176
  export type ConvertResult = {
153
177
  profiling: object[] | boolean;
package/lib-esm/convert.d.ts.map CHANGED
@@ -1 +1 @@
1
- {"version":3,"file":"convert.d.ts","sourceRoot":"","sources":["../src/convert.js"],"names":[],"mappings":"AA8BA;;;;;;;;;;;;;;;GAeG;AAEH;;;;;;;;;;;;;;;GAeG;AAEH;;;;;;;;;GASG;AAEH;;;;;;;;;;;;GAYG;AAEH;;;;;;;GAOG;AAEH;;;;;;;GAOG;AAEH,+BALW,MAAM,GAAC,WAAW,GAAC,UAAU,yCAE3B,aAAa,CAsSzB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;uBA7Ua,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"}
1
+ {"version":3,"file":"convert.d.ts","sourceRoot":"","sources":["../src/convert.js"],"names":[],"mappings":"AA8BA;;;;;;;;;;;;;;;GAeG;AAEH;;;;;;;;;;;;;;;GAeG;AAEH;;;;;;;;;GASG;AAEH;;;;;;;;;;;GAWG;AAEH;;;;;;;;;;;;;GAaG;AAEH;;;;;;;GAOG;AAEH;;;;;;;GAOG;AACH,+BAJW,MAAM,GAAC,WAAW,GAAC,UAAU,yCAE3B,aAAa,CAqSzB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;uBA1Va,OAAO,MAAM,EAAE,GAAG,CAAC;;;UAcnB,MAAM;UACN,MAAM;UACN,MAAM;UACN,MAAM;UACN,MAAM;UACN,MAAM;YACN,MAAM;;;aAMN,QAAQ,EAAE;aACV,OAAO;UACP,MAAM;UACN,MAAM;SACN,MAAM;;;;;;;;eAWL,MAAM,EAAE,GAAG,OAAO;UAClB,MAAM,EAAE;aACR,MAAM,EAAE;aACR,KAAK,EAAE"}
package/lib-esm/convert.js CHANGED
@@ -37,7 +37,7 @@ const defaultOptions = {
37
37
  * @property {boolean} [noContour=false] - Don't calculate countour in case of 2D.
38
38
  * @property {number} [nbContourLevels=7] - Number of positive / negative contour levels to calculate.
39
39
  * @property {number} [noiseMultiplier=5] - Define for 2D the level as 5 times the median as default.
40
- * @property {import('@types/pino').Logger} [logger] - A logger like 'pino'
40
+ * @property {import('cheminfo-types').Logger} [logger] - A logger like 'pino'
41
41
  * @property {boolean} [profiling=false] - Add profiling information.
42
42
  */
43
43
  /**
@@ -66,6 +66,18 @@ const defaultOptions = {
66
66
  * @property {number} [xFactor] - x axis scaling factor
67
67
  * @property {number} [nbPoints] - Number of points
68
68
  */
69
+ /**
70
+ *
71
+ * @typedef {object} MinMax
72
+ * @property {number[][]} [z]
73
+ * @property {number} minX
74
+ * @property {number} maxX
75
+ * @property {number} minY
76
+ * @property {number} maxY
77
+ * @property {number} minZ
78
+ * @property {number} maxZ
79
+ * @property {number} median
80
+ */
69
81
  /**
70
82
  *
71
83
  * @typedef {object} Entry
@@ -78,6 +90,7 @@ const defaultOptions = {
78
90
  * @property {string} [dataType]
79
91
  * @property {string} [dataClass]
80
92
  * @property {boolean} [twoD]
93
+ * @property {MinMax} [minMax]
81
94
  */
82
95
  /**
83
96
  *
package/lib-esm/convert.js.map CHANGED
@@ -1 +1 @@
1
- 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package/lib-esm/postProcessing.d.ts.map CHANGED
@@ -1 +1 @@
1
- {"version":3,"file":"postProcessing.d.ts","sourceRoot":"","sources":["../src/postProcessing.js"],"names":[],"mappings":"AAMA,0FAyCC"}
1
+ {"version":3,"file":"postProcessing.d.ts","sourceRoot":"","sources":["../src/postProcessing.js"],"names":[],"mappings":"AAQA,0FA2CC"}
package/lib-esm/postProcessing.js CHANGED
@@ -1,3 +1,4 @@
1
+ import { parseString } from 'dynamic-typing';
1
2
  import add2D from './2d/add2D';
2
3
  import { complexChromatogram } from './complexChromatogram';
3
4
  import postProcessingNMR from './postProcessingNMR';
@@ -6,6 +7,7 @@ import simpleChromatogram from './simpleChromatogram';
6
7
  export default function postProcessing(entriesFlat, result, options) {
7
8
  // converting Hz to ppm
8
9
  postProcessingNMR(entriesFlat);
10
+ createArray(entriesFlat, options);
9
11
  for (let entry of entriesFlat) {
10
12
  if (Object.keys(entry.ntuples).length > 0) {
11
13
  let newNtuples = [];
@@ -41,4 +43,45 @@ export default function postProcessing(entriesFlat, result, options) {
41
43
  delete entry.tmp;
42
44
  }
43
45
  }
46
+ function createArray(entriesFlat, options) {
47
+ for (const entry of entriesFlat) {
48
+ for (const key in entry.meta) {
49
+ const value = entry.meta[key];
50
+ if (typeof value === 'string') {
51
+ if (value[0] === '{') {
52
+ // could be an array
53
+ if (value[value.length - 1] === '}') {
54
+ const array = value
55
+ .slice(1, -1)
56
+ .split(/[,; ]+/)
57
+ .filter((e) => e);
58
+ for (let i = 0; i < array.length; i++) {
59
+ entry.meta[key + String(i)] = options.dynamicTyping
60
+ ? parseString(array[i])
61
+ : array[i];
62
+ }
63
+ }
64
+ }
65
+ else if (value[0] === '(') {
66
+ const lines = value.split(/\r?\n/);
67
+ const regexp = /^\((?<from>\d+)\.\.(?<to>\d+)\)$/;
68
+ if (regexp.test(lines[0])) {
69
+ // parsing '(0..63)'
70
+ const [from, to] = lines[0].match(regexp).slice(1).map(Number);
71
+ const array = lines
72
+ .slice(1)
73
+ .join(' ')
74
+ .split(/[,; ]+/)
75
+ .filter((e) => e);
76
+ for (let i = from; i <= to; i++) {
77
+ entry.meta[key + String(i)] = options.dynamicTyping
78
+ ? parseString(array[i - from])
79
+ : array[i - from];
80
+ }
81
+ }
82
+ }
83
+ }
84
+ }
85
+ }
86
+ }
44
87
  //# sourceMappingURL=postProcessing.js.map
package/lib-esm/postProcessing.js.map CHANGED
@@ -1 +1 @@
1
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1
+ {"version":3,"file":"postProcessing.js","sourceRoot":"","sources":["../src/postProcessing.js"],"names":[],"mappings":"AAAA,OAAO,EAAE,WAAW,EAAE,MAAM,gBAAgB,CAAC;AAE7C,OAAO,KAAK,MAAM,YAAY,CAAC;AAC/B,OAAO,EAAE,mBAAmB,EAAE,MAAM,uBAAuB,CAAC;AAC5D,OAAO,iBAAiB,MAAM,qBAAqB,CAAC;AACpD,OAAO,SAAS,MAAM,aAAa,CAAC;AACpC,OAAO,kBAAkB,MAAM,sBAAsB,CAAC;AAEtD,MAAM,CAAC,OAAO,UAAU,cAAc,CAAC,WAAW,EAAE,MAAM,EAAE,OAAO;IACjE,uBAAuB;IACvB,iBAAiB,CAAC,WAAW,CAAC,CAAC;IAE/B,WAAW,CAAC,WAAW,EAAE,OAAO,CAAC,CAAC;IAElC,KAAK,IAAI,KAAK,IAAI,WAAW,EAAE;QAC7B,IAAI,MAAM,CAAC,IAAI,CAAC,KAAK,CAAC,OAAO,CAAC,CAAC,MAAM,GAAG,CAAC,EAAE;YACzC,IAAI,UAAU,GAAG,EAAE,CAAC;YACpB,IAAI,IAAI,GAAG,MAAM,CAAC,IAAI,CAAC,KAAK,CAAC,OAAO,CAAC,CAAC;YACtC,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,IAAI,CAAC,MAAM,EAAE,CAAC,EAAE,EAAE;gBACpC,IAAI,GAAG,GAAG,IAAI,CAAC,CAAC,CAAC,CAAC;gBAClB,IAAI,MAAM,GAAG,KAAK,CAAC,OAAO,CAAC,GAAG,CAAC,CAAC;gBAChC,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,MAAM,CAAC,MAAM,EAAE,CAAC,EAAE,EAAE;oBACtC,IAAI,CAAC,UAAU,CAAC,CAAC,CAAC;wBAAE,UAAU,CAAC,CAAC,CAAC,GAAG,EAAE,CAAC;oBACvC,UAAU,CAAC,CAAC,CAAC,CAAC,GAAG,CAAC,GAAG,MAAM,CAAC,CAAC,CAAC,CAAC;iBAChC;aACF;YACD,KAAK,CAAC,OAAO,GAAG,UAAU,CAAC;SAC5B;QAED,IAAI,KAAK,CAAC,IAAI,IAAI,OAAO,CAAC,MAAM,EAAE;YAChC,KAAK,CAAC,KAAK,EAAE,OAAO,CAAC,CAAC;YAEtB,SAAS,CAAC,MAAM,EAAE,oCAAoC,EAAE,OAAO,CAAC,CAAC;YAEjE,IAAI,CAAC,OAAO,CAAC,WAAW,EAAE;gBACxB,OAAO,KAAK,CAAC,OAAO,CAAC;aACtB;SACF;QAED,iEAAiE;QACjE,IAAI,OAAO,CAAC,YAAY,EAAE;YACxB,IAAI,KAAK,CAAC,OAAO,CAAC,MAAM,GAAG,CAAC,EAAE;gBAC5B,mBAAmB,CAAC,KAAK,CAAC,CAAC;aAC5B;iBAAM;gBACL,kBAAkB,CAAC,KAAK,CAAC,CAAC;aAC3B;YACD,SAAS,CAAC,MAAM,EAAE,mCAAmC,EAAE,OAAO,CAAC,CAAC;SACjE;QAED,OAAO,KAAK,CAAC,GAAG,CAAC;KAClB;AACH,CAAC;AAED,SAAS,WAAW,CAAC,WAAW,EAAE,OAAO;IACvC,KAAK,MAAM,KAAK,IAAI,WAAW,EAAE;QAC/B,KAAK,MAAM,GAAG,IAAI,KAAK,CAAC,IAAI,EAAE;YAC5B,MAAM,KAAK,GAAG,KAAK,CAAC,IAAI,CAAC,GAAG,CAAC,CAAC;YAC9B,IAAI,OAAO,KAAK,KAAK,QAAQ,EAAE;gBAC7B,IAAI,KAAK,CAAC,CAAC,CAAC,KAAK,GAAG,EAAE;oBACpB,oBAAoB;oBACpB,IAAI,KAAK,CAAC,KAAK,CAAC,MAAM,GAAG,CAAC,CAAC,KAAK,GAAG,EAAE;wBACnC,MAAM,KAAK,GAAG,KAAK;6BAChB,KAAK,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC;6BACZ,KAAK,CAAC,QAAQ,CAAC;6BACf,MAAM,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,CAAC,CAAC,CAAC;wBACpB,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,KAAK,CAAC,MAAM,EAAE,CAAC,EAAE,EAAE;4BACrC,KAAK,CAAC,IAAI,CAAC,GAAG,GAAG,MAAM,CAAC,CAAC,CAAC,CAAC,GAAG,OAAO,CAAC,aAAa;gCACjD,CAAC,CAAC,WAAW,CAAC,KAAK,CAAC,CAAC,CAAC,CAAC;gCACvB,CAAC,CAAC,KAAK,CAAC,CAAC,CAAC,CAAC;yBACd;qBACF;iBACF;qBAAM,IAAI,KAAK,CAAC,CAAC,CAAC,KAAK,GAAG,EAAE;oBAC3B,MAAM,KAAK,GAAG,KAAK,CAAC,KAAK,CAAC,OAAO,CAAC,CAAC;oBACnC,MAAM,MAAM,GAAG,kCAAkC,CAAC;oBAClD,IAAI,MAAM,CAAC,IAAI,CAAC,KAAK,CAAC,CAAC,CAAC,CAAC,EAAE;wBACzB,qBAAqB;wBACrB,MAAM,CAAC,IAAI,EAAE,EAAE,CAAC,GAAG,KAAK,CAAC,CAAC,CAAC,CAAC,KAAK,CAAC,MAAM,CAAC,CAAC,KAAK,CAAC,CAAC,CAAC,CAAC,GAAG,CAAC,MAAM,CAAC,CAAC;wBAC/D,MAAM,KAAK,GAAG,KAAK;6BAChB,KAAK,CAAC,CAAC,CAAC;6BACR,IAAI,CAAC,GAAG,CAAC;6BACT,KAAK,CAAC,QAAQ,CAAC;6BACf,MAAM,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,CAAC,CAAC,CAAC;wBACpB,KAAK,IAAI,CAAC,GAAG,IAAI,EAAE,CAAC,IAAI,EAAE,EAAE,CAAC,EAAE,EAAE;4BAC/B,KAAK,CAAC,IAAI,CAAC,GAAG,GAAG,MAAM,CAAC,CAAC,CAAC,CAAC,GAAG,OAAO,CAAC,aAAa;gCACjD,CAAC,CAAC,WAAW,CAAC,KAAK,CAAC,CAAC,GAAG,IAAI,CAAC,CAAC;gCAC9B,CAAC,CAAC,KAAK,CAAC,CAAC,GAAG,IAAI,CAAC,CAAC;yBACrB;qBACF;iBACF;aACF;SACF;KACF;AACH,CAAC"}
package/package.json CHANGED
@@ -1,6 +1,6 @@
1
1
  {
2
2
  "name": "jcampconverter",
3
- "version": "9.1.0",
3
+ "version": "9.2.0",
4
4
  "description": "Parse and convert JCAMP data",
5
5
  "main": "lib/index.js",
6
6
  "module": "lib-esm/index.js",
@@ -44,28 +44,29 @@
44
44
  },
45
45
  "homepage": "https://github.com/cheminfo/jcampconverter#readme",
46
46
  "devDependencies": {
47
- "@types/jest": "^29.4.4",
47
+ "@types/jest": "^29.5.5",
48
48
  "@types/pino": "^7.0.5",
49
- "@vitest/coverage-c8": "^0.29.3",
49
+ "@vitest/coverage-v8": "^0.34.5",
50
50
  "benchmark": "^2.1.4",
51
- "c8": "^7.13.0",
51
+ "c8": "^8.0.1",
52
52
  "cheminfo-build": "^1.2.0",
53
- "eslint": "^8.36.0",
54
- "eslint-config-cheminfo-typescript": "^11.3.0",
53
+ "eslint": "^8.49.0",
54
+ "eslint-config-cheminfo-typescript": "^12.0.4",
55
55
  "esm": "^3.2.25",
56
- "fifo-logger": "^0.6.0",
56
+ "fifo-logger": "^0.6.1",
57
57
  "jest-matcher-deep-close-to": "^3.0.2",
58
- "jscpd": "^3.5.3",
59
- "prettier": "^2.8.4",
60
- "rimraf": "^4.4.0",
61
- "typescript": "^4.9.5",
62
- "vitest": "^0.29.3"
58
+ "jscpd": "^3.5.10",
59
+ "ml-spectra-processing": "^12.5.1",
60
+ "prettier": "^3.0.3",
61
+ "rimraf": "^5.0.1",
62
+ "typescript": "^5.2.2",
63
+ "vitest": "^0.34.5"
63
64
  },
64
65
  "dependencies": {
66
+ "cheminfo-types": "^1.7.2",
65
67
  "dynamic-typing": "^1.0.0",
66
68
  "ensure-string": "^1.2.0",
67
69
  "gyromagnetic-ratio": "^1.0.0",
68
- "ml-array-median": "^1.1.6",
69
- "ml-spectra-processing": "^12.0.0"
70
+ "ml-array-median": "^1.1.6"
70
71
  }
71
72
  }
package/src/convert.js CHANGED
@@ -41,7 +41,7 @@ const defaultOptions = {
41
41
  * @property {boolean} [noContour=false] - Don't calculate countour in case of 2D.
42
42
  * @property {number} [nbContourLevels=7] - Number of positive / negative contour levels to calculate.
43
43
  * @property {number} [noiseMultiplier=5] - Define for 2D the level as 5 times the median as default.
44
- * @property {import('@types/pino').Logger} [logger] - A logger like 'pino'
44
+ * @property {import('cheminfo-types').Logger} [logger] - A logger like 'pino'
45
45
  * @property {boolean} [profiling=false] - Add profiling information.
46
46
  */
47
47
 
@@ -73,6 +73,19 @@ const defaultOptions = {
73
73
  * @property {number} [nbPoints] - Number of points
74
74
  */
75
75
 
76
+ /**
77
+ *
78
+ * @typedef {object} MinMax
79
+ * @property {number[][]} [z]
80
+ * @property {number} minX
81
+ * @property {number} maxX
82
+ * @property {number} minY
83
+ * @property {number} maxY
84
+ * @property {number} minZ
85
+ * @property {number} maxZ
86
+ * @property {number} median
87
+ */
88
+
76
89
  /**
77
90
  *
78
91
  * @typedef {object} Entry
@@ -85,6 +98,7 @@ const defaultOptions = {
85
98
  * @property {string} [dataType]
86
99
  * @property {string} [dataClass]
87
100
  * @property {boolean} [twoD]
101
+ * @property {MinMax} [minMax]
88
102
  */
89
103
 
90
104
  /**
@@ -104,7 +118,6 @@ const defaultOptions = {
104
118
  * @param {ConvertOptions} [options]
105
119
  * @returns {ConvertResult}
106
120
  */
107
-
108
121
  export function convert(jcamp, options = {}) {
109
122
  jcamp = ensureString(jcamp);
110
123
  options = { ...defaultOptions, ...options };
package/src/postProcessing.js CHANGED
@@ -1,3 +1,5 @@
1
+ import { parseString } from 'dynamic-typing';
2
+
1
3
  import add2D from './2d/add2D';
2
4
  import { complexChromatogram } from './complexChromatogram';
3
5
  import postProcessingNMR from './postProcessingNMR';
@@ -8,6 +10,8 @@ export default function postProcessing(entriesFlat, result, options) {
8
10
  // converting Hz to ppm
9
11
  postProcessingNMR(entriesFlat);
10
12
 
13
+ createArray(entriesFlat, options);
14
+
11
15
  for (let entry of entriesFlat) {
12
16
  if (Object.keys(entry.ntuples).length > 0) {
13
17
  let newNtuples = [];
@@ -46,3 +50,44 @@ export default function postProcessing(entriesFlat, result, options) {
46
50
  delete entry.tmp;
47
51
  }
48
52
  }
53
+
54
+ function createArray(entriesFlat, options) {
55
+ for (const entry of entriesFlat) {
56
+ for (const key in entry.meta) {
57
+ const value = entry.meta[key];
58
+ if (typeof value === 'string') {
59
+ if (value[0] === '{') {
60
+ // could be an array
61
+ if (value[value.length - 1] === '}') {
62
+ const array = value
63
+ .slice(1, -1)
64
+ .split(/[,; ]+/)
65
+ .filter((e) => e);
66
+ for (let i = 0; i < array.length; i++) {
67
+ entry.meta[key + String(i)] = options.dynamicTyping
68
+ ? parseString(array[i])
69
+ : array[i];
70
+ }
71
+ }
72
+ } else if (value[0] === '(') {
73
+ const lines = value.split(/\r?\n/);
74
+ const regexp = /^\((?<from>\d+)\.\.(?<to>\d+)\)$/;
75
+ if (regexp.test(lines[0])) {
76
+ // parsing '(0..63)'
77
+ const [from, to] = lines[0].match(regexp).slice(1).map(Number);
78
+ const array = lines
79
+ .slice(1)
80
+ .join(' ')
81
+ .split(/[,; ]+/)
82
+ .filter((e) => e);
83
+ for (let i = from; i <= to; i++) {
84
+ entry.meta[key + String(i)] = options.dynamicTyping
85
+ ? parseString(array[i - from])
86
+ : array[i - from];
87
+ }
88
+ }
89
+ }
90
+ }
91
+ }
92
+ }
93
+ }