nmr-processing 3.3.4 → 5.0.0
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/CHANGELOG.md +42 -0
- package/lib/assignment/get13CAssignments.d.ts +35 -0
- package/lib/assignment/get13CAssignments.js +54 -0
- package/lib/assignment/get13CAssignments.js.map +1 -0
- package/lib/assignment/get1HAssignments.d.ts +42 -0
- package/lib/assignment/get1HAssignments.js +55 -0
- package/lib/assignment/get1HAssignments.js.map +1 -0
- package/lib/assignment/utils/buildAssignments.d.ts +33 -0
- package/lib/assignment/utils/buildAssignments.js +93 -0
- package/lib/assignment/utils/buildAssignments.js.map +1 -0
- package/lib/assignment/utils/createMapPossibleAssignments.d.ts +15 -0
- package/lib/assignment/utils/createMapPossibleAssignments.js +51 -0
- package/lib/assignment/utils/createMapPossibleAssignments.js.map +1 -0
- package/lib/assignment/utils/exploreTreeRec.d.ts +22 -0
- package/lib/assignment/utils/exploreTreeRec.js +77 -0
- package/lib/assignment/utils/exploreTreeRec.js.map +1 -0
- package/lib/assignment/utils/generateID.d.ts +1 -0
- package/lib/assignment/utils/generateID.js +13 -0
- package/lib/assignment/utils/generateID.js.map +1 -0
- package/lib/assignment/utils/partialScore.d.ts +16 -0
- package/lib/assignment/utils/partialScore.js +91 -0
- package/lib/assignment/utils/partialScore.js.map +1 -0
- package/lib/index.d.ts +2 -5
- package/lib/index.js +2 -5
- package/lib/index.js.map +1 -1
- package/lib/peaks/peaksFilterImpurities.js +1 -1
- package/lib/peaks/peaksFilterImpurities.js.map +1 -1
- package/lib/peaks/peaksToRanges.js +11 -17
- package/lib/peaks/peaksToRanges.js.map +1 -1
- package/lib/peaks/util/determineRealTop.js +3 -2
- package/lib/peaks/util/determineRealTop.js.map +1 -1
- package/lib/peaks/util/jAnalyzer.js +33 -35
- package/lib/peaks/util/jAnalyzer.js.map +1 -1
- package/lib/ranges/rangesToXY.d.ts +2 -2
- package/lib/ranges/rangesToXY.js +10 -2
- package/lib/ranges/rangesToXY.js.map +1 -1
- package/lib/signals/signals2DToZ.d.ts +2 -2
- package/lib/signals/signalsToXY.d.ts +2 -2
- package/lib/signals/simulation/simulate1D.d.ts +4 -3
- package/lib/signals/simulation/simulate1D.js.map +1 -1
- package/lib/types/NMRPeak1D.d.ts +2 -9
- package/lib/types/NMRRange.d.ts +1 -0
- package/lib/types/NMRSignal1D.d.ts +1 -0
- package/lib/types/NMRSignal2D.d.ts +3 -4
- package/lib/types/NMRZone.d.ts +4 -3
- package/lib/xy/xyAutoPeaksPicking.d.ts +4 -60
- package/lib/xy/xyAutoPeaksPicking.js +3 -3
- package/lib/xy/xyAutoPeaksPicking.js.map +1 -1
- package/lib/xyz/xyzAutoPeaksPicking.js +4 -2
- package/lib/xyz/xyzAutoPeaksPicking.js.map +1 -1
- package/lib-esm/assignment/get13CAssignments.js +47 -0
- package/lib-esm/assignment/get13CAssignments.js.map +1 -0
- package/lib-esm/assignment/get1HAssignments.js +48 -0
- package/lib-esm/assignment/get1HAssignments.js.map +1 -0
- package/lib-esm/assignment/utils/buildAssignments.js +86 -0
- package/lib-esm/assignment/utils/buildAssignments.js.map +1 -0
- package/lib-esm/assignment/utils/createMapPossibleAssignments.js +47 -0
- package/lib-esm/assignment/utils/createMapPossibleAssignments.js.map +1 -0
- package/lib-esm/assignment/utils/exploreTreeRec.js +73 -0
- package/lib-esm/assignment/utils/exploreTreeRec.js.map +1 -0
- package/lib-esm/assignment/utils/generateID.js +10 -0
- package/lib-esm/assignment/utils/generateID.js.map +1 -0
- package/lib-esm/assignment/utils/partialScore.js +87 -0
- package/lib-esm/assignment/utils/partialScore.js.map +1 -0
- package/lib-esm/index.js +2 -5
- package/lib-esm/index.js.map +1 -1
- package/lib-esm/peaks/peaksFilterImpurities.js +1 -1
- package/lib-esm/peaks/peaksFilterImpurities.js.map +1 -1
- package/lib-esm/peaks/peaksToRanges.js +11 -17
- package/lib-esm/peaks/peaksToRanges.js.map +1 -1
- package/lib-esm/peaks/util/determineRealTop.js +4 -3
- package/lib-esm/peaks/util/determineRealTop.js.map +1 -1
- package/lib-esm/peaks/util/jAnalyzer.js +33 -35
- package/lib-esm/peaks/util/jAnalyzer.js.map +1 -1
- package/lib-esm/ranges/rangesToXY.js +10 -2
- package/lib-esm/ranges/rangesToXY.js.map +1 -1
- package/lib-esm/signals/simulation/simulate1D.js.map +1 -1
- package/lib-esm/xy/xyAutoPeaksPicking.js +3 -3
- package/lib-esm/xy/xyAutoPeaksPicking.js.map +1 -1
- package/lib-esm/xyz/xyzAutoPeaksPicking.js +4 -2
- package/lib-esm/xyz/xyzAutoPeaksPicking.js.map +1 -1
- package/package.json +4 -4
- package/src/assignment/get13CAssignments.ts +100 -0
- package/src/assignment/get1HAssignments.ts +116 -0
- package/src/assignment/utils/buildAssignments.ts +155 -0
- package/src/assignment/utils/createMapPossibleAssignments.ts +76 -0
- package/src/assignment/utils/exploreTreeRec.ts +138 -0
- package/src/assignment/utils/generateID.ts +11 -0
- package/src/assignment/utils/partialScore.ts +128 -0
- package/src/index.ts +3 -6
- package/src/peaks/peaksFilterImpurities.ts +1 -1
- package/src/peaks/peaksToRanges.ts +11 -17
- package/src/peaks/util/determineRealTop.ts +4 -6
- package/src/peaks/util/jAnalyzer.ts +34 -36
- package/src/ranges/rangesToXY.ts +14 -7
- package/src/signals/signals2DToZ.ts +2 -2
- package/src/signals/signalsToXY.ts +2 -2
- package/src/signals/simulation/simulate1D.ts +4 -3
- package/src/types/NMRPeak1D.ts +3 -9
- package/src/types/NMRRange.ts +1 -0
- package/src/types/NMRSignal1D.ts +1 -0
- package/src/types/NMRSignal2D.ts +4 -4
- package/src/types/NMRZone.ts +4 -3
- package/src/types/ml-spectra-processing/index.d.ts +8 -8
- package/src/types/ml-tree-set/index.d.ts +18 -0
- package/src/types/openchemlib-utils/index..d.ts +2 -2
- package/src/xy/xyAutoPeaksPicking.ts +19 -58
- package/src/xyz/xyzAutoPeaksPicking.ts +4 -2
- package/src/types/ml-gsd/index.d.ts +0 -164
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export function createMapPossibleAssignments(props) {
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const { restrictionByCS, predictions, targets, useIntegrationRestriction } = props;
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const { tolerance: toleranceCS, chemicalShiftRestriction } = restrictionByCS;
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let errorAbs = Math.abs(toleranceCS);
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const expandMap = {};
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for (const diaID in predictions) {
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let prediction = predictions[diaID];
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if (prediction.error)
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prediction.error = Math.abs(prediction.error);
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expandMap[diaID] = [];
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if (targets) {
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for (const targetID in targets) {
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let target = targets[targetID];
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const { nbAtoms } = prediction;
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const { integration } = target;
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const couldBeAssigned = useIntegrationRestriction
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? integration > 0
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? nbAtoms - integration < 1
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: true
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: true;
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if (couldBeAssigned) {
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if (!chemicalShiftRestriction ||
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typeof prediction.delta === 'undefined') {
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// Chemical shift is not a restriction
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expandMap[diaID].push(targetID);
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}
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else {
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let error = errorAbs;
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if (prediction.error) {
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error = Math.max(error, prediction.error);
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}
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const delta = target.signals && target.signals.length > 0
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? target.signals[0].delta
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: (target.to + target.from) / 2;
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let distAfterLimit = Math.abs(prediction.delta - delta - errorAbs);
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if (distAfterLimit < 4 * errorAbs) {
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expandMap[diaID].push(targetID);
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}
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}
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}
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}
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}
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expandMap[diaID].push('*');
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}
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return expandMap;
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}
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//# sourceMappingURL=createMapPossibleAssignments.js.map
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{"version":3,"file":"createMapPossibleAssignments.js","sourceRoot":"","sources":["../../../src/assignment/utils/createMapPossibleAssignments.ts"],"names":[],"mappings":"AAoBA,MAAM,UAAU,4BAA4B,CAC1C,KAAmC;IAEnC,MAAM,EAAE,eAAe,EAAE,WAAW,EAAE,OAAO,EAAE,yBAAyB,EAAE,GACxE,KAAK,CAAC;IAER,MAAM,EAAE,SAAS,EAAE,WAAW,EAAE,wBAAwB,EAAE,GAAG,eAAe,CAAC;IAE7E,IAAI,QAAQ,GAAG,IAAI,CAAC,GAAG,CAAC,WAAW,CAAC,CAAC;IACrC,MAAM,SAAS,GAA0B,EAAE,CAAC;IAC5C,KAAK,MAAM,KAAK,IAAI,WAAW,EAAE;QAC/B,IAAI,UAAU,GAAG,WAAW,CAAC,KAAK,CAAC,CAAC;QACpC,IAAI,UAAU,CAAC,KAAK;YAAE,UAAU,CAAC,KAAK,GAAG,IAAI,CAAC,GAAG,CAAC,UAAU,CAAC,KAAK,CAAC,CAAC;QACpE,SAAS,CAAC,KAAK,CAAC,GAAG,EAAE,CAAC;QAEtB,IAAI,OAAO,EAAE;YACX,KAAK,MAAM,QAAQ,IAAI,OAAO,EAAE;gBAC9B,IAAI,MAAM,GAAG,OAAO,CAAC,QAAQ,CAAC,CAAC;gBAC/B,MAAM,EAAE,OAAO,EAAE,GAAG,UAAU,CAAC;gBAC/B,MAAM,EAAE,WAAW,EAAE,GAAG,MAAM,CAAC;gBAE/B,MAAM,eAAe,GAAG,yBAAyB;oBAC/C,CAAC,CAAC,WAAW,GAAG,CAAC;wBACf,CAAC,CAAC,OAAO,GAAG,WAAW,GAAG,CAAC;wBAC3B,CAAC,CAAC,IAAI;oBACR,CAAC,CAAC,IAAI,CAAC;gBAET,IAAI,eAAe,EAAE;oBACnB,IACE,CAAC,wBAAwB;wBACzB,OAAO,UAAU,CAAC,KAAK,KAAK,WAAW,EACvC;wBACA,sCAAsC;wBACtC,SAAS,CAAC,KAAK,CAAC,CAAC,IAAI,CAAC,QAAQ,CAAC,CAAC;qBACjC;yBAAM;wBACL,IAAI,KAAK,GAAG,QAAQ,CAAC;wBACrB,IAAI,UAAU,CAAC,KAAK,EAAE;4BACpB,KAAK,GAAG,IAAI,CAAC,GAAG,CAAC,KAAK,EAAE,UAAU,CAAC,KAAK,CAAC,CAAC;yBAC3C;wBACD,MAAM,KAAK,GACT,MAAM,CAAC,OAAO,IAAI,MAAM,CAAC,OAAO,CAAC,MAAM,GAAG,CAAC;4BACzC,CAAC,CAAC,MAAM,CAAC,OAAO,CAAC,CAAC,CAAC,CAAC,KAAK;4BACzB,CAAC,CAAC,CAAC,MAAM,CAAC,EAAE,GAAG,MAAM,CAAC,IAAI,CAAC,GAAG,CAAC,CAAC;wBAEpC,IAAI,cAAc,GAAG,IAAI,CAAC,GAAG,CAAC,UAAU,CAAC,KAAK,GAAG,KAAK,GAAG,QAAQ,CAAC,CAAC;wBACnE,IAAI,cAAc,GAAG,CAAC,GAAG,QAAQ,EAAE;4BACjC,SAAS,CAAC,KAAK,CAAC,CAAC,IAAI,CAAC,QAAQ,CAAC,CAAC;yBACjC;qBACF;iBACF;aACF;SACF;QACD,SAAS,CAAC,KAAK,CAAC,CAAC,IAAI,CAAC,GAAG,CAAC,CAAC;KAC5B;IACD,OAAO,SAAS,CAAC;AACnB,CAAC"}
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import { partialScore } from './partialScore';
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export function exploreTreeRec(props, currentIndex, partial, store) {
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const { nSources, restrictionByCS, timeout, timeStart, maxSolutions, targets, predictions, lowerBoundScore, nbAllowedUnAssigned, possibleAssignmentMap, useIntegrationRestriction, diaIDPeerPossibleAssignment, } = props;
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const currentDate = new Date();
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if (currentDate.getTime() - timeStart > timeout) {
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new Error('timeout expired');
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return store;
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}
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const diaID = diaIDPeerPossibleAssignment[currentIndex];
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const possibleAssignments = possibleAssignmentMap[diaID];
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for (let targetID of possibleAssignments) {
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partial[currentIndex] = targetID;
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let score = partialScore(partial, {
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useIntegrationRestriction,
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diaIDPeerPossibleAssignment,
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nbAllowedUnAssigned,
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restrictionByCS,
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predictions,
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targets,
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});
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if (score === 0) {
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if (targetID === '*') {
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partial[currentIndex] = null;
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}
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continue;
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}
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if (currentIndex === nSources - 1 && score >= lowerBoundScore) {
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addSolution(store, { predictions, partial, score, maxSolutions });
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}
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else if (currentIndex < nSources - 1) {
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exploreTreeRec({
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nSources,
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restrictionByCS,
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timeout,
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timeStart,
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maxSolutions,
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targets,
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predictions,
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lowerBoundScore,
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nbAllowedUnAssigned,
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possibleAssignmentMap,
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useIntegrationRestriction,
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diaIDPeerPossibleAssignment,
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}, currentIndex + 1, JSON.parse(JSON.stringify(partial)), store);
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}
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}
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}
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function addSolution(store, props) {
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let { score, maxSolutions, partial, predictions } = props;
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score /= doubleAssignmentPenalty(partial, predictions);
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store.nSolutions++;
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let solution = {
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assignment: JSON.parse(JSON.stringify(partial)),
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score: score,
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};
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if (store.nSolutions >= maxSolutions) {
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if (solution.score > store.solutions.last().score) {
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store.solutions.pollLast();
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store.solutions.add(solution);
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}
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}
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else {
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store.solutions.add(solution);
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store.nSolutions++;
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}
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}
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function doubleAssignmentPenalty(partial, predictions) {
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const nbSources = Object.keys(predictions).length;
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let assignments = new Set(partial);
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let nbDoubleAssignment = nbSources - assignments.size;
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return nbDoubleAssignment > 0 ? 2 * nbDoubleAssignment : 1;
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}
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//# sourceMappingURL=exploreTreeRec.js.map
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{"version":3,"file":"exploreTreeRec.js","sourceRoot":"","sources":["../../../src/assignment/utils/exploreTreeRec.ts"],"names":[],"mappings":"AAQA,OAAO,EAAE,YAAY,EAAE,MAAM,gBAAgB,CAAC;AAgB9C,MAAM,UAAU,cAAc,CAC5B,KAA0B,EAC1B,YAAoB,EACpB,OAA6B,EAC7B,KAAyB;IAEzB,MAAM,EACJ,QAAQ,EACR,eAAe,EACf,OAAO,EACP,SAAS,EACT,YAAY,EACZ,OAAO,EACP,WAAW,EACX,eAAe,EACf,mBAAmB,EACnB,qBAAqB,EACrB,yBAAyB,EACzB,2BAA2B,GAC5B,GAAG,KAAK,CAAC;IAEV,MAAM,WAAW,GAAG,IAAI,IAAI,EAAE,CAAC;IAC/B,IAAI,WAAW,CAAC,OAAO,EAAE,GAAG,SAAS,GAAG,OAAO,EAAE;QAC/C,IAAI,KAAK,CAAC,iBAAiB,CAAC,CAAC;QAC7B,OAAO,KAAK,CAAC;KACd;IAED,MAAM,KAAK,GAAG,2BAA2B,CAAC,YAAY,CAAC,CAAC;IACxD,MAAM,mBAAmB,GAAG,qBAAqB,CAAC,KAAK,CAAC,CAAC;IACzD,KAAK,IAAI,QAAQ,IAAI,mBAAmB,EAAE;QACxC,OAAO,CAAC,YAAY,CAAC,GAAG,QAAQ,CAAC;QACjC,IAAI,KAAK,GAAG,YAAY,CAAC,OAAO,EAAE;YAChC,yBAAyB;YACzB,2BAA2B;YAC3B,mBAAmB;YACnB,eAAe;YACf,WAAW;YACX,OAAO;SACR,CAAC,CAAC;QAEH,IAAI,KAAK,KAAK,CAAC,EAAE;YACf,IAAI,QAAQ,KAAK,GAAG,EAAE;gBACpB,OAAO,CAAC,YAAY,CAAC,GAAG,IAAI,CAAC;aAC9B;YACD,SAAS;SACV;QAED,IAAI,YAAY,KAAK,QAAQ,GAAG,CAAC,IAAI,KAAK,IAAI,eAAe,EAAE;YAC7D,WAAW,CAAC,KAAK,EAAE,EAAE,WAAW,EAAE,OAAO,EAAE,KAAK,EAAE,YAAY,EAAE,CAAC,CAAC;SACnE;aAAM,IAAI,YAAY,GAAG,QAAQ,GAAG,CAAC,EAAE;YACtC,cAAc,CACZ;gBACE,QAAQ;gBACR,eAAe;gBACf,OAAO;gBACP,SAAS;gBACT,YAAY;gBACZ,OAAO;gBACP,WAAW;gBACX,eAAe;gBACf,mBAAmB;gBACnB,qBAAqB;gBACrB,yBAAyB;gBACzB,2BAA2B;aAC5B,EACD,YAAY,GAAG,CAAC,EAChB,IAAI,CAAC,KAAK,CAAC,IAAI,CAAC,SAAS,CAAC,OAAO,CAAC,CAAC,EACnC,KAAK,CACN,CAAC;SACH;KACF;AACH,CAAC;AAcD,SAAS,WAAW,CAAC,KAAyB,EAAE,KAAuB;IACrE,IAAI,EAAE,KAAK,EAAE,YAAY,EAAE,OAAO,EAAE,WAAW,EAAE,GAAG,KAAK,CAAC;IAC1D,KAAK,IAAI,uBAAuB,CAAC,OAAO,EAAE,WAAW,CAAC,CAAC;IACvD,KAAK,CAAC,UAAU,EAAE,CAAC;IACnB,IAAI,QAAQ,GAAuB;QACjC,UAAU,EAAE,IAAI,CAAC,KAAK,CAAC,IAAI,CAAC,SAAS,CAAC,OAAO,CAAC,CAAC;QAC/C,KAAK,EAAE,KAAK;KACb,CAAC;IAEF,IAAI,KAAK,CAAC,UAAU,IAAI,YAAY,EAAE;QACpC,IAAI,QAAQ,CAAC,KAAK,GAAG,KAAK,CAAC,SAAS,CAAC,IAAI,EAAE,CAAC,KAAK,EAAE;YACjD,KAAK,CAAC,SAAS,CAAC,QAAQ,EAAE,CAAC;YAC3B,KAAK,CAAC,SAAS,CAAC,GAAG,CAAC,QAAQ,CAAC,CAAC;SAC/B;KACF;SAAM;QACL,KAAK,CAAC,SAAS,CAAC,GAAG,CAAC,QAAQ,CAAC,CAAC;QAC9B,KAAK,CAAC,UAAU,EAAE,CAAC;KACpB;AACH,CAAC;AAED,SAAS,uBAAuB,CAC9B,OAA6B,EAC7B,WAAqC;IAErC,MAAM,SAAS,GAAG,MAAM,CAAC,IAAI,CAAC,WAAW,CAAC,CAAC,MAAM,CAAC;IAClD,IAAI,WAAW,GAAG,IAAI,GAAG,CAAC,OAAO,CAAC,CAAC;IACnC,IAAI,kBAAkB,GAAG,SAAS,GAAG,WAAW,CAAC,IAAI,CAAC;IACtD,OAAO,kBAAkB,GAAG,CAAC,CAAC,CAAC,CAAC,CAAC,GAAG,kBAAkB,CAAC,CAAC,CAAC,CAAC,CAAC;AAC7D,CAAC"}
|
|
@@ -0,0 +1,10 @@
|
|
|
1
|
+
const BASE62 = '0123456789abcdefghijklmnopqrstuvwxyzABCDEFGHIJKLMNOPQRSTUVWXYZ';
|
|
2
|
+
const LENGTH = 8;
|
|
3
|
+
export default function generateID() {
|
|
4
|
+
let id = '';
|
|
5
|
+
for (let i = 0; i < LENGTH; i++) {
|
|
6
|
+
id += BASE62.charAt(Math.floor(Math.random() * 62));
|
|
7
|
+
}
|
|
8
|
+
return id;
|
|
9
|
+
}
|
|
10
|
+
//# sourceMappingURL=generateID.js.map
|
|
@@ -0,0 +1 @@
|
|
|
1
|
+
{"version":3,"file":"generateID.js","sourceRoot":"","sources":["../../../src/assignment/utils/generateID.ts"],"names":[],"mappings":"AAAA,MAAM,MAAM,GAAG,gEAAgE,CAAC;AAEhF,MAAM,MAAM,GAAG,CAAC,CAAC;AAEjB,MAAM,CAAC,OAAO,UAAU,UAAU;IAChC,IAAI,EAAE,GAAG,EAAE,CAAC;IACZ,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,MAAM,EAAE,CAAC,EAAE,EAAE;QAC/B,EAAE,IAAI,MAAM,CAAC,MAAM,CAAC,IAAI,CAAC,KAAK,CAAC,IAAI,CAAC,MAAM,EAAE,GAAG,EAAE,CAAC,CAAC,CAAC;KACrD;IACD,OAAO,EAAE,CAAC;AACZ,CAAC"}
|
|
@@ -0,0 +1,87 @@
|
|
|
1
|
+
export function partialScore(partial, options) {
|
|
2
|
+
const { useIntegrationRestriction, diaIDPeerPossibleAssignment, nbAllowedUnAssigned, restrictionByCS, predictions, targets, } = options;
|
|
3
|
+
const { useChemicalShiftScore } = restrictionByCS;
|
|
4
|
+
let countStars = 0;
|
|
5
|
+
let totalPartial = partial.length;
|
|
6
|
+
let partialInverse = {};
|
|
7
|
+
let activeDomainOnPrediction = [];
|
|
8
|
+
for (let i = 0; i < partial.length; i++) {
|
|
9
|
+
const targetID = partial[i];
|
|
10
|
+
if (targetID && targetID !== '*') {
|
|
11
|
+
activeDomainOnPrediction.push(i);
|
|
12
|
+
if (!partialInverse[targetID]) {
|
|
13
|
+
partialInverse[targetID] = [];
|
|
14
|
+
}
|
|
15
|
+
partialInverse[targetID].push(diaIDPeerPossibleAssignment[i]);
|
|
16
|
+
}
|
|
17
|
+
if (targetID === '*')
|
|
18
|
+
countStars++;
|
|
19
|
+
}
|
|
20
|
+
if (countStars > nbAllowedUnAssigned)
|
|
21
|
+
return 0;
|
|
22
|
+
const activeDomainOnTarget = Object.keys(partialInverse);
|
|
23
|
+
if (activeDomainOnTarget.length === 0) {
|
|
24
|
+
return 0;
|
|
25
|
+
}
|
|
26
|
+
if (useIntegrationRestriction) {
|
|
27
|
+
for (let targetID of activeDomainOnTarget) {
|
|
28
|
+
let targetToSource = partialInverse[targetID];
|
|
29
|
+
let total = 0;
|
|
30
|
+
for (const diaID of targetToSource) {
|
|
31
|
+
const prediction = predictions[diaID];
|
|
32
|
+
total += prediction.allHydrogens;
|
|
33
|
+
}
|
|
34
|
+
const { integration } = targets[targetID];
|
|
35
|
+
if (total - integration >= 0.5) {
|
|
36
|
+
return 0;
|
|
37
|
+
}
|
|
38
|
+
}
|
|
39
|
+
}
|
|
40
|
+
//chemical shift score
|
|
41
|
+
let chemicalShiftScore = useChemicalShiftScore
|
|
42
|
+
? chemicalShiftScoring(partial, options)
|
|
43
|
+
: 1;
|
|
44
|
+
const penaltyByStarts = countStars / totalPartial;
|
|
45
|
+
return chemicalShiftScore - penaltyByStarts;
|
|
46
|
+
}
|
|
47
|
+
function chemicalShiftScoring(partial, options) {
|
|
48
|
+
const { tolerance } = options.restrictionByCS;
|
|
49
|
+
const { diaIDPeerPossibleAssignment, predictions, targets } = options;
|
|
50
|
+
let chemicalShiftScore = 0;
|
|
51
|
+
let count = 0;
|
|
52
|
+
for (let index = 0; index < partial.length; index++) {
|
|
53
|
+
const targetID = partial[index];
|
|
54
|
+
if (targetID && targetID !== '*') {
|
|
55
|
+
count++;
|
|
56
|
+
let diaID = diaIDPeerPossibleAssignment[index];
|
|
57
|
+
let source = predictions[diaID];
|
|
58
|
+
let target = targets[targetID];
|
|
59
|
+
let error = tolerance;
|
|
60
|
+
if (source.error) {
|
|
61
|
+
error = Math.max(source.error, tolerance);
|
|
62
|
+
}
|
|
63
|
+
if (typeof source.delta === 'undefined') {
|
|
64
|
+
// Chemical shift is not a restriction
|
|
65
|
+
chemicalShiftScore += 1;
|
|
66
|
+
}
|
|
67
|
+
else {
|
|
68
|
+
const delta = target.signals && target.signals.length > 0
|
|
69
|
+
? target.signals[0].delta
|
|
70
|
+
: (target.to + target.from) / 2;
|
|
71
|
+
let diff = Math.abs(source.delta - delta);
|
|
72
|
+
if (diff < error) {
|
|
73
|
+
chemicalShiftScore += 1;
|
|
74
|
+
}
|
|
75
|
+
else {
|
|
76
|
+
diff = Math.abs(diff - error);
|
|
77
|
+
chemicalShiftScore += (-0.25 / error) * diff + 1;
|
|
78
|
+
}
|
|
79
|
+
}
|
|
80
|
+
}
|
|
81
|
+
}
|
|
82
|
+
if (count > 0) {
|
|
83
|
+
chemicalShiftScore /= count;
|
|
84
|
+
}
|
|
85
|
+
return chemicalShiftScore;
|
|
86
|
+
}
|
|
87
|
+
//# sourceMappingURL=partialScore.js.map
|
|
@@ -0,0 +1 @@
|
|
|
1
|
+
{"version":3,"file":"partialScore.js","sourceRoot":"","sources":["../../../src/assignment/utils/partialScore.ts"],"names":[],"mappings":"AAoBA,MAAM,UAAU,YAAY,CAC1B,OAA6B,EAC7B,OAA4B;IAE5B,MAAM,EACJ,yBAAyB,EACzB,2BAA2B,EAC3B,mBAAmB,EACnB,eAAe,EACf,WAAW,EACX,OAAO,GACR,GAAG,OAAO,CAAC;IACZ,MAAM,EAAE,qBAAqB,EAAE,GAAG,eAAe,CAAC;IAClD,IAAI,UAAU,GAAG,CAAC,CAAC;IACnB,IAAI,YAAY,GAAG,OAAO,CAAC,MAAM,CAAC;IAClC,IAAI,cAAc,GAEd,EAAE,CAAC;IACP,IAAI,wBAAwB,GAAa,EAAE,CAAC;IAE5C,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,OAAO,CAAC,MAAM,EAAE,CAAC,EAAE,EAAE;QACvC,MAAM,QAAQ,GAAG,OAAO,CAAC,CAAC,CAAC,CAAC;QAC5B,IAAI,QAAQ,IAAI,QAAQ,KAAK,GAAG,EAAE;YAChC,wBAAwB,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC;YACjC,IAAI,CAAC,cAAc,CAAC,QAAQ,CAAC,EAAE;gBAC7B,cAAc,CAAC,QAAQ,CAAC,GAAG,EAAE,CAAC;aAC/B;YACD,cAAc,CAAC,QAAQ,CAAC,CAAC,IAAI,CAAC,2BAA2B,CAAC,CAAC,CAAC,CAAC,CAAC;SAC/D;QACD,IAAI,QAAQ,KAAK,GAAG;YAAE,UAAU,EAAE,CAAC;KACpC;IACD,IAAI,UAAU,GAAG,mBAAmB;QAAE,OAAO,CAAC,CAAC;IAE/C,MAAM,oBAAoB,GAAG,MAAM,CAAC,IAAI,CAAC,cAAc,CAAC,CAAC;IAEzD,IAAI,oBAAoB,CAAC,MAAM,KAAK,CAAC,EAAE;QACrC,OAAO,CAAC,CAAC;KACV;IAED,IAAI,yBAAyB,EAAE;QAC7B,KAAK,IAAI,QAAQ,IAAI,oBAAoB,EAAE;YACzC,IAAI,cAAc,GAAG,cAAc,CAAC,QAAQ,CAAC,CAAC;YAC9C,IAAI,KAAK,GAAG,CAAC,CAAC;YACd,KAAK,MAAM,KAAK,IAAI,cAAc,EAAE;gBAClC,MAAM,UAAU,GAAG,WAAW,CAAC,KAAK,CAAC,CAAC;gBACtC,KAAK,IAAI,UAAU,CAAC,YAAY,CAAC;aAClC;YAED,MAAM,EAAE,WAAW,EAAE,GAAG,OAAO,CAAC,QAAQ,CAAC,CAAC;YAC1C,IAAI,KAAK,GAAG,WAAW,IAAI,GAAG,EAAE;gBAC9B,OAAO,CAAC,CAAC;aACV;SACF;KACF;IAED,sBAAsB;IACtB,IAAI,kBAAkB,GAAG,qBAAqB;QAC5C,CAAC,CAAC,oBAAoB,CAAC,OAAO,EAAE,OAAO,CAAC;QACxC,CAAC,CAAC,CAAC,CAAC;IAEN,MAAM,eAAe,GAAG,UAAU,GAAG,YAAY,CAAC;IAElD,OAAO,kBAAkB,GAAG,eAAe,CAAC;AAC9C,CAAC;AAED,SAAS,oBAAoB,CAC3B,OAA6B,EAC7B,OAA4B;IAE5B,MAAM,EAAE,SAAS,EAAE,GAAG,OAAO,CAAC,eAAe,CAAC;IAC9C,MAAM,EAAE,2BAA2B,EAAE,WAAW,EAAE,OAAO,EAAE,GAAG,OAAO,CAAC;IAEtE,IAAI,kBAAkB,GAAG,CAAC,CAAC;IAC3B,IAAI,KAAK,GAAG,CAAC,CAAC;IACd,KAAK,IAAI,KAAK,GAAG,CAAC,EAAE,KAAK,GAAG,OAAO,CAAC,MAAM,EAAE,KAAK,EAAE,EAAE;QACnD,MAAM,QAAQ,GAAG,OAAO,CAAC,KAAK,CAAC,CAAC;QAChC,IAAI,QAAQ,IAAI,QAAQ,KAAK,GAAG,EAAE;YAChC,KAAK,EAAE,CAAC;YACR,IAAI,KAAK,GAAG,2BAA2B,CAAC,KAAK,CAAC,CAAC;YAC/C,IAAI,MAAM,GAAG,WAAW,CAAC,KAAK,CAAC,CAAC;YAChC,IAAI,MAAM,GAAG,OAAO,CAAC,QAAQ,CAAC,CAAC;YAC/B,IAAI,KAAK,GAAG,SAAS,CAAC;YACtB,IAAI,MAAM,CAAC,KAAK,EAAE;gBAChB,KAAK,GAAG,IAAI,CAAC,GAAG,CAAC,MAAM,CAAC,KAAK,EAAE,SAAS,CAAC,CAAC;aAC3C;YACD,IAAI,OAAO,MAAM,CAAC,KAAK,KAAK,WAAW,EAAE;gBACvC,sCAAsC;gBACtC,kBAAkB,IAAI,CAAC,CAAC;aACzB;iBAAM;gBACL,MAAM,KAAK,GACT,MAAM,CAAC,OAAO,IAAI,MAAM,CAAC,OAAO,CAAC,MAAM,GAAG,CAAC;oBACzC,CAAC,CAAC,MAAM,CAAC,OAAO,CAAC,CAAC,CAAC,CAAC,KAAK;oBACzB,CAAC,CAAC,CAAC,MAAM,CAAC,EAAE,GAAG,MAAM,CAAC,IAAI,CAAC,GAAG,CAAC,CAAC;gBACpC,IAAI,IAAI,GAAG,IAAI,CAAC,GAAG,CAAC,MAAM,CAAC,KAAK,GAAG,KAAK,CAAC,CAAC;gBAC1C,IAAI,IAAI,GAAG,KAAK,EAAE;oBAChB,kBAAkB,IAAI,CAAC,CAAC;iBACzB;qBAAM;oBACL,IAAI,GAAG,IAAI,CAAC,GAAG,CAAC,IAAI,GAAG,KAAK,CAAC,CAAC;oBAC9B,kBAAkB,IAAI,CAAC,CAAC,IAAI,GAAG,KAAK,CAAC,GAAG,IAAI,GAAG,CAAC,CAAC;iBAClD;aACF;SACF;KACF;IACD,IAAI,KAAK,GAAG,CAAC,EAAE;QACb,kBAAkB,IAAI,KAAK,CAAC;KAC7B;IACD,OAAO,kBAAkB,CAAC;AAC5B,CAAC"}
|
package/lib-esm/index.js
CHANGED
|
@@ -1,8 +1,3 @@
|
|
|
1
|
-
/**
|
|
2
|
-
* @typedef {Object} DataXY
|
|
3
|
-
* @property {Array<Number>} x Array of x values
|
|
4
|
-
* @property {Array<Number>} y Array of y values
|
|
5
|
-
*/
|
|
6
1
|
export * from './constants/gyromagneticRatio';
|
|
7
2
|
export * from './constants/impurities';
|
|
8
3
|
export * from './constants/couplingPatterns';
|
|
@@ -13,6 +8,8 @@ export * from './prediction/predictCOSY';
|
|
|
13
8
|
export * from './prediction/predictHSQC';
|
|
14
9
|
export * from './prediction/predictHMBC';
|
|
15
10
|
export * from './prediction/predictAll';
|
|
11
|
+
export * from './assignment/get1HAssignments';
|
|
12
|
+
export * from './assignment/get13CAssignments';
|
|
16
13
|
export * from './ranges/rangesToACS';
|
|
17
14
|
export * from './ranges/rangesToXY';
|
|
18
15
|
export * from './signals/signalsToRanges';
|
package/lib-esm/index.js.map
CHANGED
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"index.js","sourceRoot":"","sources":["../src/index.ts"],"names":[],"mappings":"AAAA
|
|
1
|
+
{"version":3,"file":"index.js","sourceRoot":"","sources":["../src/index.ts"],"names":[],"mappings":"AAAA,cAAc,+BAA+B,CAAC;AAC9C,cAAc,wBAAwB,CAAC;AACvC,cAAc,8BAA8B,CAAC;AAE7C,cAAc,+BAA+B,CAAC;AAE9C,cAAc,4BAA4B,CAAC;AAC3C,cAAc,4BAA4B,CAAC;AAC3C,cAAc,0BAA0B,CAAC;AACzC,cAAc,0BAA0B,CAAC;AACzC,cAAc,0BAA0B,CAAC;AACzC,cAAc,yBAAyB,CAAC;AAExC,cAAc,+BAA+B,CAAC;AAC9C,cAAc,gCAAgC,CAAC;AAE/C,cAAc,sBAAsB,CAAC;AACrC,cAAc,qBAAqB,CAAC;AAEpC,cAAc,2BAA2B,CAAC;AAC1C,cAAc,uBAAuB,CAAC;AACtC,cAAc,wBAAwB,CAAC;AAEvC,cAAc,uBAAuB,CAAC;AACtC,cAAc,6BAA6B,CAAC;AAE5C,cAAc,yBAAyB,CAAC;AACxC,cAAc,0BAA0B,CAAC;AAEzC,cAAc,2BAA2B,CAAC;AAC1C,cAAc,uBAAuB,CAAC;AAEtC,cAAc,yBAAyB,CAAC;AACxC,cAAc,8BAA8B,CAAC;AAC7C,cAAc,8BAA8B,CAAC"}
|
|
@@ -29,7 +29,7 @@ function checkImpurity(peakList, impurity, options) {
|
|
|
29
29
|
while (i--) {
|
|
30
30
|
j = peakList.length;
|
|
31
31
|
while (j--) {
|
|
32
|
-
tolerance = error + peakList[j].
|
|
32
|
+
tolerance = error + peakList[j].width;
|
|
33
33
|
difference = Math.abs(impurity[i].shift - peakList[j].x);
|
|
34
34
|
if (difference < tolerance) {
|
|
35
35
|
// && (impurity[i].multiplicity === '' || (impurity[i].multiplicity.indexOf(peakList[j].multiplicity)) { // some impurities has multiplicities like 'bs' but at presents it is unsupported
|
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"peaksFilterImpurities.js","sourceRoot":"","sources":["../../src/peaks/peaksFilterImpurities.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,UAAU,EAAE,MAAM,yBAAyB,CAAC;AAIrD,MAAM,OAAO,GAAG,CAAC,SAAS,EAAE,KAAK,EAAE,KAAK,CAAC,CAAC;AA2B1C;;GAEG;AAEH,MAAM,UAAU,qBAAqB,CACnC,QAAqB,EACrB,UAAwC,EAAE;IAE1C,IAAI,EAAE,OAAO,EAAE,KAAK,GAAG,KAAK,EAAE,MAAM,GAAG,KAAK,EAAE,GAAG,OAAO,CAAC;IAEzD,IAAI,OAAO,EAAE;QACX,IAAI,OAAO,KAAK,UAAU;YAAE,OAAO,GAAG,MAAM,CAAC;QAC7C,IAAI,OAAO,KAAK,MAAM;YAAE,OAAO,GAAG,OAAO,CAAC;QAC1C,IAAI,iBAAiB,GAAG,UAAU,CAAC,OAAO,CAAC,CAAC;QAC5C,KAAK,IAAI,QAAQ,IAAI,OAAO,EAAE;YAC5B,IAAI,cAAc,GAAG,iBAAiB,CAAC,QAAQ,CAAC,CAAC;YACjD,aAAa,CAAC,QAAQ,EAAE,cAAc,EAAE;gBACtC,KAAK;gBACL,MAAM;gBACN,IAAI,EAAE,QAAQ;aACf,CAAC,CAAC;SACJ;KACF;IACD,OAAO,QAAQ,CAAC;AAClB,CAAC;AAED,SAAS,aAAa,CACpB,QAAqB,EACrB,QAA0B,EAC1B,OAA6B;IAE7B,IAAI,EAAE,IAAI,EAAE,KAAK,EAAE,MAAM,EAAE,GAAG,OAAO,CAAC;IACtC,IAAI,CAAC,EAAE,SAAS,EAAE,UAAU,CAAC;IAC7B,IAAI,CAAC,GAAG,QAAQ,CAAC,MAAM,CAAC;IACxB,OAAO,CAAC,EAAE,EAAE;QACV,CAAC,GAAG,QAAQ,CAAC,MAAM,CAAC;QACpB,OAAO,CAAC,EAAE,EAAE;YACV,SAAS,GAAG,KAAK,GAAG,QAAQ,CAAC,CAAC,CAAC,CAAC,KAAK,CAAC
|
|
1
|
+
{"version":3,"file":"peaksFilterImpurities.js","sourceRoot":"","sources":["../../src/peaks/peaksFilterImpurities.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,UAAU,EAAE,MAAM,yBAAyB,CAAC;AAIrD,MAAM,OAAO,GAAG,CAAC,SAAS,EAAE,KAAK,EAAE,KAAK,CAAC,CAAC;AA2B1C;;GAEG;AAEH,MAAM,UAAU,qBAAqB,CACnC,QAAqB,EACrB,UAAwC,EAAE;IAE1C,IAAI,EAAE,OAAO,EAAE,KAAK,GAAG,KAAK,EAAE,MAAM,GAAG,KAAK,EAAE,GAAG,OAAO,CAAC;IAEzD,IAAI,OAAO,EAAE;QACX,IAAI,OAAO,KAAK,UAAU;YAAE,OAAO,GAAG,MAAM,CAAC;QAC7C,IAAI,OAAO,KAAK,MAAM;YAAE,OAAO,GAAG,OAAO,CAAC;QAC1C,IAAI,iBAAiB,GAAG,UAAU,CAAC,OAAO,CAAC,CAAC;QAC5C,KAAK,IAAI,QAAQ,IAAI,OAAO,EAAE;YAC5B,IAAI,cAAc,GAAG,iBAAiB,CAAC,QAAQ,CAAC,CAAC;YACjD,aAAa,CAAC,QAAQ,EAAE,cAAc,EAAE;gBACtC,KAAK;gBACL,MAAM;gBACN,IAAI,EAAE,QAAQ;aACf,CAAC,CAAC;SACJ;KACF;IACD,OAAO,QAAQ,CAAC;AAClB,CAAC;AAED,SAAS,aAAa,CACpB,QAAqB,EACrB,QAA0B,EAC1B,OAA6B;IAE7B,IAAI,EAAE,IAAI,EAAE,KAAK,EAAE,MAAM,EAAE,GAAG,OAAO,CAAC;IACtC,IAAI,CAAC,EAAE,SAAS,EAAE,UAAU,CAAC;IAC7B,IAAI,CAAC,GAAG,QAAQ,CAAC,MAAM,CAAC;IACxB,OAAO,CAAC,EAAE,EAAE;QACV,CAAC,GAAG,QAAQ,CAAC,MAAM,CAAC;QACpB,OAAO,CAAC,EAAE,EAAE;YACV,SAAS,GAAG,KAAK,GAAG,QAAQ,CAAC,CAAC,CAAC,CAAC,KAAK,CAAC;YACtC,UAAU,GAAG,IAAI,CAAC,GAAG,CAAC,QAAQ,CAAC,CAAC,CAAC,CAAC,KAAK,GAAG,QAAQ,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC;YACzD,IAAI,UAAU,GAAG,SAAS,EAAE;gBAC1B,0LAA0L;gBAC1L,IAAI,MAAM,EAAE;oBACV,QAAQ,CAAC,MAAM,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC;iBACvB;qBAAM;oBACL,QAAQ,CAAC,CAAC,CAAC,CAAC,IAAI,GAAG,IAAI,CAAC;iBACzB;aACF;SACF;KACF;AACH,CAAC"}
|
|
@@ -17,22 +17,20 @@ const assignSignal = (peak, frequency, nucleus) => {
|
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17
17
|
delta: NaN,
|
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18
18
|
nbPeaks: 1,
|
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19
19
|
kind: 'signal',
|
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20
|
-
startX: peak.x - peak.
|
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21
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-
stopX: peak.x + peak.
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20
|
+
startX: peak.x - peak.width,
|
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21
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+
stopX: peak.x + peak.width,
|
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22
22
|
observe: frequency,
|
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23
23
|
nucleus,
|
|
24
24
|
integralData: {
|
|
25
|
-
from: peak.x - peak.
|
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26
|
-
to: peak.x + peak.
|
|
25
|
+
from: peak.x - peak.width * 3,
|
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26
|
+
to: peak.x + peak.width * 3,
|
|
27
27
|
value: 0,
|
|
28
28
|
},
|
|
29
29
|
peaks: [
|
|
30
30
|
{
|
|
31
31
|
x: peak.x,
|
|
32
32
|
intensity: peak.y,
|
|
33
|
-
|
|
34
|
-
width: peak.shape.width,
|
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35
|
-
},
|
|
33
|
+
width: peak.width,
|
|
36
34
|
},
|
|
37
35
|
],
|
|
38
36
|
};
|
|
@@ -81,9 +79,7 @@ export function peaksToRanges(data, peakList, options = {}) {
|
|
|
81
79
|
peaksO.push({
|
|
82
80
|
x: peakR.x,
|
|
83
81
|
y: peakR.intensity,
|
|
84
|
-
|
|
85
|
-
width: peakR.shape.width,
|
|
86
|
-
},
|
|
82
|
+
width: peakR.width,
|
|
87
83
|
});
|
|
88
84
|
signal.mask.splice(j, 1);
|
|
89
85
|
signal.mask2.splice(j, 1);
|
|
@@ -194,19 +190,17 @@ function detectSignals(data, peakList, options = {}) {
|
|
|
194
190
|
signals.push(signal1D);
|
|
195
191
|
}
|
|
196
192
|
else {
|
|
197
|
-
let tmp = peak.x + peak.
|
|
193
|
+
let tmp = peak.x + peak.width;
|
|
198
194
|
signal1D.stopX = Math.max(signal1D.stopX, tmp);
|
|
199
195
|
signal1D.startX = Math.min(signal1D.startX, tmp);
|
|
200
196
|
signal1D.nbPeaks++;
|
|
201
197
|
signal1D.peaks.push({
|
|
202
198
|
x: peak.x,
|
|
203
199
|
intensity: peak.y,
|
|
204
|
-
|
|
205
|
-
width: peak.shape.width,
|
|
206
|
-
},
|
|
200
|
+
width: peak.width,
|
|
207
201
|
});
|
|
208
|
-
signal1D.integralData.from = Math.min(signal1D.integralData.from, peak.x - peak.
|
|
209
|
-
signal1D.integralData.to = Math.max(signal1D.integralData.to, peak.x + peak.
|
|
202
|
+
signal1D.integralData.from = Math.min(signal1D.integralData.from, peak.x - peak.width * 3);
|
|
203
|
+
signal1D.integralData.to = Math.max(signal1D.integralData.to, peak.x + peak.width * 3);
|
|
210
204
|
if (peak.kind)
|
|
211
205
|
signal1D.kind = peak.kind;
|
|
212
206
|
}
|
|
@@ -250,6 +244,6 @@ function detectSignals(data, peakList, options = {}) {
|
|
|
250
244
|
* @private
|
|
251
245
|
*/
|
|
252
246
|
function computeArea(peak) {
|
|
253
|
-
return Math.abs(peak.intensity * peak.
|
|
247
|
+
return Math.abs(peak.intensity * peak.width * 1.57); // todo add an option with this value: 1.772453851
|
|
254
248
|
}
|
|
255
249
|
//# sourceMappingURL=peaksToRanges.js.map
|
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"peaksToRanges.js","sourceRoot":"","sources":["../../src/peaks/peaksToRanges.ts"],"names":[],"mappings":"AACA,OAAO,EAAE,aAAa,EAAE,MAAM,uBAAuB,CAAC;AAOtD,OAAO,SAAS,MAAM,kBAAkB,CAAC;AAEzC,OAAO,EAAE,UAAU,EAAE,MAAM,mBAAmB,CAAC;AA8D/C,SAAS,8BAA8B,CACrC,MAAoB;IAEpB,uBAAuB;IACvB,mEAAmE;IACnE,IAAI,CAAC,MAAM,CAAC,IAAI;QAAE,MAAM,IAAI,KAAK,CAAC,oCAAoC,CAAC,CAAC;IACxE,IAAI,CAAC,MAAM,CAAC,KAAK;QAAE,MAAM,IAAI,KAAK,CAAC,qCAAqC,CAAC,CAAC;IAC1E,IAAI,CAAC,MAAM,CAAC,WAAW,EAAE;QACvB,MAAM,IAAI,KAAK,CAAC,2CAA2C,CAAC,CAAC;KAC9D;AACH,CAAC;AAED,MAAM,YAAY,GAAG,CACnB,IAAe,EACf,SAAiB,EACjB,OAAe,EACD,EAAE;IAChB,OAAO;QACL,KAAK,EAAE,GAAG;QACV,OAAO,EAAE,CAAC;QACV,IAAI,EAAE,QAAQ;QACd,MAAM,EAAE,IAAI,CAAC,CAAC,GAAG,IAAI,CAAC,KAAK
|
|
1
|
+
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@@ -1,6 +1,5 @@
|
|
|
1
1
|
import LM from 'ml-levenberg-marquardt';
|
|
2
|
-
import {
|
|
3
|
-
const { fct: gaussian2DFct } = gaussian2D;
|
|
2
|
+
import { Gaussian2D } from 'ml-peak-shape-generator';
|
|
4
3
|
const direction8X = [-1, -1, -1, 0, 0, 1, 1, 1];
|
|
5
4
|
const direction8Y = [-1, 0, 1, -1, 1, -1, 0, 1];
|
|
6
5
|
const direction16X = [-2, -2, -2, -2, -2, -1, -1, 0, 0, 1, 1, 2, 2, 2, 2, 2];
|
|
@@ -106,6 +105,7 @@ function fitGaussian(data, options) {
|
|
|
106
105
|
};
|
|
107
106
|
}
|
|
108
107
|
function paramGaussian2D(intervalX, intervalY, nCols) {
|
|
108
|
+
const gaussian2D = new Gaussian2D();
|
|
109
109
|
return (p) => {
|
|
110
110
|
return (t) => {
|
|
111
111
|
let nL = p.length / 5;
|
|
@@ -113,9 +113,10 @@ function paramGaussian2D(intervalX, intervalY, nCols) {
|
|
|
113
113
|
let xIndex = t % nCols;
|
|
114
114
|
let yIndex = (t - xIndex) / nCols;
|
|
115
115
|
for (let i = 0; i < nL; i++) {
|
|
116
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+
gaussian2D.fwhm = { x: p[i + 3 * nL], y: p[i + 4 * nL] };
|
|
116
117
|
result +=
|
|
117
118
|
p[i + 2 * nL] *
|
|
118
|
-
|
|
119
|
+
gaussian2D.fct((xIndex - p[i]) * intervalX, (yIndex - p[i + nL]) * intervalY);
|
|
119
120
|
}
|
|
120
121
|
return result;
|
|
121
122
|
};
|
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"determineRealTop.js","sourceRoot":"","sources":["../../../src/peaks/util/determineRealTop.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,MAAM,wBAAwB,CAAC;AACxC,OAAO,EAAE,UAAU,EAAE,MAAM,yBAAyB,CAAC;AAIrD,MAAM,
|
|
1
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+
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