jcampconverter 8.2.2 → 8.2.5

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 (140) hide show
  1. package/lib/2d/add2D.d.ts +2 -0
  2. package/lib/2d/add2D.d.ts.map +1 -0
  3. package/lib/2d/add2D.js +17 -0
  4. package/lib/2d/add2D.js.map +1 -0
  5. package/lib/2d/convertTo3DZ.d.ts +11 -0
  6. package/lib/2d/convertTo3DZ.d.ts.map +1 -0
  7. package/lib/2d/convertTo3DZ.js +59 -0
  8. package/lib/2d/convertTo3DZ.js.map +1 -0
  9. package/lib/2d/generateContourLines.d.ts +8 -0
  10. package/lib/2d/generateContourLines.d.ts.map +1 -0
  11. package/lib/2d/generateContourLines.js +163 -0
  12. package/lib/2d/generateContourLines.js.map +1 -0
  13. package/lib/complexChromatogram.d.ts +4 -0
  14. package/lib/complexChromatogram.d.ts.map +1 -0
  15. package/lib/complexChromatogram.js +49 -0
  16. package/lib/complexChromatogram.js.map +1 -0
  17. package/lib/convert.d.ts +147 -0
  18. package/lib/convert.d.ts.map +1 -0
  19. package/lib/convert.js +391 -0
  20. package/lib/convert.js.map +1 -0
  21. package/lib/convertToFloatArray.d.ts +2 -0
  22. package/lib/convertToFloatArray.d.ts.map +1 -0
  23. package/lib/convertToFloatArray.js +11 -0
  24. package/lib/convertToFloatArray.js.map +1 -0
  25. package/lib/createTree.d.ts +29 -0
  26. package/lib/createTree.d.ts.map +1 -0
  27. package/lib/createTree.js +98 -0
  28. package/lib/createTree.js.map +1 -0
  29. package/lib/index.d.ts +3 -0
  30. package/lib/index.d.ts.map +1 -0
  31. package/lib/index.js +8 -1214
  32. package/lib/index.js.map +1 -0
  33. package/lib/parse/fastParseXYData.d.ts +2 -0
  34. package/lib/parse/fastParseXYData.d.ts.map +1 -0
  35. package/lib/parse/fastParseXYData.js +192 -0
  36. package/lib/parse/fastParseXYData.js.map +1 -0
  37. package/lib/parse/parsePeakTable.d.ts +2 -0
  38. package/lib/parse/parsePeakTable.d.ts.map +1 -0
  39. package/lib/parse/parsePeakTable.js +67 -0
  40. package/lib/parse/parsePeakTable.js.map +1 -0
  41. package/lib/parse/parseXYA.d.ts +2 -0
  42. package/lib/parse/parseXYA.d.ts.map +1 -0
  43. package/lib/parse/parseXYA.js +17 -0
  44. package/lib/parse/parseXYA.js.map +1 -0
  45. package/lib/postProcessing.d.ts +2 -0
  46. package/lib/postProcessing.d.ts.map +1 -0
  47. package/lib/postProcessing.js +50 -0
  48. package/lib/postProcessing.js.map +1 -0
  49. package/lib/postProcessingNMR.d.ts +2 -0
  50. package/lib/postProcessingNMR.d.ts.map +1 -0
  51. package/lib/postProcessingNMR.js +94 -0
  52. package/lib/postProcessingNMR.js.map +1 -0
  53. package/lib/prepareNtuplesDatatable.d.ts +2 -0
  54. package/lib/prepareNtuplesDatatable.d.ts.map +1 -0
  55. package/lib/prepareNtuplesDatatable.js +87 -0
  56. package/lib/prepareNtuplesDatatable.js.map +1 -0
  57. package/lib/prepareSpectrum.d.ts +2 -0
  58. package/lib/prepareSpectrum.d.ts.map +1 -0
  59. package/lib/prepareSpectrum.js +10 -0
  60. package/lib/prepareSpectrum.js.map +1 -0
  61. package/lib/profiling.d.ts +2 -0
  62. package/lib/profiling.d.ts.map +1 -0
  63. package/lib/profiling.js +12 -0
  64. package/lib/profiling.js.map +1 -0
  65. package/lib/simpleChromatogram.d.ts +2 -0
  66. package/lib/simpleChromatogram.d.ts.map +1 -0
  67. package/lib/simpleChromatogram.js +16 -0
  68. package/lib/simpleChromatogram.js.map +1 -0
  69. package/lib-esm/2d/add2D.d.ts +2 -0
  70. package/lib-esm/2d/add2D.d.ts.map +1 -0
  71. package/lib-esm/2d/add2D.js +11 -0
  72. package/lib-esm/2d/add2D.js.map +1 -0
  73. package/lib-esm/2d/convertTo3DZ.d.ts +11 -0
  74. package/lib-esm/2d/convertTo3DZ.d.ts.map +1 -0
  75. package/lib-esm/2d/convertTo3DZ.js +53 -0
  76. package/lib-esm/2d/convertTo3DZ.js.map +1 -0
  77. package/lib-esm/2d/generateContourLines.d.ts +8 -0
  78. package/lib-esm/2d/generateContourLines.d.ts.map +1 -0
  79. package/lib-esm/2d/generateContourLines.js +160 -0
  80. package/lib-esm/2d/generateContourLines.js.map +1 -0
  81. package/lib-esm/complexChromatogram.d.ts +4 -0
  82. package/lib-esm/complexChromatogram.d.ts.map +1 -0
  83. package/lib-esm/complexChromatogram.js +43 -0
  84. package/lib-esm/complexChromatogram.js.map +1 -0
  85. package/lib-esm/convert.d.ts +147 -0
  86. package/lib-esm/convert.d.ts.map +1 -0
  87. package/lib-esm/convert.js +384 -0
  88. package/lib-esm/convert.js.map +1 -0
  89. package/lib-esm/convertToFloatArray.d.ts +2 -0
  90. package/lib-esm/convertToFloatArray.d.ts.map +1 -0
  91. package/lib-esm/convertToFloatArray.js +8 -0
  92. package/lib-esm/convertToFloatArray.js.map +1 -0
  93. package/lib-esm/createTree.d.ts +29 -0
  94. package/lib-esm/createTree.d.ts.map +1 -0
  95. package/lib-esm/createTree.js +94 -0
  96. package/lib-esm/createTree.js.map +1 -0
  97. package/lib-esm/index.d.ts +3 -0
  98. package/lib-esm/index.d.ts.map +1 -0
  99. package/lib-esm/index.js +3 -0
  100. package/lib-esm/index.js.map +1 -0
  101. package/lib-esm/parse/fastParseXYData.d.ts +2 -0
  102. package/lib-esm/parse/fastParseXYData.d.ts.map +1 -0
  103. package/lib-esm/parse/fastParseXYData.js +189 -0
  104. package/lib-esm/parse/fastParseXYData.js.map +1 -0
  105. package/lib-esm/parse/parsePeakTable.d.ts +2 -0
  106. package/lib-esm/parse/parsePeakTable.d.ts.map +1 -0
  107. package/lib-esm/parse/parsePeakTable.js +64 -0
  108. package/lib-esm/parse/parsePeakTable.js.map +1 -0
  109. package/lib-esm/parse/parseXYA.d.ts +2 -0
  110. package/lib-esm/parse/parseXYA.d.ts.map +1 -0
  111. package/lib-esm/parse/parseXYA.js +14 -0
  112. package/lib-esm/parse/parseXYA.js.map +1 -0
  113. package/lib-esm/postProcessing.d.ts +2 -0
  114. package/lib-esm/postProcessing.d.ts.map +1 -0
  115. package/lib-esm/postProcessing.js +44 -0
  116. package/lib-esm/postProcessing.js.map +1 -0
  117. package/lib-esm/postProcessingNMR.d.ts +2 -0
  118. package/lib-esm/postProcessingNMR.d.ts.map +1 -0
  119. package/lib-esm/postProcessingNMR.js +91 -0
  120. package/lib-esm/postProcessingNMR.js.map +1 -0
  121. package/lib-esm/prepareNtuplesDatatable.d.ts +2 -0
  122. package/lib-esm/prepareNtuplesDatatable.d.ts.map +1 -0
  123. package/lib-esm/prepareNtuplesDatatable.js +84 -0
  124. package/lib-esm/prepareNtuplesDatatable.js.map +1 -0
  125. package/lib-esm/prepareSpectrum.d.ts +2 -0
  126. package/lib-esm/prepareSpectrum.d.ts.map +1 -0
  127. package/lib-esm/prepareSpectrum.js +7 -0
  128. package/lib-esm/prepareSpectrum.js.map +1 -0
  129. package/lib-esm/profiling.d.ts +2 -0
  130. package/lib-esm/profiling.d.ts.map +1 -0
  131. package/lib-esm/profiling.js +9 -0
  132. package/lib-esm/profiling.js.map +1 -0
  133. package/lib-esm/simpleChromatogram.d.ts +2 -0
  134. package/lib-esm/simpleChromatogram.d.ts.map +1 -0
  135. package/lib-esm/simpleChromatogram.js +13 -0
  136. package/lib-esm/simpleChromatogram.js.map +1 -0
  137. package/package.json +23 -18
  138. package/src/convert.js +72 -19
  139. package/src/createTree.js +16 -3
  140. package/CHANGELOG.md +0 -427
package/lib/convert.js ADDED
@@ -0,0 +1,391 @@
1
+ "use strict";
2
+ var __importDefault = (this && this.__importDefault) || function (mod) {
3
+ return (mod && mod.__esModule) ? mod : { "default": mod };
4
+ };
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+ Object.defineProperty(exports, "__esModule", { value: true });
6
+ exports.convert = void 0;
7
+ const dynamic_typing_1 = require("dynamic-typing");
8
+ const ensure_string_1 = require("ensure-string");
9
+ const complexChromatogram_1 = require("./complexChromatogram");
10
+ const convertToFloatArray_1 = __importDefault(require("./convertToFloatArray"));
11
+ const fastParseXYData_1 = __importDefault(require("./parse/fastParseXYData"));
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+ const parsePeakTable_1 = __importDefault(require("./parse/parsePeakTable"));
13
+ const parseXYA_1 = __importDefault(require("./parse/parseXYA"));
14
+ const postProcessing_1 = __importDefault(require("./postProcessing"));
15
+ const prepareNtuplesDatatable_1 = __importDefault(require("./prepareNtuplesDatatable"));
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+ const prepareSpectrum_1 = __importDefault(require("./prepareSpectrum"));
17
+ const profiling_1 = __importDefault(require("./profiling"));
18
+ // the following RegExp can only be used for XYdata, some peakTables have values with a "E-5" ...
19
+ const ntuplesSeparatorRegExp = /[ \t]*,[ \t]*/;
20
+ const defaultOptions = {
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+ keepRecordsRegExp: /^$/,
22
+ canonicDataLabels: true,
23
+ canonicMetadataLabels: false,
24
+ dynamicTyping: true,
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+ withoutXY: false,
26
+ chromatogram: false,
27
+ keepSpectra: false,
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+ noContour: false,
29
+ nbContourLevels: 7,
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+ noiseMultiplier: 5,
31
+ profiling: false,
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+ };
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+ /**
34
+ *
35
+ * @typedef {object} ConvertOptions
36
+ * @property {RegExp} [options.keepRecordsRegExp=/^$/] - By default we don't keep meta information.
37
+ * @property {boolean} [options.canonicDataLabels=true] - Canonize the Labels (uppercase without symbol).
38
+ * @property {boolean} [options.canonicMetadataLabels=false] - Canonize the metadata Labels (uppercase without symbol).
39
+ * @property {boolean} [options.dynamicTyping=false] - Convert numbers to Number.
40
+ * @property {boolean} [options.withoutXY=false] - Remove the XY data.
41
+ * @property {boolean} [options.chromatogram=false] - Special post-processing for GC / HPLC / MS.
42
+ * @property {boolean} [options.keepSpectra=false] - Force to keep the spectra in case of 2D.
43
+ * @property {boolean} [options.noContour=false] - Don't calculate countour in case of 2D.
44
+ * @property {number} [options.nbContourLevels=7] - Number of positive / negative contour levels to calculate.
45
+ * @property {number} [options.noiseMultiplier=5] - Define for 2D the level as 5 times the median as default.
46
+ * @property {boolean} [options.profiling=false] - Add profiling information.
47
+ */
48
+ /**
49
+ *
50
+ * @typedef {object} Ntuples
51
+ * @property {string[]} [varname]
52
+ * @property {string[]} [symbol]
53
+ * @property {string[]} [vartype]
54
+ * @property {string[]} [varform]
55
+ * @property {number[]} [vardim]
56
+ * @property {string[]} [units]
57
+ * @property {number[]} [factor]
58
+ * @property {number[]} [first]
59
+ * @property {number[]} [last]
60
+ * @property {number[]} [min]
61
+ * @property {number[]} [max]
62
+ * @property {string[]} [nucleus]
63
+ */
64
+ /**
65
+ * @typedef { Record<string, any> } Spectrum
66
+ * @property {Record<string, number[]>} [data]
67
+ * @property {number} [firstX]
68
+ * @property {number} [lastX]
69
+ * @property {number} [deltaX]
70
+ * @property {number} [yFactor]
71
+ * @property {number} [xFactor]
72
+ * @property {number} [nbPoints]
73
+ */
74
+ /**
75
+ *
76
+ * @typedef {object} Entry
77
+ * @property {Spectrum[]} spectra
78
+ * @property {Ntuples} ntuples
79
+ * @property {object} meta
80
+ * @property {object} tmp
81
+ * @property {string} [title]
82
+ * @property {string} [dataType]
83
+ * @property {string} [dataClass]
84
+ * @property {boolean} [twoD]
85
+ */
86
+ /**
87
+ *
88
+ * @typedef { object } ConvertResult
89
+ * @property { object[] | boolean } profiling
90
+ * @property { string[] } logs
91
+ * @property { object[] } entries
92
+ * @property { Entry[] } flatten
93
+ */
94
+ /**
95
+ * Parse a jcamp.
96
+ *
97
+ * @param {string|ArrayBuffer|Uint8Array} jcamp
98
+ * @param {ConvertOptions} [options]
99
+ * @returns {ConvertResult}
100
+ */
101
+ function convert(jcamp, options = {}) {
102
+ jcamp = (0, ensure_string_1.ensureString)(jcamp);
103
+ options = { ...defaultOptions, ...options };
104
+ options.wantXY = !options.withoutXY;
105
+ options.start = Date.now();
106
+ let entriesFlat = [];
107
+ let result = {
108
+ profiling: options.profiling ? [] : false,
109
+ logs: [],
110
+ entries: [],
111
+ };
112
+ let tmpResult = { children: [] };
113
+ let currentEntry = tmpResult;
114
+ let parentsStack = [];
115
+ let spectrum = {};
116
+ if (typeof jcamp !== 'string') {
117
+ throw new TypeError('the JCAMP should be a string');
118
+ }
119
+ (0, profiling_1.default)(result, 'Before split to LDRS', options);
120
+ let ldrs = jcamp.replace(/[\r\n]+##/g, '\n##').split('\n##');
121
+ (0, profiling_1.default)(result, 'Split to LDRS', options);
122
+ if (ldrs[0])
123
+ ldrs[0] = ldrs[0].replace(/^[\r\n ]*##/, '');
124
+ for (let ldr of ldrs) {
125
+ // This is a new LDR
126
+ let position = ldr.indexOf('=');
127
+ let dataLabel = position > 0 ? ldr.substring(0, position) : ldr;
128
+ let dataValue = position > 0 ? ldr.substring(position + 1).trim() : '';
129
+ let canonicDataLabel = dataLabel.replace(/[_ -]/g, '').toUpperCase();
130
+ if (canonicDataLabel === 'DATATABLE') {
131
+ let endLine = dataValue.indexOf('\n');
132
+ if (endLine === -1)
133
+ endLine = dataValue.indexOf('\r');
134
+ if (endLine > 0) {
135
+ // ##DATA TABLE= (X++(I..I)), XYDATA
136
+ // We need to find the variables
137
+ let infos = dataValue.substring(0, endLine).split(/[ ,;\t]+/);
138
+ (0, prepareNtuplesDatatable_1.default)(currentEntry, spectrum, infos[0]);
139
+ spectrum.datatable = infos[0];
140
+ if (infos[1] && infos[1].indexOf('PEAKS') > -1) {
141
+ canonicDataLabel = 'PEAKTABLE';
142
+ }
143
+ else if (infos[1] &&
144
+ (infos[1].indexOf('XYDATA') || infos[0].indexOf('++') > 0)) {
145
+ canonicDataLabel = 'XYDATA';
146
+ spectrum.deltaX =
147
+ (spectrum.lastX - spectrum.firstX) / (spectrum.nbPoints - 1);
148
+ }
149
+ }
150
+ }
151
+ if (canonicDataLabel === 'XYDATA') {
152
+ if (options.wantXY) {
153
+ (0, prepareSpectrum_1.default)(spectrum);
154
+ // well apparently we should still consider it is a PEAK TABLE if there are no '++' after
155
+ if (dataValue.match(/.*\+\+.*/)) {
156
+ // ex: (X++(Y..Y))
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+ spectrum.deltaX =
158
+ (spectrum.lastX - spectrum.firstX) / (spectrum.nbPoints - 1);
159
+ (0, fastParseXYData_1.default)(spectrum, dataValue, result);
160
+ }
161
+ else {
162
+ (0, parsePeakTable_1.default)(spectrum, dataValue, result);
163
+ }
164
+ currentEntry.spectra.push(spectrum);
165
+ spectrum = {};
166
+ }
167
+ continue;
168
+ }
169
+ else if (canonicDataLabel === 'PEAKTABLE') {
170
+ if (options.wantXY) {
171
+ (0, prepareSpectrum_1.default)(spectrum);
172
+ (0, parsePeakTable_1.default)(spectrum, dataValue, result);
173
+ currentEntry.spectra.push(spectrum);
174
+ spectrum = {};
175
+ }
176
+ continue;
177
+ }
178
+ if (canonicDataLabel === 'PEAKASSIGNMENTS') {
179
+ if (options.wantXY) {
180
+ if (dataValue.match(/.*(XYA).*/)) {
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+ // ex: (XYA)
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+ (0, parseXYA_1.default)(spectrum, dataValue);
183
+ }
184
+ currentEntry.spectra.push(spectrum);
185
+ spectrum = {};
186
+ }
187
+ continue;
188
+ }
189
+ if (canonicDataLabel === 'TITLE') {
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+ let parentEntry = currentEntry;
191
+ if (!parentEntry.children) {
192
+ parentEntry.children = [];
193
+ }
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+ currentEntry = {
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+ spectra: [],
196
+ ntuples: {},
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+ info: {},
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+ meta: {},
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+ tmp: {}, // tmp information we need to keep for postprocessing
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+ };
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+ parentEntry.children.push(currentEntry);
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+ parentsStack.push(parentEntry);
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+ entriesFlat.push(currentEntry);
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+ currentEntry.title = dataValue;
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+ }
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+ else if (canonicDataLabel === 'DATATYPE') {
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+ currentEntry.dataType = dataValue;
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+ if (dataValue.match(/(^nd|\snd\s)/i)) {
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+ currentEntry.twoD = true;
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+ }
211
+ }
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+ else if (canonicDataLabel === 'NTUPLES') {
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+ if (dataValue.match(/(^nd|\snd\s)/i)) {
214
+ currentEntry.twoD = true;
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+ }
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+ }
217
+ else if (canonicDataLabel === 'DATACLASS') {
218
+ currentEntry.dataClass = dataValue;
219
+ }
220
+ else if (canonicDataLabel === 'XUNITS') {
221
+ spectrum.xUnits = dataValue;
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+ }
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+ else if (canonicDataLabel === 'YUNITS') {
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+ spectrum.yUnits = dataValue;
225
+ }
226
+ else if (canonicDataLabel === 'FIRSTX') {
227
+ spectrum.firstX = Number(dataValue);
228
+ }
229
+ else if (canonicDataLabel === 'LASTX') {
230
+ spectrum.lastX = Number(dataValue);
231
+ }
232
+ else if (canonicDataLabel === 'FIRSTY') {
233
+ spectrum.firstY = Number(dataValue);
234
+ }
235
+ else if (canonicDataLabel === 'LASTY') {
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+ spectrum.lastY = Number(dataValue);
237
+ }
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+ else if (canonicDataLabel === 'NPOINTS') {
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+ spectrum.nbPoints = Number(dataValue);
240
+ }
241
+ else if (canonicDataLabel === 'XFACTOR') {
242
+ spectrum.xFactor = Number(dataValue);
243
+ }
244
+ else if (canonicDataLabel === 'YFACTOR') {
245
+ spectrum.yFactor = Number(dataValue);
246
+ }
247
+ else if (canonicDataLabel === 'MAXX') {
248
+ spectrum.maxX = Number(dataValue);
249
+ }
250
+ else if (canonicDataLabel === 'MINX') {
251
+ spectrum.minX = Number(dataValue);
252
+ }
253
+ else if (canonicDataLabel === 'MAXY') {
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+ spectrum.maxY = Number(dataValue);
255
+ }
256
+ else if (canonicDataLabel === 'MINY') {
257
+ spectrum.minY = Number(dataValue);
258
+ }
259
+ else if (canonicDataLabel === 'DELTAX') {
260
+ spectrum.deltaX = Number(dataValue);
261
+ }
262
+ else if (canonicDataLabel === '.OBSERVEFREQUENCY' ||
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+ canonicDataLabel === '$SFO1') {
264
+ if (!spectrum.observeFrequency) {
265
+ spectrum.observeFrequency = Number(dataValue);
266
+ }
267
+ }
268
+ else if (canonicDataLabel === '.OBSERVENUCLEUS') {
269
+ if (!spectrum.xType) {
270
+ currentEntry.xType = dataValue.replace(/[^a-zA-Z0-9]/g, '');
271
+ }
272
+ }
273
+ else if (canonicDataLabel === '$OFFSET') {
274
+ // OFFSET for Bruker spectra
275
+ currentEntry.shiftOffsetNum = 0;
276
+ if (!spectrum.shiftOffsetVal) {
277
+ spectrum.shiftOffsetVal = Number(dataValue);
278
+ }
279
+ }
280
+ else if (canonicDataLabel === '$REFERENCEPOINT') {
281
+ // OFFSET for Varian spectra
282
+ // if we activate this part it does not work for ACD specmanager
283
+ // } else if (canonicDataLabel=='.SHIFTREFERENCE') { // OFFSET FOR Bruker Spectra
284
+ // var parts = dataValue.split(/ *, */);
285
+ // currentEntry.shiftOffsetNum = parseInt(parts[2].trim());
286
+ // spectrum.shiftOffsetVal = Number(parts[3].trim());
287
+ }
288
+ else if (canonicDataLabel === 'VARNAME') {
289
+ currentEntry.ntuples.varname = dataValue.split(ntuplesSeparatorRegExp);
290
+ }
291
+ else if (canonicDataLabel === 'SYMBOL') {
292
+ currentEntry.ntuples.symbol = dataValue.split(ntuplesSeparatorRegExp);
293
+ }
294
+ else if (canonicDataLabel === 'VARTYPE') {
295
+ currentEntry.ntuples.vartype = dataValue.split(ntuplesSeparatorRegExp);
296
+ }
297
+ else if (canonicDataLabel === 'VARFORM') {
298
+ currentEntry.ntuples.varform = dataValue.split(ntuplesSeparatorRegExp);
299
+ }
300
+ else if (canonicDataLabel === 'VARDIM') {
301
+ currentEntry.ntuples.vardim = (0, convertToFloatArray_1.default)(dataValue.split(ntuplesSeparatorRegExp));
302
+ }
303
+ else if (canonicDataLabel === 'UNITS') {
304
+ currentEntry.ntuples.units = dataValue.split(ntuplesSeparatorRegExp);
305
+ }
306
+ else if (canonicDataLabel === 'FACTOR') {
307
+ currentEntry.ntuples.factor = (0, convertToFloatArray_1.default)(dataValue.split(ntuplesSeparatorRegExp));
308
+ }
309
+ else if (canonicDataLabel === 'FIRST') {
310
+ currentEntry.ntuples.first = (0, convertToFloatArray_1.default)(dataValue.split(ntuplesSeparatorRegExp));
311
+ }
312
+ else if (canonicDataLabel === 'LAST') {
313
+ currentEntry.ntuples.last = (0, convertToFloatArray_1.default)(dataValue.split(ntuplesSeparatorRegExp));
314
+ }
315
+ else if (canonicDataLabel === 'MIN') {
316
+ currentEntry.ntuples.min = (0, convertToFloatArray_1.default)(dataValue.split(ntuplesSeparatorRegExp));
317
+ }
318
+ else if (canonicDataLabel === 'MAX') {
319
+ currentEntry.ntuples.max = (0, convertToFloatArray_1.default)(dataValue.split(ntuplesSeparatorRegExp));
320
+ }
321
+ else if (canonicDataLabel === '.NUCLEUS') {
322
+ if (currentEntry.ntuples) {
323
+ currentEntry.ntuples.nucleus = dataValue.split(ntuplesSeparatorRegExp);
324
+ }
325
+ }
326
+ else if (canonicDataLabel === 'PAGE') {
327
+ spectrum.page = dataValue.trim();
328
+ spectrum.pageValue = Number(dataValue.replace(/^.*=/, ''));
329
+ spectrum.pageSymbol = spectrum.page.replace(/[=].*/, '');
330
+ }
331
+ else if (canonicDataLabel === 'RETENTIONTIME') {
332
+ spectrum.pageValue = Number(dataValue);
333
+ }
334
+ else if ((0, complexChromatogram_1.isMSField)(canonicDataLabel)) {
335
+ spectrum[(0, complexChromatogram_1.convertMSFieldToLabel)(canonicDataLabel)] = dataValue;
336
+ }
337
+ else if (canonicDataLabel === 'SAMPLEDESCRIPTION') {
338
+ spectrum.sampleDescription = dataValue;
339
+ }
340
+ else if (canonicDataLabel.startsWith('$NUC')) {
341
+ if (!currentEntry.tmp[canonicDataLabel] && !dataValue.includes('off')) {
342
+ currentEntry.tmp[canonicDataLabel] = dataValue.replace(/[<>]/g, '');
343
+ }
344
+ }
345
+ else if (canonicDataLabel === 'END') {
346
+ currentEntry = parentsStack.pop();
347
+ }
348
+ if (currentEntry &&
349
+ currentEntry.info &&
350
+ currentEntry.meta &&
351
+ canonicDataLabel.match(options.keepRecordsRegExp)) {
352
+ let value = dataValue.trim();
353
+ let target, label;
354
+ if (dataLabel.startsWith('$')) {
355
+ label = options.canonicMetadataLabels
356
+ ? canonicDataLabel.substring(1)
357
+ : dataLabel.substring(1);
358
+ target = currentEntry.meta;
359
+ }
360
+ else {
361
+ label = options.canonicDataLabels ? canonicDataLabel : dataLabel;
362
+ target = currentEntry.info;
363
+ }
364
+ if (options.dynamicTyping) {
365
+ value = (0, dynamic_typing_1.parseString)(value);
366
+ }
367
+ if (target[label]) {
368
+ if (!Array.isArray(target[label])) {
369
+ target[label] = [target[label]];
370
+ }
371
+ target[label].push(value);
372
+ }
373
+ else {
374
+ target[label] = value;
375
+ }
376
+ }
377
+ }
378
+ (0, profiling_1.default)(result, 'Finished parsing', options);
379
+ (0, postProcessing_1.default)(entriesFlat, result, options);
380
+ (0, profiling_1.default)(result, 'Total time', options);
381
+ /*
382
+ if (result.children && result.children.length>0) {
383
+ result = { ...result, ...result.children[0] };
384
+ }
385
+ */
386
+ result.entries = tmpResult.children;
387
+ result.flatten = entriesFlat;
388
+ return result;
389
+ }
390
+ exports.convert = convert;
391
+ //# sourceMappingURL=convert.js.map
@@ -0,0 +1 @@
1
+ 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@@ -0,0 +1,2 @@
1
+ export default function convertToFloatArray(stringArray: any): number[];
2
+ //# sourceMappingURL=convertToFloatArray.d.ts.map
@@ -0,0 +1 @@
1
+ {"version":3,"file":"convertToFloatArray.d.ts","sourceRoot":"","sources":["../src/convertToFloatArray.js"],"names":[],"mappings":"AAAA,wEAMC"}
@@ -0,0 +1,11 @@
1
+ "use strict";
2
+ Object.defineProperty(exports, "__esModule", { value: true });
3
+ function convertToFloatArray(stringArray) {
4
+ let floatArray = [];
5
+ for (let i = 0; i < stringArray.length; i++) {
6
+ floatArray.push(Number(stringArray[i]));
7
+ }
8
+ return floatArray;
9
+ }
10
+ exports.default = convertToFloatArray;
11
+ //# sourceMappingURL=convertToFloatArray.js.map
@@ -0,0 +1 @@
1
+ {"version":3,"file":"convertToFloatArray.js","sourceRoot":"","sources":["../src/convertToFloatArray.js"],"names":[],"mappings":";;AAAA,SAAwB,mBAAmB,CAAC,WAAW;IACrD,IAAI,UAAU,GAAG,EAAE,CAAC;IACpB,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,WAAW,CAAC,MAAM,EAAE,CAAC,EAAE,EAAE;QAC3C,UAAU,CAAC,IAAI,CAAC,MAAM,CAAC,WAAW,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC;KACzC;IACD,OAAO,UAAU,CAAC;AACpB,CAAC;AAND,sCAMC"}
@@ -0,0 +1,29 @@
1
+ /**
2
+ *
3
+ * @typedef {object} CreateTreeOptions
4
+ * @property {boolean} [flatten=false]
5
+ */
6
+ /**
7
+ *
8
+ * @typedef {object} Tree
9
+ * @property {string} title
10
+ * @property {string} jcamp
11
+ * @property {Tree[]} [children]
12
+ */
13
+ /**
14
+ * Parse the jcamp to extract the structure as a tree.
15
+ *
16
+ * @param {string|ArrayBuffer|Uint8Array} jcamp
17
+ * @param {CreateTreeOptions} [options={}]
18
+ * @returns {Tree[]}
19
+ */
20
+ export function createTree(jcamp: string | ArrayBuffer | Uint8Array, options?: CreateTreeOptions | undefined): Tree[];
21
+ export type CreateTreeOptions = {
22
+ flatten?: boolean | undefined;
23
+ };
24
+ export type Tree = {
25
+ title: string;
26
+ jcamp: string;
27
+ children?: Tree[] | undefined;
28
+ };
29
+ //# sourceMappingURL=createTree.d.ts.map
@@ -0,0 +1 @@
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+ {"version":3,"file":"createTree.d.ts","sourceRoot":"","sources":["../src/createTree.js"],"names":[],"mappings":"AAEA;;;;GAIG;AAEH;;;;;;GAMG;AAEH;;;;;;GAMG;AACH,kCAJW,MAAM,GAAC,WAAW,GAAC,UAAU,4CAE3B,IAAI,EAAE,CA2ElB;;;;;WArFa,MAAM;WACN,MAAM"}
@@ -0,0 +1,98 @@
1
+ "use strict";
2
+ Object.defineProperty(exports, "__esModule", { value: true });
3
+ exports.createTree = void 0;
4
+ const ensure_string_1 = require("ensure-string");
5
+ /**
6
+ *
7
+ * @typedef {object} CreateTreeOptions
8
+ * @property {boolean} [flatten=false]
9
+ */
10
+ /**
11
+ *
12
+ * @typedef {object} Tree
13
+ * @property {string} title
14
+ * @property {string} jcamp
15
+ * @property {Tree[]} [children]
16
+ */
17
+ /**
18
+ * Parse the jcamp to extract the structure as a tree.
19
+ *
20
+ * @param {string|ArrayBuffer|Uint8Array} jcamp
21
+ * @param {CreateTreeOptions} [options={}]
22
+ * @returns {Tree[]}
23
+ */
24
+ function createTree(jcamp, options = {}) {
25
+ jcamp = (0, ensure_string_1.ensureString)(jcamp);
26
+ const { flatten = false } = options;
27
+ if (typeof jcamp !== 'string') {
28
+ throw new TypeError('the JCAMP should be a string');
29
+ }
30
+ let lines = jcamp.split(/[\r\n]+/);
31
+ let flat = [];
32
+ let stack = [];
33
+ let result = [];
34
+ let current;
35
+ let ntupleLevel = 0;
36
+ let spaces = jcamp.includes('## ');
37
+ for (let i = 0; i < lines.length; i++) {
38
+ let line = lines[i];
39
+ let labelLine = spaces ? line.replace(/ /g, '') : line;
40
+ if (labelLine.substring(0, 9) === '##NTUPLES') {
41
+ ntupleLevel++;
42
+ }
43
+ if (labelLine.substring(0, 7) === '##TITLE') {
44
+ let title = [labelLine.substring(8).trim()];
45
+ for (let j = i + 1; j < lines.length; j++) {
46
+ if (lines[j].startsWith('##')) {
47
+ break;
48
+ }
49
+ else {
50
+ title.push(lines[j].trim());
51
+ }
52
+ }
53
+ stack.push({
54
+ title: title.join('\n'),
55
+ jcamp: `${line}\n`,
56
+ children: [],
57
+ });
58
+ current = stack[stack.length - 1];
59
+ flat.push(current);
60
+ }
61
+ else if (labelLine.substring(0, 5) === '##END' && ntupleLevel === 0) {
62
+ current.jcamp += `${line}\n`;
63
+ let finished = stack.pop();
64
+ if (stack.length !== 0) {
65
+ current = stack[stack.length - 1];
66
+ current.children.push(finished);
67
+ }
68
+ else {
69
+ current = undefined;
70
+ result.push(finished);
71
+ }
72
+ }
73
+ else if (current && current.jcamp) {
74
+ current.jcamp += `${line}\n`;
75
+ let match = labelLine.match(/^##(.*?)=(.+)/);
76
+ if (match) {
77
+ let canonicDataLabel = match[1].replace(/[ _-]/g, '').toUpperCase();
78
+ if (canonicDataLabel === 'DATATYPE') {
79
+ current.dataType = match[2].trim();
80
+ }
81
+ }
82
+ }
83
+ if (labelLine.substring(0, 5) === '##END' && ntupleLevel > 0) {
84
+ ntupleLevel--;
85
+ }
86
+ }
87
+ if (flatten) {
88
+ flat.forEach((entry) => {
89
+ entry.children = undefined;
90
+ });
91
+ return flat;
92
+ }
93
+ else {
94
+ return result;
95
+ }
96
+ }
97
+ exports.createTree = createTree;
98
+ //# sourceMappingURL=createTree.js.map
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+ {"version":3,"file":"createTree.js","sourceRoot":"","sources":["../src/createTree.js"],"names":[],"mappings":";;;AAAA,iDAA6C;AAE7C;;;;GAIG;AAEH;;;;;;GAMG;AAEH;;;;;;GAMG;AACH,SAAgB,UAAU,CAAC,KAAK,EAAE,OAAO,GAAG,EAAE;IAC5C,KAAK,GAAG,IAAA,4BAAY,EAAC,KAAK,CAAC,CAAC;IAC5B,MAAM,EAAE,OAAO,GAAG,KAAK,EAAE,GAAG,OAAO,CAAC;IACpC,IAAI,OAAO,KAAK,KAAK,QAAQ,EAAE;QAC7B,MAAM,IAAI,SAAS,CAAC,8BAA8B,CAAC,CAAC;KACrD;IAED,IAAI,KAAK,GAAG,KAAK,CAAC,KAAK,CAAC,SAAS,CAAC,CAAC;IACnC,IAAI,IAAI,GAAG,EAAE,CAAC;IACd,IAAI,KAAK,GAAG,EAAE,CAAC;IACf,IAAI,MAAM,GAAG,EAAE,CAAC;IAChB,IAAI,OAAO,CAAC;IACZ,IAAI,WAAW,GAAG,CAAC,CAAC;IAEpB,IAAI,MAAM,GAAG,KAAK,CAAC,QAAQ,CAAC,KAAK,CAAC,CAAC;IAEnC,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,KAAK,CAAC,MAAM,EAAE,CAAC,EAAE,EAAE;QACrC,IAAI,IAAI,GAAG,KAAK,CAAC,CAAC,CAAC,CAAC;QACpB,IAAI,SAAS,GAAG,MAAM,CAAC,CAAC,CAAC,IAAI,CAAC,OAAO,CAAC,IAAI,EAAE,EAAE,CAAC,CAAC,CAAC,CAAC,IAAI,CAAC;QAEvD,IAAI,SAAS,CAAC,SAAS,CAAC,CAAC,EAAE,CAAC,CAAC,KAAK,WAAW,EAAE;YAC7C,WAAW,EAAE,CAAC;SACf;QAED,IAAI,SAAS,CAAC,SAAS,CAAC,CAAC,EAAE,CAAC,CAAC,KAAK,SAAS,EAAE;YAC3C,IAAI,KAAK,GAAG,CAAC,SAAS,CAAC,SAAS,CAAC,CAAC,CAAC,CAAC,IAAI,EAAE,CAAC,CAAC;YAC5C,KAAK,IAAI,CAAC,GAAG,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,KAAK,CAAC,MAAM,EAAE,CAAC,EAAE,EAAE;gBACzC,IAAI,KAAK,CAAC,CAAC,CAAC,CAAC,UAAU,CAAC,IAAI,CAAC,EAAE;oBAC7B,MAAM;iBACP;qBAAM;oBACL,KAAK,CAAC,IAAI,CAAC,KAAK,CAAC,CAAC,CAAC,CAAC,IAAI,EAAE,CAAC,CAAC;iBAC7B;aACF;YACD,KAAK,CAAC,IAAI,CAAC;gBACT,KAAK,EAAE,KAAK,CAAC,IAAI,CAAC,IAAI,CAAC;gBACvB,KAAK,EAAE,GAAG,IAAI,IAAI;gBAClB,QAAQ,EAAE,EAAE;aACb,CAAC,CAAC;YACH,OAAO,GAAG,KAAK,CAAC,KAAK,CAAC,MAAM,GAAG,CAAC,CAAC,CAAC;YAClC,IAAI,CAAC,IAAI,CAAC,OAAO,CAAC,CAAC;SACpB;aAAM,IAAI,SAAS,CAAC,SAAS,CAAC,CAAC,EAAE,CAAC,CAAC,KAAK,OAAO,IAAI,WAAW,KAAK,CAAC,EAAE;YACrE,OAAO,CAAC,KAAK,IAAI,GAAG,IAAI,IAAI,CAAC;YAC7B,IAAI,QAAQ,GAAG,KAAK,CAAC,GAAG,EAAE,CAAC;YAC3B,IAAI,KAAK,CAAC,MAAM,KAAK,CAAC,EAAE;gBACtB,OAAO,GAAG,KAAK,CAAC,KAAK,CAAC,MAAM,GAAG,CAAC,CAAC,CAAC;gBAClC,OAAO,CAAC,QAAQ,CAAC,IAAI,CAAC,QAAQ,CAAC,CAAC;aACjC;iBAAM;gBACL,OAAO,GAAG,SAAS,CAAC;gBACpB,MAAM,CAAC,IAAI,CAAC,QAAQ,CAAC,CAAC;aACvB;SACF;aAAM,IAAI,OAAO,IAAI,OAAO,CAAC,KAAK,EAAE;YACnC,OAAO,CAAC,KAAK,IAAI,GAAG,IAAI,IAAI,CAAC;YAC7B,IAAI,KAAK,GAAG,SAAS,CAAC,KAAK,CAAC,eAAe,CAAC,CAAC;YAC7C,IAAI,KAAK,EAAE;gBACT,IAAI,gBAAgB,GAAG,KAAK,CAAC,CAAC,CAAC,CAAC,OAAO,CAAC,QAAQ,EAAE,EAAE,CAAC,CAAC,WAAW,EAAE,CAAC;gBACpE,IAAI,gBAAgB,KAAK,UAAU,EAAE;oBACnC,OAAO,CAAC,QAAQ,GAAG,KAAK,CAAC,CAAC,CAAC,CAAC,IAAI,EAAE,CAAC;iBACpC;aACF;SACF;QAED,IAAI,SAAS,CAAC,SAAS,CAAC,CAAC,EAAE,CAAC,CAAC,KAAK,OAAO,IAAI,WAAW,GAAG,CAAC,EAAE;YAC5D,WAAW,EAAE,CAAC;SACf;KACF;IACD,IAAI,OAAO,EAAE;QACX,IAAI,CAAC,OAAO,CAAC,CAAC,KAAK,EAAE,EAAE;YACrB,KAAK,CAAC,QAAQ,GAAG,SAAS,CAAC;QAC7B,CAAC,CAAC,CAAC;QACH,OAAO,IAAI,CAAC;KACb;SAAM;QACL,OAAO,MAAM,CAAC;KACf;AACH,CAAC;AAzED,gCAyEC"}
package/lib/index.d.ts ADDED
@@ -0,0 +1,3 @@
1
+ export { createTree } from "./createTree";
2
+ export { convert } from "./convert";
3
+ //# sourceMappingURL=index.d.ts.map
@@ -0,0 +1 @@
1
+ {"version":3,"file":"index.d.ts","sourceRoot":"","sources":["../src/index.js"],"names":[],"mappings":""}