@datagrok/sequence-translator 1.4.1 → 1.4.2

package/dist/package.js

@@ -1,3 +1,3 @@
 /*! For license information please see package.js.LICENSE.txt */
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Uint32Array(65536),p={gapOpen:1,gapExtend:.6,scoringMatrix:[[4,-1,-2,-2,0,-1,-1,0,-2,-1,-1,-1,-1,-2,-1,1,0,-3,-2,0,-2,-1,0,-4],[-1,5,0,-2,-3,1,0,-2,0,-3,-2,2,-1,-3,-2,-1,-1,-3,-2,-3,-1,0,-1,-4],[-2,0,6,1,-3,0,0,0,1,-3,-3,0,-2,-3,-2,1,0,-4,-2,-3,3,0,-1,-4],[-2,-2,1,6,-3,0,2,-1,-1,-3,-4,-1,-3,-3,-1,0,-1,-4,-3,-3,4,1,-1,-4],[0,-3,-3,-3,9,-3,-4,-3,-3,-1,-1,-3,-1,-2,-3,-1,-1,-2,-2,-1,-3,-3,-2,-4],[-1,1,0,0,-3,5,2,-2,0,-3,-2,1,0,-3,-1,0,-1,-2,-1,-2,0,3,-1,-4],[-1,0,0,2,-4,2,5,-2,0,-3,-3,1,-2,-3,-1,0,-1,-3,-2,-2,1,4,-1,-4],[0,-2,0,-1,-3,-2,-2,6,-2,-4,-4,-2,-3,-3,-2,0,-2,-2,-3,-3,-1,-2,-1,-4],[-2,0,1,-1,-3,0,0,-2,8,-3,-3,-1,-2,-1,-2,-1,-2,-2,2,-3,0,0,-1,-4],[-1,-3,-3,-3,-1,-3,-3,-4,-3,4,2,-3,1,0,-3,-2,-1,-3,-1,3,-3,-3,-1,-4],[-1,-2,-3,-4,-1,-2,-3,-4,-3,2,4,-2,2,0,-3,-2,-1,-2,-1,1,-4,-3,-1,-4],[-1,2,0,-1,-3,1,1,-2,-1,-3,-2,5,-1,-3,-1,0,-1,-3,-2,-2,0,1,-1,-4],[-1,-1,-2,-3,-1,0,-2,-3,-2,1,2,-1,5,0,-2,-1,-1,-1,-1,1,-3,-1,-1,-4],[-2,-3,-3,-3,-2,-3,-3,-3,-1,0,0,-3,0,6,-4,-2,-2,1,3,-1,-3,-3,-1,-4],[-1,-2,-2,-1,-3,-1,-1,-2,-2,-3,-3,-1,-2,-4,7,-1,-1,-4,-3,-2,-2,-1,-2,-4],[1,-1,1,0,-1,0,0,0,-1,-2,-2,0,-1,-2,-1,4,1,-3,-2,-2,0,0,0,-4],[0,-1,0,-1,-1,-1,-1,-2,-2,-1,-1,-1,-1,-2,-1,1,5,-2,-2,0,-1,-1,0,-4],[-3,-3,-4,-4,-2,-2,-3,-2,-2,-3,-2,-3,-1,1,-4,-3,-2,11,2,-3,-4,-3,-2,-4],[-2,-2,-2,-3,-2,-1,-2,-3,2,-1,-1,-2,-1,3,-3,-2,-2,2,7,-1,-3,-2,-1,-4],[0,-3,-3,-3,-1,-2,-2,-3,-3,3,1,-2,1,-1,-2,-2,0,-3,-1,4,-3,-2,-1,-4],[-2,-1,3,4,-3,0,1,-1,0,-3,-4,0,-3,-3,-2,0,-1,-4,-3,-3,4,1,-1,-4],[-1,0,0,1,-3,3,4,-2,0,-3,-3,1,-1,-3,-1,0,-1,-3,-2,-2,1,4,-1,-4],[0,-1,-1,-1,-2,-1,-1,-1,-1,-1,-1,-1,-1,-1,-2,0,0,-2,-1,-1,-1,-1,-1,-4],[-4,-4,-4,-4,-4,-4,-4,-4,-4,-4,-4,-4,-4,-4,-4,-4,-4,-4,-4,-4,-4,-4,-4,1]],alphabetIndexes:{A:0,R:1,N:2,D:3,C:4,Q:5,E:6,G:7,H:8,I:9,L:10,K:11,M:12,F:13,P:14,S:15,T:16,W:17,Y:18,V:19,B:20,Z:21,X:22,"*":23}};var g;!function(t){t.HAMMING="Hamming",t.LEVENSHTEIN="Levenshtein",t.NEEDLEMANN_WUNSCH="Needlemann-Wunsch",t.MONOMER_CHEMICAL_DISTANCE="Monomer chemical distance"}(g||(g={}));const m={[g.HAMMING]:f,[g.LEVENSHTEIN]:function(){return(t,e)=>((t,e)=>{if(t.length<e.length){const n=e;e=t,t=n}return 0===e.length?t.length:t.length<=32?((t,e)=>{const n=t.length,r=e.length,i=1<<n-1;let o=-1,s=0,a=n,u=n;for(;u--;)d[t.charCodeAt(u)]|=1<<u;for(u=0;u<r;u++){let t=d[e.charCodeAt(u)];const n=t|s;t|=(t&o)+o^o,s|=~(t|o),o&=t,s&i&&a++,o&i&&a--,s=s<<1|1,o=o<<1|~(n|s),s&=n}for(u=n;u--;)d[t.charCodeAt(u)]=0;return a})(t,e):((t,e)=>{const n=e.length,r=t.length,i=[],o=[],s=Math.ceil(n/32),a=Math.ceil(r/32);for(let t=0;t<s;t++)o[t]=-1,i[t]=0;let u=0;for(;u<a-1;u++){let s=0,a=-1;const l=32*u,c=Math.min(32,r)+l;for(let e=l;e<c;e++)d[t.charCodeAt(e)]|=1<<e;for(let t=0;t<n;t++){const n=d[e.charCodeAt(t)],r=o[t/32|0]>>>t&1,u=i[t/32|0]>>>t&1,l=n|s,c=((n|u)&a)+a^a|n|u;let h=s|~(c|a),f=a&c;h>>>31^r&&(o[t/32|0]^=1<<t),f>>>31^u&&(i[t/32|0]^=1<<t),h=h<<1|r,f=f<<1|u,a=f|~(l|h),s=h&l}for(let e=l;e<c;e++)d[t.charCodeAt(e)]=0}let l=0,c=-1;const h=32*u,f=Math.min(32,r-h)+h;for(let e=h;e<f;e++)d[t.charCodeAt(e)]|=1<<e;let p=r;for(let t=0;t<n;t++){const n=d[e.charCodeAt(t)],s=o[t/32|0]>>>t&1,a=i[t/32|0]>>>t&1,u=n|l,h=((n|a)&c)+c^c|n|a;let f=l|~(h|c),g=c&h;p+=f>>>r-1&1,p-=g>>>r-1&1,f>>>31^s&&(o[t/32|0]^=1<<t),g>>>31^a&&(i[t/32|0]^=1<<t),f=f<<1|s,g=g<<1|a,c=g|~(u|f),l=f&u}for(let e=h;e<f;e++)d[t.charCodeAt(e)]=0;return p})(t,e)})(t,e)/Math.max(t.length,e.length)},[g.NEEDLEMANN_WUNSCH]:function(t){const e=new Uint16Array(65536),{gapOpen:n,gapExtend:r,scoringMatrix:i,alphabetIndexes:o}={...p,...t};Object.entries(o).forEach((([t,n])=>e[t.charCodeAt(0)]=n));const s=[new Float32Array(1e4),new Float32Array(1e4)];return(t,o)=>{const a=new Array(t.length+1).fill(!1),u=new Array(t.length+1).fill(!1);let l=0,c=1;for(let e=1;e<t.length+1;e++)s[0][e]=-r-(e-1)*r,s[1][e]=0;s[0][0]=0;for(let h=1;h<o.length+1;h++){s[c][0]=-r-(h-1)*r;for(let f=1;f<t.length+1;f++){const d=s[l][f-1]+i[e[t.charCodeAt(f-1)]][e[o.charCodeAt(h-1)]],p=s[l][f]-(a[f]||1===h||h===o.length?r:n),g=s[c][f-1]-(u[f-1]||1===f||f===t.length?r:n);s[c][f]=Math.max(d,g,p),s[c][f]===d?(a[f]=!1,u[f]=!1):s[c][f]===g?(a[f]=!1,u[f]=!0):(a[f]=!0,u[f]=!1)}l=c,c=(c+1)%2}const h=Math.min(t.length,o.length);return(h-s[l][t.length])/h}},[g.MONOMER_CHEMICAL_DISTANCE]:f};a.Tanimoto,a.Dice,a.Asymmetric,a.BraunBlanquet,a.Cosine,a.Kulczynski,a.McConnaughey,a.RogotGoldberg,a.Russel,a.Sokal,a.Hamming,a.Euclidean,a.Tanimoto,a.Dice,a.Asymmetric,a.BraunBlanquet,a.Cosine,a.Kulczynski,a.McConnaughey,a.RogotGoldberg,a.Russel,a.Sokal,a.Hamming,a.Euclidean,a.Tanimoto,a.Dice,a.Cosine,a.Tanimoto,a.Asymmetric,a.Cosine,a.Sokal,g.HAMMING,g.LEVENSHTEIN,g.MONOMER_CHEMICAL_DISTANCE,g.NEEDLEMANN_WUNSCH;const v={monomerType:"Backbone",smiles:"",name:"",author:"Datagrok",molfile:"",naturalAnalog:"",rgroups:[],createDate:null,id:0,polymerType:"PEPTIDE",symbol:""},y="p",b=new RegExp(`[rd]\\((\\w)\\)${y}?`,"g");class w{constructor(t,e,n){this.name=t,this.alphabet=e,this.cutoff=n}}class C extends w{constructor(t,e,n){super(t.name,t.alphabet,t.cutoff),this.freq=e,this.similarity=n}}const A=wu;var x,_,E,S,T,I=n.n(A);(T=x||(x={})).FASTA="fasta",T.SEPARATOR="separator",T.HELM="helm",(S=_||(_={})).DNA="DNA",S.RNA="RNA",S.PT="PT",S.UN="UN",function(t){t.aligned="aligned",t.alphabet="alphabet",t.alphabetSize=".alphabetSize",t.alphabetIsMultichar=".alphabetIsMultichar",t.separator="separator",t.isHelmCompatible=".isHelmCompatible",t.positionNames=".positionNames",t.positionLabels=".positionLabels",t.regions=".regions"}(E||(E={}));const N=/(?:\[([A-Za-z0-9_\-,()]+)\])|([A-Za-z\-])/g,O=new class{constructor(){this.fasta={peptide:new Set(["G","L","Y","S","E","Q","D","N","F","A","K","R","H","C","V","P","W","I","M","T"]),dna:new Set(["A","C","G","T"]),rna:new Set(["A","C","G","U"])}}},M=[new w(_.PT,O.fasta.peptide,.5),new w(_.DNA,O.fasta.dna,.55),new w(_.RNA,O.fasta.rna,.55)];class L extends Float32Array{}function B(t){let e=0;for(let n=0;n<t.length;n++)e+=t[n]*t[n];return Math.sqrt(e)}class P{static makePalette(t,e=!1,n=P){const r={};return t.forEach((t=>{const n=t[0],i=t[1];n.forEach(((t,n)=>{r[t]=this.colourPalette[i][e?0:n]}))})),new n(r)}constructor(t){this._palette=t}get(t){return this._palette[t]}}P.undefinedColor="rgb(100,100,100)",P.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 R extends P{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,R)),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,R)),this.grokGroups}static get RasMol(){return void 0===this.rasMol&&(this.rasMol=new R({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 R.aaSynonyms?R.aaSynonyms[t]:t;return super.get(e)}}R.aaSynonyms={MeNle:"L",MeA:"A",MeG:"G",MeF:"F"};class D{static getPalette(t="grok"){switch(t){case"grok":return R.GrokGroups;case"lesk":return R.Lesk;default:throw new Error(`ChemPalette: scheme \`${t}\` does not exist`)}}static getInnerOuter(t){let e=0,n="",r="";for(const i of t)"("==i?e++:")"==i?e--:e?n+=i:r+=i;return isNaN(parseInt(n))?[r,n]:[r,""]}static getColorAAPivot(t="",e="grok"){const n=this.getPalette(e);let[r,i]=this.getInnerOuter(t);if(r=r.length>6?`${r.slice(0,3)}...`:r,i=i.length>6?`${i.slice(0,3)}...`:i,1==t.length||"("==t[1]){const e=t[0]?.toUpperCase();return e in n?[n.get(e),e,i,1]:[this.undefinedColor,r,i,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,i,2]:[this.undefinedColor,r,i,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,i,3]:[this.undefinedColor,r,i,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,i,4]:[this.undefinedColor,r,i,4]}return[this.undefinedColor,r,i,0]}}D.SemType="Aminoacids",D.SemTypeMultipleAlignment="AminoacidsMultipleAlignment",D.undefinedColor="rgb(100,100,100)",D.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"},D.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"},D.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(*)*"},D.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 F{}F.SemType="Nucleotides",F.SemTypeMultipleAlignment="NucleotidesMultipleAlignment",F.Names={A:"Adenine",C:"Cytosine",G:"Guanine",T:"Thymine",U:"Uracil"};class k{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}}class H{}class U extends H{static buildPalette(){return[].concat(...Object.values(P.colourPalette))}get(t){const n=k.hashCode(t)%U.palette.length;return function(t){if(null==t)return"rgb(100,100,100)";const n=e.Color.fromHtml(t),r=e.Color.g(n),i=e.Color.r(n),o=e.Color.b(n),s=Math.sqrt(Math.pow(0-i,2)+Math.pow(0-r,2)+Math.pow(0-o,2));return s>210?`rgb(${i/s*210},${r/s*210},${o/s*210})`:e.Color.toRgb(n)}(U.palette[n])}}U.palette=U.buildPalette();class V{get length(){return this.mList.length}get canonicals(){return this.mList}get originals(){return this.mList}isGap(t){return this.getOriginal(t)===this.gapOriginalMonomer}getCanonical(t){if(this.length<=t)throw new Error("Index out of bounds");return this.mList[t]}getOriginal(t){if(this.length<=t)throw new Error("Index out of bounds");return this.mList[t]}constructor(t,e){this.mList=t,this.gapOriginalMonomer=e}}class j{get length(){return this.seqS.length}get canonicals(){return this.seqS}get originals(){return this.seqS}isGap(t){return this.getOriginal(t)===X[x.FASTA]}getCanonical(t){if(this.length<=t)throw new Error("Index out of bounds");return this.isGap(t)?"":this.seqS[t]}getOriginal(t){if(this.length<=t)throw new Error("Index out of bounds");return this.seqS[t]}constructor(t){this.seqS=t}}const q=t=>{const e=I()(t.toString().matchAll(N)).map((t=>t[2]??t[1])).toArray();return new V(e,X[x.FASTA])},G=t=>t?new j(t):new V([],X[x.FASTA]);function W(t,e=void 0){return n=>{if(n){let r;const i=new RegExp(String.raw`"-"|'-'|[^${t}]+`,"g");if(void 0!==e){i.lastIndex=0,r=new Array(Math.ceil(e));let t=null,o=0;for(;null!==(t=i.exec(n))&&o<e;)r[o++]=t[0].replace('"-"',"").replace("'-'","");r.splice(o)}else r=n.replaceAll('"-"',"").replaceAll("'-'","").split(t,e);return new V(r,X[x.SEPARATOR])}return new V([],X[x.SEPARATOR])}}const z=/(PEPTIDE1|DNA1|RNA1)\{([^}]+)}/g,Y=/\[([^\[\]]+)]/g,K=t=>{z.lastIndex=0;const e=z.exec(t.toString()),n=e?e[2]:null,r=n?n.split("."):[];return new V(r.map((t=>{Y.lastIndex=0;const e=Y.exec(t);return e&&e.length>=2?e[1]:t})),X[x.HELM])};function J(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 i=[],o=[];for(const n of r)i.push(n in t?t[n]:0),o.push(e.has(n)?1:0);const s=new L(i),a=new L(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}(s,a)/(B(s)*B(a))}(t,e.alphabet,n);return new C(e,t,r)}));let i;const o=Math.max(...r.map((t=>t.similarity>t.cutoff?t.similarity:-1)));return i=o>0?r.find((t=>t.similarity===o)).name:_.UN,i}const Q=new class{constructor(){this.seqHandler="seq-handler",this.notationProvider="seq-handler.notation-provider"}},X={[x.FASTA]:"-",[x.SEPARATOR]:"",[x.HELM]:"*"};class Z{constructor(t){if(this._splitter=null,this.cached=!0,this._splitted=null,this.columnVersion=null,this._stats=null,this._maxLength=null,this._posList=null,this._joiner=void 0,t.type!==e.TYPE.STRING)throw new Error(`Unexpected column type '${t.type}', must be '${e.TYPE.STRING}'.`);this._column=t;const n=this._column.meta.units;if(null==n)throw new Error("Units are not specified in column");if(this._units=n,this._notation=this.getNotation(),this._defaultGapOriginal=this.isFasta()?X[x.FASTA]:this.isHelm()?X[x.HELM]:X[x.SEPARATOR],!this.column.tags.has(E.aligned)||!this.column.tags.has(E.alphabet)||!this.column.tags.has(E.alphabetIsMultichar)&&!this.isHelm()&&this.alphabet===_.UN)if(this.isFasta())Z.setUnitsToFastaColumn(this);else if(this.isSeparator()){const e=t.getTag(E.separator);Z.setUnitsToSeparatorColumn(this,e)}else{if(!this.isHelm())throw new Error(`Unexpected units '${this.column.meta.units}'.`);Z.setUnitsToHelmColumn(this)}if(!this.column.tags.has(E.alphabetIsMultichar))if(this.isHelm())this.column.setTag(E.alphabetIsMultichar,"true");else if(["UN"].includes(this.alphabet))throw new Error(`For column '${this.column.name}' of alphabet '${this.alphabet}' tag '${E.alphabetIsMultichar}' is mandatory.`);this.notationProvider=this.column.temp[Q.notationProvider]??null,this.columnVersion=this.column.version}static setUnitsToFastaColumn(t){if(t.column.semType!==e.SEMTYPE.MACROMOLECULE||t.column.meta.units!==x.FASTA)throw new Error(`The column of notation '${x.FASTA}' must be '${e.SEMTYPE.MACROMOLECULE}'.`);t.column.meta.units=x.FASTA,Z.setTags(t)}static setUnitsToSeparatorColumn(t,n){if(t.column.semType!==e.SEMTYPE.MACROMOLECULE||t.column.meta.units!==x.SEPARATOR)throw new Error(`The column of notation '${x.SEPARATOR}' must be '${e.SEMTYPE.MACROMOLECULE}'.`);if(!n)throw new Error(`The column of notation '${x.SEPARATOR}' must have the separator tag.`);t.column.meta.units=x.SEPARATOR,t.column.setTag(E.separator,n),Z.setTags(t)}static setUnitsToHelmColumn(t){if(t.column.semType!==e.SEMTYPE.MACROMOLECULE)throw new Error(`The column of notation '${x.HELM}' must be '${e.SEMTYPE.MACROMOLECULE}'`);t.column.meta.units=x.HELM,Z.setTags(t)}static setTags(t){const e=t.column.meta.units;if([x.FASTA,x.SEPARATOR].includes(e)){if(!t.column.getTag(E.alphabet)&&0===Object.keys(t.stats.freq).length)throw new Error("Alphabet is empty and not annotated.");let e=t.column.getTag(E.aligned);null===e&&(e=t.stats.sameLength?"SEQ.MSA":"SEQ",t.column.setTag(E.aligned,e));let n=t.column.getTag(E.alphabet);if(null===n&&(n=J(t.stats.freq,M),t.column.setTag(E.alphabet,n)),n===_.UN){const e=Object.keys(t.stats.freq).length,n=Object.keys(t.stats.freq).some((t=>t.length>1));t.column.setTag(E.alphabetSize,e.toString()),t.column.setTag(E.alphabetIsMultichar,n?"true":"false")}}}get column(){return this._column}get length(){return this._column.length}get units(){return this._units}get notation(){return this._notation}get defaultGapOriginal(){return this._defaultGapOriginal}get separator(){const t=this.column.getTag(E.separator)??void 0;if(this.notation===x.SEPARATOR&&void 0===t)throw new Error(`Separator is mandatory  for column '${this.column.name}' of notation '${this.notation}'.`);return t}get aligned(){const t=this.column.getTag(E.aligned);if(!t&&(this.isFasta()||this.isSeparator()))throw new Error("Tag aligned not set");return t}get alphabet(){const t=this.column.getTag(E.alphabet);if(!t&&(this.isFasta()||this.isSeparator()))throw new Error("Tag alphabet not set");return t}get helmCompatible(){return this.column.getTag(E.isHelmCompatible)}getAlphabetSize(){if(this.notation==x.HELM||this.alphabet==_.UN){const t=this.column.getTag(E.alphabetSize);let e;if(t)e=parseInt(t);else{const t=this.stats;e=Object.keys(t.freq).length}return e}switch(this.alphabet){case _.PT:return 20;case _.DNA:case _.RNA:return 4;case"NT":return console.warn("Unexpected alphabet 'NT'."),4;default:throw new Error(`Unexpected alphabet '${this.alphabet}'.`)}}getAlphabetIsMultichar(){return this.notation===x.HELM||this.alphabet===_.UN&&"true"===this.column.getTag(E.alphabetIsMultichar)}getSplitted(t,e){if(this.cached&&void 0===e){this.column.version===this.columnVersion&&null!==this._splitted||(this.columnVersion=this.column.version,this._splitted=new Array(this.column.length));let e=this._splitted[t]?this._splitted[t].deref():void 0;if(!e){const n=this.column.get(t);e=this.splitter(n),this._splitted[t]=new WeakRef(e)}return e}{const n=this.column.get(t);return this.getSplitter(e)(n)}}async getHelm(t,e){const n=this.column.get(t);return this.notationProvider?(await this.notationProvider.getHelm(this.column,e)).get(t):this.convertToHelm(n)}get stats(){if(null===this._stats){const t={};let e=!0,n=null;const r=this.column.length;for(let i=0;i<r;++i){const r=this.getSplitted(i);null==n?n=r.length:r.length!==n&&(e=!1);for(const e of r.canonicals)e in t||(t[e]=0),t[e]+=1}this._stats={freq:t,sameLength:e}}return this._stats}get maxLength(){return null===this._maxLength&&(this._maxLength=0===this.column.length?0:Math.max(...I().count(0).take(this.column.length).map((t=>this.getSplitted(t).length)))),this._maxLength}get posList(){if(null===this._posList){const t=this.column.getTag(E.positionNames);this._posList=t?t.split(", ").map((t=>t.trim())):I().count(1).take(this.maxLength).map((t=>t.toString())).toArray()}return this._posList}isFasta(){return this.notation===x.FASTA}isSeparator(){return this.notation===x.SEPARATOR}isHelm(){return this.notation===x.HELM}isRna(){return this.alphabet===_.RNA}isDna(){return this.alphabet===_.DNA}isPeptide(){return this.alphabet===_.PT}isMsa(){return!!this.aligned&&this.aligned.toUpperCase().includes("MSA")}isHelmCompatible(){return"true"===this.helmCompatible}isGap(t){return!t||t===this._defaultGapOriginal}getNotation(){if(this.units.toLowerCase().startsWith(x.FASTA))return x.FASTA;if(this.units.toLowerCase().startsWith(x.SEPARATOR))return x.SEPARATOR;if(this.units.toLowerCase().startsWith(x.HELM))return x.HELM;throw new Error(`Column '${this.column.name}' has unexpected notation '${this.units}'.`)}getHelmWrappers(){return[this.isDna()||this.isRna()||this.isHelmCompatible()?"RNA1{":"PEPTIDE1{",this.isDna()?"d(":this.isRna()?"r(":"",this.isDna()||this.isRna()?")p":"","}$$$$"]}getNewColumn(t,n,r,i){const o=this.column,s=t.toLowerCase()+"("+o.name+")",a=r??o.dataFrame.columns.getUnusedName(s),u=e.Column.fromList("string",a,i??new Array(this.column.length).fill(""));if(u.semType=e.SEMTYPE.MACROMOLECULE,u.meta.units=t,t===x.SEPARATOR){if(!n)throw new Error(`Notation '${x.SEPARATOR}' requires separator value.`);u.setTag(E.separator,n)}u.setTag(e.TAGS.CELL_RENDERER,t===x.HELM?"helm":"sequence");const l=o.getTag(E.aligned);l&&u.setTag(E.aligned,l);let c=o.getTag(E.alphabet);c||this.notation!==x.HELM||t===x.HELM||(c=_.UN),null!=c&&u.setTag(E.alphabet,c);let h=o.getTag(E.alphabetSize);null!=c&&h&&u.setTag(E.alphabetSize,h);const f=o.getTag(E.alphabetIsMultichar);return null!=c&&void 0!==f&&u.setTag(E.alphabetIsMultichar,f),t==x.HELM&&(h=this.getAlphabetSize().toString(),u.setTag(E.alphabetSize,h)),u}getNewColumnFromList(t,e){return this.getNewColumn(this.notation,this.separator,t,e)}static getNewColumn(t){const e=Z.forColumn(t),n=e.notation;return e.getNewColumn(n)}static unitsStringIsValid(t){return t=t.toLowerCase(),[x.FASTA,x.SEPARATOR,x.HELM].some((e=>t.startsWith(e.toLowerCase())))}static getNewColumnFromParams(t,n,r){if(!Z.unitsStringIsValid(r))throw new Error("Invalid format of 'units' parameter");const i=e.Column.fromList("string",n,new Array(t).fill(""));return i.semType=e.SEMTYPE.MACROMOLECULE,i.meta.units=r,i}getSplitter(t){let e=null;if(e=this.notationProvider?this.notationProvider.splitter:null,e)return e;if(this.units.toLowerCase().startsWith(x.FASTA))return null===this.column.getTag(E.alphabet)||this.getAlphabetIsMultichar()?q:G;if(this.units.toLowerCase().startsWith(x.SEPARATOR))return W(this.separator,t);if(this.units.toLowerCase().startsWith(x.HELM))return K;throw new Error(`Unexpected units ${this.units} .`)}split(t){return this.splitter(t)}getDistanceFunctionName(){if(!this.isFasta())throw new Error("Only FASTA notation is supported");if(this.isMsa())return g.HAMMING;switch(this.alphabet){case _.DNA:case _.RNA:case _.PT:}return g.LEVENSHTEIN}getDistanceFunction(){return m[this.getDistanceFunctionName()]()}async checkHelmCompatibility(){if(this.column.tags.has(E.isHelmCompatible))return"true"===this.column.getTag(E.isHelmCompatible);const t=(await nt()).getMonomerLib().getMonomerSymbolsByType("PEPTIDE"),e=new Set(t),n=(W(this.separator),new Set),r=this.column.length,i=this.column.getRawData();for(let t=0;t<r;++t){const r=i[t];if(!(r in n)){n.add(r);const i=this.getSplitted(t);for(const t of i.canonicals)if(!e.has(t))return this.column.setTag(E.isHelmCompatible,"false"),!1}}return this.column.setTag(E.isHelmCompatible,"true"),!0}get splitter(){return null===this._splitter&&(this._splitter=this.getSplitter()),this._splitter}toFasta(t){return t===x.FASTA}toSeparator(t){return t===x.SEPARATOR}toHelm(t){return t===x.HELM}convertHelmToFastaSeparator(t,e,n,r){r||(r=this.toFasta(e)?X[x.FASTA]:X[x.SEPARATOR]),n||(n=this.toFasta(e)?"":this.separator);const i=t.startsWith("RNA"),o=this.splitter(t),s=[];for(let t=0;t<o.length;++t){let n=o.getOriginal(t);if(i&&(n=n.replace(b,"")),n===X[x.HELM])s.push(r);else if(this.toFasta(e)&&n.length>1){const t="["+n+"]";s.push(t)}else s.push(n)}return s.join(n)}convert(t,e){const n=this.getJoiner({notation:t,separator:e}),r=this.getNewColumn(t,e);return r.init((t=>{const e=this.getSplitted(t);return n(e)})),r}getRegion(t,e,n){const r=this.getNewColumn(this.notation,this.separator);r.name=n;const i=t??0,o=e??this.maxLength-1,s=this.getJoiner(),a=o-i+1,u=X[this.notation];r.init((t=>{const e=this.getSplitted(t),n=new Array(a);for(let t=0;t<a;++t){const r=i+t;n[t]=r<e.length?e.getOriginal(r):u}return s(new V(n,u))}));const l=t=>{const e=t.split(",").map((t=>t.trim())),n=new Array(a);for(let t=0;t<a;++t){const r=i+t;n[t]=r<e.length?e[r]:"?"}return n.join(", ")},c=this.column.getTag(E.positionNames);c&&r.setTag(E.positionNames,l(c));const h=this.column.getTag(E.positionLabels);return h&&r.setTag(E.positionLabels,l(h)),r}get joiner(){return this._joiner||(this._joiner=this.getJoiner()),this._joiner}getJoiner(t){const e=t?t.notation:this.notation,n=t?t.separator:this.separator;let r;const i=this;switch(e){case x.FASTA:r=function(t){return i.joinToFasta(t,i.isHelm())};break;case x.SEPARATOR:if(!n)throw new Error(`Separator is mandatory for notation '${e}'.`);r=function(t){return tt(t,n,i.isHelm())};break;case x.HELM:{const t=i.alphabet===_.DNA||i.alphabet===_.RNA,e=i.getHelmWrappers();r=function(n){return et(n,e,t)};break}default:throw new Error(`Unexpected notation '${e}'.`)}return r}getConverter(t,e=void 0){if(t===x.SEPARATOR&&!e)throw new Error(`Target separator is not specified for target units '${x.SEPARATOR}'.`);const n=this;if(t===x.FASTA)return function(t){return n.convertToFasta(t)};if(t===x.HELM)return function(t){return n.convertToHelm(t)};if(t===x.SEPARATOR)return function(t){return n.convertToSeparator(t,e)};throw new Error}static forColumn(t){let e=t.temp[Q.seqHandler];return e&&e.columnVersion===t.version||(e=t.temp[Q.seqHandler]=new Z(t)),e}joinToFasta(t,e){const n=new Array(t.length);for(let r=0;r<t.length;++r){const i=t.getOriginal(r);let o=t.getOriginal(r);e&&(o=o.replace(b,"$1")),""===i?o=X[x.FASTA]:i===y?o="":o.length>1&&(o="["+o+"]"),n[r]=o}return n.join("")}convertToFasta(t){const e=this.splitter,n=this.isHelm()?this.splitterAsHelmNucl(t):e(t);return this.joinToFasta(n,this.isHelm())}convertToSeparator(t,e){return tt(this.isHelm()?this.splitterAsHelmNucl(t):this.splitter(t),e,this.isHelm())}convertToHelm(t){if(this.notation==x.HELM)return t;const e=this.getHelmWrappers(),n=t.startsWith("DNA")||t.startsWith("RNA");return et(this.splitter(t),e,n)}splitterAsHelmNucl(t){const e=this.splitter(t),n=new Array(e.length),r=t.startsWith("DNA"),i=t.startsWith("RNA");for(let t=0;t<e.length;++t){let o=e.getOriginal(t);(r||i)&&(o=o.replace(b,"$1"),o=o===y?null:o),n[t]=o||null}return new V(n.filter((t=>!!t)),X[x.HELM])}}function tt(t,e,n){const r=new Array(t.length);for(let e=0;e<t.length;++e){const i=t.getCanonical(e);let o=t.getOriginal(e);n&&(o=o.replace(b,"$1")),""===i?o=X[x.SEPARATOR]:i===y&&(o=""),r[e]=o}return r.join(e)}function et(t,e,n){const[r,i,o,s]=e,a=new Array(t.length);for(let e=0;e<t.length;++e){const r=t.getCanonical(e);let s=t.getOriginal(e);""===r?s=X[x.HELM]:(n&&(s=s.replace(b,"$1")),s=1===s.length?`${i}${s}${o}`:`${i}[${s}]${o}`),a[e]=s}return`${r}${a.join(".")}${s}`}async function nt(){const t=e.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()}class rt{constructor(t,e,n=""){this.target=t,this.debugEnabled=e,this.prefix=n}error(t,e,n){return this.target.error(this.prefix+t,e,n)}warning(t,e){return this.target.warning(this.prefix+t,e)}info(t,e){return this.target.info(this.prefix+t,e)}debug(t,e){if(this.debugEnabled)return this.target.debug(this.prefix+t,e)}}const it="System:AppData/SequenceTranslator/monomers-sample",ot="pattern-app-data.json",st="formats-to-helm.json",at="codes-to-symbols.json",ut="linkers.json",lt=["A","G","C","U"];var ct;function ht(t){return t.sort(((t,e)=>e.length-t.length))}function ft(t,e){const n=document.createElement("a");n.setAttribute("href","data:text/plain;charset=utf-8,"+e),n.setAttribute("download",t),n.click()}async function dt(e,n,r="Oligo app"){try{return await e()}catch(e){const n=e.hasOwnProperty("message")?e.message:e.toString();throw t.shell.error(`${r} error: `+n),e}finally{n&&n()}}!function(t){t.HELM="HELM",t.AXOLABS="Axolabs"}(ct||(ct={}));class pt{constructor(t,e){this.sequence=t,this.th=e,this.libWrapper=this.th.monomerLibWrapper}getInvalidCodeIndex(t){if(t===ct.HELM)return this.sequence.length;const e=["r","d"],n=ht(this.libWrapper.getCodesByFormat(t));let r=0;for(;r<this.sequence.length;){const t=n.find((t=>t===this.sequence.substring(r,r+t.length)));if(!t)break;if(r>1&&lt.includes(this.sequence[r])&&e.includes(this.sequence[r-2]))break;if(e.includes(this.sequence[r+1])&&lt.includes(this.sequence[r])){r++;break}r+=t.length}return r===this.sequence.length&&(r=-1),r}isValidSequence(t){return-1===this.getInvalidCodeIndex(t)}}class gt{constructor(t,e,n,r){this.patternAppData=t,this.codesToHelmDict=e,this.codesToSymbolsDict=n,this.monomersWithPhosphate=r}}async function mt(e){const n=await Promise.all([ot,st,at,ut].map((n=>async function(e,n){const r=e.endsWith("/")?`${e}${n}`:`${e}/${n}`;try{const e=await t.dapi.files.readAsText(r);return JSON.parse(e)}catch(t){console.error(`Error loading json from '${r}':`,t)}}(e,n))));return new gt(n[0],n[1],n[2],n[3])}class vt{constructor(t,e){if(this.lib=t,this.jsonData=e,null===this.lib)throw new Error("SequenceTranslator: monomer library is null");this.allMonomers=this.getAllMonomers()}formatMonomerForViewer(t){const e={};return e.name=t.symbol,e.symbol=t.symbol,e.molfile=t.molfile,this.getAllFormats().forEach((n=>{if(n===ct.HELM)return;const r=this.jsonData.codesToSymbolsDict[n],i=Object.keys(r).filter((e=>r[e]===t.symbol));e[n]=i.join(", ")})),e}getAllMonomers(){const t=this.lib.getPolymerTypes();let e=[];for(const n of t){const t=this.lib.getMonomerSymbolsByType(n).map((t=>this.lib.getMonomer(n,t))).filter((t=>null!==t));e=e.concat(t)}return e}getMonomer(t){const e=this.lib.getMonomer("RNA",t);if(void 0===e)throw new Error(`SequenceTranslator: no monomer with symbol ${t}`);return e}getMolfileBySymbol(t){return this.getMonomer(t).molfile}getNaturalAnalogBySymbol(t){const e=this.getMonomer(t).naturalAnalog;if(!e)throw new Error(`ST: no natural analog for ${t}`);return e}isModification(t){return!!this.getMolfileBySymbol(t).includes("MODIFICATION")}getCodeToSymbolMap(t){return new Map(Object.entries(this.jsonData.codesToSymbolsDict[t]))}getCodesByFormat(t){return Object.keys(this.jsonData.codesToSymbolsDict[t])}getAllFormats(){return Object.keys(this.jsonData.codesToSymbolsDict)}getTableForViewer(){const t=this.allMonomers.map((t=>this.formatMonomerForViewer(t)));return e.DataFrame.fromObjects(t)}getCodesToWeightsMap(){const t=new Map;return Object.entries(this.jsonData.codesToSymbolsDict).forEach((([e,n])=>{Object.entries(n).forEach((([e,n])=>{const r=this.getMonomer(n),i=r.meta?.molecularWeight;t.set(e,i)}))})),t}}const yt="<?>",bt=(t,e)=>e.length-t.length;class wt{constructor(t){this.th=t,this.formats=this.getFormats()}getFormatNames(){return this.formats.sort()}getCodesByFormat(t){if(this.validateFormat(t),this.isHelm(t))throw new Error("Codes cannot be obtained for HELM");return this.getFormatCodes(t)}getHelmToFormatDict(t){return this.validateFormat(t),function(t){const e={};return Object.values(t).forEach((t=>{Object.entries(t).forEach((([t,n])=>{const r=n.replace(/\)p/g,")").replace(/\]p/g,"]");void 0===e[r]?e[r]=[t]:e[r].push(t)}))})),Object.entries(e).forEach((([t,n])=>{const r=n.sort(bt);e[t]=r[0]})),e}(this.th.jsonData.codesToHelmDict[t])}getFormatToHelmDict(t){this.validateFormat(t);const e=this.th.jsonData.codesToHelmDict[t];return Object.assign({},...Object.values(e))}getTargetFormatHelmCodes(t){this.validateFormat(t);const e=this.getHelmToFormatDict(t);return Object.keys(e).sort(bt)}getTargetFormatHelmCodesRegExp(t){this.validateFormat(t);const e=this.getTargetFormatHelmCodes(t);return new RegExp(Ct(e)+"|.","g")}getFormatRegExp(t){if(this.validateFormat(t),this.isHelm(t))throw new Error("Helm RegExp can be built for non-HELM target formats");return this.getNonHelmFormatRegExp(t)}getPhosphateHelmCodesRegExp(t){this.validateFormat(t);const e=this.th.jsonData.codesToHelmDict[t],n=Ct(Array.from(new Set(Object.values(e.phosphateBackbone))).sort(bt));return new RegExp(`p.(${n})`,"g")}isValidFormat(t){return this.formats.includes(t)}getFormats(){return Object.keys(this.th.jsonData.codesToHelmDict)}validateFormat(t){if(!this.isValidFormat(t))throw new Error(`Invalid format: ${t}`)}isHelm(t){return t===ct.HELM}getFormatCodes(t){const e=this.getFormatToHelmDict(t);return Object.keys(e).sort(bt)}getNonHelmFormatRegExp(t){const e=this.getCodesByFormat(t);return new RegExp(Ct(e)+"|\\([^()]*\\)|.","g")}}function Ct(t){return t.map((t=>t.replace(/[.*+?^${}()|[\]\\]/g,"\\$&"))).map((t=>t.includes("(")||t.includes(")")?t:`(?<!\\([^()]*)${t}(?![^()]*\\))`)).join("|")}const At={LEFT:"RNA1{",RIGHT:"}$$$$"};class xt{constructor(t,e,n){this.sequence=t,this.sourceFormat=e,this.th=n,this.formats=new wt(this.th)}convertTo(t){const e=this.formats.getFormatNames();if(this.sourceFormat===ct.HELM&&e.includes(t))return this.helmToFormat(this.sequence,t);if(e.includes(this.sourceFormat)&&t===ct.HELM)return this.formatToHelm(this.sequence,this.sourceFormat);if([this.sourceFormat,t].every((t=>e.includes(t)))){const e=this.formatToHelm(this.sequence,this.sourceFormat);return this.helmToFormat(e,t)}throw new Error(`ST: unsupported translation direction ${this.sourceFormat} -> ${t}`)}helmToFormat(t,e){const n=new RegExp(Ct(Object.values(At)),"g");let r=t.replace(n,"");const i=this.formats.getHelmToFormatDict(e),o=this.formats.getTargetFormatHelmCodes(e),s=this.formats.getTargetFormatHelmCodesRegExp(e);return r=r.replace(s,(t=>o.includes(t)?i[t]:"p"===t||"."===t?t:"?")).replace(/\?+/g,yt).replace(/p\.|\./g,""),r=r.replace(/<empty>/g,""),r=r.replace(/\/\//g,"/"),r}formatToHelm(t,e){const n=this.formats.getFormatToHelmDict(e),r=this.formats.getCodesByFormat(e),i=this.formats.getFormatRegExp(e),o=this.formats.getPhosphateHelmCodesRegExp(e);let s=t?t.replace(i,(t=>r.includes(t)?n[t]+".":"?")):"";return s=s.replace(/\?+/g,`${yt}.`),s=s.slice(0,-1),"p"===s[s.length-1]&&(s=s.slice(0,-1)),s=s.replace(o,((t,e)=>e)),s=s.replace(/<empty>/g,""),`${At.LEFT+s+At.RIGHT}`}}class _t{constructor(t,e){this.sequence=t,this.th=e,this.libWrapper=this.th.monomerLibWrapper,this.formats=Object.keys(this.th.jsonData.codesToHelmDict)}getFormat(){if(this.sequence.startsWith("RNA"))return ct.HELM;const t=this.getListOfPossibleSynthesizersByFirstMatchedCode();if(0===t.length)return null;const e=this.th.createSequenceValidator(this.sequence),n=Array(t.length).fill(0);for(let r=0;r<t.length;++r){const i=t[r];n[r]=e.getInvalidCodeIndex(i)}const r=n.some((t=>-1===t))?-1:Math.max(...n);return t[n.indexOf(r)]}getListOfPossibleSynthesizersByFirstMatchedCode(){const t=this.sequence,e=[];for(const n of this.formats){const r=ht(this.libWrapper.getCodesByFormat(n));let i=0;for(let e=0;e<t.length;e++)if(")"===t[e]&&e!==t.length-1){i=e+1;break}r.some((e=>e===t.slice(i,i+e.length)))&&e.push(n)}return e}}const Et=ui,St=$;var Tt=n.n(St);function It(t,e){let n=0;const r=e.createFormatDetector(t).getFormat();null!==r&&(n=new pt(t,e).getInvalidCodeIndex(r));const i=n<0||""===t,o=Et.span([]);Tt()(o).css("-webkit-text-fill-color","var(--grey-6)");const s=Et.span([]);return Tt()(s).css("-webkit-text-fill-color","red"),i?o.innerHTML=t:(o.innerHTML=t.slice(0,n),s.innerHTML=t.slice(n)),[o,s]}class Nt extends e.Package{get monomerLib(){if(!this._monomerLib)throw new Error("Monomer lib not loaded");return this._monomerLib}get jsonData(){if(!this._jsonData)throw new Error("Json data not loaded");return this._jsonData}get monomerLibWrapper(){if(!this._monomerLibWrapper)throw new Error("Monomer lib wrapper not loaded");return this._monomerLibWrapper}constructor(t={debug:!1}){super(),this.highlightInvalidSubsequence=t=>It(t,this),super._logger=new rt(super.logger,t.debug)}async initLibData(){return this.initPromise||(this.initPromise=(async()=>{let e=(await this.getSettings()).MonomersPath;e&&await t.dapi.files.exists(e)||(this.logger.warning(`Monomers path '${e}' not found. Fallback to monomers sample path '${it}'.`),e=it),[this._jsonData,this._monomerLib]=await Promise.all([mt(e),Ot(e)]),this._monomerLibWrapper=new vt(this.monomerLib,this.jsonData)})()),this.initPromise}async getTranslationHelper(){return await t.functions.call(`${this.name}:getTranslationHelper`)}createSequenceValidator(t){return new pt(t,this)}createFormatConverter(t,e){return new xt(t,e,this)}createFormatDetector(t){return new _t(t,this)}}async function Ot(t){const n=e.TaskBarProgressIndicator.create("Initializing Oligo Toolkit monomer library ...");try{const e=await nt();return await e.readLibrary(t,"monomer-lib.json")}finally{n.close()}}class Mt{constructor(t,e){this.appName=t,this.parentAppName=e}async getAppView(){const n=e.TaskBarProgressIndicator.create(`Loading ${this.appName}...`),r=t.shell.v?.root;r&&Et.setUpdateIndicator(r,!0);try{return await this.constructView()}finally{n.close(),r&&Et.setUpdateIndicator(r,!1)}}}class Lt extends Mt{constructor(t){super(t),this.view=e.View.create(),this.configureView()}async constructView(){await this.initView();const t=this.parentAppName?this.parentAppName+"/"+this.appName:this.appName;return this.view.path=`/apps/${kr.name}/${t.replace(/\s/g,"")}/`,this.view}async initView(){const t=await this.getContent();this.view.append(t)}configureView(){this.view.box=!0,this.view.name=this.appName;const e=t.shell.windows;e.showProperties=!1,e.showToolbox=!1,e.showHelp=!1}getView(){return this.view}}const Bt=["SS","AS"],Pt={SS:"Sense strand",AS:"Anti sense"},Rt=["3'","5'"],Dt="OligoToolkit";var Ft,kt,Ht,Ut;!function(t){t.IS_ANTISENSE_STRAND_INCLUDED="isAntisenseStrandIncluded",t.NUCLEOTIDE_SEQUENCES="nucleotideSequences",t.PHOSPHOROTHIOATE_LINKAGE_FLAGS="phosphorothioateLinkageFlags",t.STRAND_TERMINUS_MODIFICATIONS="strandTerminusModifications"}(Ft||(Ft={})),function(t){t.PATTERN_NAME="patternName",t.PATTERN_COMMENT="patternComment",t.NUCLEOTIDES_WITH_NUMERIC_LABELS="nucleotidesWithNumericLabels"}(kt||(kt={})),function(t){t.PATTERN_CONFIG="patternConfig",t.AUTHOR_ID="authorID",t.DATE="date"}(Ht||(Ht={})),function(t){t.CREATE="create",t.MODIFY="modify"}(Ut||(Ut={}));const $t=[Ft.IS_ANTISENSE_STRAND_INCLUDED,Ft.NUCLEOTIDE_SEQUENCES,Ft.PHOSPHOROTHIOATE_LINKAGE_FLAGS,Ft.STRAND_TERMINUS_MODIFICATIONS],Vt=(kt.PATTERN_NAME,kt.PATTERN_COMMENT,kt.NUCLEOTIDES_WITH_NUMERIC_LABELS,{patternConfig:{patternName:"<default example>",isAntisenseStrandIncluded:!0,nucleotideSequences:{SS:["RNA","RNA","RNA","RNA","RNA","RNA","RNA","RNA","RNA","RNA","RNA","RNA","RNA","RNA","RNA","RNA","RNA","RNA","RNA","RNA","RNA","RNA","RNA"],AS:["RNA","RNA","RNA","RNA","RNA","RNA","RNA","RNA","RNA","RNA","RNA","RNA","RNA","RNA","RNA","RNA","RNA","RNA","RNA","RNA","RNA","RNA","RNA"]},phosphorothioateLinkageFlags:{SS:[!0,!0,!0,!0,!0,!0,!0,!0,!0,!0,!0,!0,!0,!0,!0,!0,!0,!0,!0,!0,!0,!0,!0,!0],AS:[!0,!0,!0,!0,!0,!0,!0,!0,!0,!0,!0,!0,!0,!0,!0,!0,!0,!0,!0,!0,!0,!0,!0,!0]},strandTerminusModifications:{SS:{"3'":"","5'":""},AS:{"3'":"","5'":""}},patternComment:"",nucleotidesWithNumericLabels:["RNA"]},authorID:""}),jt="2024-01-01T18:00:00.000Z";class qt extends Error{constructor(t){super(t),this.name="PatternNameExistsError"}}class Gt extends Error{constructor(t){super(t),this.name="PatternExistsError"}}var Wt=n(802),zt=n.n(Wt);class Yt{constructor(t){this.th=t,this.otherUsersPatternNameToHash=new Map,this.currentUserPatternNameToHash=new Map}static async getInstance(){const t=await kr.getTranslationHelper(),e=new Yt(t);e.currentUserName=await e.fetchCurrentUserName(),e.currentUserId=await e.fetchCurrentUserId();const n=await e.fetchPatterns();return await e.initializePatternMaps(n),e}getCurrentUserPatternNames(){return Array.from(this.currentUserPatternNameToHash.keys()).sort(((t,e)=>t.toLowerCase().localeCompare(e.toLowerCase())))}getOtherUsersPatternNames(){return Array.from(this.otherUsersPatternNameToHash.keys()).sort(((t,e)=>t.toLowerCase().localeCompare(e.toLowerCase())))}getCurrentUserName(){return this.currentUserName}validatePatternNameUniqueness(t){if(this.currentUserPatternNameToHash.has(t))throw new qt(`Pattern with name ${t} already exists`)}validatePatternUniqueness(t){if(Array.from(this.currentUserPatternNameToHash.values()).concat(Array.from(this.otherUsersPatternNameToHash.values())).includes(t))throw new Gt(t)}getPatternHash(t,e){const n=e?this.currentUserPatternNameToHash.get(t):this.otherUsersPatternNameToHash.get(t);if(void 0===n)throw new Error(`Pattern with name ${t} not found`);return n}async getPatternRecordByHash(e){if(null===e||""===e)return null;try{const n=await t.dapi.userDataStorage.getValue(Dt,e,!1);return JSON.parse(n)}catch{return null}}async getPatternConfig(t){if(""===t||null===t)return null;const e=await this.getPatternRecordByHash(t);return null===e?null:e[Ht.PATTERN_CONFIG]}getDefaultPatternRecord(){const t=Vt;return t[Ht.AUTHOR_ID]=this.currentUserId,t}getDefaultPatternConfig(){return Vt[Ht.PATTERN_CONFIG]}getAuthorCategoryByHash(t){if(this.isCurrentUserPattern(t))return this.getCurrentUserAuthorshipCategory();if(this.isOtherUserPattern(t))return this.getOtherUsersAuthorshipCategory();throw new Error(`Pattern with hash ${t} not found`)}isCurrentUserPattern(t){return Array.from(this.currentUserPatternNameToHash.values()).includes(t)}isOtherUserPattern(t){return Array.from(this.otherUsersPatternNameToHash.values()).includes(t)}getPatternNameByHash(t){const e=[this.currentUserPatternNameToHash,this.otherUsersPatternNameToHash];for(const n of e)for(const[e,r]of n.entries())if(r===t)return e;throw new Error(`Pattern with hash ${t} not found`)}getHashOfPatternToBeLoadedAfterDeletion(){const t=this.getCurrentUserPatternNames()[0];if(!t)throw new Error("Cannot load pattern after deletion, as there are no patterns left");const e=this.currentUserPatternNameToHash.get(t);if(void 0===e)throw new Error(`Pattern with name ${t} not found`);return e}async getRecordFromPattern(e){return{[Ht.PATTERN_CONFIG]:e,[Ht.AUTHOR_ID]:await t.dapi.users.current().then((t=>t.id))}}getHash(t){const e=$t.reduce(((e,n)=>(e[n]=t[n],e)),{});return zt().sha1(e)}async savePatternToUserStorage(e){const n=e.getPatternConfig();try{const r=this.getHash(n);this.validatePatternUniqueness(r);const i=n[kt.PATTERN_NAME];this.validatePatternNameUniqueness(i);const o=await this.getRecordFromPattern(n),s=(new Date).toISOString();o[Ht.DATE]={[Ut.CREATE]:s,[Ut.MODIFY]:s};const a=JSON.stringify(o);await t.dapi.userDataStorage.postValue(Dt,r,a,!1),this.currentUserPatternNameToHash.set(i,r),e.selectAuthor(this.getCurrentUserAuthorshipCategory()),e.updatePatternList(),e.requestPatternLoad(r),e.updateUrlState(r)}catch(t){if(t instanceof qt||t instanceof Gt)throw t;console.error("Error while saving pattern to user storage",t)}}async overwriteExistingPatternInUserStorage(e){const n=e.getPatternConfig(),r=n[kt.PATTERN_NAME],i=this.currentUserPatternNameToHash.get(r);if(void 0===i)throw new Error("Old hash is undefined");const o=this.getHash(n),s=await this.getRecordFromPattern(n),a=(new Date).toISOString();s[Ht.DATE]={[Ut.MODIFY]:a};const u=await t.dapi.userDataStorage.getValue(Dt,i,!1),l=JSON.parse(u);void 0!==l[Ht.DATE]&&null!=l[Ht.DATE][Ut.CREATE]&&(s[Ht.DATE][Ut.CREATE]=l[Ht.DATE][Ut.CREATE]);const c=JSON.stringify(s);await t.dapi.userDataStorage.postValue(Dt,o,c,!1),await t.dapi.userDataStorage.remove(Dt,i,!1),this.currentUserPatternNameToHash.set(r,o),e.requestPatternLoad(o),e.updateUrlState(o)}async deletePattern(e,n){const r=this.currentUserPatternNameToHash.get(e);if(e===this.getDefaultPatternName())return void t.shell.warning("Cannot delete default pattern");if(void 0===r)throw new Error(`Pattern with name ${e} not found`);await t.dapi.userDataStorage.remove(Dt,r,!1),this.currentUserPatternNameToHash.delete(e),n.updatePatternList();const i=this.getHashOfPatternToBeLoadedAfterDeletion();n.requestPatternLoad(i)}fetchDefaultNucleobase(){return this.fetchAvailableNucleotideBases()[0]}fetchAvailableNucleotideBases(){const t=Object.keys(this.th.jsonData.patternAppData)[0];return Object.keys(this.th.jsonData.patternAppData[t])}async fetchCurrentUserName(){return(await t.dapi.users.current()).friendlyName}async fetchCurrentUserId(){return(await t.dapi.users.current()).id}async fetchPatterns(){return await t.dapi.userDataStorage.get(Dt,!1)}async initializePatternMaps(t){if(!this.currentUserId)throw new Error("Current user ID is not set");const e=new Map;for(const[n,r]of Object.entries(t))await this.extractDataFromRecordToMaps(n,r,e);this.setDefaultPattern()}setDefaultPattern(){const t=Vt[Ht.PATTERN_CONFIG];this.currentUserPatternNameToHash.set(t[kt.PATTERN_NAME],"")}async extractDataFromRecordToMaps(e,n,r){const i=JSON.parse(n),o=i[Ht.PATTERN_CONFIG].patternName,s=i[Ht.AUTHOR_ID];if(this.isCurrentUserId(s))this.currentUserPatternNameToHash.set(o,e);else{if(!r.has(s)){let e="<UNKNOWN_USER>";try{e=(await t.dapi.users.find(s)).friendlyName}catch(t){}r.set(s,e)}const n=o+` (created by ${r.get(s)})`;this.otherUsersPatternNameToHash.set(n,e)}}getDefaultPatternName(){return Vt[Ht.PATTERN_CONFIG][kt.PATTERN_NAME]}getCurrentUserAuthorshipCategory(){return this.currentUserName+" (me)"}getOtherUsersAuthorshipCategory(){return"Other users"}isCurrentUserId(t){return t===this.currentUserId}}const Kt=rxjs,Jt=rxjs.operators;function Qt(t){return t.endsWith("(o)")}function Xt(t){const e=Object.values(t).flat().reduce(((t,e)=>(t[e]=(t[e]||0)+1,t)),{});return Object.entries(e).reduce(((t,e)=>t[1]>e[1]?t:e),["",0])[0]}var Zt;function te(t){const e=Array.from(new Set(t));return Array.from(e).sort(((t,e)=>t.toLowerCase().localeCompare(e.toLowerCase())))}!function(t){t.getTruncatedStrandData=function(t,e,n){return{nucleotides:t.slice(0,n),ptoFlags:e.slice(0,n+1)}},t.getExtendedStrandData=function(t,e,n,r){const i=n-t.length,o=t.concat(new Array(n-t.length).fill(r)),s=0===t.length?n+1:i;return{nucleotides:o,ptoFlags:e.concat(new Array(s).fill(!0))}}}(Zt||(Zt={}));var ee=n(543),ne=n.n(ee);class re{constructor(t,e){this.dataManager=t,this._patternListUpdated$=new Kt.Subject,this._patternLoadRequested$=new Kt.Subject,this._patternLoaded$=new Kt.Subject,this._uniqueNucleotides$=new Kt.BehaviorSubject([]),this._patternDeletionRequested$=new Kt.Subject,this._tableSelection$=new Kt.BehaviorSubject(null),this._svgSaveRequested$=new Kt.Subject,this._loadPatternInNewTabRequested$=new Kt.Subject,this._urlStateUpdated$=new Kt.Subject,this._patternHasUnsavedChanges$=new Kt.BehaviorSubject(!1),this._selectedStrandColumn=new Kt.BehaviorSubject(null),this._selectedIdColumn=new Kt.BehaviorSubject(null),this.initializeAuthorSelection(e),this.initializePatternState(e),this._lastLoadedPatternConfig=new Kt.BehaviorSubject(ne().cloneDeep(this.getPatternConfig())),this.setupSubscriptions()}setupSubscriptions(){this._nucleotideSequences$.subscribe((()=>{this.updateUniqueNucleotides(),this.updateSequenceBase()})),this._isAntisenseStrandActive$.subscribe((t=>{t||Rt.forEach((t=>{this.updateTerminusModification("AS",t,"")}))})),this.patternStateChanged$.pipe((0,Jt.debounceTime)(20)).subscribe((()=>{const t=this._lastLoadedPatternConfig.getValue(),e=this.getPatternConfig(),n=!ne().isEqual(e,t);this._patternHasUnsavedChanges$.next(n)}))}updateUniqueNucleotides(){const t=(e=this._nucleotideSequences$.getValue(),te(Object.values(e).flat()));var e;this._uniqueNucleotides$.next(t)}updateSequenceBase(){const t=Xt(this._nucleotideSequences$.getValue());this._sequenceBase$.next(t)}get nucleotideSequencesChanged$(){return this._nucleotideSequences$.asObservable()}initializeAuthorSelection(t){const e=t[Ht.AUTHOR_ID];this.dataManager.isCurrentUserId(e)?this._patternAuthorSelection$=new Kt.BehaviorSubject(this.dataManager.getCurrentUserAuthorshipCategory()):this._patternAuthorSelection$=new Kt.BehaviorSubject(this.dataManager.getOtherUsersAuthorshipCategory())}initializePatternState(t){const e=t[Ht.PATTERN_CONFIG];this._patternName$=new Kt.BehaviorSubject(e[kt.PATTERN_NAME]),this._isAntisenseStrandActive$=new Kt.BehaviorSubject(e[Ft.IS_ANTISENSE_STRAND_INCLUDED]),this._nucleotideSequences$=new Kt.BehaviorSubject(e[Ft.NUCLEOTIDE_SEQUENCES]),this._phosphorothioateLinkageFlags=new Kt.BehaviorSubject(e[Ft.PHOSPHOROTHIOATE_LINKAGE_FLAGS]),this._terminalModifications=new Kt.BehaviorSubject(e[Ft.STRAND_TERMINUS_MODIFICATIONS]),this._comment$=new Kt.BehaviorSubject(e[kt.PATTERN_COMMENT]),this._modificationsWithNumericLabels$=new Kt.BehaviorSubject(e[kt.NUCLEOTIDES_WITH_NUMERIC_LABELS]),this._sequenceBase$=new Kt.BehaviorSubject(Xt(e[Ft.NUCLEOTIDE_SEQUENCES]))}getPatternName(){return this._patternName$.getValue()}updatePatternName(t){this._patternName$.next(t)}get antisenseStrandToggled$(){return this._isAntisenseStrandActive$.asObservable()}isAntisenseStrandActive(){return this._isAntisenseStrandActive$.getValue()}toggleAntisenseStrand(t){t?this.updateStrandLength("AS",this.getNucleotideSequences().SS.length):this.updateStrandLength("AS",0),this._isAntisenseStrandActive$.next(t)}getNucleotideSequences(){return this._nucleotideSequences$.getValue()}updateNucleotideSequences(t){this._nucleotideSequences$.next(t)}updateStrandLength(t,e){const n=this.getNucleotideSequences()[t];if(n.length===e)return;const r=this.getPhosphorothioateLinkageFlags()[t];if(0===e)return void this.setNewStrandData([],[],t);if(n.length>e){const{nucleotides:i,ptoFlags:o}=Zt.getTruncatedStrandData(n,r,e);return void this.setNewStrandData(i,o,t)}const i=this.getSequenceBase(),{nucleotides:o,ptoFlags:s}=Zt.getExtendedStrandData(n,r,e,i);this.setNewStrandData(o,s,t)}setNewStrandData(t,e,n){this.updateNucleotideSequences({...this.getNucleotideSequences(),[n]:t}),this.updatePhosphorothioateLinkageFlags({...this.getPhosphorothioateLinkageFlags(),[n]:e})}getPhosphorothioateLinkageFlags(){return this._phosphorothioateLinkageFlags.getValue()}updatePhosphorothioateLinkageFlags(t){this._phosphorothioateLinkageFlags.next(t)}get phosphorothioateLingeFlagsChanged$(){return this._phosphorothioateLinkageFlags.asObservable()}getTerminalModifications(){return this._terminalModifications.getValue()}updateTerminalModifications(t){this._terminalModifications.next(t)}updateTerminusModification(t,e,n){const r=this.getTerminalModifications();r[t][e]=n,this.updateTerminalModifications(r)}terminalModificationsUpdated$(){return this._terminalModifications.asObservable()}getComment(){return this._comment$.getValue()}updateComment(t){this._comment$.next(t)}getModificationsWithNumericLabels(){return this._modificationsWithNumericLabels$.getValue()}updateModificationsWithNumericLabels(t){const e=function(t){return te(t).filter((t=>!Qt(t)))}(t);this._modificationsWithNumericLabels$.next(e)}get patternLoadRequested$(){return this._patternLoadRequested$.asObservable()}requestPatternLoad(t){this._patternLoadRequested$.next(t)}get patternListUpdated$(){return this._patternListUpdated$.asObservable()}updatePatternList(){this._patternListUpdated$.next()}get tableSelectionChanged$(){return this._tableSelection$.asObservable()}selectTable(t){this._tableSelection$.next(t)}getTableSelection(){return this._tableSelection$.getValue()}requestPatternDeletion(t){this._patternDeletionRequested$.next(t)}get patternDeletionRequested$(){return this._patternDeletionRequested$.asObservable()}replaceSequenceBase(t){const e=this._nucleotideSequences$.getValue(),n={};Bt.forEach((r=>{n[r]=e[r].map((()=>t))})),this._nucleotideSequences$.next(n);const r=this._modificationsWithNumericLabels$.getValue();r.includes(t)||this.updateModificationsWithNumericLabels(r.concat(t))}get patternStateChanged$(){return Kt.merge(this._patternName$.pipe((0,Jt.debounceTime)(300),(0,Jt.map)((()=>{}))),this._isAntisenseStrandActive$,this._nucleotideSequences$,this._phosphorothioateLinkageFlags,this._terminalModifications,this._comment$.pipe((0,Jt.debounceTime)(300)),this._modificationsWithNumericLabels$)}getSequenceBase(){return this._sequenceBase$.getValue()}uniqueNucleotidesChanged$(){return this.patternStateChanged$.pipe((0,Jt.switchMap)((()=>this._uniqueNucleotides$)))}getUniqueNucleotides(){return this._uniqueNucleotides$.getValue()}get svgSaveRequested$(){return this._svgSaveRequested$.asObservable()}requestSvgSave(){this._svgSaveRequested$.next()}setAllPTOLinkages(t){const e=this.getPhosphorothioateLinkageFlags();Bt.forEach((n=>{e[n]=e[n].map((()=>t))})),this.updatePhosphorothioateLinkageFlags(e)}setPatternConfig(t){this._patternName$.next(t[kt.PATTERN_NAME]),this._isAntisenseStrandActive$.next(t[Ft.IS_ANTISENSE_STRAND_INCLUDED]),this._nucleotideSequences$.next(t[Ft.NUCLEOTIDE_SEQUENCES]),this._phosphorothioateLinkageFlags.next(t[Ft.PHOSPHOROTHIOATE_LINKAGE_FLAGS]),this._terminalModifications.next(t[Ft.STRAND_TERMINUS_MODIFICATIONS]),this._comment$.next(t[kt.PATTERN_COMMENT]),this._modificationsWithNumericLabels$.next(t[kt.NUCLEOTIDES_WITH_NUMERIC_LABELS])}setLastLoadedPatternConfig(t){this._lastLoadedPatternConfig.next(ne().cloneDeep(t))}getPatternConfig(){return{[kt.PATTERN_NAME]:this.getPatternName(),[Ft.IS_ANTISENSE_STRAND_INCLUDED]:this.isAntisenseStrandActive(),[Ft.NUCLEOTIDE_SEQUENCES]:this.getNucleotideSequences(),[Ft.PHOSPHOROTHIOATE_LINKAGE_FLAGS]:this.getPhosphorothioateLinkageFlags(),[Ft.STRAND_TERMINUS_MODIFICATIONS]:this.getTerminalModifications(),[kt.PATTERN_COMMENT]:this.getComment(),[kt.NUCLEOTIDES_WITH_NUMERIC_LABELS]:this.getModificationsWithNumericLabels()}}setPhosphorothioateLinkageFlag(t,e,n){const r=this.getPhosphorothioateLinkageFlags();r[t][e]=n,this.updatePhosphorothioateLinkageFlags(r)}setNucleotide(t,e,n){const r=this.getNucleotideSequences();r[t][e]=n;const i=this.getModificationsWithNumericLabels();this.updateModificationsWithNumericLabels(i.concat(n)),this.updateNucleotideSequences(r)}get strandsUpdated$(){return Kt.merge(this._isAntisenseStrandActive$.asObservable().pipe((0,Jt.map)((()=>{}))),this._nucleotideSequences$.asObservable().pipe((0,Jt.map)((()=>{}))),this._patternLoaded$.asObservable().pipe((0,Jt.map)((()=>{})))).pipe((0,Jt.debounceTime)(10))}get strandsLinkagesAndTerminalsUpdated$(){return Kt.merge(this.strandsUpdated$,this._phosphorothioateLinkageFlags.asObservable().pipe((0,Jt.map)((()=>{}))),this._terminalModifications.asObservable().pipe((0,Jt.map)((()=>{}))))}updateControlsUponPatternLoaded(t){this._patternLoaded$.next(t)}get patternLoaded$(){return this._patternLoaded$.asObservable()}get userSelection$(){return this._patternAuthorSelection$.asObservable().pipe((0,Jt.skip)(1))}selectAuthor(t){if("string"!=typeof t)throw new Error("Selected user must be defined");this._patternAuthorSelection$.next(t)}getSelectedAuthor(){return this._patternAuthorSelection$.getValue()}get loadPatternInNewTabRequested$(){return this._loadPatternInNewTabRequested$.asObservable()}requestLoadPatternInNewTab(t){this._loadPatternInNewTabRequested$.next(t)}updateUrlState(t){this._urlStateUpdated$.next(t)}get urlStateUpdated$(){return this._urlStateUpdated$.asObservable()}get patternHasUnsavedChanges$(){return this._patternHasUnsavedChanges$.asObservable()}selectStrandColumn(t,e){this._selectedStrandColumn.next({...this._selectedStrandColumn.getValue(),[t]:e})}getSelectedStrandColumn(t){const e=this._selectedStrandColumn.getValue();return e?e[t]:null}selectIdColumn(t){this._selectedIdColumn.next(t)}getSelectedIdColumn(){return this._selectedIdColumn.getValue()}get updateSvgContainer$(){return this.patternStateChanged$.pipe((0,Jt.debounceTime)(100))}}const ie="pattern";class oe{constructor(){this.urlSearchParams=new URLSearchParams(window.location.search)}subscribeToObservables(t){t.urlStateUpdated$.subscribe((t=>this.setPatternURL(t))),t.loadPatternInNewTabRequested$.subscribe((t=>{const e=`${window.location.origin}${window.location.pathname}?${ie}=${t}`;window.open(e,"_blank")})),window.addEventListener("popstate",(()=>{this.urlSearchParams=new URLSearchParams(window.location.search);const e=this.getPatternHash();null!==e&&t.requestPatternLoad(e)}))}getPatternHash(){return this.urlSearchParams.get(ie)}setPatternURL(t){null!==t&&""!==t?(this.urlSearchParams.set(ie,t),window.history.pushState({},"",`${window.location.pathname}?${this.urlSearchParams}`)):this.clearPatternURL()}clearPatternURL(){this.urlSearchParams.delete(ie),window.history.pushState({},"",`${window.location.pathname}`)}}var se=n(72),ae=n.n(se),ue=n(825),le=n.n(ue),ce=n(659),he=n.n(ce),fe=n(56),de=n.n(fe),pe=n(540),ge=n.n(pe),me=n(113),ve=n.n(me),ye=n(252),be={};be.styleTagTransform=ve(),be.setAttributes=de(),be.insert=he().bind(null,"head"),be.domAPI=le(),be.insertStyleElement=ge(),ae()(ye.A,be),ye.A&&ye.A.locals&&ye.A.locals;class we{constructor(t){this.eventBus=t,this.columnControlsContainer=Et.div([]),this.eventBus.tableSelectionChanged$.subscribe((()=>this.handleTableChoice())),this.refreshColumnControls()}getColumnControlsContainer(){return this.columnControlsContainer}get selectedTable(){return this.eventBus.getTableSelection()}handleTableChoice(){this.refreshColumnControls()}refreshColumnControls(){Tt()(this.columnControlsContainer).empty(),Tt()(this.columnControlsContainer).append(this.constructColumnControls())}constructColumnControls(){const t=this.createStrandColumnInput(),e=t.SS,n=t.AS;this.eventBus.antisenseStrandToggled$.subscribe((t=>{Tt()(n).toggle(t)}));const r=this.createIdColumnInput();return[e,n,r]}createStrandColumnInput(){const t=this.selectedTable?this.selectedTable.columns.names().sort(((t,e)=>t.localeCompare(e))):[];return Object.fromEntries(Bt.map((e=>{const n=Et.input.choice(`${Pt[e]} column`,{value:t[0],items:t,onValueChanged:t=>this.eventBus.selectStrandColumn(e,t)});return this.eventBus.selectStrandColumn(e,t[0]),[e,n.root]})))}createIdColumnInput(){const t=this.selectedTable?this.selectedTable.columns.names():[],e=Et.input.choice("ID column",{value:t[0],items:t,onValueChanged:t=>this.eventBus.selectIdColumn(t)});return this.eventBus.selectIdColumn(t[0]),e.root}}class Ce{constructor(t){this.eventBus=t,this.availableTables=[],this.tableInputContainer=Et.div([]),this.subscribeToTableEvents(),this.refreshTableInput()}getTableInputContainer(){return this.tableInputContainer}subscribeToTableEvents(){t.events.onTableAdded.subscribe((t=>this.handleTableAdded(t))),t.events.onTableRemoved.subscribe((t=>this.handleTableRemoved(t))),this.eventBus.tableSelectionChanged$.subscribe((()=>this.handleTableChoice()))}getTableFromEventData(t){if(!t&&t.args&&t.args.dataFrame instanceof e.DataFrame)throw new Error("EventData does not contain a dataframe",t);return t.args.dataFrame}handleTableAdded(t){const e=this.getTableFromEventData(t);this.availableTables.some((t=>t.name===e.name))||(this.availableTables.push(e),this.eventBus.selectTable(e),this.refreshTableInput())}handleTableRemoved(t){const e=this.getTableFromEventData(t);this.availableTables=this.availableTables.filter((t=>t.name!==e.name));const n=this.availableTables[0];this.eventBus.selectTable(n||null),this.refreshTableInput()}refreshTableInput(){const t=this.createTableInput();Tt()(this.tableInputContainer).empty(),this.tableInputContainer.append(t.root)}createTableInput(){const t=this.eventBus.getTableSelection();return Et.input.table("Tables",{value:t,items:this.availableTables,onValueChanged:t=>{null!==t&&this.eventBus.selectTable(t)}})}handleTableChoice(){const t=this.eventBus.getTableSelection();t&&(this.isTableDisplayed(t)||this.displayTable(t))}isTableDisplayed(e){return t.shell.tableNames.includes(e.name)}displayTable(e){const n=t.shell.v;t.shell.addTableView(e),t.shell.v=n}}function Ae(t,e,n,r){const i=function(t,e,n){const r=new Array(t.length+e.filter((t=>t)).length+Rt.length);r[0]=n["5'"],r[r.length-1]=n["3'"];let i=1;return e[0]&&(r[i]="ps",i++),t.forEach(((t,n)=>{r[n+i]=t,e[n+1]&&(r[n+i+1]="ps",i++)})),r}(t.split("").map(((t,n)=>{const r=function(t,e,n){const r=Object.keys(n.patternAppData)[0],i=n.patternAppData[r][e].substitution;return t.replace(/([AGCTU])/,i)}(t,e[n],kr.jsonData);return r})),n,r);return i.join("")}class xe{constructor(t){this.eventBus=t,this.tableInputManager=new Ce(t),this.columnInputManager=new we(t)}createControls(){const t=Et.h1("Bulk convert"),e=this.tableInputManager.getTableInputContainer(),n=this.columnInputManager.getColumnControlsContainer(),r=Et.bigButton("Convert",(()=>this.processConvertButtonClick()));return[t,e,n,Et.buttonsInput([r])]}processConvertButtonClick(){!function(e){const n=e.getTableSelection();if(!n)return void t.shell.warning("Please select a table");const r=Bt.filter((t=>!("AS"===t&&!e.isAntisenseStrandActive()))).map((t=>({strand:t,column:e.getSelectedStrandColumn(t)}))).filter((t=>t.column));if(0===r.length)return void t.shell.warning("Select a sense strand column");const i=e.getSelectedIdColumn();if(!i)throw new Error("No ID column selected");n.getCol(i);const o=r.map((t=>({strand:t.strand,column:n.getCol(t.column)})));!function(t,e){const n=e.getNucleotideSequences();return t.every((t=>{const e=n[t.strand].length;return t.column.toList().every((t=>t.length===e))}))}(o,e)?t.shell.warning("Some strands in the table input do not match pattern length"):o.forEach((t=>{const r=t.column,i=t.strand,o=e.getNucleotideSequences()[i],s=e.getTerminalModifications()[i],a=e.getPhosphorothioateLinkageFlags()[i],u=`${e.getPatternName()}(${r.name})`;n.columns.addNewString(u).init((t=>Ae(r.get(t),o,a,s)))}))}(this.eventBus)}}class _e{constructor(t,e,n){this.eventBus=t,this.initialPatternConfig=e,this.subscriptions=n}create(){return Et.divV([Et.h1("PTO"),Et.divH([this.createAllPtoActivationInput().root,...this.createFirstPtoInputs().map((t=>t.root))],{style:{gap:"12px"}})])}areAllPtoLinkagesSet(t){return Bt.map((e=>t[e].filter((t=>t)).length)).reduce(((t,e)=>t+e),0)===Bt.map((t=>this.initialPatternConfig.nucleotideSequences[t].length)).reduce(((t,e)=>t+e),0)+Bt.filter((e=>t[e].length)).length}createAllPtoActivationInput(){const t=this.initialPatternConfig.phosphorothioateLinkageFlags,e=this.areAllPtoLinkagesSet(t),n=Et.input.bool("All PTO",{value:e});n.onInput.subscribe((()=>{const t=n.value;this.eventBus.setAllPTOLinkages(t)}));const r=this.eventBus.phosphorothioateLingeFlagsChanged$.subscribe((()=>{const t=this.eventBus.getPatternConfig().phosphorothioateLinkageFlags,e=this.areAllPtoLinkagesSet(t);n.value=e}));return this.subscriptions.add(r),this.addStyleToPtoInput(n),Et.tooltip.bind(n.captionLabel,"Activate all phosphothioates"),n}addStyleToPtoInput(t){const e=t.captionLabel;e.classList.add("ui-label-right"),Object.assign(e.style,{textAlign:"left",maxWidth:"100px",minWidth:"40px",width:"auto"})}createFirstPtoInputs(){return Bt.map((t=>{if(!this.eventBus.isAntisenseStrandActive()&&"AS"===t)return;const e=this.isFirstPtoActive(t),n=Et.input.bool(`First ${t} PTO`,{value:e});n.onInput.subscribe((()=>{const e=n.value;this.eventBus.setPhosphorothioateLinkageFlag(t,0,e)}));const r=this.eventBus.phosphorothioateLingeFlagsChanged$.subscribe((e=>{const r=e[t][0];n.value=r}));return this.subscriptions.add(r),this.addStyleToPtoInput(n),Et.tooltip.bind(n.captionLabel,`Activate first phosphothioate in ${t}`),n})).filter((t=>void 0!==t))}isFirstPtoActive(t){return this.initialPatternConfig.phosphorothioateLinkageFlags[t][0]}}class Ee{constructor(t,e,n){this.eventBus=t,this.dataManager=e,this.subscriptions=n;const r=this.eventBus.nucleotideSequencesChanged$.subscribe((()=>{this.displayedInputLabels=this.computeDisplayedInputLabels()}));this.subscriptions.add(r)}create(){const t=Bt.map((t=>this.constructControlsPanel(t)));return Et.divH(t,{style:{gap:"24px"}})}constructControlsPanel(t){if(!this.eventBus.isAntisenseStrandActive()&&"AS"===t)return Et.div([]);const e=this.constructHeader(),n=this.createControls(t);return Et.block([Et.h1(`${Pt[t]}`),e,n],{style:{paddingTop:"12px"}})}constructHeader(){return Et.divH([Et.div([Et.divText("#")],{style:{width:"20px"}}),Et.block75([Et.divText("Modification")]),Et.div([Et.divText("PTO")])])}createControls(t){const e=this.createNucleobaseInputs(t),n=this.createLabelDivs(t),r=this.createPTOFlagInputs(t);return Et.div(e.map(((t,e)=>Et.divH([n[e],Et.block75([t.root]),r[e].root],{style:{alignItems:"center"}}))))}createNucleobaseInputs(t){const e=this.dataManager.fetchAvailableNucleotideBases().sort(((t,e)=>t.toLowerCase().localeCompare(e.toLowerCase())));return this.eventBus.getNucleotideSequences()[t].map(((n,r)=>{const i=Et.input.choice("",{value:n,items:e});return i.onInput.subscribe((()=>{const e=i.value;this.eventBus.setNucleotide(t,r,e)})),i}))}createPTOFlagInputs(t){return this.eventBus.getPhosphorothioateLinkageFlags()[t].slice(1).map(((e,n)=>{const r=Et.input.bool("",{value:e});r.onInput.subscribe((()=>{const e=r.value;this.eventBus.setPhosphorothioateLinkageFlag(t,n+1,e)}));const i=this.eventBus.phosphorothioateLingeFlagsChanged$.subscribe((e=>{const i=e[t][n+1];r.value=i}));return this.subscriptions.add(i),r}))}computeDisplayedInputLabels(){const t=this.eventBus.getNucleotideSequences(),e=new Map;return Bt.forEach((n=>{let r=1;const i=t[n].map((t=>{if(Qt(t))return"";const e=String(r);return r++,e}));e.set(n,i)})),e}createLabelDivs(t){const e=this.createLabels(t).map((t=>Et.div([t],{style:{width:"20px"}}))),n=this.eventBus.nucleotideSequencesChanged$.subscribe((()=>{this.createLabels(t).forEach(((t,n)=>{Tt()(e[n]).empty(),Tt()(e[n]).append(t)}))}));return this.subscriptions.add(n),e}createLabels(t){return this.eventBus.getNucleotideSequences()[t].map(((e,n)=>{const r=this.displayedInputLabels.get(t)[n];return Et.label(r)}))}}class Se{constructor(){this.rxjsSubscriptions=[],this.dgSubscriptions=[]}add(t){t instanceof Kt.Subscription?this.rxjsSubscriptions.push(t):this.dgSubscriptions.push(t)}unsubscribeAll(){for(const t of[this.rxjsSubscriptions,this.dgSubscriptions])t.forEach((t=>t.unsubscribe())),t.length=0}}class Te{constructor(t,e){this.eventBus=t,this.dataManager=e,this.subscriptions=new Se}static open(t,e){Te.isDialogOpen||(Te.instance||(Te.instance=new Te(t,e)),Te.instance.openDialog())}openDialog(){this.initialPatternConfig=ne().cloneDeep(this.eventBus.getPatternConfig()),Te.isDialogOpen=!0,this.createDialog().show()}createDialog(){const t=Et.divV([]);this.subscriptions.add(this.eventBus.strandsUpdated$.subscribe((()=>this.onStrandsUpdated(t))));const e=Et.dialog("Edit strands").add(t).onOK((()=>{})).onCancel((()=>this.resetToInitialState()));return this.subscriptions.add(e.onClose.subscribe((()=>{Te.isDialogOpen=!1,this.subscriptions.unsubscribeAll()}))),e}onStrandsUpdated(t){const e=new _e(this.eventBus,this.initialPatternConfig,this.subscriptions).create(),n=new Ee(this.eventBus,this.dataManager,this.subscriptions).create();Tt()(t).empty(),Tt()(t).append(e,n)}resetToInitialState(){this.eventBus.setPatternConfig(this.initialPatternConfig)}}Te.isDialogOpen=!1;class Ie{constructor(t){this.eventBus=t,this.subscriptions=new Se}static open(t){Ie.isDialogOpen||(Ie.instance||(Ie.instance=new Ie(t)),Ie.instance.openDialog())}openDialog(){this.initialPatternConfig=ne().cloneDeep(this.eventBus.getPatternConfig()),Ie.isDialogOpen=!0,this.createDialog().show()}createDialog(){const t=Et.divV([]);this.subscriptions.add(this.eventBus.strandsUpdated$.subscribe((()=>this.onStrandsUpdated(t))));const e=Et.dialog("Edit terminal modifications").add(t).onOK((()=>{})).onCancel((()=>this.resetToInitialState()));return this.subscriptions.add(e.onClose.subscribe((()=>{Ie.isDialogOpen=!1,this.subscriptions.unsubscribeAll()}))),e}onStrandsUpdated(t){const e=new Ne(this.eventBus).create();Tt()(t).empty(),Tt()(t).append(e)}resetToInitialState(){this.eventBus.setPatternConfig(this.initialPatternConfig)}}Ie.isDialogOpen=!1;class Ne{constructor(t){this.eventBus=t}create(){const t=Bt.map((t=>this.constructControlsPanel(t)));return Et.divH(t,{style:{gap:"24px"}})}constructControlsPanel(t){if(!this.eventBus.isAntisenseStrandActive()&&"AS"===t)return Et.div([]);const e=this.createInputs(t);return Et.block([Et.h1(`${Pt[t]}`),e],{style:{paddingTop:"12px"}})}createInputs(t){const e=("SS"===t?[...Rt].reverse():Rt).map((e=>this.createInputForTerminus(t,e)));return Et.form(e)}createInputForTerminus(t,e){const n=this.eventBus.getTerminalModifications()[t][e],r=Et.input.textArea(e,{value:n});return this.applyStylingToInput(r),r.onInput.subscribe((()=>{const n=r.value;null!==n&&this.eventBus.updateTerminusModification(t,e,n)})),r}applyStylingToInput(t){const e=t.root.getElementsByTagName("textarea")[0];Tt()(e).css("resize","none")}}class Oe{constructor(t,e){this.eventBus=t,this.dataManager=e}createControls(){const t=this.createAntisenseStrandToggle(),e=this.createStrandLengthInputs(),n=e.SS.root,r=e.AS.root,i=this.createSequenceBaseInput().root,o=this.createPatternCommentInput().root,s=this.createPatternNameInputBlock(),a=this.createEditPatternButton(),u=this.createEditTerminalModificationsButton();return[Et.h1("Edit"),t,n,r,i,s,o,Et.buttonsInput([u,a])]}createEditPatternButton(){const t=Et.button("Edit strands",(()=>Te.open(this.eventBus,this.dataManager)));return Et.tooltip.bind(t,"Edit strand modifications and PTOs"),t}createEditTerminalModificationsButton(){const t=Et.button("Edit terminals",(()=>Ie.open(this.eventBus)));return Et.tooltip.bind(t,"Edit terminal modifications"),Tt()(t).css("margin-right","20px"),t}createAntisenseStrandToggle(){const t=Et.input.toggle(`${Pt.AS} strand`,{value:this.eventBus.isAntisenseStrandActive()});return t.onInput.subscribe((()=>this.eventBus.toggleAntisenseStrand(t.value))),this.eventBus.patternLoaded$.subscribe((()=>{t.value=this.eventBus.isAntisenseStrandActive()})),t.setTooltip("Toggle antisense strand"),t.root}createStrandLengthInputs(){const e=t=>{const e=this.eventBus.getNucleotideSequences()[t].length,r=Et.input.int(`${Pt[t]} length`,{value:e});return r.onInput.subscribe((()=>n(t,r))),this.eventBus.nucleotideSequencesChanged$.subscribe((()=>{r.value=this.eventBus.getNucleotideSequences()[t].length})),r.setTooltip(`Number of nucleotides in ${t}, including overhangs`),[t,r]},n=(e,n)=>{const r=n.value;null!==r&&(r<=0&&(t.shell.warning("Sequence length must be greater than 0"),n.value=1),r>34&&(t.shell.warning("Sequence length must be less than 35"),n.value=34),this.eventBus.updateStrandLength(e,n.value))},r=Object.fromEntries(Bt.map((t=>e(t))));return this.eventBus.antisenseStrandToggled$.subscribe((t=>{Tt()(r.AS.root).toggle(t)})),r}createSequenceBaseInput(){const t=this.dataManager.fetchAvailableNucleotideBases().sort(((t,e)=>t.toLowerCase().localeCompare(e.toLowerCase()))),e=this.dataManager.fetchDefaultNucleobase(),n=Et.input.choice("Sequence basis",{value:e,items:t});return n.onInput.subscribe((()=>this.eventBus.replaceSequenceBase(n.value))),this.eventBus.nucleotideSequencesChanged$.subscribe((()=>{n.value=this.eventBus.getSequenceBase()})),n.setTooltip("Most frequent nucleobase in the strands"),n}createPatternCommentInput(){const t=Et.input.textArea("Comment",{value:this.eventBus.getComment()});return Tt()(t.root).addClass("st-pattern-text-input"),t.onInput.subscribe((()=>this.eventBus.updateComment(t.value))),this.eventBus.patternLoaded$.subscribe((()=>{t.value=this.eventBus.getComment()})),t}createPatternNameInputBlock(){const t=Et.input.textArea("Pattern name",{value:this.eventBus.getPatternName()});return Tt()(t.root).addClass("st-pattern-text-input"),t.onInput.subscribe((()=>this.eventBus.updatePatternName(t.value))),this.eventBus.patternLoaded$.subscribe((()=>{t.value=this.eventBus.getPatternName()})),t.setTooltip("Name under which pattern will be saved"),t.root}}class Me{constructor(t,e){this.eventBus=t,this.dataManager=e,this.subscriptions=new Se,this.authorSelectedByUser=!1,this.eventBus.patternLoadRequested$.subscribe((t=>this.handlePatternChoice(t))),this.eventBus.patternDeletionRequested$.subscribe((async t=>{await this.dataManager.deletePattern(t,this.eventBus)}))}async handlePatternChoice(t){let e=await this.dataManager.getPatternConfig(t);null===e&&(e=this.dataManager.getDefaultPatternConfig()),this.eventBus.setPatternConfig(e),this.eventBus.updateControlsUponPatternLoaded(t),this.eventBus.setLastLoadedPatternConfig(e)}isCurrentUserSelected(){return this.eventBus.getSelectedAuthor()!==this.dataManager.getOtherUsersAuthorshipCategory()}createControls(){const t=this.getPatternInputsContainer();return[Et.h1("Load"),t]}getPatternInputsContainer(){const t=Et.divH(this.createPatternInputs());return this.eventBus.patternListUpdated$.subscribe((()=>{this.subscriptions.unsubscribeAll(),Tt()(t).empty(),Tt()(t).append(this.createPatternInputs())})),t}createPatternInputs(){const t=this.createAuthorChoiceInput(),e=this.createPatternChoiceInputContainer(),n=this.createDeletePatternButton();return[t.root,e,n]}createPatternChoiceInputContainer(){const t=this.createPatternChoiceInput(),e=Et.div([t.root]),n=this.eventBus.userSelection$.subscribe((()=>{Tt()(e).empty(),Tt()(e).append(this.createPatternChoiceInput().root)}));return this.subscriptions.add(n),e}createAuthorChoiceInput(){const t=[this.dataManager.getCurrentUserAuthorshipCategory()];this.dataManager.getOtherUsersPatternNames().length>0&&t.push(this.dataManager.getOtherUsersAuthorshipCategory());const e=Et.input.choice("Author",{value:this.eventBus.getSelectedAuthor(),items:t});return e.onInput.subscribe((()=>{if(this.authorSelectedByUser=!0,null===e.value)throw new Error("author choice must be non-null");this.eventBus.selectAuthor(e.value)})),this.setAuthorChoiceInputStyle(e),e.setTooltip("Select pattern author"),e}setAuthorChoiceInputStyle(t){Tt()(t.input).css({"max-width":"100px","min-width":"100px"}),Tt()(t.root).css({"padding-right":"30px","padding-left":"30px"})}createPatternChoiceInput(){const t=this.isCurrentUserSelected()?this.dataManager.getCurrentUserPatternNames():this.dataManager.getOtherUsersPatternNames();if(this.authorSelectedByUser){const e=this.dataManager.getPatternHash(t[0],this.isCurrentUserSelected());this.eventBus.requestPatternLoad(e),this.eventBus.updateUrlState(e),this.authorSelectedByUser=!1}const e=this.getPatternName(t),n=Et.input.choice("Pattern",{value:e,items:t});return n.setTooltip("Select pattern to load"),Tt()(n.input).css({"max-width":"100px","min-width":"100px"}),this.subscriptions.add(n.onInput.subscribe((()=>{const t=this.dataManager.getPatternHash(n.value,this.isCurrentUserSelected());this.eventBus.requestPatternLoad(t),this.eventBus.updateUrlState(t)}))),this.subscriptions.add(this.eventBus.patternLoaded$.subscribe((()=>{const e=this.eventBus.getPatternName();n.value!==e&&(n.value=this.getPatternName(t))}))),n}getPatternName(t){return t.find((t=>t.split(" (")[0]===this.eventBus.getPatternName()))??t[0]}createDeletePatternButton(){const e=Et.button(Et.iconFA("trash-alt"),(()=>{this.eventBus.getPatternName()!==this.dataManager.getDefaultPatternName()?this.showDeletePatternDialog():t.shell.warning("Cannot delete example pattern")}));Et.tooltip.bind(e,"Delete pattern from user storage");const n=this.eventBus.userSelection$.subscribe((()=>{e.disabled=!this.isCurrentUserSelected()}));return this.subscriptions.add(n),e}showDeletePatternDialog(){const t=Et.dialog("Delete pattern"),e=this.eventBus.getPatternName();t.add(Et.divText(`Are you sure you want to delete pattern ${e}?`)),t.onOK((()=>this.eventBus.requestPatternDeletion(e))),t.show()}}class Le{constructor(t,e){this.eventBus=t,this.dataManager=e}getLayout(){const t=new Me(this.eventBus,this.dataManager),e=new Oe(this.eventBus,this.dataManager),n=new xe(this.eventBus),r=t.createControls(),i=e.createControls(),o=n.createControls(),s=Et.div(r);Tt()(s).css({"padding-bottom":"20px"});const a=Et.div([...i,...o],"ui-form"),u=Et.div([s,a]);return Tt()(u).css({padding:"25px"}),Et.box(u,{style:{maxWidth:"450px"}})}}var Be=n(146);class Pe{constructor(t,e,n){this.svgElementFactory=t,this.config=e,this.yShift=n}shiftElements(t){this.svgElements.forEach((e=>{const n=e.getAttribute("transform")||"",r=`translate(${t.x},${t.y})`;e.setAttribute("transform",`${n} ${r}`)}))}}class Re{constructor(){}static getInstance(){return Re.instance||(Re.instance=new Re,Re.instance.canvas=document.createElement("canvas")),Re.instance}static getTextDimensions(t,e){const n=Re.getInstance().canvas.getContext("2d");if(!n)throw new Error("Canvas 2D context is not available");return n.font=`${e}px Arial`,{width:1.1*n.measureText(t).width,height:1.1*e}}}function De(t){const e=Object.keys(kr.jsonData.patternAppData)[0];if(!e)throw new Error(`No format found in '${ot}'`);return kr.jsonData.patternAppData[e][t].color||""}class Fe extends Pe{constructor(t,e,n){super(t,e,n);const r=Bt.filter((t=>e.nucleotideSequences[t].length>0));this.strands=r.map((t=>new ke(this.svgElementFactory,e,n,t))),this.terminalModifications=r.map(((t,r)=>new Ue(this.svgElementFactory,e,n,t,this.strands[r]))),this.labels=r.map(((t,r)=>new He(this.svgElementFactory,e,n,t,this.terminalModifications[r])))}get svgElements(){return[...this.strands,...this.terminalModifications,...this.labels].map((t=>t.svgElements)).flat()}getContentWidth(){return Math.max(...this.labels.map((t=>t.getContentWidth())))}getContentHeight(){return this.strands.reduce(((t,e)=>t+e.getContentHeight()),0)}}class ke extends Pe{constructor(t,e,n,r){super(t,e,n),this.svgElementFactory=t,this.config=e,this.yShift=n,this.strand=r,this.nucleotideNumericLabels=this.computeNucleotideNumericLabels(),"AS"===this.strand&&(this.config.phosphorothioateLinkageFlags[this.strand].reverse(),this.config.nucleotideSequences[this.strand].reverse(),this.nucleotideNumericLabels.reverse()),this._svgElements=[this.createStrandCircles(),this.createPTOLinkageStars()].flat()}computeNucleotideNumericLabels(){let t=0;return this.config.nucleotideSequences[this.strand].map((e=>Qt(e)?null:(t++,t)))}get svgElements(){return this._svgElements}getStrandCircleYShift(){return $e(this.strand,this.yShift)}createStrandCircles(){const t={x:80,y:this.getStrandCircleYShift()};return this.config.nucleotideSequences[this.strand].map(((e,n)=>this.createNucleotideElementGroup(e,n,t))).flat()}createNucleotideElementGroup(t,e,n){return[...this.createNucleotideCircleElements(t,e,n),this.config.nucleotidesWithNumericLabels.includes(t)?this.createNucleotideNumericLabel(e,n):null].filter((t=>null!==t))}createNucleotideCircleElements(t,e,n){const r=De(t),i={...n,x:n.x+30*e};return[this.svgElementFactory.createCircleElement(i,15,r),this.createNucleotideLetterLabel(e,n,t)]}getNucleotideCircleCenterPosition(t,e){return{x:e.x+30*t,y:e.y}}createNucleotideLetterLabel(t,e,n){if(!lt.includes(n))return null;const r=function(t){return!Qt(t)&&lt.includes(t)?t:""}(n),i=function(t){const e=De(t),n=e.match(/\d+/g)?.map(Number);if(!n||n.length<3)return"#ffffff";const[r,i,o]=n;return.299*r+.587*i+.114*o>186?"#333333":"#ffffff"}(n),o=this.getPositionForNucleotideLabel(t,e);return this.svgElementFactory.createTextElement(r,o,17,i)}getPositionForNucleotideLabel(t,e){const n=this.getNucleotideCircleCenterPosition(t,e),r=Re.getTextDimensions("A",17);return{x:n.x-r.width/2,y:n.y+r.height/3}}getNumericLabelYShift(t){return"SS"===this.strand?t.y-20:t.y+15+5+15}createNucleotideNumericLabel(t,e){const n=this.nucleotideNumericLabels[t];if(null===n)return null;const r=Re.getTextDimensions(n.toString(),15).width,i={x:e.x+30*t-r/2,y:this.getNumericLabelYShift(e)};return this.svgElementFactory.createTextElement(n.toString(),i,15,"var(--grey-6)")}createPTOLinkageStars(){const t=this.config.phosphorothioateLinkageFlags[this.strand],e=this.getStrandCircleYShift()+12;return t.map(((t,n)=>{if(!t)return null;const r={x:65+30*n,y:e};return this.svgElementFactory.createStarElement(r,"red")})).filter((t=>null!==t))}getContentWidth(){return 30*this.config.nucleotideSequences[this.strand].length}getContentHeight(){return 62}}class He extends Pe{constructor(t,e,n,r,i){super(t,e,n),this.svgElementFactory=t,this.config=e,this.yShift=n,this.strand=r,this.terminalModifications=i,this._svgElements=this.createSVGElements()}createSVGElements(){return[this.createLeftLabel(),this.createRightLabel()]}getLeftLabelWidth(){return 55}getRightLabelWidth(){return 20}createLeftLabel(){const t="SS"===this.strand?"5'":"3'",e=`${this.strand}: ${t}  `,n=Re.getTextDimensions(e,17),r={x:10,y:$e(this.strand,this.yShift)+n.height/3};return this.svgElementFactory.createTextElement(e,r,17,"var(--grey-6)")}createRightLabel(){const t="  "+("SS"===this.strand?"3'":"5'"),e=Re.getTextDimensions(t,17),n={x:65+this.terminalModifications.getContentWidth()+5,y:$e(this.strand,this.yShift)+e.height/3};return this.svgElementFactory.createTextElement(t,n,17,"var(--grey-6)")}get svgElements(){return this._svgElements}getContentWidth(){return this.terminalModifications.getContentWidth()+this.getLeftLabelWidth()+this.getRightLabelWidth()+10}getContentHeight(){return this.terminalModifications.getContentHeight()}}class Ue extends Pe{constructor(t,e,n,r,i){super(t,e,n),this.svgElementFactory=t,this.config=e,this.yShift=n,this.strand=r,this.strandSvgWrapper=i,this._svgElements=this.createSVGElements()}createSVGElements(){return this.createTerminalModifications()}getTerminalModification(t){return this.config.strandTerminusModifications[this.strand][t]}getTerminalModificationTextDimensions(t){const e=this.getTerminalModification(t);return Re.getTextDimensions(e,17)}getLeftTerminus(){return"SS"===this.strand?"5'":"3'"}createTerminalModification(t){const e=this.getTerminalModification(t),n=this.getTerminalModificationTextDimensions(t),r=t===this.getLeftTerminus(),i={x:r?65:65+this.getTerminalModificationTextDimensions(this.getLeftTerminus()).width+this.strandSvgWrapper.getContentWidth(),y:$e(this.strand,this.yShift)+n.height/3};return r&&this.strandSvgWrapper.shiftElements({x:n.width,y:0}),this.svgElementFactory.createTextElement(e,i,17,"red")}createTerminalModifications(){return("AS"===this.strand?Rt:Array.from(Rt).reverse()).map((t=>this.createTerminalModification(t)))}get svgElements(){return this._svgElements}getContentWidth(){return this.strandSvgWrapper.getContentWidth()+Rt.map((t=>this.getTerminalModificationTextDimensions(t).width)).reduce(((t,e)=>t+e),0)}getContentHeight(){return this.strandSvgWrapper.getContentHeight()}}function $e(t,e){return"SS"===t?e+5+15+15:e+52+10+15}class Ve{constructor(){this.xmlNamespace="http://www.w3.org/2000/svg"}createElement(t){return document.createElementNS(this.xmlNamespace,t)}setAttributes(t,e){Object.entries(e).forEach((([e,n])=>{t.setAttribute(e,String(n))}))}createCanvas(t,e){const n=this.createElement("svg");return this.setAttributes(n,{id:"mySvg",width:t,height:e}),n}createCircleElement(t,e,n){const r=this.createElement("circle");return this.setAttributes(r,{cx:t.x,cy:t.y,r:e,fill:n}),r}createTextElement(t,e,n,r){const i=this.createElement("text");return this.setAttributes(i,{x:e.x,y:e.y,"font-size":n,"font-weight":"normal","font-family":"Arial",fill:r}),i.textContent=t,i}createStarElement(t,e){const n=this.createElement("polygon"),r=this.computeStarVertexCoordinates(t).map((t=>t.join(","))).join(" ");return this.setAttributes(n,{points:r,fill:e}),n}computeStarVertexCoordinates(t){const e=Math.PI/5,n=-e/2;return Array.from({length:10},((r,i)=>{const o=i%2==0?6:3,s=i*e+n;return[t.x+Math.cos(s)*o,t.y+Math.sin(s)*o]}))}createRectangleElement(t,e,n,r){const i=this.createElement("rect");return this.setAttributes(i,{x:t.x,y:t.y,width:e,height:n,fill:r}),i}}class je extends Pe{constructor(t,e,n){super(t,e,n),this.svgElementFactory=t,this.config=e,this.yShift=n,this._svgElements=[],this.titleText=this.getTitleText(),this._svgElements=[this.getTitle()]}get svgElements(){return this._svgElements}getTitle(){return this.svgElementFactory.createTextElement(this.titleText,{x:15,y:this.yShift+17},17,"black")}getContentWidth(){return Re.getTextDimensions(this.titleText,17).width}getContentHeight(){return Re.getTextDimensions(this.titleText,17).height}getTitleText(){const t=`${this.config.nucleotideSequences.SS.length}`,e=this.config.isAntisenseStrandIncluded?`/${this.config.nucleotideSequences.AS.length}`:"";return`${this.config.patternName} for ${t}${e}-mer`}}class qe extends Pe{constructor(t,e,n){super(t,e,n),this._svgElements=[];const{elements:r,width:i}=this.createLegendItems();this._svgElements=r,this.width=i}isPhosphorothioatePresent(){return Object.values(this.config.phosphorothioateLinkageFlags).flat().some((t=>t))}getModificationTypesList(){return[...new Set(Object.values(this.config.nucleotideSequences).flat().sort(((t,e)=>t.toLowerCase().localeCompare(e.toLowerCase()))))]}get svgElements(){return this._svgElements}createLegendItem(t,e){const n={x:e,y:this.yShift-6},r=t.includes("linkage")?this.svgElementFactory.createStarElement(n,"red"):this.svgElementFactory.createCircleElement(n,6,De(t));e+=12;const i={y:this.yShift,x:e};return{elements:[r,this.svgElementFactory.createTextElement(t,i,15,"var(--grey-6)")],width:12+Re.getTextDimensions(t,15).width}}createLegendItems(){let t=10;const e=[],n=e=>t+=e+15;if(this.isPhosphorothioatePresent()){const{elements:r,width:i}=this.createLegendItem("PTO linkage",t);n(i),e.push(r)}return this.getModificationTypesList().forEach((r=>{const{elements:i,width:o}=this.createLegendItem(r,t);n(o),e.push(i)})),{elements:e.flat(),width:t}}getContentHeight(){return 20}getContentWidth(){return this.width}}class Ge{constructor(t){this.svgElementFactory=new Ve;const e=ne().cloneDeep(t);let n=10;this.title=new je(this.svgElementFactory,e,n),n+=this.title.getContentHeight(),this.strands=new Fe(this.svgElementFactory,e,n),n+=this.strands.getContentHeight()+10,this.legend=new qe(this.svgElementFactory,e,n)}renderPattern(){const t=this.getGlobalWidth(),e=this.getGlobalHeight(),n=this.svgElementFactory.createCanvas(t,e),r=[this.title,this.strands,this.legend].map((t=>t.svgElements)).flat();return n.append(...r),n}getGlobalWidth(){const t=[this.title,this.strands,this.legend];return Math.max(...t.map((t=>t.getContentWidth())))}getGlobalHeight(){return[this.title,this.strands,this.legend].reduce(((t,e)=>t+e.getContentHeight()),10)}}class We{constructor(t){this.eventBus=t,this.svgDisplayDiv=Et.div([]),t.updateSvgContainer$.subscribe((()=>this.updateSvgContainer())),t.svgSaveRequested$.subscribe((()=>this.saveSvgAsPng()))}static createSvgDiv(t){return new We(t).svgDisplayDiv}updateSvgContainer(){$(this.svgDisplayDiv).empty();const t=this.eventBus.getPatternConfig();this.svgElement=this.createSvg(t),this.svgDisplayDiv.append(this.svgElement)}createSvg(t){return new Ge(t).renderPattern()}saveSvgAsPng(){const t=this.eventBus.getPatternName();Be.saveSvgAsPng(this.svgElement,t,{backgroundColor:"white"})}}class ze{constructor(t){this.eventBus=t,this.togglesContainer=Et.div([]),this.eventBus.uniqueNucleotidesChanged$().subscribe((()=>{this.updateContainer()}))}getContainer(){return this.togglesContainer}updateContainer(){Tt()(this.togglesContainer).empty(),Tt()(this.togglesContainer).append(this.createInputs())}createInputs(){const t=this.eventBus.getUniqueNucleotides().filter((t=>!Qt(t))).map((t=>this.createSingleInput(t)));return t.sort(((t,e)=>t.captionLabel.textContent.localeCompare(e.captionLabel.textContent))),Et.divH(t.map((t=>t.root)))}createSingleInput(t){const e=this.eventBus.getModificationsWithNumericLabels().includes(t),n=Et.input.bool(t,{value:e,onValueChanged:e=>this.handleNumericLabelToggle(t,e)});return Tt()(n.root).css("padding-right","20px"),n.setTooltip(`Show numeric labels for ${t}`),n}handleNumericLabelToggle(t,e){const n=this.eventBus.getModificationsWithNumericLabels();if(n.includes(t)===e)return;const r=e?n.concat(t):n.filter((e=>e!==t));this.eventBus.updateModificationsWithNumericLabels(r)}}class Ye{constructor(t,e){this.eventBus=t,this.dataManager=e,this.subscriptions=new Se}createContainer(){return Et.div([Et.h1("Translation example"),this.createTranslationExamples()],{style:{paddingTop:"20px"}})}createTranslationExamples(){const t=Et.divH([...this.getExampleElements()],"ui-form");return this.eventBus.antisenseStrandToggled$.subscribe((()=>{this.subscriptions.unsubscribeAll(),Tt()(t).empty(),Tt()(t).append(this.getExampleElements())})),t}getExampleElements(){return Bt.map((t=>new Ke(t,this.eventBus,this.subscriptions).create()))}}class Ke{constructor(t,e,n){this.strand=t,this.eventBus=e,this.subscriptions=n}create(){return this.eventBus.isAntisenseStrandActive()||"AS"!==this.strand?(this.inputExample=this.createInputExample(),this.outputExample=this.createOutputExample(this.inputExample.value),this.subscribeToEvents(),Et.block50([Et.h2(Pt[this.strand]),this.inputExample.root,this.outputExample.root],{style:{paddingRight:"20px"}})):Et.div([])}subscribeToEvents(){const t=this.eventBus.strandsLinkagesAndTerminalsUpdated$.subscribe((()=>{const t=this.generateExampleSequence();this.inputExample.value=t,this.outputExample.value=this.computeOutputValue(t)}));"AS"===this.strand&&this.subscriptions.add(t)}createInputExample(){const t=this.createTextInputForExamples(),e=this.generateExampleSequence();return t.value=e,t.setTooltip(`Example raw nucleotides input for ${Pt[this.strand]}`),t}generateExampleSequence(){return this.eventBus.getNucleotideSequences()[this.strand].map(((t,e)=>lt[e%lt.length])).join("")}createOutputExample(t){const e=this.createTextInputForExamples();return e.value=this.computeOutputValue(t),e.setTooltip(`Pattern applied to the example input for ${Pt[this.strand]}`),e}computeOutputValue(t){const e=this.eventBus.getNucleotideSequences()[this.strand],n=this.eventBus.getTerminalModifications()[this.strand];return Ae(t,e,this.eventBus.getPhosphorothioateLinkageFlags()[this.strand],n)}createTextInputForExamples(){const t=Et.input.textArea("",{value:""});return this.applyStylingToInput(t),t}applyStylingToInput(t){const e=t.root.getElementsByTagName("textarea")[0];e.setAttribute("readonly","true"),Tt()(e).css("resize","none"),Tt()(t.root).css("opacity","75%")}}class Je{constructor(t,e){this.eventBus=t,this.dataManager=e,this.svgDisplay=We.createSvgDiv(t)}getLayout(){const t=new ze(this.eventBus).getContainer(),e=this.generateDownloadControls(),n=new Ye(this.eventBus,this.dataManager).createContainer();return Et.panel([this.svgDisplay,t,e,n],{style:{overflowX:"scroll",padding:"12px 24px"}})}generateDownloadControls(){return Et.divH([this.createSavePatternButton(),this.createDownloadPngButton(),this.createShareLinkButton(),this.createInfoButton()],{style:{gap:"12px",marginTop:"12px"}})}createDownloadPngButton(){const t=Et.button("Get PNG",(()=>this.eventBus.requestSvgSave()));return Et.tooltip.bind(t,"Download pattern as PNG"),t}createInfoButton(){const t=Et.button(Et.iconFA("info-circle"),(()=>this.openInfoDialog()));return this.eventBus.patternHasUnsavedChanges$.subscribe((e=>{t.disabled=e})),Et.tooltip.bind(t,"View pattern metadata"),t}async openInfoDialog(){let e=this.dataManager.getCurrentUserName(),n=this.dataManager.getDefaultPatternName(),r=jt,i=jt;const o=new URLSearchParams(window.location.search).get("pattern");if(null!==o){const s=await this.dataManager.getPatternRecordByHash(o);if(null!==s){const o=s[Ht.AUTHOR_ID];if(e=(await t.dapi.users.find(o)).friendlyName,n=s[Ht.PATTERN_CONFIG][kt.PATTERN_NAME],void 0!==s[Ht.DATE]){const t=s[Ht.DATE][Ut.CREATE];void 0!==t&&(r=t);const e=s[Ht.DATE][Ut.MODIFY];void 0!==e&&(i=e)}}}const s=Et.divV([Et.divText(`Pattern Name: ${n}`),Et.divText(`Author: ${e}`),Et.divText(`Created: ${Xe(new Date(r))}`),Et.divText(`Modified: ${Xe(new Date(i))}`)]);t.shell.info(s)}createShareLinkButton(){const e=Et.button(Et.iconFA("link"),(()=>navigator.clipboard.writeText(window.location.href).then((()=>t.shell.info("Link to pattern copied to clipboard")))));return this.eventBus.patternHasUnsavedChanges$.subscribe((t=>{e.disabled=t})),Et.tooltip.bind(e,"Share pattern link"),e}createSavePatternButton(){const t=Et.button("Save",(()=>this.processSaveButtonClick()));return this.eventBus.patternHasUnsavedChanges$.subscribe((e=>{t.disabled=!e})),Et.tooltip.bind(t,"Save pattern to user storage"),t}processSaveButtonClick(){const e=this.eventBus.getPatternName();e!==this.dataManager.getDefaultPatternName()?""!==e?this.dataManager.savePatternToUserStorage(this.eventBus).then((()=>{t.shell.info(`Pattern ${e} saved`)})).catch((t=>this.handleErrorWhileSavingPattern(t))):t.shell.warning("Insert pattern name"):t.shell.warning("Cannot save default pattern")}handleErrorWhileSavingPattern(e){e instanceof qt?new Qe(this.eventBus,this.dataManager).show():e instanceof Gt?t.shell.warning(Et.div([Et.divText("Pattern already exists"),Et.button("Load",(()=>{const t=e.message;this.eventBus.requestLoadPatternInNewTab(t)}))])):console.error("Error while saving pattern",e)}}class Qe{constructor(t,e){this.eventBus=t,this.dataManager=e}show(){const t=this.eventBus.getPatternName(),e=Et.dialog(`Pattern "${t}" already exists`);e.add(Et.divText(`Pattern "${t}" already exists. Do you want to overwrite it?`)),e.show(),e.onOK((()=>this.processOverwriteNamesakePattern()))}processOverwriteNamesakePattern(){const e=this.eventBus.getPatternName();this.dataManager.overwriteExistingPatternInUserStorage(this.eventBus).then((()=>{t.shell.info(`Pattern ${e} overwritten`)})).catch((e=>{console.error("Error while overwriting pattern in user storage",e),t.shell.error("Error while overwriting pattern")}))}}function Xe(t){return t.toLocaleString().split(":").slice(0,-1).join(":")}class Ze extends Lt{constructor(t){super("Oligo Pattern"),this.th=t}getContent(){return async function(){const t=await Yt.getInstance(),e=new oe,n=await async function(t,e){const n=e.getPatternHash();if(!n)return e.clearPatternURL(),t.getDefaultPatternRecord();let r=await t.getPatternRecordByHash(n);return r||(e.clearPatternURL(),r=t.getDefaultPatternRecord()),r}(t,e),r=new re(t,n);e.subscribeToObservables(r);const i=new Le(r,t).getLayout(),o=new Je(r,t).getLayout();return Et.splitH([i,o],{},!0)}()}}var tn=n(507),en={};function nn(t){var e;return"string"==typeof t||t instanceof String?t:("object"==typeof t||t instanceof Object)&&"$thrownJsError"in t?nn(t.$thrownJsError):t instanceof Error?null!==(e=t.stack)&&void 0!==e?e:t.message:t.toString()}en.styleTagTransform=ve(),en.setAttributes=de(),en.insert=he().bind(null,"head"),en.domAPI=le(),en.insertStyleElement=ge(),ae()(tn.A,en),tn.A&&tn.A.locals&&tn.A.locals;var rn,on=n(74),sn={};sn.styleTagTransform=ve(),sn.setAttributes=de(),sn.insert=he().bind(null,"head"),sn.domAPI=le(),sn.insertStyleElement=ge(),ae()(on.A,sn),on.A&&on.A.locals&&on.A.locals;class an{constructor(t,e,n=!0){this.textInputBase=t,this.painter=e,Tt()(this.root).addClass("st-colored-text-input"),n&&this.textInputBase.onChanged.subscribe((()=>{Tt()(this.textArea).css("height",0),Tt()(this.textArea).css("height",this.textArea.scrollHeight+"px")})),this.highlights=Et.div([]),this.root.appendChild(this.highlights),this.colorize(),this.textInputBase.onChanged.subscribe((()=>this.colorize()))}get textArea(){return this.textInputBase.root.getElementsByTagName("textarea").item(0)}get inputBase(){return this.textInputBase}get root(){return this.textInputBase.root}colorize(){const t=this.painter(this.textInputBase.value);this.highlights.innerHTML="",t.forEach((t=>this.highlights.appendChild(t)))}}!function(t){t.TYPE="V2000",t[t.NUM_OF_HEADER_LINES=3]="NUM_OF_HEADER_LINES",t[t.NUM_OF_COUNTS_DIGITS=3]="NUM_OF_COUNTS_DIGITS",t[t.ATOM_TYPE_COL=4]="ATOM_TYPE_COL",t[t.FIRST_BONDED_ATOM_COL=1]="FIRST_BONDED_ATOM_COL",t[t.BOND_TYPE_COL=3]="BOND_TYPE_COL",t[t.RGP_SHIFT=8]="RGP_SHIFT",t[t.MAX_ATOM_COUNT=999]="MAX_ATOM_COUNT",t.RGP_LINE_START="M  RGP",t.ATOM_ALIAS_LINE_START="A  ",t.END="M  END"}(rn||(rn={}));class un{constructor(t){this.init(t)}init(t){this.fileContent=t.replace(/\r/g,""),this._atomCount=void 0,this._atomTypes=void 0,this._bondCount=void 0,this._bondTypes=void 0,this.xyzAtomCoordinates=void 0,this._pairsOfBondedAtoms=void 0}get atomCount(){return void 0===this._atomCount&&this.setAtomAndBondCounts(),this._atomCount}get bondCount(){return void 0===this._bondCount&&this.setAtomAndBondCounts(),this._bondCount}get x(){var t;return null!==(t=this.xyzAtomCoordinates)&&void 0!==t||(this.xyzAtomCoordinates=this.parseAtomCoordinates()),this.xyzAtomCoordinates.x}get y(){var t;return null!==(t=this.xyzAtomCoordinates)&&void 0!==t||(this.xyzAtomCoordinates=this.parseAtomCoordinates()),this.xyzAtomCoordinates.y}get z(){var t;return null!==(t=this.xyzAtomCoordinates)&&void 0!==t||(this.xyzAtomCoordinates=this.parseAtomCoordinates()),this.xyzAtomCoordinates.z}get atomTypes(){var t;return null!==(t=this._atomTypes)&&void 0!==t||(this._atomTypes=this.parseAtomTypes()),this._atomTypes}get pairsOfBondedAtoms(){var t;return null!==(t=this._pairsOfBondedAtoms)&&void 0!==t||(this._pairsOfBondedAtoms=this.parseBondedAtomPairs()),this._pairsOfBondedAtoms}get bondTypes(){var t;return null!==(t=this._bondTypes)&&void 0!==t||(this._bondTypes=this.parseBondTypes()),this._bondTypes}setAtomAndBondCounts(){const{atomCount:t,bondCount:e}=this.parseAtomAndBondCounts();this._atomCount=t,this._bondCount=e}getNextColumnIdx(t){for(;!this.isWhitespace(t);)++t;for(;this.isWhitespace(t);)++t;return t}shiftIdxToSpecifiedColumn(t,e){let n=t;const r=this.isWhitespace(n)?e:e-1;for(let t=0;t<r;t++)n=this.getNextColumnIdx(n);return n}parseAtomTypes(){const t=this.atomCount,e=new Array(t);let n=this.getAtomBlockIdx();for(let r=0;r<t;r++)n=this.shiftIdxToAtomType(n),e[r]=this.parseAtomType(n),n=this.getNextLineIdx(n);return e}parseAtomCoordinates(){const t=new Float32Array(this.atomCount),e=new Float32Array(this.atomCount),n=new Float32Array(this.atomCount);let r=this.getAtomBlockIdx();for(let i=0;i<this.atomCount;i++){r=this.shiftIdxToXColumn(r);for(const o of[t,e,n])o[i]=this.parseFloatValue(r),r=this.getNextColumnIdx(r);r=this.getNextLineIdx(r)}return{x:t,y:e,z:n}}parseBondedAtomPairs(){const t=new Array(this.bondCount);let e=this.getBondBlockIdx();for(let n=0;n<this.bondCount;n++){e=this.shiftIdxToBondedAtomsPair(e);const r=new Uint16Array(2);r[0]=this.parseIntValue(e),e=this.getNextColumnIdx(e),r[1]=this.parseIntValue(e),t[n]=r,e=this.getNextLineIdx(e)}return t}parseBondTypes(){const t=this.bondCount,e=new Uint16Array(t);let n=this.getBondBlockIdx();for(let r=0;r<t;r++)n=this.shiftIdxToBondType(n),e[r]=this.parseIntValue(n),n=this.getNextLineIdx(n);return e}isWhitespace(t){const e=this.fileContent[t];return" "===e||"\t"===e}getNextLineIdx(t){return"\n"!==this.fileContent[t]?this.fileContent.indexOf("\n",t)+1:t+1}parseFloatValue(t){return this.parseNumericValue(parseFloat,t)}parseIntValue(t){return this.parseNumericValue(parseInt,t)}parseNumericValue(t,e){let n=e+1;for(;!this.isWhitespace(n);)++n;return t(this.fileContent.substring(e,n))}}class ln extends un{constructor(t){super(t),this.init(t)}init(t){super.init(t)}parseAtomType(t){let e=t,n=e;return this.isQuote(e)?(n=this.getNextIdenticalChar(e),e++):n=this.fileContent.indexOf(" ",n),this.fileContent.substring(e,n)}isQuote(t){const e=this.fileContent[t].charCodeAt(0);return 39===e||34===e}getNextIdenticalChar(t){const e=this.fileContent[t];return e?this.fileContent.indexOf(e,t+1):-1}isQuery(){return this.isQueryOrFragment(((t,e)=>{return 39===t||34===t||76===t&&!((n=this.fileContent.charCodeAt(e+1))>64&&n<91||n>96&&n<123);var n}))}isFragment(){return this.isQueryOrFragment((t=>82===t||42===t))}isQueryOrFragment(t){const e=this.atomCount;let n=this.getAtomBlockIdx();for(let r=0;r<e;r++){if(n=this.shiftIdxToAtomType(n),t(this.fileContent.charCodeAt(n),n))return!0;n=this.getNextLineIdx(n)}return!1}}class cn extends ln{constructor(t){super(t)}getAtomLines(){const t=this.getAtomBlockIdx(),e=this.getBondBlockIdx();return this.fileContent.substring(t,e).split("\n").slice(0,this.atomCount)}getBondLines(){const t=this.getBondBlockIdx();return this.fileContent.substring(t).split("\n").slice(0,this.bondCount)}getRGroupIdToAtomicIdxMap(){const t=new Map,e=this.fileContent.split("\n");e.filter((t=>t.startsWith(rn.RGP_LINE_START))).forEach((e=>{const n=this.getAtomIdxToRgpIdxList(e);for(const[e,r]of n){if(t.has(e))throw new Error(`R group ${e} is already in the map`);t.set(e,r)}}));const n=e.map(((t,e)=>{if(t.startsWith(rn.ATOM_ALIAS_LINE_START))return e})).filter((t=>void 0!==t)),r=n.map((t=>e[t])),i=n.map((t=>e[t+1]));r.forEach(((e,n)=>{const r=parseInt(e.split(/\s+/)[1])-1,o=parseInt(i[n].substring(1));if(t.has(o))throw new Error(`R group ${o} is already in the map`);t.set(o,r)}));const o=this.getRGroupAtomicIndices().filter((e=>!Array.from(t.values()).includes(e)));if(0!==o.length)throw new Error(`Unaccounted R group indices: ${o}`);return t}getAtomIdxToRgpIdxList(t){const e=t.split(/\s+/).filter((t=>t)).slice(3).map((t=>parseInt(t))),n=new Array(e.length/2);for(let t=0;t<e.length;t+=2)n[t/2]=[e[t+1],e[t]-1];return n}getRGroupAtomicIndices(){return this.atomTypes.map(((t,e)=>{if(t.includes("R#"))return e})).filter((t=>void 0!==t))}static isValidMolfile(t){return-1!==t.indexOf(rn.TYPE)&&-1!==t.indexOf(rn.END)}shiftIdxToAtomType(t){return this.shiftIdxToSpecifiedColumn(t,rn.ATOM_TYPE_COL)}getCountsLineIdx(){let t=0;for(let e=0;e<rn.NUM_OF_HEADER_LINES;++e)t=this.getNextLineIdx(t);return t}getAtomBlockIdx(){let t=this.getCountsLineIdx();return t=this.getNextLineIdx(t),t}shiftIdxToXColumn(t){return this.getNextColumnIdx(t)}shiftIdxToBondedAtomsPair(t){return this.shiftIdxToSpecifiedColumn(t,rn.FIRST_BONDED_ATOM_COL)}shiftIdxToBondType(t){return this.shiftIdxToSpecifiedColumn(t,rn.BOND_TYPE_COL)}getBondBlockIdx(){let t=this.getAtomBlockIdx();for(let e=0;e<this.atomCount;e++)t=this.getNextLineIdx(t);return t}parseAtomAndBondCounts(){let t=this.getCountsLineIdx(),e=t+rn.NUM_OF_COUNTS_DIGITS;const n=parseInt(this.fileContent.substring(t,e));return t=e,e+=rn.NUM_OF_COUNTS_DIGITS,{atomCount:n,bondCount:parseInt(this.fileContent.substring(t,e))}}}class hn extends ln{constructor(t){super(t),this.init(t)}getAtomLines(){const t=this.getAtomBlockIdx(),e=this.getBondBlockIdx();return this.fileContent.substring(t,e).split("\n").slice(0,this.atomCount)}getBondLines(){const t=this.getBondBlockIdx();return this.fileContent.substring(t).split("\n").slice(0,this.bondCount)}getRGroupIdToAtomicIdxMap(){const t=new Map;return this.getAtomLines().forEach(((e,n)=>{const r=e.match(/RGROUPS=\(([\d\s]+)\)/);if(r){const e=r[1].split(/\s+/).map((t=>parseInt(t)));if(e.length>2)throw new Error(`R group data ${e} has more than 2 elements`);const i=e[1];if(t.has(i))throw new Error(`R group ${i} is already in the map`);t.set(i,n)}})),t}shiftIdxToAtomType(t){return this.shiftIdxToSpecifiedColumn(t,4)}getCountsLineIdx(){return this.fileContent.indexOf("M  V30 COUNTS ")}getAtomBlockIdx(){let t=this.fileContent.indexOf("M  V30 BEGIN ATOM");return t=this.getNextLineIdx(t),t}shiftIdxToXColumn(t){let e=this.shiftIdxToAtomType(t);return this.isQuote(e)?(e=this.getNextIdenticalChar(e),e=this.getNextColumnIdx(e),e):this.shiftIdxToSpecifiedColumn(t,5)}shiftIdxToBondedAtomsPair(t){return this.shiftIdxToSpecifiedColumn(t,5)}shiftIdxToBondType(t){return this.shiftIdxToSpecifiedColumn(t,4)}getBondBlockIdx(){return this.getNextLineIdx(this.fileContent.indexOf("M  V30 BEGIN BOND"))}static isValidMolfile(t){return-1!==t.indexOf("V3000")&&-1!==t.indexOf("M  END")}parseAtomAndBondCounts(){let t=this.fileContent.indexOf("M  V30 COUNTS ")+14,e=this.fileContent.indexOf(" ",t+1);const n=parseInt(this.fileContent.substring(t,e));return t=e+1,e=this.fileContent.indexOf(" ",t+1),{atomCount:n,bondCount:parseInt(this.fileContent.substring(t,e))}}}class fn{constructor(){}static getInstance(t){if(fn.isMolfileV2K(t))return new cn(t);if(fn.isMolfileV3K(t))return new hn(t);throw new Error("Malformed molfile")}static isMolfileV2K(t){return cn.isValidMolfile(t)}static isMolfileV3K(t){return hn.isValidMolfile(t)}}const dn=class extends Error{constructor(t){super(t)}};class pn{constructor(t){this.molblock=t}get molblock(){return this._validMolBlock}set molblock(t){if(""!==t){try{this.validateMolBlock(t)}catch(e){e instanceof dn&&(t="");const n=nn(e);console.error(n)}this._validMolBlock=t}else this._validMolBlock=t}validateMolBlock(t){if(""===t)throw new dn("MoleculeImage: invalid molblock")}async drawMolBlockOnCanvas(e){try{await t.functions.call("Chem:canvasMol",{x:0,y:0,w:e.width,h:e.height,canvas:e,molString:this.molblock,scaffoldMolString:"",options:{normalizeDepiction:!1,straightenDepiction:!1}})}catch(t){const e=nn(t);console.error(e)}}getMoleculeDimensions(){const t=fn.getInstance(this.molblock),e=Math.max(...t.x)-Math.min(...t.x);return{height:Math.max(...t.y)-Math.min(...t.y),width:e}}async zoomIn(){const t=Et.dialog({title:"Molecule",showFooter:!1}),e=.7*Tt()(window).height(),n=this.getMoleculeDimensions(),r=e/n.height,i=e,o=n.width*r,s=Et.canvas(o,i);await this.drawMolBlockOnCanvas(s);const a=Et.block([s],{style:{overflowX:"scroll"}});t.add(a).showModal(!0),Tt()(t.root).find(".d4-dialog-contents").removeClass("ui-form"),Tt()(t.root).find(".d4-dialog-contents").removeClass("ui-panel"),Tt()(t.root).find(".d4-dialog-contents").addClass("ui-box"),Tt()(t.root).find(".d4-dialog-contents").css("padding","0")}async drawMolecule(t,e,n){t.innerHTML="";const r=Et.canvas(e*window.devicePixelRatio,n*window.devicePixelRatio);r.style.width=`${e}px`,r.style.height=`${n}px`,r.style.cursor="zoom-in",this.drawMolBlockOnCanvas(r),r.addEventListener("click",(async()=>{await this.zoomIn()})),t.append(Et.tooltip.bind(r,"Click to zoom"))}}class gn extends Error{constructor(t,e){super(t,e)}}class mn{constructor(t,e){this.sequence=t,this.codeMap=e}parseSequence(){const t=this.parseRawSequence();return this.addLinkers(t)}addLinkers(t){const e=[];return t.forEach(((n,r)=>{const i=this.getSymbolForCode(n);r>0&&function(t){return kr.jsonData.monomersWithPhosphate.left.includes(t)}(i)&&e.pop(),e.push(i);const o=vn(i),s=r===t.length-1,a=r+1<t.length&&vn(this.getSymbolForCode(t[r+1]));o||function(t){return kr.jsonData.monomersWithPhosphate.right.includes(t)}(i)||a||s||e.push("p")})),e}getSymbolForCode(t){let e=this.codeMap.get(t);return e??(e=t),e}parseRawSequence(){const t=this.getAllCodesOfFormat(),e=[];let n=0;for(;n<this.sequence.length;){const r=t.find((t=>t===this.sequence.substring(n,n+t.length)));if(void 0===r)throw new gn(`Unable to match a monomer for the rest of the sequence '${this.sequence.slice(n)}'.`);e.push(r),n+=r.length}return e}getAllCodesOfFormat(){return ht(Array.from(this.codeMap.keys()))}}function vn(t){return kr.jsonData.monomersWithPhosphate.phosphate.includes(t)}class yn{constructor(t,e=!1,n){this.invert=e,this.lib=kr.monomerLibWrapper;const r=this.lib.getCodeToSymbolMap(n);this.parser=new mn(t,r)}convert(){const t=this.parser.parseSequence(),e=[];t.forEach(((t,n)=>{const r=this.getMonomerMolfile(t,n);e.push(r)}));let n=this.getPolymerMolfile(e);return this.invert&&(n=this.reflect(n),n=this.invertBondConfiguration(n)),n}invertBondConfiguration(t){const e=t.indexOf("M  V30 BEGIN BOND"),n=t.indexOf("M  V30 END BOND");let r=t.substring(e,n);return r=r.replace(/(CFG=)([13])/g,((t,e,n)=>"1"===n?`${e}3`:"3"===n?`${e}1`:t)),t.substring(0,e)+r+t.substring(n)}getMonomerMolfile(t,e){const n=this.lib.getMolfileBySymbol(t);return this.lib.isModification(t)?0===e?this.reflect(n):n:this.rotateNucleotidesV3000(n)}getPolymerMolfile(t){return this.linkV3000(t)}reflect(t){const e=this.extractAtomDataV3000(t),n=e.atomIndex.length,r=e.atomIndex.indexOf(1),i=e.atomIndex.indexOf(n),o=(e.x[i]+e.x[r])/2,s=(e.y[i]+e.y[r])/2;for(let t=0;t<n;t++)e.x[t]-=o,e.y[t]-=s;for(let t=0;t<n;t++)e.x[t]=-e.x[t];const a=e.x[r];for(let t=0;t<n;t++)e.x[t]-=a;let u=t.indexOf("M  V30 BEGIN ATOM");u=t.indexOf("\n",u);let l=u;for(let r=0;r<n;r++)u=t.indexOf("V30",u)+4,u=t.indexOf(" ",u)+1,u=t.indexOf(" ",u)+1,l=t.indexOf(" ",u)+1,l=t.indexOf(" ",l),u=(t=t.slice(0,u)+e.x[r]+" "+e.y[r]+t.slice(l)).indexOf("\n",u)+1;return t}extractAtomDataV3000(t){const e=this.extractAtomsBondsNumbersV3000(t);let n=t.indexOf("M  V30 BEGIN ATOM");n=t.indexOf("\n",n);let r=n;const i=Array(e.natom),o=Array(e.natom),s=Array(e.natom),a=Array(e.natom);for(let u=0;u<e.natom;u++)n=t.indexOf("V30",n)+4,r=t.indexOf(" ",n),i[u]=parseInt(t.substring(n,r)),n=r+1,r=t.indexOf(" ",n),o[u]=t.substring(n,r),n=r+1,r=t.indexOf(" ",n),s[u]=parseFloat(t.substring(n,r)),n=r+1,r=t.indexOf(" ",n),a[u]=parseFloat(t.substring(n,r)),n=t.indexOf("\n",n)+1;return{atomIndex:i,atomType:o,x:s,y:a}}extractAtomsBondsNumbersV3000(t){let e=(t=t.replaceAll("\r","")).indexOf("COUNTS")+7,n=t.indexOf(" ",e);const r=parseInt(t.substring(e,n));return e=n+1,n=t.indexOf(" ",e),{natom:r,nbond:parseInt(t.substring(e,n))}}rotateNucleotidesV3000(t){const e=this.extractAtomDataV3000(t),n=e.atomIndex.length,r=e.atomIndex.indexOf(1),i=e.atomIndex.indexOf(n);n>8&&this.fix5Prime(e,r,i);const o=(e.x[i]+e.x[r])/2,s=(e.y[i]+e.y[r])/2;for(let t=0;t<n;t++)e.x[t]-=o,e.y[t]-=s;let a=0;if(0===e.x[r])a=e.y[r]>e.y[i]?Math.PI/2:3*Math.PI/2;else if(0===e.y[r])a=e.x[r]>e.x[i]?Math.PI:0;else{const t=e.y[r]/e.x[r];a=t>0?e.x[r]>0?Math.PI-Math.atan(t):2*Math.PI-Math.atan(t):e.x[r]>0?-Math.PI-Math.atan(t):Math.atan(t)}const u=Math.cos(a),l=Math.sin(a);for(let t=0;t<n;t++){const n=e.x[t];e.x[t]=n*u-e.y[t]*l,e.y[t]=n*l+e.y[t]*u}const c=e.x[r];for(let t=0;t<n;t++)e.x[t]-=c;let h=t.indexOf("M  V30 BEGIN ATOM");h=t.indexOf("\n",h);let f=h;for(let r=0;r<n;r++)h=t.indexOf("V30",h)+4,h=t.indexOf(" ",h)+1,h=t.indexOf(" ",h)+1,f=t.indexOf(" ",h)+1,f=t.indexOf(" ",f),h=(t=t.slice(0,h)+e.x[r]+" "+e.y[r]+t.slice(f)).indexOf("\n",h)+1;return t}linkV3000(t,e=!0){let n="\n  Datagrok macromolecule handler\n\n";n+="  0  0  0  0  0  0            999 V3000\n",n+="M  V30 BEGIN CTAB\n";let r="",i="",o="";const s=[];let a=0,u=0,l=0;for(let e=0;e<t.length;e++){const n=t[e].includes("MODIFICATION")&&0===e;let o=0;n&&(o=this.extractAtomDataV3000(t[e]).atomIndex.length),t[e]=t[e].replaceAll("(-\nM  V30 ","(").replaceAll("-\nM  V30 ","").replaceAll(" )",")");const c=this.extractAtomsBondsNumbersV3000(t[e]),h=this.extractAtomDataV3000(t[e]);let f=t[e].indexOf("M  V30 BEGIN ATOM");f=t[e].indexOf("\n",f);let d=f,p=f;for(let r=0;r<c.natom;r++)if(1!==h.atomIndex[r]||0===e){d=t[e].indexOf("V30",d)+4,p=t[e].indexOf(" ",d);let r=0;n?(r=parseInt(t[e].substring(d,p)),1===r?r=o:r===o&&(r=1),r+=a):r=parseInt(t[e].substring(d,p))+a,t[e]=t[e].slice(0,d)+r+t[e].slice(p),d=t[e].indexOf(" ",d)+1,d=t[e].indexOf(" ",d)+1,p=t[e].indexOf(" ",d);const i=l-h.x[0];let s=Math.round(1e4*(parseFloat(t[e].substring(d,p))+i))/1e4;t[e]=t[e].slice(0,d)+s+t[e].slice(p),d=t[e].indexOf(" ",d)+1,p=t[e].indexOf(" ",d),s=Math.round(1e4*parseFloat(t[e].substring(d,p)))/1e4,t[e]=t[e].slice(0,d)+s+t[e].slice(p),d=t[e].indexOf("\n",d)+1}else d=t[e].indexOf("M  V30",d)-1,p=t[e].indexOf("\n",d+1),t[e]=t[e].slice(0,d)+t[e].slice(p);const g=t[e].indexOf("M  V30 END ATOM");r+=t[e].substring(f+1,g);let m=t[e].indexOf("M  V30 BEGIN BOND");m=t[e].indexOf("\n",m),d=m,p=m;for(let r=0;r<c.nbond;r++){d=t[e].indexOf("V30",d)+4,p=t[e].indexOf(" ",d);const r=parseInt(t[e].substring(d,p))+u;t[e]=t[e].slice(0,d)+r+t[e].slice(p),d=t[e].indexOf(" ",d)+1,d=t[e].indexOf(" ",d)+1,p=t[e].indexOf(" ",d);let i=0;n?(i=parseInt(t[e].substring(d,p)),1===i?i=o:i===o&&(i=1),i+=a):i=parseInt(t[e].substring(d,p))+a,t[e]=t[e].slice(0,d)+i+t[e].slice(p),d=t[e].indexOf(" ",d)+1,p=Math.min(t[e].indexOf("\n",d),t[e].indexOf(" ",d)),i=0,n?(i=parseInt(t[e].substring(d,p)),1===i?i=o:i===o&&(i=1),i+=a):i=parseInt(t[e].substring(d,p))+a,t[e]=t[e].slice(0,d)+i+t[e].slice(p),d=t[e].indexOf("\n",d)+1}const v=t[e].indexOf("M  V30 END BOND");i+=t[e].substring(m+1,v);let y=t[e].indexOf("M  V30 MDLV30/STEABS ATOMS=(");for(;-1!==y;){y+=28;const n=t[e].indexOf(")",y);t[e].substring(y,n).split(" ").slice(1).forEach((t=>{s.push(parseInt(t)+a)})),y=n,y=t[e].indexOf("M  V30 MDLV30/STEABS ATOMS=(",y)}a+=c.natom-1,u+=c.nbond,l+=n?Math.max(...h.x):h.x[c.natom-1]-h.x[0]}const c=Math.ceil(s.length/4);o+="M  V30 MDLV30/STEABS ATOMS=("+s.length+" -\n";for(let t=0;t<c;t++){o+="M  V30 ";const e=t+1===c?s.length-4*(c-1):4;for(let n=0;n<e;n++)o+=n+1===e?t===c-1?s[4*t+n]+")\n":s[4*t+n]+" -\n":s[4*t+n]+" "}return a++,n+="M  V30 COUNTS "+a+" "+u+" 0 0 0\n",n+="M  V30 BEGIN ATOM\n",n+=r,n+="M  V30 END ATOM\n",n+="M  V30 BEGIN BOND\n",n+=i,n+="M  V30 END BOND\n",e&&s.length>0?(n+="M  V30 BEGIN COLLECTION\n",n+=o,n+="M  V30 END COLLECTION\n"):n=n.replace(/ CFG=\d/g," "),n+="M  V30 END CTAB\n",n+="M  END",n}fix5Prime(t,e,n){const r=e+1,i=t.x[r],o=t.y[r],s=t.x[n]-i,a=t.y[n]-o,u=t.x[e]-i,l=t.y[e]-o,c=u*Math.cos(2*Math.PI/3)-l*Math.sin(2*Math.PI/3),h=u*Math.sin(2*Math.PI/3)+l*Math.cos(2*Math.PI/3),f=u-s,d=l-a,p=c-s,g=h-a;Math.sqrt(g*g+p*p)>=Math.sqrt(d*d+f*f)&&(t.x[e]=c+i,t.y[e]=h+o)}}function bn(t,e=!0){let n="\n  Datagrok macromolecule handler\n\n";n+="  0  0  0  0  0  0            999 V3000\n",n+="M  V30 BEGIN CTAB\n";let r="",i="",o="";const s=[];let a=0,u=0,l=0;if(t.antiStrands.length>0)for(let e=0;e<t.antiStrands.length;e++)t.antiStrands[e]=wn(t.antiStrands[e]);let c=!1;const h=t.senseStrands.concat(t.antiStrands);let f=0;for(let e=0;e<h.length;e++){h[e]=h[e].replaceAll("(-\nM  V30 ","(").replaceAll("-\nM  V30 ","").replaceAll(" )",")");const n=Cn(h[e]),o=An(h[e]);if(e>=t.senseStrands.length?!1===c&&(c=!0,l=0):f=Math.min(f,Math.min(...o.y.filter((t=>t<0)))),c){const t=Math.min(...o.x)-l,e=Math.max(...o.y)+5;for(let e=0;e<o.x.length;e++)o.x[e]-=t;for(let t=0;t<o.y.length;t++)o.y[t]-=e-f}let d=h[e].indexOf("M  V30 BEGIN ATOM");d=h[e].indexOf("\n",d);let p=d,g=d;for(let t=0;t<n.natom;t++){p=h[e].indexOf("V30",p)+4,g=h[e].indexOf(" ",p);const n=parseInt(h[e].substring(p,g))+a;h[e]=h[e].slice(0,p)+n+h[e].slice(g),p=h[e].indexOf(" ",p)+1,p=h[e].indexOf(" ",p)+1,g=h[e].indexOf(" ",p);let r=Math.round(1e4*o.x[t])/1e4;h[e]=h[e].slice(0,p)+r+h[e].slice(g),p=h[e].indexOf(" ",p)+1,g=h[e].indexOf(" ",p),r=Math.round(1e4*o.y[t])/1e4,h[e]=h[e].slice(0,p)+r+h[e].slice(g),p=h[e].indexOf("\n",p)+1}const m=h[e].indexOf("M  V30 END ATOM");r+=h[e].substring(d+1,m);let v=h[e].indexOf("M  V30 BEGIN BOND");v=h[e].indexOf("\n",v),p=v,g=v;for(let t=0;t<n.nbond;t++){p=h[e].indexOf("V30",p)+4,g=h[e].indexOf(" ",p);const t=parseInt(h[e].substring(p,g))+u;h[e]=h[e].slice(0,p)+t+h[e].slice(g),p=h[e].indexOf(" ",p)+1,p=h[e].indexOf(" ",p)+1,g=h[e].indexOf(" ",p);let n=parseInt(h[e].substring(p,g))+a;h[e]=h[e].slice(0,p)+n+h[e].slice(g),p=h[e].indexOf(" ",p)+1,g=Math.min(h[e].indexOf("\n",p),h[e].indexOf(" ",p)),n=parseInt(h[e].substring(p,g))+a,h[e]=h[e].slice(0,p)+n+h[e].slice(g),p=h[e].indexOf("\n",p)+1}const y=h[e].indexOf("M  V30 END BOND");i+=h[e].substring(v+1,y);let b=h[e].indexOf("M  V30 MDLV30/STEABS ATOMS=(");for(;-1!==b;){b+=28;const t=h[e].indexOf(")",b);h[e].substring(b,t).split(" ").slice(1).forEach((t=>{s.push(parseInt(t)+a)})),b=t,b=h[e].indexOf("M  V30 MDLV30/STEABS ATOMS=(",b)}a+=n.natom,u+=n.nbond,l+=Math.max(...o.x)+5}const d=Math.ceil(s.length/4);o+="M  V30 MDLV30/STEABS ATOMS=("+s.length+" -\n";for(let t=0;t<d;t++){o+="M  V30 ";const e=t+1===d?s.length-4*(d-1):4;for(let n=0;n<e;n++)o+=n+1===e?t===d-1?s[4*t+n]+")\n":s[4*t+n]+" -\n":s[4*t+n]+" "}return n+="M  V30 COUNTS "+a+" "+u+" 0 0 0\n",n+="M  V30 BEGIN ATOM\n",n+=r,n+="M  V30 END ATOM\n",n+="M  V30 BEGIN BOND\n",n+=i,n+="M  V30 END BOND\n",e&&s.length>0?(n+="M  V30 BEGIN COLLECTION\n",n+=o,n+="M  V30 END COLLECTION\n"):n=n.replace(/ CFG=\d/g," "),n+="M  V30 END CTAB\n",n+="M  END",n}function wn(t){const e=An(t),n=e.atomIndex.length,r=(Math.max(...e.x)+Math.min(...e.x))/2,i=(Math.max(...e.y)+Math.min(...e.y))/2;for(let t=0;t<n;t++)e.x[t]-=r,e.y[t]-=i;const o=Math.PI,s=Math.cos(o),a=Math.sin(o);for(let t=0;t<n;t++){const n=e.x[t];e.x[t]=n*s-e.y[t]*a,e.y[t]=n*a+e.y[t]*s}const u=Math.max(...e.y);for(let t=0;t<n;t++)e.x[t]+=r,e.y[t]-=u;let l=t.indexOf("M  V30 BEGIN ATOM");l=t.indexOf("\n",l);let c=l;for(let r=0;r<n;r++)l=t.indexOf("V30",l)+4,l=t.indexOf(" ",l)+1,l=t.indexOf(" ",l)+1,c=t.indexOf(" ",l)+1,c=t.indexOf(" ",c),l=(t=t.slice(0,l)+e.x[r]+" "+e.y[r]+t.slice(c)).indexOf("\n",l)+1;return t}function Cn(t){let e=(t=t.replaceAll("\r","")).indexOf("COUNTS")+7,n=t.indexOf(" ",e);const r=parseInt(t.substring(e,n));return e=n+1,n=t.indexOf(" ",e),{natom:r,nbond:parseInt(t.substring(e,n))}}function An(t){const e=Cn(t);let n=t.indexOf("M  V30 BEGIN ATOM");n=t.indexOf("\n",n);let r=n;const i=Array(e.natom),o=Array(e.natom),s=Array(e.natom),a=Array(e.natom);for(let u=0;u<e.natom;u++)n=t.indexOf("V30",n)+4,r=t.indexOf(" ",n),i[u]=parseInt(t.substring(n,r)),n=r+1,r=t.indexOf(" ",n),o[u]=t.substring(n,r),n=r+1,r=t.indexOf(" ",n),s[u]=parseFloat(t.substring(n,r)),n=r+1,r=t.indexOf(" ",n),a[u]=parseFloat(t.substring(n,r)),n=t.indexOf("\n",n)+1;return{atomIndex:i,atomType:o,x:s,y:a}}function xn(t,e,n){if(""===t)return"";const r=n.createFormatDetector(t).getFormat();if(!r)return"";let i="";try{i=new yn(t,e,r).convert()}catch(t){const e=nn(t);console.error(e)}return i}function _n(t,e,n,r,i){const o=[t,e,n].filter((t=>""!==t.strand));return 1===o.length?xn(o[0].strand,o[0].invert,i):bn({senseStrands:[xn(t.strand,t.invert,i)],antiStrands:[xn(e.strand,e.invert,i),xn(n.strand,n.invert,i)].filter((t=>""!==t))},r)}const En=["ss","as","as2"];class Sn{constructor(){this.th=kr,this.onInput=new Kt.Subject,this.onInvalidInput=new Kt.Subject,this.inputBase=Object.fromEntries(En.map((t=>{const e=Et.input.textArea(t.toUpperCase(),{value:"",onValueChanged:()=>{this.onInput.next(),Tt()(e.root.getElementsByTagName("div")).css("padding-left","38px")}});return[t,e]}))),this.useChiralInput=Et.input.bool("Use chiral",{value:!0}),this.saveAllStrandsInput=Et.input.bool("Save as one entity",{value:!0}),Et.tooltip.bind(this.saveAllStrandsInput.root,"Save SDF with all strands in one molfile"),this.directionInversion=Object.fromEntries(En.map((t=>[t,!1]))),this.moleculeImgDiv=Et.block([]),Tt()(this.moleculeImgDiv).addClass("st-structure-mol-img"),e.debounce(this.onInput,300).subscribe((async()=>{await this.updateMoleculeImg()})),e.debounce(this.onInvalidInput,1e3).subscribe((async()=>{t.shell.warning("Insert Sense strand")}))}async getHtmlDivElement(t){const e=this.getTableInput(t),n=this.getBoolInputsAndButton();await this.updateMoleculeImg();const r=Et.divH([n,this.moleculeImgDiv]);Tt()(r).addClass("st-structure-bottom");const i=Et.divV([e,r]);return Tt()(i).addClass("st-structure-body"),i}getBoolInputsAndButton(){const e=Et.buttonsInput([Et.bigButton("Save SDF",(()=>{const e=this.getStrandData();!function(e,n,r,i,o,s){const a=[e.strand,n.strand,r.strand].filter((t=>""!==t));if(0===a.length||1===a.length&&""===e.strand)t.shell.warning("Enter SENSE_STRAND and optionally ANTISENSE_STRAND/AS2 to save SDF");else{let u;if(o)u=_n(e,n,r,i,s)+"\n$$$$\n";else{const h=xn(e.strand,e.invert,s),f=xn(n.strand,n.invert,s),d=xn(r.strand,r.invert,s);u=h+"\n> <Sequence>\nSense Strand\n$$$$\n",f&&(u+=f+"\n> <Sequence>\nAnti Sense\n$$$$\n"),d&&(u+=d+"\n> <Sequence>\nAnti Sense 2\n$$$$\n")}const l=new Date;function c(t){return t>=10?t.toString():"0"+t.toString()}ft(`SequenceTranslator-${l.getFullYear()+"-"+c(l.getMonth()+1)+"-"+c(l.getDate())+"_"+c(l.getHours())+"-"+c(l.getMinutes())+"-"+c(l.getSeconds())}.sdf`,encodeURIComponent(u))}}(e.ss,e.as,e.as2,this.useChiralInput.value,this.saveAllStrandsInput.value,this.th)}))]),n=[this.saveAllStrandsInput.root,this.useChiralInput.root,e],r=Et.divV(n);for(const t of n)Tt()(t).addClass("st-structure-bool-button-block");return r}getTableInput(t){const e=Object.fromEntries(En.map((e=>[e,new an(this.inputBase[e],t.highlightInvalidSubsequence)]))),n=Object.fromEntries(En.map(((t,e)=>{const n=0===e?"5′ → 3′":"3′ → 5′";return[t,Et.input.choice(`${t.toUpperCase()} direction`,{value:n,items:["5′ → 3′","3′ → 5′"]})]})));En.forEach(((t,e)=>{n[t].onChanged.subscribe((n=>{let r="3′ → 5′"===n;e>0&&(r=!r),this.directionInversion[t]=r,this.onInput.next()}))}));const r=["Sense Strand","Anti Sense","Anti Sense 2"],i=new Map(En.map(((t,e)=>[t,r[e]]))),o=(Object.fromEntries(En.map((t=>[t,Et.label(i.get(t))]))),Object.fromEntries(En.map((t=>{const n=Et.icons.delete((()=>{e[t].inputBase.value=""})),r=Et.button(n,(()=>{}));return Et.tooltip.bind(r,`Clear ${t.toUpperCase()}`),[t,n]})))),s=Et.form([],"st-structure-inputs"),a=Et.divV([],"st-structure-clear-buttons"),u=Et.form([],"st-direction-inputs");for(const t of En)s.append(this.inputBase[t].root),a.append(o[t]),u.append(n[t].root);return Et.divH([s,a,u])}getStrandData(){return Object.fromEntries(En.map((t=>{const e=this.directionInversion[t];return[t,{strand:this.inputBase[t].value.replace(/\s*/g,""),invert:e}]})))}getMolfile(t,e,n){return _n(t,e,n,this.useChiralInput.value,this.th)}async updateMoleculeImg(){let t="";try{const e=this.getStrandData();Object.values(e).some((t=>""!==t.strand))&&(t=this.getMolfile(e.ss,e.as,e.as2))}catch(t){const e=nn(t);console.error(e)}const e=new pn(t);await e.drawMolecule(this.moleculeImgDiv,650,150),Tt()(this.moleculeImgDiv).find("canvas").css("float","inherit")}}class Tn extends Lt{constructor(t){super("Oligo Structure"),this.th=t,this.layout=new Sn}getContent(){return this.layout.getHtmlDivElement(this.th)}}async function In(e){try{const n={overflowX:"scroll"},r=Et.div([],{style:n}),i=An(e),o=.7*Tt()(window).height(),s=Math.max(...i.x)-Math.min(...i.x),a=Math.max(...i.y)-Math.min(...i.y),u=o/a,l=u*s,c=u*a,h=Et.canvas(l*window.devicePixelRatio,c*window.devicePixelRatio);h.style.width=`${l}px`,h.style.height=`${c}px`,await async function(e,n){await t.functions.call("Chem:canvasMol",{x:0,y:0,w:e.width,h:e.height,canvas:e,molString:n,scaffoldMolString:"",options:{normalizeDepiction:!1,straightenDepiction:!1}})}(h,e),r.appendChild(h),Et.dialog("Molecule").add(r).showModal(!0)}catch(t){const e=nn(t);console.error(e)}}class Nn{static async view(){const e=kr.monomerLibWrapper.getTableForViewer();e.name="Monomer Library";const n=t.shell.addTableView(e);n.grid.props.allowEdit=!1,n.grid.onCellDoubleClick.subscribe((async t=>{const e=t.cell.value;"Molecule"===t.tableColumn?.semType&&await In(e)}))}}const On="Copied",Mn="Nucleotides";function Ln(t,e){const n=new RegExp("\\([^()]*\\)","g"),r=t.match(n);return r?r.map((t=>{const n=t.replace(/[\[\]()]/g,"");return lt.includes(n)?n:e.getNaturalAnalogBySymbol(n)})).map((t=>t||yt)).join(""):null}var Bn=n(254),Pn={};Pn.styleTagTransform=ve(),Pn.setAttributes=de(),Pn.insert=he().bind(null,"head"),Pn.domAPI=le(),Pn.insertStyleElement=ge(),ae()(Bn.A,Pn),Bn.A&&Bn.A.locals&&Bn.A.locals;const Rn=["Sequence"];class Dn{constructor(t){this.th=t,this.inputFormats=Object.keys(kr.jsonData.codesToHelmDict).concat(ct.HELM),this.onInput=new Kt.Subject,this.moleculeImgDiv=Et.div([]),this.moleculeImgDiv.className="mol-host",this.moleculeImgDiv.style.border="1px solid var(--grey-2)",this.moleculeImgDiv.style.borderRadius="1px",this.moleculeImgDiv.style.marginTop="12px",this.outputTableDiv=Et.div([]),this.formatChoiceInput=Et.input.choice("",{value:ct.HELM,items:this.inputFormats,onValueChanged:async(t,e)=>{this.format=t,this.updateTable(),await this.updateMolImg()}}),Tt()(this.formatChoiceInput.root.getElementsByTagName("select")[0]).css("width","20%"),this.sequenceInputBase=Et.input.textArea("",{value:"Afcgacsu",onValueChanged:()=>{this.onInput.next()}}),this.init(),e.debounce(this.onInput,300).subscribe((async()=>{this.init(),this.formatChoiceInput.value=this.format,this.updateTable(),await this.updateMolImg()})),this.eventBus=Un.getInstance()}async getHtmlElement(){const t=this.constructSingleSequenceControls(),e=this.constructBulkTranslationControls(),n=Et.box(Et.panel([t,e,Et.block([Et.box(this.moleculeImgDiv)])]));return this.formatChoiceInput.value=this.format,this.updateTable(),await this.updateMolImg(),n}constructBulkTranslationControls(){const t=Et.h1("Bulk");Et.tooltip.bind(t,"Bulk translation from table input");const e=new Fn(this.eventBus).createUIComponents(),n=Et.input.choice("Input format",{value:ct.AXOLABS,items:this.inputFormats,onValueChanged:t=>this.eventBus.selectInputFormat(t)}),r=Et.input.choice("Output format",{value:Mn,items:(i=this.th,Object.keys(i.jsonData.codesToHelmDict).concat([ct.HELM,Mn]).sort()),onValueChanged:t=>this.eventBus.selectOutputFormat(t)});var i;const o=this.createConvertBulkButton(),s=Et.div([...e,n,r,o],"ui-form");return Et.block25([t,s])}createConvertBulkButton(){const t=Et.bigButton("Convert",(()=>this.processConvertBulkButtonClick()));return Et.tooltip.bind(t,"Convert sequences from table input"),Tt()(t).css({float:"right","margin-top":"20px"}),t}processConvertBulkButtonClick(){const n=this.eventBus.getSelectedTable();if(!n)return void t.shell.warning("No table selected");const r=this.eventBus.getSelectedInputFormat(),i=this.eventBus.getSelectedOutputFormat(),o=this.eventBus.getSelectedColumn("Sequence");if(!o)return void t.shell.warning("No sequence column selected");const s=`${o.name} (${i})`,a=e.Column.fromList(e.TYPE.STRING,s,o.toList().map((t=>{const e=function(t,e,n,r){const i=r.createFormatConverter(t,e);return n===Mn?Ln(i.convertTo(ct.HELM),r.monomerLibWrapper):i.convertTo(n)}(t,r,i,this.th);return e})));if(i===Mn||i===ct.HELM){a.semType=e.SEMTYPE.MACROMOLECULE;const t=i==Mn?x.FASTA:x.HELM;a.meta.units=t;const n=Z.forColumn(a);(i==Mn?Z.setUnitsToFastaColumn:Z.setUnitsToHelmColumn)(n)}n.columns.add(a),t.data.detectSemanticTypes(n),t.shell.v=t.shell.getTableView(n.name)}constructSingleSequenceControls(){const t=new an(this.sequenceInputBase,(t=>It(t,this.th))),e=Et.button("Get SDF",(()=>{this.saveMolfile()}),"Save structure as SDF"),n=Et.button("Copy SMILES",(()=>{this.copySmiles()}),"Copy SMILES for the sequence"),r=Et.div([this.formatChoiceInput]),i=Et.button(Et.icons.delete((()=>{t.inputBase.value=""})),(()=>{}));Et.tooltip.bind(i,"Clear input");const o={format:r,textInput:t.root,clearBtn:i},s=Et.table([o],(t=>[t.format,t.textInput,t.clearBtn]));s.classList.add("st-translator-input-table");const a=Et.block([this.outputTableDiv,e,n]);return Et.block75([Et.h1("Single sequence"),s,a])}saveMolfile(){const t=new yn(this.sequence,!1,this.formatChoiceInput.value).convert()+"\n$$$$";ft(this.sequence+".sdf",encodeURIComponent(t))}copySmiles(){const n=e.chem.convert(this.molfile,e.chem.Notation.MolBlock,e.chem.Notation.Smiles);navigator.clipboard.writeText(n).then((()=>t.shell.info(On)))}updateTable(){this.outputTableDiv.innerHTML="";const e=this.format?this.th.createSequenceValidator(this.sequence).getInvalidCodeIndex(this.format):0,n=function(t,e,n,r){const i=Object.keys(r.jsonData.codesToHelmDict).concat([ct.HELM]);if(!t||-1!==e&&n!==ct.HELM)return{};if(!i.includes(n))throw new Error(`${n} format is not supported by SequenceTranslator`);const o=i.filter((t=>t!=n)).sort(((t,e)=>t.localeCompare(e))),s=r.createFormatConverter(t,n),a=Object.fromEntries(o.map((t=>{let e;try{e=s.convertTo(t)}catch{e=null}return[t,e]})).filter((([t,e])=>e))),u=Ln(n===ct.HELM?t:a[ct.HELM],r.monomerLibWrapper);return u&&(a.Nucleotides=u),a}(this.sequence,e,this.format,this.th),r=[];for(const e of Object.keys(n)){const i="indexOfFirstInvalidChar"in n?Et.divH([]):Et.link(n[e],(()=>navigator.clipboard.writeText(n[e]).then((()=>t.shell.info(On)))),"Copy sequence","");r.push({format:e,sequence:i})}const i=Et.table(r,(t=>[t.format,t.sequence]),["FORMAT","SEQUENCE"]);this.outputTableDiv.append(i),this.outputTableDiv.classList.add("st-translator-output-table")}async updateMolImg(){const t=new pn(this.molfile);await t.drawMolecule(this.moleculeImgDiv,500,170)}init(){this.sequence=this.getFormattedSequence(),this.format=this.th.createFormatDetector(this.sequence).getFormat(),this.molfile=this.getMolfile()}getFormattedSequence(){return this.sequenceInputBase.value.replace(/\s/g,"")}getMolfile(){if(!this.format)return"";if(this.format===ct.HELM){const t=this.th.createFormatConverter(this.sequence,this.format).convertTo(ct.AXOLABS);return new yn(t,!1,ct.AXOLABS).convert()}return new yn(this.sequence,!1,this.format).convert()}}class Fn{constructor(t){this.tableInputManager=new kn(t),this.columnInputManager=new Hn(t)}createUIComponents(){return[this.tableInputManager.getTableInputContainer(),this.columnInputManager.getColumnControlsContainer()]}}class kn{constructor(t){this.eventBus=t,this.availableTables=[],this.tableInputContainer=Et.div([]),this.subscribeToTableEvents(),this.refreshTableInput()}getTableInputContainer(){return this.tableInputContainer}subscribeToTableEvents(){t.events.onTableAdded.subscribe((t=>this.handleTableAdded(t))),t.events.onTableRemoved.subscribe((t=>this.handleTableRemoved(t))),this.eventBus.tableSelected$.subscribe((()=>this.handleTableChoice()))}getTableFromEventData(t){return t.args.dataFrame}handleTableAdded(t){const e=this.getTableFromEventData(t);this.availableTables.some((t=>t.name===e.name))||(this.availableTables.push(e),this.eventBus.selectTable(e),this.refreshTableInput())}handleTableRemoved(t){const e=this.getTableFromEventData(t);this.availableTables=this.availableTables.filter((t=>t.name!==e.name));const n=this.availableTables[0];this.eventBus.selectTable(n||null),this.refreshTableInput()}refreshTableInput(){const t=this.createTableInput();Tt()(this.tableInputContainer).empty(),this.tableInputContainer.append(t.root)}createTableInput(){const t=this.eventBus.getSelectedTable();return Et.input.table("Table",{value:t,items:this.availableTables,onValueChanged:t=>{null!==t&&this.eventBus.selectTable(t)}})}handleTableChoice(){const t=this.eventBus.getSelectedTable();t&&(this.isTableDisplayed(t)||this.displayTable(t))}isTableDisplayed(e){return t.shell.tableNames.includes(e.name)}displayTable(e){const n=t.shell.v;t.shell.addTableView(e),t.shell.v=n}}class Hn{constructor(t){this.eventBus=t,this.columnControlsContainer=Et.div([]),this.eventBus.tableSelected$.subscribe((()=>this.handleTableChoice())),this.refreshColumnControls()}getColumnControlsContainer(){return this.columnControlsContainer}handleTableChoice(){this.refreshColumnControls()}refreshColumnControls(){const t=this.createColumnInputs();Tt()(this.columnControlsContainer).empty();const e=t.map((t=>t.root));this.columnControlsContainer.append(...e)}createColumnInputs(){const t=this.eventBus.getSelectedTable(),e=null!==t?t.columns.names().sort(((t,e)=>t.localeCompare(e))):[];return Rn.map((n=>this.createColumnInput(n,e,t)))}createColumnInput(t,e,n){const r=t.toLowerCase(),i=e.find((t=>t.toLowerCase().includes(r)))||e[0];return this.selectColumnIfTableNotNull(n,i,t),Et.input.choice(`${t}`,{value:i,items:e,onValueChanged:e=>this.selectColumnIfTableNotNull(n,e,t)})}selectColumnIfTableNotNull(t,e,n){if(null!==t){const r=t.getCol(e);this.eventBus.selectColumn(n,r)}}}class Un{constructor(){this._tableSelection$=new Kt.BehaviorSubject(null),this._columnSelection=Object.fromEntries(Rn.map((t=>[t,new Kt.BehaviorSubject(null)]))),this._inputFormatSelection$=new Kt.BehaviorSubject(ct.AXOLABS),this._outputFormatSelection$=new Kt.BehaviorSubject(Mn)}static getInstance(){return void 0===Un._instance&&(Un._instance=new Un),Un._instance}get tableSelected$(){return this._tableSelection$.asObservable()}getSelectedTable(){return 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e=await t.functions.call("Bio:getMonomerLibHelper",{});return(await e.getFileManager()).getValidLibraryPaths()}const hr="\n\n\n 22 24  0  0  0  0  0  0  0  0999 V2000\n    0.3128   -0.7509    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n    0.3128    0.0740    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n   -0.4054   -1.1623    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n   -1.1081   -0.7509    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n   -0.4054    0.4877    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0\n   -1.1081    0.0740    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n   -1.8175   -1.1623    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n    1.0222    0.4877    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n   -1.8175    0.4877    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n   -2.5292   -0.7509    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n    1.0222    1.3127    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n    1.7227    1.7263    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n   -0.4054   -1.9896    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0\n   -2.5292    0.0740    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n    2.4544    1.3127    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n    1.7406    0.0740    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n    1.0222   -1.1623    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0\n    2.4544    0.4877    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n   -1.8175   -1.9896    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0\n   -3.2453    0.4877    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0\n    3.1670    1.7285    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0\n    1.7149    2.5513    0.0000 R#  0  0  0  0  0  0  0  0  0  0  0  0\n  2  1  2  0  0  0  0\n  3  1  1  0  0  0  0\n  4  3  1  0  0  0  0\n  5  2  1  0  0  0  0\n  6  5  1  0  0  0  0\n  7  4  1  0  0  0  0\n  8  2  1  0  0  0  0\n  9  6  1  0  0  0  0\n 10  7  2  0  0  0  0\n 11  8  2  0  0  0  0\n 12 11  1  0  0  0  0\n 13  3  2  0  0  0  0\n 14  9  2  0  0  0  0\n 15 18  1  0  0  0  0\n 16  8  1  0  0  0  0\n 17  1  1  0  0  0  0\n 18 16  2  0  0  0  0\n 19  7  1  0  0  0  0\n 20 14  1  0  0  0  0\n  6  4  2  0  0  0  0\n 15 12  2  0  0  0  0\n 14 10  1  0  0  0  0\n 15 21  1  0  0  0  0\n 12 22  1  0  0  0  0\nM  RGP  1  22   1\nM  END";const fr={symbol:"Short Name",name:"Medium Name",smiles:"SMILES"},dr=[{capGroupSmiles:"[*:1][H]",alternateId:"R1-H",capGroupName:"H",label:"R1"},{capGroupSmiles:"O[*:2]",alternateId:"R2-OH",capGroupName:"OH",label:"R2"},{capGroupSmiles:"[*:3][H]",alternateId:"R3-H",capGroupName:"H",label:"R3"}],pr="No dataframe with macromolecule columns open",gr="Get HELM",mr="Add HELM column",vr="Chirality engine",yr="Poly Tool Conversion",br="Poly Tool Enumeration",wr="Rules used";function Cr(n){(async function(n){const r=[],i=()=>{for(const t of r)t.unsubscribe()};try{const[o,s]=await Promise.all([cr(),Yn()]),a=n&&n.rowIndex>=0?n.value:hr;let u=await(async()=>e.chem.isMolBlock(a)?a:await t.functions.call("Chem:convertMolNotation",{molecule:a,sourceNotation:n?.column.getTag(e.TAGS.UNITS)??e.chem.Notation.Unknown,targetNotation:e.chem.Notation.MolBlock}))();const l=new e.chem.Sketcher(e.chem.SKETCHER_MODE.EXTERNAL);l.syncCurrentObject=!1,l.onChanged.subscribe((t=>{u=l.getMolFile()})),l.root.classList.add("ui-input-editor"),l.root.style.marginTop="3px",l.setMolFile(u);const c=Et.input.choice("Library to use",{value:null,items:o});l.root.setAttribute("style","min-width:250px!important;"),l.root.setAttribute("style","max-width:250px!important;"),c.input.setAttribute("style","min-width:250px!important;");const h=Et.div([l.root,c.root]);r.push(t.events.onCurrentCellChanged.subscribe((()=>{const n=t.shell.tv.dataFrame.currentCell;n.column.semType===e.SEMTYPE.MOLECULE&&l.setValue(n.value)})));const f=async()=>{try{const n=l.getMolFile();if(void 0===n||""===n)t.shell.warning("PolyTool: no molecule was provided");else if(n.includes("R#")){const r=await async function(e,n){const r=await async function(e){const n=await t.functions.call("Bio:getMonomerLibHelper",{});return(await n.readLibrary(lr,e)).getMonomerSymbolsByType("PEPTIDE")}(n),i=await async function(e){const n=await t.functions.call("Bio:getMonomerLibHelper",{}),r=await n.readLibrary(lr,e),i=r.getMonomerSymbolsByType("PEPTIDE");return new Array(i.length),r.getMonomerMolsByPolymerType("PEPTIDE")}(n),o=new Array(r.length),s=await t.functions.call("Chem:getRdKitModule"),a=s.get_mol(e),u=a.get_smiles();a.delete();const l=new Array(r.length);for(let t=0;t<r.length;t++){const e=i[r[t]],n=s.get_mol(e);l[t]=n.get_smiles(),n.delete()}for(let t=0;t<r.length;t++){let e=null;try{const n=`${`${u}.${l[t]}`.replaceAll("[1*]C","C([1*])").replaceAll("[1*]c","c([1*])").replaceAll("[1*]O","O([1*])").replaceAll("[1*]N","N([1*])")}`.replaceAll("([1*])","9").replaceAll("[1*]","9");e=s.get_mol(n,JSON.stringify({mappedDummiesAreRGroups:!0}));const r=e.get_v3Kmolblock();o[t]=r}catch(e){o[t]=""}finally{e?.delete()}}return o}(n,c.value),i=e.Column.fromStrings("Enumerated",r),o=e.DataFrame.fromColumns([i]);t.shell.addTableView(o)}else t.shell.warning("PolyTool: no R group was provided")}catch(t){ur(t)}},d=Et.dialog(br).add(h).onOK((()=>{f().finally((()=>{i()}))})).onCancel((()=>{i()}));return r.push(d.onClose.subscribe((()=>{i()}))),d}catch(t){throw i(),t}})(n).then((t=>{t.show({resizable:!0})})).catch((e=>{t.shell.warning("To run PolyTool Enumeration, sketch the molecule and specify the R group to vary")}))}async function Ar(n,r,i,o){const s=e.TaskBarProgressIndicator.create("PolyTool converting...");try{const s=(t,e)=>t?t.columns.getUnusedName(e):e;await Yn();const a=n.dataFrame,u=await async function(n){const r=new e.FileSource(er),i=[],o={homodimerCode:null,heterodimerCode:null,linkRules:i};for(let e=0;e<n.length;e++){const s=await r.readAsText(n[e].replace(er,"")),a=JSON.parse(s);for(let e=0;e<a.length;e++)if(void 0!==a[e].type&&void 0!==a[e].code)switch(a[e].type){case rr:{const t=a[e].monomericSubstitution;t.code=a[e].code,i.push(t);break}case ir:o.homodimerCode&&t.shell.warning("PolyTool: homodimer code is duplicated in rules."),o.homodimerCode=a[e].code;break;case or:o.heterodimerCode&&t.shell.warning("PolyTool: heterodimer code is duplicated in rules."),o.heterodimerCode=a[e].code;break;default:t.shell.warning(`PolyTool: Unexpected type - '${a[e]}'.`)}else t.shell.warning("Polytool: rules contain invalid rule")}return o}(o),l=function(t,e){const n=new Array(t.length);for(let r=0;r<t.length;r++)if(void 0===t[r])n[r]="";else{const i=ar.fromNotation(t[r],e);n[r]=i.getHelm()}return n}(n.toList(),u),c=s(a,`transformed(${n.name})`),h=e.Column.fromType(e.COLUMN_TYPE.STRING,c,l.length).init((t=>l[t]));h.semType=e.SEMTYPE.MACROMOLECULE,h.meta.units=x.HELM,h.setTag(e.TAGS.CELL_RENDERER,"helm"),r&&a&&a.columns.add(h,!0);const f=await Xn(),d=(await f.helmToAtomicLevel(h,i,r)).molCol;return d.name=s(a,`molfile(${n.name})`),d.semType=e.SEMTYPE.MOLECULE,a&&(a.columns.add(d,!0),await t.data.detectSemanticTypes(a)),[h,d]}finally{s.close()}}var xr,_r;function Er(t){let e;switch(t){case xr.BASE:case xr.SUGAR:case xr.LINKER:case xr.NUCLEOTIDE:case"nucleotide":e="RNA";break;case xr.AA:e="PEPTIDE";break;case xr.CHEM:e="CHEM";break;case xr.BLOB:e="BLOB";break;default:e="PEPTIDE",console.warn(`Unexpected HelmType '${t}'`)}return e}!function(t){t.BASE="HELM_BASE",t.SUGAR="HELM_SUGAR",t.LINKER="HELM_LINKER",t.AA="HELM_AA",t.CHEM="HELM_CHEM",t.BLOB="HELM_BLOB",t.NUCLEOTIDE="HELM_NUCLETIDE"}(xr||(xr={}));class Sr extends e.InputBase{constructor(t,e){super(Et.input.column(t,e).dart,e?.onValueChanged),this.options=e}setColumnInputTable(t){Et.input.setColumnInputTable(this,t,this.options?.filter)}}Et.input.column2=function(t,e){return new Sr(t,e)},function(t){t.Single="single",t.Matrix="matrix"}(_r||(_r={}));const Tr="PEPTIDE1{R.[Aca].T.G.H.F.G.A.A.Y.P.E.[meI]}$$$$";function Ir(t,e,n){const r=new Array(n.length);for(let i=0;i<n.length;i++){const o=n[i],s=r[i]=t.clone(),a=s.atoms[e].elem;s.atoms[e].elem=o;const u=a?.length>1?`[${a}]`:a,l=o?.length>1?`[${o}]`:o;s.name=`${t.name}-${u}${e+1}${l}`}return r}class Nr extends e.JsInputBase{get inputType(){return"Positions"}get dataType(){return e.TYPE.DATA_FRAME}getInput(){return this.gridHost}getValue(){return this.grid.dataFrame}setValue(t){this.grid.dataFrame=t}getStringValue(){return this.grid.dataFrame.toCsv()}setStringValue(t){this.grid.dataFrame=e.DataFrame.fromCsv(t)}get placeholdersValue(){return function(t){const e={};for(let n=0;n<t.rowCount;n++){const r=parseInt(t.get("Position",n));if(!isNaN(r)){const i=t.get("Monomers",n).split(/,(?![^(]*\))/).map((t=>('"'===(t=t.trim()).slice(0,1)&&'"'===t.slice(-1)&&(t=t.slice(1,-1)),"'"===t.slice(0,1)&&"'"===t.slice(-1)&&(t=t.slice(1,-1)),t.trim()))).filter((t=>!!t));e[r-1]=i}}return e}(this.grid.dataFrame)}constructor(t,e,n){super(),this.subs=[],t&&(this.captionLabel.innerText=t),this.gridHost=Et.div([],{classes:"ui-input-editor",style:{width:"100%",height:"100%",marginTop:"-8px",marginBottom:"8px",paddingBottom:"4px"}}),this.grid=e,this.gridHost.append(this.grid.root),null!=n?this.updateGridHeight(n+.7):(this.updateGridHeight(this.grid.dataFrame.rowCount+.6),this.subs.push(this.grid.dataFrame.onRowsAdded.subscribe((()=>{this.updateGridHeight(this.grid.dataFrame.rowCount+.6)})))),this.grid.root.style.width="100%",this.subs.push(this.grid.dataFrame.onDataChanged.subscribe((()=>{this.fireChanged()}))),this.subs.push(Et.onSizeChanged(this.grid.root).subscribe((()=>{this.grid.columns.byIndex(2).width=this.grid.root.clientWidth-this.grid.horzScroll.root.offsetWidth-this.grid.columns.byIndex(0).width-this.grid.columns.byIndex(1).width-10}))),this.root.classList.add("ui-input-polytool-pos-grid"),this.root.append(this.gridHost)}detach(){for(const t of this.subs)t.unsubscribe()}static async create(t,n,r){const i=e.DataFrame.fromObjects([{Position:"",Monomers:""}]),o=await i.plot.fromType(e.VIEWER.GRID,n);return o.sort(["Position"]),new Nr(t,o,r)}updateGridHeight(t){const e=this.grid.colHeaderHeight+t*this.grid.props.rowHeight+6+2;this.grid.root.style.height=`${e}px`}gridRootOnSizeChanged(){this.grid.columns.byIndex(2).width=this.grid.root.clientWidth-this.grid.horzScroll.root.offsetWidth-this.grid.columns.byIndex(0).width-this.grid.columns.byIndex(1).width-10}}async function Or(n){const r=window.innerWidth,i=window.innerHeight;try{let o;const s=()=>{if(null==o)return;const t=Tt()(o.root).find("div.d4-dialog-contents").get(0),e=t.clientHeight,n={0:1},r=Object.values(n).reduce(((t,e)=>t+e),0),i=e-I().count(0).take(t.children.length).filter((t=>!(t in n))).map((e=>t.children[e])).filter((t=>t instanceof HTMLElement)).map((t=>t.offsetHeight)).reduce(((t,e)=>t+e),0)-38;o.inputs.forEach(((t,e)=>{if(e in n){const o=i*n[e]/r;t.root.style.height=`${o}px`}}))};o=await async function(n,r){const i="ST: PT: HelmDialog()";let o;const s=[],a=()=>{for(const t of s)t.unsubscribe();o.placeholders.detach()};try{const u=(await nt()).getMonomerLib(),l=(await Xn(),e.DataFrame.fromColumns([])),[c,h]=await Promise.all([cr(),Yn()]);let f=null;const d=Et.divText("",{style:{marginLeft:"8px",marginTop:"2px"}}),p=Et.divText("",{style:{color:"red"}});o={enumeratorType:Et.input.choice("Enumerator type",{value:_r.Single,items:Object.values(_r)}),macromolecule:h.createHelmInput("Macromolecule",{editable:!1}),placeholders:await Nr.create("Placeholders",{showAddNewRowIcon:!0,showRemoveRowIcon:!0,showRowHeader:!1,showCellTooltip:!1}),toAtomicLevel:Et.input.bool("To atomic level",{value:!1}),keepOriginal:Et.input.bool("Keep original",{value:!1}),trivialNameCol:Et.input.column2("Trivial name",{table:n?.dataFrame,filter:t=>t.type===e.COLUMN_TYPE.STRING&&t!=n?.column,onValueChanged:()=>{const t=o.trivialNameCol.value;let e=null;n&&t&&(e={value:t.get(n.rowIndex),colName:t.name}),f=e,d.textContent=f?`Original ID: ${f.value}`:""},nullable:!0})},o.trivialNameCol.addOptions(d);let g=null;o.placeholders.addValidator((t=>{const e=[];try{const t=[];for(const[n,r]of Object.entries(o.placeholders.placeholdersValue)){const i=parseInt(n);if(i>=o.macromolecule.molValue.atoms.length){e.push(`There is no monomer at position ${i+1}.`);continue}const s=Er(o.macromolecule.molValue.atoms[i].biotype());for(const e of r){const n=u.getMonomer(s,e);n&&n.lib||t.push({polymerType:s,symbol:e})}}const n={};for(const e of t){let t=n[e.polymerType];t||(t=n[e.polymerType]=[]),t.push(e.symbol)}const r=Object.entries(n).map((([t,e])=>`${t}: ${e.join(", ")}`)).join("\n");Object.keys(r).length>0&&e.push(`Placeholders contain missed monomers: ${r}`),g=e.length>0?e.join("\n"):null}catch(t){const[e,n]=ur(t,!1);g=e}return setTimeout((()=>{v()}),0),g})),s.push(o.macromolecule.onMouseMove.subscribe((t=>{try{kr.logger.debug(`${i}, placeholdersInput.onMouseMove()`);const e=t.offsetX,n=t.offsetY,r=o.macromolecule.molValue,s=h.getHoveredAtom(e,n,r,o.macromolecule.root.clientHeight);if(s){const e=s._parent.atoms.indexOf(s),n=((e+1).toString(),o.placeholders.placeholdersValue[e]);if(n){const e=Et.divText(n.join(", "));o.macromolecule.showTooltip(e,s),t.preventDefault(),t.stopPropagation()}}}catch(t){ur(t,!1)}}))),s.push(o.macromolecule.onClick.subscribe((t=>{try{kr.logger.debug(`${i}, placeholdersInput.onClick()`);const e=t.offsetX,n=t.offsetY,r=o.macromolecule.molValue,s=h.getHoveredAtom(e,n,r,o.macromolecule.root.clientHeight);if(s){const t=(s._parent.atoms.indexOf(s)+1).toString(),e=o.placeholders.grid.dataFrame,n=e.columns.byName("Position").toList();let r=n.indexOf(t);-1===r&&(r=n.findIndex((t=>isNaN(t))),-1===r&&(r=e.rows.addNew([t,""]).idx),e.set("Position",r,t)),e.currentCell=e.cell(r,"Monomers")}}catch(t){ur(t)}}))),s.push(o.placeholders.grid.dataFrame.onDataChanged.subscribe((()=>{m()}))),s.push((0,Kt.fromEvent)(o.placeholders.grid.root,"keydown").subscribe((t=>{"Enter"===t.key&&t.stopPropagation()}))),s.push(Et.onSizeChanged(o.placeholders.root).subscribe((()=>{r&&r()}))),s.push(t.events.onCurrentCellChanged.subscribe((()=>{const n=t.shell.tv.dataFrame.currentCell;n.column.semType===e.SEMTYPE.MACROMOLECULE&&b(n)}))),o.macromolecule.root.style.setProperty("min-width","250px","important");const m=()=>{const t=o.macromolecule.molValue;for(let e=0;e<t.atoms.length;e++)t.atoms[e].highlighted=e in o.placeholders.placeholdersValue;o.macromolecule.redraw()},v=()=>{const t=g,e=p;t?(e.innerText=t,e.style.removeProperty("display")):(e.innerText="",e.style.setProperty("display","none"))},y=t=>{t?(o.trivialNameCol.setColumnInputTable(t),o.trivialNameCol.root.style.removeProperty("display")):(o.trivialNameCol.setColumnInputTable(l),o.trivialNameCol.root.style.setProperty("display","none")),r&&r()},b=async t=>{let n,r;if(t&&t.rowIndex>=0&&t?.column.semType==e.SEMTYPE.MACROMOLECULE){const e=Z.forColumn(t.column);n=await e.getHelm(t.rowIndex),r=t.dataFrame}else n=Tr;o.macromolecule.stringValue=n,y(r)};await b(n);const w=async()=>{try{const n=o.macromolecule.stringValue;if(I().enumerate(o.macromolecule.molValue.atoms).filter((([t,e])=>t.highlighted)).map((([t,e])=>e)).toArray(),void 0===n||""===n)t.shell.warning("PolyTool: no molecule was provided");else{if(0===Object.keys(o.placeholders.placeholdersValue).length)return void t.shell.warning(`${br}: placeholders are empty`);await Yn();const r={type:o.enumeratorType.value,placeholders:o.placeholders.placeholdersValue,keepOriginal:o.keepOriginal.value},i=await async function(t,n,r,i){const o=e.TaskBarProgressIndicator.create("PolyTool enumerating...");try{await Yn();const o=function(t,e,n){const r=new JSDraw2.MolHandler,i=new org.helm.webeditor.Plugin(r);org.helm.webeditor.IO.parseHelm(i,t,new JSDraw2.Point(0,0),void 0);const o=r.m;let s;switch(o.name=e,n.type){case _r.Single:s=function(t,e){return Object.entries(e).map((([e,n])=>Ir(t,parseInt(e),n))).reduce(((t,e)=>t.concat(e)),[])}(r.m,n.placeholders);break;case _r.Matrix:s=function(t,e){let n=[t];for(const[t,r]of Object.entries(e)){const e=parseInt(t),i=n.map((t=>Ir(t,e,r)));n=i.reduce(((t,e)=>t.concat(e)),[])}return n}(r.m,n.placeholders)}n.keepOriginal&&(s=[o,...s]);const a=s.map((t=>[org.helm.webeditor.IO.getHelm(t),t.name]));return a}(t,n?.value??"",r),s=e.Column.fromType(e.COLUMN_TYPE.STRING,"Enumerated",o.length).init((t=>o[t][0])),a=e.DataFrame.fromColumns([s]);if(i){const t=await Xn(),n=await t.helmToAtomicLevel(s,!0,!0);n.molCol.semType=e.SEMTYPE.MOLECULE,a.columns.add(n.molCol,!1),a.columns.add(n.molHighlightCol,!1)}if(n){const t=e.Column.fromType(e.COLUMN_TYPE.STRING,n.colName,o.length).init((t=>o[t][1]));a.columns.add(t)}return a}finally{o.close()}}(n,f,r,o.toAtomicLevel.value);t.shell.addTableView(i)}}catch(t){ur(t)}},C=Et.dialog({title:br,showFooter:!0}).add(o.macromolecule).add(o.placeholders).add(o.enumeratorType).add(o.trivialNameCol).add(o.toAtomicLevel).add(o.keepOriginal).add(p).onOK((()=>{w()}));return s.push(C.onClose.subscribe((()=>{a()}))),C.history((()=>({macromolecule:o.macromolecule.stringValue,placeholders:o.placeholders.stringValue,enumeratorType:o.enumeratorType.value,trivialNameCol:o.trivialNameCol.stringValue,toAtomicLevel:o.toAtomicLevel.value,keepOriginal:o.keepOriginal.value})),(t=>{o.macromolecule.stringValue=t.macromolecule,o.placeholders.stringValue=t.placeholders,o.enumeratorType.value=t.enumeratorType,o.trivialNameCol.stringValue=t.trivialNameCol,o.toAtomicLevel.value=t.toAtomicLevel,o.keepOriginal.value=t.keepOriginal})),C}catch(t){throw a(),t}}(n,s);let a=!0;Et.onSizeChanged(o.root).subscribe((()=>{if(a){o.inputs;const t=Tt()(o.root),e=(t.find("div.d4-dialog-header").get(0).offsetHeight,t.find("div.d4-dialog-footer").get(0).offsetHeight,.7*r),n=.7*i;o.root.style.width=`${Math.min(r,e)}px`,o.root.style.height=`${Math.min(i,n)}px`,o.root.style.left=`${Math.floor((r-o.root.offsetWidth)/2)}px`,o.root.style.top=`${Math.floor((i-o.root.offsetHeight)/2)}px`,a=!1}s()})),s(),kr.logger.debug("PolyToolEnumerateHelmUI: dialog before show"),o.show({width:Math.max(350,.7*r),resizable:!0}),kr.logger.debug("PolyToolEnumerateHelmUI: dialog after show")}catch(e){const[n,r]=Qn(e);t.shell.warning("To run PolyTool Enumeration, sketch the macromolecule and select monomers to vary"),kr.logger.error(n,void 0,r)}}class Mr{constructor(t){this.rawLib=t}isValid(){return this.rawLib.every((t=>"object"==typeof t&&Object.values(fr).every((e=>e in t&&"string"==typeof t[e]))))}getJsonMonomerLib(){const t=[];return this.rawLib.forEach((e=>{const n=this.prepareMonomer(e);t.push(n)})),t}prepareMonomer(t){const 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this.incrementVersion(e),this}xor(t,e=!0){if(this._length!=t._length)throw new Error("Array lengths differ.");for(let e=0,n=this.lengthInInts;e<n;e++)this._data[e]^=t._data[e];return this.incrementVersion(e),this}insertAt(t,e,n=!1){if(this.assureInRange(t,0,this._length,"pos"),0==e)return;const r=this._length;this.setLength(this._length+e);for(let n=r-1;n>=t;n--)this.setBit(n+e,this.getBit(n));for(let r=t;r<t+e;r++)this.setBit(r,n)}removeAt(t,e=1){if(e<0)throw new Error("n cannot be negative");if(this.assureInRange(t,0,this._length-e,"pos"),this.contains(!0))for(let n=t;n<this._length-e;n++)this.setBit(n,this.getBit(n+e));this.setLength(this._length-e)}removeByMask(t,e=!0){if(this._length!=t.length)throw new Error("length != mask.length");if(t==this)this.setLength(t.countBits(!e)),this.setAll(!e);else{let n=0;for(let r=-1;-1!=(r=t.findNext(r,!e));)this.setFast(n++,this.getBit(r));this._length=n,this._version++}return 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g;!function(t){t.HAMMING="Hamming",t.LEVENSHTEIN="Levenshtein",t.NEEDLEMANN_WUNSCH="Needlemann-Wunsch",t.MONOMER_CHEMICAL_DISTANCE="Monomer chemical distance"}(g||(g={}));const m={[g.HAMMING]:f,[g.LEVENSHTEIN]:function(){return(t,e)=>((t,e)=>{if(t.length<e.length){const n=e;e=t,t=n}return 0===e.length?t.length:t.length<=32?((t,e)=>{const n=t.length,r=e.length,i=1<<n-1;let o=-1,s=0,a=n,u=n;for(;u--;)d[t.charCodeAt(u)]|=1<<u;for(u=0;u<r;u++){let t=d[e.charCodeAt(u)];const n=t|s;t|=(t&o)+o^o,s|=~(t|o),o&=t,s&i&&a++,o&i&&a--,s=s<<1|1,o=o<<1|~(n|s),s&=n}for(u=n;u--;)d[t.charCodeAt(u)]=0;return a})(t,e):((t,e)=>{const n=e.length,r=t.length,i=[],o=[],s=Math.ceil(n/32),a=Math.ceil(r/32);for(let t=0;t<s;t++)o[t]=-1,i[t]=0;let u=0;for(;u<a-1;u++){let s=0,a=-1;const l=32*u,c=Math.min(32,r)+l;for(let e=l;e<c;e++)d[t.charCodeAt(e)]|=1<<e;for(let t=0;t<n;t++){const n=d[e.charCodeAt(t)],r=o[t/32|0]>>>t&1,u=i[t/32|0]>>>t&1,l=n|s,c=((n|u)&a)+a^a|n|u;let 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e=1;e<t.length+1;e++)s[0][e]=-r-(e-1)*r,s[1][e]=0;s[0][0]=0;for(let h=1;h<o.length+1;h++){s[c][0]=-r-(h-1)*r;for(let f=1;f<t.length+1;f++){const d=s[l][f-1]+i[e[t.charCodeAt(f-1)]][e[o.charCodeAt(h-1)]],p=s[l][f]-(a[f]||1===h||h===o.length?r:n),g=s[c][f-1]-(u[f-1]||1===f||f===t.length?r:n);s[c][f]=Math.max(d,g,p),s[c][f]===d?(a[f]=!1,u[f]=!1):s[c][f]===g?(a[f]=!1,u[f]=!0):(a[f]=!0,u[f]=!1)}l=c,c=(c+1)%2}const h=Math.min(t.length,o.length);return(h-s[l][t.length])/h}},[g.MONOMER_CHEMICAL_DISTANCE]:f};a.Tanimoto,a.Dice,a.Asymmetric,a.BraunBlanquet,a.Cosine,a.Kulczynski,a.McConnaughey,a.RogotGoldberg,a.Russel,a.Sokal,a.Hamming,a.Euclidean,a.Tanimoto,a.Dice,a.Asymmetric,a.BraunBlanquet,a.Cosine,a.Kulczynski,a.McConnaughey,a.RogotGoldberg,a.Russel,a.Sokal,a.Hamming,a.Euclidean,a.Tanimoto,a.Dice,a.Cosine,a.Tanimoto,a.Asymmetric,a.Cosine,a.Sokal,g.HAMMING,g.LEVENSHTEIN,g.MONOMER_CHEMICAL_DISTANCE,g.NEEDLEMANN_WUNSCH;const y={monomerType:"Backbone",smiles:"",name:"",author:"Datagrok",molfile:"",naturalAnalog:"",rgroups:[],createDate:null,id:0,polymerType:"PEPTIDE",symbol:""},v="p",b=new RegExp(`[rd]\\((\\w)\\)${v}?`,"g"),w=wu;var C,A,x,_,E,T=n.n(w);class S{constructor(t,e,n){this.name=t,this.alphabet=e,this.cutoff=n}}class I extends S{constructor(t,e,n){super(t.name,t.alphabet,t.cutoff),this.freq=e,this.similarity=n}}(E=C||(C={})).FASTA="fasta",E.SEPARATOR="separator",E.HELM="helm",(_=A||(A={})).DNA="DNA",_.RNA="RNA",_.PT="PT",_.UN="UN",function(t){t.aligned="aligned",t.alphabet="alphabet",t.alphabetSize=".alphabetSize",t.alphabetIsMultichar=".alphabetIsMultichar",t.separator="separator",t.isHelmCompatible=".isHelmCompatible",t.positionNames=".positionNames",t.positionLabels=".positionLabels",t.regions=".regions"}(x||(x={}));const N=/(?:\[([A-Za-z0-9_\-,()]+)\])|([A-Za-z\-])/g,M=new class{constructor(){this.fasta={peptide:new Set(["G","L","Y","S","E","Q","D","N","F","A","K","R","H","C","V","P","W","I","M","T"]),dna:new Set(["A","C","G","T"]),rna:new Set(["A","C","G","U"])}}},O=[new S(A.PT,M.fasta.peptide,.5),new S(A.DNA,M.fasta.dna,.55),new S(A.RNA,M.fasta.rna,.55)],L={[C.FASTA]:"-",[C.SEPARATOR]:"",[C.HELM]:"*"};class B extends Float32Array{}function P(t){let e=0;for(let n=0;n<t.length;n++)e+=t[n]*t[n];return Math.sqrt(e)}class R{static makePalette(t,e=!1,n=R){const r={};return t.forEach((t=>{const n=t[0],i=t[1];n.forEach(((t,n)=>{r[t]=this.colourPalette[i][e?0:n]}))})),new n(r)}constructor(t){this._palette=t}get(t,e){return this._palette[t]}}R.undefinedColor="rgb(100,100,100)",R.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 D extends R{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,D)),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,D)),this.grokGroups}static get RasMol(){return void 0===this.rasMol&&(this.rasMol=new D({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 D.aaSynonyms?D.aaSynonyms[t]:t;return super.get(e)}}D.aaSynonyms={MeNle:"L",MeA:"A",MeG:"G",MeF:"F"};class F{static getPalette(t="grok"){switch(t){case"grok":return D.GrokGroups;case"lesk":return D.Lesk;default:throw new Error(`ChemPalette: scheme \`${t}\` does not exist`)}}static getInnerOuter(t){let e=0,n="",r="";for(const i of t)"("==i?e++:")"==i?e--:e?n+=i:r+=i;return isNaN(parseInt(n))?[r,n]:[r,""]}static getColorAAPivot(t="",e="grok"){const n=this.getPalette(e);let[r,i]=this.getInnerOuter(t);if(r=r.length>6?`${r.slice(0,3)}...`:r,i=i.length>6?`${i.slice(0,3)}...`:i,1==t.length||"("==t[1]){const e=t[0]?.toUpperCase();return e in n?[n.get(e),e,i,1]:[this.undefinedColor,r,i,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,i,2]:[this.undefinedColor,r,i,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,i,3]:[this.undefinedColor,r,i,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,i,4]:[this.undefinedColor,r,i,4]}return[this.undefinedColor,r,i,0]}}F.SemType="Aminoacids",F.SemTypeMultipleAlignment="AminoacidsMultipleAlignment",F.undefinedColor="rgb(100,100,100)",F.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"},F.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"},F.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(*)*"},F.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 H{}function U(t,n=!0){if(null==t)return"rgb(100,100,100)";const r=e.Color.fromHtml(t);if(n){const t=e.Color.g(r),n=e.Color.r(r),i=e.Color.b(r),o=Math.sqrt(Math.pow(0-n,2)+Math.pow(0-t,2)+Math.pow(0-i,2));if(o>210)return`rgb(${n/o*210},${t/o*210},${i/o*210})`}return e.Color.toRgb(r)}H.SemType="Nucleotides",H.SemTypeMultipleAlignment="NucleotidesMultipleAlignment",H.Names={A:"Adenine",C:"Cytosine",G:"Guanine",T:"Thymine",U:"Uracil"};class k{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}}class V{}class j extends V{static buildPalette(){return rt().then((t=>{t.awaitLoaded().then((()=>{const e=t.getMonomerLib();e.onChanged.subscribe((()=>{j.customMonomerColors={},j.polymerTypes=e.getPolymerTypes();for(const t of this.polymerTypes){const n=e.getMonomerSymbolsByType(t);for(const r of n){const n=e.getMonomer(t,r);n?.meta?.colors?.default?.background&&(this.customMonomerColors[r]||(this.customMonomerColors[r]={}),this.customMonomerColors[r][t]=U(n.meta.colors.default.background,!1))}}}))}))})),[].concat(...Object.values(R.colourPalette))}get(t,e){const n=j.customMonomerColors[t],r=e??"PEPTIDE";if(n&&n[r])return n[r];const i=k.hashCode(t)%j.palette.length;return U(j.palette[i])}}j.palette=j.buildPalette(),j.customMonomerColors={},j.polymerTypes=[];class q{get length(){return this.mList.length}isGap(t){return this.getOriginal(t)===this.gapOriginalMonomer}getCanonical(t){if(this.length<=t)throw new Error("Index out of bounds");const e=this.mList[t];return e!==this.gapOriginalMonomer?e:""}getOriginal(t){if(this.length<=t)throw new Error("Index out of bounds");return this.mList[t]}constructor(t,e){this.mList=t,this.gapOriginalMonomer=e}}class G{get length(){return this.seqS.length}isGap(t){return this.getOriginal(t)===L[C.FASTA]}getCanonical(t){if(this.length<=t)throw new Error("Index out of bounds");return this.isGap(t)?"":this.seqS[t]}getOriginal(t){if(this.length<=t)throw new Error("Index out of bounds");return this.seqS[t]}constructor(t){this.seqS=t}}const W=t=>{const e=T()(t.toString().matchAll(N)).map((t=>t[2]??t[1])).toArray();return new q(e,L[C.FASTA])},z=t=>t?new G(t):new q([],L[C.FASTA]);function Y(t,e=void 0){return n=>{if(n){let r;const i=new RegExp(String.raw`"-"|'-'|[^${t}]+`,"g");if(void 0!==e){i.lastIndex=0,r=new Array(Math.ceil(e));let t=null,o=0;for(;null!==(t=i.exec(n))&&o<e;)r[o++]=t[0].replace('"-"',"").replace("'-'","");r.splice(o)}else r=n.replaceAll('"-"',"").replaceAll("'-'","").split(t,e);return new q(r,L[C.SEPARATOR])}return new q([],L[C.SEPARATOR])}}const K=/(PEPTIDE1|DNA1|RNA1)\{([^}]+)}/g,J=/\[([^\[\]]+)]/g,Q=t=>{K.lastIndex=0;const e=K.exec(t.toString()),n=e?e[2]:null,r=n?n.split("."):[];return new q(r.map((t=>{J.lastIndex=0;const e=J.exec(t);return e&&e.length>=2?e[1]:t})),L[C.HELM])};function X(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 i=[],o=[];for(const n of r)i.push(n in t?t[n]:0),o.push(e.has(n)?1:0);const s=new B(i),a=new B(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}(s,a)/(P(s)*P(a))}(t,e.alphabet,n);return new I(e,t,r)}));let i;const o=Math.max(...r.map((t=>t.similarity>t.cutoff?t.similarity:-1)));return i=o>0?r.find((t=>t.similarity===o)).name:A.UN,i}const Z=new class{constructor(){this.seqHandler="seq-handler",this.notationProvider="seq-handler.notation-provider"}};class tt{constructor(t){if(this._splitter=null,this.cached=!0,this._splitted=null,this.columnVersion=null,this._stats=null,this._maxLength=null,this._posList=null,this._joiner=void 0,t.type!==e.TYPE.STRING)throw new Error(`Unexpected column type '${t.type}', must be '${e.TYPE.STRING}'.`);this._column=t;const n=this._column.meta.units;if(null==n)throw new Error("Units are not specified in column");if(this._units=n,this._notation=this.getNotation(),this._defaultGapOriginal=this.isFasta()?L[C.FASTA]:this.isHelm()?L[C.HELM]:L[C.SEPARATOR],!this.column.tags.has(x.aligned)||!this.column.tags.has(x.alphabet)||!this.column.tags.has(x.alphabetIsMultichar)&&!this.isHelm()&&this.alphabet===A.UN)if(this.isFasta())tt.setUnitsToFastaColumn(this);else if(this.isSeparator()){const e=t.getTag(x.separator);tt.setUnitsToSeparatorColumn(this,e)}else{if(!this.isHelm())throw new Error(`Unexpected units '${this.column.meta.units}'.`);tt.setUnitsToHelmColumn(this)}if(!this.column.tags.has(x.alphabetIsMultichar))if(this.isHelm())this.column.setTag(x.alphabetIsMultichar,"true");else if(["UN"].includes(this.alphabet))throw new Error(`For column '${this.column.name}' of alphabet '${this.alphabet}' tag '${x.alphabetIsMultichar}' is mandatory.`);this.notationProvider=this.column.temp[Z.notationProvider]??null,this.columnVersion=this.column.version}static setUnitsToFastaColumn(t){if(t.column.semType!==e.SEMTYPE.MACROMOLECULE||t.column.meta.units!==C.FASTA)throw new Error(`The column of notation '${C.FASTA}' must be '${e.SEMTYPE.MACROMOLECULE}'.`);t.column.meta.units=C.FASTA,tt.setTags(t)}static setUnitsToSeparatorColumn(t,n){if(t.column.semType!==e.SEMTYPE.MACROMOLECULE||t.column.meta.units!==C.SEPARATOR)throw new Error(`The column of notation '${C.SEPARATOR}' must be '${e.SEMTYPE.MACROMOLECULE}'.`);if(!n)throw new Error(`The column of notation '${C.SEPARATOR}' must have the separator tag.`);t.column.meta.units=C.SEPARATOR,t.column.setTag(x.separator,n),tt.setTags(t)}static setUnitsToHelmColumn(t){if(t.column.semType!==e.SEMTYPE.MACROMOLECULE)throw new Error(`The column of notation '${C.HELM}' must be '${e.SEMTYPE.MACROMOLECULE}'`);t.column.meta.units=C.HELM,tt.setTags(t)}static setTags(t){const e=t.column.meta.units;if([C.FASTA,C.SEPARATOR].includes(e)){if(!t.column.getTag(x.alphabet)&&0===Object.keys(t.stats.freq).length)throw new Error("Alphabet is empty and not annotated.");let e=t.column.getTag(x.aligned);null===e&&(e=t.stats.sameLength?"SEQ.MSA":"SEQ",t.column.setTag(x.aligned,e));let n=t.column.getTag(x.alphabet);if(null===n&&(n=X(t.stats.freq,O),t.column.setTag(x.alphabet,n)),n===A.UN){const e=Object.keys(t.stats.freq).length,n=Object.keys(t.stats.freq).some((t=>t.length>1));t.column.setTag(x.alphabetSize,e.toString()),t.column.setTag(x.alphabetIsMultichar,n?"true":"false")}}}get column(){return this._column}get length(){return this._column.length}get units(){return this._units}get notation(){return this._notation}get defaultGapOriginal(){return this._defaultGapOriginal}get separator(){const t=this.column.getTag(x.separator)??void 0;if(this.notation===C.SEPARATOR&&void 0===t)throw new Error(`Separator is mandatory  for column '${this.column.name}' of notation '${this.notation}'.`);return t}get aligned(){const t=this.column.getTag(x.aligned);if(!t&&(this.isFasta()||this.isSeparator()))throw new Error("Tag aligned not set");return t}get alphabet(){const t=this.column.getTag(x.alphabet);if(!t&&(this.isFasta()||this.isSeparator()))throw new Error("Tag alphabet not set");return t}get helmCompatible(){return this.column.getTag(x.isHelmCompatible)}getAlphabetSize(){if(this.notation==C.HELM||this.alphabet==A.UN){const t=this.column.getTag(x.alphabetSize);let e;if(t)e=parseInt(t);else{const t=this.stats;e=Object.keys(t.freq).length}return e}switch(this.alphabet){case A.PT:return 20;case A.DNA:case A.RNA:return 4;case"NT":return console.warn("Unexpected alphabet 'NT'."),4;default:throw new Error(`Unexpected alphabet '${this.alphabet}'.`)}}getAlphabetIsMultichar(){return this.notation===C.HELM||this.alphabet===A.UN&&"true"===this.column.getTag(x.alphabetIsMultichar)}getSplitted(t,e){if(this.cached&&void 0===e){this.column.version===this.columnVersion&&null!==this._splitted||(this.columnVersion=this.column.version,this._splitted=new Array(this.column.length));let e=this._splitted[t]?this._splitted[t].deref():void 0;if(!e){const n=this.column.get(t);e=this.splitter(n),this._splitted[t]=new WeakRef(e)}return e}{const n=this.column.get(t);return this.getSplitter(e)(n)}}async getHelm(t,e){const n=this.column.get(t);return this.notationProvider?(await this.notationProvider.getHelm(this.column,e)).get(t):this.convertToHelm(n)}get stats(){if(null===this._stats){const t={};let e=!0,n=null;const r=this.column.length;for(let i=0;i<r;++i){const r=this.getSplitted(i);null==n?n=r.length:r.length!==n&&(e=!1);for(let e=0;e<r.length;++e){const n=r.getCanonical(e);n in t||(t[n]=0),t[n]+=1}}this._stats={freq:t,sameLength:e}}return this._stats}get maxLength(){return null===this._maxLength&&(this._maxLength=0===this.column.length?0:Math.max(...T().count(0).take(this.column.length).map((t=>this.getSplitted(t).length)))),this._maxLength}get posList(){if(null===this._posList){const t=this.column.getTag(x.positionNames);this._posList=t?t.split(", ").map((t=>t.trim())):T().count(1).take(this.maxLength).map((t=>t.toString())).toArray()}return this._posList}isFasta(){return this.notation===C.FASTA}isSeparator(){return this.notation===C.SEPARATOR}isHelm(){return this.notation===C.HELM}isRna(){return this.alphabet===A.RNA}isDna(){return this.alphabet===A.DNA}isPeptide(){return this.alphabet===A.PT}isMsa(){return!!this.aligned&&this.aligned.toUpperCase().includes("MSA")}isHelmCompatible(){return"true"===this.helmCompatible}isGap(t){return!t||t===this._defaultGapOriginal}getNotation(){if(this.units.toLowerCase().startsWith(C.FASTA))return C.FASTA;if(this.units.toLowerCase().startsWith(C.SEPARATOR))return C.SEPARATOR;if(this.units.toLowerCase().startsWith(C.HELM))return C.HELM;throw new Error(`Column '${this.column.name}' has unexpected notation '${this.units}'.`)}getHelmWrappers(){return[this.isDna()||this.isRna()||this.isHelmCompatible()?"RNA1{":"PEPTIDE1{",this.isDna()?"d(":this.isRna()?"r(":"",this.isDna()||this.isRna()?")p":"","}$$$$"]}getNewColumn(t,n,r,i){const o=this.column,s=t.toLowerCase()+"("+o.name+")",a=r??o.dataFrame?.columns.getUnusedName(s)??s,u=e.Column.fromList("string",a,i??new Array(this.column.length).fill(""));if(u.semType=e.SEMTYPE.MACROMOLECULE,u.meta.units=t,t===C.SEPARATOR){if(!n)throw new Error(`Notation '${C.SEPARATOR}' requires separator value.`);u.setTag(x.separator,n)}u.setTag(e.TAGS.CELL_RENDERER,t===C.HELM?"helm":"sequence");const l=o.getTag(x.aligned);l&&u.setTag(x.aligned,l);let c=o.getTag(x.alphabet);c||this.notation!==C.HELM||t===C.HELM||(c=A.UN),null!=c&&u.setTag(x.alphabet,c);let h=o.getTag(x.alphabetSize);null!=c&&h&&u.setTag(x.alphabetSize,h);const f=o.getTag(x.alphabetIsMultichar);return null!=c&&void 0!==f&&u.setTag(x.alphabetIsMultichar,f),t==C.HELM&&(h=this.getAlphabetSize().toString(),u.setTag(x.alphabetSize,h)),u}getNewColumnFromList(t,e){return this.getNewColumn(this.notation,this.separator,t,e)}static getNewColumn(t){const e=tt.forColumn(t),n=e.notation;return e.getNewColumn(n)}static unitsStringIsValid(t){return t=t.toLowerCase(),[C.FASTA,C.SEPARATOR,C.HELM].some((e=>t.startsWith(e.toLowerCase())))}static getNewColumnFromParams(t,n,r){if(!tt.unitsStringIsValid(r))throw new Error("Invalid format of 'units' parameter");const i=e.Column.fromList("string",n,new Array(t).fill(""));return i.semType=e.SEMTYPE.MACROMOLECULE,i.meta.units=r,i}getSplitter(t){let e=null;if(e=this.notationProvider?this.notationProvider.splitter:null,e)return e;if(this.units.toLowerCase().startsWith(C.FASTA))return null===this.column.getTag(x.alphabet)||this.getAlphabetIsMultichar()?W:z;if(this.units.toLowerCase().startsWith(C.SEPARATOR))return Y(this.separator,t);if(this.units.toLowerCase().startsWith(C.HELM))return Q;throw new Error(`Unexpected units ${this.units} .`)}split(t){return this.splitter(t)}getDistanceFunctionName(){if(!this.isFasta())throw new Error("Only FASTA notation is supported");if(this.isMsa())return g.HAMMING;switch(this.alphabet){case A.DNA:case A.RNA:case A.PT:}return g.LEVENSHTEIN}getDistanceFunction(){return m[this.getDistanceFunctionName()]()}async checkHelmCompatibility(){if(this.column.tags.has(x.isHelmCompatible))return"true"===this.column.getTag(x.isHelmCompatible);const t=(await rt()).getMonomerLib().getMonomerSymbolsByType("PEPTIDE"),e=new Set(t),n=(Y(this.separator),new Set),r=this.column.length,i=this.column.getRawData();for(let t=0;t<r;++t){const r=i[t];if(!(r in n)){n.add(r);const i=this.getSplitted(t);for(let t=0;t<i.length;++t){const n=i.getCanonical(t);if(!e.has(n))return this.column.setTag(x.isHelmCompatible,"false"),!1}}}return this.column.setTag(x.isHelmCompatible,"true"),!0}get splitter(){return null===this._splitter&&(this._splitter=this.getSplitter()),this._splitter}toFasta(t){return t===C.FASTA}toSeparator(t){return t===C.SEPARATOR}toHelm(t){return t===C.HELM}convertHelmToFastaSeparator(t,e,n,r){r||(r=this.toFasta(e)?L[C.FASTA]:L[C.SEPARATOR]),n||(n=this.toFasta(e)?"":this.separator);const i=t.startsWith("RNA"),o=this.splitter(t),s=[];for(let t=0;t<o.length;++t){let n=o.getOriginal(t);if(i&&(n=n.replace(b,"")),n===L[C.HELM])s.push(r);else if(this.toFasta(e)&&n.length>1){const t="["+n+"]";s.push(t)}else s.push(n)}return s.join(n)}convert(t,e){const n=this.getJoiner({notation:t,separator:e}),r=this.getNewColumn(t,e);return r.init((t=>{const e=this.getSplitted(t);return n(e)})),r}getRegion(t,e,n){const r=this.getNewColumn(this.notation,this.separator);r.name=n;const i=t??0,o=e??this.maxLength-1,s=this.getJoiner(),a=o-i+1,u=L[this.notation];r.init((t=>{const e=this.getSplitted(t),n=new Array(a);for(let t=0;t<a;++t){const r=i+t;n[t]=r<e.length?e.getOriginal(r):u}return s(new q(n,u))}));const l=t=>{const e=t.split(",").map((t=>t.trim())),n=new Array(a);for(let t=0;t<a;++t){const r=i+t;n[t]=r<e.length?e[r]:"?"}return n.join(", ")},c=this.column.getTag(x.positionNames);c&&r.setTag(x.positionNames,l(c));const h=this.column.getTag(x.positionLabels);return h&&r.setTag(x.positionLabels,l(h)),r}get joiner(){return this._joiner||(this._joiner=this.getJoiner()),this._joiner}getJoiner(t){const e=t?t.notation:this.notation,n=t?t.separator:this.separator;let r;const i=this;switch(e){case C.FASTA:r=function(t){return i.joinToFasta(t,i.isHelm())};break;case C.SEPARATOR:if(!n)throw new Error(`Separator is mandatory for notation '${e}'.`);r=function(t){return et(t,n,i.isHelm())};break;case C.HELM:{const t=i.alphabet===A.DNA||i.alphabet===A.RNA,e=i.getHelmWrappers();r=function(n){return nt(n,e,t)};break}default:throw new Error(`Unexpected notation '${e}'.`)}return r}getConverter(t,e=void 0){if(t===C.SEPARATOR&&!e)throw new Error(`Target separator is not specified for target units '${C.SEPARATOR}'.`);const n=this;if(t===C.FASTA)return function(t){return n.convertToFasta(t)};if(t===C.HELM)return function(t){return n.convertToHelm(t)};if(t===C.SEPARATOR)return function(t){return n.convertToSeparator(t,e)};throw new Error}static forColumn(t){let e=t.temp[Z.seqHandler];return e&&e.columnVersion===t.version||(e=t.temp[Z.seqHandler]=new tt(t)),e}joinToFasta(t,e){const n=new Array(t.length);for(let r=0;r<t.length;++r){const i=t.getOriginal(r);let o=t.getOriginal(r);e&&(o=o.replace(b,"$1")),""===i?o=L[C.FASTA]:i===v?o="":o.length>1&&(o="["+o+"]"),n[r]=o}return n.join("")}convertToFasta(t){const e=this.splitter,n=this.isHelm()?this.splitterAsHelmNucl(t):e(t);return this.joinToFasta(n,this.isHelm())}convertToSeparator(t,e){return et(this.isHelm()?this.splitterAsHelmNucl(t):this.splitter(t),e,this.isHelm())}convertToHelm(t){if(this.notation==C.HELM)return t;const e=this.getHelmWrappers(),n=t.startsWith("DNA")||t.startsWith("RNA");return nt(this.splitter(t),e,n)}splitterAsHelmNucl(t){const e=this.splitter(t),n=new Array(e.length),r=t.startsWith("DNA"),i=t.startsWith("RNA");for(let t=0;t<e.length;++t){let o=e.getOriginal(t);(r||i)&&(o=o.replace(b,"$1"),o=o===v?null:o),n[t]=o||null}return new q(n.filter((t=>!!t)),L[C.HELM])}}function et(t,e,n){const r=new Array(t.length);for(let e=0;e<t.length;++e){const i=t.getCanonical(e);let o=t.getOriginal(e);n&&(o=o.replace(b,"$1")),""===i?o=L[C.SEPARATOR]:i===v&&(o=""),r[e]=o}return r.join(e)}function nt(t,e,n){const[r,i,o,s]=e,a=new Array(t.length);for(let e=0;e<t.length;++e){const r=t.getCanonical(e);let s=t.getOriginal(e);""===r?s=L[C.HELM]:(n&&(s=s.replace(b,"$1")),s=1===s.length?`${i}${s}${o}`:`${i}[${s}]${o}`),a[e]=s}return`${r}${a.join(".")}${s}`}async function rt(){const t=e.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()}class it{constructor(t,e,n=""){this.target=t,this.debugEnabled=e,this.prefix=n}error(t,e,n){return this.target.error(this.prefix+t,e,n)}warning(t,e){return this.target.warning(this.prefix+t,e)}info(t,e){return this.target.info(this.prefix+t,e)}debug(t,e){if(this.debugEnabled)return this.target.debug(this.prefix+t,e)}}const ot="System:AppData/SequenceTranslator/monomers-sample",st="pattern-app-data.json",at="formats-to-helm.json",ut="codes-to-symbols.json",lt="linkers.json",ct=["A","G","C","U"];var ht;function ft(t){return t.sort(((t,e)=>e.length-t.length))}function dt(t,e){const n=document.createElement("a");n.setAttribute("href","data:text/plain;charset=utf-8,"+e),n.setAttribute("download",t),n.click()}async function pt(e,n,r="Oligo app"){try{return await e()}catch(e){const n=e.hasOwnProperty("message")?e.message:e.toString();throw t.shell.error(`${r} error: `+n),e}finally{n&&n()}}!function(t){t.HELM="HELM",t.AXOLABS="Axolabs"}(ht||(ht={}));class gt{constructor(t,e){this.sequence=t,this.th=e,this.libWrapper=this.th.monomerLibWrapper}getInvalidCodeIndex(t){if(t===ht.HELM)return this.sequence.length;const e=["r","d"],n=ft(this.libWrapper.getCodesByFormat(t));let r=0;for(;r<this.sequence.length;){const t=n.find((t=>t===this.sequence.substring(r,r+t.length)));if(!t)break;if(r>1&&ct.includes(this.sequence[r])&&e.includes(this.sequence[r-2]))break;if(e.includes(this.sequence[r+1])&&ct.includes(this.sequence[r])){r++;break}r+=t.length}return r===this.sequence.length&&(r=-1),r}isValidSequence(t){return-1===this.getInvalidCodeIndex(t)}}class mt{constructor(t,e,n,r){this.patternAppData=t,this.codesToHelmDict=e,this.codesToSymbolsDict=n,this.monomersWithPhosphate=r}}async function yt(e){const n=await Promise.all([st,at,ut,lt].map((n=>async function(e,n){const r=e.endsWith("/")?`${e}${n}`:`${e}/${n}`;try{const e=await t.dapi.files.readAsText(r);return JSON.parse(e)}catch(t){console.error(`Error loading json from '${r}':`,t)}}(e,n))));return new mt(n[0],n[1],n[2],n[3])}class vt{constructor(t,e){if(this.lib=t,this.jsonData=e,null===this.lib)throw new Error("SequenceTranslator: monomer library is null");this.allMonomers=this.getAllMonomers()}formatMonomerForViewer(t){const e={};return e.name=t.symbol,e.symbol=t.symbol,e.molfile=t.molfile,this.getAllFormats().forEach((n=>{if(n===ht.HELM)return;const r=this.jsonData.codesToSymbolsDict[n],i=Object.keys(r).filter((e=>r[e]===t.symbol));e[n]=i.join(", ")})),e}getAllMonomers(){const t=this.lib.getPolymerTypes();let e=[];for(const n of t){const t=this.lib.getMonomerSymbolsByType(n).map((t=>this.lib.getMonomer(n,t))).filter((t=>null!==t));e=e.concat(t)}return e}getMonomer(t){const e=this.lib.getMonomer("RNA",t);if(void 0===e)throw new Error(`SequenceTranslator: no monomer with symbol ${t}`);return e}getMolfileBySymbol(t){return this.getMonomer(t).molfile}getNaturalAnalogBySymbol(t){const e=this.getMonomer(t).naturalAnalog;if(!e)throw new Error(`ST: no natural analog for ${t}`);return e}isModification(t){return!!this.getMolfileBySymbol(t).includes("MODIFICATION")}getCodeToSymbolMap(t){return new Map(Object.entries(this.jsonData.codesToSymbolsDict[t]))}getCodesByFormat(t){return Object.keys(this.jsonData.codesToSymbolsDict[t])}getAllFormats(){return Object.keys(this.jsonData.codesToSymbolsDict)}getTableForViewer(){const t=this.allMonomers.map((t=>this.formatMonomerForViewer(t)));return e.DataFrame.fromObjects(t)}getCodesToWeightsMap(){const t=new Map;return Object.entries(this.jsonData.codesToSymbolsDict).forEach((([e,n])=>{Object.entries(n).forEach((([e,n])=>{const r=this.getMonomer(n),i=r.meta?.molecularWeight;t.set(e,i)}))})),t}}const bt="<?>",wt=(t,e)=>e.length-t.length;class Ct{constructor(t){this.th=t,this.formats=this.getFormats()}getFormatNames(){return this.formats.sort()}getCodesByFormat(t){if(this.validateFormat(t),this.isHelm(t))throw new Error("Codes cannot be obtained for HELM");return this.getFormatCodes(t)}getHelmToFormatDict(t){return this.validateFormat(t),function(t){const e={};return Object.values(t).forEach((t=>{Object.entries(t).forEach((([t,n])=>{const r=n.replace(/\)p/g,")").replace(/\]p/g,"]");void 0===e[r]?e[r]=[t]:e[r].push(t)}))})),Object.entries(e).forEach((([t,n])=>{const r=n.sort(wt);e[t]=r[0]})),e}(this.th.jsonData.codesToHelmDict[t])}getFormatToHelmDict(t){this.validateFormat(t);const e=this.th.jsonData.codesToHelmDict[t];return Object.assign({},...Object.values(e))}getTargetFormatHelmCodes(t){this.validateFormat(t);const e=this.getHelmToFormatDict(t);return Object.keys(e).sort(wt)}getTargetFormatHelmCodesRegExp(t){this.validateFormat(t);const e=this.getTargetFormatHelmCodes(t);return new RegExp(At(e)+"|.","g")}getFormatRegExp(t){if(this.validateFormat(t),this.isHelm(t))throw new Error("Helm RegExp can be built for non-HELM target formats");return this.getNonHelmFormatRegExp(t)}getPhosphateHelmCodesRegExp(t){this.validateFormat(t);const e=this.th.jsonData.codesToHelmDict[t],n=At(Array.from(new Set(Object.values(e.phosphateBackbone))).sort(wt));return new RegExp(`p.(${n})`,"g")}isValidFormat(t){return this.formats.includes(t)}getFormats(){return Object.keys(this.th.jsonData.codesToHelmDict)}validateFormat(t){if(!this.isValidFormat(t))throw new Error(`Invalid format: ${t}`)}isHelm(t){return t===ht.HELM}getFormatCodes(t){const e=this.getFormatToHelmDict(t);return Object.keys(e).sort(wt)}getNonHelmFormatRegExp(t){const e=this.getCodesByFormat(t);return new RegExp(At(e)+"|\\([^()]*\\)|.","g")}}function At(t){return t.map((t=>t.replace(/[.*+?^${}()|[\]\\]/g,"\\$&"))).map((t=>t.includes("(")||t.includes(")")?t:`(?<!\\([^()]*)${t}(?![^()]*\\))`)).join("|")}const xt={LEFT:"RNA1{",RIGHT:"}$$$$"};class _t{constructor(t,e,n){this.sequence=t,this.sourceFormat=e,this.th=n,this.formats=new Ct(this.th)}convertTo(t){const e=this.formats.getFormatNames();if(this.sourceFormat===ht.HELM&&e.includes(t))return this.helmToFormat(this.sequence,t);if(e.includes(this.sourceFormat)&&t===ht.HELM)return this.formatToHelm(this.sequence,this.sourceFormat);if([this.sourceFormat,t].every((t=>e.includes(t)))){const e=this.formatToHelm(this.sequence,this.sourceFormat);return this.helmToFormat(e,t)}throw new Error(`ST: unsupported translation direction ${this.sourceFormat} -> ${t}`)}helmToFormat(t,e){const n=new RegExp(At(Object.values(xt)),"g");let r=t.replace(n,"");const i=this.formats.getHelmToFormatDict(e),o=this.formats.getTargetFormatHelmCodes(e),s=this.formats.getTargetFormatHelmCodesRegExp(e);return r=r.replace(s,(t=>o.includes(t)?i[t]:"p"===t||"."===t?t:"?")).replace(/\?+/g,bt).replace(/p\.|\./g,""),r=r.replace(/<empty>/g,""),r=r.replace(/\/\//g,"/"),r}formatToHelm(t,e){const n=this.formats.getFormatToHelmDict(e),r=this.formats.getCodesByFormat(e),i=this.formats.getFormatRegExp(e),o=this.formats.getPhosphateHelmCodesRegExp(e);let s=t?t.replace(i,(t=>r.includes(t)?n[t]+".":"?")):"";return s=s.replace(/\?+/g,`${bt}.`),s=s.slice(0,-1),"p"===s[s.length-1]&&(s=s.slice(0,-1)),s=s.replace(o,((t,e)=>e)),s=s.replace(/<empty>/g,""),`${xt.LEFT+s+xt.RIGHT}`}}class Et{constructor(t,e){this.sequence=t,this.th=e,this.libWrapper=this.th.monomerLibWrapper,this.formats=Object.keys(this.th.jsonData.codesToHelmDict)}getFormat(){if(this.sequence.startsWith("RNA"))return ht.HELM;const t=this.getListOfPossibleSynthesizersByFirstMatchedCode();if(0===t.length)return null;const e=this.th.createSequenceValidator(this.sequence),n=Array(t.length).fill(0);for(let r=0;r<t.length;++r){const i=t[r];n[r]=e.getInvalidCodeIndex(i)}const r=n.some((t=>-1===t))?-1:Math.max(...n);return t[n.indexOf(r)]}getListOfPossibleSynthesizersByFirstMatchedCode(){const t=this.sequence,e=[];for(const n of this.formats){const r=ft(this.libWrapper.getCodesByFormat(n));let i=0;for(let e=0;e<t.length;e++)if(")"===t[e]&&e!==t.length-1){i=e+1;break}r.some((e=>e===t.slice(i,i+e.length)))&&e.push(n)}return e}}const Tt=ui,St=$;var It=n.n(St);function Nt(t,e){let n=0;const r=e.createFormatDetector(t).getFormat();null!==r&&(n=new gt(t,e).getInvalidCodeIndex(r));const i=n<0||""===t,o=Tt.span([]);It()(o).css("-webkit-text-fill-color","var(--grey-6)");const s=Tt.span([]);return It()(s).css("-webkit-text-fill-color","red"),i?o.innerHTML=t:(o.innerHTML=t.slice(0,n),s.innerHTML=t.slice(n)),[o,s]}class Mt extends e.Package{get monomerLib(){if(!this._monomerLib)throw new Error("Monomer lib not loaded");return this._monomerLib}get jsonData(){if(!this._jsonData)throw new Error("Json data not loaded");return this._jsonData}get monomerLibWrapper(){if(!this._monomerLibWrapper)throw new Error("Monomer lib wrapper not loaded");return this._monomerLibWrapper}constructor(t={debug:!1}){super(),this.highlightInvalidSubsequence=t=>Nt(t,this),super._logger=new it(super.logger,t.debug)}async initLibData(){return this.initPromise||(this.initPromise=(async()=>{let e=(await this.getSettings()).MonomersPath;e&&await t.dapi.files.exists(e)||(this.logger.warning(`Monomers path '${e}' not found. Fallback to monomers sample path '${ot}'.`),e=ot),[this._jsonData,this._monomerLib]=await Promise.all([yt(e),Ot(e)]),this._monomerLibWrapper=new vt(this.monomerLib,this.jsonData)})()),this.initPromise}async getTranslationHelper(){return await t.functions.call(`${this.name}:getTranslationHelper`)}createSequenceValidator(t){return new gt(t,this)}createFormatConverter(t,e){return new _t(t,e,this)}createFormatDetector(t){return new Et(t,this)}}async function Ot(t){const n=e.TaskBarProgressIndicator.create("Initializing Oligo Toolkit monomer library ...");try{const e=await rt();return await e.readLibrary(t,"monomer-lib.json")}finally{n.close()}}class Lt{constructor(t,e){this.appName=t,this.parentAppName=e}async getAppView(){const n=e.TaskBarProgressIndicator.create(`Loading ${this.appName}...`),r=t.shell.v?.root;r&&Tt.setUpdateIndicator(r,!0);try{return await this.constructView()}finally{n.close(),r&&Tt.setUpdateIndicator(r,!1)}}}class Bt extends Lt{constructor(t){super(t),this.view=e.View.create(),this.configureView()}async constructView(){await this.initView();const t=this.parentAppName?this.parentAppName+"/"+this.appName:this.appName;return this.view.path=`/apps/${$r.name}/${t.replace(/\s/g,"")}/`,this.view}async initView(){const t=await this.getContent();this.view.append(t)}configureView(){this.view.box=!0,this.view.name=this.appName;const e=t.shell.windows;e.showProperties=!1,e.showToolbox=!1,e.showHelp=!1}getView(){return this.view}}const Pt=["SS","AS"],Rt={SS:"Sense strand",AS:"Anti sense"},Dt=["3'","5'"],Ft="OligoToolkit";var Ht,Ut,kt,$t;!function(t){t.IS_ANTISENSE_STRAND_INCLUDED="isAntisenseStrandIncluded",t.NUCLEOTIDE_SEQUENCES="nucleotideSequences",t.PHOSPHOROTHIOATE_LINKAGE_FLAGS="phosphorothioateLinkageFlags",t.STRAND_TERMINUS_MODIFICATIONS="strandTerminusModifications"}(Ht||(Ht={})),function(t){t.PATTERN_NAME="patternName",t.PATTERN_COMMENT="patternComment",t.NUCLEOTIDES_WITH_NUMERIC_LABELS="nucleotidesWithNumericLabels"}(Ut||(Ut={})),function(t){t.PATTERN_CONFIG="patternConfig",t.AUTHOR_ID="authorID",t.DATE="date"}(kt||(kt={})),function(t){t.CREATE="create",t.MODIFY="modify"}($t||($t={}));const Vt=[Ht.IS_ANTISENSE_STRAND_INCLUDED,Ht.NUCLEOTIDE_SEQUENCES,Ht.PHOSPHOROTHIOATE_LINKAGE_FLAGS,Ht.STRAND_TERMINUS_MODIFICATIONS],jt=(Ut.PATTERN_NAME,Ut.PATTERN_COMMENT,Ut.NUCLEOTIDES_WITH_NUMERIC_LABELS,{patternConfig:{patternName:"<default example>",isAntisenseStrandIncluded:!0,nucleotideSequences:{SS:["RNA","RNA","RNA","RNA","RNA","RNA","RNA","RNA","RNA","RNA","RNA","RNA","RNA","RNA","RNA","RNA","RNA","RNA","RNA","RNA","RNA","RNA","RNA"],AS:["RNA","RNA","RNA","RNA","RNA","RNA","RNA","RNA","RNA","RNA","RNA","RNA","RNA","RNA","RNA","RNA","RNA","RNA","RNA","RNA","RNA","RNA","RNA"]},phosphorothioateLinkageFlags:{SS:[!0,!0,!0,!0,!0,!0,!0,!0,!0,!0,!0,!0,!0,!0,!0,!0,!0,!0,!0,!0,!0,!0,!0,!0],AS:[!0,!0,!0,!0,!0,!0,!0,!0,!0,!0,!0,!0,!0,!0,!0,!0,!0,!0,!0,!0,!0,!0,!0,!0]},strandTerminusModifications:{SS:{"3'":"","5'":""},AS:{"3'":"","5'":""}},patternComment:"",nucleotidesWithNumericLabels:["RNA"]},authorID:""}),qt="2024-01-01T18:00:00.000Z";class Gt extends Error{constructor(t){super(t),this.name="PatternNameExistsError"}}class Wt extends Error{constructor(t){super(t),this.name="PatternExistsError"}}var zt=n(802),Yt=n.n(zt);class Kt{constructor(t){this.th=t,this.otherUsersPatternNameToHash=new Map,this.currentUserPatternNameToHash=new Map}static async getInstance(){const t=await $r.getTranslationHelper(),e=new Kt(t);e.currentUserName=await e.fetchCurrentUserName(),e.currentUserId=await e.fetchCurrentUserId();const n=await e.fetchPatterns();return await e.initializePatternMaps(n),e}getCurrentUserPatternNames(){return Array.from(this.currentUserPatternNameToHash.keys()).sort(((t,e)=>t.toLowerCase().localeCompare(e.toLowerCase())))}getOtherUsersPatternNames(){return Array.from(this.otherUsersPatternNameToHash.keys()).sort(((t,e)=>t.toLowerCase().localeCompare(e.toLowerCase())))}getCurrentUserName(){return this.currentUserName}validatePatternNameUniqueness(t){if(this.currentUserPatternNameToHash.has(t))throw new Gt(`Pattern with name ${t} already exists`)}validatePatternUniqueness(t){if(Array.from(this.currentUserPatternNameToHash.values()).concat(Array.from(this.otherUsersPatternNameToHash.values())).includes(t))throw new Wt(t)}getPatternHash(t,e){const n=e?this.currentUserPatternNameToHash.get(t):this.otherUsersPatternNameToHash.get(t);if(void 0===n)throw new Error(`Pattern with name ${t} not found`);return n}async getPatternRecordByHash(e){if(null===e||""===e)return null;try{const n=await t.dapi.userDataStorage.getValue(Ft,e,!1);return JSON.parse(n)}catch{return null}}async getPatternConfig(t){if(""===t||null===t)return null;const e=await this.getPatternRecordByHash(t);return null===e?null:e[kt.PATTERN_CONFIG]}getDefaultPatternRecord(){const t=jt;return t[kt.AUTHOR_ID]=this.currentUserId,t}getDefaultPatternConfig(){return jt[kt.PATTERN_CONFIG]}getAuthorCategoryByHash(t){if(this.isCurrentUserPattern(t))return this.getCurrentUserAuthorshipCategory();if(this.isOtherUserPattern(t))return this.getOtherUsersAuthorshipCategory();throw new Error(`Pattern with hash ${t} not found`)}isCurrentUserPattern(t){return Array.from(this.currentUserPatternNameToHash.values()).includes(t)}isOtherUserPattern(t){return Array.from(this.otherUsersPatternNameToHash.values()).includes(t)}getPatternNameByHash(t){const e=[this.currentUserPatternNameToHash,this.otherUsersPatternNameToHash];for(const n of e)for(const[e,r]of n.entries())if(r===t)return e;throw new Error(`Pattern with hash ${t} not found`)}getHashOfPatternToBeLoadedAfterDeletion(){const t=this.getCurrentUserPatternNames()[0];if(!t)throw new Error("Cannot load pattern after deletion, as there are no patterns left");const e=this.currentUserPatternNameToHash.get(t);if(void 0===e)throw new Error(`Pattern with name ${t} not found`);return e}async getRecordFromPattern(e){return{[kt.PATTERN_CONFIG]:e,[kt.AUTHOR_ID]:await t.dapi.users.current().then((t=>t.id))}}getHash(t){const e=Vt.reduce(((e,n)=>(e[n]=t[n],e)),{});return Yt().sha1(e)}async savePatternToUserStorage(e){const n=e.getPatternConfig();try{const r=this.getHash(n);this.validatePatternUniqueness(r);const i=n[Ut.PATTERN_NAME];this.validatePatternNameUniqueness(i);const o=await this.getRecordFromPattern(n),s=(new Date).toISOString();o[kt.DATE]={[$t.CREATE]:s,[$t.MODIFY]:s};const a=JSON.stringify(o);await t.dapi.userDataStorage.postValue(Ft,r,a,!1),this.currentUserPatternNameToHash.set(i,r),e.selectAuthor(this.getCurrentUserAuthorshipCategory()),e.updatePatternList(),e.requestPatternLoad(r),e.updateUrlState(r)}catch(t){if(t instanceof Gt||t instanceof Wt)throw t;console.error("Error while saving pattern to user storage",t)}}async overwriteExistingPatternInUserStorage(e){const n=e.getPatternConfig(),r=n[Ut.PATTERN_NAME],i=this.currentUserPatternNameToHash.get(r);if(void 0===i)throw new Error("Old hash is undefined");const o=this.getHash(n),s=await this.getRecordFromPattern(n),a=(new Date).toISOString();s[kt.DATE]={[$t.MODIFY]:a};const u=await t.dapi.userDataStorage.getValue(Ft,i,!1),l=JSON.parse(u);void 0!==l[kt.DATE]&&null!=l[kt.DATE][$t.CREATE]&&(s[kt.DATE][$t.CREATE]=l[kt.DATE][$t.CREATE]);const c=JSON.stringify(s);await t.dapi.userDataStorage.postValue(Ft,o,c,!1),await t.dapi.userDataStorage.remove(Ft,i,!1),this.currentUserPatternNameToHash.set(r,o),e.requestPatternLoad(o),e.updateUrlState(o)}async deletePattern(e,n){const r=this.currentUserPatternNameToHash.get(e);if(e===this.getDefaultPatternName())return void t.shell.warning("Cannot delete default pattern");if(void 0===r)throw new Error(`Pattern with name ${e} not found`);await t.dapi.userDataStorage.remove(Ft,r,!1),this.currentUserPatternNameToHash.delete(e),n.updatePatternList();const i=this.getHashOfPatternToBeLoadedAfterDeletion();n.requestPatternLoad(i)}fetchDefaultNucleobase(){return this.fetchAvailableNucleotideBases()[0]}fetchAvailableNucleotideBases(){const t=Object.keys(this.th.jsonData.patternAppData)[0];return Object.keys(this.th.jsonData.patternAppData[t])}async fetchCurrentUserName(){return(await t.dapi.users.current()).friendlyName}async fetchCurrentUserId(){return(await t.dapi.users.current()).id}async fetchPatterns(){return await t.dapi.userDataStorage.get(Ft,!1)}async initializePatternMaps(t){if(!this.currentUserId)throw new Error("Current user ID is not set");const e=new Map;for(const[n,r]of Object.entries(t))await this.extractDataFromRecordToMaps(n,r,e);this.setDefaultPattern()}setDefaultPattern(){const t=jt[kt.PATTERN_CONFIG];this.currentUserPatternNameToHash.set(t[Ut.PATTERN_NAME],"")}async extractDataFromRecordToMaps(e,n,r){const i=JSON.parse(n),o=i[kt.PATTERN_CONFIG].patternName,s=i[kt.AUTHOR_ID];if(this.isCurrentUserId(s))this.currentUserPatternNameToHash.set(o,e);else{if(!r.has(s)){let e="<UNKNOWN_USER>";try{e=(await t.dapi.users.find(s)).friendlyName}catch(t){}r.set(s,e)}const n=o+` (created by ${r.get(s)})`;this.otherUsersPatternNameToHash.set(n,e)}}getDefaultPatternName(){return jt[kt.PATTERN_CONFIG][Ut.PATTERN_NAME]}getCurrentUserAuthorshipCategory(){return this.currentUserName+" (me)"}getOtherUsersAuthorshipCategory(){return"Other users"}isCurrentUserId(t){return t===this.currentUserId}}const Jt=rxjs,Qt=rxjs.operators;function Xt(t){return t.endsWith("(o)")}function Zt(t){const e=Object.values(t).flat().reduce(((t,e)=>(t[e]=(t[e]||0)+1,t)),{});return Object.entries(e).reduce(((t,e)=>t[1]>e[1]?t:e),["",0])[0]}var te;function ee(t){const e=Array.from(new Set(t));return Array.from(e).sort(((t,e)=>t.toLowerCase().localeCompare(e.toLowerCase())))}!function(t){t.getTruncatedStrandData=function(t,e,n){return{nucleotides:t.slice(0,n),ptoFlags:e.slice(0,n+1)}},t.getExtendedStrandData=function(t,e,n,r){const i=n-t.length,o=t.concat(new Array(n-t.length).fill(r)),s=0===t.length?n+1:i;return{nucleotides:o,ptoFlags:e.concat(new Array(s).fill(!0))}}}(te||(te={}));var ne=n(543),re=n.n(ne);class ie{constructor(t,e){this.dataManager=t,this._patternListUpdated$=new Jt.Subject,this._patternLoadRequested$=new Jt.Subject,this._patternLoaded$=new Jt.Subject,this._uniqueNucleotides$=new Jt.BehaviorSubject([]),this._patternDeletionRequested$=new Jt.Subject,this._tableSelection$=new Jt.BehaviorSubject(null),this._svgSaveRequested$=new Jt.Subject,this._loadPatternInNewTabRequested$=new Jt.Subject,this._urlStateUpdated$=new Jt.Subject,this._patternHasUnsavedChanges$=new Jt.BehaviorSubject(!1),this._selectedStrandColumn=new Jt.BehaviorSubject(null),this._selectedIdColumn=new Jt.BehaviorSubject(null),this.initializeAuthorSelection(e),this.initializePatternState(e),this._lastLoadedPatternConfig=new Jt.BehaviorSubject(re().cloneDeep(this.getPatternConfig())),this.setupSubscriptions()}setupSubscriptions(){this._nucleotideSequences$.subscribe((()=>{this.updateUniqueNucleotides(),this.updateSequenceBase()})),this._isAntisenseStrandActive$.subscribe((t=>{t||Dt.forEach((t=>{this.updateTerminusModification("AS",t,"")}))})),this.patternStateChanged$.pipe((0,Qt.debounceTime)(20)).subscribe((()=>{const t=this._lastLoadedPatternConfig.getValue(),e=this.getPatternConfig(),n=!re().isEqual(e,t);this._patternHasUnsavedChanges$.next(n)}))}updateUniqueNucleotides(){const t=(e=this._nucleotideSequences$.getValue(),ee(Object.values(e).flat()));var e;this._uniqueNucleotides$.next(t)}updateSequenceBase(){const t=Zt(this._nucleotideSequences$.getValue());this._sequenceBase$.next(t)}get nucleotideSequencesChanged$(){return this._nucleotideSequences$.asObservable()}initializeAuthorSelection(t){const e=t[kt.AUTHOR_ID];this.dataManager.isCurrentUserId(e)?this._patternAuthorSelection$=new Jt.BehaviorSubject(this.dataManager.getCurrentUserAuthorshipCategory()):this._patternAuthorSelection$=new Jt.BehaviorSubject(this.dataManager.getOtherUsersAuthorshipCategory())}initializePatternState(t){const e=t[kt.PATTERN_CONFIG];this._patternName$=new Jt.BehaviorSubject(e[Ut.PATTERN_NAME]),this._isAntisenseStrandActive$=new Jt.BehaviorSubject(e[Ht.IS_ANTISENSE_STRAND_INCLUDED]),this._nucleotideSequences$=new Jt.BehaviorSubject(e[Ht.NUCLEOTIDE_SEQUENCES]),this._phosphorothioateLinkageFlags=new Jt.BehaviorSubject(e[Ht.PHOSPHOROTHIOATE_LINKAGE_FLAGS]),this._terminalModifications=new Jt.BehaviorSubject(e[Ht.STRAND_TERMINUS_MODIFICATIONS]),this._comment$=new Jt.BehaviorSubject(e[Ut.PATTERN_COMMENT]),this._modificationsWithNumericLabels$=new Jt.BehaviorSubject(e[Ut.NUCLEOTIDES_WITH_NUMERIC_LABELS]),this._sequenceBase$=new Jt.BehaviorSubject(Zt(e[Ht.NUCLEOTIDE_SEQUENCES]))}getPatternName(){return this._patternName$.getValue()}updatePatternName(t){this._patternName$.next(t)}get antisenseStrandToggled$(){return this._isAntisenseStrandActive$.asObservable()}isAntisenseStrandActive(){return this._isAntisenseStrandActive$.getValue()}toggleAntisenseStrand(t){t?this.updateStrandLength("AS",this.getNucleotideSequences().SS.length):this.updateStrandLength("AS",0),this._isAntisenseStrandActive$.next(t)}getNucleotideSequences(){return this._nucleotideSequences$.getValue()}updateNucleotideSequences(t){this._nucleotideSequences$.next(t)}updateStrandLength(t,e){const n=this.getNucleotideSequences()[t];if(n.length===e)return;const r=this.getPhosphorothioateLinkageFlags()[t];if(0===e)return void this.setNewStrandData([],[],t);if(n.length>e){const{nucleotides:i,ptoFlags:o}=te.getTruncatedStrandData(n,r,e);return void this.setNewStrandData(i,o,t)}const i=this.getSequenceBase(),{nucleotides:o,ptoFlags:s}=te.getExtendedStrandData(n,r,e,i);this.setNewStrandData(o,s,t)}setNewStrandData(t,e,n){this.updateNucleotideSequences({...this.getNucleotideSequences(),[n]:t}),this.updatePhosphorothioateLinkageFlags({...this.getPhosphorothioateLinkageFlags(),[n]:e})}getPhosphorothioateLinkageFlags(){return this._phosphorothioateLinkageFlags.getValue()}updatePhosphorothioateLinkageFlags(t){this._phosphorothioateLinkageFlags.next(t)}get phosphorothioateLingeFlagsChanged$(){return this._phosphorothioateLinkageFlags.asObservable()}getTerminalModifications(){return this._terminalModifications.getValue()}updateTerminalModifications(t){this._terminalModifications.next(t)}updateTerminusModification(t,e,n){const r=this.getTerminalModifications();r[t][e]=n,this.updateTerminalModifications(r)}terminalModificationsUpdated$(){return this._terminalModifications.asObservable()}getComment(){return this._comment$.getValue()}updateComment(t){this._comment$.next(t)}getModificationsWithNumericLabels(){return this._modificationsWithNumericLabels$.getValue()}updateModificationsWithNumericLabels(t){const e=function(t){return ee(t).filter((t=>!Xt(t)))}(t);this._modificationsWithNumericLabels$.next(e)}get patternLoadRequested$(){return this._patternLoadRequested$.asObservable()}requestPatternLoad(t){this._patternLoadRequested$.next(t)}get patternListUpdated$(){return this._patternListUpdated$.asObservable()}updatePatternList(){this._patternListUpdated$.next()}get tableSelectionChanged$(){return this._tableSelection$.asObservable()}selectTable(t){this._tableSelection$.next(t)}getTableSelection(){return this._tableSelection$.getValue()}requestPatternDeletion(t){this._patternDeletionRequested$.next(t)}get patternDeletionRequested$(){return this._patternDeletionRequested$.asObservable()}replaceSequenceBase(t){const e=this._nucleotideSequences$.getValue(),n={};Pt.forEach((r=>{n[r]=e[r].map((()=>t))})),this._nucleotideSequences$.next(n);const r=this._modificationsWithNumericLabels$.getValue();r.includes(t)||this.updateModificationsWithNumericLabels(r.concat(t))}get patternStateChanged$(){return Jt.merge(this._patternName$.pipe((0,Qt.debounceTime)(300),(0,Qt.map)((()=>{}))),this._isAntisenseStrandActive$,this._nucleotideSequences$,this._phosphorothioateLinkageFlags,this._terminalModifications,this._comment$.pipe((0,Qt.debounceTime)(300)),this._modificationsWithNumericLabels$)}getSequenceBase(){return this._sequenceBase$.getValue()}uniqueNucleotidesChanged$(){return this.patternStateChanged$.pipe((0,Qt.switchMap)((()=>this._uniqueNucleotides$)))}getUniqueNucleotides(){return this._uniqueNucleotides$.getValue()}get svgSaveRequested$(){return this._svgSaveRequested$.asObservable()}requestSvgSave(){this._svgSaveRequested$.next()}setAllPTOLinkages(t){const e=this.getPhosphorothioateLinkageFlags();Pt.forEach((n=>{e[n]=e[n].map((()=>t))})),this.updatePhosphorothioateLinkageFlags(e)}setPatternConfig(t){this._patternName$.next(t[Ut.PATTERN_NAME]),this._isAntisenseStrandActive$.next(t[Ht.IS_ANTISENSE_STRAND_INCLUDED]),this._nucleotideSequences$.next(t[Ht.NUCLEOTIDE_SEQUENCES]),this._phosphorothioateLinkageFlags.next(t[Ht.PHOSPHOROTHIOATE_LINKAGE_FLAGS]),this._terminalModifications.next(t[Ht.STRAND_TERMINUS_MODIFICATIONS]),this._comment$.next(t[Ut.PATTERN_COMMENT]),this._modificationsWithNumericLabels$.next(t[Ut.NUCLEOTIDES_WITH_NUMERIC_LABELS])}setLastLoadedPatternConfig(t){this._lastLoadedPatternConfig.next(re().cloneDeep(t))}getPatternConfig(){return{[Ut.PATTERN_NAME]:this.getPatternName(),[Ht.IS_ANTISENSE_STRAND_INCLUDED]:this.isAntisenseStrandActive(),[Ht.NUCLEOTIDE_SEQUENCES]:this.getNucleotideSequences(),[Ht.PHOSPHOROTHIOATE_LINKAGE_FLAGS]:this.getPhosphorothioateLinkageFlags(),[Ht.STRAND_TERMINUS_MODIFICATIONS]:this.getTerminalModifications(),[Ut.PATTERN_COMMENT]:this.getComment(),[Ut.NUCLEOTIDES_WITH_NUMERIC_LABELS]:this.getModificationsWithNumericLabels()}}setPhosphorothioateLinkageFlag(t,e,n){const r=this.getPhosphorothioateLinkageFlags();r[t][e]=n,this.updatePhosphorothioateLinkageFlags(r)}setNucleotide(t,e,n){const r=this.getNucleotideSequences();r[t][e]=n;const i=this.getModificationsWithNumericLabels();this.updateModificationsWithNumericLabels(i.concat(n)),this.updateNucleotideSequences(r)}get strandsUpdated$(){return Jt.merge(this._isAntisenseStrandActive$.asObservable().pipe((0,Qt.map)((()=>{}))),this._nucleotideSequences$.asObservable().pipe((0,Qt.map)((()=>{}))),this._patternLoaded$.asObservable().pipe((0,Qt.map)((()=>{})))).pipe((0,Qt.debounceTime)(10))}get strandsLinkagesAndTerminalsUpdated$(){return Jt.merge(this.strandsUpdated$,this._phosphorothioateLinkageFlags.asObservable().pipe((0,Qt.map)((()=>{}))),this._terminalModifications.asObservable().pipe((0,Qt.map)((()=>{}))))}updateControlsUponPatternLoaded(t){this._patternLoaded$.next(t)}get patternLoaded$(){return this._patternLoaded$.asObservable()}get userSelection$(){return this._patternAuthorSelection$.asObservable().pipe((0,Qt.skip)(1))}selectAuthor(t){if("string"!=typeof t)throw new Error("Selected user must be defined");this._patternAuthorSelection$.next(t)}getSelectedAuthor(){return this._patternAuthorSelection$.getValue()}get loadPatternInNewTabRequested$(){return this._loadPatternInNewTabRequested$.asObservable()}requestLoadPatternInNewTab(t){this._loadPatternInNewTabRequested$.next(t)}updateUrlState(t){this._urlStateUpdated$.next(t)}get urlStateUpdated$(){return this._urlStateUpdated$.asObservable()}get patternHasUnsavedChanges$(){return this._patternHasUnsavedChanges$.asObservable()}selectStrandColumn(t,e){this._selectedStrandColumn.next({...this._selectedStrandColumn.getValue(),[t]:e})}getSelectedStrandColumn(t){const e=this._selectedStrandColumn.getValue();return e?e[t]:null}selectIdColumn(t){this._selectedIdColumn.next(t)}getSelectedIdColumn(){return this._selectedIdColumn.getValue()}get updateSvgContainer$(){return this.patternStateChanged$.pipe((0,Qt.debounceTime)(100))}}const oe="pattern";class se{constructor(){this.urlSearchParams=new URLSearchParams(window.location.search)}subscribeToObservables(t){t.urlStateUpdated$.subscribe((t=>this.setPatternURL(t))),t.loadPatternInNewTabRequested$.subscribe((t=>{const e=`${window.location.origin}${window.location.pathname}?${oe}=${t}`;window.open(e,"_blank")})),window.addEventListener("popstate",(()=>{this.urlSearchParams=new URLSearchParams(window.location.search);const e=this.getPatternHash();null!==e&&t.requestPatternLoad(e)}))}getPatternHash(){return this.urlSearchParams.get(oe)}setPatternURL(t){null!==t&&""!==t?(this.urlSearchParams.set(oe,t),window.history.pushState({},"",`${window.location.pathname}?${this.urlSearchParams}`)):this.clearPatternURL()}clearPatternURL(){this.urlSearchParams.delete(oe),window.history.pushState({},"",`${window.location.pathname}`)}}var ae=n(72),ue=n.n(ae),le=n(825),ce=n.n(le),he=n(659),fe=n.n(he),de=n(56),pe=n.n(de),ge=n(540),me=n.n(ge),ye=n(113),ve=n.n(ye),be=n(252),we={};we.styleTagTransform=ve(),we.setAttributes=pe(),we.insert=fe().bind(null,"head"),we.domAPI=ce(),we.insertStyleElement=me(),ue()(be.A,we),be.A&&be.A.locals&&be.A.locals;class Ce{constructor(t){this.eventBus=t,this.columnControlsContainer=Tt.div([]),this.eventBus.tableSelectionChanged$.subscribe((()=>this.handleTableChoice())),this.refreshColumnControls()}getColumnControlsContainer(){return this.columnControlsContainer}get selectedTable(){return this.eventBus.getTableSelection()}handleTableChoice(){this.refreshColumnControls()}refreshColumnControls(){It()(this.columnControlsContainer).empty(),It()(this.columnControlsContainer).append(this.constructColumnControls())}constructColumnControls(){const t=this.createStrandColumnInput(),e=t.SS,n=t.AS;this.eventBus.antisenseStrandToggled$.subscribe((t=>{It()(n).toggle(t)}));const r=this.createIdColumnInput();return[e,n,r]}createStrandColumnInput(){const t=this.selectedTable?this.selectedTable.columns.names().sort(((t,e)=>t.localeCompare(e))):[];return Object.fromEntries(Pt.map((e=>{const n=Tt.input.choice(`${Rt[e]} column`,{value:t[0],items:t,onValueChanged:t=>this.eventBus.selectStrandColumn(e,t)});return this.eventBus.selectStrandColumn(e,t[0]),[e,n.root]})))}createIdColumnInput(){const t=this.selectedTable?this.selectedTable.columns.names():[],e=Tt.input.choice("ID column",{value:t[0],items:t,onValueChanged:t=>this.eventBus.selectIdColumn(t)});return this.eventBus.selectIdColumn(t[0]),e.root}}class Ae{constructor(t){this.eventBus=t,this.availableTables=[],this.tableInputContainer=Tt.div([]),this.subscribeToTableEvents(),this.refreshTableInput()}getTableInputContainer(){return this.tableInputContainer}subscribeToTableEvents(){t.events.onTableAdded.subscribe((t=>this.handleTableAdded(t))),t.events.onTableRemoved.subscribe((t=>this.handleTableRemoved(t))),this.eventBus.tableSelectionChanged$.subscribe((()=>this.handleTableChoice()))}getTableFromEventData(t){if(!t&&t.args&&t.args.dataFrame instanceof e.DataFrame)throw new Error("EventData does not contain a dataframe",t);return t.args.dataFrame}handleTableAdded(t){const e=this.getTableFromEventData(t);this.availableTables.some((t=>t.name===e.name))||(this.availableTables.push(e),this.eventBus.selectTable(e),this.refreshTableInput())}handleTableRemoved(t){const e=this.getTableFromEventData(t);this.availableTables=this.availableTables.filter((t=>t.name!==e.name));const n=this.availableTables[0];this.eventBus.selectTable(n||null),this.refreshTableInput()}refreshTableInput(){const t=this.createTableInput();It()(this.tableInputContainer).empty(),this.tableInputContainer.append(t.root)}createTableInput(){const t=this.eventBus.getTableSelection();return Tt.input.table("Tables",{value:t,items:this.availableTables,onValueChanged:t=>{null!==t&&this.eventBus.selectTable(t)}})}handleTableChoice(){const t=this.eventBus.getTableSelection();t&&(this.isTableDisplayed(t)||this.displayTable(t))}isTableDisplayed(e){return t.shell.tableNames.includes(e.name)}displayTable(e){const n=t.shell.v;t.shell.addTableView(e),t.shell.v=n}}function xe(t,e,n,r){const i=function(t,e,n){const r=new Array(t.length+e.filter((t=>t)).length+Dt.length);r[0]=n["5'"],r[r.length-1]=n["3'"];let i=1;return e[0]&&(r[i]="ps",i++),t.forEach(((t,n)=>{r[n+i]=t,e[n+1]&&(r[n+i+1]="ps",i++)})),r}(t.split("").map(((t,n)=>{const r=function(t,e,n){const r=Object.keys(n.patternAppData)[0],i=n.patternAppData[r][e].substitution;return t.replace(/([AGCTU])/,i)}(t,e[n],$r.jsonData);return r})),n,r);return i.join("")}class _e{constructor(t){this.eventBus=t,this.tableInputManager=new Ae(t),this.columnInputManager=new Ce(t)}createControls(){const t=Tt.h1("Bulk convert"),e=this.tableInputManager.getTableInputContainer(),n=this.columnInputManager.getColumnControlsContainer(),r=Tt.bigButton("Convert",(()=>this.processConvertButtonClick()));return[t,e,n,Tt.buttonsInput([r])]}processConvertButtonClick(){!function(e){const n=e.getTableSelection();if(!n)return void t.shell.warning("Please select a table");const r=Pt.filter((t=>!("AS"===t&&!e.isAntisenseStrandActive()))).map((t=>({strand:t,column:e.getSelectedStrandColumn(t)}))).filter((t=>t.column));if(0===r.length)return void t.shell.warning("Select a sense strand column");const i=e.getSelectedIdColumn();if(!i)throw new Error("No ID column selected");n.getCol(i);const o=r.map((t=>({strand:t.strand,column:n.getCol(t.column)})));!function(t,e){const n=e.getNucleotideSequences();return t.every((t=>{const e=n[t.strand].length;return t.column.toList().every((t=>t.length===e))}))}(o,e)?t.shell.warning("Some strands in the table input do not match pattern length"):o.forEach((t=>{const r=t.column,i=t.strand,o=e.getNucleotideSequences()[i],s=e.getTerminalModifications()[i],a=e.getPhosphorothioateLinkageFlags()[i],u=`${e.getPatternName()}(${r.name})`;n.columns.addNewString(u).init((t=>xe(r.get(t),o,a,s)))}))}(this.eventBus)}}class Ee{constructor(t,e,n){this.eventBus=t,this.initialPatternConfig=e,this.subscriptions=n}create(){return Tt.divV([Tt.h1("PTO"),Tt.divH([this.createAllPtoActivationInput().root,...this.createFirstPtoInputs().map((t=>t.root))],{style:{gap:"12px"}})])}areAllPtoLinkagesSet(t){return Pt.map((e=>t[e].filter((t=>t)).length)).reduce(((t,e)=>t+e),0)===Pt.map((t=>this.initialPatternConfig.nucleotideSequences[t].length)).reduce(((t,e)=>t+e),0)+Pt.filter((e=>t[e].length)).length}createAllPtoActivationInput(){const t=this.initialPatternConfig.phosphorothioateLinkageFlags,e=this.areAllPtoLinkagesSet(t),n=Tt.input.bool("All PTO",{value:e});n.onInput.subscribe((()=>{const t=n.value;this.eventBus.setAllPTOLinkages(t)}));const r=this.eventBus.phosphorothioateLingeFlagsChanged$.subscribe((()=>{const t=this.eventBus.getPatternConfig().phosphorothioateLinkageFlags,e=this.areAllPtoLinkagesSet(t);n.value=e}));return this.subscriptions.add(r),this.addStyleToPtoInput(n),Tt.tooltip.bind(n.captionLabel,"Activate all phosphothioates"),n}addStyleToPtoInput(t){const e=t.captionLabel;e.classList.add("ui-label-right"),Object.assign(e.style,{textAlign:"left",maxWidth:"100px",minWidth:"40px",width:"auto"})}createFirstPtoInputs(){return Pt.map((t=>{if(!this.eventBus.isAntisenseStrandActive()&&"AS"===t)return;const e=this.isFirstPtoActive(t),n=Tt.input.bool(`First ${t} PTO`,{value:e});n.onInput.subscribe((()=>{const e=n.value;this.eventBus.setPhosphorothioateLinkageFlag(t,0,e)}));const r=this.eventBus.phosphorothioateLingeFlagsChanged$.subscribe((e=>{const r=e[t][0];n.value=r}));return this.subscriptions.add(r),this.addStyleToPtoInput(n),Tt.tooltip.bind(n.captionLabel,`Activate first phosphothioate in ${t}`),n})).filter((t=>void 0!==t))}isFirstPtoActive(t){return this.initialPatternConfig.phosphorothioateLinkageFlags[t][0]}}class Te{constructor(t,e,n){this.eventBus=t,this.dataManager=e,this.subscriptions=n;const r=this.eventBus.nucleotideSequencesChanged$.subscribe((()=>{this.displayedInputLabels=this.computeDisplayedInputLabels()}));this.subscriptions.add(r)}create(){const t=Pt.map((t=>this.constructControlsPanel(t)));return Tt.divH(t,{style:{gap:"24px"}})}constructControlsPanel(t){if(!this.eventBus.isAntisenseStrandActive()&&"AS"===t)return Tt.div([]);const e=this.constructHeader(),n=this.createControls(t);return Tt.block([Tt.h1(`${Rt[t]}`),e,n],{style:{paddingTop:"12px"}})}constructHeader(){return Tt.divH([Tt.div([Tt.divText("#")],{style:{width:"20px"}}),Tt.block75([Tt.divText("Modification")]),Tt.div([Tt.divText("PTO")])])}createControls(t){const e=this.createNucleobaseInputs(t),n=this.createLabelDivs(t),r=this.createPTOFlagInputs(t);return Tt.div(e.map(((t,e)=>Tt.divH([n[e],Tt.block75([t.root]),r[e].root],{style:{alignItems:"center"}}))))}createNucleobaseInputs(t){const e=this.dataManager.fetchAvailableNucleotideBases().sort(((t,e)=>t.toLowerCase().localeCompare(e.toLowerCase())));return this.eventBus.getNucleotideSequences()[t].map(((n,r)=>{const i=Tt.input.choice("",{value:n,items:e});return i.onInput.subscribe((()=>{const e=i.value;this.eventBus.setNucleotide(t,r,e)})),i}))}createPTOFlagInputs(t){return this.eventBus.getPhosphorothioateLinkageFlags()[t].slice(1).map(((e,n)=>{const r=Tt.input.bool("",{value:e});r.onInput.subscribe((()=>{const e=r.value;this.eventBus.setPhosphorothioateLinkageFlag(t,n+1,e)}));const i=this.eventBus.phosphorothioateLingeFlagsChanged$.subscribe((e=>{const i=e[t][n+1];r.value=i}));return this.subscriptions.add(i),r}))}computeDisplayedInputLabels(){const t=this.eventBus.getNucleotideSequences(),e=new Map;return Pt.forEach((n=>{let r=1;const i=t[n].map((t=>{if(Xt(t))return"";const e=String(r);return r++,e}));e.set(n,i)})),e}createLabelDivs(t){const e=this.createLabels(t).map((t=>Tt.div([t],{style:{width:"20px"}}))),n=this.eventBus.nucleotideSequencesChanged$.subscribe((()=>{this.createLabels(t).forEach(((t,n)=>{It()(e[n]).empty(),It()(e[n]).append(t)}))}));return this.subscriptions.add(n),e}createLabels(t){return this.eventBus.getNucleotideSequences()[t].map(((e,n)=>{const r=this.displayedInputLabels.get(t)[n];return Tt.label(r)}))}}class Se{constructor(){this.rxjsSubscriptions=[],this.dgSubscriptions=[]}add(t){t instanceof Jt.Subscription?this.rxjsSubscriptions.push(t):this.dgSubscriptions.push(t)}unsubscribeAll(){for(const t of[this.rxjsSubscriptions,this.dgSubscriptions])t.forEach((t=>t.unsubscribe())),t.length=0}}class Ie{constructor(t,e){this.eventBus=t,this.dataManager=e,this.subscriptions=new Se}static open(t,e){Ie.isDialogOpen||(Ie.instance||(Ie.instance=new Ie(t,e)),Ie.instance.openDialog())}openDialog(){this.initialPatternConfig=re().cloneDeep(this.eventBus.getPatternConfig()),Ie.isDialogOpen=!0,this.createDialog().show()}createDialog(){const t=Tt.divV([]);this.subscriptions.add(this.eventBus.strandsUpdated$.subscribe((()=>this.onStrandsUpdated(t))));const e=Tt.dialog("Edit strands").add(t).onOK((()=>{})).onCancel((()=>this.resetToInitialState()));return this.subscriptions.add(e.onClose.subscribe((()=>{Ie.isDialogOpen=!1,this.subscriptions.unsubscribeAll()}))),e}onStrandsUpdated(t){const e=new Ee(this.eventBus,this.initialPatternConfig,this.subscriptions).create(),n=new Te(this.eventBus,this.dataManager,this.subscriptions).create();It()(t).empty(),It()(t).append(e,n)}resetToInitialState(){this.eventBus.setPatternConfig(this.initialPatternConfig)}}Ie.isDialogOpen=!1;class Ne{constructor(t){this.eventBus=t,this.subscriptions=new Se}static open(t){Ne.isDialogOpen||(Ne.instance||(Ne.instance=new Ne(t)),Ne.instance.openDialog())}openDialog(){this.initialPatternConfig=re().cloneDeep(this.eventBus.getPatternConfig()),Ne.isDialogOpen=!0,this.createDialog().show()}createDialog(){const t=Tt.divV([]);this.subscriptions.add(this.eventBus.strandsUpdated$.subscribe((()=>this.onStrandsUpdated(t))));const e=Tt.dialog("Edit terminal modifications").add(t).onOK((()=>{})).onCancel((()=>this.resetToInitialState()));return this.subscriptions.add(e.onClose.subscribe((()=>{Ne.isDialogOpen=!1,this.subscriptions.unsubscribeAll()}))),e}onStrandsUpdated(t){const e=new Me(this.eventBus).create();It()(t).empty(),It()(t).append(e)}resetToInitialState(){this.eventBus.setPatternConfig(this.initialPatternConfig)}}Ne.isDialogOpen=!1;class Me{constructor(t){this.eventBus=t}create(){const t=Pt.map((t=>this.constructControlsPanel(t)));return Tt.divH(t,{style:{gap:"24px"}})}constructControlsPanel(t){if(!this.eventBus.isAntisenseStrandActive()&&"AS"===t)return Tt.div([]);const e=this.createInputs(t);return Tt.block([Tt.h1(`${Rt[t]}`),e],{style:{paddingTop:"12px"}})}createInputs(t){const e=("SS"===t?[...Dt].reverse():Dt).map((e=>this.createInputForTerminus(t,e)));return Tt.form(e)}createInputForTerminus(t,e){const n=this.eventBus.getTerminalModifications()[t][e],r=Tt.input.textArea(e,{value:n});return this.applyStylingToInput(r),r.onInput.subscribe((()=>{const n=r.value;null!==n&&this.eventBus.updateTerminusModification(t,e,n)})),r}applyStylingToInput(t){const e=t.root.getElementsByTagName("textarea")[0];It()(e).css("resize","none")}}class Oe{constructor(t,e){this.eventBus=t,this.dataManager=e}createControls(){const t=this.createAntisenseStrandToggle(),e=this.createStrandLengthInputs(),n=e.SS.root,r=e.AS.root,i=this.createSequenceBaseInput().root,o=this.createPatternCommentInput().root,s=this.createPatternNameInputBlock(),a=this.createEditPatternButton(),u=this.createEditTerminalModificationsButton();return[Tt.h1("Edit"),t,n,r,i,s,o,Tt.buttonsInput([u,a])]}createEditPatternButton(){const t=Tt.button("Edit strands",(()=>Ie.open(this.eventBus,this.dataManager)));return Tt.tooltip.bind(t,"Edit strand modifications and PTOs"),t}createEditTerminalModificationsButton(){const t=Tt.button("Edit terminals",(()=>Ne.open(this.eventBus)));return Tt.tooltip.bind(t,"Edit terminal modifications"),It()(t).css("margin-right","20px"),t}createAntisenseStrandToggle(){const t=Tt.input.toggle(`${Rt.AS} strand`,{value:this.eventBus.isAntisenseStrandActive()});return t.onInput.subscribe((()=>this.eventBus.toggleAntisenseStrand(t.value))),this.eventBus.patternLoaded$.subscribe((()=>{t.value=this.eventBus.isAntisenseStrandActive()})),t.setTooltip("Toggle antisense strand"),t.root}createStrandLengthInputs(){const e=t=>{const e=this.eventBus.getNucleotideSequences()[t].length,r=Tt.input.int(`${Rt[t]} length`,{value:e});return r.onInput.subscribe((()=>n(t,r))),this.eventBus.nucleotideSequencesChanged$.subscribe((()=>{r.value=this.eventBus.getNucleotideSequences()[t].length})),r.setTooltip(`Number of nucleotides in ${t}, including overhangs`),[t,r]},n=(e,n)=>{const r=n.value;null!==r&&(r<=0&&(t.shell.warning("Sequence length must be greater than 0"),n.value=1),r>34&&(t.shell.warning("Sequence length must be less than 35"),n.value=34),this.eventBus.updateStrandLength(e,n.value))},r=Object.fromEntries(Pt.map((t=>e(t))));return this.eventBus.antisenseStrandToggled$.subscribe((t=>{It()(r.AS.root).toggle(t)})),r}createSequenceBaseInput(){const t=this.dataManager.fetchAvailableNucleotideBases().sort(((t,e)=>t.toLowerCase().localeCompare(e.toLowerCase()))),e=this.dataManager.fetchDefaultNucleobase(),n=Tt.input.choice("Sequence basis",{value:e,items:t});return n.onInput.subscribe((()=>this.eventBus.replaceSequenceBase(n.value))),this.eventBus.nucleotideSequencesChanged$.subscribe((()=>{n.value=this.eventBus.getSequenceBase()})),n.setTooltip("Most frequent nucleobase in the strands"),n}createPatternCommentInput(){const t=Tt.input.textArea("Comment",{value:this.eventBus.getComment()});return It()(t.root).addClass("st-pattern-text-input"),t.onInput.subscribe((()=>this.eventBus.updateComment(t.value))),this.eventBus.patternLoaded$.subscribe((()=>{t.value=this.eventBus.getComment()})),t}createPatternNameInputBlock(){const t=Tt.input.textArea("Pattern name",{value:this.eventBus.getPatternName()});return It()(t.root).addClass("st-pattern-text-input"),t.onInput.subscribe((()=>this.eventBus.updatePatternName(t.value))),this.eventBus.patternLoaded$.subscribe((()=>{t.value=this.eventBus.getPatternName()})),t.setTooltip("Name under which pattern will be saved"),t.root}}class Le{constructor(t,e){this.eventBus=t,this.dataManager=e,this.subscriptions=new Se,this.authorSelectedByUser=!1,this.eventBus.patternLoadRequested$.subscribe((t=>this.handlePatternChoice(t))),this.eventBus.patternDeletionRequested$.subscribe((async t=>{await this.dataManager.deletePattern(t,this.eventBus)}))}async handlePatternChoice(t){let e=await this.dataManager.getPatternConfig(t);null===e&&(e=this.dataManager.getDefaultPatternConfig()),this.eventBus.setPatternConfig(e),this.eventBus.updateControlsUponPatternLoaded(t),this.eventBus.setLastLoadedPatternConfig(e)}isCurrentUserSelected(){return this.eventBus.getSelectedAuthor()!==this.dataManager.getOtherUsersAuthorshipCategory()}createControls(){const t=this.getPatternInputsContainer();return[Tt.h1("Load"),t]}getPatternInputsContainer(){const t=Tt.divH(this.createPatternInputs());return this.eventBus.patternListUpdated$.subscribe((()=>{this.subscriptions.unsubscribeAll(),It()(t).empty(),It()(t).append(this.createPatternInputs())})),t}createPatternInputs(){const t=this.createAuthorChoiceInput(),e=this.createPatternChoiceInputContainer(),n=this.createDeletePatternButton();return[t.root,e,n]}createPatternChoiceInputContainer(){const t=this.createPatternChoiceInput(),e=Tt.div([t.root]),n=this.eventBus.userSelection$.subscribe((()=>{It()(e).empty(),It()(e).append(this.createPatternChoiceInput().root)}));return this.subscriptions.add(n),e}createAuthorChoiceInput(){const t=[this.dataManager.getCurrentUserAuthorshipCategory()];this.dataManager.getOtherUsersPatternNames().length>0&&t.push(this.dataManager.getOtherUsersAuthorshipCategory());const e=Tt.input.choice("Author",{value:this.eventBus.getSelectedAuthor(),items:t});return e.onInput.subscribe((()=>{if(this.authorSelectedByUser=!0,null===e.value)throw new Error("author choice must be non-null");this.eventBus.selectAuthor(e.value)})),this.setAuthorChoiceInputStyle(e),e.setTooltip("Select pattern author"),e}setAuthorChoiceInputStyle(t){It()(t.input).css({"max-width":"100px","min-width":"100px"}),It()(t.root).css({"padding-right":"30px","padding-left":"30px"})}createPatternChoiceInput(){const t=this.isCurrentUserSelected()?this.dataManager.getCurrentUserPatternNames():this.dataManager.getOtherUsersPatternNames();if(this.authorSelectedByUser){const e=this.dataManager.getPatternHash(t[0],this.isCurrentUserSelected());this.eventBus.requestPatternLoad(e),this.eventBus.updateUrlState(e),this.authorSelectedByUser=!1}const e=this.getPatternName(t),n=Tt.input.choice("Pattern",{value:e,items:t});return n.setTooltip("Select pattern to load"),It()(n.input).css({"max-width":"100px","min-width":"100px"}),this.subscriptions.add(n.onInput.subscribe((()=>{const t=this.dataManager.getPatternHash(n.value,this.isCurrentUserSelected());this.eventBus.requestPatternLoad(t),this.eventBus.updateUrlState(t)}))),this.subscriptions.add(this.eventBus.patternLoaded$.subscribe((()=>{const e=this.eventBus.getPatternName();n.value!==e&&(n.value=this.getPatternName(t))}))),n}getPatternName(t){return t.find((t=>t.split(" (")[0]===this.eventBus.getPatternName()))??t[0]}createDeletePatternButton(){const e=Tt.button(Tt.iconFA("trash-alt"),(()=>{this.eventBus.getPatternName()!==this.dataManager.getDefaultPatternName()?this.showDeletePatternDialog():t.shell.warning("Cannot delete example pattern")}));Tt.tooltip.bind(e,"Delete pattern from user storage");const n=this.eventBus.userSelection$.subscribe((()=>{e.disabled=!this.isCurrentUserSelected()}));return this.subscriptions.add(n),e}showDeletePatternDialog(){const t=Tt.dialog("Delete pattern"),e=this.eventBus.getPatternName();t.add(Tt.divText(`Are you sure you want to delete pattern ${e}?`)),t.onOK((()=>this.eventBus.requestPatternDeletion(e))),t.show()}}class Be{constructor(t,e){this.eventBus=t,this.dataManager=e}getLayout(){const t=new Le(this.eventBus,this.dataManager),e=new Oe(this.eventBus,this.dataManager),n=new _e(this.eventBus),r=t.createControls(),i=e.createControls(),o=n.createControls(),s=Tt.div(r);It()(s).css({"padding-bottom":"20px"});const a=Tt.div([...i,...o],"ui-form"),u=Tt.div([s,a]);return It()(u).css({padding:"25px"}),Tt.box(u,{style:{maxWidth:"450px"}})}}var Pe=n(146);class Re{constructor(t,e,n){this.svgElementFactory=t,this.config=e,this.yShift=n}shiftElements(t){this.svgElements.forEach((e=>{const n=e.getAttribute("transform")||"",r=`translate(${t.x},${t.y})`;e.setAttribute("transform",`${n} ${r}`)}))}}class De{constructor(){}static getInstance(){return De.instance||(De.instance=new De,De.instance.canvas=document.createElement("canvas")),De.instance}static getTextDimensions(t,e){const n=De.getInstance().canvas.getContext("2d");if(!n)throw new Error("Canvas 2D context is not available");return n.font=`${e}px Arial`,{width:1.1*n.measureText(t).width,height:1.1*e}}}function Fe(t){const e=Object.keys($r.jsonData.patternAppData)[0];if(!e)throw new Error(`No format found in '${st}'`);return $r.jsonData.patternAppData[e][t].color||""}class He extends Re{constructor(t,e,n){super(t,e,n);const r=Pt.filter((t=>e.nucleotideSequences[t].length>0));this.strands=r.map((t=>new Ue(this.svgElementFactory,e,n,t))),this.terminalModifications=r.map(((t,r)=>new $e(this.svgElementFactory,e,n,t,this.strands[r]))),this.labels=r.map(((t,r)=>new ke(this.svgElementFactory,e,n,t,this.terminalModifications[r])))}get svgElements(){return[...this.strands,...this.terminalModifications,...this.labels].map((t=>t.svgElements)).flat()}getContentWidth(){return Math.max(...this.labels.map((t=>t.getContentWidth())))}getContentHeight(){return this.strands.reduce(((t,e)=>t+e.getContentHeight()),0)}}class Ue extends Re{constructor(t,e,n,r){super(t,e,n),this.svgElementFactory=t,this.config=e,this.yShift=n,this.strand=r,this.nucleotideNumericLabels=this.computeNucleotideNumericLabels(),"AS"===this.strand&&(this.config.phosphorothioateLinkageFlags[this.strand].reverse(),this.config.nucleotideSequences[this.strand].reverse(),this.nucleotideNumericLabels.reverse()),this._svgElements=[this.createStrandCircles(),this.createPTOLinkageStars()].flat()}computeNucleotideNumericLabels(){let t=0;return this.config.nucleotideSequences[this.strand].map((e=>Xt(e)?null:(t++,t)))}get svgElements(){return this._svgElements}getStrandCircleYShift(){return Ve(this.strand,this.yShift)}createStrandCircles(){const t={x:80,y:this.getStrandCircleYShift()};return this.config.nucleotideSequences[this.strand].map(((e,n)=>this.createNucleotideElementGroup(e,n,t))).flat()}createNucleotideElementGroup(t,e,n){return[...this.createNucleotideCircleElements(t,e,n),this.config.nucleotidesWithNumericLabels.includes(t)?this.createNucleotideNumericLabel(e,n):null].filter((t=>null!==t))}createNucleotideCircleElements(t,e,n){const r=Fe(t),i={...n,x:n.x+30*e};return[this.svgElementFactory.createCircleElement(i,15,r),this.createNucleotideLetterLabel(e,n,t)]}getNucleotideCircleCenterPosition(t,e){return{x:e.x+30*t,y:e.y}}createNucleotideLetterLabel(t,e,n){if(!ct.includes(n))return null;const r=function(t){return!Xt(t)&&ct.includes(t)?t:""}(n),i=function(t){const e=Fe(t),n=e.match(/\d+/g)?.map(Number);if(!n||n.length<3)return"#ffffff";const[r,i,o]=n;return.299*r+.587*i+.114*o>186?"#333333":"#ffffff"}(n),o=this.getPositionForNucleotideLabel(t,e);return this.svgElementFactory.createTextElement(r,o,17,i)}getPositionForNucleotideLabel(t,e){const n=this.getNucleotideCircleCenterPosition(t,e),r=De.getTextDimensions("A",17);return{x:n.x-r.width/2,y:n.y+r.height/3}}getNumericLabelYShift(t){return"SS"===this.strand?t.y-20:t.y+15+5+15}createNucleotideNumericLabel(t,e){const n=this.nucleotideNumericLabels[t];if(null===n)return null;const r=De.getTextDimensions(n.toString(),15).width,i={x:e.x+30*t-r/2,y:this.getNumericLabelYShift(e)};return this.svgElementFactory.createTextElement(n.toString(),i,15,"var(--grey-6)")}createPTOLinkageStars(){const t=this.config.phosphorothioateLinkageFlags[this.strand],e=this.getStrandCircleYShift()+12;return t.map(((t,n)=>{if(!t)return null;const r={x:65+30*n,y:e};return this.svgElementFactory.createStarElement(r,"red")})).filter((t=>null!==t))}getContentWidth(){return 30*this.config.nucleotideSequences[this.strand].length}getContentHeight(){return 62}}class ke extends Re{constructor(t,e,n,r,i){super(t,e,n),this.svgElementFactory=t,this.config=e,this.yShift=n,this.strand=r,this.terminalModifications=i,this._svgElements=this.createSVGElements()}createSVGElements(){return[this.createLeftLabel(),this.createRightLabel()]}getLeftLabelWidth(){return 55}getRightLabelWidth(){return 20}createLeftLabel(){const t="SS"===this.strand?"5'":"3'",e=`${this.strand}: ${t}  `,n=De.getTextDimensions(e,17),r={x:10,y:Ve(this.strand,this.yShift)+n.height/3};return this.svgElementFactory.createTextElement(e,r,17,"var(--grey-6)")}createRightLabel(){const t="  "+("SS"===this.strand?"3'":"5'"),e=De.getTextDimensions(t,17),n={x:65+this.terminalModifications.getContentWidth()+5,y:Ve(this.strand,this.yShift)+e.height/3};return this.svgElementFactory.createTextElement(t,n,17,"var(--grey-6)")}get svgElements(){return this._svgElements}getContentWidth(){return this.terminalModifications.getContentWidth()+this.getLeftLabelWidth()+this.getRightLabelWidth()+10}getContentHeight(){return this.terminalModifications.getContentHeight()}}class $e extends Re{constructor(t,e,n,r,i){super(t,e,n),this.svgElementFactory=t,this.config=e,this.yShift=n,this.strand=r,this.strandSvgWrapper=i,this._svgElements=this.createSVGElements()}createSVGElements(){return this.createTerminalModifications()}getTerminalModification(t){return this.config.strandTerminusModifications[this.strand][t]}getTerminalModificationTextDimensions(t){const e=this.getTerminalModification(t);return De.getTextDimensions(e,17)}getLeftTerminus(){return"SS"===this.strand?"5'":"3'"}createTerminalModification(t){const e=this.getTerminalModification(t),n=this.getTerminalModificationTextDimensions(t),r=t===this.getLeftTerminus(),i={x:r?65:65+this.getTerminalModificationTextDimensions(this.getLeftTerminus()).width+this.strandSvgWrapper.getContentWidth(),y:Ve(this.strand,this.yShift)+n.height/3};return r&&this.strandSvgWrapper.shiftElements({x:n.width,y:0}),this.svgElementFactory.createTextElement(e,i,17,"red")}createTerminalModifications(){return("AS"===this.strand?Dt:Array.from(Dt).reverse()).map((t=>this.createTerminalModification(t)))}get svgElements(){return this._svgElements}getContentWidth(){return this.strandSvgWrapper.getContentWidth()+Dt.map((t=>this.getTerminalModificationTextDimensions(t).width)).reduce(((t,e)=>t+e),0)}getContentHeight(){return this.strandSvgWrapper.getContentHeight()}}function Ve(t,e){return"SS"===t?e+5+15+15:e+52+10+15}class je{constructor(){this.xmlNamespace="http://www.w3.org/2000/svg"}createElement(t){return document.createElementNS(this.xmlNamespace,t)}setAttributes(t,e){Object.entries(e).forEach((([e,n])=>{t.setAttribute(e,String(n))}))}createCanvas(t,e){const n=this.createElement("svg");return this.setAttributes(n,{id:"mySvg",width:t,height:e}),n}createCircleElement(t,e,n){const r=this.createElement("circle");return this.setAttributes(r,{cx:t.x,cy:t.y,r:e,fill:n}),r}createTextElement(t,e,n,r){const i=this.createElement("text");return this.setAttributes(i,{x:e.x,y:e.y,"font-size":n,"font-weight":"normal","font-family":"Arial",fill:r}),i.textContent=t,i}createStarElement(t,e){const n=this.createElement("polygon"),r=this.computeStarVertexCoordinates(t).map((t=>t.join(","))).join(" ");return this.setAttributes(n,{points:r,fill:e}),n}computeStarVertexCoordinates(t){const e=Math.PI/5,n=-e/2;return Array.from({length:10},((r,i)=>{const o=i%2==0?6:3,s=i*e+n;return[t.x+Math.cos(s)*o,t.y+Math.sin(s)*o]}))}createRectangleElement(t,e,n,r){const i=this.createElement("rect");return this.setAttributes(i,{x:t.x,y:t.y,width:e,height:n,fill:r}),i}}class qe extends Re{constructor(t,e,n){super(t,e,n),this.svgElementFactory=t,this.config=e,this.yShift=n,this._svgElements=[],this.titleText=this.getTitleText(),this._svgElements=[this.getTitle()]}get svgElements(){return this._svgElements}getTitle(){return this.svgElementFactory.createTextElement(this.titleText,{x:15,y:this.yShift+17},17,"black")}getContentWidth(){return De.getTextDimensions(this.titleText,17).width}getContentHeight(){return De.getTextDimensions(this.titleText,17).height}getTitleText(){const t=`${this.config.nucleotideSequences.SS.length}`,e=this.config.isAntisenseStrandIncluded?`/${this.config.nucleotideSequences.AS.length}`:"";return`${this.config.patternName} for ${t}${e}-mer`}}class Ge extends Re{constructor(t,e,n){super(t,e,n),this._svgElements=[];const{elements:r,width:i}=this.createLegendItems();this._svgElements=r,this.width=i}isPhosphorothioatePresent(){return Object.values(this.config.phosphorothioateLinkageFlags).flat().some((t=>t))}getModificationTypesList(){return[...new Set(Object.values(this.config.nucleotideSequences).flat().sort(((t,e)=>t.toLowerCase().localeCompare(e.toLowerCase()))))]}get svgElements(){return this._svgElements}createLegendItem(t,e){const n={x:e,y:this.yShift-6},r=t.includes("linkage")?this.svgElementFactory.createStarElement(n,"red"):this.svgElementFactory.createCircleElement(n,6,Fe(t));e+=12;const i={y:this.yShift,x:e};return{elements:[r,this.svgElementFactory.createTextElement(t,i,15,"var(--grey-6)")],width:12+De.getTextDimensions(t,15).width}}createLegendItems(){let t=10;const e=[],n=e=>t+=e+15;if(this.isPhosphorothioatePresent()){const{elements:r,width:i}=this.createLegendItem("PTO linkage",t);n(i),e.push(r)}return this.getModificationTypesList().forEach((r=>{const{elements:i,width:o}=this.createLegendItem(r,t);n(o),e.push(i)})),{elements:e.flat(),width:t}}getContentHeight(){return 20}getContentWidth(){return this.width}}class We{constructor(t){this.svgElementFactory=new je;const e=re().cloneDeep(t);let n=10;this.title=new qe(this.svgElementFactory,e,n),n+=this.title.getContentHeight(),this.strands=new He(this.svgElementFactory,e,n),n+=this.strands.getContentHeight()+10,this.legend=new Ge(this.svgElementFactory,e,n)}renderPattern(){const t=this.getGlobalWidth(),e=this.getGlobalHeight(),n=this.svgElementFactory.createCanvas(t,e),r=[this.title,this.strands,this.legend].map((t=>t.svgElements)).flat();return n.append(...r),n}getGlobalWidth(){const t=[this.title,this.strands,this.legend];return Math.max(...t.map((t=>t.getContentWidth())))}getGlobalHeight(){return[this.title,this.strands,this.legend].reduce(((t,e)=>t+e.getContentHeight()),10)}}class ze{constructor(t){this.eventBus=t,this.svgDisplayDiv=Tt.div([]),t.updateSvgContainer$.subscribe((()=>this.updateSvgContainer())),t.svgSaveRequested$.subscribe((()=>this.saveSvgAsPng()))}static createSvgDiv(t){return new ze(t).svgDisplayDiv}updateSvgContainer(){$(this.svgDisplayDiv).empty();const t=this.eventBus.getPatternConfig();this.svgElement=this.createSvg(t),this.svgDisplayDiv.append(this.svgElement)}createSvg(t){return new We(t).renderPattern()}saveSvgAsPng(){const t=this.eventBus.getPatternName();Pe.saveSvgAsPng(this.svgElement,t,{backgroundColor:"white"})}}class Ye{constructor(t){this.eventBus=t,this.togglesContainer=Tt.div([]),this.eventBus.uniqueNucleotidesChanged$().subscribe((()=>{this.updateContainer()}))}getContainer(){return this.togglesContainer}updateContainer(){It()(this.togglesContainer).empty(),It()(this.togglesContainer).append(this.createInputs())}createInputs(){const t=this.eventBus.getUniqueNucleotides().filter((t=>!Xt(t))).map((t=>this.createSingleInput(t)));return t.sort(((t,e)=>t.captionLabel.textContent.localeCompare(e.captionLabel.textContent))),Tt.divH(t.map((t=>t.root)))}createSingleInput(t){const e=this.eventBus.getModificationsWithNumericLabels().includes(t),n=Tt.input.bool(t,{value:e,onValueChanged:e=>this.handleNumericLabelToggle(t,e)});return It()(n.root).css("padding-right","20px"),n.setTooltip(`Show numeric labels for ${t}`),n}handleNumericLabelToggle(t,e){const n=this.eventBus.getModificationsWithNumericLabels();if(n.includes(t)===e)return;const r=e?n.concat(t):n.filter((e=>e!==t));this.eventBus.updateModificationsWithNumericLabels(r)}}class Ke{constructor(t,e){this.eventBus=t,this.dataManager=e,this.subscriptions=new Se}createContainer(){return Tt.div([Tt.h1("Translation example"),this.createTranslationExamples()],{style:{paddingTop:"20px"}})}createTranslationExamples(){const t=Tt.divH([...this.getExampleElements()],"ui-form");return this.eventBus.antisenseStrandToggled$.subscribe((()=>{this.subscriptions.unsubscribeAll(),It()(t).empty(),It()(t).append(this.getExampleElements())})),t}getExampleElements(){return Pt.map((t=>new Je(t,this.eventBus,this.subscriptions).create()))}}class Je{constructor(t,e,n){this.strand=t,this.eventBus=e,this.subscriptions=n}create(){return this.eventBus.isAntisenseStrandActive()||"AS"!==this.strand?(this.inputExample=this.createInputExample(),this.outputExample=this.createOutputExample(this.inputExample.value),this.subscribeToEvents(),Tt.block50([Tt.h2(Rt[this.strand]),this.inputExample.root,this.outputExample.root],{style:{paddingRight:"20px"}})):Tt.div([])}subscribeToEvents(){const t=this.eventBus.strandsLinkagesAndTerminalsUpdated$.subscribe((()=>{const t=this.generateExampleSequence();this.inputExample.value=t,this.outputExample.value=this.computeOutputValue(t)}));"AS"===this.strand&&this.subscriptions.add(t)}createInputExample(){const t=this.createTextInputForExamples(),e=this.generateExampleSequence();return t.value=e,t.setTooltip(`Example raw nucleotides input for ${Rt[this.strand]}`),t}generateExampleSequence(){return this.eventBus.getNucleotideSequences()[this.strand].map(((t,e)=>ct[e%ct.length])).join("")}createOutputExample(t){const e=this.createTextInputForExamples();return e.value=this.computeOutputValue(t),e.setTooltip(`Pattern applied to the example input for ${Rt[this.strand]}`),e}computeOutputValue(t){const e=this.eventBus.getNucleotideSequences()[this.strand],n=this.eventBus.getTerminalModifications()[this.strand];return xe(t,e,this.eventBus.getPhosphorothioateLinkageFlags()[this.strand],n)}createTextInputForExamples(){const t=Tt.input.textArea("",{value:""});return this.applyStylingToInput(t),t}applyStylingToInput(t){const e=t.root.getElementsByTagName("textarea")[0];e.setAttribute("readonly","true"),It()(e).css("resize","none"),It()(t.root).css("opacity","75%")}}class Qe{constructor(t,e){this.eventBus=t,this.dataManager=e,this.svgDisplay=ze.createSvgDiv(t)}getLayout(){const t=new Ye(this.eventBus).getContainer(),e=this.generateDownloadControls(),n=new Ke(this.eventBus,this.dataManager).createContainer();return Tt.panel([this.svgDisplay,t,e,n],{style:{overflowX:"scroll",padding:"12px 24px"}})}generateDownloadControls(){return Tt.divH([this.createSavePatternButton(),this.createDownloadPngButton(),this.createShareLinkButton(),this.createInfoButton()],{style:{gap:"12px",marginTop:"12px"}})}createDownloadPngButton(){const t=Tt.button("Get PNG",(()=>this.eventBus.requestSvgSave()));return Tt.tooltip.bind(t,"Download pattern as PNG"),t}createInfoButton(){const t=Tt.button(Tt.iconFA("info-circle"),(()=>this.openInfoDialog()));return this.eventBus.patternHasUnsavedChanges$.subscribe((e=>{t.disabled=e})),Tt.tooltip.bind(t,"View pattern metadata"),t}async openInfoDialog(){let e=this.dataManager.getCurrentUserName(),n=this.dataManager.getDefaultPatternName(),r=qt,i=qt;const o=new URLSearchParams(window.location.search).get("pattern");if(null!==o){const s=await this.dataManager.getPatternRecordByHash(o);if(null!==s){const o=s[kt.AUTHOR_ID];if(e=(await t.dapi.users.find(o)).friendlyName,n=s[kt.PATTERN_CONFIG][Ut.PATTERN_NAME],void 0!==s[kt.DATE]){const t=s[kt.DATE][$t.CREATE];void 0!==t&&(r=t);const e=s[kt.DATE][$t.MODIFY];void 0!==e&&(i=e)}}}const s=Tt.divV([Tt.divText(`Pattern Name: ${n}`),Tt.divText(`Author: ${e}`),Tt.divText(`Created: ${Ze(new Date(r))}`),Tt.divText(`Modified: ${Ze(new Date(i))}`)]);t.shell.info(s)}createShareLinkButton(){const e=Tt.button(Tt.iconFA("link"),(()=>navigator.clipboard.writeText(window.location.href).then((()=>t.shell.info("Link to pattern copied to clipboard")))));return this.eventBus.patternHasUnsavedChanges$.subscribe((t=>{e.disabled=t})),Tt.tooltip.bind(e,"Share pattern link"),e}createSavePatternButton(){const t=Tt.button("Save",(()=>this.processSaveButtonClick()));return this.eventBus.patternHasUnsavedChanges$.subscribe((e=>{t.disabled=!e})),Tt.tooltip.bind(t,"Save pattern to user storage"),t}processSaveButtonClick(){const e=this.eventBus.getPatternName();e!==this.dataManager.getDefaultPatternName()?""!==e?this.dataManager.savePatternToUserStorage(this.eventBus).then((()=>{t.shell.info(`Pattern ${e} saved`)})).catch((t=>this.handleErrorWhileSavingPattern(t))):t.shell.warning("Insert pattern name"):t.shell.warning("Cannot save default pattern")}handleErrorWhileSavingPattern(e){e instanceof Gt?new Xe(this.eventBus,this.dataManager).show():e instanceof Wt?t.shell.warning(Tt.div([Tt.divText("Pattern already exists"),Tt.button("Load",(()=>{const t=e.message;this.eventBus.requestLoadPatternInNewTab(t)}))])):console.error("Error while saving pattern",e)}}class Xe{constructor(t,e){this.eventBus=t,this.dataManager=e}show(){const t=this.eventBus.getPatternName(),e=Tt.dialog(`Pattern "${t}" already exists`);e.add(Tt.divText(`Pattern "${t}" already exists. Do you want to overwrite it?`)),e.show(),e.onOK((()=>this.processOverwriteNamesakePattern()))}processOverwriteNamesakePattern(){const e=this.eventBus.getPatternName();this.dataManager.overwriteExistingPatternInUserStorage(this.eventBus).then((()=>{t.shell.info(`Pattern ${e} overwritten`)})).catch((e=>{console.error("Error while overwriting pattern in user storage",e),t.shell.error("Error while overwriting pattern")}))}}function Ze(t){return t.toLocaleString().split(":").slice(0,-1).join(":")}class tn extends Bt{constructor(t){super("Oligo Pattern"),this.th=t}getContent(){return async function(){const t=await Kt.getInstance(),e=new se,n=await async function(t,e){const n=e.getPatternHash();if(!n)return e.clearPatternURL(),t.getDefaultPatternRecord();let r=await t.getPatternRecordByHash(n);return r||(e.clearPatternURL(),r=t.getDefaultPatternRecord()),r}(t,e),r=new ie(t,n);e.subscribeToObservables(r);const i=new Be(r,t).getLayout(),o=new Qe(r,t).getLayout();return Tt.splitH([i,o],{},!0)}()}}var en=n(507),nn={};function rn(t){var e;return"string"==typeof t||t instanceof String?t:("object"==typeof t||t instanceof Object)&&"$thrownJsError"in t?rn(t.$thrownJsError):t instanceof Error?null!==(e=t.stack)&&void 0!==e?e:t.message:t.toString()}nn.styleTagTransform=ve(),nn.setAttributes=pe(),nn.insert=fe().bind(null,"head"),nn.domAPI=ce(),nn.insertStyleElement=me(),ue()(en.A,nn),en.A&&en.A.locals&&en.A.locals;var on,sn=n(74),an={};an.styleTagTransform=ve(),an.setAttributes=pe(),an.insert=fe().bind(null,"head"),an.domAPI=ce(),an.insertStyleElement=me(),ue()(sn.A,an),sn.A&&sn.A.locals&&sn.A.locals;class un{constructor(t,e,n=!0){this.textInputBase=t,this.painter=e,It()(this.root).addClass("st-colored-text-input"),n&&this.textInputBase.onChanged.subscribe((()=>{It()(this.textArea).css("height",0),It()(this.textArea).css("height",this.textArea.scrollHeight+"px")})),this.highlights=Tt.div([]),this.root.appendChild(this.highlights),this.colorize(),this.textInputBase.onChanged.subscribe((()=>this.colorize()))}get textArea(){return this.textInputBase.root.getElementsByTagName("textarea").item(0)}get inputBase(){return this.textInputBase}get root(){return this.textInputBase.root}colorize(){const t=this.painter(this.textInputBase.value);this.highlights.innerHTML="",t.forEach((t=>this.highlights.appendChild(t)))}}!function(t){t.TYPE="V2000",t[t.NUM_OF_HEADER_LINES=3]="NUM_OF_HEADER_LINES",t[t.NUM_OF_COUNTS_DIGITS=3]="NUM_OF_COUNTS_DIGITS",t[t.ATOM_TYPE_COL=4]="ATOM_TYPE_COL",t[t.FIRST_BONDED_ATOM_COL=1]="FIRST_BONDED_ATOM_COL",t[t.BOND_TYPE_COL=3]="BOND_TYPE_COL",t[t.RGP_SHIFT=8]="RGP_SHIFT",t[t.MAX_ATOM_COUNT=999]="MAX_ATOM_COUNT",t.RGP_LINE_START="M  RGP",t.ATOM_ALIAS_LINE_START="A  ",t.END="M  END"}(on||(on={}));class ln{constructor(t){this.init(t)}init(t){this.fileContent=t.replace(/\r/g,""),this._atomCount=void 0,this._atomTypes=void 0,this._bondCount=void 0,this._bondTypes=void 0,this.xyzAtomCoordinates=void 0,this._pairsOfBondedAtoms=void 0}get atomCount(){return void 0===this._atomCount&&this.setAtomAndBondCounts(),this._atomCount}get bondCount(){return void 0===this._bondCount&&this.setAtomAndBondCounts(),this._bondCount}get x(){var t;return null!==(t=this.xyzAtomCoordinates)&&void 0!==t||(this.xyzAtomCoordinates=this.parseAtomCoordinates()),this.xyzAtomCoordinates.x}get y(){var t;return null!==(t=this.xyzAtomCoordinates)&&void 0!==t||(this.xyzAtomCoordinates=this.parseAtomCoordinates()),this.xyzAtomCoordinates.y}get z(){var t;return null!==(t=this.xyzAtomCoordinates)&&void 0!==t||(this.xyzAtomCoordinates=this.parseAtomCoordinates()),this.xyzAtomCoordinates.z}get atomTypes(){var t;return null!==(t=this._atomTypes)&&void 0!==t||(this._atomTypes=this.parseAtomTypes()),this._atomTypes}get pairsOfBondedAtoms(){var t;return null!==(t=this._pairsOfBondedAtoms)&&void 0!==t||(this._pairsOfBondedAtoms=this.parseBondedAtomPairs()),this._pairsOfBondedAtoms}get bondTypes(){var t;return null!==(t=this._bondTypes)&&void 0!==t||(this._bondTypes=this.parseBondTypes()),this._bondTypes}setAtomAndBondCounts(){const{atomCount:t,bondCount:e}=this.parseAtomAndBondCounts();this._atomCount=t,this._bondCount=e}getNextColumnIdx(t){for(;!this.isWhitespace(t);)++t;for(;this.isWhitespace(t);)++t;return t}shiftIdxToSpecifiedColumn(t,e){let n=t;const r=this.isWhitespace(n)?e:e-1;for(let t=0;t<r;t++)n=this.getNextColumnIdx(n);return n}parseAtomTypes(){const t=this.atomCount,e=new Array(t);let n=this.getAtomBlockIdx();for(let r=0;r<t;r++)n=this.shiftIdxToAtomType(n),e[r]=this.parseAtomType(n),n=this.getNextLineIdx(n);return e}parseAtomCoordinates(){const t=new Float32Array(this.atomCount),e=new Float32Array(this.atomCount),n=new Float32Array(this.atomCount);let r=this.getAtomBlockIdx();for(let i=0;i<this.atomCount;i++){r=this.shiftIdxToXColumn(r);for(const o of[t,e,n])o[i]=this.parseFloatValue(r),r=this.getNextColumnIdx(r);r=this.getNextLineIdx(r)}return{x:t,y:e,z:n}}parseBondedAtomPairs(){const t=new Array(this.bondCount);let e=this.getBondBlockIdx();for(let n=0;n<this.bondCount;n++){e=this.shiftIdxToBondedAtomsPair(e);const r=new Uint16Array(2);r[0]=this.parseIntValue(e),e=this.getNextColumnIdx(e),r[1]=this.parseIntValue(e),t[n]=r,e=this.getNextLineIdx(e)}return t}parseBondTypes(){const t=this.bondCount,e=new Uint16Array(t);let n=this.getBondBlockIdx();for(let r=0;r<t;r++)n=this.shiftIdxToBondType(n),e[r]=this.parseIntValue(n),n=this.getNextLineIdx(n);return e}isWhitespace(t){const e=this.fileContent[t];return" "===e||"\t"===e}getNextLineIdx(t){return"\n"!==this.fileContent[t]?this.fileContent.indexOf("\n",t)+1:t+1}parseFloatValue(t){return this.parseNumericValue(parseFloat,t)}parseIntValue(t){return this.parseNumericValue(parseInt,t)}parseNumericValue(t,e){let n=e+1;for(;!this.isWhitespace(n);)++n;return t(this.fileContent.substring(e,n))}}class cn extends ln{constructor(t){super(t),this.init(t)}init(t){super.init(t)}parseAtomType(t){let e=t,n=e;return this.isQuote(e)?(n=this.getNextIdenticalChar(e),e++):n=this.fileContent.indexOf(" ",n),this.fileContent.substring(e,n)}isQuote(t){const e=this.fileContent[t].charCodeAt(0);return 39===e||34===e}getNextIdenticalChar(t){const e=this.fileContent[t];return e?this.fileContent.indexOf(e,t+1):-1}isQuery(){return this.isQueryOrFragment(((t,e)=>{return 39===t||34===t||76===t&&!((n=this.fileContent.charCodeAt(e+1))>64&&n<91||n>96&&n<123);var n}))}isFragment(){return this.isQueryOrFragment((t=>82===t||42===t))}isQueryOrFragment(t){const e=this.atomCount;let n=this.getAtomBlockIdx();for(let r=0;r<e;r++){if(n=this.shiftIdxToAtomType(n),t(this.fileContent.charCodeAt(n),n))return!0;n=this.getNextLineIdx(n)}return!1}}class hn extends cn{constructor(t){super(t)}getAtomLines(){const t=this.getAtomBlockIdx(),e=this.getBondBlockIdx();return this.fileContent.substring(t,e).split("\n").slice(0,this.atomCount)}getBondLines(){const t=this.getBondBlockIdx();return this.fileContent.substring(t).split("\n").slice(0,this.bondCount)}getRGroupIdToAtomicIdxMap(){const t=new Map,e=this.fileContent.split("\n");e.filter((t=>t.startsWith(on.RGP_LINE_START))).forEach((e=>{const n=this.getAtomIdxToRgpIdxList(e);for(const[e,r]of n){if(t.has(e))throw new Error(`R group ${e} is already in the map`);t.set(e,r)}}));const n=e.map(((t,e)=>{if(t.startsWith(on.ATOM_ALIAS_LINE_START))return e})).filter((t=>void 0!==t)),r=n.map((t=>e[t])),i=n.map((t=>e[t+1]));r.forEach(((e,n)=>{const r=parseInt(e.split(/\s+/)[1])-1,o=parseInt(i[n].substring(1));if(t.has(o))throw new Error(`R group ${o} is already in the map`);t.set(o,r)}));const o=this.getRGroupAtomicIndices().filter((e=>!Array.from(t.values()).includes(e)));if(0!==o.length)throw new Error(`Unaccounted R group indices: ${o}`);return t}getAtomIdxToRgpIdxList(t){const e=t.split(/\s+/).filter((t=>t)).slice(3).map((t=>parseInt(t))),n=new Array(e.length/2);for(let t=0;t<e.length;t+=2)n[t/2]=[e[t+1],e[t]-1];return n}getRGroupAtomicIndices(){return this.atomTypes.map(((t,e)=>{if(t.includes("R#"))return e})).filter((t=>void 0!==t))}static isValidMolfile(t){return-1!==t.indexOf(on.TYPE)&&-1!==t.indexOf(on.END)}shiftIdxToAtomType(t){return this.shiftIdxToSpecifiedColumn(t,on.ATOM_TYPE_COL)}getCountsLineIdx(){let t=0;for(let e=0;e<on.NUM_OF_HEADER_LINES;++e)t=this.getNextLineIdx(t);return t}getAtomBlockIdx(){let t=this.getCountsLineIdx();return t=this.getNextLineIdx(t),t}shiftIdxToXColumn(t){return this.getNextColumnIdx(t)}shiftIdxToBondedAtomsPair(t){return this.shiftIdxToSpecifiedColumn(t,on.FIRST_BONDED_ATOM_COL)}shiftIdxToBondType(t){return this.shiftIdxToSpecifiedColumn(t,on.BOND_TYPE_COL)}getBondBlockIdx(){let t=this.getAtomBlockIdx();for(let e=0;e<this.atomCount;e++)t=this.getNextLineIdx(t);return t}parseAtomAndBondCounts(){let t=this.getCountsLineIdx(),e=t+on.NUM_OF_COUNTS_DIGITS;const n=parseInt(this.fileContent.substring(t,e));return t=e,e+=on.NUM_OF_COUNTS_DIGITS,{atomCount:n,bondCount:parseInt(this.fileContent.substring(t,e))}}}class fn extends cn{constructor(t){super(t),this.init(t)}getAtomLines(){const t=this.getAtomBlockIdx(),e=this.getBondBlockIdx();return this.fileContent.substring(t,e).split("\n").slice(0,this.atomCount)}getBondLines(){const t=this.getBondBlockIdx();return this.fileContent.substring(t).split("\n").slice(0,this.bondCount)}getRGroupIdToAtomicIdxMap(){const t=new Map;return this.getAtomLines().forEach(((e,n)=>{const r=e.match(/RGROUPS=\(([\d\s]+)\)/);if(r){const e=r[1].split(/\s+/).map((t=>parseInt(t)));if(e.length>2)throw new Error(`R group data ${e} has more than 2 elements`);const i=e[1];if(t.has(i))throw new Error(`R group ${i} is already in the map`);t.set(i,n)}})),t}shiftIdxToAtomType(t){return this.shiftIdxToSpecifiedColumn(t,4)}getCountsLineIdx(){return this.fileContent.indexOf("M  V30 COUNTS ")}getAtomBlockIdx(){let t=this.fileContent.indexOf("M  V30 BEGIN ATOM");return t=this.getNextLineIdx(t),t}shiftIdxToXColumn(t){let e=this.shiftIdxToAtomType(t);return this.isQuote(e)?(e=this.getNextIdenticalChar(e),e=this.getNextColumnIdx(e),e):this.shiftIdxToSpecifiedColumn(t,5)}shiftIdxToBondedAtomsPair(t){return this.shiftIdxToSpecifiedColumn(t,5)}shiftIdxToBondType(t){return this.shiftIdxToSpecifiedColumn(t,4)}getBondBlockIdx(){return this.getNextLineIdx(this.fileContent.indexOf("M  V30 BEGIN BOND"))}static isValidMolfile(t){return-1!==t.indexOf("V3000")&&-1!==t.indexOf("M  END")}parseAtomAndBondCounts(){let t=this.fileContent.indexOf("M  V30 COUNTS ")+14,e=this.fileContent.indexOf(" ",t+1);const n=parseInt(this.fileContent.substring(t,e));return t=e+1,e=this.fileContent.indexOf(" ",t+1),{atomCount:n,bondCount:parseInt(this.fileContent.substring(t,e))}}}class dn{constructor(){}static getInstance(t){if(dn.isMolfileV2K(t))return new hn(t);if(dn.isMolfileV3K(t))return new fn(t);throw new Error("Malformed molfile")}static isMolfileV2K(t){return hn.isValidMolfile(t)}static isMolfileV3K(t){return fn.isValidMolfile(t)}}const pn=class extends Error{constructor(t){super(t)}};class gn{constructor(t){this.molblock=t}get molblock(){return this._validMolBlock}set molblock(t){if(""!==t){try{this.validateMolBlock(t)}catch(e){e instanceof pn&&(t="");const n=rn(e);console.error(n)}this._validMolBlock=t}else this._validMolBlock=t}validateMolBlock(t){if(""===t)throw new pn("MoleculeImage: invalid molblock")}async drawMolBlockOnCanvas(e){try{await t.functions.call("Chem:canvasMol",{x:0,y:0,w:e.width,h:e.height,canvas:e,molString:this.molblock,scaffoldMolString:"",options:{normalizeDepiction:!1,straightenDepiction:!1}})}catch(t){const e=rn(t);console.error(e)}}getMoleculeDimensions(){const t=dn.getInstance(this.molblock),e=Math.max(...t.x)-Math.min(...t.x);return{height:Math.max(...t.y)-Math.min(...t.y),width:e}}async zoomIn(){const t=Tt.dialog({title:"Molecule",showFooter:!1}),e=.7*It()(window).height(),n=this.getMoleculeDimensions(),r=e/n.height,i=e,o=n.width*r,s=Tt.canvas(o,i);await this.drawMolBlockOnCanvas(s);const a=Tt.block([s],{style:{overflowX:"scroll"}});t.add(a).showModal(!0),It()(t.root).find(".d4-dialog-contents").removeClass("ui-form"),It()(t.root).find(".d4-dialog-contents").removeClass("ui-panel"),It()(t.root).find(".d4-dialog-contents").addClass("ui-box"),It()(t.root).find(".d4-dialog-contents").css("padding","0")}async drawMolecule(t,e,n){t.innerHTML="";const r=Tt.canvas(e*window.devicePixelRatio,n*window.devicePixelRatio);r.style.width=`${e}px`,r.style.height=`${n}px`,r.style.cursor="zoom-in",this.drawMolBlockOnCanvas(r),r.addEventListener("click",(async()=>{await this.zoomIn()})),t.append(Tt.tooltip.bind(r,"Click to zoom"))}}class mn extends Error{constructor(t,e){super(t,e)}}class yn{constructor(t,e){this.sequence=t,this.codeMap=e}parseSequence(){const t=this.parseRawSequence();return this.addLinkers(t)}addLinkers(t){const e=[];return t.forEach(((n,r)=>{const i=this.getSymbolForCode(n);r>0&&function(t){return $r.jsonData.monomersWithPhosphate.left.includes(t)}(i)&&e.pop(),e.push(i);const o=vn(i),s=r===t.length-1,a=r+1<t.length&&vn(this.getSymbolForCode(t[r+1]));o||function(t){return $r.jsonData.monomersWithPhosphate.right.includes(t)}(i)||a||s||e.push("p")})),e}getSymbolForCode(t){let e=this.codeMap.get(t);return e??(e=t),e}parseRawSequence(){const t=this.getAllCodesOfFormat(),e=[];let n=0;for(;n<this.sequence.length;){const r=t.find((t=>t===this.sequence.substring(n,n+t.length)));if(void 0===r)throw new mn(`Unable to match a monomer for the rest of the sequence '${this.sequence.slice(n)}'.`);e.push(r),n+=r.length}return e}getAllCodesOfFormat(){return ft(Array.from(this.codeMap.keys()))}}function vn(t){return $r.jsonData.monomersWithPhosphate.phosphate.includes(t)}class bn{constructor(t,e=!1,n){this.invert=e,this.lib=$r.monomerLibWrapper;const r=this.lib.getCodeToSymbolMap(n);this.parser=new yn(t,r)}convert(){const t=this.parser.parseSequence(),e=[];t.forEach(((t,n)=>{const r=this.getMonomerMolfile(t,n);e.push(r)}));let n=this.getPolymerMolfile(e);return this.invert&&(n=this.reflect(n),n=this.invertBondConfiguration(n)),n}invertBondConfiguration(t){const e=t.indexOf("M  V30 BEGIN BOND"),n=t.indexOf("M  V30 END BOND");let r=t.substring(e,n);return r=r.replace(/(CFG=)([13])/g,((t,e,n)=>"1"===n?`${e}3`:"3"===n?`${e}1`:t)),t.substring(0,e)+r+t.substring(n)}getMonomerMolfile(t,e){const n=this.lib.getMolfileBySymbol(t);return this.lib.isModification(t)?0===e?this.reflect(n):n:this.rotateNucleotidesV3000(n)}getPolymerMolfile(t){return this.linkV3000(t)}reflect(t){const e=this.extractAtomDataV3000(t),n=e.atomIndex.length,r=e.atomIndex.indexOf(1),i=e.atomIndex.indexOf(n),o=(e.x[i]+e.x[r])/2,s=(e.y[i]+e.y[r])/2;for(let t=0;t<n;t++)e.x[t]-=o,e.y[t]-=s;for(let t=0;t<n;t++)e.x[t]=-e.x[t];const a=e.x[r];for(let t=0;t<n;t++)e.x[t]-=a;let u=t.indexOf("M  V30 BEGIN ATOM");u=t.indexOf("\n",u);let l=u;for(let r=0;r<n;r++)u=t.indexOf("V30",u)+4,u=t.indexOf(" ",u)+1,u=t.indexOf(" ",u)+1,l=t.indexOf(" ",u)+1,l=t.indexOf(" ",l),u=(t=t.slice(0,u)+e.x[r]+" "+e.y[r]+t.slice(l)).indexOf("\n",u)+1;return t}extractAtomDataV3000(t){const e=this.extractAtomsBondsNumbersV3000(t);let n=t.indexOf("M  V30 BEGIN ATOM");n=t.indexOf("\n",n);let r=n;const i=Array(e.natom),o=Array(e.natom),s=Array(e.natom),a=Array(e.natom);for(let u=0;u<e.natom;u++)n=t.indexOf("V30",n)+4,r=t.indexOf(" ",n),i[u]=parseInt(t.substring(n,r)),n=r+1,r=t.indexOf(" ",n),o[u]=t.substring(n,r),n=r+1,r=t.indexOf(" ",n),s[u]=parseFloat(t.substring(n,r)),n=r+1,r=t.indexOf(" ",n),a[u]=parseFloat(t.substring(n,r)),n=t.indexOf("\n",n)+1;return{atomIndex:i,atomType:o,x:s,y:a}}extractAtomsBondsNumbersV3000(t){let e=(t=t.replaceAll("\r","")).indexOf("COUNTS")+7,n=t.indexOf(" ",e);const r=parseInt(t.substring(e,n));return e=n+1,n=t.indexOf(" ",e),{natom:r,nbond:parseInt(t.substring(e,n))}}rotateNucleotidesV3000(t){const e=this.extractAtomDataV3000(t),n=e.atomIndex.length,r=e.atomIndex.indexOf(1),i=e.atomIndex.indexOf(n);n>8&&this.fix5Prime(e,r,i);const o=(e.x[i]+e.x[r])/2,s=(e.y[i]+e.y[r])/2;for(let t=0;t<n;t++)e.x[t]-=o,e.y[t]-=s;let a=0;if(0===e.x[r])a=e.y[r]>e.y[i]?Math.PI/2:3*Math.PI/2;else if(0===e.y[r])a=e.x[r]>e.x[i]?Math.PI:0;else{const t=e.y[r]/e.x[r];a=t>0?e.x[r]>0?Math.PI-Math.atan(t):2*Math.PI-Math.atan(t):e.x[r]>0?-Math.PI-Math.atan(t):Math.atan(t)}const u=Math.cos(a),l=Math.sin(a);for(let t=0;t<n;t++){const n=e.x[t];e.x[t]=n*u-e.y[t]*l,e.y[t]=n*l+e.y[t]*u}const c=e.x[r];for(let t=0;t<n;t++)e.x[t]-=c;let h=t.indexOf("M  V30 BEGIN ATOM");h=t.indexOf("\n",h);let f=h;for(let r=0;r<n;r++)h=t.indexOf("V30",h)+4,h=t.indexOf(" ",h)+1,h=t.indexOf(" ",h)+1,f=t.indexOf(" ",h)+1,f=t.indexOf(" ",f),h=(t=t.slice(0,h)+e.x[r]+" "+e.y[r]+t.slice(f)).indexOf("\n",h)+1;return t}linkV3000(t,e=!0){let n="\n  Datagrok macromolecule handler\n\n";n+="  0  0  0  0  0  0            999 V3000\n",n+="M  V30 BEGIN CTAB\n";let r="",i="",o="";const s=[];let a=0,u=0,l=0;for(let e=0;e<t.length;e++){const n=t[e].includes("MODIFICATION")&&0===e;let o=0;n&&(o=this.extractAtomDataV3000(t[e]).atomIndex.length),t[e]=t[e].replaceAll("(-\nM  V30 ","(").replaceAll("-\nM  V30 ","").replaceAll(" )",")");const c=this.extractAtomsBondsNumbersV3000(t[e]),h=this.extractAtomDataV3000(t[e]);let f=t[e].indexOf("M  V30 BEGIN ATOM");f=t[e].indexOf("\n",f);let d=f,p=f;for(let r=0;r<c.natom;r++)if(1!==h.atomIndex[r]||0===e){d=t[e].indexOf("V30",d)+4,p=t[e].indexOf(" ",d);let r=0;n?(r=parseInt(t[e].substring(d,p)),1===r?r=o:r===o&&(r=1),r+=a):r=parseInt(t[e].substring(d,p))+a,t[e]=t[e].slice(0,d)+r+t[e].slice(p),d=t[e].indexOf(" ",d)+1,d=t[e].indexOf(" ",d)+1,p=t[e].indexOf(" ",d);const i=l-h.x[0];let s=Math.round(1e4*(parseFloat(t[e].substring(d,p))+i))/1e4;t[e]=t[e].slice(0,d)+s+t[e].slice(p),d=t[e].indexOf(" ",d)+1,p=t[e].indexOf(" ",d),s=Math.round(1e4*parseFloat(t[e].substring(d,p)))/1e4,t[e]=t[e].slice(0,d)+s+t[e].slice(p),d=t[e].indexOf("\n",d)+1}else d=t[e].indexOf("M  V30",d)-1,p=t[e].indexOf("\n",d+1),t[e]=t[e].slice(0,d)+t[e].slice(p);const g=t[e].indexOf("M  V30 END ATOM");r+=t[e].substring(f+1,g);let m=t[e].indexOf("M  V30 BEGIN BOND");m=t[e].indexOf("\n",m),d=m,p=m;for(let r=0;r<c.nbond;r++){d=t[e].indexOf("V30",d)+4,p=t[e].indexOf(" ",d);const r=parseInt(t[e].substring(d,p))+u;t[e]=t[e].slice(0,d)+r+t[e].slice(p),d=t[e].indexOf(" ",d)+1,d=t[e].indexOf(" ",d)+1,p=t[e].indexOf(" ",d);let i=0;n?(i=parseInt(t[e].substring(d,p)),1===i?i=o:i===o&&(i=1),i+=a):i=parseInt(t[e].substring(d,p))+a,t[e]=t[e].slice(0,d)+i+t[e].slice(p),d=t[e].indexOf(" ",d)+1,p=Math.min(t[e].indexOf("\n",d),t[e].indexOf(" ",d)),i=0,n?(i=parseInt(t[e].substring(d,p)),1===i?i=o:i===o&&(i=1),i+=a):i=parseInt(t[e].substring(d,p))+a,t[e]=t[e].slice(0,d)+i+t[e].slice(p),d=t[e].indexOf("\n",d)+1}const y=t[e].indexOf("M  V30 END BOND");i+=t[e].substring(m+1,y);let v=t[e].indexOf("M  V30 MDLV30/STEABS ATOMS=(");for(;-1!==v;){v+=28;const n=t[e].indexOf(")",v);t[e].substring(v,n).split(" ").slice(1).forEach((t=>{s.push(parseInt(t)+a)})),v=n,v=t[e].indexOf("M  V30 MDLV30/STEABS ATOMS=(",v)}a+=c.natom-1,u+=c.nbond,l+=n?Math.max(...h.x):h.x[c.natom-1]-h.x[0]}const c=Math.ceil(s.length/4);o+="M  V30 MDLV30/STEABS ATOMS=("+s.length+" -\n";for(let t=0;t<c;t++){o+="M  V30 ";const e=t+1===c?s.length-4*(c-1):4;for(let n=0;n<e;n++)o+=n+1===e?t===c-1?s[4*t+n]+")\n":s[4*t+n]+" -\n":s[4*t+n]+" "}return a++,n+="M  V30 COUNTS "+a+" "+u+" 0 0 0\n",n+="M  V30 BEGIN ATOM\n",n+=r,n+="M  V30 END ATOM\n",n+="M  V30 BEGIN BOND\n",n+=i,n+="M  V30 END BOND\n",e&&s.length>0?(n+="M  V30 BEGIN COLLECTION\n",n+=o,n+="M  V30 END COLLECTION\n"):n=n.replace(/ CFG=\d/g," "),n+="M  V30 END CTAB\n",n+="M  END",n}fix5Prime(t,e,n){const r=e+1,i=t.x[r],o=t.y[r],s=t.x[n]-i,a=t.y[n]-o,u=t.x[e]-i,l=t.y[e]-o,c=u*Math.cos(2*Math.PI/3)-l*Math.sin(2*Math.PI/3),h=u*Math.sin(2*Math.PI/3)+l*Math.cos(2*Math.PI/3),f=u-s,d=l-a,p=c-s,g=h-a;Math.sqrt(g*g+p*p)>=Math.sqrt(d*d+f*f)&&(t.x[e]=c+i,t.y[e]=h+o)}}function wn(t,e=!0){let n="\n  Datagrok macromolecule handler\n\n";n+="  0  0  0  0  0  0            999 V3000\n",n+="M  V30 BEGIN CTAB\n";let r="",i="",o="";const s=[];let a=0,u=0,l=0;if(t.antiStrands.length>0)for(let e=0;e<t.antiStrands.length;e++)t.antiStrands[e]=Cn(t.antiStrands[e]);let c=!1;const h=t.senseStrands.concat(t.antiStrands);let f=0;for(let e=0;e<h.length;e++){h[e]=h[e].replaceAll("(-\nM  V30 ","(").replaceAll("-\nM  V30 ","").replaceAll(" )",")");const n=An(h[e]),o=xn(h[e]);if(e>=t.senseStrands.length?!1===c&&(c=!0,l=0):f=Math.min(f,Math.min(...o.y.filter((t=>t<0)))),c){const t=Math.min(...o.x)-l,e=Math.max(...o.y)+5;for(let e=0;e<o.x.length;e++)o.x[e]-=t;for(let t=0;t<o.y.length;t++)o.y[t]-=e-f}let d=h[e].indexOf("M  V30 BEGIN ATOM");d=h[e].indexOf("\n",d);let p=d,g=d;for(let t=0;t<n.natom;t++){p=h[e].indexOf("V30",p)+4,g=h[e].indexOf(" ",p);const n=parseInt(h[e].substring(p,g))+a;h[e]=h[e].slice(0,p)+n+h[e].slice(g),p=h[e].indexOf(" ",p)+1,p=h[e].indexOf(" ",p)+1,g=h[e].indexOf(" ",p);let r=Math.round(1e4*o.x[t])/1e4;h[e]=h[e].slice(0,p)+r+h[e].slice(g),p=h[e].indexOf(" ",p)+1,g=h[e].indexOf(" ",p),r=Math.round(1e4*o.y[t])/1e4,h[e]=h[e].slice(0,p)+r+h[e].slice(g),p=h[e].indexOf("\n",p)+1}const m=h[e].indexOf("M  V30 END ATOM");r+=h[e].substring(d+1,m);let y=h[e].indexOf("M  V30 BEGIN BOND");y=h[e].indexOf("\n",y),p=y,g=y;for(let t=0;t<n.nbond;t++){p=h[e].indexOf("V30",p)+4,g=h[e].indexOf(" ",p);const t=parseInt(h[e].substring(p,g))+u;h[e]=h[e].slice(0,p)+t+h[e].slice(g),p=h[e].indexOf(" ",p)+1,p=h[e].indexOf(" ",p)+1,g=h[e].indexOf(" ",p);let n=parseInt(h[e].substring(p,g))+a;h[e]=h[e].slice(0,p)+n+h[e].slice(g),p=h[e].indexOf(" ",p)+1,g=Math.min(h[e].indexOf("\n",p),h[e].indexOf(" ",p)),n=parseInt(h[e].substring(p,g))+a,h[e]=h[e].slice(0,p)+n+h[e].slice(g),p=h[e].indexOf("\n",p)+1}const v=h[e].indexOf("M  V30 END BOND");i+=h[e].substring(y+1,v);let b=h[e].indexOf("M  V30 MDLV30/STEABS ATOMS=(");for(;-1!==b;){b+=28;const t=h[e].indexOf(")",b);h[e].substring(b,t).split(" ").slice(1).forEach((t=>{s.push(parseInt(t)+a)})),b=t,b=h[e].indexOf("M  V30 MDLV30/STEABS ATOMS=(",b)}a+=n.natom,u+=n.nbond,l+=Math.max(...o.x)+5}const d=Math.ceil(s.length/4);o+="M  V30 MDLV30/STEABS ATOMS=("+s.length+" -\n";for(let t=0;t<d;t++){o+="M  V30 ";const e=t+1===d?s.length-4*(d-1):4;for(let n=0;n<e;n++)o+=n+1===e?t===d-1?s[4*t+n]+")\n":s[4*t+n]+" -\n":s[4*t+n]+" "}return n+="M  V30 COUNTS "+a+" "+u+" 0 0 0\n",n+="M  V30 BEGIN ATOM\n",n+=r,n+="M  V30 END ATOM\n",n+="M  V30 BEGIN BOND\n",n+=i,n+="M  V30 END BOND\n",e&&s.length>0?(n+="M  V30 BEGIN COLLECTION\n",n+=o,n+="M  V30 END COLLECTION\n"):n=n.replace(/ CFG=\d/g," "),n+="M  V30 END CTAB\n",n+="M  END",n}function Cn(t){const e=xn(t),n=e.atomIndex.length,r=(Math.max(...e.x)+Math.min(...e.x))/2,i=(Math.max(...e.y)+Math.min(...e.y))/2;for(let t=0;t<n;t++)e.x[t]-=r,e.y[t]-=i;const o=Math.PI,s=Math.cos(o),a=Math.sin(o);for(let t=0;t<n;t++){const n=e.x[t];e.x[t]=n*s-e.y[t]*a,e.y[t]=n*a+e.y[t]*s}const u=Math.max(...e.y);for(let t=0;t<n;t++)e.x[t]+=r,e.y[t]-=u;let l=t.indexOf("M  V30 BEGIN ATOM");l=t.indexOf("\n",l);let c=l;for(let r=0;r<n;r++)l=t.indexOf("V30",l)+4,l=t.indexOf(" ",l)+1,l=t.indexOf(" ",l)+1,c=t.indexOf(" ",l)+1,c=t.indexOf(" ",c),l=(t=t.slice(0,l)+e.x[r]+" "+e.y[r]+t.slice(c)).indexOf("\n",l)+1;return t}function An(t){let e=(t=t.replaceAll("\r","")).indexOf("COUNTS")+7,n=t.indexOf(" ",e);const r=parseInt(t.substring(e,n));return e=n+1,n=t.indexOf(" ",e),{natom:r,nbond:parseInt(t.substring(e,n))}}function xn(t){const e=An(t);let n=t.indexOf("M  V30 BEGIN ATOM");n=t.indexOf("\n",n);let r=n;const i=Array(e.natom),o=Array(e.natom),s=Array(e.natom),a=Array(e.natom);for(let u=0;u<e.natom;u++)n=t.indexOf("V30",n)+4,r=t.indexOf(" ",n),i[u]=parseInt(t.substring(n,r)),n=r+1,r=t.indexOf(" ",n),o[u]=t.substring(n,r),n=r+1,r=t.indexOf(" ",n),s[u]=parseFloat(t.substring(n,r)),n=r+1,r=t.indexOf(" ",n),a[u]=parseFloat(t.substring(n,r)),n=t.indexOf("\n",n)+1;return{atomIndex:i,atomType:o,x:s,y:a}}function _n(t,e,n){if(""===t)return"";const r=n.createFormatDetector(t).getFormat();if(!r)return"";let i="";try{i=new bn(t,e,r).convert()}catch(t){const e=rn(t);console.error(e)}return i}function En(t,e,n,r,i){const o=[t,e,n].filter((t=>""!==t.strand));return 1===o.length?_n(o[0].strand,o[0].invert,i):wn({senseStrands:[_n(t.strand,t.invert,i)],antiStrands:[_n(e.strand,e.invert,i),_n(n.strand,n.invert,i)].filter((t=>""!==t))},r)}const Tn=["ss","as","as2"];class Sn{constructor(){this.th=$r,this.onInput=new Jt.Subject,this.onInvalidInput=new Jt.Subject,this.inputBase=Object.fromEntries(Tn.map((t=>{const e=Tt.input.textArea(t.toUpperCase(),{value:"",onValueChanged:()=>{this.onInput.next(),It()(e.root.getElementsByTagName("div")).css("padding-left","38px")}});return[t,e]}))),this.useChiralInput=Tt.input.bool("Use chiral",{value:!0}),this.saveAllStrandsInput=Tt.input.bool("Save as one entity",{value:!0}),Tt.tooltip.bind(this.saveAllStrandsInput.root,"Save SDF with all strands in one molfile"),this.directionInversion=Object.fromEntries(Tn.map((t=>[t,!1]))),this.moleculeImgDiv=Tt.block([]),It()(this.moleculeImgDiv).addClass("st-structure-mol-img"),e.debounce(this.onInput,300).subscribe((async()=>{await this.updateMoleculeImg()})),e.debounce(this.onInvalidInput,1e3).subscribe((async()=>{t.shell.warning("Insert Sense strand")}))}async getHtmlDivElement(t){const e=this.getTableInput(t),n=this.getBoolInputsAndButton();await this.updateMoleculeImg();const r=Tt.divH([n,this.moleculeImgDiv]);It()(r).addClass("st-structure-bottom");const i=Tt.divV([e,r]);return It()(i).addClass("st-structure-body"),i}getBoolInputsAndButton(){const e=Tt.buttonsInput([Tt.bigButton("Save SDF",(()=>{const e=this.getStrandData();!function(e,n,r,i,o,s){const a=[e.strand,n.strand,r.strand].filter((t=>""!==t));if(0===a.length||1===a.length&&""===e.strand)t.shell.warning("Enter SENSE_STRAND and optionally ANTISENSE_STRAND/AS2 to save SDF");else{let u;if(o)u=En(e,n,r,i,s)+"\n$$$$\n";else{const h=_n(e.strand,e.invert,s),f=_n(n.strand,n.invert,s),d=_n(r.strand,r.invert,s);u=h+"\n> <Sequence>\nSense Strand\n$$$$\n",f&&(u+=f+"\n> <Sequence>\nAnti Sense\n$$$$\n"),d&&(u+=d+"\n> <Sequence>\nAnti Sense 2\n$$$$\n")}const l=new Date;function c(t){return t>=10?t.toString():"0"+t.toString()}dt(`SequenceTranslator-${l.getFullYear()+"-"+c(l.getMonth()+1)+"-"+c(l.getDate())+"_"+c(l.getHours())+"-"+c(l.getMinutes())+"-"+c(l.getSeconds())}.sdf`,encodeURIComponent(u))}}(e.ss,e.as,e.as2,this.useChiralInput.value,this.saveAllStrandsInput.value,this.th)}))]),n=[this.saveAllStrandsInput.root,this.useChiralInput.root,e],r=Tt.divV(n);for(const t of n)It()(t).addClass("st-structure-bool-button-block");return r}getTableInput(t){const e=Object.fromEntries(Tn.map((e=>[e,new un(this.inputBase[e],t.highlightInvalidSubsequence)]))),n=Object.fromEntries(Tn.map(((t,e)=>{const n=0===e?"5′ → 3′":"3′ → 5′";return[t,Tt.input.choice(`${t.toUpperCase()} direction`,{value:n,items:["5′ → 3′","3′ → 5′"]})]})));Tn.forEach(((t,e)=>{n[t].onChanged.subscribe((n=>{let r="3′ → 5′"===n;e>0&&(r=!r),this.directionInversion[t]=r,this.onInput.next()}))}));const r=["Sense Strand","Anti Sense","Anti Sense 2"],i=new Map(Tn.map(((t,e)=>[t,r[e]]))),o=(Object.fromEntries(Tn.map((t=>[t,Tt.label(i.get(t))]))),Object.fromEntries(Tn.map((t=>{const n=Tt.icons.delete((()=>{e[t].inputBase.value=""})),r=Tt.button(n,(()=>{}));return Tt.tooltip.bind(r,`Clear ${t.toUpperCase()}`),[t,n]})))),s=Tt.form([],"st-structure-inputs"),a=Tt.divV([],"st-structure-clear-buttons"),u=Tt.form([],"st-direction-inputs");for(const t of Tn)s.append(this.inputBase[t].root),a.append(o[t]),u.append(n[t].root);return Tt.divH([s,a,u])}getStrandData(){return Object.fromEntries(Tn.map((t=>{const e=this.directionInversion[t];return[t,{strand:this.inputBase[t].value.replace(/\s*/g,""),invert:e}]})))}getMolfile(t,e,n){return En(t,e,n,this.useChiralInput.value,this.th)}async updateMoleculeImg(){let t="";try{const e=this.getStrandData();Object.values(e).some((t=>""!==t.strand))&&(t=this.getMolfile(e.ss,e.as,e.as2))}catch(t){const e=rn(t);console.error(e)}const e=new gn(t);await e.drawMolecule(this.moleculeImgDiv,650,150),It()(this.moleculeImgDiv).find("canvas").css("float","inherit")}}class In extends Bt{constructor(t){super("Oligo Structure"),this.th=t,this.layout=new Sn}getContent(){return this.layout.getHtmlDivElement(this.th)}}async function Nn(e){try{const n={overflowX:"scroll"},r=Tt.div([],{style:n}),i=xn(e),o=.7*It()(window).height(),s=Math.max(...i.x)-Math.min(...i.x),a=Math.max(...i.y)-Math.min(...i.y),u=o/a,l=u*s,c=u*a,h=Tt.canvas(l*window.devicePixelRatio,c*window.devicePixelRatio);h.style.width=`${l}px`,h.style.height=`${c}px`,await async function(e,n){await t.functions.call("Chem:canvasMol",{x:0,y:0,w:e.width,h:e.height,canvas:e,molString:n,scaffoldMolString:"",options:{normalizeDepiction:!1,straightenDepiction:!1}})}(h,e),r.appendChild(h),Tt.dialog("Molecule").add(r).showModal(!0)}catch(t){const e=rn(t);console.error(e)}}class Mn{static async view(){const e=$r.monomerLibWrapper.getTableForViewer();e.name="Monomer Library";const n=t.shell.addTableView(e);n.grid.props.allowEdit=!1,n.grid.onCellDoubleClick.subscribe((async t=>{const e=t.cell.value;"Molecule"===t.tableColumn?.semType&&await Nn(e)}))}}const On="Copied",Ln="Nucleotides";function Bn(t,e){const n=new RegExp("\\([^()]*\\)","g"),r=t.match(n);return r?r.map((t=>{const n=t.replace(/[\[\]()]/g,"");return ct.includes(n)?n:e.getNaturalAnalogBySymbol(n)})).map((t=>t||bt)).join(""):null}var Pn=n(254),Rn={};Rn.styleTagTransform=ve(),Rn.setAttributes=pe(),Rn.insert=fe().bind(null,"head"),Rn.domAPI=ce(),Rn.insertStyleElement=me(),ue()(Pn.A,Rn),Pn.A&&Pn.A.locals&&Pn.A.locals;const Dn=["Sequence"];class Fn{constructor(t){this.th=t,this.inputFormats=Object.keys($r.jsonData.codesToHelmDict).concat(ht.HELM),this.onInput=new Jt.Subject,this.moleculeImgDiv=Tt.div([]),this.moleculeImgDiv.className="mol-host",this.moleculeImgDiv.style.border="1px solid var(--grey-2)",this.moleculeImgDiv.style.borderRadius="1px",this.moleculeImgDiv.style.marginTop="12px",this.outputTableDiv=Tt.div([]),this.formatChoiceInput=Tt.input.choice("",{value:ht.HELM,items:this.inputFormats,onValueChanged:async(t,e)=>{this.format=t,this.updateTable(),await this.updateMolImg()}}),It()(this.formatChoiceInput.root.getElementsByTagName("select")[0]).css("width","20%"),this.sequenceInputBase=Tt.input.textArea("",{value:"Afcgacsu",onValueChanged:()=>{this.onInput.next()}}),this.init(),e.debounce(this.onInput,300).subscribe((async()=>{this.init(),this.formatChoiceInput.value=this.format,this.updateTable(),await this.updateMolImg()})),this.eventBus=$n.getInstance()}async getHtmlElement(){const t=this.constructSingleSequenceControls(),e=this.constructBulkTranslationControls(),n=Tt.box(Tt.panel([t,e,Tt.block([Tt.box(this.moleculeImgDiv)])]));return this.formatChoiceInput.value=this.format,this.updateTable(),await this.updateMolImg(),n}constructBulkTranslationControls(){const t=Tt.h1("Bulk");Tt.tooltip.bind(t,"Bulk translation from table input");const e=new Hn(this.eventBus).createUIComponents(),n=Tt.input.choice("Input format",{value:ht.AXOLABS,items:this.inputFormats,onValueChanged:t=>this.eventBus.selectInputFormat(t)}),r=Tt.input.choice("Output format",{value:Ln,items:(i=this.th,Object.keys(i.jsonData.codesToHelmDict).concat([ht.HELM,Ln]).sort()),onValueChanged:t=>this.eventBus.selectOutputFormat(t)});var i;const o=this.createConvertBulkButton(),s=Tt.div([...e,n,r,o],"ui-form");return Tt.block25([t,s])}createConvertBulkButton(){const t=Tt.bigButton("Convert",(()=>this.processConvertBulkButtonClick()));return Tt.tooltip.bind(t,"Convert sequences from table input"),It()(t).css({float:"right","margin-top":"20px"}),t}processConvertBulkButtonClick(){const n=this.eventBus.getSelectedTable();if(!n)return void t.shell.warning("No table selected");const r=this.eventBus.getSelectedInputFormat(),i=this.eventBus.getSelectedOutputFormat(),o=this.eventBus.getSelectedColumn("Sequence");if(!o)return void t.shell.warning("No sequence column selected");const s=`${o.name} (${i})`,a=e.Column.fromList(e.TYPE.STRING,s,o.toList().map((t=>{const e=function(t,e,n,r){const i=r.createFormatConverter(t,e);return n===Ln?Bn(i.convertTo(ht.HELM),r.monomerLibWrapper):i.convertTo(n)}(t,r,i,this.th);return e})));if(i===Ln||i===ht.HELM){a.semType=e.SEMTYPE.MACROMOLECULE;const t=i==Ln?C.FASTA:C.HELM;a.meta.units=t;const n=tt.forColumn(a);(i==Ln?tt.setUnitsToFastaColumn:tt.setUnitsToHelmColumn)(n)}n.columns.add(a),t.data.detectSemanticTypes(n),t.shell.v=t.shell.getTableView(n.name)}constructSingleSequenceControls(){const t=new un(this.sequenceInputBase,(t=>Nt(t,this.th))),e=Tt.button("Get SDF",(()=>{this.saveMolfile()}),"Save structure as SDF"),n=Tt.button("Copy SMILES",(()=>{this.copySmiles()}),"Copy SMILES for the sequence"),r=Tt.div([this.formatChoiceInput]),i=Tt.button(Tt.icons.delete((()=>{t.inputBase.value=""})),(()=>{}));Tt.tooltip.bind(i,"Clear input");const o={format:r,textInput:t.root,clearBtn:i},s=Tt.table([o],(t=>[t.format,t.textInput,t.clearBtn]));s.classList.add("st-translator-input-table");const a=Tt.block([this.outputTableDiv,e,n]);return Tt.block75([Tt.h1("Single sequence"),s,a])}saveMolfile(){const t=new bn(this.sequence,!1,this.formatChoiceInput.value).convert()+"\n$$$$";dt(this.sequence+".sdf",encodeURIComponent(t))}copySmiles(){const n=e.chem.convert(this.molfile,e.chem.Notation.MolBlock,e.chem.Notation.Smiles);navigator.clipboard.writeText(n).then((()=>t.shell.info(On)))}updateTable(){this.outputTableDiv.innerHTML="";const e=this.format?this.th.createSequenceValidator(this.sequence).getInvalidCodeIndex(this.format):0,n=function(t,e,n,r){const i=Object.keys(r.jsonData.codesToHelmDict).concat([ht.HELM]);if(!t||-1!==e&&n!==ht.HELM)return{};if(!i.includes(n))throw new Error(`${n} format is not supported by SequenceTranslator`);const o=i.filter((t=>t!=n)).sort(((t,e)=>t.localeCompare(e))),s=r.createFormatConverter(t,n),a=Object.fromEntries(o.map((t=>{let e;try{e=s.convertTo(t)}catch{e=null}return[t,e]})).filter((([t,e])=>e))),u=Bn(n===ht.HELM?t:a[ht.HELM],r.monomerLibWrapper);return u&&(a.Nucleotides=u),a}(this.sequence,e,this.format,this.th),r=[];for(const e of Object.keys(n)){const i="indexOfFirstInvalidChar"in n?Tt.divH([]):Tt.link(n[e],(()=>navigator.clipboard.writeText(n[e]).then((()=>t.shell.info(On)))),"Copy sequence","");r.push({format:e,sequence:i})}const i=Tt.table(r,(t=>[t.format,t.sequence]),["FORMAT","SEQUENCE"]);this.outputTableDiv.append(i),this.outputTableDiv.classList.add("st-translator-output-table")}async updateMolImg(){const t=new gn(this.molfile);await t.drawMolecule(this.moleculeImgDiv,500,170)}init(){this.sequence=this.getFormattedSequence(),this.format=this.th.createFormatDetector(this.sequence).getFormat(),this.molfile=this.getMolfile()}getFormattedSequence(){return this.sequenceInputBase.value.replace(/\s/g,"")}getMolfile(){if(!this.format)return"";if(this.format===ht.HELM){const t=this.th.createFormatConverter(this.sequence,this.format).convertTo(ht.AXOLABS);return new bn(t,!1,ht.AXOLABS).convert()}return new bn(this.sequence,!1,this.format).convert()}}class Hn{constructor(t){this.tableInputManager=new Un(t),this.columnInputManager=new kn(t)}createUIComponents(){return[this.tableInputManager.getTableInputContainer(),this.columnInputManager.getColumnControlsContainer()]}}class Un{constructor(t){this.eventBus=t,this.availableTables=[],this.tableInputContainer=Tt.div([]),this.subscribeToTableEvents(),this.refreshTableInput()}getTableInputContainer(){return this.tableInputContainer}subscribeToTableEvents(){t.events.onTableAdded.subscribe((t=>this.handleTableAdded(t))),t.events.onTableRemoved.subscribe((t=>this.handleTableRemoved(t))),this.eventBus.tableSelected$.subscribe((()=>this.handleTableChoice()))}getTableFromEventData(t){return t.args.dataFrame}handleTableAdded(t){const e=this.getTableFromEventData(t);this.availableTables.some((t=>t.name===e.name))||(this.availableTables.push(e),this.eventBus.selectTable(e),this.refreshTableInput())}handleTableRemoved(t){const e=this.getTableFromEventData(t);this.availableTables=this.availableTables.filter((t=>t.name!==e.name));const n=this.availableTables[0];this.eventBus.selectTable(n||null),this.refreshTableInput()}refreshTableInput(){const t=this.createTableInput();It()(this.tableInputContainer).empty(),this.tableInputContainer.append(t.root)}createTableInput(){const t=this.eventBus.getSelectedTable();return Tt.input.table("Table",{value:t,items:this.availableTables,onValueChanged:t=>{null!==t&&this.eventBus.selectTable(t)}})}handleTableChoice(){const t=this.eventBus.getSelectedTable();t&&(this.isTableDisplayed(t)||this.displayTable(t))}isTableDisplayed(e){return t.shell.tableNames.includes(e.name)}displayTable(e){const n=t.shell.v;t.shell.addTableView(e),t.shell.v=n}}class kn{constructor(t){this.eventBus=t,this.columnControlsContainer=Tt.div([]),this.eventBus.tableSelected$.subscribe((()=>this.handleTableChoice())),this.refreshColumnControls()}getColumnControlsContainer(){return this.columnControlsContainer}handleTableChoice(){this.refreshColumnControls()}refreshColumnControls(){const t=this.createColumnInputs();It()(this.columnControlsContainer).empty();const e=t.map((t=>t.root));this.columnControlsContainer.append(...e)}createColumnInputs(){const t=this.eventBus.getSelectedTable(),e=null!==t?t.columns.names().sort(((t,e)=>t.localeCompare(e))):[];return Dn.map((n=>this.createColumnInput(n,e,t)))}createColumnInput(t,e,n){const r=t.toLowerCase(),i=e.find((t=>t.toLowerCase().includes(r)))||e[0];return this.selectColumnIfTableNotNull(n,i,t),Tt.input.choice(`${t}`,{value:i,items:e,onValueChanged:e=>this.selectColumnIfTableNotNull(n,e,t)})}selectColumnIfTableNotNull(t,e,n){if(null!==t){const r=t.getCol(e);this.eventBus.selectColumn(n,r)}}}class $n{constructor(){this._tableSelection$=new Jt.BehaviorSubject(null),this._columnSelection=Object.fromEntries(Dn.map((t=>[t,new Jt.BehaviorSubject(null)]))),this._inputFormatSelection$=new Jt.BehaviorSubject(ht.AXOLABS),this._outputFormatSelection$=new Jt.BehaviorSubject(Ln)}static getInstance(){return void 0===$n._instance&&($n._instance=new $n),$n._instance}get tableSelected$(){return this._tableSelection$.asObservable()}getSelectedTable(){return this._tableSelection$.getValue()}selectTable(t){this._tableSelection$.next(t)}selectColumn(t,e){this._columnSelection[t].next(e)}getSelectedColumn(t){return this._columnSelection[t].getValue()}getSelectedInputFormat(){return this._inputFormatSelection$.getValue()}selectInputFormat(t){this._inputFormatSelection$.next(t)}selectOutputFormat(t){this._outputFormatSelection$.next(t)}getSelectedOutputFormat(){return this._outputFormatSelection$.getValue()}}class Vn extends Bt{constructor(t){super("Oligo Translator"),this.th=t,this.th=$r,this.layout=new Fn(this.th);const e=Tt.iconFA("book",Mn.view,"View monomer library");this.topPanel=[e],this.view.setRibbonPanels([this.topPanel])}getContent(){return this.layout.getHtmlElement()}}class jn extends Bt{constructor(t,e){super(t),this.content=e}getContent(){return Promise.resolve(this.content)}}class qn extends Lt{constructor(t,n){super("Oligo Toolkit"),this.externalViewFactories=t,this.th=n;const r=this.getViewFactories(this.th);this.multiView=new e.MultiView({viewFactories:r})}getViewFactories(t){function n(n){e.View.create();const r=new n(t);return r.initView().catch((t=>console.error(`Failed to initialize ${n.name}: ${t}`))),()=>r.getView()}let r={TRANSLATOR:n(Vn),PATTERN:n(tn),STRUCTURE:n(In)};return this.externalViewFactories&&(r=Object.assign({},r,this.externalViewFactories)),r}getCurrentPanePath(){let t=this.multiView.tabs.currentPane.name;return t=t.charAt(0).toUpperCase()+t.substring(1).toLowerCase(),`/apps/${$r.name}/OligoToolkit/${t}`}setUrl(){this.multiView.path=this.getCurrentPanePath()}async constructView(){return this.multiView.tabs.onTabChanged.subscribe((()=>this.setUrl())),this.setUrl(),this.multiView}}n(982),e.DataFrame.fromCsv('countries,fasta,smiles,molregno,LON,Zip Code,Street Address Line 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this.getUserSettings(),r=n.excluded.indexOf(e);r>-1&&n.excluded.splice(r,1),this.setUserSettings(n),yield t.dapi.files.delete(this.path+e),t.shell.info(`File ${e} successfully deleted`)}))}getNewAvailable(){return tr(this,void 0,void 0,(function*(){return new Promise(((n,r)=>{e.Utils.openFile({accept:this.ext,open:e=>tr(this,void 0,void 0,(function*(){const r=e.name,i=yield e.arrayBuffer();yield t.dapi.files.write(this.path+`${e.name}`,new Uint8Array(i)),n(r)}))})}))}))}}const nr="System:AppData/SequenceTranslator/polytool-rules/",rr="Polytool",ir="link",or="fragmentDuplication",sr="differentFragments";class ar extends er{constructor(t,e,n){super(t,e,n)}}class ur{constructor(t,e){this.linkages=e,this.monomers=t}static fromHelm(t){const e=t.split("$"),n=e[0].split("|"),r=e[1].split("|"),i=new Array(n.length),o=[];for(let t=0;t<n.length;t++){const e=n[t].indexOf("{"),r=n[t].indexOf("}");i[t]=n[t].slice(e+1,r).split(".")}for(let t=0;t<r.length;t++)if(""!==r[t]&&"V2.0"!==r[t]){const e=r[t].split(","),n=e[0].replace("PEPTIDE","")-1,i=e[1].replace("PEPTIDE","")-1,s=e[2].split("-"),a=s[0].split(":"),u=s[1].split(":");o.push({fChain:n,sChain:i,fMonomer:a[0],sMonomer:u[0],fR:a[1].replace("R",""),sR:u[1].replace("R","")})}return new ur(i,o)}static fromNotation(t,e){const n=e.heterodimerCode,r=e.homodimerCode,i=[],o=[],s=null!==n?t.split(`(${e.heterodimerCode})`):"";null!==n&&s.length>1?(o.push({fChain:0,sChain:1,fMonomer:1,sMonomer:1,fR:1,sR:1}),i.push(s[1].replaceAll("{","").replaceAll("}","")),i.push(s[2].replaceAll("{","").replaceAll("}",""))):i.push(t);for(let t=0;t<i.length;t++)if(null!==r&&i[t].includes(`(${r})`)){const e=i.length;o.push({fChain:t,sChain:e,fMonomer:1,sMonomer:1,fR:1,sR:1});const n=i[t].replace(`(${r})`,""),s=n.indexOf("{"),a=n.slice(0,s),u=n.replace(a,"").replaceAll("{","").replaceAll("}","");i[t]=a+u,i.push(u)}const a=new Array(i.length);for(let t=0;t<i.length;t++){const n=i[t].split("-"),r=this.getLinkedPositions(n,e.linkRules),[s,u,l,c,h]=this.getAllCycles(e.linkRules,n,r),f=new Array(s.length);for(let t=0;t<s.length;t++)f[t]=`[${s[t]}]`;for(let e=0;e<u.length;e++)o.push({fChain:t,sChain:t,fMonomer:u[e],sMonomer:l[e],fR:c[e],sR:h[e]});a[t]=f}return new ur(a,o)}getHelmChanged(t,e){let n=0,r=0,i=0;t:for(let e=0;e<this.monomers.length;e++)for(let o=0;o<this.monomers[e].length;o++){if(n==t){r=e,i=o;break t}n++}const o=this.monomers[r][i];this.monomers[r][i]=`[${e}]`;const s=this.getHelm();return this.monomers[r][i]=o,s}getHelm(){let t="";for(let e=0;e<this.monomers.length;e++){e>0&&(t+="|"),t+=`PEPTIDE${e+1}{`;for(let n=0;n<this.monomers[e].length;n++)n>0&&(t+="."),t+=this.monomers[e][n];t+="}"}t+="$";for(let e=0;e<this.linkages.length;e++)e>0&&(t+="|"),t+=`PEPTIDE${this.linkages[e].fChain+1},PEPTIDE${this.linkages[e].sChain+1},`,t+=`${this.linkages[e].fMonomer}:R${this.linkages[e].fR}-`,t+=`${this.linkages[e].sMonomer}:R${this.linkages[e].sR}`;return t+="$$$",t}static getLinkedPositions(t,e){const n=new Array(e.length);for(let r=0;r<e.length;r++){let i=!1,o=!1,s=!1,a=-1,u=-1;const l=`(${e[r].code})`;for(let n=0;n<t.length;n++)if(t[n].includes(l)){if(i){if(s&&t[n]==e[r].secondMonomer+l){o=!0,u=n;break}if(s||t[n]!=e[r].firstMonomer+l)continue;o=!0,u=n;break}if(t[n]==e[r].firstMonomer+l)i=!0,s=!0,a=n;else{if(t[n]!=e[r].secondMonomer+l)continue;i=!0,s=!1,a=n}}n[r]=i&&o?s?[a,u]:[u,a]:[-1,-1]}return n}static getAllCycles(t,e,n){const r=[],i=[],o=[],s=[],a=t.length;for(let u=0;u<a;u++){if(-1==n[u][0])continue;const a=e[n[u][0]],l=e[n[u][1]];e[n[u][0]]=e[n[u][0]].replace(a,t[u].firstSubstitution),e[n[u][1]]=e[n[u][1]].replace(l,t[u].secondSubstitution),r.push(n[u][0]+1),i.push(n[u][1]+1),o.push(t[u].firstLinkingGroup),s.push(t[u].secondLinkingGroup)}return[e,r,i,o,s]}}function lr(e,n=!0){const[r,i]=Xn(e);return $r.logger.error(r,void 0,i),n&&t.shell.error(r),[r,i]}const cr="System:AppData/Bio/monomer-libraries/";async function hr(){const e=await t.functions.call("Bio:getMonomerLibHelper",{});return(await e.getFileManager()).getValidLibraryPaths()}const fr="\n\n\n 22 24  0  0  0  0  0  0  0  0999 V2000\n    0.3128   -0.7509    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n    0.3128    0.0740    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n   -0.4054   -1.1623    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n   -1.1081   -0.7509    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n   -0.4054    0.4877    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0\n   -1.1081    0.0740    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n   -1.8175   -1.1623    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n    1.0222    0.4877    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n   -1.8175    0.4877    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n   -2.5292   -0.7509    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n    1.0222    1.3127    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n    1.7227    1.7263    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n   -0.4054   -1.9896    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0\n   -2.5292    0.0740    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n    2.4544    1.3127    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n    1.7406    0.0740    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n    1.0222   -1.1623    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0\n    2.4544    0.4877    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n   -1.8175   -1.9896    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0\n   -3.2453    0.4877    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0\n    3.1670    1.7285    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0\n    1.7149    2.5513    0.0000 R#  0  0  0  0  0  0  0  0  0  0  0  0\n  2  1  2  0  0  0  0\n  3  1  1  0  0  0  0\n  4  3  1  0  0  0  0\n  5  2  1  0  0  0  0\n  6  5  1  0  0  0  0\n  7  4  1  0  0  0  0\n  8  2  1  0  0  0  0\n  9  6  1  0  0  0  0\n 10  7  2  0  0  0  0\n 11  8  2  0  0  0  0\n 12 11  1  0  0  0  0\n 13  3  2  0  0  0  0\n 14  9  2  0  0  0  0\n 15 18  1  0  0  0  0\n 16  8  1  0  0  0  0\n 17  1  1  0  0  0  0\n 18 16  2  0  0  0  0\n 19  7  1  0  0  0  0\n 20 14  1  0  0  0  0\n  6  4  2  0  0  0  0\n 15 12  2  0  0  0  0\n 14 10  1  0  0  0  0\n 15 21  1  0  0  0  0\n 12 22  1  0  0  0  0\nM  RGP  1  22   1\nM  END";const dr={symbol:"Short Name",name:"Medium Name",smiles:"SMILES"},pr=[{capGroupSmiles:"[*:1][H]",alternateId:"R1-H",capGroupName:"H",label:"R1"},{capGroupSmiles:"O[*:2]",alternateId:"R2-OH",capGroupName:"OH",label:"R2"},{capGroupSmiles:"[*:3][H]",alternateId:"R3-H",capGroupName:"H",label:"R3"}],gr="No dataframe with macromolecule columns open",mr="Get HELM",yr="Add HELM column",vr="Chirality engine",br="Poly Tool Conversion",wr="Poly Tool Enumeration",Cr="Rules used";function Ar(n){(async function(n){const r=[],i=()=>{for(const t of r)t.unsubscribe()};try{const[o,s]=await Promise.all([hr(),Kn()]),a=n&&n.rowIndex>=0?n.value:fr;let u=await(async()=>e.chem.isMolBlock(a)?a:await t.functions.call("Chem:convertMolNotation",{molecule:a,sourceNotation:n?.column.getTag(e.TAGS.UNITS)??e.chem.Notation.Unknown,targetNotation:e.chem.Notation.MolBlock}))();const l=new e.chem.Sketcher(e.chem.SKETCHER_MODE.EXTERNAL);l.syncCurrentObject=!1,l.onChanged.subscribe((t=>{u=l.getMolFile()})),l.root.classList.add("ui-input-editor"),l.root.style.marginTop="3px",l.setMolFile(u);const c=Tt.input.choice("Library to use",{value:null,items:o});l.root.setAttribute("style","min-width:250px!important;"),l.root.setAttribute("style","max-width:250px!important;"),c.input.setAttribute("style","min-width:250px!important;");const h=Tt.div([l.root,c.root]);r.push(t.events.onCurrentCellChanged.subscribe((()=>{const n=t.shell.tv.dataFrame.currentCell;n.column.semType===e.SEMTYPE.MOLECULE&&l.setValue(n.value)})));const f=async()=>{try{const n=l.getMolFile();if(void 0===n||""===n)t.shell.warning("PolyTool: no molecule was provided");else if(n.includes("R#")){const r=await async function(e,n){const r=await async function(e){const n=await t.functions.call("Bio:getMonomerLibHelper",{});return(await n.readLibrary(cr,e)).getMonomerSymbolsByType("PEPTIDE")}(n),i=await async function(e){const n=await t.functions.call("Bio:getMonomerLibHelper",{}),r=await n.readLibrary(cr,e),i=r.getMonomerSymbolsByType("PEPTIDE");return new Array(i.length),r.getMonomerMolsByPolymerType("PEPTIDE")}(n),o=new Array(r.length),s=await t.functions.call("Chem:getRdKitModule"),a=s.get_mol(e),u=a.get_smiles();a.delete();const l=new Array(r.length);for(let t=0;t<r.length;t++){const e=i[r[t]],n=s.get_mol(e);l[t]=n.get_smiles(),n.delete()}for(let t=0;t<r.length;t++){let e=null;try{const n=`${`${u}.${l[t]}`.replaceAll("[1*]C","C([1*])").replaceAll("[1*]c","c([1*])").replaceAll("[1*]O","O([1*])").replaceAll("[1*]N","N([1*])")}`.replaceAll("([1*])","9").replaceAll("[1*]","9");e=s.get_mol(n,JSON.stringify({mappedDummiesAreRGroups:!0}));const r=e.get_v3Kmolblock();o[t]=r}catch(e){o[t]=""}finally{e?.delete()}}return o}(n,c.value),i=e.Column.fromStrings("Enumerated",r),o=e.DataFrame.fromColumns([i]);t.shell.addTableView(o)}else t.shell.warning("PolyTool: no R group was provided")}catch(t){lr(t)}},d=Tt.dialog(wr).add(h).onOK((()=>{f().finally((()=>{i()}))})).onCancel((()=>{i()}));return r.push(d.onClose.subscribe((()=>{i()}))),d.history((()=>({mol:l.getMolFile(),screenLibrary:c.value})),(t=>{l.setMolFile(t.mol),c.value=t.screenLibrary})),d}catch(t){throw i(),t}})(n).then((t=>{t.show({resizable:!0})})).catch((e=>{t.shell.warning("To run PolyTool Enumeration, sketch the molecule and specify the R group to vary")}))}async function xr(n,r,i,o){const s=e.TaskBarProgressIndicator.create("PolyTool converting...");try{const s=(t,e)=>t?t.columns.getUnusedName(e):e;await Kn();const a=n.dataFrame,u=await async function(n){const r=new e.FileSource(nr),i=[],o={homodimerCode:null,heterodimerCode:null,linkRules:i};for(let e=0;e<n.length;e++){const s=await r.readAsText(n[e].replace(nr,"")),a=JSON.parse(s);for(let e=0;e<a.length;e++)if(void 0!==a[e].type&&void 0!==a[e].code)switch(a[e].type){case ir:{const t=a[e].monomericSubstitution;t.code=a[e].code,i.push(t);break}case or:o.homodimerCode&&t.shell.warning("PolyTool: homodimer code is duplicated in rules."),o.homodimerCode=a[e].code;break;case sr:o.heterodimerCode&&t.shell.warning("PolyTool: heterodimer code is duplicated in rules."),o.heterodimerCode=a[e].code;break;default:t.shell.warning(`PolyTool: Unexpected type - '${a[e]}'.`)}else t.shell.warning("Polytool: rules contain invalid rule")}return o}(o),l=function(t,e){const n=new Array(t.length);for(let r=0;r<t.length;r++)if(void 0===t[r])n[r]="";else{const i=ur.fromNotation(t[r],e);n[r]=i.getHelm()}return n}(n.toList(),u),c=s(a,`transformed(${n.name})`),h=e.Column.fromType(e.COLUMN_TYPE.STRING,c,l.length).init((t=>l[t]));h.semType=e.SEMTYPE.MACROMOLECULE,h.meta.units=C.HELM,h.setTag(e.TAGS.CELL_RENDERER,"helm"),r&&a&&a.columns.add(h,!0);const f=await Zn(),d=(await f.helmToAtomicLevel(h,i,r)).molCol;return d.name=s(a,`molfile(${n.name})`),d.semType=e.SEMTYPE.MOLECULE,a&&(a.columns.add(d,!0),await t.data.detectSemanticTypes(a)),[h,d]}finally{s.close()}}var _r,Er;function Tr(t){let e;switch(t){case _r.BASE:case _r.SUGAR:case _r.LINKER:case _r.NUCLEOTIDE:case"nucleotide":e="RNA";break;case _r.AA:e="PEPTIDE";break;case _r.CHEM:e="CHEM";break;case _r.BLOB:e="BLOB";break;default:e="PEPTIDE",console.warn(`Unexpected HelmType '${t}'`)}return e}!function(t){t.BASE="HELM_BASE",t.SUGAR="HELM_SUGAR",t.LINKER="HELM_LINKER",t.AA="HELM_AA",t.CHEM="HELM_CHEM",t.BLOB="HELM_BLOB",t.NUCLEOTIDE="HELM_NUCLETIDE"}(_r||(_r={}));class Sr extends e.InputBase{constructor(t,e){super(Tt.input.column(t,e).dart,e?.onValueChanged),this.options=e}setColumnInputTable(t){Tt.input.setColumnInputTable(this,t,this.options?.filter)}}Tt.input.column2=function(t,e){return new Sr(t,e)},function(t){t.Single="single",t.Matrix="matrix"}(Er||(Er={}));const Ir="PEPTIDE1{R.[Aca].T.G.H.F.G.A.A.Y.P.E.[meI]}$$$$";function Nr(t,e,n,r){const i=new Array(r.length*(n-e+1));for(let o=0;o<r.length;++o){const s=n-e+1;for(let n=0;n<s;++n){const a=e+n,u=r[o],l=i[o*s+n]=t.clone(),c=l.atoms[a].elem;l.atoms[a].elem=u;const h=c?.length>1?`[${c}]`:c,f=u?.length>1?`[${u}]`:u;l.name=`${t.name}-${h}${a+1}${f}`}}return i}class Mr extends e.JsInputBase{get inputType(){return"Positions"}get dataType(){return e.TYPE.DATA_FRAME}getInput(){return this.gridHost}getValue(){return this.grid.dataFrame}setValue(t){this.grid.dataFrame=t}getStringValue(){return this.grid.dataFrame.toCsv()}setStringValue(t){this.grid.dataFrame=e.DataFrame.fromCsv(t)}get placeholdersValue(){return function(t){const e=[];for(let n=0;n<t.rowCount;n++){const r=parseInt(t.get("Position",n));if(!isNaN(r)){const i=Or(t.get("Monomers",n));e.push({position:r,monomers:i})}}return e}(this.grid.dataFrame)}constructor(t,e,n){super(),this.subs=[],t&&(this.captionLabel.innerText=t),this.gridHost=Tt.div([],{classes:"ui-input-editor",style:{width:"100%",height:"100%",marginTop:"-8px",marginBottom:"8px",paddingBottom:"4px"}}),this.grid=e,this.gridHost.append(this.grid.root),null!=n?this.updateGridHeight(n+.7):(this.updateGridHeight(this.grid.dataFrame.rowCount+.6),this.subs.push(this.grid.dataFrame.onRowsAdded.subscribe((()=>{this.updateGridHeight(this.grid.dataFrame.rowCount+.6)})))),this.grid.root.style.width="100%",this.subs.push(this.grid.dataFrame.onDataChanged.subscribe((()=>{this.fireChanged()}))),this.subs.push(Tt.onSizeChanged(this.grid.root).subscribe((()=>{this.grid.columns.byIndex(2).width=this.grid.root.clientWidth-this.grid.horzScroll.root.offsetWidth-this.grid.columns.byIndex(0).width-this.grid.columns.byIndex(1).width-10}))),this.root.classList.add("ui-input-polytool-pos-grid"),this.root.append(this.gridHost)}detach(){for(const t of this.subs)t.unsubscribe()}static async create(t,n,r){const i=e.DataFrame.fromColumns([e.Column.fromType(e.COLUMN_TYPE.INT,"Position",0),e.Column.fromType(e.COLUMN_TYPE.STRING,"Monomers",0)]),o=await i.plot.fromType(e.VIEWER.GRID,n);return o.sort(["Position"]),new Mr(t,o,r)}updateGridHeight(t){const e=this.grid.colHeaderHeight+t*this.grid.props.rowHeight+6+2;this.grid.root.style.height=`${e}px`}gridRootOnSizeChanged(){this.grid.columns.byIndex(2).width=this.grid.root.clientWidth-this.grid.horzScroll.root.offsetWidth-this.grid.columns.byIndex(0).width-this.grid.columns.byIndex(1).width-10}}function Or(t){return t.split(/,(?![^(]*\))/).map((t=>('"'===(t=t.trim()).slice(0,1)&&'"'===t.slice(-1)&&(t=t.slice(1,-1)),"'"===t.slice(0,1)&&"'"===t.slice(-1)&&(t=t.slice(1,-1)),t.trim()))).filter((t=>!!t))}class Lr extends e.JsInputBase{get inputType(){return"Breadth"}get dataType(){return e.TYPE.DATA_FRAME}getInput(){return this.gridHost}getValue(){return this.grid.dataFrame}setValue(t){this.grid.dataFrame=t}getStringValue(){return this.grid.dataFrame.toCsv()}setStringValue(t){this.grid.dataFrame=e.DataFrame.fromCsv(t)}get placeholdersBreadthValue(){return function(t){const e=[];for(let n=0;n<t.rowCount;n++){const r=parseInt(t.get("Start",n)),i=parseInt(t.get("End",n));if(!isNaN(r)&&!isNaN(i)){const o=Or(t.get("Monomers",n));e.push({start:r,end:i,monomers:o})}}return e}(this.grid.dataFrame)}constructor(t,e,n){super(),this.subs=[],t&&(this.captionLabel.innerText=t),this.gridHost=Tt.div([],{classes:"ui-input-editor",style:{width:"100%",height:"100%",marginTop:"-8px",marginBottom:"8px",paddingBottom:"4px"}}),this.grid=e,this.gridHost.append(this.grid.root),null!=n?this.updateGridHeight(n+.7):(this.updateGridHeight(this.grid.dataFrame.rowCount+.6),this.subs.push(this.grid.dataFrame.onRowsAdded.subscribe((()=>{this.updateGridHeight(this.grid.dataFrame.rowCount+.6)})))),this.grid.root.style.width="100%",this.subs.push(this.grid.dataFrame.onDataChanged.subscribe((()=>{this.fireChanged()}))),this.subs.push(Tt.onSizeChanged(this.grid.root).subscribe((()=>{this.grid.columns.byIndex(3).width=this.grid.root.clientWidth-this.grid.horzScroll.root.offsetWidth-this.grid.columns.byIndex(0).width-this.grid.columns.byIndex(1).width-this.grid.columns.byIndex(2).width-10}))),this.root.classList.add("ui-input-polytool-pos-grid"),this.root.append(this.gridHost)}detach(){for(const t of this.subs)t.unsubscribe()}static async create(t,n,r){const i=e.DataFrame.fromColumns([e.Column.fromType(e.COLUMN_TYPE.INT,"Start",0),e.Column.fromType(e.COLUMN_TYPE.INT,"End",0),e.Column.fromType(e.COLUMN_TYPE.STRING,"Monomers",0)]),o=await i.plot.fromType(e.VIEWER.GRID,n);return o.sort(["Start","End"]),new Lr(t,o,r)}updateGridHeight(t){const e=this.grid.colHeaderHeight+t*this.grid.props.rowHeight+6+2;this.grid.root.style.height=`${e}px`}gridRootOnSizeChanged(){this.grid.columns.byIndex(3).width=this.grid.root.clientWidth-this.grid.horzScroll.root.offsetWidth-this.grid.columns.byIndex(0).width-this.grid.columns.byIndex(1).width-this.grid.columns.byIndex(2).width-10}}async function Br(n){const r=window.innerWidth,i=window.innerHeight;try{let o;const s=()=>{if(null==o)return;const t=It()(o.root).find("div.d4-dialog-contents").get(0),e=t.clientHeight,n={0:1},r=Object.values(n).reduce(((t,e)=>t+e),0),i=e-T().count(0).take(t.children.length).filter((t=>!(t in n))).map((e=>t.children[e])).filter((t=>t instanceof HTMLElement)).map((t=>t.offsetHeight)).reduce(((t,e)=>t+e),0)-38;o.inputs.forEach(((t,e)=>{if(e in n){const o=i*n[e]/r;t.root.style.height=`${o}px`}}))};o=await async function(n,r){const i="ST: PT: HelmDialog()";let o;const s=[],a=()=>{for(const t of s)t.unsubscribe();o.placeholders.detach()};try{const u=(await rt()).getMonomerLib(),l=(await Zn(),e.DataFrame.fromColumns([])),[c,h]=await Promise.all([hr(),Kn()]);let f=null;const d=Tt.divText("",{style:{marginLeft:"8px",marginTop:"2px"}}),p=Tt.divText("",{style:{color:"red"}});o={macromolecule:h.createHelmInput("Macromolecule",{editable:!1}),placeholders:await Mr.create("Placeholders",{showAddNewRowIcon:!0,showRemoveRowIcon:!0,showRowHeader:!1,showCellTooltip:!1}),enumeratorType:Tt.input.choice("Enumerator type",{value:Er.Single,items:Object.values(Er)}),placeholdersBreadth:await Lr.create("Breadth",{showAddNewRowIcon:!0,showRemoveRowIcon:!0,showRowHeader:!1,showCellTooltip:!1}),toAtomicLevel:Tt.input.bool("To atomic level",{value:!1}),keepOriginal:Tt.input.bool("Keep original",{value:!1}),trivialNameCol:Tt.input.column2("Trivial name",{table:n?.dataFrame,filter:t=>t.type===e.COLUMN_TYPE.STRING&&t!=n?.column,onValueChanged:()=>{const t=o.trivialNameCol.value;let e=null;n&&t&&(e={value:t.get(n.rowIndex),colName:t.name}),f=e,d.textContent=f?`Original ID: ${f.value}`:""},nullable:!0})},o.trivialNameCol.addOptions(d);let g=null;o.placeholders.addValidator((t=>{const e=[];try{const t=[];for(const n of o.placeholders.placeholdersValue){const r=n.position;if(r>=o.macromolecule.molValue.atoms.length){e.push(`There is no monomer at position ${r+1}.`);continue}const i=Tr(o.macromolecule.molValue.atoms[r].biotype());for(const e of n.monomers){const n=u.getMonomer(i,e);n&&n.lib||t.push({polymerType:i,symbol:e})}}const n={};for(const e of t){let t=n[e.polymerType];t||(t=n[e.polymerType]=[]),t.push(e.symbol)}const r=Object.entries(n).map((([t,e])=>`${t}: ${e.join(", ")}`)).join("\n");Object.keys(r).length>0&&e.push(`Placeholders contain missed monomers: ${r}`),g=e.length>0?e.join("\n"):null}catch(t){const[e,n]=lr(t,!1);g=e}return setTimeout((()=>{y()}),0),g})),s.push(o.macromolecule.onMouseMove.subscribe((t=>{try{$r.logger.debug(`${i}, placeholdersInput.onMouseMove()`);const e=t.offsetX,n=t.offsetY,r=o.macromolecule.molValue,s=h.getHoveredAtom(e,n,r,o.macromolecule.root.clientHeight);if(s){const e=s._parent.atoms.indexOf(s),n=o.placeholders.placeholdersValue.find((t=>t.position===e))?.monomers;if(n){const e=Tt.divText(n.join(", "));o.macromolecule.showTooltip(e,s),t.preventDefault(),t.stopPropagation()}}}catch(t){lr(t,!1)}}))),s.push(o.macromolecule.onClick.subscribe((t=>{try{$r.logger.debug(`${i}, placeholdersInput.onClick()`);const e=t.offsetX,n=t.offsetY,r=o.macromolecule.molValue,s=h.getHoveredAtom(e,n,r,o.macromolecule.root.clientHeight);if(s){const t=(s._parent.atoms.indexOf(s)+1).toString(),e=o.placeholders.grid.dataFrame,n=e.columns.byName("Position").toList();let r=n.indexOf(t);-1===r&&(r=n.findIndex((t=>isNaN(t))),-1===r&&(r=e.rows.addNew([t,""]).idx),e.set("Position",r,t)),e.currentCell=e.cell(r,"Monomers")}}catch(t){lr(t)}}))),s.push(o.placeholders.grid.dataFrame.onDataChanged.subscribe((()=>{m()}))),s.push((0,Jt.fromEvent)(o.placeholders.grid.root,"keydown").subscribe((t=>{"Enter"===t.key&&t.stopPropagation()}))),s.push(Tt.onSizeChanged(o.placeholders.root).subscribe((()=>{r&&r()}))),s.push(t.events.onCurrentCellChanged.subscribe((()=>{const n=t.shell.tv.dataFrame.currentCell;n.column.semType===e.SEMTYPE.MACROMOLECULE&&b(n)}))),o.macromolecule.root.style.setProperty("min-width","250px","important");const m=()=>{const t=o.macromolecule.molValue;for(let e=0;e<t.atoms.length;e++)t.atoms[e].highlighted=e in o.placeholders.placeholdersValue;o.macromolecule.redraw()},y=()=>{const t=g,e=p;t?(e.innerText=t,e.style.removeProperty("display")):(e.innerText="",e.style.setProperty("display","none"))},v=t=>{t?(o.trivialNameCol.setColumnInputTable(t),o.trivialNameCol.root.style.removeProperty("display")):(o.trivialNameCol.setColumnInputTable(l),o.trivialNameCol.root.style.setProperty("display","none")),r&&r()},b=async t=>{let n,r;if(t&&t.rowIndex>=0&&t?.column.semType==e.SEMTYPE.MACROMOLECULE){const e=tt.forColumn(t.column);n=await e.getHelm(t.rowIndex),r=t.dataFrame}else n=Ir;o.macromolecule.stringValue=n,v(r)};await b(n);const w=async()=>{try{const n=o.macromolecule.stringValue;if(T().enumerate(o.macromolecule.molValue.atoms).filter((([t,e])=>t.highlighted)).map((([t,e])=>e)).toArray(),void 0===n||""===n)t.shell.warning("PolyTool: no molecule was provided");else{if(0===Object.keys(o.placeholders.placeholdersValue).length&&0===Object.keys(o.placeholdersBreadth.placeholdersBreadthValue).length)return void t.shell.warning(`${wr}: placeholders are empty`);await Kn();const r={placeholders:o.placeholders.placeholdersValue,type:o.enumeratorType.value,placeholdersBreadth:o.placeholdersBreadth.placeholdersBreadthValue,keepOriginal:o.keepOriginal.value},i=await async function(t,n,r,i){const o=e.TaskBarProgressIndicator.create("PolyTool enumerating...");try{await Kn();const o=function(t,e,n){const r=new JSDraw2.MolHandler,i=new org.helm.webeditor.Plugin(r);org.helm.webeditor.IO.parseHelm(i,t,new JSDraw2.Point(0,0),void 0);const o=r.m;o.name=e;let s=[];if(n.placeholders)switch(n.type){case Er.Single:s=function(t,e){return e.map((e=>Nr(t,e.position,e.position,e.monomers))).reduce(((t,e)=>t.concat(e)),[])}(r.m,n.placeholders);break;case Er.Matrix:s=function(t,e){let n=[t];for(const t of e){const e=n.map((e=>Nr(e,t.position,t.position,t.monomers)));n=e.reduce(((t,e)=>t.concat(e)),[])}return n}(r.m,n.placeholders)}let a=[];n.placeholdersBreadth&&(a=function(t,e){let n=[t];for(const t of e){const e=n.map((e=>Nr(e,t.start,t.end,t.monomers)));n=e.reduce(((t,e)=>t.concat(e)),[])}return n}(r.m,n.placeholdersBreadth)),s=s.concat(a),n.keepOriginal&&(s=[o,...s]);const u=s.map((t=>[org.helm.webeditor.IO.getHelm(t),t.name]));return u}(t,n?.value??"",r),s=e.Column.fromType(e.COLUMN_TYPE.STRING,"Enumerated",o.length).init((t=>o[t][0])),a=e.DataFrame.fromColumns([s]);if(i){const t=await Zn(),n=await t.helmToAtomicLevel(s,!0,!0);n.molCol.semType=e.SEMTYPE.MOLECULE,a.columns.add(n.molCol,!1)}if(n){const t=e.Column.fromType(e.COLUMN_TYPE.STRING,n.colName,o.length).init((t=>o[t][1]));a.columns.add(t)}return a}finally{o.close()}}(n,f,r,o.toAtomicLevel.value);t.shell.addTableView(i)}}catch(t){lr(t)}},C=Tt.dialog({title:wr,showFooter:!0}).add(o.macromolecule).add(o.placeholders).add(o.enumeratorType).add(o.placeholdersBreadth).add(o.trivialNameCol).add(o.toAtomicLevel).add(o.keepOriginal).add(p).onOK((()=>{w()}));return s.push(C.onClose.subscribe((()=>{a()}))),C.history((()=>({macromolecule:o.macromolecule.stringValue,placeholders:o.placeholders.stringValue,enumeratorType:o.enumeratorType.value,placeholdersBreadth:o.placeholdersBreadth.stringValue,trivialNameCol:o.trivialNameCol.stringValue,toAtomicLevel:o.toAtomicLevel.value,keepOriginal:o.keepOriginal.value})),(t=>{o.macromolecule.stringValue=t.macromolecule,o.placeholders.stringValue=t.placeholders,o.enumeratorType.value=t.enumeratorType,o.placeholdersBreadth.stringValue=t.placeholdersBreadth,o.trivialNameCol.stringValue=t.trivialNameCol,o.toAtomicLevel.value=t.toAtomicLevel,o.keepOriginal.value=t.keepOriginal})),C}catch(t){throw a(),t}}(n,s);let a=!0;Tt.onSizeChanged(o.root).subscribe((()=>{if(a){o.inputs;const t=It()(o.root),e=(t.find("div.d4-dialog-header").get(0).offsetHeight,t.find("div.d4-dialog-footer").get(0).offsetHeight,.7*r),n=.7*i;o.root.style.width=`${Math.min(r,e)}px`,o.root.style.height=`${Math.min(i,n)}px`,o.root.style.left=`${Math.floor((r-o.root.offsetWidth)/2)}px`,o.root.style.top=`${Math.floor((i-o.root.offsetHeight)/2)}px`,a=!1}s()})),s(),$r.logger.debug("PolyToolEnumerateHelmUI: dialog before show"),o.show({width:Math.max(350,.7*r),resizable:!0}),$r.logger.debug("PolyToolEnumerateHelmUI: dialog after show")}catch(e){const[n,r]=Xn(e);t.shell.warning("To run PolyTool Enumeration, sketch the macromolecule and select monomers to vary"),$r.logger.error(n,void 0,r)}}class Pr{constructor(t){this.rawLib=t}isValid(){return this.rawLib.every((t=>"object"==typeof t&&Object.values(dr).every((e=>e in t&&"string"==typeof t[e]))))}getJsonMonomerLib(){const t=[];return this.rawLib.forEach((e=>{const n=this.prepareMonomer(e);t.push(n)})),t}prepareMonomer(t){const e={...y};Object.entries(dr).forEach((([n,r])=>{const i=t[r];e[n]=i}));let n="smiles";const r=t[dr[n]],i=new Rr(r),o=i.getCappedSmiles();return e[n]=o,n="rgroups",e[n]=Dr.getRGroups(i.getNumberOfRGroups()),n="molfile",e[n]=new Fr(i.getSmilesWithRGroups()).getMolfile(),e}}class Rr{constructor(t){let e=0;this.smilesWithRGroups=t.replace(/\[R(\d+)\]/g,((t,n)=>(++e,`[${n}*]`))),this.numberOfRGroups=e}getSmilesWithRGroups(){return this.smilesWithRGroups}getCappedSmiles(){return this.capRGroups()}getNumberOfRGroups(){return this.numberOfRGroups}capRGroups(){let t=this.smilesWithRGroups.replace("[1*]","[H:1]");return t=t.replace("[2*]","[OH:2]"),t.replace("[3*]","[H:3]")}}class Dr{constructor(){}static getRGroups(t){return pr.slice(0,t)}}class Fr{constructor(t){this.smilesWithRGroups=t}getMolfile(){let t=e.chem.convert(this.smilesWithRGroups,e.chem.Notation.Smiles,e.chem.Notation.MolBlock);return t=this.restoreRGPLine(t),t=this.fixRGroupSymbols(t),t}restoreRGPLine(t){return t.replace("M  ISO","M  RGP")}fixRGroupSymbols(t){return t.replace(/\bR\b/g,"R#")}}class Hr{constructor(t,n){this.fileName=t,this.fileContent=n,this.validateFileType();const r=e.DataFrame.fromCsv(this.fileContent),i=this.toJson(r);this.polyToolMonomerLib=new Pr(i),this.validateContent()}async getJson(){return this.polyToolMonomerLib.getJsonMonomerLib()}toJson(t){return Array.from({length:t.rowCount},((e,n)=>t.columns.names().reduce(((e,r)=>(e[r]=t.get(r,n),e)),{})))}validateFileType(){if(!this.fileName.endsWith(".csv"))throw new Error(`File ${this.fileName} is not an CSV file`)}validateContent(){if(!this.polyToolMonomerLib.isValid())throw new Error("Invalid format of CSV monomer lib")}}var Ur;!function(t){t.table="table",t.seqCol="seqCol",t.generateHelm="generateHelm",t.chiralityEngine="chiralityEngine",t.rules="rules"}(Ur||(Ur={}));class kr{constructor(t){this.call=t,this.ruleInputs=new ar(nr,rr,".json")}async initInputs(){const t=t=>this.call.inputParams[t];this.inputs={table:(()=>{const e=t(Ur.table);return Tt.input.table(e.property.caption,{value:e.value})})(),seqCol:(()=>{const e=t(Ur.seqCol);return Tt.input.column(e.property.caption,{value:e.value,table:e.value.dataFrame})})(),generateHelm:Tt.input.forProperty(t(Ur.generateHelm).property),chiralityEngine:Tt.input.forProperty(t(Ur.chiralityEngine).property),rules:{header:Tt.inlineText([Cr]),form:await this.ruleInputs.getForm()}}}static async create(t){const e=new kr(t);return await e.initInputs(),e}async getParams(){return{table:this.inputs.table.value,seqCol:this.inputs.seqCol.value,generateHelm:this.inputs.generateHelm.value,chiralityEngine:this.inputs.chiralityEngine.value,rules:await this.ruleInputs.getActive()}}async showDialog(){const t=Tt.div([this.inputs.table,this.inputs.seqCol,this.inputs.generateHelm,this.inputs.chiralityEngine,this.inputs.rules.header,this.inputs.rules.form],{style:{minWidth:"320px"}});return new Promise(((e,n)=>{Tt.dialog({title:br}).add(t).onOK((async()=>{const t=await this.getParams(),n=(await this.call.func.prepare(t).call(!0)).getOutputParamValue();e(n)})).onCancel((()=>{n(new Error("Cancelled by user"))})).show()}))}widget(){throw new Error("not implemented")}}const $r=new Mt({debug:!0});async function Vr(){await $r.initLibData();const e=await async function(e){const n={"Mermadesynthesis:merMadeSynthesis":{tabName:"SYNTHESIZE",parameters:Yn(e)}},r={};for(const[e,i]of Object.entries(n)){let n;try{n=await t.functions.call(e,i.parameters);const o=new jn(i.tabName,n);o.initView(),r[i.tabName]=()=>o.getView()}catch(t){console.warn(`Plugin ${e} not loaded, reason:`,t);continue}}return r}($r);if(!e)throw new Error("External app view factories not loaded");const n=new qn(e,$r);return await n.getAppView()}async function jr(){return await ei("Oligo Translator")}async function qr(){return await ei("Oligo Pattern")}async function Gr(){return await ei("Oligo Structure")}async function Wr(){return await $r.initLibData(),$r}function zr(){const t=$r.monomerLibWrapper.getCodesToWeightsMap();return Object.fromEntries(t)}function Yr(t){const e=$r.createSequenceValidator(t),n=$r.createFormatDetector(t).getFormat();return null!==n&&e.isValidSequence(n)}function Kr(t,e){return new bn(t,e,"GCRS").convert()}function Jr(t){return wn(t,!0)}async function Qr(){await async function(){await pt((async()=>{const e=await jr();t.shell.addView(e)}))}()}async function Xr(){await async function(){await pt((async()=>{const e=await qr();t.shell.addView(e)}))}()}async function Zr(){await zn()}async function ti(t,e,n){return await $r.initLibData(),$r.createFormatConverter(t,e).convertTo(n)}async function ei(t){await $r.initLibData();const e=function(t,e){switch(t){case"Oligo Translator":return new Vn(e);case"Oligo Pattern":return new tn(e);case"Oligo Structure":return new In(e);default:throw new Error(`Unknown app name: ${t}`)}}(t,$r);return await e.getAppView()}async function ni(){await async function(){let n;try{n=await async function(){const n=[],r=()=>{for(const t of n)t.unsubscribe()};try{const i=t.shell.t.columns.bySemTypeAll(e.SEMTYPE.MACROMOLECULE);if(!i)throw new Error(gr);const o=Tt.input.column("Column",{table:t.shell.t,value:i[0],filter:t=>t.semType===e.SEMTYPE.MACROMOLECULE});o.value=o.value;const s=Tt.input.bool(mr,{value:!0});Tt.tooltip.bind(s.root,yr);const a=Tt.input.bool(vr,{value:!1}),u=new ar(nr,rr,".json"),l=Tt.inlineText([Cr]);Tt.tooltip.bind(l,"Add or specify rules to use");const c=await u.getForm(),h=Tt.div([o,s,a,l,c]),f=async()=>{try{const t=await u.getActive();await xr(o.value,s.value,a.value,t)}catch(t){lr(t)}},d=Tt.dialog(br).add(h).onOK((()=>{f()}));return n.push(d.onClose.subscribe((()=>{r()}))),d.history((()=>({generateHelm:s.value,chiralityEngine:a.value})),(t=>{s.value=t.generateHelm,a.value=t.chiralityEngine})),d}catch(t){throw r(),t}}(),n.show()}catch(e){const[n,r]=Xn(e);t.shell.warning("To run PolyTool Conversion, open a dataframe with macromolecules"),$r.logger.error(n,void 0,r)}}()}async function ri(t){const e=await kr.create(t);return await e.showDialog()}async function ii(t,e,n,r,i){return(await xr(e,n,r,i))[0]}async function oi(){await Br(t.shell.tv?.dataFrame.currentCell)}async function si(){Ar()}async function ai(n,r){var i;(function(t){t.semType=e.SEMTYPE.MACROMOLECULE,t.setTag("aligned","SEQ"),t.setTag("alphabet",A.PT)})(i=r),i.meta.units=C.SEPARATOR,i.setTag("separator","-"),await t.data.detectSemanticTypes(n)}async function li(t){const n=await t.readAsString(),r=new Hr(t.fileName,n),i=await r.getJson(),o=t.fileName.replace(/\.csv$/,".json"),s=JSON.stringify(i,null,2);e.Utils.download(o,s)}function ci(t){!function(t){try{const n=t.args.item;if(n){const r=t.args.menu;(n instanceof e.GridCell||"GridCell"==n.constructor.name)&&function(t,n){if($r.logger.debug("ST: addContextMenuForCell(), start"),t&&t.tableColumn)switch(t.tableColumn.semType){case e.SEMTYPE.MACROMOLECULE:return n.item("PolyTool-Enumerate",(()=>{Br(t.cell)})),!0;case e.SEMTYPE.MOLECULE:return n.item("PolyTool-Enumerate",(()=>{Ar(t.cell)})),!0}return!1}(n,r)&&t.preventDefault()}}catch(t){lr(t),window.$sequenceTranslator||(window.$sequenceTranslator={}),window.$sequenceTranslator.contextMenuError=t}}(t)}async function hi(){await Br()}async function fi(){Ar()}})(),sequencetranslator=r})();
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