nmr-correlation
Advanced tools
Comparing version 2.1.0 to 2.1.1
# Changelog | ||
### [2.1.1](https://www.github.com/cheminfo/nmr-correlation/compare/v2.1.0...v2.1.1) (2021-10-15) | ||
### Bug Fixes | ||
* deletion of obsolete links in 1D too ([da60776](https://www.github.com/cheminfo/nmr-correlation/commit/da607765b03ffd5a8197e8bdf38e30701f84690a)) | ||
* deletion of obsolete links to non-existing signals ([c173249](https://www.github.com/cheminfo/nmr-correlation/commit/c1732495a31abd0ff5ee3478f0bbd0e0c87861a6)) | ||
* do not delete moved link with empty match array ([aa7c8c5](https://www.github.com/cheminfo/nmr-correlation/commit/aa7c8c506a2315c87601661a470397ad0b310450)) | ||
* missing consideration of moved signals in addFromData1D ([5986216](https://www.github.com/cheminfo/nmr-correlation/commit/5986216b0b141bc4ad2701e4ac0ba156f92fc21a)) | ||
* remove correlations without any link ([e8d5e6a](https://www.github.com/cheminfo/nmr-correlation/commit/e8d5e6ab87b446f4c87a51a0646175706f5fb97e)) | ||
* removed unnecessary experiment type and id from correlation options ([28ed3c4](https://www.github.com/cheminfo/nmr-correlation/commit/28ed3c4c23ef79ed10d77cfba332859c7b327322)) | ||
* restorage of previously set correlation properties and possibilty to skip the addFromData method ([3d3b81b](https://www.github.com/cheminfo/nmr-correlation/commit/3d3b81b8e1aefa15ac0fa3259b3e85d5f916f79c)) | ||
* using wrong index in atom types array in removeDeletedAndNotLinkedCorrelations ([658cbe2](https://www.github.com/cheminfo/nmr-correlation/commit/658cbe2af647cc0720b41056cb56dfce953b67b5)) | ||
## [2.1.0](https://www.github.com/cheminfo/nmr-correlation/compare/v2.0.3...v2.1.0) (2021-09-10) | ||
@@ -4,0 +18,0 @@ |
@@ -10,11 +10,11 @@ import { buildState } from '../utilities/build/buildState'; | ||
export function buildCorrelationData(spectra, options) { | ||
const { tolerance = {}, mf = '', values: prevValues = [] } = options; | ||
const values = spectra ? buildValues(spectra, mf, tolerance, prevValues) : []; | ||
const values = spectra ? buildValues(spectra, options) : []; | ||
delete options.values; | ||
delete options.skipDataUpdate; | ||
return { | ||
values, | ||
options, | ||
state: buildState(values, mf), | ||
state: buildState(values, options.mf || ''), | ||
}; | ||
} | ||
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@@ -12,2 +12,3 @@ export * from './build/buildCorrelationData'; | ||
export * from './utilities/general/getAtomTypeFromNucleus'; | ||
export * from './utilities/general/getCorrelationDelta'; | ||
export * from './utilities/general/getCorrelationIndex'; | ||
@@ -17,5 +18,7 @@ export * from './utilities/general/getCorrelationsByAtomType'; | ||
export * from './utilities/general/getLabels'; | ||
export * from './utilities/general/getLinkDelta'; | ||
export * from './utilities/general/getLinkDim'; | ||
export * from './utilities/general/isEditedHSQC'; | ||
import * as Types_1 from './types/index'; | ||
export { Types_1 as Types }; | ||
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@@ -10,3 +10,4 @@ import { spectraDataSet1 } from '../../../data/spectraDataSet1'; | ||
const prevValues = []; | ||
expect(buildValues(spectra, mf, tolerance, prevValues)).toStrictEqual([]); | ||
const options = { tolerance, mf, values: prevValues }; | ||
expect(buildValues(spectra, options)).toStrictEqual([]); | ||
}); | ||
@@ -18,3 +19,4 @@ it('test 2, mf only', () => { | ||
const prevValues = []; | ||
expect(buildValues(spectra, mf, tolerance, prevValues)).toHaveLength(4); | ||
const options = { tolerance, mf, values: prevValues }; | ||
expect(buildValues(spectra, options)).toHaveLength(4); | ||
}); | ||
@@ -31,17 +33,21 @@ it('test 3, prev value (will be deleted)', () => { | ||
const prevValues = [correlation]; | ||
expect(buildValues(spectra, mf, tolerance, prevValues)).toStrictEqual([]); | ||
const options = { tolerance, mf, values: prevValues }; | ||
expect(buildValues(spectra, options)).toStrictEqual([]); | ||
}); | ||
it('test 4, spectra data: only take first 13C spectrum, no mf', () => { | ||
const tolerance = { C: 0.25, H: 0.05 }; | ||
expect(buildValues(spectraDataSet1, '', tolerance, [])).toHaveLength(5); | ||
const options = { tolerance }; | ||
expect(buildValues(spectraDataSet1, options)).toHaveLength(5); | ||
}); | ||
it('test 5, spectra data: only take first 13C spectrum, no mf, increased tolerance for H', () => { | ||
const tolerance = { C: 0.25, H: 0.1 }; | ||
expect(buildValues(spectraDataSet1, '', tolerance, [])).toHaveLength(4); | ||
const options = { tolerance }; | ||
expect(buildValues(spectraDataSet1, options)).toHaveLength(4); | ||
}); | ||
it('test 6, spectra data: only take first 13C spectrum, with mf', () => { | ||
const tolerance = { C: 0.25, H: 0.05 }; | ||
expect(buildValues(spectraDataSet1, 'C6H6', tolerance, [])).toHaveLength(12); | ||
const options = { tolerance, mf: 'C6H6' }; | ||
expect(buildValues(spectraDataSet1, options)).toHaveLength(12); | ||
}); | ||
}); | ||
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@@ -7,3 +7,2 @@ import { buildCorrelation } from '../../correlation/buildCorrelation'; | ||
label: { origin: 'C1' }, | ||
signal: { delta: 30.2, id: 'id1' }, | ||
}); | ||
@@ -13,3 +12,2 @@ const correlation2 = buildCorrelation({ | ||
label: { origin: 'C2' }, | ||
signal: { delta: 40.7, id: 'id2' }, | ||
}); | ||
@@ -19,3 +17,2 @@ const correlation3 = buildCorrelation({ | ||
label: { origin: 'H1' }, | ||
signal: { delta: 1.0, id: 'id3' }, | ||
}); | ||
@@ -25,3 +22,2 @@ const correlation4 = buildCorrelation({ | ||
label: { origin: 'H2' }, | ||
signal: { delta: 2.1, id: 'id4' }, | ||
}); | ||
@@ -37,2 +33,2 @@ it('test', () => { | ||
}); | ||
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import { setProtonsCountFromData } from '../protonsCount/setProtonsCountFromData'; | ||
import { getSignals } from '../signals/getSignals'; | ||
import { addFromData1D } from './addFromData1D'; | ||
import { addFromData2D } from './addFromData2D'; | ||
import { addFromData } from './addFromData'; | ||
import { updatePseudoCorrelations } from './pseudo/updatePseudoCorrelations'; | ||
import { removeDeletedCorrelations } from './removeDeletedCorrelations'; | ||
import { removeObsoleteLinksAndNotLinkedCorrelations } from './removeObsoleteLinksAndNotLinkedCorrelations'; | ||
import { setAttachmentsAndProtonEquivalences } from './setAttachmentsAndProtonEquivalences'; | ||
@@ -19,11 +18,13 @@ import { setLabels } from './setLabels'; | ||
*/ | ||
export function buildValues(spectra, mf, tolerance, values) { | ||
export function buildValues(spectra, options) { | ||
const { tolerance = {}, mf = '', values: prevValues = [] } = options; | ||
const signals = getSignals(spectra); | ||
let _correlations = values ? values.slice() : []; | ||
// remove deleted correlations | ||
_correlations = removeDeletedCorrelations(_correlations, signals.signals1D, signals.signals2D); | ||
// add signals from either 1D or 2D if not already existing as correlation | ||
// if a signal already exists then add a link within matched correlation | ||
_correlations = addFromData1D(_correlations, signals.signals1D, tolerance); | ||
_correlations = addFromData2D(_correlations, signals.signals2D, tolerance); | ||
let _correlations = prevValues ? prevValues.slice() : []; | ||
if (options.skipDataUpdate !== true) { | ||
// remove obsolete links/correlations | ||
_correlations = removeObsoleteLinksAndNotLinkedCorrelations(_correlations, signals.signals1D, signals.signals2D); | ||
// add signals from either 1D or 2D if not already existing as correlation | ||
// if a signal already exists then add a link within matched correlation | ||
_correlations = addFromData(_correlations, signals.signals1D, signals.signals2D, tolerance); | ||
} | ||
// set the number of attached protons via DEPT or edited HSQC | ||
@@ -43,2 +44,2 @@ _correlations = setProtonsCountFromData(_correlations, signals.signalsDEPT, signals.signals2D, tolerance); | ||
} | ||
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@@ -38,3 +38,8 @@ import lodashIsEqual from 'lodash/isEqual'; | ||
correlations.forEach((correlation) => { | ||
const linksToRemove = correlation.link.filter((link) => link.match.length === 0 && link.experimentType !== '1d'); | ||
const linksToRemove = correlation.link.filter((link) => { | ||
var _a; | ||
return link.match.length === 0 && | ||
link.experimentType !== '1d' && | ||
((_a = link.edited) === null || _a === void 0 ? void 0 : _a.moved) !== true; | ||
}); | ||
linksToRemove.forEach((link) => removeLink(correlation, link.id)); | ||
@@ -44,2 +49,2 @@ }); | ||
} | ||
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@@ -0,1 +1,2 @@ | ||
import { getCorrelationDelta } from '../general/getCorrelationDelta'; | ||
import { getCorrelationsByAtomType } from '../general/getCorrelationsByAtomType'; | ||
@@ -32,9 +33,16 @@ /** | ||
const compareCorrelations = (corr1, corr2) => { | ||
if (corr1.pseudo === false && corr2.pseudo === false) { | ||
if (corr1.signal.delta < corr2.signal.delta) { | ||
return -1; | ||
if (corr1.pseudo === false && | ||
corr2.pseudo === false && | ||
corr1.link.length > 0 && | ||
corr2.link.length > 0) { | ||
const corr1Delta = getCorrelationDelta(corr1); | ||
const corr2Delta = getCorrelationDelta(corr2); | ||
if (corr1Delta !== undefined && corr2Delta !== undefined) { | ||
if (corr1Delta < corr2Delta) { | ||
return -1; | ||
} | ||
else if (corr1Delta > corr2Delta) { | ||
return 1; | ||
} | ||
} | ||
else if (corr1.signal.delta > corr2.signal.delta) { | ||
return 1; | ||
} | ||
} | ||
@@ -67,2 +75,2 @@ if (corr1.pseudo === false && corr2.pseudo === true) { | ||
} | ||
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@@ -10,6 +10,3 @@ import { generateID } from '../general/generateID'; | ||
id: options.id || generateID(), | ||
experimentType: options.experimentType, | ||
experimentID: options.experimentID, | ||
atomType: options.atomType, | ||
signal: options.signal, | ||
label: options.label || {}, | ||
@@ -25,2 +22,2 @@ link: options.link || [], | ||
} | ||
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@@ -18,4 +18,5 @@ import { generateID } from '../general/generateID'; | ||
pseudo: options.pseudo || false, | ||
edited: options.edited || {}, | ||
}; | ||
} | ||
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@@ -10,5 +10,10 @@ import { buildCorrelation } from './buildCorrelation'; | ||
export function setCorrelation(data, id, correlation) { | ||
const correlationIndex = data.values.findIndex((_correlation) => _correlation.id === id); | ||
const _values = data.values.slice(); | ||
_values.splice(correlationIndex, 1, buildCorrelation({ ...correlation })); | ||
const correlationIndex = _values.findIndex((_correlation) => _correlation.id === id); | ||
if (correlationIndex >= 0) { | ||
_values.splice(correlationIndex, 1, buildCorrelation({ ...correlation })); | ||
} | ||
else { | ||
_values.push(correlation); | ||
} | ||
return { | ||
@@ -20,2 +25,2 @@ values: _values, | ||
} | ||
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import { checkMatch } from '../general/checkMatch'; | ||
import { getCorrelationDelta } from '../general/getCorrelationDelta'; | ||
/** | ||
@@ -13,6 +14,8 @@ * Sets proton counts from DEPT90 signals and DEPT135/edited HSQC signals. | ||
for (let i = 0; i < correlations.length; i++) { | ||
if (correlations[i].edited.protonsCount) { | ||
const correlation = correlations[i]; | ||
if (correlation.edited.protonsCount) { | ||
// do not overwrite a manually edited value | ||
continue; | ||
} | ||
const correlationDelta = getCorrelationDelta(correlation); | ||
const match = [-1, -1]; | ||
@@ -22,3 +25,4 @@ for (let k = 0; k < signals90.length; k++) { | ||
// signals90[k].sign === 1 && | ||
checkMatch(correlations[i].signal.delta, signals90[k].delta, toleranceAtomType)) { | ||
correlationDelta !== undefined && | ||
checkMatch(correlationDelta, signals90[k].delta, toleranceAtomType)) { | ||
match[0] = k; | ||
@@ -29,3 +33,4 @@ break; | ||
for (let k = 0; k < signals135.length; k++) { | ||
if (checkMatch(correlations[i].signal.delta, signals135[k].delta, toleranceAtomType)) { | ||
if (correlationDelta !== undefined && | ||
checkMatch(correlationDelta, signals135[k].delta, toleranceAtomType)) { | ||
match[1] = k; | ||
@@ -38,3 +43,3 @@ break; | ||
// CH | ||
correlations[i].protonsCount = [1]; | ||
correlation.protonsCount = [1]; | ||
continue; | ||
@@ -50,3 +55,3 @@ } | ||
// CH3 | ||
correlations[i].protonsCount = [3]; | ||
correlation.protonsCount = [3]; | ||
} | ||
@@ -56,3 +61,3 @@ else { | ||
// CH or CH3 | ||
correlations[i].protonsCount = [1, 3]; | ||
correlation.protonsCount = [1, 3]; | ||
} | ||
@@ -63,3 +68,3 @@ } | ||
// CH2 | ||
correlations[i].protonsCount = [2]; | ||
correlation.protonsCount = [2]; | ||
} | ||
@@ -71,7 +76,7 @@ } | ||
// qC | ||
correlations[i].protonsCount = [0]; | ||
correlation.protonsCount = [0]; | ||
} | ||
else { | ||
// no information | ||
correlations[i].protonsCount = []; | ||
correlation.protonsCount = []; | ||
} | ||
@@ -82,2 +87,2 @@ } | ||
} | ||
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@@ -13,12 +13,12 @@ "use strict"; | ||
function buildCorrelationData(spectra, options) { | ||
const { tolerance = {}, mf = '', values: prevValues = [] } = options; | ||
const values = spectra ? (0, buildValues_1.buildValues)(spectra, mf, tolerance, prevValues) : []; | ||
const values = spectra ? (0, buildValues_1.buildValues)(spectra, options) : []; | ||
delete options.values; | ||
delete options.skipDataUpdate; | ||
return { | ||
values, | ||
options, | ||
state: (0, buildState_1.buildState)(values, mf), | ||
state: (0, buildState_1.buildState)(values, options.mf || ''), | ||
}; | ||
} | ||
exports.buildCorrelationData = buildCorrelationData; | ||
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@@ -12,2 +12,3 @@ export * from './build/buildCorrelationData'; | ||
export * from './utilities/general/getAtomTypeFromNucleus'; | ||
export * from './utilities/general/getCorrelationDelta'; | ||
export * from './utilities/general/getCorrelationIndex'; | ||
@@ -17,3 +18,5 @@ export * from './utilities/general/getCorrelationsByAtomType'; | ||
export * from './utilities/general/getLabels'; | ||
export * from './utilities/general/getLinkDelta'; | ||
export * from './utilities/general/getLinkDim'; | ||
export * from './utilities/general/isEditedHSQC'; | ||
export * as Types from './types/index'; |
@@ -37,2 +37,3 @@ "use strict"; | ||
__exportStar(require("./utilities/general/getAtomTypeFromNucleus"), exports); | ||
__exportStar(require("./utilities/general/getCorrelationDelta"), exports); | ||
__exportStar(require("./utilities/general/getCorrelationIndex"), exports); | ||
@@ -42,4 +43,6 @@ __exportStar(require("./utilities/general/getCorrelationsByAtomType"), exports); | ||
__exportStar(require("./utilities/general/getLabels"), exports); | ||
__exportStar(require("./utilities/general/getLinkDelta"), exports); | ||
__exportStar(require("./utilities/general/getLinkDim"), exports); | ||
__exportStar(require("./utilities/general/isEditedHSQC"), exports); | ||
exports.Types = __importStar(require("./types/index")); | ||
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import { Correlation } from './correlation/correlation'; | ||
import { CorrelationData } from './correlation/correlationData'; | ||
import { CorrelationSignal } from './correlation/correlationSignal'; | ||
import { Link } from './correlation/link'; | ||
@@ -22,2 +21,2 @@ import { Options } from './correlation/options'; | ||
import { Zones } from './spectrum/zones'; | ||
export { Correlation, CorrelationData, CorrelationSignal, Info1D, Info2D, Link, Options, Range, Ranges, Signal1D, Signal2D, Spectrum1D, Spectrum2D, Spectra, State, StateAtomType, StateAtomTypeError, Tolerance, Values, Zone, Zones, }; | ||
export { Correlation, CorrelationData, Info1D, Info2D, Link, Options, Range, Ranges, Signal1D, Signal2D, Spectrum1D, Spectrum2D, Spectra, State, StateAtomType, StateAtomTypeError, Tolerance, Values, Zone, Zones, }; |
@@ -12,3 +12,4 @@ "use strict"; | ||
const prevValues = []; | ||
expect((0, buildValues_1.buildValues)(spectra, mf, tolerance, prevValues)).toStrictEqual([]); | ||
const options = { tolerance, mf, values: prevValues }; | ||
expect((0, buildValues_1.buildValues)(spectra, options)).toStrictEqual([]); | ||
}); | ||
@@ -20,3 +21,4 @@ it('test 2, mf only', () => { | ||
const prevValues = []; | ||
expect((0, buildValues_1.buildValues)(spectra, mf, tolerance, prevValues)).toHaveLength(4); | ||
const options = { tolerance, mf, values: prevValues }; | ||
expect((0, buildValues_1.buildValues)(spectra, options)).toHaveLength(4); | ||
}); | ||
@@ -33,17 +35,21 @@ it('test 3, prev value (will be deleted)', () => { | ||
const prevValues = [correlation]; | ||
expect((0, buildValues_1.buildValues)(spectra, mf, tolerance, prevValues)).toStrictEqual([]); | ||
const options = { tolerance, mf, values: prevValues }; | ||
expect((0, buildValues_1.buildValues)(spectra, options)).toStrictEqual([]); | ||
}); | ||
it('test 4, spectra data: only take first 13C spectrum, no mf', () => { | ||
const tolerance = { C: 0.25, H: 0.05 }; | ||
expect((0, buildValues_1.buildValues)(spectraDataSet1_1.spectraDataSet1, '', tolerance, [])).toHaveLength(5); | ||
const options = { tolerance }; | ||
expect((0, buildValues_1.buildValues)(spectraDataSet1_1.spectraDataSet1, options)).toHaveLength(5); | ||
}); | ||
it('test 5, spectra data: only take first 13C spectrum, no mf, increased tolerance for H', () => { | ||
const tolerance = { C: 0.25, H: 0.1 }; | ||
expect((0, buildValues_1.buildValues)(spectraDataSet1_1.spectraDataSet1, '', tolerance, [])).toHaveLength(4); | ||
const options = { tolerance }; | ||
expect((0, buildValues_1.buildValues)(spectraDataSet1_1.spectraDataSet1, options)).toHaveLength(4); | ||
}); | ||
it('test 6, spectra data: only take first 13C spectrum, with mf', () => { | ||
const tolerance = { C: 0.25, H: 0.05 }; | ||
expect((0, buildValues_1.buildValues)(spectraDataSet1_1.spectraDataSet1, 'C6H6', tolerance, [])).toHaveLength(12); | ||
const options = { tolerance, mf: 'C6H6' }; | ||
expect((0, buildValues_1.buildValues)(spectraDataSet1_1.spectraDataSet1, options)).toHaveLength(12); | ||
}); | ||
}); | ||
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@@ -9,3 +9,2 @@ "use strict"; | ||
label: { origin: 'C1' }, | ||
signal: { delta: 30.2, id: 'id1' }, | ||
}); | ||
@@ -15,3 +14,2 @@ const correlation2 = (0, buildCorrelation_1.buildCorrelation)({ | ||
label: { origin: 'C2' }, | ||
signal: { delta: 40.7, id: 'id2' }, | ||
}); | ||
@@ -21,3 +19,2 @@ const correlation3 = (0, buildCorrelation_1.buildCorrelation)({ | ||
label: { origin: 'H1' }, | ||
signal: { delta: 1.0, id: 'id3' }, | ||
}); | ||
@@ -27,3 +24,2 @@ const correlation4 = (0, buildCorrelation_1.buildCorrelation)({ | ||
label: { origin: 'H2' }, | ||
signal: { delta: 2.1, id: 'id4' }, | ||
}); | ||
@@ -39,2 +35,2 @@ it('test', () => { | ||
}); | ||
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@@ -1,2 +0,2 @@ | ||
import { Tolerance } from '../../types/correlation/tolerance'; | ||
import { Options } from '../../types'; | ||
import { Values } from '../../types/correlation/values'; | ||
@@ -12,2 +12,2 @@ import { Spectra } from '../../types/spectrum/spectra'; | ||
*/ | ||
export declare function buildValues(spectra: Spectra, mf: string, tolerance: Tolerance, values: Values): Values; | ||
export declare function buildValues(spectra: Spectra, options: Options): Values; |
@@ -6,6 +6,5 @@ "use strict"; | ||
const getSignals_1 = require("../signals/getSignals"); | ||
const addFromData1D_1 = require("./addFromData1D"); | ||
const addFromData2D_1 = require("./addFromData2D"); | ||
const addFromData_1 = require("./addFromData"); | ||
const updatePseudoCorrelations_1 = require("./pseudo/updatePseudoCorrelations"); | ||
const removeDeletedCorrelations_1 = require("./removeDeletedCorrelations"); | ||
const removeObsoleteLinksAndNotLinkedCorrelations_1 = require("./removeObsoleteLinksAndNotLinkedCorrelations"); | ||
const setAttachmentsAndProtonEquivalences_1 = require("./setAttachmentsAndProtonEquivalences"); | ||
@@ -23,11 +22,13 @@ const setLabels_1 = require("./setLabels"); | ||
*/ | ||
function buildValues(spectra, mf, tolerance, values) { | ||
function buildValues(spectra, options) { | ||
const { tolerance = {}, mf = '', values: prevValues = [] } = options; | ||
const signals = (0, getSignals_1.getSignals)(spectra); | ||
let _correlations = values ? values.slice() : []; | ||
// remove deleted correlations | ||
_correlations = (0, removeDeletedCorrelations_1.removeDeletedCorrelations)(_correlations, signals.signals1D, signals.signals2D); | ||
// add signals from either 1D or 2D if not already existing as correlation | ||
// if a signal already exists then add a link within matched correlation | ||
_correlations = (0, addFromData1D_1.addFromData1D)(_correlations, signals.signals1D, tolerance); | ||
_correlations = (0, addFromData2D_1.addFromData2D)(_correlations, signals.signals2D, tolerance); | ||
let _correlations = prevValues ? prevValues.slice() : []; | ||
if (options.skipDataUpdate !== true) { | ||
// remove obsolete links/correlations | ||
_correlations = (0, removeObsoleteLinksAndNotLinkedCorrelations_1.removeObsoleteLinksAndNotLinkedCorrelations)(_correlations, signals.signals1D, signals.signals2D); | ||
// add signals from either 1D or 2D if not already existing as correlation | ||
// if a signal already exists then add a link within matched correlation | ||
_correlations = (0, addFromData_1.addFromData)(_correlations, signals.signals1D, signals.signals2D, tolerance); | ||
} | ||
// set the number of attached protons via DEPT or edited HSQC | ||
@@ -48,2 +49,2 @@ _correlations = (0, setProtonsCountFromData_1.setProtonsCountFromData)(_correlations, signals.signalsDEPT, signals.signals2D, tolerance); | ||
exports.buildValues = buildValues; | ||
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@@ -44,3 +44,8 @@ "use strict"; | ||
correlations.forEach((correlation) => { | ||
const linksToRemove = correlation.link.filter((link) => link.match.length === 0 && link.experimentType !== '1d'); | ||
const linksToRemove = correlation.link.filter((link) => { | ||
var _a; | ||
return link.match.length === 0 && | ||
link.experimentType !== '1d' && | ||
((_a = link.edited) === null || _a === void 0 ? void 0 : _a.moved) !== true; | ||
}); | ||
linksToRemove.forEach((link) => (0, removeLink_1.removeLink)(correlation, link.id)); | ||
@@ -51,2 +56,2 @@ }); | ||
exports.setMatches = setMatches; | ||
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"use strict"; | ||
Object.defineProperty(exports, "__esModule", { value: true }); | ||
exports.sortCorrelations = void 0; | ||
const getCorrelationDelta_1 = require("../general/getCorrelationDelta"); | ||
const getCorrelationsByAtomType_1 = require("../general/getCorrelationsByAtomType"); | ||
@@ -35,9 +36,16 @@ /** | ||
const compareCorrelations = (corr1, corr2) => { | ||
if (corr1.pseudo === false && corr2.pseudo === false) { | ||
if (corr1.signal.delta < corr2.signal.delta) { | ||
return -1; | ||
if (corr1.pseudo === false && | ||
corr2.pseudo === false && | ||
corr1.link.length > 0 && | ||
corr2.link.length > 0) { | ||
const corr1Delta = (0, getCorrelationDelta_1.getCorrelationDelta)(corr1); | ||
const corr2Delta = (0, getCorrelationDelta_1.getCorrelationDelta)(corr2); | ||
if (corr1Delta !== undefined && corr2Delta !== undefined) { | ||
if (corr1Delta < corr2Delta) { | ||
return -1; | ||
} | ||
else if (corr1Delta > corr2Delta) { | ||
return 1; | ||
} | ||
} | ||
else if (corr1.signal.delta > corr2.signal.delta) { | ||
return 1; | ||
} | ||
} | ||
@@ -71,2 +79,2 @@ if (corr1.pseudo === false && corr2.pseudo === true) { | ||
exports.sortCorrelations = sortCorrelations; | ||
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@@ -13,6 +13,3 @@ "use strict"; | ||
id: options.id || (0, generateID_1.generateID)(), | ||
experimentType: options.experimentType, | ||
experimentID: options.experimentID, | ||
atomType: options.atomType, | ||
signal: options.signal, | ||
label: options.label || {}, | ||
@@ -29,2 +26,2 @@ link: options.link || [], | ||
exports.buildCorrelation = buildCorrelation; | ||
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@@ -21,5 +21,6 @@ "use strict"; | ||
pseudo: options.pseudo || false, | ||
edited: options.edited || {}, | ||
}; | ||
} | ||
exports.buildLink = buildLink; | ||
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@@ -13,5 +13,10 @@ "use strict"; | ||
function setCorrelation(data, id, correlation) { | ||
const correlationIndex = data.values.findIndex((_correlation) => _correlation.id === id); | ||
const _values = data.values.slice(); | ||
_values.splice(correlationIndex, 1, (0, buildCorrelation_1.buildCorrelation)({ ...correlation })); | ||
const correlationIndex = _values.findIndex((_correlation) => _correlation.id === id); | ||
if (correlationIndex >= 0) { | ||
_values.splice(correlationIndex, 1, (0, buildCorrelation_1.buildCorrelation)({ ...correlation })); | ||
} | ||
else { | ||
_values.push(correlation); | ||
} | ||
return { | ||
@@ -24,2 +29,2 @@ values: _values, | ||
exports.setCorrelation = setCorrelation; | ||
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@@ -5,2 +5,3 @@ "use strict"; | ||
const checkMatch_1 = require("../general/checkMatch"); | ||
const getCorrelationDelta_1 = require("../general/getCorrelationDelta"); | ||
/** | ||
@@ -17,6 +18,8 @@ * Sets proton counts from DEPT90 signals and DEPT135/edited HSQC signals. | ||
for (let i = 0; i < correlations.length; i++) { | ||
if (correlations[i].edited.protonsCount) { | ||
const correlation = correlations[i]; | ||
if (correlation.edited.protonsCount) { | ||
// do not overwrite a manually edited value | ||
continue; | ||
} | ||
const correlationDelta = (0, getCorrelationDelta_1.getCorrelationDelta)(correlation); | ||
const match = [-1, -1]; | ||
@@ -26,3 +29,4 @@ for (let k = 0; k < signals90.length; k++) { | ||
// signals90[k].sign === 1 && | ||
(0, checkMatch_1.checkMatch)(correlations[i].signal.delta, signals90[k].delta, toleranceAtomType)) { | ||
correlationDelta !== undefined && | ||
(0, checkMatch_1.checkMatch)(correlationDelta, signals90[k].delta, toleranceAtomType)) { | ||
match[0] = k; | ||
@@ -33,3 +37,4 @@ break; | ||
for (let k = 0; k < signals135.length; k++) { | ||
if ((0, checkMatch_1.checkMatch)(correlations[i].signal.delta, signals135[k].delta, toleranceAtomType)) { | ||
if (correlationDelta !== undefined && | ||
(0, checkMatch_1.checkMatch)(correlationDelta, signals135[k].delta, toleranceAtomType)) { | ||
match[1] = k; | ||
@@ -42,3 +47,3 @@ break; | ||
// CH | ||
correlations[i].protonsCount = [1]; | ||
correlation.protonsCount = [1]; | ||
continue; | ||
@@ -54,3 +59,3 @@ } | ||
// CH3 | ||
correlations[i].protonsCount = [3]; | ||
correlation.protonsCount = [3]; | ||
} | ||
@@ -60,3 +65,3 @@ else { | ||
// CH or CH3 | ||
correlations[i].protonsCount = [1, 3]; | ||
correlation.protonsCount = [1, 3]; | ||
} | ||
@@ -67,3 +72,3 @@ } | ||
// CH2 | ||
correlations[i].protonsCount = [2]; | ||
correlation.protonsCount = [2]; | ||
} | ||
@@ -75,7 +80,7 @@ } | ||
// qC | ||
correlations[i].protonsCount = [0]; | ||
correlation.protonsCount = [0]; | ||
} | ||
else { | ||
// no information | ||
correlations[i].protonsCount = []; | ||
correlation.protonsCount = []; | ||
} | ||
@@ -87,2 +92,2 @@ } | ||
exports.setProtonsCount = setProtonsCount; | ||
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{ | ||
"name": "nmr-correlation", | ||
"version": "2.1.0", | ||
"version": "2.1.1", | ||
"description": "Build and manipulation of correlations from 1D and 2D NMR data", | ||
@@ -5,0 +5,0 @@ "main": "./lib/index.js", |
@@ -38,2 +38,22 @@ import { spectraDataSet1 } from '../../data/spectraDataSet1'; | ||
id: result.values[0].id, | ||
link: [ | ||
{ | ||
atomType: ['C'], | ||
axis: undefined, | ||
edited: {}, | ||
experimentID: 'spectrum13C', | ||
experimentLabel: '', | ||
experimentType: '1d', | ||
id: result.values[0].link[0].id, | ||
match: [], | ||
pseudo: false, | ||
signal: { | ||
delta: 16.4, | ||
id: 'spectrum13C_range2_1', | ||
kind: 'signal', | ||
multiplicity: 'q', | ||
peaks: [], | ||
}, | ||
}, | ||
], | ||
}; | ||
@@ -48,2 +68,22 @@ const _expectedCorrelationC2: Correlation = { | ||
id: result.values[2].id, | ||
link: [ | ||
{ | ||
atomType: ['C'], | ||
axis: undefined, | ||
edited: {}, | ||
experimentID: 'spectrum13C', | ||
experimentLabel: '', | ||
experimentType: '1d', | ||
id: result.values[2].link[0].id, | ||
match: [], | ||
pseudo: false, | ||
signal: { | ||
delta: 110.9, | ||
id: 'spectrum13C_range1_1', | ||
kind: 'signal', | ||
multiplicity: 'd', | ||
peaks: [], | ||
}, | ||
}, | ||
], | ||
}; | ||
@@ -53,7 +93,47 @@ const _expectedCorrelationH1: Correlation = { | ||
id: result.values[3].id, | ||
link: [ | ||
{ | ||
atomType: ['H'], | ||
axis: undefined, | ||
edited: {}, | ||
experimentID: 'spectrum1H', | ||
experimentLabel: '', | ||
experimentType: '1d', | ||
id: result.values[3].link[0].id, | ||
match: [], | ||
pseudo: false, | ||
signal: { | ||
delta: 1.7, | ||
id: 'spectrum1H_range1_1', | ||
kind: 'signal', | ||
multiplicity: 'd', | ||
peaks: [], | ||
}, | ||
}, | ||
{ ...expectedCorrelationH1.link[0], id: result.values[3].link[1].id }, | ||
], | ||
}; | ||
_expectedCorrelationH1.link[0].id = result.values[3].link[0].id; | ||
const _expectedCorrelationH2: Correlation = { | ||
...expectedCorrelationH2, | ||
id: result.values[4].id, | ||
link: [ | ||
{ | ||
atomType: ['H'], | ||
axis: undefined, | ||
edited: {}, | ||
experimentID: 'spectrum1H', | ||
experimentLabel: '', | ||
experimentType: '1d', | ||
id: result.values[4].link[0].id, | ||
match: [], | ||
pseudo: false, | ||
signal: { | ||
delta: 1.8, | ||
id: 'spectrum1H_range1_2', | ||
kind: 'signal', | ||
multiplicity: 'd', | ||
peaks: [], | ||
}, | ||
}, | ||
], | ||
}; | ||
@@ -88,2 +168,22 @@ | ||
protonsCount: [1, 3], // there is no DEPT90 signal: we can not not distinguish between one or three | ||
link: [ | ||
{ | ||
atomType: ['C'], | ||
axis: undefined, | ||
edited: {}, | ||
experimentID: 'spectrum13C', | ||
experimentLabel: '', | ||
experimentType: '1d', | ||
id: result.values[0].link[0].id, | ||
match: [], | ||
pseudo: false, | ||
signal: { | ||
delta: 16.4, | ||
id: 'spectrum13C_range2_1', | ||
kind: 'signal', | ||
multiplicity: 'q', | ||
peaks: [], | ||
}, | ||
}, | ||
], | ||
}; | ||
@@ -99,3 +199,23 @@ const _expectedCorrelationC2: Correlation = { | ||
id: result.values[2].id, | ||
protonsCount: [0], // no signal in DEP90 or DEPT135 | ||
protonsCount: [0], // no signal in DEP90 or DEPT135, | ||
link: [ | ||
{ | ||
atomType: ['C'], | ||
axis: undefined, | ||
edited: {}, | ||
experimentID: 'spectrum13C', | ||
experimentLabel: '', | ||
experimentType: '1d', | ||
id: result.values[2].link[0].id, | ||
match: [], | ||
pseudo: false, | ||
signal: { | ||
delta: 110.9, | ||
id: 'spectrum13C_range1_1', | ||
kind: 'signal', | ||
multiplicity: 'd', | ||
peaks: [], | ||
}, | ||
}, | ||
], | ||
}; | ||
@@ -106,7 +226,69 @@ const _expectedCorrelationH1: Correlation = { | ||
equivalence: 2, | ||
link: [ | ||
{ | ||
atomType: ['H'], | ||
axis: undefined, | ||
edited: {}, | ||
experimentID: 'spectrum1H', | ||
experimentLabel: '', | ||
experimentType: '1d', | ||
id: result.values[3].link[0].id, | ||
match: [], | ||
pseudo: false, | ||
signal: { | ||
delta: 1.7, | ||
id: 'spectrum1H_range1_1', | ||
kind: 'signal', | ||
multiplicity: 'd', | ||
peaks: [], | ||
}, | ||
}, | ||
{ | ||
atomType: ['H', 'C'], | ||
axis: 'x', | ||
edited: {}, | ||
experimentID: 'spectrumHSQC', | ||
experimentLabel: '', | ||
experimentType: 'hsqc', | ||
id: result.values[3].link[1].id, | ||
match: [1], | ||
pseudo: false, | ||
signal: { | ||
id: 'spectrumHSQC_zone1_1', | ||
kind: 'signal', | ||
peaks: [], | ||
sign: 0, | ||
x: { | ||
delta: 1.7, | ||
}, | ||
y: { | ||
delta: 51.3, | ||
}, | ||
}, | ||
}, | ||
], | ||
}; | ||
_expectedCorrelationH1.link[0].id = result.values[3].link[0].id; | ||
const _expectedCorrelationH2: Correlation = { | ||
...expectedCorrelationH2, | ||
id: result.values[4].id, | ||
link: [ | ||
{ | ||
atomType: ['H'], | ||
axis: undefined, | ||
edited: {}, | ||
experimentID: 'spectrum1H', | ||
experimentLabel: '', | ||
experimentType: '1d', | ||
id: result.values[4].link[0].id, | ||
match: [], | ||
pseudo: false, | ||
signal: { | ||
delta: 1.8, | ||
id: 'spectrum1H_range1_2', | ||
kind: 'signal', | ||
multiplicity: 'd', | ||
peaks: [], | ||
}, | ||
}, | ||
], | ||
}; | ||
@@ -126,8 +308,2 @@ | ||
atomType: 'C', | ||
experimentType: '1d', | ||
experimentID: 'spectrum13C', | ||
signal: { | ||
id: 'spectrum13C_range2_1', | ||
delta: 16.4, | ||
}, | ||
label: { origin: 'C1' }, | ||
@@ -137,9 +313,2 @@ }); | ||
atomType: 'C', | ||
experimentType: 'hsqc', | ||
experimentID: 'spectrumHSQC', | ||
signal: { | ||
id: 'spectrumHSQC_zone1_1', | ||
delta: 51.3, | ||
sign: 0, | ||
}, | ||
label: { origin: 'C2' }, | ||
@@ -168,2 +337,3 @@ attachment: { H: [3] }, | ||
}, | ||
edited: {}, | ||
}), | ||
@@ -174,8 +344,2 @@ ], | ||
atomType: 'C', | ||
experimentType: '1d', | ||
experimentID: 'spectrum13C', | ||
signal: { | ||
id: 'spectrum13C_range1_1', | ||
delta: 110.9, | ||
}, | ||
label: { origin: 'C3' }, | ||
@@ -185,9 +349,2 @@ }); | ||
atomType: 'H', | ||
experimentType: 'hsqc', | ||
experimentID: 'spectrumHSQC', | ||
signal: { | ||
id: 'spectrumHSQC_zone1_1', | ||
delta: 1.7, | ||
sign: 0, | ||
}, | ||
label: { origin: 'H1' }, | ||
@@ -216,2 +373,3 @@ attachment: { C: [1] }, | ||
}, | ||
edited: {}, | ||
}), | ||
@@ -222,8 +380,2 @@ ], | ||
atomType: 'H', | ||
experimentType: '1d', | ||
experimentID: 'spectrum1H', | ||
signal: { | ||
id: 'spectrum1H_range1_2', | ||
delta: 1.8, | ||
}, | ||
label: { origin: 'H2' }, | ||
@@ -288,13 +440,12 @@ }); | ||
atomType: 'C', | ||
experimentType: 'hsqc', | ||
experimentID: 'spectrumEditedHSQC', | ||
signal: { | ||
id: 'spectrumEditedHSQC_zone1_1', | ||
delta: 16.4, | ||
sign: 1, | ||
}, | ||
label: { origin: 'C1' }, | ||
attachment: { H: [2] }, | ||
link: [ | ||
{ ...link1, axis: 'y', match: [2], id: result.values[0].link[0].id }, | ||
{ | ||
...link1, | ||
axis: 'y', | ||
match: [2], | ||
id: result.values[0].link[0].id, | ||
edited: {}, | ||
}, | ||
], | ||
@@ -306,13 +457,12 @@ protonsCount: [1, 3], | ||
atomType: 'C', | ||
experimentType: 'hsqc', | ||
experimentID: 'spectrumEditedHSQC', | ||
signal: { | ||
id: 'spectrumEditedHSQC_zone2_1', | ||
delta: 51.3, | ||
sign: -1, | ||
}, | ||
label: { origin: 'C2' }, | ||
attachment: { H: [3] }, | ||
link: [ | ||
{ ...link2, axis: 'y', match: [3], id: result.values[1].link[0].id }, | ||
{ | ||
...link2, | ||
axis: 'y', | ||
match: [3], | ||
id: result.values[1].link[0].id, | ||
edited: {}, | ||
}, | ||
], | ||
@@ -324,13 +474,12 @@ protonsCount: [2], | ||
atomType: 'H', | ||
experimentType: 'hsqc', | ||
experimentID: 'spectrumEditedHSQC', | ||
signal: { | ||
id: 'spectrumEditedHSQC_zone1_1', | ||
delta: 1.7, | ||
sign: 1, | ||
}, | ||
label: { origin: 'H1' }, | ||
attachment: { C: [0] }, | ||
link: [ | ||
{ ...link1, axis: 'x', match: [0], id: result.values[2].link[0].id }, | ||
{ | ||
...link1, | ||
axis: 'x', | ||
match: [0], | ||
id: result.values[2].link[0].id, | ||
edited: {}, | ||
}, | ||
], | ||
@@ -341,13 +490,12 @@ }); | ||
atomType: 'H', | ||
experimentType: 'hsqc', | ||
experimentID: 'spectrumEditedHSQC', | ||
signal: { | ||
id: 'spectrumEditedHSQC_zone2_1', | ||
delta: 1.8, | ||
sign: -1, | ||
}, | ||
label: { origin: 'H2' }, | ||
attachment: { C: [1] }, | ||
link: [ | ||
{ ...link2, axis: 'x', match: [1], id: result.values[3].link[0].id }, | ||
{ | ||
...link2, | ||
axis: 'x', | ||
match: [1], | ||
id: result.values[3].link[0].id, | ||
edited: {}, | ||
}, | ||
], | ||
@@ -354,0 +502,0 @@ equivalence: 2, |
@@ -17,6 +17,6 @@ import { CorrelationData } from '../types/correlation/correlationData'; | ||
): CorrelationData { | ||
const { tolerance = {}, mf = '', values: prevValues = [] } = options; | ||
const values = spectra ? buildValues(spectra, mf, tolerance, prevValues) : []; | ||
const values = spectra ? buildValues(spectra, options) : []; | ||
delete options.values; | ||
delete options.skipDataUpdate; | ||
@@ -26,4 +26,4 @@ return { | ||
options, | ||
state: buildState(values, mf), | ||
state: buildState(values, options.mf || ''), | ||
}; | ||
} |
@@ -15,2 +15,3 @@ export * from './build/buildCorrelationData'; | ||
export * from './utilities/general/getAtomTypeFromNucleus'; | ||
export * from './utilities/general/getCorrelationDelta'; | ||
export * from './utilities/general/getCorrelationIndex'; | ||
@@ -20,4 +21,6 @@ export * from './utilities/general/getCorrelationsByAtomType'; | ||
export * from './utilities/general/getLabels'; | ||
export * from './utilities/general/getLinkDelta'; | ||
export * from './utilities/general/getLinkDim'; | ||
export * from './utilities/general/isEditedHSQC'; | ||
export * as Types from './types/index'; |
import { CorrelationAndLinkFields } from './correlationAndLinkFields'; | ||
import { CorrelationSignal } from './correlationSignal'; | ||
import { Link } from './link'; | ||
@@ -7,3 +6,2 @@ | ||
atomType: string; | ||
signal: CorrelationSignal; | ||
label: { [key: string]: string }; | ||
@@ -15,3 +13,2 @@ link: Array<Link>; | ||
hybridization: string; | ||
edited: { [key: string]: boolean }; | ||
} |
export interface CorrelationAndLinkFields { | ||
id: string; | ||
experimentType: string; | ||
experimentID: string; | ||
pseudo: boolean; | ||
edited: { [key: string]: boolean }; | ||
} |
export interface CorrelationAndLinkOptions { | ||
id?: string; | ||
experimentType?: string; | ||
experimentID?: string; | ||
pseudo?: boolean; | ||
edited?: { [key: string]: boolean }; | ||
} |
import { CorrelationAndLinkOptions } from './correlationAndLinkOptions'; | ||
import { CorrelationSignal } from './correlationSignal'; | ||
import { Link } from './link'; | ||
@@ -7,3 +6,2 @@ | ||
atomType?: string; | ||
signal?: CorrelationSignal; | ||
label?: { [key: string]: string }; | ||
@@ -15,3 +13,2 @@ link?: Array<Link>; | ||
hybridization?: string; | ||
edited?: { [key: string]: boolean }; | ||
} |
@@ -9,5 +9,7 @@ import { Signal1D } from '../spectrum/signal1D'; | ||
signal: Signal1D | Signal2D; | ||
axis: string; | ||
axis: string | undefined; | ||
match: Array<number>; | ||
experimentLabel: string; | ||
experimentType: string; | ||
experimentID: string; | ||
} |
@@ -8,2 +8,4 @@ import { Signal1D } from '../spectrum/signal1D'; | ||
atomType?: Array<string>; | ||
experimentType?: string; | ||
experimentID?: string; | ||
signal?: Signal1D | Signal2D; | ||
@@ -10,0 +12,0 @@ axis?: string; |
@@ -9,2 +9,3 @@ import { Values } from '..'; | ||
values?: Values; | ||
skipDataUpdate?: boolean; | ||
} |
import { Correlation } from './correlation/correlation'; | ||
import { CorrelationData } from './correlation/correlationData'; | ||
import { CorrelationSignal } from './correlation/correlationSignal'; | ||
import { Link } from './correlation/link'; | ||
@@ -26,3 +25,2 @@ import { Options } from './correlation/options'; | ||
CorrelationData, | ||
CorrelationSignal, | ||
Info1D, | ||
@@ -29,0 +27,0 @@ Info2D, |
import { spectraDataSet1 } from '../../../data/spectraDataSet1'; | ||
import { Spectra, Tolerance, Values } from '../../../types/index'; | ||
import { Options, Spectra, Tolerance, Values } from '../../../types/index'; | ||
import { buildCorrelation } from '../../correlation/buildCorrelation'; | ||
@@ -12,3 +12,4 @@ import { buildValues } from '../buildValues'; | ||
const prevValues: Values = []; | ||
expect(buildValues(spectra, mf, tolerance, prevValues)).toStrictEqual([]); | ||
const options: Options = { tolerance, mf, values: prevValues }; | ||
expect(buildValues(spectra, options)).toStrictEqual([]); | ||
}); | ||
@@ -21,3 +22,4 @@ | ||
const prevValues: Values = []; | ||
expect(buildValues(spectra, mf, tolerance, prevValues)).toHaveLength(4); | ||
const options: Options = { tolerance, mf, values: prevValues }; | ||
expect(buildValues(spectra, options)).toHaveLength(4); | ||
}); | ||
@@ -35,3 +37,4 @@ | ||
const prevValues: Values = [correlation]; | ||
expect(buildValues(spectra, mf, tolerance, prevValues)).toStrictEqual([]); | ||
const options: Options = { tolerance, mf, values: prevValues }; | ||
expect(buildValues(spectra, options)).toStrictEqual([]); | ||
}); | ||
@@ -41,3 +44,4 @@ | ||
const tolerance: Tolerance = { C: 0.25, H: 0.05 }; | ||
expect(buildValues(spectraDataSet1, '', tolerance, [])).toHaveLength(5); | ||
const options: Options = { tolerance }; | ||
expect(buildValues(spectraDataSet1, options)).toHaveLength(5); | ||
}); | ||
@@ -47,3 +51,4 @@ | ||
const tolerance: Tolerance = { C: 0.25, H: 0.1 }; | ||
expect(buildValues(spectraDataSet1, '', tolerance, [])).toHaveLength(4); | ||
const options: Options = { tolerance }; | ||
expect(buildValues(spectraDataSet1, options)).toHaveLength(4); | ||
}); | ||
@@ -53,6 +58,5 @@ | ||
const tolerance: Tolerance = { C: 0.25, H: 0.05 }; | ||
expect(buildValues(spectraDataSet1, 'C6H6', tolerance, [])).toHaveLength( | ||
12, | ||
); | ||
const options: Options = { tolerance, mf: 'C6H6' }; | ||
expect(buildValues(spectraDataSet1, options)).toHaveLength(12); | ||
}); | ||
}); |
@@ -8,3 +8,2 @@ import { buildCorrelation } from '../../correlation/buildCorrelation'; | ||
label: { origin: 'C1' }, | ||
signal: { delta: 30.2, id: 'id1' }, | ||
}); | ||
@@ -14,3 +13,2 @@ const correlation2 = buildCorrelation({ | ||
label: { origin: 'C2' }, | ||
signal: { delta: 40.7, id: 'id2' }, | ||
}); | ||
@@ -20,3 +18,2 @@ const correlation3 = buildCorrelation({ | ||
label: { origin: 'H1' }, | ||
signal: { delta: 1.0, id: 'id3' }, | ||
}); | ||
@@ -26,3 +23,2 @@ const correlation4 = buildCorrelation({ | ||
label: { origin: 'H2' }, | ||
signal: { delta: 2.1, id: 'id4' }, | ||
}); | ||
@@ -29,0 +25,0 @@ it('test', () => { |
@@ -1,2 +0,2 @@ | ||
import { Tolerance } from '../../types/correlation/tolerance'; | ||
import { Options } from '../../types'; | ||
import { Values } from '../../types/correlation/values'; | ||
@@ -8,6 +8,5 @@ import { ExperimentSignals } from '../../types/experiment/experimentSignals'; | ||
import { addFromData1D } from './addFromData1D'; | ||
import { addFromData2D } from './addFromData2D'; | ||
import { addFromData } from './addFromData'; | ||
import { updatePseudoCorrelations } from './pseudo/updatePseudoCorrelations'; | ||
import { removeDeletedCorrelations } from './removeDeletedCorrelations'; | ||
import { removeObsoleteLinksAndNotLinkedCorrelations } from './removeObsoleteLinksAndNotLinkedCorrelations'; | ||
import { setAttachmentsAndProtonEquivalences } from './setAttachmentsAndProtonEquivalences'; | ||
@@ -26,21 +25,24 @@ import { setLabels } from './setLabels'; | ||
*/ | ||
export function buildValues( | ||
spectra: Spectra, | ||
mf: string, | ||
tolerance: Tolerance, | ||
values: Values, | ||
): Values { | ||
export function buildValues(spectra: Spectra, options: Options): Values { | ||
const { tolerance = {}, mf = '', values: prevValues = [] } = options; | ||
const signals: ExperimentSignals = getSignals(spectra); | ||
let _correlations = values ? values.slice() : []; | ||
// remove deleted correlations | ||
_correlations = removeDeletedCorrelations( | ||
_correlations, | ||
signals.signals1D, | ||
signals.signals2D, | ||
); | ||
// add signals from either 1D or 2D if not already existing as correlation | ||
// if a signal already exists then add a link within matched correlation | ||
_correlations = addFromData1D(_correlations, signals.signals1D, tolerance); | ||
_correlations = addFromData2D(_correlations, signals.signals2D, tolerance); | ||
let _correlations = prevValues ? prevValues.slice() : []; | ||
if (options.skipDataUpdate !== true) { | ||
// remove obsolete links/correlations | ||
_correlations = removeObsoleteLinksAndNotLinkedCorrelations( | ||
_correlations, | ||
signals.signals1D, | ||
signals.signals2D, | ||
); | ||
// add signals from either 1D or 2D if not already existing as correlation | ||
// if a signal already exists then add a link within matched correlation | ||
_correlations = addFromData( | ||
_correlations, | ||
signals.signals1D, | ||
signals.signals2D, | ||
tolerance, | ||
); | ||
} | ||
// set the number of attached protons via DEPT or edited HSQC | ||
@@ -53,3 +55,2 @@ _correlations = setProtonsCountFromData( | ||
); | ||
// sort by atom type and shift value | ||
@@ -56,0 +57,0 @@ _correlations = sortCorrelations(_correlations); |
@@ -51,3 +51,6 @@ import lodashIsEqual from 'lodash/isEqual'; | ||
const linksToRemove = correlation.link.filter( | ||
(link) => link.match.length === 0 && link.experimentType !== '1d', | ||
(link) => | ||
link.match.length === 0 && | ||
link.experimentType !== '1d' && | ||
link.edited?.moved !== true, | ||
); | ||
@@ -54,0 +57,0 @@ linksToRemove.forEach((link) => removeLink(correlation, link.id)); |
import { Correlation } from '../../types/correlation/correlation'; | ||
import { Values } from '../../types/correlation/values'; | ||
import { getCorrelationDelta } from '../general/getCorrelationDelta'; | ||
import { getCorrelationsByAtomType } from '../general/getCorrelationsByAtomType'; | ||
@@ -37,7 +38,16 @@ | ||
const compareCorrelations = (corr1: Correlation, corr2: Correlation) => { | ||
if (corr1.pseudo === false && corr2.pseudo === false) { | ||
if (corr1.signal.delta < corr2.signal.delta) { | ||
return -1; | ||
} else if (corr1.signal.delta > corr2.signal.delta) { | ||
return 1; | ||
if ( | ||
corr1.pseudo === false && | ||
corr2.pseudo === false && | ||
corr1.link.length > 0 && | ||
corr2.link.length > 0 | ||
) { | ||
const corr1Delta = getCorrelationDelta(corr1); | ||
const corr2Delta = getCorrelationDelta(corr2); | ||
if (corr1Delta !== undefined && corr2Delta !== undefined) { | ||
if (corr1Delta < corr2Delta) { | ||
return -1; | ||
} else if (corr1Delta > corr2Delta) { | ||
return 1; | ||
} | ||
} | ||
@@ -44,0 +54,0 @@ } |
@@ -13,6 +13,3 @@ import { Correlation } from '../../types/correlation/correlation'; | ||
id: options.id || generateID(), | ||
experimentType: options.experimentType, | ||
experimentID: options.experimentID, | ||
atomType: options.atomType, | ||
signal: options.signal, | ||
label: options.label || {}, | ||
@@ -19,0 +16,0 @@ link: options.link || [], |
@@ -21,3 +21,4 @@ import { Link } from '../../types/correlation/link'; | ||
pseudo: options.pseudo || false, | ||
edited: options.edited || {}, | ||
} as Link; | ||
} |
@@ -18,7 +18,11 @@ import { Correlation } from '../../types/correlation/correlation'; | ||
): CorrelationData { | ||
const correlationIndex = data.values.findIndex( | ||
const _values = data.values.slice(); | ||
const correlationIndex = _values.findIndex( | ||
(_correlation) => _correlation.id === id, | ||
); | ||
const _values = data.values.slice(); | ||
_values.splice(correlationIndex, 1, buildCorrelation({ ...correlation })); | ||
if (correlationIndex >= 0) { | ||
_values.splice(correlationIndex, 1, buildCorrelation({ ...correlation })); | ||
} else { | ||
_values.push(correlation); | ||
} | ||
@@ -25,0 +29,0 @@ return { |
import { Values } from '../../types/correlation/values'; | ||
import { checkMatch } from '../general/checkMatch'; | ||
import { getCorrelationDelta } from '../general/getCorrelationDelta'; | ||
@@ -20,6 +21,8 @@ /** | ||
for (let i = 0; i < correlations.length; i++) { | ||
if (correlations[i].edited.protonsCount) { | ||
const correlation = correlations[i]; | ||
if (correlation.edited.protonsCount) { | ||
// do not overwrite a manually edited value | ||
continue; | ||
} | ||
const correlationDelta = getCorrelationDelta(correlation); | ||
@@ -30,7 +33,4 @@ const match = [-1, -1]; | ||
// signals90[k].sign === 1 && | ||
checkMatch( | ||
correlations[i].signal.delta, | ||
signals90[k].delta, | ||
toleranceAtomType, | ||
) | ||
correlationDelta !== undefined && | ||
checkMatch(correlationDelta, signals90[k].delta, toleranceAtomType) | ||
) { | ||
@@ -43,7 +43,4 @@ match[0] = k; | ||
if ( | ||
checkMatch( | ||
correlations[i].signal.delta, | ||
signals135[k].delta, | ||
toleranceAtomType, | ||
) | ||
correlationDelta !== undefined && | ||
checkMatch(correlationDelta, signals135[k].delta, toleranceAtomType) | ||
) { | ||
@@ -58,3 +55,3 @@ match[1] = k; | ||
// CH | ||
correlations[i].protonsCount = [1]; | ||
correlation.protonsCount = [1]; | ||
continue; | ||
@@ -70,7 +67,7 @@ } | ||
// CH3 | ||
correlations[i].protonsCount = [3]; | ||
correlation.protonsCount = [3]; | ||
} else { | ||
// in case of DEPT135 is given only | ||
// CH or CH3 | ||
correlations[i].protonsCount = [1, 3]; | ||
correlation.protonsCount = [1, 3]; | ||
} | ||
@@ -80,3 +77,3 @@ } else { | ||
// CH2 | ||
correlations[i].protonsCount = [2]; | ||
correlation.protonsCount = [2]; | ||
} | ||
@@ -87,6 +84,6 @@ } else { | ||
// qC | ||
correlations[i].protonsCount = [0]; | ||
correlation.protonsCount = [0]; | ||
} else { | ||
// no information | ||
correlations[i].protonsCount = []; | ||
correlation.protonsCount = []; | ||
} | ||
@@ -93,0 +90,0 @@ } |
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