jcampconverter 9.1.1 → 9.2.1

package/README.md

@@ -4,12 +4,10 @@
 [![npm download][download-image]][download-url]
 [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.5091526.svg)](https://doi.org/10.5281/zenodo.5091526)
 
-
 # JCAMP-DX converter
 
 Parse and convert JCAMP-DX data
 
-
 ## Installation
 
 ### Node JS
@@ -29,7 +27,7 @@ Returns an object with information about the converted file and uncompressed spe
 
 **Arguments**
 
-- `jcamp` - String or ArrayBuffer containing the JCAMP data
+- `jcamp` - String or ArrayBuffer containing the JCAMP-DX data
 - `options` - Object with options to pass to the converter
 
 **Options**

package/jcampconverter.cjs

@@ -0,0 +1,8 @@
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s=[],l=Object.keys(a.ntuples);for(let p=0;p<l.length;p++){let i=l[p],f=a.ntuples[i];for(let m=0;m<f.length;m++)s[m]||(s[m]={}),s[m][i]=f[m]}a.ntuples=s}a.twoD&&r.wantXY&&(j(a,r),L(t,"Finished countour plot calculation",r),r.keepSpectra||delete a.spectra),r.chromatogram&&(a.spectra.length>1?ae(a):H(a),L(t,"Finished chromatogram calculation",r)),delete a.tmp}}function ye(e,t){for(let r of e)for(let a in r.meta){let s=r.meta[a];if(typeof s=="string"){if(s[0]==="{"){if(s[s.length-1]==="}"){let l=s.slice(1,-1).split(/[,; ]+/).filter(p=>p);for(let p=0;p<l.length;p++)r.meta[a+String(p)]=t.dynamicTyping?(0,G.parseString)(l[p]):l[p]}}else if(s[0]==="("){let l=s.split(/\r?\n/),p=/^\((?<from>\d+)\.\.(?<to>\d+)\)$/;if(p.test(l[0])){let[i,f]=l[0].match(p).slice(1).map(Number),m=l.slice(1).join(" ").split(/[,; ]+/).filter(c=>c);for(let c=i;c<=f;c++)r.meta[a+String(c)]=t.dynamicTyping?(0,G.parseString)(m[c-i]):m[c-i]}}}}}function _(e,t,r){let 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package/{lib/convert.d.ts → jcampconverter.d.ts}

@@ -1,182 +1,222 @@
-/**
- * Conversion options
- * @typedef {object} ConvertOptions
- * @property {RegExp} [keepRecordsRegExp=/^$/] - By default we don't keep meta information.
- * @property {boolean} [canonicDataLabels=true] - Canonize the Labels (uppercase without symbol).
- * @property {boolean} [canonicMetadataLabels=false] - Canonize the metadata Labels (uppercase without symbol).
- * @property {boolean} [dynamicTyping=false] - Convert numbers to Number.
- * @property {boolean} [withoutXY=false] - Remove the XY data.
- * @property {boolean} [chromatogram=false] - Special post-processing for GC / HPLC / MS.
- * @property {boolean} [keepSpectra=false] - Force to keep the spectra in case of 2D.
- * @property {boolean} [noContour=false] - Don't calculate countour in case of 2D.
- * @property {number} [nbContourLevels=7] - Number of positive / negative contour levels to calculate.
- * @property {number} [noiseMultiplier=5] - Define for 2D the level as 5 times the median as default.
- * @property {import('cheminfo-types').Logger} [logger] - A logger like 'pino'
- * @property {boolean} [profiling=false] - Add profiling information.
- */
-/**
- *
- * @typedef {object} Ntuples
- * @property {string[]} [varname]
- * @property {string[]} [symbol]
- * @property {string[]} [vartype]
- * @property {string[]} [varform]
- * @property {number[]} [vardim]
- * @property {string[]} [units]
- * @property {number[]} [factor]
- * @property {number[]} [first]
- * @property {number[]} [last]
- * @property {number[]} [min]
- * @property {number[]} [max]
- * @property {string[]} [nucleus]
- */
-/**
- * @typedef { Record<string, any> } Spectrum
- * @property {Record<string, number[]>} [data]
- * @property {number} [firstX] - first X value
- * @property {number} [lastX] - last X value
- * @property {number} [deltaX] - distance between 2 consecutive x axis values
- * @property {number} [yFactor] - y axis scaling factor
- * @property {number} [xFactor] - x axis scaling factor
- * @property {number} [nbPoints] - Number of points
- */
-/**
- *
- * @typedef {object} MinMax
- * @property {number[][]} [z]
- * @property {number} minX
- * @property {number} maxX
- * @property {number} minY
- * @property {number} maxY
- * @property {number} minZ
- * @property {number} maxZ
- * @property {number} median
- */
-/**
- *
- * @typedef {object} Entry
- * @property {Spectrum[]} spectra
- * @property {Ntuples} ntuples
- * @property {object} meta
- * @property {object} info
- * @property {object} tmp
- * @property {string} [title]
- * @property {string} [dataType]
- * @property {string} [dataClass]
- * @property {boolean} [twoD]
- * @property {MinMax} [minMax]
- */
-/**
- *
- * @typedef { object } ConvertResult
- * @property { object[] | boolean } profiling
- * @property { string[] } logs
- * @property { object[] } entries
- * @property { Entry[] } flatten
- */
-/**
- * Parse a jcamp.
- * The data can be provide as a string or array buffer. In this later case
- * we will convert it first to a string before parsing.
- * @param {string|ArrayBuffer|Uint8Array} jcamp
- * @param {ConvertOptions} [options]
- * @returns {ConvertResult}
- */
-export function convert(jcamp: string | ArrayBuffer | Uint8Array, options?: ConvertOptions | undefined): ConvertResult;
-/**
- * Conversion options
- */
-export type ConvertOptions = {
-    /**
-     * - By default we don't keep meta information.
-     */
-    keepRecordsRegExp?: RegExp | undefined;
-    /**
-     * - Canonize the Labels (uppercase without symbol).
-     */
-    canonicDataLabels?: boolean | undefined;
-    /**
-     * - Canonize the metadata Labels (uppercase without symbol).
-     */
-    canonicMetadataLabels?: boolean | undefined;
-    /**
-     * - Convert numbers to Number.
-     */
-    dynamicTyping?: boolean | undefined;
-    /**
-     * - Remove the XY data.
-     */
-    withoutXY?: boolean | undefined;
-    /**
-     * - Special post-processing for GC / HPLC / MS.
-     */
-    chromatogram?: boolean | undefined;
-    /**
-     * - Force to keep the spectra in case of 2D.
-     */
-    keepSpectra?: boolean | undefined;
-    /**
-     * - Don't calculate countour in case of 2D.
-     */
-    noContour?: boolean | undefined;
-    /**
-     * - Number of positive / negative contour levels to calculate.
-     */
-    nbContourLevels?: number | undefined;
-    /**
-     * - Define for 2D the level as 5 times the median as default.
-     */
-    noiseMultiplier?: number | undefined;
-    /**
-     * - A logger like 'pino'
-     */
-    logger?: import("cheminfo-types").Logger | undefined;
-    /**
-     * - Add profiling information.
-     */
-    profiling?: boolean | undefined;
-};
-export type Ntuples = {
-    varname?: string[] | undefined;
-    symbol?: string[] | undefined;
-    vartype?: string[] | undefined;
-    varform?: string[] | undefined;
-    vardim?: number[] | undefined;
-    units?: string[] | undefined;
-    factor?: number[] | undefined;
-    first?: number[] | undefined;
-    last?: number[] | undefined;
-    min?: number[] | undefined;
-    max?: number[] | undefined;
-    nucleus?: string[] | undefined;
-};
-export type Spectrum = Record<string, any>;
-export type MinMax = {
-    z?: number[][] | undefined;
-    minX: number;
-    maxX: number;
-    minY: number;
-    maxY: number;
-    minZ: number;
-    maxZ: number;
-    median: number;
-};
-export type Entry = {
-    spectra: Spectrum[];
-    ntuples: Ntuples;
-    meta: object;
-    info: object;
-    tmp: object;
-    title?: string | undefined;
-    dataType?: string | undefined;
-    dataClass?: string | undefined;
-    twoD?: boolean | undefined;
-    minMax?: MinMax | undefined;
-};
-export type ConvertResult = {
-    profiling: object[] | boolean;
-    logs: string[];
-    entries: object[];
-    flatten: Entry[];
-};
-//# sourceMappingURL=convert.d.ts.map
+import { Logger } from 'cheminfo-types';
+
+/**
+ * Conversion options
+ * @typedef {object} ConvertOptions@typedef {object} ConvertOptions
+ * @property {RegExp} [keepRecordsRegExp=/^$/] - By default we don't keep meta information.
+ * @property {boolean} [canonicDataLabels=true] - Canonize the Labels (uppercase without symbol).
+ * @property {boolean} [canonicMetadataLabels=false] - Canonize the metadata Labels (uppercase without symbol).
+ * @property {boolean} [dynamicTyping=false] - Convert numbers to Number.
+ * @property {boolean} [withoutXY=false] - Remove the XY data.
+ * @property {boolean} [chromatogram=false] - Special post-processing for GC / HPLC / MS.
+ * @property {boolean} [keepSpectra=false] - Force to keep the spectra in case of 2D.
+ * @property {boolean} [noContour=false] - Don't calculate countour in case of 2D.
+ * @property {number} [nbContourLevels=7] - Number of positive / negative contour levels to calculate.
+ * @property {number} [noiseMultiplier=5] - Define for 2D the level as 5 times the median as default.
+ * @property {import('cheminfo-types').Logger} [logger] - A logger like 'pino'
+ * @property {boolean} [profiling=false] - Add profiling information.
+ */
+/**
+ *
+ * @typedef {object} Ntuples@typedef {object} Ntuples
+ * @property {string[]} [varname]
+ * @property {string[]} [symbol]
+ * @property {string[]} [vartype]
+ * @property {string[]} [varform]
+ * @property {number[]} [vardim]
+ * @property {string[]} [units]
+ * @property {number[]} [factor]
+ * @property {number[]} [first]
+ * @property {number[]} [last]
+ * @property {number[]} [min]
+ * @property {number[]} [max]
+ * @property {string[]} [nucleus]
+ */
+/**
+ * @typedef { Record<string, any> } Spectrum
+ * @property {Record<string, number[]>} [data]
+ * @property {number} [firstX] - first X value
+ * @property {number} [lastX] - last X value
+ * @property {number} [deltaX] - distance between 2 consecutive x axis values
+ * @property {number} [yFactor] - y axis scaling factor
+ * @property {number} [xFactor] - x axis scaling factor
+ * @property {number} [nbPoints] - Number of points
+ */
+/**
+ *
+ * @typedef {object} MinMax@typedef {object} MinMax
+ * @property {number[][]} [z]
+ * @property {number} minX
+ * @property {number} maxX
+ * @property {number} minY
+ * @property {number} maxY
+ * @property {number} minZ
+ * @property {number} maxZ
+ * @property {number} median
+ */
+/**
+ *
+ * @typedef {object} Entry@typedef {object} Entry
+ * @property {Spectrum[]} spectra
+ * @property {Ntuples} ntuples
+ * @property {object} meta
+ * @property {object} info
+ * @property {object} tmp
+ * @property {string} [title]
+ * @property {string} [dataType]
+ * @property {string} [dataClass]
+ * @property {boolean} [twoD]
+ * @property {MinMax} [minMax]
+ */
+/**
+ *
+ * @typedef { object } ConvertResult@typedef { object } ConvertResult
+ * @property { object[] | boolean } profiling
+ * @property { string[] } logs
+ * @property { object[] } entries
+ * @property { Entry[] } flatten
+ */
+/**
+ * Parse a jcamp.
+ * The data can be provide as a string or array buffer. In this later case
+ * we will convert it first to a string before parsing.
+ * @param {string|ArrayBuffer|Uint8Array} jcamp
+ * @param {ConvertOptions} [options]
+ * @returns {ConvertResult}
+ */
+export declare function convert(jcamp: string | ArrayBuffer | Uint8Array, options?: ConvertOptions | undefined): ConvertResult;
+
+/**
+ * Conversion options
+ */
+declare type ConvertOptions = {
+    /**
+     * - By default we don't keep meta information.
+     */
+    keepRecordsRegExp?: RegExp | undefined;
+    /**
+     * - Canonize the Labels (uppercase without symbol).
+     */
+    canonicDataLabels?: boolean | undefined;
+    /**
+     * - Canonize the metadata Labels (uppercase without symbol).
+     */
+    canonicMetadataLabels?: boolean | undefined;
+    /**
+     * - Convert numbers to Number.
+     */
+    dynamicTyping?: boolean | undefined;
+    /**
+     * - Remove the XY data.
+     */
+    withoutXY?: boolean | undefined;
+    /**
+     * - Special post-processing for GC / HPLC / MS.
+     */
+    chromatogram?: boolean | undefined;
+    /**
+     * - Force to keep the spectra in case of 2D.
+     */
+    keepSpectra?: boolean | undefined;
+    /**
+     * - Don't calculate countour in case of 2D.
+     */
+    noContour?: boolean | undefined;
+    /**
+     * - Number of positive / negative contour levels to calculate.
+     */
+    nbContourLevels?: number | undefined;
+    /**
+     * - Define for 2D the level as 5 times the median as default.
+     */
+    noiseMultiplier?: number | undefined;
+    /**
+     * - A logger like 'pino'
+     */
+    logger?: Logger | undefined;
+    /**
+     * - Add profiling information.
+     */
+    profiling?: boolean | undefined;
+};
+
+declare type ConvertResult = {
+    profiling: object[] | boolean;
+    logs: string[];
+    entries: object[];
+    flatten: Entry[];
+};
+
+/**
+ *
+ * @typedef {object} CreateTreeOptions@typedef {object} CreateTreeOptions
+ * @property {boolean} [flatten=false]
+ */
+/**
+ *
+ * @typedef {object} Tree@typedef {object} Tree
+ * @property {string} title
+ * @property {string} jcamp
+ * @property {Tree[]} [children]
+ */
+/**
+ * Parse the jcamp to extract the structure as a tree.
+ *
+ * @param {string|ArrayBuffer|Uint8Array} jcamp
+ * @param {CreateTreeOptions} [options={}]
+ * @returns {Tree[]}
+ */
+export declare function createTree(jcamp: string | ArrayBuffer | Uint8Array, options?: CreateTreeOptions | undefined): Tree[];
+
+declare type CreateTreeOptions = {
+    flatten?: boolean | undefined;
+};
+
+declare type Entry = {
+    spectra: Spectrum[];
+    ntuples: Ntuples;
+    meta: object;
+    info: object;
+    tmp: object;
+    title?: string | undefined;
+    dataType?: string | undefined;
+    dataClass?: string | undefined;
+    twoD?: boolean | undefined;
+    minMax?: MinMax | undefined;
+};
+
+declare type MinMax = {
+    z?: number[][] | undefined;
+    minX: number;
+    maxX: number;
+    minY: number;
+    maxY: number;
+    minZ: number;
+    maxZ: number;
+    median: number;
+};
+
+declare type Ntuples = {
+    varname?: string[] | undefined;
+    symbol?: string[] | undefined;
+    vartype?: string[] | undefined;
+    varform?: string[] | undefined;
+    vardim?: number[] | undefined;
+    units?: string[] | undefined;
+    factor?: number[] | undefined;
+    first?: number[] | undefined;
+    last?: number[] | undefined;
+    min?: number[] | undefined;
+    max?: number[] | undefined;
+    nucleus?: string[] | undefined;
+};
+
+declare type Spectrum = Record<string, any>;
+
+declare type Tree = {
+    title: string;
+    jcamp: string;
+    children?: Tree[] | undefined;
+};
+
+export { }

package/jcampconverter.mjs

@@ -0,0 +1,8 @@
+import{ensureString as fe}from"ensure-string";function ne(e,i={}){e=fe(e);let{flatten:p=!1}=i;if(typeof e!="string")throw new TypeError("the JCAMP should be a string");let a=e.split(/[\r\n]+/),s=[],t=[],o=[],l,r=0,m=e.includes("## ");for(let c=0;c<a.length;c++){let b=a[c],f=m?b.replace(/ /g,""):b;if(f.substring(0,9)==="##NTUPLES"&&r++,f.substring(0,7)==="##TITLE"){let n=[f.substring(8).trim()];for(let u=c+1;u<a.length&&!a[u].startsWith("##");u++)n.push(a[u].trim());t.push({title:n.join(`
+`),jcamp:`${b}
+`,children:[]}),l=t[t.length-1],s.push(l)}else if(f.substring(0,5)==="##END"&&r===0){l.jcamp+=`${b}
+`;let n=t.pop();t.length!==0?(l=t[t.length-1],l.children.push(n)):(l=void 0,o.push(n))}else if(l&&l.jcamp){l.jcamp+=`${b}
+`;let n=f.match(/^##(.*?)=(.+)/);if(n){let u=n[1].replace(/[ _-]/g,"").toUpperCase();u==="DATATYPE"&&(l.dataType=n[2].trim()),u==="DATACLASS"&&(l.dataClass=n[2].trim())}}f.substring(0,5)==="##END"&&r>0&&r--}return p?(s.forEach(c=>{c.children=void 0}),s):o}import{parseString as me}from"dynamic-typing";import{ensureString as ce}from"ensure-string";var R=["TIC",".RIC","SCANNUMBER"];function J(e){let i=e.spectra,p=i.length,a={times:new Array(p),series:{ms:{dimension:2,data:new Array(p)}}},s=[];for(let t=0;t<R.length;t++){let o=$(R[t]);i[0][o]&&(s.push(o),a.series[o]={dimension:1,data:new Array(p)})}for(let t=0;t<p;t++){let o=i[t];a.times[t]=o.pageValue;for(let l=0;l<s.length;l++)a.series[s[l]].data[t]=Number(o[s[l]]);o.data&&(a.series.ms.data[t]=[o.data.x,o.data.y])}e.chromatogram=a}function Q(e){return R.indexOf(e)!==-1}function $(e){return e.toLowerCase().replace(/[^a-z0-9]/g,"")}function Y(e){let i=[];for(let p=0;p<e.length;p++)i.push(Number(e[p]));return i}function U(e,i){let p=e.yFactor,a=e.deltaX;e.isXYdata=!0;let s={x:[],y:[]};e.data=s;let t=e.firstX,o=e.firstY,l=!1,r,m=0;for(;m<i.length;m++)if(r=i.charCodeAt(m),r===13||r===10)l=!0;else if(l)break;let c=!0,b=!1,f=!1,n=0,u=!1,d=!1,h=0,T=0,A=!1,N=!1,y=!1,S=0;for(;m<=i.length;m++)if(m===i.length?r=13:r=i.charCodeAt(m),d)(r===13||r===10)&&(c=!0,d=!1);else if(r<=57&&r>=48)N=!0,S>0?h+=(r-48)/Math.pow(10,S++):(h*=10,h+=r-48);else if(r===44||r===46)N=!0,S++;else{if(N){if(c)c=!1,f&&(y=!0);else if(y)y=!1;else{b?(n=A?0-h:h,f=!0,b=!1):u||(T=A?0-h:h);let O=u?h-1:1;for(let F=0;F<O;F++)f?o+=n:o=T,s.x.push(t),s.y.push(o*p),t+=a}A=!1,h=0,S=0,N=!1,u=!1}if(r<74&&r>63)N=!0,f=!1,h=r-64;else if(r>96&&r<106)N=!0,f=!1,h=r-96,A=!0;else if(r===115)N=!0,u=!0,h=9;else if(r>82&&r<91)N=!0,u=!0,h=r-82;else if(r>73&&r<83)N=!0,b=!0,h=r-73;else if(r>105&&r<115)N=!0,b=!0,h=r-105,A=!0;else if(r===36&&i.charCodeAt(m+1)===36)N=!0,d=!0;else if(r===37)N=!0,b=!0,h=0,A=!1;else if(r===45){let O=i.charCodeAt(m+1);(O>=48&&O<=57||O===44||O===46)&&(N=!0,c||(f=!1),A=!0)}else(r===13||r===10)&&(c=!0,d=!1)}}var ee=/\$\$.*/,te=/[,\t ]+/;function P(e,i,p){if(e.isPeaktable=!0,!e.variables||Object.keys(e.variables)===2?oe(e,i,p):pe(e,i,p),e.variables)for(let a in e.variables)e.variables[a].data=e.data[a]}function oe(e,i,p){let a={x:[],y:[]};e.data=a;let s=i.split(/,? *,?[;\r\n]+ */);for(let t=1;t<s.length;t++){let o=s[t].trim().replace(ee,"").split(te);if(o.length%2===0)for(let l=0;l<o.length;l=l+2)a.x.push(Number(o[l])*e.xFactor),a.y.push(Number(o[l+1])*e.yFactor);else p.logs.push(`Format error: ${o}`)}}function pe(e,i,p){let a={},s=Object.keys(e.variables),t=s.length;s.forEach(l=>a[l]=[]),e.data=a;let o=i.split(/,? *,?[;\r\n]+ */);for(let l=1;l<o.length;l++){let r=o[l].trim().replace(ee,"").split(te);if(r.length%t===0)for(let m=0;m<r.length;m++)a[s[m%t]].push(Number(r[m]));else p.logs.push(`Format error: ${r}`)}}function V(e,i){e.isXYAdata=!0;let p={};e.data=p;let a=i.split(/\r?\n/),s=a[0].replace(/^.*?([A-Z]+).*$/,"$1").split("").map(t=>t.toLowerCase());for(let t=1;t<a.length;t++){let o=a[t].replace(/^\((.*)\)$/,"$1").split(/ *, */);for(let l=0;l<s.length;l++){let r=o[l];switch(s[l]){case"x":case"y":case"w":r=Number.parseFloat(r);break;case"a":r=r.replace(/^<(.*)>$/,"$1");break;case"m":break;default:continue}p[s[l]]||(p[s[l]]=[]),p[s[l]].push(r)}}}import{parseString as se}from"dynamic-typing";import le from"ml-array-median";function I(e){let i=e[0].data.y[0],p=i,a=e.length,s=e[0].data.x.length,t=new Array(a);for(let f=0;f<a;f++){t[f]=e[f].data.y;for(let n=0;n<s;n++){let u=t[f][n];u<i&&(i=u),u>p&&(p=u)}}let o=e[0].data.x[0],l=e[0].data.x[e[0].data.x.length-1],r=e[0].pageValue,m=e[a-1].pageValue;if(o>l)for(let f of t)f.reverse();r>m&&t.reverse();let c=[];for(let f=0;f<t.length;f++){let n=Float64Array.from(t[f]);for(let u=0;u<n.length;u++)n[u]<0&&(n[u]=-n[u]);c.push(le(n))}let b=le(c);return{z:t,minX:Math.min(o,l),maxX:Math.max(o,l),minY:Math.min(r,m),maxY:Math.max(r,m),minZ:i,maxZ:p,noise:b}}function E(e,i){let p=e.noise,a=e.z,s,t,o,l,r,m,c,b,f=a.length,n=a[0].length,u,d,h,T,A=e.minX,y=(e.maxX-A)/(n-1),S=e.minY,F=(e.maxY-S)/(f-1),ae=e.minZ,H=e.maxZ,G=i.nbContourLevels*2,K=new Array(G),x;for(let M=0;M<G;M++){let D={};K[M]=D;let re=M%2,_=(H-i.noiseMultiplier*p)*Math.exp((M>>1)-i.nbContourLevels);re===0?x=_+i.noiseMultiplier*p:x=0-_-i.noiseMultiplier*p;let g=[];if(D.zValue=x,D.lines=g,!(x<=ae||x>=H))for(let v=0;v<f-1;v++){let W=a[v],z=a[v+1];for(let X=0;X<n-1;X++)s=W[X],t=W[X+1],o=z[X],l=z[X+1],r=s>x,m=t>x,c=o>x,b=l>x,r!==m&&r!==c&&(u=X+(x-s)/(t-s),d=v,h=X,T=v+(x-s)/(o-s),g.push(u*y+A),g.push(d*F+S),g.push(h*y+A),g.push(T*F+S)),b!==m&&b!==c&&(u=X+1,d=v+1-(x-l)/(t-l),h=X+1-(x-l)/(o-l),T=v+1,g.push(u*y+A),g.push(d*F+S),g.push(h*y+A),g.push(T*F+S)),m!==c&&(u=(X+1-(x-t)/(o-t))*y+A,d=(v+(x-t)/(o-t))*F+S,m!==r&&(h=X+1-(x-t)/(s-t),T=v,g.push(u),g.push(d),g.push(h*y+A),g.push(T*F+S)),c!==r&&(h=X,T=v+1-(x-o)/(s-o),g.push(u),g.push(d),g.push(h*y+A),g.push(T*F+S)),m!==b&&(h=X+1,T=v+(x-t)/(l-t),g.push(u),g.push(d),g.push(h*y+A),g.push(T*F+S)),c!==b&&(h=X+(x-o)/(l-o),T=v+1,g.push(u),g.push(d),g.push(h*y+A),g.push(T*F+S)))}}return{minX:e.minX,maxX:e.maxX,minY:e.minY,maxY:e.maxY,segments:K}}function k(e,i){let p=I(e.spectra);i.noContour||(e.contourLines=E(p,i),delete p.z),e.minMax=p}import{gyromagneticRatio as ie}from"gyromagnetic-ratio";function Z(e){for(let i of e){let p=0,a=0;for(let s of i.spectra){if(i.ntuples&&i.ntuples.symbol?(!p&&s.observeFrequency&&(p=s.observeFrequency),!a&&s.shiftOffsetVal&&(a=s.shiftOffsetVal)):(p=s.observeFrequency,a=s.shiftOffsetVal),p&&s.xUnits&&s.xUnits.toUpperCase().includes("HZ")){s.xUnits="PPM",s.xFactor=s.xFactor/p,s.firstX=s.firstX/p,s.lastX=s.lastX/p,s.deltaX=s.deltaX/p;for(let t=0;t<s.data.x.length;t++)s.data.x[t]/=p}if(a&&s.xUnits.toLowerCase().includes("ppm")){let t=s.firstX-a;s.firstX=s.firstX-t,s.lastX=s.lastX-t;for(let o=0;o<s.data.x.length;o++)s.data.x[o]-=t}if(i.ntuples&&i.ntuples.nucleus&&i.ntuples.symbol)for(let t=0;t<i.ntuples.nucleus.length;t++){let o=i.ntuples.symbol[t],l=i.ntuples.nucleus[t];if(o.match(/^[F|T]/)&&!l){if(o.match(/[F|T]1/))if(i.tmp.$NUC2)i.ntuples.nucleus[t]=i.tmp.$NUC2;else{let r=i.ntuples.symbol.indexOf(o.replace(/^([F|T]).*/,"$12"));r&&i.ntuples.nucleus[r]&&(i.ntuples.nucleus[t]=i.ntuples.nucleus[r])}o.match(/[F|T]2/)&&(i.ntuples.nucleus[t]=i.tmp.$NUC1)}o.match(/[F|T]2/)&&(i.yType=i.ntuples.nucleus[0])}if(p&&i.ntuples&&i.ntuples.symbol&&i.ntuples.nucleus){let t="",o=i.ntuples.symbol.indexOf(s.pageSymbol);if(i.ntuples.units&&i.ntuples.units[o]&&(t=i.ntuples.units[o]),t!=="PPM"){if(o!==0)throw Error("Not sure about this ntuples format");let l=ie[i.ntuples.nucleus[0]],r=ie[i.ntuples.nucleus[1]];if(!l||!r)throw Error("Problem with determination of gyromagnetic ratio");let m=l/r*p;s.pageValue/=m}}}}}function L(e,i,p={}){p.logger?.trace(i),e.profiling&&e.profiling.push({action:i,time:Date.now()-p.start})}function j(e){let i=e.spectra[0].data;e.chromatogram={times:i.x.slice(),series:{intensity:{dimension:1,data:i.y.slice()}}}}function B(e,i,p){Z(e),ue(e,p);for(let a of e){if(Object.keys(a.ntuples).length>0){let s=[],t=Object.keys(a.ntuples);for(let o=0;o<t.length;o++){let l=t[o],r=a.ntuples[l];for(let m=0;m<r.length;m++)s[m]||(s[m]={}),s[m][l]=r[m]}a.ntuples=s}a.twoD&&p.wantXY&&(k(a,p),L(i,"Finished countour plot calculation",p),p.keepSpectra||delete a.spectra),p.chromatogram&&(a.spectra.length>1?J(a):j(a),L(i,"Finished chromatogram calculation",p)),delete a.tmp}}function ue(e,i){for(let p of e)for(let a in p.meta){let s=p.meta[a];if(typeof s=="string"){if(s[0]==="{"){if(s[s.length-1]==="}"){let t=s.slice(1,-1).split(/[,; ]+/).filter(o=>o);for(let o=0;o<t.length;o++)p.meta[a+String(o)]=i.dynamicTyping?se(t[o]):t[o]}}else if(s[0]==="("){let t=s.split(/\r?\n/),o=/^\((?<from>\d+)\.\.(?<to>\d+)\)$/;if(o.test(t[0])){let[l,r]=t[0].match(o).slice(1).map(Number),m=t.slice(1).join(" ").split(/[,; ]+/).filter(c=>c);for(let c=l;c<=r;c++)p.meta[a+String(c)]=i.dynamicTyping?se(m[c-l]):m[c-l]}}}}}function q(e,i,p){let a=-1,s=-1,t="",o="";if(p.indexOf("++")>0)t=p.replace(/.*\(([a-zA-Z0-9]+)\+\+.*/,"$1"),o=p.replace(/.*\.\.([a-zA-Z0-9]+).*/,"$1");else{p=p.replace(/[^a-zA-Z]/g,""),t=p.charAt(0),o=p.charAt(1),i.variables={};for(let l of p){let r=l.toLowerCase(),m=e.ntuples.symbol.indexOf(l);if(m===-1)throw Error(`Symbol undefined: ${l}`);i.variables[r]={};for(let c in e.ntuples)e.ntuples[c][m]&&(i.variables[r][c.replace(/^var/,"")]=e.ntuples[c][m])}}a=e.ntuples.symbol.indexOf(t),s=e.ntuples.symbol.indexOf(o),a===-1&&(a=0),s===-1&&(s=0),e.ntuples.first&&(e.ntuples.first.length>a&&(i.firstX=e.ntuples.first[a]),e.ntuples.first.length>s&&(i.firstY=e.ntuples.first[s])),e.ntuples.last&&(e.ntuples.last.length>a&&(i.lastX=e.ntuples.last[a]),e.ntuples.last.length>s&&(i.lastY=e.ntuples.last[s])),e.ntuples.vardim&&e.ntuples.vardim.length>a&&(i.nbPoints=e.ntuples.vardim[a]),e.ntuples.factor&&(e.ntuples.factor.length>a&&(i.xFactor=e.ntuples.factor[a]),e.ntuples.factor.length>s&&(i.yFactor=e.ntuples.factor[s])),e.ntuples.units&&(e.ntuples.units.length>a&&(e.ntuples.varname&&e.ntuples.varname[a]?i.xUnits=`${e.ntuples.varname[a]} [${e.ntuples.units[a]}]`:i.xUnits=e.ntuples.units[a]),e.ntuples.units.length>s&&(e.ntuples.varname&&e.ntuples.varname[s]?i.yUnits=`${e.ntuples.varname[s]} [${e.ntuples.units[s]}]`:i.yUnits=e.ntuples.units[s]))}function w(e){e.xFactor||(e.xFactor=1),e.yFactor||(e.yFactor=1)}var C=/[ \t]*,[ \t]*/,he={keepRecordsRegExp:/^$/,canonicDataLabels:!0,canonicMetadataLabels:!1,dynamicTyping:!0,withoutXY:!1,chromatogram:!1,keepSpectra:!1,noContour:!1,nbContourLevels:7,noiseMultiplier:5,profiling:!1};function de(e,i={}){e=ce(e),i={...he,...i},i.logger?.debug("Starting jcamp conversion"),i.wantXY=!i.withoutXY,i.start=Date.now();let p=[],a={profiling:i.profiling?[]:!1,logs:[],entries:[]},s={children:[]},t=s,o=[],l={};if(typeof e!="string")throw new TypeError("the JCAMP should be a string");L(a,"Before split to LDRS",i);let r=e.replace(/[\r\n]+##/g,`
+##`).split(`
+##`);L(a,"Split to LDRS",i),r[0]&&(r[0]=r[0].replace(/^[\r\n ]*##/,""));for(let m of r){let c=m.indexOf("="),b=c>0?m.substring(0,c):m,f=c>0?m.substring(c+1).trim():"",n=b.replace(/[_ -]/g,"").toUpperCase();if(n==="DATATABLE"){let u=f.indexOf(`
+`);if(u===-1&&(u=f.indexOf("\r")),u>0){let d=f.substring(0,u).split(/[ ,;\t]+/);q(t,l,d[0]),l.datatable=d[0],d[1]&&d[1].indexOf("PEAKS")>-1?n="PEAKTABLE":d[1]&&(d[1].indexOf("XYDATA")||d[0].indexOf("++")>0)&&(n="XYDATA",l.nbPoints&&(l.deltaX=(l.lastX-l.firstX)/(l.nbPoints-1)))}}if(n==="XYDATA"){i.wantXY&&(w(l),f.match(/.*\+\+.*/)?(l.nbPoints&&(l.deltaX=(l.lastX-l.firstX)/(l.nbPoints-1)),U(l,f,a)):P(l,f,a),t.spectra.push(l),l={});continue}else if(n==="PEAKTABLE"){i.wantXY&&(w(l),P(l,f,a),t.spectra.push(l),l={});continue}if(n==="PEAKASSIGNMENTS"){i.wantXY&&(f.match(/.*([^A-Z]*).*/)&&V(l,f),t.spectra.push(l),l={});continue}if(n==="TITLE"){let u=t;u.children||(u.children=[]),t={spectra:[],ntuples:{},info:{},meta:{},tmp:{}},u.children.push(t),o.push(u),p.push(t),t.title=f}else n==="DATATYPE"?(t.dataType=f,f.match(/(^nd|\snd\s)/i)&&(t.twoD=!0)):n==="NTUPLES"?f.match(/(^nd|\snd\s)/i)&&(t.twoD=!0):n==="DATACLASS"?t.dataClass=f:n==="XUNITS"?l.xUnits=f:n==="YUNITS"?l.yUnits=f:n==="FIRSTX"?l.firstX=Number(f):n==="LASTX"?l.lastX=Number(f):n==="FIRSTY"?l.firstY=Number(f):n==="LASTY"?l.lastY=Number(f):n==="NPOINTS"?l.nbPoints=Number(f):n==="XFACTOR"?l.xFactor=Number(f):n==="YFACTOR"?l.yFactor=Number(f):n==="MAXX"?l.maxX=Number(f):n==="MINX"?l.minX=Number(f):n==="MAXY"?l.maxY=Number(f):n==="MINY"?l.minY=Number(f):n==="DELTAX"?l.deltaX=Number(f):n===".OBSERVEFREQUENCY"||n==="$SFO1"?l.observeFrequency||(l.observeFrequency=Number(f)):n===".OBSERVENUCLEUS"?l.xType||(t.xType=f.replace(/[^a-zA-Z0-9]/g,"")):n==="$OFFSET"?(t.shiftOffsetNum=0,l.shiftOffsetVal||(l.shiftOffsetVal=Number(f))):n==="$REFERENCEPOINT"||(n==="VARNAME"?t.ntuples.varname=f.split(C):n==="SYMBOL"?t.ntuples.symbol=f.split(C):n==="VARTYPE"?t.ntuples.vartype=f.split(C):n==="VARFORM"?t.ntuples.varform=f.split(C):n==="VARDIM"?t.ntuples.vardim=Y(f.split(C)):n==="UNITS"?t.ntuples.units=f.split(C):n==="FACTOR"?t.ntuples.factor=Y(f.split(C)):n==="FIRST"?t.ntuples.first=Y(f.split(C)):n==="LAST"?t.ntuples.last=Y(f.split(C)):n==="MIN"?t.ntuples.min=Y(f.split(C)):n==="MAX"?t.ntuples.max=Y(f.split(C)):n===".NUCLEUS"?t.ntuples&&(t.ntuples.nucleus=f.split(C)):n==="PAGE"?(l.page=f.trim(),l.pageValue=Number(f.replace(/^.*=/,"")),l.pageSymbol=l.page.replace(/[=].*/,"")):n==="RETENTIONTIME"?l.pageValue=Number(f):Q(n)?l[$(n)]=f:n==="SAMPLEDESCRIPTION"?l.sampleDescription=f:n.startsWith("$NUC")?!t.tmp[n]&&!f.includes("off")&&(t.tmp[n]=f.replace(/[<>]/g,"")):n==="END"&&(t=o.pop()));if(t&&t.info&&t.meta&&n.match(i.keepRecordsRegExp)){let u=f.trim(),d,h;b.startsWith("$")?(h=i.canonicMetadataLabels?n.substring(1):b.substring(1),d=t.meta):(h=i.canonicDataLabels?n:b,d=t.info),i.dynamicTyping&&(u=me(u)),d[h]?(Array.isArray(d[h])||(d[h]=[d[h]]),d[h].push(u)):d[h]=u}}return L(a,"Finished parsing",i),B(p,a,i),L(a,"Total time",i),a.entries=s.children,a.flatten=p,a}export{de as convert,ne as createTree};

package/package.json

@@ -1,38 +1,45 @@
 {
   "name": "jcampconverter",
-  "version": "9.1.1",
+  "version": "9.2.1",
   "description": "Parse and convert JCAMP data",
-  "main": "lib/index.js",
-  "module": "lib-esm/index.js",
-  "types": "lib/index.d.ts",
+  "types": "jcampconverter.d.ts",
+  "main": "jcampconverter.cjs",
+  "module": "jcampconverter.mjs",
+  "exports": {
+    ".": {
+      "types": "./jcampconverter.d.ts",
+      "require": "./jcampconverter.cjs",
+      "default": "./jcampconverter.mjs"
+    }
+  },
   "files": [
-    "lib",
-    "src",
-    "lib-esm"
+    "jcampconverter.d.ts",
+    "jcampconverter.cjs",
+    "jcampconverter.mjs"
   ],
   "scripts": {
-    "build": "cheminfo-build --entry src/index.js --root JcampConverter",
+    "api-extractor": "api-extractor run --local",
+    "build": "cheminfo-build --entry src/index.js --root JcampConverter --no-source-map && rm dist/jcampconverter.js",
+    "bundle": "npm run bundle-cjs && npm run bundle-esm",
+    "bundle-common": "esbuild src/index.js --bundle --packages=external --minify",
+    "bundle-cjs": "npm run bundle-common -- --format=cjs --outfile=jcampconverter.cjs",
+    "bundle-esm": "npm run bundle-common -- --format=esm --outfile=jcampconverter.mjs",
+    "bundle-types": "npm run tsc && npm run api-extractor",
     "check-types": "tsc --noEmit",
-    "clean": "rimraf lib lib-esm",
+    "clean": "rimraf dist types",
     "eslint": "eslint src __tests__",
     "eslint-fix": "npm run eslint -- --fix",
     "jscpd": "jscpd -l 10 -i \"**/__tests__/**\" -t 1 src",
-    "prepack": "npm run tsc",
+    "prepack": "npm run bundle && npm run bundle-types",
     "prettier": "prettier --check src",
     "prettier-write": "prettier --write src",
     "test": "npm run test-only && npm run eslint && npm run prettier && npm run check-types",
     "test-only": "vitest run --globals --coverage",
-    "tsc": "npm run clean && npm run tsc-cjs && npm run tsc-esm",
-    "tsc-cjs": "tsc --project tsconfig.cjs.json",
-    "tsc-esm": "tsc --project tsconfig.esm.json",
+    "tsc": "tsc --project tsconfig.types.json",
     "benchmark": "node benchmark/benchmark.js",
     "deopt": "node --trace-opt --trace-deopt --code-comments debug/deoptimize.js > deopt.log",
     "hydra": "node --trace-hydrogen --trace-phase=Z --trace-deopt --code-comments --hydrogen-track-positions --redirect-code-traces --redirect-code-traces-to=code.asm debug/deoptimize.js"
   },
-  "repository": {
-    "type": "git",
-    "url": "https://github.com/cheminfo/jcampconverter.git"
-  },
   "keywords": [
     "jcamp",
     "converter"
@@ -40,33 +47,34 @@
   "author": "Luc Patiny",
   "license": "MIT",
   "bugs": {
-    "url": "https://github.com/cheminfo/jcampconverter/issues"
+    "url": "https://github.com/cheminfo/nmrium/issues/new?title=%5Bjcampconverter%5D"
   },
-  "homepage": "https://github.com/cheminfo/jcampconverter#readme",
   "devDependencies": {
-    "@types/jest": "^29.5.1",
+    "@microsoft/api-extractor": "^7.37.2",
+    "@types/jest": "^29.5.5",
     "@types/pino": "^7.0.5",
-    "@vitest/coverage-c8": "^0.30.1",
+    "@vitest/coverage-v8": "^0.34.5",
     "benchmark": "^2.1.4",
-    "c8": "^7.13.0",
+    "c8": "^8.0.1",
     "cheminfo-build": "^1.2.0",
-    "eslint": "^8.39.0",
-    "eslint-config-cheminfo-typescript": "^11.3.1",
+    "esbuild": "^0.19.3",
+    "eslint": "^8.49.0",
+    "eslint-config-cheminfo-typescript": "^12.0.4",
     "esm": "^3.2.25",
     "fifo-logger": "^0.6.1",
     "jest-matcher-deep-close-to": "^3.0.2",
-    "jscpd": "^3.5.4",
-    "prettier": "^2.8.8",
-    "rimraf": "^5.0.0",
-    "typescript": "^5.0.4",
-    "vitest": "^0.30.1"
+    "jscpd": "^3.5.10",
+    "ml-spectra-processing": "^12.5.1",
+    "prettier": "^3.0.3",
+    "rimraf": "^5.0.1",
+    "typescript": "^5.2.2",
+    "vitest": "^0.34.5"
   },
   "dependencies": {
-    "cheminfo-types": "^1.7.0",
+    "cheminfo-types": "^1.7.2",
     "dynamic-typing": "^1.0.0",
     "ensure-string": "^1.2.0",
     "gyromagnetic-ratio": "^1.0.0",
-    "ml-array-median": "^1.1.6",
-    "ml-spectra-processing": "^12.2.0"
+    "ml-array-median": "^1.1.6"
   }
 }

package/lib/2d/add2D.d.ts

@@ -1,2 +0,0 @@
-export default function add2D(result: any, options: any): void;
-//# sourceMappingURL=add2D.d.ts.map

package/lib/2d/add2D.d.ts.map

@@ -1 +0,0 @@
-{"version":3,"file":"add2D.d.ts","sourceRoot":"","sources":["../../src/2d/add2D.js"],"names":[],"mappings":"AAGA,+DAOC"}