jcampconverter 9.6.4 → 10.0.1

package/README.md

@@ -1,6 +1,5 @@
 [![NPM version][npm-image]][npm-url]
 [![build status][ci-image]][ci-url]
-[![Test coverage][codecov-image]][codecov-url]
 [![npm download][download-image]][download-url]
 [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.5091526.svg)](https://doi.org/10.5281/zenodo.5091526)
 
@@ -82,8 +81,6 @@ npm run benchmark
 
 [npm-image]: https://img.shields.io/npm/v/jcampconverter.svg
 [npm-url]: https://npmjs.org/package/jcampconverter
-[codecov-image]: https://img.shields.io/codecov/c/github/cheminfo/jcampconverter.svg
-[codecov-url]: https://codecov.io/gh/cheminfo/jcampconverter
 [ci-image]: https://github.com/cheminfo/jcampconverter/workflows/Node.js%20CI/badge.svg?branch=main
 [ci-url]: https://github.com/cheminfo/jcampconverter/actions?query=workflow%3A%22Node.js+CI%22
 [download-image]: https://img.shields.io/npm/dm/jcampconverter.svg

package/jcampconverter.cjs

@@ -1,8 +1,9 @@
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-##`);L(a,"Split to LDRS",i),o[0]&&(o[0]=o[0].replace(/^[\r\n ]*##/,""));for(let p of o){let c=p.indexOf("="),d=c>0?p.substring(0,c):p,u=c>0?d.match(i.noTrimRegExp)?p.substring(c+1):p.substring(c+1).trim():"",f=d.replace(/[_ -]/g,"").toUpperCase();if(f==="DATATABLE"){let m=u.indexOf(`
-`);if(m===-1&&(m=u.indexOf("\r")),m>0){let h=u.substring(0,m).split(/[ ,;\t]+/);_(t,l,h[0]),l.datatable=h[0],h[1]&&h[1].indexOf("PEAKS")>-1?f="PEAKTABLE":h[1]&&(h[1].indexOf("XYDATA")||h[0].indexOf("++")>0)&&(f="XYDATA",l.nbPoints&&(l.deltaX=(l.lastX-l.firstX)/(l.nbPoints-1)))}}if(f==="XYDATA"){i.wantXY&&(E(l),u.match(/.*\+\+.*/)?(l.nbPoints&&(l.deltaX=(l.lastX-l.firstX)/(l.nbPoints-1)),B(l,u,a)):w(l,u,a),t.spectra.push(l),l={});continue}else if(f==="PEAKTABLE"){i.wantXY&&(E(l),w(l,u,a),t.spectra.push(l),l={});continue}if(f==="PEAKASSIGNMENTS"){i.wantXY&&(u.match(/.*([^A-Z]*).*/)&&k(l,u),t.spectra.push(l),l={});continue}if(f==="TITLE"){let m=t;m.children||(m.children=[]),t={spectra:[],ntuples:{},info:{},meta:{},tmp:{}},m.children.push(t),r.push(m),s.push(t),t.title=u}else f==="DATATYPE"?(t.dataType=u,u.match(/(^nd|\snd\s)/i)&&(t.twoD=!0)):f==="NTUPLES"?u.match(/(^nd|\snd\s)/i)&&(t.twoD=!0):f==="DATACLASS"?t.dataClass=u:f==="JCAMPDX"?t.jcampDX=M(u):f==="JCAMPCS"?t.jcampCS=M(u):f==="XUNITS"?l.xUnits=u:f==="YUNITS"?l.yUnits=u:f==="FIRSTX"?l.firstX=Number(u):f==="LASTX"?l.lastX=Number(u):f==="FIRSTY"?l.firstY=Number(u):f==="LASTY"?l.lastY=Number(u):f==="NPOINTS"?l.nbPoints=Number(u):f==="XFACTOR"?l.xFactor=Number(u):f==="YFACTOR"?l.yFactor=Number(u):f==="MAXX"?l.maxX=Number(u):f==="MINX"?l.minX=Number(u):f==="MAXY"?l.maxY=Number(u):f==="MINY"?l.minY=Number(u):f==="DELTAX"?l.deltaX=Number(u):f===".OBSERVEFREQUENCY"||f==="$SFO1"?l.observeFrequency||(l.observeFrequency=Number(u)):f===".OBSERVENUCLEUS"?l.xType||(t.xType=u.replace(/[^a-zA-Z0-9]/g,"")):f==="$OFFSET"?(t.shiftOffsetNum=0,l.shiftOffsetVal||(l.shiftOffsetVal=Number(u))):f==="$REFERENCEPOINT"||(f==="VARNAME"?t.ntuples.varname=u.split(F):f==="SYMBOL"?t.ntuples.symbol=u.split(F):f==="VARTYPE"?t.ntuples.vartype=u.split(F):f==="VARFORM"?t.ntuples.varform=u.split(F):f==="VARDIM"?t.ntuples.vardim=Y(u.split(F)):f==="UNITS"?t.ntuples.units=u.split(F):f==="FACTOR"?t.ntuples.factor=Y(u.split(F)):f==="FIRST"?t.ntuples.first=Y(u.split(F)):f==="LAST"?t.ntuples.last=Y(u.split(F)):f==="MIN"?t.ntuples.min=Y(u.split(F)):f==="MAX"?t.ntuples.max=Y(u.split(F)):f===".NUCLEUS"?t.ntuples&&(t.ntuples.nucleus=u.split(F).map(m=>m.replace(/[^a-zA-Z0-9]/g,""))):f==="PAGE"?(l.page=u.trim(),l.pageValue=Number(u.replace(/^.*=/,"")),l.pageSymbol=l.page.replace(/[=].*/,"")):f==="RETENTIONTIME"?l.pageValue=Number(u):fe(f)?l[V(f)]=u:f==="SAMPLEDESCRIPTION"?l.sampleDescription=u:f.startsWith("$NUC")?!t.tmp[f]&&!u.includes("off")&&(t.tmp[f]=u.replace(/[<>]/g,"")):f==="END"&&(t=r.pop()));if(t&&t.info&&t.meta&&f.match(i.keepRecordsRegExp)){let m,h;d.startsWith("$")?(h=i.canonicMetadataLabels?f.substring(1):d.substring(1),m=t.meta):(h=i.canonicDataLabels?f:d,m=t.info),i.dynamicTyping&&(u=(0,me.parseString)(u)),m[h]?(Array.isArray(m[h])||(m[h]=[m[h]]),m[h].push(u)):m[h]=u}}if(L(a,"Finished parsing",i),W(s,a,i),L(a,"Total time",i),a.entries=n.children,a.flatten=s,i.logger){i.logger.debug("Finished jcamp conversion");for(let p of a.flatten)i.logger.debug(`${p.dataType} - ${p.title}`)}return a}function de(e,i={}){let{logger:s,OCL:a}=i;if(!e.info.ATOMLIST||!e.info.BONDLIST){s?.warn("No ATOMLIST or BONDLIST in the JCAMP-CS entry");return}we(e,s);let n=Re(e.info.ATOMLIST),t=Pe(e.info.BONDLIST),r=De(e.info.CHARGE,s),l=Oe(a,n,t,r,s);return{molecule:l,molfile:l.toMolfile()}}function Oe(e,i,s,a,n){let t={S:e.Molecule.cBondTypeSingle,D:e.Molecule.cBondTypeDouble,T:e.Molecule.cBondTypeTriple,Q:e.Molecule.cBondTypeQuadruple},r={},l=new e.Molecule(i.length,s.length);for(let o of i){let p=e.Molecule.getAtomicNoFromLabel(o.element);p||(n?.error(`Atomic number of ${o.element} could not be determined`),p=e.Molecule.getAtomicNoFromLabel("X")),r[o.atomNumber]=l.addAtom(p),l.setAtomMapNo(r[o.atomNumber],o.atomNumber)}for(let o of s){if(r[o.atomNumber1]===void 0){n?.error(`A bond goes to atomNumber ${o.atomNumber1} that does not exists`);continue}if(r[o.atomNumber2]===void 0){n?.error(`A bond goes to atomNumber ${o.atomNumber2} that does not exists`);continue}let p=l.addBond(r[o.atomNumber1],r[o.atomNumber2]);l.setBondType(p,t[o.bondType])}for(let o of a){if(r[o.atomNumber]===void 0){n?.error(`A charge goes to atomNumber ${o.atomNumber1} that does not exists`);continue}l.setAtomCharge(r[o.atomNumber],o.value)}return l}function Re(e){let i=e.split(/\r?\n/).map(a=>M(a)).filter(a=>a),s=[];for(let a of i){let[n,t,r]=a.trim().split(/\s+/);s.push({atomNumber:Number(n),element:t,nbImplicitHydrogens:r?.length>0?Number(r):void 0})}return s}function Pe(e){let i=e.split(/\r?\n/).map(a=>M(a)).filter(a=>a),s=[];for(let a of i){let[n,t,r]=a.trim().split(/\s+/);s.push({atomNumber1:Number(n),atomNumber2:Number(t),bondType:r})}return s}function De(e,i){if(!e)return[];let s=e.split(/\r?\n/).map(n=>M(n)).filter(n=>n),a=[];for(let n of s){let[t,r,l]=n.trim().split(/\s+/);l!==void 0&&i?.warn("Charge on multiple atom is not supported"),a.push({atomNumber:Number(r),value:Number(t)})}return a}function we(e,i){let s=["STEREOPAIR","STEREOCENTER","RADICAL","STEREOMOLECULE"];for(let a of s)e.info[a]&&i?.warn(`JCAMP-CS parser do not support: ${a}`)}
+##`);t.logger?.trace({profiling:!0},"Split to LDRS"),p[0]&&(p[0]=p[0].replace(/^[\r\n ]*##/,""));for(let u of p){let b=u.indexOf("="),h=b>0?u.slice(0,Math.max(0,b)):u,s=b>0?h.match(t.noTrimRegExp)?u.slice(Math.max(0,b+1)):u.slice(Math.max(0,b+1)).trim():"",l=h.replaceAll(/[_ -]/g,"").toUpperCase();if(l==="DATATABLE"){let c=s.indexOf(`
+`);if(c===-1&&(c=s.indexOf("\r")),c>0){let d=s.slice(0,Math.max(0,c)).split(/[ ,;\t]+/);ee(n,r,d[0]),r.datatable=d[0],d[1]?.includes("PEAKS")?l="PEAKTABLE":d[1]&&(d[1].indexOf("XYDATA")||d[0].indexOf("++")>0)&&(l="XYDATA",r.nbPoints&&r.lastX!==void 0&&r.firstX!==void 0&&(r.deltaX=(r.lastX-r.firstX)/(r.nbPoints-1)))}}if(l==="XYDATA"){t.wantXY&&(U(r),s.match(/.*\+\+.*/)?(r.nbPoints&&r.lastX!==void 0&&r.firstX!==void 0&&(r.deltaX=(r.lastX-r.firstX)/(r.nbPoints-1)),j(r,s,t)):w(r,s,t),n?.spectra.push(r),r={data:{}});continue}else if(l==="PEAKTABLE"){t.wantXY&&(U(r),w(r,s,t),n?.spectra.push(r),r={data:{}});continue}if(l==="PEAKASSIGNMENTS"){t.wantXY&&(s.match(/.*[^A-Z]*.*/)&&Z(r,s),n?.spectra.push(r),r={data:{}});continue}if(t.removeComments&&(s=s.split(/\r?\n/).map(c=>c.replace(/ *\$\$.*$/,"")).join(`
+`)),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

@@ -1,253 +1,218 @@
 import { Logger } from 'cheminfo-types';
+import type { Molecule } from 'openchemlib';
+import { openchemlib } from 'openchemlib';
+
+declare interface Add2DOptions extends GenerateContourLinesOptions {
+    /**
+     * Don't calculate contour in case of 2D.
+     */
+    noContour?: boolean;
+}
+
+declare interface Chromatogram {
+    times: number[];
+    series: Record<string, {
+        dimension: number;
+        data: any[];
+    }>;
+}
+
+declare interface ContourLines {
+    minX: number;
+    maxX: number;
+    minY: number;
+    maxY: number;
+    segments: Array<{
+        zValue?: number;
+        lines?: number[];
+    }>;
+}
 
 /**
- * Conversion options
- * @typedef {object} ConvertOptions@typedef {object} ConvertOptions
- * @property {RegExp} [keepRecordsRegExp=/^$/] - By default we don't keep meta information.
- * @property {boolean} [canonicDataLabels=true] - Canonize the Labels (uppercase without symbol).
- * @property {boolean} [canonicMetadataLabels=false] - Canonize the metadata Labels (uppercase without symbol).
- * @property {boolean} [dynamicTyping=false] - Convert numbers to Number.
- * @property {boolean} [withoutXY=false] - Remove the XY data.
- * @property {boolean} [chromatogram=false] - Special post-processing for GC / HPLC / MS.
- * @property {boolean} [keepSpectra=false] - Force to keep the spectra in case of 2D.
- * @property {RegExp} [noTrimRegExp=/^$/] - For which fields we should not trim ?
- * @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 {Record<String, string | string[] | number | number[] | boolean | boolean[] | undefined>} meta
- * @property {Record<String, string | string[] | number | number[] | boolean | boolean[] | undefined>} info
- * @property {Record<String, string | string[] | number | number[] | boolean | boolean[] | undefined>} tmp
- * @property {string} [title]
- * @property {string} [dataType]
- * @property {string} [dataClass]
- * @property {string?} [jcampDX]
- * @property {string?} [jcampCS]
- * @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
+ * Parse JCAMP-DX data.
+ * The data can be provided as a string or array buffer. In this latter case
  * we will convert it first to a string before parsing.
- * @param {string|ArrayBuffer|Uint8Array} jcamp
- * @param {ConvertOptions} [options]
- * @returns {ConvertResult}
+ * @param jcamp
+ * @param optionsParam
+ * @returns Converted result.
  */
-export declare function convert(jcamp: string | ArrayBuffer | Uint8Array, options?: ConvertOptions | undefined): ConvertResult;
+export declare function convert(jcamp: string | ArrayBuffer | Uint8Array, optionsParam?: ConvertOptions): ConvertResult;
 
 /**
- * Conversion options
+ * Conversion options.
  */
-declare type ConvertOptions = {
+declare interface ConvertOptions extends Partial<Add2DOptions> {
     /**
-     * - By default we don't keep meta information.
+     * If it is true, anywhere out of XYDATA, PEAKTABLE n PEAKASSIGNMENTS the comments are removed
+     * @default false
      */
-    keepRecordsRegExp?: RegExp | undefined;
+    removeComments?: boolean;
     /**
-     * - Canonize the Labels (uppercase without symbol).
+     * By default we don't keep meta information.
+     * @default `/^$/`
      */
-    canonicDataLabels?: boolean | undefined;
+    keepRecordsRegExp?: RegExp;
     /**
-     * - Canonize the metadata Labels (uppercase without symbol).
+     * Canonize the Labels (uppercase without symbol).
      */
-    canonicMetadataLabels?: boolean | undefined;
+    canonicDataLabels?: boolean;
     /**
-     * - Convert numbers to Number.
+     * Canonize the metadata Labels (uppercase without symbol).
      */
-    dynamicTyping?: boolean | undefined;
+    canonicMetadataLabels?: boolean;
     /**
-     * - Remove the XY data.
+     * Convert numbers to Number.
      */
-    withoutXY?: boolean | undefined;
+    dynamicTyping?: boolean;
     /**
-     * - Special post-processing for GC / HPLC / MS.
+     * Remove the XY data.
      */
-    chromatogram?: boolean | undefined;
+    withoutXY?: boolean;
     /**
-     * - Force to keep the spectra in case of 2D.
+     * Special post-processing for GC / HPLC / MS.
      */
-    keepSpectra?: boolean | undefined;
+    chromatogram?: boolean;
     /**
-     * - For which fields we should not trim ?
+     * Force to keep the spectra in case of 2D.
      */
-    noTrimRegExp?: RegExp | undefined;
+    keepSpectra?: boolean;
     /**
-     * - Don't calculate countour in case of 2D.
+     * For which fields we should not trim ?
+     * @default `/^$/`
      */
-    noContour?: boolean | undefined;
+    noTrimRegExp?: RegExp;
     /**
-     * - Number of positive / negative contour levels to calculate.
+     * A logger like `pino`.
      */
-    nbContourLevels?: number | undefined;
+    logger?: Logger;
     /**
-     * - Define for 2D the level as 5 times the median as default.
+     * Add profiling information.
      */
-    noiseMultiplier?: number | undefined;
-    /**
-     * - A logger like 'pino'
-     */
-    logger?: Logger | undefined;
-    /**
-     * - Add profiling information.
-     */
-    profiling?: boolean | undefined;
-};
+    wantXY?: boolean;
+    start?: number;
+    fastParse?: boolean;
+}
 
-declare type ConvertResult = {
-    profiling: object[] | boolean;
-    logs: string[];
-    entries: object[];
+declare interface ConvertResult {
+    entries: Entry[];
     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[]}
+ * Parse the JCAMP-DX to extract the structure as a tree.
+ * @param jcamp
+ * @param options
+ * @returns Tree.
  */
-export declare function createTree(jcamp: string | ArrayBuffer | Uint8Array, options?: CreateTreeOptions | undefined): Tree[];
+export declare function createTree(jcamp: string | ArrayBuffer | Uint8Array, options?: CreateTreeOptions): Stack[];
 
-declare type CreateTreeOptions = {
-    flatten?: boolean | undefined;
-};
+declare interface CreateTreeOptions {
+    flatten?: boolean;
+}
 
-declare type Entry = {
+declare interface Entry {
     spectra: Spectrum[];
     ntuples: Ntuples;
     meta: Record<string, string | string[] | number | number[] | boolean | boolean[] | undefined>;
     info: Record<string, string | string[] | number | number[] | boolean | boolean[] | undefined>;
     tmp: Record<string, string | string[] | number | number[] | boolean | boolean[] | undefined>;
-    title?: string | undefined;
-    dataType?: string | undefined;
-    dataClass?: string | undefined;
-    jcampDX?: string | null | undefined;
-    jcampCS?: string | null | undefined;
-    twoD?: boolean | undefined;
-    minMax?: MinMax | undefined;
-};
-
-declare type MinMax = {
-    z?: number[][] | undefined;
+    title?: string;
+    dataType?: string;
+    dataClass?: string;
+    jcampDX?: string;
+    jcampCS?: string;
+    twoD?: boolean;
+    minMax?: MinMax;
+    children?: Entry[];
+    shiftOffsetVal?: number;
+    shiftOffsetNum?: number;
+    xType?: string;
+    yType?: string;
+    chromatogram?: Chromatogram;
+    contourLines?: ContourLines;
+}
+
+declare interface GenerateContourLinesOptions {
+    /**
+     * Number of positive / negative contour levels to calculate.
+     * @default `7`
+     */
+    nbContourLevels: number;
+    /**
+     * Define for 2D the level as 5 times the median as default.
+     * @default `5`
+     */
+    noiseMultiplier: number;
+}
+
+declare interface MinMax {
+    z: number[][];
     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;
-};
+    median?: number;
+    noice?: number;
+}
+
+declare interface Ntuples {
+    varname?: string[];
+    symbol?: string[];
+    vartype?: string[];
+    varform?: string[];
+    vardim?: number[];
+    units?: string[];
+    factor?: number[];
+    first?: number[];
+    last?: number[];
+    min?: number[];
+    max?: number[];
+    nucleus?: string[];
+    [key: string]: any | undefined;
+}
+
+declare type OCL = openchemlib;
+
+declare interface ParsedCS {
+    molfile: string;
+    molecule: Molecule;
+}
 
 /**
  *
- * @typedef {object} ParsedCS@typedef {object} ParsedCS
- * @property {string} molfile
- * @property {import("openchemlib").OCL} molecule
- */
-/**
- *
- * @param {import("./convert.js").Entry} entry
- * @param {object} [options={}]
- * @param {import("fifo-logger").Logger} [options.logger]
- * @param {import("openchemlib").OCL} [options.OCL]
+ * @param entry
+ * @param options
  * @returns ParsedCS
  */
-export declare function parseJcampCS(entry: Entry, options?: {
-    logger?: any;
-    OCL?: any;
-} | undefined): {
-    molecule: any;
-    molfile: any;
-} | undefined;
+export declare function parseJcampCS(entry: Entry, options: ParseJcampCSOptions): ParsedCS | undefined;
+
+declare interface ParseJcampCSOptions {
+    OCL: OCL;
+    logger?: Logger;
+}
 
-declare type Spectrum = Record<string, any>;
+declare interface Spectrum {
+    [key: string]: any;
+    data: Record<string, number[]>;
+    firstX?: number;
+    firstY?: number;
+    lastX?: number;
+    deltaX?: number;
+    yFactor?: number;
+    xFactor?: number;
+    nbPoints?: number;
+}
 
-declare type Tree = {
+declare interface Stack {
     title: string;
     jcamp: string;
-    children?: Tree[] | undefined;
-};
+    children: Stack[] | undefined;
+    jcampDX?: string;
+    jcampCS?: string;
+    dataType?: string;
+    dataClass?: string;
+}
 
 export { }

package/jcampconverter.mjs

@@ -1,8 +1,9 @@
-import{ensureString as ue}from"ensure-string";var P=/\s*\$\$.*/;function M(e){return e.replace(P,"")}function pe(e,a={}){e=ue(e);let{flatten:s=!1}=a;if(typeof e!="string")throw new TypeError("the JCAMP should be a string");let i=e.split(/\r?\n/),o=[],t=[],r=[],l,n=0,p=e.includes("## ");for(let c=0;c<i.length;c++){let d=i[c],u=p?d.replace(/ /g,""):d;if(u.substring(0,9)==="##NTUPLES"&&n++,u.substring(0,7)==="##TITLE"){let f=[u.substring(8).trim()];for(let m=c+1;m<i.length&&!i[m].startsWith("##");m++)f.push(i[m].trim());t.push({title:f.join(`
-`),jcamp:`${d}
-`,children:[]}),l=t[t.length-1],o.push(l)}else if(u.substring(0,5)==="##END"&&n===0){l.jcamp+=`${d}
-`;let f=t.pop();t.length!==0?(l=t[t.length-1],l.children.push(f)):(l=void 0,r.push(f))}else if(l&&l.jcamp){l.jcamp+=`${d}
-`;let f=u.match(/^##(.*?)=(.+)/);if(f){let m=f[1].replace(/[ _-]/g,"").toUpperCase();m==="DATATYPE"?l.dataType=f[2].trim():m==="DATACLASS"?l.dataClass=f[2].trim():m==="JCAMPDX"?l.jcampDX=M(f[2].trim()):m==="JCAMPCS"&&(l.jcampCS=M(f[2].trim()))}}u.substring(0,5)==="##END"&&n>0&&n--}return s?(o.forEach(c=>{c.children=void 0}),o):r}import{parseString as ge}from"dynamic-typing";import{ensureString as be}from"ensure-string";var E=["TIC",".RIC","SCANNUMBER"];function te(e){let a=e.spectra,s=a.length,i={times:new Array(s),series:{ms:{dimension:2,data:new Array(s)}}},o=[];for(let t=0;t<E.length;t++){let r=I(E[t]);a[0][r]&&(o.push(r),i.series[r]={dimension:1,data:new Array(s)})}for(let t=0;t<s;t++){let r=a[t];i.times[t]=r.pageValue;for(let l=0;l<o.length;l++)i.series[o[l]].data[t]=Number(r[o[l]]);r.data&&(i.series.ms.data[t]=[r.data.x,r.data.y])}e.chromatogram=i}function le(e){return E.indexOf(e)!==-1}function I(e){return e.toLowerCase().replace(/[^a-z0-9]/g,"")}function Y(e){let a=[];for(let s=0;s<e.length;s++)a.push(Number(e[s]));return a}function U(e,a){let s=e.yFactor,i=e.deltaX;e.isXYdata=!0;let o={x:[],y:[]};e.data=o;let t=e.firstX,r=e.firstY,l=!1,n,p=0;for(;p<a.length;p++)if(n=a.charCodeAt(p),n===13||n===10)l=!0;else if(l)break;let c=!0,d=!1,u=!1,f=0,m=!1,h=!1,g=0,A=0,N=!1,y=!1,C=!1,T=0;for(;p<=a.length;p++)if(p===a.length?n=13:n=a.charCodeAt(p),h)(n===13||n===10)&&(c=!0,h=!1);else if(n<=57&&n>=48)y=!0,T>0?g+=(n-48)/10**T++:(g*=10,g+=n-48);else if(n===44||n===46)y=!0,T++;else{if(y){if(c)c=!1,u&&(C=!0);else if(C)C=!1;else{d?(f=N?0-g:g,u=!0,d=!1):m||(A=N?0-g:g);let O=m?g-1:1;for(let v=0;v<O;v++)u?r+=f:r=A,o.x.push(t),o.y.push(r*s),t+=i}N=!1,g=0,T=0,y=!1,m=!1}if(n<74&&n>63)y=!0,u=!1,g=n-64;else if(n>96&&n<106)y=!0,u=!1,g=n-96,N=!0;else if(n===115)y=!0,m=!0,g=9;else if(n>82&&n<91)y=!0,m=!0,g=n-82;else if(n>73&&n<83)y=!0,d=!0,g=n-73;else if(n>105&&n<115)y=!0,d=!0,g=n-105,N=!0;else if(n===36&&a.charCodeAt(p+1)===36)y=!0,h=!0;else if(n===37)y=!0,d=!0,g=0,N=!1;else if(n===45){let O=a.charCodeAt(p+1);(O>=48&&O<=57||O===44||O===46)&&(y=!0,c||(u=!1),N=!0)}else(n===13||n===10)&&(c=!0,h=!1)}}var se=/[,\t ]+/;function D(e,a,s){if(e.isPeaktable=!0,!e.variables||Object.keys(e.variables)===2?me(e,a,s):ce(e,a,s),e.variables)for(let i in e.variables)e.variables[i].data=e.data[i]}function me(e,a,s){let i={x:[],y:[]};e.data=i;let o=a.split(/,? *,?[;\r\n]+ */);for(let t=1;t<o.length;t++){let r=o[t].trim().replace(P,"").split(se);if(r.length%2===0)for(let l=0;l<r.length;l=l+2)i.x.push(Number(r[l])*e.xFactor),i.y.push(Number(r[l+1])*e.yFactor);else s.logs.push(`Format error: ${r}`)}}function ce(e,a,s){let i={},o=Object.keys(e.variables),t=o.length;o.forEach(l=>i[l]=[]),e.data=i;let r=a.split(/,? *,?[;\r\n]+ */);for(let l=1;l<r.length;l++){let n=r[l].trim().replace(P,"").split(se);if(n.length%t===0)for(let p=0;p<n.length;p++)i[o[p%t]].push(Number(n[p]));else s.logs.push(`Wrong number of columns: ${n}`)}}function V(e,a){e.isXYAdata=!0;let s={};e.data=s;let i=a.split(/\r?\n/),o=i[0].replace(/^.*?([A-Z]+).*$/,"$1").split("").map(t=>t.toLowerCase());for(let t=1;t<i.length;t++){let r=i[t].replace(/^\((.*)\)$/,"$1").split(/ *, */);for(let l=0;l<o.length;l++){let n=r[l];switch(o[l]){case"x":case"y":case"w":n=Number.parseFloat(n);break;case"a":n=n.replace(/^<(.*)>$/,"$1");break;case"m":break;default:continue}s[o[l]]||(s[o[l]]=[]),s[o[l]].push(n)}}}import{parseString as ne}from"dynamic-typing";import{getGyromagneticRatio as ae}from"gyromagnetic-ratio";import re from"ml-array-median";function ie(e){return Array.isArray(e)?e[0]:e}function B(e){let{spectra:a}=e,s=a[0].data.y[0],i=s,o=a.length,t=a[0].data.x.length,r=new Array(o);for(let f=0;f<o;f++){r[f]=a[f].data.y;for(let m=0;m<t;m++){let h=r[f][m];h<s&&(s=h),h>i&&(i=h)}}let l=a[0].data.x[0],n=a[0].data.x[a[0].data.x.length-1],{firstY:p,lastY:c}=he(e);if(l>n)for(let f of r)f.reverse();p>c&&r.reverse();let d=[];for(let f=0;f<r.length;f++){let m=Float64Array.from(r[f]);for(let h=0;h<m.length;h++)m[h]<0&&(m[h]=-m[h]);d.push(re(m))}let u=re(d);return{z:r,minX:Math.min(l,n),maxX:Math.max(l,n),minY:Math.min(p,c),maxY:Math.max(p,c),minZ:s,maxZ:i,noise:u}}function he(e){let{spectra:a,ntuples:s,info:i}=e;if(s)for(let o=0;o<s.length;o++){let{symbol:t,nucleus:r,units:l}=s[o];if(t.match(/[F|T]1/)&&l?.toUpperCase().match("HZ")){let n=ie(i[".OBSERVEFREQUENCY"]),{nucleus:p}=s.find(h=>h.symbol.match(/[F|T]2/));if([n,p,r].some(h=>!h))break;let c=ae(p),d=ae(r),{first:u,last:f}=s[o],m=n*d/c;return{firstY:u/m,lastY:f/m}}}return{firstY:a[0].pageValue,lastY:a[a.length-1].pageValue}}function k(e,a){let s=e.noise,i=e.z,o,t,r,l,n,p,c,d,u=i.length,f=i[0].length,m,h,g,A,N=e.minX,C=(e.maxX-N)/(f-1),T=e.minY,v=(e.maxY-T)/(u-1),oe=e.minZ,K=e.maxZ,Q=a.nbContourLevels*2,W=new Array(Q),x;for(let R=0;R<Q;R++){let $={};W[R]=$;let fe=R%2,_=(K-a.noiseMultiplier*s)*Math.exp((R>>1)-a.nbContourLevels);fe===0?x=_+a.noiseMultiplier*s:x=0-_-a.noiseMultiplier*s;let b=[];if($.zValue=x,$.lines=b,!(x<=oe||x>=K))for(let X=0;X<u-1;X++){let z=i[X],ee=i[X+1];for(let S=0;S<f-1;S++)o=z[S],t=z[S+1],r=ee[S],l=ee[S+1],n=o>x,p=t>x,c=r>x,d=l>x,n!==p&&n!==c&&(m=S+(x-o)/(t-o),h=X,g=S,A=X+(x-o)/(r-o),b.push(m*C+N),b.push(h*v+T),b.push(g*C+N),b.push(A*v+T)),d!==p&&d!==c&&(m=S+1,h=X+1-(x-l)/(t-l),g=S+1-(x-l)/(r-l),A=X+1,b.push(m*C+N),b.push(h*v+T),b.push(g*C+N),b.push(A*v+T)),p!==c&&(m=(S+1-(x-t)/(r-t))*C+N,h=(X+(x-t)/(r-t))*v+T,p!==n&&(g=S+1-(x-t)/(o-t),A=X,b.push(m),b.push(h),b.push(g*C+N),b.push(A*v+T)),c!==n&&(g=S,A=X+1-(x-r)/(o-r),b.push(m),b.push(h),b.push(g*C+N),b.push(A*v+T)),p!==d&&(g=S+1,A=X+(x-t)/(l-t),b.push(m),b.push(h),b.push(g*C+N),b.push(A*v+T)),c!==d&&(g=S+(x-r)/(l-r),A=X+1,b.push(m),b.push(h),b.push(g*C+N),b.push(A*v+T)))}}return{minX:e.minX,maxX:e.maxX,minY:e.minY,maxY:e.maxY,segments:W}}function Z(e,a){let s=B(e);a.noContour||(e.contourLines=k(s,a),delete s.z),e.minMax=s}import{getGyromagneticRatio as j}from"gyromagnetic-ratio";function 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e.ntuples)e.ntuples[c][p]&&(a.variables[n][c.replace(/^var/,"")]=e.ntuples[c][p])}}i=e.ntuples.symbol.indexOf(t),o=e.ntuples.symbol.indexOf(r),i===-1&&(i=0),o===-1&&(o=0),e.ntuples.first&&(e.ntuples.first.length>i&&(a.firstX=e.ntuples.first[i]),e.ntuples.first.length>o&&(a.firstY=e.ntuples.first[o])),e.ntuples.last&&(e.ntuples.last.length>i&&(a.lastX=e.ntuples.last[i]),e.ntuples.last.length>o&&(a.lastY=e.ntuples.last[o])),e.ntuples.vardim&&e.ntuples.vardim.length>i&&(a.nbPoints=e.ntuples.vardim[i]),e.ntuples.factor&&(e.ntuples.factor.length>i&&(a.xFactor=e.ntuples.factor[i]),e.ntuples.factor.length>o&&(a.yFactor=e.ntuples.factor[o])),e.ntuples.units&&(e.ntuples.units.length>i&&(e.ntuples.varname&&e.ntuples.varname[i]?a.xUnits=`${e.ntuples.varname[i]} [${e.ntuples.units[i]}]`:a.xUnits=e.ntuples.units[i]),e.ntuples.units.length>o&&(e.ntuples.varname&&e.ntuples.varname[o]?a.yUnits=`${e.ntuples.varname[o]} [${e.ntuples.units[o]}]`:a.yUnits=e.ntuples.units[o]))}function w(e){e.xFactor||(e.xFactor=1),e.yFactor||(e.yFactor=1)}var F=/[ \t]*,[ \t]*/,xe={keepRecordsRegExp:/^$/,canonicDataLabels:!0,canonicMetadataLabels:!1,dynamicTyping:!0,withoutXY:!1,noTrimRegExp:/^$/,chromatogram:!1,keepSpectra:!1,noContour:!1,nbContourLevels:7,noiseMultiplier:5,profiling:!1};function Ne(e,a={}){e=be(e),a={...xe,...a},a.logger?.debug("Starting jcamp conversion"),a.wantXY=!a.withoutXY,a.start=Date.now();let s=[],i={profiling:a.profiling?[]:!1,logs:[],entries:[]},o={children:[]},t=o,r=[],l={};if(typeof e!="string")throw new TypeError("the JCAMP should be a string");L(i,"Before split to LDRS",a);let n=e.replace(/[\r\n]+##/g,`
+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(`
+`),jcamp:`${b}
+`,children:[]}),l=i.at(-1),f.push(l)}else if(h.startsWith("##END")&&r===0&&l){l.jcamp+=`${b}
+`;let s=i.pop();if(!s)throw new Error("Not finished");i.length>0?(l=i.at(-1),l.children?.push(s)):(l=void 0,t.push(s))}else if(l?.jcamp){l.jcamp+=`${b}
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${p.title}`)}return i}function Ae(e,a={}){let{logger:s,OCL:i}=a;if(!e.info.ATOMLIST||!e.info.BONDLIST){s?.warn("No ATOMLIST or BONDLIST in the JCAMP-CS entry");return}Xe(e,s);let o=Se(e.info.ATOMLIST),t=ye(e.info.BONDLIST),r=Ce(e.info.CHARGE,s),l=Te(i,o,t,r,s);return{molecule:l,molfile:l.toMolfile()}}function Te(e,a,s,i,o){let t={S:e.Molecule.cBondTypeSingle,D:e.Molecule.cBondTypeDouble,T:e.Molecule.cBondTypeTriple,Q:e.Molecule.cBondTypeQuadruple},r={},l=new e.Molecule(a.length,s.length);for(let n of a){let p=e.Molecule.getAtomicNoFromLabel(n.element);p||(o?.error(`Atomic number of ${n.element} could not be determined`),p=e.Molecule.getAtomicNoFromLabel("X")),r[n.atomNumber]=l.addAtom(p),l.setAtomMapNo(r[n.atomNumber],n.atomNumber)}for(let n of s){if(r[n.atomNumber1]===void 0){o?.error(`A bond goes to atomNumber ${n.atomNumber1} that does not exists`);continue}if(r[n.atomNumber2]===void 0){o?.error(`A bond goes to atomNumber ${n.atomNumber2} that does not exists`);continue}let p=l.addBond(r[n.atomNumber1],r[n.atomNumber2]);l.setBondType(p,t[n.bondType])}for(let n of i){if(r[n.atomNumber]===void 0){o?.error(`A charge goes to atomNumber ${n.atomNumber1} that does not exists`);continue}l.setAtomCharge(r[n.atomNumber],n.value)}return l}function Se(e){let a=e.split(/\r?\n/).map(i=>M(i)).filter(i=>i),s=[];for(let i of a){let[o,t,r]=i.trim().split(/\s+/);s.push({atomNumber:Number(o),element:t,nbImplicitHydrogens:r?.length>0?Number(r):void 0})}return s}function ye(e){let a=e.split(/\r?\n/).map(i=>M(i)).filter(i=>i),s=[];for(let i of a){let[o,t,r]=i.trim().split(/\s+/);s.push({atomNumber1:Number(o),atomNumber2:Number(t),bondType:r})}return s}function Ce(e,a){if(!e)return[];let s=e.split(/\r?\n/).map(o=>M(o)).filter(o=>o),i=[];for(let o of s){let[t,r,l]=o.trim().split(/\s+/);l!==void 0&&a?.warn("Charge on multiple atom is not supported"),i.push({atomNumber:Number(r),value:Number(t)})}return i}function Xe(e,a){let s=["STEREOPAIR","STEREOCENTER","RADICAL","STEREOMOLECULE"];for(let i of s)e.info[i]&&a?.warn(`JCAMP-CS parser do not support: ${i}`)}export{Ne as convert,pe as createTree,Ae as parseJcampCS};
+##`);n.logger?.trace({profiling:!0},"Split to LDRS"),p[0]&&(p[0]=p[0].replace(/^[\r\n ]*##/,""));for(let u of p){let b=u.indexOf("="),h=b>0?u.slice(0,Math.max(0,b)):u,s=b>0?h.match(n.noTrimRegExp)?u.slice(Math.max(0,b+1)):u.slice(Math.max(0,b+1)).trim():"",a=h.replaceAll(/[_ -]/g,"").toUpperCase();if(a==="DATATABLE"){let c=s.indexOf(`
+`);if(c===-1&&(c=s.indexOf("\r")),c>0){let d=s.slice(0,Math.max(0,c)).split(/[ ,;\t]+/);z(t,r,d[0]),r.datatable=d[0],d[1]?.includes("PEAKS")?a="PEAKTABLE":d[1]&&(d[1].indexOf("XYDATA")||d[0].indexOf("++")>0)&&(a="XYDATA",r.nbPoints&&r.lastX!==void 0&&r.firstX!==void 0&&(r.deltaX=(r.lastX-r.firstX)/(r.nbPoints-1)))}}if(a==="XYDATA"){n.wantXY&&(w(r),s.match(/.*\+\+.*/)?(r.nbPoints&&r.lastX!==void 0&&r.firstX!==void 0&&(r.deltaX=(r.lastX-r.firstX)/(r.nbPoints-1)),V(r,s,n)):P(r,s,n),t?.spectra.push(r),r={data:{}});continue}else if(a==="PEAKTABLE"){n.wantXY&&(w(r),P(r,s,n),t?.spectra.push(r),r={data:{}});continue}if(a==="PEAKASSIGNMENTS"){n.wantXY&&(s.match(/.*[^A-Z]*.*/)&&B(r,s),t?.spectra.push(r),r={data:{}});continue}if(n.removeComments&&(s=s.split(/\r?\n/).map(c=>c.replace(/ *\$\$.*$/,"")).join(`
+`)),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

@@ -1,10 +1,16 @@
 {
   "name": "jcampconverter",
-  "version": "9.6.4",
+  "version": "10.0.1",
   "description": "Parse and convert JCAMP data",
-  "types": "jcampconverter.d.ts",
-  "main": "jcampconverter.cjs",
-  "module": "jcampconverter.mjs",
+  "keywords": [
+    "jcamp",
+    "converter"
+  ],
+  "author": "Luc Patiny",
+  "license": "MIT",
+  "types": "./jcampconverter.d.ts",
+  "require": "./jcampconverter.cjs",
+  "module": "./jcampconverter.mjs",
   "exports": {
     ".": {
       "types": "./jcampconverter.d.ts",
@@ -19,63 +25,54 @@
   ],
   "scripts": {
     "api-extractor": "api-extractor run --local",
-    "build": "cheminfo-build --entry src/index.js --root JcampConverter --no-source-map && rm dist/jcampconverter.js",
+    "benchmark": "node benchmark/benchmark.js",
+    "build": "tsc --project tsconfig.cheminfo-build.json && cheminfo-build --entry lib/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-common": "esbuild src/index.ts --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 dist types",
+    "clean": "rimraf dist lib types",
+    "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",
     "eslint": "eslint src __tests__",
     "eslint-fix": "npm run eslint -- --fix",
     "jscpd": "jscpd -l 10 -i \"**/__tests__/**\" -t 1 src",
     "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": "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"
+    "prettier": "prettier --check src __tests__",
+    "prettier-write": "prettier --write src __tests__",
+    "test": "npm run test-only && npm run check-types && npm run eslint && npm run prettier",
+    "test-only": "vitest run --coverage",
+    "tsc": "tsc --project tsconfig.types.json"
   },
-  "keywords": [
-    "jcamp",
-    "converter"
-  ],
-  "author": "Luc Patiny",
-  "license": "MIT",
   "bugs": {
     "url": "https://github.com/cheminfo/nmrium/issues/new?title=%5Bjcampconverter%5D"
   },
   "devDependencies": {
-    "@microsoft/api-extractor": "^7.42.3",
-    "@types/jest": "^29.5.12",
-    "@types/pino": "^7.0.5",
-    "@vitest/coverage-v8": "^1.3.1",
+    "@microsoft/api-extractor": "^7.47.10",
+    "@vitest/coverage-v8": "^2.1.3",
     "benchmark": "^2.1.4",
-    "c8": "^9.1.0",
     "cheminfo-build": "^1.2.0",
-    "esbuild": "^0.20.1",
-    "eslint": "^8.57.0",
-    "eslint-config-cheminfo-typescript": "^12.2.0",
-    "esm": "^3.2.25",
-    "fifo-logger": "^0.6.1",
+    "esbuild": "^0.24.0",
+    "eslint": "^9.12.0",
+    "eslint-config-cheminfo-typescript": "^16.0.0",
+    "fifo-logger": "^1.0.0",
+    "jcamp-data-test": "^0.8.1",
     "jest-matcher-deep-close-to": "^3.0.2",
-    "jscpd": "^3.5.10",
-    "ml-spectra-processing": "^14.2.0",
-    "openchemlib": "^8.9.0",
-    "prettier": "^3.2.5",
-    "rimraf": "^5.0.5",
-    "typescript": "^5.4.2",
-    "vitest": "^1.3.1"
+    "jscpd": "^4.0.5",
+    "ml-spectra-processing": "^14.6.0",
+    "openchemlib": "^8.15.0",
+    "prettier": "^3.3.3",
+    "rimraf": "^6.0.1",
+    "typescript": "^5.6.3",
+    "vitest": "^2.1.3"
   },
   "dependencies": {
-    "cheminfo-types": "^1.7.2",
-    "dynamic-typing": "^1.0.0",
+    "cheminfo-types": "^1.8.0",
+    "dynamic-typing": "^1.0.1",
     "ensure-string": "^1.2.0",
-    "gyromagnetic-ratio": "^1.1.1",
+    "gyromagnetic-ratio": "^1.2.0",
     "ml-array-median": "^1.1.6"
   }
 }