@datagrok/helm 2.1.16 → 2.1.17

package/.eslintrc.json

@@ -25,8 +25,7 @@
     "linebreak-style": "off",
     "curly": [
       "error",
-      "multi-or-nest",
-      "consistent"
+      "multi-or-nest"
     ],
     "brace-style": ["error", "1tbs", {"allowSingleLine": true}],
     "block-spacing": [2, "always"],

package/CHANGELOG.md

@@ -0,0 +1,22 @@
+# Helm changelog
+
+## 2.2.0 (WIP)
+
+### Bug fixes
+
+* Fix Helm cell renderer, allowing to render with gaps by skipping.
+* Fix message WebEditor not supporting Helm with gaps.
+* Prevent display tooltip by fallback cell renderer while WebEditor renders.
+* Reset monomer placer on monomer lib changed.
+
+## 2.1.16 (2023-07-21)
+
+This release focuses on stability.
+
+*Dependency: datagarok-api >= 1.10.2*
+
+### Bug Fixes
+
+* Fixed the **To Atomic Level** function for helm sequences.
+* `Neither peptide, nor nucleotide` error when calling **Helm Web Editor**
+* Macromolecule detector for alphabet UN.

package/dist/package-test.js

@@ -1,2 +1,2 @@
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M=function(t,e,n,r){return new(n||(n=Promise))((function(s,o){function i(t){try{l(r.next(t))}catch(t){o(t)}}function a(t){try{l(r.throw(t))}catch(t){o(t)}}function l(t){var e;t.done?s(t.value):(e=t.value,e instanceof n?e:new n((function(t){t(e)}))).then(i,a)}l((r=r.apply(t,e||[])).next())}))};C("Helm",(()=>{const t=[["L-hArg(Et,Et)","E","F","G","C","E"],["L-hArg(Et,Et)","L-hArg(Et,Et)","E","F","G"],["dhp","m1A","p","r","T","p","r","T","p","r","G","p"],["r","mo6pur","p","r","T","p","r","T","p","r","G","p"],["afhna","mo6pur","36SS","r","T","p"]],e=["comples-monomer","complex-monomer+side-chain","complex-monomer+side-chain-RNA","complex-side-chain","complex+side-chain+linker"];g("parseHelm",(()=>M(void 0,void 0,void 0,(function*(){const 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t=1;t<e.length+1;t++)a[0][t]=-r-(t-1)*s;for(let t=1;t<n.length+1;t++){a[h][0]=-r-(t-1)*s;for(let g=1;g<e.length+1;g++){const f=a[u][g-1]+o[i[e[g-1]]][i[n[t-1]]],p=a[u][g]-(l[g]?s:r),d=a[h][g-1]-(c[g-1]?s:r);a[h][g]=Math.max(f,d,p),a[h][g]===f?(l[g]=!1,c[g]=!1):a[h][g]===d?(l[g]=!1,c[g]=!0):(l[g]=!0,c[g]=!1)}u=h,h=(h+1)%2}const g=e.split("").map((t=>o[i[t]][i[t]])).reduce(((t,e)=>t+e),0),f=n.split("").map((t=>o[i[t]][i[t]])).reduce(((t,e)=>t+e),0),p=Math.max(g,f);return(p-a[u][e.length])/p}}},U=new class{constructor(){this.uhTemp=`units-handler.${n.SEMTYPE.MACROMOLECULE}`}};class D{static setUnitsToFastaColumn(t){if(t.column.semType!==n.SEMTYPE.MACROMOLECULE||"fasta"!==t.column.getTag(n.TAGS.UNITS))throw new Error(`The column of notation 'fasta' must be '${n.SEMTYPE.MACROMOLECULE}'.`);t.column.setTag(n.TAGS.UNITS,"fasta"),D.setTags(t)}static setUnitsToSeparatorColumn(t,e){if(t.column.semType!==n.SEMTYPE.MACROMOLECULE||"separator"!==t.column.getTag(n.TAGS.UNITS))throw new Error(`The column of notation 'separator' must be '${n.SEMTYPE.MACROMOLECULE}'.`);if(!e)throw new Error("The column of notation 'separator' must have the separator tag.");t.column.setTag(n.TAGS.UNITS,"separator"),t.column.setTag("separator",e),D.setTags(t)}static setUnitsToHelmColumn(t){if(t.column.semType!==n.SEMTYPE.MACROMOLECULE)throw new Error(`The column of notation 'helm' must be '${n.SEMTYPE.MACROMOLECULE}'`);t.column.setTag(n.TAGS.UNITS,"helm"),D.setTags(t)}static setTags(t){const e=t.column.getTag(n.TAGS.UNITS),r=t.stats;if(Object.keys(r.freq).some((t=>t.length>1)),["fasta","separator"].includes(e)){if(0===Object.keys(r.freq).length)throw new Error("Alphabet is empty");const e=r.sameLength?"SEQ.MSA":"SEQ";t.column.setTag("aligned",e);const n=function(t,e,n="-"){const r=e.map((e=>{const r=function(t,e,n="-"){const r=new Set([...new Set(Object.keys(t)),...e]);r.delete(n);const s=[],o=[];for(const n of r)s.push(n in t?t[n]:0),o.push(e.has(n)?1:0);const i=new F(s),a=new F(o);return function(t,e){if(t.length!=e.length)throw new Error("The dimensionality of the vectors must match");let n=0;for(let r=0;r<t.length;r++)n+=t[r]*e[r];return n}(i,a)/(W(i)*W(a))}(t,e.alphabet,n);return new I(e,t,r)}));let s;const o=Math.max(...r.map((t=>t.similarity>t.cutoff?t.similarity:-1)));s=o>0?r.find((t=>t.similarity===o)).name:"UN";return s}(r.freq,G);if(t.column.setTag("alphabet",n),"UN"===n){const e=Object.keys(r.freq).length,n=Object.keys(r.freq).some((t=>t.length>1));t.column.setTag(".alphabetSize",e.toString()),t.column.setTag(".alphabetIsMultichar",n?"true":"false")}}}get column(){return this._column}get units(){return this._units}get notation(){return this._notation}get defaultGapSymbol(){return this._defaultGapSymbol}get separator(){const t=this.column.getTag("separator")??void 0;if("separator"===this.notation&&void 0===t)throw new Error(`Separator is mandatory  for column '${this.column.name}' of notation '${this.notation}'.`);return t}get aligned(){const t=this.column.getTag("aligned");if(!t&&(this.isFasta()||this.isSeparator()))throw new Error("Tag aligned not set");return t}get alphabet(){const t=this.column.getTag("alphabet");if(!t&&(this.isFasta()||this.isSeparator()))throw new Error("Tag alphabet not set");return t}get helmCompatible(){return this.column.getTag(".isHelmCompatible")}getAlphabetSize(){if("helm"==this.notation||"UN"==this.alphabet){const t=this.column.getTag(".alphabetSize");let e;if(t)e=parseInt(t);else{const t=this.stats;e=Object.keys(t.freq).length}return e}switch(this.alphabet){case"PT":return 20;case"DNA":case"RNA":return 4;case"NT":return console.warn("Unexpected alphabet 'NT'."),4;default:throw new Error(`Unexpected alphabet '${this.alphabet}'.`)}}getAlphabetIsMultichar(){return"helm"===this.notation||"UN"===this.alphabet&&"true"===this.column.getTag(".alphabetIsMultichar")}get splitted(){if(null===this._splitted){const t=this.getSplitter(),e=this._column.length;this._splitted=new Array(e);const n=this._column.getRawData(),r=this._column.categories;for(let s=0;s<e;s++){const e=r[n[s]];this._splitted[s]=t(e)}}return this._splitted}get stats(){if(null===this._stats){const t={};let e=!0,n=null;for(const r of this.splitted){null==n?n=r.length:r.length!==n&&(e=!1);for(const e of r)e in t||(t[e]=0),t[e]+=1}this._stats={freq:t,sameLength:e}}return this._stats}isFasta(){return"fasta"===this.notation}isSeparator(){return"separator"===this.notation}isHelm(){return"helm"===this.notation}isRna(){return"RNA"===this.alphabet}isDna(){return"DNA"===this.alphabet}isPeptide(){return"PT"===this.alphabet}isMsa(){return!!this.aligned&&this.aligned.toUpperCase().includes("MSA")}isHelmCompatible(){return"true"===this.helmCompatible}getNotation(){if(this.units.toLowerCase().startsWith("fasta"))return"fasta";if(this.units.toLowerCase().startsWith("separator"))return"separator";if(this.units.toLowerCase().startsWith("helm"))return"helm";throw new Error(`Column '${this.column.name}' has unexpected notation '${this.units}'.`)}getNewColumn(t,e){const r=this.column,s=r.length,o=t.toLowerCase()+"("+r.name+")",i=r.dataFrame.columns.getUnusedName(o),a=n.Column.fromList("string",i,new Array(s).fill(""));if(a.semType=n.SEMTYPE.MACROMOLECULE,a.setTag(n.TAGS.UNITS,t),"separator"===t){if(!e)throw new Error("Notation 'separator' requires separator value.");a.setTag("separator",e)}a.setTag(n.TAGS.CELL_RENDERER,"Macromolecule");const l=r.getTag("aligned");l&&a.setTag("aligned",l);const c=r.getTag("alphabet");c&&a.setTag("alphabet",c);let u=r.getTag(".alphabetSize");u&&a.setTag(".alphabetSize",u);const h=r.getTag(".alphabetIsMultichar");return void 0!==h&&a.setTag(".alphabetIsMultichar",h),"helm"==t&&(u=this.getAlphabetSize().toString(),a.setTag(".alphabetSize",u)),a}static getNewColumn(t){const e=D.getOrCreate(t),n=e.notation;return e.getNewColumn(n)}static unitsStringIsValid(t){return t=t.toLowerCase(),["fasta","separator","helm"].some((e=>t.startsWith(e.toLowerCase())))}static getNewColumnFromParams(t,e,r){if(!D.unitsStringIsValid(r))throw new Error("Invalid format of 'units' parameter");const s=n.Column.fromList("string",e,new Array(t).fill(""));return s.semType=n.SEMTYPE.MACROMOLECULE,s.setTag(n.TAGS.UNITS,r),s}getSplitter(){return function(t){if(t.semType!==n.SEMTYPE.MACROMOLECULE)throw new Error(`Get splitter for semType "${n.SEMTYPE.MACROMOLECULE}" only.`);return function(t,e,n){if(t.toLowerCase().startsWith("fasta"))return q;if(t.toLowerCase().startsWith("separator"))return K(e,void 0);if(t.toLowerCase().startsWith("helm"))return X;throw new Error(`Unexpected units ${t} .`)}(t.getTag(n.TAGS.UNITS),t.getTag("separator"))}(this._column)}getDistanceFunctionName(){if(!this.isFasta())throw new Error("Only FASTA notation is supported");if(this.isMsa())return x.HAMMING;switch(this.alphabet){case"DNA":case"RNA":default:return x.LEVENSHTEIN;case"PT":return x.NEEDLEMANN_WUNSCH}}getDistanceFunction(){return k[this.getDistanceFunctionName()]()}async checkHelmCompatibility(){if(this.column.tags.has(".isHelmCompatible"))return"true"===this.column.getTag(".isHelmCompatible");const t=(await Z()).getBioLib().getMonomerSymbolsByType("PEPTIDE".toString()),e=new Set(t),n=K(this.separator);for(const t of this.column.categories){const r=n(t);for(const t of r)if(!e.has(t))return this.column.setTag(".isHelmCompatible","false"),!1}return this.column.setTag(".isHelmCompatible","true"),!0}constructor(t){if(this._splitted=null,this._stats=null,t.type!=n.TYPE.STRING)throw new Error(`Unexpected column type '${t.type}', must be '${n.TYPE.STRING}'.`);this._column=t;const e=this._column.getTag(n.TAGS.UNITS);if(null==e)throw new Error("Units are not specified in column");if(this._units=e,this._notation=this.getNotation(),this._defaultGapSymbol=this.isFasta()?D._defaultGapSymbolsDict.FASTA:this.isHelm()?D._defaultGapSymbolsDict.HELM:D._defaultGapSymbolsDict.SEPARATOR,!this.column.tags.has("aligned")||!this.column.tags.has("alphabet")||!this.column.tags.has(".alphabetIsMultichar")&&!this.isHelm()&&"UN"===this.alphabet)if(this.isFasta())D.setUnitsToFastaColumn(this);else if(this.isSeparator()){const e=t.getTag("separator");D.setUnitsToSeparatorColumn(this,e)}else{if(!this.isHelm())throw new Error(`Unexpected units '${this.column.getTag(n.TAGS.UNITS)}'.`);D.setUnitsToHelmColumn(this)}if(!this.column.tags.has(".alphabetIsMultichar"))if(this.isHelm())this.column.setTag(".alphabetIsMultichar","true");else if(["UN"].includes(this.alphabet))throw new Error(`For column '${this.column.name}' of alphabet '${this.alphabet}' tag '.alphabetIsMultichar' is mandatory.`)}static getOrCreate(t){return U.uhTemp in t.temp||(t.temp[U.uhTemp]=new D(t)),t.temp[U.uhTemp]}}D._defaultGapSymbolsDict={HELM:"*",SEPARATOR:"",FASTA:"-"};class F extends Float32Array{}function W(t){let e=0;for(let n=0;n<t.length;n++)e+=t[n]*t[n];return Math.sqrt(e)}class V{static makePalette(t,e=!1,n=V){const r={};return t.forEach((t=>{const n=t[0],s=t[1];n.forEach(((t,n)=>{r[t]=this.colourPalette[s][e?0:n]}))})),new n(r)}constructor(t){this._palette=t}get(t){return this._palette[t]}}V.undefinedColor="rgb(100,100,100)",V.colourPalette={orange:["rgb(255,187,120)","rgb(245,167,100)","rgb(235,137,70)","rgb(205, 111, 71)"],all_green:["rgb(44,160,44)","rgb(74,160,74)","rgb(23,103,57)","rgb(30,110,96)","rgb(60,131,95)","rgb(24,110,79)","rgb(152,223,138)","rgb(182, 223, 138)","rgb(152, 193, 138)"],all_blue:["rgb(31,119,180)","rgb(23,190,207)","rgb(122, 102, 189)","rgb(158,218,229)","rgb(141, 124, 217)","rgb(31, 120, 150)"],magenta:["rgb(162,106,192)","rgb(197,165,224)","rgb(208,113,218)"],red:["rgb(214,39,40)","rgb(255,152,150)"],st_blue:["rgb(23,190,207)","rgb(158,218,229)","rgb(31,119,180)"],dark_blue:["rgb(31,119,180)","rgb(31, 120, 150)"],light_blue:["rgb(23,190,207)","rgb(158,218,229)","rgb(108, 218, 229)","rgb(23,190,227)"],lilac_blue:["rgb(124,102,211)","rgb(149,134,217)","rgb(97, 81, 150)"],dark_green:["rgb(23,103,57)","rgb(30,110,96)","rgb(60,131,95)","rgb(24,110,79)"],green:["rgb(44,160,44)","rgb(74,160,74)"],light_green:["rgb(152,223,138)","rgb(182, 223, 138)","rgb(152, 193, 138)"],st_green:["rgb(44,160,44)","rgb(152,223,138)","rgb(39, 174, 96)","rgb(74,160,74)"],pink:["rgb(247,182,210)"],brown:["rgb(140,86,75)","rgb(102, 62, 54)"],gray:["rgb(127,127,127)","rgb(199,199,199)","rgb(196,156,148)","rgb(222, 222, 180)"],yellow:["rgb(188,189,34)"],white:["rgb(230,230,230)"]};class Y extends V{static get Lesk(){return void 0===this.lesk&&(this.lesk=this.makePalette([[["G","A","S","T"],"orange"],[["C","V","I","L","P","F","Y","M","W"],"all_green"],[["N","Q","H"],"magenta"],[["D","E"],"red"],[["K","R"],"all_blue"]],!1,Y)),this.lesk}static get GrokGroups(){return void 0===this.grokGroups&&(this.grokGroups=this.makePalette([[["C","U"],"yellow"],[["G","P"],"red"],[["A","V","I","L","M","F","Y","W"],"all_green"],[["R","H","K"],"light_blue"],[["D","E"],"dark_blue"],[["S","T","N","Q"],"orange"]],!1,Y)),this.grokGroups}static get RasMol(){return void 0===this.rasMol&&(this.rasMol=new Y({D:"#E60A0A",E:"#E60A0A",C:"#E6E600",M:"#E6E600",K:"#145AFF",R:"#145AFF",S:"#FA9600",T:"#FA9600",F:"#3232AA",Y:"#3232AA",N:"#00DCDC",Q:"#00DCDC",G:"#EBEBEB",L:"#0F820F",V:"#0F820F",I:"#0F820F",A:"#C8C8C8",W:"#B45AB4",H:"#8282D2",P:"#DC9682",others:"#BEA06E"})),this.rasMol}get(t){const e=t in Y.aaSynonyms?Y.aaSynonyms[t]:t;return super.get(e)}}Y.aaSynonyms={MeNle:"L",MeA:"A",MeG:"G",MeF:"F"};class j{static getPalette(t="grok"){switch(t){case"grok":return Y.GrokGroups;case"lesk":return Y.Lesk;default:throw new Error(`ChemPalette: scheme \`${t}\` does not exist`)}}static getInnerOuter(t){let e=0,n="",r="";for(const s of t)"("==s?e++:")"==s?e--:e?n+=s:r+=s;return isNaN(parseInt(n))?[r,n]:[r,""]}static getColorAAPivot(t="",e="grok"){const n=this.getPalette(e);let[r,s]=this.getInnerOuter(t);if(r=r.length>6?`${r.slice(0,3)}...`:r,s=s.length>6?`${s.slice(0,3)}...`:s,1==t.length||"("==t[1]){const e=t[0]?.toUpperCase();return e in n?[n.get(e),e,s,1]:[this.undefinedColor,r,s,1]}if("d"==t[0]&&t[1]in n&&(2==t.length||"("==t[2])){const e=t[1]?.toUpperCase();return e in n?[n.get(e),e,s,2]:[this.undefinedColor,r,s,2]}if(t.substring(0,3)in this.AAFullNames&&(3==t.length||"("==t[3])){const e=this.AAFullNames[t.substring(0,3)];return e in n?[n.get(e),e,s,3]:[this.undefinedColor,r,s,3]}if(t[0]?.toLowerCase()==t[0]&&t.substring(1,3)in this.AAFullNames&&(4==t.length||"("==t[4])){const e=this.AAFullNames[t.substring(1,3)];return e in n?[n.get(e),e,s,4]:[this.undefinedColor,r,s,4]}return[this.undefinedColor,r,s,0]}}j.SemType="Aminoacids",j.SemTypeMultipleAlignment="AminoacidsMultipleAlignment",j.undefinedColor="rgb(100,100,100)",j.Names={G:"Glycine",L:"Leucine",Y:"Tyrosine",S:"Serine",E:"Glutamic acid",Q:"Glutamine",D:"Aspartic acid",N:"Asparagine",F:"Phenylalanine",A:"Alanine",K:"Lysine",R:"Arginine",H:"Histidine",C:"Cysteine",V:"Valine",P:"Proline",W:"Tryptophan",I:"Isoleucine",M:"Methionine",T:"Threonine"},j.AASmiles={G:"NCC(=O)O",L:"N[C@H](CC(C)C)C(=O)O",Y:"NC(CC1=CC=C(O)C=C1)C(=O)O",S:"NC(CO)C(=O)O",E:"N[C@@H](CCC(O)=O)C(=O)O",Q:"N[C@@H](CCC(N)=O)C(=O)O",D:"N[C@@H](CC(O)=O)C(=O)O",N:"N[C@@H](CC(N)=O)C(=O)O",F:"NC(CC1=CC=CC=C1)C(=O)O",A:"N[C@H](C)C(=O)O",K:"NC(CCCCN)C(=O)O",R:"N[C@H](CCCNC(=N)C)C(=O)O",H:"NC(CC1=CN=C[N]1)C(=O)O",C:"N[C@@H](CS)C(=O)O",V:"NC(C(C)C)C(=O)O",P:"N(CCC1)C1C(=O)O",W:"N[C@@H](Cc1c2ccccc2n([H])c1)C(=O)O",I:"N[C@H]([C@H](C)CC)C(=O)O",M:"NC(CCSC)C(=O)O",T:"NC(C(O)C)C(=O)O"},j.AASmilesTruncated={G:"*C*",L:"CC(C)C[C@H](*)*",Y:"C1=CC(=CC=C1CC(*)*)O",S:"OCC(*)C*",E:"*[C@@H](CCC(O)=O)*",Q:"*N[C@@H](CCC(N)=O)*",D:"*[C@@H](CC(O)=O)*",N:"*[C@@H](CC(N)=O)*",F:"C1=CC=C(C=C1)CC(*)*",A:"C[C@H](*)*",K:"C(CCN)CC(*)*",R:"*[C@H](CCCNC(=N)C)*",H:"C1=C(NC=N1)CC(*)*",C:"C([C@@H](*)*)S",V:"CC(C)C(*)*",P:"C1CCN(*)C1*",W:"*[C@@H](Cc1c2ccccc2n([H])c1)*",I:"CC[C@H](C)[C@H](*)*",M:"CSCCC(*)*",T:"CC(O)C(*)*"},j.AAFullNames={Ala:"A",Arg:"R",Asn:"N",Asp:"D",Cys:"C",Gln:"Q",Glu:"E",Gly:"G",His:"H",Ile:"I",Leu:"L",Lys:"K",Met:"M",Phe:"F",Pro:"P",Ser:"S",Thr:"T",Trp:"W",Tyr:"Y",Val:"V"};class Q{}Q.SemType="Nucleotides",Q.SemTypeMultipleAlignment="NucleotidesMultipleAlignment",Q.Names={A:"Adenine",C:"Cytosine",G:"Guanine",T:"Thymine",U:"Uracil"};class B extends class{}{static buildPalette(){return[].concat(...Object.values(V.colourPalette))}get(t){const e=class{static hashCode(t){let e=0;if(0===t.length)return e;for(let n=0;n<t.length;n++)e=(e<<5)-e+t.charCodeAt(n),e|=0;return e}}.hashCode(t)%B.palette.length;return function(t){if(null==t)return"rgb(100,100,100)";const e=n.Color.fromHtml(t),r=n.Color.g(e),s=n.Color.r(e),o=n.Color.b(e),i=Math.sqrt(Math.pow(0-s,2)+Math.pow(0-r,2)+Math.pow(0-o,2));return i>210?`rgb(${s/i*210},${r/i*210},${o/i*210})`:n.Color.toRgb(e)}(B.palette[e])}}function q(t){return t.toString().replace(L,".$1").slice(1).split(".").map((t=>t.startsWith("[")&&t.endsWith("]")?t.slice(1,-1):"-"===t?"":t))}function K(t,e){return n=>n.split(t,e)}B.palette=B.buildPalette();const z=/(PEPTIDE1|DNA1|RNA1)\{([^}]+)}/g,J=/\[([^\[\]]+)]/g;function X(t){z.lastIndex=0;const e=z.exec(t.toString()),n=e?e[2]:null;return(n?n.split("."):[]).map((t=>{J.lastIndex=0;const e=J.exec(t);return e&&e.length>=2?e[1]:t}))}async function Z(){const t=n.Func.find({package:"Bio",name:"getMonomerLibHelper"});if(0===t.length)throw new Error('Package "Bio" must be installed for MonomerLibHelper.');return(await t[0].prepare().call()).getOutputParamValue()}var tt=function(t,e,n,r){return new(n||(n=Promise))((function(s,o){function i(t){try{l(r.next(t))}catch(t){o(t)}}function a(t){try{l(r.throw(t))}catch(t){o(t)}}function l(t){var e;t.done?s(t.value):(e=t.value,e instanceof n?e:new n((function(t){t(e)}))).then(i,a)}l((r=r.apply(t,e||[])).next())}))};const et="Libraries",nt={"HELMCoreLibrary.json":"HELMCoreLibrary.json"};C("findMonomers",(()=>{let t,e=null;E((()=>tt(void 0,void 0,void 0,(function*(){t=yield Z(),e=yield r.dapi.userDataStorage.get(et,!0),yield r.dapi.userDataStorage.post(et,nt,!0),yield t.loadLibraries(!0)})))),T((()=>tt(void 0,void 0,void 0,(function*(){yield r.dapi.userDataStorage.put(et,e,!0)}))));const n={withoutMissed:{test:"PEPTIDE1{meI.hHis.Aca.N.T.dE.Thr_PO3H2.Aca.D-Tyr_Et}$$$$",tgt:new Set},withMissed:{test:"PEPTIDE1{meI.missed2.Aca.N.T.dE.Thr_PO3H2.Aca.D-Tyr_Et}$$$$",tgt:new Set(["missed2"])}};for(const[t,e]of Object.entries(n))g(t,(()=>tt(void 0,void 0,void 0,(function*(){s(e.test,e.tgt)}))));function s(t,e){d(function(t){const e=Object.keys(org.helm.webeditor.monomerTypeList()),n=[],r=[];for(let t=0;t<e.length;t++)n.push(new scil.helm.Monomers.getMonomerSet(e[t])),Object.keys(n[t]).forEach((e=>{r.push(n[t][e].id)}));return new Set(t.filter((t=>!r.includes(t))))}(w(t)),e)}}));const rt=$;var st=t.n(rt),ot=function(t,e,n,r){return new(n||(n=Promise))((function(s,o){function i(t){try{l(r.next(t))}catch(t){o(t)}}function a(t){try{l(r.throw(t))}catch(t){o(t)}}function l(t){var e;t.done?s(t.value):(e=t.value,e instanceof n?e:new n((function(t){t(e)}))).then(i,a)}l((r=r.apply(t,e||[])).next())}))};C("renderers",(()=>{g("missedInLib",(()=>ot(void 0,void 0,void 0,(function*(){yield function(){return ot(this,void 0,void 0,(function*(){const t=yield r.dapi.files.readCsv("System:AppData/Helm/tests/sample_HELM-missedInLib.csv"),e=t.getCol("HELM"),o=r.shell.addTableView(t);yield function(t,e="Timeout exceeded",n=500,r=50){return s(this,void 0,void 0,(function*(){return new Promise(((s,o)=>{setTimeout((()=>{clearInterval(i),o(new Error(e))}),n);const i=setInterval((()=>{t()&&(clearInterval(i),s())}),r)}))}))}((()=>st()(o.root).find(".d4-grid canvas").length>0),"Table view canvas not found",100),f(e.semType,n.SEMTYPE.MACROMOLECULE),f(e.getTag(n.TAGS.UNITS),"helm"),f(e.getTag(n.TAGS.CELL_RENDERER),"helm");const i=e.getTag(".cell-renderer.render.error");if(i){const t=JSON.parse(i),e=new Error(t.message);throw e.stack=t.stack,e}}))}()}))))}));const it=new n.Package;function at(t,e,l){return c=this,g=void 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n?[n.get(t),t,s,3]:[this.undefinedColor,r,s,3]}if(e[0]?.toLowerCase()==e[0]&&e.substring(1,3)in this.AAFullNames&&(4==e.length||"("==e[4])){const t=this.AAFullNames[e.substring(1,3)];return t in n?[n.get(t),t,s,4]:[this.undefinedColor,r,s,4]}return[this.undefinedColor,r,s,0]}}R.SemType="Aminoacids",R.SemTypeMultipleAlignment="AminoacidsMultipleAlignment",R.undefinedColor="rgb(100,100,100)",R.Names={G:"Glycine",L:"Leucine",Y:"Tyrosine",S:"Serine",E:"Glutamic acid",Q:"Glutamine",D:"Aspartic acid",N:"Asparagine",F:"Phenylalanine",A:"Alanine",K:"Lysine",R:"Arginine",H:"Histidine",C:"Cysteine",V:"Valine",P:"Proline",W:"Tryptophan",I:"Isoleucine",M:"Methionine",T:"Threonine"},R.AASmiles={G:"NCC(=O)O",L:"N[C@H](CC(C)C)C(=O)O",Y:"NC(CC1=CC=C(O)C=C1)C(=O)O",S:"NC(CO)C(=O)O",E:"N[C@@H](CCC(O)=O)C(=O)O",Q:"N[C@@H](CCC(N)=O)C(=O)O",D:"N[C@@H](CC(O)=O)C(=O)O",N:"N[C@@H](CC(N)=O)C(=O)O",F:"NC(CC1=CC=CC=C1)C(=O)O",A:"N[C@H](C)C(=O)O",K:"NC(CCCCN)C(=O)O",R:"N[C@H](CCCNC(=N)C)C(=O)O",H:"NC(CC1=CN=C[N]1)C(=O)O",C:"N[C@@H](CS)C(=O)O",V:"NC(C(C)C)C(=O)O",P:"N(CCC1)C1C(=O)O",W:"N[C@@H](Cc1c2ccccc2n([H])c1)C(=O)O",I:"N[C@H]([C@H](C)CC)C(=O)O",M:"NC(CCSC)C(=O)O",T:"NC(C(O)C)C(=O)O"},R.AASmilesTruncated={G:"*C*",L:"CC(C)C[C@H](*)*",Y:"C1=CC(=CC=C1CC(*)*)O",S:"OCC(*)C*",E:"*[C@@H](CCC(O)=O)*",Q:"*N[C@@H](CCC(N)=O)*",D:"*[C@@H](CC(O)=O)*",N:"*[C@@H](CC(N)=O)*",F:"C1=CC=C(C=C1)CC(*)*",A:"C[C@H](*)*",K:"C(CCN)CC(*)*",R:"*[C@H](CCCNC(=N)C)*",H:"C1=C(NC=N1)CC(*)*",C:"C([C@@H](*)*)S",V:"CC(C)C(*)*",P:"C1CCN(*)C1*",W:"*[C@@H](Cc1c2ccccc2n([H])c1)*",I:"CC[C@H](C)[C@H](*)*",M:"CSCCC(*)*",T:"CC(O)C(*)*"},R.AAFullNames={Ala:"A",Arg:"R",Asn:"N",Asp:"D",Cys:"C",Gln:"Q",Glu:"E",Gly:"G",His:"H",Ile:"I",Leu:"L",Lys:"K",Met:"M",Phe:"F",Pro:"P",Ser:"S",Thr:"T",Trp:"W",Tyr:"Y",Val:"V"};class D{}D.SemType="Nucleotides",D.SemTypeMultipleAlignment="NucleotidesMultipleAlignment",D.Names={A:"Adenine",C:"Cytosine",G:"Guanine",T:"Thymine",U:"Uracil"};class x extends class{}{static buildPalette(){return[].concat(...Object.values(L.colourPalette))}get(e){const t=class{static hashCode(e){let t=0;if(0===e.length)return t;for(let n=0;n<e.length;n++)t=(t<<5)-t+e.charCodeAt(n),t|=0;return t}}.hashCode(e)%x.palette.length;return function(e){if(null==e)return"rgb(100,100,100)";const t=n.Color.fromHtml(e),r=n.Color.g(t),s=n.Color.r(t),o=n.Color.b(t),i=Math.sqrt(Math.pow(0-s,2)+Math.pow(0-r,2)+Math.pow(0-o,2));return i>210?`rgb(${s/i*210},${r/i*210},${o/i*210})`:n.Color.toRgb(t)}(x.palette[t])}}x.palette=x.buildPalette();new Uint32Array(65536);var F,_;(_=F||(F={})).HAMMING="Hamming",_.LEVENSHTEIN="Levenshtein",_.NEEDLEMANN_WUNSCH="Needlemann-Wunsch",F.HAMMING,F.LEVENSHTEIN,F.NEEDLEMANN_WUNSCH,new class{constructor(){this.uhTemp=`units-handler.${n.SEMTYPE.MACROMOLECULE}`}},S.FASTA,S.SEPARATOR,S.HELM;var V=function(e,t,n,r){return new(n||(n=Promise))((function(s,o){function i(e){try{a(r.next(e))}catch(e){o(e)}}function l(e){try{a(r.throw(e))}catch(e){o(e)}}function a(e){var t;e.done?s(e.value):(t=e.value,t instanceof n?t:new n((function(e){e(t)}))).then(i,l)}a((r=r.apply(e,t||[])).next())}))};const W="Libraries",U={"HELMCoreLibrary.json":"HELMCoreLibrary.json"};m("findMonomers",(()=>{let e,t=null;E((()=>V(void 0,void 0,void 0,(function*(){e=yield async function(){const e=n.Func.find({package:"Bio",name:"getMonomerLibHelper"});if(0===e.length)throw new Error('Package "Bio" must be installed for MonomerLibHelper.');return(await e[0].prepare().call()).getOutputParamValue()}(),t=yield r.dapi.userDataStorage.get(W,!0),yield r.dapi.userDataStorage.post(W,U,!0),yield e.loadLibraries(!0)})))),b((()=>V(void 0,void 0,void 0,(function*(){yield r.dapi.userDataStorage.put(W,t,!0)}))));const s={withoutMissed:{test:"PEPTIDE1{meI.hHis.Aca.N.T.dE.Thr_PO3H2.Aca.D-Tyr_Et}$$$$",tgt:new Set},withMissed:{test:"PEPTIDE1{meI.missed2.Aca.N.T.dE.Thr_PO3H2.Aca.D-Tyr_Et}$$$$",tgt:new Set(["missed2"])}};for(const[e,t]of Object.entries(s))C(e,(()=>V(void 0,void 0,void 0,(function*(){o(t.test,t.tgt)}))));function o(e,t){h(function(e){const t=Object.keys(org.helm.webeditor.monomerTypeList()),n=[],r=[];for(let e=0;e<t.length;e++)n.push(new scil.helm.Monomers.getMonomerSet(t[e])),Object.keys(n[e]).forEach((t=>{r.push(n[e][t].id)}));return new Set(e.filter((e=>!r.includes(e))))}(T(e)),t)}}));const j=$;var Y=e.n(j),K=function(e,t,n,r){return new(n||(n=Promise))((function(s,o){function i(e){try{a(r.next(e))}catch(e){o(e)}}function l(e){try{a(r.throw(e))}catch(e){o(e)}}function a(e){var t;e.done?s(e.value):(t=e.value,t instanceof n?t:new n((function(e){e(t)}))).then(i,l)}a((r=r.apply(e,t||[])).next())}))};m("renderers",(()=>{C("missedInLib",(()=>K(void 0,void 0,void 0,(function*(){yield function(){return K(this,void 0,void 0,(function*(){const e=yield r.dapi.files.readCsv("System:AppData/Helm/tests/sample_HELM-missedInLib.csv"),t=e.getCol("HELM"),o=r.shell.addTableView(e);yield function(e,t="Timeout exceeded",n=500,r=50){return s(this,void 0,void 0,(function*(){return new Promise(((s,o)=>{setTimeout((()=>{clearInterval(i),o(new Error(t))}),n);const i=setInterval((()=>{e()&&(clearInterval(i),s())}),r)}))}))}((()=>Y()(o.root).find(".d4-grid canvas").length>0),"Table view canvas not found",100),g(t.semType,n.SEMTYPE.MACROMOLECULE),g(t.getTag(n.TAGS.UNITS),S.HELM),g(t.getTag(n.TAGS.CELL_RENDERER),"helm");const i=t.getTag(".cell-renderer.render.error");if(i){const e=JSON.parse(i),t=new Error(e.message);throw t.stack=e.stack,t}}))}()}))))}));const Q=new n.Package;function B(e,t,a){return c=this,C=void 0,f=function*(){const c=yield function(e){var t,a,c,C,g;return s(this,void 0,void 0,(function*(){const f=null===(a=null===(t=r.functions.getCurrentCall())||void 0===t?void 0:t.func)||void 0===a?void 0:a.package;yield function(e,t){return s(this,void 0,void 0,(function*(){if(l[e])return;const t=o;if(void 0!==t["Auto Tests"]||Object.keys(t).find((e=>e.startsWith(i))))return void(l[e]=!0);const n=[],a=yield r.dapi.functions.filter(`package.id = "${e}"`).list(),c=new RegExp(/skip:\s*([^,\s]+)|wait:\s*(\d+)|cat:\s*([^,\s]+)/g);for(const e of a){const o=e.options.test;if(o&&Array.isArray(o)&&o.length)for(let l=0;l<o.length;l++){const a=o[l].matchAll(c),u={};Array.from(a).forEach((e=>{e[0].startsWith("skip")?u.skip=e[1]:e[0].startsWith("wait")?u.wait=parseInt(e[2]):e[0].startsWith("cat")&&(u.cat=e[3])}));const C=new d(i,1===o.length?e.name:`${e.name} ${l+1}`,(()=>s(this,void 0,void 0,(function*(){const t=yield r.functions.eval(A(o[l],e));if(u.wait&&(yield N(u.wait)),"boolean"==typeof t&&!t)throw`Failed: ${o[l]}, expected true, got ${t}`}))),{skipReason:u.skip});if(u.cat){const e="Auto Tests: "+u.cat;C.category=e,void 0===t[e]&&(t[e]={tests:[],clear:!0}),t[e].tests.push(C)}else n.push(C)}}l[e]=!0,n.length&&(t["Auto Tests"]={tests:n,clear:!0})}))}(f.id);const h=[];console.log("Running tests"),null!=e||(e={}),null!==(c=(g=e).testContext)&&void 0!==c||(g.testContext=new u),r.shell.lastError="";for(const[t,s]of Object.entries(o)){if(null!=(null==e?void 0:e.category)&&!t.toLowerCase().startsWith(null==e?void 0:e.category.toLowerCase()))continue;console.log(`Started ${t} category`);try{s.before&&(yield s.before())}catch(e){s.beforeStatus=e.toString()}const o=null!==(C=s.tests)&&void 0!==C?C:[],i=[];if(s.clear)for(let t=0;t<o.length;t++)i.push(yield y(o[t],null==e?void 0:e.test,s.timeout)),r.shell.closeAll(),n.Balloon.closeAll();else for(let t=0;t<o.length;t++)i.push(yield y(o[t],null==e?void 0:e.test,s.timeout));const l=(yield Promise.all(i)).filter((e=>"skipped"!=e.result));try{s.after&&(yield s.after())}catch(e){s.afterStatus=e.toString()}s.afterStatus&&l.push({category:t,name:"init",result:s.afterStatus,success:!1,ms:0,skipped:!1}),s.beforeStatus&&l.push({category:t,name:"init",result:s.beforeStatus,success:!1,ms:0,skipped:!1}),h.push(...l)}if(e.testContext.catchUnhandled&&(yield N(1e3),r.shell.lastError.length>0&&h.push({category:"Unhandled exceptions",name:"exceptions",result:r.shell.lastError,success:!1,ms:0,skipped:!1})),e.testContext.report){const e=new n.Logger,t=h.filter((e=>e.success)).length,r=h.filter((e=>e.skipped)).length,s=h.filter((e=>!e.success)),o="Package @package tested: @successful successful, @skipped skipped, @failed failed tests",i={successful:t,skipped:r,failed:s.length,package:f};for(const e of s)Object.assign(i,{[`${e.category} | ${e.name}`]:e.result});e.log(o,i,"package-tested")}return h}))}({category:e,test:t,testContext:a});return n.DataFrame.fromObjects(c)},new((g=void 0)||(g=Promise))((function(e,t){function n(e){try{s(f.next(e))}catch(e){t(e)}}function r(e){try{s(f.throw(e))}catch(e){t(e)}}function s(t){var s;t.done?e(t.value):(s=t.value,s instanceof g?s:new g((function(e){e(s)}))).then(n,r)}s((f=f.apply(c,C||[])).next())}));var c,C,g,f}helm_test=t})();
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