npm - @datagrok/sequence-translator - Versions diffs - 1.2.6 → 1.2.9 - Mend

@datagrok/sequence-translator 1.2.6 → 1.2.9

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Files changed (102) hide show

package/dist/package.js CHANGED Viewed

@@ -1,2 +1,3 @@
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l=Object.keys(s.Rv).concat([o.NI.HELM]);if(!t||-1!==e&&n!==o.NI.HELM)return{};if(!l.includes(n))throw new Error(`${n} format is not supported by SequenceTranslator`);const c=l.filter((t=>t!=n)).sort(((t,e)=>t.localeCompare(e))),u=new i.I(t,n),d=Object.fromEntries(c.map((t=>{let e;try{e=u.convertTo(t)}catch{e=null}return[t,e]})).filter((([t,e])=>e))),h=function(t,e){const n=new RegExp("\\([^()]*\\)","g"),i=t.match(n);if(!i)return null;return i.map((t=>{const n=t.replace(/[\[\]()]/g,"");return o.mc.includes(n)?n:e.getNaturalAnalogBySymbol(n)})).map((t=>t||r.s8)).join("")}(n===o.NI.HELM?t:d[o.NI.HELM],a.A.getInstance());return h&&(d.Nucleotides=h),d}},456:(t,e,n)=>{n.d(e,{I:()=>u});var o=n(29),r=n(544),i=n(996);const s=(t,e)=>e.length-t.length;class a{constructor(){this.formats=this.getFormats()}formats;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 o=n.replace(/\)p/g,")").replace(/\]p/g,"]");void 0===e[o]?e[o]=[t]:e[o].push(t)}))})),Object.entries(e).forEach((([t,n])=>{const o=n.sort(s);e[t]=o[0]})),e}(i.Rv[t])}getFormatToHelmDict(t){this.validateFormat(t);const e=i.Rv[t];return Object.assign({},...Object.values(e))}getTargetFormatHelmCodes(t){this.validateFormat(t);const e=this.getHelmToFormatDict(t);return Object.keys(e).sort(s)}getTargetFormatHelmCodesRegExp(t){this.validateFormat(t);const e=this.getTargetFormatHelmCodes(t);return new RegExp(l(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=i.Rv[t],n=l(Array.from(new Set(Object.values(e[r.DD.LINKAGE]))).sort(s));return new RegExp(`${r.$3}.(${n})`,"g")}isValidFormat(t){return this.formats.includes(t)}getFormats(){return Object.keys(i.Rv)}validateFormat(t){if(!this.isValidFormat(t))throw new Error(`Invalid format: ${t}`)}isHelm(t){return t===o.NI.HELM}getFormatCodes(t){const e=this.getFormatToHelmDict(t);return Object.keys(e).sort(s)}getNonHelmFormatRegExp(t){const e=this.getCodesByFormat(t);return new RegExp(l(e)+"|\\([^()]*\\)|.","g")}}function l(t){return t.map((t=>t.replace(/[.*+?^${}()|[\]\\]/g,"\\$&"))).map((t=>t.includes("(")||t.includes(")")?t:`(?<!\\([^()]*)${t}(?![^()]*\\))`)).join("|")}const c={LEFT:"RNA1{",RIGHT:"}$$$$"};class u{sequence;sourceFormat;constructor(t,e){this.sequence=t,this.sourceFormat=e}formats=new a;convertTo(t){const e=this.formats.getFormatNames();if(this.sourceFormat===o.NI.HELM&&e.includes(t))return this.helmToFormat(this.sequence,t);if(e.includes(this.sourceFormat)&&t===o.NI.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(l(Object.values(c)),"g");let o=t.replace(n,"");const i=this.formats.getHelmToFormatDict(e),s=this.formats.getTargetFormatHelmCodes(e),a=this.formats.getTargetFormatHelmCodesRegExp(e);return o=o.replace(a,(t=>s.includes(t)?i[t]:"p"===t||"."===t?t:"?")).replace(/\?+/g,r.s8).replace(/p\.|\./g,""),o=o.replace(/<empty>/g,""),o=o.replace(/\/\//g,"/"),o}formatToHelm(t,e){const n=this.formats.getFormatToHelmDict(e),o=this.formats.getCodesByFormat(e),i=this.formats.getFormatRegExp(e),s=this.formats.getPhosphateHelmCodesRegExp(e);let a=t.replace(i,(t=>o.includes(t)?n[t]+".":"?"));return a=a.replace(/\?+/g,`${r.s8}.`),a=a.slice(0,-1),a[a.length-1]===r.$3&&(a=a.slice(0,-1)),a=a.replace(s,((t,e)=>e)),a=a.replace(/<empty>/g,""),`${c.LEFT+a+c.RIGHT}`}}},593:(t,e,n)=>{n.r(e),n.d(e,{_package:()=>pe,demoOligoPattern:()=>Oe,demoOligoStructure:()=>Ie,demoTranslateSequence:()=>Ee,getCodeToWeightsMap:()=>Ce,getMolfileFromGcrsSequence:()=>we,initSequenceTranslatorLibData:()=>xe,linkStrands:()=>ye,oligoPatternApp:()=>Ae,oligoStructureApp:()=>ve,oligoToolkitApp:()=>ge,oligoTranslatorApp:()=>fe,translateOligonucleotideSequence:()=>Se,validateSequence:()=>be});var o=n(976),r=n(469);const i=ui,s=rxjs;var a=n(379),l=n.n(a),c=n(795),u=n.n(c),d=n(569),h=n.n(d),p=n(565),m=n.n(p),g=n(216),f=n.n(g),A=n(589),v=n.n(A),x=n(602),C={};C.styleTagTransform=v(),C.setAttributes=m(),C.insert=h().bind(null,"head"),C.domAPI=u(),C.insertStyleElement=f(),l()(x.Z,C),x.Z&&x.Z.locals&&x.Z.locals;var b=n(947),w=n(669),y=n(29),E=n(559),O=n(996);class I{sequence;constructor(t){this.sequence=t,this.libWrapper=E.A.getInstance(),this.formats=Object.keys(O.Rv)}libWrapper;formats;getFormat(){if(this.sequence.startsWith("RNA"))return y.NI.HELM;const t=this.getListOfPossibleSynthesizersByFirstMatchedCode();if(0===t.length)return null;const e=new b.b(this.sequence),n=Array(t.length).fill(0);for(let o=0;o<t.length;++o){const r=t[o];n[o]=e.getInvalidCodeIndex(r)}const o=n.some((t=>-1===t))?-1:Math.max(...n);return t[n.indexOf(o)]}getListOfPossibleSynthesizersByFirstMatchedCode(){const t=this.sequence;let e=[];for(const n of this.formats){let o=(0,w.xB)(this.libWrapper.getCodesByFormat(n)),r=0;for(let e=0;e<t.length;e++)if(")"===t[e]&&e!==t.length-1){r=e+1;break}o.some((e=>e===t.slice(r,r+e.length)))&&e.push(n)}return e}}const S=$;var T=n.n(S);function M(t){let e=0;const n=new I(t).getFormat();null!==n&&(e=new b.b(t).getInvalidCodeIndex(n));const o=e<0||""===t,r=i.span([]);T()(r).css("-webkit-text-fill-color","var(--grey-6)");const s=i.span([]);return T()(s).css("-webkit-text-fill-color","red"),o?r.innerHTML=t:(r.innerHTML=t.slice(0,e),s.innerHTML=t.slice(e)),[r,s]}var B=n(490),N={};N.styleTagTransform=v(),N.setAttributes=m(),N.insert=h().bind(null,"head"),N.domAPI=u(),N.insertStyleElement=f(),l()(B.Z,N),B.Z&&B.Z.locals&&B.Z.locals;class L{textInputBase;painter;constructor(t,e,n=!0){this.textInputBase=t,this.painter=e,T()(this.root).addClass("colored-text-input"),n&&this.textInputBase.onChanged((()=>{T()(this.textArea).css("height",0),T()(this.textArea).css("height",this.textArea.scrollHeight+"px")})),this.highlights=i.div([]),this.root.appendChild(this.highlights),this.colorize(),this.textInputBase.onChanged((()=>this.colorize()))}highlights;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)))}}var D=n(900);class F{sequence;codeMap;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,o)=>{const r=this.getSymbolForCode(n);o>0&&function(t){return O.iA.left.includes(t)}(r)&&e.pop(),e.push(r);const i=V(r),s=o===t.length-1,a=o+1<t.length&&V(this.getSymbolForCode(t[o+1]));i||function(t){return O.iA.right.includes(t)}(r)||a||s||e.push(D.$)})),e}getSymbolForCode(t){let e=this.codeMap.get(t);return e??=t,e}parseRawSequence(){const t=this.getAllCodesOfFormat(),e=[];let n=0;for(;n<this.sequence.length;){const o=t.find((t=>t===this.sequence.substring(n,n+t.length)));e.push(o),n+=o.length}return e}getAllCodesOfFormat(){let t=Array.from(this.codeMap.keys());return(0,w.xB)(t)}}function V(t){return O.iA.phosphate.includes(t)}class k{invert;constructor(t,e=!1,n){this.invert=e,this.lib=E.A.getInstance();const o=this.lib.getCodeToSymbolMap(n);this.parser=new F(t,o)}parser;lib;convert(){const t=this.parser.parseSequence(),e=[];t.forEach(((t,n)=>{const o=this.getMonomerMolfile(t,n);e.push(o)}));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 o=t.substring(e,n);return o=o.replace(/(CFG=)([13])/g,((t,e,n)=>"1"===n?`${e}3`:"3"===n?`${e}1`:t)),t.substring(0,e)+o+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,o=e.atomIndex.indexOf(1),r=e.atomIndex.indexOf(n),i=(e.x[r]+e.x[o])/2,s=(e.y[r]+e.y[o])/2;for(let t=0;t<n;t++)e.x[t]-=i,e.y[t]-=s;for(let t=0;t<n;t++)e.x[t]=-e.x[t];const a=e.x[o];for(let t=0;t<n;t++)e.x[t]-=a;let l=t.indexOf("M  V30 BEGIN ATOM");l=t.indexOf("\n",l);let c=l;for(let o=0;o<n;o++)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[o]+" "+e.y[o]+t.slice(c)).indexOf("\n",l)+1;return t}extractAtomDataV3000(t){const e=this.extractAtomsBondsNumbersV3000(t);let n=t.indexOf("M  V30 BEGIN ATOM");n=t.indexOf("\n",n);let o=n;const r=Array(e.natom),i=Array(e.natom),s=Array(e.natom),a=Array(e.natom);for(let l=0;l<e.natom;l++)n=t.indexOf("V30",n)+4,o=t.indexOf(" ",n),r[l]=parseInt(t.substring(n,o)),n=o+1,o=t.indexOf(" ",n),i[l]=t.substring(n,o),n=o+1,o=t.indexOf(" ",n),s[l]=parseFloat(t.substring(n,o)),n=o+1,o=t.indexOf(" ",n),a[l]=parseFloat(t.substring(n,o)),n=t.indexOf("\n",n)+1;return{atomIndex:r,atomType:i,x:s,y:a}}extractAtomsBondsNumbersV3000(t){let e=(t=t.replaceAll("\r","")).indexOf("COUNTS")+7,n=t.indexOf(" ",e);const o=parseInt(t.substring(e,n));return e=n+1,n=t.indexOf(" ",e),{natom:o,nbond:parseInt(t.substring(e,n))}}rotateNucleotidesV3000(t){const e=this.extractAtomDataV3000(t),n=e.atomIndex.length,o=e.atomIndex.indexOf(1),r=e.atomIndex.indexOf(n);n>8&&this.fix5Prime(e,o,r);const i=(e.x[r]+e.x[o])/2,s=(e.y[r]+e.y[o])/2;for(let t=0;t<n;t++)e.x[t]-=i,e.y[t]-=s;let a=0;if(0===e.x[o])a=e.y[o]>e.y[r]?Math.PI/2:3*Math.PI/2;else if(0===e.y[o])a=e.x[o]>e.x[r]?Math.PI:0;else{const t=e.y[o]/e.x[o];a=t>0?e.x[o]>0?Math.PI-Math.atan(t):2*Math.PI-Math.atan(t):e.x[o]>0?-Math.PI-Math.atan(t):Math.atan(t)}const l=Math.cos(a),c=Math.sin(a);for(let t=0;t<n;t++){const n=e.x[t];e.x[t]=n*l-e.y[t]*c,e.y[t]=n*c+e.y[t]*l}const u=e.x[o];for(let t=0;t<n;t++)e.x[t]-=u;let d=t.indexOf("M  V30 BEGIN ATOM");d=t.indexOf("\n",d);let h=d;for(let o=0;o<n;o++)d=t.indexOf("V30",d)+4,d=t.indexOf(" ",d)+1,d=t.indexOf(" ",d)+1,h=t.indexOf(" ",d)+1,h=t.indexOf(" ",h),d=(t=t.slice(0,d)+e.x[o]+" "+e.y[o]+t.slice(h)).indexOf("\n",d)+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 o="",r="",i="";const s=[];let a=0,l=0,c=0;for(let e=0;e<t.length;e++){const n=t[e].includes("MODIFICATION")&&0===e;let i=0;n&&(i=this.extractAtomDataV3000(t[e]).atomIndex.length),t[e]=t[e].replaceAll("(-\nM  V30 ","(").replaceAll("-\nM  V30 ","").replaceAll(" )",")");const u=this.extractAtomsBondsNumbersV3000(t[e]),d=this.extractAtomDataV3000(t[e]);let h=t[e].indexOf("M  V30 BEGIN ATOM");h=t[e].indexOf("\n",h);let p=h,m=h;for(let o=0;o<u.natom;o++)if(1!==d.atomIndex[o]||0===e){p=t[e].indexOf("V30",p)+4,m=t[e].indexOf(" ",p);let o=0;n?(o=parseInt(t[e].substring(p,m)),1===o?o=i:o===i&&(o=1),o+=a):o=parseInt(t[e].substring(p,m))+a,t[e]=t[e].slice(0,p)+o+t[e].slice(m),p=t[e].indexOf(" ",p)+1,p=t[e].indexOf(" ",p)+1,m=t[e].indexOf(" ",p);const r=c-d.x[0];let s=Math.round(1e4*(parseFloat(t[e].substring(p,m))+r))/1e4;t[e]=t[e].slice(0,p)+s+t[e].slice(m),p=t[e].indexOf(" ",p)+1,m=t[e].indexOf(" ",p),s=Math.round(1e4*parseFloat(t[e].substring(p,m)))/1e4,t[e]=t[e].slice(0,p)+s+t[e].slice(m),p=t[e].indexOf("\n",p)+1}else p=t[e].indexOf("M  V30",p)-1,m=t[e].indexOf("\n",p+1),t[e]=t[e].slice(0,p)+t[e].slice(m);const g=t[e].indexOf("M  V30 END ATOM");o+=t[e].substring(h+1,g);let f=t[e].indexOf("M  V30 BEGIN BOND");f=t[e].indexOf("\n",f),p=f,m=f;for(let o=0;o<u.nbond;o++){p=t[e].indexOf("V30",p)+4,m=t[e].indexOf(" ",p);const o=parseInt(t[e].substring(p,m))+l;t[e]=t[e].slice(0,p)+o+t[e].slice(m),p=t[e].indexOf(" ",p)+1,p=t[e].indexOf(" ",p)+1,m=t[e].indexOf(" ",p);let r=0;n?(r=parseInt(t[e].substring(p,m)),1===r?r=i:r===i&&(r=1),r+=a):r=parseInt(t[e].substring(p,m))+a,t[e]=t[e].slice(0,p)+r+t[e].slice(m),p=t[e].indexOf(" ",p)+1,m=Math.min(t[e].indexOf("\n",p),t[e].indexOf(" ",p)),r=0,n?(r=parseInt(t[e].substring(p,m)),1===r?r=i:r===i&&(r=1),r+=a):r=parseInt(t[e].substring(p,m))+a,t[e]=t[e].slice(0,p)+r+t[e].slice(m),p=t[e].indexOf("\n",p)+1}const A=t[e].indexOf("M  V30 END BOND");r+=t[e].substring(f+1,A);let v=t[e].indexOf("M  V30 MDLV30/STEABS ATOMS=(");for(;-1!==v;){v+=28;const n=t[e].indexOf(")",v);t[e].substring(v,n).split(" ").slice(1).forEach((t=>{s.push(parseInt(t)+a)})),v=n,v=t[e].indexOf("M  V30 MDLV30/STEABS ATOMS=(",v)}a+=u.natom-1,l+=u.nbond,c+=n?Math.max(...d.x):d.x[u.natom-1]-d.x[0]}const u=Math.ceil(s.length/4);i+="M  V30 MDLV30/STEABS ATOMS=("+s.length+" -\n";for(let t=0;t<u;t++){i+="M  V30 ";const e=t+1===u?s.length-4*(u-1):4;for(let n=0;n<e;n++)i+=n+1===e?t===u-1?s[4*t+n]+")\n":s[4*t+n]+" -\n":s[4*t+n]+" "}return a++,n+="M  V30 COUNTS "+a+" "+l+" 0 0 0\n",n+="M  V30 BEGIN ATOM\n",n+=o,n+="M  V30 END ATOM\n",n+="M  V30 BEGIN BOND\n",n+=r,n+="M  V30 END BOND\n",e&&s.length>0?(n+="M  V30 BEGIN COLLECTION\n",n+=i,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 o=e+1,r=t.x[o],i=t.y[o],s=t.x[n]-r,a=t.y[n]-i,l=t.x[e]-r,c=t.y[e]-i,u=l*Math.cos(2*Math.PI/3)-c*Math.sin(2*Math.PI/3),d=l*Math.sin(2*Math.PI/3)+c*Math.cos(2*Math.PI/3),h=l-s,p=c-a,m=u-s,g=d-a;Math.sqrt(g*g+m*m)>=Math.sqrt(p*p+h*h)&&(t.x[e]=u+r,t.y[e]=d+i)}}var P,H=n(864),_=n(622);!function(t){t.HEADER="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.RGP_LINE="M  RGP",t.A_LINE="A  ",t.END="M  END"}(P||(P={}));class R extends _.w{constructor(t){super(t)}static validate(t){return-1!==t.indexOf(P.HEADER)&&-1!==t.indexOf(P.END)}shiftIdxToAtomType(t){return this.shiftIdxToSpecifiedColumn(t,P.ATOM_TYPE_COL)}getCountsLineIdx(){let t=0;for(let e=0;e<P.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,P.FIRST_BONDED_ATOM_COL)}shiftIdxToBondType(t){return this.shiftIdxToSpecifiedColumn(t,P.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+P.NUM_OF_COUNTS_DIGITS;const n=parseInt(this.fileContent.substring(t,e));return t=e,e+=P.NUM_OF_COUNTS_DIGITS,{atomCount:n,bondCount:parseInt(this.fileContent.substring(t,e))}}}var j=n(577);class q{constructor(){}static getInstance(t){if(R.validate(t))return new R(t);if(j.u.validate(t))return new j.u(t);throw new Error("Malformed molfile")}}var G=n(604);const U=class extends Error{constructor(t){super(t)}};class W{constructor(t){this.molblock=t}_validMolBlock;get molblock(){return this._validMolBlock}set molblock(t){if(""!==t){try{this.validateMolBlock(t)}catch(e){e instanceof U&&(t="");const n=(0,G.O)(e);console.error(n)}this._validMolBlock=t}else this._validMolBlock=t}validateMolBlock(t){if(""===t)throw new U("MoleculeImage: invalid molblock")}async drawMolBlockOnCanvas(t){try{await r.functions.call("Chem:canvasMol",{x:0,y:0,w:t.width,h:t.height,canvas:t,molString:this.molblock,scaffoldMolString:"",options:{normalizeDepiction:!1,straightenDepiction:!1}})}catch(t){const e=(0,G.O)(t);console.error(e)}}getMoleculeDimensions(){const t=q.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=i.dialog({title:"Molecule",showFooter:!1}),e=.7*T()(window).height(),n=this.getMoleculeDimensions(),o=e/n.height,r=e,s=n.width*o,a=i.canvas(s,r);await this.drawMolBlockOnCanvas(a);const l=i.block([a],{style:{overflowX:"scroll"}});t.add(l).showModal(!0),T()(t.root).find(".d4-dialog-contents").removeClass("ui-form"),T()(t.root).find(".d4-dialog-contents").removeClass("ui-panel"),T()(t.root).find(".d4-dialog-contents").addClass("ui-box"),T()(t.root).find(".d4-dialog-contents").css("padding","0")}async drawMolecule(t,e,n){t.innerHTML="";const o=i.canvas(e*window.devicePixelRatio,n*window.devicePixelRatio);o.style.width=`${e}px`,o.style.height=`${n}px`,o.style.cursor="zoom-in",this.drawMolBlockOnCanvas(o),o.addEventListener("click",(async()=>{await this.zoomIn()})),t.append(i.tooltip.bind(o,"Click to zoom"))}}var Y=n(713),z=n(511),X=n(456);class Z{constructor(){const t=Object.keys(O.Rv).concat(y.NI.HELM);this.moleculeImgDiv=i.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=i.div([]),this.formatChoiceInput=i.choiceInput("",y.NI.HELM,t,(async()=>{this.format=this.formatChoiceInput.value,this.updateTable(),await this.updateMolImg()})),this.sequenceInputBase=i.textInput("",z.T,(()=>{this.onInput.next()})),this.init(),o.debounce(this.onInput,300).subscribe((async()=>{this.init(),this.formatChoiceInput.value=this.format,this.updateTable(),await this.updateMolImg()}))}onInput=new s.Subject;moleculeImgDiv;outputTableDiv;formatChoiceInput;sequenceInputBase;molfile;sequence;format;async getHtmlElement(){const t=new L(this.sequenceInputBase,M),e=i.button("Get SDF",(()=>{this.saveMolfile()}),"Save structure as SDF"),n=i.button("Copy SMILES",(()=>{this.copySmiles()}),"Copy SMILES for the sequence"),o=i.div([this.formatChoiceInput]),r=i.button(i.icons.delete((()=>{t.inputBase.value=""})),(()=>{}));i.tooltip.bind(r,"Clear input");const s={format:o,textInput:t.root,clearBtn:r},a=i.table([s],(t=>[t.format,t.textInput,t.clearBtn]));a.classList.add("st-translator-input-table");const l=i.block([this.outputTableDiv,e,n]),c=i.box(i.panel([a,l,i.block([i.box(this.moleculeImgDiv)])]));return this.formatChoiceInput.value=this.format,this.updateTable(),await this.updateMolImg(),c}saveMolfile(){const t=new k(this.sequence,!1,this.formatChoiceInput.value).convert()+"\n$$$$";(0,w.LR)(this.sequence+".sdf",encodeURIComponent(t))}copySmiles(){const t=o.chem.convert(this.molfile,o.chem.Notation.MolBlock,o.chem.Notation.Smiles);navigator.clipboard.writeText(t).then((()=>r.shell.info(Y.AU)))}updateTable(){this.outputTableDiv.innerHTML="";const t=this.format?new b.b(this.sequence).getInvalidCodeIndex(this.format):0,e=(0,H.D)(this.sequence,t,this.format),n=[];for(const t of Object.keys(e)){const o="indexOfFirstInvalidChar"in 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K=n(753),Q={};Q.styleTagTransform=v(),Q.setAttributes=m(),Q.insert=h().bind(null,"head"),Q.domAPI=u(),Q.insertStyleElement=f(),l()(K.Z,Q),K.Z&&K.Z.locals&&K.Z.locals;var J=n(261);function tt(t,e){if(""===t)return"";const n=new I(t).getFormat();if(!n)return"";let o="";try{o=new k(t,e,n).convert()}catch(t){const e=(0,G.O)(t);console.error(e)}return o}function et(t,e,n,o){const r=[t,e,n].filter((t=>""!==t.strand));if(1===r.length)return tt(r[0].strand,r[0].invert);{const r=tt(t.strand,t.invert),i=[tt(e.strand,e.invert),tt(n.strand,n.invert)].filter((t=>""!==t));return(0,J.v5)({senseStrands:[r],antiStrands:i},o)}}const nt=["ss","as","as2"];class ot{constructor(){this.onInput=new s.Subject,this.onInvalidInput=new s.Subject,this.inputBase=Object.fromEntries(nt.map((t=>[t,i.textInput("","",(()=>{this.onInput.next()}))]))),this.useChiralInput=i.boolInput("Use chiral",!0),this.saveAllStrandsInput=i.boolInput("Save as one entity",!0),i.tooltip.bind(this.saveAllStrandsInput.root,"Save SDF with all strands in one molfile"),this.directionInversion=Object.fromEntries(nt.map((t=>[t,!1]))),this.moleculeImgDiv=i.block([]),T()(this.moleculeImgDiv).addClass("st-structure-mol-img"),o.debounce(this.onInput,300).subscribe((async()=>{await this.updateMoleculeImg()})),o.debounce(this.onInvalidInput,1e3).subscribe((async()=>{r.shell.warning("Insert Sense strand")}))}onInput;onInvalidInput;useChiralInput;saveAllStrandsInput;inputBase;directionInversion;moleculeImgDiv;async getHtmlDivElement(){const t=this.getTableInput(),e=this.getBoolInputsAndButton();await this.updateMoleculeImg();const n=i.divH([e,this.moleculeImgDiv]);T()(n).addClass("st-structure-bottom");const o=i.divV([t,n]);return T()(o).addClass("st-structure-body"),o}getBoolInputsAndButton(){const t=i.buttonsInput([i.bigButton("Save SDF",(()=>{const t=this.getStrandData();!function(t,e,n,o,i){const s=[t.strand,e.strand,n.strand].filter((t=>""!==t));if(0===s.length||1===s.length&&""===t.strand)r.shell.warning("Enter SS and optionally AS/AS2 to save SDF");else{let a;if(i)a=et(t,e,n,o)+"\n$$$$\n";else{const d=tt(t.strand,t.invert),h=tt(e.strand,e.invert),p=tt(n.strand,n.invert);a=d+"\n> <Sequence>\nSense Strand\n$$$$\n",h&&(a+=h+"\n> <Sequence>\nAnti Sense\n$$$$\n"),p&&(a+=p+"\n> <Sequence>\nAnti Sense 2\n$$$$\n")}const l=new Date;function c(t){return t>=10?t.toString():"0"+t.toString()}const u=l.getFullYear()+"-"+c(l.getMonth()+1)+"-"+c(l.getDate())+"_"+c(l.getHours())+"-"+c(l.getMinutes())+"-"+c(l.getSeconds());(0,w.LR)(`SequenceTranslator-${u}.sdf`,encodeURIComponent(a))}}(t.ss,t.as,t.as2,this.useChiralInput.value,this.saveAllStrandsInput.value)}))]),e=[this.saveAllStrandsInput.root,this.useChiralInput.root,t],n=i.divV(e);for(const t of e)T()(t).addClass("st-structure-bool-button-block");return n}getTableInput(){const t=Object.fromEntries(nt.map((t=>[t,new L(this.inputBase[t],M)]))),e=Object.fromEntries(nt.map(((t,e)=>{const n=0===e?"5′ → 3′":"3′ → 5′";return[t,i.choiceInput(`${t.toUpperCase()} direction`,n,["5′ → 3′","3′ → 5′"])]})));nt.forEach(((t,n)=>{e[t].onChanged((()=>{let o="3′ → 5′"===e[t].value;n>0&&(o=!o),this.directionInversion[t]=o,this.onInput.next()}))}));const n=["Sense Strand","Anti Sense","Anti Sense 2"],o=new Map(nt.map(((t,e)=>[t,n[e]]))),r=Object.fromEntries(nt.map((t=>[t,i.label(o.get(t))]))),s=Object.fromEntries(nt.map((e=>{const n=i.icons.delete((()=>{t[e].inputBase.value=""})),o=i.button(n,(()=>{}));return i.tooltip.bind(o,`Clear ${e.toUpperCase()}`),[e,n]}))),a=nt.map((n=>({label:r[n],textInput:t[n].root,clear:s[n],choiceInput:e[n].root}))),l=i.table(a,(t=>[t.label,t.textInput,t.clear,t.choiceInput]));T()(l).css("margin-top","10px");for(const t of nt){let n=r[t].parentElement;n.classList.add("st-structure-input-form"),T()(n).css("padding-top","3px"),n=e[t].root.parentElement,n.classList.add("st-structure-input-form","st-structure-direction-choice"),n=this.inputBase[t].root.parentElement,n.classList.add("st-structure-text-input-td")}return l}getStrandData(){return Object.fromEntries(nt.map(((t,e)=>{let n=this.directionInversion[t];return[t,{strand:this.inputBase[t].value.replace(/\s*/g,""),invert:n}]})))}getMolfile(t,e,n){return et(t,e,n,this.useChiralInput.value)}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=(0,G.O)(t);console.error(e)}const e=new W(t);await e.drawMolecule(this.moleculeImgDiv,650,150),T()(this.moleculeImgDiv).find("canvas").css("float","inherit")}}const rt="SequenceTranslator",it="SS",st="AS",at=[it,st],lt={[it]:"Sense strand",[st]:"Anti sense"},ct="THREE_PRIME",ut="FIVE_PRIME",dt=[ct,ut],ht={[ct]:3,[ut]:5};function pt(t){return"(o)"===t.slice(-3)}function mt(t){let e=0;for(;e<t.length&&pt(t[e]);)e++;return e===t.length-1?0:e}function gt(t,e){const n=document.createElement("canvas").getContext("2d");return n.font=String(e),2*n.measureText(t).width}function ft(t,e){return pt(t[e])||!y.mc.includes(t[e])?"":t[e]}function At(t){const e=O.al[t].color.match(/\d+/g).map((t=>Number(t)));return.299*e[0]+.587*e[1]+.114*e[2]>186?"#33333":"#ffffff"}function vt(t){return O.al[t].color}const xt={xmlns:"http://www.w3.org/2000/svg",render:function(t,e){const n=document.createElementNS(this.xmlns,"svg");return n.setAttribute("id","mySvg"),n.setAttribute("width",String(t)),n.setAttribute("height",String(e)),n},circle:function(t,e,n,o){const r=document.createElementNS(this.xmlns,"circle");return r.setAttribute("cx",String(t)),r.setAttribute("cy",String(e)),r.setAttribute("r",String(n)),r.setAttribute("fill",o),r},text:function(t,e,n,o,r){const i=document.createElementNS(this.xmlns,"text");return i.setAttribute("x",String(e)),i.setAttribute("y",String(n)),i.setAttribute("font-size",String(o)),i.setAttribute("font-weight","normal"),i.setAttribute("font-family","Arial"),i.setAttribute("fill",r),i.innerHTML=t,i},star:function(t,e,n){const 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t(e){x[e].innerHTML="",C[e]=C[e].concat(Array(v[e]-b[e].length).fill(A)),b[e]=b[e].concat(Array(v[e]-b[e].length).fill(f));let o=0;for(let r=0;r<w[e].value;r++)C[e][r]=i.boolInput("",C[e][r].value,(()=>{s(),n()})),b[e][r]=i.choiceInput("",b[e][r].value,p,(e=>{g.includes(e)||(g.push(e),k.append(i.divText("",{style:{width:"25px"}}),i.boolInput(e,!0,(t=>{if(t)g.includes(e)||g.push(e);else{const t=g.indexOf(e,0);t>-1&&g.splice(t,1)}s()})).root)),t(st),s(),n()})),T()(b[e][r].root).addClass("st-pattern-choice-input"),pt(b[e][r].value)||o++,x[e].append(i.divH([i.div([i.label(pt(b[e][r].value)?"":String(o))],{style:{width:"20px"}}),i.block75([b[e][r].root]),i.div([C[e][r]])],{style:{alignItems:"center"}}))}function e(){Object.values(w).every((t=>t.value<35))?(at.forEach((e=>{w[e].value>v[e]&&(v[e]=w[e].value),t(e)})),s(),at.forEach((t=>{""===I[t].value&&(E[t].value=Ct(w[t].value,f.value))})),n()):i.dialog("Out of range").add(i.divText("Sequence length should be less than "+35..toString()+" due 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n}(n.asBases.concat(n.ssBases)),j.value=n.asBases.length>0,q.value=t;let o=["ssBases","asBases"];at.forEach(((t,e)=>{b[t]=[];const r=o[e];for(let e=0;e<n[r].length;e++)b[t].push(i.choiceInput("",n[r][e],p))})),o=["ssPtoLinkages","asPtoLinkages"],at.forEach(((t,e)=>{const r=o[e];S[t].value=n[r][0],C[t]=[];for(let e=1;e<n[r].length;e++)C[t].push(i.boolInput("",n[r][e]))})),o=["ssBases","asBases"],at.forEach(((t,e)=>{w[t].value=n[o[e]].length}));const r=[["ssThreeModification","ssFiveModification"],["asThreeModification","asFiveModification"]];at.forEach(((t,e)=>{dt.forEach(((o,i)=>{M[t][o].value=n[r[e][i]]}))})),$.value=n.comment})),e.close()}async function l(){const t=await async function(){return await r.dapi.users.current().then((t=>" (created by "+t.friendlyName+")"))}();return q.value=q.stringValue.includes("(created by 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pattern","",u,(t=>a(t))),o.root.append(l.input),o.root.append(o.input),o.input.style.maxWidth="120px",o.input.style.marginLeft="12px",o.setTooltip("Apply Existing Pattern"),F.innerHTML="",F.append(o.root),o.root.append(i.div([i.button(i.iconFA("trash-alt",(()=>{})),(async()=>{null===o.value?r.shell.warning("Choose pattern to delete"):await bt(q.value)?r.shell.warning("Cannot delete pattern, created by other user"):await r.dapi.userDataStorage.remove(rt,o.value,!1).then((()=>r.shell.info("Pattern '"+o.value+"' deleted"))),await c()}))],"ui-input-options"))}));l.input.style.maxWidth="142px",o.root.append(l.input),o.root.append(o.input),o.input.style.maxWidth="100px",o.setTooltip("Apply Existing Pattern"),F.innerHTML="",F.append(o.root),o.root.append(i.div([i.button(i.iconFA("trash-alt",(()=>{})),(async()=>{null===o.value?r.shell.warning("Choose pattern to delete"):await bt(q.value)?r.shell.warning("Cannot delete pattern, created by other user"):await r.dapi.userDataStorage.remove(rt,o.value,!1).then((()=>r.shell.info("Pattern '"+o.value+"' deleted"))),await c()}))],"ui-input-options"))}))}async function u(){await r.dapi.userDataStorage.get(rt,!1).then((t=>{if(Object.keys(t).includes(q.value)){const t=i.dialog("Pattern already exists");T()(t.getButton("OK")).hide(),t.add(i.divText("Pattern name '"+q.value+"' already exists.")).add(i.divText("Replace pattern?")).addButton("YES",(async()=>{await r.dapi.userDataStorage.remove(rt,q.value,!1).then((()=>l())),t.close()})).show()}else l()})),await c()}function d(t,e){const n=function(t){const e=H.value.getCol(t);let n=!0;for(let t=1;t<e.length;t++)if(e.get(t-1).length!==e.get(t).length&&0!==e.get(t).length){n=!1;break}if(!n){const n=i.dialog("Sequences lengths mismatch");T()(n.getButton("OK")).hide(),n.add(i.divText("The sequence length should match the number of Raw sequences in the input file")).add(i.divText("'ADD COLUMN' to see sequences lengths")).addButton("ADD COLUMN",(()=>{H.value.columns.addNewInt("Sequences lengths in "+t).init((t=>e.get(t).length)),r.shell.info("Column with lengths added to '"+H.value.name+"'"),n.close(),r.shell.v=r.shell.getTableView(H.value.name)})).show()}return e.get(0).length!==w[it].value&&i.dialog("Length was updated by value to from imported file").add(i.divText("Latest modifications may not take effect during translation")).onOK((()=>r.shell.info("Lengths changed"))).show(),n}(t),o=H.value.getCol(t).get(0);n&&o.length!==w[e].value&&(w[e].value=H.value.getCol(t).get(0).length),E[e].value=o}function h(t){const e=H.value.getCol(t);if(e.type!==o.TYPE.INT)r.shell.error("Column should contain integers only");else if(e.categories.filter((t=>""!==t)).length<e.toList().filter((t=>""!==t)).length){const t=(n=e.getRawData(),Array.from(new Set(n)).filter((t=>n.indexOf(t)!==n.lastIndexOf(t))));i.dialog("Non-unique IDs").add(i.divText("Press 'OK' to select rows with non-unique values")).onOK((()=>{H.value.selection.init((n=>t.indexOf(e.get(n))>-1)),r.shell.v=r.shell.getTableView(H.value.name),r.shell.info("Rows are selected in table '"+H.value.name+"'")})).show()}var n}const p=Object.keys(O.al),m=p[0],g=[m],f=i.choiceInput("Sequence basis",m,p,(t=>{var e;e=t,at.forEach((t=>{for(let n=0;n<b[t].length;n++)b[t][n].value=e})),s(),n()})),A=i.boolInput("Fully PTO",!0,(t=>{var e;at.forEach((e=>{S[e].value=t})),e=t,at.forEach((t=>{for(let n=0;n<C[t].length;n++)C[t][n].value=e})),s(),n()}));A.captionLabel.classList.add("ui-label-right"),A.captionLabel.style.textAlign="left",A.captionLabel.style.maxWidth="100px",A.captionLabel.style.maxWidth="100px",A.captionLabel.style.minWidth="40px",A.captionLabel.style.width="auto";const v=Object.fromEntries(at.map((t=>[t,23]))),x=Object.fromEntries(at.map((t=>[t,i.div([])]))),C=Object.fromEntries(at.map((t=>[t,Array(23).fill(i.boolInput("",!0))]))),b=Object.fromEntries(at.map((t=>[t,Array(23).fill(i.choiceInput("",m,p))]))),w=Object.fromEntries(at.map((t=>{const n=i.intInput(`${lt[t]} length`,23,(()=>e()));return n.setTooltip(`Length of ${lt[t].toLowerCase()}, including overhangs`),[t,n]}))),y=Object.fromEntries(at.map((t=>[t,""]))),E=Object.fromEntries(at.map((t=>[t,i.textInput("",Ct(w[t].value,f.value))]))),I=Object.fromEntries(at.map((t=>{const e=i.choiceInput(`${lt[t]} column`,"",[],(e=>{d(e,t),y[t]=e}));return[t,e]}))),S=Object.fromEntries(at.map((t=>{const e=i.boolInput(`First ${t} PTO`,A.value,(()=>s()));return e.setTooltip(`ps linkage before first nucleotide of ${lt[t].toLowerCase()}`),e.captionLabel.classList.add("ui-label-right"),e.captionLabel.style.textAlign="left",e.captionLabel.style.maxWidth="100px",e.captionLabel.style.minWidth="40px",e.captionLabel.style.width="auto",[t,e]}))),M=Object.fromEntries(at.map((t=>{const e=Object.fromEntries(dt.map((e=>{const o=i.stringInput(`${t} ${ht[e]}' Modification`,"",(()=>{s(),n()}));return o.setTooltip(`Additional ${t} ${ht[e]}' Modification`),[e,o]})));return[t,e]}))),B=Object.fromEntries(at.map((t=>{const e=i.textInput("",yt(E[t].value,b[t],C[t],M[t][ct],M[t][ut],S[t].value));return e.input.style.minWidth="none",e.input.style.flexGrow="1",T()(e.root.lastChild).css("height","auto"),[t,e]}))),N=Object.fromEntries(at.map((t=>[t,i.block([i.h1(`${lt[t]}`),i.divH([i.div([i.divText("#")],{style:{width:"20px"}}),i.block75([i.divText("Modification")]),i.div([i.divText("PTO")])]),x[t]],{style:{paddingTop:"12px"}})])));at.forEach((t=>{E[t].input.style.resize="none",B[t].input.style.resize="none",E[t].input.style.minWidth="none",E[t].input.style.flexGrow="1",B[t].input.style.minWidth="none",B[t].input.style.flexGrow="1";let e=i.div([i.button(i.iconFA("copy",(()=>{})),(()=>{navigator.clipboard.writeText(B[t].value).then((()=>r.shell.info("Sequence was copied to clipboard")))}))],"ui-input-options");e.style.height="inherit",B[t].root.append(e)}));const L=i.div([]),D=i.div([],"ui-form ui-form-wide"),F=i.div([]),V=i.form([]),k=i.divH([i.boolInput(m,!0,(t=>{if(t)g.includes(m)||g.push(m);else{const t=g.indexOf(m,0);t>-1&&g.splice(t,1)}s(),n()})).root]),P=i.div([w[st].root]),H=function(t){const e=i.tableInput("Tables",t[0],t,(()=>{const t=e.value;if(null===t)return void console.warn("Table is null");const n=t.name;if(!r.shell.tableNames.includes(n)){const e=r.shell.v;r.shell.addTableView(t),r.shell.v=e}const o=t.columns.names();at.forEach((t=>{const e=o[0];d(e,t),y[t]=e;const n=i.choiceInput(`${lt[t]} column`,e,o,(e=>{d(e,t),y[t]=e,console.log(`clicked ${t} var:`,y[t])}));T()(I[t].root).replaceWith(n.root)})),_=o[0];const s=i.choiceInput("ID column",o[0],o,(t=>{h(t),_=t}));T()(R.root).replaceWith(s.root)}));return e}([]);let _="";const R=i.choiceInput("ID column","",[],(t=>{h(t),_=t}));c();const j=i.boolInput("Anti sense strand",!0,(t=>{N[st].hidden=!t,I[st].root.hidden=!t,P.hidden=!t,V.hidden=!t,D.hidden=!t,S[st].root.hidden=!t,s()}));j.setTooltip("Create antisense strand sections on SVG and table to the right");const q=i.textInput("Save as","Pattern name",(()=>s()));q.setTooltip("Name Of New Pattern"),dt.forEach((t=>{V.append(M[st][t].root)}));const $=i.textInput("Comment","",(()=>s())),G=i.bigButton("Save",(()=>{if(""!==q.value)u().then((()=>r.shell.info("Pattern saved")));else{const t=i.stringInput("Enter name","");i.dialog("Pattern Name").add(t.root).onOK((()=>{q.value=t.value,u().then((()=>r.shell.info("Pattern saved")))})).show()}}));q.addOptions(G);const U=i.bigButton("Convert",(()=>{const t=[!0,j.value];if(console.log("strand vars:",Object.values(y)),at.some(((e,n)=>t[n]&&""===y[e])))r.shell.info("Please select table and columns on which to apply pattern");else if(at.some((t=>w[t].value!==E[t].value.length))){const t=i.dialog("Length Mismatch");T()(t.getButton("OK")).hide(),t.add(i.divText("Length of sequences in columns doesn't match entered length. Update length value?")).addButton("YES",(()=>{at.forEach((t=>{w[t].value=H.value.getCol(I[t].value).getString(0).length})),t.close()})).show()}else{""!==_&&function(t,e,n){const o="ID "+n,i=r.shell.table(t).columns;i.contains(o)&&i.remove(o);const s=i.byName(e);i.addNewString(o).init((t=>""===s.getString(t)?"":s.get(t)+"_"+n))}(H.value.name,_,wt(q.value));const t=[!0,j.value];at.forEach(((e,n)=>{t[n]&&function(t,e,n,o,i,s,a){const l="Axolabs "+e,c=r.shell.table(t).columns;c.contains(l)&&c.remove(l);const u=c.byName(e);c.addNewString(l).init((t=>""===u.getString(t)?"":yt(u.getString(t),n,o,i,s,a)))}(H.value.name,y[e],b[e],C[e],M[e][ut],M[e][ct],S[e].value)})),r.shell.v=r.shell.getTableView(H.value.name),r.shell.info((j.value?"Columns were":"Column was")+" added to table '"+H.value.name+"'"),n()}}));D.append(E[st].root),D.append(B[st].root),e(),i.div([i.h1("Conversion preview"),E[it].root,B[it].root,D],"ui-form ui-form-wide"),i.block50([i.h1("Convert options"),H.root,I[it].root,I[st].root,R.root,i.buttonsInput([U])]).classList.add("ui-form");const W=i.link("Download",(()=>Pt.saveSvgAsPng(document.getElementById("mySvg"),q.value,{backgroundColor:"white"})),"Download pattern as PNG image",""),Y=i.link("Edit pattern",(()=>{i.dialog("Edit pattern").add(i.divV([i.h1("PTO"),i.divH([A.root,S[it].root,S[st].root],{style:{gap:"12px"}})])).add(i.divH([N[it],N[st]],{style:{gap:"24px"}})).onOK((()=>{r.shell.info("Saved")})).show()}),"Edit pattern","");return w[it].addCaption("Length"),i.splitH([i.box(i.div([i.h1("Pattern"),j.root,w[it],w[st],f.root,$.root,F,q.root,i.h1("Convert"),H.root,I[it],I[st],R.root,i.buttonsInput([U])],"ui-form"),{style:{maxWidth:"450px"}}),i.panel([L,k,i.divH([W,Y],{style:{gap:"12px",marginTop:"12px"}}),i.divH([i.divV([i.h1("Sense strand"),E[it].root,B[it].root],"ui-block"),i.divV([i.h1("Anti sense"),E[st],B[st]],"ui-block")],{style:{gap:"24px",marginTop:"24px"}}),i.h1("Additional modifications"),i.form([M[it][ut],M[it][ct]]),V],{style:{overflowX:"scroll",padding:"12px 24px"}})],{},!0)}}async function _t(t){try{const e={overflowX:"scroll"},n=i.div([],{style:e}),o=(0,J.$U)(t),s=.7*T()(window).height(),a=Math.max(...o.x)-Math.min(...o.x),l=Math.max(...o.y)-Math.min(...o.y),c=s/l,u=c*a,d=c*l,h=i.canvas(u*window.devicePixelRatio,d*window.devicePixelRatio);h.style.width=`${u}px`,h.style.height=`${d}px`,await async function(t,e){await r.functions.call("Chem:canvasMol",{x:0,y:0,w:t.width,h:t.height,canvas:t,molString:e,scaffoldMolString:"",options:{normalizeDepiction:!1,straightenDepiction:!1}})}(h,t),n.appendChild(h),i.dialog("Molecule").add(n).showModal(!0)}catch(t){const e=(0,G.O)(t);console.error(e)}}class Rt{static async view(){const t=E.A.getInstance().getTableForViewer();t.name="Monomer Library";const e=r.shell.addTableView(t);e.grid.props.allowEdit=!1,e.grid.onCellDoubleClick.subscribe((async t=>{const e=t.cell.value;"Molecule"===t.tableColumn?.semType&&await _t(e)}))}}class jt{appName;parentAppName;constructor(t,e){this.appName=t,this.parentAppName=e}async createAppLayout(){const t=o.TaskBarProgressIndicator.create(`Loading ${this.appName}...`);let e=r.shell.v?.root;e&&i.setUpdateIndicator(e,!0),await(0,w.Y3)((async()=>{await this.addView()}),(()=>t.close())),e&&i.setUpdateIndicator(e,!1)}}class qt extends jt{constructor(t){super(t),this.view=o.View.create(),this.setupView()}view;async addView(){await this.initView();const t=this.parentAppName?this.parentAppName+"/"+this.appName:this.appName;this.view.path=`/apps/${pe.name}/${t.replace(/\s/g,"")}/`,r.shell.addView(this.view)}async initView(){const t=await this.getHtml();this.view.append(t)}setupView(){this.view.box=!0,this.view.name=this.appName;const t=r.shell.windows;t.showProperties=!1,t.showToolbox=!1,t.showHelp=!1}getView(){return this.view}}class $t extends jt{constructor(t){super("Oligo Toolkit"),this.externalViewFactories=t;const e=this.getViewFactories();this.multiView=new o.MultiView({viewFactories:e})}multiView;externalViewFactories;getViewFactories(){function t(t){const e=new t(o.View.create());return e.initView(),()=>e.getView()}let e={TRANSLATOR:t(Wt),PATTERN:t(Yt),STRUCTURE:t(zt)};return this.externalViewFactories&&(e=Object.assign({},e,this.externalViewFactories)),e}getPath(){let t=this.multiView.tabs.currentPane.name;return t=t.charAt(0).toUpperCase()+t.substring(1).toLowerCase(),`/apps/${pe.name}/OligoToolkit/${t}`}setUrl(){this.multiView.path=this.getPath()}async addView(){this.multiView.tabs.onTabChanged.subscribe((()=>this.setUrl())),this.setUrl(),r.shell.addView(this.multiView)}}class Gt extends qt{constructor(t,e){super(t),this.layout=e}layout;getHtml(){return Promise.resolve(this.layout)}}class Ut{constructor(){}static getUI(t){switch(t){case"Oligo Translator":return new Wt;case"Oligo Pattern":return new Yt;case"Oligo Structure":return new zt;default:throw new Error(`Unknown app name: ${t}`)}}}class Wt extends qt{constructor(){super("Oligo Translator");const t=i.iconFA("book",Rt.view,"View monomer library");this.topPanel=[t],this.view.setRibbonPanels([this.topPanel]),this.ui=new Z}topPanel;ui;getHtml(){return this.ui.getHtmlElement()}}class Yt extends qt{constructor(){super("Oligo Pattern"),this.ui=new Ht}ui;getHtml(){return Promise.resolve(this.ui.htmlDivElement)}}class zt extends qt{constructor(){super("Oligo Structure"),this.ui=new ot}ui;getHtml(){return this.ui.getHtmlDivElement()}}var Xt,Zt,Kt=n(895);wu;class Qt{constructor(t,e,n){this.name=t,this.alphabet=e,this.cutoff=n}}(Zt=Xt||(Xt={})).FASTA="fasta",Zt.SEPARATOR="separator",Zt.HELM="helm";const Jt=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"])}}};new Qt("PT",Jt.fasta.peptide,.5),new Qt("DNA",Jt.fasta.dna,.55),new Qt("RNA",Jt.fasta.rna,.55);class te extends Float32Array{}class ee{static makePalette(t,e=!1,n=ee){const o={};return t.forEach((t=>{const n=t[0],r=t[1];n.forEach(((t,n)=>{o[t]=this.colourPalette[r][e?0:n]}))})),new n(o)}constructor(t){this._palette=t}get(t){return this._palette[t]}}ee.undefinedColor="rgb(100,100,100)",ee.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 ne extends ee{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,ne)),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,ne)),this.grokGroups}static get RasMol(){return void 0===this.rasMol&&(this.rasMol=new ne({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 ne.aaSynonyms?ne.aaSynonyms[t]:t;return super.get(e)}}ne.aaSynonyms={MeNle:"L",MeA:"A",MeG:"G",MeF:"F"};class oe{static getPalette(t="grok"){switch(t){case"grok":return ne.GrokGroups;case"lesk":return ne.Lesk;default:throw new Error(`ChemPalette: scheme \`${t}\` does not exist`)}}static getInnerOuter(t){let e=0,n="",o="";for(const r of t)"("==r?e++:")"==r?e--:e?n+=r:o+=r;return isNaN(parseInt(n))?[o,n]:[o,""]}static getColorAAPivot(t="",e="grok"){const n=this.getPalette(e);let[o,r]=this.getInnerOuter(t);if(o=o.length>6?`${o.slice(0,3)}...`:o,r=r.length>6?`${r.slice(0,3)}...`:r,1==t.length||"("==t[1]){const e=t[0]?.toUpperCase();return e in n?[n.get(e),e,r,1]:[this.undefinedColor,o,r,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,r,2]:[this.undefinedColor,o,r,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,r,3]:[this.undefinedColor,o,r,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,r,4]:[this.undefinedColor,o,r,4]}return[this.undefinedColor,o,r,0]}}oe.SemType="Aminoacids",oe.SemTypeMultipleAlignment="AminoacidsMultipleAlignment",oe.undefinedColor="rgb(100,100,100)",oe.Names={G:"Glycine",L:"Leucine",Y:"Tyrosine",S:"Serine",E:"Glutamic acid",Q:"Glutamine",D:"Aspartic 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a{constructor(){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(s);e[t]=r[0]})),e}(o.$D[t])}getFormatToHelmDict(t){this.validateFormat(t);const e=o.$D[t];return Object.assign({},...Object.values(e))}getTargetFormatHelmCodes(t){this.validateFormat(t);const e=this.getHelmToFormatDict(t);return Object.keys(e).sort(s)}getTargetFormatHelmCodesRegExp(t){this.validateFormat(t);const e=this.getTargetFormatHelmCodes(t);return new RegExp(u(e)+"|.","g")}getFormatRegExp(t){if(this.validateFormat(t),this.isHelm(t))throw new Error("Helm RegExp 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r=n(82),i=n.n(r),o=n(328),s=n(620),a=n(448);const u={monomerType:"Backbone",smiles:"",name:"",author:"Datagrok",molfile:"",naturalAnalog:"",rgroups:[],createDate:null,id:0,polymerType:"PEPTIDE",symbol:""},l="p",c=new RegExp(`[rd]\\((\\w)\\)${l}?`,"g");class h{constructor(t,e,n){this.name=t,this.alphabet=e,this.cutoff=n}}class f extends h{constructor(t,e,n){super(t.name,t.alphabet,t.cutoff),this.freq=e,this.similarity=n}}const d=wu;var p,g,m=n.n(d);(g=p||(p={})).FASTA="fasta",g.SEPARATOR="separator",g.HELM="helm";const v=/(?:\[([A-Za-z0-9_\-,()]+)\])|([A-Za-z\-])/g,y=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"])}}},b=[new h("PT",y.fasta.peptide,.5),new h("DNA",y.fasta.dna,.55),new h("RNA",y.fasta.rna,.55)];class A extends Float32Array{}function C(t){let e=0;for(let n=0;n<t.length;n++)e+=t[n]*t[n];return Math.sqrt(e)}class w{static 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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,x)),this.grokGroups}static get RasMol(){return void 0===this.rasMol&&(this.rasMol=new x({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 x.aaSynonyms?x.aaSynonyms[t]:t;return super.get(e)}}x.aaSynonyms={MeNle:"L",MeA:"A",MeG:"G",MeF:"F"};class _{static getPalette(t="grok"){switch(t){case"grok":return x.GrokGroups;case"lesk":return x.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]}}_.SemType="Aminoacids",_.SemTypeMultipleAlignment="AminoacidsMultipleAlignment",_.undefinedColor="rgb(100,100,100)",_.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"},_.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"},_.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(*)*"},_.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 S{}S.SemType="Nucleotides",S.SemTypeMultipleAlignment="NucleotidesMultipleAlignment",S.Names={A:"Adenine",C:"Cytosine",G:"Guanine",T:"Thymine",U:"Uracil"};class E{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 T{}class I extends T{static buildPalette(){return[].concat(...Object.values(w.colourPalette))}get(t){const e=E.hashCode(t)%I.palette.length;return function(t){if(null==t)return"rgb(100,100,100)";const e=r.Color.fromHtml(t),n=r.Color.g(e),i=r.Color.r(e),o=r.Color.b(e),s=Math.sqrt(Math.pow(0-i,2)+Math.pow(0-n,2)+Math.pow(0-o,2));return s>210?`rgb(${i/s*210},${n/s*210},${o/s*210})`:r.Color.toRgb(e)}(I.palette[e])}}I.palette=I.buildPalette();class N{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 O{get length(){return this.seqS.length}get canonicals(){return this.seqS}get originals(){return this.seqS}isGap(t){return this.getOriginal(t)===G[p.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 L=t=>{const e=m()(t.toString().matchAll(v)).map((t=>t[2]??t[1])).toArray();return new N(e,G[p.FASTA])},M=t=>t?new O(t):new N([],G[p.FASTA]);function B(t,e=void 0){return n=>{if(n){const r=n.replaceAll('"-"',"").replaceAll("'-'","").split(t,e);return new N(r,G[p.SEPARATOR])}return new N([],G[p.SEPARATOR])}}const P=/(PEPTIDE1|DNA1|RNA1)\{([^}]+)}/g,R=/\[([^\[\]]+)]/g,F=t=>{P.lastIndex=0;const e=P.exec(t.toString()),n=e?e[2]:null,r=n?n.split("."):[];return new N(r.map((t=>{R.lastIndex=0;const e=R.exec(t);return e&&e.length>=2?e[1]:t})),G[p.HELM])};function D(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 A(i),a=new A(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)/(C(s)*C(a))}(t,e.alphabet,n);return new f(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}function U(t={}){const e=function(){if(!t||!t.scoringMatrix||!t.alphabetIndexes)return(t,e)=>t===e?0:1;if(t.scoringMatrix.length!==Object.keys(t.alphabetIndexes).length)throw new Error("Scoring matrix and alphabet indexes should have the same length");const e=t.alphabetIndexes,n=t.scoringMatrix,r=Math.min(...Object.keys(e).map((t=>t.charCodeAt(0))))+1,i=new Float32Array((n.length+r)*(n.length+r));return Object.entries(e).forEach((([t,r])=>{const o=n[r];Object.entries(e).forEach((([e,r])=>{i[t.charCodeAt(0)*n.length+e.charCodeAt(0)]=o[r]}))})),(t,e)=>1-i[t.charCodeAt(0)*n.length+e.charCodeAt(0)]}(),n=t?.threshold??0;return(t,r)=>{let i=0;const o=t.length,s=r.length,a=Math.max(o,s)*(1-n);o!==s&&(i=Math.abs(o-s));let u=0;for(let n=0;n<Math.min(o,s);n++)if(t[n]!==r[n]&&(u+=e(t[n],r[n]),u>a))return 1;return u+=i,u/=Math.max(o,s),u}}const k=new Uint32Array(65536),H={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 V;!function(t){t.HAMMING="Hamming",t.LEVENSHTEIN="Levenshtein",t.NEEDLEMANN_WUNSCH="Needlemann-Wunsch",t.MONOMER_CHEMICAL_DISTANCE="Monomer chemical distance"}(V||(V={}));const j={[V.HAMMING]:U,[V.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--;)k[t.charCodeAt(u)]|=1<<u;for(u=0;u<r;u++){let t=k[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--;)k[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++)k[t.charCodeAt(e)]|=1<<e;for(let t=0;t<n;t++){const n=k[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++)k[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++)k[t.charCodeAt(e)]|=1<<e;let d=r;for(let t=0;t<n;t++){const n=k[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),p=c&h;d+=f>>>r-1&1,d-=p>>>r-1&1,f>>>31^s&&(o[t/32|0]^=1<<t),p>>>31^a&&(i[t/32|0]^=1<<t),f=f<<1|s,p=p<<1|a,c=p|~(u|f),l=f&u}for(let e=h;e<f;e++)k[t.charCodeAt(e)]=0;return d})(t,e)})(t,e)/Math.max(t.length,e.length)},[V.NEEDLEMANN_WUNSCH]:function(t){const e=new Uint16Array(65536),{gapOpen:n,gapExtend:r,scoringMatrix:i,alphabetIndexes:o}={...H,...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}},[V.MONOMER_CHEMICAL_DISTANCE]:U},q=new class{constructor(){this.seqHandler="seq-handler",this.notationProvider="seq-handler.notation-provider"}},G={[p.FASTA]:"-",[p.SEPARATOR]:"",[p.HELM]:"*"};class W{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!==r.TYPE.STRING)throw new Error(`Unexpected column type '${t.type}', must be '${r.TYPE.STRING}'.`);this._column=t;const e=this._column.getTag(r.TAGS.UNITS);if(null==e)throw new Error("Units are not specified in column");if(this._units=e,this._notation=this.getNotation(),this._defaultGapOriginal=this.isFasta()?G[p.FASTA]:this.isHelm()?G[p.HELM]:G[p.SEPARATOR],!this.column.tags.has("aligned")||!this.column.tags.has("alphabet")||!this.column.tags.has(".alphabetIsMultichar")&&!this.isHelm()&&"UN"===this.alphabet)if(this.isFasta())W.setUnitsToFastaColumn(this);else if(this.isSeparator()){const e=t.getTag("separator");W.setUnitsToSeparatorColumn(this,e)}else{if(!this.isHelm())throw new Error(`Unexpected units '${this.column.getTag(r.TAGS.UNITS)}'.`);W.setUnitsToHelmColumn(this)}if(!this.column.tags.has(".alphabetIsMultichar"))if(this.isHelm())this.column.setTag(".alphabetIsMultichar","true");else if(["UN"].includes(this.alphabet))throw new Error(`For column '${this.column.name}' of alphabet '${this.alphabet}' tag '.alphabetIsMultichar' is mandatory.`);this.notationProvider=this.column.temp[q.notationProvider]??null,this.columnVersion=this.column.version}static setUnitsToFastaColumn(t){if(t.column.semType!==r.SEMTYPE.MACROMOLECULE||t.column.getTag(r.TAGS.UNITS)!==p.FASTA)throw new Error(`The column of notation '${p.FASTA}' must be '${r.SEMTYPE.MACROMOLECULE}'.`);t.column.setTag(r.TAGS.UNITS,p.FASTA),W.setTags(t)}static setUnitsToSeparatorColumn(t,e){if(t.column.semType!==r.SEMTYPE.MACROMOLECULE||t.column.getTag(r.TAGS.UNITS)!==p.SEPARATOR)throw new Error(`The column of notation '${p.SEPARATOR}' must be '${r.SEMTYPE.MACROMOLECULE}'.`);if(!e)throw new Error(`The column of notation '${p.SEPARATOR}' must have the separator tag.`);t.column.setTag(r.TAGS.UNITS,p.SEPARATOR),t.column.setTag("separator",e),W.setTags(t)}static setUnitsToHelmColumn(t){if(t.column.semType!==r.SEMTYPE.MACROMOLECULE)throw new Error(`The column of notation '${p.HELM}' must be '${r.SEMTYPE.MACROMOLECULE}'`);t.column.setTag(r.TAGS.UNITS,p.HELM),W.setTags(t)}static setTags(t){const e=t.column.getTag(r.TAGS.UNITS),n=t.stats;if(Object.keys(n.freq).some((t=>t.length>1)),[p.FASTA,p.SEPARATOR].includes(e)){if(!t.column.getTag("alphabet")&&0===Object.keys(n.freq).length)throw new Error("Alphabet is empty and not annotated.");let e=t.column.getTag("aligned");null===e&&(e=n.sameLength?"SEQ.MSA":"SEQ",t.column.setTag("aligned",e));let r=t.column.getTag("alphabet");if(null===r&&(r=D(n.freq,b),t.column.setTag("alphabet",r)),"UN"===r){const e=Object.keys(n.freq).length,r=Object.keys(n.freq).some((t=>t.length>1));t.column.setTag(".alphabetSize",e.toString()),t.column.setTag(".alphabetIsMultichar",r?"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("separator")??void 0;if(this.notation===p.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("aligned");if(!t&&(this.isFasta()||this.isSeparator()))throw new Error("Tag aligned not set");return t}get alphabet(){const t=this.column.getTag("alphabet");if(!t&&(this.isFasta()||this.isSeparator()))throw new Error("Tag alphabet not set");return t}get helmCompatible(){return this.column.getTag(".isHelmCompatible")}getAlphabetSize(){if(this.notation==p.HELM||"UN"==this.alphabet){const t=this.column.getTag(".alphabetSize");let e;if(t)e=parseInt(t);else{const t=this.stats;e=Object.keys(t.freq).length}return e}switch(this.alphabet){case"PT":return 20;case"DNA":case"RNA":return 4;case"NT":return console.warn("Unexpected alphabet 'NT'."),4;default:throw new Error(`Unexpected alphabet '${this.alphabet}'.`)}}getAlphabetIsMultichar(){return this.notation===p.HELM||"UN"===this.alphabet&&"true"===this.column.getTag(".alphabetIsMultichar")}getSplitted(t){if(this.cached){this.column.version===this.columnVersion&&null!==this._splitted||(this.columnVersion=this.column.version,this._splitted=new Array(this.column.length));let e=this._splitted[t]?this._splitted[t].deref():void 0;if(!e){const n=this.column.get(t);e=this.splitter(n),this._splitted[t]=new WeakRef(e)}return e}{const e=this.column.get(t);return this.splitter(e)}}get stats(){if(null===this._stats){const t={};let e=!0,n=null;const r=this.column.length;for(let i=0;i<r;++i){const r=this.getSplitted(i);null==n?n=r.length:r.length!==n&&(e=!1);for(const e of r.canonicals)e in t||(t[e]=0),t[e]+=1}this._stats={freq:t,sameLength:e}}return this._stats}get maxLength(){return null===this._maxLength&&(this._maxLength=0===this.column.length?0:Math.max(...m().count(0).take(this.column.length).map((t=>this.getSplitted(t).length)))),this._maxLength}get posList(){if(null===this._posList){const t=this.column.getTag(".positionNames");this._posList=t?t.split(", ").map((t=>t.trim())):m().count(1).take(this.maxLength).map((t=>t.toString())).toArray()}return this._posList}isFasta(){return this.notation===p.FASTA}isSeparator(){return this.notation===p.SEPARATOR}isHelm(){return this.notation===p.HELM}isRna(){return"RNA"===this.alphabet}isDna(){return"DNA"===this.alphabet}isPeptide(){return"PT"===this.alphabet}isMsa(){return!!this.aligned&&this.aligned.toUpperCase().includes("MSA")}isHelmCompatible(){return"true"===this.helmCompatible}isGap(t){return!t||t===this._defaultGapOriginal}getNotation(){if(this.units.toLowerCase().startsWith(p.FASTA))return p.FASTA;if(this.units.toLowerCase().startsWith(p.SEPARATOR))return p.SEPARATOR;if(this.units.toLowerCase().startsWith(p.HELM))return p.HELM;throw new Error(`Column '${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,e,n,i){const o=this.column,s=t.toLowerCase()+"("+o.name+")",a=n??o.dataFrame.columns.getUnusedName(s),u=r.Column.fromList("string",a,i??new Array(this.column.length).fill(""));if(u.semType=r.SEMTYPE.MACROMOLECULE,u.setTag(r.TAGS.UNITS,t),t===p.SEPARATOR){if(!e)throw new Error(`Notation '${p.SEPARATOR}' requires separator value.`);u.setTag("separator",e)}u.setTag(r.TAGS.CELL_RENDERER,"sequence");const l=o.getTag("aligned");l&&u.setTag("aligned",l);let c=o.getTag("alphabet");c||this.notation!==p.HELM||t===p.HELM||(c="UN"),null!=c&&u.setTag("alphabet",c);let h=o.getTag(".alphabetSize");null!=c&&h&&u.setTag(".alphabetSize",h);const f=o.getTag(".alphabetIsMultichar");return null!=c&&void 0!==f&&u.setTag(".alphabetIsMultichar",f),t==p.HELM&&(h=this.getAlphabetSize().toString(),u.setTag(".alphabetSize",h)),u}getNewColumnFromList(t,e){return this.getNewColumn(this.notation,this.separator,t,e)}static getNewColumn(t){const e=W.forColumn(t),n=e.notation;return e.getNewColumn(n)}static unitsStringIsValid(t){return t=t.toLowerCase(),[p.FASTA,p.SEPARATOR,p.HELM].some((e=>t.startsWith(e.toLowerCase())))}static getNewColumnFromParams(t,e,n){if(!W.unitsStringIsValid(n))throw new Error("Invalid format of 'units' parameter");const i=r.Column.fromList("string",e,new Array(t).fill(""));return i.semType=r.SEMTYPE.MACROMOLECULE,i.setTag(r.TAGS.UNITS,n),i}getSplitter(t){let e=null;if(e=this.notationProvider?this.notationProvider.splitter:null,e)return e;if(this.units.toLowerCase().startsWith(p.FASTA))return null===this.column.getTag("alphabet")||this.getAlphabetIsMultichar()?L:M;if(this.units.toLowerCase().startsWith(p.SEPARATOR))return B(this.separator,t);if(this.units.toLowerCase().startsWith(p.HELM))return F;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");return this.isMsa()?V.HAMMING:(this.alphabet,V.LEVENSHTEIN)}getDistanceFunction(){return j[this.getDistanceFunctionName()]()}async checkHelmCompatibility(){if(this.column.tags.has(".isHelmCompatible"))return"true"===this.column.getTag(".isHelmCompatible");const t=(await rt()).getBioLib().getMonomerSymbolsByType("PEPTIDE".toString()),e=new Set(t),n=(B(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(".isHelmCompatible","false"),!1}}return this.column.setTag(".isHelmCompatible","true"),!0}get splitter(){return null===this._splitter&&(this._splitter=this.getSplitter()),this._splitter}toFasta(t){return t===p.FASTA}toSeparator(t){return t===p.SEPARATOR}toHelm(t){return t===p.HELM}convertHelmToFastaSeparator(t,e,n,r){r||(r=this.toFasta(e)?G[p.FASTA]:G[p.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(c,"")),n===G[p.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=G[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 N(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(".positionNames");c&&r.setTag(".positionNames",l(c));const h=this.column.getTag(".positionLabels");return h&&r.setTag(".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 p.FASTA:r=function(t){return i.joinToFasta(t,i.isHelm())};break;case p.SEPARATOR:if(!n)throw new Error(`Separator is mandatory for notation '${e}'.`);r=function(t){return z(t,n,i.isHelm())};break;case p.HELM:{const t="DNA"===i.alphabet||"RNA"===i.alphabet,e=i.getHelmWrappers();r=function(n){return Y(n,e,t)};break}default:throw new Error(`Unexpected notation '${e}'.`)}return r}getConverter(t,e=void 0){if(t===p.SEPARATOR&&!e)throw new Error(`Target separator is not specified for target units '${p.SEPARATOR}'.`);const n=this;if(t===p.FASTA)return function(t){return n.convertToFasta(t)};if(t===p.HELM)return function(t){return n.convertToHelm(t)};if(t===p.SEPARATOR)return function(t){return n.convertToSeparator(t,e)};throw new Error}static forColumn(t){let e=t.temp[q.seqHandler];return e&&e.columnVersion===t.version||(e=t.temp[q.seqHandler]=new W(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(c,"$1")),""===i?o=G[p.FASTA]:i===l?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 z(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 Y(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(c,"$1"),o=o===l?null:o),n[t]=o||null}return new N(n.filter((t=>!!t)),G[p.HELM])}}function z(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(c,"$1")),""===i?o=G[p.SEPARATOR]:i===l&&(o=""),r[e]=o}return r.join(e)}function Y(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=G[p.HELM]:(n&&(s=s.replace(c,"$1")),s=1===s.length?`${i}${s}${o}`:`${i}[${s}]${o}`),a[e]=s}return`${r}${a.join(".")}${s}`}class K{constructor(t,e=!1){if(this._length=0,this._version=0,this._updateLevel=0,this._selectedCount=0,this._selectedCountVersion=-1,this._selectedIndexesVersion=-1,this._versionedName="",this._versionedNameVersion=-1,this.SHRINK_THRESHOLD=256,"number"==typeof t){const n=t,r=K._createBuffer(n);if(e)for(let t=0;t<r.length;t++)r[t]=-1;this._data=r,this._length=n}else{if(!(t instanceof Uint32Array))throw new Error("Invalid constructor");this._data=t,this._length=e}}getRawData(){return this._data}assureGoez(t,e){if(t<0)throw new Error(`${e} should be greater than zero`)}assureInRange(t,e,n,r){if(t<e||t>n)throw new Error(`Argument ${r} (${t}) out of range (${e}, ${n})`)}copy(t,e,n){for(let r=0;r<n;r++)e[r]=t[r]}copyFrom(t){if(this._length!=t._length)throw new Error(`Lengths differ (${this._length} != ${t._length})`);this.copy(t._data,this._data,this.lengthInInts),this._version++}get length(){return this._length}get buffer(){return this._data}set buffer(t){this._data=t,this._version++}get version(){return this._version}set version(t){this._version=t}incrementVersion(t=!0){this._version++}get lengthInInts(){return Math.floor((this._length+31)/32)}get versionedName(){return this._version==this._versionedNameVersion?this._versionedName:""}set versionedName(t){this._versionedName=t,this._versionedNameVersion=this._version}get self(){return this}setLength(t){if(t<0)throw new Error("should be >= 0");if(t==this._length)return;const e=Math.floor((t+31)/32);if(e>this._data.length||e+this.SHRINK_THRESHOLD<this._data.length){const t=new Uint32Array(e);this.copy(this._data,t,e>this._data.length?this._data.length:e),this._data=t}t>this._length&&(this._length%32>0&&(this._data[this.lengthInInts-1]&=(1<<(this._length%32&31))-1),this._data.fill(0,this.lengthInInts,e)),this._length=t,this._version++}static fromAnd(t,e){if(t._length!=e._length)throw new Error(`Lengths differ (${t._length} != ${e._length})`);const n=new K(t._length);n._length=t._length,n._data=K._createBuffer(n._length),n._version=0;const r=t.lengthInInts;for(let i=0;i<r;i++)n._data[i]=t._data[i]&e._data[i];return n}static _createBuffer(t){return new Uint32Array(Math.floor((t+31)/32))}static fromValues(t){const e=new K(t.length);e._version=0;for(let n=0;n<e._length;n++)t[n]&&(e._data[Math.floor(n/32)]|=1<<(n%32&31));return e}static fromSeq(t,e){const n=new K(t);for(let r=0;r<t;++r)n.setBit(r,e(r));return n._version=0,n}static fromString(t){return K.fromSeq(t.length,(e=>"1"==t.charAt(e)))}static fromUint32Array(t,e){const n=new K(t);return n._data=e,n}static fromBytes(t){const e=t.length,n=new K(8*e);n._data=new Uint32Array(Math.floor((e+3)/4)),n._length=8*e;let r=0,i=0;for(;e-i>=4;)n._data[r++]=255&t[i]|(255&t[i+1])<<8|(255&t[i+2])<<16|(255&t[i+3])<<24,i+=4;return e-i==3&&(n._data[r]=(255&t[i+2])<<16),e-i==2&&(n._data[r]|=(255&t[i+1])<<8),e-i==1&&(n._data[r]|=255&t[i]),n._version=0,n}toString(){return`${this._length} bits, ${this.countBits(!0)} set`}equals(t){if(this==t)return!0;if(null==t)return!1;if(this._length!=t._length)return!1;if(0==this._length)return!0;for(let e=0;e<this._data.length-1;e++)if(this._data[e]!=t._data[e])return!1;for(let e=8*(this._data.length-1);e<this._length;e++)if(this.getBit(e)!=t.getBit(e))return!1;return!0}clone(){const t=new K(0,!1);return t._data=Uint32Array.from(this._data),t._length=this._length,t._version=this._version,t}init(t,e){this.setAll(!1,!1);for(let e=0;e<this._length;e++)t(e)&&(this._data[Math.floor(e/32)]|=1<<(e%32&31));return this.incrementVersion(e),this}invert(t=!0){for(let t=0;t<this._data.length;t++)this._data[t]^=-1;this.incrementVersion(t)}setAll(t,e=!1){const n=t?-1:0,r=this.lengthInInts;for(let t=0;t<r;t++)this._data[t]=n;this.incrementVersion(e)}setIndexes(t,e=!0,n=!0,r=!0){n&&this.setAll(!e,!1);for(const n of t)this.setFast(n,e);this.incrementVersion(r)}everyIndex(t,e=!0){for(const n of t)if(this.getBit(n)!=e)return!1;return!0}anyIndex(t,e=!0){for(const n of t)if(this.getBit(n)==e)return!0;return!1}setWhere(t,e=!0,n=!0,r=!0,i=!0){if(n&&i&&this.setAll(!e,!1),i)for(let n=0;n<this._length;n++)t(n)&&this.setFast(n,e);else for(let n=0;n<this._length;n++)this.setFast(n,t(n)?e:!e);this.incrementVersion(r)}getRange(t,e){this.assureInRange(t,0,this._length-1,"from"),this.assureInRange(e,0,this._length,"to");const n=[];for(let r=t;r<e;++r)n.push(this.getBit(r));return K.fromValues(n)}getRangeAsList(t,e){this.assureInRange(t,0,this._length-1,"from"),this.assureInRange(e,0,this._length,"to");const n=[];for(let r=t;r<e;++r)n.push(this.getBit(r));return n}setRange(t,e,n,r=!0){this.assureInRange(t,0,this._length-1,"from"),this.assureInRange(e,0,this._length-1,"to");const i=Math.min(t,e),o=Math.max(t,e);if(n)for(let t=i;t<=o;t++)this.setTrue(t);else for(let t=i;t<=o;t++)this.setFalse(t);return this.incrementVersion(r),this}setRandom(t,e,n=!0){if(t<0||t>this._length)throw new Error("n must be >= 0 && <= Count");t>this._length/2&&this.setRandom(this._length-t,!e),this.setAll(!e);for(let n=0;n<t;){const t=Math.floor(Math.random()*this._length);this.getBit(t)!=e&&(this.setFast(t,e),n++)}this.incrementVersion(n)}and(t,e=!0){if(this._length!=t._length)throw new Error("Array lengths differ.");for(let e=0,n=this.lengthInInts;e<n;e++)this._data[e]&=t._data[e];return this.incrementVersion(e),this}andNot(t,e=!0){if(this._length!=t._length)throw new Error("Array lengths differ.");const n=this.lengthInInts;for(let e=0;e<n;e++)this._data[e]&=~t._data[e];return this.incrementVersion(e),this}notAnd(t,e=!0){if(this._length!=t._length)throw new Error("Array lengths differ.");for(let e=0,n=this.lengthInInts;e<n;e++)this._data[e]=~this._data[e]&t._data[e];return this.incrementVersion(e),this}not(t=!0){for(let t=0,e=this.lengthInInts;t<e;t++)this._data[t]=~this._data[t];return this.incrementVersion(t),this}or(t,e=!0){if(this._length!=t._length)throw new Error("Array lengths differ.");for(let e=0,n=this.lengthInInts;e<n;e++)this._data[e]|=t._data[e];return this.incrementVersion(e),this}xor(t,e=!0){if(this._length!=t._length)throw new Error("Array lengths differ.");for(let e=0,n=this.lengthInInts;e<n;e++)this._data[e]^=t._data[e];return this.incrementVersion(e),this}insertAt(t,e,n=!1){if(this.assureInRange(t,0,this._length,"pos"),0==e)return;const r=this._length;this.setLength(this._length+e);for(let n=r-1;n>=t;n--)this.setBit(n+e,this.getBit(n));for(let r=t;r<t+e;r++)this.setBit(r,n)}removeAt(t,e=1){if(e<0)throw new Error("n cannot be negative");if(this.assureInRange(t,0,this._length-e,"pos"),this.contains(!0))for(let n=t;n<this._length-e;n++)this.setBit(n,this.getBit(n+e));this.setLength(this._length-e)}removeByMask(t,e=!0){if(this._length!=t.length)throw new Error("length != mask.length");if(t==this)this.setLength(t.countBits(!e)),this.setAll(!e);else{let n=0;for(let r=-1;-1!=(r=t.findNext(r,!e));)this.setFast(n++,this.getBit(r));this._length=n,this._version++}return this}getBit(t){return!!(this._data[Math.floor(t/32)]&1<<(31&t))}setBit(t,e,n=!0){this.setFast(t,e),this._version++}setFast(t,e){e?this._data[Math.floor(t/32)]|=1<<(31&t):this._data[Math.floor(t/32)]&=~(1<<(31&t))}setTrue(t){this._data[Math.floor(t/32)]|=1<<(31&t)}setFalse(t){this._data[Math.floor(t/32)]&=~(1<<(31&t))}trueCount(){return this.countBits(!0)}falseCount(){return this.countBits(!1)}countBits(t){if(0==this._length)return 0;if(this._selectedCountVersion!=this._version){this._selectedCount=0;const t=this.lengthInInts;let e=0;for(;e<t-1;e++)for(let t=this._data[e];0!=t;t>>>=8)this._selectedCount+=K._onBitCount[255&t];let n=this._data[e];const r=31&this._length;for(0!=r&&(n&=~(4294967295<<r));0!=n;n>>>=8)this._selectedCount+=K._onBitCount[255&n];this._selectedCountVersion=this._version}return t?this._selectedCount:this._length-this._selectedCount}countWhere(t){let e=0;if(this.trueCount()==this._length)for(let n=0;n<this._length;n++)e+=t(n)?1:0;else for(let n=-1;-1!=(n=this.findNext(n,!0));)e+=t(n)?1:0;return e}andWithCountBits(t,e){if(0==this._length)return 0;let n=0;const r=this.lengthInInts;let i=0;for(;i<r-1;i++)for(let e=this._data[i]&t._data[i];0!=e;e>>>=8)n+=K._onBitCount[255&e];let o=this._data[i]&t._data[i];const s=31&this._length;for(0!=s&&(o&=~(4294967295<<s));0!=o;o>>>=8)n+=K._onBitCount[255&o];return e?n:this._length-n}clear(){this.setLength(0)}contains(t){return this.findNext(-1,t)>=0}get allTrue(){return this.countBits(!0)==this._length}get allFalse(){return this.countBits(!1)==this._length}get anyTrue(){return this.countBits(!0)>0}get anyFalse(){return this.countBits(!1)>0}findNext(t,e=!0){if(this.assureInRange(t,-1,this._length,"index"),t>=this._length-1)return-1;let n=31&(t=t<0?0:t+1);const r=this.lengthInInts;for(let i=Math.floor(t/32);i<r;i++){let r=e?this._data[i]:~this._data[i];if(0!=n)r&=4294967295<<n&4294967295,n=0;else if(!e&&-4294967296==r)continue;for(let e=0;0!=r;e+=8,r>>>=8){const n=K._firstOnBit[255&r];if(n>=0)return(t=n+32*i+e)>=this._length?-1:t}}return-1}findPrev(t,e=!0){if(0==t)return-1;this.assureInRange(t,-1,this._length,"index");let n=1+(t=t<0?this._length-1:t-1)&31;for(let r=Math.floor(t/32);r>=0;r--){let t=e?this._data[r]:~this._data[r];0!=n&&(t&=~(4294967295<<n),n=0);for(let e=24;0!=t;e-=8,t<<=8){const n=K._lastOnBit[t>>>24];if(n>=0)return n+32*r+e}}return-1}}var Q,X,J,Z,tt,et,nt;async function rt(){const t=r.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()}K._onBitCount=Int8Array.from([0,1,1,2,1,2,2,3,1,2,2,3,2,3,3,4,1,2,2,3,2,3,3,4,2,3,3,4,3,4,4,5,1,2,2,3,2,3,3,4,2,3,3,4,3,4,4,5,2,3,3,4,3,4,4,5,3,4,4,5,4,5,5,6,1,2,2,3,2,3,3,4,2,3,3,4,3,4,4,5,2,3,3,4,3,4,4,5,3,4,4,5,4,5,5,6,2,3,3,4,3,4,4,5,3,4,4,5,4,5,5,6,3,4,4,5,4,5,5,6,4,5,5,6,5,6,6,7,1,2,2,3,2,3,3,4,2,3,3,4,3,4,4,5,2,3,3,4,3,4,4,5,3,4,4,5,4,5,5,6,2,3,3,4,3,4,4,5,3,4,4,5,4,5,5,6,3,4,4,5,4,5,5,6,4,5,5,6,5,6,6,7,2,3,3,4,3,4,4,5,3,4,4,5,4,5,5,6,3,4,4,5,4,5,5,6,4,5,5,6,5,6,6,7,3,4,4,5,4,5,5,6,4,5,5,6,5,6,6,7,4,5,5,6,5,6,6,7,5,6,6,7,6,7,7,8]),K._firstOnBit=Int8Array.from([-1,0,1,0,2,0,1,0,3,0,1,0,2,0,1,0,4,0,1,0,2,0,1,0,3,0,1,0,2,0,1,0,5,0,1,0,2,0,1,0,3,0,1,0,2,0,1,0,4,0,1,0,2,0,1,0,3,0,1,0,2,0,1,0,6,0,1,0,2,0,1,0,3,0,1,0,2,0,1,0,4,0,1,0,2,0,1,0,3,0,1,0,2,0,1,0,5,0,1,0,2,0,1,0,3,0,1,0,2,0,1,0,4,0,1,0,2,0,1,0,3,0,1,0,2,0,1,0,7,0,1,0,2,0,1,0,3,0,1,0,2,0,1,0,4,0,1,0,2,0,1,0,3,0,1,0,2,0,1,0,5,0,1,0,2,0,1,0,3,0,1,0,2,0,1,0,4,0,1,0,2,0,1,0,3,0,1,0,2,0,1,0,6,0,1,0,2,0,1,0,3,0,1,0,2,0,1,0,4,0,1,0,2,0,1,0,3,0,1,0,2,0,1,0,5,0,1,0,2,0,1,0,3,0,1,0,2,0,1,0,4,0,1,0,2,0,1,0,3,0,1,0,2,0,1,0]),K._lastOnBit=Int8Array.from([-1,0,1,1,2,2,2,2,3,3,3,3,3,3,3,3,4,4,4,4,4,4,4,4,4,4,4,4,4,4,4,4,5,5,5,5,5,5,5,5,5,5,5,5,5,5,5,5,5,5,5,5,5,5,5,5,5,5,5,5,5,5,5,5,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7]),function(t){t.Levenshtein="Levenshtein",t.JaroWinkler="Jaro-Winkler",t.Manhattan="Manhattan",t.Onehot="One-Hot"}(Q||(Q={})),function(t){t.Euclidean="Euclidean"}(X||(X={})),function(t){t.Tanimoto="Tanimoto",t.Dice="Dice",t.Asymmetric="Asymmetric",t.BraunBlanquet="Braun-Blanquet",t.Cosine="Cosine",t.Kulczynski="Kulczynski",t.McConnaughey="Mc-Connaughey",t.RogotGoldberg="Rogot-Goldberg",t.Russel="Russel",t.Sokal="Sokal",t.Hamming="Hamming",t.Euclidean="Euclidean"}(J||(J={})),function(t){t.TanimotoIntArray="TanimotoIntArray"}(Z||(Z={})),function(t){t.Vector="Vector",t.String="String",t.BitArray="BitArray",t.MacroMolecule="MacroMolecule",t.Number="Number",t.IntArray="IntArray",t.NumberArray="NumberArray"}(tt||(tt={})),function(t){t.Difference="Difference"}(et||(et={})),function(t){t.CommonItems="Common Items"}(nt||(nt={})),J.Tanimoto,J.Dice,J.Asymmetric,J.BraunBlanquet,J.Cosine,J.Kulczynski,J.McConnaughey,J.RogotGoldberg,J.Russel,J.Sokal,J.Hamming,J.Euclidean,J.Tanimoto,J.Dice,J.Asymmetric,J.BraunBlanquet,J.Cosine,J.Kulczynski,J.McConnaughey,J.RogotGoldberg,J.Russel,J.Sokal,J.Hamming,J.Euclidean,J.Tanimoto,J.Dice,J.Cosine,J.Tanimoto,J.Asymmetric,J.Cosine,J.Sokal,V.HAMMING,V.LEVENSHTEIN,V.MONOMER_CHEMICAL_DISTANCE,V.NEEDLEMANN_WUNSCH;var it=n(373),ot=n(124);class st extends r.Package{get monomerLib(){if(!this._monomerLib)throw new Error("Monomer lib not loaded");return this._monomerLib}async initMonomerLib(){if(void 0!==this._monomerLib)return;const t=r.TaskBarProgressIndicator.create("Initializing Oligo Toolkit monomer library ...");await(0,ot.TX)((async()=>{const t=await rt();this._monomerLib=await t.readLibrary(it.so,it.c6)}),(()=>t.close()))}}var at=n(686),ut=n(838);class lt{constructor(t){this.sequence=t,this.libWrapper=a.k.getInstance(),this.formats=Object.keys(s.$D)}getFormat(){if(this.sequence.startsWith("RNA"))return at.NO.HELM;const t=this.getListOfPossibleSynthesizersByFirstMatchedCode();if(0===t.length)return null;const e=new ut.q(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=(0,ot.iD)(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 ct=ui;class ht{constructor(t,e){this.appName=t,this.parentAppName=e}async getAppView(){const t=r.TaskBarProgressIndicator.create(`Loading ${this.appName}...`),e=o.shell.v?.root;e&&ct.setUpdateIndicator(e,!0);try{return await this.constructView()}finally{t.close(),e&&ct.setUpdateIndicator(e,!1)}}}class ft extends ht{constructor(t){super(t),this.view=r.View.create(),this.configureView()}async constructView(){await this.initView();const t=this.parentAppName?this.parentAppName+"/"+this.appName:this.appName;return this.view.path=`/apps/${Hn.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 t=o.shell.windows;t.showProperties=!1,t.showToolbox=!1,t.showHelp=!1}getView(){return this.view}}const dt=["SS","AS"],pt={SS:"Sense strand",AS:"Anti sense"},gt=[0,1],mt=["3'","5'"],vt={SS:{0:"3'",1:"5'"},AS:{0:"5'",1:"3'"}},yt="OligoToolkit";var bt,At,Ct;!function(t){t.IS_ANTISENSE_STRAND_INCLUDED="isAntisenseStrandIncluded",t.NUCLEOTIDE_SEQUENCES="nucleotideSequences",t.PHOSPHOROTHIOATE_LINKAGE_FLAGS="phosphorothioateLinkageFlags",t.STRAND_TERMINUS_MODIFICATIONS="strandTerminusModifications"}(bt||(bt={})),function(t){t.PATTERN_NAME="patternName",t.PATTERN_COMMENT="patternComment",t.NUCLEOTIDES_WITH_NUMERIC_LABELS="nucleotidesWithNumericLabels"}(At||(At={})),function(t){t.PATTERN_CONFIG="patternConfig",t.AUTHOR_ID="authorID"}(Ct||(Ct={}));const wt=[bt.IS_ANTISENSE_STRAND_INCLUDED,bt.NUCLEOTIDE_SEQUENCES,bt.PHOSPHOROTHIOATE_LINKAGE_FLAGS,bt.STRAND_TERMINUS_MODIFICATIONS],xt=(At.PATTERN_NAME,At.PATTERN_COMMENT,At.NUCLEOTIDES_WITH_NUMERIC_LABELS,Ct.PATTERN_CONFIG,Ct.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 St extends Error{constructor(t){super(t),this.name="PatternExistsError"}}var Et=n(802),Tt=n.n(Et);class It{constructor(){this.otherUsersPatternNameToHash=new Map,this.currentUserPatternNameToHash=new Map}static async getInstance(){const t=new It;t.currentUserName=await t.fetchCurrentUserName(),t.currentUserId=await t.fetchCurrentUserId();const e=await t.fetchPatterns();return await t.initializePatternMaps(e),t}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 St(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(t){if(null===t||""===t)return null;try{const e=await o.dapi.userDataStorage.getValue(yt,t,!1);return JSON.parse(e)}catch{return null}}async getPatternConfig(t){if(""===t||null===t)return null;const e=await this.getPatternRecord(t);return null===e?null:e[Ct.PATTERN_CONFIG]}getDefaultPatternRecord(){const t=xt;return t[Ct.AUTHOR_ID]=this.currentUserId,t}getDefaultPatternConfig(){return xt[Ct.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(t){const e={[Ct.PATTERN_CONFIG]:t,[Ct.AUTHOR_ID]:await o.dapi.users.current().then((t=>t.id))};return JSON.stringify(e)}getHash(t){const e=wt.reduce(((e,n)=>(e[n]=t[n],e)),{});return Tt().sha1(e)}async savePatternToUserStorage(t){const e=t.getPatternConfig();try{const n=this.getHash(e);this.validatePatternUniqueness(n);const r=e[At.PATTERN_NAME];this.validatePatternNameUniqueness(r);const i=await this.getRecordFromPattern(e);await o.dapi.userDataStorage.postValue(yt,n,i,!1),this.currentUserPatternNameToHash.set(r,n),t.selectAuthor(this.getCurrentUserAuthorshipCategory()),t.updatePatternList()}catch(t){if(t instanceof _t||t instanceof St)throw t;console.error("Error while saving pattern to user storage",t)}}async overwritePatternInUserStorage(t){const e=t.getPatternConfig(),n=this.getHash(e),r=e[At.PATTERN_NAME],i=await this.getRecordFromPattern(e);await o.dapi.userDataStorage.postValue(yt,n,i,!1),this.currentUserPatternNameToHash.set(r,n),t.updatePatternList()}async deletePattern(t,e){const n=this.currentUserPatternNameToHash.get(t);if(t===this.getDefaultPatternName())return void o.shell.warning("Cannot delete default pattern");if(void 0===n)throw new Error(`Pattern with name ${t} not found`);await o.dapi.userDataStorage.remove(yt,n,!1),this.currentUserPatternNameToHash.delete(t),e.updatePatternList();const r=this.getHashOfPatternToBeLoadedAfterDeletion();e.requestPatternLoad(r)}fetchDefaultNucleobase(){return this.fetchAvailableNucleotideBases()[0]}fetchAvailableNucleotideBases(){const t=Object.keys(s.a1)[0];return Object.keys(s.a1[t])}async fetchCurrentUserName(){return(await o.dapi.users.current()).friendlyName}async fetchCurrentUserId(){return(await o.dapi.users.current()).id}async fetchPatterns(){return await o.dapi.userDataStorage.get(yt,!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=xt[Ct.PATTERN_CONFIG];this.currentUserPatternNameToHash.set(t[At.PATTERN_NAME],"")}async extractDataFromRecordToMaps(t,e,n){const r=JSON.parse(e),i=r[Ct.PATTERN_CONFIG].patternName,s=r[Ct.AUTHOR_ID];if(this.isCurrentUserId(s))this.currentUserPatternNameToHash.set(i,t);else{if(!n.has(s)){const t=(await o.dapi.users.find(s)).friendlyName;n.set(s,t)}const e=i+` (created by ${n.get(s)})`;this.otherUsersPatternNameToHash.set(e,t)}}getDefaultPatternName(){return xt[Ct.PATTERN_CONFIG][At.PATTERN_NAME]}getCurrentUserAuthorshipCategory(){return this.currentUserName+" (me)"}getOtherUsersAuthorshipCategory(){return"Other users"}isCurrentUserId(t){return t===this.currentUserId}}const Nt=rxjs,Ot=rxjs.operators;function Lt(t){return t.endsWith("(o)")}function Mt(t){const e=Object.values(t).flat().reduce(((t,e)=>(t[e]=(t[e]||0)+1,t)),{});return Object.entries(e).reduce(((t,e)=>t[1]>e[1]?t:e),["",0])[0]}var Bt;function Pt(t){const e=Array.from(new Set(t));return Array.from(e).sort(((t,e)=>t.toLowerCase().localeCompare(e.toLowerCase())))}!function(t){t.getTruncatedStrandData=function(t,e,n){return{nucleotides:t.slice(0,n),ptoFlags:e.slice(0,n+1)}},t.getExtendedStrandData=function(t,e,n,r){const i=n-t.length,o=t.concat(new Array(n-t.length).fill(r)),s=0===t.length?n+1:i;return{nucleotides:o,ptoFlags:e.concat(new Array(s).fill(!0))}}}(Bt||(Bt={}));var Rt=n(543),Ft=n.n(Rt);class Dt{constructor(t,e){this.dataManager=t,this._patternListUpdated$=new Nt.Subject,this._patternLoadRequested$=new Nt.Subject,this._patternLoaded$=new Nt.Subject,this._uniqueNucleotides$=new Nt.BehaviorSubject([]),this._patternDeletionRequested$=new Nt.Subject,this._tableSelection$=new Nt.BehaviorSubject(null),this._svgSaveRequested$=new Nt.Subject,this._loadPatternInNewTabRequested$=new Nt.Subject,this._urlStateUpdated$=new Nt.Subject,this._patternHasUnsavedChanges$=new Nt.BehaviorSubject(!1),this._selectedColumn=new Nt.BehaviorSubject(null),this.initializeAuthorSelection(e),this.initializePatternState(e),this._lastLoadedPatternConfig=new Nt.BehaviorSubject(Ft().cloneDeep(this.getPatternConfig())),this.setupSubscriptions()}setupSubscriptions(){this._nucleotideSequences$.subscribe((()=>{this.updateUniqueNucleotides(),this.updateSequenceBase()})),this._isAntisenseStrandActive$.subscribe((t=>{t||mt.forEach((t=>{this.updateTerminusModification("AS",t,"")}))})),this.patternStateChanged$.pipe((0,Ot.debounceTime)(20)).subscribe((()=>{const t=this._lastLoadedPatternConfig.getValue(),e=this.getPatternConfig(),n=!Ft().isEqual(e,t);this._patternHasUnsavedChanges$.next(n)}))}updateUniqueNucleotides(){const t=(e=this._nucleotideSequences$.getValue(),Pt(Object.values(e).flat()));var e;this._uniqueNucleotides$.next(t)}updateSequenceBase(){const t=Mt(this._nucleotideSequences$.getValue());this._sequenceBase$.next(t)}get nucleotideSequencesChanged$(){return this._nucleotideSequences$.asObservable()}initializeAuthorSelection(t){const e=t[Ct.AUTHOR_ID];this.dataManager.isCurrentUserId(e)?this._patternAuthorSelection$=new Nt.BehaviorSubject(this.dataManager.getCurrentUserAuthorshipCategory()):this._patternAuthorSelection$=new Nt.BehaviorSubject(this.dataManager.getOtherUsersAuthorshipCategory())}initializePatternState(t){const e=t[Ct.PATTERN_CONFIG];this._patternName$=new Nt.BehaviorSubject(e[At.PATTERN_NAME]),this._isAntisenseStrandActive$=new Nt.BehaviorSubject(e[bt.IS_ANTISENSE_STRAND_INCLUDED]),this._nucleotideSequences$=new Nt.BehaviorSubject(e[bt.NUCLEOTIDE_SEQUENCES]),this._phosphorothioateLinkageFlags=new Nt.BehaviorSubject(e[bt.PHOSPHOROTHIOATE_LINKAGE_FLAGS]),this._terminalModifications=new Nt.BehaviorSubject(e[bt.STRAND_TERMINUS_MODIFICATIONS]),this._comment$=new Nt.BehaviorSubject(e[At.PATTERN_COMMENT]),this._modificationsWithNumericLabels$=new Nt.BehaviorSubject(e[At.NUCLEOTIDES_WITH_NUMERIC_LABELS]),this._sequenceBase$=new Nt.BehaviorSubject(Mt(e[bt.NUCLEOTIDE_SEQUENCES]))}getPatternName(){return this._patternName$.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$.next(t)}updateStrandLength(t,e){const n=this.getNucleotideSequences()[t];if(n.length===e)return;const r=this.getPhosphorothioateLinkageFlags()[t];if(0===e)return void this.setNewStrandData([],[],t);if(n.length>e){const{nucleotides:i,ptoFlags:o}=Bt.getTruncatedStrandData(n,r,e);return void this.setNewStrandData(i,o,t)}const i=this.getSequenceBase(),{nucleotides:o,ptoFlags:s}=Bt.getExtendedStrandData(n,r,e,i);this.setNewStrandData(o,s,t)}setNewStrandData(t,e,n){this.updateNucleotideSequences({...this.getNucleotideSequences(),[n]:t}),this.updatePhosphorothioateLinkageFlags({...this.getPhosphorothioateLinkageFlags(),[n]:e})}getPhosphorothioateLinkageFlags(){return this._phosphorothioateLinkageFlags.getValue()}updatePhosphorothioateLinkageFlags(t){this._phosphorothioateLinkageFlags.next(t)}get phosphorothioateLingeFlagsChanged$(){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 Pt(t).filter((t=>!Lt(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$.getValue(),n={};dt.forEach((r=>{n[r]=e[r].map((()=>t))})),this._nucleotideSequences$.next(n);const r=this._modificationsWithNumericLabels$.getValue();r.includes(t)||this.updateModificationsWithNumericLabels(r.concat(t))}get patternStateChanged$(){return Nt.merge(this._patternName$.pipe((0,Ot.debounceTime)(300),(0,Ot.map)((()=>{}))),this._isAntisenseStrandActive$,this._nucleotideSequences$,this._phosphorothioateLinkageFlags,this._terminalModifications,this._comment$.pipe((0,Ot.debounceTime)(300)),this._modificationsWithNumericLabels$)}getSequenceBase(){return this._sequenceBase$.getValue()}uniqueNucleotidesChanged$(){return this.patternStateChanged$.pipe((0,Ot.switchMap)((()=>this._uniqueNucleotides$)))}getUniqueNucleotides(){return this._uniqueNucleotides$.getValue()}get svgSaveRequested$(){return this._svgSaveRequested$.asObservable()}requestSvgSave(){this._svgSaveRequested$.next()}setAllPTOLinkages(t){const e=this.getPhosphorothioateLinkageFlags();dt.forEach((n=>{e[n]=e[n].map((()=>t))})),this.updatePhosphorothioateLinkageFlags(e)}setPatternConfig(t){this._patternName$.next(t[At.PATTERN_NAME]),this._isAntisenseStrandActive$.next(t[bt.IS_ANTISENSE_STRAND_INCLUDED]),this._nucleotideSequences$.next(t[bt.NUCLEOTIDE_SEQUENCES]),this._phosphorothioateLinkageFlags.next(t[bt.PHOSPHOROTHIOATE_LINKAGE_FLAGS]),this._terminalModifications.next(t[bt.STRAND_TERMINUS_MODIFICATIONS]),this._comment$.next(t[At.PATTERN_COMMENT]),this._modificationsWithNumericLabels$.next(t[At.NUCLEOTIDES_WITH_NUMERIC_LABELS])}setLastLoadedPatternConfig(t){this._lastLoadedPatternConfig.next(Ft().cloneDeep(t))}getPatternConfig(){return{[At.PATTERN_NAME]:this.getPatternName(),[bt.IS_ANTISENSE_STRAND_INCLUDED]:this.isAntisenseStrandActive(),[bt.NUCLEOTIDE_SEQUENCES]:this.getNucleotideSequences(),[bt.PHOSPHOROTHIOATE_LINKAGE_FLAGS]:this.getPhosphorothioateLinkageFlags(),[bt.STRAND_TERMINUS_MODIFICATIONS]:this.getTerminalModifications(),[At.PATTERN_COMMENT]:this.getComment(),[At.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$(){return Nt.merge(this._isAntisenseStrandActive$.asObservable().pipe((0,Ot.map)((()=>{}))),this._nucleotideSequences$.asObservable().pipe((0,Ot.map)((()=>{}))),this._patternLoaded$.asObservable().pipe((0,Ot.map)((()=>{})))).pipe((0,Ot.debounceTime)(10))}get strandsLinkagesAndTerminalsUpdated$(){return Nt.merge(this.strandsUpdated$,this._phosphorothioateLinkageFlags.asObservable().pipe((0,Ot.map)((()=>{}))),this._terminalModifications.asObservable().pipe((0,Ot.map)((()=>{}))))}updateControlsUponPatternLoaded(t){this._patternLoaded$.next(t)}get patternLoaded$(){return this._patternLoaded$.asObservable()}get userSelection$(){return this._patternAuthorSelection$.asObservable().pipe((0,Ot.skip)(1))}selectAuthor(t){this._patternAuthorSelection$.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$.asObservable()}selectColumn(t,e){this._selectedColumn.next({strand:t,colName:e})}getSelectedColumn(t){return this._selectedColumn.getValue()?.colName??null}}const Ut="pattern";class kt{constructor(){this.urlSearchParams=new URLSearchParams(window.location.search)}subscribeToObservables(t){t.urlStateUpdated$.subscribe((t=>this.setPatternURL(t))),t.loadPatternInNewTabRequested$.subscribe((t=>{const e=`${window.location.origin}${window.location.pathname}?${Ut}=${t}`;window.open(e,"_blank")})),window.addEventListener("popstate",(()=>{this.urlSearchParams=new URLSearchParams(window.location.search);const e=this.getPatternHash();null!==e&&t.requestPatternLoad(e)}))}getPatternHash(){return this.urlSearchParams.get(Ut)}setPatternURL(t){null!==t&&""!==t?(this.urlSearchParams.set(Ut,t),window.history.pushState({},"",`${window.location.pathname}?${this.urlSearchParams}`)):this.clearPatternURL()}clearPatternURL(){this.urlSearchParams.delete(Ut),window.history.pushState({},"",`${window.location.pathname}`)}}const $t=$;var Ht=n.n($t),Vt=n(72),jt=n.n(Vt),qt=n(825),Gt=n.n(qt),Wt=n(659),zt=n.n(Wt),Yt=n(56),Kt=n.n(Yt),Qt=n(540),Xt=n.n(Qt),Jt=n(113),Zt=n.n(Jt),te=n(252),ee={};ee.styleTagTransform=Zt(),ee.setAttributes=Kt(),ee.insert=zt().bind(null,"head"),ee.domAPI=Gt(),ee.insertStyleElement=Xt(),jt()(te.A,ee),te.A&&te.A.locals&&te.A.locals;class ne{constructor(t){this.eventBus=t,this.columnControlsContainer=ct.div([]),this.eventBus.tableSelectionChanged$.subscribe((()=>this.handleTableChoice())),this.refreshColumnControls()}getColumnControlsContainer(){return this.columnControlsContainer}get selectedTable(){return this.eventBus.getTableSelection()}handleTableChoice(){this.refreshColumnControls()}refreshColumnControls(){Ht()(this.columnControlsContainer).empty(),Ht()(this.columnControlsContainer).append(this.constructColumnControls())}constructColumnControls(){const t=this.createStrandColumnInput();return[t.SS,t.AS,this.createIdColumnInput()]}createStrandColumnInput(){const t=this.selectedTable?this.selectedTable.columns.names().sort(((t,e)=>t.localeCompare(e))):[];return Object.fromEntries(dt.map((e=>{const n=ct.choiceInput(`${pt[e]} column`,t[0],t,(t=>this.eventBus.selectColumn(e,t)));return[e,n.root]})))}createIdColumnInput(){const t=this.selectedTable?this.selectedTable.columns.names():[];return ct.choiceInput("ID column",t[0],t,(()=>{})).root}}class re{constructor(t){this.eventBus=t,this.availableTables=[],this.tableInputContainer=ct.div([]),this.subscribeToTableEvents(),this.refreshTableInput()}getTableInputContainer(){return this.tableInputContainer}subscribeToTableEvents(){o.events.onTableAdded.subscribe((t=>this.handleTableAdded(t))),o.events.onTableRemoved.subscribe((t=>this.handleTableRemoved(t))),this.eventBus.tableSelectionChanged$.subscribe((()=>this.handleTableChoice()))}getTableFromEventData(t){if(!t&&t.args&&t.args.dataFrame instanceof r.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();Ht()(this.tableInputContainer).empty(),this.tableInputContainer.append(t.root)}createTableInput(){const t=this.eventBus.getTableSelection();return ct.tableInput("Tables",t,this.availableTables,(t=>{null!==t&&t instanceof r.DataFrame&&this.eventBus.selectTable(t)}))}handleTableChoice(){const t=this.eventBus.getTableSelection();t&&(this.isTableDisplayed(t)||this.displayTable(t))}isTableDisplayed(t){return o.shell.tableNames.includes(t.name)}displayTable(t){const e=o.shell.v;o.shell.addTableView(t),o.shell.v=e}}class ie{constructor(t){this.eventBus=t,this.tableInputManager=new re(t),this.columnInputManager=new ne(t)}createControls(){const t=ct.h1("Bulk convert"),e=this.tableInputManager.getTableInputContainer(),n=this.columnInputManager.getColumnControlsContainer(),r=ct.bigButton("Convert",(()=>this.processConvertButtonClick()));return[t,e,n,ct.buttonsInput([r])]}processConvertButtonClick(){}}class oe{constructor(t,e,n){this.eventBus=t,this.initialPatternConfig=e,this.subscriptions=n}create(){return ct.divV([ct.h1("PTO"),ct.divH([this.createAllPtoActivationInput().root,...this.createFirstPtoInputs().map((t=>t.root))],{style:{gap:"12px"}})])}areAllPtoLinkagesSet(t){return dt.map((e=>t[e].filter((t=>t)).length)).reduce(((t,e)=>t+e),0)===dt.map((t=>this.initialPatternConfig.nucleotideSequences[t].length)).reduce(((t,e)=>t+e),0)+dt.filter((e=>t[e].length)).length}createAllPtoActivationInput(){const t=this.initialPatternConfig.phosphorothioateLinkageFlags,e=this.areAllPtoLinkagesSet(t),n=ct.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),ct.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 dt.map((t=>{if(!this.eventBus.isAntisenseStrandActive()&&"AS"===t)return;const e=this.isFirstPtoActive(t),n=ct.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),ct.tooltip.bind(n.captionLabel,`Activate first phosphothioate in ${t}`),n})).filter((t=>void 0!==t))}isFirstPtoActive(t){return this.initialPatternConfig.phosphorothioateLinkageFlags[t][0]}}class se{constructor(t,e,n){this.eventBus=t,this.dataManager=e,this.subscriptions=n;const r=this.eventBus.nucleotideSequencesChanged$.subscribe((()=>{this.displayedInputLabels=this.computeDisplayedInputLabels()}));this.subscriptions.add(r)}create(){const t=dt.map((t=>this.constructControlsPanel(t)));return ct.divH(t,{style:{gap:"24px"}})}constructControlsPanel(t){if(!this.eventBus.isAntisenseStrandActive()&&"AS"===t)return ct.div([]);const e=this.constructHeader(),n=this.createControls(t);return ct.block([ct.h1(`${pt[t]}`),e,n],{style:{paddingTop:"12px"}})}constructHeader(){return ct.divH([ct.div([ct.divText("#")],{style:{width:"20px"}}),ct.block75([ct.divText("Modification")]),ct.div([ct.divText("PTO")])])}createControls(t){const e=this.createNucleobaseInputs(t),n=this.createLabelDivs(t),r=this.createPTOFlagInputs(t);return ct.div(e.map(((t,e)=>ct.divH([n[e],ct.block75([t.root]),r[e].root],{style:{alignItems:"center"}}))))}createNucleobaseInputs(t){const e=this.dataManager.fetchAvailableNucleotideBases().sort(((t,e)=>t.toLowerCase().localeCompare(e.toLowerCase())));return this.eventBus.getNucleotideSequences()[t].map(((n,r)=>{const i=ct.choiceInput("",n,e);return i.onInput((()=>{const e=i.value;this.eventBus.setNucleotide(t,r,e)})),i}))}createPTOFlagInputs(t){return this.eventBus.getPhosphorothioateLinkageFlags()[t].slice(1).map(((e,n)=>{const r=ct.boolInput("",e);r.onInput((()=>{const e=r.value;this.eventBus.setPhosphorothioateLinkageFlag(t,n+1,e)}));const i=this.eventBus.phosphorothioateLingeFlagsChanged$.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 dt.forEach((n=>{let r=1;const i=t[n].map((t=>{if(Lt(t))return"";const e=String(r);return r++,e}));e.set(n,i)})),e}createLabelDivs(t){const e=this.createLabels(t).map((t=>ct.div([t],{style:{width:"20px"}}))),n=this.eventBus.nucleotideSequencesChanged$.subscribe((()=>{this.createLabels(t).forEach(((t,n)=>{Ht()(e[n]).empty(),Ht()(e[n]).append(t)}))}));return this.subscriptions.add(n),e}createLabels(t){return this.eventBus.getNucleotideSequences()[t].map(((e,n)=>{const r=this.displayedInputLabels.get(t)[n];return ct.label(r)}))}}class ae{constructor(){this.rxjsSubscriptions=[],this.dgSubscriptions=[]}add(t){t instanceof Nt.Subscription?this.rxjsSubscriptions.push(t):this.dgSubscriptions.push(t)}unsubscribeAll(){for(const t of[this.rxjsSubscriptions,this.dgSubscriptions])t.forEach((t=>t.unsubscribe())),t.length=0}}class ue{constructor(t,e){this.eventBus=t,this.dataManager=e,this.subscriptions=new ae}static open(t,e){ue.isDialogOpen||(ue.instance||(ue.instance=new ue(t,e)),ue.instance.openDialog())}openDialog(){this.initialPatternConfig=Ft().cloneDeep(this.eventBus.getPatternConfig()),ue.isDialogOpen=!0,this.createDialog().show()}createDialog(){const t=ct.divV([]);this.subscriptions.add(this.eventBus.strandsUpdated$.subscribe((()=>this.onStrandsUpdated(t))));const e=ct.dialog("Edit strands").add(t).onOK((()=>{})).onCancel((()=>this.resetToInitialState()));return this.subscriptions.add(e.onClose.subscribe((()=>{ue.isDialogOpen=!1,this.subscriptions.unsubscribeAll()}))),e}onStrandsUpdated(t){const e=new oe(this.eventBus,this.initialPatternConfig,this.subscriptions).create(),n=new se(this.eventBus,this.dataManager,this.subscriptions).create();Ht()(t).empty(),Ht()(t).append(e,n)}resetToInitialState(){this.eventBus.setPatternConfig(this.initialPatternConfig)}}ue.isDialogOpen=!1;class le{constructor(t){this.eventBus=t,this.subscriptions=new ae}static open(t){le.isDialogOpen||(le.instance||(le.instance=new le(t)),le.instance.openDialog())}openDialog(){this.initialPatternConfig=Ft().cloneDeep(this.eventBus.getPatternConfig()),le.isDialogOpen=!0,this.createDialog().show()}createDialog(){const t=ct.divV([]);this.subscriptions.add(this.eventBus.strandsUpdated$.subscribe((()=>this.onStrandsUpdated(t))));const e=ct.dialog("Edit terminal modifications").add(t).onOK((()=>{})).onCancel((()=>this.resetToInitialState()));return this.subscriptions.add(e.onClose.subscribe((()=>{le.isDialogOpen=!1,this.subscriptions.unsubscribeAll()}))),e}onStrandsUpdated(t){const e=new ce(this.eventBus).create();Ht()(t).empty(),Ht()(t).append(e)}resetToInitialState(){this.eventBus.setPatternConfig(this.initialPatternConfig)}}le.isDialogOpen=!1;class ce{constructor(t){this.eventBus=t}create(){const t=dt.map((t=>this.constructControlsPanel(t)));return ct.divH(t,{style:{gap:"24px"}})}constructControlsPanel(t){if(!this.eventBus.isAntisenseStrandActive()&&"AS"===t)return ct.div([]);const e=this.createInputs(t);return ct.block([ct.h1(`${pt[t]}`),e],{style:{paddingTop:"12px"}})}createInputs(t){const e=("SS"===t?[...mt].reverse():mt).map((e=>this.createInputForTerminus(t,e)));return ct.form(e)}createInputForTerminus(t,e){const n=this.eventBus.getTerminalModifications()[t][e],r=ct.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];Ht()(e).css("resize","none")}}class he{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[ct.h1("Edit"),t,n,r,i,s,o,ct.buttonsInput([u,a])]}createEditPatternButton(){const t=ct.button("Edit strands",(()=>ue.open(this.eventBus,this.dataManager)));return ct.tooltip.bind(t,"Edit strand modifications and PTOs"),t}createEditTerminalModificationsButton(){const t=ct.button("Edit terminals",(()=>le.open(this.eventBus)));return ct.tooltip.bind(t,"Edit terminal modifications"),Ht()(t).css("margin-right","20px"),t}createAntisenseStrandToggle(){const t=ct.switchInput(`${pt.AS} strand`,this.eventBus.isAntisenseStrandActive());return t.onInput((()=>this.eventBus.toggleAntisenseStrand(t.value))),this.eventBus.patternLoaded$.subscribe((()=>{t.value=this.eventBus.isAntisenseStrandActive()})),t.setTooltip("Toggle antisense strand"),t.root}createStrandLengthInputs(){const t=t=>{const n=this.eventBus.getNucleotideSequences()[t].length,r=ct.intInput(`${pt[t]} length`,n);return r.onInput((()=>e(t,r))),this.eventBus.nucleotideSequencesChanged$.subscribe((()=>{r.value=this.eventBus.getNucleotideSequences()[t].length})),r.setTooltip(`Number of nucleotides in ${t}, including overhangs`),[t,r]},e=(t,e)=>{const n=e.value;null!==n&&(n<=0&&(o.shell.warning("Sequence length must be greater than 0"),e.value=1),n>34&&(o.shell.warning("Sequence length must be less than 35"),e.value=34),this.eventBus.updateStrandLength(t,e.value))},n=Object.fromEntries(dt.map((e=>t(e))));return this.eventBus.antisenseStrandToggled$.subscribe((t=>{Ht()(n.AS.root).toggle(t)})),n}createSequenceBaseInput(){const t=this.dataManager.fetchAvailableNucleotideBases().sort(((t,e)=>t.toLowerCase().localeCompare(e.toLowerCase()))),e=this.dataManager.fetchDefaultNucleobase(),n=ct.choiceInput("Sequence basis",e,t);return n.onInput((()=>this.eventBus.replaceSequenceBase(n.value))),this.eventBus.nucleotideSequencesChanged$.subscribe((()=>{n.value=this.eventBus.getSequenceBase()})),n.setTooltip("Most frequent nucleobase in the strands"),n}createPatternCommentInput(){const t=ct.textInput("Comment",this.eventBus.getComment());return Ht()(t.root).addClass("st-pattern-text-input"),t.onInput((()=>this.eventBus.updateComment(t.value))),this.eventBus.patternLoaded$.subscribe((()=>{t.value=this.eventBus.getComment()})),t}createPatternNameInputBlock(){const t=ct.textInput("Pattern name",this.eventBus.getPatternName());return Ht()(t.root).addClass("st-pattern-text-input"),t.onInput((()=>this.eventBus.updatePatternName(t.value))),this.eventBus.patternLoaded$.subscribe((()=>{t.value=this.eventBus.getPatternName()})),t.setTooltip("Name under which pattern will be saved"),t.root}}class fe{constructor(t,e){this.eventBus=t,this.dataManager=e,this.subscriptions=new ae,this.authorSelectedByUser=!1,this.eventBus.patternLoadRequested$.subscribe((t=>this.handlePatternChoice(t))),this.eventBus.patternDeletionRequested$.subscribe((async t=>{await this.dataManager.deletePattern(t,this.eventBus)}))}async handlePatternChoice(t){let e=await this.dataManager.getPatternConfig(t);null===e&&(e=this.dataManager.getDefaultPatternConfig()),this.eventBus.setPatternConfig(e),this.eventBus.updateControlsUponPatternLoaded(t),this.eventBus.setLastLoadedPatternConfig(e)}isCurrentUserSelected(){return this.eventBus.getSelectedAuthor()!==this.dataManager.getOtherUsersAuthorshipCategory()}createControls(){const t=this.getPatternInputsContainer();return[ct.h1("Load"),t]}getPatternInputsContainer(){const t=ct.divH(this.createPatternInputs());return this.eventBus.patternListUpdated$.subscribe((()=>{this.subscriptions.unsubscribeAll(),Ht()(t).empty(),Ht()(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=ct.div([t.root]),n=this.eventBus.userSelection$.subscribe((()=>{Ht()(e).empty(),Ht()(e).append(this.createPatternChoiceInput().root)}));return this.subscriptions.add(n),e}createAuthorChoiceInput(){const t=[this.dataManager.getCurrentUserAuthorshipCategory()];this.dataManager.getOtherUsersPatternNames().length>0&&t.push(this.dataManager.getOtherUsersAuthorshipCategory());const e=ct.choiceInput("Author",this.eventBus.getSelectedAuthor(),t,(t=>{this.authorSelectedByUser=!0,this.eventBus.selectAuthor(t)}));return this.setAuthorChoiceInputStyle(e),e.setTooltip("Select pattern author"),e}setAuthorChoiceInputStyle(t){Ht()(t.input).css({"max-width":"100px","min-width":"100px"}),Ht()(t.root).css({"padding-right":"30px","padding-left":"30px"})}createPatternChoiceInput(){const t=this.isCurrentUserSelected()?this.dataManager.getCurrentUserPatternNames():this.dataManager.getOtherUsersPatternNames();if(this.authorSelectedByUser){const e=this.dataManager.getPatternHash(t[0],this.isCurrentUserSelected());this.eventBus.requestPatternLoad(e),this.eventBus.updateUrlState(e),this.authorSelectedByUser=!1}const e=this.getPatternName(t),n=ct.choiceInput("Pattern",e,t);return n.setTooltip("Select pattern to load"),Ht()(n.input).css({"max-width":"100px","min-width":"100px"}),this.subscriptions.add(n.onInput((()=>{const t=this.dataManager.getPatternHash(n.value,this.isCurrentUserSelected());this.eventBus.requestPatternLoad(t),this.eventBus.updateUrlState(t)}))),this.subscriptions.add(this.eventBus.patternLoaded$.subscribe((()=>{const e=this.eventBus.getPatternName();n.value?.includes(e)||(n.value=this.getPatternName(t))}))),n}getPatternName(t){return t.find((t=>t.includes(this.eventBus.getPatternName())))??t[0]}createDeletePatternButton(){const t=ct.button(ct.iconFA("trash-alt"),(()=>{this.eventBus.getPatternName()!==this.dataManager.getDefaultPatternName()?this.showDeletePatternDialog():o.shell.warning("Cannot delete example pattern")}));ct.tooltip.bind(t,"Delete pattern from user storage");const e=this.eventBus.userSelection$.subscribe((()=>{t.disabled=!this.isCurrentUserSelected()}));return this.subscriptions.add(e),t}showDeletePatternDialog(){const t=ct.dialog("Delete pattern"),e=this.eventBus.getPatternName();t.add(ct.divText(`Are you sure you want to delete pattern ${e}?`)),t.onOK((()=>this.eventBus.requestPatternDeletion(e))),t.show()}}class de{constructor(t,e){this.eventBus=t,this.dataManager=e}getLayout(){const t=new fe(this.eventBus,this.dataManager),e=new he(this.eventBus,this.dataManager),n=new ie(this.eventBus),r=t.createControls(),i=e.createControls(),o=n.createControls(),s=ct.div(r);Ht()(s).css({"padding-bottom":"20px"});const a=ct.div([...i,...o],"ui-form"),u=ct.div([s,a]);return Ht()(u).css({padding:"25px"}),ct.box(u,{style:{maxWidth:"450px"}})}}class pe{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]}))}}const ge={0:{SS:"SS: 5'",AS:"AS: 3'"},1:{SS:"3'",AS:"5'"}},me={SS:{NUMERIC_LABEL:30,NUCLEOBASE_CIRCLE:52.5,NUCLEOBASE_LABEL:60},AS:{NUMERIC_LABEL:127.5,NUCLEOBASE_CIRCLE:97.5,NUCLEOBASE_LABEL:105}};function ve(t){const e=Object.keys(s.a1)[0];if(!e)throw new Error("No format found in PATTERN_APP_DATA");return s.a1[e][t].color||""}class ye{constructor(t){this.config=t;const e=this.computeRightOverhangNucleotideCounts(),n=this.computeMaxEffectiveStrandLength(e),r=this.computeMaxWidthOfRightOverhangs(e),i=this.computeStrandLabelWidth(),o=this.computeMaxWidthOfTerminusLabels();this.initializeCalculators(e,n,r,i,o)}initializeCalculators(t,e,n,r,i){this.canvasDimensions=new Ae(this.config,e,n,r,i),this.nucleotidePositionCalculator=new Ce(this.config,e,t,i),this.legendPositionCalculator=new we(this.config,this.canvasDimensions),this.labelPositionCalculator=new xe(this.config,n,i,r,t,this.nucleotidePositionCalculator),this.linkageStarPositionCalculator=new _e(this.nucleotidePositionCalculator,t)}computeRightOverhangNucleotideCounts(){return dt.reduce(((t,e)=>(t[e]=this.countOverhangNucleotidesAtStartOfStrand(e),t)),{})}computeMaxEffectiveStrandLength(t){return Math.max(...dt.map((e=>this.config.nucleotideSequences[e].length-t[e])))}computeMaxWidthOfRightOverhangs(t){return Math.max(t.SS,t.AS)}getCanvasWidth(){return this.canvasDimensions.getCanvasWidth()}getCanvasHeight(){return this.canvasDimensions.getCanvasHeight()}getNucleotideCirclePosition(t,e){return this.nucleotidePositionCalculator.getNucleotideCirclePosition(t,e)}getNucleotideLabelTextPosition(t,e){return this.nucleotidePositionCalculator.getNucleotideLabelTextPosition(t,e)}getNumericLabelPosition(t,e,n){return this.nucleotidePositionCalculator.getNumericLabelPosition(t,e,n)}getLegendCirclePosition(t,e,n){return this.legendPositionCalculator.getLegendCirclePosition(t,e,n)}getLegendTextPosition(t,e,n){return this.legendPositionCalculator.getLegendTextPosition(t,e,n)}getStarLabelPosition(){return this.legendPositionCalculator.getStarLabelPosition()}getPhosphorothioateLinkageLabelPosition(){return this.legendPositionCalculator.getPhosphorothioateLinkageLabelPosition()}getTerminusLabelPosition(t,e){return this.labelPositionCalculator.getTerminusLabelPosition(t,e)}getStrandEndLabelPosition(t,e){return this.labelPositionCalculator.getStrandEndLabelPosition(t,e)}getTitleTextPosition(){return this.labelPositionCalculator.getTitleTextPosition()}getCommentLabelPosition(){return this.labelPositionCalculator.getCommentLabelPosition()}getCenterPositionOfLinkageStar(t,e){return this.linkageStarPositionCalculator.getCenterPositionOfLinkageStar(t,e)}computeStrandLabelWidth(){return Object.fromEntries(gt.map((t=>[t,this.getMaxWidthStrandEndLabelsByEnd(t)])))}computeMaxWidthOfTerminusLabels(){return gt.reduce(((t,e)=>(t[e]=this.getMaxWidthOfTerminusLabelsByEnd(e),t)),{})}getMaxWidthOfTerminusLabelsByEnd(t){return this.calculateMaxWidthOfStrandEndLabel((e=>this.config.strandTerminusModifications[e][vt[e][t]]))}getMaxWidthStrandEndLabelsByEnd(t){return this.calculateMaxWidthOfStrandEndLabel((e=>ge[t][e]))}calculateMaxWidthOfStrandEndLabel(t){const e=be.getInstance();return Math.max(...dt.map((n=>e.computeTextWidth(t(n),17,"Arial"))))}countOverhangNucleotidesAtStartOfStrand(t){const e=this.config.nucleotideSequences[t];let n=0;for(const t of e){if(!Lt(t))break;n++}return n}}class be{constructor(){this.canvas=document.createElement("canvas"),this.context=this.canvas.getContext("2d"),this.pixelRatio=window.devicePixelRatio||1,this.canvas.width*=this.pixelRatio,this.canvas.height*=this.pixelRatio}static getInstance(){return be.instance||(be.instance=new be),be.instance}computeTextWidth(t,e,n){return this.context?(this.context.font=`${e*this.pixelRatio}px ${n}`,this.context.measureText(t).width/this.pixelRatio):0}}class Ae{constructor(t,e,n,r,i){this.config=t,this.maxEffectiveStrandLength=e,this.maxWidthOfRightOverhangs=n,this.strandLabelWidth=r,this.maxTerminusWidthByEnd=i}getCanvasWidth(){const t=30*(this.maxEffectiveStrandLength+this.maxWidthOfRightOverhangs);return gt.reduce(((t,e)=>t+(this.strandLabelWidth[e]+this.maxTerminusWidthByEnd[e])),0)+t+30}getCanvasHeight(){return 15*(this.config.isAntisenseStrandIncluded?11:9)}}class Ce{constructor(t,e,n,r){this.config=t,this.maxEffectiveStrandLength=e,this.rightOverhangNucleotideCounts=n,this.maxTerminusWidthByEnd=r}getNucleotideCirclePosition(t,e){return{x:this.computeNucleotideCircleXPositionByStrand(t,e),y:me[e].NUCLEOBASE_CIRCLE}}getNucleotideLabelTextPosition(t,e){return{x:this.computeNucleotideCircleXPositionByStrand(t,e)+-5,y:me[e].NUCLEOBASE_LABEL}}computeNucleotideCircleXPositionByStrand(t,e){const n=this.rightOverhangNucleotideCounts[e];return this.computeNucleobaseCircleXPosition(t,n)}computeNucleobaseCircleXPosition(t,e){return this.maxTerminusWidthByEnd[1]+30*(this.maxEffectiveStrandLength-t+e+1)}getNumericLabelPosition(t,e,n){const r=this.getVisualStrandIndex(t,e),i=this.computeNumericLabelXOffset(this.config.nucleotideSequences[e],r,n);return{x:this.computeNucleotideCircleXPositionByStrand(t,e)+i,y:me[e].NUMERIC_LABEL}}computeNumericLabelXOffset(t,e,n){return n>=0&&n<10||at.AL.includes(t[e])?-5:-10}getVisualStrandIndex(t,e){return"SS"===e?t:this.config.nucleotideSequences[e].length-t}}class we{constructor(t,e){this.config=t,this.canvasDimensionCalculator=e}getLegendCirclePosition(t,e,n){return{x:this.computeLegendCircleXPosition(t,e,n),y:this.getLegendVerticalPosition()}}getLegendTextPosition(t,e,n){return{x:this.computeLegendCircleXPosition(t,e,n)+6+4,y:this.getLegendTextVerticalPosition()}}computeLegendCircleXPosition(t,e,n){const r=n?1:0,i=e.length+r,o=(t+r)*(this.canvasDimensionCalculator.getCanvasWidth()/i)+6;return Math.round(o)}getStarLabelPosition(){return{x:15,y:this.getLegendVerticalPosition()}}getPhosphorothioateLinkageLabelPosition(){return{x:22,y:this.getLegendTextVerticalPosition()}}getLegendVerticalPosition(){return 15*(this.config.isAntisenseStrandIncluded?9.5:6)}getLegendTextVerticalPosition(){return(this.config.isAntisenseStrandIncluded?150:me.AS.NUCLEOBASE_CIRCLE)-3}}class xe{constructor(t,e,n,r,i,o){this.config=t,this.maxWidthOfRightOverhangs=e,this.maxTerminusWidthByEnd=n,this.strandLabelWidth=r,this.rightOverhangNucleotideCounts=i,this.nucleotidePositionCalculator=o,this.xPositionOfTerminusModifications=this.computeXPositionOfTerminusModifications()}getTerminusLabelPosition(t,e){return{x:this.xPositionOfTerminusModifications[e][t],y:me[t].NUCLEOBASE_LABEL}}getStrandEndLabelPosition(t,e){return{x:this.getXPositionOfStrandLabels()[e],y:me[t].NUCLEOBASE_LABEL}}getTitleTextPosition(){return{x:15,y:15}}getCommentLabelPosition(){const t=15*(this.config.isAntisenseStrandIncluded?11:8.5);return{x:this.getXPositionOfStrandLabels()[0],y:t}}getXPositionOfStrandLabels(){return{0:0,1:Math.max(...dt.map((t=>this.xPositionOfTerminusModifications[1][t])))+this.maxTerminusWidthByEnd[0]+30*this.maxWidthOfRightOverhangs}}computeXPositionOfTerminusModifications(){return Object.fromEntries(gt.map((t=>[t,Object.fromEntries(dt.map((e=>[e,0===t?this.strandLabelWidth[0]-5:30*this.rightOverhangNucleotideCounts[e]+this.nucleotidePositionCalculator.computeNucleobaseCircleXPosition(-.5,0)])))])))}}class _e{constructor(t,e){this.nucleotidePositionCalculator=t,this.rightOverhangNucleotideCounts=e}getCenterPositionOfLinkageStar(t,e){return{x:this.getXPositionOfLinkageStar(t,e),y:this.getYPositionOfLinkageStar(e)}}getXPositionOfLinkageStar(t,e){return this.nucleotidePositionCalculator.computeNucleobaseCircleXPosition(t,this.rightOverhangNucleotideCounts[e])+15}getYPositionOfLinkageStar(t){return me[t].NUCLEOBASE_LABEL+5}}class Se{constructor(t){this.setupPatternConfig(t),this.patternDimensionsCalculator=new ye(this.config),this.svgFactory=new Ie(new pe,this.config,this.patternDimensionsCalculator),this.strandElementManager=new Ne(this.svgFactory,this.config),this.legendBuilder=new Ee(this.svgFactory,this.config)}renderPattern(){const t=this.createLabelElements(),e=this.countNucleotidesExcludingOverhangs(),n=this.strandElementManager.createStrandElements(e),r=this.svgFactory.createTitleElement(this.config.patternName,e,this.config.isAntisenseStrandIncluded),i=this.legendBuilder.getLegendItems(),o=this.svgFactory.createCanvas();return o.append(...t,...n,r,...i),o}countNucleotidesExcludingOverhangs(){return dt.reduce(((t,e)=>(t[e]=this.config.nucleotideSequences[e].filter((t=>!Lt(t))).length,t)),{})}createLabelElements(){const t=this.getStrandEndLabels(),e=this.getTerminusModificationLabels();return[...dt.flatMap((n=>[...Object.values(t[n]),...Object.values(e[n])]))].filter((t=>null!==t))}setupPatternConfig(t){this.config=JSON.parse(JSON.stringify(t)),this.config.nucleotideSequences.SS.reverse(),this.config.phosphorothioateLinkageFlags.SS.reverse()}getStrandEndLabels(){return dt.reduce(((t,e)=>(t[e]=gt.reduce(((t,n)=>(t[n]=this.svgFactory.createLabelForStrandEnd(e,n),t)),{}),t)),{})}getTerminusModificationLabels(){return dt.reduce(((t,e)=>(t[e]=mt.reduce(((t,n)=>(t[n]=this.svgFactory.createTerminusModificationLabel(e,n),t)),{}),t)),{})}}class Ee{constructor(t,e){this.svgFactory=t,this.config=e,this.containsPhosphorothioateLinkages=this.checkAnyPhosphorothioateLinkages()}getLegendItems(){return[this.svgFactory.createCommentLabel(),...this.createLegendItemsForNucleotideTypes(),...this.createLegendItemForPhosphorothioateLinkage(this.containsPhosphorothioateLinkages)]}createLegendItemsForNucleotideTypes(){const t=this.extractNucleotideTypes(),e=[];return t.forEach(((n,r)=>{const i=this.svgFactory.createLegendCircle(n,r,t,this.containsPhosphorothioateLinkages),o=this.svgFactory.createLegendText(n,r,t,this.containsPhosphorothioateLinkages);e.push(i,o)})),e}createLegendItemForPhosphorothioateLinkage(t){return[this.svgFactory.createLinkageStarLegendLabel(t),this.svgFactory.createPhosphorothioateLinkageLabel(t)].filter((t=>null!==t))}extractNucleotideTypes(){return[...new Set(this.config.nucleotideSequences.SS.concat(this.config.isAntisenseStrandIncluded?this.config.nucleotideSequences.AS:[]))]}checkAnyPhosphorothioateLinkages(){return[...this.config.phosphorothioateLinkageFlags.SS,...this.config.isAntisenseStrandIncluded?this.config.phosphorothioateLinkageFlags.AS:[]].some((t=>t))}}class Te{constructor(t){this.nucleotideCounts=JSON.parse(JSON.stringify(t))}decrementIfNotOverhang(t,e){t||this.nucleotideCounts[e]--}getCurrentCount(t){return this.nucleotideCounts[t]}}class Ie{constructor(t,e,n){this.svgElementFactory=t,this.config=e,this.dimensionsCalculator=n}createCanvas(){const t=this.dimensionsCalculator.getCanvasWidth(),e=this.dimensionsCalculator.getCanvasHeight();return this.svgElementFactory.createCanvas(t,e)}createTitleElement(t,e,n){const r=this.getTitleText(t,e,n),i=this.dimensionsCalculator.getTitleTextPosition();return this.svgElementFactory.createTextElement(r,i,17,"black")}getTitleText(t,e,n){return`${t} for ${e.SS}${n?`/${e.AS}`:""}-mer`}createPhosphorothioateLinkageStar(t,e){if(!this.config.phosphorothioateLinkageFlags[t][e])return null;const n=this.dimensionsCalculator.getCenterPositionOfLinkageStar(e,t);return this.svgElementFactory.createStarElement(n,"red")}createNucleotideNumericLabel(t,e,n){const r=this.config.nucleotideSequences[e][t],i=Lt(r),o=this.dimensionsCalculator.getNumericLabelPosition(t,e,n),s=!i&&this.config.nucleotidesWithNumericLabels.includes(r)?String(n):"";return this.svgElementFactory.createTextElement(s,o,14,"var(--grey-6)")}createNucleotideCircle(t,e){const n=this.config.nucleotideSequences[e][t],r=this.dimensionsCalculator.getNucleotideCirclePosition(t,e);return this.svgElementFactory.createCircleElement(r,15,ve(n))}createNucleotideNameLabel(t,e){const n=this.config.nucleotideSequences[e][t],r=this.dimensionsCalculator.getNucleotideLabelTextPosition(t,e);var i;return this.svgElementFactory.createTextElement(!Lt(i=n)&&at.AL.includes(i)?i:"",r,17,function(t){const e=ve(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))}createCommentLabel(){const t=this.dimensionsCalculator.getCommentLabelPosition();return this.svgElementFactory.createTextElement(this.config.patternComment,t,14,"var(--grey-6)")}createLinkageStarLegendLabel(t){const e=this.dimensionsCalculator.getStarLabelPosition();return t?this.svgElementFactory.createStarElement(e,"red"):null}createPhosphorothioateLinkageLabel(t){const e=this.dimensionsCalculator.getPhosphorothioateLinkageLabelPosition();return t?this.svgElementFactory.createTextElement("ps linkage",e,14,"var(--grey-6)"):null}createLabelForStrandEnd(t,e){if(!("SS"===t||"AS"===t&&this.config.isAntisenseStrandIncluded))return null;const n=ge[e][t],r=this.dimensionsCalculator.getStrandEndLabelPosition(t,e);return this.svgElementFactory.createTextElement(n,r,17,"var(--grey-6)")}createTerminusModificationLabel(t,e){if("AS"===t&&!this.config.isAntisenseStrandIncluded)return null;const n="SS"===t&&"5'"===e||"AS"===t&&"3'"===e?0:1,r=this.config.strandTerminusModifications[t][e],i=this.dimensionsCalculator.getTerminusLabelPosition(t,n);return this.svgElementFactory.createTextElement(r,i,17,"red")}createLegendCircle(t,e,n,r){const i=ve(t),o=this.dimensionsCalculator.getLegendCirclePosition(e,n,r);return this.svgElementFactory.createCircleElement(o,6,i)}createLegendText(t,e,n,r){const i=this.dimensionsCalculator.getLegendTextPosition(e,n,r);return this.svgElementFactory.createTextElement(t,i,14,"var(--grey-6)")}}class Ne{constructor(t,e){this.svgFactory=t,this.config=e}createStrandElements(t){const e=[],n=new Te(t);return dt.forEach((r=>{("SS"===r||"AS"===r&&this.config.isAntisenseStrandIncluded)&&this.config.nucleotideSequences[r].forEach(((i,o)=>{const s=this.createElementsForNucleotide(o,r,n,t);e.push(...s)}))})),e}createElementsForNucleotide(t,e,n,r){const i=Lt(this.config.nucleotideSequences[e][t]);n.decrementIfNotOverhang(i,e);const o="SS"===e?n.getCurrentCount(e)+1:r[e]-n.getCurrentCount(e),s=this.svgFactory.createNucleotideNumericLabel(t,e,o),a=this.svgFactory.createNucleotideCircle(t,e),u=this.svgFactory.createNucleotideNameLabel(t,e),l=this.svgFactory.createPhosphorothioateLinkageStar(e,t),c=this.config.nucleotideSequences[e].length;return[s,a,u,l,this.svgFactory.createPhosphorothioateLinkageStar(e,c)].filter((t=>null!==t))}}var Oe=n(146);class Le{constructor(t){this.eventBus=t,this.svgDisplayDiv=ct.div([]),t.patternStateChanged$.subscribe((()=>this.updateSvgContainer())),t.svgSaveRequested$.subscribe((()=>this.saveSvgAsPng()))}static createSvgDiv(t){return new Le(t).svgDisplayDiv}updateSvgContainer(){$(this.svgDisplayDiv).empty();const t=this.eventBus.getPatternConfig();this.svgElement=this.createSvg(t),this.svgDisplayDiv.append(this.svgElement)}createSvg(t){return new Se(t).renderPattern()}saveSvgAsPng(){const t=this.eventBus.getPatternName();Oe.saveSvgAsPng(this.svgElement,t,{backgroundColor:"white"})}}class Me{constructor(t){this.eventBus=t,this.togglesContainer=ct.div([]),this.eventBus.uniqueNucleotidesChanged$().subscribe((()=>{this.updateContainer()}))}getContainer(){return this.togglesContainer}updateContainer(){Ht()(this.togglesContainer).empty(),Ht()(this.togglesContainer).append(this.createInputs())}createInputs(){const t=this.eventBus.getUniqueNucleotides().filter((t=>!Lt(t))).map((t=>this.createSingleInput(t)));return t.sort(((t,e)=>t.captionLabel.textContent.localeCompare(e.captionLabel.textContent))),ct.divH(t.map((t=>t.root)))}createSingleInput(t){const e=this.eventBus.getModificationsWithNumericLabels().includes(t),n=ct.boolInput(t,e,(e=>this.handleNumericLabelToggle(t,e)));return Ht()(n.root).css("padding-right","20px"),n.setTooltip(`Show numeric labels for ${t}`),n}handleNumericLabelToggle(t,e){const n=this.eventBus.getModificationsWithNumericLabels();if(n.includes(t)===e)return;const r=e?n.concat(t):n.filter((e=>e!==t));this.eventBus.updateModificationsWithNumericLabels(r)}}class Be{constructor(t,e){this.eventBus=t,this.dataManager=e,this.subscriptions=new ae}createContainer(){return ct.div([ct.h1("Translation example"),this.createTranslationExamples()],{style:{paddingTop:"20px"}})}createTranslationExamples(){const t=ct.divH([...this.getExampleElements()],"ui-form");return this.eventBus.antisenseStrandToggled$.subscribe((()=>{this.subscriptions.unsubscribeAll(),Ht()(t).empty(),Ht()(t).append(this.getExampleElements())})),t}getExampleElements(){return dt.map((t=>new Pe(t,this.eventBus,this.subscriptions).create()))}}class Pe{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(),ct.block50([ct.h2(pt[this.strand]),this.inputExample.root,this.outputExample.root],{style:{paddingRight:"20px"}})):ct.div([])}subscribeToEvents(){const t=this.eventBus.strandsLinkagesAndTerminalsUpdated$.subscribe((()=>{const t=this.generateExampleSequence();this.inputExample.value=t,this.outputExample.value=this.computeOutputValue(t)}));"AS"===this.strand&&this.subscriptions.add(t)}createInputExample(){const t=this.createTextInputForExamples(),e=this.generateExampleSequence();return t.value=e,t.setTooltip(`Example raw nucleotides input for ${pt[this.strand]}`),t}generateExampleSequence(){return this.eventBus.getNucleotideSequences()[this.strand].map(((t,e)=>at.AL[e%at.AL.length])).join("")}createOutputExample(t){const e=this.createTextInputForExamples();return e.value=this.computeOutputValue(t),e.setTooltip(`Pattern applied to the example input for ${pt[this.strand]}`),e}computeOutputValue(t){const e=this.eventBus.getNucleotideSequences()[this.strand],n=this.eventBus.getTerminalModifications()[this.strand];return function(t,e,n,r){const i=function(t,e,n){const r=new Array(t.length+e.filter((t=>t)).length+mt.length);r[0]=n["5'"],r[r.length-1]=n["3'"];let i=1;return e[0]&&(r[i]="ps",i++),t.forEach(((t,n)=>{r[n+i]=t,e[n+1]&&(r[n+i+1]="ps",i++)})),r}(t.split("").map(((t,n)=>{const r=function(t,e){const n=Object.keys(s.a1)[0],r=s.a1[n][e].substitution;return t.replace(/([AGCTU])/,r)}(t,e[n]);return r})),n,r);return i.join("")}(t,e,this.eventBus.getPhosphorothioateLinkageFlags()[this.strand],n)}createTextInputForExamples(){const t=ct.textInput("","");return this.applyStylingToInput(t),t}applyStylingToInput(t){const e=t.root.getElementsByTagName("textarea")[0];e.setAttribute("readonly","true"),Ht()(e).css("resize","none"),Ht()(t.root).css("opacity","75%")}}class Re{constructor(t,e){this.eventBus=t,this.dataManager=e,this.svgDisplay=Le.createSvgDiv(t)}getLayout(){const t=new Me(this.eventBus).getContainer(),e=this.generateDownloadControls(),n=new Be(this.eventBus,this.dataManager).createContainer();return ct.panel([this.svgDisplay,t,e,n],{style:{overflowX:"scroll",padding:"12px 24px"}})}generateDownloadControls(){return ct.divH([this.createSavePatternButton(),this.createDownloadPngButton(),this.createShareLinkButton()],{style:{gap:"12px",marginTop:"12px"}})}createDownloadPngButton(){const t=ct.button("Get PNG",(()=>this.eventBus.requestSvgSave()));return ct.tooltip.bind(t,"Download pattern as PNG"),t}createShareLinkButton(){const t=ct.button(ct.iconFA("link"),(()=>navigator.clipboard.writeText(window.location.href).then((()=>o.shell.info("Link to pattern copied to clipboard")))));return this.eventBus.patternHasUnsavedChanges$.subscribe((e=>{t.disabled=e})),ct.tooltip.bind(t,"Share pattern link"),t}createSavePatternButton(){const t=ct.button("Save",(()=>this.processSaveButtonClick()));return this.eventBus.patternHasUnsavedChanges$.subscribe((e=>{t.disabled=!e})),ct.tooltip.bind(t,"Save pattern to user storage"),t}processSaveButtonClick(){const t=this.eventBus.getPatternName();t!==this.dataManager.getDefaultPatternName()?""!==t?this.dataManager.savePatternToUserStorage(this.eventBus).then((()=>{o.shell.info(`Pattern ${t} saved`)})).catch((t=>this.handleErrorWhileSavingPattern(t))):o.shell.warning("Insert pattern name"):o.shell.warning("Cannot save default pattern")}handleErrorWhileSavingPattern(t){t instanceof _t?new Fe(this.eventBus,this.dataManager).show():t instanceof St?o.shell.warning(ct.div([ct.divText("Pattern already exists"),ct.button("Load",(()=>{const e=t.message;this.eventBus.requestLoadPatternInNewTab(e)}))])):console.error("Error while saving pattern",t)}}class Fe{constructor(t,e){this.eventBus=t,this.dataManager=e}show(){const t=this.eventBus.getPatternName(),e=ct.dialog(`Pattern "${t}" already exists`);e.add(ct.divText(`Pattern "${t}" already exists. Do you want to overwrite it?`)),e.show(),e.onOK((()=>this.processOverwriteNamesakePattern()))}processOverwriteNamesakePattern(){const t=this.eventBus.getPatternName();this.dataManager.overwritePatternInUserStorage(this.eventBus).then((()=>{o.shell.info(`Pattern ${t} overwritten`)})).catch((t=>{console.error("Error while overwriting pattern in user storage",t),o.shell.error("Error while overwriting pattern")}))}}class De extends ft{constructor(){super("Oligo Pattern")}getContent(){return async function(){const t=await It.getInstance(),e=new kt,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 Dt(t,n);e.subscribeToObservables(r);const i=new de(r,t).getLayout(),o=new Re(r,t).getLayout();return ct.splitH([i,o],{},!0)}()}}var Ue=n(507),ke={};function $e(t){var e;return"string"==typeof t||t instanceof String?t:("object"==typeof t||t instanceof Object)&&"$thrownJsError"in t?$e(t.$thrownJsError):t instanceof Error?null!==(e=t.stack)&&void 0!==e?e:t.message:t.toString()}ke.styleTagTransform=Zt(),ke.setAttributes=Kt(),ke.insert=zt().bind(null,"head"),ke.domAPI=Gt(),ke.insertStyleElement=Xt(),jt()(Ue.A,ke),Ue.A&&Ue.A.locals&&Ue.A.locals;var He,Ve=n(74),je={};je.styleTagTransform=Zt(),je.setAttributes=Kt(),je.insert=zt().bind(null,"head"),je.domAPI=Gt(),je.insertStyleElement=Xt(),jt()(Ve.A,je),Ve.A&&Ve.A.locals&&Ve.A.locals;class qe{constructor(t,e,n=!0){this.textInputBase=t,this.painter=e,Ht()(this.root).addClass("colored-text-input"),n&&this.textInputBase.onChanged((()=>{Ht()(this.textArea).css("height",0),Ht()(this.textArea).css("height",this.textArea.scrollHeight+"px")})),this.highlights=ct.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 Ge(t){let e=0;const n=new lt(t).getFormat();null!==n&&(e=new ut.q(t).getInvalidCodeIndex(n));const r=e<0||""===t,i=ct.span([]);Ht()(i).css("-webkit-text-fill-color","var(--grey-6)");const o=ct.span([]);return Ht()(o).css("-webkit-text-fill-color","red"),r?i.innerHTML=t:(i.innerHTML=t.slice(0,e),o.innerHTML=t.slice(e)),[i,o]}!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"}(He||(He={}));class We{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 ze extends We{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 Ye extends ze{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(He.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(He.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(He.TYPE)&&-1!==t.indexOf(He.END)}shiftIdxToAtomType(t){return this.shiftIdxToSpecifiedColumn(t,He.ATOM_TYPE_COL)}getCountsLineIdx(){let t=0;for(let e=0;e<He.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,He.FIRST_BONDED_ATOM_COL)}shiftIdxToBondType(t){return this.shiftIdxToSpecifiedColumn(t,He.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+He.NUM_OF_COUNTS_DIGITS;const n=parseInt(this.fileContent.substring(t,e));return t=e,e+=He.NUM_OF_COUNTS_DIGITS,{atomCount:n,bondCount:parseInt(this.fileContent.substring(t,e))}}}class Ke extends ze{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 ${i} is already in the map`);t.set(i,n)}})),t}shiftIdxToAtomType(t){return this.shiftIdxToSpecifiedColumn(t,4)}getCountsLineIdx(){return this.fileContent.indexOf("M  V30 COUNTS ")}getAtomBlockIdx(){let t=this.fileContent.indexOf("M  V30 BEGIN ATOM");return t=this.getNextLineIdx(t),t}shiftIdxToXColumn(t){let e=this.shiftIdxToAtomType(t);return this.isQuote(e)?(e=this.getNextIdenticalChar(e),e=this.getNextColumnIdx(e),e):this.shiftIdxToSpecifiedColumn(t,5)}shiftIdxToBondedAtomsPair(t){return this.shiftIdxToSpecifiedColumn(t,5)}shiftIdxToBondType(t){return this.shiftIdxToSpecifiedColumn(t,4)}getBondBlockIdx(){return this.getNextLineIdx(this.fileContent.indexOf("M  V30 BEGIN BOND"))}static isValidMolfile(t){return-1!==t.indexOf("V3000")&&-1!==t.indexOf("M  END")}parseAtomAndBondCounts(){let t=this.fileContent.indexOf("M  V30 COUNTS ")+14,e=this.fileContent.indexOf(" ",t+1);const n=parseInt(this.fileContent.substring(t,e));return t=e+1,e=this.fileContent.indexOf(" ",t+1),{atomCount:n,bondCount:parseInt(this.fileContent.substring(t,e))}}}class Qe{constructor(){}static getInstance(t){if(Qe.isMolfileV2K(t))return new Ye(t);if(Qe.isMolfileV3K(t))return new Ke(t);throw new Error("Malformed molfile")}static isMolfileV2K(t){return Ye.isValidMolfile(t)}static isMolfileV3K(t){return Ke.isValidMolfile(t)}}const Xe=class extends Error{constructor(t){super(t)}};class Je{constructor(t){this.molblock=t}get molblock(){return this._validMolBlock}set molblock(t){if(""!==t){try{this.validateMolBlock(t)}catch(e){e instanceof Xe&&(t="");const n=$e(e);console.error(n)}this._validMolBlock=t}else this._validMolBlock=t}validateMolBlock(t){if(""===t)throw new Xe("MoleculeImage: invalid molblock")}async drawMolBlockOnCanvas(t){try{await o.functions.call("Chem:canvasMol",{x:0,y:0,w:t.width,h:t.height,canvas:t,molString:this.molblock,scaffoldMolString:"",options:{normalizeDepiction:!1,straightenDepiction:!1}})}catch(t){const e=$e(t);console.error(e)}}getMoleculeDimensions(){const t=Qe.getInstance(this.molblock),e=Math.max(...t.x)-Math.min(...t.x);return{height:Math.max(...t.y)-Math.min(...t.y),width:e}}async zoomIn(){const t=ct.dialog({title:"Molecule",showFooter:!1}),e=.7*Ht()(window).height(),n=this.getMoleculeDimensions(),r=e/n.height,i=e,o=n.width*r,s=ct.canvas(o,i);await this.drawMolBlockOnCanvas(s);const a=ct.block([s],{style:{overflowX:"scroll"}});t.add(a).showModal(!0),Ht()(t.root).find(".d4-dialog-contents").removeClass("ui-form"),Ht()(t.root).find(".d4-dialog-contents").removeClass("ui-panel"),Ht()(t.root).find(".d4-dialog-contents").addClass("ui-box"),Ht()(t.root).find(".d4-dialog-contents").css("padding","0")}async drawMolecule(t,e,n){t.innerHTML="";const r=ct.canvas(e*window.devicePixelRatio,n*window.devicePixelRatio);r.style.width=`${e}px`,r.style.height=`${n}px`,r.style.cursor="zoom-in",this.drawMolBlockOnCanvas(r),r.addEventListener("click",(async()=>{await this.zoomIn()})),t.append(ct.tooltip.bind(r,"Click to zoom"))}}class Ze{constructor(t,e){this.sequence=t,this.codeMap=e}parseSequence(){const t=this.parseRawSequence();return this.addLinkers(t)}addLinkers(t){const e=[];return t.forEach(((n,r)=>{const i=this.getSymbolForCode(n);r>0&&function(t){return s.TJ.left.includes(t)}(i)&&e.pop(),e.push(i);const o=tn(i),a=r===t.length-1,u=r+1<t.length&&tn(this.getSymbolForCode(t[r+1]));o||function(t){return s.TJ.right.includes(t)}(i)||u||a||e.push("p")})),e}getSymbolForCode(t){let e=this.codeMap.get(t);return e??(e=t),e}parseRawSequence(){const t=this.getAllCodesOfFormat(),e=[];let n=0;for(;n<this.sequence.length;){const r=t.find((t=>t===this.sequence.substring(n,n+t.length)));e.push(r),n+=r.length}return e}getAllCodesOfFormat(){const t=Array.from(this.codeMap.keys());return(0,ot.iD)(t)}}function tn(t){return s.TJ.phosphate.includes(t)}class en{constructor(t,e=!1,n){this.invert=e,this.lib=a.k.getInstance();const r=this.lib.getCodeToSymbolMap(n);this.parser=new Ze(t,r)}convert(){const t=this.parser.parseSequence(),e=[];t.forEach(((t,n)=>{const r=this.getMonomerMolfile(t,n);e.push(r)}));let n=this.getPolymerMolfile(e);return this.invert&&(n=this.reflect(n),n=this.invertBondConfiguration(n)),n}invertBondConfiguration(t){const e=t.indexOf("M  V30 BEGIN BOND"),n=t.indexOf("M  V30 END BOND");let r=t.substring(e,n);return r=r.replace(/(CFG=)([13])/g,((t,e,n)=>"1"===n?`${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)}}var nn=n(670);function rn(t,e){if(""===t)return"";const n=new lt(t).getFormat();if(!n)return"";let r="";try{r=new en(t,e,n).convert()}catch(t){const e=$e(t);console.error(e)}return r}function on(t,e,n,r){const i=[t,e,n].filter((t=>""!==t.strand));if(1===i.length)return rn(i[0].strand,i[0].invert);{const i=rn(t.strand,t.invert),o=[rn(e.strand,e.invert),rn(n.strand,n.invert)].filter((t=>""!==t));return(0,nn.vS)({senseStrands:[i],antiStrands:o},r)}}const sn=["ss","as","as2"];class an{constructor(){this.onInput=new Nt.Subject,this.onInvalidInput=new Nt.Subject,this.inputBase=Object.fromEntries(sn.map((t=>[t,ct.textInput("","",(()=>{this.onInput.next()}))]))),this.useChiralInput=ct.boolInput("Use chiral",!0),this.saveAllStrandsInput=ct.boolInput("Save as one entity",!0),ct.tooltip.bind(this.saveAllStrandsInput.root,"Save SDF with all strands in one molfile"),this.directionInversion=Object.fromEntries(sn.map((t=>[t,!1]))),this.moleculeImgDiv=ct.block([]),Ht()(this.moleculeImgDiv).addClass("st-structure-mol-img"),r.debounce(this.onInput,300).subscribe((async()=>{await this.updateMoleculeImg()})),r.debounce(this.onInvalidInput,1e3).subscribe((async()=>{o.shell.warning("Insert Sense strand")}))}async getHtmlDivElement(){const t=this.getTableInput(),e=this.getBoolInputsAndButton();await this.updateMoleculeImg();const n=ct.divH([e,this.moleculeImgDiv]);Ht()(n).addClass("st-structure-bottom");const r=ct.divV([t,n]);return Ht()(r).addClass("st-structure-body"),r}getBoolInputsAndButton(){const t=ct.buttonsInput([ct.bigButton("Save SDF",(()=>{const t=this.getStrandData();!function(t,e,n,r,i){const s=[t.strand,e.strand,n.strand].filter((t=>""!==t));if(0===s.length||1===s.length&&""===t.strand)o.shell.warning("Enter SENSE_STRAND and optionally ANTISENSE_STRAND/AS2 to save SDF");else{let a;if(i)a=on(t,e,n,r)+"\n$$$$\n";else{const h=rn(t.strand,t.invert),f=rn(e.strand,e.invert),d=rn(n.strand,n.invert);a=h+"\n> <Sequence>\nSense Strand\n$$$$\n",f&&(a+=f+"\n> <Sequence>\nAnti Sense\n$$$$\n"),d&&(a+=d+"\n> <Sequence>\nAnti Sense 2\n$$$$\n")}const u=new Date;function l(t){return t>=10?t.toString():"0"+t.toString()}const c=u.getFullYear()+"-"+l(u.getMonth()+1)+"-"+l(u.getDate())+"_"+l(u.getHours())+"-"+l(u.getMinutes())+"-"+l(u.getSeconds());(0,ot.RG)(`SequenceTranslator-${c}.sdf`,encodeURIComponent(a))}}(t.ss,t.as,t.as2,this.useChiralInput.value,this.saveAllStrandsInput.value)}))]),e=[this.saveAllStrandsInput.root,this.useChiralInput.root,t],n=ct.divV(e);for(const t of e)Ht()(t).addClass("st-structure-bool-button-block");return n}getTableInput(){const t=Object.fromEntries(sn.map((t=>[t,new qe(this.inputBase[t],Ge)]))),e=Object.fromEntries(sn.map(((t,e)=>{const n=0===e?"5′ → 3′":"3′ → 5′";return[t,ct.choiceInput(`${t.toUpperCase()} direction`,n,["5′ → 3′","3′ → 5′"])]})));sn.forEach(((t,n)=>{e[t].onChanged((()=>{let r="3′ → 5′"===e[t].value;n>0&&(r=!r),this.directionInversion[t]=r,this.onInput.next()}))}));const n=["Sense Strand","Anti Sense","Anti Sense 2"],r=new Map(sn.map(((t,e)=>[t,n[e]]))),i=Object.fromEntries(sn.map((t=>[t,ct.label(r.get(t))]))),o=Object.fromEntries(sn.map((e=>{const n=ct.icons.delete((()=>{t[e].inputBase.value=""})),r=ct.button(n,(()=>{}));return ct.tooltip.bind(r,`Clear ${e.toUpperCase()}`),[e,n]}))),s=sn.map((n=>({label:i[n],textInput:t[n].root,clear:o[n],choiceInput:e[n].root}))),a=ct.table(s,(t=>[t.label,t.textInput,t.clear,t.choiceInput]));Ht()(a).css("margin-top","10px");for(const t of sn){let n=i[t].parentElement;n.classList.add("st-structure-input-form"),Ht()(n).css("padding-top","3px"),n=e[t].root.parentElement,n.classList.add("st-structure-input-form","st-structure-direction-choice"),n=this.inputBase[t].root.parentElement,n.classList.add("st-structure-text-input-td")}return a}getStrandData(){return Object.fromEntries(sn.map((t=>{const e=this.directionInversion[t];return[t,{strand:this.inputBase[t].value.replace(/\s*/g,""),invert:e}]})))}getMolfile(t,e,n){return on(t,e,n,this.useChiralInput.value)}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=$e(t);console.error(e)}const e=new Je(t);await e.drawMolecule(this.moleculeImgDiv,650,150),Ht()(this.moleculeImgDiv).find("canvas").css("float","inherit")}}class un extends ft{constructor(){super("Oligo Structure"),this.layout=new an}getContent(){return this.layout.getHtmlDivElement()}}async function ln(t){try{const e={overflowX:"scroll"},n=ct.div([],{style:e}),r=(0,nn.cx)(t),i=.7*Ht()(window).height(),s=Math.max(...r.x)-Math.min(...r.x),a=Math.max(...r.y)-Math.min(...r.y),u=i/a,l=u*s,c=u*a,h=ct.canvas(l*window.devicePixelRatio,c*window.devicePixelRatio);h.style.width=`${l}px`,h.style.height=`${c}px`,await async function(t,e){await o.functions.call("Chem:canvasMol",{x:0,y:0,w:t.width,h:t.height,canvas:t,molString:e,scaffoldMolString:"",options:{normalizeDepiction:!1,straightenDepiction:!1}})}(h,t),n.appendChild(h),ct.dialog("Molecule").add(n).showModal(!0)}catch(t){const e=$e(t);console.error(e)}}class cn{static async view(){const t=a.k.getInstance().getTableForViewer();t.name="Monomer Library";const e=o.shell.addTableView(t);e.grid.props.allowEdit=!1,e.grid.onCellDoubleClick.subscribe((async t=>{const e=t.cell.value;"Molecule"===t.tableColumn?.semType&&await ln(e)}))}}var hn=n(480),fn=n(348),dn=n(67),pn=n(254),gn={};gn.styleTagTransform=Zt(),gn.setAttributes=Kt(),gn.insert=zt().bind(null,"head"),gn.domAPI=Gt(),gn.insertStyleElement=Xt(),jt()(pn.A,gn),pn.A&&pn.A.locals&&pn.A.locals;const mn=["Sequence"];class vn{constructor(){this.inputFormats=Object.keys(s.$D).concat(at.NO.HELM),this.onInput=new Nt.Subject,this.moleculeImgDiv=ct.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=ct.div([]),this.formatChoiceInput=ct.choiceInput("",at.NO.HELM,this.inputFormats,(async()=>{this.format=this.formatChoiceInput.value,this.updateTable(),await this.updateMolImg()})),this.sequenceInputBase=ct.textInput("","Afcgacsu",(()=>{this.onInput.next()})),this.init(),r.debounce(this.onInput,300).subscribe((async()=>{this.init(),this.formatChoiceInput.value=this.format,this.updateTable(),await this.updateMolImg()})),this.eventBus=Cn.getInstance()}async getHtmlElement(){const t=this.constructSingleSequenceControls(),e=this.constructBulkTranslationControls(),n=ct.box(ct.panel([t,e,ct.block([ct.box(this.moleculeImgDiv)])]));return this.formatChoiceInput.value=this.format,this.updateTable(),await this.updateMolImg(),n}constructBulkTranslationControls(){const t=ct.h1("Bulk");ct.tooltip.bind(t,"Bulk translation from table input");const e=new yn(this.eventBus).createUIComponents(),n=ct.choiceInput("Input format",at.NO.AXOLABS,this.inputFormats,(t=>this.eventBus.selectInputFormat(t))),r=ct.choiceInput("Output format",dn.qP,(0,hn.OT)(),(t=>this.eventBus.selectOutputFormat(t))),i=this.createConvertBulkButton(),o=ct.div([...e,n,r,i],"ui-form");return ct.block25([t,o])}createConvertBulkButton(){const t=ct.bigButton("Convert",(()=>this.processConvertBulkButtonClick()));return ct.tooltip.bind(t,"Convert sequences from table input"),$(t).css({float:"right","margin-top":"20px"}),t}processConvertBulkButtonClick(){const t=this.eventBus.getSelectedTable();if(!t)return void o.shell.warning("No table selected");const e=this.eventBus.getSelectedInputFormat(),n=this.eventBus.getSelectedOutputFormat(),i=this.eventBus.getSelectedColumn("Sequence");if(!i)return void o.shell.warning("No sequence column selected");const s=`${i.name} (${n})`,a=r.Column.fromList(r.TYPE.STRING,s,i.toList().map((t=>(0,hn.C6)(t,e,n))));if(n===dn.qP||n===at.NO.HELM){a.semType=r.SEMTYPE.MACROMOLECULE;const t=n==dn.qP?p.FASTA:p.HELM;a.setTag(r.TAGS.UNITS,t);const e=W.forColumn(a);(n==dn.qP?W.setUnitsToFastaColumn:W.setUnitsToHelmColumn)(e)}t.columns.add(a),o.data.detectSemanticTypes(t),o.shell.v=o.shell.getTableView(t.name)}constructSingleSequenceControls(){const t=new qe(this.sequenceInputBase,Ge),e=ct.button("Get SDF",(()=>{this.saveMolfile()}),"Save structure as SDF"),n=ct.button("Copy SMILES",(()=>{this.copySmiles()}),"Copy SMILES for the sequence"),r=ct.div([this.formatChoiceInput]),i=ct.button(ct.icons.delete((()=>{t.inputBase.value=""})),(()=>{}));ct.tooltip.bind(i,"Clear input");const o={format:r,textInput:t.root,clearBtn:i},s=ct.table([o],(t=>[t.format,t.textInput,t.clearBtn]));s.classList.add("st-translator-input-table");const a=ct.block([this.outputTableDiv,e,n]);return ct.block75([ct.h1("Single sequence"),s,a])}saveMolfile(){const t=new en(this.sequence,!1,this.formatChoiceInput.value).convert()+"\n$$$$";(0,ot.RG)(this.sequence+".sdf",encodeURIComponent(t))}copySmiles(){const t=r.chem.convert(this.molfile,r.chem.Notation.MolBlock,r.chem.Notation.Smiles);navigator.clipboard.writeText(t).then((()=>o.shell.info(dn.n_)))}updateTable(){this.outputTableDiv.innerHTML="";const t=this.format?new ut.q(this.sequence).getInvalidCodeIndex(this.format):0,e=(0,hn.bD)(this.sequence,t,this.format),n=[];for(const t of Object.keys(e)){const r="indexOfFirstInvalidChar"in e?ct.divH([]):ct.link(e[t],(()=>navigator.clipboard.writeText(e[t]).then((()=>o.shell.info(dn.n_)))),dn.U_,"");n.push({format:t,sequence:r})}const r=ct.table(n,(t=>[t.format,t.sequence]),["FORMAT","SEQUENCE"]);this.outputTableDiv.append(r),this.outputTableDiv.classList.add("st-translator-output-table")}async updateMolImg(){const t=new Je(this.molfile);await t.drawMolecule(this.moleculeImgDiv,500,170)}init(){this.sequence=this.getFormattedSequence(),this.format=new lt(this.sequence).getFormat(),this.molfile=this.getMolfile()}getFormattedSequence(){return this.sequenceInputBase.value.replace(/\s/g,"")}getMolfile(){if(!this.format)return"";if(this.format===at.NO.HELM){const t=new fn.y(this.sequence,this.format).convertTo(at.NO.AXOLABS);return new en(t,!1,at.NO.AXOLABS).convert()}return new en(this.sequence,!1,this.format).convert()}}class yn{constructor(t){this.tableInputManager=new bn(t),this.columnInputManager=new An(t)}createUIComponents(){return[this.tableInputManager.getTableInputContainer(),this.columnInputManager.getColumnControlsContainer()]}}class bn{constructor(t){this.eventBus=t,this.availableTables=[],this.tableInputContainer=ct.div([]),this.subscribeToTableEvents(),this.refreshTableInput()}getTableInputContainer(){return this.tableInputContainer}subscribeToTableEvents(){o.events.onTableAdded.subscribe((t=>this.handleTableAdded(t))),o.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 ct.tableInput("Table",t,this.availableTables,(t=>{null!==t&&t instanceof r.DataFrame&&this.eventBus.selectTable(t)}))}handleTableChoice(){const t=this.eventBus.getSelectedTable();t&&(this.isTableDisplayed(t)||this.displayTable(t))}isTableDisplayed(t){return o.shell.tableNames.includes(t.name)}displayTable(t){const e=o.shell.v;o.shell.addTableView(t),o.shell.v=e}}class An{constructor(t){this.eventBus=t,this.columnControlsContainer=ct.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),ct.choiceInput(`${t}`,i,e,(e=>this.selectColumnIfTableNotNull(n,e,t)))}selectColumnIfTableNotNull(t,e,n){if(null!==t){const r=t.getCol(e);this.eventBus.selectColumn(n,r)}}}class Cn{constructor(){this._tableSelection$=new Nt.BehaviorSubject(null),this._columnSelection=Object.fromEntries(mn.map((t=>[t,new Nt.BehaviorSubject(null)]))),this._inputFormatSelection$=new Nt.BehaviorSubject(at.NO.AXOLABS),this._outputFormatSelection$=new Nt.BehaviorSubject(dn.qP)}static getInstance(){return void 0===Cn._instance&&(Cn._instance=new Cn),Cn._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 wn extends ft{constructor(){super("Oligo Translator"),this.layout=new vn;const t=ct.iconFA("book",cn.view,"View monomer library");this.topPanel=[t],this.view.setRibbonPanels([this.topPanel])}getContent(){return this.layout.getHtmlElement()}}class xn extends ft{constructor(t,e){super(t),this.content=e}getContent(){return Promise.resolve(this.content)}}class _n extends ht{constructor(t){super("Oligo Toolkit"),this.externalViewFactories=t;const e=this.getViewFactories();this.multiView=new r.MultiView({viewFactories:e})}getViewFactories(){function t(t){const e=r.View.create(),n=new t(e);return n.initView().catch((e=>console.error(`Failed to initialize ${t.name}: ${e}`))),()=>n.getView()}let e={TRANSLATOR:t(wn),PATTERN:t(De),STRUCTURE:t(un)};return this.externalViewFactories&&(e=Object.assign({},e,this.externalViewFactories)),e}getCurrentPanePath(){let t=this.multiView.tabs.currentPane.name;return t=t.charAt(0).toUpperCase()+t.substring(1).toLowerCase(),`/apps/${Hn.name}/OligoToolkit/${t}`}setUrl(){this.multiView.path=this.getCurrentPanePath()}async constructView(){return this.multiView.tabs.onTabChanged.subscribe((()=>this.setUrl())),this.setUrl(),this.multiView}}var Sn=n(415);function En(){const t=ct.textInput("","");return{coloredInput:new qe(t,Ge),codes:s.QC}}const Tn="System:AppData/Bio/polytool-rules/",In="Polytool";class Nn{constructor(t){this.helmColumn=t}getLinkedPositions(t,e){const n=t.map((t=>t.replace("[","").replace("]",""))),r=new Array(e.length);for(let t=0;t<e.length;t++){let i=!1,o=!1,s=!1,a=-1,u=-1;const l=`(${e[t].code})`;for(let r=0;r<n.length;r++)if(n[r].includes(l)){if(i){if(s&&n[r]==e[t].secondMonomer+l){o=!0,u=r;break}if(s||n[r]!=e[t].firstMonomer+l)continue;o=!0,u=r;break}if(n[r]==e[t].firstMonomer+l)i=!0,s=!0,a=r;else{if(n[r]!=e[t].secondMonomer+l)continue;i=!0,s=!1,a=r}}r[t]=i&&o?s?[a,u]:[u,a]:[-1,-1]}return r}getRules(t){const e=t.map((t=>t.rowCount)).reduce(((t,e)=>t+e)),n=new Array(e);let r=0;for(let e=0;e<t.length;e++){const i=t[e].columns.byName("code"),o=t[e].columns.byName("monomer1"),s=t[e].columns.byName("monomer2"),a=t[e].columns.byName("modification1"),u=t[e].columns.byName("modification2"),l=t[e].columns.byName("R1"),c=t[e].columns.byName("R2");for(let h=0;h<t[e].rowCount;h++,r++)n[r]={code:i.get(h),firstMonomer:o.get(h),secondMonomer:s.get(h),firstModification:a.get(h),secondModification:u.get(h),firstR:l.get(h),secondR:c.get(h)}}return n}getDimeric(t){const e=t.replace("PEPTIDE1{","").replace("}$$$$","").split("."),n=[];for(let t=0;t<e.length;t++)if(e[t].includes("(#2)")){e[t]=e[t].replace("(#2)","");const r=t+1;let i=0;for(let t=r+1;t<e.length;t++)if(e[t].includes("}")){i=t;break}e[r]=e[r].replace("{",""),e[i]=e[i].replace("}",""),n.push([r,i])}return[e,n]}getAllCycles(t,e,n){const r=[],i=[],o=[],s=[],a=t.length;for(let u=0;u<a;u++){if(-1==n[u][0])continue;const a=e[n[u][0]].replace("[","").replace("]",""),l=e[n[u][1]].replace("[","").replace("]","");e[n[u][0]]=e[n[u][0]].replace(a,t[u].firstModification),e[n[u][1]]=e[n[u][1]].replace(l,t[u].secondModification),r.push(n[u][0]+1),i.push(n[u][1]+1),o.push(t[u].firstR),s.push(t[u].secondR)}return[e,r,i,o,s]}getHelmCycle(t,e,n){let r="";for(let i=0;i<t.allPos1.length;i++)r+=0==i?`PEPTIDE${e},PEPTIDE${n},`:`|PEPTIDE${e},PEPTIDE${n},`,r+=`${t.allPos1[i]}:R${t.allAttaches1[i]}-${t.allPos2[i]}:R${t.allAttaches2[i]}`;return r}getTransformedHelm(t,e){const[n,r]=this.getDimeric(t),i=this.getLinkedPositions(n,e),[o,s,a,u,l]=this.getAllCycles(e,n,i);t="PEPTIDE1{";for(let e=0;e<o.length;e++)t+=e!=o.length-1?o[e]+".":o[e];t+="}";const c=new Array(r.length),h=new Array(r.length);for(let t=0;t<r.length;t++){let e=`|PEPTIDE${t+2}{`;const n=r[t][1]-r[t][0],i=[],l=[],f=[],d=[];for(let i=0;i<=n;i++){const s=i+r[t][0];e+=i!=n?o[s]+".":o[s]}e+="}";for(let e=0;e<s.length;e++)s[e]-1>=r[t][0]&&s[e]-1<=r[t][1]&&(i.push(s[e]-r[t][0]),l.push(a[e]-r[t][0]),f.push(u[e]),d.push(u[e]));const p=this.getHelmCycle({allPos1:i,allPos2:l,allAttaches1:f,allAttaches2:d},t+2,t+2);c[t]=e,h[t]=this.getHelmCycle({allPos1:[r[t][0]],allPos2:[1],allAttaches1:[1],allAttaches2:[1]},1,t+2),h.push(p)}for(let e=0;e<c.length;e++)t+=c[e];t+="$",t+=this.getHelmCycle({allPos1:s,allPos2:a,allAttaches1:u,allAttaches2:l},1,1);for(let e=0;e<h.length;e++)t+="|",t+=h[e];return t+"$$$"}transform(t){const e=this.getRules(t);return this.helmColumn.toList().map((t=>this.getTransformedHelm(t,e)))}}class On{constructor(){}static getInstance(t){return new Nn(t)}}var Ln=function(t,e,n,r){return new(n||(n=Promise))((function(i,o){function s(t){try{u(r.next(t))}catch(t){o(t)}}function a(t){try{u(r.throw(t))}catch(t){o(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(s,a)}u((r=r.apply(t,e||[])).next())}))};class Mn{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 Ln(this,void 0,void 0,(function*(){if(this.settings)return this.settings;const t=yield o.dapi.userDataStorage.getValue(this.userStorageName,"Settings",!0),e=t?JSON.parse(t):{excluded:[],explicit:[]};return e.explicit=e.explicit instanceof Array?e.explicit:[],e.excluded=e.excluded instanceof Array?e.excluded:[],this.settings=e}))}setUserSettings(t){return Ln(this,void 0,void 0,(function*(){this.settings=t,yield o.dapi.userDataStorage.postValue(this.userStorageName,"Settings",JSON.stringify(t),!0)}))}getAllAvailable(){return Ln(this,void 0,void 0,(function*(){return(yield o.dapi.files.list(this.path)).map((t=>t.fullPath.replace(`${this.path}`,"")))}))}getActive(){return Ln(this,void 0,void 0,(function*(){const t=yield this.getUserSettings();return t.explicit.length>0?t.explicit:(yield this.getAllAvailable()).filter((e=>!t.excluded.includes(e)))}))}createInput(t,e){const n=ct.boolInput(t,e,(e=>this.updateSelectionStatus(t,e)));return n.addOptions(ct.button(ct.iconFA("trash"),(()=>{ct.dialog({title:"Warning"}).add(ct.divText(`Delete file '${t}'?`)).onOK((()=>{n.root.remove(),this.availableRemove(t)})).show()}),`Delete ${t}`)),n}getInputs(){return Ln(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 Ln(this,void 0,void 0,(function*(){const t=yield this.getInputs(),e=ct.divV(t);return ct.divV([e,ct.button("ADD",(()=>Ln(this,void 0,void 0,(function*(){let t="";t=yield this.getNewAvailable(),""!==t&&e.append(this.createInput(t,!0).root)}))))])}))}updateSelectionStatus(t,e){return Ln(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(t){return Ln(this,void 0,void 0,(function*(){const e=yield this.getUserSettings(),n=e.excluded.indexOf(t);n>-1&&e.excluded.splice(n,1),yield Promise.all([this.setUserSettings(e),o.dapi.files.delete(this.path+t)]),o.shell.info(`File ${t} successfully deleted`)}))}getNewAvailable(){return Ln(this,void 0,void 0,(function*(){return new Promise(((t,e)=>{r.Utils.openFile({accept:this.ext,open:e=>Ln(this,void 0,void 0,(function*(){const n=e.name,r=yield e.arrayBuffer();yield o.dapi.files.write(this.path+`${e.name}`,new Uint8Array(r)),t(n)}))})}))}))}}class Bn extends Mn{constructor(t,e,n){super(t,e,n)}}const Pn={symbol:"Short Name",name:"Medium Name",smiles:"SMILES"},Rn=[{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 Fn{constructor(t){this.rawLib=t}isValid(){return this.rawLib.every((t=>"object"==typeof t&&Object.values(Pn).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={...u};Object.entries(Pn).forEach((([n,r])=>{const i=t[r];e[n]=i}));let n="smiles";const r=t[Pn[n]],i=new Dn(r),o=i.getCappedSmiles();return e[n]=o,n="rgroups",e[n]=Un.getRGroups(i.getNumberOfRGroups()),n="molfile",e[n]=new kn(i.getSmilesWithRGroups()).getMolfile(),e}}class Dn{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 Un{constructor(){}static getRGroups(t){return Rn.slice(0,t)}}class kn{constructor(t){this.smilesWithRGroups=t}getMolfile(){let t=r.chem.convert(this.smilesWithRGroups,r.chem.Notation.Smiles,r.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 $n{constructor(t,e){this.fileName=t,this.fileContent=e,this.validateFileType();const n=r.DataFrame.fromCsv(this.fileContent),i=this.toJson(n);this.polyToolMonomerLib=new Fn(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 Hn=new st;async function Vn(){await Wn();const t=await async function(){const t={"Mermadesynthesis:merMadeSynthesis":{tabName:"SYNTHESIZE",parameters:En()}},e={};for(const[n,r]of Object.entries(t)){let t;try{t=await o.functions.call(n,r.parameters);const i=new xn(r.tabName,t);i.initView(),e[r.tabName]=()=>i.getView()}catch(t){console.warn(`Plugin ${n} not loaded, reason:`,t);continue}}return e}();if(!t)throw new Error("External app view factories not loaded");const e=new _n(t);return await e.getAppView()}async function jn(){return await er("Oligo Translator")}async function qn(){return await er("Oligo Pattern")}async function Gn(){return await er("Oligo Structure")}async function Wn(){await(0,s.hH)(),await Hn.initMonomerLib()}function zn(){const t=a.k.getInstance().getCodesToWeightsMap();return Object.fromEntries(t)}function Yn(t){const e=new ut.q(t),n=new lt(t).getFormat();return null!==n&&e.isValidSequence(n)}function Kn(t,e){return new en(t,e,"GCRS").convert()}function Qn(t){return(0,nn.vS)(t,!0)}async function Xn(){await async function(){await(0,ot.TX)((async()=>{const t=await jn();o.shell.addView(t)}))}()}async function Jn(){await async function(){await(0,ot.TX)((async()=>{const t=await qn();o.shell.addView(t)}))}()}async function Zn(){await async function(){await(0,ot.TX)((async()=>{const t=await Gn();o.shell.addView(t),["Afcgacsu","Afcgacsu","Afcgacsu"].forEach((async(t,e)=>{await async function(t,e){await(0,Sn.cb)(500);const n=document.querySelectorAll(".colored-text-input > textarea")[t];n.value=e;const r=new Event("input");n.dispatchEvent(r)}(e,t)}))}))}()}async function tr(t,e,n){return await Wn(),new fn.y(t,e).convertTo(n)}async function er(t){await Wn();const e=function(t){switch(t){case"Oligo Translator":return new wn;case"Oligo Pattern":return new De;case"Oligo Structure":return new un;default:throw new Error(`Unknown app name: ${t}`)}}(t);return await e.getAppView()}async function nr(){let t;try{t=await async function(){const t=o.shell.t.columns.bySemTypeAll(r.SEMTYPE.MACROMOLECULE);if(!t)throw new Error("No dataframe with macromolecule columns open");const e=ct.columnInput("Column",o.shell.t,t[0],null,{filter:t=>t.semType===r.SEMTYPE.MACROMOLECULE}),n=ct.boolInput("Get HELM",!0);ct.tooltip.bind(n.root,"Add HELM column");const i=ct.boolInput("Chirality engine",!1),s=new Bn(Tn,In,".csv"),a=await s.getForm(),u=ct.div([e,n,i,"Rules used",a]);return ct.dialog("Poly Tool").add(u).onOK((async()=>{const t=e.value;if(!t)return void o.shell.warning("No marcomolecule column chosen!");const a=await s.getActive();!async function(t,e,n,i){const s=t.dataFrame,a=W.forColumn(t).convert(p.HELM),u=On.getInstance(a),l=new r.FileSource(Tn),c=new Array(n.length);for(let t=0;t<n.length;t++){const e=await l.readAsText(n[t].replace(Tn,""));c[t]=r.DataFrame.fromCsv(e)}const h=u.transform(c),f=s.columns.getUnusedName("transformed("+t.name+")"),d=r.Column.fromList("string",f,h);var g;(g=d).setTag("quality",r.SEMTYPE.MACROMOLECULE),g.setTag("aligned","SEQ"),g.setTag("alphabet","PT"),d.setTag("units",p.HELM);const m=await o.functions.call("Bio:getMolFromHelm",{df:s,helmCol:d,chiralityEngine:i});m.name=s.columns.getUnusedName("molfile("+t.name+")"),m.semType=r.SEMTYPE.MOLECULE,e&&(d.setTag("cell.renderer","helm"),s.columns.add(d)),s.columns.add(m,!0),await o.data.detectSemanticTypes(s)}(t,n.value,a,i.value)}))}(),t.show()}catch(t){o.shell.warning("To run PolyTool, open a dataframe with macromolecules")}}async function rr(t,e){var n;(function(t){t.setTag("quality",r.SEMTYPE.MACROMOLECULE),t.setTag("aligned","SEQ"),t.setTag("alphabet","PT")})(n=e),n.setTag("units",p.SEPARATOR),n.setTag("separator","-"),await o.data.detectSemanticTypes(t)}async function ir(t){const e=await t.readAsString(),n=new $n(t.fileName,e),r=await n.getJson(),o=t.fileName.replace(/\.csv$/,".json"),s=JSON.stringify(r,null,2);i().Utils.download(o,s)}},82:t=>{"use strict";t.exports=DG},328:t=>{"use 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