nmr-processing 7.4.3 → 8.2.0
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.
- package/lib/assignment/getAssignments.js +1 -1
- package/lib/assignment/getAssignments.js.map +1 -1
- package/lib/assignment/utils/getAssignment/checkIDs.d.ts +1 -1
- package/lib/assignment/utils/getAssignment/checkIDs.js.map +1 -1
- package/lib/databases/getDatabase.d.ts +6 -1
- package/lib/databases/getDatabase.js +13 -3
- package/lib/databases/getDatabase.js.map +1 -1
- package/lib/index.d.ts +4 -2
- package/lib/index.js +3 -1
- package/lib/index.js.map +1 -1
- package/lib/peaks/NMRPeak1D.d.ts +0 -1
- package/lib/peaks/peaksToRanges.d.ts +16 -0
- package/lib/peaks/peaksToRanges.js +2 -1
- package/lib/peaks/peaksToRanges.js.map +1 -1
- package/lib/peaks/solventSuppression.d.ts +3 -0
- package/lib/peaks/solventSuppression.js +155 -0
- package/lib/peaks/solventSuppression.js.map +1 -0
- package/lib/peaks/util/jAnalyzer.d.ts +1 -1
- package/lib/peaks/util/jAnalyzer.js +3 -2
- package/lib/peaks/util/jAnalyzer.js.map +1 -1
- package/lib/prediction/predictAllSpectra.d.ts +22 -4
- package/lib/prediction/predictAllSpectra.js +102 -16
- package/lib/prediction/predictAllSpectra.js.map +1 -1
- package/lib/ranges/markSolventSignal.d.ts +3 -0
- package/lib/ranges/markSolventSignal.js +107 -0
- package/lib/ranges/markSolventSignal.js.map +1 -0
- package/lib/ranges/rangesToXY.js +27 -3
- package/lib/ranges/rangesToXY.js.map +1 -1
- package/lib/signals/addDummySignals.d.ts +2 -0
- package/lib/signals/addDummySignals.js +56 -0
- package/lib/signals/addDummySignals.js.map +1 -0
- package/lib/signals/hackSignalsToXY.js +2 -48
- package/lib/signals/hackSignalsToXY.js.map +1 -1
- package/lib/signals/simulation/simulate1D.d.ts +1 -39
- package/lib/signals/simulation/simulate1D.js +13 -240
- package/lib/signals/simulation/simulate1D.js.map +1 -1
- package/lib/signals/simulation/simulateXYPeaks.d.ts +47 -0
- package/lib/signals/simulation/simulateXYPeaks.js +246 -0
- package/lib/signals/simulation/simulateXYPeaks.js.map +1 -0
- package/lib/utilities/getFrequency.d.ts +1 -1
- package/lib/utilities/getFrequency.js +4 -4
- package/lib/utilities/getFrequency.js.map +1 -1
- package/lib/xyz/NMRSignal2D.d.ts +3 -3
- package/lib/xyz/util/formatZone.d.ts +3 -0
- package/lib/xyz/util/formatZone.js +38 -0
- package/lib/xyz/util/formatZone.js.map +1 -0
- package/lib/xyz/xyzAutoZonesPicking.d.ts +1 -2
- package/lib/xyz/xyzAutoZonesPicking.js +2 -34
- package/lib/xyz/xyzAutoZonesPicking.js.map +1 -1
- package/lib/xyz/xyzJResAnalyzer.d.ts +6 -1
- package/lib/xyz/xyzJResAnalyzer.js +9 -8
- package/lib/xyz/xyzJResAnalyzer.js.map +1 -1
- package/lib-esm/assignment/getAssignments.js +1 -1
- package/lib-esm/assignment/getAssignments.js.map +1 -1
- package/lib-esm/assignment/utils/getAssignment/checkIDs.js.map +1 -1
- package/lib-esm/databases/getDatabase.js +13 -3
- package/lib-esm/databases/getDatabase.js.map +1 -1
- package/lib-esm/index.js +3 -1
- package/lib-esm/index.js.map +1 -1
- package/lib-esm/peaks/peaksToRanges.js +1 -1
- package/lib-esm/peaks/peaksToRanges.js.map +1 -1
- package/lib-esm/peaks/solventSuppression.js +151 -0
- package/lib-esm/peaks/solventSuppression.js.map +1 -0
- package/lib-esm/peaks/util/jAnalyzer.js +3 -2
- package/lib-esm/peaks/util/jAnalyzer.js.map +1 -1
- package/lib-esm/prediction/predictAllSpectra.js +102 -16
- package/lib-esm/prediction/predictAllSpectra.js.map +1 -1
- package/lib-esm/ranges/markSolventSignal.js +100 -0
- package/lib-esm/ranges/markSolventSignal.js.map +1 -0
- package/lib-esm/ranges/rangesToXY.js +27 -3
- package/lib-esm/ranges/rangesToXY.js.map +1 -1
- package/lib-esm/signals/addDummySignals.js +52 -0
- package/lib-esm/signals/addDummySignals.js.map +1 -0
- package/lib-esm/signals/hackSignalsToXY.js +2 -48
- package/lib-esm/signals/hackSignalsToXY.js.map +1 -1
- package/lib-esm/signals/simulation/simulate1D.js +14 -238
- package/lib-esm/signals/simulation/simulate1D.js.map +1 -1
- package/lib-esm/signals/simulation/simulateXYPeaks.js +239 -0
- package/lib-esm/signals/simulation/simulateXYPeaks.js.map +1 -0
- package/lib-esm/utilities/getFrequency.js +1 -1
- package/lib-esm/utilities/getFrequency.js.map +1 -1
- package/lib-esm/xyz/util/formatZone.js +34 -0
- package/lib-esm/xyz/util/formatZone.js.map +1 -0
- package/lib-esm/xyz/xyzAutoZonesPicking.js +1 -33
- package/lib-esm/xyz/xyzAutoZonesPicking.js.map +1 -1
- package/lib-esm/xyz/xyzJResAnalyzer.js +9 -8
- package/lib-esm/xyz/xyzJResAnalyzer.js.map +1 -1
- package/package.json +14 -12
- package/src/assignment/getAssignments.ts +1 -1
- package/src/assignment/utils/getAssignment/checkIDs.ts +1 -1
- package/src/databases/getDatabase.ts +19 -2
- package/src/index.ts +5 -2
- package/src/peaks/NMRPeak1D.ts +0 -1
- package/src/peaks/peaksToRanges.ts +1 -1
- package/src/peaks/solventSuppression.ts +209 -0
- package/src/peaks/util/jAnalyzer.ts +5 -3
- package/src/prediction/predictAllSpectra.ts +151 -14
- package/src/ranges/markSolventSignal.ts +121 -0
- package/src/ranges/rangesToXY.ts +33 -4
- package/src/signals/addDummySignals.ts +77 -0
- package/src/signals/hackSignalsToXY.ts +2 -72
- package/src/signals/simulation/simulate1D.ts +14 -319
- package/src/signals/simulation/simulateXYPeaks.ts +332 -0
- package/src/utilities/getFrequency.ts +1 -1
- package/src/xyz/NMRSignal2D.ts +3 -3
- package/src/xyz/util/formatZone.ts +36 -0
- package/src/xyz/xyzAutoZonesPicking.ts +1 -35
- package/src/xyz/xyzJResAnalyzer.ts +14 -7
- package/lib/constants/gyromagneticRatio.d.ts +0 -6
- package/lib/constants/gyromagneticRatio.js +0 -26
- package/lib/constants/gyromagneticRatio.js.map +0 -1
- package/lib-esm/constants/gyromagneticRatio.js +0 -23
- package/lib-esm/constants/gyromagneticRatio.js.map +0 -1
- package/src/constants/gyromagneticRatio.ts +0 -49
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+
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@@ -1,24 +1,25 @@
|
|
|
1
1
|
import simpleClustering from 'ml-simple-clustering';
|
|
2
2
|
import jAnalyzer from '../peaks/util/jAnalyzer';
|
|
3
|
+
import { formatZones } from './util/formatZone';
|
|
3
4
|
export function xyzJResAnalyzer(signals, options = {}) {
|
|
4
|
-
let { reference = 0, referenceMaxShiftError = 0.08, tolerances = [10, 100], nuclei = ['1H', '1H'], observedFrequencies = [400, 400], jAnalyzer = {
|
|
5
|
+
let { reference = 0, getZones = false, referenceMaxShiftError = 0.08, tolerances = [10, 100], nuclei = ['1H', '1H'], observedFrequencies = [400, 400], jAnalyzer = {
|
|
5
6
|
jAxisKey: { jAxis: 'y', intensity: 'z' },
|
|
6
7
|
}, } = options;
|
|
7
|
-
let temporalSignals = compilePattern(signals, {
|
|
8
|
+
let temporalSignals = compilePattern([...signals], {
|
|
8
9
|
observedFrequencies,
|
|
9
10
|
tolerances,
|
|
10
11
|
nuclei,
|
|
11
12
|
jAnalyzer,
|
|
12
13
|
});
|
|
13
14
|
//check if the signal are symmetric around the reference
|
|
14
|
-
let
|
|
15
|
+
let signals2D = [];
|
|
15
16
|
for (const tempSignal of temporalSignals) {
|
|
16
17
|
let delta = tempSignal.y.delta;
|
|
17
18
|
if (Math.abs(delta - reference) > referenceMaxShiftError)
|
|
18
19
|
continue;
|
|
19
|
-
|
|
20
|
+
signals2D.push(tempSignal);
|
|
20
21
|
}
|
|
21
|
-
return
|
|
22
|
+
return getZones ? formatZones(signals2D) : signals2D;
|
|
22
23
|
}
|
|
23
24
|
function compilePattern(signals, options) {
|
|
24
25
|
let { observedFrequencies, tolerances, nuclei, jAnalyzer: jAnalyzerOptions, } = options;
|
|
@@ -67,9 +68,9 @@ function compilePattern(signals, options) {
|
|
|
67
68
|
}
|
|
68
69
|
if (peaksO.length > 0) {
|
|
69
70
|
peaksO.reverse();
|
|
70
|
-
let
|
|
71
|
-
for (const
|
|
72
|
-
newSignals.push(
|
|
71
|
+
let signals2D = createSignals2D(peaksO, signalOptions);
|
|
72
|
+
for (const signal of signals2D) {
|
|
73
|
+
newSignals.push(signal);
|
|
73
74
|
}
|
|
74
75
|
}
|
|
75
76
|
}
|
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"xyzJResAnalyzer.js","sourceRoot":"","sources":["../../src/xyz/xyzJResAnalyzer.ts"],"names":[],"mappings":"AACA,OAAO,gBAAgB,MAAM,sBAAsB,CAAC;AAGpD,OAAO,SAAS,MAAM,yBAAyB,CAAC;
|
|
1
|
+
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AAC,CAAC;YACb,KAAK,IAAI,KAAK,GAAG,OAAO,CAAC,MAAM,GAAG,CAAC,EAAE,KAAK,IAAI,CAAC,EAAE,KAAK,EAAE,EAAE;gBACxD,IAAI,OAAO,CAAC,KAAK,CAAC,KAAK,CAAC,EAAE;oBACxB,MAAM,CAAC,OAAO,EAAE,CAAC;oBACjB,IAAI,CAAC,KAAK,CAAC,KAAK,CAAC,CAAC,KAAK;wBAAE,KAAK,CAAC,KAAK,CAAC,CAAC,KAAK,GAAG,IAAI,CAAC;oBACnD,OAAO,CAAC,IAAI,CAAC,KAAK,CAAC,KAAK,CAAC,CAAC,CAAC;oBAC3B,MAAM,CAAC,MAAM,IAAI,KAAK,CAAC,KAAK,CAAC,CAAC,CAAC,GAAG,KAAK,CAAC,KAAK,CAAC,CAAC,CAAC,CAAC;oBACjD,MAAM,CAAC,MAAM,IAAI,KAAK,CAAC,KAAK,CAAC,CAAC,CAAC,GAAG,KAAK,CAAC,KAAK,CAAC,CAAC,CAAC,CAAC;oBACjD,IAAI,IAAI,KAAK,CAAC,KAAK,CAAC,CAAC,CAAC,CAAC;oBACvB,IAAI,KAAK,CAAC,KAAK,CAAC,CAAC,IAAI,GAAG,OAAO,CAAC,CAAC,CAAC,EAAE;wBAClC,OAAO,CAAC,CAAC,CAAC,GAAG,KAAK,CAAC,KAAK,CAAC,CAAC,IAAI,CAAC;qBAChC;oBACD,IAAI,KAAK,CAAC,KAAK,CAAC,CAAC,IAAI,GAAG,OAAO,CAAC,CAAC,CAAC,EAAE;wBAClC,OAAO,CAAC,CAAC,CAAC,GAAG,KAAK,CAAC,KAAK,CAAC,CAAC,IAAI,CAAC;qBAChC;oBACD,IAAI,KAAK,CAAC,KAAK,CAAC,CAAC,IAAI,GAAG,OAAO,CAAC,CAAC,CAAC,EAAE;wBAClC,OAAO,CAAC,CAAC,CAAC,GAAG,KAAK,CAAC,KAAK,CAAC,CAAC,IAAI,CAAC;qBAChC;oBACD,IAAI,KAAK,CAAC,KAAK,CAAC,CAAC,IAAI,GAAG,OAAO,CAAC,CAAC,CAAC,EAAE;wBAClC,OAAO,CAAC,CAAC,CAAC,GAAG,KAAK,CAAC,KAAK,CAAC,CAAC,IAAI,CAAC;qBAChC;iBACF;aACF;YAED,MAAM,CAAC,MAAM,GAAG;gBACd,EAAE,IAAI,EAAE,OAAO,CAAC,CAAC,CAAC,EAAE,EAAE,EAAE,OAAO,CAAC,CAAC,CAAC,EAAE;gBACpC,EAAE,IAAI,EAAE,OAAO,CAAC,CAAC,CAAC,EAAE,EAAE,EAAE,OAAO,CAAC,CAAC,CAAC,EAAE;aACrC,CAAC;YACF,MAAM,CAAC,MAAM,IAAI,IAAI,CAAC;YACtB,MAAM,CAAC,MAAM,IAAI,IAAI,CAAC;YACtB,MAAM,CAAC,MAAM,GAAG,MAAM,CAAC,MAAM,CAAC;YAC9B,MAAM,CAAC,KAAK,GAAG,OAAO,CAAC;YACvB,OAAO,CAAC,IAAI,CAAC,MAAsB,CAAC,CAAC;SACtC;KACF;IACD,OAAO,OAAO,CAAC;AACjB,CAAC"}
|
package/package.json
CHANGED
|
@@ -1,6 +1,6 @@
|
|
|
1
1
|
{
|
|
2
2
|
"name": "nmr-processing",
|
|
3
|
-
"version": "
|
|
3
|
+
"version": "8.2.0",
|
|
4
4
|
"description": "Pure functions allowing to process NMR spectra.",
|
|
5
5
|
"main": "./lib/index.js",
|
|
6
6
|
"module": "./lib-esm/index.js",
|
|
@@ -38,44 +38,46 @@
|
|
|
38
38
|
},
|
|
39
39
|
"homepage": "https://github.com/cheminfo/nmr-processing#readme",
|
|
40
40
|
"devDependencies": {
|
|
41
|
-
"@types/jest": "^27.
|
|
41
|
+
"@types/jest": "^27.5.0",
|
|
42
42
|
"cheminfo-build": "^1.1.11",
|
|
43
43
|
"cheminfo-types": "^1.1.0",
|
|
44
|
-
"eslint": "^8.
|
|
44
|
+
"eslint": "^8.14.0",
|
|
45
45
|
"eslint-config-cheminfo-typescript": "^10.4.0",
|
|
46
|
-
"jest": "^
|
|
46
|
+
"jest": "^28.0.3",
|
|
47
47
|
"jest-matcher-deep-close-to": "^3.0.2",
|
|
48
48
|
"md5": "^2.3.0",
|
|
49
49
|
"ml-array-median": "^1.1.6",
|
|
50
50
|
"nmr-xy-testdata": "^0.5.1",
|
|
51
51
|
"openchemlib": "^7.4.3",
|
|
52
|
-
"prettier": "^2.6.
|
|
52
|
+
"prettier": "^2.6.2",
|
|
53
53
|
"rimraf": "^3.0.2",
|
|
54
|
-
"ts-jest": "^
|
|
55
|
-
"typescript": "^4.6.
|
|
54
|
+
"ts-jest": "^28.0.1",
|
|
55
|
+
"typescript": "^4.6.4"
|
|
56
56
|
},
|
|
57
57
|
"dependencies": {
|
|
58
58
|
"binary-search": "^1.3.6",
|
|
59
59
|
"cross-fetch": "^3.1.5",
|
|
60
60
|
"form-data": "^4.0.0",
|
|
61
|
+
"gyromagnetic-ratio": "^1.0.0",
|
|
61
62
|
"is-any-array": "^2.0.0",
|
|
63
|
+
"linear-sum-assignment": "^1.0.4",
|
|
62
64
|
"ml-array-mean": "^1.1.6",
|
|
63
65
|
"ml-array-rescale": "^1.3.7",
|
|
64
66
|
"ml-array-sequential-fill": "^1.1.8",
|
|
65
67
|
"ml-array-sum": "^1.1.6",
|
|
66
|
-
"ml-gsd": "^
|
|
68
|
+
"ml-gsd": "^11.2.0",
|
|
67
69
|
"ml-hclust": "^3.1.0",
|
|
68
70
|
"ml-levenberg-marquardt": "^4.1.0",
|
|
69
|
-
"ml-matrix": "^6.
|
|
71
|
+
"ml-matrix": "^6.10.0",
|
|
70
72
|
"ml-matrix-convolution": "^1.0.0",
|
|
71
73
|
"ml-matrix-peaks-finder": "^1.0.0",
|
|
72
74
|
"ml-peak-shape-generator": "^4.1.1",
|
|
73
75
|
"ml-simple-clustering": "^0.1.0",
|
|
74
76
|
"ml-sparse-matrix": "^2.1.0",
|
|
75
|
-
"ml-spectra-processing": "^11.
|
|
77
|
+
"ml-spectra-processing": "^11.5.0",
|
|
76
78
|
"ml-tree-set": "^0.1.1",
|
|
77
79
|
"nmr-correlation": "^2.2.5",
|
|
78
|
-
"openchemlib-utils": "^1.
|
|
79
|
-
"spectrum-generator": "^8.0.
|
|
80
|
+
"openchemlib-utils": "^1.11.0",
|
|
81
|
+
"spectrum-generator": "^8.0.2"
|
|
80
82
|
}
|
|
81
83
|
}
|
|
@@ -42,7 +42,7 @@ export function hasIDs(
|
|
|
42
42
|
}
|
|
43
43
|
}
|
|
44
44
|
|
|
45
|
-
export function addIDs
|
|
45
|
+
export function addIDs<T extends NMRRange[] | NMRZone[]>(data: T) {
|
|
46
46
|
for (const element of data) {
|
|
47
47
|
if (!element.id) element.id = generateID();
|
|
48
48
|
for (let signal of element.signals || []) {
|
|
@@ -6,16 +6,33 @@ import { DatabaseNMREntry } from './DatabaseNMREntry';
|
|
|
6
6
|
|
|
7
7
|
export async function getDatabase(
|
|
8
8
|
url = 'https://docs.google.com/spreadsheets/d/1uwyq_L38PMRWCcT4If_EhPbHKyY3q_2tpjV8vr5_zh0/edit?usp=sharing',
|
|
9
|
+
options: {
|
|
10
|
+
/**
|
|
11
|
+
* @default 'tsv'
|
|
12
|
+
*/
|
|
13
|
+
format?: 'tsv' | 'json';
|
|
14
|
+
} = {},
|
|
9
15
|
) {
|
|
16
|
+
const { format = 'tsv' } = options;
|
|
17
|
+
|
|
10
18
|
if (url.includes('google.com')) {
|
|
11
19
|
url = `https://googledocs.cheminfo.org/spreadsheets/d/${extractGoogleUUID(
|
|
12
20
|
url,
|
|
13
21
|
)}/export?format=tsv`;
|
|
14
22
|
}
|
|
15
23
|
|
|
24
|
+
let parsed;
|
|
16
25
|
const response = await fetch(url);
|
|
17
|
-
|
|
18
|
-
|
|
26
|
+
switch (format) {
|
|
27
|
+
case 'tsv':
|
|
28
|
+
parsed = parseData(await response.text());
|
|
29
|
+
break;
|
|
30
|
+
case 'json':
|
|
31
|
+
parsed = await response.json();
|
|
32
|
+
break;
|
|
33
|
+
default:
|
|
34
|
+
throw new Error('unknown database format');
|
|
35
|
+
}
|
|
19
36
|
|
|
20
37
|
const results = [];
|
|
21
38
|
|
package/src/index.ts
CHANGED
|
@@ -1,4 +1,4 @@
|
|
|
1
|
-
export * from '
|
|
1
|
+
export * from 'gyromagnetic-ratio';
|
|
2
2
|
export * from './constants/impurities';
|
|
3
3
|
export * from './constants/couplingPatterns';
|
|
4
4
|
|
|
@@ -37,8 +37,11 @@ export * from './databases/getDatabase';
|
|
|
37
37
|
export * from './databases/carbonImpurities';
|
|
38
38
|
export * from './databases/protonImpurities';
|
|
39
39
|
|
|
40
|
+
export * from './peaks/solventSuppression';
|
|
41
|
+
export * from './ranges/markSolventSignal';
|
|
42
|
+
|
|
40
43
|
export type { NMRSignal1D } from './signals/NMRSignal1D';
|
|
41
|
-
export type { NMRSignal2D,
|
|
44
|
+
export type { NMRSignal2D, Signal2DProjection } from './xyz/NMRSignal2D';
|
|
42
45
|
export type { NMRRange } from './xy/NMRRange';
|
|
43
46
|
export type { NMRZone } from './xyz/NMRZone';
|
|
44
47
|
export type { NMRPeak1D } from './peaks/NMRPeak1D';
|
package/src/peaks/NMRPeak1D.ts
CHANGED
|
@@ -0,0 +1,209 @@
|
|
|
1
|
+
import { PointXY } from 'cheminfo-types';
|
|
2
|
+
import { linearSumAssignment } from 'linear-sum-assignment';
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3
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import { Matrix } from 'ml-matrix';
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import { gaussianFct } from 'ml-peak-shape-generator';
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5
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import { xFindClosestIndex, xMaxValue } from 'ml-spectra-processing';
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import { NMRSignal1D } from '../signals/NMRSignal1D';
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import { addDummySignals } from '../signals/addDummySignals';
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import { signalsToSpinSystem } from '../signals/simulation/signalsToSpinSystem';
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import { simulateXYPeaks } from '../signals/simulation/simulateXYPeaks';
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import { splitSpinSystem } from '../signals/simulation/splitSpinSystem';
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import { NMRPeak1D } from './NMRPeak1D';
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export function solventSuppression<T extends NMRPeak1D>(
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peakList: T[],
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solvent: NMRSignal1D[],
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options: any = {},
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) {
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const peaks = [...peakList].sort((a, b) => a.x - b.x);
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const xValues = peaks.map((peak) => peak.x);
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const { markSolventPeaks = false, solventZoneExtension = 1.2 } = options;
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for (const solventSignal of solvent) {
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let solventXYPeaks = solventSignal.peaks
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? solventSignal.peaks
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: getSolventPeaks(solventSignal);
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solventXYPeaks.sort((a, b) => a.x - b.x);
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let upIndex = xFindClosestIndex(
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xValues,
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solventXYPeaks[solventXYPeaks.length - 1].x + solventZoneExtension,
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);
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let lowIndex = xFindClosestIndex(
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xValues,
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solventXYPeaks[0].x - solventZoneExtension,
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);
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if (upIndex === lowIndex) continue;
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const nearPeaks = peaks.slice(lowIndex, upIndex + 1);
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const amplitudeResiduals = [];
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const deltaResiduals = [];
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const positionResiduals = [];
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for (let peak of nearPeaks) {
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const { peaks: shiftedSolventPeaks, delta: currentDelta } =
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getShiftedSolventPeaks(peak, solventSignal, solventXYPeaks);
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const closestPeaks = getClosestPeaks(shiftedSolventPeaks, nearPeaks);
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let deltaResidual = 0;
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let amplitudeResidual = 0;
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let positionResidual = 0;
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for (let i = 0; i < closestPeaks.length; i++) {
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amplitudeResidual += Math.abs(
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shiftedSolventPeaks[i].y - closestPeaks[i].y,
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);
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deltaResidual += Math.abs(shiftedSolventPeaks[i].x - closestPeaks[i].x);
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}
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if (closestPeaks.length === 0) {
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deltaResidual = Number.MAX_SAFE_INTEGER;
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amplitudeResidual = Number.MAX_SAFE_INTEGER;
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positionResidual = Number.MAX_SAFE_INTEGER;
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} else {
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positionResidual = gaussianFct(
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Math.abs(solventSignal.delta - currentDelta),
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0.5,
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);
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}
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amplitudeResiduals.push(amplitudeResidual);
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deltaResiduals.push(deltaResidual);
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positionResiduals.push(positionResidual);
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}
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const maxAmplitude = xMaxValue(amplitudeResiduals);
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const maxDelta = xMaxValue(deltaResiduals);
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const maxPosition = xMaxValue(positionResiduals);
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let minIndex = -1;
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let minScore = Number.MAX_SAFE_INTEGER;
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let score = [];
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for (let i = 0; i < deltaResiduals.length; i++) {
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const value =
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(amplitudeResiduals[i] / maxAmplitude +
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deltaResiduals[i] / maxDelta +
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1 -
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positionResiduals[i] / maxPosition) /
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3;
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score.push(value);
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if (minScore > value) {
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minIndex = i;
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minScore = value;
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}
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}
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if (minScore < 0) {
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new Error('There is not a correct match with the pattern');
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return peaks;
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}
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const { peaks: shiftedSolventPeaks } = getShiftedSolventPeaks(
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nearPeaks[minIndex],
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solventSignal,
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solventXYPeaks,
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);
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const diff = getDiffMatrix(shiftedSolventPeaks, nearPeaks);
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const { rowAssignments, gain } = linearSumAssignment(diff, {
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maximaze: false,
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});
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if (gain < 0) {
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new Error('The gain is below to zero');
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return peaks;
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}
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if (markSolventPeaks) {
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for (let index of rowAssignments) {
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peaks[index + lowIndex].kind = 'solvent';
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}
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} else {
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rowAssignments.sort((a, b) => b - a);
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for (let index of rowAssignments) {
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peaks.splice(index + lowIndex, 1);
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}
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}
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}
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return peaks;
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}
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function getSolventPeaks(
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signal: NMRSignal1D,
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options: { frequency?: number; maxClusterSize?: number } = {},
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) {
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let signals = addDummySignals([signal]);
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let spinSystem = signalsToSpinSystem(signals);
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const { frequency = 400, maxClusterSize = 8 } = options;
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spinSystem.clusters = splitSpinSystem(spinSystem, {
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frequency,
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maxClusterSize,
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});
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const peaks = simulateXYPeaks(spinSystem);
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return peaks.filter((peak) => peak.x < 1000);
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}
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function getShiftedSolventPeaks<T extends PointXY>(
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peak: T,
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solventSignal: any,
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solventXYPeaks: T[],
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) {
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const shiftedSolventPeaks: PointXY[] = JSON.parse(
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JSON.stringify(solventXYPeaks),
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);
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// shift x values of solventPeaks to center it to the current peak.
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let deltaPPM = peak.x - solventSignal.delta;
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if (solventXYPeaks.length > 1 && solventXYPeaks.length % 2 === 0) {
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deltaPPM += solventXYPeaks[0].x;
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}
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const maxIntensity = shiftedSolventPeaks.reduce(
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(max, current) => (current.y > max ? current.y : max),
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shiftedSolventPeaks[0].y,
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);
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let currentDelta = 0;
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for (let shiftedSolventPeak of shiftedSolventPeaks) {
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shiftedSolventPeak.x += deltaPPM;
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shiftedSolventPeak.y /= maxIntensity;
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currentDelta += shiftedSolventPeak.x;
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}
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return {
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peaks: shiftedSolventPeaks,
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delta: currentDelta / shiftedSolventPeaks.length,
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};
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}
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function getClosestPeaks(shiftedSolventPeaks: PointXY[], nearPeaks: PointXY[]) {
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const diff = getDiffMatrix(shiftedSolventPeaks, nearPeaks);
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const { rowAssignments, gain } = linearSumAssignment(diff, {
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maximaze: false,
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});
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if (gain === -1) return [];
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+
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const assignmentPeaks = [];
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let maxValue = Number.MIN_SAFE_INTEGER;
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for (let index of rowAssignments) {
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if (maxValue < nearPeaks[index].y) maxValue = nearPeaks[index].y;
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assignmentPeaks.push({ ...nearPeaks[index] });
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}
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assignmentPeaks.forEach((peak, i, arr) => (arr[i].y /= maxValue));
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return assignmentPeaks;
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}
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function getDiffMatrix<T extends PointXY>(rows: T[], columns: T[]) {
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const nbColumns = columns.length;
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const nbRows = rows.length;
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const diff = new Matrix(nbRows, nbColumns);
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for (let r = 0; r < nbRows; r++) {
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for (let c = 0; c < nbColumns; c++) {
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diff.set(r, c, Math.abs(rows[r].x - columns[c].x));
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}
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}
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return diff;
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}
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@@ -29,7 +29,7 @@ interface IntergralData {
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29
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to: number;
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}
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31
31
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32
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-
export type Peak1DIntern = Omit<NMRPeak1D, 'y' | 'shape'
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32
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+
export type Peak1DIntern = Omit<NMRPeak1D, 'y' | 'shape'> & {
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intensity: number;
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34
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};
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35
35
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@@ -62,10 +62,12 @@ type SignalInternMandatory = MakeMandatory<
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62
62
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function checkSignalForCompilePattern(
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63
63
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signal: SignalIntern,
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64
64
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): asserts signal is SignalInternMandatory {
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65
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-
if (!signal
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65
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+
if (!('symRank' in signal)) {
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66
66
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throw new Error('Internal error, symRank was not calculated');
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67
67
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}
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68
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-
if (!
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68
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+
if (!('mask' in signal)) {
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69
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throw new Error('Internal Error, mask was not added');
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70
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+
}
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69
71
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}
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70
72
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71
73
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export interface OpitonsCompilePatter {
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