jcampconverter 10.0.0 → 10.0.1
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/jcampconverter.cjs +6 -6
- package/jcampconverter.d.ts +5 -0
- package/jcampconverter.mjs +6 -6
- package/package.json +2 -1
package/jcampconverter.cjs
CHANGED
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-
"use strict";var he=Object.create;var $=Object.defineProperty;var xe=Object.getOwnPropertyDescriptor;var ye=Object.getOwnPropertyNames;var Ae=Object.getPrototypeOf,
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"use strict";var he=Object.create;var $=Object.defineProperty;var xe=Object.getOwnPropertyDescriptor;var ye=Object.getOwnPropertyNames;var Ae=Object.getPrototypeOf,Ce=Object.prototype.hasOwnProperty;var Se=(e,f)=>{for(var t in f)$(e,t,{get:f[t],enumerable:!0})},se=(e,f,t,o)=>{if(f&&typeof f=="object"||typeof f=="function")for(let a of ye(f))!Ce.call(e,a)&&a!==t&&$(e,a,{get:()=>f[a],enumerable:!(o=xe(f,a))||o.enumerable});return e};var Ne=(e,f,t)=>(t=e!=null?he(Ae(e)):{},se(f||!e||!e.__esModule?$(t,"default",{value:e,enumerable:!0}):t,e)),Te=e=>se($({},"__esModule",{value:!0}),e);var $e={};Se($e,{convert:()=>de,createTree:()=>ie,parseJcampCS:()=>be});module.exports=Te($e);var oe=require("ensure-string");var P=/\s*\$\$.*/;function O(e){return e.replace(P,"")}function ie(e,f={}){e=(0,oe.ensureString)(e);let{flatten:t=!1}=f,o=e.split(/\r?\n/),a=[],i=[],n=[],m={title:"",jcamp:"",children:[]},r=0,p=e.includes("## ");for(let u=0;u<o.length;u++){let b=o[u],h=p?b.replaceAll(" ",""):b;if(h.startsWith("##NTUPLES")&&r++,h.startsWith("##TITLE")){let s=[h.slice(8).trim()];for(let l=u+1;l<o.length&&!o[l].startsWith("##");l++)s.push(o[l].trim());i.push({title:s.join(`
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`),jcamp:`${b}
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`,children:[]}),m=
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`;let s=
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`;let s=h.match(/^##(.*?)=(.+)/);if(s){let l=s[1].replaceAll(/[ _-]/g,"").toUpperCase();l==="DATATYPE"?m.dataType=s[2].trim():l==="DATACLASS"?m.dataClass=s[2].trim():l==="JCAMPDX"?m.jcampDX=O(s[2].trim()):l==="JCAMPCS"&&(m.jcampCS=O(s[2].trim()))}}h.startsWith("##END")&&r>0&&r--}if(t){for(let u of a)u.children=void 0;return a}else return n}var ce=require("dynamic-typing"),pe=require("ensure-string");var ae=["TIC",".RIC","SCANNUMBER"];function le(e){let f=e.spectra,t=f.length,i={times:new Array(t),series:{ms:{dimension:2,data:new Array(t)}}},a=[];for(let o of ae){let n=B(o);f[0][n]&&(a.push(n),i.series[n]={dimension:1,data:new Array(t)})}for(let o=0;o<t;o++){let n=f[o];i.times[o]=n.pageValue;for(let m of a)i.series[m].data[o]=Number(n[m]);n.data&&(i.series.ms.data[o]=[n.data.x,n.data.y])}e.chromatogram=i}function fe(e){return ae.includes(e)}function B(e){return e.toLowerCase().replaceAll(/[^a-z0-9]/g,"")}function E(e){return e.map(Number)}function j(e,f,t){let{logger:i}=t;i&&(e.xFactor||i.info("The xFactor is not defined, it will be set to 1"),e.yFactor||i.info("The yFactor is not defined, it will be set to 1"));let a=e.yFactor??1,o=e.xFactor??1,n=e.deltaX??1,m=Math.abs(n*.1),r=.01;e.isXYdata=!0;let p={x:[],y:[]};e.data=p;let u=e.firstX||0,b=e.firstY||0,h=!1,s,l=0;for(;l<f.length;l++)if(s=f.codePointAt(l),s===13||s===10)h=!0;else if(h)break;let c=0,d=!0,A=!1,y=!1,k=0,N=!1,C=!1,g=0,X=0,M=!1,S=!1,Y=!1,R=0;for(;l<=f.length;l++)if(l===f.length?s=13:s=f.codePointAt(l),C)(s===13||s===10)&&(d=!0,C=!1,c++);else if(s<=57&&s>=48)S=!0,R>0?g+=(s-48)/10**R++:(g*=10,g+=s-48);else if(s===44||s===46)S=!0,R++;else{if(S){if(M&&(g=g*-1,M=!1),d)g*=o,i&&(y?Math.abs(u-n-g)>m&&(Math.abs(u-g)<m?i.trace(`Data line ${c}: After a DIFFERENCE the next line should repeat the last value and this does not seem to be the case: Current value: ${g} - Expected: ${u}.`):Math.abs(u-n-g)>10*m?i.trace(`Data line ${c}: The difference between the first value ${g} and the expected first x value ${u} based on increment after a DIFFERENCE is too high`):i.trace(`Data line ${c}: The difference between the first value ${g} and the expected first x value ${u} based on increment after a DIFFERENCE is too high`)):Math.abs(u-g)>m&&i.trace(`Data line ${c}: The difference between the first value ${g} and the first x value ${u} is too high`)),d=!1,y&&(Y=!0);else if(Y)Y=!1,i&&Math.abs(b-g)>r&&i.trace(`Data line ${c}: After a duplicate the next line should repeat the same value ${g} !== ${b}`),b=g;else{A?(k=M?0-g:g,y=!0,A=!1):N||(X=M?0-g:g);let x=N?g-1:1;for(let F=0;F<x;F++)y?b+=k:b=X,p.x.push(u),p.y.push(b*a),u+=n}M=!1,g=0,R=0,S=!1,N=!1}if(s<74&&s>63)S=!0,y=!1,g=s-64;else if(s>96&&s<106)S=!0,y=!1,g=s-96,M=!0;else if(s===115)S=!0,N=!0,g=9;else if(s>82&&s<91)S=!0,N=!0,g=s-82;else if(s>73&&s<83)S=!0,A=!0,g=s-73;else if(s>105&&s<115)S=!0,A=!0,g=s-105,M=!0;else if(s===36&&f.codePointAt(l+1)===36)S=!0,C=!0;else if(s===37)S=!0,A=!0,g=0,M=!1;else if(s===45){let x=f.codePointAt(l+1);(x!==void 0&&x>=48&&x<=57||x===44||x===46)&&(S=!0,d||(y=!1),M=!0)}else(s===13||s===10)&&(d=!0,C=!1,c++)}i&&y&&i.warn("The last value is a difference, it should be repeated on the next line")}var me=/[,\t ]+/;function w(e,f,t){if(e.isPeaktable=!0,!e.variables||Object.keys(e.variables).length===2?ve(e,f,t):Xe(e,f,t),e.variables)for(let i in e.variables)e.variables[i].data=e.data?.[i]}function ve(e,f,t){let{logger:i}=t,a={x:[],y:[]};e.data=a;let o=f.split(/,? *,?[;\r\n]+ */);for(let n=1;n<o.length;n++){let m=o[n].trim().replace(P,"").split(me);if(m.length%2===0)for(let r=0;r<m.length;r=r+2)e.xFactor!==void 0&&e.yFactor!==void 0&&(a.x.push(Number(m[r])*e.xFactor),a.y.push(Number(m[r+1])*e.yFactor));else i?.warn(`Format error: ${m.toString()}`)}}function Xe(e,f,t){let{logger:i}=t,a={},o=Object.keys(e.variables),n=o.length;for(let r of o)a[r]=[];e.data=a;let m=f.split(/,? *,?[;\r\n]+ */);for(let r=1;r<m.length;r++){let p=m[r].trim().replace(P,"").split(me);if(p.length%n===0)for(let u=0;u<p.length;u++)a[o[u%n]].push(Number(p[u]));else i?.warn(`Wrong number of columns: ${p.toString()}`)}}function Z(e,f){e.isXYAdata=!0;let t={};e.data=t;let i=f.split(/\r?\n/),a=i[0].replace(/^.*?([A-Z]+).*$/,"$1").split("").map(o=>o.toLowerCase());for(let o=1;o<i.length;o++){let n=i[o].replace(/^\((.*)\)$/,"$1").split(/ *, */);for(let m=0;m<a.length;m++){let r=n[m];switch(a[m]){case"x":case"y":case"w":r=Number.parseFloat(r);break;case"a":r=r.replace(/^<(.*)>$/,"$1");break;case"m":break;default:continue}t[a[m]]||(t[a[m]]=[]),t[a[m]].push(r)}}}var Q=require("dynamic-typing");var G=require("gyromagnetic-ratio"),W=Ce(require("ml-array-median"));function ue(e){return Array.isArray(e)?e[0]:e}function H(e){let{spectra:f}=e,t=f[0].data.y[0],i=t,a=f.length,o=f[0].data.x.length||0,n=new Array(a);for(let s=0;s<a;s++){n[s]=f[s].data.y;for(let l=0;l<o;l++){let c=n[s][l];c<t&&(t=c),c>i&&(i=c)}}let m=f[0].data.x[0],r=f[0].data.x.at(-1),{firstY:p,lastY:u}=Le(e);if(m>r)for(let s of n)s.reverse();p>u&&n.reverse();let b=[];for(let s of n){let l=Float64Array.from(s);for(let c=0;c<l.length;c++)l[c]<0&&(l[c]=-l[c]);b.push((0,W.default)(l))}let h=(0,W.default)(b);return{z:n,minX:Math.min(m,r),maxX:Math.max(m,r),minY:Math.min(p,u),maxY:Math.max(p,u),minZ:t,maxZ:i,noise:h}}function Le(e){let{spectra:f,ntuples:t,info:i}=e;if(t)for(let a of t){let{symbol:o,nucleus:n,units:m}=a;if(o.match(/[F|T]1/)&&m?.toUpperCase().match("HZ")){let r=ue(i[".OBSERVEFREQUENCY"]),{nucleus:p}=t.find(c=>c.symbol.match(/[F|T]2/));if([r,p,n].some(c=>!c))break;let u=(0,G.getGyromagneticRatio)(p),b=(0,G.getGyromagneticRatio)(n),{first:h,last:s}=a,l=b!==null&&u!==null?r*b/u:r;return{firstY:h/l,lastY:s/l}}}return{firstY:f[0].pageValue,lastY:f.at(-1).pageValue}}function J(e,f){let t=e.noise,i=e.z,a,o,n,m,r,p,u,b,h=i.length,s=i[0].length,l,c,d,A,y=e.minX,N=(e.maxX-y)/(s-1),C=e.minY,X=(e.maxY-C)/(h-1),M=e.minZ,S=e.maxZ,Y=f.nbContourLevels*2,R=new Array(Y),x;for(let F=0;F<Y;F++){let V={};R[F]=V;let ge=F%2,te=(S-f.noiseMultiplier*t)*Math.exp((F>>1)-f.nbContourLevels);ge===0?x=te+f.noiseMultiplier*t:x=0-te-f.noiseMultiplier*t;let D=[];if(V.zValue=x,V.lines=D,!(x<=M||x>=S))for(let v=0;v<h-1;v++){let ne=i[v],re=i[v+1];for(let 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t.spectra){if(t.ntuples?.symbol?(!i&&o.observeFrequency&&(i=o.observeFrequency),!a&&o.shiftOffsetVal&&(a=o.shiftOffsetVal)):(i=o.observeFrequency,a=o.shiftOffsetVal),i&&o.xUnits?.toUpperCase().includes("HZ")&&(o.xUnits="PPM",o.xFactor=o.xFactor!==void 0?o.xFactor/i:void 0,o.firstX=o.firstX!==void 0?o.firstX/i:void 0,o.lastX=o.lastX!==void 0?o.lastX/i:void 0,o.deltaX=o.deltaX!==void 0?o.deltaX/i:void 0,o.data))for(let n=0;n<o.data.x.length;n++)o.data.x[n]/=i;if(a&&o.xUnits.toLowerCase().includes("ppm")&&o.firstX!==void 0&&o.lastX!==void 0){let n=o.firstX-a;if(o.firstX=o.firstX-n,o.lastX=o.lastX-n,o.data)for(let m=0;m<o.data.x.length;m++)o.data.x[m]-=n}if(t.ntuples?.nucleus&&t.ntuples.symbol)for(let n=0;n<t.ntuples.nucleus.length;n++){let m=t.ntuples.symbol[n],r=t.ntuples.nucleus[n];if(m.match(/^[F|T]/)&&!r){if(m.match(/[F|T]1/))if(t.tmp.$NUC2&&typeof t.tmp.$NUC2=="string")t.ntuples.nucleus[n]=t.tmp.$NUC2;else{let p=t.ntuples.symbol.indexOf(m.replace(/^([F|T]).*/,"$12"));p&&t.ntuples.nucleus[p]&&(t.ntuples.nucleus[n]=t.ntuples.nucleus[p])}m.match(/[F|T]2/)&&typeof t.tmp.$NUC1=="string"&&(t.ntuples.nucleus[n]=t.tmp.$NUC1)}m.match(/[F|T]2/)&&(t.yType=t.ntuples.nucleus[0],t.xType&&!(0,I.getGyromagneticRatio)(t.xType)&&(t.xType=t.ntuples.nucleus[1]))}if(i&&t.ntuples?.symbol&&t.ntuples.nucleus){let n="",m=t.ntuples.symbol.indexOf(o.pageSymbol);t.ntuples.units?.[m]&&(n=t.ntuples.units[m]);let{nucleus:r}=t.ntuples;if(!n.toLowerCase().match(/(ppm|seconds)/)&&r.length>1){if(m!==0){let h="Not sure about this ntuples format";if(f){f.warn(h);continue}else throw new Error(h)}let{nucleus:p}=t.ntuples,u=(0,I.getGyromagneticRatio)(p[0]),b=(0,I.getGyromagneticRatio)(p[1]);if(!u||!b){let h=`Problem with determination of gyromagnetic ratio for ${p.join("-")}`;if(f)f.error(h);else throw new Error(h)}else{let h=u/b*i;o.pageValue/=h}}}}}}function K(e){let f=e.spectra[0].data;e.chromatogram={times:f.x.slice(),series:{intensity:{dimension:1,data:f.y.slice()}}}}function _(e,f,t){z(e,t.logger),Me(e,t);for(let i of e){if(Object.keys(i.ntuples).length>0){let a=[],o=Object.keys(i.ntuples);for(let n of o){let m=i.ntuples[n];if(m)for(let r=0;r<m.length;r++)a[r]||(a[r]={}),a[r][n]=m[r]}i.ntuples=a}i.twoD&&t.wantXY&&(q(i,t),t.logger?.trace({profiling:!0},"Finished countour plot calculation"),t.keepSpectra||delete i.spectra),t.chromatogram&&(i.spectra.length>1?le(i):K(i),t.logger?.trace({profiling:!0},"Finished chromatogram calculation")),delete i.tmp}}function Me(e,f){for(let t of e)for(let i in t.meta){let a=t.meta[i];if(typeof a=="string"){if(a.startsWith("{")){if(!a.includes(":")&&a.endsWith("}")){let o=a.slice(1,-1).split(/[,; ]+/).filter(Boolean);for(let n=0;n<o.length;n++)t.meta[i+String(n)]=f.dynamicTyping?(0,Q.parseString)(o[n]):o[n]}}else if(a.startsWith("(")){let o=a.split(/\r?\n/),n=/^\((?<from>\d+)\.\.(?<to>\d+)\).*$/;if(n.test(o[0])){let[m,r]=o[0].match(n)?.slice(1).map(Number)??[],p=o.slice(1).join(" ").split(/[,; ]+/).filter(Boolean);for(let u=m;u<=r;u++)f.dynamicTyping&&typeof p[u-m]=="string"?t.meta[i+String(u)]=(0,Q.parseString)(p[u-m]):t.meta[i+String(u)]=p[u-m]}}}}}function ee(e,f,t){let i=-1,a=-1,o="",n="";if(t.indexOf("++")>0)o=t.replace(/.*\(([a-zA-Z0-9]+)\+\+.*/,"$1"),n=t.replace(/.*\.\.([a-zA-Z0-9]+).*/,"$1");else{t=t.replaceAll(/[^a-zA-Z%]/g,""),o=t.charAt(0),n=t.charAt(1),f.variables={};for(let m of t){let r=m.toLowerCase(),p=e.ntuples.symbol?.indexOf(m)||0;if(p===-1)throw new Error(`Symbol undefined: ${m}`);f.variables[r]={};for(let u in e.ntuples)e.ntuples[u]?.[p]&&(f.variables[r][u.replace(/^var/,"")]=e.ntuples[u]?.[p])}}i=e.ntuples.symbol?.indexOf(o)??-1,a=e.ntuples.symbol?.indexOf(n)??-1,i===-1&&(i=0),a===-1&&(a=0),e.ntuples.first&&(e.ntuples.first.length>i&&(f.firstX=e.ntuples.first[i]),e.ntuples.first.length>a&&(f.firstY=e.ntuples.first[a])),e.ntuples.last&&(e.ntuples.last.length>i&&(f.lastX=e.ntuples.last[i]),e.ntuples.last.length>a&&(f.lastY=e.ntuples.last[a])),e.ntuples.vardim&&e.ntuples.vardim.length>i&&(f.nbPoints=e.ntuples.vardim[i]),e.ntuples.factor&&(e.ntuples.factor.length>i&&(f.xFactor=e.ntuples.factor[i]),e.ntuples.factor.length>a&&(f.yFactor=e.ntuples.factor[a])),e.ntuples.units&&(e.ntuples.units.length>i&&(e.ntuples.varname?.[i]?f.xUnits=`${e.ntuples.varname[i]} [${e.ntuples.units[i]}]`:f.xUnits=e.ntuples.units[i]),e.ntuples.units.length>a&&(e.ntuples.varname?.[a]?f.yUnits=`${e.ntuples.varname[a]} [${e.ntuples.units[a]}]`:f.yUnits=e.ntuples.units[a]))}function U(e){e.xFactor||(e.xFactor=1),e.yFactor||(e.yFactor=1)}var L=/[ \t]*,[ \t]*/,Oe={keepRecordsRegExp:/^$/,canonicDataLabels:!0,canonicMetadataLabels:!1,dynamicTyping:!0,withoutXY:!1,noTrimRegExp:/^$/,chromatogram:!1,keepSpectra:!1,noContour:!1,nbContourLevels:7,noiseMultiplier:5};function de(e,f={}){e=(0,pe.ensureString)(e);let t={...Oe,...f};t.logger?.debug("Starting jcamp conversion"),t.wantXY=!t.withoutXY,t.start=Date.now();let i=[],a={entries:[],flatten:[]},o={children:[],spectra:[],ntuples:{},info:{},meta:{},tmp:{}},n=o,m=[],r={data:{}};t.logger?.trace({profiling:!0},"Before split to LDRS");let p=e.replaceAll(/[\r\n]+##/g,`
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`,children:[]}),m=i.at(-1),a.push(m)}else if(h.startsWith("##END")&&r===0&&m){m.jcamp+=`${b}
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`;let s=i.pop();if(!s)throw new Error("Not finished");i.length>0?(m=i.at(-1),m.children?.push(s)):(m=void 0,n.push(s))}else if(m?.jcamp){m.jcamp+=`${b}
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`;let s=h.match(/^##(.*?)=(.+)/);if(s){let l=s[1].replaceAll(/[ _-]/g,"").toUpperCase();l==="DATATYPE"?m.dataType=s[2].trim():l==="DATACLASS"?m.dataClass=s[2].trim():l==="JCAMPDX"?m.jcampDX=O(s[2].trim()):l==="JCAMPCS"&&(m.jcampCS=O(s[2].trim()))}}h.startsWith("##END")&&r>0&&r--}if(t){for(let u of a)u.children=void 0;return a}else return n}var ce=require("dynamic-typing"),pe=require("ensure-string");var ae=["TIC",".RIC","SCANNUMBER"];function le(e){let f=e.spectra,t=f.length,o={times:new Array(t),series:{ms:{dimension:2,data:new Array(t)}}},a=[];for(let i of ae){let n=B(i);f[0][n]&&(a.push(n),o.series[n]={dimension:1,data:new Array(t)})}for(let i=0;i<t;i++){let n=f[i];o.times[i]=n.pageValue;for(let m of a)o.series[m].data[i]=Number(n[m]);n.data&&(o.series.ms.data[i]=[n.data.x,n.data.y])}e.chromatogram=o}function fe(e){return ae.includes(e)}function B(e){return e.toLowerCase().replaceAll(/[^a-z0-9]/g,"")}function E(e){return e.map(Number)}function 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+
`)),l==="TITLE"){let c=n;c.children||(c.children=[]),n={spectra:[],ntuples:{},info:{},meta:{},tmp:{}},c.children.push(n),m.push(c),o.push(n),n.title=s}else l==="DATATYPE"?(n.dataType=s,s.match(/^nd|\snd\s/i)&&(n.twoD=!0)):l==="NTUPLES"?s.match(/^nd|\snd\s/i)&&(n.twoD=!0):l==="DATACLASS"?n.dataClass=s:l==="JCAMPDX"?n.jcampDX=O(s):l==="JCAMPCS"?n.jcampCS=O(s):l==="XUNITS"?r.xUnits=s:l==="YUNITS"?r.yUnits=s:l==="FIRSTX"?r.firstX=Number(s):l==="LASTX"?r.lastX=Number(s):l==="FIRSTY"?r.firstY=Number(s):l==="LASTY"?r.lastY=Number(s):l==="NPOINTS"?r.nbPoints=Number(s):l==="XFACTOR"?r.xFactor=Number(s):l==="YFACTOR"?r.yFactor=Number(s):l==="MAXX"?r.maxX=Number(s):l==="MINX"?r.minX=Number(s):l==="MAXY"?r.maxY=Number(s):l==="MINY"?r.minY=Number(s):l==="DELTAX"?r.deltaX=Number(s):l===".OBSERVEFREQUENCY"||l==="$SFO1"?r.observeFrequency||(r.observeFrequency=Number(s)):l===".OBSERVENUCLEUS"?r.xType||(n.xType=s.replaceAll(/[^a-zA-Z0-9]/g,"")):l==="$OFFSET"?(n.shiftOffsetNum=0,r.shiftOffsetVal||(r.shiftOffsetVal=Number(s))):l==="$REFERENCEPOINT"||(l==="VARNAME"?n.ntuples.varname=s.split(L):l==="SYMBOL"?n.ntuples.symbol=s.split(L):l==="VARTYPE"?n.ntuples.vartype=s.split(L):l==="VARFORM"?n.ntuples.varform=s.split(L):l==="VARDIM"?n.ntuples.vardim=E(s.split(L)):l==="UNITS"?n.ntuples.units=s.split(L):l==="FACTOR"?n.ntuples.factor=E(s.split(L)):l==="FIRST"?n.ntuples.first=E(s.split(L)):l==="LAST"?n.ntuples.last=E(s.split(L)):l==="MIN"?n.ntuples.min=E(s.split(L)):l==="MAX"?n.ntuples.max=E(s.split(L)):l===".NUCLEUS"?n.ntuples&&(n.ntuples.nucleus=s.split(L).map(c=>c.replaceAll(/[^a-zA-Z0-9]/g,""))):l==="PAGE"?(r.page=s.trim(),r.pageValue=Number(s.replace(/^.*=/,"")),r.pageSymbol=r.page.replace(/[=].*/,"")):l==="RETENTIONTIME"?r.pageValue=Number(s):fe(l)?r[B(l)]=s:l==="SAMPLEDESCRIPTION"?r.sampleDescription=s:l.startsWith("$NUC")?!n.tmp[l]&&!s.includes("off")&&(n.tmp[l]=s.replaceAll(/[<>]/g,"")):l==="END"&&(n=m.pop()));if(n?.info&&n.meta&&l.match(t.keepRecordsRegExp)){let c,d;h.startsWith("$")?(d=t.canonicMetadataLabels?l.slice(1):h.slice(1),c=n.meta):(d=t.canonicDataLabels?l:h,c=n.info),t.dynamicTyping&&(s=(0,ce.parseString)(s)),c[d]?(Array.isArray(c[d])||(c[d]=[c[d]]),c[d].push(s)):c[d]=s}}if(t.logger?.trace({profiling:!0},"Finished parsing"),_(o,a,t),t.logger?.trace({profiling:!0},"Total time"),a.entries=i.children||[],a.flatten=o,t.logger){t.logger.debug("Finished jcamp conversion");for(let u of a.flatten)t.logger.debug(`${u.dataType} - ${u.title}`)}return a}function be(e,f){let{logger:t,OCL:o}=f;if(!e.info.ATOMLIST||!e.info.BONDLIST){t?.warn("No ATOMLIST or BONDLIST in the JCAMP-CS entry");return}Ye(e,t);let a=Ee(e.info.ATOMLIST),i=Re(e.info.BONDLIST),n=De(e.info.CHARGE,t),m=Fe(o,a,i,n,t);return{molecule:m,molfile:m.toMolfile()}}function Fe(e,f,t,o,a){let i={S:e.Molecule.cBondTypeSingle,D:e.Molecule.cBondTypeDouble,T:e.Molecule.cBondTypeTriple,Q:e.Molecule.cBondTypeQuadruple},n={},m=new e.Molecule(f.length,t.length);for(let r of f){let p=e.Molecule.getAtomicNoFromLabel(r.element);p||(a?.error(`Atomic number of ${r.element} could not be determined`),p=e.Molecule.getAtomicNoFromLabel("X")),n[r.atomNumber]=m.addAtom(p),m.setAtomMapNo(n[r.atomNumber],r.atomNumber,!1)}for(let r of t){if(n[r.atomNumber1]===void 0){a?.error(`A bond goes to atomNumber ${r.atomNumber1} that does not exists`);continue}if(n[r.atomNumber2]===void 0){a?.error(`A bond goes to atomNumber ${r.atomNumber2} that does not exists`);continue}let p=m.addBond(n[r.atomNumber1],n[r.atomNumber2]);m.setBondType(p,i[r.bondType])}for(let r of o){if(n[r.atomNumber]===void 0){a?.error(`A charge goes to atomNumber ${r.atomNumber} that does not exists`);continue}m.setAtomCharge(n[r.atomNumber],r.value)}return m}function Ee(e){let f=e.split(/\r?\n/).map(o=>O(o)).filter(Boolean),t=[];for(let o of f){let[a,i,n]=o.trim().split(/\s+/);t.push({atomNumber:Number(a),element:i,nbImplicitHydrogens:n?.length>0?Number(n):void 0})}return t}function Re(e){let f=e.split(/\r?\n/).map(o=>O(o)).filter(Boolean),t=[];for(let o of f){let[a,i,n]=o.trim().split(/\s+/);t.push({atomNumber1:Number(a),atomNumber2:Number(i),bondType:n})}return t}function De(e,f){if(!e)return[];let t=e.split(/\r?\n/).map(a=>O(a)).filter(Boolean),o=[];for(let a of t){let[i,n,m]=a.trim().split(/\s+/);m!==void 0&&f?.warn("Charge on multiple atom is not supported"),o.push({atomNumber:Number(n),value:Number(i)})}return o}function Ye(e,f){let t=["STEREOPAIR","STEREOCENTER","RADICAL","STEREOMOLECULE"];for(let o of t)e.info[o]&&f?.warn(`JCAMP-CS parser do not support: ${o}`)}
|
package/jcampconverter.d.ts
CHANGED
|
@@ -42,6 +42,11 @@ export declare function convert(jcamp: string | ArrayBuffer | Uint8Array, option
|
|
|
42
42
|
* Conversion options.
|
|
43
43
|
*/
|
|
44
44
|
declare interface ConvertOptions extends Partial<Add2DOptions> {
|
|
45
|
+
/**
|
|
46
|
+
* If it is true, anywhere out of XYDATA, PEAKTABLE n PEAKASSIGNMENTS the comments are removed
|
|
47
|
+
* @default false
|
|
48
|
+
*/
|
|
49
|
+
removeComments?: boolean;
|
|
45
50
|
/**
|
|
46
51
|
* By default we don't keep meta information.
|
|
47
52
|
* @default `/^$/`
|
package/jcampconverter.mjs
CHANGED
|
@@ -1,9 +1,9 @@
|
|
|
1
|
-
import{ensureString as fe}from"ensure-string";var $=/\s*\$\$.*/;function O(e){return e.replace($,"")}function me(e,m={}){e=fe(e);let{flatten:n=!1}=m,
|
|
1
|
+
import{ensureString as fe}from"ensure-string";var $=/\s*\$\$.*/;function O(e){return e.replace($,"")}function me(e,m={}){e=fe(e);let{flatten:n=!1}=m,o=e.split(/\r?\n/),f=[],i=[],t=[],l={title:"",jcamp:"",children:[]},r=0,p=e.includes("## ");for(let u=0;u<o.length;u++){let b=o[u],h=p?b.replaceAll(" ",""):b;if(h.startsWith("##NTUPLES")&&r++,h.startsWith("##TITLE")){let s=[h.slice(8).trim()];for(let a=u+1;a<o.length&&!o[a].startsWith("##");a++)s.push(o[a].trim());i.push({title:s.join(`
|
|
2
2
|
`),jcamp:`${b}
|
|
3
|
-
`,children:[]}),l=
|
|
4
|
-
`;let s=
|
|
5
|
-
`;let s=h.match(/^##(.*?)=(.+)/);if(s){let a=s[1].replaceAll(/[ _-]/g,"").toUpperCase();a==="DATATYPE"?l.dataType=s[2].trim():a==="DATACLASS"?l.dataClass=s[2].trim():a==="JCAMPDX"?l.jcampDX=O(s[2].trim()):a==="JCAMPCS"&&(l.jcampCS=O(s[2].trim()))}}h.startsWith("##END")&&r>0&&r--}if(n){for(let u of f)u.children=void 0;return f}else return t}import{parseString as be}from"dynamic-typing";import{ensureString as ge}from"ensure-string";var ee=["TIC",".RIC","SCANNUMBER"];function te(e){let m=e.spectra,n=m.length,i={times:new Array(n),series:{ms:{dimension:2,data:new Array(n)}}},f=[];for(let o of ee){let t=k(o);m[0][t]&&(f.push(t),i.series[t]={dimension:1,data:new Array(n)})}for(let o=0;o<n;o++){let t=m[o];i.times[o]=t.pageValue;for(let l of f)i.series[l].data[o]=Number(t[l]);t.data&&(i.series.ms.data[o]=[t.data.x,t.data.y])}e.chromatogram=i}function ne(e){return ee.includes(e)}function k(e){return e.toLowerCase().replaceAll(/[^a-z0-9]/g,"")}function E(e){return e.map(Number)}function V(e,m,n){let{logger:i}=n;i&&(e.xFactor||i.info("The xFactor is not defined, it will be set to 1"),e.yFactor||i.info("The yFactor is not defined, it will be set to 1"));let f=e.yFactor??1,o=e.xFactor??1,t=e.deltaX??1,l=Math.abs(t*.1),r=.01;e.isXYdata=!0;let p={x:[],y:[]};e.data=p;let u=e.firstX||0,b=e.firstY||0,h=!1,s,a=0;for(;a<m.length;a++)if(s=m.codePointAt(a),s===13||s===10)h=!0;else if(h)break;let c=0,d=!0,A=!1,y=!1,I=0,N=!1,C=!1,g=0,X=0,M=!1,S=!1,Y=!1,R=0;for(;a<=m.length;a++)if(a===m.length?s=13:s=m.codePointAt(a),C)(s===13||s===10)&&(d=!0,C=!1,c++);else if(s<=57&&s>=48)S=!0,R>0?g+=(s-48)/10**R++:(g*=10,g+=s-48);else if(s===44||s===46)S=!0,R++;else{if(S){if(M&&(g=g*-1,M=!1),d)g*=o,i&&(y?Math.abs(u-t-g)>l&&(Math.abs(u-g)<l?i.trace(`Data line ${c}: After a DIFFERENCE the next line should repeat the last value and this does not seem to be the case: Current value: ${g} - Expected: ${u}.`):Math.abs(u-t-g)>10*l?i.trace(`Data line ${c}: The difference between the first value ${g} and the expected first x value ${u} based on increment after a DIFFERENCE is too high`):i.trace(`Data line ${c}: The difference between the first value ${g} and the expected first x value ${u} based on increment after a DIFFERENCE is too high`)):Math.abs(u-g)>l&&i.trace(`Data line ${c}: The difference between the first value ${g} and the first x value ${u} is too high`)),d=!1,y&&(Y=!0);else if(Y)Y=!1,i&&Math.abs(b-g)>r&&i.trace(`Data line ${c}: After a duplicate the next line should repeat the same value ${g} !== ${b}`),b=g;else{A?(I=M?0-g:g,y=!0,A=!1):N||(X=M?0-g:g);let x=N?g-1:1;for(let F=0;F<x;F++)y?b+=I:b=X,p.x.push(u),p.y.push(b*f),u+=t}M=!1,g=0,R=0,S=!1,N=!1}if(s<74&&s>63)S=!0,y=!1,g=s-64;else if(s>96&&s<106)S=!0,y=!1,g=s-96,M=!0;else if(s===115)S=!0,N=!0,g=9;else if(s>82&&s<91)S=!0,N=!0,g=s-82;else if(s>73&&s<83)S=!0,A=!0,g=s-73;else if(s>105&&s<115)S=!0,A=!0,g=s-105,M=!0;else if(s===36&&m.codePointAt(a+1)===36)S=!0,C=!0;else if(s===37)S=!0,A=!0,g=0,M=!1;else if(s===45){let x=m.codePointAt(a+1);(x!==void 0&&x>=48&&x<=57||x===44||x===46)&&(S=!0,d||(y=!1),M=!0)}else(s===13||s===10)&&(d=!0,C=!1,c++)}i&&y&&i.warn("The last value is a difference, it should be repeated on the next line")}var re=/[,\t ]+/;function P(e,m,n){if(e.isPeaktable=!0,!e.variables||Object.keys(e.variables).length===2?ue(e,m,n):ce(e,m,n),e.variables)for(let i in e.variables)e.variables[i].data=e.data?.[i]}function ue(e,m,n){let{logger:i}=n,f={x:[],y:[]};e.data=f;let o=m.split(/,? *,?[;\r\n]+ */);for(let t=1;t<o.length;t++){let l=o[t].trim().replace($,"").split(re);if(l.length%2===0)for(let r=0;r<l.length;r=r+2)e.xFactor!==void 0&&e.yFactor!==void 0&&(f.x.push(Number(l[r])*e.xFactor),f.y.push(Number(l[r+1])*e.yFactor));else i?.warn(`Format error: ${l.toString()}`)}}function ce(e,m,n){let{logger:i}=n,f={},o=Object.keys(e.variables),t=o.length;for(let r of o)f[r]=[];e.data=f;let l=m.split(/,? *,?[;\r\n]+ */);for(let r=1;r<l.length;r++){let p=l[r].trim().replace($,"").split(re);if(p.length%t===0)for(let u=0;u<p.length;u++)f[o[u%t]].push(Number(p[u]));else i?.warn(`Wrong number of columns: ${p.toString()}`)}}function B(e,m){e.isXYAdata=!0;let n={};e.data=n;let i=m.split(/\r?\n/),f=i[0].replace(/^.*?([A-Z]+).*$/,"$1").split("").map(o=>o.toLowerCase());for(let o=1;o<i.length;o++){let t=i[o].replace(/^\((.*)\)$/,"$1").split(/ *, */);for(let l=0;l<f.length;l++){let r=t[l];switch(f[l]){case"x":case"y":case"w":r=Number.parseFloat(r);break;case"a":r=r.replace(/^<(.*)>$/,"$1");break;case"m":break;default:continue}n[f[l]]||(n[f[l]]=[]),n[f[l]].push(r)}}}import{parseString as ae}from"dynamic-typing";import{getGyromagneticRatio as ie}from"gyromagnetic-ratio";import oe from"ml-array-median";function se(e){return Array.isArray(e)?e[0]:e}function j(e){let{spectra:m}=e,n=m[0].data.y[0],i=n,f=m.length,o=m[0].data.x.length||0,t=new Array(f);for(let s=0;s<f;s++){t[s]=m[s].data.y;for(let a=0;a<o;a++){let c=t[s][a];c<n&&(n=c),c>i&&(i=c)}}let l=m[0].data.x[0],r=m[0].data.x.at(-1),{firstY:p,lastY:u}=pe(e);if(l>r)for(let s of t)s.reverse();p>u&&t.reverse();let b=[];for(let s of t){let a=Float64Array.from(s);for(let c=0;c<a.length;c++)a[c]<0&&(a[c]=-a[c]);b.push(oe(a))}let h=oe(b);return{z:t,minX:Math.min(l,r),maxX:Math.max(l,r),minY:Math.min(p,u),maxY:Math.max(p,u),minZ:n,maxZ:i,noise:h}}function pe(e){let{spectra:m,ntuples:n,info:i}=e;if(n)for(let f of n){let{symbol:o,nucleus:t,units:l}=f;if(o.match(/[F|T]1/)&&l?.toUpperCase().match("HZ")){let r=se(i[".OBSERVEFREQUENCY"]),{nucleus:p}=n.find(c=>c.symbol.match(/[F|T]2/));if([r,p,t].some(c=>!c))break;let u=ie(p),b=ie(t),{first:h,last:s}=f,a=b!==null&&u!==null?r*b/u:r;return{firstY:h/a,lastY:s/a}}}return{firstY:m[0].pageValue,lastY:m.at(-1).pageValue}}function Z(e,m){let n=e.noise,i=e.z,f,o,t,l,r,p,u,b,h=i.length,s=i[0].length,a,c,d,A,y=e.minX,N=(e.maxX-y)/(s-1),C=e.minY,X=(e.maxY-C)/(h-1),M=e.minZ,S=e.maxZ,Y=m.nbContourLevels*2,R=new Array(Y),x;for(let F=0;F<Y;F++){let U={};R[F]=U;let le=F%2,K=(S-m.noiseMultiplier*n)*Math.exp((F>>1)-m.nbContourLevels);le===0?x=K+m.noiseMultiplier*n:x=0-K-m.noiseMultiplier*n;let D=[];if(U.zValue=x,U.lines=D,!(x<=M||x>=S))for(let v=0;v<h-1;v++){let Q=i[v],_=i[v+1];for(let T=0;T<s-1;T++)f=Q[T],o=Q[T+1],t=_[T],l=_[T+1],r=f>x,p=o>x,u=t>x,b=l>x,r!==p&&r!==u&&(a=T+(x-f)/(o-f),c=v,d=T,A=v+(x-f)/(t-f),D.push(a*N+y,c*X+C,d*N+y,A*X+C)),b!==p&&b!==u&&(a=T+1,c=v+1-(x-l)/(o-l),d=T+1-(x-l)/(t-l),A=v+1,D.push(a*N+y,c*X+C,d*N+y,A*X+C)),p!==u&&(a=(T+1-(x-o)/(t-o))*N+y,c=(v+(x-o)/(t-o))*X+C,p!==r&&(d=T+1-(x-o)/(f-o),A=v,D.push(a,c,d*N+y,A*X+C)),u!==r&&(d=T,A=v+1-(x-t)/(f-t),D.push(a,c,d*N+y,A*X+C)),p!==b&&(d=T+1,A=v+(x-o)/(l-o),D.push(a,c,d*N+y,A*X+C)),u!==b&&(d=T+(x-t)/(l-t),A=v+1,D.push(a,c,d*N+y,A*X+C)))}}return{minX:e.minX,maxX:e.maxX,minY:e.minY,maxY:e.maxY,segments:R}}function G(e,m){let n=j(e);m.noContour||(e.contourLines=Z(n,m),delete n.z),e.minMax=n}import{getGyromagneticRatio as W}from"gyromagnetic-ratio";function H(e,m){for(let n of e){let i=0,f=0;for(let o of n.spectra){if(n.ntuples?.symbol?(!i&&o.observeFrequency&&(i=o.observeFrequency),!f&&o.shiftOffsetVal&&(f=o.shiftOffsetVal)):(i=o.observeFrequency,f=o.shiftOffsetVal),i&&o.xUnits?.toUpperCase().includes("HZ")&&(o.xUnits="PPM",o.xFactor=o.xFactor!==void 0?o.xFactor/i:void 0,o.firstX=o.firstX!==void 0?o.firstX/i:void 0,o.lastX=o.lastX!==void 0?o.lastX/i:void 0,o.deltaX=o.deltaX!==void 0?o.deltaX/i:void 0,o.data))for(let t=0;t<o.data.x.length;t++)o.data.x[t]/=i;if(f&&o.xUnits.toLowerCase().includes("ppm")&&o.firstX!==void 0&&o.lastX!==void 0){let t=o.firstX-f;if(o.firstX=o.firstX-t,o.lastX=o.lastX-t,o.data)for(let l=0;l<o.data.x.length;l++)o.data.x[l]-=t}if(n.ntuples?.nucleus&&n.ntuples.symbol)for(let t=0;t<n.ntuples.nucleus.length;t++){let l=n.ntuples.symbol[t],r=n.ntuples.nucleus[t];if(l.match(/^[F|T]/)&&!r){if(l.match(/[F|T]1/))if(n.tmp.$NUC2&&typeof n.tmp.$NUC2=="string")n.ntuples.nucleus[t]=n.tmp.$NUC2;else{let p=n.ntuples.symbol.indexOf(l.replace(/^([F|T]).*/,"$12"));p&&n.ntuples.nucleus[p]&&(n.ntuples.nucleus[t]=n.ntuples.nucleus[p])}l.match(/[F|T]2/)&&typeof n.tmp.$NUC1=="string"&&(n.ntuples.nucleus[t]=n.tmp.$NUC1)}l.match(/[F|T]2/)&&(n.yType=n.ntuples.nucleus[0],n.xType&&!W(n.xType)&&(n.xType=n.ntuples.nucleus[1]))}if(i&&n.ntuples?.symbol&&n.ntuples.nucleus){let t="",l=n.ntuples.symbol.indexOf(o.pageSymbol);n.ntuples.units?.[l]&&(t=n.ntuples.units[l]);let{nucleus:r}=n.ntuples;if(!t.toLowerCase().match(/(ppm|seconds)/)&&r.length>1){if(l!==0){let h="Not sure about this ntuples format";if(m){m.warn(h);continue}else throw new Error(h)}let{nucleus:p}=n.ntuples,u=W(p[0]),b=W(p[1]);if(!u||!b){let h=`Problem with determination of gyromagnetic ratio for ${p.join("-")}`;if(m)m.error(h);else throw new Error(h)}else{let h=u/b*i;o.pageValue/=h}}}}}}function J(e){let m=e.spectra[0].data;e.chromatogram={times:m.x.slice(),series:{intensity:{dimension:1,data:m.y.slice()}}}}function q(e,m,n){H(e,n.logger),de(e,n);for(let i of e){if(Object.keys(i.ntuples).length>0){let f=[],o=Object.keys(i.ntuples);for(let t of o){let l=i.ntuples[t];if(l)for(let r=0;r<l.length;r++)f[r]||(f[r]={}),f[r][t]=l[r]}i.ntuples=f}i.twoD&&n.wantXY&&(G(i,n),n.logger?.trace({profiling:!0},"Finished countour plot calculation"),n.keepSpectra||delete i.spectra),n.chromatogram&&(i.spectra.length>1?te(i):J(i),n.logger?.trace({profiling:!0},"Finished chromatogram calculation")),delete i.tmp}}function de(e,m){for(let n of e)for(let i in n.meta){let f=n.meta[i];if(typeof f=="string"){if(f.startsWith("{")){if(!f.includes(":")&&f.endsWith("}")){let o=f.slice(1,-1).split(/[,; ]+/).filter(Boolean);for(let t=0;t<o.length;t++)n.meta[i+String(t)]=m.dynamicTyping?ae(o[t]):o[t]}}else if(f.startsWith("(")){let o=f.split(/\r?\n/),t=/^\((?<from>\d+)\.\.(?<to>\d+)\).*$/;if(t.test(o[0])){let[l,r]=o[0].match(t)?.slice(1).map(Number)??[],p=o.slice(1).join(" ").split(/[,; ]+/).filter(Boolean);for(let 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e.ntuples)e.ntuples[u]?.[p]&&(m.variables[r][u.replace(/^var/,"")]=e.ntuples[u]?.[p])}}i=e.ntuples.symbol?.indexOf(o)??-1,f=e.ntuples.symbol?.indexOf(t)??-1,i===-1&&(i=0),f===-1&&(f=0),e.ntuples.first&&(e.ntuples.first.length>i&&(m.firstX=e.ntuples.first[i]),e.ntuples.first.length>f&&(m.firstY=e.ntuples.first[f])),e.ntuples.last&&(e.ntuples.last.length>i&&(m.lastX=e.ntuples.last[i]),e.ntuples.last.length>f&&(m.lastY=e.ntuples.last[f])),e.ntuples.vardim&&e.ntuples.vardim.length>i&&(m.nbPoints=e.ntuples.vardim[i]),e.ntuples.factor&&(e.ntuples.factor.length>i&&(m.xFactor=e.ntuples.factor[i]),e.ntuples.factor.length>f&&(m.yFactor=e.ntuples.factor[f])),e.ntuples.units&&(e.ntuples.units.length>i&&(e.ntuples.varname?.[i]?m.xUnits=`${e.ntuples.varname[i]} [${e.ntuples.units[i]}]`:m.xUnits=e.ntuples.units[i]),e.ntuples.units.length>f&&(e.ntuples.varname?.[f]?m.yUnits=`${e.ntuples.varname[f]} [${e.ntuples.units[f]}]`:m.yUnits=e.ntuples.units[f]))}function 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3
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u=l;u<=r;u++)m.dynamicTyping&&typeof p[u-l]=="string"?n.meta[o+String(u)]=ae(p[u-l]):n.meta[o+String(u)]=p[u-l]}}}}}function z(e,m,n){let o=-1,f=-1,i="",t="";if(n.indexOf("++")>0)i=n.replace(/.*\(([a-zA-Z0-9]+)\+\+.*/,"$1"),t=n.replace(/.*\.\.([a-zA-Z0-9]+).*/,"$1");else{n=n.replaceAll(/[^a-zA-Z%]/g,""),i=n.charAt(0),t=n.charAt(1),m.variables={};for(let l of n){let r=l.toLowerCase(),p=e.ntuples.symbol?.indexOf(l)||0;if(p===-1)throw new Error(`Symbol undefined: ${l}`);m.variables[r]={};for(let u in e.ntuples)e.ntuples[u]?.[p]&&(m.variables[r][u.replace(/^var/,"")]=e.ntuples[u]?.[p])}}o=e.ntuples.symbol?.indexOf(i)??-1,f=e.ntuples.symbol?.indexOf(t)??-1,o===-1&&(o=0),f===-1&&(f=0),e.ntuples.first&&(e.ntuples.first.length>o&&(m.firstX=e.ntuples.first[o]),e.ntuples.first.length>f&&(m.firstY=e.ntuples.first[f])),e.ntuples.last&&(e.ntuples.last.length>o&&(m.lastX=e.ntuples.last[o]),e.ntuples.last.length>f&&(m.lastY=e.ntuples.last[f])),e.ntuples.vardim&&e.ntuples.vardim.length>o&&(m.nbPoints=e.ntuples.vardim[o]),e.ntuples.factor&&(e.ntuples.factor.length>o&&(m.xFactor=e.ntuples.factor[o]),e.ntuples.factor.length>f&&(m.yFactor=e.ntuples.factor[f])),e.ntuples.units&&(e.ntuples.units.length>o&&(e.ntuples.varname?.[o]?m.xUnits=`${e.ntuples.varname[o]} [${e.ntuples.units[o]}]`:m.xUnits=e.ntuples.units[o]),e.ntuples.units.length>f&&(e.ntuples.varname?.[f]?m.yUnits=`${e.ntuples.varname[f]} [${e.ntuples.units[f]}]`:m.yUnits=e.ntuples.units[f]))}function w(e){e.xFactor||(e.xFactor=1),e.yFactor||(e.yFactor=1)}var L=/[ \t]*,[ \t]*/,he={removeComments:!1,keepRecordsRegExp:/^$/,canonicDataLabels:!0,canonicMetadataLabels:!1,dynamicTyping:!0,withoutXY:!1,noTrimRegExp:/^$/,chromatogram:!1,keepSpectra:!1,noContour:!1,nbContourLevels:7,noiseMultiplier:5};function xe(e,m={}){e=ge(e);let n={...he,...m};n.logger?.debug("Starting jcamp conversion"),n.wantXY=!n.withoutXY,n.start=Date.now();let o=[],f={entries:[],flatten:[]},i={children:[],spectra:[],ntuples:{},info:{},meta:{},tmp:{}},t=i,l=[],r={data:{}};n.logger?.trace({profiling:!0},"Before split to LDRS");let p=e.replaceAll(/[\r\n]+##/g,`
|
|
6
6
|
##`).split(`
|
|
7
7
|
##`);n.logger?.trace({profiling:!0},"Split to LDRS"),p[0]&&(p[0]=p[0].replace(/^[\r\n ]*##/,""));for(let u of p){let b=u.indexOf("="),h=b>0?u.slice(0,Math.max(0,b)):u,s=b>0?h.match(n.noTrimRegExp)?u.slice(Math.max(0,b+1)):u.slice(Math.max(0,b+1)).trim():"",a=h.replaceAll(/[_ -]/g,"").toUpperCase();if(a==="DATATABLE"){let c=s.indexOf(`
|
|
8
|
-
`);if(c===-1&&(c=s.indexOf("\r")),c>0){let d=s.slice(0,Math.max(0,c)).split(/[ ,;\t]+/);z(t,r,d[0]),r.datatable=d[0],d[1]?.includes("PEAKS")?a="PEAKTABLE":d[1]&&(d[1].indexOf("XYDATA")||d[0].indexOf("++")>0)&&(a="XYDATA",r.nbPoints&&r.lastX!==void 0&&r.firstX!==void 0&&(r.deltaX=(r.lastX-r.firstX)/(r.nbPoints-1)))}}if(a==="XYDATA"){n.wantXY&&(w(r),s.match(/.*\+\+.*/)?(r.nbPoints&&r.lastX!==void 0&&r.firstX!==void 0&&(r.deltaX=(r.lastX-r.firstX)/(r.nbPoints-1)),V(r,s,n)):P(r,s,n),t?.spectra.push(r),r={data:{}});continue}else if(a==="PEAKTABLE"){n.wantXY&&(w(r),P(r,s,n),t?.spectra.push(r),r={data:{}});continue}if(a==="PEAKASSIGNMENTS"){n.wantXY&&(s.match(/.*[^A-Z]*.*/)&&B(r,s),t?.spectra.push(r),r={data:{}});continue}if(s=s.split(/\r?\n/).map(c=>c.replace(/ *\$\$.*$/,"")).join(`
|
|
9
|
-
`),a==="TITLE"){let c=t;c.children||(c.children=[]),t={spectra:[],ntuples:{},info:{},meta:{},tmp:{}},c.children.push(t),l.push(c),
|
|
8
|
+
`);if(c===-1&&(c=s.indexOf("\r")),c>0){let d=s.slice(0,Math.max(0,c)).split(/[ ,;\t]+/);z(t,r,d[0]),r.datatable=d[0],d[1]?.includes("PEAKS")?a="PEAKTABLE":d[1]&&(d[1].indexOf("XYDATA")||d[0].indexOf("++")>0)&&(a="XYDATA",r.nbPoints&&r.lastX!==void 0&&r.firstX!==void 0&&(r.deltaX=(r.lastX-r.firstX)/(r.nbPoints-1)))}}if(a==="XYDATA"){n.wantXY&&(w(r),s.match(/.*\+\+.*/)?(r.nbPoints&&r.lastX!==void 0&&r.firstX!==void 0&&(r.deltaX=(r.lastX-r.firstX)/(r.nbPoints-1)),V(r,s,n)):P(r,s,n),t?.spectra.push(r),r={data:{}});continue}else if(a==="PEAKTABLE"){n.wantXY&&(w(r),P(r,s,n),t?.spectra.push(r),r={data:{}});continue}if(a==="PEAKASSIGNMENTS"){n.wantXY&&(s.match(/.*[^A-Z]*.*/)&&B(r,s),t?.spectra.push(r),r={data:{}});continue}if(n.removeComments&&(s=s.split(/\r?\n/).map(c=>c.replace(/ *\$\$.*$/,"")).join(`
|
|
9
|
+
`)),a==="TITLE"){let c=t;c.children||(c.children=[]),t={spectra:[],ntuples:{},info:{},meta:{},tmp:{}},c.children.push(t),l.push(c),o.push(t),t.title=s}else a==="DATATYPE"?(t.dataType=s,s.match(/^nd|\snd\s/i)&&(t.twoD=!0)):a==="NTUPLES"?s.match(/^nd|\snd\s/i)&&(t.twoD=!0):a==="DATACLASS"?t.dataClass=s:a==="JCAMPDX"?t.jcampDX=O(s):a==="JCAMPCS"?t.jcampCS=O(s):a==="XUNITS"?r.xUnits=s:a==="YUNITS"?r.yUnits=s:a==="FIRSTX"?r.firstX=Number(s):a==="LASTX"?r.lastX=Number(s):a==="FIRSTY"?r.firstY=Number(s):a==="LASTY"?r.lastY=Number(s):a==="NPOINTS"?r.nbPoints=Number(s):a==="XFACTOR"?r.xFactor=Number(s):a==="YFACTOR"?r.yFactor=Number(s):a==="MAXX"?r.maxX=Number(s):a==="MINX"?r.minX=Number(s):a==="MAXY"?r.maxY=Number(s):a==="MINY"?r.minY=Number(s):a==="DELTAX"?r.deltaX=Number(s):a===".OBSERVEFREQUENCY"||a==="$SFO1"?r.observeFrequency||(r.observeFrequency=Number(s)):a===".OBSERVENUCLEUS"?r.xType||(t.xType=s.replaceAll(/[^a-zA-Z0-9]/g,"")):a==="$OFFSET"?(t.shiftOffsetNum=0,r.shiftOffsetVal||(r.shiftOffsetVal=Number(s))):a==="$REFERENCEPOINT"||(a==="VARNAME"?t.ntuples.varname=s.split(L):a==="SYMBOL"?t.ntuples.symbol=s.split(L):a==="VARTYPE"?t.ntuples.vartype=s.split(L):a==="VARFORM"?t.ntuples.varform=s.split(L):a==="VARDIM"?t.ntuples.vardim=E(s.split(L)):a==="UNITS"?t.ntuples.units=s.split(L):a==="FACTOR"?t.ntuples.factor=E(s.split(L)):a==="FIRST"?t.ntuples.first=E(s.split(L)):a==="LAST"?t.ntuples.last=E(s.split(L)):a==="MIN"?t.ntuples.min=E(s.split(L)):a==="MAX"?t.ntuples.max=E(s.split(L)):a===".NUCLEUS"?t.ntuples&&(t.ntuples.nucleus=s.split(L).map(c=>c.replaceAll(/[^a-zA-Z0-9]/g,""))):a==="PAGE"?(r.page=s.trim(),r.pageValue=Number(s.replace(/^.*=/,"")),r.pageSymbol=r.page.replace(/[=].*/,"")):a==="RETENTIONTIME"?r.pageValue=Number(s):ne(a)?r[k(a)]=s:a==="SAMPLEDESCRIPTION"?r.sampleDescription=s:a.startsWith("$NUC")?!t.tmp[a]&&!s.includes("off")&&(t.tmp[a]=s.replaceAll(/[<>]/g,"")):a==="END"&&(t=l.pop()));if(t?.info&&t.meta&&a.match(n.keepRecordsRegExp)){let c,d;h.startsWith("$")?(d=n.canonicMetadataLabels?a.slice(1):h.slice(1),c=t.meta):(d=n.canonicDataLabels?a:h,c=t.info),n.dynamicTyping&&(s=be(s)),c[d]?(Array.isArray(c[d])||(c[d]=[c[d]]),c[d].push(s)):c[d]=s}}if(n.logger?.trace({profiling:!0},"Finished parsing"),q(o,f,n),n.logger?.trace({profiling:!0},"Total time"),f.entries=i.children||[],f.flatten=o,n.logger){n.logger.debug("Finished jcamp conversion");for(let u of f.flatten)n.logger.debug(`${u.dataType} - ${u.title}`)}return f}function ye(e,m){let{logger:n,OCL:o}=m;if(!e.info.ATOMLIST||!e.info.BONDLIST){n?.warn("No ATOMLIST or BONDLIST in the JCAMP-CS entry");return}Te(e,n);let f=Ce(e.info.ATOMLIST),i=Se(e.info.BONDLIST),t=Ne(e.info.CHARGE,n),l=Ae(o,f,i,t,n);return{molecule:l,molfile:l.toMolfile()}}function Ae(e,m,n,o,f){let i={S:e.Molecule.cBondTypeSingle,D:e.Molecule.cBondTypeDouble,T:e.Molecule.cBondTypeTriple,Q:e.Molecule.cBondTypeQuadruple},t={},l=new e.Molecule(m.length,n.length);for(let r of m){let p=e.Molecule.getAtomicNoFromLabel(r.element);p||(f?.error(`Atomic number of ${r.element} could not be determined`),p=e.Molecule.getAtomicNoFromLabel("X")),t[r.atomNumber]=l.addAtom(p),l.setAtomMapNo(t[r.atomNumber],r.atomNumber,!1)}for(let r of n){if(t[r.atomNumber1]===void 0){f?.error(`A bond goes to atomNumber ${r.atomNumber1} that does not exists`);continue}if(t[r.atomNumber2]===void 0){f?.error(`A bond goes to atomNumber ${r.atomNumber2} that does not exists`);continue}let p=l.addBond(t[r.atomNumber1],t[r.atomNumber2]);l.setBondType(p,i[r.bondType])}for(let r of o){if(t[r.atomNumber]===void 0){f?.error(`A charge goes to atomNumber ${r.atomNumber} that does not exists`);continue}l.setAtomCharge(t[r.atomNumber],r.value)}return l}function Ce(e){let m=e.split(/\r?\n/).map(o=>O(o)).filter(Boolean),n=[];for(let o of m){let[f,i,t]=o.trim().split(/\s+/);n.push({atomNumber:Number(f),element:i,nbImplicitHydrogens:t?.length>0?Number(t):void 0})}return n}function Se(e){let m=e.split(/\r?\n/).map(o=>O(o)).filter(Boolean),n=[];for(let o of m){let[f,i,t]=o.trim().split(/\s+/);n.push({atomNumber1:Number(f),atomNumber2:Number(i),bondType:t})}return n}function Ne(e,m){if(!e)return[];let n=e.split(/\r?\n/).map(f=>O(f)).filter(Boolean),o=[];for(let f of n){let[i,t,l]=f.trim().split(/\s+/);l!==void 0&&m?.warn("Charge on multiple atom is not supported"),o.push({atomNumber:Number(t),value:Number(i)})}return o}function Te(e,m){let n=["STEREOPAIR","STEREOCENTER","RADICAL","STEREOMOLECULE"];for(let o of n)e.info[o]&&m?.warn(`JCAMP-CS parser do not support: ${o}`)}export{xe as convert,me as createTree,ye as parseJcampCS};
|
package/package.json
CHANGED
|
@@ -1,6 +1,6 @@
|
|
|
1
1
|
{
|
|
2
2
|
"name": "jcampconverter",
|
|
3
|
-
"version": "10.0.
|
|
3
|
+
"version": "10.0.1",
|
|
4
4
|
"description": "Parse and convert JCAMP data",
|
|
5
5
|
"keywords": [
|
|
6
6
|
"jcamp",
|
|
@@ -58,6 +58,7 @@
|
|
|
58
58
|
"eslint": "^9.12.0",
|
|
59
59
|
"eslint-config-cheminfo-typescript": "^16.0.0",
|
|
60
60
|
"fifo-logger": "^1.0.0",
|
|
61
|
+
"jcamp-data-test": "^0.8.1",
|
|
61
62
|
"jest-matcher-deep-close-to": "^3.0.2",
|
|
62
63
|
"jscpd": "^4.0.5",
|
|
63
64
|
"ml-spectra-processing": "^14.6.0",
|