@zakodium/nmrium-core 0.4.5 → 0.4.7
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/dist/nmrium-core.d.ts +13 -4
- package/dist/nmrium-core.js +3 -3
- package/package.json +2 -2
package/dist/nmrium-core.d.ts
CHANGED
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@@ -214,7 +214,7 @@ declare interface ContourOptions_2 {
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export declare type ContoursLevels = Record<string, Level>;
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-
export declare const CURRENT_EXPORT_VERSION =
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export declare const CURRENT_EXPORT_VERSION = 11;
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export declare type CustomWorkspaces = Record<string, InnerWorkspace>;
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@@ -477,9 +477,17 @@ export declare type MoleculesView = Record<string, MoleculeView>;
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export declare interface MoleculeView {
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floating: FloatingElement;
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/**
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-
* Show/Hide
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* Show/Hide molecule label.
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*/
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-
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showLabel: boolean;
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/**
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* Defines which type of annotation is displayed on atoms.
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* "none": Show atoms only
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* "atom-numbers": Show atom numbers
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* "custom-labels": Show custom atom labels
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* @default "none"
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*/
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atomAnnotation: 'none' | 'atom-numbers' | 'custom-labels';
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}
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declare type MultipleSpectraAnalysis = Record<string, MultipleSpectraAnalysisPreferences>;
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@@ -491,7 +499,7 @@ export declare interface MultipleSpectraAnalysisPreferences {
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export declare class NMRiumCore {
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#private;
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-
readonly version =
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readonly version = 11;
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registerPlugin(plugin: NMRiumPlugin): void;
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registerPlugins(plugins: NMRiumPlugin[]): void;
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private migrate;
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@@ -1421,6 +1429,7 @@ export declare interface WorkspacePreferences {
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export?: ExportPreferences;
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peaksLabel?: PeaksLabel;
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acsExportSettings?: ACSExportSettings;
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defaultMoleculeSettings?: MoleculeView;
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}
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/**
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package/dist/nmrium-core.js
CHANGED
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@@ -1,6 +1,6 @@
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1
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-
var be={NORMAL:"NORMAL",FORMULA:"FORMULA"};var Re={RELATIVE:"relative",ABSOLUTE:"absolute",MIN:"min",MAX:"max"};var Ce=[{name:"pixels",unit:"px"},{name:"inches",unit:"in"},{name:"feet",unit:"ft"},{name:"yards",unit:"yd"},{name:"centimeters",unit:"cm"},{name:"millimeters",unit:"mm"},{name:"meters",unit:"m"},{name:"points",unit:"pt"},{name:"picas",unit:"pc"}];var P=10;var Ie=[{key:"CT",description:"CT from NMR Solutions"}];import{isAnyArray as Me}from"is-any-array";import{xMultiply as U}from"ml-spectra-processing";var Oe=crypto.randomUUID.bind(crypto),N=Oe;function h(e){let{id:t=N(),meta:o,peaks:r={},filters:i=[],info:n={},ranges:a={},integrals:s={},selector:c,sourceId:l,dependentVariables:p=[],...m}=e,u={id:t,meta:o,filters:i},{data:d=De(p[0].components)}=e;if(Array.isArray(n.nucleus)&&(n.nucleus=n.nucleus[0]),u.data={x:[],re:[],im:[],...d},"scaleFactor"in 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o;throw new RangeError("An array with a index out of boundaries")}return e}var ze=new Set(["t1ir","T1"]);function oe(e){let t=[];for(let o of e){let{info:{pulseSequence:r,isFid:i}}=o,{data:n,info:a,meta:{vdlistValues:s=[]}}=o;if(!(r&&ze.has(r))||s.length===0){t.push(o);continue}let l=i?"re":"rr",p={};for(let y in a)p[y]=_(a[y]);let{z:m,maxX:u,minX:d}=n[l],f=je({from:d,to:u,size:m[0].length}),[g,S]=Le(o);for(let y=0;y<s.length;y++){let te={re:f,x:f};for(let re in n)te[ke(re)]=n[re].z.at(g*(y+S));t.push(h({data:te,info:{...p,name:`${p.name}_${s[y]}`,dimension:1,vd:s[y]}}))}}return t}function ke(e){return["rr","re"].includes(e)?"re":["im","ri","ir","ii"].includes(e)?"im":"x"}function Le(e){let{meta:{PAGE:t}}=e,o=!0;if(t){let r=i=>Number.parseFloat(i.replace(/[F|T]1=/,""));o=r(t[0])>r(t[2])}return o?[-1,1]:[1,0]}var Ue=2,Ve=1;function _e(e){let{spectra:t=[],molecules:o}=e,r=[];for(let i of t){let{info:n}=i;switch(n.dimension){case Ve:r.push(h(i));break;case 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var Re={NORMAL:"NORMAL",FORMULA:"FORMULA"};var Ie={RELATIVE:"relative",ABSOLUTE:"absolute",MIN:"min",MAX:"max"};var Ce=[{name:"pixels",unit:"px"},{name:"inches",unit:"in"},{name:"feet",unit:"ft"},{name:"yards",unit:"yd"},{name:"centimeters",unit:"cm"},{name:"millimeters",unit:"mm"},{name:"meters",unit:"m"},{name:"points",unit:"pt"},{name:"picas",unit:"pc"}];var P=11;var Oe=[{key:"CT",description:"CT from NMR Solutions"}];import{isAnyArray as ve}from"is-any-array";import{xMultiply as j}from"ml-spectra-processing";var Me=crypto.randomUUID.bind(crypto),N=Me;function h(e){let{id:t=N(),meta:o,peaks:r={},filters:i=[],info:n={},ranges:a={},integrals:s={},selector:c,sourceId:l,dependentVariables:p=[],...m}=e,u={id:t,meta:o,filters:i},{data:d=De(p[0].components)}=e;if(Array.isArray(n.nucleus)&&(n.nucleus=n.nucleus[0]),u.data={x:[],re:[],im:[],...d},"scaleFactor"in 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o;throw new RangeError("An array with a index out of boundaries")}return e}var Le=new Set(["t1ir","T1"]);function ie(e){let t=[];for(let o of e){let{info:{pulseSequence:r,isFid:i}}=o,{data:n,info:a,meta:{vdlistValues:s=[]}}=o;if(!(r&&Le.has(r))||s.length===0){t.push(o);continue}let l=i?"re":"rr",p={};for(let y in a)p[y]=_(a[y]);let{z:m,maxX:u,minX:d}=n[l],f=ke({from:d,to:u,size:m[0].length}),[g,S]=je(o);for(let y=0;y<s.length;y++){let re={re:f,x:f};for(let oe in n)re[Ue(oe)]=n[oe].z.at(g*(y+S));t.push(h({data:re,info:{...p,name:`${p.name}_${s[y]}`,dimension:1,vd:s[y]}}))}}return t}function Ue(e){return["rr","re"].includes(e)?"re":["im","ri","ir","ii"].includes(e)?"im":"x"}function je(e){let{meta:{PAGE:t}}=e,o=!0;if(t){let r=i=>Number.parseFloat(i.replace(/[F|T]1=/,""));o=r(t[0])>r(t[2])}return o?[-1,1]:[1,0]}var Ve=2,_e=1;function Be(e){let{spectra:t=[],molecules:o}=e,r=[];for(let i of t){let{info:n}=i;switch(n.dimension){case _e:r.push(h(i));break;case Ve:r.push(C(i));break;default:throw new Error("dimension does not supported")}}return{molecules:o,spectra:ie(r)}}function Ke(e){return e}function x(e,t){return JSON.parse(JSON.stringify(e),function(r,i){if(r in t){this[t[r]]=i;return}return i})}function B(e){if(e?.version===1)return e;let t={...e,version:1},o={j:"js",signal:"signals",integral:"integration",peak:"peaks",diaID:"diaIDs"};for(let r of t.spectra){if(r.ranges){let i=x(r.ranges,o);r.ranges=Array.isArray(i)?{values:i}:i}else if(r.zones){let i=x(r.zones,o);r.zones=Array.isArray(i)?{values:i}:i}r.peaks&&(r.peaks=Array.isArray(r.peaks)?{values:r.peaks}:r.peaks),r.integrals&&(r.integrals=Array.isArray(r.integrals)?{values:r.integrals}:r.integrals)}return t}function K(e){if(e?.version===2)return e;let t={...e,version:2},o={peaks:{delta:"x",originDelta:"originalX",intensity:"y"},ranges:{atomIDs:"atoms",intensity:"y"}};for(let r of t.spectra)r.peaks?r.peaks=x(r.peaks,o.peaks):r.ranges?r.ranges=x(r.ranges,o.ranges):r.zones&&(r.zones.values=Xe(r.zones.values));return t}function Xe(e){return e.map(t=>(t.signals&&(t.signals=t.signals.map(o=>{if(o.x&&o.y){let{x:{fromTo:r,...i},y:{fromTo:n,...a}}=o;o={...o,x:{...i,...r},y:{...a,...n}}}else{let{fromTo:r,deltaX:i,resolutionX:n,nucleusX:a,deltaY:s,resolutionY:c,nucleusY:l,shiftX:p,shiftY:m,...u}=o;o={...u,x:{from:r[0].from,to:r[0].to,delta:i,resolution:n,nucleus:a},y:{from:r[1].from,to:r[1].to,delta:s,resolution:c,nucleus:l}}}return o},[])),t),[])}var We={name:"apodization",label:"Apodization",value:{lineBroadening:1,gaussBroadening:0,lineBroadeningCenter:0}};function X(e){if(e?.version===3)return e;let t={...e,version:3};for(let o of t.spectra)if(Array.isArray(o?.filters)&&o?.filters.length>0){let r=o.filters.findIndex(i=>i.name==="lineBroadening");if(r!==-1){let i={...o.filters[r],...We};o.filters[r]=o.filters[r-1],o.filters[r-1]=i}}return t}function W(e){if(e?.version===4)return e;let{version:t,...o}=e,r=[],i={};for(let{source:s,...c}of o.spectra){let l={},{info:p={},display:m={}}=c;if(p?.dimension===2&&!s?.jcampURL)if(p.isFt)l.data={rr:c.data};else continue;if(s?.jcampURL){let{jcampURL:f,jcampSpectrumIndex:g}=s,S=f.match(/(?<baseURL>^\w+:\/{2}\w+\/)(?<relativePath>.*)/);i[f]||(i[f]={baseURL:S?.groups.baseURL||"",relativePath:S?.groups.relativePath||f.replace(/^\.\//,"")}),l.sourceSelector={files:[i[f].relativePath]},g!==void 0&&(l.sourceSelector.jcamp={index:g})}l.filters=Ye(c.filters);let{name:u,...d}=m;u&&(l.info={...p,name:u}),l.display=d,r.push({...c,...l})}let n={data:{...o,spectra:r},version:4},a={entries:Object.values(i)};return a.entries.length>0&&(n.data.source=a),n}function Ye(e=[]){let t=[];for(let o of e){let{name:r,value:i}=o;switch(r){case"zeroFilling":t.push({...o,value:{nbPoints:i}});break;case"shiftX":case"shift2DX":case"shift2DY":t.push({...o,value:{shift:i}});break;default:t.push({...o})}}return t}function Y(e){if(e?.version===5)return e;let t={...e,version:5},o={originFrom:"originalFrom",originTo:"originalTo",originDelta:"originalDelta",originX:"originalX",originY:"originalY",originZ:"originalZ"};for(let r of t?.data?.spectra||[])for(let i of["peaks","ranges","zones"])r?.[i]&&(r[i]=x(r[i],o));return t}function $(e){if(e?.version===6)return e;let t={...e,version:6};for(let o of t?.data?.spectra||[]){let{digitalFilter:r,fft:i,phaseCorrection:n}=$e(o);i?.flag&&r?.flag&&n&&Math.floor(r.value.digitalFilterValue)%2>0&&(n.value.ph0-=180)}return t}function $e(e,t=["phaseCorrection","fft","digitalFilter"]){let{filters:o=[]}=e,r={};for(let i of t)r[i]=o.find(n=>n.name===i);return r}function O(e,t="localStorage"){if(e?.version===7)return e;if(t==="nmrium")return ne(e);let o={...e,version:7};for(let r in e.workspaces)o.workspaces[r]=ne(o.workspaces[r]);return o}function ne(e){let{formatting:{nuclei:t,panels:o}={nuclei:null,panels:null},version:r,...i}=e,n={...i};return t&&(n.nuclei=Ze(t)),o&&(n.panels=o),n}function Ze(e){let t=[],o={name:"nucleus",ppm:"ppmFormat",hz:"hzFormat"};for(let r in e)t.push(x(e[r],o));return t}function Z(e){if(e?.version===7)return e;let t={...e,version:7};return t?.settings&&(t.settings=O(t.settings,"nmrium")),t}function M(e,t="localStorage"){if(e?.version===8)return e;if(t==="nmrium")return se(e);let o={...e,version:8};for(let r in e.workspaces)o.workspaces[r]=se(o.workspaces[r]);return o}function se(e){let{version:t,...o}=e,r={...o};return r.display.panels=Ge(e),r}function Ge(e){let t={},o=e.display.panels;for(let r of Object.keys(o)){let{display:i,open:n}=o[r];t[r]={display:i,visible:i,open:n}}return t}function G(e){if(e?.version===8)return e;let t={...e,version:8};t?.settings&&(t.settings=M(t.settings,"nmrium"));for(let o of t?.data?.spectra||[]){let{filters:r=[]}=o;for(let s=0;s<r.length;s++){let{flag:c,isDeleteAllow:l,label:p,...m}=r[s];r[s]={...m,enabled:c}}let i=r.findIndex(s=>s.name==="apodization");if(i!==-1){let s=r[i],{lineBroadening:c,gaussBroadening:l,lineBroadeningCenter:p}=s.value;s.value={exponential:{apply:!0,options:{lineBroadening:l>0?-c:c}}},l>0&&(s.value.gaussian={apply:!0,options:{lineBroadening:.6*l,lineBroadeningCenter:p}}),r[i]=s}let n=r.findIndex(s=>s.name==="apodizationDimension1"),a=r.findIndex(s=>s.name==="apodizationDimension2");if(n!==-1){let s=r[n],{shapes:c}=s.value.compose;s.value=ae(c)}if(a!==-1){let s=r[a],{shapes:c}=s.value.compose;s.value=ae(c)}}return t}function ae(e){let t={};for(let{shape:o}of e){let{kind:r,options:i}=o;if(r==="sineBell"){let{exponent:n,offset:a}=i,s=n===2?"sineSquare":"sineBell";t[s]={apply:!0,options:{offset:a}}}}return t}function J(e){let{version:t,plugins:o,...r}=e;return t===9?e:{version:9,plugins:{},...r}}function q(e){if(e?.version>=10)return e;let t={...e,version:10};if(e.data){let{source:o,spectra:r,...i}=e.data,n=o?crypto.randomUUID():void 0,a=o?[{...o,id:n}]:[];t.data={...i,sources:a,spectra:o?r.map(s=>({...s,sourceId:n})):r}}return t}function H(e){let{version:t}=e;if(t>=11)return e;let o={...e,version:11};return e?.view?.molecules&&(o.view=Je(e.view)),o}function Je(e){let{molecules:t,...o}=e,r={};for(let[i,n]of Object.entries(t)){let{showAtomNumber:a,...s}=n;r[i]={...s,atomAnnotation:"none",showLabel:!1}}return{molecules:r,...o}}function b(e,t){e.plugins||(e.plugins={});let o=e.plugins;for(let r of t.values()){if(!r.shouldSerialize){delete o[r.id];continue}o[r.id]||(o[r.id]={id:r.id,version:r.version}),o[r.id].id=r.id,o[r.id].version=r.version}}var qe=[B,K,X,W,Y,$,Z,G,J,q,H];function le(e,t,o){let r=structuredClone(e),i=Object.entries(e?.plugins??{});for(let[s,{version:c}]of i){let l=o.get(s);if(!(l&&l.version>=c)){if(l){console.warn(`Plugin "${l.id}" is loaded with a version older (${l.version}) than the one used to save the state (${c}).
|
|
2
2
|
NMRium may fail to load the state.
|
|
3
3
|
Please update the plugin to the latest version.`);continue}console.warn(`Plugin "${s}@${c}" is not registered. NMRium may fail to load the state.
|
|
4
|
-
Please consider open this file with the plugin installed.`)}}let n=new Set,a=()=>{let s=r.version;for(let c of o.values())for(let l of c.migrations){if(n.has(l)||s<l.minCore||l.maxCore&&s>l.maxCore)continue;if((r.plugins?.[c.id]?.version||0)===c.version)break;r=l.up(r),n.add(l)}};for(let s=e?.version||0;s<t;s++){let c=Ge[s];r=c(r),a()}return a(),b(r,o),r}import{FileCollection as ot}from"file-collection";var le={SDF:"sdf",MOL:"mol",NMRIUM:"nmrium",NMRIUM_ARCHIVE:"nmrium.zip",JSON:"json",JCAMP:"jcamp",DX:"dx",JDX:"jdx",JDF:"jdf",NMREDATA:"nmredata",SMILES:"smiles",SMI:"smi"};function D(e){return e.includes(".")?e.replace(/^.*\./,"").toLowerCase():""}function v(e,t={},o){let{data:r,...i}=e;if(!r)return e;let{spectra:n=[]}=r,{keep1D:a=!0,keep2D:s=!0,onlyReal:c}=t,l=c?"ft":t.dataSelection||"both",p=[];for(let m of n){if(!m.info){p.push(m);continue}let{isFid:u,dimension:d,name:f}=m.info;if(!F(d===1&&!a,f,o)&&!F(d===2&&!s,f,o)&&!F(u&&l==="ft",f,o)&&!F(!u&&l==="fid",f,o))if(c&&!u)if(m.info.isComplex=!1,Je(m)){let{rr:g}=m.data;p.push({...m,data:{rr:g}})}else{let{re:g,x:S}=m.data;p.push({...m,data:{re:g,x:S}})}else p.push(m)}return{data:{...r,spectra:p},...i}}function F(e,t,o){return e?(o?.warn(`Skipping ${t} because it didn't match the import filters.`),!0):!1}function Je(e){let{info:t}=e;return t?.dimension===2}function A(e){let{nmriumState:t,plugins:o,options:r}=e;for(let i of o.values()){let n=i.onReadProcess?.onProcessing;n&&n(t,r)}}async function w(e,t,o={}){let{sourceSelector:r,converter:i,logger:n}=o,a=[],s=[];for(let u of t.values()){let{onReadProcess:d}=u;d&&(d?.onFiles&&a.push(u),d?.supportedExtensions?.length&&d?.onFile&&s.push(u))}let c=await Promise.allSettled(a.map(u=>u.onReadProcess.onFiles(e,o))),l=[],p=await Promise.allSettled(e.files.flatMap(u=>{let d=D(u.name).toLowerCase();return s.flatMap(f=>{let{supportedExtensions:g,onFile:S}=f.onReadProcess;return g.includes(d)?(l.push({file:u,plugin:f}),S(u,{logger:n,sourceSelector:r,converter:i})):[]})})),m={spectra:[],molecules:[]};for(let u=0;u<c.length;u++){let d=c[u];switch(d.status){case"fulfilled":{let{spectra:f=[],molecules:g=[]}=d.value||{};m.spectra.push(...f),m.molecules.push(...g);break}case"rejected":{let f=d.reason,g=a[u];o.logger?.error(`Load file collection with plugin ${g.id}@${g.version} fails with: ${f}`);break}}}for(let u=0;u<p.length;u++){let d=p[u];switch(d.status){case"fulfilled":{let{spectra:f=[],molecules:g=[]}=d.value||{};m.spectra.push(...f),m.molecules.push(...g);break}case"rejected":{let f=d.reason,{file:g,plugin:S}=l[u];o.logger?.error(`Load file ${g.relativePath} with plugin ${S.id}@${S.version} fails with: ${f}`);break}}}return m}import{FileCollection as et}from"file-collection";import{FileCollection as Qe}from"file-collection";import ce from"lodash.merge";import{xIsEquallySpaced as qe}from"ml-spectra-processing";async function T(e){let{input:t,spectraResult:o,unserializedSpectrum:r,options:i,plugins:n,migrator:a}=e,c=(await R({input:t,migrator:a,plugins:n,options:{...i,sourceSelector:r.sourceSelector}}))?.nmriumState?.data?.spectra??[],l=c.pop();if(l){o.push(ue(r,l));for(let p of c)o.push(ue(r,He(p)))}}function ue(e,t){!e.fileCollectionId&&e.sourceId&&(e.fileCollectionId=e.sourceId),!t.fileCollectionId&&t.sourceId&&(t.fileCollectionId=t.sourceId);let{data:o,...r}=e;if("ranges"in t){let{data:i,...n}=t;return{...ce(n,r),data:i}}else if("zones"in t){let{data:i,...n}=t;return{...ce(n,r),data:i}}else return t}function He(e){return{...e,id:N()}}function E(e){let{spectrum:t,spectraResult:o,logger:r}=e,{dimension:i}=t.info;if(i===1){if(!qe(t.data)){r?.error('The ".nmrium" file is corrupted; the X-axis values are not equally distant.');return}o.push(h(t))}else i===2&&o.push(I(t))}async function j(e){let{input:t,moleculesResult:o,unserializedMolecule:r,options:i,plugins:n,migrator:a}=e,{sourceSelector:s,sourceId:c}=r,p=(await R({input:t,migrator:a,plugins:n,options:{...i,sourceSelector:s}}))?.nmriumState?.data?.molecules??[];for(let m of p)o.push({...m,sourceId:c,fileCollectionId:c})}function z(e){let{molecule:t,moleculesResult:o}=e;o.push(t)}async function k(e){let{nmriumObjectInput:t,options:o={},migrator:r,plugins:i}=e,n=r(t),{data:a,...s}=n;if(!a)return[{...s},new Map];let c={data:{...a,spectra:[],molecules:[]},...s},l=c.data,{sources:p=[],spectra:m,molecules:u}=l,d=await Promise.all(p.map(async S=>{let y=await Qe.fromSource(S,{unzip:{zipExtensions:["zip","nmredata"]}});return[S.id,y]})),f=new Map(d),g=[];for(let S of a.spectra){let y=f.get(S.sourceId);if(!y){E({spectrum:S,spectraResult:m,logger:o.logger});continue}g.push(T({input:y,spectraResult:m,unserializedSpectrum:S,migrator:r,plugins:i,options:o}))}for(let S of a.molecules??[]){let y=f.get(S.sourceId);if(!y){z({molecule:S,moleculesResult:u,logger:o.logger});continue}g.push(j({input:y,unserializedMolecule:S,moleculesResult:u,migrator:r,plugins:i,options:o}))}return await Promise.allSettled(g),[c,f]}async function pe(e){let{file:t,options:o={},migrator:r,plugins:i}=e,n=await t.arrayBuffer(),a=await(rt(n)?tt(n):t.text());return k({nmriumObjectInput:JSON.parse(a),plugins:i,migrator:r,options:o})}async function tt(e){let t=await et.fromZip(e);if(t.files.length===0)throw new Error("compressed nmrium file is corrupted");return t.files[0].text()}function rt(e){if(e.byteLength<4)return!1;let t=new Uint8Array(e);return t[0]===80&&t[1]===75&&(t[2]===3||t[2]===5||t[2]===7)&&(t[3]===4||t[3]===6||t[3]===8)}async function R(e){let{options:t={},input:o,migrator:r,plugins:i}=e,n=st(await it(o),t.sourceSelector?.files),a=at(n);if(a){let[u]=await pe({file:a,migrator:r,plugins:i,options:t});return{nmriumState:u,containsNmrium:!0,fileCollection:n}}let s=await w(n,i,t),c=v({version:10,data:s},t?.sourceSelector?.general,t.logger),{onLoadProcessing:l,experimentalFeatures:p}=t,m={...l,autoProcessing:l?.autoProcessing??!1,experimentalFeatures:p};return A({nmriumState:c,plugins:i,options:m}),{nmriumState:c,containsNmrium:!1,fileCollection:n}}function it(e){return Array.isArray(e)?Promise.reject(new Error("For a set of fileCollectionItems pass a FileCollection instance")):nt(e)?Promise.resolve(e):new ot().appendExtendedSource({...e,uuid:crypto.randomUUID()})}function nt(e){return typeof e=="object"&&"files"in e}function st(e,t){if(!t)return e;let o=new Set(t);return e.filter(r=>o.has(r.relativePath))}function at(e){return e.files.find(t=>D(t.name).toLowerCase()===le.NMRIUM)}function C(e,t){let o={};for(let r in e)t.includes(r)||(o[r]=e[r]);return o}var lt=["data","originalData","info","originalInfo","meta","customInfo"],ct=["data","originalData","info","originalInfo","meta","customInfo"],ut=["sourceSelector","sourceId","fileCollectionId","originalData","originalInfo"];function me(e,t,o={}){let{version:r,data:i}=e;if(i.actionType)return e;let n={version:r,plugins:e.plugins},{includeData:a}=o;a!=="noData"&&(n.data=pt({...i},a));let{includeSettings:s,includeView:c}=o;return s&&(n.settings=e.settings),c&&(n.view=e.view),b(n,t),n}function pt(e,t="rawData"){let{spectra:o}=e;switch(t){case"dataSource":return mt(e);case"selfContained":case"selfContainedExternalDatasource":return ft(e);case"rawData":return{...C(e,["sources"]),spectra:o.map(St)};default:return e}}function mt(e){let{spectra:t}=e;if(!e.sources)throw new Error("sources property should exists for dataSource serialization");return{...e,spectra:t.map(dt)}}function ft(e){let{spectra:t}=e;return{...e,spectra:t.map(gt)}}function dt(e){return C(e,lt)}function gt(e){return C(e,ct)}function St(e){let{data:t,info:o,originalData:r,originalInfo:i}=e,n=C(e,ut);return n.data=r||t,n.info=i||o,n}import{FileCollection as yt}from"file-collection";async function de(e){let{spectra:t,molecules:o,fileCollections:r,serializedState:i,includeData:n=!0}=e,a=new yt({filter:{ignoreDotfiles:!1}}),s=new Set,c=[];for(let l of t)fe({builder:a,fileCollections:r,fileCollectionId:l.fileCollectionId,includeData:n,alreadyAdded:s,asyncTasks:c});for(let l of o)fe({builder:a,fileCollections:r,fileCollectionId:l.fileCollectionId,includeData:n,alreadyAdded:s,asyncTasks:c});return await Promise.all(c),a.toIum({*getExtraFiles(){yield{relativePath:"state.json",data:i},yield{relativePath:".META-NMRIUM/NMRIUM_ARCHIVE.json",data:JSON.stringify(Pt({fileCollections:r,toSerialize:s}),null,2)},n?yield{relativePath:".META-NMRIUM/EMBED_ALL_DATA",data:""}:yield{relativePath:".META-NMRIUM/USE_EXTERNAL_SOURCES",data:""},yield{relativePath:"index.txt",data:xt({fileCollections:r,toIndex:s})}}})}function fe(e){let{builder:t,fileCollections:o,fileCollectionId:r,includeData:i,alreadyAdded:n,asyncTasks:a}=e;if(!r||n.has(r))return;let s=o[r];s&&(n.add(r),a.push(s.toIum({includeData:i}).then(c=>{let l=new Blob([c],{type:"application/zip"});return t.appendExtendedSource({uuid:r,name:r,relativePath:`${r}.ium.zip`,size:l.size,text:()=>l.text(),stream:()=>l.stream(),arrayBuffer:()=>l.arrayBuffer()},{unzip:{zipExtensions:[]}})})))}function Pt(e){let{fileCollections:t,toSerialize:o}=e,r={};for(let i of o){let n=t[i];if(!n)continue;let{logger:a,...s}=n.options;r[i]={sourceUUID:i,filePath:`${i}.ium.zip`,options:s}}return r}function xt(e){let{fileCollections:t,toIndex:o}=e,r=[];for(let i of o){let n=t[i];if(n){r.push(`data/${i}.ium.zip`);for(let a of n.sources)r.push(` data/${a.relativePath}`);r.push(`
|
|
4
|
+
Please consider open this file with the plugin installed.`)}}let n=new Set,a=()=>{let s=r.version;for(let c of o.values())for(let l of c.migrations){if(n.has(l)||s<l.minCore||l.maxCore&&s>l.maxCore)continue;if((r.plugins?.[c.id]?.version||0)===c.version)break;r=l.up(r),n.add(l)}};for(let s=e?.version||0;s<t;s++){let c=qe[s];r=c(r),a()}return a(),b(r,o),r}var He=["topbar.right","topbar.about_us.modal"],Qe=[],$r=[...He,...Qe],et={},Q={};{let e=et,t=Q;for(let[o,r]of Object.entries(e))t[r]||(t[r]=[]),t[r]?.push(o)}function*ce(e){let{slot:t,plugins:o,supportedToDeprecatedSlots:r=Q}=e,i=r[t];for(let[n,a]of o.entries()){let s=a.ui;if(!s)continue;let c=s[t];if(c){yield[n,c];continue}if(i)for(let l of i){let p=a.ui?.[l];if(p){yield[n,p],console.warn(`Plugin ${a.id} used deprecated slot "${l}". 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tt(e){let{info:t}=e;return t?.dimension===2}function A(e){let{nmriumState:t,plugins:o,options:r}=e;for(let i of o.values()){let n=i.onReadProcess?.onProcessing;n&&n(t,r)}}async function w(e,t,o={}){let{sourceSelector:r,converter:i,logger:n}=o,a=[],s=[];for(let u of t.values()){let{onReadProcess:d}=u;d&&(d?.onFiles&&a.push(u),d?.supportedExtensions?.length&&d?.onFile&&s.push(u))}let c=await Promise.allSettled(a.map(u=>u.onReadProcess.onFiles(e,o))),l=[],p=await Promise.allSettled(e.files.flatMap(u=>{let d=v(u.name).toLowerCase();return s.flatMap(f=>{let{supportedExtensions:g,onFile:S}=f.onReadProcess;return g.includes(d)?(l.push({file:u,plugin:f}),S(u,{logger:n,sourceSelector:r,converter:i})):[]})})),m={spectra:[],molecules:[]};for(let u=0;u<c.length;u++){let d=c[u];switch(d.status){case"fulfilled":{let{spectra:f=[],molecules:g=[]}=d.value||{};m.spectra.push(...f),m.molecules.push(...g);break}case"rejected":{let f=d.reason,g=a[u];o.logger?.error(`Load file collection with plugin ${g.id}@${g.version} fails with: ${f}`);break}}}for(let u=0;u<p.length;u++){let d=p[u];switch(d.status){case"fulfilled":{let{spectra:f=[],molecules:g=[]}=d.value||{};m.spectra.push(...f),m.molecules.push(...g);break}case"rejected":{let f=d.reason,{file:g,plugin:S}=l[u];o.logger?.error(`Load file ${g.relativePath} with plugin ${S.id}@${S.version} fails with: ${f}`);break}}}return m}import{FileCollection as nt}from"file-collection";import{FileCollection as it}from"file-collection";import pe from"lodash.merge";import{xIsEquallySpaced as rt}from"ml-spectra-processing";async function E(e){let{input:t,spectraResult:o,unserializedSpectrum:r,options:i,plugins:n,migrator:a}=e,c=(await R({input:t,migrator:a,plugins:n,options:{...i,sourceSelector:r.sourceSelector}}))?.nmriumState?.data?.spectra??[],l=c.pop();if(l){o.push(me(r,l));for(let p of c)o.push(me(r,ot(p)))}}function me(e,t){!e.fileCollectionId&&e.sourceId&&(e.fileCollectionId=e.sourceId),!t.fileCollectionId&&t.sourceId&&(t.fileCollectionId=t.sourceId);let{data:o,...r}=e;if("ranges"in t){let{data:i,...n}=t;return{...pe(n,r),data:i}}else if("zones"in t){let{data:i,...n}=t;return{...pe(n,r),data:i}}else return t}function ot(e){return{...e,id:N()}}function T(e){let{spectrum:t,spectraResult:o,logger:r}=e,{dimension:i}=t.info;if(i===1){if(!rt(t.data)){r?.error('The ".nmrium" file is corrupted; the X-axis values are not equally distant.');return}o.push(h(t))}else i===2&&o.push(C(t))}async function z(e){let{input:t,moleculesResult:o,unserializedMolecule:r,options:i,plugins:n,migrator:a}=e,{sourceSelector:s,sourceId:c}=r,p=(await R({input:t,migrator:a,plugins:n,options:{...i,sourceSelector:s}}))?.nmriumState?.data?.molecules??[];for(let m of p)o.push({...m,sourceId:c,fileCollectionId:c})}function k(e){let{molecule:t,moleculesResult:o}=e;o.push(t)}async function L(e){let{nmriumObjectInput:t,options:o={},migrator:r,plugins:i}=e,n=r(t),{data:a,...s}=n;if(!a)return[{...s},new Map];let c={data:{...a,spectra:[],molecules:[]},...s},l=c.data,{sources:p=[],spectra:m,molecules:u}=l,d=await Promise.all(p.map(async S=>{let y=await it.fromSource(S,{unzip:{zipExtensions:["zip","nmredata"]}});return[S.id,y]})),f=new Map(d),g=[];for(let S of a.spectra){let y=f.get(S.sourceId);if(!y){T({spectrum:S,spectraResult:m,logger:o.logger});continue}g.push(E({input:y,spectraResult:m,unserializedSpectrum:S,migrator:r,plugins:i,options:o}))}for(let S of a.molecules??[]){let y=f.get(S.sourceId);if(!y){k({molecule:S,moleculesResult:u,logger:o.logger});continue}g.push(z({input:y,unserializedMolecule:S,moleculesResult:u,migrator:r,plugins:i,options:o}))}return await Promise.allSettled(g),[c,f]}async function fe(e){let{file:t,options:o={},migrator:r,plugins:i}=e,n=await t.arrayBuffer(),a=await(at(n)?st(n):t.text());return L({nmriumObjectInput:JSON.parse(a),plugins:i,migrator:r,options:o})}async function st(e){let t=await nt.fromZip(e);if(t.files.length===0)throw new Error("compressed nmrium file is corrupted");return t.files[0].text()}function at(e){if(e.byteLength<4)return!1;let t=new Uint8Array(e);return t[0]===80&&t[1]===75&&(t[2]===3||t[2]===5||t[2]===7)&&(t[3]===4||t[3]===6||t[3]===8)}async function R(e){let{options:t={},input:o,migrator:r,plugins:i}=e,n=pt(await ct(o),t.sourceSelector?.files),a=mt(n);if(a){let[u]=await fe({file:a,migrator:r,plugins:i,options:t});return{nmriumState:u,containsNmrium:!0,fileCollection:n}}let s=await w(n,i,t),c=F({version:11,data:s},t?.sourceSelector?.general,t.logger),{onLoadProcessing:l,experimentalFeatures:p}=t,m={...l,autoProcessing:l?.autoProcessing??!1,experimentalFeatures:p};return A({nmriumState:c,plugins:i,options:m}),{nmriumState:c,containsNmrium:!1,fileCollection:n}}function ct(e){return Array.isArray(e)?Promise.reject(new Error("For a set of fileCollectionItems pass a FileCollection instance")):ut(e)?Promise.resolve(e):new lt().appendExtendedSource({...e,uuid:crypto.randomUUID()})}function ut(e){return typeof e=="object"&&"files"in e}function pt(e,t){if(!t)return e;let o=new Set(t);return e.filter(r=>o.has(r.relativePath))}function mt(e){return e.files.find(t=>v(t.name).toLowerCase()===ue.NMRIUM)}import{FileCollection as ee}from"file-collection";async function de(e){let t={},o=[];for(let r of e.sources)switch(r.relativePath){case".META-NMRIUM/VERSION":o.push(r.text().then(i=>{t.version=Number.parseInt(i,10)}));break;case"state.json":o.push(r.text().then(i=>{t.state=JSON.parse(i)}));break;case".META-NMRIUM/NMRIUM_ARCHIVE.json":o.push(r.text().then(i=>{t.archive=JSON.parse(i)}));break;case".META-NMRIUM/EMBED_ALL_DATA":t.embed=r;break;case".META-NMRIUM/USE_EXTERNAL_SOURCES":t.external=r;break;default:}return await Promise.all(o),t}function ge(e){if(typeof e.version!="number"||Number.isNaN(e.version))throw new Error("Not a valid NMRium archive");if(!e.archive)throw new Error("Not a valid NMRium archive");if(!e.state)throw new Error("NMRium Archive corrupted, state.json is missing");if(!e.embed&&!e.external)throw new Error("NMRium Archive corrupted, no embedded data or external sources")}async function Se(e){let{options:t,plugins:o,migrator:r}=e,i=await ee.fromIum(e.input),n=await de(i);ge(n);let a=r(n.state),s={...a,data:{...a.data,spectra:[],molecules:[]}},c=s.data.spectra,l=s.data.molecules,p=ft(a.data.sources),m=dt(i,n.archive),u=[];for(let f of a.data.spectra)u.push(St({archive:n,externalSources:p,embedFiles:m,unserializedSpectrum:f,spectraResult:c,options:t,plugins:o,migrator:r}));for(let f of a.data.molecules??[])u.push(yt({archive:n,externalSources:p,embedFiles:m,unserializedMolecule:f,moleculesResult:l,options:t,plugins:o,migrator:r}));await Promise.allSettled(u);let d=await gt(m,p);return[s,d]}function ft(e){e??=[];let t=new Map(e.map(r=>[r.id,r])),o=new Map;return{get(r){let i=t.get(r);if(!i)return;let n=o.get(r);return n||(n=ee.fromSource(i,{unzip:{zipExtensions:["zip","nmredata"]}}),o.set(r,n)),n},async all(){let r=new Map;return await Promise.all(U(o.entries(),async([i,n])=>{r.set(i,await n)})),r},[Symbol("debug")]:{sources:e,mapSources:t,fileCollections:o}}}function dt(e,t){let o=new Map,r=new Map(e.sources.map(i=>[i.relativePath,i]));return{get(i){let n=t[i];if(!n)return;let a=r.get(n.filePath);if(!a)return;let s=o.get(i);return s||(s=ee.fromIum(a.stream()),o.set(i,s)),s},async all(){let i=new Map;return await Promise.all(U(o.entries(),async([n,a])=>{i.set(n,await a)})),i},[Symbol("debug")]:{ium:e,record:t,iumSources:r,fileCollections:o}}}async function gt(e,t){let o=new Map;return await Promise.allSettled(U(await e.all(),async([r,i])=>{o.set(r,i)})),await Promise.allSettled(U(await t.all(),async([r,i])=>{o.has(r)||o.set(r,i)})),o}function*U(e,t){for(let o of e)yield t(o)}async function St(e){let{archive:t,externalSources:o,embedFiles:r}=e,{unserializedSpectrum:i,spectraResult:n}=e,{options:a,plugins:s,migrator:c}=e,l=await ye({archive:t,externalSources:o,embedFiles:r,pickableInput:i});if(!l)return T({spectrum:i,spectraResult:n,logger:a?.logger});await E({input:l,unserializedSpectrum:i,spectraResult:n,options:a,plugins:s,migrator:c})}async function yt(e){let{archive:t,externalSources:o,embedFiles:r}=e,{unserializedMolecule:i,moleculesResult:n}=e,{options:a,plugins:s,migrator:c}=e,l=await ye({archive:t,externalSources:o,embedFiles:r,pickableInput:i});if(!l)return k({molecule:i,moleculesResult:n,logger:a?.logger});await z({input:l,unserializedMolecule:i,moleculesResult:n,options:a,plugins:s,migrator:c})}async function ye(e){let{archive:t,externalSources:o,embedFiles:r,pickableInput:i}=e,{fileCollectionId:n,sourceId:a}=i,s;return t.external&&a&&(s=await o.get(a)),!s&&t.external&&a&&n&&(s=await r.get(n)),!s&&t.embed&&n&&(s=await r.get(n)),s}import{FileCollection as Pt}from"file-collection";async function Pe(e){let{source:t,plugins:o,options:r={}}=e,{converter:i,...n}=r,a={spectra:[],molecules:[]},s=await Pt.fromSource(t,{unzip:{zipExtensions:["zip","nmredata"]}}),{spectra:c=[],molecules:l=[]}=await w(s,o,{converter:{...i,bruker:{keepFiles:!0,...Reflect.get(i??{},"bruker")}},...n});a.spectra.push(...c),a.molecules.push(...l);let p=crypto.randomUUID(),m={...t,id:p};for(let g of a.spectra)g.sourceId=p;for(let g of a.molecules)g.sourceId=p;a.sources??=[],a.sources.push(m);let u=F({version:11,data:a},r?.sourceSelector?.general),{onLoadProcessing:d}=n,f={filters:d?.filters,autoProcessing:d?.autoProcessing??!1,experimentalFeatures:r.experimentalFeatures};return A({nmriumState:u,plugins:o,options:f}),[u,s]}function I(e,t){let o={};for(let r in e)t.includes(r)||(o[r]=e[r]);return o}var xt=["data","originalData","info","originalInfo","meta","customInfo"],Nt=["data","originalData","info","originalInfo","meta","customInfo"],ht=["sourceSelector","sourceId","fileCollectionId","originalData","originalInfo"];function xe(e,t,o={}){let{version:r,data:i}=e;if(i.actionType)return e;let n={version:r,plugins:e.plugins},{includeData:a}=o;a!=="noData"&&(n.data=bt({...i},a));let{includeSettings:s,includeView:c}=o;return s&&(n.settings=e.settings),c&&(n.view=e.view),b(n,t),n}function bt(e,t="rawData"){let{spectra:o}=e;switch(t){case"dataSource":return Rt(e);case"selfContained":case"selfContainedExternalDatasource":return It(e);case"rawData":return{...I(e,["sources"]),spectra:o.map(Mt)};default:return e}}function Rt(e){let{spectra:t}=e;if(!e.sources)throw new Error("sources property should exists for dataSource serialization");return{...e,spectra:t.map(Ct)}}function It(e){let{spectra:t}=e;return{...e,spectra:t.map(Ot)}}function Ct(e){return I(e,xt)}function Ot(e){return I(e,Nt)}function Mt(e){let{data:t,info:o,originalData:r,originalInfo:i}=e,n=I(e,ht);return n.data=r||t,n.info=i||o,n}import{FileCollection as vt}from"file-collection";async function he(e){let{spectra:t,molecules:o,fileCollections:r,serializedState:i,includeData:n=!0}=e,a=new vt({filter:{ignoreDotfiles:!1}}),s=new Set,c=[];for(let l of t)Ne({builder:a,fileCollections:r,fileCollectionId:l.fileCollectionId,includeData:n,alreadyAdded:s,asyncTasks:c});for(let l of o)Ne({builder:a,fileCollections:r,fileCollectionId:l.fileCollectionId,includeData:n,alreadyAdded:s,asyncTasks:c});return await Promise.all(c),a.toIum({*getExtraFiles(){yield{relativePath:".META-NMRIUM/VERSION",data:"0"},yield{relativePath:"state.json",data:i},yield{relativePath:".META-NMRIUM/NMRIUM_ARCHIVE.json",data:JSON.stringify(Dt({fileCollections:r,toSerialize:s}),null,2)},n?yield{relativePath:".META-NMRIUM/EMBED_ALL_DATA",data:""}:yield{relativePath:".META-NMRIUM/USE_EXTERNAL_SOURCES",data:""},yield{relativePath:"index.txt",data:Ft({fileCollections:r,toIndex:s})}}})}function Ne(e){let{builder:t,fileCollections:o,fileCollectionId:r,includeData:i,alreadyAdded:n,asyncTasks:a}=e;if(!r||n.has(r))return;let s=o[r];s&&(n.add(r),a.push(s.toIum({includeData:i}).then(c=>{let l=new Blob([c],{type:"application/zip"});return t.appendExtendedSource({uuid:r,name:r,relativePath:`${r}.ium.zip`,size:l.size,text:()=>l.text(),stream:()=>l.stream(),arrayBuffer:()=>l.arrayBuffer()},{unzip:{zipExtensions:[]}})})))}function Dt(e){let{fileCollections:t,toSerialize:o}=e,r={};for(let i of o){let n=t[i];if(!n)continue;let{logger:a,...s}=n.options;r[i]={sourceUUID:i,filePath:`${i}.ium.zip`,options:s}}return r}function Ft(e){let{fileCollections:t,toIndex:o}=e,r=[];for(let i of o){let n=t[i];if(n){r.push(`data/${i}.ium.zip`);for(let a of n.sources)r.push(` data/${a.relativePath}`);r.push(`
|
|
5
5
|
`)}}return r.join(`
|
|
6
|
-
`)}var
|
|
6
|
+
`)}var te=class{version=11;#e=new Map;registerPlugin(t){if(this.#e.has(t.id)){console.warn(`Plugin ${t.id} is already registered. skip.`),console.debug("Plugin already registered:",this.#e.get(t.id)),console.debug("Plugin to register:",t);return}this.#e.set(t.id,t)}registerPlugins(t){for(let o of t)this.registerPlugin(o)}migrate(t){return le(t,this.version,this.#e)}read(t,o={}){return R({input:t,migrator:this.migrate.bind(this),plugins:this.#e,options:o})}readNMRiumArchive(t,o={}){return Se({input:t,options:o,plugins:this.#e,migrator:this.migrate.bind(this)})}readNMRiumObject(t,o){return L({nmriumObjectInput:t,options:o,plugins:this.#e,migrator:this.migrate.bind(this)})}readFromWebSource(t,o){return Pe({source:t,options:o,plugins:this.#e})}serializeNmriumState(t,o){return xe(t,this.#e,o)}serializeNmriumArchive(t){return he(t)}serializePlugins(){let t={plugins:{}};return b(t,this.#e),t.plugins}slot(t){return ce({slot:t,plugins:this.#e})}};function At(e,t){if(t>11)return 0;let o=-1;for(let r=0;r<e.length;r++)if(e[r].version>t){o=r;break}return o}var be=[{version:6,fun:O},{version:7,fun:M}];function wt(e){let{version:t}=e||{},o=At(be,t);if(o===-1)return{...e,version:11};let r=be.slice(o);for(let i of r)e=i.fun(e);return e}export{Re as ANALYSIS_COLUMN_TYPES,Ie as ANALYSIS_COLUMN_VALUES_KEYS,P as CURRENT_EXPORT_VERSION,Oe as EXTERNAL_API_KEYS,te as NMRiumCore,Ke as defineNMRiumPlugin,Be as formatSpectra,N as generateID,_ as getOneIfArray,wt as migrateSettings,Ce as units};
|
package/package.json
CHANGED
|
@@ -1,6 +1,6 @@
|
|
|
1
1
|
{
|
|
2
2
|
"name": "@zakodium/nmrium-core",
|
|
3
|
-
"version": "0.4.
|
|
3
|
+
"version": "0.4.7",
|
|
4
4
|
"description": "The core of NMRium: types, state, state migration and plugin system.",
|
|
5
5
|
"author": "Zakodium Sàrl",
|
|
6
6
|
"license": "CC-BY-NC-SA-4.0",
|
|
@@ -45,5 +45,5 @@
|
|
|
45
45
|
"volta": {
|
|
46
46
|
"extends": "../../../package.json"
|
|
47
47
|
},
|
|
48
|
-
"gitHead": "
|
|
48
|
+
"gitHead": "b38eec0f45c19f73ef4b6b6eb3190ac6cbc43ac1"
|
|
49
49
|
}
|