@datagrok/sequence-translator 1.3.4 → 1.3.9

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 s=-1,o=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|o;t|=(t&s)+s^s,o|=~(t|s),s&=t,o&i&&a++,s&i&&a--,o=o<<1|1,s=s<<1|~(n|o),o&=n}for(u=n;u--;)d[t.charCodeAt(u)]=0;return a})(t,e):((t,e)=>{const n=e.length,r=t.length,i=[],s=[],o=Math.ceil(n/32),a=Math.ceil(r/32);for(let t=0;t<o;t++)s[t]=-1,i[t]=0;let u=0;for(;u<a-1;u++){let o=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=s[t/32|0]>>>t&1,u=i[t/32|0]>>>t&1,l=n|o,c=((n|u)&a)+a^a|n|u;let h=o|~(c|a),f=a&c;h>>>31^r&&(s[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),o=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)],o=s[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^o&&(s[t/32|0]^=1<<t),g>>>31^a&&(i[t/32|0]^=1<<t),f=f<<1|o,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:s}={...p,...t};Object.entries(s).forEach((([t,n])=>e[t.charCodeAt(0)]=n));const o=[new Float32Array(1e4),new Float32Array(1e4)];return(t,s)=>{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++)o[0][e]=-n-(e-1)*r,o[1][e]=0;o[0][0]=0;for(let h=1;h<s.length+1;h++){o[c][0]=-n-(h-1)*r;for(let f=1;f<t.length+1;f++){const d=o[l][f-1]+i[e[t.charCodeAt(f-1)]][e[s.charCodeAt(h-1)]],p=o[l][f]-(a[f]?r:n),g=o[c][f-1]-(u[f-1]?r:n);o[c][f]=Math.max(d,g,p),o[c][f]===d?(a[f]=!1,u[f]=!1):o[c][f]===g?(a[f]=!1,u[f]=!0):(a[f]=!0,u[f]=!1)}l=c,c=(c+1)%2}const h=Math.max(t.length,s.length);return(h-o[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 A extends w{constructor(t,e,n){super(t.name,t.alphabet,t.cutoff),this.freq=e,this.similarity=n}}const C=wu;var x,_,S,E,T,I=n.n(C);(T=x||(x={})).FASTA="fasta",T.SEPARATOR="separator",T.HELM="helm",(E=_||(_={})).DNA="DNA",E.RNA="RNA",E.PT="PT",E.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"}(S||(S={}));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 U{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 k{}class H extends k{static buildPalette(){return[].concat(...Object.values(P.colourPalette))}get(t){const n=U.hashCode(t)%H.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),s=e.Color.b(n),o=Math.sqrt(Math.pow(0-i,2)+Math.pow(0-r,2)+Math.pow(0-s,2));return o>210?`rgb(${i/o*210},${r/o*210},${s/o*210})`:e.Color.toRgb(n)}(H.palette[n])}}H.palette=H.buildPalette();class j{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 V{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 j(e,X[x.FASTA])},G=t=>t?new V(t):new j([],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,s=0;for(;null!==(t=i.exec(n))&&s<e;)r[s++]=t[0].replace('"-"',"").replace("'-'","");r.splice(s)}else r=n.replaceAll('"-"',"").replaceAll("'-'","").split(t,e);return new j(r,X[x.SEPARATOR])}return new j([],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 j(r.map((t=>{Y.lastIndex=0;const e=Y.exec(t);return e&&e.length>=2?e[1]:t})),X[x.HELM])};function Q(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=[],s=[];for(const n of r)i.push(n in t?t[n]:0),s.push(e.has(n)?1:0);const o=new L(i),a=new L(s);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}(o,a)/(B(o)*B(a))}(t,e.alphabet,n);return new A(e,t,r)}));let i;const s=Math.max(...r.map((t=>t.similarity>t.cutoff?t.similarity:-1)));return i=s>0?r.find((t=>t.similarity===s)).name:_.UN,i}const J=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.getTag(e.TAGS.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(S.aligned)||!this.column.tags.has(S.alphabet)||!this.column.tags.has(S.alphabetIsMultichar)&&!this.isHelm()&&this.alphabet===_.UN)if(this.isFasta())Z.setUnitsToFastaColumn(this);else if(this.isSeparator()){const e=t.getTag(S.separator);Z.setUnitsToSeparatorColumn(this,e)}else{if(!this.isHelm())throw new Error(`Unexpected units '${this.column.getTag(e.TAGS.UNITS)}'.`);Z.setUnitsToHelmColumn(this)}if(!this.column.tags.has(S.alphabetIsMultichar))if(this.isHelm())this.column.setTag(S.alphabetIsMultichar,"true");else if(["UN"].includes(this.alphabet))throw new Error(`For column '${this.column.name}' of alphabet '${this.alphabet}' tag '${S.alphabetIsMultichar}' is mandatory.`);this.notationProvider=this.column.temp[J.notationProvider]??null,this.columnVersion=this.column.version}static setUnitsToFastaColumn(t){if(t.column.semType!==e.SEMTYPE.MACROMOLECULE||t.column.getTag(e.TAGS.UNITS)!==x.FASTA)throw new Error(`The column of notation '${x.FASTA}' must be '${e.SEMTYPE.MACROMOLECULE}'.`);t.column.setTag(e.TAGS.UNITS,x.FASTA),Z.setTags(t)}static setUnitsToSeparatorColumn(t,n){if(t.column.semType!==e.SEMTYPE.MACROMOLECULE||t.column.getTag(e.TAGS.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 '${x.SEPARATOR}' must have the separator tag.`);t.column.setTag(e.TAGS.UNITS,x.SEPARATOR),t.column.setTag(S.separator,n),Z.setTags(t)}static setUnitsToHelmColumn(t){if(t.column.semType!==e.SEMTYPE.MACROMOLECULE)throw new Error(`The column of notation '${x.HELM}' must be '${e.SEMTYPE.MACROMOLECULE}'`);t.column.setTag(e.TAGS.UNITS,x.HELM),Z.setTags(t)}static setTags(t){const n=t.column.getTag(e.TAGS.UNITS);if([x.FASTA,x.SEPARATOR].includes(n)){if(!t.column.getTag(S.alphabet)&&0===Object.keys(t.stats.freq).length)throw new Error("Alphabet is empty and not annotated.");let e=t.column.getTag(S.aligned);null===e&&(e=t.stats.sameLength?"SEQ.MSA":"SEQ",t.column.setTag(S.aligned,e));let n=t.column.getTag(S.alphabet);if(null===n&&(n=Q(t.stats.freq,M),t.column.setTag(S.alphabet,n)),n===_.UN){const e=Object.keys(t.stats.freq).length,n=Object.keys(t.stats.freq).some((t=>t.length>1));t.column.setTag(S.alphabetSize,e.toString()),t.column.setTag(S.alphabetIsMultichar,n?"true":"false")}}}get column(){return this._column}get length(){return this._column.length}get units(){return this._units}get notation(){return this._notation}get defaultGapOriginal(){return this._defaultGapOriginal}get separator(){const t=this.column.getTag(S.separator)??void 0;if(this.notation===x.SEPARATOR&&void 0===t)throw new Error(`Separator is mandatory  for column '${this.column.name}' of notation '${this.notation}'.`);return t}get aligned(){const t=this.column.getTag(S.aligned);if(!t&&(this.isFasta()||this.isSeparator()))throw new Error("Tag aligned not set");return t}get alphabet(){const t=this.column.getTag(S.alphabet);if(!t&&(this.isFasta()||this.isSeparator()))throw new Error("Tag alphabet not set");return t}get helmCompatible(){return this.column.getTag(S.isHelmCompatible)}getAlphabetSize(){if(this.notation==x.HELM||this.alphabet==_.UN){const t=this.column.getTag(S.alphabetSize);let e;if(t)e=parseInt(t);else{const t=this.stats;e=Object.keys(t.freq).length}return e}switch(this.alphabet){case _.PT:return 20;case _.DNA:case _.RNA:return 4;case"NT":return console.warn("Unexpected alphabet 'NT'."),4;default:throw new Error(`Unexpected alphabet '${this.alphabet}'.`)}}getAlphabetIsMultichar(){return this.notation===x.HELM||this.alphabet===_.UN&&"true"===this.column.getTag(S.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)}}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(S.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 s=this.column,o=t.toLowerCase()+"("+s.name+")",a=r??s.dataFrame.columns.getUnusedName(o),u=e.Column.fromList("string",a,i??new Array(this.column.length).fill(""));if(u.semType=e.SEMTYPE.MACROMOLECULE,u.setTag(e.TAGS.UNITS,t),t===x.SEPARATOR){if(!n)throw new Error(`Notation '${x.SEPARATOR}' requires separator value.`);u.setTag(S.separator,n)}u.setTag(e.TAGS.CELL_RENDERER,t===x.HELM?"helm":"sequence");const l=s.getTag(S.aligned);l&&u.setTag(S.aligned,l);let c=s.getTag(S.alphabet);c||this.notation!==x.HELM||t===x.HELM||(c=_.UN),null!=c&&u.setTag(S.alphabet,c);let h=s.getTag(S.alphabetSize);null!=c&&h&&u.setTag(S.alphabetSize,h);const f=s.getTag(S.alphabetIsMultichar);return null!=c&&void 0!==f&&u.setTag(S.alphabetIsMultichar,f),t==x.HELM&&(h=this.getAlphabetSize().toString(),u.setTag(S.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.setTag(e.TAGS.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(S.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(S.isHelmCompatible))return"true"===this.column.getTag(S.isHelmCompatible);const t=(await nt()).getBioLib().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(S.isHelmCompatible,"false"),!1}}return this.column.setTag(S.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"),s=this.splitter(t),o=[];for(let t=0;t<s.length;++t){let n=s.getOriginal(t);if(i&&(n=n.replace(b,"")),n===X[x.HELM])o.push(r);else if(this.toFasta(e)&&n.length>1){const t="["+n+"]";o.push(t)}else o.push(n)}return o.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,s=e??this.maxLength-1,o=this.getJoiner(),a=s-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 o(new j(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(S.positionNames);c&&r.setTag(S.positionNames,l(c));const h=this.column.getTag(S.positionLabels);return h&&r.setTag(S.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[J.seqHandler];return e&&e.columnVersion===t.version||(e=t.temp[J.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 s=t.getOriginal(r);e&&(s=s.replace(b,"$1")),""===i?s=X[x.FASTA]:i===y?s="":s.length>1&&(s="["+s+"]"),n[r]=s}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){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 s=e.getOriginal(t);(r||i)&&(s=s.replace(b,"$1"),s=s===y?null:s),n[t]=s||null}return new j(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 s=t.getOriginal(e);n&&(s=s.replace(b,"$1")),""===i?s=X[x.SEPARATOR]:i===y&&(s=""),r[e]=s}return r.join(e)}function et(t,e,n){const[r,i,s,o]=e,a=new Array(t.length);for(let e=0;e<t.length;++e){const r=t.getCanonical(e);let o=t.getOriginal(e);""===r?o=X[x.HELM]:(n&&(o=o.replace(b,"$1")),o=1===o.length?`${i}${o}${s}`:`${i}[${o}]${s}`),a[e]=o}return`${r}${a.join(".")}${o}`}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()}const rt="System:AppData/SequenceTranslator/monomers-sample",it="pattern-app-data.json",st="formats-to-helm.json",ot="codes-to-symbols.json",at="linkers.json",ut=["A","G","C","U"];var lt;function ct(t){return t.sort(((t,e)=>e.length-t.length))}function ht(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 ft(e,n,r="Oligo app"){try{return await e()}catch(e){const n=e.hasOwnProperty("message")?e.message:e.toString();throw t.shell.error(`${r} error: `+n),e}finally{n&&n()}}!function(t){t.HELM="HELM",t.AXOLABS="Axolabs"}(lt||(lt={}));class dt{constructor(t,e){this.sequence=t,this.th=e,this.libWrapper=this.th.monomerLibWrapper}getInvalidCodeIndex(t){if(t===lt.HELM)return this.sequence.length;const e=["r","d"],n=ct(this.libWrapper.getCodesByFormat(t));let r=0;for(;r<this.sequence.length;){const t=n.find((t=>t===this.sequence.substring(r,r+t.length)));if(!t)break;if(r>1&&ut.includes(this.sequence[r])&&e.includes(this.sequence[r-2]))break;if(e.includes(this.sequence[r+1])&&ut.includes(this.sequence[r])){r++;break}r+=t.length}return r===this.sequence.length&&(r=-1),r}isValidSequence(t){return-1===this.getInvalidCodeIndex(t)}}class pt{constructor(t,e,n,r){this.patternAppData=t,this.codesToHelmDict=e,this.codesToSymbolsDict=n,this.monomersWithPhosphate=r}}async function gt(e){const n=await Promise.all([it,st,ot,at].map((n=>async function(e,n){const r=e.endsWith("/")?`${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 pt(n[0],n[1],n[2],n[3])}class mt{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===lt.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 vt="<?>",yt=(t,e)=>e.length-t.length;class bt{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(yt);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(yt)}getTargetFormatHelmCodesRegExp(t){this.validateFormat(t);const e=this.getTargetFormatHelmCodes(t);return new RegExp(wt(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=wt(Array.from(new Set(Object.values(e.phosphateBackbone))).sort(yt));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: ${t}`)}isHelm(t){return t===lt.HELM}getFormatCodes(t){const e=this.getFormatToHelmDict(t);return Object.keys(e).sort(yt)}getNonHelmFormatRegExp(t){const e=this.getCodesByFormat(t);return new RegExp(wt(e)+"|\\([^()]*\\)|.","g")}}function wt(t){return t.map((t=>t.replace(/[.*+?^${}()|[\]\\]/g,"\\$&"))).map((t=>t.includes("(")||t.includes(")")?t:`(?<!\\([^()]*)${t}(?![^()]*\\))`)).join("|")}const At={LEFT:"RNA1{",RIGHT:"}$$$$"};class Ct{constructor(t,e,n){this.sequence=t,this.sourceFormat=e,this.th=n,this.formats=new bt(this.th)}convertTo(t){const e=this.formats.getFormatNames();if(this.sourceFormat===lt.HELM&&e.includes(t))return this.helmToFormat(this.sequence,t);if(e.includes(this.sourceFormat)&&t===lt.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} -> ${t}`)}helmToFormat(t,e){const n=new RegExp(wt(Object.values(At)),"g");let r=t.replace(n,"");const i=this.formats.getHelmToFormatDict(e),s=this.formats.getTargetFormatHelmCodes(e),o=this.formats.getTargetFormatHelmCodesRegExp(e);return r=r.replace(o,(t=>s.includes(t)?i[t]:"p"===t||"."===t?t:"?")).replace(/\?+/g,vt).replace(/p\.|\./g,""),r=r.replace(/<empty>/g,""),r=r.replace(/\/\//g,"/"),r}formatToHelm(t,e){const n=this.formats.getFormatToHelmDict(e),r=this.formats.getCodesByFormat(e),i=this.formats.getFormatRegExp(e),s=this.formats.getPhosphateHelmCodesRegExp(e);let o=t?t.replace(i,(t=>r.includes(t)?n[t]+".":"?")):"";return o=o.replace(/\?+/g,`${vt}.`),o=o.slice(0,-1),"p"===o[o.length-1]&&(o=o.slice(0,-1)),o=o.replace(s,((t,e)=>e)),o=o.replace(/<empty>/g,""),`${At.LEFT+o+At.RIGHT}`}}class xt{constructor(t,e){this.sequence=t,this.th=e,this.libWrapper=this.th.monomerLibWrapper,this.formats=Object.keys(this.th.jsonData.codesToHelmDict)}getFormat(){if(this.sequence.startsWith("RNA"))return lt.HELM;const t=this.getListOfPossibleSynthesizersByFirstMatchedCode();if(0===t.length)return null;const e=this.th.createSequenceValidator(this.sequence),n=Array(t.length).fill(0);for(let r=0;r<t.length;++r){const i=t[r];n[r]=e.getInvalidCodeIndex(i)}const r=n.some((t=>-1===t))?-1:Math.max(...n);return t[n.indexOf(r)]}getListOfPossibleSynthesizersByFirstMatchedCode(){const t=this.sequence,e=[];for(const n of this.formats){const r=ct(this.libWrapper.getCodesByFormat(n));let i=0;for(let e=0;e<t.length;e++)if(")"===t[e]&&e!==t.length-1){i=e+1;break}r.some((e=>e===t.slice(i,i+e.length)))&&e.push(n)}return e}}const _t=ui,St=$;var Et=n.n(St);function Tt(t,e){let n=0;const r=e.createFormatDetector(t).getFormat();null!==r&&(n=new dt(t,e).getInvalidCodeIndex(r));const i=n<0||""===t,s=_t.span([]);Et()(s).css("-webkit-text-fill-color","var(--grey-6)");const o=_t.span([]);return Et()(o).css("-webkit-text-fill-color","red"),i?s.innerHTML=t:(s.innerHTML=t.slice(0,n),o.innerHTML=t.slice(n)),[s,o]}class It 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(){super(),this.highlightInvalidSubsequence=t=>Tt(t,this)}async initLibData(){return this.initPromise||(this.initPromise=(async()=>{let e=(await this.getSettings()).MonomersPath;e&&await t.dapi.files.exists(e)||(yr.logger.warning(`Monomers path '${e}' not found. Fallback to monomers sample path '${rt}'.`),e=rt),[this._jsonData,this._monomerLib]=await Promise.all([gt(e),Nt(e)]),this._monomerLibWrapper=new mt(this.monomerLib,this.jsonData)})()),this.initPromise}async getTranslationHelper(){return await t.functions.call(`${this.name}:getTranslationHelper`)}createSequenceValidator(t){return new dt(t,this)}createFormatConverter(t,e){return new Ct(t,e,this)}createFormatDetector(t){return new xt(t,this)}}async function Nt(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 Ot{constructor(t,e){this.appName=t,this.parentAppName=e}async getAppView(){const n=e.TaskBarProgressIndicator.create(`Loading ${this.appName}...`),r=t.shell.v?.root;r&&_t.setUpdateIndicator(r,!0);try{return await this.constructView()}finally{n.close(),r&&_t.setUpdateIndicator(r,!1)}}}class Mt extends Ot{constructor(t){super(t),this.view=e.View.create(),this.configureView()}async constructView(){await this.initView();const t=this.parentAppName?this.parentAppName+"/"+this.appName:this.appName;return this.view.path=`/apps/${yr.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 Lt=["SS","AS"],Bt={SS:"Sense strand",AS:"Anti sense"},Pt=["3'","5'"],Rt="OligoToolkit";var Dt,Ft,Ut;!function(t){t.IS_ANTISENSE_STRAND_INCLUDED="isAntisenseStrandIncluded",t.NUCLEOTIDE_SEQUENCES="nucleotideSequences",t.PHOSPHOROTHIOATE_LINKAGE_FLAGS="phosphorothioateLinkageFlags",t.STRAND_TERMINUS_MODIFICATIONS="strandTerminusModifications"}(Dt||(Dt={})),function(t){t.PATTERN_NAME="patternName",t.PATTERN_COMMENT="patternComment",t.NUCLEOTIDES_WITH_NUMERIC_LABELS="nucleotidesWithNumericLabels"}(Ft||(Ft={})),function(t){t.PATTERN_CONFIG="patternConfig",t.AUTHOR_ID="authorID"}(Ut||(Ut={}));const kt=[Dt.IS_ANTISENSE_STRAND_INCLUDED,Dt.NUCLEOTIDE_SEQUENCES,Dt.PHOSPHOROTHIOATE_LINKAGE_FLAGS,Dt.STRAND_TERMINUS_MODIFICATIONS],Ht=(Ft.PATTERN_NAME,Ft.PATTERN_COMMENT,Ft.NUCLEOTIDES_WITH_NUMERIC_LABELS,Ut.PATTERN_CONFIG,Ut.AUTHOR_ID,{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:""});class $t extends Error{constructor(t){super(t),this.name="PatternNameExistsError"}}class jt extends Error{constructor(t){super(t),this.name="PatternExistsError"}}var Vt=n(802),qt=n.n(Vt);class Gt{constructor(t){this.th=t,this.otherUsersPatternNameToHash=new Map,this.currentUserPatternNameToHash=new Map}static async getInstance(){const t=await yr.getTranslationHelper(),e=new Gt(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 $t(`Pattern with name ${t} already exists`)}validatePatternUniqueness(t){if(Array.from(this.currentUserPatternNameToHash.values()).concat(Array.from(this.otherUsersPatternNameToHash.values())).includes(t))throw new jt(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 getPatternRecord(e){if(null===e||""===e)return null;try{const n=await t.dapi.userDataStorage.getValue(Rt,e,!1);return JSON.parse(n)}catch{return null}}async getPatternConfig(t){if(""===t||null===t)return null;const e=await this.getPatternRecord(t);return null===e?null:e[Ut.PATTERN_CONFIG]}getDefaultPatternRecord(){const t=Ht;return t[Ut.AUTHOR_ID]=this.currentUserId,t}getDefaultPatternConfig(){return Ht[Ut.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){const n={[Ut.PATTERN_CONFIG]:e,[Ut.AUTHOR_ID]:await t.dapi.users.current().then((t=>t.id))};return JSON.stringify(n)}getHash(t){const e=kt.reduce(((e,n)=>(e[n]=t[n],e)),{});return qt().sha1(e)}async savePatternToUserStorage(e){const n=e.getPatternConfig();try{const r=this.getHash(n);this.validatePatternUniqueness(r);const i=n[Ft.PATTERN_NAME];this.validatePatternNameUniqueness(i);const s=await this.getRecordFromPattern(n);await t.dapi.userDataStorage.postValue(Rt,r,s,!1),this.currentUserPatternNameToHash.set(i,r),e.selectAuthor(this.getCurrentUserAuthorshipCategory()),e.updatePatternList()}catch(t){if(t instanceof $t||t instanceof jt)throw t;console.error("Error while saving pattern to user storage",t)}}async overwritePatternInUserStorage(e){const n=e.getPatternConfig(),r=this.getHash(n),i=n[Ft.PATTERN_NAME],s=await this.getRecordFromPattern(n);await t.dapi.userDataStorage.postValue(Rt,r,s,!1),this.currentUserPatternNameToHash.set(i,r),e.updatePatternList()}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(Rt,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(Rt,!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=Ht[Ut.PATTERN_CONFIG];this.currentUserPatternNameToHash.set(t[Ft.PATTERN_NAME],"")}async extractDataFromRecordToMaps(e,n,r){const i=JSON.parse(n),s=i[Ut.PATTERN_CONFIG].patternName,o=i[Ut.AUTHOR_ID];if(this.isCurrentUserId(o))this.currentUserPatternNameToHash.set(s,e);else{if(!r.has(o)){const e=(await t.dapi.users.find(o)).friendlyName;r.set(o,e)}const n=s+` (created by ${r.get(o)})`;this.otherUsersPatternNameToHash.set(n,e)}}getDefaultPatternName(){return Ht[Ut.PATTERN_CONFIG][Ft.PATTERN_NAME]}getCurrentUserAuthorshipCategory(){return this.currentUserName+" (me)"}getOtherUsersAuthorshipCategory(){return"Other users"}isCurrentUserId(t){return t===this.currentUserId}}const Wt=rxjs,zt=rxjs.operators;function Yt(t){return t.endsWith("(o)")}function Kt(t){const e=Object.values(t).flat().reduce(((t,e)=>(t[e]=(t[e]||0)+1,t)),{});return Object.entries(e).reduce(((t,e)=>t[1]>e[1]?t:e),["",0])[0]}var Qt;function Jt(t){const e=Array.from(new Set(t));return Array.from(e).sort(((t,e)=>t.toLowerCase().localeCompare(e.toLowerCase())))}!function(t){t.getTruncatedStrandData=function(t,e,n){return{nucleotides:t.slice(0,n),ptoFlags:e.slice(0,n+1)}},t.getExtendedStrandData=function(t,e,n,r){const i=n-t.length,s=t.concat(new Array(n-t.length).fill(r)),o=0===t.length?n+1:i;return{nucleotides:s,ptoFlags:e.concat(new Array(o).fill(!0))}}}(Qt||(Qt={}));var Xt=n(543),Zt=n.n(Xt);class te{constructor(t,e){this.dataManager=t,this._patternListUpdated$=new Wt.Subject,this._patternLoadRequested$=new Wt.Subject,this._patternLoaded$=new Wt.Subject,this._uniqueNucleotides$=new Wt.BehaviorSubject([]),this._patternDeletionRequested$=new Wt.Subject,this._tableSelection$=new Wt.BehaviorSubject(null),this._svgSaveRequested$=new Wt.Subject,this._loadPatternInNewTabRequested$=new Wt.Subject,this._urlStateUpdated$=new Wt.Subject,this._patternHasUnsavedChanges$=new Wt.BehaviorSubject(!1),this._selectedStrandColumn=new Wt.BehaviorSubject(null),this._selectedIdColumn=new Wt.BehaviorSubject(null),this.initializeAuthorSelection(e),this.initializePatternState(e),this._lastLoadedPatternConfig=new Wt.BehaviorSubject(Zt().cloneDeep(this.getPatternConfig())),this.setupSubscriptions()}setupSubscriptions(){this._nucleotideSequences$.subscribe((()=>{this.updateUniqueNucleotides(),this.updateSequenceBase()})),this._isAntisenseStrandActive$.subscribe((t=>{t||Pt.forEach((t=>{this.updateTerminusModification("AS",t,"")}))})),this.patternStateChanged$.pipe((0,zt.debounceTime)(20)).subscribe((()=>{const t=this._lastLoadedPatternConfig.getValue(),e=this.getPatternConfig(),n=!Zt().isEqual(e,t);this._patternHasUnsavedChanges$.next(n)}))}updateUniqueNucleotides(){const t=(e=this._nucleotideSequences$.getValue(),Jt(Object.values(e).flat()));var e;this._uniqueNucleotides$.next(t)}updateSequenceBase(){const t=Kt(this._nucleotideSequences$.getValue());this._sequenceBase$.next(t)}get nucleotideSequencesChanged$(){return this._nucleotideSequences$.asObservable()}initializeAuthorSelection(t){const e=t[Ut.AUTHOR_ID];this.dataManager.isCurrentUserId(e)?this._patternAuthorSelection$=new Wt.BehaviorSubject(this.dataManager.getCurrentUserAuthorshipCategory()):this._patternAuthorSelection$=new Wt.BehaviorSubject(this.dataManager.getOtherUsersAuthorshipCategory())}initializePatternState(t){const e=t[Ut.PATTERN_CONFIG];this._patternName$=new Wt.BehaviorSubject(e[Ft.PATTERN_NAME]),this._isAntisenseStrandActive$=new Wt.BehaviorSubject(e[Dt.IS_ANTISENSE_STRAND_INCLUDED]),this._nucleotideSequences$=new Wt.BehaviorSubject(e[Dt.NUCLEOTIDE_SEQUENCES]),this._phosphorothioateLinkageFlags=new Wt.BehaviorSubject(e[Dt.PHOSPHOROTHIOATE_LINKAGE_FLAGS]),this._terminalModifications=new Wt.BehaviorSubject(e[Dt.STRAND_TERMINUS_MODIFICATIONS]),this._comment$=new Wt.BehaviorSubject(e[Ft.PATTERN_COMMENT]),this._modificationsWithNumericLabels$=new Wt.BehaviorSubject(e[Ft.NUCLEOTIDES_WITH_NUMERIC_LABELS]),this._sequenceBase$=new Wt.BehaviorSubject(Kt(e[Dt.NUCLEOTIDE_SEQUENCES]))}getPatternName(){return this._patternName$.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$.next(t)}updateStrandLength(t,e){const n=this.getNucleotideSequences()[t];if(n.length===e)return;const r=this.getPhosphorothioateLinkageFlags()[t];if(0===e)return void this.setNewStrandData([],[],t);if(n.length>e){const{nucleotides:i,ptoFlags:s}=Qt.getTruncatedStrandData(n,r,e);return void this.setNewStrandData(i,s,t)}const i=this.getSequenceBase(),{nucleotides:s,ptoFlags:o}=Qt.getExtendedStrandData(n,r,e,i);this.setNewStrandData(s,o,t)}setNewStrandData(t,e,n){this.updateNucleotideSequences({...this.getNucleotideSequences(),[n]:t}),this.updatePhosphorothioateLinkageFlags({...this.getPhosphorothioateLinkageFlags(),[n]:e})}getPhosphorothioateLinkageFlags(){return this._phosphorothioateLinkageFlags.getValue()}updatePhosphorothioateLinkageFlags(t){this._phosphorothioateLinkageFlags.next(t)}get phosphorothioateLingeFlagsChanged$(){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 Jt(t).filter((t=>!Yt(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$.getValue(),n={};Lt.forEach((r=>{n[r]=e[r].map((()=>t))})),this._nucleotideSequences$.next(n);const r=this._modificationsWithNumericLabels$.getValue();r.includes(t)||this.updateModificationsWithNumericLabels(r.concat(t))}get patternStateChanged$(){return Wt.merge(this._patternName$.pipe((0,zt.debounceTime)(300),(0,zt.map)((()=>{}))),this._isAntisenseStrandActive$,this._nucleotideSequences$,this._phosphorothioateLinkageFlags,this._terminalModifications,this._comment$.pipe((0,zt.debounceTime)(300)),this._modificationsWithNumericLabels$)}getSequenceBase(){return this._sequenceBase$.getValue()}uniqueNucleotidesChanged$(){return this.patternStateChanged$.pipe((0,zt.switchMap)((()=>this._uniqueNucleotides$)))}getUniqueNucleotides(){return this._uniqueNucleotides$.getValue()}get svgSaveRequested$(){return this._svgSaveRequested$.asObservable()}requestSvgSave(){this._svgSaveRequested$.next()}setAllPTOLinkages(t){const e=this.getPhosphorothioateLinkageFlags();Lt.forEach((n=>{e[n]=e[n].map((()=>t))})),this.updatePhosphorothioateLinkageFlags(e)}setPatternConfig(t){this._patternName$.next(t[Ft.PATTERN_NAME]),this._isAntisenseStrandActive$.next(t[Dt.IS_ANTISENSE_STRAND_INCLUDED]),this._nucleotideSequences$.next(t[Dt.NUCLEOTIDE_SEQUENCES]),this._phosphorothioateLinkageFlags.next(t[Dt.PHOSPHOROTHIOATE_LINKAGE_FLAGS]),this._terminalModifications.next(t[Dt.STRAND_TERMINUS_MODIFICATIONS]),this._comment$.next(t[Ft.PATTERN_COMMENT]),this._modificationsWithNumericLabels$.next(t[Ft.NUCLEOTIDES_WITH_NUMERIC_LABELS])}setLastLoadedPatternConfig(t){this._lastLoadedPatternConfig.next(Zt().cloneDeep(t))}getPatternConfig(){return{[Ft.PATTERN_NAME]:this.getPatternName(),[Dt.IS_ANTISENSE_STRAND_INCLUDED]:this.isAntisenseStrandActive(),[Dt.NUCLEOTIDE_SEQUENCES]:this.getNucleotideSequences(),[Dt.PHOSPHOROTHIOATE_LINKAGE_FLAGS]:this.getPhosphorothioateLinkageFlags(),[Dt.STRAND_TERMINUS_MODIFICATIONS]:this.getTerminalModifications(),[Ft.PATTERN_COMMENT]:this.getComment(),[Ft.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$(){return Wt.merge(this._isAntisenseStrandActive$.asObservable().pipe((0,zt.map)((()=>{}))),this._nucleotideSequences$.asObservable().pipe((0,zt.map)((()=>{}))),this._patternLoaded$.asObservable().pipe((0,zt.map)((()=>{})))).pipe((0,zt.debounceTime)(10))}get strandsLinkagesAndTerminalsUpdated$(){return Wt.merge(this.strandsUpdated$,this._phosphorothioateLinkageFlags.asObservable().pipe((0,zt.map)((()=>{}))),this._terminalModifications.asObservable().pipe((0,zt.map)((()=>{}))))}updateControlsUponPatternLoaded(t){this._patternLoaded$.next(t)}get patternLoaded$(){return this._patternLoaded$.asObservable()}get userSelection$(){return this._patternAuthorSelection$.asObservable().pipe((0,zt.skip)(1))}selectAuthor(t){this._patternAuthorSelection$.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$.pipe((0,zt.debounceTime)(100))}}const ee="pattern";class ne{constructor(){this.urlSearchParams=new URLSearchParams(window.location.search)}subscribeToObservables(t){t.urlStateUpdated$.subscribe((t=>this.setPatternURL(t))),t.loadPatternInNewTabRequested$.subscribe((t=>{const e=`${window.location.origin}${window.location.pathname}?${ee}=${t}`;window.open(e,"_blank")})),window.addEventListener("popstate",(()=>{this.urlSearchParams=new URLSearchParams(window.location.search);const e=this.getPatternHash();null!==e&&t.requestPatternLoad(e)}))}getPatternHash(){return this.urlSearchParams.get(ee)}setPatternURL(t){null!==t&&""!==t?(this.urlSearchParams.set(ee,t),window.history.pushState({},"",`${window.location.pathname}?${this.urlSearchParams}`)):this.clearPatternURL()}clearPatternURL(){this.urlSearchParams.delete(ee),window.history.pushState({},"",`${window.location.pathname}`)}}var re=n(72),ie=n.n(re),se=n(825),oe=n.n(se),ae=n(659),ue=n.n(ae),le=n(56),ce=n.n(le),he=n(540),fe=n.n(he),de=n(113),pe=n.n(de),ge=n(252),me={};me.styleTagTransform=pe(),me.setAttributes=ce(),me.insert=ue().bind(null,"head"),me.domAPI=oe(),me.insertStyleElement=fe(),ie()(ge.A,me),ge.A&&ge.A.locals&&ge.A.locals;class ve{constructor(t){this.eventBus=t,this.columnControlsContainer=_t.div([]),this.eventBus.tableSelectionChanged$.subscribe((()=>this.handleTableChoice())),this.refreshColumnControls()}getColumnControlsContainer(){return this.columnControlsContainer}get selectedTable(){return this.eventBus.getTableSelection()}handleTableChoice(){this.refreshColumnControls()}refreshColumnControls(){Et()(this.columnControlsContainer).empty(),Et()(this.columnControlsContainer).append(this.constructColumnControls())}constructColumnControls(){const t=this.createStrandColumnInput(),e=t.SS,n=t.AS;this.eventBus.antisenseStrandToggled$.subscribe((t=>{Et()(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(Lt.map((e=>{const n=_t.choiceInput(`${Bt[e]} column`,t[0],t,(t=>this.eventBus.selectStrandColumn(e,t)));return this.eventBus.selectStrandColumn(e,t[0]),[e,n.root]})))}createIdColumnInput(){const t=this.selectedTable?this.selectedTable.columns.names():[],e=_t.choiceInput("ID column",t[0],t,(t=>this.eventBus.selectIdColumn(t)));return this.eventBus.selectIdColumn(t[0]),e.root}}class ye{constructor(t){this.eventBus=t,this.availableTables=[],this.tableInputContainer=_t.div([]),this.subscribeToTableEvents(),this.refreshTableInput()}getTableInputContainer(){return this.tableInputContainer}subscribeToTableEvents(){t.events.onTableAdded.subscribe((t=>this.handleTableAdded(t))),t.events.onTableRemoved.subscribe((t=>this.handleTableRemoved(t))),this.eventBus.tableSelectionChanged$.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();Et()(this.tableInputContainer).empty(),this.tableInputContainer.append(t.root)}createTableInput(){const t=this.eventBus.getTableSelection();return _t.tableInput("Tables",t,this.availableTables,(t=>{null!==t&&t instanceof e.DataFrame&&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}}class be{constructor(t){this.eventBus=t,this.tableInputManager=new ye(t),this.columnInputManager=new ve(t)}createControls(){const t=_t.h1("Bulk convert"),e=this.tableInputManager.getTableInputContainer(),n=this.columnInputManager.getColumnControlsContainer(),r=_t.bigButton("Convert",(()=>this.processConvertButtonClick()));return[t,e,n,_t.buttonsInput([r])]}processConvertButtonClick(){!function(e){const n=e.getTableSelection();if(!n)return void t.shell.warning("Please select a table");const r=Lt.filter((t=>!("AS"===t&&!e.isAntisenseStrandActive()))).map((t=>e.getSelectedStrandColumn(t))).filter((t=>t));if(0===r.length)return void t.shell.warning("Please column for sense strand");const i=e.getSelectedIdColumn();if(!i)throw new Error("No ID column selected");n.getCol(i),r.map((t=>n.getCol(t)))}(this.eventBus)}}class we{constructor(t,e,n){this.eventBus=t,this.initialPatternConfig=e,this.subscriptions=n}create(){return _t.divV([_t.h1("PTO"),_t.divH([this.createAllPtoActivationInput().root,...this.createFirstPtoInputs().map((t=>t.root))],{style:{gap:"12px"}})])}areAllPtoLinkagesSet(t){return Lt.map((e=>t[e].filter((t=>t)).length)).reduce(((t,e)=>t+e),0)===Lt.map((t=>this.initialPatternConfig.nucleotideSequences[t].length)).reduce(((t,e)=>t+e),0)+Lt.filter((e=>t[e].length)).length}createAllPtoActivationInput(){const t=this.initialPatternConfig.phosphorothioateLinkageFlags,e=this.areAllPtoLinkagesSet(t),n=_t.boolInput("All PTO",e);n.onInput((()=>{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),_t.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 Lt.map((t=>{if(!this.eventBus.isAntisenseStrandActive()&&"AS"===t)return;const e=this.isFirstPtoActive(t),n=_t.boolInput(`First ${t} PTO`,e);n.onInput((()=>{const e=n.value;this.eventBus.setPhosphorothioateLinkageFlag(t,0,e)}));const r=this.eventBus.phosphorothioateLingeFlagsChanged$.subscribe((e=>{const r=e[t][0];n.value=r}));return this.subscriptions.add(r),this.addStyleToPtoInput(n),_t.tooltip.bind(n.captionLabel,`Activate first phosphothioate in ${t}`),n})).filter((t=>void 0!==t))}isFirstPtoActive(t){return this.initialPatternConfig.phosphorothioateLinkageFlags[t][0]}}class Ae{constructor(t,e,n){this.eventBus=t,this.dataManager=e,this.subscriptions=n;const r=this.eventBus.nucleotideSequencesChanged$.subscribe((()=>{this.displayedInputLabels=this.computeDisplayedInputLabels()}));this.subscriptions.add(r)}create(){const t=Lt.map((t=>this.constructControlsPanel(t)));return _t.divH(t,{style:{gap:"24px"}})}constructControlsPanel(t){if(!this.eventBus.isAntisenseStrandActive()&&"AS"===t)return _t.div([]);const e=this.constructHeader(),n=this.createControls(t);return _t.block([_t.h1(`${Bt[t]}`),e,n],{style:{paddingTop:"12px"}})}constructHeader(){return _t.divH([_t.div([_t.divText("#")],{style:{width:"20px"}}),_t.block75([_t.divText("Modification")]),_t.div([_t.divText("PTO")])])}createControls(t){const e=this.createNucleobaseInputs(t),n=this.createLabelDivs(t),r=this.createPTOFlagInputs(t);return _t.div(e.map(((t,e)=>_t.divH([n[e],_t.block75([t.root]),r[e].root],{style:{alignItems:"center"}}))))}createNucleobaseInputs(t){const e=this.dataManager.fetchAvailableNucleotideBases().sort(((t,e)=>t.toLowerCase().localeCompare(e.toLowerCase())));return this.eventBus.getNucleotideSequences()[t].map(((n,r)=>{const i=_t.choiceInput("",n,e);return i.onInput((()=>{const e=i.value;this.eventBus.setNucleotide(t,r,e)})),i}))}createPTOFlagInputs(t){return this.eventBus.getPhosphorothioateLinkageFlags()[t].slice(1).map(((e,n)=>{const r=_t.boolInput("",e);r.onInput((()=>{const e=r.value;this.eventBus.setPhosphorothioateLinkageFlag(t,n+1,e)}));const i=this.eventBus.phosphorothioateLingeFlagsChanged$.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 Lt.forEach((n=>{let r=1;const i=t[n].map((t=>{if(Yt(t))return"";const e=String(r);return r++,e}));e.set(n,i)})),e}createLabelDivs(t){const e=this.createLabels(t).map((t=>_t.div([t],{style:{width:"20px"}}))),n=this.eventBus.nucleotideSequencesChanged$.subscribe((()=>{this.createLabels(t).forEach(((t,n)=>{Et()(e[n]).empty(),Et()(e[n]).append(t)}))}));return this.subscriptions.add(n),e}createLabels(t){return this.eventBus.getNucleotideSequences()[t].map(((e,n)=>{const r=this.displayedInputLabels.get(t)[n];return _t.label(r)}))}}class Ce{constructor(){this.rxjsSubscriptions=[],this.dgSubscriptions=[]}add(t){t instanceof Wt.Subscription?this.rxjsSubscriptions.push(t):this.dgSubscriptions.push(t)}unsubscribeAll(){for(const t of[this.rxjsSubscriptions,this.dgSubscriptions])t.forEach((t=>t.unsubscribe())),t.length=0}}class xe{constructor(t,e){this.eventBus=t,this.dataManager=e,this.subscriptions=new Ce}static open(t,e){xe.isDialogOpen||(xe.instance||(xe.instance=new xe(t,e)),xe.instance.openDialog())}openDialog(){this.initialPatternConfig=Zt().cloneDeep(this.eventBus.getPatternConfig()),xe.isDialogOpen=!0,this.createDialog().show()}createDialog(){const t=_t.divV([]);this.subscriptions.add(this.eventBus.strandsUpdated$.subscribe((()=>this.onStrandsUpdated(t))));const e=_t.dialog("Edit strands").add(t).onOK((()=>{})).onCancel((()=>this.resetToInitialState()));return this.subscriptions.add(e.onClose.subscribe((()=>{xe.isDialogOpen=!1,this.subscriptions.unsubscribeAll()}))),e}onStrandsUpdated(t){const e=new we(this.eventBus,this.initialPatternConfig,this.subscriptions).create(),n=new Ae(this.eventBus,this.dataManager,this.subscriptions).create();Et()(t).empty(),Et()(t).append(e,n)}resetToInitialState(){this.eventBus.setPatternConfig(this.initialPatternConfig)}}xe.isDialogOpen=!1;class _e{constructor(t){this.eventBus=t,this.subscriptions=new Ce}static open(t){_e.isDialogOpen||(_e.instance||(_e.instance=new _e(t)),_e.instance.openDialog())}openDialog(){this.initialPatternConfig=Zt().cloneDeep(this.eventBus.getPatternConfig()),_e.isDialogOpen=!0,this.createDialog().show()}createDialog(){const t=_t.divV([]);this.subscriptions.add(this.eventBus.strandsUpdated$.subscribe((()=>this.onStrandsUpdated(t))));const e=_t.dialog("Edit terminal modifications").add(t).onOK((()=>{})).onCancel((()=>this.resetToInitialState()));return this.subscriptions.add(e.onClose.subscribe((()=>{_e.isDialogOpen=!1,this.subscriptions.unsubscribeAll()}))),e}onStrandsUpdated(t){const e=new Se(this.eventBus).create();Et()(t).empty(),Et()(t).append(e)}resetToInitialState(){this.eventBus.setPatternConfig(this.initialPatternConfig)}}_e.isDialogOpen=!1;class Se{constructor(t){this.eventBus=t}create(){const t=Lt.map((t=>this.constructControlsPanel(t)));return _t.divH(t,{style:{gap:"24px"}})}constructControlsPanel(t){if(!this.eventBus.isAntisenseStrandActive()&&"AS"===t)return _t.div([]);const e=this.createInputs(t);return _t.block([_t.h1(`${Bt[t]}`),e],{style:{paddingTop:"12px"}})}createInputs(t){const e=("SS"===t?[...Pt].reverse():Pt).map((e=>this.createInputForTerminus(t,e)));return _t.form(e)}createInputForTerminus(t,e){const n=this.eventBus.getTerminalModifications()[t][e],r=_t.textInput(e,n);return this.applyStylingToInput(r),r.onInput((()=>{const n=r.value;null!==n&&this.eventBus.updateTerminusModification(t,e,n)})),r}applyStylingToInput(t){const e=t.root.getElementsByTagName("textarea")[0];Et()(e).css("resize","none")}}class Ee{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,s=this.createPatternCommentInput().root,o=this.createPatternNameInputBlock(),a=this.createEditPatternButton(),u=this.createEditTerminalModificationsButton();return[_t.h1("Edit"),t,n,r,i,o,s,_t.buttonsInput([u,a])]}createEditPatternButton(){const t=_t.button("Edit strands",(()=>xe.open(this.eventBus,this.dataManager)));return _t.tooltip.bind(t,"Edit strand modifications and PTOs"),t}createEditTerminalModificationsButton(){const t=_t.button("Edit terminals",(()=>_e.open(this.eventBus)));return _t.tooltip.bind(t,"Edit terminal modifications"),Et()(t).css("margin-right","20px"),t}createAntisenseStrandToggle(){const t=_t.switchInput(`${Bt.AS} strand`,this.eventBus.isAntisenseStrandActive());return t.onInput((()=>this.eventBus.toggleAntisenseStrand(t.value))),this.eventBus.patternLoaded$.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=_t.intInput(`${Bt[t]} length`,e);return r.onInput((()=>n(t,r))),this.eventBus.nucleotideSequencesChanged$.subscribe((()=>{r.value=this.eventBus.getNucleotideSequences()[t].length})),r.setTooltip(`Number of nucleotides in ${t}, including overhangs`),[t,r]},n=(e,n)=>{const r=n.value;null!==r&&(r<=0&&(t.shell.warning("Sequence length must be greater than 0"),n.value=1),r>34&&(t.shell.warning("Sequence length must be less than 35"),n.value=34),this.eventBus.updateStrandLength(e,n.value))},r=Object.fromEntries(Lt.map((t=>e(t))));return this.eventBus.antisenseStrandToggled$.subscribe((t=>{Et()(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=_t.choiceInput("Sequence basis",e,t);return n.onInput((()=>this.eventBus.replaceSequenceBase(n.value))),this.eventBus.nucleotideSequencesChanged$.subscribe((()=>{n.value=this.eventBus.getSequenceBase()})),n.setTooltip("Most frequent nucleobase in the strands"),n}createPatternCommentInput(){const t=_t.textInput("Comment",this.eventBus.getComment());return Et()(t.root).addClass("st-pattern-text-input"),t.onInput((()=>this.eventBus.updateComment(t.value))),this.eventBus.patternLoaded$.subscribe((()=>{t.value=this.eventBus.getComment()})),t}createPatternNameInputBlock(){const t=_t.textInput("Pattern name",this.eventBus.getPatternName());return Et()(t.root).addClass("st-pattern-text-input"),t.onInput((()=>this.eventBus.updatePatternName(t.value))),this.eventBus.patternLoaded$.subscribe((()=>{t.value=this.eventBus.getPatternName()})),t.setTooltip("Name under which pattern will be saved"),t.root}}class Te{constructor(t,e){this.eventBus=t,this.dataManager=e,this.subscriptions=new Ce,this.authorSelectedByUser=!1,this.eventBus.patternLoadRequested$.subscribe((t=>this.handlePatternChoice(t))),this.eventBus.patternDeletionRequested$.subscribe((async t=>{await this.dataManager.deletePattern(t,this.eventBus)}))}async handlePatternChoice(t){let e=await this.dataManager.getPatternConfig(t);null===e&&(e=this.dataManager.getDefaultPatternConfig()),this.eventBus.setPatternConfig(e),this.eventBus.updateControlsUponPatternLoaded(t),this.eventBus.setLastLoadedPatternConfig(e)}isCurrentUserSelected(){return this.eventBus.getSelectedAuthor()!==this.dataManager.getOtherUsersAuthorshipCategory()}createControls(){const t=this.getPatternInputsContainer();return[_t.h1("Load"),t]}getPatternInputsContainer(){const t=_t.divH(this.createPatternInputs());return this.eventBus.patternListUpdated$.subscribe((()=>{this.subscriptions.unsubscribeAll(),Et()(t).empty(),Et()(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=_t.div([t.root]),n=this.eventBus.userSelection$.subscribe((()=>{Et()(e).empty(),Et()(e).append(this.createPatternChoiceInput().root)}));return this.subscriptions.add(n),e}createAuthorChoiceInput(){const t=[this.dataManager.getCurrentUserAuthorshipCategory()];this.dataManager.getOtherUsersPatternNames().length>0&&t.push(this.dataManager.getOtherUsersAuthorshipCategory());const e=_t.choiceInput("Author",this.eventBus.getSelectedAuthor(),t,(t=>{this.authorSelectedByUser=!0,this.eventBus.selectAuthor(t)}));return this.setAuthorChoiceInputStyle(e),e.setTooltip("Select pattern author"),e}setAuthorChoiceInputStyle(t){Et()(t.input).css({"max-width":"100px","min-width":"100px"}),Et()(t.root).css({"padding-right":"30px","padding-left":"30px"})}createPatternChoiceInput(){const t=this.isCurrentUserSelected()?this.dataManager.getCurrentUserPatternNames():this.dataManager.getOtherUsersPatternNames();if(this.authorSelectedByUser){const e=this.dataManager.getPatternHash(t[0],this.isCurrentUserSelected());this.eventBus.requestPatternLoad(e),this.eventBus.updateUrlState(e),this.authorSelectedByUser=!1}const e=this.getPatternName(t),n=_t.choiceInput("Pattern",e,t);return n.setTooltip("Select pattern to load"),Et()(n.input).css({"max-width":"100px","min-width":"100px"}),this.subscriptions.add(n.onInput((()=>{const t=this.dataManager.getPatternHash(n.value,this.isCurrentUserSelected());this.eventBus.requestPatternLoad(t),this.eventBus.updateUrlState(t)}))),this.subscriptions.add(this.eventBus.patternLoaded$.subscribe((()=>{const e=this.eventBus.getPatternName();n.value!==e&&(n.value=this.getPatternName(t))}))),n}getPatternName(t){return t.find((t=>t===this.eventBus.getPatternName()))??t[0]}createDeletePatternButton(){const e=_t.button(_t.iconFA("trash-alt"),(()=>{this.eventBus.getPatternName()!==this.dataManager.getDefaultPatternName()?this.showDeletePatternDialog():t.shell.warning("Cannot delete example pattern")}));_t.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=_t.dialog("Delete pattern"),e=this.eventBus.getPatternName();t.add(_t.divText(`Are you sure you want to delete pattern ${e}?`)),t.onOK((()=>this.eventBus.requestPatternDeletion(e))),t.show()}}class Ie{constructor(t,e){this.eventBus=t,this.dataManager=e}getLayout(){const t=new Te(this.eventBus,this.dataManager),e=new Ee(this.eventBus,this.dataManager),n=new be(this.eventBus),r=t.createControls(),i=e.createControls(),s=n.createControls(),o=_t.div(r);Et()(o).css({"padding-bottom":"20px"});const a=_t.div([...i,...s],"ui-form"),u=_t.div([o,a]);return Et()(u).css({padding:"25px"}),_t.box(u,{style:{maxWidth:"450px"}})}}var Ne=n(146);class Oe{constructor(t,e,n){this.svgElementFactory=t,this.config=e,this.yShift=n}shiftElements(t){this.svgElements.forEach((e=>{const n=e.getAttribute("transform")||"",r=`translate(${t.x},${t.y})`;e.setAttribute("transform",`${n} ${r}`)}))}}class Me{constructor(){}static getInstance(){return Me.instance||(Me.instance=new Me,Me.instance.canvas=document.createElement("canvas")),Me.instance}static getTextDimensions(t,e){const n=Me.getInstance().canvas.getContext("2d");if(!n)throw new Error("Canvas 2D context is not available");return n.font=`${e}px Arial`,{width:1.1*n.measureText(t).width,height:1.1*e}}}function Le(t){const e=Object.keys(yr.jsonData.patternAppData)[0];if(!e)throw new Error(`No format found in '${it}'`);return yr.jsonData.patternAppData[e][t].color||""}class Be extends Oe{constructor(t,e,n){super(t,e,n);const r=Lt.filter((t=>e.nucleotideSequences[t].length>0));this.strands=r.map((t=>new Pe(this.svgElementFactory,e,n,t))),this.terminalModifications=r.map(((t,r)=>new De(this.svgElementFactory,e,n,t,this.strands[r]))),this.labels=r.map(((t,r)=>new Re(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 Pe extends Oe{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=>Yt(e)?null:(t++,t)))}get svgElements(){return this._svgElements}getStrandCircleYShift(){return Fe(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=Le(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(!ut.includes(n))return null;const r=function(t){return!Yt(t)&&ut.includes(t)?t:""}(n),i=function(t){const e=Le(t),n=e.match(/\d+/g)?.map(Number);if(!n||n.length<3)return"#ffffff";const[r,i,s]=n;return.299*r+.587*i+.114*s>186?"#333333":"#ffffff"}(n),s=this.getPositionForNucleotideLabel(t,e);return this.svgElementFactory.createTextElement(r,s,17,i)}getPositionForNucleotideLabel(t,e){const n=this.getNucleotideCircleCenterPosition(t,e),r=Me.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=Me.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 Re extends Oe{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=Me.getTextDimensions(e,17),r={x:10,y:Fe(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=Me.getTextDimensions(t,17),n={x:65+this.terminalModifications.getContentWidth()+5,y:Fe(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 De extends Oe{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 Me.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:Fe(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?Pt:Array.from(Pt).reverse()).map((t=>this.createTerminalModification(t)))}get svgElements(){return this._svgElements}getContentWidth(){return this.strandSvgWrapper.getContentWidth()+Pt.map((t=>this.getTerminalModificationTextDimensions(t).width)).reduce(((t,e)=>t+e),0)}getContentHeight(){return this.strandSvgWrapper.getContentHeight()}}function Fe(t,e){return"SS"===t?e+5+15+15:e+52+10+15}class Ue{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 s=i%2==0?6:3,o=i*e+n;return[t.x+Math.cos(o)*s,t.y+Math.sin(o)*s]}))}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 ke extends Oe{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 Me.getTextDimensions(this.titleText,17).width}getContentHeight(){return Me.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 He extends Oe{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,Le(t));e+=12;const i={y:this.yShift,x:e};return{elements:[r,this.svgElementFactory.createTextElement(t,i,15,"var(--grey-6)")],width:12+Me.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:s}=this.createLegendItem(r,t);n(s),e.push(i)})),{elements:e.flat(),width:t}}getContentHeight(){return 20}getContentWidth(){return this.width}}class $e{constructor(t){this.svgElementFactory=new Ue;const e=Zt().cloneDeep(t);let n=10;this.title=new ke(this.svgElementFactory,e,n),n+=this.title.getContentHeight(),this.strands=new Be(this.svgElementFactory,e,n),n+=this.strands.getContentHeight()+10,this.legend=new He(this.svgElementFactory,e,n)}renderPattern(){const t=this.getGlobalWidth(),e=this.getGlobalHeight(),n=this.svgElementFactory.createCanvas(t,e),r=[this.title,this.strands,this.legend].map((t=>t.svgElements)).flat();return n.append(...r),n}getGlobalWidth(){const t=[this.title,this.strands,this.legend];return Math.max(...t.map((t=>t.getContentWidth())))}getGlobalHeight(){return[this.title,this.strands,this.legend].reduce(((t,e)=>t+e.getContentHeight()),10)}}class je{constructor(t){this.eventBus=t,this.svgDisplayDiv=_t.div([]),t.updateSvgContainer$.subscribe((()=>this.updateSvgContainer())),t.svgSaveRequested$.subscribe((()=>this.saveSvgAsPng()))}static createSvgDiv(t){return new je(t).svgDisplayDiv}updateSvgContainer(){$(this.svgDisplayDiv).empty();const t=this.eventBus.getPatternConfig();this.svgElement=this.createSvg(t),this.svgDisplayDiv.append(this.svgElement)}createSvg(t){return new $e(t).renderPattern()}saveSvgAsPng(){const t=this.eventBus.getPatternName();Ne.saveSvgAsPng(this.svgElement,t,{backgroundColor:"white"})}}class Ve{constructor(t){this.eventBus=t,this.togglesContainer=_t.div([]),this.eventBus.uniqueNucleotidesChanged$().subscribe((()=>{this.updateContainer()}))}getContainer(){return this.togglesContainer}updateContainer(){Et()(this.togglesContainer).empty(),Et()(this.togglesContainer).append(this.createInputs())}createInputs(){const t=this.eventBus.getUniqueNucleotides().filter((t=>!Yt(t))).map((t=>this.createSingleInput(t)));return t.sort(((t,e)=>t.captionLabel.textContent.localeCompare(e.captionLabel.textContent))),_t.divH(t.map((t=>t.root)))}createSingleInput(t){const e=this.eventBus.getModificationsWithNumericLabels().includes(t),n=_t.boolInput(t,e,(e=>this.handleNumericLabelToggle(t,e)));return Et()(n.root).css("padding-right","20px"),n.setTooltip(`Show numeric labels for ${t}`),n}handleNumericLabelToggle(t,e){const n=this.eventBus.getModificationsWithNumericLabels();if(n.includes(t)===e)return;const r=e?n.concat(t):n.filter((e=>e!==t));this.eventBus.updateModificationsWithNumericLabels(r)}}class qe{constructor(t,e){this.eventBus=t,this.dataManager=e,this.subscriptions=new Ce}createContainer(){return _t.div([_t.h1("Translation example"),this.createTranslationExamples()],{style:{paddingTop:"20px"}})}createTranslationExamples(){const t=_t.divH([...this.getExampleElements()],"ui-form");return this.eventBus.antisenseStrandToggled$.subscribe((()=>{this.subscriptions.unsubscribeAll(),Et()(t).empty(),Et()(t).append(this.getExampleElements())})),t}getExampleElements(){return Lt.map((t=>new Ge(t,this.eventBus,this.subscriptions).create()))}}class Ge{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(),_t.block50([_t.h2(Bt[this.strand]),this.inputExample.root,this.outputExample.root],{style:{paddingRight:"20px"}})):_t.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 ${Bt[this.strand]}`),t}generateExampleSequence(){return this.eventBus.getNucleotideSequences()[this.strand].map(((t,e)=>ut[e%ut.length])).join("")}createOutputExample(t){const e=this.createTextInputForExamples();return e.value=this.computeOutputValue(t),e.setTooltip(`Pattern applied to the example input for ${Bt[this.strand]}`),e}computeOutputValue(t){const e=this.eventBus.getNucleotideSequences()[this.strand],n=this.eventBus.getTerminalModifications()[this.strand];return function(t,e,n,r){const i=function(t,e,n){const r=new Array(t.length+e.filter((t=>t)).length+Pt.length);r[0]=n["5'"],r[r.length-1]=n["3'"];let i=1;return e[0]&&(r[i]="ps",i++),t.forEach(((t,n)=>{r[n+i]=t,e[n+1]&&(r[n+i+1]="ps",i++)})),r}(t.split("").map(((t,n)=>{const r=function(t,e,n){const r=Object.keys(n.patternAppData)[0],i=n.patternAppData[r][e].substitution;return t.replace(/([AGCTU])/,i)}(t,e[n],yr.jsonData);return r})),n,r);return i.join("")}(t,e,this.eventBus.getPhosphorothioateLinkageFlags()[this.strand],n)}createTextInputForExamples(){const t=_t.textInput("","");return this.applyStylingToInput(t),t}applyStylingToInput(t){const e=t.root.getElementsByTagName("textarea")[0];e.setAttribute("readonly","true"),Et()(e).css("resize","none"),Et()(t.root).css("opacity","75%")}}class We{constructor(t,e){this.eventBus=t,this.dataManager=e,this.svgDisplay=je.createSvgDiv(t)}getLayout(){const t=new Ve(this.eventBus).getContainer(),e=this.generateDownloadControls(),n=new qe(this.eventBus,this.dataManager).createContainer();return _t.panel([this.svgDisplay,t,e,n],{style:{overflowX:"scroll",padding:"12px 24px"}})}generateDownloadControls(){return _t.divH([this.createSavePatternButton(),this.createDownloadPngButton(),this.createShareLinkButton()],{style:{gap:"12px",marginTop:"12px"}})}createDownloadPngButton(){const t=_t.button("Get PNG",(()=>this.eventBus.requestSvgSave()));return _t.tooltip.bind(t,"Download pattern as PNG"),t}createShareLinkButton(){const e=_t.button(_t.iconFA("link"),(()=>navigator.clipboard.writeText(window.location.href).then((()=>t.shell.info("Link to pattern copied to clipboard")))));return this.eventBus.patternHasUnsavedChanges$.subscribe((t=>{e.disabled=t})),_t.tooltip.bind(e,"Share pattern link"),e}createSavePatternButton(){const t=_t.button("Save",(()=>this.processSaveButtonClick()));return this.eventBus.patternHasUnsavedChanges$.subscribe((e=>{t.disabled=!e})),_t.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 $t?new ze(this.eventBus,this.dataManager).show():e instanceof jt?t.shell.warning(_t.div([_t.divText("Pattern already exists"),_t.button("Load",(()=>{const t=e.message;this.eventBus.requestLoadPatternInNewTab(t)}))])):console.error("Error while saving pattern",e)}}class ze{constructor(t,e){this.eventBus=t,this.dataManager=e}show(){const t=this.eventBus.getPatternName(),e=_t.dialog(`Pattern "${t}" already exists`);e.add(_t.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.overwritePatternInUserStorage(this.eventBus).then((()=>{t.shell.info(`Pattern ${e} overwritten`)})).catch((e=>{console.error("Error while overwriting pattern in user storage",e),t.shell.error("Error while overwriting pattern")}))}}class Ye extends Mt{constructor(t){super("Oligo Pattern"),this.th=t}getContent(){return async function(){const t=await Gt.getInstance(),e=new ne,n=await async function(t,e){const n=e.getPatternHash();if(!n)return e.clearPatternURL(),t.getDefaultPatternRecord();let r=await t.getPatternRecord(n);return r||(e.clearPatternURL(),r=t.getDefaultPatternRecord()),r}(t,e),r=new te(t,n);e.subscribeToObservables(r);const i=new Ie(r,t).getLayout(),s=new We(r,t).getLayout();return _t.splitH([i,s],{},!0)}()}}var Ke=n(507),Qe={};function Je(t){var e;return"string"==typeof t||t instanceof String?t:("object"==typeof t||t instanceof Object)&&"$thrownJsError"in t?Je(t.$thrownJsError):t instanceof Error?null!==(e=t.stack)&&void 0!==e?e:t.message:t.toString()}Qe.styleTagTransform=pe(),Qe.setAttributes=ce(),Qe.insert=ue().bind(null,"head"),Qe.domAPI=oe(),Qe.insertStyleElement=fe(),ie()(Ke.A,Qe),Ke.A&&Ke.A.locals&&Ke.A.locals;var Xe,Ze=n(74),tn={};tn.styleTagTransform=pe(),tn.setAttributes=ce(),tn.insert=ue().bind(null,"head"),tn.domAPI=oe(),tn.insertStyleElement=fe(),ie()(Ze.A,tn),Ze.A&&Ze.A.locals&&Ze.A.locals;class en{constructor(t,e,n=!0){this.textInputBase=t,this.painter=e,Et()(this.root).addClass("colored-text-input"),n&&this.textInputBase.onChanged((()=>{Et()(this.textArea).css("height",0),Et()(this.textArea).css("height",this.textArea.scrollHeight+"px")})),this.highlights=_t.div([]),this.root.appendChild(this.highlights),this.colorize(),this.textInputBase.onChanged((()=>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"}(Xe||(Xe={}));class nn{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 s of[t,e,n])s[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 rn extends nn{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 sn extends rn{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(Xe.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(Xe.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,s=parseInt(i[n].substring(1));if(t.has(s))throw new Error(`R group ${s} is already in the map`);t.set(s,r)}));const s=this.getRGroupAtomicIndices().filter((e=>!Array.from(t.values()).includes(e)));if(0!==s.length)throw new Error(`Unaccounted R group indices: ${s}`);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(Xe.TYPE)&&-1!==t.indexOf(Xe.END)}shiftIdxToAtomType(t){return this.shiftIdxToSpecifiedColumn(t,Xe.ATOM_TYPE_COL)}getCountsLineIdx(){let t=0;for(let e=0;e<Xe.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,Xe.FIRST_BONDED_ATOM_COL)}shiftIdxToBondType(t){return this.shiftIdxToSpecifiedColumn(t,Xe.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+Xe.NUM_OF_COUNTS_DIGITS;const n=parseInt(this.fileContent.substring(t,e));return t=e,e+=Xe.NUM_OF_COUNTS_DIGITS,{atomCount:n,bondCount:parseInt(this.fileContent.substring(t,e))}}}class on extends rn{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 an{constructor(){}static getInstance(t){if(an.isMolfileV2K(t))return new sn(t);if(an.isMolfileV3K(t))return new on(t);throw new Error("Malformed molfile")}static isMolfileV2K(t){return sn.isValidMolfile(t)}static isMolfileV3K(t){return on.isValidMolfile(t)}}const un=class extends Error{constructor(t){super(t)}};class ln{constructor(t){this.molblock=t}get molblock(){return this._validMolBlock}set molblock(t){if(""!==t){try{this.validateMolBlock(t)}catch(e){e instanceof un&&(t="");const n=Je(e);console.error(n)}this._validMolBlock=t}else this._validMolBlock=t}validateMolBlock(t){if(""===t)throw new un("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=Je(t);console.error(e)}}getMoleculeDimensions(){const t=an.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=_t.dialog({title:"Molecule",showFooter:!1}),e=.7*Et()(window).height(),n=this.getMoleculeDimensions(),r=e/n.height,i=e,s=n.width*r,o=_t.canvas(s,i);await this.drawMolBlockOnCanvas(o);const a=_t.block([o],{style:{overflowX:"scroll"}});t.add(a).showModal(!0),Et()(t.root).find(".d4-dialog-contents").removeClass("ui-form"),Et()(t.root).find(".d4-dialog-contents").removeClass("ui-panel"),Et()(t.root).find(".d4-dialog-contents").addClass("ui-box"),Et()(t.root).find(".d4-dialog-contents").css("padding","0")}async drawMolecule(t,e,n){t.innerHTML="";const r=_t.canvas(e*window.devicePixelRatio,n*window.devicePixelRatio);r.style.width=`${e}px`,r.style.height=`${n}px`,r.style.cursor="zoom-in",this.drawMolBlockOnCanvas(r),r.addEventListener("click",(async()=>{await this.zoomIn()})),t.append(_t.tooltip.bind(r,"Click to zoom"))}}class cn extends Error{constructor(t,e){super(t,e)}}class hn{constructor(t,e){this.sequence=t,this.codeMap=e}parseSequence(){const t=this.parseRawSequence();return this.addLinkers(t)}addLinkers(t){const e=[];return t.forEach(((n,r)=>{const i=this.getSymbolForCode(n);r>0&&function(t){return yr.jsonData.monomersWithPhosphate.left.includes(t)}(i)&&e.pop(),e.push(i);const s=fn(i),o=r===t.length-1,a=r+1<t.length&&fn(this.getSymbolForCode(t[r+1]));s||function(t){return yr.jsonData.monomersWithPhosphate.right.includes(t)}(i)||a||o||e.push("p")})),e}getSymbolForCode(t){let e=this.codeMap.get(t);return e??(e=t),e}parseRawSequence(){const t=this.getAllCodesOfFormat(),e=[];let n=0;for(;n<this.sequence.length;){const r=t.find((t=>t===this.sequence.substring(n,n+t.length)));if(void 0===r)throw new cn(`Unable to match a monomer for the rest of the sequence '${this.sequence.slice(n)}'.`);e.push(r),n+=r.length}return e}getAllCodesOfFormat(){return ct(Array.from(this.codeMap.keys()))}}function fn(t){return yr.jsonData.monomersWithPhosphate.phosphate.includes(t)}class dn{constructor(t,e=!1,n){this.invert=e,this.lib=yr.monomerLibWrapper;const r=this.lib.getCodeToSymbolMap(n);this.parser=new hn(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),s=(e.x[i]+e.x[r])/2,o=(e.y[i]+e.y[r])/2;for(let t=0;t<n;t++)e.x[t]-=s,e.y[t]-=o;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),s=Array(e.natom),o=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),s[u]=t.substring(n,r),n=r+1,r=t.indexOf(" ",n),o[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:s,x:o,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 s=(e.x[i]+e.x[r])/2,o=(e.y[i]+e.y[r])/2;for(let t=0;t<n;t++)e.x[t]-=s,e.y[t]-=o;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="",s="";const o=[];let a=0,u=0,l=0;for(let e=0;e<t.length;e++){const n=t[e].includes("MODIFICATION")&&0===e;let s=0;n&&(s=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=s:r===s&&(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 o=Math.round(1e4*(parseFloat(t[e].substring(d,p))+i))/1e4;t[e]=t[e].slice(0,d)+o+t[e].slice(p),d=t[e].indexOf(" ",d)+1,p=t[e].indexOf(" ",d),o=Math.round(1e4*parseFloat(t[e].substring(d,p)))/1e4,t[e]=t[e].slice(0,d)+o+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=s:i===s&&(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=s:i===s&&(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=>{o.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(o.length/4);s+="M  V30 MDLV30/STEABS ATOMS=("+o.length+" -\n";for(let t=0;t<c;t++){s+="M  V30 ";const e=t+1===c?o.length-4*(c-1):4;for(let n=0;n<e;n++)s+=n+1===e?t===c-1?o[4*t+n]+")\n":o[4*t+n]+" -\n":o[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&&o.length>0?(n+="M  V30 BEGIN COLLECTION\n",n+=s,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],s=t.y[r],o=t.x[n]-i,a=t.y[n]-s,u=t.x[e]-i,l=t.y[e]-s,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-o,d=l-a,p=c-o,g=h-a;Math.sqrt(g*g+p*p)>=Math.sqrt(d*d+f*f)&&(t.x[e]=c+i,t.y[e]=h+s)}}function pn(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="",s="";const o=[];let a=0,u=0,l=0;if(t.antiStrands.length>0)for(let e=0;e<t.antiStrands.length;e++)t.antiStrands[e]=gn(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=mn(h[e]),s=vn(h[e]);if(e>=t.senseStrands.length?!1===c&&(c=!0,l=0):f=Math.min(f,Math.min(...s.y.filter((t=>t<0)))),c){const t=Math.min(...s.x)-l,e=Math.max(...s.y)+5;for(let e=0;e<s.x.length;e++)s.x[e]-=t;for(let t=0;t<s.y.length;t++)s.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*s.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*s.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=>{o.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(...s.x)+5}const d=Math.ceil(o.length/4);s+="M  V30 MDLV30/STEABS ATOMS=("+o.length+" -\n";for(let t=0;t<d;t++){s+="M  V30 ";const e=t+1===d?o.length-4*(d-1):4;for(let n=0;n<e;n++)s+=n+1===e?t===d-1?o[4*t+n]+")\n":o[4*t+n]+" -\n":o[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&&o.length>0?(n+="M  V30 BEGIN COLLECTION\n",n+=s,n+="M  V30 END COLLECTION\n"):n=n.replace(/ CFG=\d/g," "),n+="M  V30 END CTAB\n",n+="M  END",n}function gn(t){const e=vn(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 s=Math.PI,o=Math.cos(s),a=Math.sin(s);for(let t=0;t<n;t++){const n=e.x[t];e.x[t]=n*o-e.y[t]*a,e.y[t]=n*a+e.y[t]*o}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 mn(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 vn(t){const e=mn(t);let n=t.indexOf("M  V30 BEGIN ATOM");n=t.indexOf("\n",n);let r=n;const i=Array(e.natom),s=Array(e.natom),o=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),s[u]=t.substring(n,r),n=r+1,r=t.indexOf(" ",n),o[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:s,x:o,y:a}}function yn(t,e,n){if(""===t)return"";const r=n.createFormatDetector(t).getFormat();if(!r)return"";let i="";try{i=new dn(t,e,r).convert()}catch(t){const e=Je(t);console.error(e)}return i}function bn(t,e,n,r,i){const s=[t,e,n].filter((t=>""!==t.strand));return 1===s.length?yn(s[0].strand,s[0].invert,i):pn({senseStrands:[yn(t.strand,t.invert,i)],antiStrands:[yn(e.strand,e.invert,i),yn(n.strand,n.invert,i)].filter((t=>""!==t))},r)}const wn=["ss","as","as2"];class An{constructor(){this.th=yr,this.onInput=new Wt.Subject,this.onInvalidInput=new Wt.Subject,this.inputBase=Object.fromEntries(wn.map((t=>[t,_t.textInput("","",(()=>{this.onInput.next()}))]))),this.useChiralInput=_t.boolInput("Use chiral",!0),this.saveAllStrandsInput=_t.boolInput("Save as one entity",!0),_t.tooltip.bind(this.saveAllStrandsInput.root,"Save SDF with all strands in one molfile"),this.directionInversion=Object.fromEntries(wn.map((t=>[t,!1]))),this.moleculeImgDiv=_t.block([]),Et()(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=_t.divH([n,this.moleculeImgDiv]);Et()(r).addClass("st-structure-bottom");const i=_t.divV([e,r]);return Et()(i).addClass("st-structure-body"),i}getBoolInputsAndButton(){const e=_t.buttonsInput([_t.bigButton("Save SDF",(()=>{const e=this.getStrandData();!function(e,n,r,i,s,o){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(s)u=bn(e,n,r,i,o)+"\n$$$$\n";else{const h=yn(e.strand,e.invert,o),f=yn(n.strand,n.invert,o),d=yn(r.strand,r.invert,o);u=h+"\n> <Sequence>\nSense Strand\n$$$$\n",f&&(u+=f+"\n> <Sequence>\nAnti Sense\n$$$$\n"),d&&(u+=d+"\n> <Sequence>\nAnti Sense 2\n$$$$\n")}const l=new Date;function c(t){return t>=10?t.toString():"0"+t.toString()}ht(`SequenceTranslator-${l.getFullYear()+"-"+c(l.getMonth()+1)+"-"+c(l.getDate())+"_"+c(l.getHours())+"-"+c(l.getMinutes())+"-"+c(l.getSeconds())}.sdf`,encodeURIComponent(u))}}(e.ss,e.as,e.as2,this.useChiralInput.value,this.saveAllStrandsInput.value,this.th)}))]),n=[this.saveAllStrandsInput.root,this.useChiralInput.root,e],r=_t.divV(n);for(const t of n)Et()(t).addClass("st-structure-bool-button-block");return r}getTableInput(t){const e=Object.fromEntries(wn.map((e=>[e,new en(this.inputBase[e],t.highlightInvalidSubsequence)]))),n=Object.fromEntries(wn.map(((t,e)=>{const n=0===e?"5′ → 3′":"3′ → 5′";return[t,_t.choiceInput(`${t.toUpperCase()} direction`,n,["5′ → 3′","3′ → 5′"])]})));wn.forEach(((t,e)=>{n[t].onChanged((()=>{let r="3′ → 5′"===n[t].value;e>0&&(r=!r),this.directionInversion[t]=r,this.onInput.next()}))}));const r=["Sense Strand","Anti Sense","Anti Sense 2"],i=new Map(wn.map(((t,e)=>[t,r[e]]))),s=Object.fromEntries(wn.map((t=>[t,_t.label(i.get(t))]))),o=Object.fromEntries(wn.map((t=>{const n=_t.icons.delete((()=>{e[t].inputBase.value=""})),r=_t.button(n,(()=>{}));return _t.tooltip.bind(r,`Clear ${t.toUpperCase()}`),[t,n]}))),a=wn.map((t=>({label:s[t],textInput:e[t].root,clear:o[t],choiceInput:n[t].root}))),u=_t.table(a,(t=>[t.label,t.textInput,t.clear,t.choiceInput]));Et()(u).css("margin-top","10px");for(const t of wn){let e=s[t].parentElement;e.classList.add("st-structure-input-form"),Et()(e).css("padding-top","3px"),e=n[t].root.parentElement,e.classList.add("st-structure-input-form","st-structure-direction-choice"),e=this.inputBase[t].root.parentElement,e.classList.add("st-structure-text-input-td")}return u}getStrandData(){return Object.fromEntries(wn.map((t=>{const e=this.directionInversion[t];return[t,{strand:this.inputBase[t].value.replace(/\s*/g,""),invert:e}]})))}getMolfile(t,e,n){return bn(t,e,n,this.useChiralInput.value,this.th)}async updateMoleculeImg(){let t="";try{const e=this.getStrandData();Object.values(e).some((t=>""!==t.strand))&&(t=this.getMolfile(e.ss,e.as,e.as2))}catch(t){const e=Je(t);console.error(e)}const e=new ln(t);await e.drawMolecule(this.moleculeImgDiv,650,150),Et()(this.moleculeImgDiv).find("canvas").css("float","inherit")}}class Cn extends Mt{constructor(t){super("Oligo Structure"),this.th=t,this.layout=new An}getContent(){return this.layout.getHtmlDivElement(this.th)}}async function xn(e){try{const n={overflowX:"scroll"},r=_t.div([],{style:n}),i=vn(e),s=.7*Et()(window).height(),o=Math.max(...i.x)-Math.min(...i.x),a=Math.max(...i.y)-Math.min(...i.y),u=s/a,l=u*o,c=u*a,h=_t.canvas(l*window.devicePixelRatio,c*window.devicePixelRatio);h.style.width=`${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),_t.dialog("Molecule").add(r).showModal(!0)}catch(t){const e=Je(t);console.error(e)}}class _n{static async view(){const e=yr.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 xn(e)}))}}const Sn="Copied",En="Nucleotides";function Tn(t,e){const n=new RegExp("\\([^()]*\\)","g"),r=t.match(n);return r?r.map((t=>{const n=t.replace(/[\[\]()]/g,"");return ut.includes(n)?n:e.getNaturalAnalogBySymbol(n)})).map((t=>t||vt)).join(""):null}var In=n(254),Nn={};Nn.styleTagTransform=pe(),Nn.setAttributes=ce(),Nn.insert=ue().bind(null,"head"),Nn.domAPI=oe(),Nn.insertStyleElement=fe(),ie()(In.A,Nn),In.A&&In.A.locals&&In.A.locals;const On=["Sequence"];class Mn{constructor(t){this.th=t,this.inputFormats=Object.keys(yr.jsonData.codesToHelmDict).concat(lt.HELM),this.onInput=new Wt.Subject,this.moleculeImgDiv=_t.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=_t.div([]),this.formatChoiceInput=_t.choiceInput("",lt.HELM,this.inputFormats,(async()=>{this.format=this.formatChoiceInput.value,this.updateTable(),await this.updateMolImg()})),this.sequenceInputBase=_t.textInput("","Afcgacsu",(()=>{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=Rn.getInstance()}async getHtmlElement(){const t=this.constructSingleSequenceControls(),e=this.constructBulkTranslationControls(),n=_t.box(_t.panel([t,e,_t.block([_t.box(this.moleculeImgDiv)])]));return this.formatChoiceInput.value=this.format,this.updateTable(),await this.updateMolImg(),n}constructBulkTranslationControls(){const t=_t.h1("Bulk");_t.tooltip.bind(t,"Bulk translation from table input");const e=new Ln(this.eventBus).createUIComponents(),n=_t.choiceInput("Input format",lt.AXOLABS,this.inputFormats,(t=>this.eventBus.selectInputFormat(t))),r=_t.choiceInput("Output format",En,(i=this.th,Object.keys(i.jsonData.codesToHelmDict).concat([lt.HELM,En]).sort()),(t=>this.eventBus.selectOutputFormat(t)));var i;const s=this.createConvertBulkButton(),o=_t.div([...e,n,r,s],"ui-form");return _t.block25([t,o])}createConvertBulkButton(){const t=_t.bigButton("Convert",(()=>this.processConvertBulkButtonClick()));return _t.tooltip.bind(t,"Convert sequences from table input"),$(t).css({float:"right","margin-top":"20px"}),t}processConvertBulkButtonClick(){const n=this.eventBus.getSelectedTable();if(!n)return void t.shell.warning("No table selected");const r=this.eventBus.getSelectedInputFormat(),i=this.eventBus.getSelectedOutputFormat(),s=this.eventBus.getSelectedColumn("Sequence");if(!s)return void t.shell.warning("No sequence column selected");const o=`${s.name} (${i})`,a=e.Column.fromList(e.TYPE.STRING,o,s.toList().map((t=>{const e=function(t,e,n,r){const i=r.createFormatConverter(t,e);return n===En?Tn(i.convertTo(lt.HELM),r.monomerLibWrapper):i.convertTo(n)}(t,r,i,this.th);return e})));if(i===En||i===lt.HELM){a.semType=e.SEMTYPE.MACROMOLECULE;const t=i==En?x.FASTA:x.HELM;a.setTag(e.TAGS.UNITS,t);const n=Z.forColumn(a);(i==En?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 en(this.sequenceInputBase,(t=>Tt(t,this.th))),e=_t.button("Get SDF",(()=>{this.saveMolfile()}),"Save structure as SDF"),n=_t.button("Copy SMILES",(()=>{this.copySmiles()}),"Copy SMILES for the sequence"),r=_t.div([this.formatChoiceInput]),i=_t.button(_t.icons.delete((()=>{t.inputBase.value=""})),(()=>{}));_t.tooltip.bind(i,"Clear input");const s={format:r,textInput:t.root,clearBtn:i},o=_t.table([s],(t=>[t.format,t.textInput,t.clearBtn]));o.classList.add("st-translator-input-table");const a=_t.block([this.outputTableDiv,e,n]);return _t.block75([_t.h1("Single sequence"),o,a])}saveMolfile(){const t=new dn(this.sequence,!1,this.formatChoiceInput.value).convert()+"\n$$$$";ht(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(Sn)))}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([lt.HELM]);if(!t||-1!==e&&n!==lt.HELM)return{};if(!i.includes(n))throw new Error(`${n} format is not supported by SequenceTranslator`);const s=i.filter((t=>t!=n)).sort(((t,e)=>t.localeCompare(e))),o=r.createFormatConverter(t,n),a=Object.fromEntries(s.map((t=>{let e;try{e=o.convertTo(t)}catch{e=null}return[t,e]})).filter((([t,e])=>e))),u=Tn(n===lt.HELM?t:a[lt.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 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curves""}}",text,,\n,,,,,,,,,,,,,,,,,,,,,').columns.add(e.Column.fromList(e.TYPE.BYTE_ARRAY,"BinaryImage",Array.from(new Uint8Array(11))));var kn,Hn=function(t,e,n,r){return new(n||(n=Promise))((function(i,s){function o(t){try{u(r.next(t))}catch(t){s(t)}}function a(t){try{u(r.throw(t))}catch(t){s(t)}}function u(t){var e;t.done?i(t.value):(e=t.value,e instanceof n?e:new n((function(t){t(e)}))).then(o,a)}u((r=r.apply(t,e||[])).next())}))};async function $n(){await ft((async()=>{const e=await Cr();t.shell.addView(e),["Afcgacsu","Afcgacsu","Afcgacsu"].forEach((async(t,e)=>{await async function(t,e){await function(t){return Hn(this,void 0,void 0,(function*(){yield new Promise((e=>setTimeout(e,t)))}))}(500);const n=document.querySelectorAll(".colored-text-input > textarea")[t];n.value=e;const r=new Event("input");n.dispatchEvent(r)}(e,t)}))}))}function jn(t){const e=_t.textInput("","");return{coloredInput:new en(e,t.highlightInvalidSubsequence),codes:t.jsonData.codesToSymbolsDict}}console.log.bind(console),console.info.bind(console),console.warn.bind(console),console.error.bind(console),function(t){t.notNull=function(t,e){if(null==t)throw new Error(`${null==e?"Value":e} not defined`)}}(kn||(kn={})),e.DataFrame.fromColumns([e.Column.fromStrings("col",["val1","val2","val3"])]);var Vn=function(t,e,n,r){return new(n||(n=Promise))((function(i,s){function o(t){try{u(r.next(t))}catch(t){s(t)}}function a(t){try{u(r.throw(t))}catch(t){s(t)}}function u(t){var e;t.done?i(t.value):(e=t.value,e instanceof n?e:new n((function(t){t(e)}))).then(o,a)}u((r=r.apply(t,e||[])).next())}))};class qn{constructor(t,e,n=".csv"){this.path=t,this.userStorageName=e,this.ext=n,"/"!==this.path[this.path.length-1]&&(this.path+="/"),"."!==this.ext[0]&&(this.ext="."+this.ext)}getUserSettings(){return Vn(this,void 0,void 0,(function*(){if(this.settings)return this.settings;const e=yield t.dapi.userDataStorage.getValue(this.userStorageName,"Settings",!0),n=e?JSON.parse(e):{excluded:[],explicit:[]};return n.explicit=n.explicit instanceof Array?n.explicit:[],n.excluded=n.excluded instanceof Array?n.excluded:[],this.settings=n}))}setUserSettings(e){return Vn(this,void 0,void 0,(function*(){this.settings=e,yield t.dapi.userDataStorage.postValue(this.userStorageName,"Settings",JSON.stringify(e),!0)}))}getAllAvailable(){return Vn(this,void 0,void 0,(function*(){return(yield t.dapi.files.list(this.path)).map((t=>t.fullPath.replace(`${this.path}`,"")))}))}getActive(){return Vn(this,void 0,void 0,(function*(){const t=yield this.getUserSettings();return t.explicit.length>0?t.explicit:(yield this.getAllAvailable()).filter((e=>!t.excluded.includes(e)))}))}createInput(t,e){const n=_t.boolInput(t,e,(e=>this.updateSelectionStatus(t,e)));return n.addOptions(_t.button(_t.iconFA("trash"),(()=>{_t.dialog({title:"Warning"}).add(_t.divText(`Delete file '${t}'?`)).onOK((()=>{n.root.remove(),this.availableRemove(t)})).show()}),`Delete ${t}`)),n}getInputs(){return Vn(this,void 0,void 0,(function*(){const t=yield this.getAllAvailable(),e=yield this.getActive(),n=new Array(t.length);for(let r=0;r<t.length;r++){const i=e.includes(t[r]);n[r]=this.createInput(t[r],i)}return n}))}getForm(){return Vn(this,void 0,void 0,(function*(){const t=yield this.getInputs(),e=_t.divV(t);return _t.divV([e,_t.button("ADD",(()=>Vn(this,void 0,void 0,(function*(){let t="";t=yield this.getNewAvailable(),""!==t&&e.append(this.createInput(t,!0).root)}))))])}))}updateSelectionStatus(t,e){return Vn(this,void 0,void 0,(function*(){const n=yield this.getUserSettings();if(!n.excluded.includes(t)!==e){if(e){const e=n.excluded.indexOf(t);e>-1&&n.excluded.splice(e,1)}else n.excluded.push(t);this.setUserSettings(n)}}))}availableRemove(e){return Vn(this,void 0,void 0,(function*(){const n=yield this.getUserSettings(),r=n.excluded.indexOf(e);r>-1&&n.excluded.splice(r,1),yield Promise.all([this.setUserSettings(n),t.dapi.files.delete(this.path+e)]),t.shell.info(`File ${e} successfully deleted`)}))}getNewAvailable(){return Vn(this,void 0,void 0,(function*(){return new Promise(((n,r)=>{e.Utils.openFile({accept:this.ext,open:e=>Vn(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 Gn="System:AppData/SequenceTranslator/polytool-rules/",Wn="Polytool",zn="link",Yn="fragmentDuplication",Kn="differentFragments";class Qn extends qn{constructor(t,e,n){super(t,e,n)}}class Jn{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),s=[];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,o=e[2].split("-"),a=o[0].split(":"),u=o[1].split(":");s.push({fChain:n,sChain:i,fMonomer:a[0],sMonomer:u[0],fR:a[1].replace("R",""),sR:u[1].replace("R","")})}return new Jn(i,s)}static fromNotation(t,e){const n=e.heterodimerCode,r=e.homodimerCode,i=[],s=[],o=null!==n?t.split(`(${e.heterodimerCode})`):"";null!==n&&o.length>1?(s.push({fChain:0,sChain:1,fMonomer:1,sMonomer:1,fR:1,sR:1}),i.push(o[1].replaceAll("{","").replaceAll("}","")),i.push(o[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;s.push({fChain:t,sChain:e,fMonomer:1,sMonomer:1,fR:1,sR:1});const n=i[t].replace(`(${r})`,""),o=n.indexOf("{"),a=n.slice(0,o),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),[o,u,l,c,h]=this.getAllCycles(e.linkRules,n,r),f=new Array(o.length);for(let t=0;t<o.length;t++)f[t]=`[${o[t]}]`;for(let e=0;e<u.length;e++)s.push({fChain:t,sChain:t,fMonomer:u[e],sMonomer:l[e],fR:c[e],sR:h[e]});a[t]=f}return new Jn(a,s)}getHelmChanged(t,e){let n=0,r=0,i=0;t:for(let e=0;e<this.monomers.length;e++)for(let s=0;s<this.monomers[e].length;s++){if(n==t){r=e,i=s;break t}n++}const s=this.monomers[r][i];this.monomers[r][i]=`[${e}]`;const o=this.getHelm();return this.monomers[r][i]=s,o}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,s=!1,o=!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(o&&t[n]==e[r].secondMonomer+l){s=!0,u=n;break}if(o||t[n]!=e[r].firstMonomer+l)continue;s=!0,u=n;break}if(t[n]==e[r].firstMonomer+l)i=!0,o=!0,a=n;else{if(t[n]!=e[r].secondMonomer+l)continue;i=!0,o=!1,a=n}}n[r]=i&&s?o?[a,u]:[u,a]:[-1,-1]}return n}static getAllCycles(t,e,n){const r=[],i=[],s=[],o=[],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),s.push(t[u].firstLinkingGroup),o.push(t[u].secondLinkingGroup)}return[e,r,i,s,o]}}const Xn="System:AppData/Bio/monomer-libraries/",Zn="PEPTIDE1{[R].[F].[T].[G].[H].[F].[G].[A].[A].[Y].[P].[E].[NH2]}$$$$";class tr{constructor(t,e){this.helmString=Zn,this.helmHelper=t,this.editor=e,this.webEditorHost=null,this.webEditorApp=null,[].push((0,Wt.fromEvent)(e.host,"click").subscribe((()=>{this.webEditorHost=_t.div(),this.webEditorApp=t.createWebEditorApp(this.webEditorHost,this.getHelmString()),_t.dialog({showHeader:!1,showFooter:!0}).add(this.webEditorHost).onOK((()=>{try{const t=this.webEditorApp.canvas.getHelm(!0).replace(/<\/span>/g,"").replace(/<span style='background:#bbf;'>/g,"");e.editor.setHelm(t),this.helmString=t,this.helmSelection=[];const n=this.webEditorApp?.canvas.helm.jsd.m.atoms;for(let t=0;t<n.length;t++)n[t].selected&&this.helmSelection.push(t)}catch(t){}finally{Et()(this.webEditorHost).empty(),this.webEditorHost=null,this.webEditorApp=null}})).onCancel((()=>{Et()(this.webEditorHost).empty(),this.webEditorHost=null,this.webEditorApp=null})).show({modal:!0,fullScreen:!0})})))}static async init(){const t=await async function(){const t="Helm",n=e.Func.find({package:t,name:"getHelmHelper"});if(0===n.length)throw new Error(`Package '${t}' must be installed for HelmHelper.`);return(await n[0].prepare().call()).getOutputParamValue()}(),n=t.createHelmWebEditor();return n.host.style.width="200px",n.host.style.height="100px",n.host.style.paddingLeft="40px",n.editor.setHelm(Zn),new tr(t,n)}getHelmString(){return this.helmString}getHelmSelections(){return this.helmSelection}getDiv(){const t=_t.divText("Macromolecule",{style:{paddingTop:"43px",color:"var(--grey-4)"}});return _t.divH([t,this.editor.host],{style:{paddingLeft:"48px"}})}}const er="No dataframe with macromolecule columns open",nr="No marcomolecule column chosen!",rr="Get HELM",ir="Add HELM column",sr="Chirality engine",or="Poly Tool Conversion",ar="Poly Tool Enumeration",ur="Rules used";async function lr(){const n=t.shell.t.columns.bySemTypeAll(e.SEMTYPE.MACROMOLECULE);if(!n)throw new Error(er);const r=_t.columnInput("Column",t.shell.t,n[0],null,{filter:t=>t.semType===e.SEMTYPE.MACROMOLECULE}),i=_t.boolInput(rr,!0);_t.tooltip.bind(i.root,ir);const s=_t.boolInput(sr,!1),o=new Qn(Gn,Wn,".json"),a=_t.inlineText([ur]);_t.tooltip.bind(a,"Add or specify rules to use");const u=await o.getForm(),l=_t.div([r,i,s,a,u]);return _t.dialog(or).add(l).onOK((async()=>{const n=e.TaskBarProgressIndicator.create("PolyTool converting");try{const n=r.value;if(!n)return void t.shell.warning(nr);const a=await o.getActive();!async function(n,r,i,s){const o=n.dataFrame,a=await async function(n){const r=new e.FileSource(Gn),i=[],s={homodimerCode:null,heterodimerCode:null,linkRules:i};for(let e=0;e<n.length;e++){const o=await r.readAsText(n[e].replace(Gn,"")),a=JSON.parse(o);for(let e=0;e<a.length;e++)if(void 0!==a[e].type&&void 0!==a[e].code)switch(a[e].type){case zn:{const t=a[e].monomericSubstitution;t.code=a[e].code,i.push(t);break}case Yn:s.homodimerCode&&t.shell.warning("PolyTool: homodimer code is duplicated in rules."),s.homodimerCode=a[e].code;break;case Kn:s.heterodimerCode&&t.shell.warning("PolyTool: heterodimer code is duplicated in rules."),s.heterodimerCode=a[e].code;break;default:t.shell.warning(`PolyTool: Unexpected type - '${a[e]}'.`)}else t.shell.warning("Polytool: rules contain invalid rule")}return s}(i),u=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=Jn.fromNotation(t[r],e);n[r]=i.getHelm()}return n}(n.toList(),a),l=o.columns.getUnusedName("transformed("+n.name+")"),c=e.Column.fromList("string",l,u);var h;(h=c).setTag("quality",e.SEMTYPE.MACROMOLECULE),h.setTag("aligned","SEQ"),h.setTag("alphabet",_.PT),c.setTag("units",x.HELM),r&&(c.setTag("cell.renderer","helm"),o.columns.add(c));const f=await t.functions.call("Bio:getMolFromHelm",{df:o,helmCol:c,chiralityEngine:s});f.name=o.columns.getUnusedName("molfile("+n.name+")"),f.semType=e.SEMTYPE.MOLECULE,o.columns.add(f,!0),await t.data.detectSemanticTypes(o)}(n,i.value,a,s.value)}catch(e){!function(e){const n=e instanceof Error?e.message:e.toString(),r=e instanceof Error?e.stack:void 0;t.shell.error(n),yr.logger.error(e.message,void 0,r)}(e)}finally{n.close()}}))}async function cr(){const n=await tr.init(),r=await async function(){const e=await t.functions.call("Bio:getMonomerLibHelper",{});return(await e.getFileManager()).getValidLibraryPaths()}(),i=_t.choiceInput("Library to use",null,r);i.input.setAttribute("style","min-width:250px!important;");const s=_t.div([n.getDiv(),i.root]);return _t.dialog(ar).add(s).onOK((async()=>{try{const r=n.getHelmString(),s=n.getHelmSelections();if(void 0===r||""===r)t.shell.warning("PolyTool: no molecule was provided");else if(void 0===s||s.length<1)t.shell.warning("PolyTool: no selection was provided");else{const n=await async function(e,n,r){const i=await async function(e){const n=await t.functions.call("Bio:getMonomerLibHelper",{});return(await n.readLibrary(Xn,e)).getMonomerSymbolsByType("PEPTIDE")}(r),s=Jn.fromHelm(e),o=n.length*i.length,a=new Array(o);for(let t=0;t<n.length;t++)for(let e=0;e<i.length;e++)a[t*i.length+e]=s.getHelmChanged(n[t],i[e]);return a}(r,s,i.value),o=e.Column.fromStrings("Enumerated",n),a=e.DataFrame.fromColumns([o]);t.shell.addTableView(a)}}catch(t){}})).onCancel((()=>{}))}const hr={symbol:"Short Name",name:"Medium Name",smiles:"SMILES"},fr=[{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"}];class dr{constructor(t){this.rawLib=t}isValid(){return this.rawLib.every((t=>"object"==typeof t&&Object.values(hr).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={...v};Object.entries(hr).forEach((([n,r])=>{const i=t[r];e[n]=i}));let n="smiles";const r=t[hr[n]],i=new pr(r),s=i.getCappedSmiles();return e[n]=s,n="rgroups",e[n]=gr.getRGroups(i.getNumberOfRGroups()),n="molfile",e[n]=new mr(i.getSmilesWithRGroups()).getMolfile(),e}}class pr{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 gr{constructor(){}static getRGroups(t){return fr.slice(0,t)}}class mr{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 vr{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 dr(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")}}const yr=new It;async function br(){await yr.initLibData();const e=await async function(e){const n={"Mermadesynthesis:merMadeSynthesis":{tabName:"SYNTHESIZE",parameters:jn(e)}},r={};for(const[e,i]of Object.entries(n)){let n;try{n=await t.functions.call(e,i.parameters);const s=new Fn(i.tabName,n);s.initView(),r[i.tabName]=()=>s.getView()}catch(t){console.warn(`Plugin ${e} not loaded, reason:`,t);continue}}return r}(yr);if(!e)throw new Error("External app view factories not loaded");const n=new Un(e,yr);return await n.getAppView()}async function wr(){return await Lr("Oligo Translator")}async function Ar(){return await Lr("Oligo Pattern")}async function Cr(){return await Lr("Oligo Structure")}async function xr(){return await yr.initLibData(),yr}function _r(){const t=yr.monomerLibWrapper.getCodesToWeightsMap();return Object.fromEntries(t)}function Sr(t){const e=yr.createSequenceValidator(t),n=yr.createFormatDetector(t).getFormat();return null!==n&&e.isValidSequence(n)}function Er(t,e){return new dn(t,e,"GCRS").convert()}function Tr(t){return pn(t,!0)}async function Ir(){await async function(){await ft((async()=>{const e=await wr();t.shell.addView(e)}))}()}async function Nr(){await async function(){await ft((async()=>{const e=await 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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]=-n-(e-1)*r,s[1][e]=0;s[0][0]=0;for(let h=1;h<o.length+1;h++){s[c][0]=-n-(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]?r:n),g=s[c][f-1]-(u[f-1]?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.max(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 A{constructor(t,e,n){this.name=t,this.alphabet=e,this.cutoff=n}}class w extends A{constructor(t,e,n){super(t.name,t.alphabet,t.cutoff),this.freq=e,this.similarity=n}}const C=wu;var x,_,E,S,T,I=n.n(C);(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 A(_.PT,O.fasta.peptide,.5),new A(_.DNA,O.fasta.dna,.55),new A(_.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 U{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 k{}class H extends k{static buildPalette(){return[].concat(...Object.values(P.colourPalette))}get(t){const n=U.hashCode(t)%H.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)}(H.palette[n])}}H.palette=H.buildPalette();class j{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 V{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 j(e,X[x.FASTA])},G=t=>t?new V(t):new j([],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 j(r,X[x.SEPARATOR])}return new j([],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 j(r.map((t=>{Y.lastIndex=0;const e=Y.exec(t);return e&&e.length>=2?e[1]:t})),X[x.HELM])};function Q(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 w(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 J=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[J.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 '${e.SEMTYPE.MACROMOLECULE}'`);t.column.meta.units=x.HELM,Z.setTags(t)}static setTags(t){const e=t.column.meta.units;if([x.FASTA,x.SEPARATOR].includes(e)){if(!t.column.getTag(E.alphabet)&&0===Object.keys(t.stats.freq).length)throw new Error("Alphabet is empty and not annotated.");let e=t.column.getTag(E.aligned);null===e&&(e=t.stats.sameLength?"SEQ.MSA":"SEQ",t.column.setTag(E.aligned,e));let n=t.column.getTag(E.alphabet);if(null===n&&(n=Q(t.stats.freq,M),t.column.setTag(E.alphabet,n)),n===_.UN){const e=Object.keys(t.stats.freq).length,n=Object.keys(t.stats.freq).some((t=>t.length>1));t.column.setTag(E.alphabetSize,e.toString()),t.column.setTag(E.alphabetIsMultichar,n?"true":"false")}}}get column(){return this._column}get length(){return this._column.length}get units(){return this._units}get notation(){return this._notation}get defaultGapOriginal(){return this._defaultGapOriginal}get separator(){const t=this.column.getTag(E.separator)??void 0;if(this.notation===x.SEPARATOR&&void 0===t)throw new Error(`Separator is mandatory  for column '${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)}}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()).getBioLib().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 j(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[J.seqHandler];return e&&e.columnVersion===t.version||(e=t.temp[J.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){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 j(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()}const rt="System:AppData/SequenceTranslator/monomers-sample",it="pattern-app-data.json",ot="formats-to-helm.json",st="codes-to-symbols.json",at="linkers.json",ut=["A","G","C","U"];var lt;function ct(t){return t.sort(((t,e)=>e.length-t.length))}function ht(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 ft(e,n,r="Oligo app"){try{return await e()}catch(e){const n=e.hasOwnProperty("message")?e.message:e.toString();throw t.shell.error(`${r} error: `+n),e}finally{n&&n()}}!function(t){t.HELM="HELM",t.AXOLABS="Axolabs"}(lt||(lt={}));class dt{constructor(t,e){this.sequence=t,this.th=e,this.libWrapper=this.th.monomerLibWrapper}getInvalidCodeIndex(t){if(t===lt.HELM)return this.sequence.length;const e=["r","d"],n=ct(this.libWrapper.getCodesByFormat(t));let r=0;for(;r<this.sequence.length;){const t=n.find((t=>t===this.sequence.substring(r,r+t.length)));if(!t)break;if(r>1&&ut.includes(this.sequence[r])&&e.includes(this.sequence[r-2]))break;if(e.includes(this.sequence[r+1])&&ut.includes(this.sequence[r])){r++;break}r+=t.length}return r===this.sequence.length&&(r=-1),r}isValidSequence(t){return-1===this.getInvalidCodeIndex(t)}}class pt{constructor(t,e,n,r){this.patternAppData=t,this.codesToHelmDict=e,this.codesToSymbolsDict=n,this.monomersWithPhosphate=r}}async function gt(e){const n=await Promise.all([it,ot,st,at].map((n=>async function(e,n){const r=e.endsWith("/")?`${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 pt(n[0],n[1],n[2],n[3])}class mt{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===lt.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 vt="<?>",yt=(t,e)=>e.length-t.length;class bt{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(yt);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(yt)}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(yt));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: ${t}`)}isHelm(t){return t===lt.HELM}getFormatCodes(t){const e=this.getFormatToHelmDict(t);return Object.keys(e).sort(yt)}getNonHelmFormatRegExp(t){const e=this.getCodesByFormat(t);return new RegExp(At(e)+"|\\([^()]*\\)|.","g")}}function At(t){return t.map((t=>t.replace(/[.*+?^${}()|[\]\\]/g,"\\$&"))).map((t=>t.includes("(")||t.includes(")")?t:`(?<!\\([^()]*)${t}(?![^()]*\\))`)).join("|")}const wt={LEFT:"RNA1{",RIGHT:"}$$$$"};class Ct{constructor(t,e,n){this.sequence=t,this.sourceFormat=e,this.th=n,this.formats=new bt(this.th)}convertTo(t){const e=this.formats.getFormatNames();if(this.sourceFormat===lt.HELM&&e.includes(t))return this.helmToFormat(this.sequence,t);if(e.includes(this.sourceFormat)&&t===lt.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} -> ${t}`)}helmToFormat(t,e){const n=new RegExp(At(Object.values(wt)),"g");let r=t.replace(n,"");const i=this.formats.getHelmToFormatDict(e),o=this.formats.getTargetFormatHelmCodes(e),s=this.formats.getTargetFormatHelmCodesRegExp(e);return r=r.replace(s,(t=>o.includes(t)?i[t]:"p"===t||"."===t?t:"?")).replace(/\?+/g,vt).replace(/p\.|\./g,""),r=r.replace(/<empty>/g,""),r=r.replace(/\/\//g,"/"),r}formatToHelm(t,e){const n=this.formats.getFormatToHelmDict(e),r=this.formats.getCodesByFormat(e),i=this.formats.getFormatRegExp(e),o=this.formats.getPhosphateHelmCodesRegExp(e);let s=t?t.replace(i,(t=>r.includes(t)?n[t]+".":"?")):"";return s=s.replace(/\?+/g,`${vt}.`),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,""),`${wt.LEFT+s+wt.RIGHT}`}}class xt{constructor(t,e){this.sequence=t,this.th=e,this.libWrapper=this.th.monomerLibWrapper,this.formats=Object.keys(this.th.jsonData.codesToHelmDict)}getFormat(){if(this.sequence.startsWith("RNA"))return lt.HELM;const t=this.getListOfPossibleSynthesizersByFirstMatchedCode();if(0===t.length)return null;const e=this.th.createSequenceValidator(this.sequence),n=Array(t.length).fill(0);for(let r=0;r<t.length;++r){const i=t[r];n[r]=e.getInvalidCodeIndex(i)}const r=n.some((t=>-1===t))?-1:Math.max(...n);return t[n.indexOf(r)]}getListOfPossibleSynthesizersByFirstMatchedCode(){const t=this.sequence,e=[];for(const n of this.formats){const r=ct(this.libWrapper.getCodesByFormat(n));let i=0;for(let e=0;e<t.length;e++)if(")"===t[e]&&e!==t.length-1){i=e+1;break}r.some((e=>e===t.slice(i,i+e.length)))&&e.push(n)}return e}}const _t=ui,Et=$;var St=n.n(Et);function Tt(t,e){let n=0;const r=e.createFormatDetector(t).getFormat();null!==r&&(n=new dt(t,e).getInvalidCodeIndex(r));const i=n<0||""===t,o=_t.span([]);St()(o).css("-webkit-text-fill-color","var(--grey-6)");const s=_t.span([]);return St()(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 It 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(){super(),this.highlightInvalidSubsequence=t=>Tt(t,this)}async initLibData(){return this.initPromise||(this.initPromise=(async()=>{let e=(await this.getSettings()).MonomersPath;e&&await t.dapi.files.exists(e)||(_r.logger.warning(`Monomers path '${e}' not found. Fallback to monomers sample path '${rt}'.`),e=rt),[this._jsonData,this._monomerLib]=await Promise.all([gt(e),Nt(e)]),this._monomerLibWrapper=new mt(this.monomerLib,this.jsonData)})()),this.initPromise}async getTranslationHelper(){return await t.functions.call(`${this.name}:getTranslationHelper`)}createSequenceValidator(t){return new dt(t,this)}createFormatConverter(t,e){return new Ct(t,e,this)}createFormatDetector(t){return new xt(t,this)}}async function Nt(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 Ot{constructor(t,e){this.appName=t,this.parentAppName=e}async getAppView(){const n=e.TaskBarProgressIndicator.create(`Loading ${this.appName}...`),r=t.shell.v?.root;r&&_t.setUpdateIndicator(r,!0);try{return await this.constructView()}finally{n.close(),r&&_t.setUpdateIndicator(r,!1)}}}class Mt extends Ot{constructor(t){super(t),this.view=e.View.create(),this.configureView()}async constructView(){await this.initView();const t=this.parentAppName?this.parentAppName+"/"+this.appName:this.appName;return this.view.path=`/apps/${_r.name}/${t.replace(/\s/g,"")}/`,this.view}async initView(){const t=await this.getContent();this.view.append(t)}configureView(){this.view.box=!0,this.view.name=this.appName;const e=t.shell.windows;e.showProperties=!1,e.showToolbox=!1,e.showHelp=!1}getView(){return this.view}}const Lt=["SS","AS"],Bt={SS:"Sense strand",AS:"Anti sense"},Pt=["3'","5'"],Rt="OligoToolkit";var Dt,Ft,Ut;!function(t){t.IS_ANTISENSE_STRAND_INCLUDED="isAntisenseStrandIncluded",t.NUCLEOTIDE_SEQUENCES="nucleotideSequences",t.PHOSPHOROTHIOATE_LINKAGE_FLAGS="phosphorothioateLinkageFlags",t.STRAND_TERMINUS_MODIFICATIONS="strandTerminusModifications"}(Dt||(Dt={})),function(t){t.PATTERN_NAME="patternName",t.PATTERN_COMMENT="patternComment",t.NUCLEOTIDES_WITH_NUMERIC_LABELS="nucleotidesWithNumericLabels"}(Ft||(Ft={})),function(t){t.PATTERN_CONFIG="patternConfig",t.AUTHOR_ID="authorID"}(Ut||(Ut={}));const kt=[Dt.IS_ANTISENSE_STRAND_INCLUDED,Dt.NUCLEOTIDE_SEQUENCES,Dt.PHOSPHOROTHIOATE_LINKAGE_FLAGS,Dt.STRAND_TERMINUS_MODIFICATIONS],$t=(Ft.PATTERN_NAME,Ft.PATTERN_COMMENT,Ft.NUCLEOTIDES_WITH_NUMERIC_LABELS,Ut.PATTERN_CONFIG,Ut.AUTHOR_ID,{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:""});class Ht extends Error{constructor(t){super(t),this.name="PatternNameExistsError"}}class jt extends Error{constructor(t){super(t),this.name="PatternExistsError"}}var Vt=n(802),qt=n.n(Vt);class Gt{constructor(t){this.th=t,this.otherUsersPatternNameToHash=new Map,this.currentUserPatternNameToHash=new Map}static async getInstance(){const t=await _r.getTranslationHelper(),e=new Gt(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 Ht(`Pattern with name ${t} already exists`)}validatePatternUniqueness(t){if(Array.from(this.currentUserPatternNameToHash.values()).concat(Array.from(this.otherUsersPatternNameToHash.values())).includes(t))throw new jt(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 ${t} not found`);return n}async getPatternRecord(e){if(null===e||""===e)return null;try{const n=await t.dapi.userDataStorage.getValue(Rt,e,!1);return JSON.parse(n)}catch{return null}}async getPatternConfig(t){if(""===t||null===t)return null;const e=await this.getPatternRecord(t);return null===e?null:e[Ut.PATTERN_CONFIG]}getDefaultPatternRecord(){const t=$t;return t[Ut.AUTHOR_ID]=this.currentUserId,t}getDefaultPatternConfig(){return $t[Ut.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){const n={[Ut.PATTERN_CONFIG]:e,[Ut.AUTHOR_ID]:await t.dapi.users.current().then((t=>t.id))};return JSON.stringify(n)}getHash(t){const e=kt.reduce(((e,n)=>(e[n]=t[n],e)),{});return qt().sha1(e)}async savePatternToUserStorage(e){const n=e.getPatternConfig();try{const r=this.getHash(n);this.validatePatternUniqueness(r);const i=n[Ft.PATTERN_NAME];this.validatePatternNameUniqueness(i);const o=await this.getRecordFromPattern(n);await t.dapi.userDataStorage.postValue(Rt,r,o,!1),this.currentUserPatternNameToHash.set(i,r),e.selectAuthor(this.getCurrentUserAuthorshipCategory()),e.updatePatternList()}catch(t){if(t instanceof Ht||t instanceof jt)throw t;console.error("Error while saving pattern to user storage",t)}}async overwritePatternInUserStorage(e){const n=e.getPatternConfig(),r=this.getHash(n),i=n[Ft.PATTERN_NAME],o=await this.getRecordFromPattern(n);await t.dapi.userDataStorage.postValue(Rt,r,o,!1),this.currentUserPatternNameToHash.set(i,r),e.updatePatternList()}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 ${e} not found`);await t.dapi.userDataStorage.remove(Rt,r,!1),this.currentUserPatternNameToHash.delete(e),n.updatePatternList();const i=this.getHashOfPatternToBeLoadedAfterDeletion();n.requestPatternLoad(i)}fetchDefaultNucleobase(){return this.fetchAvailableNucleotideBases()[0]}fetchAvailableNucleotideBases(){const t=Object.keys(this.th.jsonData.patternAppData)[0];return Object.keys(this.th.jsonData.patternAppData[t])}async fetchCurrentUserName(){return(await t.dapi.users.current()).friendlyName}async fetchCurrentUserId(){return(await t.dapi.users.current()).id}async fetchPatterns(){return await t.dapi.userDataStorage.get(Rt,!1)}async initializePatternMaps(t){if(!this.currentUserId)throw new Error("Current user ID is not set");const e=new Map;for(const[n,r]of Object.entries(t))await this.extractDataFromRecordToMaps(n,r,e);this.setDefaultPattern()}setDefaultPattern(){const t=$t[Ut.PATTERN_CONFIG];this.currentUserPatternNameToHash.set(t[Ft.PATTERN_NAME],"")}async extractDataFromRecordToMaps(e,n,r){const i=JSON.parse(n),o=i[Ut.PATTERN_CONFIG].patternName,s=i[Ut.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 $t[Ut.PATTERN_CONFIG][Ft.PATTERN_NAME]}getCurrentUserAuthorshipCategory(){return this.currentUserName+" (me)"}getOtherUsersAuthorshipCategory(){return"Other users"}isCurrentUserId(t){return t===this.currentUserId}}const Wt=rxjs,zt=rxjs.operators;function Yt(t){return t.endsWith("(o)")}function Kt(t){const e=Object.values(t).flat().reduce(((t,e)=>(t[e]=(t[e]||0)+1,t)),{});return Object.entries(e).reduce(((t,e)=>t[1]>e[1]?t:e),["",0])[0]}var Qt;function Jt(t){const e=Array.from(new Set(t));return Array.from(e).sort(((t,e)=>t.toLowerCase().localeCompare(e.toLowerCase())))}!function(t){t.getTruncatedStrandData=function(t,e,n){return{nucleotides:t.slice(0,n),ptoFlags:e.slice(0,n+1)}},t.getExtendedStrandData=function(t,e,n,r){const i=n-t.length,o=t.concat(new Array(n-t.length).fill(r)),s=0===t.length?n+1:i;return{nucleotides:o,ptoFlags:e.concat(new Array(s).fill(!0))}}}(Qt||(Qt={}));var Xt=n(543),Zt=n.n(Xt);class te{constructor(t,e){this.dataManager=t,this._patternListUpdated$=new Wt.Subject,this._patternLoadRequested$=new Wt.Subject,this._patternLoaded$=new Wt.Subject,this._uniqueNucleotides$=new Wt.BehaviorSubject([]),this._patternDeletionRequested$=new Wt.Subject,this._tableSelection$=new Wt.BehaviorSubject(null),this._svgSaveRequested$=new Wt.Subject,this._loadPatternInNewTabRequested$=new Wt.Subject,this._urlStateUpdated$=new Wt.Subject,this._patternHasUnsavedChanges$=new Wt.BehaviorSubject(!1),this._selectedStrandColumn=new Wt.BehaviorSubject(null),this._selectedIdColumn=new Wt.BehaviorSubject(null),this.initializeAuthorSelection(e),this.initializePatternState(e),this._lastLoadedPatternConfig=new Wt.BehaviorSubject(Zt().cloneDeep(this.getPatternConfig())),this.setupSubscriptions()}setupSubscriptions(){this._nucleotideSequences$.subscribe((()=>{this.updateUniqueNucleotides(),this.updateSequenceBase()})),this._isAntisenseStrandActive$.subscribe((t=>{t||Pt.forEach((t=>{this.updateTerminusModification("AS",t,"")}))})),this.patternStateChanged$.pipe((0,zt.debounceTime)(20)).subscribe((()=>{const t=this._lastLoadedPatternConfig.getValue(),e=this.getPatternConfig(),n=!Zt().isEqual(e,t);this._patternHasUnsavedChanges$.next(n)}))}updateUniqueNucleotides(){const t=(e=this._nucleotideSequences$.getValue(),Jt(Object.values(e).flat()));var e;this._uniqueNucleotides$.next(t)}updateSequenceBase(){const t=Kt(this._nucleotideSequences$.getValue());this._sequenceBase$.next(t)}get nucleotideSequencesChanged$(){return this._nucleotideSequences$.asObservable()}initializeAuthorSelection(t){const e=t[Ut.AUTHOR_ID];this.dataManager.isCurrentUserId(e)?this._patternAuthorSelection$=new Wt.BehaviorSubject(this.dataManager.getCurrentUserAuthorshipCategory()):this._patternAuthorSelection$=new Wt.BehaviorSubject(this.dataManager.getOtherUsersAuthorshipCategory())}initializePatternState(t){const e=t[Ut.PATTERN_CONFIG];this._patternName$=new Wt.BehaviorSubject(e[Ft.PATTERN_NAME]),this._isAntisenseStrandActive$=new Wt.BehaviorSubject(e[Dt.IS_ANTISENSE_STRAND_INCLUDED]),this._nucleotideSequences$=new Wt.BehaviorSubject(e[Dt.NUCLEOTIDE_SEQUENCES]),this._phosphorothioateLinkageFlags=new Wt.BehaviorSubject(e[Dt.PHOSPHOROTHIOATE_LINKAGE_FLAGS]),this._terminalModifications=new Wt.BehaviorSubject(e[Dt.STRAND_TERMINUS_MODIFICATIONS]),this._comment$=new Wt.BehaviorSubject(e[Ft.PATTERN_COMMENT]),this._modificationsWithNumericLabels$=new Wt.BehaviorSubject(e[Ft.NUCLEOTIDES_WITH_NUMERIC_LABELS]),this._sequenceBase$=new Wt.BehaviorSubject(Kt(e[Dt.NUCLEOTIDE_SEQUENCES]))}getPatternName(){return this._patternName$.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$.next(t)}updateStrandLength(t,e){const n=this.getNucleotideSequences()[t];if(n.length===e)return;const r=this.getPhosphorothioateLinkageFlags()[t];if(0===e)return void this.setNewStrandData([],[],t);if(n.length>e){const{nucleotides:i,ptoFlags:o}=Qt.getTruncatedStrandData(n,r,e);return void this.setNewStrandData(i,o,t)}const i=this.getSequenceBase(),{nucleotides:o,ptoFlags:s}=Qt.getExtendedStrandData(n,r,e,i);this.setNewStrandData(o,s,t)}setNewStrandData(t,e,n){this.updateNucleotideSequences({...this.getNucleotideSequences(),[n]:t}),this.updatePhosphorothioateLinkageFlags({...this.getPhosphorothioateLinkageFlags(),[n]:e})}getPhosphorothioateLinkageFlags(){return this._phosphorothioateLinkageFlags.getValue()}updatePhosphorothioateLinkageFlags(t){this._phosphorothioateLinkageFlags.next(t)}get phosphorothioateLingeFlagsChanged$(){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 Jt(t).filter((t=>!Yt(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$.getValue(),n={};Lt.forEach((r=>{n[r]=e[r].map((()=>t))})),this._nucleotideSequences$.next(n);const r=this._modificationsWithNumericLabels$.getValue();r.includes(t)||this.updateModificationsWithNumericLabels(r.concat(t))}get patternStateChanged$(){return Wt.merge(this._patternName$.pipe((0,zt.debounceTime)(300),(0,zt.map)((()=>{}))),this._isAntisenseStrandActive$,this._nucleotideSequences$,this._phosphorothioateLinkageFlags,this._terminalModifications,this._comment$.pipe((0,zt.debounceTime)(300)),this._modificationsWithNumericLabels$)}getSequenceBase(){return this._sequenceBase$.getValue()}uniqueNucleotidesChanged$(){return this.patternStateChanged$.pipe((0,zt.switchMap)((()=>this._uniqueNucleotides$)))}getUniqueNucleotides(){return this._uniqueNucleotides$.getValue()}get svgSaveRequested$(){return this._svgSaveRequested$.asObservable()}requestSvgSave(){this._svgSaveRequested$.next()}setAllPTOLinkages(t){const e=this.getPhosphorothioateLinkageFlags();Lt.forEach((n=>{e[n]=e[n].map((()=>t))})),this.updatePhosphorothioateLinkageFlags(e)}setPatternConfig(t){this._patternName$.next(t[Ft.PATTERN_NAME]),this._isAntisenseStrandActive$.next(t[Dt.IS_ANTISENSE_STRAND_INCLUDED]),this._nucleotideSequences$.next(t[Dt.NUCLEOTIDE_SEQUENCES]),this._phosphorothioateLinkageFlags.next(t[Dt.PHOSPHOROTHIOATE_LINKAGE_FLAGS]),this._terminalModifications.next(t[Dt.STRAND_TERMINUS_MODIFICATIONS]),this._comment$.next(t[Ft.PATTERN_COMMENT]),this._modificationsWithNumericLabels$.next(t[Ft.NUCLEOTIDES_WITH_NUMERIC_LABELS])}setLastLoadedPatternConfig(t){this._lastLoadedPatternConfig.next(Zt().cloneDeep(t))}getPatternConfig(){return{[Ft.PATTERN_NAME]:this.getPatternName(),[Dt.IS_ANTISENSE_STRAND_INCLUDED]:this.isAntisenseStrandActive(),[Dt.NUCLEOTIDE_SEQUENCES]:this.getNucleotideSequences(),[Dt.PHOSPHOROTHIOATE_LINKAGE_FLAGS]:this.getPhosphorothioateLinkageFlags(),[Dt.STRAND_TERMINUS_MODIFICATIONS]:this.getTerminalModifications(),[Ft.PATTERN_COMMENT]:this.getComment(),[Ft.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$(){return Wt.merge(this._isAntisenseStrandActive$.asObservable().pipe((0,zt.map)((()=>{}))),this._nucleotideSequences$.asObservable().pipe((0,zt.map)((()=>{}))),this._patternLoaded$.asObservable().pipe((0,zt.map)((()=>{})))).pipe((0,zt.debounceTime)(10))}get strandsLinkagesAndTerminalsUpdated$(){return Wt.merge(this.strandsUpdated$,this._phosphorothioateLinkageFlags.asObservable().pipe((0,zt.map)((()=>{}))),this._terminalModifications.asObservable().pipe((0,zt.map)((()=>{}))))}updateControlsUponPatternLoaded(t){this._patternLoaded$.next(t)}get patternLoaded$(){return this._patternLoaded$.asObservable()}get userSelection$(){return this._patternAuthorSelection$.asObservable().pipe((0,zt.skip)(1))}selectAuthor(t){this._patternAuthorSelection$.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$.pipe((0,zt.debounceTime)(100))}}const ee="pattern";class ne{constructor(){this.urlSearchParams=new URLSearchParams(window.location.search)}subscribeToObservables(t){t.urlStateUpdated$.subscribe((t=>this.setPatternURL(t))),t.loadPatternInNewTabRequested$.subscribe((t=>{const e=`${window.location.origin}${window.location.pathname}?${ee}=${t}`;window.open(e,"_blank")})),window.addEventListener("popstate",(()=>{this.urlSearchParams=new URLSearchParams(window.location.search);const e=this.getPatternHash();null!==e&&t.requestPatternLoad(e)}))}getPatternHash(){return this.urlSearchParams.get(ee)}setPatternURL(t){null!==t&&""!==t?(this.urlSearchParams.set(ee,t),window.history.pushState({},"",`${window.location.pathname}?${this.urlSearchParams}`)):this.clearPatternURL()}clearPatternURL(){this.urlSearchParams.delete(ee),window.history.pushState({},"",`${window.location.pathname}`)}}var re=n(72),ie=n.n(re),oe=n(825),se=n.n(oe),ae=n(659),ue=n.n(ae),le=n(56),ce=n.n(le),he=n(540),fe=n.n(he),de=n(113),pe=n.n(de),ge=n(252),me={};me.styleTagTransform=pe(),me.setAttributes=ce(),me.insert=ue().bind(null,"head"),me.domAPI=se(),me.insertStyleElement=fe(),ie()(ge.A,me),ge.A&&ge.A.locals&&ge.A.locals;class ve{constructor(t){this.eventBus=t,this.columnControlsContainer=_t.div([]),this.eventBus.tableSelectionChanged$.subscribe((()=>this.handleTableChoice())),this.refreshColumnControls()}getColumnControlsContainer(){return this.columnControlsContainer}get selectedTable(){return this.eventBus.getTableSelection()}handleTableChoice(){this.refreshColumnControls()}refreshColumnControls(){St()(this.columnControlsContainer).empty(),St()(this.columnControlsContainer).append(this.constructColumnControls())}constructColumnControls(){const t=this.createStrandColumnInput(),e=t.SS,n=t.AS;this.eventBus.antisenseStrandToggled$.subscribe((t=>{St()(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(Lt.map((e=>{const n=_t.input.choice(`${Bt[e]} column`,{value:t[0],items:t,onValueChanged:t=>this.eventBus.selectStrandColumn(e,t.value)});return this.eventBus.selectStrandColumn(e,t[0]),[e,n.root]})))}createIdColumnInput(){const t=this.selectedTable?this.selectedTable.columns.names():[],e=_t.input.choice("ID column",{value:t[0],items:t,onValueChanged:t=>this.eventBus.selectIdColumn(t.value)});return this.eventBus.selectIdColumn(t[0]),e.root}}class ye{constructor(t){this.eventBus=t,this.availableTables=[],this.tableInputContainer=_t.div([]),this.subscribeToTableEvents(),this.refreshTableInput()}getTableInputContainer(){return this.tableInputContainer}subscribeToTableEvents(){t.events.onTableAdded.subscribe((t=>this.handleTableAdded(t))),t.events.onTableRemoved.subscribe((t=>this.handleTableRemoved(t))),this.eventBus.tableSelectionChanged$.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();St()(this.tableInputContainer).empty(),this.tableInputContainer.append(t.root)}createTableInput(){const t=this.eventBus.getTableSelection();return _t.input.table("Tables",{value:t,items:this.availableTables,onValueChanged:t=>{null!==t.value&&this.eventBus.selectTable(t.value)}})}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 be(t,e,n,r){const i=function(t,e,n){const r=new Array(t.length+e.filter((t=>t)).length+Pt.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 Ae{constructor(t){this.eventBus=t,this.tableInputManager=new ye(t),this.columnInputManager=new ve(t)}createControls(){const t=_t.h1("Bulk convert"),e=this.tableInputManager.getTableInputContainer(),n=this.columnInputManager.getColumnControlsContainer(),r=_t.bigButton("Convert",(()=>this.processConvertButtonClick()));return[t,e,n,_t.buttonsInput([r])]}processConvertButtonClick(){!function(e){const n=e.getTableSelection();if(!n)return void t.shell.warning("Please select a table");const r=Lt.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=>be(r.get(t),o,a,s)))}))}(this.eventBus)}}class we{constructor(t,e,n){this.eventBus=t,this.initialPatternConfig=e,this.subscriptions=n}create(){return _t.divV([_t.h1("PTO"),_t.divH([this.createAllPtoActivationInput().root,...this.createFirstPtoInputs().map((t=>t.root))],{style:{gap:"12px"}})])}areAllPtoLinkagesSet(t){return Lt.map((e=>t[e].filter((t=>t)).length)).reduce(((t,e)=>t+e),0)===Lt.map((t=>this.initialPatternConfig.nucleotideSequences[t].length)).reduce(((t,e)=>t+e),0)+Lt.filter((e=>t[e].length)).length}createAllPtoActivationInput(){const t=this.initialPatternConfig.phosphorothioateLinkageFlags,e=this.areAllPtoLinkagesSet(t),n=_t.input.bool("All PTO",{value:e});n.onInput((()=>{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),_t.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 Lt.map((t=>{if(!this.eventBus.isAntisenseStrandActive()&&"AS"===t)return;const e=this.isFirstPtoActive(t),n=_t.input.bool(`First ${t} PTO`,{value:e});n.onInput((()=>{const e=n.value;this.eventBus.setPhosphorothioateLinkageFlag(t,0,e)}));const r=this.eventBus.phosphorothioateLingeFlagsChanged$.subscribe((e=>{const r=e[t][0];n.value=r}));return this.subscriptions.add(r),this.addStyleToPtoInput(n),_t.tooltip.bind(n.captionLabel,`Activate first phosphothioate in ${t}`),n})).filter((t=>void 0!==t))}isFirstPtoActive(t){return this.initialPatternConfig.phosphorothioateLinkageFlags[t][0]}}class Ce{constructor(t,e,n){this.eventBus=t,this.dataManager=e,this.subscriptions=n;const r=this.eventBus.nucleotideSequencesChanged$.subscribe((()=>{this.displayedInputLabels=this.computeDisplayedInputLabels()}));this.subscriptions.add(r)}create(){const t=Lt.map((t=>this.constructControlsPanel(t)));return _t.divH(t,{style:{gap:"24px"}})}constructControlsPanel(t){if(!this.eventBus.isAntisenseStrandActive()&&"AS"===t)return _t.div([]);const e=this.constructHeader(),n=this.createControls(t);return _t.block([_t.h1(`${Bt[t]}`),e,n],{style:{paddingTop:"12px"}})}constructHeader(){return _t.divH([_t.div([_t.divText("#")],{style:{width:"20px"}}),_t.block75([_t.divText("Modification")]),_t.div([_t.divText("PTO")])])}createControls(t){const e=this.createNucleobaseInputs(t),n=this.createLabelDivs(t),r=this.createPTOFlagInputs(t);return _t.div(e.map(((t,e)=>_t.divH([n[e],_t.block75([t.root]),r[e].root],{style:{alignItems:"center"}}))))}createNucleobaseInputs(t){const e=this.dataManager.fetchAvailableNucleotideBases().sort(((t,e)=>t.toLowerCase().localeCompare(e.toLowerCase())));return this.eventBus.getNucleotideSequences()[t].map(((n,r)=>{const i=_t.input.choice("",{value:n,items:e});return i.onInput((()=>{const e=i.value;this.eventBus.setNucleotide(t,r,e)})),i}))}createPTOFlagInputs(t){return this.eventBus.getPhosphorothioateLinkageFlags()[t].slice(1).map(((e,n)=>{const r=_t.input.bool("",{value:e});r.onInput((()=>{const e=r.value;this.eventBus.setPhosphorothioateLinkageFlag(t,n+1,e)}));const i=this.eventBus.phosphorothioateLingeFlagsChanged$.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 Lt.forEach((n=>{let r=1;const i=t[n].map((t=>{if(Yt(t))return"";const e=String(r);return r++,e}));e.set(n,i)})),e}createLabelDivs(t){const e=this.createLabels(t).map((t=>_t.div([t],{style:{width:"20px"}}))),n=this.eventBus.nucleotideSequencesChanged$.subscribe((()=>{this.createLabels(t).forEach(((t,n)=>{St()(e[n]).empty(),St()(e[n]).append(t)}))}));return this.subscriptions.add(n),e}createLabels(t){return this.eventBus.getNucleotideSequences()[t].map(((e,n)=>{const r=this.displayedInputLabels.get(t)[n];return _t.label(r)}))}}class xe{constructor(){this.rxjsSubscriptions=[],this.dgSubscriptions=[]}add(t){t instanceof Wt.Subscription?this.rxjsSubscriptions.push(t):this.dgSubscriptions.push(t)}unsubscribeAll(){for(const t of[this.rxjsSubscriptions,this.dgSubscriptions])t.forEach((t=>t.unsubscribe())),t.length=0}}class _e{constructor(t,e){this.eventBus=t,this.dataManager=e,this.subscriptions=new xe}static open(t,e){_e.isDialogOpen||(_e.instance||(_e.instance=new _e(t,e)),_e.instance.openDialog())}openDialog(){this.initialPatternConfig=Zt().cloneDeep(this.eventBus.getPatternConfig()),_e.isDialogOpen=!0,this.createDialog().show()}createDialog(){const t=_t.divV([]);this.subscriptions.add(this.eventBus.strandsUpdated$.subscribe((()=>this.onStrandsUpdated(t))));const e=_t.dialog("Edit strands").add(t).onOK((()=>{})).onCancel((()=>this.resetToInitialState()));return this.subscriptions.add(e.onClose.subscribe((()=>{_e.isDialogOpen=!1,this.subscriptions.unsubscribeAll()}))),e}onStrandsUpdated(t){const e=new we(this.eventBus,this.initialPatternConfig,this.subscriptions).create(),n=new Ce(this.eventBus,this.dataManager,this.subscriptions).create();St()(t).empty(),St()(t).append(e,n)}resetToInitialState(){this.eventBus.setPatternConfig(this.initialPatternConfig)}}_e.isDialogOpen=!1;class Ee{constructor(t){this.eventBus=t,this.subscriptions=new xe}static open(t){Ee.isDialogOpen||(Ee.instance||(Ee.instance=new Ee(t)),Ee.instance.openDialog())}openDialog(){this.initialPatternConfig=Zt().cloneDeep(this.eventBus.getPatternConfig()),Ee.isDialogOpen=!0,this.createDialog().show()}createDialog(){const t=_t.divV([]);this.subscriptions.add(this.eventBus.strandsUpdated$.subscribe((()=>this.onStrandsUpdated(t))));const e=_t.dialog("Edit terminal modifications").add(t).onOK((()=>{})).onCancel((()=>this.resetToInitialState()));return this.subscriptions.add(e.onClose.subscribe((()=>{Ee.isDialogOpen=!1,this.subscriptions.unsubscribeAll()}))),e}onStrandsUpdated(t){const e=new Se(this.eventBus).create();St()(t).empty(),St()(t).append(e)}resetToInitialState(){this.eventBus.setPatternConfig(this.initialPatternConfig)}}Ee.isDialogOpen=!1;class Se{constructor(t){this.eventBus=t}create(){const t=Lt.map((t=>this.constructControlsPanel(t)));return _t.divH(t,{style:{gap:"24px"}})}constructControlsPanel(t){if(!this.eventBus.isAntisenseStrandActive()&&"AS"===t)return _t.div([]);const e=this.createInputs(t);return _t.block([_t.h1(`${Bt[t]}`),e],{style:{paddingTop:"12px"}})}createInputs(t){const e=("SS"===t?[...Pt].reverse():Pt).map((e=>this.createInputForTerminus(t,e)));return _t.form(e)}createInputForTerminus(t,e){const n=this.eventBus.getTerminalModifications()[t][e],r=_t.input.textArea(e,{value:n});return this.applyStylingToInput(r),r.onInput((()=>{const n=r.value;null!==n&&this.eventBus.updateTerminusModification(t,e,n)})),r}applyStylingToInput(t){const e=t.root.getElementsByTagName("textarea")[0];St()(e).css("resize","none")}}class Te{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[_t.h1("Edit"),t,n,r,i,s,o,_t.buttonsInput([u,a])]}createEditPatternButton(){const t=_t.button("Edit strands",(()=>_e.open(this.eventBus,this.dataManager)));return _t.tooltip.bind(t,"Edit strand modifications and PTOs"),t}createEditTerminalModificationsButton(){const t=_t.button("Edit terminals",(()=>Ee.open(this.eventBus)));return _t.tooltip.bind(t,"Edit terminal modifications"),St()(t).css("margin-right","20px"),t}createAntisenseStrandToggle(){const t=_t.input.toggle(`${Bt.AS} strand`,{value:this.eventBus.isAntisenseStrandActive()});return t.onInput((()=>this.eventBus.toggleAntisenseStrand(t.value))),this.eventBus.patternLoaded$.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=_t.input.int(`${Bt[t]} length`,{value:e});return r.onInput((()=>n(t,r))),this.eventBus.nucleotideSequencesChanged$.subscribe((()=>{r.value=this.eventBus.getNucleotideSequences()[t].length})),r.setTooltip(`Number of nucleotides in ${t}, including overhangs`),[t,r]},n=(e,n)=>{const r=n.value;null!==r&&(r<=0&&(t.shell.warning("Sequence length must be greater than 0"),n.value=1),r>34&&(t.shell.warning("Sequence length must be less than 35"),n.value=34),this.eventBus.updateStrandLength(e,n.value))},r=Object.fromEntries(Lt.map((t=>e(t))));return this.eventBus.antisenseStrandToggled$.subscribe((t=>{St()(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=_t.input.choice("Sequence basis",{value:e,items:t});return n.onInput((()=>this.eventBus.replaceSequenceBase(n.value))),this.eventBus.nucleotideSequencesChanged$.subscribe((()=>{n.value=this.eventBus.getSequenceBase()})),n.setTooltip("Most frequent nucleobase in the strands"),n}createPatternCommentInput(){const t=_t.input.textArea("Comment",{value:this.eventBus.getComment()});return St()(t.root).addClass("st-pattern-text-input"),t.onInput((()=>this.eventBus.updateComment(t.value))),this.eventBus.patternLoaded$.subscribe((()=>{t.value=this.eventBus.getComment()})),t}createPatternNameInputBlock(){const t=_t.input.textArea("Pattern name",{value:this.eventBus.getPatternName()});return St()(t.root).addClass("st-pattern-text-input"),t.onInput((()=>this.eventBus.updatePatternName(t.value))),this.eventBus.patternLoaded$.subscribe((()=>{t.value=this.eventBus.getPatternName()})),t.setTooltip("Name under which pattern will be saved"),t.root}}class Ie{constructor(t,e){this.eventBus=t,this.dataManager=e,this.subscriptions=new xe,this.authorSelectedByUser=!1,this.eventBus.patternLoadRequested$.subscribe((t=>this.handlePatternChoice(t))),this.eventBus.patternDeletionRequested$.subscribe((async t=>{await this.dataManager.deletePattern(t,this.eventBus)}))}async handlePatternChoice(t){let e=await this.dataManager.getPatternConfig(t);null===e&&(e=this.dataManager.getDefaultPatternConfig()),this.eventBus.setPatternConfig(e),this.eventBus.updateControlsUponPatternLoaded(t),this.eventBus.setLastLoadedPatternConfig(e)}isCurrentUserSelected(){return this.eventBus.getSelectedAuthor()!==this.dataManager.getOtherUsersAuthorshipCategory()}createControls(){const t=this.getPatternInputsContainer();return[_t.h1("Load"),t]}getPatternInputsContainer(){const t=_t.divH(this.createPatternInputs());return this.eventBus.patternListUpdated$.subscribe((()=>{this.subscriptions.unsubscribeAll(),St()(t).empty(),St()(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=_t.div([t.root]),n=this.eventBus.userSelection$.subscribe((()=>{St()(e).empty(),St()(e).append(this.createPatternChoiceInput().root)}));return this.subscriptions.add(n),e}createAuthorChoiceInput(){const t=[this.dataManager.getCurrentUserAuthorshipCategory()];this.dataManager.getOtherUsersPatternNames().length>0&&t.push(this.dataManager.getOtherUsersAuthorshipCategory());const e=_t.input.choice("Author",{value:this.eventBus.getSelectedAuthor(),items:t,onValueChanged:t=>{this.authorSelectedByUser=!0,this.eventBus.selectAuthor(t.value)}});return this.setAuthorChoiceInputStyle(e),e.setTooltip("Select pattern author"),e}setAuthorChoiceInputStyle(t){St()(t.input).css({"max-width":"100px","min-width":"100px"}),St()(t.root).css({"padding-right":"30px","padding-left":"30px"})}createPatternChoiceInput(){const t=this.isCurrentUserSelected()?this.dataManager.getCurrentUserPatternNames():this.dataManager.getOtherUsersPatternNames();if(this.authorSelectedByUser){const e=this.dataManager.getPatternHash(t[0],this.isCurrentUserSelected());this.eventBus.requestPatternLoad(e),this.eventBus.updateUrlState(e),this.authorSelectedByUser=!1}const e=this.getPatternName(t),n=_t.input.choice("Pattern",{value:e,items:t});return n.setTooltip("Select pattern to load"),St()(n.input).css({"max-width":"100px","min-width":"100px"}),this.subscriptions.add(n.onInput((()=>{const t=this.dataManager.getPatternHash(n.value,this.isCurrentUserSelected());this.eventBus.requestPatternLoad(t),this.eventBus.updateUrlState(t)}))),this.subscriptions.add(this.eventBus.patternLoaded$.subscribe((()=>{const e=this.eventBus.getPatternName();n.value!==e&&(n.value=this.getPatternName(t))}))),n}getPatternName(t){return t.find((t=>t===this.eventBus.getPatternName()))??t[0]}createDeletePatternButton(){const e=_t.button(_t.iconFA("trash-alt"),(()=>{this.eventBus.getPatternName()!==this.dataManager.getDefaultPatternName()?this.showDeletePatternDialog():t.shell.warning("Cannot delete example pattern")}));_t.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=_t.dialog("Delete pattern"),e=this.eventBus.getPatternName();t.add(_t.divText(`Are you sure you want to delete pattern ${e}?`)),t.onOK((()=>this.eventBus.requestPatternDeletion(e))),t.show()}}class Ne{constructor(t,e){this.eventBus=t,this.dataManager=e}getLayout(){const t=new Ie(this.eventBus,this.dataManager),e=new Te(this.eventBus,this.dataManager),n=new Ae(this.eventBus),r=t.createControls(),i=e.createControls(),o=n.createControls(),s=_t.div(r);St()(s).css({"padding-bottom":"20px"});const a=_t.div([...i,...o],"ui-form"),u=_t.div([s,a]);return St()(u).css({padding:"25px"}),_t.box(u,{style:{maxWidth:"450px"}})}}var Oe=n(146);class Me{constructor(t,e,n){this.svgElementFactory=t,this.config=e,this.yShift=n}shiftElements(t){this.svgElements.forEach((e=>{const n=e.getAttribute("transform")||"",r=`translate(${t.x},${t.y})`;e.setAttribute("transform",`${n} ${r}`)}))}}class Le{constructor(){}static getInstance(){return Le.instance||(Le.instance=new Le,Le.instance.canvas=document.createElement("canvas")),Le.instance}static getTextDimensions(t,e){const n=Le.getInstance().canvas.getContext("2d");if(!n)throw new Error("Canvas 2D context is not available");return n.font=`${e}px Arial`,{width:1.1*n.measureText(t).width,height:1.1*e}}}function Be(t){const e=Object.keys(_r.jsonData.patternAppData)[0];if(!e)throw new Error(`No format found in '${it}'`);return _r.jsonData.patternAppData[e][t].color||""}class Pe extends Me{constructor(t,e,n){super(t,e,n);const r=Lt.filter((t=>e.nucleotideSequences[t].length>0));this.strands=r.map((t=>new Re(this.svgElementFactory,e,n,t))),this.terminalModifications=r.map(((t,r)=>new Fe(this.svgElementFactory,e,n,t,this.strands[r]))),this.labels=r.map(((t,r)=>new De(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 Re extends Me{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=>Yt(e)?null:(t++,t)))}get svgElements(){return this._svgElements}getStrandCircleYShift(){return Ue(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=Be(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(!ut.includes(n))return null;const r=function(t){return!Yt(t)&&ut.includes(t)?t:""}(n),i=function(t){const e=Be(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=Le.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=Le.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 De extends Me{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=Le.getTextDimensions(e,17),r={x:10,y:Ue(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=Le.getTextDimensions(t,17),n={x:65+this.terminalModifications.getContentWidth()+5,y:Ue(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 Fe extends Me{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 Le.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:Ue(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?Pt:Array.from(Pt).reverse()).map((t=>this.createTerminalModification(t)))}get svgElements(){return this._svgElements}getContentWidth(){return this.strandSvgWrapper.getContentWidth()+Pt.map((t=>this.getTerminalModificationTextDimensions(t).width)).reduce(((t,e)=>t+e),0)}getContentHeight(){return this.strandSvgWrapper.getContentHeight()}}function Ue(t,e){return"SS"===t?e+5+15+15:e+52+10+15}class ke{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 $e extends Me{constructor(t,e,n){super(t,e,n),this.svgElementFactory=t,this.config=e,this.yShift=n,this._svgElements=[],this.titleText=this.getTitleText(),this._svgElements=[this.getTitle()]}get svgElements(){return this._svgElements}getTitle(){return this.svgElementFactory.createTextElement(this.titleText,{x:15,y:this.yShift+17},17,"black")}getContentWidth(){return Le.getTextDimensions(this.titleText,17).width}getContentHeight(){return Le.getTextDimensions(this.titleText,17).height}getTitleText(){const t=`${this.config.nucleotideSequences.SS.length}`,e=this.config.isAntisenseStrandIncluded?`/${this.config.nucleotideSequences.AS.length}`:"";return`${this.config.patternName} for ${t}${e}-mer`}}class He extends Me{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,Be(t));e+=12;const i={y:this.yShift,x:e};return{elements:[r,this.svgElementFactory.createTextElement(t,i,15,"var(--grey-6)")],width:12+Le.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 je{constructor(t){this.svgElementFactory=new ke;const e=Zt().cloneDeep(t);let n=10;this.title=new $e(this.svgElementFactory,e,n),n+=this.title.getContentHeight(),this.strands=new Pe(this.svgElementFactory,e,n),n+=this.strands.getContentHeight()+10,this.legend=new He(this.svgElementFactory,e,n)}renderPattern(){const t=this.getGlobalWidth(),e=this.getGlobalHeight(),n=this.svgElementFactory.createCanvas(t,e),r=[this.title,this.strands,this.legend].map((t=>t.svgElements)).flat();return n.append(...r),n}getGlobalWidth(){const t=[this.title,this.strands,this.legend];return Math.max(...t.map((t=>t.getContentWidth())))}getGlobalHeight(){return[this.title,this.strands,this.legend].reduce(((t,e)=>t+e.getContentHeight()),10)}}class Ve{constructor(t){this.eventBus=t,this.svgDisplayDiv=_t.div([]),t.updateSvgContainer$.subscribe((()=>this.updateSvgContainer())),t.svgSaveRequested$.subscribe((()=>this.saveSvgAsPng()))}static createSvgDiv(t){return new Ve(t).svgDisplayDiv}updateSvgContainer(){$(this.svgDisplayDiv).empty();const t=this.eventBus.getPatternConfig();this.svgElement=this.createSvg(t),this.svgDisplayDiv.append(this.svgElement)}createSvg(t){return new je(t).renderPattern()}saveSvgAsPng(){const t=this.eventBus.getPatternName();Oe.saveSvgAsPng(this.svgElement,t,{backgroundColor:"white"})}}class qe{constructor(t){this.eventBus=t,this.togglesContainer=_t.div([]),this.eventBus.uniqueNucleotidesChanged$().subscribe((()=>{this.updateContainer()}))}getContainer(){return this.togglesContainer}updateContainer(){St()(this.togglesContainer).empty(),St()(this.togglesContainer).append(this.createInputs())}createInputs(){const t=this.eventBus.getUniqueNucleotides().filter((t=>!Yt(t))).map((t=>this.createSingleInput(t)));return t.sort(((t,e)=>t.captionLabel.textContent.localeCompare(e.captionLabel.textContent))),_t.divH(t.map((t=>t.root)))}createSingleInput(t){const e=this.eventBus.getModificationsWithNumericLabels().includes(t),n=_t.input.bool(t,{value:e,onValueChanged:e=>this.handleNumericLabelToggle(t,e.value)});return St()(n.root).css("padding-right","20px"),n.setTooltip(`Show numeric labels for ${t}`),n}handleNumericLabelToggle(t,e){const n=this.eventBus.getModificationsWithNumericLabels();if(n.includes(t)===e)return;const r=e?n.concat(t):n.filter((e=>e!==t));this.eventBus.updateModificationsWithNumericLabels(r)}}class Ge{constructor(t,e){this.eventBus=t,this.dataManager=e,this.subscriptions=new xe}createContainer(){return _t.div([_t.h1("Translation example"),this.createTranslationExamples()],{style:{paddingTop:"20px"}})}createTranslationExamples(){const t=_t.divH([...this.getExampleElements()],"ui-form");return this.eventBus.antisenseStrandToggled$.subscribe((()=>{this.subscriptions.unsubscribeAll(),St()(t).empty(),St()(t).append(this.getExampleElements())})),t}getExampleElements(){return Lt.map((t=>new We(t,this.eventBus,this.subscriptions).create()))}}class We{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(),_t.block50([_t.h2(Bt[this.strand]),this.inputExample.root,this.outputExample.root],{style:{paddingRight:"20px"}})):_t.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 ${Bt[this.strand]}`),t}generateExampleSequence(){return this.eventBus.getNucleotideSequences()[this.strand].map(((t,e)=>ut[e%ut.length])).join("")}createOutputExample(t){const e=this.createTextInputForExamples();return e.value=this.computeOutputValue(t),e.setTooltip(`Pattern applied to the example input for ${Bt[this.strand]}`),e}computeOutputValue(t){const e=this.eventBus.getNucleotideSequences()[this.strand],n=this.eventBus.getTerminalModifications()[this.strand];return be(t,e,this.eventBus.getPhosphorothioateLinkageFlags()[this.strand],n)}createTextInputForExamples(){const t=_t.input.textArea("",{value:""});return this.applyStylingToInput(t),t}applyStylingToInput(t){const e=t.root.getElementsByTagName("textarea")[0];e.setAttribute("readonly","true"),St()(e).css("resize","none"),St()(t.root).css("opacity","75%")}}class ze{constructor(t,e){this.eventBus=t,this.dataManager=e,this.svgDisplay=Ve.createSvgDiv(t)}getLayout(){const t=new qe(this.eventBus).getContainer(),e=this.generateDownloadControls(),n=new Ge(this.eventBus,this.dataManager).createContainer();return _t.panel([this.svgDisplay,t,e,n],{style:{overflowX:"scroll",padding:"12px 24px"}})}generateDownloadControls(){return _t.divH([this.createSavePatternButton(),this.createDownloadPngButton(),this.createShareLinkButton()],{style:{gap:"12px",marginTop:"12px"}})}createDownloadPngButton(){const t=_t.button("Get PNG",(()=>this.eventBus.requestSvgSave()));return _t.tooltip.bind(t,"Download pattern as PNG"),t}createShareLinkButton(){const e=_t.button(_t.iconFA("link"),(()=>navigator.clipboard.writeText(window.location.href).then((()=>t.shell.info("Link to pattern copied to clipboard")))));return this.eventBus.patternHasUnsavedChanges$.subscribe((t=>{e.disabled=t})),_t.tooltip.bind(e,"Share pattern link"),e}createSavePatternButton(){const t=_t.button("Save",(()=>this.processSaveButtonClick()));return this.eventBus.patternHasUnsavedChanges$.subscribe((e=>{t.disabled=!e})),_t.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 ${e} saved`)})).catch((t=>this.handleErrorWhileSavingPattern(t))):t.shell.warning("Insert pattern name"):t.shell.warning("Cannot save default pattern")}handleErrorWhileSavingPattern(e){e instanceof Ht?new Ye(this.eventBus,this.dataManager).show():e instanceof jt?t.shell.warning(_t.div([_t.divText("Pattern already exists"),_t.button("Load",(()=>{const t=e.message;this.eventBus.requestLoadPatternInNewTab(t)}))])):console.error("Error while saving pattern",e)}}class Ye{constructor(t,e){this.eventBus=t,this.dataManager=e}show(){const t=this.eventBus.getPatternName(),e=_t.dialog(`Pattern "${t}" already exists`);e.add(_t.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.overwritePatternInUserStorage(this.eventBus).then((()=>{t.shell.info(`Pattern ${e} overwritten`)})).catch((e=>{console.error("Error while overwriting pattern in user storage",e),t.shell.error("Error while overwriting pattern")}))}}class Ke extends Mt{constructor(t){super("Oligo Pattern"),this.th=t}getContent(){return async function(){const t=await Gt.getInstance(),e=new ne,n=await async function(t,e){const n=e.getPatternHash();if(!n)return e.clearPatternURL(),t.getDefaultPatternRecord();let r=await t.getPatternRecord(n);return r||(e.clearPatternURL(),r=t.getDefaultPatternRecord()),r}(t,e),r=new te(t,n);e.subscribeToObservables(r);const i=new Ne(r,t).getLayout(),o=new ze(r,t).getLayout();return _t.splitH([i,o],{},!0)}()}}var Qe=n(507),Je={};function Xe(t){var e;return"string"==typeof t||t instanceof String?t:("object"==typeof t||t instanceof Object)&&"$thrownJsError"in t?Xe(t.$thrownJsError):t instanceof Error?null!==(e=t.stack)&&void 0!==e?e:t.message:t.toString()}Je.styleTagTransform=pe(),Je.setAttributes=ce(),Je.insert=ue().bind(null,"head"),Je.domAPI=se(),Je.insertStyleElement=fe(),ie()(Qe.A,Je),Qe.A&&Qe.A.locals&&Qe.A.locals;var Ze,tn=n(74),en={};en.styleTagTransform=pe(),en.setAttributes=ce(),en.insert=ue().bind(null,"head"),en.domAPI=se(),en.insertStyleElement=fe(),ie()(tn.A,en),tn.A&&tn.A.locals&&tn.A.locals;class nn{constructor(t,e,n=!0){this.textInputBase=t,this.painter=e,St()(this.root).addClass("colored-text-input"),n&&this.textInputBase.onChanged((()=>{St()(this.textArea).css("height",0),St()(this.textArea).css("height",this.textArea.scrollHeight+"px")})),this.highlights=_t.div([]),this.root.appendChild(this.highlights),this.colorize(),this.textInputBase.onChanged((()=>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"}(Ze||(Ze={}));class rn{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 on extends rn{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 sn extends on{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(Ze.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(Ze.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(Ze.TYPE)&&-1!==t.indexOf(Ze.END)}shiftIdxToAtomType(t){return this.shiftIdxToSpecifiedColumn(t,Ze.ATOM_TYPE_COL)}getCountsLineIdx(){let t=0;for(let e=0;e<Ze.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,Ze.FIRST_BONDED_ATOM_COL)}shiftIdxToBondType(t){return this.shiftIdxToSpecifiedColumn(t,Ze.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+Ze.NUM_OF_COUNTS_DIGITS;const n=parseInt(this.fileContent.substring(t,e));return t=e,e+=Ze.NUM_OF_COUNTS_DIGITS,{atomCount:n,bondCount:parseInt(this.fileContent.substring(t,e))}}}class an extends on{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 un{constructor(){}static getInstance(t){if(un.isMolfileV2K(t))return new sn(t);if(un.isMolfileV3K(t))return new an(t);throw new Error("Malformed molfile")}static isMolfileV2K(t){return sn.isValidMolfile(t)}static isMolfileV3K(t){return an.isValidMolfile(t)}}const ln=class extends Error{constructor(t){super(t)}};class cn{constructor(t){this.molblock=t}get molblock(){return this._validMolBlock}set molblock(t){if(""!==t){try{this.validateMolBlock(t)}catch(e){e instanceof ln&&(t="");const n=Xe(e);console.error(n)}this._validMolBlock=t}else this._validMolBlock=t}validateMolBlock(t){if(""===t)throw new ln("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=Xe(t);console.error(e)}}getMoleculeDimensions(){const t=un.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=_t.dialog({title:"Molecule",showFooter:!1}),e=.7*St()(window).height(),n=this.getMoleculeDimensions(),r=e/n.height,i=e,o=n.width*r,s=_t.canvas(o,i);await this.drawMolBlockOnCanvas(s);const a=_t.block([s],{style:{overflowX:"scroll"}});t.add(a).showModal(!0),St()(t.root).find(".d4-dialog-contents").removeClass("ui-form"),St()(t.root).find(".d4-dialog-contents").removeClass("ui-panel"),St()(t.root).find(".d4-dialog-contents").addClass("ui-box"),St()(t.root).find(".d4-dialog-contents").css("padding","0")}async drawMolecule(t,e,n){t.innerHTML="";const r=_t.canvas(e*window.devicePixelRatio,n*window.devicePixelRatio);r.style.width=`${e}px`,r.style.height=`${n}px`,r.style.cursor="zoom-in",this.drawMolBlockOnCanvas(r),r.addEventListener("click",(async()=>{await this.zoomIn()})),t.append(_t.tooltip.bind(r,"Click to zoom"))}}class hn extends Error{constructor(t,e){super(t,e)}}class fn{constructor(t,e){this.sequence=t,this.codeMap=e}parseSequence(){const t=this.parseRawSequence();return this.addLinkers(t)}addLinkers(t){const e=[];return t.forEach(((n,r)=>{const i=this.getSymbolForCode(n);r>0&&function(t){return _r.jsonData.monomersWithPhosphate.left.includes(t)}(i)&&e.pop(),e.push(i);const o=dn(i),s=r===t.length-1,a=r+1<t.length&&dn(this.getSymbolForCode(t[r+1]));o||function(t){return _r.jsonData.monomersWithPhosphate.right.includes(t)}(i)||a||s||e.push("p")})),e}getSymbolForCode(t){let e=this.codeMap.get(t);return e??(e=t),e}parseRawSequence(){const t=this.getAllCodesOfFormat(),e=[];let n=0;for(;n<this.sequence.length;){const r=t.find((t=>t===this.sequence.substring(n,n+t.length)));if(void 0===r)throw new hn(`Unable to match a monomer for the rest of the sequence '${this.sequence.slice(n)}'.`);e.push(r),n+=r.length}return e}getAllCodesOfFormat(){return ct(Array.from(this.codeMap.keys()))}}function dn(t){return _r.jsonData.monomersWithPhosphate.phosphate.includes(t)}class pn{constructor(t,e=!1,n){this.invert=e,this.lib=_r.monomerLibWrapper;const r=this.lib.getCodeToSymbolMap(n);this.parser=new fn(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 gn(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]=mn(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=vn(h[e]),o=yn(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 mn(t){const e=yn(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 vn(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 yn(t){const e=vn(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 bn(t,e,n){if(""===t)return"";const r=n.createFormatDetector(t).getFormat();if(!r)return"";let i="";try{i=new pn(t,e,r).convert()}catch(t){const e=Xe(t);console.error(e)}return i}function An(t,e,n,r,i){const o=[t,e,n].filter((t=>""!==t.strand));return 1===o.length?bn(o[0].strand,o[0].invert,i):gn({senseStrands:[bn(t.strand,t.invert,i)],antiStrands:[bn(e.strand,e.invert,i),bn(n.strand,n.invert,i)].filter((t=>""!==t))},r)}const wn=["ss","as","as2"];class Cn{constructor(){this.th=_r,this.onInput=new Wt.Subject,this.onInvalidInput=new Wt.Subject,this.inputBase=Object.fromEntries(wn.map((t=>[t,_t.input.textArea("",{value:"",onValueChanged:()=>{this.onInput.next()}})]))),this.useChiralInput=_t.input.bool("Use chiral",{value:!0}),this.saveAllStrandsInput=_t.input.bool("Save as one entity",{value:!0}),_t.tooltip.bind(this.saveAllStrandsInput.root,"Save SDF with all strands in one molfile"),this.directionInversion=Object.fromEntries(wn.map((t=>[t,!1]))),this.moleculeImgDiv=_t.block([]),St()(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=_t.divH([n,this.moleculeImgDiv]);St()(r).addClass("st-structure-bottom");const i=_t.divV([e,r]);return St()(i).addClass("st-structure-body"),i}getBoolInputsAndButton(){const e=_t.buttonsInput([_t.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=An(e,n,r,i,s)+"\n$$$$\n";else{const h=bn(e.strand,e.invert,s),f=bn(n.strand,n.invert,s),d=bn(r.strand,r.invert,s);u=h+"\n> <Sequence>\nSense Strand\n$$$$\n",f&&(u+=f+"\n> <Sequence>\nAnti Sense\n$$$$\n"),d&&(u+=d+"\n> <Sequence>\nAnti Sense 2\n$$$$\n")}const l=new Date;function c(t){return t>=10?t.toString():"0"+t.toString()}ht(`SequenceTranslator-${l.getFullYear()+"-"+c(l.getMonth()+1)+"-"+c(l.getDate())+"_"+c(l.getHours())+"-"+c(l.getMinutes())+"-"+c(l.getSeconds())}.sdf`,encodeURIComponent(u))}}(e.ss,e.as,e.as2,this.useChiralInput.value,this.saveAllStrandsInput.value,this.th)}))]),n=[this.saveAllStrandsInput.root,this.useChiralInput.root,e],r=_t.divV(n);for(const t of n)St()(t).addClass("st-structure-bool-button-block");return r}getTableInput(t){const e=Object.fromEntries(wn.map((e=>[e,new nn(this.inputBase[e],t.highlightInvalidSubsequence)]))),n=Object.fromEntries(wn.map(((t,e)=>{const n=0===e?"5′ → 3′":"3′ → 5′";return[t,_t.input.choice(`${t.toUpperCase()} direction`,{value:n,items:["5′ → 3′","3′ → 5′"]})]})));wn.forEach(((t,e)=>{n[t].onChanged((()=>{let r="3′ → 5′"===n[t].value;e>0&&(r=!r),this.directionInversion[t]=r,this.onInput.next()}))}));const r=["Sense Strand","Anti Sense","Anti Sense 2"],i=new Map(wn.map(((t,e)=>[t,r[e]]))),o=Object.fromEntries(wn.map((t=>[t,_t.label(i.get(t))]))),s=Object.fromEntries(wn.map((t=>{const n=_t.icons.delete((()=>{e[t].inputBase.value=""})),r=_t.button(n,(()=>{}));return _t.tooltip.bind(r,`Clear ${t.toUpperCase()}`),[t,n]}))),a=wn.map((t=>({label:o[t],textInput:e[t].root,clear:s[t],choiceInput:n[t].root}))),u=_t.table(a,(t=>[t.label,t.textInput,t.clear,t.choiceInput]));St()(u).css("margin-top","10px");for(const t of wn){let e=o[t].parentElement;e.classList.add("st-structure-input-form"),St()(e).css("padding-top","3px"),e=n[t].root.parentElement,e.classList.add("st-structure-input-form","st-structure-direction-choice"),e=this.inputBase[t].root.parentElement,e.classList.add("st-structure-text-input-td")}return u}getStrandData(){return Object.fromEntries(wn.map((t=>{const e=this.directionInversion[t];return[t,{strand:this.inputBase[t].value.replace(/\s*/g,""),invert:e}]})))}getMolfile(t,e,n){return An(t,e,n,this.useChiralInput.value,this.th)}async updateMoleculeImg(){let t="";try{const e=this.getStrandData();Object.values(e).some((t=>""!==t.strand))&&(t=this.getMolfile(e.ss,e.as,e.as2))}catch(t){const e=Xe(t);console.error(e)}const e=new cn(t);await e.drawMolecule(this.moleculeImgDiv,650,150),St()(this.moleculeImgDiv).find("canvas").css("float","inherit")}}class xn extends Mt{constructor(t){super("Oligo Structure"),this.th=t,this.layout=new Cn}getContent(){return this.layout.getHtmlDivElement(this.th)}}async function _n(e){try{const n={overflowX:"scroll"},r=_t.div([],{style:n}),i=yn(e),o=.7*St()(window).height(),s=Math.max(...i.x)-Math.min(...i.x),a=Math.max(...i.y)-Math.min(...i.y),u=o/a,l=u*s,c=u*a,h=_t.canvas(l*window.devicePixelRatio,c*window.devicePixelRatio);h.style.width=`${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),_t.dialog("Molecule").add(r).showModal(!0)}catch(t){const e=Xe(t);console.error(e)}}class En{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 _n(e)}))}}const Sn="Copied",Tn="Nucleotides";function In(t,e){const n=new RegExp("\\([^()]*\\)","g"),r=t.match(n);return r?r.map((t=>{const n=t.replace(/[\[\]()]/g,"");return ut.includes(n)?n:e.getNaturalAnalogBySymbol(n)})).map((t=>t||vt)).join(""):null}var Nn=n(254),On={};On.styleTagTransform=pe(),On.setAttributes=ce(),On.insert=ue().bind(null,"head"),On.domAPI=se(),On.insertStyleElement=fe(),ie()(Nn.A,On),Nn.A&&Nn.A.locals&&Nn.A.locals;const Mn=["Sequence"];class Ln{constructor(t){this.th=t,this.inputFormats=Object.keys(_r.jsonData.codesToHelmDict).concat(lt.HELM),this.onInput=new Wt.Subject,this.moleculeImgDiv=_t.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=_t.div([]),this.formatChoiceInput=_t.input.choice("",{value:lt.HELM,items:this.inputFormats,onValueChanged:async()=>{this.format=this.formatChoiceInput.value,this.updateTable(),await this.updateMolImg()}}),this.sequenceInputBase=_t.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=Dn.getInstance()}async getHtmlElement(){const t=this.constructSingleSequenceControls(),e=this.constructBulkTranslationControls(),n=_t.box(_t.panel([t,e,_t.block([_t.box(this.moleculeImgDiv)])]));return this.formatChoiceInput.value=this.format,this.updateTable(),await this.updateMolImg(),n}constructBulkTranslationControls(){const t=_t.h1("Bulk");_t.tooltip.bind(t,"Bulk translation from table input");const e=new Bn(this.eventBus).createUIComponents(),n=_t.input.choice("Input format",{value:lt.AXOLABS,items:this.inputFormats,onValueChanged:t=>this.eventBus.selectInputFormat(t.value)}),r=_t.input.choice("Output format",{value:Tn,items:(i=this.th,Object.keys(i.jsonData.codesToHelmDict).concat([lt.HELM,Tn]).sort()),onValueChanged:t=>this.eventBus.selectOutputFormat(t.value)});var i;const o=this.createConvertBulkButton(),s=_t.div([...e,n,r,o],"ui-form");return _t.block25([t,s])}createConvertBulkButton(){const t=_t.bigButton("Convert",(()=>this.processConvertBulkButtonClick()));return _t.tooltip.bind(t,"Convert sequences from table input"),$(t).css({float:"right","margin-top":"20px"}),t}processConvertBulkButtonClick(){const n=this.eventBus.getSelectedTable();if(!n)return void t.shell.warning("No table selected");const r=this.eventBus.getSelectedInputFormat(),i=this.eventBus.getSelectedOutputFormat(),o=this.eventBus.getSelectedColumn("Sequence");if(!o)return void t.shell.warning("No sequence column selected");const s=`${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===Tn?In(i.convertTo(lt.HELM),r.monomerLibWrapper):i.convertTo(n)}(t,r,i,this.th);return e})));if(i===Tn||i===lt.HELM){a.semType=e.SEMTYPE.MACROMOLECULE;const t=i==Tn?x.FASTA:x.HELM;a.meta.units=t;const n=Z.forColumn(a);(i==Tn?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 nn(this.sequenceInputBase,(t=>Tt(t,this.th))),e=_t.button("Get SDF",(()=>{this.saveMolfile()}),"Save structure as SDF"),n=_t.button("Copy SMILES",(()=>{this.copySmiles()}),"Copy SMILES for the sequence"),r=_t.div([this.formatChoiceInput]),i=_t.button(_t.icons.delete((()=>{t.inputBase.value=""})),(()=>{}));_t.tooltip.bind(i,"Clear input");const o={format:r,textInput:t.root,clearBtn:i},s=_t.table([o],(t=>[t.format,t.textInput,t.clearBtn]));s.classList.add("st-translator-input-table");const a=_t.block([this.outputTableDiv,e,n]);return _t.block75([_t.h1("Single sequence"),s,a])}saveMolfile(){const t=new pn(this.sequence,!1,this.formatChoiceInput.value).convert()+"\n$$$$";ht(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(Sn)))}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([lt.HELM]);if(!t||-1!==e&&n!==lt.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=In(n===lt.HELM?t:a[lt.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?_t.divH([]):_t.link(n[e],(()=>navigator.clipboard.writeText(n[e]).then((()=>t.shell.info(Sn)))),"Copy sequence","");r.push({format:e,sequence:i})}const i=_t.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 cn(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===lt.HELM){const t=this.th.createFormatConverter(this.sequence,this.format).convertTo(lt.AXOLABS);return new pn(t,!1,lt.AXOLABS).convert()}return new pn(this.sequence,!1,this.format).convert()}}class Bn{constructor(t){this.tableInputManager=new Pn(t),this.columnInputManager=new Rn(t)}createUIComponents(){return[this.tableInputManager.getTableInputContainer(),this.columnInputManager.getColumnControlsContainer()]}}class Pn{constructor(t){this.eventBus=t,this.availableTables=[],this.tableInputContainer=_t.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();$(this.tableInputContainer).empty(),this.tableInputContainer.append(t.root)}createTableInput(){const t=this.eventBus.getSelectedTable();return _t.input.table("Table",{value:t,items:this.availableTables,onValueChanged:t=>{null!==t.value&&this.eventBus.selectTable(t.value)}})}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 Rn{constructor(t){this.eventBus=t,this.columnControlsContainer=_t.div([]),this.eventBus.tableSelected$.subscribe((()=>this.handleTableChoice())),this.refreshColumnControls()}getColumnControlsContainer(){return this.columnControlsContainer}handleTableChoice(){this.refreshColumnControls()}refreshColumnControls(){const t=this.createColumnInputs();$(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 Mn.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),_t.input.choice(`${t}`,{value:i,items:e,onValueChanged:e=>this.selectColumnIfTableNotNull(n,e.value,t)})}selectColumnIfTableNotNull(t,e,n){if(null!==t){const r=t.getCol(e);this.eventBus.selectColumn(n,r)}}}class Dn{constructor(){this._tableSelection$=new Wt.BehaviorSubject(null),this._columnSelection=Object.fromEntries(Mn.map((t=>[t,new Wt.BehaviorSubject(null)]))),this._inputFormatSelection$=new Wt.BehaviorSubject(lt.AXOLABS),this._outputFormatSelection$=new Wt.BehaviorSubject(Tn)}static getInstance(){return void 0===Dn._instance&&(Dn._instance=new Dn),Dn._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 Fn extends 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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 Zn(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 Zn(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=`(${e[r].code})`;for(let n=0;n<t.length;n++)if(t[n].includes(l)){if(i){if(s&&t[n]==e[r].secondMonomer+l){o=!0,u=n;break}if(s||t[n]!=e[r].firstMonomer+l)continue;o=!0,u=n;break}if(t[n]==e[r].firstMonomer+l)i=!0,s=!0,a=n;else{if(t[n]!=e[r].secondMonomer+l)continue;i=!0,s=!1,a=n}}n[r]=i&&o?s?[a,u]:[u,a]:[-1,-1]}return n}static getAllCycles(t,e,n){const r=[],i=[],o=[],s=[],a=t.length;for(let u=0;u<a;u++){if(-1==n[u][0])continue;const a=e[n[u][0]],l=e[n[u][1]];e[n[u][0]]=e[n[u][0]].replace(a,t[u].firstSubstitution),e[n[u][1]]=e[n[u][1]].replace(l,t[u].secondSubstitution),r.push(n[u][0]+1),i.push(n[u][1]+1),o.push(t[u].firstLinkingGroup),s.push(t[u].secondLinkingGroup)}return[e,r,i,o,s]}}const tr="System:AppData/Bio/monomer-libraries/";async function er(){const e=await t.functions.call("Bio:getMonomerLibHelper",{});return(await e.getFileManager()).getValidLibraryPaths()}function nr(t){return"string"==typeof t||t instanceof String?t:"StateError"===t.constructor.name?t.message:"StateError"===t.constructor.name&&"$thrownJsError"in t?nr(t.$thrownJsError):t instanceof Error?t.message:t.toString()}function rr(t){return t instanceof Error?t.stack:"StateError"===t.constructor.name&&"$thrownJsError"in t?rr(t.$thrownJsError):void 0}function ir(t){return[nr(t),rr(t)]}function or(e){const[n,r]=ir(e);_r.logger.error(n,void 0,r),t.shell.error(n)}const sr="PEPTIDE1{[R].[F].[T].[G].[H].[F].[G].[A].[A].[Y].[P].[E].[NH2]}$$$$";const ar="No dataframe with macromolecule columns open",ur="No marcomolecule column chosen!",lr="Get HELM",cr="Add HELM column",hr="Chirality engine",fr="Poly Tool Conversion",dr="Poly Tool Enumeration",pr="Rules used";async function gr(){const n=t.shell.t.columns.bySemTypeAll(e.SEMTYPE.MACROMOLECULE);if(!n)throw new Error(ar);const r=_t.input.column("Column",{table:t.shell.t,value:n[0],filter:t=>t.semType===e.SEMTYPE.MACROMOLECULE}),i=_t.input.bool(lr,{value:!0});_t.tooltip.bind(i.root,cr);const o=_t.input.bool(hr,{value:!1}),s=new Xn(zn,Yn,".json"),a=_t.inlineText([pr]);_t.tooltip.bind(a,"Add or specify rules to use");const u=await s.getForm(),l=_t.div([r,i,o,a,u]),c=_t.dialog(fr).add(l).onOK((async()=>{const n=e.TaskBarProgressIndicator.create("PolyTool converting");try{const n=r.value;if(!n)return void t.shell.warning(ur);const a=await s.getActive();!async function(n,r,i,o){const s=n.dataFrame,a=await async function(n){const r=new e.FileSource(zn),i=[],o={homodimerCode:null,heterodimerCode:null,linkRules:i};for(let e=0;e<n.length;e++){const s=await r.readAsText(n[e].replace(zn,"")),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 Kn:{const t=a[e].monomericSubstitution;t.code=a[e].code,i.push(t);break}case Qn:o.homodimerCode&&t.shell.warning("PolyTool: homodimer code is duplicated in rules."),o.homodimerCode=a[e].code;break;case Jn: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}(i),u=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=Zn.fromNotation(t[r],e);n[r]=i.getHelm()}return n}(n.toList(),a),l=s.columns.getUnusedName("transformed("+n.name+")"),c=e.Column.fromList("string",l,u);var h;(h=c).semType=e.SEMTYPE.MACROMOLECULE,h.setTag("aligned","SEQ"),h.setTag("alphabet",_.PT),c.meta.units=x.HELM,r&&(c.setTag("cell.renderer","helm"),s.columns.add(c));const f=await t.functions.call("Bio:getMolFromHelm",{df:s,helmCol:c,chiralityEngine:o});f.name=s.columns.getUnusedName("molfile("+n.name+")"),f.semType=e.SEMTYPE.MOLECULE,s.columns.add(f,!0),await t.data.detectSemanticTypes(s)}(n,i.value,a,o.value)}catch(e){!function(e){const n=e instanceof Error?e.message:e.toString(),r=e instanceof Error?e.stack:void 0;t.shell.error(n),_r.logger.error(e.message,void 0,r)}(e)}finally{n.close()}}));return c}const mr={symbol:"Short Name",name:"Medium Name",smiles:"SMILES"},vr=[{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"}];class yr{constructor(t){this.rawLib=t}isValid(){return this.rawLib.every((t=>"object"==typeof t&&Object.values(mr).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={...v};Object.entries(mr).forEach((([n,r])=>{const i=t[r];e[n]=i}));let n="smiles";const r=t[mr[n]],i=new br(r),o=i.getCappedSmiles();return e[n]=o,n="rgroups",e[n]=Ar.getRGroups(i.getNumberOfRGroups()),n="molfile",e[n]=new wr(i.getSmilesWithRGroups()).getMolfile(),e}}class br{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 Ar{constructor(){}static getRGroups(t){return vr.slice(0,t)}}class wr{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 Cr{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 yr(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")}}function xr(n){(async function(n){const[r,i]=await Promise.all([er(),qn()]),o=n?n.value:sr,s=i.createHelmInput("Macromolecule",{value:o}),a=_t.input.choice("Library to use",{value:null,items:r});s.input.setAttribute("style","min-width:250px!important;"),a.input.setAttribute("style","min-width:250px!important;");const u=_t.div([s.root,a.root]),l=t.events.onCurrentCellChanged.subscribe((()=>{const n=t.shell.tv.dataFrame.currentCell;n.column.semType===e.SEMTYPE.MACROMOLECULE&&n.column.meta.units===x.HELM&&(s.stringValue=n.value)}));return _t.dialog(dr).add(u).onOK((async()=>{try{const n=s.stringValue,r=I().enumerate(s.value.atoms).filter((([t,e])=>t.highlighted)).map((([t,e])=>e)).toArray();if(void 0===n||""===n)t.shell.warning("PolyTool: no molecule was provided");else if(void 0===r||r.length<1)t.shell.warning("PolyTool: no selection was provided");else{const i=await async function(e,n,r){const i=await async function(e){const n=await t.functions.call("Bio:getMonomerLibHelper",{});return(await n.readLibrary(tr,e)).getMonomerSymbolsByType("PEPTIDE")}(r),o=Zn.fromHelm(e),s=n.length*i.length,a=new Array(s);for(let t=0;t<n.length;t++)for(let e=0;e<i.length;e++)a[t*i.length+e]=o.getHelmChanged(n[t],i[e]);return a}(n,r,a.value),o=e.Column.fromStrings("Enumerated",i),s=e.DataFrame.fromColumns([o]);t.shell.addTableView(s)}}catch(t){or(t)}finally{l.unsubscribe()}})).onCancel((()=>{l.unsubscribe()}))})(n).then((t=>{t.show({resizable:!0})})).catch((e=>{t.shell.warning("To run PolyTool Enumeration, sketch the macromolecule and select monomers to vary")}))}const _r=new It;async function Er(){await _r.initLibData();const e=await async function(e){const n={"Mermadesynthesis:merMadeSynthesis":{tabName:"SYNTHESIZE",parameters:Vn(e)}},r={};for(const[e,i]of Object.entries(n)){let n;try{n=await t.functions.call(e,i.parameters);const o=new Un(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 kn(e,_r);return await n.getAppView()}async function Sr(){return await Ur("Oligo Translator")}async function Tr(){return await Ur("Oligo Pattern")}async function Ir(){return await Ur("Oligo Structure")}async function Nr(){return await _r.initLibData(),_r}function Or(){const t=_r.monomerLibWrapper.getCodesToWeightsMap();return Object.fromEntries(t)}function Mr(t){const e=_r.createSequenceValidator(t),n=_r.createFormatDetector(t).getFormat();return null!==n&&e.isValidSequence(n)}function Lr(t,e){return new pn(t,e,"GCRS").convert()}function Br(t){return gn(t,!0)}async function Pr(){await async function(){await ft((async()=>{const e=await Sr();t.shell.addView(e)}))}()}async function Rr(){await async function(){await ft((async()=>{const e=await Tr();t.shell.addView(e)}))}()}async function Dr(){await jn()}async function Fr(t,e,n){return await _r.initLibData(),_r.createFormatConverter(t,e).convertTo(n)}async function Ur(t){await 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