@datagrok/sequence-translator 1.10.3 → 1.10.5

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Files changed (12) hide show
  1. package/dist/package-test.js +1 -1
  2. package/dist/package-test.js.map +1 -1
  3. package/dist/package.js +1 -1
  4. package/dist/package.js.map +1 -1
  5. package/package.json +1 -1
  6. package/src/package-api.ts +17 -3
  7. package/src/package.g.ts +23 -3
  8. package/src/package.ts +43 -5
  9. package/src/polytool/conversion/pt-synthetic.ts +16 -8
  10. package/src/polytool/pt-enumerate-seq-dialog.ts +1 -1
  11. package/test-console-output-1.log +52 -52
  12. package/test-record-1.mp4 +0 -0
package/dist/package.js CHANGED
@@ -1,3 +1,3 @@
1
1
  /*! For license information please see package.js.LICENSE.txt */
2
- var sequencetranslator;(()=>{var t={6717:(t,e,n)=>{"use strict";n.d(e,{j:()=>o});var r=n(6082);async function o(){const t=r.Func.find({package:"Chem",name:"getRdKitModule"});if(0===t.length)throw new Error('Package "Chem" must be installed for getRdKitModule.');return(await t[0].prepare().call()).getOutputParamValue()}},3599:(t,e,n)=>{"use strict";n.d(e,{o:()=>r.o});var r=n(6869)},9124:(t,e,n)=>{"use strict";n.d(e,{b2:()=>i});var r=n(7389),o=n(6082);async function i(){const t="Helm",e=o.Func.find({package:t,name:"getHelmHelper"});if(0===e.length)throw new Error(`Package '${t}' must be installed for HelmHelper.`);return(await e[0].prepare().call()).getOutputParamValue()}o.JsInputBase,Error,r.input.helmAsync=async function(t,e){return(await i()).createHelmInput(t,e)}},8438:(t,e,n)=>{"use strict";function r(t){return t.startsWith("[")&&t.endsWith("]")?t.slice(1,-1):t}n.d(e,{D:()=>r})},8123:(t,e,n)=>{"use strict";n.d(e,{u:()=>r});const r={V2K_RGP_SHIFT:8,V2K_RGP_LINE:"M RGP",V2K_A_LINE:"A ",V3K_COUNTS_SHIFT:14,V3K_IDX_SHIFT:7,V3K_HEADER_FIRST_LINE:"\nDatagrok macromolecule handler\n\n",V3K_HEADER_SECOND_LINE:" 0 0 0 0 0 0 999 V3000\n",V3K_BEGIN_CTAB_BLOCK:"M V30 BEGIN CTAB\n",V3K_END_CTAB_BLOCK:"M V30 END CTAB\n",V3K_BEGIN_COUNTS_LINE:"M V30 COUNTS ",V3K_COUNTS_LINE_ENDING:" 0 0 0\n",V3K_BEGIN_ATOM_BLOCK:"M V30 BEGIN ATOM\n",V3K_END_ATOM_BLOCK:"M V30 END ATOM\n",V3K_BEGIN_BOND_BLOCK:"M V30 BEGIN BOND\n",V3K_END_BOND_BLOCK:"M V30 END BOND\n",V3K_BOND_CONFIG:" CFG=",V3K_BEGIN_DATA_LINE:"M V30 ",V3K_END:"M END",PRECISION_FACTOR:1e4,DEOXYRIBOSE:{polymerType:"RNA",symbol:"d"},RIBOSE:{polymerType:"RNA",symbol:"r"},PHOSPHATE:{polymerType:"RNA",symbol:"p"},OXYGEN:"O",HYDROGEN:"H"}},6197:(t,e,n)=>{"use strict";n.d(e,{Y:()=>o});var r=n(3599);function o(t){let e;switch(t){case r.o.BASE:case r.o.SUGAR:case r.o.LINKER:case r.o.NUCLEOTIDE:case"nucleotide":e="RNA";break;case r.o.AA:e="PEPTIDE";break;case r.o.CHEM:e="CHEM";break;case r.o.BLOB:e="BLOB";break;default:e="PEPTIDE",console.warn(`Unexpected HelmType '${t}'`)}return e}},9235:(t,e,n)=>{"use strict";n.d(e,{H:()=>u,R:()=>l});var r=n(6082),o=n(1991),i=n.n(o),s=n(330),a=n(3599);async function l(t,e,o,l,u,c,h){const d=t.length,f=t.dataFrame,p=Math.max(navigator.hardwareConcurrency-2,1),m=new Array(p).fill(null).map((()=>new Worker(new URL(n.p+n.u(455),n.b)))),g=d/p,y=new Array(p),b=c.getSeqHandler(t),v="RNA"==l?a.o.NUCLEOTIDE:a.o.AA,w=i().count(0).take(t.length).map((t=>{const e=b.getSplitted(t);return i().count(0).take(e.length).map((t=>({position:t,symbol:e.getCanonical(t),biotype:v}))).toArray()})).toArray();for(let t=0;t<p;t++){const n=m[t],r=Math.floor(t*g),i=t===p-1?d:Math.floor((t+1)*g);y[t]=new Promise((t=>{n.onmessage=e=>{t(e.data)}})),n.postMessage({seqList:w,monomersDict:e,alphabet:o,polymerType:l,start:r,end:i})}const C=[],A=[];await Promise.all(y).then((t=>{for(const e of t)C.push(...e.molfiles),A.push(...e.warnings)})),setTimeout((()=>{m.forEach((t=>{t.terminate()}))}),0);const x=(0,s.qj)(f,t.name),S=r.Column.fromType(r.COLUMN_TYPE.STRING,x,t.length).init((t=>C[t]?.molfile));return S.semType=r.SEMTYPE.MOLECULE,S.meta.units=r.UNITS.Molecule.MOLBLOCK,S.setTag(".sequence-src-col",t.name),{molCol:S,warnings:A}}function u(t,e){const n={},o={};for(const i of t){const t=e.getWebEditorMonomer(i.biotype,i.symbol).backgroundcolor,a=(0,s.vG)(t??r.Color.toRgb(r.Color.mouseOverRows))??[1,0,0,.7];for(const t of i.atoms)n[t]=a;for(const t of i.bonds)o[t]=a}return{atoms:Object.keys(n).map((t=>parseInt(t))),bonds:Object.keys(o).map((t=>parseInt(t))),highlightAtomColors:n,highlightBondColors:o}}},3561:(t,e,n)=>{"use strict";n.d(e,{Hb:()=>l,YN:()=>m,gU:()=>u});var r=n(8123),o=n(294),i=n(3151),s=n(439),a=n(6197);function l(t,e,n){const o=new Map;for(const a of t.getMonomerSymbolsByType(e)){const l=t.getMonomer(e,a);if("RNA"===e&&("Branch"===l.monomerType||n===s.YI.DNA&&l.symbol===r.u.DEOXYRIBOSE.symbol||n===s.YI.RNA&&l.symbol===r.u.RIBOSE.symbol||l.symbol===r.u.PHOSPHATE.symbol)||"PEPTIDE"===e&&"Branch"!==l.monomerType){const t={};i.f6.forEach((e=>{t[e]=l[e]})),o.set(a,t)}}return o}function u(t,e,n,i){if(0===t.length)return o.vF.createEmpty();const l=p,{atomCount:u,bondCount:h,needsCapping:f}=l(t,e,n,i),g=new Array(u),y=new Array(h);let b,v=null,w=null;"PEPTIDE"===i?b=c:(b=d,v=n===s.YI.DNA?(0,o.xb)(e,r.u.DEOXYRIBOSE):(0,o.xb)(e,r.u.RIBOSE),w=(0,o.xb)(e,r.u.PHOSPHATE));const C={i:0,nodeShift:0,bondShift:0,backbonePositionShift:new Array(2).fill(0),branchPositionShift:new Array(2).fill(0),backboneAttachNode:0,branchAttachNode:0,flipFactor:1},A={sugar:v,phosphate:w,seqLength:t.length,atomCount:u,bondCount:h},x=new o.Cg,S=[];let T,E=0;for(C.i=0;C.i<A.seqLength;++C.i){const n=t[C.i];if(n.symbol===s._S)continue;const r=(0,o.xb)(e,{symbol:n.symbol,polymerType:(0,a.Y)(n.biotype)});T=r.terminalR2Atom;const i=C.nodeShift,l=C.bondShift;b(r,g,y,C,A),r.stereoAtoms?.forEach((t=>S.push(t+E))),E+=r.atoms.x.length;const u=C.nodeShift-i,c=new Array(u);for(let t=0;t<u;++t)c[t]=i+t;const h=C.bondShift-l,d=new Array(h);for(let t=0;t<h;++t)d[t]=l+t;x.set(C.i,{biotype:n.biotype,symbol:n.symbol,atoms:c,bonds:d})}f&&function(t,e,n,o,i=r.u.OXYGEN){const s=n.nodeShift+1;t[o.atomCount]=r.u.V3K_BEGIN_DATA_LINE+s+" "+(i??r.u.OXYGEN)+" "+m(n.backbonePositionShift[0])+" "+n.flipFactor*m(n.backbonePositionShift[1])+" 0.000000 0\n";const a=n.backboneAttachNode,l=s;e[o.bondCount]=r.u.V3K_BEGIN_DATA_LINE+n.bondShift+" 1 "+a+" "+l+"\n"}(g,y,C,A,T??r.u.OXYGEN);const _=r.u.V3K_BEGIN_COUNTS_LINE+u+" "+h+r.u.V3K_COUNTS_LINE_ENDING;let I="";return I+=r.u.V3K_HEADER_FIRST_LINE,I+=r.u.V3K_HEADER_SECOND_LINE,I+=r.u.V3K_BEGIN_CTAB_BLOCK,I+=_,I+=r.u.V3K_BEGIN_ATOM_BLOCK,I+=g.join(""),I+=r.u.V3K_END_ATOM_BLOCK,I+=r.u.V3K_BEGIN_BOND_BLOCK,I+=y.join(""),I+=r.u.V3K_END_BOND_BLOCK,S.length>0&&(I+=function(t){const e=[];let n=`M V30 MDLV30/STEABS ATOMS=(${t.length}`;for(let r=0;r<t.length;r++){const o=`${n} ${t[r]}`;o.length>76?(e.push(`${n} -\n`),n=`M V30 ${t[r]}`):n=o,r===t.length-1&&e.push(`${n})\n`)}return`M V30 BEGIN COLLECTION\n${e.join("")}M V30 END COLLECTION\n`}(S)),I+=r.u.V3K_END_CTAB_BLOCK,I+=r.u.V3K_END,{molfile:I,monomers:x}}function c(t,e,n,r){r.flipFactor=(-1)**(r.i%2),h(t,e,n,r)}function h(t,e,n,o){!function(t,e,n){for(let o=0;o<t.atoms.atomTypes.length;++o){const i=n.nodeShift+o+1;e[n.nodeShift+o]=r.u.V3K_BEGIN_DATA_LINE+i+" "+t.atoms.atomTypes[o]+" "+m(n.backbonePositionShift[0]+t.atoms.x[o])+" "+m(n.backbonePositionShift[1]+n.flipFactor*t.atoms.y[o])+" "+t.atoms.kwargs[o]}}(t,e,o),f(t,n,o),function(t,e,n){if(0!==n.backboneAttachNode){const o=n.bondShift,i=n.backboneAttachNode,s=t.meta.terminalNodes[0]+n.nodeShift;e[n.bondShift-1]=r.u.V3K_BEGIN_DATA_LINE+o+" 1 "+i+" "+s+"\n"}}(t,n,o),null!==t.meta.branchShift&&t.meta.terminalNodes.length>2&&function(t,e){e.branchAttachNode=e.nodeShift+t.meta.terminalNodes[2];for(let n=0;n<2;++n)e.branchPositionShift[n]=e.backbonePositionShift[n]+t.meta.branchShift[n]}(t,o),function(t,e){e.backboneAttachNode=e.nodeShift+t.meta.terminalNodes[1],e.bondShift+=t.bonds.atomPairs.length+1,e.nodeShift+=t.atoms.atomTypes.length,e.backbonePositionShift[0]+=t.meta.backboneShift?.[0]??0,e.backbonePositionShift[1]+=e.flipFactor*(t.meta.backboneShift?.[1]??0)}(t,o)}function d(t,e,n,o,i){if(0===o.i)h(i.sugar,e,n,o);else for(const t of[i.phosphate,i.sugar])h(t,e,n,o);!function(t,e,n,o){(function(t,e,n){for(let o=0;o<t.atoms.atomTypes.length;++o){const i=n.nodeShift+o+1;e[n.nodeShift+o]=r.u.V3K_BEGIN_DATA_LINE+i+" "+t.atoms.atomTypes[o]+" "+m(n.branchPositionShift[0]+t.atoms.x[o])+" "+m(n.branchPositionShift[1]+n.flipFactor*t.atoms.y[o])+" "+t.atoms.kwargs[o]}})(t,e,o),f(t,n,o),function(t,e,n){const o=n.bondShift,i=n.branchAttachNode,s=t.meta.terminalNodes[0]+n.nodeShift;e[o-1]=r.u.V3K_BEGIN_DATA_LINE+o+" 1 "+i+" "+s+"\n"}(t,n,o);const i=o.bondShift,s=o.branchAttachNode,a=t.meta.terminalNodes[0]+o.nodeShift;n[i-1]=r.u.V3K_BEGIN_DATA_LINE+i+" 1 "+s+" "+a+"\n",o.bondShift+=t.bonds.atomPairs.length+1,o.nodeShift+=t.atoms.atomTypes.length}(t,e,n,o)}function f(t,e,n){for(let o=0;o<t.bonds.atomPairs.length;++o){const i=n.bondShift+o+1,s=t.bonds.atomPairs[o][0]+n.nodeShift,a=t.bonds.atomPairs[o][1]+n.nodeShift;let l="";if(t.bonds.bondConfiguration.has(o)){let e=t.bonds.bondConfiguration.get(o);n.flipFactor<0&&(e=1===e?3:1),l=" CFG="+e}const u=t.bonds.kwargs.has(o)?" "+t.bonds.kwargs.get(o):"";e[n.bondShift+o]=r.u.V3K_BEGIN_DATA_LINE+i+" "+t.bonds.bondTypes[o]+" "+s+" "+a+l+u+"\n"}}function p(t,e,n,i){let l=0,u=0,c=0,h=!0,d=null;for(const n of t)if(n.symbol!==s._S){if("*"==n.symbol)throw new Error("Gap canonical symbol is '', not '*");d=(0,o.xb)(e,{symbol:n.symbol,polymerType:(0,a.Y)(n.biotype)}),l+=d.atoms.x.length,u+=d.bonds.bondTypes.length,c++}if("PEPTIDE"===i)l+=1,u+=c,c>0&&((d?.meta?.rNodes?.length??0)<2||d?.terminalR2Atom?.toLowerCase()===r.u.HYDROGEN.toLowerCase())&&(h=!1,l-=1,u-=1);else{const i=n===s.YI.DNA?(0,o.xb)(e,r.u.DEOXYRIBOSE):(0,o.xb)(e,r.u.RIBOSE),a=(0,o.xb)(e,r.u.PHOSPHATE);l+=(t.length-1)*a.atoms.x.length,l+=t.length*i.atoms.x.length,l+=1,u+=(t.length-1)*a.bonds.bondTypes.length,u+=t.length*i.bonds.bondTypes.length,u-=1,u+=3*t.length}return{atomCount:l,bondCount:u,needsCapping:h}}function m(t){return Math.round(r.u.PRECISION_FACTOR*t)/r.u.PRECISION_FACTOR}},6077:(t,e,n)=>{"use strict";n.d(e,{C4:()=>p,eM:()=>m});var r=n(4328),o=n(6082),i=n(1991),s=n.n(i),a=n(439),l=n(3561),u=n(9235),c=n(294),h=n(9192),d=n(330),f=n(8123);async function p(t,e,n,i,l){if(e.semType!==o.SEMTYPE.MACROMOLECULE)return{molCol:null,warnings:[`Only the ${o.SEMTYPE.MACROMOLECULE} columns can be converted to atomic level, the chosen column has semType '${e.semType}'`]};let c=e;const f=i.getSeqHandler(e);let p,g;f.notation!==a.Hi.SEPARATOR&&f.notation!==a.Hi.BILN&&(c=f.convert(a.Hi.SEPARATOR,"."),c.name=e.name);try{g=i.getSeqHandler(c).alphabet,p=(0,d.pz)(g)}catch(t){const[e,n]=(0,h.AP)(t);return{molCol:null,warnings:[e]}}const y=function(t,e){const n=t.length,o=new Array(n),i=e.getSeqHandler(t);let a=!1;const l=i.defaultBiotype;for(let t=0;t<n;++t){const e=i.getSplitted(t);a||(a=0===e.length),o[t]=s().count(0).take(e.length).filter((t=>!e.isGap(t))).map((t=>({position:t,biotype:l,symbol:e.getCanonical(t)}))).toArray()}return a&&r.shell.warning(`Some values in the "${t.name}" column are empty`),o}(c,i),b=m(y,p,g,n,l),v=c.length,w=await(0,u.R)(c,b,g,p,n,i,l);w.warnings.length>.05*v&&r.shell.warning(`Molfile conversion resulted in ${w.warnings.length} errors`);const C=o.Func.find({name:"convertToV3KViaOCL"})[0];if(C&&w.molCol)try{const t=w.molCol.toList(),e=await C.apply({mols:t});w.molCol.init((n=>e[n]?e[n]:t[n]))}catch(t){console.error(t)}return w}function m(t,e,n,r,o){const i=(0,l.Hb)(r,e,n),s={},u={value:null};if("RNA"===e){const t=n===a.YI.RNA?[f.u.RIBOSE,f.u.PHOSPHATE]:[f.u.DEOXYRIBOSE,f.u.PHOSPHATE];for(const n of t)g(s,n.symbol,i,o,e,u)}for(let n=0;n<t.length;++n){const r=t[n];for(const t of r){const n=t.symbol;if(""!==n)try{if("RNA"===e&&3===n.split(/\(|\)/).filter((t=>!!t)).length){const t=n.split(/\(|\)/)[1];g(s,t,i,o,e,u),s[e]?.[t]&&(s[e][n]=s[e][t])}else g(s,n,i,o,e,u)}catch(t){const e=t instanceof Error?t.message:t.toString(),r=t instanceof Error?t.stack:void 0;throw console.error(`bio lib: getMonomersDictFromLib() sym='${n}', error:\n${e}\n${r}`),new Error(`Can't get monomer '${n}' from library: ${e}`)}}}return s}function g(t,e,n,r,o,i){const s={polymerType:o,symbol:e};if(!(0,c.bq)(t,s)){const a=function(t,e,n,r,o){if(e.has(t)){const s=e.get(t),a=function(t){const e=[];for(const n of t){let t=n.capGroupSmiles;t||(t=n.capGroupSMILES),t=t.replace(/(\[|\]|\*|:|\d)/g,"").replace("OH","O").replace("Oh","O"),e.push(t)}return e}(s.rgroups),u=(i=s.molfile).includes("V3000")?function(t){const e=new Map,n=/M V30 (\d+) R#.+RGROUPS=\((\d+) (\d+)\).*/gm;let r;for(;null!==(r=n.exec(t));)r.index===n.lastIndex&&n.lastIndex++,e.set(parseInt(r[1]),parseInt(r[3]));return e}(i):function(t){const e=new Map;let n=t.indexOf(f.u.V2K_A_LINE,0),r=n;for(;-1!==n;){r=t.indexOf("\n",n);const o=parseInt(t.substring(n,r).replace(/^A\s+/,""));n=t.indexOf("R",r),r=t.indexOf("\n",n);const i=parseInt(t.substring(n,r).replace(/^R/,""));e.set(o,i),n=t.indexOf(f.u.V2K_A_LINE,r)}for(n=t.indexOf(f.u.V2K_RGP_LINE,0),r=t.indexOf("\n",n);-1!==n;){n+=f.u.V2K_RGP_SHIFT,r=t.indexOf("\n",n);const o=t.substring(n,r).replaceAll(/\s+/g," ").split(" ").map((t=>parseInt(t))).slice(1);for(let t=0;t<o.length;t+=2){if(e.has(o[t])&&e.get(o[t])!==o[t+1])throw new Error(`r-group index ${o[t]} has already been added with a different value`);e.set(o[t],o[t+1])}n=t.indexOf(f.u.V2K_RGP_LINE,r)}return e}(i),c=s.molfile.includes("V3000")?s.molfile:function(t,e){const n=e.get_mol(function(t){return t.split("\n").map((t=>{const e=t.indexOf(" R# "),n=t.indexOf(" R ");if(-1===e&&-1===n)return t;const r=-1!==e?e:n,o=t.split("");for(let t=r+5;t<o.length;t++)" "!==o[t]&&(o[t]="0");return o.join("")})).join("\n")}(t)),r=n.get_v3Kmolblock();return n.delete(),r}(function(t){let e=t.indexOf(f.u.V2K_A_LINE,0);-1===e&&(e=t.indexOf(f.u.V2K_RGP_LINE));const n=t.indexOf(f.u.V3K_END,e);return t.substring(0,e)+t.substring(n)}(s.molfile),n),h=function(t){let e=(t=t.replaceAll("\r","")).indexOf(f.u.V3K_BEGIN_COUNTS_LINE)+f.u.V3K_COUNTS_SHIFT,n=t.indexOf(" ",e+1);const r=parseInt(t.substring(e,n));return e=n+1,n=t.indexOf(" ",e+1),{atomCount:r,bondCount:parseInt(t.substring(e,n))}}(c),d=function(t,e){const n=new Array(e),r=new Float32Array(e),o=new Float32Array(e),i=new Array(e);let s=t.indexOf(f.u.V3K_BEGIN_ATOM_BLOCK);s=t.indexOf("\n",s);let a=s;for(let l=0;l<e;l++){s=t.indexOf(f.u.V3K_BEGIN_DATA_LINE,s)+f.u.V3K_IDX_SHIFT,a=t.indexOf(" ",s),s=a+1,a=t.indexOf(" ",s),n[l]=t.substring(s,a);const e=new Array(2);for(let n=0;n<2;++n)s=a+1,a=t.indexOf(" ",s),e[n]=parseFloat(t.substring(s,a));r[l]=e[0],o[l]=e[1],s=a,a=t.indexOf("\n",s)+1,i[l]=t.slice(s,a),s=a}return{atomTypes:n,x:r,y:o,kwargs:i}}(c,h.atomCount),p=function(t,e){const n=new Uint32Array(e),r=new Array(e),o=new Map,i=new Map;let s=t.indexOf(f.u.V3K_BEGIN_BOND_BLOCK);s=t.indexOf("\n",s);let a=s;for(let l=0;l<e;++l){const e=new Array(3);s=t.indexOf(f.u.V3K_BEGIN_DATA_LINE,a)+f.u.V3K_IDX_SHIFT,a=t.indexOf(" ",s);for(let n=0;n<3;++n)s=a+1,a=Math.min(t.indexOf("\n",s),t.indexOf(" ",s)),e[n]=parseInt(t.slice(s,a));n[l]=e[0],r[l]=e.slice(1);const u=t.indexOf("\n",s);let c=t.slice(a,u),h=c.indexOf(f.u.V3K_BOND_CONFIG);if(-1!==h){h=c.indexOf("=",h)+1;let t=c.indexOf(" ",h);-1===t&&(t=c.length);const e=parseInt(c.slice(h,t));o.set(l,e);const n=f.u.V3K_BOND_CONFIG+e.toString();c=c.replace(n,"")}c||i.set(l,c)}return{bondTypes:n,atomPairs:r,bondConfiguration:o,kwargs:i}}(c,h.bondCount),m=function(t,e,n,r){const o={backboneShift:null,branchShift:null,terminalNodes:[],rNodes:[]};if(n&&r&&[1,2].some((t=>!Array.from(r.values()).find((e=>e==t))))){const o=[1,2].find((t=>!Array.from(r.values()).find((e=>e==t)))),i=[1,2].find((t=>Array.from(r.values()).find((e=>e==t)))),s=Array.from(r.keys()).find((t=>r.get(t)===i))-1,a=t.x[s],l=t.y[s],u=e.atomPairs.find((t=>t.includes(s+1))).find((t=>t!==s+1))-1;let 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c{}c.SemType="Nucleotides",c.SemTypeMultipleAlignment="NucleotidesMultipleAlignment",c.Names={A:"Adenine",C:"Cytosine",G:"Guanine",T:"Thymine",U:"Uracil"};var h=n(4971);function d(t,e=!0){if(null==t)return"rgb(100,100,100)";const n=r.Color.fromHtml(t);if(e){const t=r.Color.g(n),e=r.Color.r(n),o=r.Color.b(n),i=Math.sqrt(Math.pow(0-e,2)+Math.pow(0-t,2)+Math.pow(0-o,2));if(i>210)return`rgb(${e/i*210},${t/i*210},${o/i*210})`}return r.Color.toRgb(n)}class f{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 p{}class m extends p{static get palette(){return m._pallete||(m._pallete=m.buildPalette()),m._pallete}static buildPalette(){return(0,h.pj)().then((t=>{t.awaitLoaded(1/0).then((()=>{const e=t.getMonomerLib();e.onChanged.subscribe((()=>{m.customMonomerColors={},m.polymerTypes=e.getPolymerTypes();for(const t of this.polymerTypes){const n=e.getMonomerSymbolsByType(t);for(const r of n){const 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natural analog for ${t}`);return e}isModification(t){return!!this.getMolfileBySymbol(t).includes("MODIFICATION")}getCodeToSymbolMap(t){return new Map(Object.entries(this.jsonData.codesToSymbolsDict[t]))}getCodesByFormat(t){return Object.keys(this.jsonData.codesToSymbolsDict[t])}getAllFormats(){return Object.keys(this.jsonData.codesToSymbolsDict)}getTableForViewer(){const t=this.allMonomers.map((t=>this.formatMonomerForViewer(t)));return o.DataFrame.fromObjects(t)}getCodesToWeightsMap(){const t=new Map;return Object.entries(this.jsonData.codesToSymbolsDict).forEach((([e,n])=>{Object.entries(n).forEach((([e,n])=>{const r=this.getMonomer(n),o=r.meta?.molecularWeight;t.set(e,o)}))})),t}}var x=n(9537);const S=(t,e)=>e.length-t.length;class T{constructor(t){this.th=t,this.formats=this.getFormats()}getFormatNames(){return this.formats.sort()}getCodesByFormat(t){if(this.validateFormat(t),this.isHelm(t))throw new Error("Codes cannot be obtained for HELM");return this.getFormatCodes(t)}getHelmToFormatDict(t){return this.validateFormat(t),function(t){const e={};return Object.values(t).forEach((t=>{Object.entries(t).forEach((([t,n])=>{const r=n.replace(/\)p/g,")").replace(/\]p/g,"]");void 0===e[r]?e[r]=[t]:e[r].push(t)}))})),Object.entries(e).forEach((([t,n])=>{const r=n.sort(S);e[t]=r[0]})),e}(this.th.jsonData.codesToHelmDict[t])}getFormatToHelmDict(t){this.validateFormat(t);const e=this.th.jsonData.codesToHelmDict[t];return Object.assign({},...Object.values(e))}getTargetFormatHelmCodes(t){this.validateFormat(t);const e=this.getHelmToFormatDict(t);return Object.keys(e).sort(S)}getTargetFormatHelmCodesRegExp(t){this.validateFormat(t);const e=this.getTargetFormatHelmCodes(t);return new RegExp(E(e)+"|.","g")}getFormatRegExp(t){if(this.validateFormat(t),this.isHelm(t))throw new Error("Helm RegExp can be built for non-HELM target formats");return this.getNonHelmFormatRegExp(t)}getPhosphateHelmCodesRegExp(t){this.validateFormat(t);const e=this.th.jsonData.codesToHelmDict[t],n=E(Array.from(new Set(Object.values(e[x.ti.LINKAGE]))).sort(S));return new RegExp(`${x.q7}.(${n})`,"g")}isValidFormat(t){return this.formats.includes(t)}getFormats(){return Object.keys(this.th.jsonData.codesToHelmDict)}validateFormat(t){if(!this.isValidFormat(t))throw new Error(`Invalid format: ${t}`)}isHelm(t){return t===m.NO.HELM}getFormatCodes(t){const e=this.getFormatToHelmDict(t);return Object.keys(e).sort(S)}getNonHelmFormatRegExp(t){const e=this.getCodesByFormat(t);return new RegExp(E(e)+"|\\([^()]*\\)|.","g")}}function E(t){return t.map((t=>t.replace(/[.*+?^${}()|[\]\\]/g,"\\$&"))).map((t=>t.includes("(")||t.includes(")")?t:`(?<!\\([^()]*)${t}(?![^()]*\\))`)).join("|")}const _={LEFT:"RNA1{",RIGHT:"}$$$$"};class I{constructor(t,e,n){this.sequence=t,this.sourceFormat=e,this.th=n,this.formats=new T(this.th)}convertTo(t){const e=this.formats.getFormatNames();if(this.sourceFormat===m.NO.HELM&&e.includes(t))return this.helmToFormat(this.sequence,t);if(e.includes(this.sourceFormat)&&t===m.NO.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} -> ${t}`)}helmToFormat(t,e){const n=new RegExp(E(Object.values(_)),"g");let r=t.replace(n,"");const o=this.formats.getHelmToFormatDict(e),i=this.formats.getTargetFormatHelmCodes(e),s=this.formats.getTargetFormatHelmCodesRegExp(e);return r=r.replace(s,(t=>i.includes(t)?o[t]:"p"===t||"."===t?t:"?")).replace(/\?+/g,x.iL).replace(/p\.|\./g,""),r=r.replace(/<empty>/g,""),r=r.replace(/\/\//g,"/"),r}formatToHelm(t,e){const n=this.formats.getFormatToHelmDict(e),r=this.formats.getCodesByFormat(e),o=this.formats.getFormatRegExp(e),i=this.formats.getPhosphateHelmCodesRegExp(e);let s=t?t.replace(o,(t=>r.includes(t)?n[t]+".":"?")):"";return s=s.replace(/\?+/g,`${x.iL}.`),s=s.slice(0,-1),s[s.length-1]===x.q7&&(s=s.slice(0,-1)),s=s.replace(i,((t,e)=>e)),s=s.replace(/<empty>/g,""),`${_.LEFT+s+_.RIGHT}`}}class N{constructor(t,e){this.sequence=t,this.th=e,this.libWrapper=this.th.monomerLibWrapper,this.formats=Object.keys(this.th.jsonData.codesToHelmDict)}getFormat(){if(this.sequence.startsWith("RNA"))return m.NO.HELM;const t=this.getListOfPossibleSynthesizersByFirstMatchedCode();if(0===t.length)return null;const e=this.th.createSequenceValidator(this.sequence),n=Array(t.length).fill(0);for(let r=0;r<t.length;++r){const o=t[r];n[r]=e.getInvalidCodeIndex(o)}const r=n.some((t=>-1===t))?-1:Math.max(...n);return t[n.indexOf(r)]}getListOfPossibleSynthesizersByFirstMatchedCode(){const t=this.sequence,e=[];for(const n of this.formats){const r=g(this.libWrapper.getCodesByFormat(n));let o=0;for(let e=0;e<t.length;e++)if(")"===t[e]&&e!==t.length-1){o=e+1;break}r.some((e=>e===t.slice(o,o+e.length)))&&e.push(n)}return e}}var M=n(7389);const O=$;var L=n.n(O);function R(t,e){let n=0;const r=e.createFormatDetector(t).getFormat();null!==r&&(n=new v(t,e).getInvalidCodeIndex(r));const o=n<0||""===t,i=M.span([]);L()(i).css("-webkit-text-fill-color","var(--grey-6)");const s=M.span([]);return L()(s).css("-webkit-text-fill-color","red"),o?i.innerHTML=t:(i.innerHTML=t.slice(0,n),s.innerHTML=t.slice(n)),[i,s]}class P extends o.Package{get helmHelper(){if(!this._helmHelper)throw new Error("Package SequenceTranslator .helmHelper is not initialized");return this._helmHelper}get seqHelper(){return this._helmHelper.seqHelper}get monomerLib(){if(!this._monomerLib)throw new Error("Monomer lib not loaded");return this._monomerLib}get jsonData(){if(!this._jsonData)throw new Error("Json data not loaded");return this._jsonData}get monomerLibWrapper(){if(!this._monomerLibWrapper)throw new Error("Monomer lib wrapper not loaded");return this._monomerLibWrapper}get initPromise(){return this._initPromise}constructor(t={debug:!1}){super(),this.highlightInvalidSubsequence=t=>R(t,this),super._logger=new u(super.logger,t.debug)}startInit(t){this._initPromise=t}completeInit(t){this._helmHelper=t}async initLibData(){return this.initLibDataPromise||(this.initLibDataPromise=(async()=>{const t=await this.getSettings();let e=t instanceof Map?t.get("MonomersPath"):t.MonomersPath;e&&await r.dapi.files.exists(e)||(this.logger.warning(`Monomers path '${e}' not found. Fallback to monomers sample path '${c}'.`),e=c),[this._jsonData,this._monomerLib]=await Promise.all([C(e),B(e)]),this._monomerLibWrapper=new A(this.monomerLib,this.jsonData)})()),this.initLibDataPromise}async getTranslationHelper(){return await r.functions.call(`${this.name}:getTranslationHelper`)}createSequenceValidator(t){return new v(t,this)}createFormatConverter(t,e){return new I(t,e,this)}createFormatDetector(t){return new N(t,this)}}async function B(t){const e=o.TaskBarProgressIndicator.create("Initializing Oligo Toolkit monomer library ...");try{const e=await(0,l.pj)(),n=(t.endsWith("/")?t:t+"/")+"monomer-lib.json";return await e.readLibraryFromFilePath(n)}finally{e.close()}}class D{constructor(t,e){this.appName=t,this.parentAppName=e}async getAppView(){const t=o.TaskBarProgressIndicator.create(`Loading ${this.appName}...`),e=r.shell.v?.root;e&&M.setUpdateIndicator(e,!0);try{return await this.constructView()}finally{t.close(),e&&M.setUpdateIndicator(e,!1)}}}class F extends D{constructor(t){super(t),this.view=o.View.create(),this.configureView()}async constructView(){await this.initView();const t=this.parentAppName?this.parentAppName+"/"+this.appName:this.appName;return this.view.path=`/apps/${Kr.name}/${t.replace(/\s/g,"")}/`,this.view}async initView(){const t=await this.getContent();this.view.append(t)}configureView(){this.view.box=!0,this.view.name=this.appName;const t=r.shell.windows;t.showProperties=!1,t.showToolbox=!1,t.showHelp=!1}getView(){return this.view}}const k=["SS","AS"],H={SS:"Sense strand",AS:"Anti sense"},U=["3'","5'"],V="OligoToolkit";var j,q,G,z;!function(t){t.IS_ANTISENSE_STRAND_INCLUDED="isAntisenseStrandIncluded",t.NUCLEOTIDE_SEQUENCES="nucleotideSequences",t.PHOSPHOROTHIOATE_LINKAGE_FLAGS="phosphorothioateLinkageFlags",t.STRAND_TERMINUS_MODIFICATIONS="strandTerminusModifications"}(j||(j={})),function(t){t.PATTERN_NAME="patternName",t.PATTERN_COMMENT="patternComment",t.NUCLEOTIDES_WITH_NUMERIC_LABELS="nucleotidesWithNumericLabels"}(q||(q={})),function(t){t.PATTERN_CONFIG="patternConfig",t.AUTHOR_ID="authorID",t.DATE="date"}(G||(G={})),function(t){t.CREATE="create",t.MODIFY="modify"}(z||(z={}));const W=[j.IS_ANTISENSE_STRAND_INCLUDED,j.NUCLEOTIDE_SEQUENCES,j.PHOSPHOROTHIOATE_LINKAGE_FLAGS,j.STRAND_TERMINUS_MODIFICATIONS],Y=(q.PATTERN_NAME,q.PATTERN_COMMENT,q.NUCLEOTIDES_WITH_NUMERIC_LABELS,{patternConfig:{patternName:"<default example>",isAntisenseStrandIncluded:!0,nucleotideSequences:{SS:["RNA","RNA","RNA","RNA","RNA","RNA","RNA","RNA","RNA","RNA","RNA","RNA","RNA","RNA","RNA","RNA","RNA","RNA","RNA","RNA","RNA","RNA","RNA"],AS:["RNA","RNA","RNA","RNA","RNA","RNA","RNA","RNA","RNA","RNA","RNA","RNA","RNA","RNA","RNA","RNA","RNA","RNA","RNA","RNA","RNA","RNA","RNA"]},phosphorothioateLinkageFlags:{SS:[!0,!0,!0,!0,!0,!0,!0,!0,!0,!0,!0,!0,!0,!0,!0,!0,!0,!0,!0,!0,!0,!0,!0,!0],AS:[!0,!0,!0,!0,!0,!0,!0,!0,!0,!0,!0,!0,!0,!0,!0,!0,!0,!0,!0,!0,!0,!0,!0,!0]},strandTerminusModifications:{SS:{"3'":"","5'":""},AS:{"3'":"","5'":""}},patternComment:"",nucleotidesWithNumericLabels:["RNA"]},authorID:""}),K="2024-01-01T18:00:00.000Z";class J extends Error{constructor(t){super(t),this.name="PatternNameExistsError"}}class Q extends Error{constructor(t){super(t),this.name="PatternExistsError"}}var X=n(4802),Z=n.n(X);class tt{constructor(t){this.th=t,this.otherUsersPatternNameToHash=new Map,this.currentUserPatternNameToHash=new Map}static async getInstance(){const t=await Kr.getTranslationHelper(),e=new tt(t);e.currentUserName=await e.fetchCurrentUserName(),e.currentUserId=await e.fetchCurrentUserId();const n=e.fetchPatterns();return await e.initializePatternMaps(n),e}getCurrentUserPatternNames(){return Array.from(this.currentUserPatternNameToHash.keys()).sort(((t,e)=>t.toLowerCase().localeCompare(e.toLowerCase())))}getOtherUsersPatternNames(){return Array.from(this.otherUsersPatternNameToHash.keys()).sort(((t,e)=>t.toLowerCase().localeCompare(e.toLowerCase())))}getCurrentUserName(){return this.currentUserName}validatePatternNameUniqueness(t){if(this.currentUserPatternNameToHash.has(t))throw new J(`Pattern with name ${t} already exists`)}validatePatternUniqueness(t){if(Array.from(this.currentUserPatternNameToHash.values()).concat(Array.from(this.otherUsersPatternNameToHash.values())).includes(t))throw new Q(t)}getPatternHash(t,e){const n=e?this.currentUserPatternNameToHash.get(t):this.otherUsersPatternNameToHash.get(t);if(void 0===n)throw new Error(`Pattern with name ${t} not found`);return n}async getPatternRecordByHash(t){if(null===t||""===t)return null;try{const e=r.userSettings.getValue(V,t,!1)??"null";return JSON.parse(e)}catch{return null}}async getPatternConfig(t){if(""===t||null===t)return null;const e=await this.getPatternRecordByHash(t);return null===e?null:e[G.PATTERN_CONFIG]}getDefaultPatternRecord(){const t=Y;return t[G.AUTHOR_ID]=this.currentUserId,t}getDefaultPatternConfig(){return Y[G.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){return{[G.PATTERN_CONFIG]:t,[G.AUTHOR_ID]:await r.dapi.users.current().then((t=>t.id))}}getHash(t){const e=W.reduce(((e,n)=>(e[n]=t[n],e)),{});return Z().sha1(e)}async savePatternToUserStorage(t){const e=t.getPatternConfig();try{const n=this.getHash(e);this.validatePatternUniqueness(n);const o=e[q.PATTERN_NAME];this.validatePatternNameUniqueness(o);const i=await this.getRecordFromPattern(e),s=(new Date).toISOString();i[G.DATE]={[z.CREATE]:s,[z.MODIFY]:s};const a=JSON.stringify(i);r.userSettings.add(V,n,a,!1),this.currentUserPatternNameToHash.set(o,n),t.selectAuthor(this.getCurrentUserAuthorshipCategory()),t.updatePatternList(),t.requestPatternLoad(n),t.updateUrlState(n)}catch(t){if(t instanceof J||t instanceof Q)throw t;console.error("Error while saving pattern to user storage",t)}}async overwriteExistingPatternInUserStorage(t){const e=t.getPatternConfig(),n=e[q.PATTERN_NAME],o=this.currentUserPatternNameToHash.get(n);if(void 0===o)throw new Error("Old hash is undefined");const i=this.getHash(e),s=await this.getRecordFromPattern(e),a=(new Date).toISOString();s[G.DATE]={[z.MODIFY]:a};const l=r.userSettings.getValue(V,o,!1)??"null",u=JSON.parse(l);void 0!==u[G.DATE]&&null!=u[G.DATE][z.CREATE]&&(s[G.DATE][z.CREATE]=u[G.DATE][z.CREATE]);const c=JSON.stringify(s);r.userSettings.add(V,i,c,!1),r.userSettings.delete(V,o,!1),this.currentUserPatternNameToHash.set(n,i),t.requestPatternLoad(i),t.updateUrlState(i)}async deletePattern(t,e){const n=this.currentUserPatternNameToHash.get(t);if(t===this.getDefaultPatternName())return void r.shell.warning("Cannot delete default pattern");if(void 0===n)throw new Error(`Pattern with name ${t} not found`);r.userSettings.delete(V,n,!1),this.currentUserPatternNameToHash.delete(t),e.updatePatternList();const o=this.getHashOfPatternToBeLoadedAfterDeletion();e.requestPatternLoad(o)}fetchDefaultNucleobase(){return this.fetchAvailableNucleotideBases()[0]}fetchAvailableNucleotideBases(){const t=Object.keys(this.th.jsonData.patternAppData)[0];return Object.keys(this.th.jsonData.patternAppData[t])}async fetchCurrentUserName(){return(await r.dapi.users.current()).friendlyName}async fetchCurrentUserId(){return(await r.dapi.users.current()).id}fetchPatterns(){return r.userSettings.get(V,!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=Y[G.PATTERN_CONFIG];this.currentUserPatternNameToHash.set(t[q.PATTERN_NAME],"")}async extractDataFromRecordToMaps(t,e,n){const o=JSON.parse(e),i=o[G.PATTERN_CONFIG].patternName,s=o[G.AUTHOR_ID];if(this.isCurrentUserId(s))this.currentUserPatternNameToHash.set(i,t);else{if(!n.has(s)){let t="<UNKNOWN_USER>";try{t=(await r.dapi.users.find(s)).friendlyName}catch(t){}n.set(s,t)}const e=i+` (created by ${n.get(s)})`;this.otherUsersPatternNameToHash.set(e,t)}}getDefaultPatternName(){return Y[G.PATTERN_CONFIG][q.PATTERN_NAME]}getCurrentUserAuthorshipCategory(){return this.currentUserName+" (me)"}getOtherUsersAuthorshipCategory(){return"Other users"}isCurrentUserId(t){return t===this.currentUserId}}const et=rxjs,nt=rxjs.operators;function rt(t){return t.endsWith("(o)")}function ot(t){const e=Object.values(t).flat().reduce(((t,e)=>(t[e]=(t[e]||0)+1,t)),{});return Object.entries(e).reduce(((t,e)=>t[1]>e[1]?t:e),["",0])[0]}var it;function st(t){const e=Array.from(new Set(t));return Array.from(e).sort(((t,e)=>t.toLowerCase().localeCompare(e.toLowerCase())))}!function(t){t.getTruncatedStrandData=function(t,e,n){return{nucleotides:t.slice(0,n),ptoFlags:e.slice(0,n+1)}},t.getExtendedStrandData=function(t,e,n,r){const o=n-t.length,i=t.concat(new Array(n-t.length).fill(r)),s=0===t.length?n+1:o;return{nucleotides:i,ptoFlags:e.concat(new Array(s).fill(!0))}}}(it||(it={}));var at=n(2543),lt=n.n(at);class ut{constructor(t,e){this.dataManager=t,this._patternListUpdated$=new et.Subject,this._patternLoadRequested$=new et.Subject,this._patternLoaded$=new et.Subject,this._uniqueNucleotides$=new et.BehaviorSubject([]),this._patternDeletionRequested$=new et.Subject,this._tableSelection$=new et.BehaviorSubject(null),this._svgSaveRequested$=new et.Subject,this._loadPatternInNewTabRequested$=new et.Subject,this._urlStateUpdated$=new et.Subject,this._patternHasUnsavedChanges$=new et.BehaviorSubject(!1),this._selectedStrandColumn=new et.BehaviorSubject(null),this._selectedIdColumn=new et.BehaviorSubject(null),this.initializeAuthorSelection(e),this.initializePatternState(e),this._lastLoadedPatternConfig=new et.BehaviorSubject(lt().cloneDeep(this.getPatternConfig())),this.setupSubscriptions()}setupSubscriptions(){this._nucleotideSequences$.subscribe((()=>{this.updateUniqueNucleotides(),this.updateSequenceBase()})),this._isAntisenseStrandActive$.subscribe((t=>{t||U.forEach((t=>{this.updateTerminusModification("AS",t,"")}))})),this.patternStateChanged$.pipe((0,nt.debounceTime)(20)).subscribe((()=>{const t=this._lastLoadedPatternConfig.getValue(),e=this.getPatternConfig(),n=!lt().isEqual(e,t);this._patternHasUnsavedChanges$.next(n)}))}updateUniqueNucleotides(){const t=(e=this._nucleotideSequences$.getValue(),st(Object.values(e).flat()));var e;this._uniqueNucleotides$.next(t)}updateSequenceBase(){const t=ot(this._nucleotideSequences$.getValue());this._sequenceBase$.next(t)}get nucleotideSequencesChanged$(){return this._nucleotideSequences$.asObservable()}initializeAuthorSelection(t){const e=t[G.AUTHOR_ID];this.dataManager.isCurrentUserId(e)?this._patternAuthorSelection$=new et.BehaviorSubject(this.dataManager.getCurrentUserAuthorshipCategory()):this._patternAuthorSelection$=new et.BehaviorSubject(this.dataManager.getOtherUsersAuthorshipCategory())}initializePatternState(t){const e=t[G.PATTERN_CONFIG];this._patternName$=new et.BehaviorSubject(e[q.PATTERN_NAME]),this._isAntisenseStrandActive$=new et.BehaviorSubject(e[j.IS_ANTISENSE_STRAND_INCLUDED]),this._nucleotideSequences$=new et.BehaviorSubject(e[j.NUCLEOTIDE_SEQUENCES]),this._phosphorothioateLinkageFlags=new et.BehaviorSubject(e[j.PHOSPHOROTHIOATE_LINKAGE_FLAGS]),this._terminalModifications=new et.BehaviorSubject(e[j.STRAND_TERMINUS_MODIFICATIONS]),this._comment$=new et.BehaviorSubject(e[q.PATTERN_COMMENT]),this._modificationsWithNumericLabels$=new et.BehaviorSubject(e[q.NUCLEOTIDES_WITH_NUMERIC_LABELS]),this._sequenceBase$=new et.BehaviorSubject(ot(e[j.NUCLEOTIDE_SEQUENCES]))}getPatternName(){return this._patternName$.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$.next(t)}updateStrandLength(t,e){const n=this.getNucleotideSequences()[t];if(n.length===e)return;const r=this.getPhosphorothioateLinkageFlags()[t];if(0===e)return void this.setNewStrandData([],[],t);if(n.length>e){const{nucleotides:o,ptoFlags:i}=it.getTruncatedStrandData(n,r,e);return void this.setNewStrandData(o,i,t)}const o=this.getSequenceBase(),{nucleotides:i,ptoFlags:s}=it.getExtendedStrandData(n,r,e,o);this.setNewStrandData(i,s,t)}setNewStrandData(t,e,n){this.updateNucleotideSequences({...this.getNucleotideSequences(),[n]:t}),this.updatePhosphorothioateLinkageFlags({...this.getPhosphorothioateLinkageFlags(),[n]:e})}getPhosphorothioateLinkageFlags(){return this._phosphorothioateLinkageFlags.getValue()}updatePhosphorothioateLinkageFlags(t){this._phosphorothioateLinkageFlags.next(t)}get phosphorothioateLingeFlagsChanged$(){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 st(t).filter((t=>!rt(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$.getValue(),n={};k.forEach((r=>{n[r]=e[r].map((()=>t))})),this._nucleotideSequences$.next(n);const r=this._modificationsWithNumericLabels$.getValue();r.includes(t)||this.updateModificationsWithNumericLabels(r.concat(t))}get patternStateChanged$(){return et.merge(this._patternName$.pipe((0,nt.debounceTime)(300),(0,nt.map)((()=>{}))),this._isAntisenseStrandActive$,this._nucleotideSequences$,this._phosphorothioateLinkageFlags,this._terminalModifications,this._comment$.pipe((0,nt.debounceTime)(300)),this._modificationsWithNumericLabels$)}getSequenceBase(){return this._sequenceBase$.getValue()}uniqueNucleotidesChanged$(){return this.patternStateChanged$.pipe((0,nt.switchMap)((()=>this._uniqueNucleotides$)))}getUniqueNucleotides(){return this._uniqueNucleotides$.getValue()}get svgSaveRequested$(){return this._svgSaveRequested$.asObservable()}requestSvgSave(){this._svgSaveRequested$.next()}setAllPTOLinkages(t){const e=this.getPhosphorothioateLinkageFlags();k.forEach((n=>{e[n]=e[n].map((()=>t))})),this.updatePhosphorothioateLinkageFlags(e)}setPatternConfig(t){this._patternName$.next(t[q.PATTERN_NAME]),this._isAntisenseStrandActive$.next(t[j.IS_ANTISENSE_STRAND_INCLUDED]),this._nucleotideSequences$.next(t[j.NUCLEOTIDE_SEQUENCES]),this._phosphorothioateLinkageFlags.next(t[j.PHOSPHOROTHIOATE_LINKAGE_FLAGS]),this._terminalModifications.next(t[j.STRAND_TERMINUS_MODIFICATIONS]),this._comment$.next(t[q.PATTERN_COMMENT]),this._modificationsWithNumericLabels$.next(t[q.NUCLEOTIDES_WITH_NUMERIC_LABELS])}setLastLoadedPatternConfig(t){this._lastLoadedPatternConfig.next(lt().cloneDeep(t))}getPatternConfig(){return{[q.PATTERN_NAME]:this.getPatternName(),[j.IS_ANTISENSE_STRAND_INCLUDED]:this.isAntisenseStrandActive(),[j.NUCLEOTIDE_SEQUENCES]:this.getNucleotideSequences(),[j.PHOSPHOROTHIOATE_LINKAGE_FLAGS]:this.getPhosphorothioateLinkageFlags(),[j.STRAND_TERMINUS_MODIFICATIONS]:this.getTerminalModifications(),[q.PATTERN_COMMENT]:this.getComment(),[q.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 o=this.getModificationsWithNumericLabels();this.updateModificationsWithNumericLabels(o.concat(n)),this.updateNucleotideSequences(r)}get strandsUpdated$(){return et.merge(this._isAntisenseStrandActive$.asObservable().pipe((0,nt.map)((()=>{}))),this._nucleotideSequences$.asObservable().pipe((0,nt.map)((()=>{}))),this._patternLoaded$.asObservable().pipe((0,nt.map)((()=>{})))).pipe((0,nt.debounceTime)(10))}get strandsLinkagesAndTerminalsUpdated$(){return et.merge(this.strandsUpdated$,this._phosphorothioateLinkageFlags.asObservable().pipe((0,nt.map)((()=>{}))),this._terminalModifications.asObservable().pipe((0,nt.map)((()=>{}))))}updateControlsUponPatternLoaded(t){this._patternLoaded$.next(t)}get patternLoaded$(){return this._patternLoaded$.asObservable()}get userSelection$(){return this._patternAuthorSelection$.asObservable().pipe((0,nt.skip)(1))}selectAuthor(t){if("string"!=typeof t)throw new Error("Selected user must be defined");this._patternAuthorSelection$.next(t)}getSelectedAuthor(){return this._patternAuthorSelection$.getValue()}get loadPatternInNewTabRequested$(){return this._loadPatternInNewTabRequested$.asObservable()}requestLoadPatternInNewTab(t){this._loadPatternInNewTabRequested$.next(t)}updateUrlState(t){this._urlStateUpdated$.next(t)}get urlStateUpdated$(){return this._urlStateUpdated$.asObservable()}get patternHasUnsavedChanges$(){return this._patternHasUnsavedChanges$.asObservable()}selectStrandColumn(t,e){this._selectedStrandColumn.next({...this._selectedStrandColumn.getValue(),[t]:e})}getSelectedStrandColumn(t){const e=this._selectedStrandColumn.getValue();return e?e[t]:null}selectIdColumn(t){this._selectedIdColumn.next(t)}getSelectedIdColumn(){return this._selectedIdColumn.getValue()}get updateSvgContainer$(){return this.patternStateChanged$.pipe((0,nt.debounceTime)(100))}}const ct="pattern";class ht{constructor(){this.urlSearchParams=new URLSearchParams(window.location.search)}subscribeToObservables(t){t.urlStateUpdated$.subscribe((t=>this.setPatternURL(t))),t.loadPatternInNewTabRequested$.subscribe((t=>{const e=`${window.location.origin}${window.location.pathname}?${ct}=${t}`;window.open(e,"_blank")})),window.addEventListener("popstate",(()=>{this.urlSearchParams=new URLSearchParams(window.location.search);const e=this.getPatternHash();null!==e&&t.requestPatternLoad(e)}))}getPatternHash(){return this.urlSearchParams.get(ct)}setPatternURL(t){null!==t&&""!==t?(this.urlSearchParams.set(ct,t),window.history.pushState({},"",`${window.location.pathname}?${this.urlSearchParams}`)):this.clearPatternURL()}clearPatternURL(){this.urlSearchParams.delete(ct),window.history.pushState({},"",`${window.location.pathname}`)}}var dt=n(5072),ft=n.n(dt),pt=n(7825),mt=n.n(pt),gt=n(7659),yt=n.n(gt),bt=n(5056),vt=n.n(bt),wt=n(540),Ct=n.n(wt),At=n(1113),xt=n.n(At),St=n(9252),Tt={};Tt.styleTagTransform=xt(),Tt.setAttributes=vt(),Tt.insert=yt().bind(null,"head"),Tt.domAPI=mt(),Tt.insertStyleElement=Ct(),ft()(St.A,Tt),St.A&&St.A.locals&&St.A.locals;class Et{constructor(t){this.eventBus=t,this.columnControlsContainer=M.div([]),this.eventBus.tableSelectionChanged$.subscribe((()=>this.handleTableChoice())),this.refreshColumnControls()}getColumnControlsContainer(){return this.columnControlsContainer}get selectedTable(){return this.eventBus.getTableSelection()}handleTableChoice(){this.refreshColumnControls()}refreshColumnControls(){L()(this.columnControlsContainer).empty(),L()(this.columnControlsContainer).append(this.constructColumnControls())}constructColumnControls(){const t=this.createStrandColumnInput(),e=t.SS,n=t.AS;this.eventBus.antisenseStrandToggled$.subscribe((t=>{L()(n).toggle(t)}));const r=this.createIdColumnInput();return[e,n,r]}createStrandColumnInput(){const t=this.selectedTable?this.selectedTable.columns.names().sort(((t,e)=>t.localeCompare(e))):[];return Object.fromEntries(k.map((e=>{const n=M.input.choice(`${H[e]} column`,{value:t[0],items:t,onValueChanged:t=>this.eventBus.selectStrandColumn(e,t)});return this.eventBus.selectStrandColumn(e,t[0]),[e,n.root]})))}createIdColumnInput(){const t=this.selectedTable?this.selectedTable.columns.names():[],e=M.input.choice("ID column",{value:t[0],items:t,onValueChanged:t=>this.eventBus.selectIdColumn(t)});return this.eventBus.selectIdColumn(t[0]),e.root}}class _t{constructor(t){this.eventBus=t,this.availableTables=[],this.tableInputContainer=M.div([]),this.subscribeToTableEvents(),this.refreshTableInput()}getTableInputContainer(){return this.tableInputContainer}subscribeToTableEvents(){r.events.onTableAdded.subscribe((t=>this.handleTableAdded(t))),r.events.onTableRemoved.subscribe((t=>this.handleTableRemoved(t))),this.eventBus.tableSelectionChanged$.subscribe((()=>this.handleTableChoice()))}getTableFromEventData(t){if(!t&&t.args&&t.args.dataFrame instanceof o.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();L()(this.tableInputContainer).empty(),this.tableInputContainer.append(t.root)}createTableInput(){const t=this.eventBus.getTableSelection();return M.input.table("Tables",{value:t,items:this.availableTables,onValueChanged:t=>{null!==t&&this.eventBus.selectTable(t)}})}handleTableChoice(){const t=this.eventBus.getTableSelection();t&&(this.isTableDisplayed(t)||this.displayTable(t))}isTableDisplayed(t){return r.shell.tableNames.includes(t.name)}displayTable(t){const e=r.shell.v;r.shell.addTableView(t),r.shell.v=e}}function It(t,e,n,r){const o=function(t,e,n){const r=new Array(t.length+e.filter((t=>t)).length+U.length);r[0]=n["5'"],r[r.length-1]=n["3'"];let o=1;return e[0]&&(r[o]="ps",o++),t.forEach(((t,n)=>{r[n+o]=t,e[n+1]&&(r[n+o+1]="ps",o++)})),r}(t.split("").map(((t,n)=>{const r=function(t,e,n){const r=Object.keys(n.patternAppData)[0],o=n.patternAppData[r][e].substitution;return t.replace(/([AGCTU])/,o)}(t,e[n],Kr.jsonData);return r})),n,r);return o.join("")}class Nt{constructor(t){this.eventBus=t,this.tableInputManager=new _t(t),this.columnInputManager=new Et(t)}createControls(){const t=M.h1("Bulk convert"),e=this.tableInputManager.getTableInputContainer(),n=this.columnInputManager.getColumnControlsContainer(),r=M.bigButton("Convert",(()=>this.processConvertButtonClick()));return[t,e,n,M.buttonsInput([r])]}processConvertButtonClick(){!function(t){const e=t.getTableSelection();if(!e)return void r.shell.warning("Please select a table");const n=k.filter((e=>!("AS"===e&&!t.isAntisenseStrandActive()))).map((e=>({strand:e,column:t.getSelectedStrandColumn(e)}))).filter((t=>t.column));if(0===n.length)return void r.shell.warning("Select a sense strand column");const o=t.getSelectedIdColumn();if(!o)throw new Error("No ID column selected");e.getCol(o);const i=n.map((t=>({strand:t.strand,column:e.getCol(t.column)})));!function(t,e){const n=e.getNucleotideSequences();return t.every((t=>{const e=n[t.strand].length;return t.column.toList().every((t=>t.length===e))}))}(i,t)?r.shell.warning("Some strands in the table input do not match pattern length"):i.forEach((n=>{const r=n.column,o=n.strand,i=t.getNucleotideSequences()[o],s=t.getTerminalModifications()[o],a=t.getPhosphorothioateLinkageFlags()[o],l=`${t.getPatternName()}(${r.name})`;e.columns.addNewString(l).init((t=>It(r.get(t),i,a,s)))}))}(this.eventBus)}}class Mt{constructor(t,e,n){this.eventBus=t,this.initialPatternConfig=e,this.subscriptions=n}create(){return M.divV([M.h1("PTO"),M.divH([this.createAllPtoActivationInput().root,...this.createFirstPtoInputs().map((t=>t.root))],{style:{gap:"12px"}})])}areAllPtoLinkagesSet(t){return k.map((e=>t[e].filter((t=>t)).length)).reduce(((t,e)=>t+e),0)===k.map((t=>this.initialPatternConfig.nucleotideSequences[t].length)).reduce(((t,e)=>t+e),0)+k.filter((e=>t[e].length)).length}createAllPtoActivationInput(){const t=this.initialPatternConfig.phosphorothioateLinkageFlags,e=this.areAllPtoLinkagesSet(t),n=M.input.bool("All PTO",{value:e});n.onInput.subscribe((()=>{const t=n.value;this.eventBus.setAllPTOLinkages(t)}));const r=this.eventBus.phosphorothioateLingeFlagsChanged$.subscribe((()=>{const t=this.eventBus.getPatternConfig().phosphorothioateLinkageFlags,e=this.areAllPtoLinkagesSet(t);n.value=e}));return this.subscriptions.add(r),this.addStyleToPtoInput(n),M.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 k.map((t=>{if(!this.eventBus.isAntisenseStrandActive()&&"AS"===t)return;const e=this.isFirstPtoActive(t),n=M.input.bool(`First ${t} PTO`,{value:e});n.onInput.subscribe((()=>{const e=n.value;this.eventBus.setPhosphorothioateLinkageFlag(t,0,e)}));const r=this.eventBus.phosphorothioateLingeFlagsChanged$.subscribe((e=>{const r=e[t][0];n.value=r}));return this.subscriptions.add(r),this.addStyleToPtoInput(n),M.tooltip.bind(n.captionLabel,`Activate first phosphothioate in ${t}`),n})).filter((t=>void 0!==t))}isFirstPtoActive(t){return this.initialPatternConfig.phosphorothioateLinkageFlags[t][0]}}class Ot{constructor(t,e,n){this.eventBus=t,this.dataManager=e,this.subscriptions=n;const r=this.eventBus.nucleotideSequencesChanged$.subscribe((()=>{this.displayedInputLabels=this.computeDisplayedInputLabels()}));this.subscriptions.add(r)}create(){const t=k.map((t=>this.constructControlsPanel(t)));return M.divH(t,{style:{gap:"24px"}})}constructControlsPanel(t){if(!this.eventBus.isAntisenseStrandActive()&&"AS"===t)return M.div([]);const e=this.constructHeader(),n=this.createControls(t);return M.block([M.h1(`${H[t]}`),e,n],{style:{paddingTop:"12px"}})}constructHeader(){return M.divH([M.div([M.divText("#")],{style:{width:"20px"}}),M.block75([M.divText("Modification")]),M.div([M.divText("PTO")])])}createControls(t){const e=this.createNucleobaseInputs(t),n=this.createLabelDivs(t),r=this.createPTOFlagInputs(t);return M.div(e.map(((t,e)=>M.divH([n[e],M.block75([t.root]),r[e].root],{style:{alignItems:"center"}}))))}createNucleobaseInputs(t){const e=this.dataManager.fetchAvailableNucleotideBases().sort(((t,e)=>t.toLowerCase().localeCompare(e.toLowerCase())));return this.eventBus.getNucleotideSequences()[t].map(((n,r)=>{const o=M.input.choice("",{value:n,items:e});return o.onInput.subscribe((()=>{const e=o.value;this.eventBus.setNucleotide(t,r,e)})),o}))}createPTOFlagInputs(t){return this.eventBus.getPhosphorothioateLinkageFlags()[t].slice(1).map(((e,n)=>{const r=M.input.bool("",{value:e});r.onInput.subscribe((()=>{const e=r.value;this.eventBus.setPhosphorothioateLinkageFlag(t,n+1,e)}));const o=this.eventBus.phosphorothioateLingeFlagsChanged$.subscribe((e=>{const o=e[t][n+1];r.value=o}));return this.subscriptions.add(o),r}))}computeDisplayedInputLabels(){const t=this.eventBus.getNucleotideSequences(),e=new Map;return k.forEach((n=>{let r=1;const o=t[n].map((t=>{if(rt(t))return"";const e=String(r);return r++,e}));e.set(n,o)})),e}createLabelDivs(t){const e=this.createLabels(t).map((t=>M.div([t],{style:{width:"20px"}}))),n=this.eventBus.nucleotideSequencesChanged$.subscribe((()=>{this.createLabels(t).forEach(((t,n)=>{L()(e[n]).empty(),L()(e[n]).append(t)}))}));return this.subscriptions.add(n),e}createLabels(t){return this.eventBus.getNucleotideSequences()[t].map(((e,n)=>{const r=this.displayedInputLabels.get(t)[n];return M.label(r)}))}}class Lt{constructor(){this.rxjsSubscriptions=[],this.dgSubscriptions=[]}add(t){t instanceof et.Subscription?this.rxjsSubscriptions.push(t):this.dgSubscriptions.push(t)}unsubscribeAll(){for(const t of[this.rxjsSubscriptions,this.dgSubscriptions])t.forEach((t=>t.unsubscribe())),t.length=0}}class Rt{constructor(t,e){this.eventBus=t,this.dataManager=e,this.subscriptions=new Lt}static open(t,e){Rt.isDialogOpen||(Rt.instance||(Rt.instance=new Rt(t,e)),Rt.instance.openDialog())}openDialog(){this.initialPatternConfig=lt().cloneDeep(this.eventBus.getPatternConfig()),Rt.isDialogOpen=!0,this.createDialog().show()}createDialog(){const t=M.divV([]);this.subscriptions.add(this.eventBus.strandsUpdated$.subscribe((()=>this.onStrandsUpdated(t))));const e=M.dialog("Edit strands").add(t).onOK((()=>{})).onCancel((()=>this.resetToInitialState()));return this.subscriptions.add(e.onClose.subscribe((()=>{Rt.isDialogOpen=!1,this.subscriptions.unsubscribeAll()}))),e}onStrandsUpdated(t){const e=new Mt(this.eventBus,this.initialPatternConfig,this.subscriptions).create(),n=new Ot(this.eventBus,this.dataManager,this.subscriptions).create();L()(t).empty(),L()(t).append(e,n)}resetToInitialState(){this.eventBus.setPatternConfig(this.initialPatternConfig)}}Rt.isDialogOpen=!1;class Pt{constructor(t){this.eventBus=t,this.subscriptions=new Lt}static open(t){Pt.isDialogOpen||(Pt.instance||(Pt.instance=new Pt(t)),Pt.instance.openDialog())}openDialog(){this.initialPatternConfig=lt().cloneDeep(this.eventBus.getPatternConfig()),Pt.isDialogOpen=!0,this.createDialog().show()}createDialog(){const t=M.divV([]);this.subscriptions.add(this.eventBus.strandsUpdated$.subscribe((()=>this.onStrandsUpdated(t))));const e=M.dialog("Edit terminal modifications").add(t).onOK((()=>{})).onCancel((()=>this.resetToInitialState()));return this.subscriptions.add(e.onClose.subscribe((()=>{Pt.isDialogOpen=!1,this.subscriptions.unsubscribeAll()}))),e}onStrandsUpdated(t){const e=new Bt(this.eventBus).create();L()(t).empty(),L()(t).append(e)}resetToInitialState(){this.eventBus.setPatternConfig(this.initialPatternConfig)}}Pt.isDialogOpen=!1;class Bt{constructor(t){this.eventBus=t}create(){const t=k.map((t=>this.constructControlsPanel(t)));return M.divH(t,{style:{gap:"24px"}})}constructControlsPanel(t){if(!this.eventBus.isAntisenseStrandActive()&&"AS"===t)return M.div([]);const e=this.createInputs(t);return M.block([M.h1(`${H[t]}`),e],{style:{paddingTop:"12px"}})}createInputs(t){const e=("SS"===t?[...U].reverse():U).map((e=>this.createInputForTerminus(t,e)));return M.form(e)}createInputForTerminus(t,e){const n=this.eventBus.getTerminalModifications()[t][e],r=M.input.textArea(e,{value:n});return this.applyStylingToInput(r),r.onInput.subscribe((()=>{const n=r.value;null!==n&&this.eventBus.updateTerminusModification(t,e,n)})),r}applyStylingToInput(t){const e=t.root.getElementsByTagName("textarea")[0];L()(e).css("resize","none")}}class Dt{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,o=this.createSequenceBaseInput().root,i=this.createPatternCommentInput().root,s=this.createPatternNameInputBlock(),a=this.createEditPatternButton(),l=this.createEditTerminalModificationsButton();return[M.h1("Edit"),t,n,r,o,s,i,M.buttonsInput([l,a])]}createEditPatternButton(){const t=M.button("Edit strands",(()=>Rt.open(this.eventBus,this.dataManager)));return M.tooltip.bind(t,"Edit strand modifications and PTOs"),t}createEditTerminalModificationsButton(){const t=M.button("Edit terminals",(()=>Pt.open(this.eventBus)));return M.tooltip.bind(t,"Edit terminal modifications"),L()(t).css("margin-right","20px"),t}createAntisenseStrandToggle(){const t=M.input.toggle(`${H.AS} strand`,{value:this.eventBus.isAntisenseStrandActive()});return t.onInput.subscribe((()=>this.eventBus.toggleAntisenseStrand(t.value))),this.eventBus.patternLoaded$.subscribe((()=>{t.value=this.eventBus.isAntisenseStrandActive()})),t.setTooltip("Toggle antisense strand"),t.root}createStrandLengthInputs(){const t=t=>{const n=this.eventBus.getNucleotideSequences()[t].length,r=M.input.int(`${H[t]} length`,{value:n});return r.onInput.subscribe((()=>e(t,r))),this.eventBus.nucleotideSequencesChanged$.subscribe((()=>{r.value=this.eventBus.getNucleotideSequences()[t].length})),r.setTooltip(`Number of nucleotides in ${t}, including overhangs`),[t,r]},e=(t,e)=>{const n=e.value;null!==n&&(n<=0&&(r.shell.warning("Sequence length must be greater than 0"),e.value=1),n>34&&(r.shell.warning("Sequence length must be less than 35"),e.value=34),this.eventBus.updateStrandLength(t,e.value))},n=Object.fromEntries(k.map((e=>t(e))));return this.eventBus.antisenseStrandToggled$.subscribe((t=>{L()(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=M.input.choice("Sequence basis",{value:e,items:t});return n.onInput.subscribe((()=>this.eventBus.replaceSequenceBase(n.value))),this.eventBus.nucleotideSequencesChanged$.subscribe((()=>{n.value=this.eventBus.getSequenceBase()})),n.setTooltip("Most frequent nucleobase in the strands"),n}createPatternCommentInput(){const t=M.input.textArea("Comment",{value:this.eventBus.getComment()});return L()(t.root).addClass("st-pattern-text-input"),t.onInput.subscribe((()=>this.eventBus.updateComment(t.value))),this.eventBus.patternLoaded$.subscribe((()=>{t.value=this.eventBus.getComment()})),t}createPatternNameInputBlock(){const t=M.input.textArea("Pattern name",{value:this.eventBus.getPatternName()});return L()(t.root).addClass("st-pattern-text-input"),t.onInput.subscribe((()=>this.eventBus.updatePatternName(t.value))),this.eventBus.patternLoaded$.subscribe((()=>{t.value=this.eventBus.getPatternName()})),t.setTooltip("Name under which pattern will be saved"),t.root}}class Ft{constructor(t,e){this.eventBus=t,this.dataManager=e,this.subscriptions=new Lt,this.authorSelectedByUser=!1,this.eventBus.patternLoadRequested$.subscribe((t=>this.handlePatternChoice(t))),this.eventBus.patternDeletionRequested$.subscribe((async t=>{await this.dataManager.deletePattern(t,this.eventBus)}))}async handlePatternChoice(t){let e=await this.dataManager.getPatternConfig(t);null===e&&(e=this.dataManager.getDefaultPatternConfig()),this.eventBus.setPatternConfig(e),this.eventBus.updateControlsUponPatternLoaded(t),this.eventBus.setLastLoadedPatternConfig(e)}isCurrentUserSelected(){return this.eventBus.getSelectedAuthor()!==this.dataManager.getOtherUsersAuthorshipCategory()}createControls(){const t=this.getPatternInputsContainer();return[M.h1("Load"),t]}getPatternInputsContainer(){const t=M.divH(this.createPatternInputs());return this.eventBus.patternListUpdated$.subscribe((()=>{this.subscriptions.unsubscribeAll(),L()(t).empty(),L()(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=M.div([t.root]),n=this.eventBus.userSelection$.subscribe((()=>{L()(e).empty(),L()(e).append(this.createPatternChoiceInput().root)}));return this.subscriptions.add(n),e}createAuthorChoiceInput(){const t=[this.dataManager.getCurrentUserAuthorshipCategory()];this.dataManager.getOtherUsersPatternNames().length>0&&t.push(this.dataManager.getOtherUsersAuthorshipCategory());const e=M.input.choice("Author",{value:this.eventBus.getSelectedAuthor(),items:t});return e.onInput.subscribe((()=>{if(this.authorSelectedByUser=!0,null===e.value)throw new Error("author choice must be non-null");this.eventBus.selectAuthor(e.value)})),this.setAuthorChoiceInputStyle(e),e.setTooltip("Select pattern author"),e}setAuthorChoiceInputStyle(t){L()(t.input).css({"max-width":"100px","min-width":"100px"}),L()(t.root).css({"padding-right":"30px","padding-left":"30px"})}createPatternChoiceInput(){const t=this.isCurrentUserSelected()?this.dataManager.getCurrentUserPatternNames():this.dataManager.getOtherUsersPatternNames();if(this.authorSelectedByUser){const e=this.dataManager.getPatternHash(t[0],this.isCurrentUserSelected());this.eventBus.requestPatternLoad(e),this.eventBus.updateUrlState(e),this.authorSelectedByUser=!1}const e=this.getPatternName(t),n=M.input.choice("Pattern",{value:e,items:t});return n.setTooltip("Select pattern to load"),L()(n.input).css({"max-width":"100px","min-width":"100px"}),this.subscriptions.add(n.onInput.subscribe((()=>{const t=this.dataManager.getPatternHash(n.value,this.isCurrentUserSelected());this.eventBus.requestPatternLoad(t),this.eventBus.updateUrlState(t)}))),this.subscriptions.add(this.eventBus.patternLoaded$.subscribe((()=>{const e=this.eventBus.getPatternName();n.value!==e&&(n.value=this.getPatternName(t))}))),n}getPatternName(t){return t.find((t=>t.split(" (")[0]===this.eventBus.getPatternName()))??t[0]}createDeletePatternButton(){const t=M.button(M.iconFA("trash-alt"),(()=>{this.eventBus.getPatternName()!==this.dataManager.getDefaultPatternName()?this.showDeletePatternDialog():r.shell.warning("Cannot delete example pattern")}));M.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=M.dialog("Delete pattern"),e=this.eventBus.getPatternName();t.add(M.divText(`Are you sure you want to delete pattern ${e}?`)),t.onOK((()=>this.eventBus.requestPatternDeletion(e))),t.show()}}class kt{constructor(t,e){this.eventBus=t,this.dataManager=e}getLayout(){const t=new Ft(this.eventBus,this.dataManager),e=new Dt(this.eventBus,this.dataManager),n=new Nt(this.eventBus),r=t.createControls(),o=e.createControls(),i=n.createControls(),s=M.div(r);L()(s).css({"padding-bottom":"20px"});const a=M.div([...o,...i],"ui-form"),l=M.div([s,a]);return L()(l).css({padding:"25px"}),M.box(l,{style:{maxWidth:"450px"}})}}var Ht=n(9146);class Ut{constructor(t,e,n){this.svgElementFactory=t,this.config=e,this.yShift=n}shiftElements(t){this.svgElements.forEach((e=>{const n=e.getAttribute("transform")||"",r=`translate(${t.x},${t.y})`;e.setAttribute("transform",`${n} ${r}`)}))}}class $t{constructor(){}static getInstance(){return $t.instance||($t.instance=new $t,$t.instance.canvas=document.createElement("canvas")),$t.instance}static getTextDimensions(t,e){const n=$t.getInstance().canvas.getContext("2d");if(!n)throw new Error("Canvas 2D context is not available");return n.font=`${e}px Arial`,{width:1.1*n.measureText(t).width,height:1.1*e}}}function Vt(t){const e=Object.keys(Kr.jsonData.patternAppData)[0];if(!e)throw new Error(`No format found in '${h}'`);return Kr.jsonData.patternAppData[e][t].color||""}class jt extends Ut{constructor(t,e,n){super(t,e,n);const r=k.filter((t=>e.nucleotideSequences[t].length>0));this.strands=r.map((t=>new qt(this.svgElementFactory,e,n,t))),this.terminalModifications=r.map(((t,r)=>new zt(this.svgElementFactory,e,n,t,this.strands[r]))),this.labels=r.map(((t,r)=>new Gt(this.svgElementFactory,e,n,t,this.terminalModifications[r])))}get svgElements(){return[...this.strands,...this.terminalModifications,...this.labels].map((t=>t.svgElements)).flat()}getContentWidth(){return Math.max(...this.labels.map((t=>t.getContentWidth())))}getContentHeight(){return this.strands.reduce(((t,e)=>t+e.getContentHeight()),0)}}class qt extends Ut{constructor(t,e,n,r){super(t,e,n),this.svgElementFactory=t,this.config=e,this.yShift=n,this.strand=r,this.nucleotideNumericLabels=this.computeNucleotideNumericLabels(),"AS"===this.strand&&(this.config.phosphorothioateLinkageFlags[this.strand].reverse(),this.config.nucleotideSequences[this.strand].reverse(),this.nucleotideNumericLabels.reverse()),this._svgElements=[this.createStrandCircles(),this.createPTOLinkageStars()].flat()}computeNucleotideNumericLabels(){let t=0;return this.config.nucleotideSequences[this.strand].map((e=>rt(e)?null:(t++,t)))}get svgElements(){return this._svgElements}getStrandCircleYShift(){return Wt(this.strand,this.yShift)}createStrandCircles(){const t={x:80,y:this.getStrandCircleYShift()};return this.config.nucleotideSequences[this.strand].map(((e,n)=>this.createNucleotideElementGroup(e,n,t))).flat()}createNucleotideElementGroup(t,e,n){return[...this.createNucleotideCircleElements(t,e,n),this.config.nucleotidesWithNumericLabels.includes(t)?this.createNucleotideNumericLabel(e,n):null].filter((t=>null!==t))}createNucleotideCircleElements(t,e,n){const r=Vt(t),o={...n,x:n.x+30*e};return[this.svgElementFactory.createCircleElement(o,15,r),this.createNucleotideLetterLabel(e,n,t)]}getNucleotideCircleCenterPosition(t,e){return{x:e.x+30*t,y:e.y}}createNucleotideLetterLabel(t,e,n){if(!m.AL.includes(n))return null;const r=function(t){return!rt(t)&&m.AL.includes(t)?t:""}(n),o=function(t){const e=Vt(t),n=e.match(/\d+/g)?.map(Number);if(!n||n.length<3)return"#ffffff";const[r,o,i]=n;return.299*r+.587*o+.114*i>186?"#333333":"#ffffff"}(n),i=this.getPositionForNucleotideLabel(t,e);return this.svgElementFactory.createTextElement(r,i,17,o)}getPositionForNucleotideLabel(t,e){const n=this.getNucleotideCircleCenterPosition(t,e),r=$t.getTextDimensions("A",17);return{x:n.x-r.width/2,y:n.y+r.height/3}}getNumericLabelYShift(t){return"SS"===this.strand?t.y-20:t.y+15+5+15}createNucleotideNumericLabel(t,e){const n=this.nucleotideNumericLabels[t];if(null===n)return null;const r=$t.getTextDimensions(n.toString(),15).width,o={x:e.x+30*t-r/2,y:this.getNumericLabelYShift(e)};return this.svgElementFactory.createTextElement(n.toString(),o,15,"var(--grey-6)")}createPTOLinkageStars(){const t=this.config.phosphorothioateLinkageFlags[this.strand],e=this.getStrandCircleYShift()+12;return t.map(((t,n)=>{if(!t)return null;const r={x:65+30*n,y:e};return this.svgElementFactory.createStarElement(r,"red")})).filter((t=>null!==t))}getContentWidth(){return 30*this.config.nucleotideSequences[this.strand].length}getContentHeight(){return 62}}class Gt extends Ut{constructor(t,e,n,r,o){super(t,e,n),this.svgElementFactory=t,this.config=e,this.yShift=n,this.strand=r,this.terminalModifications=o,this._svgElements=this.createSVGElements()}createSVGElements(){return[this.createLeftLabel(),this.createRightLabel()]}getLeftLabelWidth(){return 55}getRightLabelWidth(){return 20}createLeftLabel(){const t="SS"===this.strand?"5'":"3'",e=`${this.strand}: ${t} `,n=$t.getTextDimensions(e,17),r={x:10,y:Wt(this.strand,this.yShift)+n.height/3};return this.svgElementFactory.createTextElement(e,r,17,"var(--grey-6)")}createRightLabel(){const t=" "+("SS"===this.strand?"3'":"5'"),e=$t.getTextDimensions(t,17),n={x:65+this.terminalModifications.getContentWidth()+5,y:Wt(this.strand,this.yShift)+e.height/3};return this.svgElementFactory.createTextElement(t,n,17,"var(--grey-6)")}get svgElements(){return this._svgElements}getContentWidth(){return this.terminalModifications.getContentWidth()+this.getLeftLabelWidth()+this.getRightLabelWidth()+10}getContentHeight(){return this.terminalModifications.getContentHeight()}}class zt extends Ut{constructor(t,e,n,r,o){super(t,e,n),this.svgElementFactory=t,this.config=e,this.yShift=n,this.strand=r,this.strandSvgWrapper=o,this._svgElements=this.createSVGElements()}createSVGElements(){return this.createTerminalModifications()}getTerminalModification(t){return this.config.strandTerminusModifications[this.strand][t]}getTerminalModificationTextDimensions(t){const e=this.getTerminalModification(t);return $t.getTextDimensions(e,17)}getLeftTerminus(){return"SS"===this.strand?"5'":"3'"}createTerminalModification(t){const e=this.getTerminalModification(t),n=this.getTerminalModificationTextDimensions(t),r=t===this.getLeftTerminus(),o={x:r?65:65+this.getTerminalModificationTextDimensions(this.getLeftTerminus()).width+this.strandSvgWrapper.getContentWidth(),y:Wt(this.strand,this.yShift)+n.height/3};return r&&this.strandSvgWrapper.shiftElements({x:n.width,y:0}),this.svgElementFactory.createTextElement(e,o,17,"red")}createTerminalModifications(){return("AS"===this.strand?U:Array.from(U).reverse()).map((t=>this.createTerminalModification(t)))}get svgElements(){return this._svgElements}getContentWidth(){return this.strandSvgWrapper.getContentWidth()+U.map((t=>this.getTerminalModificationTextDimensions(t).width)).reduce(((t,e)=>t+e),0)}getContentHeight(){return this.strandSvgWrapper.getContentHeight()}}function Wt(t,e){return"SS"===t?e+5+15+15:e+52+10+15}class Yt{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 o=this.createElement("text");return this.setAttributes(o,{x:e.x,y:e.y,"font-size":n,"font-weight":"normal","font-family":"Arial",fill:r}),o.textContent=t,o}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,o)=>{const i=o%2==0?6:3,s=o*e+n;return[t.x+Math.cos(s)*i,t.y+Math.sin(s)*i]}))}createRectangleElement(t,e,n,r){const o=this.createElement("rect");return this.setAttributes(o,{x:t.x,y:t.y,width:e,height:n,fill:r}),o}}class Kt extends Ut{constructor(t,e,n){super(t,e,n),this.svgElementFactory=t,this.config=e,this.yShift=n,this._svgElements=[],this.titleText=this.getTitleText(),this._svgElements=[this.getTitle()]}get svgElements(){return this._svgElements}getTitle(){return this.svgElementFactory.createTextElement(this.titleText,{x:15,y:this.yShift+17},17,"black")}getContentWidth(){return $t.getTextDimensions(this.titleText,17).width}getContentHeight(){return $t.getTextDimensions(this.titleText,17).height}getTitleText(){const t=`${this.config.nucleotideSequences.SS.length}`,e=this.config.isAntisenseStrandIncluded?`/${this.config.nucleotideSequences.AS.length}`:"";return`${this.config.patternName} for ${t}${e}-mer`}}class Jt extends Ut{constructor(t,e,n){super(t,e,n),this._svgElements=[];const{elements:r,width:o}=this.createLegendItems();this._svgElements=r,this.width=o}isPhosphorothioatePresent(){return Object.values(this.config.phosphorothioateLinkageFlags).flat().some((t=>t))}getModificationTypesList(){return[...new Set(Object.values(this.config.nucleotideSequences).flat().sort(((t,e)=>t.toLowerCase().localeCompare(e.toLowerCase()))))]}get svgElements(){return this._svgElements}createLegendItem(t,e){const n={x:e,y:this.yShift-6},r=t.includes("linkage")?this.svgElementFactory.createStarElement(n,"red"):this.svgElementFactory.createCircleElement(n,6,Vt(t));e+=12;const o={y:this.yShift,x:e};return{elements:[r,this.svgElementFactory.createTextElement(t,o,15,"var(--grey-6)")],width:12+$t.getTextDimensions(t,15).width}}createLegendItems(){let t=10;const e=[],n=e=>t+=e+15;if(this.isPhosphorothioatePresent()){const{elements:r,width:o}=this.createLegendItem("PTO linkage",t);n(o),e.push(r)}return this.getModificationTypesList().forEach((r=>{const{elements:o,width:i}=this.createLegendItem(r,t);n(i),e.push(o)})),{elements:e.flat(),width:t}}getContentHeight(){return 20}getContentWidth(){return this.width}}class Qt{constructor(t){this.svgElementFactory=new Yt;const e=lt().cloneDeep(t);let n=10;this.title=new Kt(this.svgElementFactory,e,n),n+=this.title.getContentHeight(),this.strands=new jt(this.svgElementFactory,e,n),n+=this.strands.getContentHeight()+10,this.legend=new Jt(this.svgElementFactory,e,n)}renderPattern(){const t=this.getGlobalWidth(),e=this.getGlobalHeight(),n=this.svgElementFactory.createCanvas(t,e),r=[this.title,this.strands,this.legend].map((t=>t.svgElements)).flat();return n.append(...r),n}getGlobalWidth(){const t=[this.title,this.strands,this.legend];return Math.max(...t.map((t=>t.getContentWidth())))}getGlobalHeight(){return[this.title,this.strands,this.legend].reduce(((t,e)=>t+e.getContentHeight()),10)}}class Xt{constructor(t){this.eventBus=t,this.svgDisplayDiv=M.div([]),t.updateSvgContainer$.subscribe((()=>this.updateSvgContainer())),t.svgSaveRequested$.subscribe((()=>this.saveSvgAsPng()))}static createSvgDiv(t){return new Xt(t).svgDisplayDiv}updateSvgContainer(){$(this.svgDisplayDiv).empty();const t=this.eventBus.getPatternConfig();this.svgElement=this.createSvg(t),this.svgDisplayDiv.append(this.svgElement)}createSvg(t){return new Qt(t).renderPattern()}saveSvgAsPng(){const t=this.eventBus.getPatternName();Ht.saveSvgAsPng(this.svgElement,t,{backgroundColor:"white"})}}class Zt{constructor(t){this.eventBus=t,this.togglesContainer=M.div([]),this.eventBus.uniqueNucleotidesChanged$().subscribe((()=>{this.updateContainer()}))}getContainer(){return this.togglesContainer}updateContainer(){L()(this.togglesContainer).empty(),L()(this.togglesContainer).append(this.createInputs())}createInputs(){const t=this.eventBus.getUniqueNucleotides().filter((t=>!rt(t))).map((t=>this.createSingleInput(t)));return t.sort(((t,e)=>t.captionLabel.textContent.localeCompare(e.captionLabel.textContent))),M.divH(t.map((t=>t.root)))}createSingleInput(t){const e=this.eventBus.getModificationsWithNumericLabels().includes(t),n=M.input.bool(t,{value:e,onValueChanged:e=>this.handleNumericLabelToggle(t,e)});return L()(n.root).css("padding-right","20px"),n.setTooltip(`Show numeric labels for ${t}`),n}handleNumericLabelToggle(t,e){const n=this.eventBus.getModificationsWithNumericLabels();if(n.includes(t)===e)return;const r=e?n.concat(t):n.filter((e=>e!==t));this.eventBus.updateModificationsWithNumericLabels(r)}}class te{constructor(t,e){this.eventBus=t,this.dataManager=e,this.subscriptions=new Lt}createContainer(){return M.div([M.h1("Translation example"),this.createTranslationExamples()],{style:{paddingTop:"20px"}})}createTranslationExamples(){const t=M.divH([...this.getExampleElements()],"ui-form");return this.eventBus.antisenseStrandToggled$.subscribe((()=>{this.subscriptions.unsubscribeAll(),L()(t).empty(),L()(t).append(this.getExampleElements())})),t}getExampleElements(){return k.map((t=>new ee(t,this.eventBus,this.subscriptions).create()))}}class ee{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(),M.block50([M.h2(H[this.strand]),this.inputExample.root,this.outputExample.root],{style:{paddingRight:"20px"}})):M.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 ${H[this.strand]}`),t}generateExampleSequence(){return this.eventBus.getNucleotideSequences()[this.strand].map(((t,e)=>m.AL[e%m.AL.length])).join("")}createOutputExample(t){const e=this.createTextInputForExamples();return e.value=this.computeOutputValue(t),e.setTooltip(`Pattern applied to the example input for ${H[this.strand]}`),e}computeOutputValue(t){const e=this.eventBus.getNucleotideSequences()[this.strand],n=this.eventBus.getTerminalModifications()[this.strand];return It(t,e,this.eventBus.getPhosphorothioateLinkageFlags()[this.strand],n)}createTextInputForExamples(){const t=M.input.textArea("",{value:""});return this.applyStylingToInput(t),t}applyStylingToInput(t){const e=t.root.getElementsByTagName("textarea")[0];e.setAttribute("readonly","true"),L()(e).css("resize","none"),L()(t.root).css("opacity","75%")}}class ne{constructor(t,e){this.eventBus=t,this.dataManager=e,this.svgDisplay=Xt.createSvgDiv(t)}getLayout(){const t=new Zt(this.eventBus).getContainer(),e=this.generateDownloadControls(),n=new te(this.eventBus,this.dataManager).createContainer();return M.panel([this.svgDisplay,t,e,n],{style:{overflowX:"scroll",padding:"12px 24px"}})}generateDownloadControls(){return M.divH([this.createSavePatternButton(),this.createDownloadPngButton(),this.createShareLinkButton(),this.createInfoButton()],{style:{gap:"12px",marginTop:"12px"}})}createDownloadPngButton(){const t=M.button("Get PNG",(()=>this.eventBus.requestSvgSave()));return M.tooltip.bind(t,"Download pattern as PNG"),t}createInfoButton(){const t=M.button(M.iconFA("info-circle"),(()=>this.openInfoDialog()));return this.eventBus.patternHasUnsavedChanges$.subscribe((e=>{t.disabled=e})),M.tooltip.bind(t,"View pattern metadata"),t}async openInfoDialog(){let t=this.dataManager.getCurrentUserName(),e=this.dataManager.getDefaultPatternName(),n=K,o=K;const i=new URLSearchParams(window.location.search).get("pattern");if(null!==i){const s=await this.dataManager.getPatternRecordByHash(i);if(null!==s){const i=s[G.AUTHOR_ID];if(t=(await r.dapi.users.find(i)).friendlyName,e=s[G.PATTERN_CONFIG][q.PATTERN_NAME],void 0!==s[G.DATE]){const t=s[G.DATE][z.CREATE];void 0!==t&&(n=t);const e=s[G.DATE][z.MODIFY];void 0!==e&&(o=e)}}}const s=M.divV([M.divText(`Pattern Name: ${e}`),M.divText(`Author: ${t}`),M.divText(`Created: ${oe(new Date(n))}`),M.divText(`Modified: ${oe(new Date(o))}`)]);r.shell.info(s)}createShareLinkButton(){const t=M.button(M.iconFA("link"),(()=>navigator.clipboard.writeText(window.location.href).then((()=>r.shell.info("Link to pattern copied to clipboard")))));return this.eventBus.patternHasUnsavedChanges$.subscribe((e=>{t.disabled=e})),M.tooltip.bind(t,"Share pattern link"),t}createSavePatternButton(){const t=M.button("Save",(()=>this.processSaveButtonClick()));return this.eventBus.patternHasUnsavedChanges$.subscribe((e=>{t.disabled=!e})),M.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((()=>{r.shell.info(`Pattern ${t} saved`)})).catch((t=>this.handleErrorWhileSavingPattern(t))):r.shell.warning("Insert pattern name"):r.shell.warning("Cannot save default pattern")}handleErrorWhileSavingPattern(t){t instanceof J?new re(this.eventBus,this.dataManager).show():t instanceof Q?r.shell.warning(M.div([M.divText("Pattern already exists"),M.button("Load",(()=>{const e=t.message;this.eventBus.requestLoadPatternInNewTab(e)}))])):console.error("Error while saving pattern",t)}}class re{constructor(t,e){this.eventBus=t,this.dataManager=e}show(){const t=this.eventBus.getPatternName(),e=M.dialog(`Pattern "${t}" already exists`);e.add(M.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.overwriteExistingPatternInUserStorage(this.eventBus).then((()=>{r.shell.info(`Pattern ${t} overwritten`)})).catch((t=>{console.error("Error while overwriting pattern in user storage",t),r.shell.error("Error while overwriting pattern")}))}}function oe(t){return t.toLocaleString().split(":").slice(0,-1).join(":")}class ie extends F{constructor(t){super("Oligo Pattern"),this.th=t}getContent(){return async function(){const t=await tt.getInstance(),e=new ht,n=await async function(t,e){const n=e.getPatternHash();if(!n)return e.clearPatternURL(),t.getDefaultPatternRecord();let r=await t.getPatternRecordByHash(n);return r||(e.clearPatternURL(),r=t.getDefaultPatternRecord()),r}(t,e),r=new ut(t,n);e.subscribeToObservables(r);const o=new kt(r,t).getLayout(),i=new ne(r,t).getLayout();return M.splitH([o,i],{},!0)}()}}var se=n(8507),ae={};function le(t){var e;return"string"==typeof t||t instanceof String?t:("object"==typeof t||t instanceof Object)&&"$thrownJsError"in t?le(t.$thrownJsError):t instanceof Error?null!==(e=t.stack)&&void 0!==e?e:t.message:t.toString()}ae.styleTagTransform=xt(),ae.setAttributes=vt(),ae.insert=yt().bind(null,"head"),ae.domAPI=mt(),ae.insertStyleElement=Ct(),ft()(se.A,ae),se.A&&se.A.locals&&se.A.locals;var ue,ce=n(2074),he={};he.styleTagTransform=xt(),he.setAttributes=vt(),he.insert=yt().bind(null,"head"),he.domAPI=mt(),he.insertStyleElement=Ct(),ft()(ce.A,he),ce.A&&ce.A.locals&&ce.A.locals;class de{constructor(t,e,n=!0){this.textInputBase=t,this.painter=e,L()(this.root).addClass("st-colored-text-input"),n&&this.textInputBase.onChanged.subscribe((()=>{L()(this.textArea).css("height",0),L()(this.textArea).css("height",this.textArea.scrollHeight+"px")})),this.highlights=M.div([]),this.root.appendChild(this.highlights),this.colorize(),this.textInputBase.onChanged.subscribe((()=>this.colorize()))}get textArea(){return this.textInputBase.root.getElementsByTagName("textarea").item(0)}get inputBase(){return this.textInputBase}get root(){return this.textInputBase.root}colorize(){const t=this.painter(this.textInputBase.value);this.highlights.innerHTML="",t.forEach((t=>this.highlights.appendChild(t)))}}!function(t){t.TYPE="V2000",t[t.NUM_OF_HEADER_LINES=3]="NUM_OF_HEADER_LINES",t[t.NUM_OF_COUNTS_DIGITS=3]="NUM_OF_COUNTS_DIGITS",t[t.ATOM_TYPE_COL=4]="ATOM_TYPE_COL",t[t.FIRST_BONDED_ATOM_COL=1]="FIRST_BONDED_ATOM_COL",t[t.BOND_TYPE_COL=3]="BOND_TYPE_COL",t[t.RGP_SHIFT=8]="RGP_SHIFT",t[t.MAX_ATOM_COUNT=999]="MAX_ATOM_COUNT",t.RGP_LINE_START="M RGP",t.ATOM_ALIAS_LINE_START="A ",t.END="M END"}(ue||(ue={}));class fe{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 o=0;o<this.atomCount;o++){r=this.shiftIdxToXColumn(r);for(const i of[t,e,n])i[o]=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 pe extends fe{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 me extends pe{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(ue.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(ue.ATOM_ALIAS_LINE_START))return e})).filter((t=>void 0!==t)),r=n.map((t=>e[t])),o=n.map((t=>e[t+1]));r.forEach(((e,n)=>{const r=parseInt(e.split(/\s+/)[1])-1,i=parseInt(o[n].substring(1));if(t.has(i))throw new Error(`R group ${i} is already in the map`);t.set(i,r)}));const i=this.getRGroupAtomicIndices().filter((e=>!Array.from(t.values()).includes(e)));if(0!==i.length)throw new Error(`Unaccounted R group indices: ${i}`);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(ue.TYPE)&&-1!==t.indexOf(ue.END)}shiftIdxToAtomType(t){return this.shiftIdxToSpecifiedColumn(t,ue.ATOM_TYPE_COL)}getCountsLineIdx(){let t=0;for(let e=0;e<ue.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,ue.FIRST_BONDED_ATOM_COL)}shiftIdxToBondType(t){return this.shiftIdxToSpecifiedColumn(t,ue.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+ue.NUM_OF_COUNTS_DIGITS;const n=parseInt(this.fileContent.substring(t,e));return t=e,e+=ue.NUM_OF_COUNTS_DIGITS,{atomCount:n,bondCount:parseInt(this.fileContent.substring(t,e))}}}class ge extends pe{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 o=e[1];if(t.has(o))throw new Error(`R group ${o} is already in the map`);t.set(o,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 ye{constructor(){}static getInstance(t){if(ye.isMolfileV2K(t))return new me(t);if(ye.isMolfileV3K(t))return new ge(t);throw new Error("Malformed molfile")}static isMolfileV2K(t){return me.isValidMolfile(t)}static isMolfileV3K(t){return ge.isValidMolfile(t)}}const be=class extends Error{constructor(t){super(t)}};class ve{constructor(t){this.molblock=t}get molblock(){return this._validMolBlock}set molblock(t){if(""!==t){try{this.validateMolBlock(t)}catch(e){e instanceof be&&(t="");const n=le(e);console.error(n)}this._validMolBlock=t}else this._validMolBlock=t}validateMolBlock(t){if(""===t)throw new be("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=le(t);console.error(e)}}getMoleculeDimensions(){const t=ye.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=M.dialog({title:"Molecule",showFooter:!1}),e=.7*L()(window).height(),n=this.getMoleculeDimensions(),r=e/n.height,o=e,i=n.width*r,s=M.canvas(i,o);await this.drawMolBlockOnCanvas(s);const a=M.block([s],{style:{overflowX:"scroll"}});t.add(a).showModal(!0),L()(t.root).find(".d4-dialog-contents").removeClass("ui-form"),L()(t.root).find(".d4-dialog-contents").removeClass("ui-panel"),L()(t.root).find(".d4-dialog-contents").addClass("ui-box"),L()(t.root).find(".d4-dialog-contents").css("padding","0")}async drawMolecule(t,e,n){t.innerHTML="";const r=M.canvas(e*window.devicePixelRatio,n*window.devicePixelRatio);r.style.width=`${e}px`,r.style.height=`${n}px`,r.style.cursor="zoom-in",this.drawMolBlockOnCanvas(r),r.addEventListener("click",(async()=>{await this.zoomIn()})),t.append(M.tooltip.bind(r,"Click to zoom"))}}class we extends Error{constructor(t,e){super(t,e)}}class Ce{constructor(t,e){this.sequence=t,this.codeMap=e}parseSequence(){const t=this.parseRawSequence();return this.addLinkers(t)}addLinkers(t){const e=[];return t.forEach(((n,r)=>{const o=this.getSymbolForCode(n);r>0&&function(t){return Kr.jsonData.monomersWithPhosphate.left.includes(t)}(o)&&e.pop(),e.push(o);const i=Ae(o),s=r===t.length-1,a=r+1<t.length&&Ae(this.getSymbolForCode(t[r+1]));i||function(t){return Kr.jsonData.monomersWithPhosphate.right.includes(t)}(o)||a||s||e.push("p")})),e}getSymbolForCode(t){let e=this.codeMap.get(t);return e??(e=t),e}parseRawSequence(){const t=this.getAllCodesOfFormat(),e=[];let n=0;for(;n<this.sequence.length;){const r=t.find((t=>t===this.sequence.substring(n,n+t.length)));if(void 0===r)throw new we(`Unable to match a monomer for the rest of the sequence '${this.sequence.slice(n)}'.`);e.push(r),n+=r.length}return e}getAllCodesOfFormat(){return g(Array.from(this.codeMap.keys()))}}function Ae(t){return Kr.jsonData.monomersWithPhosphate.phosphate.includes(t)}class xe{constructor(t,e=!1,n){this.invert=e,this.lib=Kr.monomerLibWrapper;const r=this.lib.getCodeToSymbolMap(n);this.parser=new Ce(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),o=e.atomIndex.indexOf(n),i=(e.x[o]+e.x[r])/2,s=(e.y[o]+e.y[r])/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[r];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 u=l;for(let r=0;r<n;r++)l=t.indexOf("V30",l)+4,l=t.indexOf(" ",l)+1,l=t.indexOf(" ",l)+1,u=t.indexOf(" ",l)+1,u=t.indexOf(" ",u),l=(t=t.slice(0,l)+e.x[r]+" "+e.y[r]+t.slice(u)).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 r=n;const o=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,r=t.indexOf(" ",n),o[l]=parseInt(t.substring(n,r)),n=r+1,r=t.indexOf(" ",n),i[l]=t.substring(n,r),n=r+1,r=t.indexOf(" ",n),s[l]=parseFloat(t.substring(n,r)),n=r+1,r=t.indexOf(" ",n),a[l]=parseFloat(t.substring(n,r)),n=t.indexOf("\n",n)+1;return{atomIndex:o,atomType:i,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),o=e.atomIndex.indexOf(n);n>8&&this.fix5Prime(e,r,o);const i=(e.x[o]+e.x[r])/2,s=(e.y[o]+e.y[r])/2;for(let t=0;t<n;t++)e.x[t]-=i,e.y[t]-=s;let a=0;if(0===e.x[r])a=e.y[r]>e.y[o]?Math.PI/2:3*Math.PI/2;else if(0===e.y[r])a=e.x[r]>e.x[o]?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 l=Math.cos(a),u=Math.sin(a);for(let t=0;t<n;t++){const n=e.x[t];e.x[t]=n*l-e.y[t]*u,e.y[t]=n*u+e.y[t]*l}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 d=h;for(let r=0;r<n;r++)h=t.indexOf("V30",h)+4,h=t.indexOf(" ",h)+1,h=t.indexOf(" ",h)+1,d=t.indexOf(" ",h)+1,d=t.indexOf(" ",d),h=(t=t.slice(0,h)+e.x[r]+" "+e.y[r]+t.slice(d)).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="",o="",i="";const s=[];let a=0,l=0,u=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 c=this.extractAtomsBondsNumbersV3000(t[e]),h=this.extractAtomDataV3000(t[e]);let d=t[e].indexOf("M V30 BEGIN ATOM");d=t[e].indexOf("\n",d);let f=d,p=d;for(let r=0;r<c.natom;r++)if(1!==h.atomIndex[r]||0===e){f=t[e].indexOf("V30",f)+4,p=t[e].indexOf(" ",f);let r=0;n?(r=parseInt(t[e].substring(f,p)),1===r?r=i:r===i&&(r=1),r+=a):r=parseInt(t[e].substring(f,p))+a,t[e]=t[e].slice(0,f)+r+t[e].slice(p),f=t[e].indexOf(" ",f)+1,f=t[e].indexOf(" ",f)+1,p=t[e].indexOf(" ",f);const o=u-h.x[0];let s=Math.round(1e4*(parseFloat(t[e].substring(f,p))+o))/1e4;t[e]=t[e].slice(0,f)+s+t[e].slice(p),f=t[e].indexOf(" ",f)+1,p=t[e].indexOf(" ",f),s=Math.round(1e4*parseFloat(t[e].substring(f,p)))/1e4,t[e]=t[e].slice(0,f)+s+t[e].slice(p),f=t[e].indexOf("\n",f)+1}else f=t[e].indexOf("M V30",f)-1,p=t[e].indexOf("\n",f+1),t[e]=t[e].slice(0,f)+t[e].slice(p);const m=t[e].indexOf("M V30 END ATOM");r+=t[e].substring(d+1,m);let g=t[e].indexOf("M V30 BEGIN BOND");g=t[e].indexOf("\n",g),f=g,p=g;for(let r=0;r<c.nbond;r++){f=t[e].indexOf("V30",f)+4,p=t[e].indexOf(" ",f);const r=parseInt(t[e].substring(f,p))+l;t[e]=t[e].slice(0,f)+r+t[e].slice(p),f=t[e].indexOf(" ",f)+1,f=t[e].indexOf(" ",f)+1,p=t[e].indexOf(" ",f);let o=0;n?(o=parseInt(t[e].substring(f,p)),1===o?o=i:o===i&&(o=1),o+=a):o=parseInt(t[e].substring(f,p))+a,t[e]=t[e].slice(0,f)+o+t[e].slice(p),f=t[e].indexOf(" ",f)+1,p=Math.min(t[e].indexOf("\n",f),t[e].indexOf(" ",f)),o=0,n?(o=parseInt(t[e].substring(f,p)),1===o?o=i:o===i&&(o=1),o+=a):o=parseInt(t[e].substring(f,p))+a,t[e]=t[e].slice(0,f)+o+t[e].slice(p),f=t[e].indexOf("\n",f)+1}const y=t[e].indexOf("M V30 END BOND");o+=t[e].substring(g+1,y);let b=t[e].indexOf("M V30 MDLV30/STEABS ATOMS=(");for(;-1!==b;){b+=28;const n=t[e].indexOf(")",b);t[e].substring(b,n).split(" ").slice(1).forEach((t=>{s.push(parseInt(t)+a)})),b=n,b=t[e].indexOf("M V30 MDLV30/STEABS ATOMS=(",b)}a+=c.natom-1,l+=c.nbond,u+=n?Math.max(...h.x):h.x[c.natom-1]-h.x[0]}const c=Math.ceil(s.length/4);i+="M V30 MDLV30/STEABS ATOMS=("+s.length+" -\n";for(let t=0;t<c;t++){i+="M V30 ";const e=t+1===c?s.length-4*(c-1):4;for(let n=0;n<e;n++)i+=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+" "+l+" 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+=o,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 r=e+1,o=t.x[r],i=t.y[r],s=t.x[n]-o,a=t.y[n]-i,l=t.x[e]-o,u=t.y[e]-i,c=l*Math.cos(2*Math.PI/3)-u*Math.sin(2*Math.PI/3),h=l*Math.sin(2*Math.PI/3)+u*Math.cos(2*Math.PI/3),d=l-s,f=u-a,p=c-s,m=h-a;Math.sqrt(m*m+p*p)>=Math.sqrt(f*f+d*d)&&(t.x[e]=c+o,t.y[e]=h+i)}}function Se(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="",o="",i="";const s=[];let a=0,l=0,u=0;if(t.antiStrands.length>0)for(let e=0;e<t.antiStrands.length;e++)t.antiStrands[e]=Te(t.antiStrands[e]);let c=!1;const h=t.senseStrands.concat(t.antiStrands);let d=0;for(let e=0;e<h.length;e++){h[e]=h[e].replaceAll("(-\nM V30 ","(").replaceAll("-\nM V30 ","").replaceAll(" )",")");const n=Ee(h[e]),i=_e(h[e]);if(e>=t.senseStrands.length?!1===c&&(c=!0,u=0):d=Math.min(d,Math.min(...i.y.filter((t=>t<0)))),c){const t=Math.min(...i.x)-u,e=Math.max(...i.y)+5;for(let e=0;e<i.x.length;e++)i.x[e]-=t;for(let t=0;t<i.y.length;t++)i.y[t]-=e-d}let f=h[e].indexOf("M V30 BEGIN ATOM");f=h[e].indexOf("\n",f);let p=f,m=f;for(let t=0;t<n.natom;t++){p=h[e].indexOf("V30",p)+4,m=h[e].indexOf(" ",p);const n=parseInt(h[e].substring(p,m))+a;h[e]=h[e].slice(0,p)+n+h[e].slice(m),p=h[e].indexOf(" ",p)+1,p=h[e].indexOf(" ",p)+1,m=h[e].indexOf(" ",p);let r=Math.round(1e4*i.x[t])/1e4;h[e]=h[e].slice(0,p)+r+h[e].slice(m),p=h[e].indexOf(" ",p)+1,m=h[e].indexOf(" ",p),r=Math.round(1e4*i.y[t])/1e4,h[e]=h[e].slice(0,p)+r+h[e].slice(m),p=h[e].indexOf("\n",p)+1}const g=h[e].indexOf("M V30 END ATOM");r+=h[e].substring(f+1,g);let y=h[e].indexOf("M V30 BEGIN BOND");y=h[e].indexOf("\n",y),p=y,m=y;for(let t=0;t<n.nbond;t++){p=h[e].indexOf("V30",p)+4,m=h[e].indexOf(" ",p);const t=parseInt(h[e].substring(p,m))+l;h[e]=h[e].slice(0,p)+t+h[e].slice(m),p=h[e].indexOf(" ",p)+1,p=h[e].indexOf(" ",p)+1,m=h[e].indexOf(" ",p);let n=parseInt(h[e].substring(p,m))+a;h[e]=h[e].slice(0,p)+n+h[e].slice(m),p=h[e].indexOf(" ",p)+1,m=Math.min(h[e].indexOf("\n",p),h[e].indexOf(" ",p)),n=parseInt(h[e].substring(p,m))+a,h[e]=h[e].slice(0,p)+n+h[e].slice(m),p=h[e].indexOf("\n",p)+1}const b=h[e].indexOf("M V30 END BOND");o+=h[e].substring(y+1,b);let v=h[e].indexOf("M V30 MDLV30/STEABS ATOMS=(");for(;-1!==v;){v+=28;const t=h[e].indexOf(")",v);h[e].substring(v,t).split(" ").slice(1).forEach((t=>{s.push(parseInt(t)+a)})),v=t,v=h[e].indexOf("M V30 MDLV30/STEABS ATOMS=(",v)}a+=n.natom,l+=n.nbond,u+=Math.max(...i.x)+5}const f=Math.ceil(s.length/4);i+="M V30 MDLV30/STEABS ATOMS=("+s.length+" -\n";for(let t=0;t<f;t++){i+="M V30 ";const e=t+1===f?s.length-4*(f-1):4;for(let n=0;n<e;n++)i+=n+1===e?t===f-1?s[4*t+n]+")\n":s[4*t+n]+" -\n":s[4*t+n]+" "}return n+="M V30 COUNTS "+a+" "+l+" 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+=o,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}function Te(t){const e=_e(t),n=e.atomIndex.length,r=(Math.max(...e.x)+Math.min(...e.x))/2,o=(Math.max(...e.y)+Math.min(...e.y))/2;for(let t=0;t<n;t++)e.x[t]-=r,e.y[t]-=o;const i=Math.PI,s=Math.cos(i),a=Math.sin(i);for(let t=0;t<n;t++){const n=e.x[t];e.x[t]=n*s-e.y[t]*a,e.y[t]=n*a+e.y[t]*s}const l=Math.max(...e.y);for(let t=0;t<n;t++)e.x[t]+=r,e.y[t]-=l;let u=t.indexOf("M V30 BEGIN ATOM");u=t.indexOf("\n",u);let c=u;for(let r=0;r<n;r++)u=t.indexOf("V30",u)+4,u=t.indexOf(" ",u)+1,u=t.indexOf(" ",u)+1,c=t.indexOf(" ",u)+1,c=t.indexOf(" ",c),u=(t=t.slice(0,u)+e.x[r]+" "+e.y[r]+t.slice(c)).indexOf("\n",u)+1;return t}function Ee(t){let e=(t=t.replaceAll("\r","")).indexOf("COUNTS")+7,n=t.indexOf(" ",e);const r=parseInt(t.substring(e,n));return e=n+1,n=t.indexOf(" ",e),{natom:r,nbond:parseInt(t.substring(e,n))}}function _e(t){const e=Ee(t);let n=t.indexOf("M V30 BEGIN ATOM");n=t.indexOf("\n",n);let r=n;const o=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,r=t.indexOf(" ",n),o[l]=parseInt(t.substring(n,r)),n=r+1,r=t.indexOf(" ",n),i[l]=t.substring(n,r),n=r+1,r=t.indexOf(" ",n),s[l]=parseFloat(t.substring(n,r)),n=r+1,r=t.indexOf(" ",n),a[l]=parseFloat(t.substring(n,r)),n=t.indexOf("\n",n)+1;return{atomIndex:o,atomType:i,x:s,y:a}}function Ie(t,e,n){if(""===t)return"";const r=n.createFormatDetector(t).getFormat();if(!r)return"";let o="";try{o=new xe(t,e,r).convert()}catch(t){const e=le(t);console.error(e)}return o}function Ne(t,e,n,r,o){const i=[t,e,n].filter((t=>""!==t.strand));return 1===i.length?Ie(i[0].strand,i[0].invert,o):Se({senseStrands:[Ie(t.strand,t.invert,o)],antiStrands:[Ie(e.strand,e.invert,o),Ie(n.strand,n.invert,o)].filter((t=>""!==t))},r)}const Me=["ss","as","as2"];class Oe{constructor(){this.th=Kr,this.onInput=new et.Subject,this.onInvalidInput=new et.Subject,this.inputBase=Object.fromEntries(Me.map((t=>{const e=M.input.textArea(t.toUpperCase(),{value:"",onValueChanged:()=>{this.onInput.next(),L()(e.root.getElementsByTagName("div")).css("padding-left","38px")}});return[t,e]}))),this.useChiralInput=M.input.bool("Use chiral",{value:!0}),this.saveAllStrandsInput=M.input.bool("Save as one entity",{value:!0}),M.tooltip.bind(this.saveAllStrandsInput.root,"Save SDF with all strands in one molfile"),this.directionInversion=Object.fromEntries(Me.map((t=>[t,!1]))),this.moleculeImgDiv=M.block([]),L()(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")}))}async getHtmlDivElement(t){const e=this.getTableInput(t),n=this.getBoolInputsAndButton();await this.updateMoleculeImg();const r=M.divH([n,this.moleculeImgDiv]);L()(r).addClass("st-structure-bottom");const o=M.divV([e,r]);return L()(o).addClass("st-structure-body"),o}getBoolInputsAndButton(){const t=M.buttonsInput([M.bigButton("Save SDF",(()=>{const t=this.getStrandData();!function(t,e,n,o,i,s){const a=[t.strand,e.strand,n.strand].filter((t=>""!==t));if(0===a.length||1===a.length&&""===t.strand)r.shell.warning("Enter SENSE_STRAND and optionally ANTISENSE_STRAND/AS2 to save SDF");else{let l;if(i)l=Ne(t,e,n,o,s)+"\n$$$$\n";else{const h=Ie(t.strand,t.invert,s),d=Ie(e.strand,e.invert,s),f=Ie(n.strand,n.invert,s);l=h+"\n> <Sequence>\nSense Strand\n$$$$\n",d&&(l+=d+"\n> <Sequence>\nAnti Sense\n$$$$\n"),f&&(l+=f+"\n> <Sequence>\nAnti Sense 2\n$$$$\n")}const u=new Date;function c(t){return t>=10?t.toString():"0"+t.toString()}y(`SequenceTranslator-${u.getFullYear()+"-"+c(u.getMonth()+1)+"-"+c(u.getDate())+"_"+c(u.getHours())+"-"+c(u.getMinutes())+"-"+c(u.getSeconds())}.sdf`,encodeURIComponent(l))}}(t.ss,t.as,t.as2,this.useChiralInput.value,this.saveAllStrandsInput.value,this.th)}))]),e=[this.saveAllStrandsInput.root,this.useChiralInput.root,t],n=M.divV(e);for(const t of e)L()(t).addClass("st-structure-bool-button-block");return n}getTableInput(t){const e=Object.fromEntries(Me.map((e=>[e,new de(this.inputBase[e],t.highlightInvalidSubsequence)]))),n=Object.fromEntries(Me.map(((t,e)=>{const n=0===e?"5′ → 3′":"3′ → 5′";return[t,M.input.choice(`${t.toUpperCase()} direction`,{value:n,items:["5′ → 3′","3′ → 5′"]})]})));Me.forEach(((t,e)=>{n[t].onChanged.subscribe((n=>{let r="3′ → 5′"===n;e>0&&(r=!r),this.directionInversion[t]=r,this.onInput.next()}))}));const r=["Sense Strand","Anti Sense","Anti Sense 2"],o=new Map(Me.map(((t,e)=>[t,r[e]]))),i=(Object.fromEntries(Me.map((t=>[t,M.label(o.get(t))]))),Object.fromEntries(Me.map((t=>{const n=M.icons.delete((()=>{e[t].inputBase.value=""})),r=M.button(n,(()=>{}));return M.tooltip.bind(r,`Clear ${t.toUpperCase()}`),[t,n]})))),s=M.form([],"st-structure-inputs"),a=M.divV([],"st-structure-clear-buttons"),l=M.form([],"st-direction-inputs");for(const t of Me)s.append(this.inputBase[t].root),a.append(i[t]),l.append(n[t].root);return M.divH([s,a,l])}getStrandData(){return Object.fromEntries(Me.map((t=>{const e=this.directionInversion[t];return[t,{strand:this.inputBase[t].value.replace(/\s*/g,""),invert:e}]})))}getMolfile(t,e,n){return Ne(t,e,n,this.useChiralInput.value,this.th)}async updateMoleculeImg(){let t="";try{const e=this.getStrandData();Object.values(e).some((t=>""!==t.strand))&&(t=this.getMolfile(e.ss,e.as,e.as2))}catch(t){const e=le(t);console.error(e)}const e=new ve(t);await e.drawMolecule(this.moleculeImgDiv,650,150),L()(this.moleculeImgDiv).find("canvas").css("float","inherit")}}class Le extends F{constructor(t){super("Oligo Structure"),this.th=t,this.layout=new Oe}getContent(){return this.layout.getHtmlDivElement(this.th)}}var Re=n(2003);async function Pe(t){try{const e={overflowX:"scroll"},n=M.div([],{style:e}),o=_e(t),i=.7*L()(window).height(),s=Math.max(...o.x)-Math.min(...o.x),a=Math.max(...o.y)-Math.min(...o.y),l=i/a,u=l*s,c=l*a,h=M.canvas(u*window.devicePixelRatio,c*window.devicePixelRatio);h.style.width=`${u}px`,h.style.height=`${c}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),M.dialog("Molecule").add(n).showModal(!0)}catch(t){const e=le(t);console.error(e)}}class Be{static async view(){const t=Kr.monomerLibWrapper.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 Pe(e)}))}}var De=n(3480),Fe=n(5067),ke=n(5254),He={};He.styleTagTransform=xt(),He.setAttributes=vt(),He.insert=yt().bind(null,"head"),He.domAPI=mt(),He.insertStyleElement=Ct(),ft()(ke.A,He),ke.A&&ke.A.locals&&ke.A.locals;const Ue=["Sequence"];class $e{constructor(t){this.th=t,this.inputFormats=Object.keys(Kr.jsonData.codesToHelmDict).concat(m.NO.HELM),this.seqHelper=Kr.seqHelper,this.onInput=new et.Subject,this.moleculeImgDiv=M.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=M.div([]),this.formatChoiceInput=M.input.choice("",{value:m.NO.HELM,items:this.inputFormats,onValueChanged:async(t,e)=>{this.format=t,this.updateTable(),await this.updateMolImg()}}),L()(this.formatChoiceInput.root.getElementsByTagName("select")[0]).css("width","20%"),this.sequenceInputBase=M.input.textArea("",{value:"Afcgacsu",onValueChanged:()=>{this.onInput.next()}}),this.init(),o.debounce(this.onInput,300).subscribe((async()=>{this.init(),this.formatChoiceInput.value=this.format,this.updateTable(),await this.updateMolImg()})),this.eventBus=Ge.getInstance()}async getHtmlElement(){const t=this.constructSingleSequenceControls(),e=this.constructBulkTranslationControls(),n=M.box(M.panel([t,e,M.block([M.box(this.moleculeImgDiv)])]));return this.formatChoiceInput.value=this.format,this.updateTable(),await this.updateMolImg(),n}constructBulkTranslationControls(){const t=M.h1("Bulk");M.tooltip.bind(t,"Bulk translation from table input");const e=new Ve(this.eventBus).createUIComponents(),n=M.input.choice("Input format",{value:m.NO.AXOLABS,items:this.inputFormats,onValueChanged:t=>this.eventBus.selectInputFormat(t)}),r=M.input.choice("Output format",{value:Fe.qP,items:(0,De.OT)(this.th),onValueChanged:t=>this.eventBus.selectOutputFormat(t)}),o=this.createConvertBulkButton(),i=M.div([...e,n,r,o],"ui-form");return M.block25([t,i])}createConvertBulkButton(){const t=M.bigButton("Convert",(()=>this.processConvertBulkButtonClick()));return M.tooltip.bind(t,"Convert sequences from table input"),L()(t).css({float:"right","margin-top":"20px"}),t}processConvertBulkButtonClick(){const t=this.eventBus.getSelectedTable();if(!t)return void r.shell.warning("No table selected");const e=this.eventBus.getSelectedInputFormat(),n=this.eventBus.getSelectedOutputFormat(),i=this.eventBus.getSelectedColumn("Sequence");if(!i)return void r.shell.warning("No sequence column selected");const s=`${i.name} (${n})`,a=o.Column.fromList(o.TYPE.STRING,s,i.toList().map((t=>(0,De.C6)(t,e,n,this.th))));if(n===Fe.qP||n===m.NO.HELM){a.semType=o.SEMTYPE.MACROMOLECULE;const t=n==Fe.qP?Re.Hi.FASTA:Re.Hi.HELM;a.meta.units=t;const e=this.seqHelper.getSeqHandler(a);(n==Fe.qP?this.seqHelper.setUnitsToFastaColumn:this.seqHelper.setUnitsToHelmColumn)(e)}t.columns.add(a),r.data.detectSemanticTypes(t),r.shell.v=r.shell.getTableView(t.name)}constructSingleSequenceControls(){const t=new de(this.sequenceInputBase,(t=>R(t,this.th))),e=M.button("Get SDF",(()=>{this.saveMolfile()}),"Save structure as SDF"),n=M.button("Copy SMILES",(()=>{this.copySmiles()}),"Copy SMILES for the sequence"),r=M.div([this.formatChoiceInput]),o=M.button(M.icons.delete((()=>{t.inputBase.value=""})),(()=>{}));M.tooltip.bind(o,"Clear input");const i={format:r,textInput:t.root,clearBtn:o},s=M.table([i],(t=>[t.format,t.textInput,t.clearBtn]));s.classList.add("st-translator-input-table");const a=M.block([this.outputTableDiv,e,n]);return M.block75([M.h1("Single sequence"),s,a])}saveMolfile(){const t=new xe(this.sequence,!1,this.formatChoiceInput.value).convert()+"\n$$$$";y(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(Fe.n_)))}updateTable(){this.outputTableDiv.innerHTML="";const t=this.format?this.th.createSequenceValidator(this.sequence).getInvalidCodeIndex(this.format):0,e=(0,De.bD)(this.sequence,t,this.format,this.th),n=[];for(const t of Object.keys(e)){const o="indexOfFirstInvalidChar"in e?M.divH([]):M.link(e[t],(()=>navigator.clipboard.writeText(e[t]).then((()=>r.shell.info(Fe.n_)))),Fe.U_,"");n.push({format:t,sequence:o})}const o=M.table(n,(t=>[t.format,t.sequence]),["FORMAT","SEQUENCE"]);this.outputTableDiv.append(o),this.outputTableDiv.classList.add("st-translator-output-table")}async updateMolImg(){const t=new ve(this.molfile);await t.drawMolecule(this.moleculeImgDiv,500,170)}init(){this.sequence=this.getFormattedSequence(),this.format=this.th.createFormatDetector(this.sequence).getFormat(),this.molfile=this.getMolfile()}getFormattedSequence(){return this.sequenceInputBase.value.replace(/\s/g,"")}getMolfile(){if(!this.format)return"";if(this.format===m.NO.HELM){const t=this.th.createFormatConverter(this.sequence,this.format).convertTo(m.NO.AXOLABS);return new xe(t,!1,m.NO.AXOLABS).convert()}return new xe(this.sequence,!1,this.format).convert()}}class Ve{constructor(t){this.tableInputManager=new je(t),this.columnInputManager=new qe(t)}createUIComponents(){return[this.tableInputManager.getTableInputContainer(),this.columnInputManager.getColumnControlsContainer()]}}class je{constructor(t){this.eventBus=t,this.availableTables=[],this.tableInputContainer=M.div([]),this.subscribeToTableEvents(),this.refreshTableInput()}getTableInputContainer(){return this.tableInputContainer}subscribeToTableEvents(){r.events.onTableAdded.subscribe((t=>this.handleTableAdded(t))),r.events.onTableRemoved.subscribe((t=>this.handleTableRemoved(t))),this.eventBus.tableSelected$.subscribe((()=>this.handleTableChoice()))}getTableFromEventData(t){return t.args.dataFrame}handleTableAdded(t){const e=this.getTableFromEventData(t);this.availableTables.some((t=>t.name===e.name))||(this.availableTables.push(e),this.eventBus.selectTable(e),this.refreshTableInput())}handleTableRemoved(t){const e=this.getTableFromEventData(t);this.availableTables=this.availableTables.filter((t=>t.name!==e.name));const n=this.availableTables[0];this.eventBus.selectTable(n||null),this.refreshTableInput()}refreshTableInput(){const t=this.createTableInput();L()(this.tableInputContainer).empty(),this.tableInputContainer.append(t.root)}createTableInput(){const t=this.eventBus.getSelectedTable();return M.input.table("Table",{value:t,items:this.availableTables,onValueChanged:t=>{null!==t&&this.eventBus.selectTable(t)}})}handleTableChoice(){const t=this.eventBus.getSelectedTable();t&&(this.isTableDisplayed(t)||this.displayTable(t))}isTableDisplayed(t){return r.shell.tableNames.includes(t.name)}displayTable(t){const e=r.shell.v;r.shell.addTableView(t),r.shell.v=e}}class qe{constructor(t){this.eventBus=t,this.columnControlsContainer=M.div([]),this.eventBus.tableSelected$.subscribe((()=>this.handleTableChoice())),this.refreshColumnControls()}getColumnControlsContainer(){return this.columnControlsContainer}handleTableChoice(){this.refreshColumnControls()}refreshColumnControls(){const t=this.createColumnInputs();L()(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 Ue.map((n=>this.createColumnInput(n,e,t)))}createColumnInput(t,e,n){const r=t.toLowerCase(),o=e.find((t=>t.toLowerCase().includes(r)))||e[0];return this.selectColumnIfTableNotNull(n,o,t),M.input.choice(`${t}`,{value:o,items:e,onValueChanged:e=>this.selectColumnIfTableNotNull(n,e,t)})}selectColumnIfTableNotNull(t,e,n){if(null!==t&&e){const r=t.col(e);r&&this.eventBus.selectColumn(n,r)}}}class Ge{constructor(){this._tableSelection$=new et.BehaviorSubject(null),this._columnSelection=Object.fromEntries(Ue.map((t=>[t,new et.BehaviorSubject(null)]))),this._inputFormatSelection$=new et.BehaviorSubject(m.NO.AXOLABS),this._outputFormatSelection$=new et.BehaviorSubject(Fe.qP)}static getInstance(){return void 0===Ge._instance&&(Ge._instance=new Ge),Ge._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 ze extends F{constructor(t){super("Oligo 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t=t.charAt(0).toUpperCase()+t.substring(1).toLowerCase(),`/apps/${Kr.name}/OligoToolkit/${t}`}setUrl(){this.multiView.path=this.getCurrentPanePath()}async constructView(){return this.multiView.tabs.onTabChanged.subscribe((()=>this.setUrl())),this.setUrl(),this.multiView}}var Ke=n(8070);function Je(t){const e=M.input.textArea("",{value:""});return{coloredInput:new de(e,t.highlightInvalidSubsequence),codes:t.jsonData.codesToSymbolsDict}}var Qe=n(9124),Xe=n(9192),Ze=n(8312),tn=n(1991),en=n.n(tn);const nn="object"==typeof performance&&performance&&"function"==typeof performance.now?performance:Date,rn=new Set,on="object"==typeof process&&process?process:{},sn=(t,e,n,r)=>{"function"==typeof on.emitWarning?on.emitWarning(t,e,n,r):console.error(`[${n}] ${e}: ${t}`)};let an=globalThis.AbortController,ln=globalThis.AbortSignal;if(void 0===an){ln=class{onabort;_onabort=[];reason;aborted=!1;addEventListener(t,e){this._onabort.push(e)}},an=class{constructor(){e()}signal=new 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0!==r;if(n.status&&(s&&!o?(n.status.fetchAborted=!0,n.status.fetchError=i.signal.reason,l&&(n.status.fetchAbortIgnored=!0)):n.status.fetchResolved=!0),s&&!l&&!o)return u(i.signal.reason);const h=c;return this.#h[e]===c&&(void 0===r?h.__staleWhileFetching?this.#h[e]=h.__staleWhileFetching:this.#R(t,"fetch"):(n.status&&(n.status.fetchUpdated=!0),this.set(t,r,a.options))),r},u=r=>{const{aborted:o}=i.signal,s=o&&n.allowStaleOnFetchAbort,a=s||n.allowStaleOnFetchRejection,l=a||n.noDeleteOnFetchRejection,u=c;if(this.#h[e]===c&&(l&&void 0!==u.__staleWhileFetching?s||(this.#h[e]=u.__staleWhileFetching):this.#R(t,"fetch")),a)return n.status&&void 0!==u.__staleWhileFetching&&(n.status.returnedStale=!0),u.__staleWhileFetching;if(u.__returned===u)throw r};n.status&&(n.status.fetchDispatched=!0);const c=new Promise(((e,r)=>{const s=this.#i?.(t,o,a);s&&s instanceof Promise&&s.then((t=>e(void 0===t?void 0:t)),r),i.signal.addEventListener("abort",(()=>{n.ignoreFetchAbort&&!n.allowStaleOnFetchAbort||(e(void 0),n.allowStaleOnFetchAbort&&(e=t=>l(t,!0)))}))})).then(l,(t=>(n.status&&(n.status.fetchRejected=!0,n.status.fetchError=t),u(t)))),h=Object.assign(c,{__abortController:i,__staleWhileFetching:o,__returned:void 0});return void 0===e?(this.set(t,h,{...a.options,status:void 0}),e=this.#u.get(t)):this.#h[e]=h,h}#S(t){if(!this.#A)return!1;const e=t;return!!e&&e instanceof Promise&&e.hasOwnProperty("__staleWhileFetching")&&e.__abortController instanceof an}async fetch(t,e={}){const{allowStale:n=this.allowStale,updateAgeOnGet:r=this.updateAgeOnGet,noDeleteOnStaleGet:o=this.noDeleteOnStaleGet,ttl:i=this.ttl,noDisposeOnSet:s=this.noDisposeOnSet,size:a=0,sizeCalculation:l=this.sizeCalculation,noUpdateTTL:u=this.noUpdateTTL,noDeleteOnFetchRejection:c=this.noDeleteOnFetchRejection,allowStaleOnFetchRejection:h=this.allowStaleOnFetchRejection,ignoreFetchAbort:d=this.ignoreFetchAbort,allowStaleOnFetchAbort:f=this.allowStaleOnFetchAbort,context:p,forceRefresh:m=!1,status:g,signal:y}=e;if(!this.#A)return g&&(g.fetch="get"),this.get(t,{allowStale:n,updateAgeOnGet:r,noDeleteOnStaleGet:o,status:g});const b={allowStale:n,updateAgeOnGet:r,noDeleteOnStaleGet:o,ttl:i,noDisposeOnSet:s,size:a,sizeCalculation:l,noUpdateTTL:u,noDeleteOnFetchRejection:c,allowStaleOnFetchRejection:h,allowStaleOnFetchAbort:f,ignoreFetchAbort:d,status:g,signal:y};let v=this.#u.get(t);if(void 0===v){g&&(g.fetch="miss");const e=this.#T(t,v,b,p);return e.__returned=e}{const e=this.#h[v];if(this.#S(e)){const t=n&&void 0!==e.__staleWhileFetching;return g&&(g.fetch="inflight",t&&(g.returnedStale=!0)),t?e.__staleWhileFetching:e.__returned=e}const o=this.#N(v);if(!m&&!o)return g&&(g.fetch="hit"),this.#E(v),r&&this.#P(v),g&&this.#B(g,v),e;const i=this.#T(t,v,b,p),s=void 0!==i.__staleWhileFetching&&n;return g&&(g.fetch=o?"stale":"refresh",s&&o&&(g.returnedStale=!0)),s?i.__staleWhileFetching:i.__returned=i}}async forceFetch(t,e={}){const n=await this.fetch(t,e);if(void 0===n)throw new Error("fetch() returned undefined");return n}memo(t,e={}){const n=this.#s;if(!n)throw new Error("no memoMethod provided to constructor");const{context:r,forceRefresh:o,...i}=e,s=this.get(t,i);if(!o&&void 0!==s)return s;const a=n(t,s,{options:i,context:r});return this.set(t,a,i),a}get(t,e={}){const{allowStale:n=this.allowStale,updateAgeOnGet:r=this.updateAgeOnGet,noDeleteOnStaleGet:o=this.noDeleteOnStaleGet,status:i}=e,s=this.#u.get(t);if(void 0!==s){const e=this.#h[s],a=this.#S(e);return i&&this.#B(i,s),this.#N(s)?(i&&(i.get="stale"),a?(i&&n&&void 0!==e.__staleWhileFetching&&(i.returnedStale=!0),n?e.__staleWhileFetching:void 0):(o||this.#R(t,"expire"),i&&n&&(i.returnedStale=!0),n?e:void 0)):(i&&(i.get="hit"),a?e.__staleWhileFetching:(this.#E(s),r&&this.#P(s),e))}i&&(i.get="miss")}#$(t,e){this.#f[e]=t,this.#d[t]=e}#E(t){t!==this.#m&&(t===this.#p?this.#p=this.#d[t]:this.#$(this.#f[t],this.#d[t]),this.#$(this.#m,t),this.#m=t)}delete(t){return this.#R(t,"delete")}#R(t,e){let n=!1;if(0!==this.#a){const r=this.#u.get(t);if(void 0!==r)if(n=!0,1===this.#a)this.#V(e);else{this.#D(r);const n=this.#h[r];if(this.#S(n)?n.__abortController.abort(new Error("deleted")):(this.#C||this.#x)&&(this.#C&&this.#r?.(n,t,e),this.#x&&this.#y?.push([n,t,e])),this.#u.delete(t),this.#c[r]=void 0,this.#h[r]=void 0,r===this.#m)this.#m=this.#f[r];else if(r===this.#p)this.#p=this.#d[r];else{const t=this.#f[r];this.#d[t]=this.#d[r];const e=this.#d[r];this.#f[e]=this.#f[r]}this.#a--,this.#g.push(r)}}if(this.#x&&this.#y?.length){const t=this.#y;let e;for(;e=t?.shift();)this.#o?.(...e)}return n}clear(){return this.#V("delete")}#V(t){for(const e of this.#I({allowStale:!0})){const n=this.#h[e];if(this.#S(n))n.__abortController.abort(new Error("deleted"));else{const r=this.#c[e];this.#C&&this.#r?.(n,r,t),this.#x&&this.#y?.push([n,r,t])}}if(this.#u.clear(),this.#h.fill(void 0),this.#c.fill(void 0),this.#w&&this.#v&&(this.#w.fill(0),this.#v.fill(0)),this.#b&&this.#b.fill(0),this.#p=0,this.#m=0,this.#g.length=0,this.#l=0,this.#a=0,this.#x&&this.#y){const t=this.#y;let e;for(;e=t?.shift();)this.#o?.(...e)}}}function pn(){var t;return null!==(t=window.$monomerHover)&&void 0!==t?t:null}function mn(t){window.$monomerHover=t}function gn(t,e){let n=t["substruct-providers"];n||(n=t["substruct-providers"]=[]),n.push(e),t["substruct-providers"]=n}var yn=n(6077),bn=n(3561),vn=n(9235);const wn="MonomerHoverLinks";function Cn(t,e){let n=t[wn];n||(n=t[wn]=[]),n.push(e),t[wn]=n}function An(t,e){try{const n=t.tableColumn;if(!n)return;const r=function(t){return t.temp[wn]??[]}(n);for(let n=r.length-1;n>=0;--n){const o=r[n],i=t.grid.col(o.targetCol.name);if(i&&!o.handler(t,e,i))break}}catch(t){console.error(t)}}var xn=n(6717),Sn=n(6694),Tn=n(4229),En=n(5174);function _n(t,e=!0){const[n,o]=(0,Xe.AP)(t);return Kr.logger.error(n,void 0,o),e&&r.shell.error(n),[n,o]}async function In(){return(await(0,l.pj)()).getAvaliableLibraryNames()}const Nn={symbol:"Short Name",name:"Medium Name",smiles:"SMILES"},Mn=[{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"}],On="Get HELM",Ln="Chirality engine",Rn="Highlight monomers",Pn="Poly Tool Conversion",Bn="Poly Tool Enumeration",Dn="Rules used";var Fn=n(5412);async function kn(t){await Kr.initPromise;try{const e=await async function(t){const e=[],n=()=>{for(const t of e)t.unsubscribe()};try{const[i,s]=await Promise.all([In(),(0,Qe.b2)()]),a=t&&t.rowIndex>=0?t.value:"\n\n\n 22 24 0 0 0 0 0 0 0 0999 V2000\n 0.3128 -0.7509 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n 0.3128 0.0740 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n -0.4054 -1.1623 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n -1.1081 -0.7509 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n -0.4054 0.4877 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0\n -1.1081 0.0740 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n -1.8175 -1.1623 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n 1.0222 0.4877 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n -1.8175 0.4877 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n -2.5292 -0.7509 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n 1.0222 1.3127 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n 1.7227 1.7263 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n -0.4054 -1.9896 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0\n -2.5292 0.0740 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n 2.4544 1.3127 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n 1.7406 0.0740 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n 1.0222 -1.1623 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0\n 2.4544 0.4877 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n -1.8175 -1.9896 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0\n -3.2453 0.4877 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0\n 3.1670 1.7285 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0\n 1.7149 2.5513 0.0000 R# 0 0 0 0 0 0 0 0 0 0 0 0\n 2 1 2 0 0 0 0\n 3 1 1 0 0 0 0\n 4 3 1 0 0 0 0\n 5 2 1 0 0 0 0\n 6 5 1 0 0 0 0\n 7 4 1 0 0 0 0\n 8 2 1 0 0 0 0\n 9 6 1 0 0 0 0\n 10 7 2 0 0 0 0\n 11 8 2 0 0 0 0\n 12 11 1 0 0 0 0\n 13 3 2 0 0 0 0\n 14 9 2 0 0 0 0\n 15 18 1 0 0 0 0\n 16 8 1 0 0 0 0\n 17 1 1 0 0 0 0\n 18 16 2 0 0 0 0\n 19 7 1 0 0 0 0\n 20 14 1 0 0 0 0\n 6 4 2 0 0 0 0\n 15 12 2 0 0 0 0\n 14 10 1 0 0 0 0\n 15 21 1 0 0 0 0\n 12 22 1 0 0 0 0\nM RGP 1 22 1\nM END";let u=await(async()=>o.chem.isMolBlock(a)?a:await r.functions.call("Chem:convertMolNotation",{molecule:a,sourceNotation:t?.column.getTag(o.TAGS.UNITS)??o.chem.Notation.Unknown,targetNotation:o.chem.Notation.MolBlock}))();const c=new o.chem.Sketcher(o.chem.SKETCHER_MODE.EXTERNAL);c.syncCurrentObject=!1,c.onChanged.subscribe((t=>{u=c.getMolFile()})),c.root.classList.add("ui-input-editor"),c.root.style.marginTop="3px",c.setMolFile(u);const h=M.input.choice("Library to use",{value:null,items:i});c.root.setAttribute("style","min-width:250px!important;"),c.root.setAttribute("style","max-width:250px!important;"),h.input.setAttribute("style","min-width:250px!important;");const d=M.div([c.root,h.root]);e.push(r.events.onCurrentCellChanged.subscribe((()=>{const t=r.shell.tv.dataFrame.currentCell;t.column.semType===o.SEMTYPE.MOLECULE&&c.setValue(t.value)})));const f=async()=>{try{const t=c.getMolFile();if(void 0===t||""===t)r.shell.warning("PolyTool: no molecule was provided");else if(t.includes("R#")){const e=await async function(t,e){const n=await async function(t){const e=await(0,l.pj)(),n=await e.readSingleLibraryByName(t);return n?n.getMonomerSymbolsByType("PEPTIDE"):(Kr.logger.error(`Monomer library '${t}' not found.`),[])}(e),o=await async function(t){const e=await(0,l.pj)(),n=await e.readSingleLibraryByName(t);if(!n)return Kr.logger.error(`Monomer library '${t}' not found.`),{};const r=n.getMonomerSymbolsByType("PEPTIDE");return new Array(r.length),n.getMonomerMolsByPolymerType("PEPTIDE")}(e),i=new Array(n.length),s=await r.functions.call("Chem:getRdKitModule"),a=s.get_mol(t),u=a.get_smiles();a.delete();const c=new Array(n.length);for(let t=0;t<n.length;t++){const e=o[n[t]],r=s.get_mol(e);c[t]=r.get_smiles(),r.delete()}for(let t=0;t<n.length;t++){let e=null;try{const n=`${`${u}.${c[t]}`.replaceAll("[1*]C","C([1*])").replaceAll("[1*]c","c([1*])").replaceAll("[1*]O","O([1*])").replaceAll("[1*]N","N([1*])")}`.replaceAll("([1*])","9").replaceAll("[1*]","9");e=s.get_mol(n,JSON.stringify({mappedDummiesAreRGroups:!0}));const r=e.get_v3Kmolblock();i[t]=r}catch(e){i[t]=""}finally{e?.delete()}}return i}(t,h.value),n=o.Column.fromStrings("Enumerated",e),i=o.DataFrame.fromColumns([n]);r.shell.addTableView(i)}else r.shell.warning("PolyTool: no R group was provided")}catch(t){_n(t)}},p=M.dialog(Bn).add(d).onOK((()=>{f().finally((()=>{n()}))})).onCancel((()=>{n()}));return e.push(p.onClose.subscribe((()=>{n()}))),p.history((()=>({mol:c.getMolFile(),screenLibrary:h.value})),(t=>{c.setMolFile(t.mol),h.value=t.screenLibrary})),p}catch(t){throw n(),t}}(t);e.show({resizable:!0})}catch(t){r.shell.warning("To run PolyTool Enumeration, sketch the molecule and specify the R group to vary")}}async function Hn(t,e,n,i,s,a){const l=o.TaskBarProgressIndicator.create("PolyTool converting...");try{const l=(t,e)=>t?t.columns.getUnusedName(e):e,u=await(0,Qe.b2)(),c=t.dataFrame,h=await(0,Sn.Q4)(a),[d,f,p]=(0,Tn.b)(t.toList(),h,u),m=l(c,`transformed(${t.name})`),g=o.Column.fromType(o.COLUMN_TYPE.STRING,m,d.length).init((t=>d[t]));g.semType=o.SEMTYPE.MACROMOLECULE,g.meta.units=Re.Hi.HELM,g.setTag(o.TAGS.CELL_RENDERER,"helm"),e&&c&&c.columns.add(g,!0);const y=await(0,xn.j)(),b=await(0,Ze.Q)(),v=await(0,En.A)(h),w=g.temp;w[".mm.cellRenderer.overriddenLibrary"]=v,g.temp=w;const C=await(0,Fn.m)(g,d,f,i,s,n,v,y,b);return C.name=l(c,`molfile(${t.name})`),C.semType=o.SEMTYPE.MOLECULE,c&&(c.columns.add(C,!0),await r.data.detectSemanticTypes(c)),function(t,e,n,r,o,i,s){const a=new fn({max:100});function l(t,e){const n=t.get(e);if(null==n)return null;let s=a.get(n);return s||a.set(n,s=function(t,e){const n=o.getSeqHandler(t),s=n.getSplitted(e),a=n.defaultBiotype,l=en().count(0).take(s.length).map((t=>({position:t,symbol:s.getCanonical(t),biotype:a}))).toArray(),u=n.alphabet,c=u==Re.YI.RNA||u==Re.YI.DNA?"RNA":"PEPTIDE",h=(0,yn.eM)([l],c,u,r,i);return(0,bn.gU)(l,h,u,c).monomers}(t,e)),s}const u={targetCol:n,handler:(t,n,o)=>{if(!t||!o.grid||!e.dataFrame)return!0;const i=o.grid,a=t.tableRowIndex,u=t.gridRow,c=i.cell(o.name,u),h=s[u],d=pn();if(!d||d&&(d.dataFrameId!=e.dataFrame?.id||d.gridRowIdx!=u||d.seqColName!=e.name||d.seqPosition!=n?.position)){if(d&&(mn(null),d.gridCell.render()),!n)return mn(null),!0;mn({gridCell:c,dataFrameId:e.dataFrame.id,gridRowIdx:u,seqColName:e.name,seqPosition:n?n.position:-1,getSubstruct:()=>{if(!n||"*"===n.symbol)return;const t=l(e,a);if(!t)return;const o=[],i=h[n.position];for(const e of i){const n=t.get(e);if(!n)return{atoms:[],bonds:[],highlightAtomColors:[],highlightBondColors:[]};o.push((0,vn.H)([n],r))}return function(t){var e,n,r,o;const i={atoms:[],bonds:[],highlightAtomColors:{},highlightBondColors:{}};for(const s of t)i.atoms=[...null!==(e=i.atoms)&&void 0!==e?e:[],...null!==(n=s.atoms)&&void 0!==n?n:[]],i.bonds=[...null!==(r=i.bonds)&&void 0!==r?r:[],...null!==(o=s.bonds)&&void 0!==o?o:[]],i.highlightAtomColors=Object.assign(Object.assign({},i.highlightAtomColors),s.highlightAtomColors),i.highlightBondColors=Object.assign(Object.assign({},i.highlightBondColors),s.highlightBondColors);return i}(o)}}),c.render()}return!0},getSubstruct:t=>{if("true"!=n.getTag(".sequence-src-highlight-monomers"))return;if(null==t)return;if(!e.get(t))return;const o=l(e,t);return o?(0,vn.H)(o.values(),r):void 0}};Cn(t.temp,u),gn(n.temp,u)}(t,g,C,v,b,y,p),[g,C]}finally{l.close()}}var Un=n(6197);class $n extends o.InputBase{constructor(t,e){super(M.input.column(t,e).dart,e?.onValueChanged),this.options=e}setColumnInputTable(t){M.input.setColumnInputTable(this,t,this.options?.filter)}}M.input.column2=function(t,e){return new $n(t,e)};var Vn=n(1296),jn=n(3820);class qn extends o.JsInputBase{get inputType(){return"Positions"}get dataType(){return o.TYPE.DATA_FRAME}getInput(){return this.gridHost}getValue(){return this.grid.dataFrame}setValue(t){this.setDataFrame(t)}getStringValue(){return this.grid.dataFrame.toCsv()}setStringValue(t){this.setDataFrame(o.DataFrame.fromCsv(t))}clearInput(){const t=o.DataFrame.fromColumns([o.Column.fromType(o.COLUMN_TYPE.STRING,"Remove",0),o.Column.fromType(o.COLUMN_TYPE.INT,"Position",0),o.Column.fromType(o.COLUMN_TYPE.STRING,"Monomers",0)]);this.setDataFrame(t)}get placeholdersValue(){return function(t){const e=[];for(let n=0;n<t.rowCount;n++){if(t.getCol("Position").isNone(n))continue;const r=parseInt(t.get("Position",n))-1;if(!isNaN(r)){const o=Gn(t.get("Monomers",n));e.push({position:r,monomers:o})}}return e}(this.grid.dataFrame)}constructor(t,e,n){super(),this.name=t,this.subs=[],this.dataFrameSubs=[],this.caption=t??"",this.root.classList.add("ui-input-polytool-pos-grid"),this.root.append(this.gridHost=M.div([],{classes:"ui-input-editor",style:{width:"100%",height:"100%",marginTop:"-8px",marginBottom:"8px",paddingBottom:"4px"}})),this.render(e,n).then((()=>{}))}detach(){for(const t of this.subs)t.unsubscribe();for(const t of this.dataFrameSubs)t.unsubscribe()}async render(t,e){let n;const r=o.DataFrame.fromColumns([n=o.Column.fromType(o.COLUMN_TYPE.STRING,"Remove",0),o.Column.fromType(o.COLUMN_TYPE.INT,"Position",0),o.Column.fromType(o.COLUMN_TYPE.STRING,"Monomers",0)]);n.setTag(o.TAGS.FRIENDLY_NAME,""),this.grid=await r.plot.fromType(o.VIEWER.GRID,e),this.grid.sort(["Position"]),this.grid.columns.byIndex(1).width=this.grid.props.rowHeight+2,this.grid.onCellRender.subscribe((t=>{const e=t.cell;e.tableColumn?.name==n.name&&(e?.tableRowIndex??-1)>=0&&(e.element=M.div(M.icons.delete((()=>{this.grid.dataFrame.rows.removeAt(e.tableRowIndex)}),"Delete"),{style:{height:`${e.grid.props.rowHeight}px`,color:"var(--grey-6)",display:"flex",flexDirection:"row",justifyContent:"center"}}))})),this.updateGridHeight(t??this.grid.dataFrame.rowCount+.7),this.subs.push(M.onSizeChanged(this.grid.root).subscribe(this.gridRootOnSizeChanged.bind(this))),this.subs.push((0,et.fromEvent)(this.grid.root,"keydown").subscribe((t=>{"Enter"===t.key&&t.stopPropagation()}))),this.setDataFrame(r),this.grid.root.style.width="100%",this.gridHost.append(this.grid.root)}setDataFrame(t){for(const t of this.dataFrameSubs)t.unsubscribe();this.grid.dataFrame=t,this.dataFrameSubs.push(this.grid.dataFrame.onRowsRemoved.subscribe((()=>{this.updateGridHeight(this.grid.dataFrame.rowCount+.7),this.fireChanged()}))),this.dataFrameSubs.push(this.grid.dataFrame.onRowsAdded.subscribe((()=>{this.updateGridHeight(this.grid.dataFrame.rowCount+.7)}))),this.dataFrameSubs.push(this.grid.dataFrame.onDataChanged.subscribe((()=>{this.fireChanged()}))),this.updateGridHeight(this.grid.dataFrame.rowCount+.7),this.fireChanged()}addPosition(t,e){const n=this.grid.dataFrame,r=n.columns.byName("Position").toList();let o=r.indexOf(t+1);-1===o&&(o=r.findIndex((t=>isNaN(t))),-1===o&&(o=n.rows.addNew(["",t+1,e??""]).idx),this.grid.cell("Monomers",o)),n.currentCell=n.cell(o,"Monomers")}setMonomersValue(t,e){const n=this.grid.dataFrame;n.rowCount<=t||n.set("Monomers",t,e)}static async create(t,e,n){return new qn(t,n,e)}updateGridHeight(t){const e=this.grid.colHeaderHeight+t*this.grid.props.rowHeight+6+2;this.grid.root.style.height=`${e}px`}gridRootOnSizeChanged(){this.grid.columns.byIndex(3).width=this.grid.root.clientWidth-this.grid.horzScroll.root.offsetWidth-this.grid.columns.byIndex(0).width-this.grid.columns.byIndex(1).width-this.grid.columns.byIndex(2).width-10}}function Gn(t){return t.split(/,(?![^(]*\))/).map((t=>('"'===(t=t.trim()).slice(0,1)&&'"'===t.slice(-1)&&(t=t.slice(1,-1)),"'"===t.slice(0,1)&&"'"===t.slice(-1)&&(t=t.slice(1,-1)),t.trim()))).filter((t=>!!t))}class zn extends o.JsInputBase{get inputType(){return"Breadth"}get dataType(){return o.TYPE.DATA_FRAME}getInput(){return this.gridHost}getValue(){return this.grid.dataFrame}setValue(t){this.setDataFrame(t)}getStringValue(){return this.grid.dataFrame.toCsv()}setStringValue(t){this.setDataFrame(o.DataFrame.fromCsv(t))}get placeholdersBreadthValue(){return function(t){const e=[];for(let n=0;n<t.rowCount;n++){const r=parseInt(t.get("Start",n))-1,o=parseInt(t.get("End",n))-1;if(!isNaN(r)&&!isNaN(o)){const i=Gn(t.get("Monomers",n));e.push({start:r,end:o,monomers:i})}}return e}(this.grid.dataFrame)}constructor(t,e,n){super(),this.name=t,this.subs=[],this.dataFrameSubs=[],this.caption=t??"",this.root.classList.add("ui-input-polytool-pos-grid"),this.root.append(this.gridHost=M.div([],{classes:"ui-input-editor",style:{width:"100%",height:"100%",marginTop:"-8px",marginBottom:"8px",paddingBottom:"4px"}})),this.render(e,n).then((()=>{}))}detach(){for(const t of this.subs)t.unsubscribe();for(const t of this.dataFrameSubs)t.unsubscribe()}clearInput(){const t=o.DataFrame.fromColumns([o.Column.fromType(o.COLUMN_TYPE.STRING,"Remove",0),o.Column.fromType(o.COLUMN_TYPE.INT,"Start",0),o.Column.fromType(o.COLUMN_TYPE.INT,"End",0),o.Column.fromType(o.COLUMN_TYPE.STRING,"Monomers",0)]);this.setDataFrame(t)}async render(t,e){let n;const r=o.DataFrame.fromColumns([n=o.Column.fromType(o.COLUMN_TYPE.STRING,"Remove",0),o.Column.fromType(o.COLUMN_TYPE.INT,"Start",0),o.Column.fromType(o.COLUMN_TYPE.INT,"End",0),o.Column.fromType(o.COLUMN_TYPE.STRING,"Monomers",0)]);n.setTag(o.TAGS.FRIENDLY_NAME,""),this.grid=await r.plot.fromType(o.VIEWER.GRID,e),this.grid.sort(["Start","End"]),this.grid.columns.byIndex(1).width=this.grid.props.rowHeight+2,this.grid.onCellRender.subscribe((t=>{const e=t.cell;e.tableColumn?.name==n.name&&(e?.tableRowIndex??-1)>=0&&(e.element=M.div(M.icons.delete((()=>{this.grid.dataFrame.rows.removeAt(e.tableRowIndex)}),"Delete"),{style:{height:`${e.grid.props.rowHeight}px`,color:"var(--grey-6)",display:"flex",flexDirection:"row",justifyContent:"center"}}))})),this.updateGridHeight(t??this.grid.dataFrame.rowCount+.7),this.subs.push(M.onSizeChanged(this.grid.root).subscribe(this.gridRootOnSizeChanged.bind(this))),this.subs.push((0,et.fromEvent)(this.grid.root,"keydown").subscribe((t=>{"Enter"===t.key&&t.stopPropagation()}))),this.setDataFrame(r),this.grid.root.style.width="100%",this.gridHost.append(this.grid.root)}setDataFrame(t){for(const t of this.dataFrameSubs)t.unsubscribe();this.grid.dataFrame=t,this.dataFrameSubs.push(this.grid.dataFrame.onRowsRemoved.subscribe((()=>{this.updateGridHeight(this.grid.dataFrame.rowCount+.7),this.fireChanged()}))),this.dataFrameSubs.push(this.grid.dataFrame.onRowsAdded.subscribe((()=>{this.updateGridHeight(this.grid.dataFrame.rowCount+.7)}))),this.dataFrameSubs.push(this.grid.dataFrame.onDataChanged.subscribe((()=>{this.fireChanged()}))),this.updateGridHeight(this.grid.dataFrame.rowCount+.7),this.fireChanged()}static async create(t,e,n){return new zn(t,n,e)}updateGridHeight(t){const e=this.grid.colHeaderHeight+t*this.grid.props.rowHeight+6+2;this.grid.root.style.height=`${e}px`}gridRootOnSizeChanged(){this.grid.columns.byIndex(4).width=this.grid.root.clientWidth-this.grid.horzScroll.root.offsetWidth-this.grid.columns.byIndex(0).width-this.grid.columns.byIndex(1).width-this.grid.columns.byIndex(2).width-this.grid.columns.byIndex(3).width-10}}var Wn=n(6307);async function Yn(t){await Kr.initPromise;const e=window.innerWidth,n=window.innerHeight;try{let i;function s(){if(null==i)return;const t=L()(i.root).find("div.d4-dialog-contents").get(0),e=t.clientHeight,n={0:1},r=Object.values(n).reduce(((t,e)=>t+e),0),o=e-en().count(0).take(t.children.length).filter((t=>!(t in n))).map((e=>t.children[e])).filter((t=>t instanceof HTMLElement)).map((t=>t.offsetHeight)).reduce(((t,e)=>t+e),0)-38;for(const e of en().count(0).take(t.children.length))if(e in n){const i=t.children[e],s=o*n[e]/r;i.style.height=`${s}px`}}i=await async function(t,e){const n="ST: PT: HelmDialog()";let i;const s=[];let a=Vn.aK.Single;const u=()=>{for(const t of s)t.unsubscribe();i.placeholders.detach()};try{const c=await(0,l.pj)(),h=c.getMonomerLib(),d=await(0,Ze.Q)(),f=o.DataFrame.fromColumns([]),[p,m]=await Promise.all([In(),(0,Qe.b2)()]),g=m.buildMonomersFuncsFromLib(h),y=t=>{let e,n;if(t&&t.rowIndex>=0&&t?.column.semType==o.SEMTYPE.MACROMOLECULE)e=d.getSeqHandler(t.column).getValue(t.rowIndex),n=e.tags["polytool-data-role"]??"macromolecule";else{const t=o.Column.fromList(o.COLUMN_TYPE.STRING,"seq",[jn.d]);t.semType=o.SEMTYPE.MACROMOLECULE,o.DataFrame.fromColumns([t]),t.meta.units=Re.Hi.HELM,e=d.getSeqHandler(t).getValue(0),n="macromolecule"}return[e,n]};let b,v,[w,C]=y(t),A=null;const x=M.divText("",{style:{marginLeft:"8px",marginTop:"2px"}}),S=M.divText("",{style:{color:"red"}});i={macromolecule:m.createHelmInput("Macromolecule",{editable:!1,editorOptions:{drawOptions:{monomerNumbering:1,getMonomer:(t,e)=>{const n=t;if("ATOM"!==n.T)return g.getMonomer(t,e);try{if(w.isDna()||w.isRna()){const t=w.getSplittedWithSugarsAndPhosphates().getCanonical(n.bio.continuousId-1);return g.getMonomer(n.bio.type,t)}{const t=w.getSplitted().getCanonical(n.bio.continuousId-1);return g.getMonomer(n.bio.type,t)}}catch(n){return g.getMonomer(t,e)}}}}}),placeholders:await qn.create("Placeholders",{showAddNewRowIcon:!0,showRemoveRowIcon:!0,showRowHeader:!1,showCellTooltip:!1}),enumeratorType:M.input.choice("Enumerator type",{value:a,items:Object.values(Vn.aK)}),placeholdersBreadth:await zn.create("Breadth",{showAddNewRowIcon:!0,showRemoveRowIcon:!0,showRowHeader:!1,showCellTooltip:!1}),keepOriginal:M.input.bool("Keep original",{value:!1}),toAtomicLevel:M.input.bool("To atomic level",{value:!1,onValueChanged:(t,e)=>{_()}}),generateHelm:M.input.bool(On,{value:!0}),chiralityEngine:M.input.bool(Ln,{value:!1}),highlightMonomers:M.input.bool(Rn,{value:!1}),rules:{header:M.inlineText([Dn]),form:await(v=new Sn._v(Sn.MU,Sn.yy,".json",{onValueChanged:t=>{b=t}})).getForm()},trivialNameCol:M.input.column2("Trivial name",{table:t?.dataFrame,filter:e=>e.type===o.COLUMN_TYPE.STRING&&e!=t?.column,onValueChanged:()=>{const e=i.trivialNameCol.value;let n=null;t&&e&&(n={value:e.get(t.rowIndex),colName:e.name}),A=n,x.textContent=A?`Original ID: ${A.value}`:""},nullable:!0}),library:M.input.choice("Monomer Library",{items:p,value:p[0],nullable:!0})},i.library.root.style.setProperty("display","none"),i.trivialNameCol.addOptions(x);let T=null;i.placeholders.addValidator((t=>{const e=[];try{if(i.enumeratorType.value===Vn.aK.Library){setTimeout((()=>{I()}),10);const t=i.placeholders.placeholdersValue;if(t.length>1)return"Only one placeholder is allowed for Library mode";if(1===t.length){if(null==t[0].position)return"Position is required for Library mode";if(t[0].position>i.macromolecule.molValue.atoms.length)return`There is no monomer at position ${t[0].position+1}.`}return null}if("macromolecule"!==C)return null;const t=[];for(const n of i.placeholders.placeholdersValue){const r=n.position;if(null==r)continue;if(r>=i.macromolecule.molValue.atoms.length){e.push(`There is no monomer at position ${r+1}.`);continue}const o=i.macromolecule.molValue.atoms[r];if(o){const e=o.biotype(),r=(0,Un.Y)(e);for(const e of n.monomers){const n=h.getMonomer(r,e);n&&n.lib||t.push({polymerType:r,symbol:e})}}}const n={};for(const e of t){let t=n[e.polymerType];t||(t=n[e.polymerType]=[]),t.push(e.symbol)}const r=Object.entries(n).map((([t,e])=>`${t}: ${e.join(", ")}`)).join("\n");Object.keys(r).length>0&&e.push(`Placeholders contain missed monomers: ${r}`),T=e.length>0?e.join("\n"):null}catch(t){const[e,n]=_n(t,!1);T=e}return setTimeout((()=>{I()}),0),T})),i.library.addValidator((t=>i.enumeratorType.value!==Vn.aK.Library||i.library.value?null:"Monomer Library is required for this enumerator type")),i.library.onChanged.subscribe((()=>{i.enumeratorType.value===Vn.aK.Library&&i.placeholders.setMonomersValue(0,i.library.value??"")})),i.enumeratorType.onChanged.subscribe((t=>{const e=i.enumeratorType.value===Vn.aK.Library;i.library.root.style.setProperty("display",e?"flex":"none");try{if(a!==Vn.aK.Library&&e||a===Vn.aK.Library&&!e){const t=1===i.placeholders.placeholdersValue.length?i.placeholders.placeholdersValue[0].position:null;i.placeholders.clearInput(),i.placeholdersBreadth.clearInput(),e&&null!=t&&i.placeholders.addPosition(t,i.library.value??"")}}catch(t){_n(t,!1)}a=i.enumeratorType.value})),s.push(i.macromolecule.onMouseMove.subscribe((t=>{try{Kr.logger.debug(`${n}, placeholdersInput.onMouseMove()`);const e=t.offsetX,r=t.offsetY,o=i.macromolecule.molValue,s=m.getHoveredAtom(e,r,o,i.macromolecule.root.clientHeight);if(s){const e=s._parent.atoms.indexOf(s),n=i.placeholders.placeholdersValue.find((t=>t.position===e))?.monomers;if(n){const e=M.divText(n.join(", "));i.macromolecule.showTooltip(e,s),t.preventDefault(),t.stopPropagation()}}}catch(t){_n(t,!1)}}))),s.push(i.macromolecule.onClick.subscribe((t=>{try{Kr.logger.debug(`${n}, placeholdersInput.onClick()`);const e=t.offsetX,r=t.offsetY,o=i.macromolecule.molValue,s=m.getHoveredAtom(e,r,o,i.macromolecule.root.clientHeight);if(s){const t=s._parent.atoms.indexOf(s);String(t+1);let e="";i.enumeratorType.value===Vn.aK.Library&&(i.placeholders.clearInput(),e=i.library.value??""),i.placeholders.addPosition(t,e)}}catch(t){_n(t)}}))),s.push(i.placeholders.onChanged.subscribe((()=>{E()}))),s.push(M.onSizeChanged(i.placeholders.root).subscribe((()=>{e&&e()}))),s.push(r.events.onCurrentCellChanged.subscribe((()=>{const t=r.shell.tv.dataFrame.currentCell;t.column.semType===o.SEMTYPE.MACROMOLECULE&&([w,C]=y(),O(w,C,t))}))),i.macromolecule.root.style.setProperty("min-width","250px","important");const E=()=>{const t=new Set(i.placeholders.placeholdersValue.map((t=>t.position))),e=i.macromolecule.molValue;for(let n=0;n<e.atoms.length;n++)e.atoms[n].highlighted=t.has(n);i.macromolecule.redraw()},_=()=>{i.toAtomicLevel.value&&"template"===C?(i.generateHelm.root.style.removeProperty("display"),i.chiralityEngine.root.style.removeProperty("display"),i.highlightMonomers.root.style.removeProperty("display"),i.rules.header.style.removeProperty("display"),i.rules.form.style.removeProperty("display")):(i.generateHelm.root.style.display=i.chiralityEngine.root.style.display=i.highlightMonomers.root.style.display="none",i.rules.header.style.display=i.rules.form.style.display="none"),e&&e()},I=()=>{const t=T,e=S;t?(e.innerText=t,e.style.removeProperty("display")):(e.innerText="",e.style.setProperty("display","none"))},N=t=>{t?(i.trivialNameCol.setColumnInputTable(t),i.trivialNameCol.root.style.removeProperty("display")):(i.trivialNameCol.setColumnInputTable(f),i.trivialNameCol.root.style.setProperty("display","none")),e&&e()},O=(t,e,n)=>{i.macromolecule.value=t;const r=n?.dataFrame;N(r)};O(w,C,t),_();const L=async()=>{try{const t=i.macromolecule.stringValue,e=en().enumerate(i.macromolecule.molValue.atoms).filter((([t,e])=>t.highlighted)).map((([t,e])=>e)).toArray();if(i.enumeratorType.value===Vn.aK.Library){if(0===e.length)return void r.shell.warning("PolyTool: position for enumeration was not selected");if(!i.library.value)return void r.shell.warning("PolyTool: No monomer library was selected")}if(void 0===t||""===t)r.shell.warning("PolyTool: no molecule was provided");else{if(0===Object.keys(i.placeholders.placeholdersValue).length&&0===Object.keys(i.placeholdersBreadth.placeholdersBreadthValue).length)return void r.shell.warning(`${Bn}: placeholders are empty`);await(0,Qe.b2)();const e=i.placeholders.placeholdersValue;let n=i.enumeratorType.value;if(n===Vn.aK.Library){if(1!==e.length)return void r.shell.warning("Only one placeholder is allowed for Library mode");if(!e[0].monomers||!p.includes(e[0].monomers[0]))return void r.shell.warning("Valid Monomer Library is required for this enumerator type");const t=e[0].monomers[0],o=await c.readSingleLibraryByName(t);if(!o)return void r.shell.warning(`Monomer Library '${t}' was not found`);const i=o.getMonomerSymbolsByType("PEPTIDE");e[0].monomers=i,n=Vn.aK.Single}const s={placeholders:e,type:n,breadthPlaceholders:i.placeholdersBreadth.placeholdersBreadthValue,keepOriginal:i.keepOriginal.value},a=i.toAtomicLevel.value,u=await async function(t,e,n,i,s,a){const u=o.TaskBarProgressIndicator.create("PolyTool enumerating...");try{const u=await(0,l.pj)(),c=await(0,xn.j)(),h=u.getMonomerLib(),d=(0,jn.o)(t,n?.value??"",i);let f;switch(e){case"macromolecule":f=o.Column.fromType(o.COLUMN_TYPE.STRING,"Enumerated",d.length).init((t=>d[t][0]));break;case"template":{const t=new Array(d.length);for(let e=0;e<d.length;e++){const n=d[e][0],r=Wn.s.fromHelm(n,a);t[e]=r.getNotation()}f=o.Column.fromList(o.COLUMN_TYPE.STRING,"Enumerated",t),f.semType=o.SEMTYPE.MACROMOLECULE,f.setTag("polytool-data-role","template"),Qr.applyNotationProviderForCyclized(f,"-");break}}const p=o.DataFrame.fromColumns([f]);if(await r.data.detectSemanticTypes(p),"template"==e&&Qr.applyNotationProviderForCyclized(f,"-"),s){let t;if("macromolecule"===e){t=f;const e=await a.seqHelper.helmToAtomicLevel(t,s.chiralityEngine,s.highlightMonomers);p.columns.add(e.molCol,!1);const n=e.molCol;await async function(t,e,n,r,o,i=!1){const s=r.getSeqHandler(t),a=s.alphabet==Re.YI.RNA||s.alphabet==Re.YI.DNA,l=s.isHelm()&&a,u=!s.isHelm()&&a,c=t=>null==t?null:l?i?t:Math.floor(t/3):u&&i?3*t+1:t,h=i?await r.getHelmToMolfileConverter(n):null,d=new fn({max:100});function f(t,e){const s=t.get(e);if(null==s)return null;let a=d.get(s);return a||d.set(s,a=function(t,e){const s=r.getSeqHandler(t);if(i){const t=s.getHelm(e);return r.helmToAtomicLevelSingle(t,h,!1,!1).monomers}{const t=s.getSplitted(e),r=s.defaultBiotype,i=en().count(0).take(t.length).map((e=>({position:e,symbol:t.getCanonical(e),biotype:r}))).toArray(),a=s.alphabet,l=a==Re.YI.RNA||a==Re.YI.DNA?"RNA":"PEPTIDE",u=(0,yn.eM)([i],l,a,n,o);return(0,bn.gU)(i,u,a,l).monomers}}(t,e)),a}const p={targetCol:e,handler:(e,r,o)=>{const i=o.grid,s=e.tableRowIndex,a=e.gridRow,l=i.cell(o.name,a),u=pn();if(!u||u&&(u.dataFrameId!=t.dataFrame.id||u.gridRowIdx!=a||u.seqColName!=t.name||u.seqPosition!=r?.position)){if(u&&(mn(null),u.gridCell.render()),!r)return mn(null),!0;mn({gridCell:l,dataFrameId:t.dataFrame.id,gridRowIdx:a,seqColName:t.name,seqPosition:c(r?.position)??-1,getSubstruct:()=>{if(!r||"*"===r.symbol)return;const e=f(t,s);if(!e)return;const o=e.get(c(r?.position));return o?(0,vn.H)([o],n):{atoms:[],bonds:[],highlightAtomColors:[],highlightBondColors:[]}}}),l.render()}return!0},getSubstruct:r=>{if("true"!=e.getTag(".sequence-src-highlight-monomers"))return;if(null==r)return;if(!t.get(r))return;const o=f(t,r);return o?(0,vn.H)(o.values(),n):void 0}};return Cn(t.temp,p),gn(e.temp,p),p}(t,n,h,a.seqHelper,c,!0)}else"template"===e&&(t=(await Hn(f,s.generateHelm,!1,s.chiralityEngine,!1,s.rules))[0])}if(n){const t=o.Column.fromType(o.COLUMN_TYPE.STRING,n.colName,d.length).init((t=>d[t][1]));p.columns.add(t)}return p}finally{u.close()}}(t,C,A,s,!!a&&{generateHelm:i.generateHelm.value,chiralityEngine:i.chiralityEngine.value,highlightMonomers:i.highlightMonomers.value,rules:await v.getActive()},m);r.shell.addTableView(u)}}catch(t){_n(t)}},R=M.dialog({title:Bn,showFooter:!0}).add(i.macromolecule.root).add(M.divH([M.divV([i.placeholders.root,i.enumeratorType.root,i.library.root],{style:{width:"50%"}}),M.divV([i.placeholdersBreadth.root],{style:{width:"50%"}})],{style:{width:"100%"}})).add(M.divH([M.divV([i.trivialNameCol.root,i.keepOriginal.root],{style:{width:"50%"}}),M.divV([M.divH([i.toAtomicLevel.root,i.generateHelm.root]),M.divH([i.chiralityEngine.root,i.highlightMonomers.root]),i.rules.header,i.rules.form],{style:{width:"50%"}})],{style:{width:"100%"}})).add(S).onOK((()=>{L()}));return s.push(R.onClose.subscribe((()=>{u()}))),R.history((()=>({description:`${i.enumeratorType.value} ${i.placeholders.placeholdersValue?.map((t=>(t.position?.toString()??"")+": "+t.monomers?.join(", "))).join("; ")}`,placeholders:i.placeholders.stringValue,enumeratorType:i.enumeratorType.value,placeholdersBreadth:i.placeholdersBreadth.stringValue,trivialNameCol:i.trivialNameCol.stringValue,keepOriginal:i.keepOriginal.value,toAtomicLevel:i.toAtomicLevel.value,generateHelm:i.generateHelm.value,chiralityEngine:i.chiralityEngine.value,highlightMonomers:i.highlightMonomers.value,rules:b,library:i.library.value})),(t=>{i.enumeratorType.value=t.enumeratorType??Vn.aK.Single,i.placeholders.stringValue=t.placeholders,i.placeholdersBreadth.stringValue=t.placeholdersBreadth,i.trivialNameCol.stringValue=t.trivialNameCol,i.keepOriginal.value=t.keepOriginal??!1,i.toAtomicLevel.value=t.toAtomicLevel??!0,i.generateHelm.value=t.generateHelm??!0,i.chiralityEngine.value=t.chiralityEngine??!1,i.highlightMonomers.value=t.highlightMonomers??!1,v.setActive(t.rules),i.library.value=t.library})),R}catch(t){throw u(),t}}(t,s);let a=!0;M.onSizeChanged(i.root).subscribe((()=>{if(a){const t=.7*e,r=.7*n;i.root.style.width=`${Math.min(e,t)}px`,i.root.style.height=`${Math.min(n,r)}px`,i.root.style.left=`${Math.floor((e-i.root.offsetWidth)/2)}px`,i.root.style.top=`${Math.floor((n-i.root.offsetHeight)/2)}px`,a=!1}s()})),s(),Kr.logger.debug("PolyToolEnumerateHelmUI: dialog before show"),i.show({width:Math.max(350,.7*e),resizable:!0}),Kr.logger.debug("PolyToolEnumerateHelmUI: dialog after show")}catch(u){const[c,h]=(0,Xe.AP)(u);Kr.logger.error(c,void 0,h)}}var Kn,Jn=n(3151);class Qn{constructor(t){this.rawLib=t}isValid(){return this.rawLib.every((t=>"object"==typeof t&&Object.values(Nn).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={...Jn.pe};Object.entries(Nn).forEach((([n,r])=>{const o=t[r];e[n]=o}));let n="smiles";const r=t[Nn[n]],o=new Xn(r),i=o.getCappedSmiles();return e[n]=i,n="rgroups",e[n]=Zn.getRGroups(o.getNumberOfRGroups()),n="molfile",e[n]=new tr(o.getSmilesWithRGroups()).getMolfile(),e}}class Xn{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 Zn{constructor(){}static getRGroups(t){return Mn.slice(0,t)}}class tr{constructor(t){this.smilesWithRGroups=t}getMolfile(){let t=o.chem.convert(this.smilesWithRGroups,o.chem.Notation.Smiles,o.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 er{constructor(t,e){this.fileName=t,this.fileContent=e,this.validateFileType();const n=o.DataFrame.fromCsv(this.fileContent),r=this.toJson(n);this.polyToolMonomerLib=new Qn(r),this.validateContent()}async getJson(){return this.polyToolMonomerLib.getJsonMonomerLib()}toJson(t){return Array.from({length:t.rowCount},((e,n)=>t.columns.names().reduce(((e,r)=>(e[r]=t.get(r,n),e)),{})))}validateFileType(){if(!this.fileName.endsWith(".csv"))throw new Error(`File ${this.fileName} is not an CSV file`)}validateContent(){if(!this.polyToolMonomerLib.isValid())throw new Error("Invalid format of CSV monomer lib")}}!function(t){t.table="table",t.seqCol="seqCol",t.generateHelm="generateHelm",t.chiralityEngine="chiralityEngine",t.rules="rules"}(Kn||(Kn={}));class nr{constructor(t){this.call=t,this.ruleInputs=new Sn._v(Sn.MU,Sn.yy,".json")}async initInputs(){const t=t=>this.call.inputParams[t],e=await this.ruleInputs.getForm();this.inputs={table:(()=>{const e=t(Kn.table);return M.input.table(e.property.caption,{value:e.value})})(),seqCol:(()=>{const e=t(Kn.seqCol);return M.input.column(e.property.caption,{value:e.value,table:e.value.dataFrame})})(),generateHelm:M.input.forProperty(t(Kn.generateHelm).property),chiralityEngine:M.input.forProperty(t(Kn.chiralityEngine).property),rules:{header:M.inlineText([Dn]),form:e}}}static async create(t){const e=new nr(t);return await e.initInputs(),e}async getParams(){return{table:this.inputs.table.value,seqCol:this.inputs.seqCol.value,generateHelm:this.inputs.generateHelm.value,chiralityEngine:this.inputs.chiralityEngine.value,rules:await this.ruleInputs.getActive()}}async showDialog(){const t=M.div([this.inputs.table,this.inputs.seqCol,this.inputs.generateHelm,this.inputs.chiralityEngine,this.inputs.rules.header,this.inputs.rules.form],{style:{minWidth:"320px"}});return new Promise(((e,n)=>{M.dialog({title:Pn}).add(t).onOK((async()=>{const t=await this.getParams(),n=(await this.call.func.prepare(t).call(!0)).getOutputParamValue();e(n)})).onCancel((()=>{n(new Error("Cancelled by user"))})).show()}))}widget(){throw new Error("not implemented")}}class rr{onKeyDown(t,e){}onKeyPress(t,e){}onMouseEnter(t,e){}onMouseLeave(t,e){}onMouseDown(t,e){}onMouseUp(t,e){}onMouseMove(t,e){}onClick(t,e){}onDoubleClick(t,e){}}class or extends rr{constructor(t,e,n){super(),this.gridCol=t,this.tableCol=e,this.logger=n,this.subs=[],this.dirty=!0,this.destroyed=!1,this.viewerId=++or.viewerCounter,this.errors=[],this._onRendered=new et.Subject,this.tableCol&&this.tableCol.dataFrame&&(this.subs.push(this.tableCol.dataFrame.onDataChanged.subscribe((()=>{this.dirty=!0}))),this.subs.push(this.tableCol.dataFrame.onColumnsRemoved.subscribe((t=>{try{this.destroyed||!this.tableCol||this.tableCol.dataFrame||this.destroy()}catch(t){this.logger.error(t)}})))),this.tableCol&&this.subs.push(r.events.onTableRemoved.subscribe((t=>{try{const e=t.args.dataFrame;this.tableCol?.dataFrame.id!==e.id||this.destroyed||this.destroy()}catch(t){this.logger.error(t)}}))),this.gridCol&&this.subs.push(r.events.onViewRemoving.subscribe((t=>{try{const e=t.args.view;this.gridCol?.dart&&this.gridCol.grid&&this.gridCol?.grid?.dart&&this.gridCol?.grid?.view?.id===e.id&&!this.destroyed&&this.destroy()}catch(t){this.logger.error(t)}})))}toLog(){return`${this.constructor.name}<${this.viewerId}>`}destroy(){for(const t of this.subs)t.unsubscribe();this.destroyed=!0}invalidateGrid(){this.gridCol&&this.gridCol.dart&&this.gridCol.grid?.invalidate()}reset(){this.dirty=!1}get onRendered(){return this._onRendered}invalidate(t){this.invalidateGrid()}async awaitRendered(t=1e4,e=`${t} timeout`){const n=`${this.toLog()}.awaitRendered()`;if(this.logger.debug(`${n}, start, testEvent before`),await(0,Ke.PE)(this._onRendered,(()=>{}),(()=>{this.invalidate()}),t,`${n}, ${e}`),this.errors.length>0){const t=this.errors[0];throw this.errors=[],t}this.logger.debug(`${n}, end`)}}or.viewerCounter=-1;const ir="rgb(100,100,100)",sr="rgb(0,0,0)",ar=s.zS;var lr,ur,cr;!function(t){t.maxMonomerLength=".mm.cellRenderer.maxMonomerLength"}(lr||(lr={})),function(t){t.applyToBackground=".m.cellRenderer.applyToBackground"}(ur||(ur={})),function(t){t.MSA="MSA",t.classic="classic"}(cr||(cr={}));const hr=new class{constructor(){this.color=ir,this.pivot=0,this.left=!1,this.transparencyRate=0,this.separator="",this.last=!1,this.drawStyle=cr.classic,this.maxWord=[],this.wordIdx=0,this.gridCell=null,this.referenceSequence=null,this.maxLengthOfMonomer=null,this.monomerTextSizeMap={},this.logger=void 0,this.selectedPosition=void 0,this.isMultiLineContext=!1,this.lineNumber=0}};function dr(t,e,n,r,i,s,a){var l,u,c;const h={...hr,...a};if(h.isMultiLineContext){t.textBaseline="middle",t.textAlign="center";let o=e;null!=h.maxLengthOfMonomer&&(o=ar(o,h.maxLengthOfMonomer));const a=Math.max(.1,1-(h.transparencyRate??0));t.globalAlpha=a;const l=t.measureText(o),u=l.fontBoundingBoxAscent+l.fontBoundingBoxDescent,c=r+(s-u)/2+l.fontBoundingBoxAscent;let d=h.color??ir;return d&&d!==ir||(d=sr),t.fillStyle=d,h.selectedPosition===h.wordIdx+1&&(t.save(),t.fillStyle="rgba(60, 177, 115, 0.2)",t.fillRect(n,r,i,s),t.restore(),t.fillStyle=d),t.fillText(o,n+i/2,c),t.globalAlpha=1,t.textBaseline="top",t.textAlign="start",n+i}a.logger?.debug("Bio: printLeftOrCentered(), start"),t.textAlign="start";let d=e.substring(0),f=h.last?"":h.separator;h.drawStyle===cr.MSA&&(f="");let p=!0,m=!0,g="difference";if(null!=h.gridCell&&null!=h.gridCell.cell.column&&(p=h.gridCell.cell.column.temp["color-code"]??!0,m=h.gridCell.cell.column.temp["compare-with-current"]??!0,g=h.gridCell.cell.column.temp["highlight-difference"]??"difference"),h.referenceSequence){const t=h.referenceSequence[h.wordIdx];m&&h.referenceSequence.length>0&&"difference"===g&&(h.transparencyRate=d==t?.7:h.transparencyRate),m&&h.referenceSequence.length>0&&"equal"===g&&(h.transparencyRate=d!=t?.7:h.transparencyRate)}null!=h.maxLengthOfMonomer&&(d=ar(d,h.maxLengthOfMonomer));const y=d+f;(l=h.monomerTextSizeMap)[y]??(l[y]=t.measureText(y));let b=h.monomerTextSizeMap[y];(u=h.monomerTextSizeMap)[d]??(u[d]=t.measureText(d));let v=h.monomerTextSizeMap[d].width;const w=s/2-(b.fontBoundingBoxAscent+b.fontBoundingBoxDescent)/2+1;(c=h.monomerTextSizeMap)[f]??(c[f]=t.measureText(f));const C=h.monomerTextSizeMap[f].width;function A(e,i){let a=p?h.color:sr;h.selectedPosition===h.wordIdx+1&&(t.fillStyle="rgba(60, 177, 115, 0.2)",t.fillRect(n+e-4,r-5,h.monomerTextSizeMap[d].width+8,s+10),a=o.Color.toHtml(o.Color.setAlpha(o.Color.fromHtml(a),255))),t.fillStyle=a,t.globalAlpha=1-h.transparencyRate,h.drawStyle===cr.classic&&(t.fillText(d,n+e,r+w),t.fillStyle="#808080",t.fillText(f,n+i,r+w)),h.drawStyle===cr.MSA&&t.fillText(d,n+e,r+w),t.globalAlpha=1}b=b.width,h.drawStyle===cr.MSA&&(v=h.maxWord[h.wordIdx],b=h.maxWord[h.wordIdx]);const x=(h.maxWord[h.wordIdx]??0)-(h.maxWord[0]??0);if(h.left||b>i)return A(x,x+v),n+x+v+C;{const t=(i-b)/2;return A(t,t+v),n+x+t+v}}var fr=n(3599);const pr="rgb(100,100,100)";class mr extends or{get separatorWidth(){return this.props?.fontCharWidth?this.props?.fontCharWidth:5}constructor(t,e,n,r,i){if(super(t,e,n),this.monomerLengthLimit=r,this.propsProvider=i,this.colWidth=0,this._monomerLengthList=null,this._processedMaxVisibleSeqLength=0,this._monomerLengthMap={},this._monomerStructureMap={},this._ellipsisBounds=void 0,this._totalLinesNeeded=0,this._lineHeight=20,this._cellBounds=new Map,this.sysMonomerLib=null,this.padding=5,this._leftThreeDotsPadding=0,this.props=this.propsProvider(),this._processedRows=o.BitSet.create(this.tableCol.length),this.gridCol&&this.subs.push(this.gridCol.grid.onAfterDrawContent.subscribe((()=>{this._onRendered.next()}))),this.tableCol&&this.gridCol){this.subs.push(this.tableCol.dataFrame.onCurrentRowChanged.subscribe((()=>{-1===this.tableCol.dataFrame.currentRowIdx&&(this.tableCol.temp["reference-sequence"]=null,this.tableCol.temp["current-word"]=null,this.invalidateGrid())})));const t=[Re.gp.positionShift,"renderMultiline"];this.subs.push(o.debounce(this.tableCol.dataFrame.onMetadataChanged.pipe(nt.filter((e=>e.args.source===this.tableCol&&t.includes(e.args.key)))),200).subscribe((t=>{this.reset()}))),this.subs.push(o.debounce(this.tableCol.dataFrame.onMetadataChanged.pipe(nt.filter((t=>t.args.source===this.tableCol&&t.args.key===Re.gp.positionShift))),200).subscribe((t=>{this.reset()})))}}calculateFontBasedSpacing(t){const e=t.measureText("M");let n=12;if(this.tableCol?.temp[".mm.cellRenderer.fontSize"]){const t=this.tableCol.temp[".mm.cellRenderer.fontSize"];"number"!=typeof t||isNaN(t)||(n=Math.max(t,1))}return{lineHeight:Math.max(1.4*n,e.fontBoundingBoxAscent+e.fontBoundingBoxDescent+4),monomerSpacing:Math.max(2,.2*this.props.fontCharWidth)}}shouldUseMultilineRendering(t){return"true"===t.getTag("renderMultiline")}calculateMultiLineLayoutDynamic(t,e,n,r,o,i){if(this.dirty)try{this.reset()}catch(t){const[e,n]=(0,Xe.AP)(t);this.logger.error(e,void 0,n)}const{lineHeight:s,monomerSpacing:a}=this.calculateFontBasedSpacing(t),l=e-2*this.padding;let u=0;const c=[];if(r.length>0)for(let e=o;e<r.length;e++){const n=r.getOriginal(e),o=this.props.monomerToShort(n,i);c.push({text:o,posIdx:e}),u=Math.max(u,t.measureText(o).width)}if(0===c.length)return{lineLayouts:[],lineHeight:s};const h=u;let d=Math.floor((l+a)/(h+a));d=Math.max(1,d);const f=n-2*this.padding,p=Math.max(0,Math.floor(f/s)),m=[];let g=0;for(let t=0;t<p&&g<c.length;t++){const e=[];for(let t=0;t<d&&g<c.length;t++){const n=c[g],r=this.padding+t*(h+a);e.push({posIdx:n.posIdx,x:r,width:h,om:n.text,isSeparator:!1}),g++}m.push({lineIdx:t,elements:e})}return{lineLayouts:m,lineHeight:s}}async init(){await Promise.all([(async()=>{this.seqHelper=await(0,Ze.Q)(),this.invalidateGrid()})(),(async()=>{const t=await(0,l.pj)();this.sysMonomerLib=t.getMonomerLib()})()]),this.subs.push(this.sysMonomerLib.onChanged.subscribe((()=>{this.reset()}))),this.reset()}static getFontSettings(t){let e=12;return t&&t.temp[".mm.cellRenderer.fontSize"]&&"number"==typeof t.temp[".mm.cellRenderer.fontSize"]&&!isNaN(t.temp[".mm.cellRenderer.fontSize"])&&(e=Math.max(t.temp[".mm.cellRenderer.fontSize"],1)),{font:`${e}px monospace`,fontWidth:.6*e}}toLog(){return`MonomerPlacer<${this.viewerId}>`}getMonomerLib(){return this.tableCol.temp[".mm.cellRenderer.overriddenLibrary"]??this.sysMonomerLib}reset(){this.propsProvider&&(this.props=this.propsProvider()),this._processedRows=o.BitSet.create(this.tableCol.length),this._monomerLengthList=null,this._monomerLengthMap={},this._monomerStructureMap={},this._cellBounds.clear(),super.reset(),this.invalidateGrid()}invalidateGrid(){this.gridCol&&this.gridCol.dart&&this.gridCol.grid?.invalidate()}getCellMonomerLengths(t,e){const n=this.seqHelper.getSeqHandler(this.tableCol);if(this.colWidth<e&&(this.colWidth=e,this.dirty=!0),this.dirty)try{this.reset()}catch(t){const[e,n]=(0,Xe.AP)(t);this.logger.error(e,void 0,n)}const r=n.isMsa()?this.getCellMonomerLengthsForSeqMsa():this.getCellMonomerLengthsForSeq(t);return[r,this.getSummedMonomerLengths(r)]}getSummedMonomerLengths(t){const e=new Array(t.length+1);e[0]=this.padding;for(let n=1;n<e.length;n++)e[n]=e[n-1]+t[n-1];let n=e[0];for(let t=1;t<e.length;t++)e[t]?n=e[t]:e[t]=n;return e}getCellMonomerLengthsForSeqValue(t,e){const n=this.seqHelper.getSeqHandler(this.tableCol),r=this.props.separatorWidth+1*this.props.fontCharWidth,o=this.positionShift,i=Math.ceil(e/r)+o,s=n.splitter(t),a=Math.min(i,s.length),l=new Array(a-o);let u=0;for(let t=o;t<a;++t){const r=s.getOriginal(t),i=this.props.monomerToShort(r,this.monomerLengthLimit),a=(n.isSeparator()?this.separatorWidth:this.props.separatorWidth)+i.length*this.props.fontCharWidth;if(l[t-o]=a,u+=a,u>e)break}return l}getCellMonomerLengthsForSeq(t){this.toLog(),null===this._monomerLengthList&&(this._monomerLengthList=new Array(this.tableCol.length).fill(null));const e=this.positionShift,n=this.seqHelper.getSeqHandler(this.tableCol),r=this.props.separatorWidth+1*this.props.fontCharWidth,o=Math.ceil(this.colWidth/r)+e,i=n.getSplitted(t),s=Math.min(o,i.length);let a=this._monomerLengthList[t];if(null===a||a.length!=s-e){a=this._monomerLengthList[t]=new Array(i.length);let r=0;for(let t=e;t<s;++t){const o=i.getOriginal(t),s=this.props.monomerToShort(o,this.monomerLengthLimit),l=(n.isSeparator()?this.separatorWidth:this.props.separatorWidth)+s.length*this.props.fontCharWidth;if(a[t-e]=l,r+=l,r>this.colWidth)break}}return a}getCellMonomerLengthsForSeqMsa(){var t;this.toLog(),null===this._monomerLengthList&&(this._monomerLengthList=new Array(1).fill(null)),(t=this._monomerLengthList)[0]??(t[0]=new Array(0));const e=this._monomerLengthList[0],{startIdx:n,endIdx:r}=(()=>{try{const t=this.gridCol&&this.gridCol.dart?this.gridCol.grid:null;return t&&t.dart?{startIdx:Math.max(Math.floor((t?.vertScroll.min??0)-10),0),endIdx:Math.min(Math.ceil((t?.vertScroll.max??0)+10),this.tableCol.length)}:{startIdx:0,endIdx:Math.min(this.tableCol.length,10)}}catch(t){return{startIdx:0,endIdx:Math.min(this.tableCol.length,10)}}})(),o=this.props.separatorWidth+1*this.props.fontCharWidth,i=this.positionShift,s=Math.ceil(this.colWidth/o)+i;for(let t=n;t<r;t++){if(this._processedRows.get(t)&&s<=this._processedMaxVisibleSeqLength)continue;const n=this.seqHelper.getSeqHandler(this.tableCol).getSplitted(t,s),r=Math.min(s,n.length);r-i>e.length&&e.push(...new Array(r-i-e.length).fill(o));let a=0;for(let t=i;t<r;++t){const r=n.getOriginal(t),o=this.props.monomerToShort(r,this.monomerLengthLimit),s=this.props.separatorWidth+o.length*this.props.fontCharWidth;if(e[t-i]=Math.max(e[t-i]??0,s),a+=s,a>=this.colWidth)break}this._processedMaxVisibleSeqLength=Math.max(this._processedMaxVisibleSeqLength,s),this._processedRows.set(t,!0)}return e}getPosition(t,e,n,r){const[o,i]=this.getCellMonomerLengths(t,n);return 0===this.seqHelper.getSeqHandler(this.tableCol).getSplitted(t).length?null:function(t,e,n){if((n??0)>0&&e<(t[0]??0)+n)return-1;e-=n??0;let r,o=100,i=0,s=t.length-1;for(;i<=s;){if(r=Math.floor((s+i)/2),t[r]<=e&&e<t[r+1])return r;if(e<t[r]?s=r-1:i=r+1,--o<=0)throw new Error(`Get position for pointer x = ${e} searching has not converged on ${JSON.stringify(t)}. `)}return null}(i,e,r)}setMonomerLengthLimit(t){this.monomerLengthLimit!=t&&(this.monomerLengthLimit=t,this.dirty=!0)}setSeparatorWidth(t){this.separatorWidth!=t&&(this.props.separatorWidth=t,this.dirty=!0)}get positionShift(){const t=Number.parseInt(this.tableCol?.tags[Re.gp.positionShift]??"0")??0;return isNaN(t)?0:Math.max(t,0)}render(t,e,n,r,i,s,a){const l=s.grid?.dart&&s.grid?.canvas===t.canvas;if(!this.seqHelper)return;const u=this.tableCol,c=this.positionShift;t.save();try{const a=this.seqHelper.getSeqHandler(u);let h=this.monomerLengthLimit;if(lr.maxMonomerLength in u.tags){const t=parseInt(u.getTag(lr.maxMonomerLength));h=!isNaN(t)&&t?t:50}if(".mm.cellRenderer.maxMonomerLength"in u.temp){const t=u.temp[".mm.cellRenderer.maxMonomerLength"],e="number"==typeof t?t:parseInt(t);h=!isNaN(e)&&e?e:50}if("1"===u.temp[".mm.cellRenderer.settingsChanged"]||this.monomerLengthLimit!=h){let t=0;const e=8;t=u.temp[".mm.cellRenderer.gapLength"]??t,this.setMonomerLengthLimit(h),this.setSeparatorWidth(a.isMsa()?e:t),u.temp[".mm.cellRenderer.settingsChanged"]="0",this.dirty=!0}const d=s.cell.rowIndex,f=s.cell.value;l&&(r=function(t,e,n,r,o){return t?Math.max(Math.min(t.canvas.width/o-n,r)):Math.max(e.canvas.width/o-n,0)}(s.grid,t,e,r,window.devicePixelRatio)),t.beginPath(),t.rect(e,n,r,i),t.clip(),t.font=this.props?.font??"12px monospace",t.textBaseline="top";const p=u.meta.units,m=u.getTag(Re.gp.aligned),g=u.getTag(Re.gp.separator)??"",y=l?a.getSplitted(d):a.splitter(f);let b=cr.classic;m?.includes("MSA")&&p===Re.Hi.SEPARATOR&&(b=cr.MSA);const v=u.temp["reference-sequence"],w=this.tableCol.temp["current-word"],C=(()=>{const t=(0,a.splitter)(null!=v&&""!==v?v:w??"");return en().count(0).take(t.length).slice(c).map((e=>t.getCanonical(e))).toArray()})(),A=Number.parseInt(u.getTag(Re.gp.selectedPosition)??"-200");if(this.shouldUseMultilineRendering(u)){const l=[],d=this.calculateMultiLineLayoutDynamic(t,r,i,y,c,h);let f=n+this.padding;1===d.lineLayouts.length&&(f=n+(i-d.lineHeight)/2);for(const r of d.lineLayouts){const i=f+r.lineIdx*d.lineHeight;for(const h of r.elements){const f=e+h.x,p=h,m=p.posIdx,g=y.getCanonical(m);let b=pr;const v=this.getMonomerLib();v&&(b=v.getMonomerTextColor(a.defaultBiotype,g));let w=0;if(s.tableRowIndex!==u.dataFrame.currentRowIdx&&C.length>0){const t=m-c;t>=0&&t<C.length&&g===C[t]&&(w=.7)}l.push({lineIdx:r.lineIdx,monomerIdx:m-c,bounds:new o.Rect(h.x,i-n,h.width,d.lineHeight),sequencePosition:m}),dr(t,p.om,f,i,h.width,d.lineHeight,{color:b,isMultiLineContext:!0,transparencyRate:w,selectedPosition:isNaN(A)||A<1?void 0:A,wordIdx:m})}}null!==s.tableRowIndex&&this._cellBounds.set(s.tableRowIndex,l)}else{this._leftThreeDotsPadding=this.shouldRenderShiftedThreeDots(c)?t.measureText("...").width:0;let[,o]=this.getCellMonomerLengths(s.tableRowIndex,r);l||(o=this.getSummedMonomerLengths(this.getCellMonomerLengthsForSeqValue(f,r)));const u=this.props.separatorWidth+1*this.props.fontCharWidth,d=Math.min(y.length,Math.ceil(r/u)+c);for(let l=c;l<d;++l){const u=l<y.length?y.getOriginal(l):a.defaultGapOriginal,d=l<y.length?y.getCanonical(l):a.defaultGapOriginal;let f=pr;this.getMonomerLib()&&(f=this.getMonomerLib().getMonomerTextColor(a.defaultBiotype,d));const p=l===y.length-1,m={color:f,pivot:0,left:!0,transparencyRate:0,separator:(y?.graphInfo?.disjointSeqStarts?.indexOf(l+1)??0)>0?"|":g,last:p,drawStyle:b,maxWord:o,wordIdx:l-c,gridCell:s,referenceSequence:C,maxLengthOfMonomer:h,monomerTextSizeMap:this._monomerLengthMap,logger:this.logger,selectedPosition:isNaN(A)||A<1?void 0:A-c};dr(t,u,e+this.padding+this._leftThreeDotsPadding,n,r,i,m)}if(this.shouldRenderShiftedThreeDots(c)){const a={color:pr,pivot:0,left:!0,transparencyRate:0,separator:g,last:!1,drawStyle:b,maxWord:o,wordIdx:0,gridCell:s,maxLengthOfMonomer:h,monomerTextSizeMap:this._monomerLengthMap,logger:this.logger};dr(t,"...",e+this.padding,n,r,i,a)}}}catch(t){const[e,n]=(0,Xe.AP)(t);this.logger.error(e,void 0,n),this.errors.push(t)}finally{t.restore()}}shouldRenderShiftedThreeDots(t){return t>0&&(!this.gridCol||!this.gridCol.dart||!this.gridCol.grid||!this.gridCol.grid.dart||(this.gridCol.grid.props.colHeaderHeight??0)<=50)}onMouseMove(t,e){const n=`${this.toLog()}.onMouseMove()`;if(!this.seqHelper||null==t.tableRowIndex)return;const r=this.positionShift,o=t.bounds,i=e.offsetX-t.gridColumn.left+(t.gridColumn.left-o.x),s=e.offsetY-o.y;this.gridCol?.grid?.canvas&&(this.gridCol.grid.canvas.style.cursor="default");let a=null;const l=this._cellBounds.get(t.tableRowIndex);if(l){for(const t of l)if(t.bounds.contains(i,s)){a=t.monomerIdx;break}}else{const e=this.shouldRenderShiftedThreeDots(r)&&(this._leftThreeDotsPadding??0)>0?this._leftThreeDotsPadding:0;a=this.getPosition(t.tableRowIndex,i,o.width,e)}this.logger.debug(`${n}, argsX: ${i}, argsY: ${s}, left: ${a}`);const u=this.seqHelper.getSeqHandler(this.tableCol),c=u.getSplitted(t.tableRowIndex);if(null!==a&&a>=0&&a+r<c.length){const n=u.alphabet??Re.YI.UN,o={position:a,biotype:n===Re.YI.RNA||n===Re.YI.DNA?fr.o.NUCLEOTIDE:fr.o.AA,symbol:c.getCanonical(a+r)},i=[];let s=this._monomerStructureMap[o.symbol];if(!s){const t=this.getMonomerLib();s=this._monomerStructureMap[o.symbol]=t?t.getTooltip(o.biotype,o.symbol):M.divText("Monomer library is not available")}i.push(s),M.tooltip.show(M.divV(i),e.x+16,e.y+16),An(t,o)}else-1===a?M.tooltip.show(M.divText(`${Math.min(r,c.length)} hidden monomers`),e.x+16,e.y+16):M.tooltip.hide(),An(t,null)}}class gr extends mr{constructor(t,e,n,r){super(t,e,Kr.logger,n,(()=>{const t=r.getSeqHandler(e),{font:n,fontWidth:o}=mr.getFontSettings(e);return{seqHandler:t,font:n,fontCharWidth:o,separatorWidth:11,monomerToShort:Re.zS}}))}onMouseMove(t,e){super.onMouseMove(t,e)}}class yr{get defaultGapOriginal(){return""}constructor(t,e){this.separator=t,this.helmHelper=e,this.separatorSplitter=(0,Re.dh)(this.separator),this.splitter=this._splitter.bind(this)}setUnits(){}_splitter(t){const e=this.separatorSplitter(t);return new br(en().count(0).take(e.length).map((t=>e.getOriginal(t))).toArray(),i.b9[i.Hi.SEPARATOR])}getHelm(t,e){return Wn.s.fromSeparator(t,this.helmHelper).getHelm()}createCellRendererBack(t,e){const n=new gr(t,e,4,this.helmHelper.seqHelper);return n.init().then((()=>{})),n}}class br extends s.Mu{getCanonical(t){if(this.isGap(t))return i._S;const e=this.getOriginal(t);let n=e;return e.startsWith("{")?n=e.slice(1):e.endsWith("}")?n=e.slice(0,-1):e.startsWith("(")?n=e.replace(/^\(.\d+\)/,""):e.endsWith(")")&&(n=e.replace(/\(\d+\)$/,"")),n}constructor(t,e){super(t,e)}}async function vr(){return await Qr.oligoToolkitApp()}async function wr(){await Qr.init()}async function Cr(){return await Qr.oligoTranslatorApp()}async function Ar(){return await Qr.oligoPatternApp()}async function xr(){return await Qr.oligoStructureApp()}async function Sr(){return await Qr.getTranslationHelper()}function Tr(){return Qr.getCodeToWeightsMap()}function Er(t){return Qr.validateSequence(t)}function _r(t,e){return Qr.getMolfileFromGcrsSequence(t,e)}function Ir(t){return Qr.linkStrands(t)}async function Nr(){await Qr.demoTranslateSequence()}async function Mr(){await Qr.demoOligoPattern()}async function Or(){await Qr.demoOligoStructure()}async function Lr(t,e,n){return await Qr.translateOligonucleotideSequence(t,e,n)}async function Rr(){await Qr.polyToolConvertTopMenu()}async function Pr(t){return await Qr.getPolyToolConvertEditor(t)}async function Br(t,e,n,r,o){return await Qr.polyToolConvert2(t,e,n,r,o)}async function Dr(){await Qr.polyToolEnumerateHelmTopMenu()}async function Fr(){await Qr.polyToolEnumerateChemTopMenu()}async function kr(t,e){await Qr.polyToolColumnChoice(t,e)}async function Hr(t){await Qr.createMonomerLibraryForPolyTool(t)}async function Ur(){await Qr.ptEnumeratorHelmApp()}async function $r(){await Qr.ptEnumeratorChemApp()}async function Vr(t){await Qr.getPtHelmEnumeratorDialog(t)}async function jr(t){await Qr.getPtChemEnumeratorDialog(t)}async function qr(){await Qr.getPolyToolCombineDialog()}function Gr(t,e){Qr.applyNotationProviderForCyclized(t,e)}var zr=function(t,e,n,r){var o,i=arguments.length,s=i<3?e:null===r?r=Object.getOwnPropertyDescriptor(e,n):r;if("object"==typeof Reflect&&"function"==typeof Reflect.decorate)s=Reflect.decorate(t,e,n,r);else for(var a=t.length-1;a>=0;a--)(o=t[a])&&(s=(i<3?o(s):i>3?o(e,n,s):o(e,n))||s);return i>3&&s&&Object.defineProperty(e,n,s),s},Wr=function(t,e){if("object"==typeof Reflect&&"function"==typeof Reflect.metadata)return Reflect.metadata(t,e)},Yr=function(t,e){return function(n,r){e(n,r,t)}};r.decorators||(r.decorators={}),["func","init","param","panel","editor","demo","app","appTreeBrowser","fileHandler","fileExporter","model","viewer","filter","cellRenderer","autostart","dashboard","folderViewer","semTypeDetector","packageSettingsEditor","functionAnalysis","converter","fileViewer","model","treeBrowser","polyfill"].forEach((t=>{r.decorators[t]||(r.decorators[t]=function(t){return function(t,e,n){}})}));const Kr=new P({debug:!0});let Jr=null;class Qr{static async oligoToolkitApp(){await Kr.initLibData();const t=await async function(t){const e={"Mermadesynthesis:merMadeSynthesis":{tabName:"SYNTHESIZE",parameters:Je(t)}},n={};for(const[t,o]of Object.entries(e)){let e;try{e=await r.functions.call(t,o.parameters);const i=new We(o.tabName,e);i.initView(),n[o.tabName]=()=>i.getView()}catch(e){console.warn(`Plugin ${t} not loaded, reason:`,e);continue}}return n}(Kr);if(!t)throw new Error("External app view factories not loaded");const e=new Ye(t,Kr);return await e.getAppView()}static async init(){return null===Jr&&Kr.startInit(Jr=async function(){const[t]=await Promise.all([(0,Qe.b2)()]);Kr.completeInit(t)}()),Jr}static async oligoTranslatorApp(){return await Xr("Oligo Translator")}static async oligoPatternApp(){return await Xr("Oligo Pattern")}static async oligoStructureApp(){return await Xr("Oligo Structure")}static async getTranslationHelper(){return await Kr.initLibData(),Kr}static getCodeToWeightsMap(){const t=Kr.monomerLibWrapper.getCodesToWeightsMap();return Object.fromEntries(t)}static validateSequence(t){const e=Kr.createSequenceValidator(t),n=Kr.createFormatDetector(t).getFormat();return null!==n&&e.isValidSequence(n)}static getMolfileFromGcrsSequence(t,e){return new xe(t,e,"GCRS").convert()}static linkStrands(t){return Se(t,!0)}static async demoTranslateSequence(){await async function(){await b((async()=>{const t=await Qr.oligoTranslatorApp();r.shell.addView(t)}))}()}static async demoOligoPattern(){await async function(){await b((async()=>{const t=await Qr.oligoPatternApp();r.shell.addView(t)}))}()}static async demoOligoStructure(){await async function(){await b((async()=>{const t=await Qr.oligoStructureApp();r.shell.addView(t),["Afcgacsu","Afcgacsu","Afcgacsu"].forEach((async(t,e)=>{await async function(t,e){await(0,Ke.cb)(500);const n=document.querySelectorAll(".st-colored-text-input > textarea")[t];n.value=e;const r=new Event("input");n.dispatchEvent(r)}(e,t)}))}))}()}static async translateOligonucleotideSequence(t,e,n){return await Kr.initLibData(),Kr.createFormatConverter(t,e).convertTo(n)}static async polyToolConvertTopMenu(){await async function(){await Kr.initPromise;let t=null;try{t=await async function(){const t=[],e=()=>{for(const e of t)e.unsubscribe()};try{let n;const i=r.shell.t.columns.bySemTypeAll(o.SEMTYPE.MACROMOLECULE),s=i.filter((t=>Kr.seqHelper.getSeqHandler(t).notation===Re.Hi.CUSTOM));if(!n){if(i.length<1)throw new Error("No dataframe with macromolecule columns open");if(s.length<1){const t=o.Func.find({package:"Bio",name:"toAtomicLevel"})[0];return t?(t.prepare().edit(),null):(r.shell.warning("Polytool requires a macromolecule column with custom notation. \n\nUse Top menu | Bio | Transform | To Atomic Level."),null)}n=i[0]}const a=M.input.column("Column",{table:n.dataFrame,value:n,filter:t=>s.includes(t)}),l=M.input.bool(On,{value:!0});M.tooltip.bind(l.root,"Add HELM column");const u=M.input.bool("Linearize",{value:!0});M.tooltip.bind(u.root,"Make representation linear if possible");const c=M.input.bool(Ln,{value:!0}),h=M.input.bool(Rn,{value:!0});let d;const f=new Sn._v(Sn.MU,Sn.yy,".json",{onValueChanged:t=>{d=t}}),p=M.inlineText([Dn]);M.tooltip.bind(p,"Add or specify rules to use");const m=await f.getForm(),g=M.divV([a,l,u,c,h,p,m]),y=async()=>{try{const t=await f.getActive();await Hn(a.value,l.value,u.value,c.value,h.value,t)}catch(t){_n(t)}},b=M.dialog(Pn).add(g).onOK((()=>{y()}));return t.push(b.onClose.subscribe((()=>{e()}))),b.history((()=>({generateHelm:l.value,chiralityEngine:c.value,rules:d})),(t=>{l.value=t.generateHelm,c.value=t.chiralityEngine,f.setActive(t.rules)})),b}catch(t){throw e(),t}}(),t?.show()}catch(t){const[e,n]=(0,Xe.AP)(t);r.shell.warning("To run PolyTool Conversion, open a dataframe with macromolecules"),Kr.logger.error(e,void 0,n)}}()}static async getPolyToolConvertEditor(t){const e=await nr.create(t);return await e.showDialog()}static async polyToolConvert2(t,e,n,r,o){return(await Hn(e,n,!1,r,!1,o))[0]}static async polyToolEnumerateHelmTopMenu(){await Yn(r.shell.tv?.dataFrame.currentCell)}static async polyToolEnumerateChemTopMenu(){kn()}static async polyToolColumnChoice(t,e){var n;(function(t){t.semType=o.SEMTYPE.MACROMOLECULE,t.setTag("aligned","SEQ"),t.setTag("alphabet",Re.YI.PT)})(n=e),n.meta.units=Re.Hi.SEPARATOR,n.setTag("separator","-"),await r.data.detectSemanticTypes(t)}static async createMonomerLibraryForPolyTool(t){const e=await t.readAsString(),n=new er(t.fileName,e),r=await n.getJson(),i=t.fileName.replace(/\.csv$/,".json"),s=JSON.stringify(r,null,2);o.Utils.download(i,s)}static async ptEnumeratorHelmApp(){await Yn()}static async ptEnumeratorChemApp(){kn()}static async getPtHelmEnumeratorDialog(t){return Yn(t)}static async getPtChemEnumeratorDialog(t){return kn(t)}static async getPolyToolCombineDialog(){!async function(){const t=[],e=M.divV([]),n=i=>{const s=(()=>{const t=M.divH([]),e=M.input.table("Table",{value:void 0,tooltipText:"Table with 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Use numbered R groups in correspondence with the rest of the molecule."}),g=i.input.molecule("Second reactant",{value:r,nullable:!1,tooltipText:"Reactant fragment of second monomer(s). Use numbered R groups in correspondence with the rest of the molecule."}),y=i.input.molecule("Product",{value:s,nullable:!1,tooltipText:"Product fragment of the resulting monomer from the reaction of the two reactants. Use numbered R groups in correspondence with the reactants."}),C=()=>{if(!m||!g||!y)return"Inputs not initialized yet";const t=v(b(o.chem.convert(m.value??"",o.chem.Notation.Unknown,o.chem.Notation.Smiles))),e=v(b(o.chem.convert(g.value??"",o.chem.Notation.Unknown,o.chem.Notation.Smiles))),n=v(b(o.chem.convert(y.value??"",o.chem.Notation.Unknown,o.chem.Notation.Smiles)));return t&&e&&n?-1==t.indexOf("[C:1]")?"First Reactant must contain R1-group":-1==e.indexOf("[C:2]")?"Second Reactant must contain R2-group":-1==n.indexOf("[C:1]")||-1==n.indexOf("[C:2]")?"Product must contain R1- and R2-groups":null:"First/Second Reactants and Product must all be set"};m.addValidator(C),g.addValidator(C),y.addValidator(C);const A=i.dialog(e?"Edit Reaction Rule":"Add Reaction Rule").add(h).add(p).add(d).add(f).add(m).add(g).add(y);A.addButton("Save",(()=>{const n=C();if(null!=n)return void o.shell.warning(n);const r=v(b(o.chem.convert(m.value??"",o.chem.Notation.Unknown,o.chem.Notation.Smiles))),i=v(b(o.chem.convert(g.value??"",o.chem.Notation.Unknown,o.chem.Notation.Smiles))),s=v(b(o.chem.convert(y.value??"",o.chem.Notation.Unknown,o.chem.Notation.Smiles)));t({code:h.value,resultMonomerName:p.value,firstMonomers:d.value.split(",").map((t=>t.trim())).filter((t=>t.length>0)),secondMonomers:f.value.split(",").map((t=>t.trim())).filter((t=>t.length>0)),firstReactantSmiles:r,secondReactantSmiles:i,productSmiles:s,rowIndex:e?.rowIndex}),A.close()})),A.show()}const A="Links",x="Reactions";class S{constructor(t,e){this.v=null,this.substituteReactionGridDataFrame=null,this.rules=t;const n=this.rules.getLinkRulesDf();this.linkRuleDataFrame=n.res,this.addLinkRulesFunc=n.addNewRow;const r=this.rules.getSynthesisRulesDf();this.addSynthRulesFunc=t=>{r.addNewRow(t),this.rules.setSynthesisRules(r.df),this.synthRuleDataFrame=r.df,this.substituteReactionGridDataFrame?.(),this.save()},this.synthRuleDataFrame=r.df,this.fileName=e;const o=this.rules.homodimerCode?this.rules.homodimerCode:"",s=this.rules.heterodimerCode?this.rules.heterodimerCode:"";this.homoDimerInput=i.input.string("Homo dimer",{value:o,onValueChanged:()=>{},nullable:!1}),this.heteroDimerInput=i.input.string("Hetero dimer",{value:s,onValueChanged:()=>{},nullable:!1})}async getAndAddView(){if(this.v)try{const t=Array.from(o.shell.views).find((t=>t.name===this.v.name));if(!t)throw this.v.detach(),this.v.close(),new Error("View is closed, making it null in catch statement");o.shell.v=t}catch(t){this.v=null}return this.v||(this.v=r.View.create(),this.v.name=`Manage Polytool Rules - ${this.fileName}`,this.v.append(await this.getForm()),this.v=o.shell.addView(this.v),o.shell.v=this.v),this.v}static async getInstance(t){if(!this.instances[t]){const e=await tt([t]);this.instances[t]=new S(e,t)}return this.instances[t]}save(){this.rules.homodimerCode=this.homoDimerInput.value,this.rules.heterodimerCode=this.heteroDimerInput.value,this.rules.setLinkRules(this.linkRuleDataFrame),this.rules.setSynthesisRules(this.synthRuleDataFrame);const t={homodimerCode:this.rules.homodimerCode,heterodimerCode:this.rules.heterodimerCode,linkRules:this.rules.linkRules,reactionRules:this.rules.reactionRules},e=JSON.stringify(t,void 0,2);c._package.files.writeAsText(`polytool-rules/${this.fileName}`,e),o.shell.info(`Polytool rules at ${this.fileName} was updated`)}createGridDiv(t,e,n){const r=i.h1(t,"polytool-grid-header");i.tooltip.bind(r,n),r.style.marginTop="10px",r.style.marginRight="10px",e.root.style.height="100%";const o=i.splitV([i.box(r,{style:{maxHeight:"60px"}}),e.root]);return o.style.height="100%",o}async getLinkExamplesGrid(){const t=[];for(let e=0;e<this.rules.linkRules.length;e++){const n=this.rules.linkRules[e].code,[r,o]=et(this.rules.linkRules[e]);for(let e=0;e<r.length;e++){const i=`${r[e]}(${n})-A-A-A-A-${o[e]}(${n})`;t.push(i)}}const e=await(0,h.b2)(),[n,o,i]=(0,d.b)(t,this.rules,e),s=r.Column.fromStrings("Monomers",t),a=r.Column.fromStrings("Helm",n);return c.PackageFunctions.applyNotationProviderForCyclized(s,"-"),s.semType=r.SEMTYPE.MACROMOLECULE,a.semType=r.SEMTYPE.MACROMOLECULE,a.meta.units=f.Hi.HELM,a.setTag(r.TAGS.CELL_RENDERER,"helm"),r.DataFrame.fromColumns([s,a]).plot.grid()}async getReactionExamplesGrid(){const t=[];for(let e=0;e<this.rules.reactionRules.length;e++){const n=this.rules.reactionRules[e].code,[r,o]=et(this.rules.reactionRules[e]);for(let e=0;e<r.length;e++){const i=`${r[e]}(${n})-A-A-A-A-${o[e]}(${n})`;t.push(i)}}const e=await(0,h.b2)(),[n,o,i]=(0,d.b)(t,this.rules,e),s=r.Column.fromStrings("Monomers",t),a=r.Column.fromStrings("Helm",n),l=r.DataFrame.fromColumns([s,a]);s.semType=r.SEMTYPE.MACROMOLECULE;const u=await(0,g.j)(),b=await(0,y.Q)();c.PackageFunctions.applyNotationProviderForCyclized(s,"-"),s.tags[r.TAGS.CELL_RENDERER]="Sequence",a.semType=r.SEMTYPE.MACROMOLECULE,a.meta.units=f.Hi.HELM,a.setTag(r.TAGS.CELL_RENDERER,"helm");const v=await(0,p.A)(this.rules),w=a.temp;w[".mm.cellRenderer.overriddenLibrary"]=v,a.temp=w;const C=await(0,m.m)(a,t,o,!0,!1,!1,v,u,b);return C.name="molfile(sequence)",C.semType=r.SEMTYPE.MOLECULE,l.columns.add(C),l.plot.grid()}async getForm(){const t=this.linkRuleDataFrame.plot.grid({showAddNewRowIcon:!1,allowEdit:!1,rowHeight:60});t.onCellDoubleClick.subscribe((()=>{if(!t.dataFrame||-1==t.dataFrame.currentRowIdx||null==t.dataFrame.currentRowIdx)return;const e=t.dataFrame.currentRowIdx,n={row:e,code:this.linkRuleDataFrame.get("code",e),firstMonomers:this.linkRuleDataFrame.get("firstMonomers",e),secondMonomers:this.linkRuleDataFrame.get("secondMonomers",e),firstLinkingGroup:this.linkRuleDataFrame.get("firstLinkingGroup",e),secondLinkingGroup:this.linkRuleDataFrame.get("secondLinkingGroup",e)};this.getAddNewLinkRuleDialog(n)}));const e=this.createGridDiv("Rules",t,"specification for monomers to link and linking positions"),n=this.createGridDiv("Examples",await this.getLinkExamplesGrid(),"specification for monomers to link and linking positions");e.style.width="50%",n.style.width="50%";const r=i.h1("Monomers","polytool-grid-header");i.tooltip.bind(r,"Click different cobination to see how monomers will link"),this.linkCards=await this.rules.getLinkCards();const o=i.splitV([i.box(r,{style:{maxHeight:"30px"}}),this.linkCards[0].root]);this.linkCards[0].render(),await this.linkCards[0].reset(),this.linkRuleDataFrame.currentRowIdx=0,this.linkRuleDataFrame.onCurrentRowChanged.subscribe((async()=>{const t=this.linkRuleDataFrame.currentRowIdx;-1!==t&&null!=t&&(i.empty(o),o.append(i.splitV([i.box(r,{style:{maxHeight:"30px"}}),this.linkCards[t].root])),this.linkCards[t].render(),await this.linkCards[t].reset())}));const s=i.splitH([e,o],null,!0),a=this.synthRuleDataFrame.plot.grid({showAddNewRowIcon:!1,allowEdit:!1,rowHeight:130});a.onCellDoubleClick.subscribe((()=>{if(!a.dataFrame||-1==a.dataFrame.currentRowIdx||null==a.dataFrame.currentRowIdx)return;const t=a.dataFrame.currentRowIdx;C((t=>this.addSynthRulesFunc(t)),{rowIndex:t,code:this.synthRuleDataFrame.get("code",t),firstMonomers:this.synthRuleDataFrame.get("firstMonomers",t).split(",").map((t=>t.trim())).filter((t=>t)),secondMonomers:this.synthRuleDataFrame.get("secondMonomers",t).split(",").map((t=>t.trim())).filter((t=>t)),resultMonomerName:this.synthRuleDataFrame.get("name",t),firstReactantSmiles:this.synthRuleDataFrame.get("firstReactant",t),secondReactantSmiles:this.synthRuleDataFrame.get("secondReactant",t),productSmiles:this.synthRuleDataFrame.get("product",t)})}));const l=this.createGridDiv("Rules",a),u=await this.getReactionExamplesGrid(),c=this.createGridDiv("Examples",u);this.substituteReactionGridDataFrame=async()=>{const t=await this.getReactionExamplesGrid();u.dataFrame=t.dataFrame},l.style.width="50%",c.style.width="50%";const h=i.divH([l,c]),d=i.divV([this.homoDimerInput,this.heteroDimerInput]),f=i.tabControl({Links:s,Reactions:h,Dimers:d},!1);i.tooltip.bind(f.getPane(A).header,"Specify rules to link monomers based on HELM notation"),i.tooltip.bind(f.getPane(x).header,"Specify rules to perform reactions within monomers"),i.tooltip.bind(f.getPane("Dimers").header,"Specify symbols for homodimeric and heterodimeric codes"),f.root.style.height="100%",f.root.style.width="100%",f.root.classList.add("rules-manager-form-tab-control"),f.header.style.marginBottom="10px";const p=i.divV([f.root]),m=[i.bigButton("Save",(()=>{this.save()})),i.button("Add rule",(()=>{const t=f.currentPane.name;t==A?this.getAddNewLinkRuleDialog():t==x&&C((t=>this.addSynthRulesFunc(t)))})),i.button("Remove rule",(()=>{const e=f.currentPane.name;if(e==A){if(null==this.linkRuleDataFrame||-1==this.linkRuleDataFrame.currentRowIdx||null==this.linkRuleDataFrame.currentRowIdx)return;const e=t.dataFrame.currentRowIdx;i.dialog("Are you sure you want to remove the rule?").add(i.divText("This action is irreversible!")).onOK((()=>{this.linkRuleDataFrame.rows.removeAt(e),this.rules.setLinkRules(this.linkRuleDataFrame),this.save()})).show()}else if(e==x){if(null==this.synthRuleDataFrame||-1==this.synthRuleDataFrame.currentRowIdx||null==this.synthRuleDataFrame.currentRowIdx)return;const t=a.dataFrame.currentRowIdx;i.dialog("Are you sure you want to remove the rule?").add(i.divText("This action is irreversible!")).onOK((()=>{this.synthRuleDataFrame.rows.removeAt(t),this.rules.setSynthesisRules(this.synthRuleDataFrame),this.substituteReactionGridDataFrame?.(),this.save()})).show()}}))];return this.v.setRibbonPanels([m]),p.style.height="100%",p.style.alignItems="center",f.root}getAddNewLinkRuleDialog(t){const e=i.input.int("Code",{nullable:!1,value:t?.code}),n=i.input.string("First monomers",{placeholder:"E.g. C,D,E",value:t?.firstMonomers,tooltipText:"Comma separated list of first monomers applicable for the rule. If left empty, all monomers will be considered",nullable:!0}),r=i.input.string("Second monomers",{placeholder:"E.g. C,D,E",value:t?.secondMonomers,tooltipText:"Comma separated list of second monomers applicable for the rule. If left empty, all monomers will be considered",nullable:!0}),o=t?.firstLinkingGroup?`R${t.firstLinkingGroup}`:"R3",s=t?.secondLinkingGroup?`R${t.secondLinkingGroup}`:"R3",a=i.input.choice("First linking group",{value:o,items:["R1","R2","R3","R4"],tooltipText:"Specifies which R-group of the first monomer will be used for linking",nullable:!1}),l=i.input.choice("Second linking group",{value:s,items:["R1","R2","R3","R4"],tooltipText:"Specifies which R-group of the second monomer will be used for linking",nullable:!1});i.dialog("Add new link rule").add(e).add(n).add(r).add(a).add(l).onOK((async()=>{const o=e.value,i=(n.value??"").split(",").map((t=>t.trim())).filter((t=>t)).join(","),s=(r.value??"").split(",").map((t=>t.trim())).filter((t=>t)).join(","),u=parseInt(a.value.substring(1)),c=parseInt(l.value.substring(1));this.addLinkRulesFunc({code:o,firstMonomers:i??"",secondMonomers:s??"",firstLinkingGroup:u,secondLinkingGroup:c,row:t?.row}),this.rules.setLinkRules(this.linkRuleDataFrame),this.linkCards=await this.rules.getLinkCards(),this.save()})).show()}}S.instances={};var T=n(5072),E=n.n(T),_=n(7825),I=n.n(_),N=n(7659),M=n.n(N),O=n(5056),L=n.n(O),R=n(540),P=n.n(R),B=n(1113),D=n.n(B),F=n(890),k={};k.styleTagTransform=D(),k.setAttributes=L(),k.insert=M().bind(null,"head"),k.domAPI=I(),k.insertStyleElement=P(),E()(F.A,k),F.A&&F.A.locals&&F.A.locals;var H=n(2003);class U{get selected(){return this._selected}set selected(t){this._selected=t,this.root.style.border=t?"2px solid var(--green-2)":"2px solid var(--grey-2)"}constructor(t,e){this.monomer=t,this.monomerSymbol=e,this.root=i.divV([],{classes:"monomer-card-rule-root"}),this._selected=!1}render(){if(i.empty(this.root),this.root.appendChild(i.h2(this.monomerSymbol,{style:{textAlign:"center"}})),this.monomer){const t=this.monomer.smiles&&o.chem.checkSmiles(this.monomer.smiles)?o.chem.drawMolecule(this.monomer.smiles,150,120):o.chem.drawMolecule(this.monomer.molfile??"",150,120);this.root.appendChild(t);const e=i.divH([i.divText("Monomer Name: "),i.divText(this.monomer.name)],{classes:"monomer-card-info-rules"});if(this.root.appendChild(e),i.tooltip.bind(e,this.monomer.name),this.monomer.lib?.source){const t=i.divH([i.divText("Source: "),i.divText(this.monomer.lib.source)],{classes:"monomer-card-info-rules"});this.root.appendChild(t),i.tooltip.bind(t,this.monomer.lib.source)}const n=i.divH([i.divText("Polymer Type: "),i.divText(this.monomer.polymerType)],{classes:"monomer-card-info-rules"});this.root.appendChild(n),i.tooltip.bind(n,this.monomer.polymerType),i.tooltip.bind(this.root,"Select Monomer")}else this.root.appendChild(i.divV([`Monomer ${this.monomerSymbol} not found in libraries`],{style:{textAlign:"center",height:"100%"}}))}}class ${constructor(t,e,n,r,o){this.firstMonomers=t,this.secondMonomers=e,this.code=r,this.rules=o,this.root=i.divH([],{style:{width:"100%",overflow:"hidden",visibility:"visible"},classes:"monomer-cards"});const s=!t?.length,a=!e?.length;s&&(this.firstMonomers=t=["C","D","E","F","G"]),a&&(this.secondMonomers=e=["D","C","E","F","G"]),this.actionable=!0;const l=i.divH([],{style:{overflowX:"auto",width:"100%"}}),u=i.divH([],{style:{overflowX:"auto",width:"100%"}});this.resulting=i.divH([],{style:{overflowX:"auto",width:"100%",minHeight:"150px"}});const c=i.h2("First Monomer"+(s?" (Applied to all monomers, example list shown)":""),{style:{width:"100%"}}),h=i.h2("Second Monomer"+(a?" (Applied to all monomers, example list shown)":""),{style:{width:"100%"}}),d=i.divV([c,l,h,u,this.resulting]);this.cardsFirst=t.map((t=>new U(n.getMonomer("PEPTIDE",t),t))),this.cardsSecond=e.map((t=>new U(n.getMonomer("PEPTIDE",t),t))),this.cardsFirst.forEach((t=>{t.root.onclick=()=>{this.cardsFirst.forEach((t=>t.selected=!1)),t.selected=!0,this.firstCard=t,this.reset()},l.appendChild(t.root)})),this.cardsSecond.forEach((t=>{t.root.onclick=()=>{this.cardsSecond.forEach((t=>t.selected=!1)),t.selected=!0,this.secondCard=t,this.reset()},u.appendChild(t.root)})),this.cardsFirst[0].selected=!0,this.cardsSecond[0].selected=!0,this.firstCard=this.cardsFirst[0],this.secondCard=this.cardsSecond[0],this.root.appendChild(d)}async reset(){if(this.actionable){const t=[`${this.firstCard.monomer?.symbol}(${this.code})-A-A-A-A-${this.secondCard.monomer?.symbol}(${this.code})`],e=await(0,h.b2)(),[n,s,a]=(0,d.b)(t,this.rules,e),l=r.Column.fromType(r.COLUMN_TYPE.STRING,"helm",n.length).init((t=>n[t]));l.semType=r.SEMTYPE.MACROMOLECULE,l.meta.units=H.Hi.HELM,l.setTag(r.TAGS.CELL_RENDERER,"helm");const u=await(0,g.j)(),c=await(0,y.Q)(),f=await(0,p.A)(this.rules),b=l.temp;l.temp=b;const v=(await(0,m.m)(l,n,s,!0,!1,!1,f,u,c)).get(0),w=v&&o.chem.checkSmiles(v)?o.chem.drawMolecule(v,200,200):o.chem.drawMolecule(v??"",200,200);v&&(w.style.cursor="pointer",w.onclick=()=>{const t=window.innerWidth-200,e=window.innerHeight-200,n=o.chem.checkSmiles(v)?o.chem.drawMolecule(v,t,e):o.chem.drawMolecule(v??"",t,e);i.dialog({title:"Molecule"}).add(n).showModal(!0)},i.tooltip.bind(w,"Click to expand"));const C=i.divV([i.h2("Example Result:"),i.h2(t[0])],{style:{width:"200px"}});i.empty(this.resulting),this.resulting.append(i.divH([C,w],{style:{overflowX:"auto",width:"100%",minHeight:"150px"}}))}}render(){this.actionable&&(this.cardsFirst.forEach((t=>t.render())),this.cardsSecond.forEach((t=>t.render())))}}var V=n(4971);const j="System:AppData/SequenceTranslator/polytool-rules/",q="Polytool",G="code",z="firstMonomers",W="secondMonomers",Y="name",K="firstLinkingGroup",J="secondLinkingGroup";class Q extends u{constructor(t,e,n,r){super(t,e,n,r)}createInput(t,e){const n=super.createInput(t,e),o=i.icons.edit((async()=>{const e=await S.getInstance(t);r.Dialog.getOpenDialogs()?.filter((t=>t.root.contains(o))).forEach((t=>t.close())),await e.getAndAddView()}),"Edit rules");return n.addOptions(o),n}async getForm(){const t=await super.getForm();return this.processRulesForm(t),t}async processRulesForm(t){const e=Array.from(t.getElementsByTagName("label")??[]).filter((t=>t.textContent?.endsWith(".json")&&null!=t.parentElement));for(const t of e){const e=t.textContent.trim(),n=t.parentElement.getElementsByTagName("input")[0];i.tooltip.bind(n,i.wait((async()=>{var t;return(t=Q.ruleDescriptions)[e]??(t[e]=(async()=>{try{const t=JSON.parse(await o.dapi.files.readAsText(`${j}/${e}`)),n=i.divV([i.h1(e)]),r=t.linkRules??[];if(r.length>0){n.appendChild(i.h3("Linkage Rules"));const t=i.table(r,(t=>[t.code?.toString()??"",X((t.firstMonomers??[]).join(", ")),X((t.secondMonomers??[]).join(", ")),t.firstLinkingGroup?.toString()??"",t.secondLinkingGroup?.toString()??""]),["Code","M1","M2","L1","L2"]);n.appendChild(t)}const s=t.reactionRules??[];if(s.length>0){n.appendChild(i.h3("Synthesis Rules"));const t=i.table(s,(t=>[t.code?.toString()??"",X((t.firstMonomers??[]).join(", ")),X((t.secondMonomers??[]).join(", ")),X(t.name??""),o.chem.drawMolecule(t.reaction?.split(">>")[1]??"",70,70)]),["Code","M1","M2","Name","Product"]);n.appendChild(t)}return n}catch(t){return c._package.logger.error(`Failed to load rule ${e}: ${t?.toString?.()}`),console.error(t),i.divText(`Failed to load rule ${e}`)}})()),await Q.ruleDescriptions[e]})))}}}function X(t,e=30){return t.length<=e?t:`${t.substring(0,e)}...`}Q.ruleDescriptions={};class Z{constructor(t,e,n,r){this.homodimerCode=t,this.heterodimerCode=e,this.linkRules=n,this.reactionRules=r}set homodimer(t){this.homodimerCode=t}set heterodimer(t){this.heterodimerCode=t}addLinkRules(t){for(let e=0;e<t.length;e++)this.linkRules.push(t[e])}addSynthesisRules(t){for(let e=0;e<t.length;e++)this.reactionRules.push(t[e])}getLinkRulesDf(){const t=this.linkRules.length,e=r.Column.int(G,t);e.setTag("friendlyName","Code");const n=r.Column.string(z,t);n.temp[".mm.cellRenderer.fontSize"]=16,n.setTag("friendlyName","First monomers"),n.semType=r.SEMTYPE.MACROMOLECULE,c.PackageFunctions.applyNotationProviderForCyclized(n,",");const o=r.Column.string(W,t);o.setTag("friendlyName","Second monomers"),o.temp[".mm.cellRenderer.fontSize"]=16,o.semType=r.SEMTYPE.MACROMOLECULE,c.PackageFunctions.applyNotationProviderForCyclized(o,",");const i=r.Column.int(K,t);i.setTag("friendlyName","First group");const s=r.Column.int(J,t);s.setTag("friendlyName","Second group");for(let r=0;r<t;r++)e.set(r,this.linkRules[r].code),n.set(r,this.linkRules[r].firstMonomers.toString()),o.set(r,this.linkRules[r].secondMonomers.toString()),i.set(r,this.linkRules[r].firstLinkingGroup),s.set(r,this.linkRules[r].secondLinkingGroup);const a=r.DataFrame.fromColumns([e,n,o,i,s]);return{res:a,addNewRow:t=>{if(null!=t.row&&t.row<a.rowCount&&t.row>=0)e.set(t.row,t.code),n.set(t.row,t.firstMonomers),o.set(t.row,t.secondMonomers),i.set(t.row,t.firstLinkingGroup),s.set(t.row,t.secondLinkingGroup);else{const{code:e,firstMonomers:n,secondMonomers:r,firstLinkingGroup:o,secondLinkingGroup:i}=t;a.rows.addNew([e,n??"",r??"",o??1,i??2])}}}}async getLinkCards(){const t=this.linkRules.length,e=new Array(t),n=(await(0,V.pj)()).getMonomerLib();for(let r=0;r<t;r++)e[r]=new $(this.linkRules[r].firstMonomers,this.linkRules[r].secondMonomers,n,this.linkRules[r].code,this);return e}getSynthesisRulesDf(){const t=this.reactionRules.length,e=r.Column.int(G,t);e.setTag("friendlyName","Code");const n=r.Column.string(z,t);n.setTag("friendlyName","First monomers");const o=r.Column.string(W,t);o.setTag("friendlyName","Second monomers"),n.semType=r.SEMTYPE.MACROMOLECULE,n.temp[".mm.cellRenderer.fontSize"]=16,c.PackageFunctions.applyNotationProviderForCyclized(n,","),o.semType=r.SEMTYPE.MACROMOLECULE,o.temp[".mm.cellRenderer.fontSize"]=16,c.PackageFunctions.applyNotationProviderForCyclized(o,","),o.setTag(r.TAGS.CELL_RENDERER,"Sequence"),n.setTag(r.TAGS.CELL_RENDERER,"Sequence");const i=r.Column.string(Y,t);i.setTag("friendlyName","Name");const s=r.Column.string("firstReactant",t);s.setTag("friendlyName","First reactant");const a=r.Column.string("secondReactant",t);a.setTag("friendlyName","Second reactant");const l=r.Column.string("product",t);l.setTag("friendlyName","Product");for(let r=0;r<t;r++){e.set(r,this.reactionRules[r].code),n.set(r,this.reactionRules[r].firstMonomers.toString()),o.set(r,this.reactionRules[r].secondMonomers.toString()),i.set(r,this.reactionRules[r].name);const t=this.reactionRules[r].reaction.split(">>"),u=t[0].split(".");s.set(r,u[0]),a.set(r,u[1]),l.set(r,t[1])}s.semType=r.SEMTYPE.MOLECULE,a.semType=r.SEMTYPE.MOLECULE,l.semType=r.SEMTYPE.MOLECULE;const u=r.DataFrame.fromColumns([i,s,a,l,e,n,o]);return{df:u,addNewRow:t=>{if(null!=t.rowIndex&&t.rowIndex<u.rowCount&&t.rowIndex>=0)i.set(t.rowIndex,t.resultMonomerName),e.set(t.rowIndex,t.code),n.set(t.rowIndex,t.firstMonomers.join(",")),o.set(t.rowIndex,t.secondMonomers.join(",")),s.set(t.rowIndex,t.firstReactantSmiles),a.set(t.rowIndex,t.secondReactantSmiles),l.set(t.rowIndex,t.productSmiles);else{const{resultMonomerName:e,code:n,firstMonomers:r,secondMonomers:o,firstReactantSmiles:i,secondReactantSmiles:s,productSmiles:a}=t;u.rows.addNew([e,i,s,a,n,r.join(","),o.join(",")])}}}}setLinkRules(t){const e=t.rowCount,n=new Array(e),r=t.columns.byName(G),o=t.columns.byName(z),i=t.columns.byName(W),s=t.columns.byName(K),a=t.columns.byName(J);for(let t=0;t<e;t++){const e=o.get(t).split(","),l=i.get(t).split(","),u={code:r.get(t),firstMonomers:""!==e[0]?e:[],secondMonomers:""!==l[0]?l:[],firstLinkingGroup:s.get(t),secondLinkingGroup:a.get(t)};n[t]=u}this.linkRules=n}setSynthesisRules(t){const e=t.rowCount,n=new Array(e),r=t.columns.byName(G),o=t.columns.byName(z),i=t.columns.byName(W),s=t.columns.byName(Y),a=t.columns.byName("firstReactant"),l=t.columns.byName("secondReactant"),u=t.columns.byName("product");for(let t=0;t<e;t++){const e=`${a.get(t)}.${l.get(t)}>>${u.get(t)}`,c=o.get(t).split(","),h=i.get(t).split(","),d={code:r.get(t),firstMonomers:""!==c[0]?c:[],secondMonomers:""!==h[0]?h:[],reaction:e,name:s.get(t)};n[t]=d}this.reactionRules=n}}async function tt(t){const e=new r.FileSource(j),n=new Z(null,null,[],[]);for(let r=0;r<t.length;r++){const o=await e.readAsText(t[r].replace(j,"")),i=JSON.parse(o);n.homodimer=i.homodimerCode,n.heterodimer=i.heterodimerCode,n.addLinkRules(i.linkRules),n.addSynthesisRules(i.reactionRules)}return n}function et(t){const e=t.firstMonomers.length*t.secondMonomers.length,n=new Array(e),r=new Array(e);let o=0;for(let e=0;e<t.firstMonomers.length;e++)for(let i=0;i<t.secondMonomers.length;i++)n[o]=t.firstMonomers[e],r[o]=t.secondMonomers[i],o++;return[n,r]}},5174:(t,e,n)=>{"use strict";n.d(e,{A:()=>c});var r=n(6717),o=n(1296),i=n(9192),s=n(4328),a=n(1991),l=n.n(a),u=n(4971);async function c(t){const e=(await(0,u.pj)()).getMonomerLib(),n=await(0,r.j)(),o={};let i=[],a=[];for(let r=0;r<t.reactionRules.length;r++)try{[i,a]=h(n,e,t.reactionRules[r])}catch(t){i=[],a=[],console.error(t),s.shell.warning(t)}finally{for(let t=0;t<i.length;t++)null!=i[t]&&null!=a[t]&&(o[i[t]]=a[t])}const c={PEPTIDE:o};return e.override(c,"ST-PT-reactions."+l().repeat(1).map((()=>Math.floor(36*Math.random()).toString(36))).take(4).toArray().join(""))}function h(t,e,n){const r=n.reaction,o=n.name,s=n.firstMonomers.length+n.secondMonomers.length+1,a=n.reaction.split(">>"),l=a[0].split("."),u=new Array(s),c=new Array(s),h=new Array(s),m=f(t,r),g=`${l[0]}>>[C:1]C`,y=`${l[1]}>>[C:2]C`,b=f(t,g),v=f(t,y);let w=0;for(let r=0;r<n.firstMonomers.length;r++){const i=e.getMonomer("PEPTIDE",n.firstMonomers[r]);if(i){const e=d(t,i.molfile,b,i.name);h[w]=e,u[w]=`${i.symbol}_${o}`}w++}for(let r=0;r<n.secondMonomers.length;r++){const i=e.getMonomer("PEPTIDE",n.secondMonomers[r]);if(i){const e=d(t,i.molfile,v,i.name);h[w]=e,u[w]=`${i.symbol}_${o}`}w++}let C=null;a[1]=a[1].replace("[C:1]","[1*]").replace("[C:2]","[2*]").replace("[C:3]","[3*]");let A="";try{C=t.get_mol(a[1]),A=C?.get_molblock()}catch(t){const[e,n]=(0,i.AP)(t);throw console.error(`Can not assemble monomer '${o}': ${e}.`),t}finally{C?.delete()}h[w]=A,u[w]=o;for(let t=0;t<s-1;t++)h[t]&&(h[t]=h[t].replace(" 0.0000 0.0000 0.0000 C "," 0.0000 0.0000 0.0000 R# ").replace("M RGP 2","M RGP 3 2 3"));h[s-1]=function(t){const e=t.replace("M RAD","M RGP").replace("M ISO","M RGP").split("\n"),n=e.findIndex((t=>t.startsWith("M RGP"))),r=Number(e[n].substring(9,13)),o=Number(e[n].substring(17,21)),i=Number(e[n].substring(13,17)),s=Number(e[n].substring(21,25));e[n]=e[n].substring(0,13)+` ${i}`+e[n].substring(17,21)+` ${s}`,e[3+r]=e[3+r].substring(0,30)+" R# 0 0 0 0 0 0 0 0 0 0 0 0",e[3+o]=e[3+o].substring(0,30)+" R# 0 0 0 0 0 0 0 0 0 0 0 0";let a="";for(let t=0;t<e.length;t++)a+=e[t]+"\n";return a}(h[s-1]);for(let t=0;t<s;t++){const e=t==s-1;if(!h[t]||!u[t])continue;const n={symbol:u[t],name:u[t],molfile:h[t],author:"",id:0,rgroups:p(e),smiles:"",polymerType:"PEPTIDE",monomerType:"Backbone",createDate:null};n.meta=Object.assign(n.meta??{},{colors:{default:{line:"#2083D5",text:"#2083D5",background:"#F2F2F5"}}}),u[t]=u[t],c[t]=n}return m.delete(),b.delete(),v.delete(),[u,c]}function d(t,e,n,r){let o=null,s=null,a=null,l=null,u="";try{o=new t.MolList,s=t.get_mol(e),o.append(s),a=n.run_reactants(o,1),l=a.get(0).next(),u=l?.get_molblock()}catch(t){const[e,n]=(0,i.AP)(t);throw console.error(`Can not assemble monomer '${r}': ${e}.`),t}finally{o?.delete(),s?.delete(),a?.delete(),l?.delete()}return u}function f(t,e){let n=null;try{if(n=t.get_rxn(e),!n)throw new o.J5(e)}catch(t){n?.delete();const[r,o]=(0,i.AP)(t);throw console.error(`Can not assemble monomer '${e}': ${r}.`),t}return n}function p(t){if(t){const t=new Array(2),e={capGroupSMILES:"[*:1][H]",alternateId:"R1-H",capGroupName:"H",label:"R1"},n={capGroupSMILES:"[*:2][H]",alternateId:"R2-H",capGroupName:"H",label:"R2"};return t[0]=e,t[1]=n,t}return[{capGroupSMILES:"[*:3][H]",alternateId:"R3-H",capGroupName:"H",label:"R3"}]}},3820:(t,e,n)=>{"use strict";n.d(e,{d:()=>o,o:()=>s});var r=n(1296);const o="PEPTIDE1{R.[Aca].T.G.H.F.G.A.A.Y.P.E.[meI]}$$$$";function i(t,e,n,r){const o=new Array(r.length*(n-e+1));for(let i=0;i<r.length;++i){const s=n-e+1;for(let n=0;n<s;++n){const a=e+n,l=r[i],u=o[i*s+n]=t.clone(),c=u.atoms[a].elem;u.atoms[a].elem=l;const h=c?.length>1?`[${c}]`:c,d=l?.length>1?`[${l}]`:l;u.name=`${t.name}-${h}${a+1}${d}`}}return o}function s(t,e,n){const o=new JSDraw2.MolHandler,s=new org.helm.webeditor.Plugin(o);org.helm.webeditor.IO.parseHelm(s,t,new JSDraw2.Point(0,0),void 0);const a=o.m;a.name=e;let l=[];if(n.placeholders)switch(n.type){case r.aK.Single:l=function(t,e){return e.map((e=>i(t,e.position,e.position,e.monomers))).reduce(((t,e)=>t.concat(e)),[])}(o.m,n.placeholders);break;case r.aK.Matrix:l=function(t,e){let n=[t];for(const t of e){const e=n.map((e=>i(e,t.position,t.position,t.monomers)));n=e.reduce(((t,e)=>t.concat(e)),[])}return n}(o.m,n.placeholders)}let u=[];n.breadthPlaceholders&&(u=function(t,e){if(0==e.length)return[];let n=[t];for(const t of e){const e=n.map((e=>i(e,t.start,t.end,t.monomers)));n=e.reduce(((t,e)=>t.concat(e)),[])}return n}(o.m,n.breadthPlaceholders)),l=l.concat(u),n.keepOriginal&&(l=[a,...l]);const c=l.map((t=>[org.helm.webeditor.IO.getHelm(t),t.name]));return c}},1296:(t,e,n)=>{"use strict";var r;n.d(e,{J5:()=>o,aK:()=>r}),function(t){t.Single="single",t.Matrix="matrix",t.Library="library"}(r||(r={})),Error;class o extends Error{constructor(t,e){super(`Invalid reaction '${t}'.`),this.type="InvalidReactionError"}}},6082:t=>{"use strict";t.exports=DG},4328:t=>{"use strict";t.exports=grok},7389:t=>{"use strict";t.exports=ui},1991:t=>{"use strict";t.exports=wu}},e={};function n(r){var o=e[r];if(void 0!==o)return o.exports;var i=e[r]={id:r,loaded:!1,exports:{}};return t[r].call(i.exports,i,i.exports,n),i.loaded=!0,i.exports}n.m=t,n.n=t=>{var e=t&&t.__esModule?()=>t.default:()=>t;return n.d(e,{a:e}),e},n.d=(t,e)=>{for(var r in e)n.o(e,r)&&!n.o(t,r)&&Object.defineProperty(t,r,{enumerable:!0,get:e[r]})},n.u=t=>t+".js",n.g=function(){if("object"==typeof globalThis)return globalThis;try{return this||new Function("return this")()}catch(t){if("object"==typeof window)return window}}(),n.o=(t,e)=>Object.prototype.hasOwnProperty.call(t,e),n.r=t=>{"undefined"!=typeof Symbol&&Symbol.toStringTag&&Object.defineProperty(t,Symbol.toStringTag,{value:"Module"}),Object.defineProperty(t,"__esModule",{value:!0})},n.nmd=t=>(t.paths=[],t.children||(t.children=[]),t),(()=>{var t;n.g.importScripts&&(t=n.g.location+"");var e=n.g.document;if(!t&&e&&(e.currentScript&&"SCRIPT"===e.currentScript.tagName.toUpperCase()&&(t=e.currentScript.src),!t)){var r=e.getElementsByTagName("script");if(r.length)for(var o=r.length-1;o>-1&&(!t||!/^http(s?):/.test(t));)t=r[o--].src}if(!t)throw new Error("Automatic publicPath is not supported in this browser");t=t.replace(/#.*$/,"").replace(/\?.*$/,"").replace(/\/[^\/]+$/,"/"),n.p=t})(),n.b=document.baseURI||self.location.href,n.nc=void 0;var r=n(9788);sequencetranslator=r})();
2
+ var sequencetranslator;(()=>{var t={6717:(t,e,n)=>{"use strict";n.d(e,{j:()=>o});var r=n(6082);async function o(){const t=r.Func.find({package:"Chem",name:"getRdKitModule"});if(0===t.length)throw new Error('Package "Chem" must be installed for getRdKitModule.');return(await t[0].prepare().call()).getOutputParamValue()}},3599:(t,e,n)=>{"use strict";n.d(e,{o:()=>r.o});var r=n(6869)},9124:(t,e,n)=>{"use strict";n.d(e,{b2:()=>i});var r=n(7389),o=n(6082);async function i(){const t="Helm",e=o.Func.find({package:t,name:"getHelmHelper"});if(0===e.length)throw new Error(`Package '${t}' must be installed for HelmHelper.`);return(await e[0].prepare().call()).getOutputParamValue()}o.JsInputBase,Error,r.input.helmAsync=async function(t,e){return(await i()).createHelmInput(t,e)}},8438:(t,e,n)=>{"use strict";function r(t){return t.startsWith("[")&&t.endsWith("]")?t.slice(1,-1):t}n.d(e,{D:()=>r})},8123:(t,e,n)=>{"use strict";n.d(e,{u:()=>r});const r={V2K_RGP_SHIFT:8,V2K_RGP_LINE:"M RGP",V2K_A_LINE:"A ",V3K_COUNTS_SHIFT:14,V3K_IDX_SHIFT:7,V3K_HEADER_FIRST_LINE:"\nDatagrok macromolecule handler\n\n",V3K_HEADER_SECOND_LINE:" 0 0 0 0 0 0 999 V3000\n",V3K_BEGIN_CTAB_BLOCK:"M V30 BEGIN CTAB\n",V3K_END_CTAB_BLOCK:"M V30 END CTAB\n",V3K_BEGIN_COUNTS_LINE:"M V30 COUNTS ",V3K_COUNTS_LINE_ENDING:" 0 0 0\n",V3K_BEGIN_ATOM_BLOCK:"M V30 BEGIN ATOM\n",V3K_END_ATOM_BLOCK:"M V30 END ATOM\n",V3K_BEGIN_BOND_BLOCK:"M V30 BEGIN BOND\n",V3K_END_BOND_BLOCK:"M V30 END BOND\n",V3K_BOND_CONFIG:" CFG=",V3K_BEGIN_DATA_LINE:"M V30 ",V3K_END:"M END",PRECISION_FACTOR:1e4,DEOXYRIBOSE:{polymerType:"RNA",symbol:"d"},RIBOSE:{polymerType:"RNA",symbol:"r"},PHOSPHATE:{polymerType:"RNA",symbol:"p"},OXYGEN:"O",HYDROGEN:"H"}},6197:(t,e,n)=>{"use strict";n.d(e,{Y:()=>o});var r=n(3599);function o(t){let e;switch(t){case r.o.BASE:case r.o.SUGAR:case r.o.LINKER:case r.o.NUCLEOTIDE:case"nucleotide":e="RNA";break;case r.o.AA:e="PEPTIDE";break;case r.o.CHEM:e="CHEM";break;case r.o.BLOB:e="BLOB";break;default:e="PEPTIDE",console.warn(`Unexpected HelmType '${t}'`)}return e}},9235:(t,e,n)=>{"use strict";n.d(e,{H:()=>u,R:()=>l});var r=n(6082),o=n(1991),i=n.n(o),s=n(330),a=n(3599);async function l(t,e,o,l,u,c,h){const d=t.length,f=t.dataFrame,p=Math.max(navigator.hardwareConcurrency-2,1),m=new Array(p).fill(null).map((()=>new Worker(new URL(n.p+n.u(455),n.b)))),g=d/p,y=new Array(p),b=c.getSeqHandler(t),v="RNA"==l?a.o.NUCLEOTIDE:a.o.AA,w=i().count(0).take(t.length).map((t=>{const e=b.getSplitted(t);return i().count(0).take(e.length).map((t=>({position:t,symbol:e.getCanonical(t),biotype:v}))).toArray()})).toArray();for(let t=0;t<p;t++){const n=m[t],r=Math.floor(t*g),i=t===p-1?d:Math.floor((t+1)*g);y[t]=new Promise((t=>{n.onmessage=e=>{t(e.data)}})),n.postMessage({seqList:w,monomersDict:e,alphabet:o,polymerType:l,start:r,end:i})}const C=[],A=[];await Promise.all(y).then((t=>{for(const e of t)C.push(...e.molfiles),A.push(...e.warnings)})),setTimeout((()=>{m.forEach((t=>{t.terminate()}))}),0);const x=(0,s.qj)(f,t.name),S=r.Column.fromType(r.COLUMN_TYPE.STRING,x,t.length).init((t=>C[t]?.molfile));return S.semType=r.SEMTYPE.MOLECULE,S.meta.units=r.UNITS.Molecule.MOLBLOCK,S.setTag(".sequence-src-col",t.name),{molCol:S,warnings:A}}function u(t,e){const n={},o={};for(const i of t){const t=e.getWebEditorMonomer(i.biotype,i.symbol).backgroundcolor,a=(0,s.vG)(t??r.Color.toRgb(r.Color.mouseOverRows))??[1,0,0,.7];for(const t of i.atoms)n[t]=a;for(const t of i.bonds)o[t]=a}return{atoms:Object.keys(n).map((t=>parseInt(t))),bonds:Object.keys(o).map((t=>parseInt(t))),highlightAtomColors:n,highlightBondColors:o}}},3561:(t,e,n)=>{"use strict";n.d(e,{Hb:()=>l,YN:()=>m,gU:()=>u});var r=n(8123),o=n(294),i=n(3151),s=n(439),a=n(6197);function l(t,e,n){const o=new Map;for(const a of t.getMonomerSymbolsByType(e)){const l=t.getMonomer(e,a);if("RNA"===e&&("Branch"===l.monomerType||n===s.YI.DNA&&l.symbol===r.u.DEOXYRIBOSE.symbol||n===s.YI.RNA&&l.symbol===r.u.RIBOSE.symbol||l.symbol===r.u.PHOSPHATE.symbol)||"PEPTIDE"===e&&"Branch"!==l.monomerType){const t={};i.f6.forEach((e=>{t[e]=l[e]})),o.set(a,t)}}return o}function u(t,e,n,i){if(0===t.length)return o.vF.createEmpty();const l=p,{atomCount:u,bondCount:h,needsCapping:f}=l(t,e,n,i),g=new Array(u),y=new Array(h);let b,v=null,w=null;"PEPTIDE"===i?b=c:(b=d,v=n===s.YI.DNA?(0,o.xb)(e,r.u.DEOXYRIBOSE):(0,o.xb)(e,r.u.RIBOSE),w=(0,o.xb)(e,r.u.PHOSPHATE));const C={i:0,nodeShift:0,bondShift:0,backbonePositionShift:new Array(2).fill(0),branchPositionShift:new Array(2).fill(0),backboneAttachNode:0,branchAttachNode:0,flipFactor:1},A={sugar:v,phosphate:w,seqLength:t.length,atomCount:u,bondCount:h},x=new o.Cg,S=[];let T,E=0;for(C.i=0;C.i<A.seqLength;++C.i){const n=t[C.i];if(n.symbol===s._S)continue;const r=(0,o.xb)(e,{symbol:n.symbol,polymerType:(0,a.Y)(n.biotype)});T=r.terminalR2Atom;const i=C.nodeShift,l=C.bondShift;b(r,g,y,C,A),r.stereoAtoms?.forEach((t=>S.push(t+E))),E+=r.atoms.x.length;const u=C.nodeShift-i,c=new Array(u);for(let t=0;t<u;++t)c[t]=i+t;const h=C.bondShift-l,d=new Array(h);for(let t=0;t<h;++t)d[t]=l+t;x.set(C.i,{biotype:n.biotype,symbol:n.symbol,atoms:c,bonds:d})}f&&function(t,e,n,o,i=r.u.OXYGEN){const s=n.nodeShift+1;t[o.atomCount]=r.u.V3K_BEGIN_DATA_LINE+s+" "+(i??r.u.OXYGEN)+" "+m(n.backbonePositionShift[0])+" "+n.flipFactor*m(n.backbonePositionShift[1])+" 0.000000 0\n";const a=n.backboneAttachNode,l=s;e[o.bondCount]=r.u.V3K_BEGIN_DATA_LINE+n.bondShift+" 1 "+a+" "+l+"\n"}(g,y,C,A,T??r.u.OXYGEN);const _=r.u.V3K_BEGIN_COUNTS_LINE+u+" "+h+r.u.V3K_COUNTS_LINE_ENDING;let I="";return I+=r.u.V3K_HEADER_FIRST_LINE,I+=r.u.V3K_HEADER_SECOND_LINE,I+=r.u.V3K_BEGIN_CTAB_BLOCK,I+=_,I+=r.u.V3K_BEGIN_ATOM_BLOCK,I+=g.join(""),I+=r.u.V3K_END_ATOM_BLOCK,I+=r.u.V3K_BEGIN_BOND_BLOCK,I+=y.join(""),I+=r.u.V3K_END_BOND_BLOCK,S.length>0&&(I+=function(t){const e=[];let n=`M V30 MDLV30/STEABS ATOMS=(${t.length}`;for(let r=0;r<t.length;r++){const o=`${n} ${t[r]}`;o.length>76?(e.push(`${n} -\n`),n=`M V30 ${t[r]}`):n=o,r===t.length-1&&e.push(`${n})\n`)}return`M V30 BEGIN COLLECTION\n${e.join("")}M V30 END COLLECTION\n`}(S)),I+=r.u.V3K_END_CTAB_BLOCK,I+=r.u.V3K_END,{molfile:I,monomers:x}}function c(t,e,n,r){r.flipFactor=(-1)**(r.i%2),h(t,e,n,r)}function h(t,e,n,o){!function(t,e,n){for(let o=0;o<t.atoms.atomTypes.length;++o){const i=n.nodeShift+o+1;e[n.nodeShift+o]=r.u.V3K_BEGIN_DATA_LINE+i+" "+t.atoms.atomTypes[o]+" "+m(n.backbonePositionShift[0]+t.atoms.x[o])+" "+m(n.backbonePositionShift[1]+n.flipFactor*t.atoms.y[o])+" 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r,o,i,s=n(2738);!function(t){t.FASTA="fasta",t.SEPARATOR="separator",t.HELM="helm",t.CUSTOM="custom",t.BILN="biln"}(r||(r={})),function(t){t.DNA="DNA",t.RNA="RNA",t.PT="PT",t.UN="UN"}(o||(o={})),function(t){t.aligned="aligned",t.alphabet="alphabet",t.alphabetSize=".alphabetSize",t.alphabetIsMultichar=".alphabetIsMultichar",t.separator="separator",t.isHelmCompatible=".isHelmCompatible",t.positionNames=".positionNames",t.positionLabels=".positionLabels",t.regions=".regions",t.positionShift=".positionShift",t.selectedPosition=".selectedPosition",t.polymerTypeColumnName=".polymerTypeColumnName"}(i||(i={}));const a=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"])}}},l=(new s.a(o.PT,a.fasta.peptide,.5),new s.a(o.DNA,a.fasta.dna,.55),new s.a(o.RNA,a.fasta.rna,.55),""),u={[r.FASTA]:"-",[r.SEPARATOR]:"",[r.HELM]:"*",[r.BILN]:""}},2003:(t,e,n)=>{"use 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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,l)),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,l)),this.grokGroups}static get RasMol(){return void 0===this.rasMol&&(this.rasMol=new l({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 l.aaSynonyms?l.aaSynonyms[t]:t;return super.get(e)}}l.aaSynonyms={MeNle:"L",MeA:"A",MeG:"G",MeF:"F"};class u{static getPalette(t="grok"){switch(t){case"grok":return l.GrokGroups;case"lesk":return l.Lesk;default:throw new Error(`ChemPalette: scheme \`${t}\` does not exist`)}}static getInnerOuter(t){let e=0,n="",r="";for(const o of t)"("==o?e++:")"==o?e--:e?n+=o:r+=o;return isNaN(parseInt(n))?[r,n]:[r,""]}static getColorAAPivot(t="",e="grok"){const n=this.getPalette(e);let[r,o]=this.getInnerOuter(t);if(r=r.length>6?`${r.slice(0,3)}...`:r,o=o.length>6?`${o.slice(0,3)}...`:o,1==t.length||"("==t[1]){const e=t[0]?.toUpperCase();return e in n?[n.get(e),e,o,1]:[this.undefinedColor,r,o,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,o,2]:[this.undefinedColor,r,o,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,o,3]:[this.undefinedColor,r,o,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,o,4]:[this.undefinedColor,r,o,4]}return[this.undefinedColor,r,o,0]}}u.SemType="Aminoacids",u.SemTypeMultipleAlignment="AminoacidsMultipleAlignment",u.undefinedColor="rgb(100,100,100)",u.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"},u.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"},u.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(*)*"},u.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 c{}c.SemType="Nucleotides",c.SemTypeMultipleAlignment="NucleotidesMultipleAlignment",c.Names={A:"Adenine",C:"Cytosine",G:"Guanine",T:"Thymine",U:"Uracil"};var h=n(4971);function d(t,e=!0){if(null==t)return"rgb(100,100,100)";const n=r.Color.fromHtml(t);if(e){const t=r.Color.g(n),e=r.Color.r(n),o=r.Color.b(n),i=Math.sqrt(Math.pow(0-e,2)+Math.pow(0-t,2)+Math.pow(0-o,2));if(i>210)return`rgb(${e/i*210},${t/i*210},${o/i*210})`}return r.Color.toRgb(n)}class f{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 p{}class m extends p{static get palette(){return m._pallete||(m._pallete=m.buildPalette()),m._pallete}static buildPalette(){return(0,h.pj)().then((t=>{t.awaitLoaded(1/0).then((()=>{const e=t.getMonomerLib();e.onChanged.subscribe((()=>{m.customMonomerColors={},m.polymerTypes=e.getPolymerTypes();for(const t of this.polymerTypes){const n=e.getMonomerSymbolsByType(t);for(const r of n){const n=e.getMonomer(t,r);n?.meta?.colors?.default?.background&&(this.customMonomerColors[r]||(this.customMonomerColors[r]={}),this.customMonomerColors[r][t]=d(n.meta.colors.default.background))}}}))}))})),[].concat(...Object.values(a.colourPalette))}get(t,e){const n=m.palette.length,r=m.customMonomerColors[t],o=e??"PEPTIDE";if(r&&r[o])return r[o];const i=f.hashCode(t)%n;return d(m.palette[i])}}m._pallete=null,m.customMonomerColors={},m.polymerTypes=[];var g=n(8438);n(3599);class y{get length(){return this.mList.length}get graphInfo(){}isGap(t){return this.getOriginal(t)===this.gapOriginalMonomer}getCanonical(t){if(this.length<=t)throw new Error("Index out of bounds");const e=this.mList[t];return e!==this.gapOriginalMonomer?e:s._S}getOriginal(t){if(this.length<=t)throw new Error("Index out of bounds");return this.mList[t]}getCanonicalRegion(t,e){const n=Math.min(Math.max(0,t),this.length),r=Math.max(Math.min(this.length,e),0)-n,o=this.gapOriginalMonomer;return new Array(r).fill(null).map(((t,e)=>{const r=this.mList[e+n];return r===o?s._S:r}))}getOriginalRegion(t,e){const n=Math.min(Math.max(0,t),this.length),r=Math.max(Math.min(this.length,e),0);return new Array(r-n).fill(null).map(((t,e)=>this.mList[e+n]))}get gapOriginal(){return this.gapOriginalMonomer}constructor(t,e){this.mList=t,this.gapOriginalMonomer=e}}class b extends y{constructor(t,e,n,r){super(t.flat(),r),this.mListSeparated=t,this.connections=e,this._graphInfo=void 0,this.polymerTypes=t.map(((t,e)=>new Array(t.length).fill(n[e]))).flat()}get graphInfo(){return this._graphInfo??(this._graphInfo=this.parseConnections()),this._graphInfo}parseConnections(){const t={connections:[],disjointSeqStarts:[],polymerTypes:this.polymerTypes};if((this.connections?.length??0)>0){let e=0;for(let n=0;n<this.mListSeparated.length;++n)t.disjointSeqStarts.push(e),e+=this.mListSeparated[n].length;const 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r.dapi.files.readAsText(n);return JSON.parse(t)}catch(t){console.error(`Error loading json from '${n}':`,t)}}(t,e))));return new w(e[0],e[1],e[2],e[3])}class A{constructor(t,e){if(this.lib=t,this.jsonData=e,null===this.lib)throw new Error("SequenceTranslator: monomer library is null");this.allMonomers=this.getAllMonomers()}formatMonomerForViewer(t){const e={};return e.name=t.symbol,e.symbol=t.symbol,e.molfile=t.molfile,this.getAllFormats().forEach((n=>{if(n===m.NO.HELM)return;const r=this.jsonData.codesToSymbolsDict[n],o=Object.keys(r).filter((e=>r[e]===t.symbol));e[n]=o.join(", ")})),e}getAllMonomers(){const t=this.lib.getPolymerTypes();let e=[];for(const n of t){const t=this.lib.getMonomerSymbolsByType(n).map((t=>this.lib.getMonomer(n,t))).filter((t=>null!==t));e=e.concat(t)}return e}getMonomer(t){const e=this.lib.getMonomer("RNA",t);if(void 0===e)throw new Error(`SequenceTranslator: no monomer with symbol ${t}`);return e}getMolfileBySymbol(t){return this.getMonomer(t).molfile}getNaturalAnalogBySymbol(t){const e=this.getMonomer(t).naturalAnalog;if(!e)throw new Error(`ST: no natural analog for ${t}`);return e}isModification(t){return!!this.getMolfileBySymbol(t).includes("MODIFICATION")}getCodeToSymbolMap(t){return new Map(Object.entries(this.jsonData.codesToSymbolsDict[t]))}getCodesByFormat(t){return Object.keys(this.jsonData.codesToSymbolsDict[t])}getAllFormats(){return Object.keys(this.jsonData.codesToSymbolsDict)}getTableForViewer(){const t=this.allMonomers.map((t=>this.formatMonomerForViewer(t)));return o.DataFrame.fromObjects(t)}getCodesToWeightsMap(){const t=new Map;return Object.entries(this.jsonData.codesToSymbolsDict).forEach((([e,n])=>{Object.entries(n).forEach((([e,n])=>{const r=this.getMonomer(n),o=r.meta?.molecularWeight;t.set(e,o)}))})),t}}var x=n(9537);const S=(t,e)=>e.length-t.length;class T{constructor(t){this.th=t,this.formats=this.getFormats()}getFormatNames(){return this.formats.sort()}getCodesByFormat(t){if(this.validateFormat(t),this.isHelm(t))throw new Error("Codes cannot be obtained for HELM");return this.getFormatCodes(t)}getHelmToFormatDict(t){return this.validateFormat(t),function(t){const e={};return Object.values(t).forEach((t=>{Object.entries(t).forEach((([t,n])=>{const r=n.replace(/\)p/g,")").replace(/\]p/g,"]");void 0===e[r]?e[r]=[t]:e[r].push(t)}))})),Object.entries(e).forEach((([t,n])=>{const r=n.sort(S);e[t]=r[0]})),e}(this.th.jsonData.codesToHelmDict[t])}getFormatToHelmDict(t){this.validateFormat(t);const e=this.th.jsonData.codesToHelmDict[t];return Object.assign({},...Object.values(e))}getTargetFormatHelmCodes(t){this.validateFormat(t);const e=this.getHelmToFormatDict(t);return Object.keys(e).sort(S)}getTargetFormatHelmCodesRegExp(t){this.validateFormat(t);const e=this.getTargetFormatHelmCodes(t);return new RegExp(E(e)+"|.","g")}getFormatRegExp(t){if(this.validateFormat(t),this.isHelm(t))throw new Error("Helm RegExp can be built for non-HELM target formats");return this.getNonHelmFormatRegExp(t)}getPhosphateHelmCodesRegExp(t){this.validateFormat(t);const e=this.th.jsonData.codesToHelmDict[t],n=E(Array.from(new Set(Object.values(e[x.ti.LINKAGE]))).sort(S));return new RegExp(`${x.q7}.(${n})`,"g")}isValidFormat(t){return this.formats.includes(t)}getFormats(){return Object.keys(this.th.jsonData.codesToHelmDict)}validateFormat(t){if(!this.isValidFormat(t))throw new Error(`Invalid format: ${t}`)}isHelm(t){return t===m.NO.HELM}getFormatCodes(t){const e=this.getFormatToHelmDict(t);return Object.keys(e).sort(S)}getNonHelmFormatRegExp(t){const e=this.getCodesByFormat(t);return new RegExp(E(e)+"|\\([^()]*\\)|.","g")}}function E(t){return t.map((t=>t.replace(/[.*+?^${}()|[\]\\]/g,"\\$&"))).map((t=>t.includes("(")||t.includes(")")?t:`(?<!\\([^()]*)${t}(?![^()]*\\))`)).join("|")}const _={LEFT:"RNA1{",RIGHT:"}$$$$"};class I{constructor(t,e,n){this.sequence=t,this.sourceFormat=e,this.th=n,this.formats=new T(this.th)}convertTo(t){const e=this.formats.getFormatNames();if(this.sourceFormat===m.NO.HELM&&e.includes(t))return this.helmToFormat(this.sequence,t);if(e.includes(this.sourceFormat)&&t===m.NO.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} -> ${t}`)}helmToFormat(t,e){const n=new RegExp(E(Object.values(_)),"g");let r=t.replace(n,"");const o=this.formats.getHelmToFormatDict(e),i=this.formats.getTargetFormatHelmCodes(e),s=this.formats.getTargetFormatHelmCodesRegExp(e);return r=r.replace(s,(t=>i.includes(t)?o[t]:"p"===t||"."===t?t:"?")).replace(/\?+/g,x.iL).replace(/p\.|\./g,""),r=r.replace(/<empty>/g,""),r=r.replace(/\/\//g,"/"),r}formatToHelm(t,e){const n=this.formats.getFormatToHelmDict(e),r=this.formats.getCodesByFormat(e),o=this.formats.getFormatRegExp(e),i=this.formats.getPhosphateHelmCodesRegExp(e);let s=t?t.replace(o,(t=>r.includes(t)?n[t]+".":"?")):"";return s=s.replace(/\?+/g,`${x.iL}.`),s=s.slice(0,-1),s[s.length-1]===x.q7&&(s=s.slice(0,-1)),s=s.replace(i,((t,e)=>e)),s=s.replace(/<empty>/g,""),`${_.LEFT+s+_.RIGHT}`}}class N{constructor(t,e){this.sequence=t,this.th=e,this.libWrapper=this.th.monomerLibWrapper,this.formats=Object.keys(this.th.jsonData.codesToHelmDict)}getFormat(){if(this.sequence.startsWith("RNA"))return m.NO.HELM;const t=this.getListOfPossibleSynthesizersByFirstMatchedCode();if(0===t.length)return null;const e=this.th.createSequenceValidator(this.sequence),n=Array(t.length).fill(0);for(let r=0;r<t.length;++r){const o=t[r];n[r]=e.getInvalidCodeIndex(o)}const r=n.some((t=>-1===t))?-1:Math.max(...n);return t[n.indexOf(r)]}getListOfPossibleSynthesizersByFirstMatchedCode(){const t=this.sequence,e=[];for(const n of this.formats){const r=g(this.libWrapper.getCodesByFormat(n));let o=0;for(let e=0;e<t.length;e++)if(")"===t[e]&&e!==t.length-1){o=e+1;break}r.some((e=>e===t.slice(o,o+e.length)))&&e.push(n)}return e}}var M=n(7389);const O=$;var L=n.n(O);function R(t,e){let n=0;const r=e.createFormatDetector(t).getFormat();null!==r&&(n=new v(t,e).getInvalidCodeIndex(r));const o=n<0||""===t,i=M.span([]);L()(i).css("-webkit-text-fill-color","var(--grey-6)");const s=M.span([]);return L()(s).css("-webkit-text-fill-color","red"),o?i.innerHTML=t:(i.innerHTML=t.slice(0,n),s.innerHTML=t.slice(n)),[i,s]}class P extends o.Package{get helmHelper(){if(!this._helmHelper)throw new Error("Package SequenceTranslator .helmHelper is not initialized");return this._helmHelper}get seqHelper(){return this._helmHelper.seqHelper}get monomerLib(){if(!this._monomerLib)throw new Error("Monomer lib not loaded");return this._monomerLib}get jsonData(){if(!this._jsonData)throw new Error("Json data not loaded");return this._jsonData}get monomerLibWrapper(){if(!this._monomerLibWrapper)throw new Error("Monomer lib wrapper not loaded");return this._monomerLibWrapper}get initPromise(){return this._initPromise}constructor(t={debug:!1}){super(),this.highlightInvalidSubsequence=t=>R(t,this),super._logger=new u(super.logger,t.debug)}startInit(t){this._initPromise=t}completeInit(t){this._helmHelper=t}async initLibData(){return this.initLibDataPromise||(this.initLibDataPromise=(async()=>{const t=await this.getSettings();let e=t instanceof Map?t.get("MonomersPath"):t.MonomersPath;e&&await r.dapi.files.exists(e)||(this.logger.warning(`Monomers path '${e}' not found. Fallback to monomers sample path '${c}'.`),e=c),[this._jsonData,this._monomerLib]=await Promise.all([C(e),B(e)]),this._monomerLibWrapper=new A(this.monomerLib,this.jsonData)})()),this.initLibDataPromise}async getTranslationHelper(){return await r.functions.call(`${this.name}:getTranslationHelper`)}createSequenceValidator(t){return new v(t,this)}createFormatConverter(t,e){return new I(t,e,this)}createFormatDetector(t){return new N(t,this)}}async function B(t){const e=o.TaskBarProgressIndicator.create("Initializing Oligo Toolkit monomer library ...");try{const e=await(0,l.pj)(),n=(t.endsWith("/")?t:t+"/")+"monomer-lib.json";return await e.readLibraryFromFilePath(n)}finally{e.close()}}class D{constructor(t,e){this.appName=t,this.parentAppName=e}async getAppView(){const t=o.TaskBarProgressIndicator.create(`Loading ${this.appName}...`),e=r.shell.v?.root;e&&M.setUpdateIndicator(e,!0);try{return await this.constructView()}finally{t.close(),e&&M.setUpdateIndicator(e,!1)}}}class F extends D{constructor(t){super(t),this.view=o.View.create(),this.configureView()}async constructView(){await this.initView();const t=this.parentAppName?this.parentAppName+"/"+this.appName:this.appName;return this.view.path=`/apps/${Xr.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=r.shell.windows;t.showProperties=!1,t.showToolbox=!1,t.showHelp=!1}getView(){return this.view}}const k=["SS","AS"],H={SS:"Sense strand",AS:"Anti sense"},U=["3'","5'"],V="OligoToolkit";var q,j,G,z;!function(t){t.IS_ANTISENSE_STRAND_INCLUDED="isAntisenseStrandIncluded",t.NUCLEOTIDE_SEQUENCES="nucleotideSequences",t.PHOSPHOROTHIOATE_LINKAGE_FLAGS="phosphorothioateLinkageFlags",t.STRAND_TERMINUS_MODIFICATIONS="strandTerminusModifications"}(q||(q={})),function(t){t.PATTERN_NAME="patternName",t.PATTERN_COMMENT="patternComment",t.NUCLEOTIDES_WITH_NUMERIC_LABELS="nucleotidesWithNumericLabels"}(j||(j={})),function(t){t.PATTERN_CONFIG="patternConfig",t.AUTHOR_ID="authorID",t.DATE="date"}(G||(G={})),function(t){t.CREATE="create",t.MODIFY="modify"}(z||(z={}));const W=[q.IS_ANTISENSE_STRAND_INCLUDED,q.NUCLEOTIDE_SEQUENCES,q.PHOSPHOROTHIOATE_LINKAGE_FLAGS,q.STRAND_TERMINUS_MODIFICATIONS],Y=(j.PATTERN_NAME,j.PATTERN_COMMENT,j.NUCLEOTIDES_WITH_NUMERIC_LABELS,{patternConfig:{patternName:"<default example>",isAntisenseStrandIncluded:!0,nucleotideSequences:{SS:["RNA","RNA","RNA","RNA","RNA","RNA","RNA","RNA","RNA","RNA","RNA","RNA","RNA","RNA","RNA","RNA","RNA","RNA","RNA","RNA","RNA","RNA","RNA"],AS:["RNA","RNA","RNA","RNA","RNA","RNA","RNA","RNA","RNA","RNA","RNA","RNA","RNA","RNA","RNA","RNA","RNA","RNA","RNA","RNA","RNA","RNA","RNA"]},phosphorothioateLinkageFlags:{SS:[!0,!0,!0,!0,!0,!0,!0,!0,!0,!0,!0,!0,!0,!0,!0,!0,!0,!0,!0,!0,!0,!0,!0,!0],AS:[!0,!0,!0,!0,!0,!0,!0,!0,!0,!0,!0,!0,!0,!0,!0,!0,!0,!0,!0,!0,!0,!0,!0,!0]},strandTerminusModifications:{SS:{"3'":"","5'":""},AS:{"3'":"","5'":""}},patternComment:"",nucleotidesWithNumericLabels:["RNA"]},authorID:""}),K="2024-01-01T18:00:00.000Z";class J extends Error{constructor(t){super(t),this.name="PatternNameExistsError"}}class Q extends Error{constructor(t){super(t),this.name="PatternExistsError"}}var X=n(4802),Z=n.n(X);class tt{constructor(t){this.th=t,this.otherUsersPatternNameToHash=new Map,this.currentUserPatternNameToHash=new Map}static async getInstance(){const t=await Xr.getTranslationHelper(),e=new tt(t);e.currentUserName=await e.fetchCurrentUserName(),e.currentUserId=await e.fetchCurrentUserId();const n=e.fetchPatterns();return await e.initializePatternMaps(n),e}getCurrentUserPatternNames(){return Array.from(this.currentUserPatternNameToHash.keys()).sort(((t,e)=>t.toLowerCase().localeCompare(e.toLowerCase())))}getOtherUsersPatternNames(){return Array.from(this.otherUsersPatternNameToHash.keys()).sort(((t,e)=>t.toLowerCase().localeCompare(e.toLowerCase())))}getCurrentUserName(){return this.currentUserName}validatePatternNameUniqueness(t){if(this.currentUserPatternNameToHash.has(t))throw new J(`Pattern with name ${t} already exists`)}validatePatternUniqueness(t){if(Array.from(this.currentUserPatternNameToHash.values()).concat(Array.from(this.otherUsersPatternNameToHash.values())).includes(t))throw new Q(t)}getPatternHash(t,e){const n=e?this.currentUserPatternNameToHash.get(t):this.otherUsersPatternNameToHash.get(t);if(void 0===n)throw new Error(`Pattern with name ${t} not found`);return n}async getPatternRecordByHash(t){if(null===t||""===t)return null;try{const e=r.userSettings.getValue(V,t,!1)??"null";return JSON.parse(e)}catch{return null}}async getPatternConfig(t){if(""===t||null===t)return null;const e=await this.getPatternRecordByHash(t);return null===e?null:e[G.PATTERN_CONFIG]}getDefaultPatternRecord(){const t=Y;return t[G.AUTHOR_ID]=this.currentUserId,t}getDefaultPatternConfig(){return Y[G.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){return{[G.PATTERN_CONFIG]:t,[G.AUTHOR_ID]:await r.dapi.users.current().then((t=>t.id))}}getHash(t){const e=W.reduce(((e,n)=>(e[n]=t[n],e)),{});return Z().sha1(e)}async savePatternToUserStorage(t){const e=t.getPatternConfig();try{const n=this.getHash(e);this.validatePatternUniqueness(n);const o=e[j.PATTERN_NAME];this.validatePatternNameUniqueness(o);const i=await this.getRecordFromPattern(e),s=(new Date).toISOString();i[G.DATE]={[z.CREATE]:s,[z.MODIFY]:s};const a=JSON.stringify(i);r.userSettings.add(V,n,a,!1),this.currentUserPatternNameToHash.set(o,n),t.selectAuthor(this.getCurrentUserAuthorshipCategory()),t.updatePatternList(),t.requestPatternLoad(n),t.updateUrlState(n)}catch(t){if(t instanceof J||t instanceof Q)throw t;console.error("Error while saving pattern to user storage",t)}}async overwriteExistingPatternInUserStorage(t){const e=t.getPatternConfig(),n=e[j.PATTERN_NAME],o=this.currentUserPatternNameToHash.get(n);if(void 0===o)throw new Error("Old hash is undefined");const i=this.getHash(e),s=await this.getRecordFromPattern(e),a=(new Date).toISOString();s[G.DATE]={[z.MODIFY]:a};const l=r.userSettings.getValue(V,o,!1)??"null",u=JSON.parse(l);void 0!==u[G.DATE]&&null!=u[G.DATE][z.CREATE]&&(s[G.DATE][z.CREATE]=u[G.DATE][z.CREATE]);const c=JSON.stringify(s);r.userSettings.add(V,i,c,!1),r.userSettings.delete(V,o,!1),this.currentUserPatternNameToHash.set(n,i),t.requestPatternLoad(i),t.updateUrlState(i)}async deletePattern(t,e){const n=this.currentUserPatternNameToHash.get(t);if(t===this.getDefaultPatternName())return void r.shell.warning("Cannot delete default pattern");if(void 0===n)throw new Error(`Pattern with name ${t} not found`);r.userSettings.delete(V,n,!1),this.currentUserPatternNameToHash.delete(t),e.updatePatternList();const o=this.getHashOfPatternToBeLoadedAfterDeletion();e.requestPatternLoad(o)}fetchDefaultNucleobase(){return this.fetchAvailableNucleotideBases()[0]}fetchAvailableNucleotideBases(){const t=Object.keys(this.th.jsonData.patternAppData)[0];return Object.keys(this.th.jsonData.patternAppData[t])}async fetchCurrentUserName(){return(await r.dapi.users.current()).friendlyName}async fetchCurrentUserId(){return(await r.dapi.users.current()).id}fetchPatterns(){return r.userSettings.get(V,!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=Y[G.PATTERN_CONFIG];this.currentUserPatternNameToHash.set(t[j.PATTERN_NAME],"")}async extractDataFromRecordToMaps(t,e,n){const o=JSON.parse(e),i=o[G.PATTERN_CONFIG].patternName,s=o[G.AUTHOR_ID];if(this.isCurrentUserId(s))this.currentUserPatternNameToHash.set(i,t);else{if(!n.has(s)){let t="<UNKNOWN_USER>";try{t=(await r.dapi.users.find(s)).friendlyName}catch(t){}n.set(s,t)}const e=i+` (created by ${n.get(s)})`;this.otherUsersPatternNameToHash.set(e,t)}}getDefaultPatternName(){return Y[G.PATTERN_CONFIG][j.PATTERN_NAME]}getCurrentUserAuthorshipCategory(){return this.currentUserName+" (me)"}getOtherUsersAuthorshipCategory(){return"Other users"}isCurrentUserId(t){return t===this.currentUserId}}const et=rxjs,nt=rxjs.operators;function rt(t){return t.endsWith("(o)")}function ot(t){const e=Object.values(t).flat().reduce(((t,e)=>(t[e]=(t[e]||0)+1,t)),{});return Object.entries(e).reduce(((t,e)=>t[1]>e[1]?t:e),["",0])[0]}var it;function st(t){const e=Array.from(new Set(t));return Array.from(e).sort(((t,e)=>t.toLowerCase().localeCompare(e.toLowerCase())))}!function(t){t.getTruncatedStrandData=function(t,e,n){return{nucleotides:t.slice(0,n),ptoFlags:e.slice(0,n+1)}},t.getExtendedStrandData=function(t,e,n,r){const o=n-t.length,i=t.concat(new Array(n-t.length).fill(r)),s=0===t.length?n+1:o;return{nucleotides:i,ptoFlags:e.concat(new Array(s).fill(!0))}}}(it||(it={}));var at=n(2543),lt=n.n(at);class ut{constructor(t,e){this.dataManager=t,this._patternListUpdated$=new et.Subject,this._patternLoadRequested$=new et.Subject,this._patternLoaded$=new et.Subject,this._uniqueNucleotides$=new et.BehaviorSubject([]),this._patternDeletionRequested$=new et.Subject,this._tableSelection$=new et.BehaviorSubject(null),this._svgSaveRequested$=new et.Subject,this._loadPatternInNewTabRequested$=new et.Subject,this._urlStateUpdated$=new et.Subject,this._patternHasUnsavedChanges$=new et.BehaviorSubject(!1),this._selectedStrandColumn=new et.BehaviorSubject(null),this._selectedIdColumn=new et.BehaviorSubject(null),this.initializeAuthorSelection(e),this.initializePatternState(e),this._lastLoadedPatternConfig=new et.BehaviorSubject(lt().cloneDeep(this.getPatternConfig())),this.setupSubscriptions()}setupSubscriptions(){this._nucleotideSequences$.subscribe((()=>{this.updateUniqueNucleotides(),this.updateSequenceBase()})),this._isAntisenseStrandActive$.subscribe((t=>{t||U.forEach((t=>{this.updateTerminusModification("AS",t,"")}))})),this.patternStateChanged$.pipe((0,nt.debounceTime)(20)).subscribe((()=>{const t=this._lastLoadedPatternConfig.getValue(),e=this.getPatternConfig(),n=!lt().isEqual(e,t);this._patternHasUnsavedChanges$.next(n)}))}updateUniqueNucleotides(){const t=(e=this._nucleotideSequences$.getValue(),st(Object.values(e).flat()));var e;this._uniqueNucleotides$.next(t)}updateSequenceBase(){const t=ot(this._nucleotideSequences$.getValue());this._sequenceBase$.next(t)}get nucleotideSequencesChanged$(){return this._nucleotideSequences$.asObservable()}initializeAuthorSelection(t){const e=t[G.AUTHOR_ID];this.dataManager.isCurrentUserId(e)?this._patternAuthorSelection$=new et.BehaviorSubject(this.dataManager.getCurrentUserAuthorshipCategory()):this._patternAuthorSelection$=new et.BehaviorSubject(this.dataManager.getOtherUsersAuthorshipCategory())}initializePatternState(t){const e=t[G.PATTERN_CONFIG];this._patternName$=new et.BehaviorSubject(e[j.PATTERN_NAME]),this._isAntisenseStrandActive$=new et.BehaviorSubject(e[q.IS_ANTISENSE_STRAND_INCLUDED]),this._nucleotideSequences$=new et.BehaviorSubject(e[q.NUCLEOTIDE_SEQUENCES]),this._phosphorothioateLinkageFlags=new et.BehaviorSubject(e[q.PHOSPHOROTHIOATE_LINKAGE_FLAGS]),this._terminalModifications=new et.BehaviorSubject(e[q.STRAND_TERMINUS_MODIFICATIONS]),this._comment$=new et.BehaviorSubject(e[j.PATTERN_COMMENT]),this._modificationsWithNumericLabels$=new et.BehaviorSubject(e[j.NUCLEOTIDES_WITH_NUMERIC_LABELS]),this._sequenceBase$=new et.BehaviorSubject(ot(e[q.NUCLEOTIDE_SEQUENCES]))}getPatternName(){return this._patternName$.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$.next(t)}updateStrandLength(t,e){const n=this.getNucleotideSequences()[t];if(n.length===e)return;const r=this.getPhosphorothioateLinkageFlags()[t];if(0===e)return void this.setNewStrandData([],[],t);if(n.length>e){const{nucleotides:o,ptoFlags:i}=it.getTruncatedStrandData(n,r,e);return void this.setNewStrandData(o,i,t)}const o=this.getSequenceBase(),{nucleotides:i,ptoFlags:s}=it.getExtendedStrandData(n,r,e,o);this.setNewStrandData(i,s,t)}setNewStrandData(t,e,n){this.updateNucleotideSequences({...this.getNucleotideSequences(),[n]:t}),this.updatePhosphorothioateLinkageFlags({...this.getPhosphorothioateLinkageFlags(),[n]:e})}getPhosphorothioateLinkageFlags(){return this._phosphorothioateLinkageFlags.getValue()}updatePhosphorothioateLinkageFlags(t){this._phosphorothioateLinkageFlags.next(t)}get phosphorothioateLingeFlagsChanged$(){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 st(t).filter((t=>!rt(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$.getValue(),n={};k.forEach((r=>{n[r]=e[r].map((()=>t))})),this._nucleotideSequences$.next(n);const r=this._modificationsWithNumericLabels$.getValue();r.includes(t)||this.updateModificationsWithNumericLabels(r.concat(t))}get patternStateChanged$(){return et.merge(this._patternName$.pipe((0,nt.debounceTime)(300),(0,nt.map)((()=>{}))),this._isAntisenseStrandActive$,this._nucleotideSequences$,this._phosphorothioateLinkageFlags,this._terminalModifications,this._comment$.pipe((0,nt.debounceTime)(300)),this._modificationsWithNumericLabels$)}getSequenceBase(){return this._sequenceBase$.getValue()}uniqueNucleotidesChanged$(){return this.patternStateChanged$.pipe((0,nt.switchMap)((()=>this._uniqueNucleotides$)))}getUniqueNucleotides(){return this._uniqueNucleotides$.getValue()}get svgSaveRequested$(){return this._svgSaveRequested$.asObservable()}requestSvgSave(){this._svgSaveRequested$.next()}setAllPTOLinkages(t){const e=this.getPhosphorothioateLinkageFlags();k.forEach((n=>{e[n]=e[n].map((()=>t))})),this.updatePhosphorothioateLinkageFlags(e)}setPatternConfig(t){this._patternName$.next(t[j.PATTERN_NAME]),this._isAntisenseStrandActive$.next(t[q.IS_ANTISENSE_STRAND_INCLUDED]),this._nucleotideSequences$.next(t[q.NUCLEOTIDE_SEQUENCES]),this._phosphorothioateLinkageFlags.next(t[q.PHOSPHOROTHIOATE_LINKAGE_FLAGS]),this._terminalModifications.next(t[q.STRAND_TERMINUS_MODIFICATIONS]),this._comment$.next(t[j.PATTERN_COMMENT]),this._modificationsWithNumericLabels$.next(t[j.NUCLEOTIDES_WITH_NUMERIC_LABELS])}setLastLoadedPatternConfig(t){this._lastLoadedPatternConfig.next(lt().cloneDeep(t))}getPatternConfig(){return{[j.PATTERN_NAME]:this.getPatternName(),[q.IS_ANTISENSE_STRAND_INCLUDED]:this.isAntisenseStrandActive(),[q.NUCLEOTIDE_SEQUENCES]:this.getNucleotideSequences(),[q.PHOSPHOROTHIOATE_LINKAGE_FLAGS]:this.getPhosphorothioateLinkageFlags(),[q.STRAND_TERMINUS_MODIFICATIONS]:this.getTerminalModifications(),[j.PATTERN_COMMENT]:this.getComment(),[j.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 o=this.getModificationsWithNumericLabels();this.updateModificationsWithNumericLabels(o.concat(n)),this.updateNucleotideSequences(r)}get strandsUpdated$(){return et.merge(this._isAntisenseStrandActive$.asObservable().pipe((0,nt.map)((()=>{}))),this._nucleotideSequences$.asObservable().pipe((0,nt.map)((()=>{}))),this._patternLoaded$.asObservable().pipe((0,nt.map)((()=>{})))).pipe((0,nt.debounceTime)(10))}get strandsLinkagesAndTerminalsUpdated$(){return et.merge(this.strandsUpdated$,this._phosphorothioateLinkageFlags.asObservable().pipe((0,nt.map)((()=>{}))),this._terminalModifications.asObservable().pipe((0,nt.map)((()=>{}))))}updateControlsUponPatternLoaded(t){this._patternLoaded$.next(t)}get patternLoaded$(){return this._patternLoaded$.asObservable()}get userSelection$(){return this._patternAuthorSelection$.asObservable().pipe((0,nt.skip)(1))}selectAuthor(t){if("string"!=typeof t)throw new Error("Selected user must be defined");this._patternAuthorSelection$.next(t)}getSelectedAuthor(){return this._patternAuthorSelection$.getValue()}get loadPatternInNewTabRequested$(){return this._loadPatternInNewTabRequested$.asObservable()}requestLoadPatternInNewTab(t){this._loadPatternInNewTabRequested$.next(t)}updateUrlState(t){this._urlStateUpdated$.next(t)}get urlStateUpdated$(){return this._urlStateUpdated$.asObservable()}get patternHasUnsavedChanges$(){return this._patternHasUnsavedChanges$.asObservable()}selectStrandColumn(t,e){this._selectedStrandColumn.next({...this._selectedStrandColumn.getValue(),[t]:e})}getSelectedStrandColumn(t){const e=this._selectedStrandColumn.getValue();return e?e[t]:null}selectIdColumn(t){this._selectedIdColumn.next(t)}getSelectedIdColumn(){return this._selectedIdColumn.getValue()}get updateSvgContainer$(){return this.patternStateChanged$.pipe((0,nt.debounceTime)(100))}}const ct="pattern";class ht{constructor(){this.urlSearchParams=new URLSearchParams(window.location.search)}subscribeToObservables(t){t.urlStateUpdated$.subscribe((t=>this.setPatternURL(t))),t.loadPatternInNewTabRequested$.subscribe((t=>{const e=`${window.location.origin}${window.location.pathname}?${ct}=${t}`;window.open(e,"_blank")})),window.addEventListener("popstate",(()=>{this.urlSearchParams=new URLSearchParams(window.location.search);const e=this.getPatternHash();null!==e&&t.requestPatternLoad(e)}))}getPatternHash(){return this.urlSearchParams.get(ct)}setPatternURL(t){null!==t&&""!==t?(this.urlSearchParams.set(ct,t),window.history.pushState({},"",`${window.location.pathname}?${this.urlSearchParams}`)):this.clearPatternURL()}clearPatternURL(){this.urlSearchParams.delete(ct),window.history.pushState({},"",`${window.location.pathname}`)}}var dt=n(5072),ft=n.n(dt),pt=n(7825),mt=n.n(pt),gt=n(7659),yt=n.n(gt),bt=n(5056),vt=n.n(bt),wt=n(540),Ct=n.n(wt),At=n(1113),xt=n.n(At),St=n(9252),Tt={};Tt.styleTagTransform=xt(),Tt.setAttributes=vt(),Tt.insert=yt().bind(null,"head"),Tt.domAPI=mt(),Tt.insertStyleElement=Ct(),ft()(St.A,Tt),St.A&&St.A.locals&&St.A.locals;class Et{constructor(t){this.eventBus=t,this.columnControlsContainer=M.div([]),this.eventBus.tableSelectionChanged$.subscribe((()=>this.handleTableChoice())),this.refreshColumnControls()}getColumnControlsContainer(){return this.columnControlsContainer}get selectedTable(){return this.eventBus.getTableSelection()}handleTableChoice(){this.refreshColumnControls()}refreshColumnControls(){L()(this.columnControlsContainer).empty(),L()(this.columnControlsContainer).append(this.constructColumnControls())}constructColumnControls(){const t=this.createStrandColumnInput(),e=t.SS,n=t.AS;this.eventBus.antisenseStrandToggled$.subscribe((t=>{L()(n).toggle(t)}));const r=this.createIdColumnInput();return[e,n,r]}createStrandColumnInput(){const t=this.selectedTable?this.selectedTable.columns.names().sort(((t,e)=>t.localeCompare(e))):[];return Object.fromEntries(k.map((e=>{const n=M.input.choice(`${H[e]} column`,{value:t[0],items:t,onValueChanged:t=>this.eventBus.selectStrandColumn(e,t)});return this.eventBus.selectStrandColumn(e,t[0]),[e,n.root]})))}createIdColumnInput(){const t=this.selectedTable?this.selectedTable.columns.names():[],e=M.input.choice("ID column",{value:t[0],items:t,onValueChanged:t=>this.eventBus.selectIdColumn(t)});return this.eventBus.selectIdColumn(t[0]),e.root}}class _t{constructor(t){this.eventBus=t,this.availableTables=[],this.tableInputContainer=M.div([]),this.subscribeToTableEvents(),this.refreshTableInput()}getTableInputContainer(){return this.tableInputContainer}subscribeToTableEvents(){r.events.onTableAdded.subscribe((t=>this.handleTableAdded(t))),r.events.onTableRemoved.subscribe((t=>this.handleTableRemoved(t))),this.eventBus.tableSelectionChanged$.subscribe((()=>this.handleTableChoice()))}getTableFromEventData(t){if(!t&&t.args&&t.args.dataFrame instanceof o.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();L()(this.tableInputContainer).empty(),this.tableInputContainer.append(t.root)}createTableInput(){const t=this.eventBus.getTableSelection();return M.input.table("Tables",{value:t,items:this.availableTables,onValueChanged:t=>{null!==t&&this.eventBus.selectTable(t)}})}handleTableChoice(){const t=this.eventBus.getTableSelection();t&&(this.isTableDisplayed(t)||this.displayTable(t))}isTableDisplayed(t){return r.shell.tableNames.includes(t.name)}displayTable(t){const e=r.shell.v;r.shell.addTableView(t),r.shell.v=e}}function It(t,e,n,r){const o=function(t,e,n){const r=new Array(t.length+e.filter((t=>t)).length+U.length);r[0]=n["5'"],r[r.length-1]=n["3'"];let o=1;return e[0]&&(r[o]="ps",o++),t.forEach(((t,n)=>{r[n+o]=t,e[n+1]&&(r[n+o+1]="ps",o++)})),r}(t.split("").map(((t,n)=>{const r=function(t,e,n){const r=Object.keys(n.patternAppData)[0],o=n.patternAppData[r][e].substitution;return t.replace(/([AGCTU])/,o)}(t,e[n],Xr.jsonData);return r})),n,r);return o.join("")}class Nt{constructor(t){this.eventBus=t,this.tableInputManager=new _t(t),this.columnInputManager=new Et(t)}createControls(){const t=M.h1("Bulk convert"),e=this.tableInputManager.getTableInputContainer(),n=this.columnInputManager.getColumnControlsContainer(),r=M.bigButton("Convert",(()=>this.processConvertButtonClick()));return[t,e,n,M.buttonsInput([r])]}processConvertButtonClick(){!function(t){const e=t.getTableSelection();if(!e)return void r.shell.warning("Please select a table");const n=k.filter((e=>!("AS"===e&&!t.isAntisenseStrandActive()))).map((e=>({strand:e,column:t.getSelectedStrandColumn(e)}))).filter((t=>t.column));if(0===n.length)return void r.shell.warning("Select a sense strand column");const o=t.getSelectedIdColumn();if(!o)throw new Error("No ID column selected");e.getCol(o);const i=n.map((t=>({strand:t.strand,column:e.getCol(t.column)})));!function(t,e){const n=e.getNucleotideSequences();return t.every((t=>{const e=n[t.strand].length;return t.column.toList().every((t=>t.length===e))}))}(i,t)?r.shell.warning("Some strands in the table input do not match pattern length"):i.forEach((n=>{const r=n.column,o=n.strand,i=t.getNucleotideSequences()[o],s=t.getTerminalModifications()[o],a=t.getPhosphorothioateLinkageFlags()[o],l=`${t.getPatternName()}(${r.name})`;e.columns.addNewString(l).init((t=>It(r.get(t),i,a,s)))}))}(this.eventBus)}}class Mt{constructor(t,e,n){this.eventBus=t,this.initialPatternConfig=e,this.subscriptions=n}create(){return M.divV([M.h1("PTO"),M.divH([this.createAllPtoActivationInput().root,...this.createFirstPtoInputs().map((t=>t.root))],{style:{gap:"12px"}})])}areAllPtoLinkagesSet(t){return k.map((e=>t[e].filter((t=>t)).length)).reduce(((t,e)=>t+e),0)===k.map((t=>this.initialPatternConfig.nucleotideSequences[t].length)).reduce(((t,e)=>t+e),0)+k.filter((e=>t[e].length)).length}createAllPtoActivationInput(){const t=this.initialPatternConfig.phosphorothioateLinkageFlags,e=this.areAllPtoLinkagesSet(t),n=M.input.bool("All PTO",{value:e});n.onInput.subscribe((()=>{const t=n.value;this.eventBus.setAllPTOLinkages(t)}));const r=this.eventBus.phosphorothioateLingeFlagsChanged$.subscribe((()=>{const t=this.eventBus.getPatternConfig().phosphorothioateLinkageFlags,e=this.areAllPtoLinkagesSet(t);n.value=e}));return this.subscriptions.add(r),this.addStyleToPtoInput(n),M.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 k.map((t=>{if(!this.eventBus.isAntisenseStrandActive()&&"AS"===t)return;const e=this.isFirstPtoActive(t),n=M.input.bool(`First ${t} PTO`,{value:e});n.onInput.subscribe((()=>{const e=n.value;this.eventBus.setPhosphorothioateLinkageFlag(t,0,e)}));const r=this.eventBus.phosphorothioateLingeFlagsChanged$.subscribe((e=>{const r=e[t][0];n.value=r}));return this.subscriptions.add(r),this.addStyleToPtoInput(n),M.tooltip.bind(n.captionLabel,`Activate first phosphothioate in ${t}`),n})).filter((t=>void 0!==t))}isFirstPtoActive(t){return this.initialPatternConfig.phosphorothioateLinkageFlags[t][0]}}class Ot{constructor(t,e,n){this.eventBus=t,this.dataManager=e,this.subscriptions=n;const r=this.eventBus.nucleotideSequencesChanged$.subscribe((()=>{this.displayedInputLabels=this.computeDisplayedInputLabels()}));this.subscriptions.add(r)}create(){const t=k.map((t=>this.constructControlsPanel(t)));return M.divH(t,{style:{gap:"24px"}})}constructControlsPanel(t){if(!this.eventBus.isAntisenseStrandActive()&&"AS"===t)return M.div([]);const e=this.constructHeader(),n=this.createControls(t);return M.block([M.h1(`${H[t]}`),e,n],{style:{paddingTop:"12px"}})}constructHeader(){return M.divH([M.div([M.divText("#")],{style:{width:"20px"}}),M.block75([M.divText("Modification")]),M.div([M.divText("PTO")])])}createControls(t){const e=this.createNucleobaseInputs(t),n=this.createLabelDivs(t),r=this.createPTOFlagInputs(t);return M.div(e.map(((t,e)=>M.divH([n[e],M.block75([t.root]),r[e].root],{style:{alignItems:"center"}}))))}createNucleobaseInputs(t){const e=this.dataManager.fetchAvailableNucleotideBases().sort(((t,e)=>t.toLowerCase().localeCompare(e.toLowerCase())));return this.eventBus.getNucleotideSequences()[t].map(((n,r)=>{const o=M.input.choice("",{value:n,items:e});return o.onInput.subscribe((()=>{const e=o.value;this.eventBus.setNucleotide(t,r,e)})),o}))}createPTOFlagInputs(t){return this.eventBus.getPhosphorothioateLinkageFlags()[t].slice(1).map(((e,n)=>{const r=M.input.bool("",{value:e});r.onInput.subscribe((()=>{const e=r.value;this.eventBus.setPhosphorothioateLinkageFlag(t,n+1,e)}));const o=this.eventBus.phosphorothioateLingeFlagsChanged$.subscribe((e=>{const o=e[t][n+1];r.value=o}));return this.subscriptions.add(o),r}))}computeDisplayedInputLabels(){const t=this.eventBus.getNucleotideSequences(),e=new Map;return k.forEach((n=>{let r=1;const o=t[n].map((t=>{if(rt(t))return"";const e=String(r);return r++,e}));e.set(n,o)})),e}createLabelDivs(t){const e=this.createLabels(t).map((t=>M.div([t],{style:{width:"20px"}}))),n=this.eventBus.nucleotideSequencesChanged$.subscribe((()=>{this.createLabels(t).forEach(((t,n)=>{L()(e[n]).empty(),L()(e[n]).append(t)}))}));return this.subscriptions.add(n),e}createLabels(t){return this.eventBus.getNucleotideSequences()[t].map(((e,n)=>{const r=this.displayedInputLabels.get(t)[n];return M.label(r)}))}}class Lt{constructor(){this.rxjsSubscriptions=[],this.dgSubscriptions=[]}add(t){t instanceof et.Subscription?this.rxjsSubscriptions.push(t):this.dgSubscriptions.push(t)}unsubscribeAll(){for(const t of[this.rxjsSubscriptions,this.dgSubscriptions])t.forEach((t=>t.unsubscribe())),t.length=0}}class Rt{constructor(t,e){this.eventBus=t,this.dataManager=e,this.subscriptions=new Lt}static open(t,e){Rt.isDialogOpen||(Rt.instance||(Rt.instance=new Rt(t,e)),Rt.instance.openDialog())}openDialog(){this.initialPatternConfig=lt().cloneDeep(this.eventBus.getPatternConfig()),Rt.isDialogOpen=!0,this.createDialog().show()}createDialog(){const t=M.divV([]);this.subscriptions.add(this.eventBus.strandsUpdated$.subscribe((()=>this.onStrandsUpdated(t))));const e=M.dialog("Edit strands").add(t).onOK((()=>{})).onCancel((()=>this.resetToInitialState()));return this.subscriptions.add(e.onClose.subscribe((()=>{Rt.isDialogOpen=!1,this.subscriptions.unsubscribeAll()}))),e}onStrandsUpdated(t){const e=new Mt(this.eventBus,this.initialPatternConfig,this.subscriptions).create(),n=new Ot(this.eventBus,this.dataManager,this.subscriptions).create();L()(t).empty(),L()(t).append(e,n)}resetToInitialState(){this.eventBus.setPatternConfig(this.initialPatternConfig)}}Rt.isDialogOpen=!1;class Pt{constructor(t){this.eventBus=t,this.subscriptions=new Lt}static open(t){Pt.isDialogOpen||(Pt.instance||(Pt.instance=new Pt(t)),Pt.instance.openDialog())}openDialog(){this.initialPatternConfig=lt().cloneDeep(this.eventBus.getPatternConfig()),Pt.isDialogOpen=!0,this.createDialog().show()}createDialog(){const t=M.divV([]);this.subscriptions.add(this.eventBus.strandsUpdated$.subscribe((()=>this.onStrandsUpdated(t))));const e=M.dialog("Edit terminal modifications").add(t).onOK((()=>{})).onCancel((()=>this.resetToInitialState()));return this.subscriptions.add(e.onClose.subscribe((()=>{Pt.isDialogOpen=!1,this.subscriptions.unsubscribeAll()}))),e}onStrandsUpdated(t){const e=new Bt(this.eventBus).create();L()(t).empty(),L()(t).append(e)}resetToInitialState(){this.eventBus.setPatternConfig(this.initialPatternConfig)}}Pt.isDialogOpen=!1;class Bt{constructor(t){this.eventBus=t}create(){const t=k.map((t=>this.constructControlsPanel(t)));return M.divH(t,{style:{gap:"24px"}})}constructControlsPanel(t){if(!this.eventBus.isAntisenseStrandActive()&&"AS"===t)return M.div([]);const e=this.createInputs(t);return M.block([M.h1(`${H[t]}`),e],{style:{paddingTop:"12px"}})}createInputs(t){const e=("SS"===t?[...U].reverse():U).map((e=>this.createInputForTerminus(t,e)));return M.form(e)}createInputForTerminus(t,e){const n=this.eventBus.getTerminalModifications()[t][e],r=M.input.textArea(e,{value:n});return this.applyStylingToInput(r),r.onInput.subscribe((()=>{const n=r.value;null!==n&&this.eventBus.updateTerminusModification(t,e,n)})),r}applyStylingToInput(t){const e=t.root.getElementsByTagName("textarea")[0];L()(e).css("resize","none")}}class Dt{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,o=this.createSequenceBaseInput().root,i=this.createPatternCommentInput().root,s=this.createPatternNameInputBlock(),a=this.createEditPatternButton(),l=this.createEditTerminalModificationsButton();return[M.h1("Edit"),t,n,r,o,s,i,M.buttonsInput([l,a])]}createEditPatternButton(){const t=M.button("Edit strands",(()=>Rt.open(this.eventBus,this.dataManager)));return M.tooltip.bind(t,"Edit strand modifications and PTOs"),t}createEditTerminalModificationsButton(){const t=M.button("Edit terminals",(()=>Pt.open(this.eventBus)));return M.tooltip.bind(t,"Edit terminal modifications"),L()(t).css("margin-right","20px"),t}createAntisenseStrandToggle(){const t=M.input.toggle(`${H.AS} strand`,{value:this.eventBus.isAntisenseStrandActive()});return t.onInput.subscribe((()=>this.eventBus.toggleAntisenseStrand(t.value))),this.eventBus.patternLoaded$.subscribe((()=>{t.value=this.eventBus.isAntisenseStrandActive()})),t.setTooltip("Toggle antisense strand"),t.root}createStrandLengthInputs(){const t=t=>{const n=this.eventBus.getNucleotideSequences()[t].length,r=M.input.int(`${H[t]} length`,{value:n});return r.onInput.subscribe((()=>e(t,r))),this.eventBus.nucleotideSequencesChanged$.subscribe((()=>{r.value=this.eventBus.getNucleotideSequences()[t].length})),r.setTooltip(`Number of nucleotides in ${t}, including overhangs`),[t,r]},e=(t,e)=>{const n=e.value;null!==n&&(n<=0&&(r.shell.warning("Sequence length must be greater than 0"),e.value=1),n>34&&(r.shell.warning("Sequence length must be less than 35"),e.value=34),this.eventBus.updateStrandLength(t,e.value))},n=Object.fromEntries(k.map((e=>t(e))));return this.eventBus.antisenseStrandToggled$.subscribe((t=>{L()(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=M.input.choice("Sequence basis",{value:e,items:t});return n.onInput.subscribe((()=>this.eventBus.replaceSequenceBase(n.value))),this.eventBus.nucleotideSequencesChanged$.subscribe((()=>{n.value=this.eventBus.getSequenceBase()})),n.setTooltip("Most frequent nucleobase in the strands"),n}createPatternCommentInput(){const t=M.input.textArea("Comment",{value:this.eventBus.getComment()});return L()(t.root).addClass("st-pattern-text-input"),t.onInput.subscribe((()=>this.eventBus.updateComment(t.value))),this.eventBus.patternLoaded$.subscribe((()=>{t.value=this.eventBus.getComment()})),t}createPatternNameInputBlock(){const t=M.input.textArea("Pattern name",{value:this.eventBus.getPatternName()});return L()(t.root).addClass("st-pattern-text-input"),t.onInput.subscribe((()=>this.eventBus.updatePatternName(t.value))),this.eventBus.patternLoaded$.subscribe((()=>{t.value=this.eventBus.getPatternName()})),t.setTooltip("Name under which pattern will be saved"),t.root}}class Ft{constructor(t,e){this.eventBus=t,this.dataManager=e,this.subscriptions=new Lt,this.authorSelectedByUser=!1,this.eventBus.patternLoadRequested$.subscribe((t=>this.handlePatternChoice(t))),this.eventBus.patternDeletionRequested$.subscribe((async t=>{await this.dataManager.deletePattern(t,this.eventBus)}))}async handlePatternChoice(t){let e=await this.dataManager.getPatternConfig(t);null===e&&(e=this.dataManager.getDefaultPatternConfig()),this.eventBus.setPatternConfig(e),this.eventBus.updateControlsUponPatternLoaded(t),this.eventBus.setLastLoadedPatternConfig(e)}isCurrentUserSelected(){return this.eventBus.getSelectedAuthor()!==this.dataManager.getOtherUsersAuthorshipCategory()}createControls(){const t=this.getPatternInputsContainer();return[M.h1("Load"),t]}getPatternInputsContainer(){const t=M.divH(this.createPatternInputs());return this.eventBus.patternListUpdated$.subscribe((()=>{this.subscriptions.unsubscribeAll(),L()(t).empty(),L()(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=M.div([t.root]),n=this.eventBus.userSelection$.subscribe((()=>{L()(e).empty(),L()(e).append(this.createPatternChoiceInput().root)}));return this.subscriptions.add(n),e}createAuthorChoiceInput(){const t=[this.dataManager.getCurrentUserAuthorshipCategory()];this.dataManager.getOtherUsersPatternNames().length>0&&t.push(this.dataManager.getOtherUsersAuthorshipCategory());const e=M.input.choice("Author",{value:this.eventBus.getSelectedAuthor(),items:t});return e.onInput.subscribe((()=>{if(this.authorSelectedByUser=!0,null===e.value)throw new Error("author choice must be non-null");this.eventBus.selectAuthor(e.value)})),this.setAuthorChoiceInputStyle(e),e.setTooltip("Select pattern author"),e}setAuthorChoiceInputStyle(t){L()(t.input).css({"max-width":"100px","min-width":"100px"}),L()(t.root).css({"padding-right":"30px","padding-left":"30px"})}createPatternChoiceInput(){const t=this.isCurrentUserSelected()?this.dataManager.getCurrentUserPatternNames():this.dataManager.getOtherUsersPatternNames();if(this.authorSelectedByUser){const e=this.dataManager.getPatternHash(t[0],this.isCurrentUserSelected());this.eventBus.requestPatternLoad(e),this.eventBus.updateUrlState(e),this.authorSelectedByUser=!1}const e=this.getPatternName(t),n=M.input.choice("Pattern",{value:e,items:t});return n.setTooltip("Select pattern to load"),L()(n.input).css({"max-width":"100px","min-width":"100px"}),this.subscriptions.add(n.onInput.subscribe((()=>{const t=this.dataManager.getPatternHash(n.value,this.isCurrentUserSelected());this.eventBus.requestPatternLoad(t),this.eventBus.updateUrlState(t)}))),this.subscriptions.add(this.eventBus.patternLoaded$.subscribe((()=>{const e=this.eventBus.getPatternName();n.value!==e&&(n.value=this.getPatternName(t))}))),n}getPatternName(t){return t.find((t=>t.split(" (")[0]===this.eventBus.getPatternName()))??t[0]}createDeletePatternButton(){const t=M.button(M.iconFA("trash-alt"),(()=>{this.eventBus.getPatternName()!==this.dataManager.getDefaultPatternName()?this.showDeletePatternDialog():r.shell.warning("Cannot delete example pattern")}));M.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=M.dialog("Delete pattern"),e=this.eventBus.getPatternName();t.add(M.divText(`Are you sure you want to delete pattern ${e}?`)),t.onOK((()=>this.eventBus.requestPatternDeletion(e))),t.show()}}class kt{constructor(t,e){this.eventBus=t,this.dataManager=e}getLayout(){const t=new Ft(this.eventBus,this.dataManager),e=new Dt(this.eventBus,this.dataManager),n=new Nt(this.eventBus),r=t.createControls(),o=e.createControls(),i=n.createControls(),s=M.div(r);L()(s).css({"padding-bottom":"20px"});const a=M.div([...o,...i],"ui-form"),l=M.div([s,a]);return L()(l).css({padding:"25px"}),M.box(l,{style:{maxWidth:"450px"}})}}var Ht=n(9146);class Ut{constructor(t,e,n){this.svgElementFactory=t,this.config=e,this.yShift=n}shiftElements(t){this.svgElements.forEach((e=>{const n=e.getAttribute("transform")||"",r=`translate(${t.x},${t.y})`;e.setAttribute("transform",`${n} ${r}`)}))}}class $t{constructor(){}static getInstance(){return $t.instance||($t.instance=new $t,$t.instance.canvas=document.createElement("canvas")),$t.instance}static getTextDimensions(t,e){const n=$t.getInstance().canvas.getContext("2d");if(!n)throw new Error("Canvas 2D context is not available");return n.font=`${e}px Arial`,{width:1.1*n.measureText(t).width,height:1.1*e}}}function Vt(t){const e=Object.keys(Xr.jsonData.patternAppData)[0];if(!e)throw new Error(`No format found in '${h}'`);return Xr.jsonData.patternAppData[e][t].color||""}class qt extends Ut{constructor(t,e,n){super(t,e,n);const r=k.filter((t=>e.nucleotideSequences[t].length>0));this.strands=r.map((t=>new jt(this.svgElementFactory,e,n,t))),this.terminalModifications=r.map(((t,r)=>new zt(this.svgElementFactory,e,n,t,this.strands[r]))),this.labels=r.map(((t,r)=>new Gt(this.svgElementFactory,e,n,t,this.terminalModifications[r])))}get svgElements(){return[...this.strands,...this.terminalModifications,...this.labels].map((t=>t.svgElements)).flat()}getContentWidth(){return Math.max(...this.labels.map((t=>t.getContentWidth())))}getContentHeight(){return this.strands.reduce(((t,e)=>t+e.getContentHeight()),0)}}class jt extends Ut{constructor(t,e,n,r){super(t,e,n),this.svgElementFactory=t,this.config=e,this.yShift=n,this.strand=r,this.nucleotideNumericLabels=this.computeNucleotideNumericLabels(),"AS"===this.strand&&(this.config.phosphorothioateLinkageFlags[this.strand].reverse(),this.config.nucleotideSequences[this.strand].reverse(),this.nucleotideNumericLabels.reverse()),this._svgElements=[this.createStrandCircles(),this.createPTOLinkageStars()].flat()}computeNucleotideNumericLabels(){let t=0;return this.config.nucleotideSequences[this.strand].map((e=>rt(e)?null:(t++,t)))}get svgElements(){return this._svgElements}getStrandCircleYShift(){return Wt(this.strand,this.yShift)}createStrandCircles(){const t={x:80,y:this.getStrandCircleYShift()};return this.config.nucleotideSequences[this.strand].map(((e,n)=>this.createNucleotideElementGroup(e,n,t))).flat()}createNucleotideElementGroup(t,e,n){return[...this.createNucleotideCircleElements(t,e,n),this.config.nucleotidesWithNumericLabels.includes(t)?this.createNucleotideNumericLabel(e,n):null].filter((t=>null!==t))}createNucleotideCircleElements(t,e,n){const r=Vt(t),o={...n,x:n.x+30*e};return[this.svgElementFactory.createCircleElement(o,15,r),this.createNucleotideLetterLabel(e,n,t)]}getNucleotideCircleCenterPosition(t,e){return{x:e.x+30*t,y:e.y}}createNucleotideLetterLabel(t,e,n){if(!m.AL.includes(n))return null;const r=function(t){return!rt(t)&&m.AL.includes(t)?t:""}(n),o=function(t){const e=Vt(t),n=e.match(/\d+/g)?.map(Number);if(!n||n.length<3)return"#ffffff";const[r,o,i]=n;return.299*r+.587*o+.114*i>186?"#333333":"#ffffff"}(n),i=this.getPositionForNucleotideLabel(t,e);return this.svgElementFactory.createTextElement(r,i,17,o)}getPositionForNucleotideLabel(t,e){const n=this.getNucleotideCircleCenterPosition(t,e),r=$t.getTextDimensions("A",17);return{x:n.x-r.width/2,y:n.y+r.height/3}}getNumericLabelYShift(t){return"SS"===this.strand?t.y-20:t.y+15+5+15}createNucleotideNumericLabel(t,e){const n=this.nucleotideNumericLabels[t];if(null===n)return null;const r=$t.getTextDimensions(n.toString(),15).width,o={x:e.x+30*t-r/2,y:this.getNumericLabelYShift(e)};return this.svgElementFactory.createTextElement(n.toString(),o,15,"var(--grey-6)")}createPTOLinkageStars(){const t=this.config.phosphorothioateLinkageFlags[this.strand],e=this.getStrandCircleYShift()+12;return t.map(((t,n)=>{if(!t)return null;const r={x:65+30*n,y:e};return this.svgElementFactory.createStarElement(r,"red")})).filter((t=>null!==t))}getContentWidth(){return 30*this.config.nucleotideSequences[this.strand].length}getContentHeight(){return 62}}class Gt extends Ut{constructor(t,e,n,r,o){super(t,e,n),this.svgElementFactory=t,this.config=e,this.yShift=n,this.strand=r,this.terminalModifications=o,this._svgElements=this.createSVGElements()}createSVGElements(){return[this.createLeftLabel(),this.createRightLabel()]}getLeftLabelWidth(){return 55}getRightLabelWidth(){return 20}createLeftLabel(){const t="SS"===this.strand?"5'":"3'",e=`${this.strand}: ${t} `,n=$t.getTextDimensions(e,17),r={x:10,y:Wt(this.strand,this.yShift)+n.height/3};return this.svgElementFactory.createTextElement(e,r,17,"var(--grey-6)")}createRightLabel(){const t=" "+("SS"===this.strand?"3'":"5'"),e=$t.getTextDimensions(t,17),n={x:65+this.terminalModifications.getContentWidth()+5,y:Wt(this.strand,this.yShift)+e.height/3};return this.svgElementFactory.createTextElement(t,n,17,"var(--grey-6)")}get svgElements(){return this._svgElements}getContentWidth(){return this.terminalModifications.getContentWidth()+this.getLeftLabelWidth()+this.getRightLabelWidth()+10}getContentHeight(){return this.terminalModifications.getContentHeight()}}class zt extends Ut{constructor(t,e,n,r,o){super(t,e,n),this.svgElementFactory=t,this.config=e,this.yShift=n,this.strand=r,this.strandSvgWrapper=o,this._svgElements=this.createSVGElements()}createSVGElements(){return this.createTerminalModifications()}getTerminalModification(t){return this.config.strandTerminusModifications[this.strand][t]}getTerminalModificationTextDimensions(t){const e=this.getTerminalModification(t);return $t.getTextDimensions(e,17)}getLeftTerminus(){return"SS"===this.strand?"5'":"3'"}createTerminalModification(t){const e=this.getTerminalModification(t),n=this.getTerminalModificationTextDimensions(t),r=t===this.getLeftTerminus(),o={x:r?65:65+this.getTerminalModificationTextDimensions(this.getLeftTerminus()).width+this.strandSvgWrapper.getContentWidth(),y:Wt(this.strand,this.yShift)+n.height/3};return r&&this.strandSvgWrapper.shiftElements({x:n.width,y:0}),this.svgElementFactory.createTextElement(e,o,17,"red")}createTerminalModifications(){return("AS"===this.strand?U:Array.from(U).reverse()).map((t=>this.createTerminalModification(t)))}get svgElements(){return this._svgElements}getContentWidth(){return this.strandSvgWrapper.getContentWidth()+U.map((t=>this.getTerminalModificationTextDimensions(t).width)).reduce(((t,e)=>t+e),0)}getContentHeight(){return this.strandSvgWrapper.getContentHeight()}}function Wt(t,e){return"SS"===t?e+5+15+15:e+52+10+15}class Yt{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 o=this.createElement("text");return this.setAttributes(o,{x:e.x,y:e.y,"font-size":n,"font-weight":"normal","font-family":"Arial",fill:r}),o.textContent=t,o}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,o)=>{const i=o%2==0?6:3,s=o*e+n;return[t.x+Math.cos(s)*i,t.y+Math.sin(s)*i]}))}createRectangleElement(t,e,n,r){const o=this.createElement("rect");return this.setAttributes(o,{x:t.x,y:t.y,width:e,height:n,fill:r}),o}}class Kt extends Ut{constructor(t,e,n){super(t,e,n),this.svgElementFactory=t,this.config=e,this.yShift=n,this._svgElements=[],this.titleText=this.getTitleText(),this._svgElements=[this.getTitle()]}get svgElements(){return this._svgElements}getTitle(){return this.svgElementFactory.createTextElement(this.titleText,{x:15,y:this.yShift+17},17,"black")}getContentWidth(){return $t.getTextDimensions(this.titleText,17).width}getContentHeight(){return $t.getTextDimensions(this.titleText,17).height}getTitleText(){const t=`${this.config.nucleotideSequences.SS.length}`,e=this.config.isAntisenseStrandIncluded?`/${this.config.nucleotideSequences.AS.length}`:"";return`${this.config.patternName} for ${t}${e}-mer`}}class Jt extends Ut{constructor(t,e,n){super(t,e,n),this._svgElements=[];const{elements:r,width:o}=this.createLegendItems();this._svgElements=r,this.width=o}isPhosphorothioatePresent(){return Object.values(this.config.phosphorothioateLinkageFlags).flat().some((t=>t))}getModificationTypesList(){return[...new Set(Object.values(this.config.nucleotideSequences).flat().sort(((t,e)=>t.toLowerCase().localeCompare(e.toLowerCase()))))]}get svgElements(){return this._svgElements}createLegendItem(t,e){const n={x:e,y:this.yShift-6},r=t.includes("linkage")?this.svgElementFactory.createStarElement(n,"red"):this.svgElementFactory.createCircleElement(n,6,Vt(t));e+=12;const o={y:this.yShift,x:e};return{elements:[r,this.svgElementFactory.createTextElement(t,o,15,"var(--grey-6)")],width:12+$t.getTextDimensions(t,15).width}}createLegendItems(){let t=10;const e=[],n=e=>t+=e+15;if(this.isPhosphorothioatePresent()){const{elements:r,width:o}=this.createLegendItem("PTO linkage",t);n(o),e.push(r)}return this.getModificationTypesList().forEach((r=>{const{elements:o,width:i}=this.createLegendItem(r,t);n(i),e.push(o)})),{elements:e.flat(),width:t}}getContentHeight(){return 20}getContentWidth(){return this.width}}class Qt{constructor(t){this.svgElementFactory=new Yt;const e=lt().cloneDeep(t);let n=10;this.title=new Kt(this.svgElementFactory,e,n),n+=this.title.getContentHeight(),this.strands=new qt(this.svgElementFactory,e,n),n+=this.strands.getContentHeight()+10,this.legend=new Jt(this.svgElementFactory,e,n)}renderPattern(){const t=this.getGlobalWidth(),e=this.getGlobalHeight(),n=this.svgElementFactory.createCanvas(t,e),r=[this.title,this.strands,this.legend].map((t=>t.svgElements)).flat();return n.append(...r),n}getGlobalWidth(){const t=[this.title,this.strands,this.legend];return Math.max(...t.map((t=>t.getContentWidth())))}getGlobalHeight(){return[this.title,this.strands,this.legend].reduce(((t,e)=>t+e.getContentHeight()),10)}}class Xt{constructor(t){this.eventBus=t,this.svgDisplayDiv=M.div([]),t.updateSvgContainer$.subscribe((()=>this.updateSvgContainer())),t.svgSaveRequested$.subscribe((()=>this.saveSvgAsPng()))}static createSvgDiv(t){return new Xt(t).svgDisplayDiv}updateSvgContainer(){$(this.svgDisplayDiv).empty();const t=this.eventBus.getPatternConfig();this.svgElement=this.createSvg(t),this.svgDisplayDiv.append(this.svgElement)}createSvg(t){return new Qt(t).renderPattern()}saveSvgAsPng(){const t=this.eventBus.getPatternName();Ht.saveSvgAsPng(this.svgElement,t,{backgroundColor:"white"})}}class Zt{constructor(t){this.eventBus=t,this.togglesContainer=M.div([]),this.eventBus.uniqueNucleotidesChanged$().subscribe((()=>{this.updateContainer()}))}getContainer(){return this.togglesContainer}updateContainer(){L()(this.togglesContainer).empty(),L()(this.togglesContainer).append(this.createInputs())}createInputs(){const t=this.eventBus.getUniqueNucleotides().filter((t=>!rt(t))).map((t=>this.createSingleInput(t)));return t.sort(((t,e)=>t.captionLabel.textContent.localeCompare(e.captionLabel.textContent))),M.divH(t.map((t=>t.root)))}createSingleInput(t){const e=this.eventBus.getModificationsWithNumericLabels().includes(t),n=M.input.bool(t,{value:e,onValueChanged:e=>this.handleNumericLabelToggle(t,e)});return L()(n.root).css("padding-right","20px"),n.setTooltip(`Show numeric labels for ${t}`),n}handleNumericLabelToggle(t,e){const n=this.eventBus.getModificationsWithNumericLabels();if(n.includes(t)===e)return;const r=e?n.concat(t):n.filter((e=>e!==t));this.eventBus.updateModificationsWithNumericLabels(r)}}class te{constructor(t,e){this.eventBus=t,this.dataManager=e,this.subscriptions=new Lt}createContainer(){return M.div([M.h1("Translation example"),this.createTranslationExamples()],{style:{paddingTop:"20px"}})}createTranslationExamples(){const t=M.divH([...this.getExampleElements()],"ui-form");return this.eventBus.antisenseStrandToggled$.subscribe((()=>{this.subscriptions.unsubscribeAll(),L()(t).empty(),L()(t).append(this.getExampleElements())})),t}getExampleElements(){return k.map((t=>new ee(t,this.eventBus,this.subscriptions).create()))}}class ee{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(),M.block50([M.h2(H[this.strand]),this.inputExample.root,this.outputExample.root],{style:{paddingRight:"20px"}})):M.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 ${H[this.strand]}`),t}generateExampleSequence(){return this.eventBus.getNucleotideSequences()[this.strand].map(((t,e)=>m.AL[e%m.AL.length])).join("")}createOutputExample(t){const e=this.createTextInputForExamples();return e.value=this.computeOutputValue(t),e.setTooltip(`Pattern applied to the example input for ${H[this.strand]}`),e}computeOutputValue(t){const e=this.eventBus.getNucleotideSequences()[this.strand],n=this.eventBus.getTerminalModifications()[this.strand];return It(t,e,this.eventBus.getPhosphorothioateLinkageFlags()[this.strand],n)}createTextInputForExamples(){const t=M.input.textArea("",{value:""});return this.applyStylingToInput(t),t}applyStylingToInput(t){const e=t.root.getElementsByTagName("textarea")[0];e.setAttribute("readonly","true"),L()(e).css("resize","none"),L()(t.root).css("opacity","75%")}}class ne{constructor(t,e){this.eventBus=t,this.dataManager=e,this.svgDisplay=Xt.createSvgDiv(t)}getLayout(){const t=new Zt(this.eventBus).getContainer(),e=this.generateDownloadControls(),n=new te(this.eventBus,this.dataManager).createContainer();return M.panel([this.svgDisplay,t,e,n],{style:{overflowX:"scroll",padding:"12px 24px"}})}generateDownloadControls(){return M.divH([this.createSavePatternButton(),this.createDownloadPngButton(),this.createShareLinkButton(),this.createInfoButton()],{style:{gap:"12px",marginTop:"12px"}})}createDownloadPngButton(){const t=M.button("Get PNG",(()=>this.eventBus.requestSvgSave()));return M.tooltip.bind(t,"Download pattern as PNG"),t}createInfoButton(){const t=M.button(M.iconFA("info-circle"),(()=>this.openInfoDialog()));return this.eventBus.patternHasUnsavedChanges$.subscribe((e=>{t.disabled=e})),M.tooltip.bind(t,"View pattern metadata"),t}async openInfoDialog(){let t=this.dataManager.getCurrentUserName(),e=this.dataManager.getDefaultPatternName(),n=K,o=K;const i=new URLSearchParams(window.location.search).get("pattern");if(null!==i){const s=await this.dataManager.getPatternRecordByHash(i);if(null!==s){const i=s[G.AUTHOR_ID];if(t=(await r.dapi.users.find(i)).friendlyName,e=s[G.PATTERN_CONFIG][j.PATTERN_NAME],void 0!==s[G.DATE]){const t=s[G.DATE][z.CREATE];void 0!==t&&(n=t);const e=s[G.DATE][z.MODIFY];void 0!==e&&(o=e)}}}const s=M.divV([M.divText(`Pattern Name: ${e}`),M.divText(`Author: ${t}`),M.divText(`Created: ${oe(new Date(n))}`),M.divText(`Modified: ${oe(new Date(o))}`)]);r.shell.info(s)}createShareLinkButton(){const t=M.button(M.iconFA("link"),(()=>navigator.clipboard.writeText(window.location.href).then((()=>r.shell.info("Link to pattern copied to clipboard")))));return this.eventBus.patternHasUnsavedChanges$.subscribe((e=>{t.disabled=e})),M.tooltip.bind(t,"Share pattern link"),t}createSavePatternButton(){const t=M.button("Save",(()=>this.processSaveButtonClick()));return this.eventBus.patternHasUnsavedChanges$.subscribe((e=>{t.disabled=!e})),M.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((()=>{r.shell.info(`Pattern ${t} saved`)})).catch((t=>this.handleErrorWhileSavingPattern(t))):r.shell.warning("Insert pattern name"):r.shell.warning("Cannot save default pattern")}handleErrorWhileSavingPattern(t){t instanceof J?new re(this.eventBus,this.dataManager).show():t instanceof Q?r.shell.warning(M.div([M.divText("Pattern already exists"),M.button("Load",(()=>{const e=t.message;this.eventBus.requestLoadPatternInNewTab(e)}))])):console.error("Error while saving pattern",t)}}class re{constructor(t,e){this.eventBus=t,this.dataManager=e}show(){const t=this.eventBus.getPatternName(),e=M.dialog(`Pattern "${t}" already exists`);e.add(M.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.overwriteExistingPatternInUserStorage(this.eventBus).then((()=>{r.shell.info(`Pattern ${t} overwritten`)})).catch((t=>{console.error("Error while overwriting pattern in user storage",t),r.shell.error("Error while overwriting pattern")}))}}function oe(t){return t.toLocaleString().split(":").slice(0,-1).join(":")}class ie extends F{constructor(t){super("Oligo Pattern"),this.th=t}getContent(){return async function(){const t=await tt.getInstance(),e=new ht,n=await async function(t,e){const n=e.getPatternHash();if(!n)return e.clearPatternURL(),t.getDefaultPatternRecord();let r=await t.getPatternRecordByHash(n);return r||(e.clearPatternURL(),r=t.getDefaultPatternRecord()),r}(t,e),r=new ut(t,n);e.subscribeToObservables(r);const o=new kt(r,t).getLayout(),i=new ne(r,t).getLayout();return M.splitH([o,i],{},!0)}()}}var se=n(8507),ae={};function le(t){var e;return"string"==typeof t||t instanceof String?t:("object"==typeof t||t instanceof Object)&&"$thrownJsError"in t?le(t.$thrownJsError):t instanceof Error?null!==(e=t.stack)&&void 0!==e?e:t.message:t.toString()}ae.styleTagTransform=xt(),ae.setAttributes=vt(),ae.insert=yt().bind(null,"head"),ae.domAPI=mt(),ae.insertStyleElement=Ct(),ft()(se.A,ae),se.A&&se.A.locals&&se.A.locals;var ue,ce=n(2074),he={};he.styleTagTransform=xt(),he.setAttributes=vt(),he.insert=yt().bind(null,"head"),he.domAPI=mt(),he.insertStyleElement=Ct(),ft()(ce.A,he),ce.A&&ce.A.locals&&ce.A.locals;class de{constructor(t,e,n=!0){this.textInputBase=t,this.painter=e,L()(this.root).addClass("st-colored-text-input"),n&&this.textInputBase.onChanged.subscribe((()=>{L()(this.textArea).css("height",0),L()(this.textArea).css("height",this.textArea.scrollHeight+"px")})),this.highlights=M.div([]),this.root.appendChild(this.highlights),this.colorize(),this.textInputBase.onChanged.subscribe((()=>this.colorize()))}get textArea(){return this.textInputBase.root.getElementsByTagName("textarea").item(0)}get inputBase(){return this.textInputBase}get root(){return this.textInputBase.root}colorize(){const t=this.painter(this.textInputBase.value);this.highlights.innerHTML="",t.forEach((t=>this.highlights.appendChild(t)))}}!function(t){t.TYPE="V2000",t[t.NUM_OF_HEADER_LINES=3]="NUM_OF_HEADER_LINES",t[t.NUM_OF_COUNTS_DIGITS=3]="NUM_OF_COUNTS_DIGITS",t[t.ATOM_TYPE_COL=4]="ATOM_TYPE_COL",t[t.FIRST_BONDED_ATOM_COL=1]="FIRST_BONDED_ATOM_COL",t[t.BOND_TYPE_COL=3]="BOND_TYPE_COL",t[t.RGP_SHIFT=8]="RGP_SHIFT",t[t.MAX_ATOM_COUNT=999]="MAX_ATOM_COUNT",t.RGP_LINE_START="M RGP",t.ATOM_ALIAS_LINE_START="A ",t.END="M END"}(ue||(ue={}));class fe{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 o=0;o<this.atomCount;o++){r=this.shiftIdxToXColumn(r);for(const i of[t,e,n])i[o]=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 pe extends fe{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 me extends pe{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(ue.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(ue.ATOM_ALIAS_LINE_START))return e})).filter((t=>void 0!==t)),r=n.map((t=>e[t])),o=n.map((t=>e[t+1]));r.forEach(((e,n)=>{const r=parseInt(e.split(/\s+/)[1])-1,i=parseInt(o[n].substring(1));if(t.has(i))throw new Error(`R group ${i} is already in the map`);t.set(i,r)}));const i=this.getRGroupAtomicIndices().filter((e=>!Array.from(t.values()).includes(e)));if(0!==i.length)throw new Error(`Unaccounted R group indices: ${i}`);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(ue.TYPE)&&-1!==t.indexOf(ue.END)}shiftIdxToAtomType(t){return this.shiftIdxToSpecifiedColumn(t,ue.ATOM_TYPE_COL)}getCountsLineIdx(){let t=0;for(let e=0;e<ue.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,ue.FIRST_BONDED_ATOM_COL)}shiftIdxToBondType(t){return this.shiftIdxToSpecifiedColumn(t,ue.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+ue.NUM_OF_COUNTS_DIGITS;const n=parseInt(this.fileContent.substring(t,e));return t=e,e+=ue.NUM_OF_COUNTS_DIGITS,{atomCount:n,bondCount:parseInt(this.fileContent.substring(t,e))}}}class ge extends pe{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 o=e[1];if(t.has(o))throw new Error(`R group ${o} is already in the map`);t.set(o,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 ye{constructor(){}static getInstance(t){if(ye.isMolfileV2K(t))return new me(t);if(ye.isMolfileV3K(t))return new ge(t);throw new Error("Malformed molfile")}static isMolfileV2K(t){return me.isValidMolfile(t)}static isMolfileV3K(t){return ge.isValidMolfile(t)}}const be=class extends Error{constructor(t){super(t)}};class ve{constructor(t){this.molblock=t}get molblock(){return this._validMolBlock}set molblock(t){if(""!==t){try{this.validateMolBlock(t)}catch(e){e instanceof be&&(t="");const n=le(e);console.error(n)}this._validMolBlock=t}else this._validMolBlock=t}validateMolBlock(t){if(""===t)throw new be("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=le(t);console.error(e)}}getMoleculeDimensions(){const t=ye.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=M.dialog({title:"Molecule",showFooter:!1}),e=.7*L()(window).height(),n=this.getMoleculeDimensions(),r=e/n.height,o=e,i=n.width*r,s=M.canvas(i,o);await this.drawMolBlockOnCanvas(s);const a=M.block([s],{style:{overflowX:"scroll"}});t.add(a).showModal(!0),L()(t.root).find(".d4-dialog-contents").removeClass("ui-form"),L()(t.root).find(".d4-dialog-contents").removeClass("ui-panel"),L()(t.root).find(".d4-dialog-contents").addClass("ui-box"),L()(t.root).find(".d4-dialog-contents").css("padding","0")}async drawMolecule(t,e,n){t.innerHTML="";const r=M.canvas(e*window.devicePixelRatio,n*window.devicePixelRatio);r.style.width=`${e}px`,r.style.height=`${n}px`,r.style.cursor="zoom-in",this.drawMolBlockOnCanvas(r),r.addEventListener("click",(async()=>{await this.zoomIn()})),t.append(M.tooltip.bind(r,"Click to zoom"))}}class we extends Error{constructor(t,e){super(t,e)}}class Ce{constructor(t,e){this.sequence=t,this.codeMap=e}parseSequence(){const t=this.parseRawSequence();return this.addLinkers(t)}addLinkers(t){const e=[];return t.forEach(((n,r)=>{const o=this.getSymbolForCode(n);r>0&&function(t){return Xr.jsonData.monomersWithPhosphate.left.includes(t)}(o)&&e.pop(),e.push(o);const i=Ae(o),s=r===t.length-1,a=r+1<t.length&&Ae(this.getSymbolForCode(t[r+1]));i||function(t){return Xr.jsonData.monomersWithPhosphate.right.includes(t)}(o)||a||s||e.push("p")})),e}getSymbolForCode(t){let e=this.codeMap.get(t);return e??(e=t),e}parseRawSequence(){const t=this.getAllCodesOfFormat(),e=[];let n=0;for(;n<this.sequence.length;){const r=t.find((t=>t===this.sequence.substring(n,n+t.length)));if(void 0===r)throw new we(`Unable to match a monomer for the rest of the sequence '${this.sequence.slice(n)}'.`);e.push(r),n+=r.length}return e}getAllCodesOfFormat(){return g(Array.from(this.codeMap.keys()))}}function Ae(t){return Xr.jsonData.monomersWithPhosphate.phosphate.includes(t)}class xe{constructor(t,e=!1,n){this.invert=e,this.lib=Xr.monomerLibWrapper;const r=this.lib.getCodeToSymbolMap(n);this.parser=new Ce(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),o=e.atomIndex.indexOf(n),i=(e.x[o]+e.x[r])/2,s=(e.y[o]+e.y[r])/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[r];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 u=l;for(let r=0;r<n;r++)l=t.indexOf("V30",l)+4,l=t.indexOf(" ",l)+1,l=t.indexOf(" ",l)+1,u=t.indexOf(" ",l)+1,u=t.indexOf(" ",u),l=(t=t.slice(0,l)+e.x[r]+" "+e.y[r]+t.slice(u)).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 r=n;const o=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,r=t.indexOf(" ",n),o[l]=parseInt(t.substring(n,r)),n=r+1,r=t.indexOf(" ",n),i[l]=t.substring(n,r),n=r+1,r=t.indexOf(" ",n),s[l]=parseFloat(t.substring(n,r)),n=r+1,r=t.indexOf(" ",n),a[l]=parseFloat(t.substring(n,r)),n=t.indexOf("\n",n)+1;return{atomIndex:o,atomType:i,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),o=e.atomIndex.indexOf(n);n>8&&this.fix5Prime(e,r,o);const i=(e.x[o]+e.x[r])/2,s=(e.y[o]+e.y[r])/2;for(let t=0;t<n;t++)e.x[t]-=i,e.y[t]-=s;let a=0;if(0===e.x[r])a=e.y[r]>e.y[o]?Math.PI/2:3*Math.PI/2;else if(0===e.y[r])a=e.x[r]>e.x[o]?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 l=Math.cos(a),u=Math.sin(a);for(let t=0;t<n;t++){const n=e.x[t];e.x[t]=n*l-e.y[t]*u,e.y[t]=n*u+e.y[t]*l}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 d=h;for(let r=0;r<n;r++)h=t.indexOf("V30",h)+4,h=t.indexOf(" ",h)+1,h=t.indexOf(" ",h)+1,d=t.indexOf(" ",h)+1,d=t.indexOf(" ",d),h=(t=t.slice(0,h)+e.x[r]+" "+e.y[r]+t.slice(d)).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="",o="",i="";const s=[];let a=0,l=0,u=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 c=this.extractAtomsBondsNumbersV3000(t[e]),h=this.extractAtomDataV3000(t[e]);let d=t[e].indexOf("M V30 BEGIN ATOM");d=t[e].indexOf("\n",d);let f=d,p=d;for(let r=0;r<c.natom;r++)if(1!==h.atomIndex[r]||0===e){f=t[e].indexOf("V30",f)+4,p=t[e].indexOf(" ",f);let r=0;n?(r=parseInt(t[e].substring(f,p)),1===r?r=i:r===i&&(r=1),r+=a):r=parseInt(t[e].substring(f,p))+a,t[e]=t[e].slice(0,f)+r+t[e].slice(p),f=t[e].indexOf(" ",f)+1,f=t[e].indexOf(" ",f)+1,p=t[e].indexOf(" ",f);const o=u-h.x[0];let s=Math.round(1e4*(parseFloat(t[e].substring(f,p))+o))/1e4;t[e]=t[e].slice(0,f)+s+t[e].slice(p),f=t[e].indexOf(" ",f)+1,p=t[e].indexOf(" ",f),s=Math.round(1e4*parseFloat(t[e].substring(f,p)))/1e4,t[e]=t[e].slice(0,f)+s+t[e].slice(p),f=t[e].indexOf("\n",f)+1}else f=t[e].indexOf("M V30",f)-1,p=t[e].indexOf("\n",f+1),t[e]=t[e].slice(0,f)+t[e].slice(p);const m=t[e].indexOf("M V30 END ATOM");r+=t[e].substring(d+1,m);let g=t[e].indexOf("M V30 BEGIN BOND");g=t[e].indexOf("\n",g),f=g,p=g;for(let r=0;r<c.nbond;r++){f=t[e].indexOf("V30",f)+4,p=t[e].indexOf(" ",f);const r=parseInt(t[e].substring(f,p))+l;t[e]=t[e].slice(0,f)+r+t[e].slice(p),f=t[e].indexOf(" ",f)+1,f=t[e].indexOf(" ",f)+1,p=t[e].indexOf(" ",f);let o=0;n?(o=parseInt(t[e].substring(f,p)),1===o?o=i:o===i&&(o=1),o+=a):o=parseInt(t[e].substring(f,p))+a,t[e]=t[e].slice(0,f)+o+t[e].slice(p),f=t[e].indexOf(" ",f)+1,p=Math.min(t[e].indexOf("\n",f),t[e].indexOf(" ",f)),o=0,n?(o=parseInt(t[e].substring(f,p)),1===o?o=i:o===i&&(o=1),o+=a):o=parseInt(t[e].substring(f,p))+a,t[e]=t[e].slice(0,f)+o+t[e].slice(p),f=t[e].indexOf("\n",f)+1}const y=t[e].indexOf("M V30 END BOND");o+=t[e].substring(g+1,y);let b=t[e].indexOf("M V30 MDLV30/STEABS ATOMS=(");for(;-1!==b;){b+=28;const n=t[e].indexOf(")",b);t[e].substring(b,n).split(" ").slice(1).forEach((t=>{s.push(parseInt(t)+a)})),b=n,b=t[e].indexOf("M V30 MDLV30/STEABS ATOMS=(",b)}a+=c.natom-1,l+=c.nbond,u+=n?Math.max(...h.x):h.x[c.natom-1]-h.x[0]}const c=Math.ceil(s.length/4);i+="M V30 MDLV30/STEABS ATOMS=("+s.length+" -\n";for(let t=0;t<c;t++){i+="M V30 ";const e=t+1===c?s.length-4*(c-1):4;for(let n=0;n<e;n++)i+=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+" "+l+" 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+=o,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 r=e+1,o=t.x[r],i=t.y[r],s=t.x[n]-o,a=t.y[n]-i,l=t.x[e]-o,u=t.y[e]-i,c=l*Math.cos(2*Math.PI/3)-u*Math.sin(2*Math.PI/3),h=l*Math.sin(2*Math.PI/3)+u*Math.cos(2*Math.PI/3),d=l-s,f=u-a,p=c-s,m=h-a;Math.sqrt(m*m+p*p)>=Math.sqrt(f*f+d*d)&&(t.x[e]=c+o,t.y[e]=h+i)}}function Se(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="",o="",i="";const s=[];let a=0,l=0,u=0;if(t.antiStrands.length>0)for(let e=0;e<t.antiStrands.length;e++)t.antiStrands[e]=Te(t.antiStrands[e]);let c=!1;const h=t.senseStrands.concat(t.antiStrands);let d=0;for(let e=0;e<h.length;e++){h[e]=h[e].replaceAll("(-\nM V30 ","(").replaceAll("-\nM V30 ","").replaceAll(" )",")");const n=Ee(h[e]),i=_e(h[e]);if(e>=t.senseStrands.length?!1===c&&(c=!0,u=0):d=Math.min(d,Math.min(...i.y.filter((t=>t<0)))),c){const t=Math.min(...i.x)-u,e=Math.max(...i.y)+5;for(let e=0;e<i.x.length;e++)i.x[e]-=t;for(let t=0;t<i.y.length;t++)i.y[t]-=e-d}let f=h[e].indexOf("M V30 BEGIN ATOM");f=h[e].indexOf("\n",f);let p=f,m=f;for(let t=0;t<n.natom;t++){p=h[e].indexOf("V30",p)+4,m=h[e].indexOf(" ",p);const n=parseInt(h[e].substring(p,m))+a;h[e]=h[e].slice(0,p)+n+h[e].slice(m),p=h[e].indexOf(" ",p)+1,p=h[e].indexOf(" ",p)+1,m=h[e].indexOf(" ",p);let r=Math.round(1e4*i.x[t])/1e4;h[e]=h[e].slice(0,p)+r+h[e].slice(m),p=h[e].indexOf(" ",p)+1,m=h[e].indexOf(" ",p),r=Math.round(1e4*i.y[t])/1e4,h[e]=h[e].slice(0,p)+r+h[e].slice(m),p=h[e].indexOf("\n",p)+1}const g=h[e].indexOf("M V30 END ATOM");r+=h[e].substring(f+1,g);let y=h[e].indexOf("M V30 BEGIN BOND");y=h[e].indexOf("\n",y),p=y,m=y;for(let t=0;t<n.nbond;t++){p=h[e].indexOf("V30",p)+4,m=h[e].indexOf(" ",p);const t=parseInt(h[e].substring(p,m))+l;h[e]=h[e].slice(0,p)+t+h[e].slice(m),p=h[e].indexOf(" ",p)+1,p=h[e].indexOf(" ",p)+1,m=h[e].indexOf(" ",p);let n=parseInt(h[e].substring(p,m))+a;h[e]=h[e].slice(0,p)+n+h[e].slice(m),p=h[e].indexOf(" ",p)+1,m=Math.min(h[e].indexOf("\n",p),h[e].indexOf(" ",p)),n=parseInt(h[e].substring(p,m))+a,h[e]=h[e].slice(0,p)+n+h[e].slice(m),p=h[e].indexOf("\n",p)+1}const b=h[e].indexOf("M V30 END BOND");o+=h[e].substring(y+1,b);let v=h[e].indexOf("M V30 MDLV30/STEABS ATOMS=(");for(;-1!==v;){v+=28;const t=h[e].indexOf(")",v);h[e].substring(v,t).split(" ").slice(1).forEach((t=>{s.push(parseInt(t)+a)})),v=t,v=h[e].indexOf("M V30 MDLV30/STEABS ATOMS=(",v)}a+=n.natom,l+=n.nbond,u+=Math.max(...i.x)+5}const f=Math.ceil(s.length/4);i+="M V30 MDLV30/STEABS ATOMS=("+s.length+" -\n";for(let t=0;t<f;t++){i+="M V30 ";const e=t+1===f?s.length-4*(f-1):4;for(let n=0;n<e;n++)i+=n+1===e?t===f-1?s[4*t+n]+")\n":s[4*t+n]+" -\n":s[4*t+n]+" "}return n+="M V30 COUNTS "+a+" "+l+" 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+=o,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}function Te(t){const e=_e(t),n=e.atomIndex.length,r=(Math.max(...e.x)+Math.min(...e.x))/2,o=(Math.max(...e.y)+Math.min(...e.y))/2;for(let t=0;t<n;t++)e.x[t]-=r,e.y[t]-=o;const i=Math.PI,s=Math.cos(i),a=Math.sin(i);for(let t=0;t<n;t++){const n=e.x[t];e.x[t]=n*s-e.y[t]*a,e.y[t]=n*a+e.y[t]*s}const l=Math.max(...e.y);for(let t=0;t<n;t++)e.x[t]+=r,e.y[t]-=l;let u=t.indexOf("M V30 BEGIN ATOM");u=t.indexOf("\n",u);let c=u;for(let r=0;r<n;r++)u=t.indexOf("V30",u)+4,u=t.indexOf(" ",u)+1,u=t.indexOf(" ",u)+1,c=t.indexOf(" ",u)+1,c=t.indexOf(" ",c),u=(t=t.slice(0,u)+e.x[r]+" "+e.y[r]+t.slice(c)).indexOf("\n",u)+1;return t}function Ee(t){let e=(t=t.replaceAll("\r","")).indexOf("COUNTS")+7,n=t.indexOf(" ",e);const r=parseInt(t.substring(e,n));return e=n+1,n=t.indexOf(" ",e),{natom:r,nbond:parseInt(t.substring(e,n))}}function _e(t){const e=Ee(t);let n=t.indexOf("M V30 BEGIN ATOM");n=t.indexOf("\n",n);let r=n;const o=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,r=t.indexOf(" ",n),o[l]=parseInt(t.substring(n,r)),n=r+1,r=t.indexOf(" ",n),i[l]=t.substring(n,r),n=r+1,r=t.indexOf(" ",n),s[l]=parseFloat(t.substring(n,r)),n=r+1,r=t.indexOf(" ",n),a[l]=parseFloat(t.substring(n,r)),n=t.indexOf("\n",n)+1;return{atomIndex:o,atomType:i,x:s,y:a}}function Ie(t,e,n){if(""===t)return"";const r=n.createFormatDetector(t).getFormat();if(!r)return"";let o="";try{o=new xe(t,e,r).convert()}catch(t){const e=le(t);console.error(e)}return o}function Ne(t,e,n,r,o){const i=[t,e,n].filter((t=>""!==t.strand));return 1===i.length?Ie(i[0].strand,i[0].invert,o):Se({senseStrands:[Ie(t.strand,t.invert,o)],antiStrands:[Ie(e.strand,e.invert,o),Ie(n.strand,n.invert,o)].filter((t=>""!==t))},r)}const Me=["ss","as","as2"];class Oe{constructor(){this.th=Xr,this.onInput=new et.Subject,this.onInvalidInput=new et.Subject,this.inputBase=Object.fromEntries(Me.map((t=>{const e=M.input.textArea(t.toUpperCase(),{value:"",onValueChanged:()=>{this.onInput.next(),L()(e.root.getElementsByTagName("div")).css("padding-left","38px")}});return[t,e]}))),this.useChiralInput=M.input.bool("Use chiral",{value:!0}),this.saveAllStrandsInput=M.input.bool("Save as one entity",{value:!0}),M.tooltip.bind(this.saveAllStrandsInput.root,"Save SDF with all strands in one molfile"),this.directionInversion=Object.fromEntries(Me.map((t=>[t,!1]))),this.moleculeImgDiv=M.block([]),L()(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")}))}async getHtmlDivElement(t){const e=this.getTableInput(t),n=this.getBoolInputsAndButton();await this.updateMoleculeImg();const r=M.divH([n,this.moleculeImgDiv]);L()(r).addClass("st-structure-bottom");const o=M.divV([e,r]);return L()(o).addClass("st-structure-body"),o}getBoolInputsAndButton(){const t=M.buttonsInput([M.bigButton("Save SDF",(()=>{const t=this.getStrandData();!function(t,e,n,o,i,s){const a=[t.strand,e.strand,n.strand].filter((t=>""!==t));if(0===a.length||1===a.length&&""===t.strand)r.shell.warning("Enter SENSE_STRAND and optionally ANTISENSE_STRAND/AS2 to save SDF");else{let l;if(i)l=Ne(t,e,n,o,s)+"\n$$$$\n";else{const h=Ie(t.strand,t.invert,s),d=Ie(e.strand,e.invert,s),f=Ie(n.strand,n.invert,s);l=h+"\n> <Sequence>\nSense Strand\n$$$$\n",d&&(l+=d+"\n> <Sequence>\nAnti Sense\n$$$$\n"),f&&(l+=f+"\n> <Sequence>\nAnti Sense 2\n$$$$\n")}const u=new Date;function c(t){return t>=10?t.toString():"0"+t.toString()}y(`SequenceTranslator-${u.getFullYear()+"-"+c(u.getMonth()+1)+"-"+c(u.getDate())+"_"+c(u.getHours())+"-"+c(u.getMinutes())+"-"+c(u.getSeconds())}.sdf`,encodeURIComponent(l))}}(t.ss,t.as,t.as2,this.useChiralInput.value,this.saveAllStrandsInput.value,this.th)}))]),e=[this.saveAllStrandsInput.root,this.useChiralInput.root,t],n=M.divV(e);for(const t of e)L()(t).addClass("st-structure-bool-button-block");return n}getTableInput(t){const e=Object.fromEntries(Me.map((e=>[e,new de(this.inputBase[e],t.highlightInvalidSubsequence)]))),n=Object.fromEntries(Me.map(((t,e)=>{const n=0===e?"5′ → 3′":"3′ → 5′";return[t,M.input.choice(`${t.toUpperCase()} direction`,{value:n,items:["5′ → 3′","3′ → 5′"]})]})));Me.forEach(((t,e)=>{n[t].onChanged.subscribe((n=>{let r="3′ → 5′"===n;e>0&&(r=!r),this.directionInversion[t]=r,this.onInput.next()}))}));const r=["Sense Strand","Anti Sense","Anti Sense 2"],o=new Map(Me.map(((t,e)=>[t,r[e]]))),i=(Object.fromEntries(Me.map((t=>[t,M.label(o.get(t))]))),Object.fromEntries(Me.map((t=>{const n=M.icons.delete((()=>{e[t].inputBase.value=""})),r=M.button(n,(()=>{}));return M.tooltip.bind(r,`Clear ${t.toUpperCase()}`),[t,n]})))),s=M.form([],"st-structure-inputs"),a=M.divV([],"st-structure-clear-buttons"),l=M.form([],"st-direction-inputs");for(const t of Me)s.append(this.inputBase[t].root),a.append(i[t]),l.append(n[t].root);return M.divH([s,a,l])}getStrandData(){return Object.fromEntries(Me.map((t=>{const e=this.directionInversion[t];return[t,{strand:this.inputBase[t].value.replace(/\s*/g,""),invert:e}]})))}getMolfile(t,e,n){return Ne(t,e,n,this.useChiralInput.value,this.th)}async updateMoleculeImg(){let t="";try{const e=this.getStrandData();Object.values(e).some((t=>""!==t.strand))&&(t=this.getMolfile(e.ss,e.as,e.as2))}catch(t){const e=le(t);console.error(e)}const e=new ve(t);await e.drawMolecule(this.moleculeImgDiv,650,150),L()(this.moleculeImgDiv).find("canvas").css("float","inherit")}}class Le extends F{constructor(t){super("Oligo Structure"),this.th=t,this.layout=new Oe}getContent(){return this.layout.getHtmlDivElement(this.th)}}var Re=n(2003);async function Pe(t){try{const e={overflowX:"scroll"},n=M.div([],{style:e}),o=_e(t),i=.7*L()(window).height(),s=Math.max(...o.x)-Math.min(...o.x),a=Math.max(...o.y)-Math.min(...o.y),l=i/a,u=l*s,c=l*a,h=M.canvas(u*window.devicePixelRatio,c*window.devicePixelRatio);h.style.width=`${u}px`,h.style.height=`${c}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),M.dialog("Molecule").add(n).showModal(!0)}catch(t){const e=le(t);console.error(e)}}class Be{static async view(){const t=Xr.monomerLibWrapper.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 Pe(e)}))}}var De=n(3480),Fe=n(5067),ke=n(5254),He={};He.styleTagTransform=xt(),He.setAttributes=vt(),He.insert=yt().bind(null,"head"),He.domAPI=mt(),He.insertStyleElement=Ct(),ft()(ke.A,He),ke.A&&ke.A.locals&&ke.A.locals;const Ue=["Sequence"];class $e{constructor(t){this.th=t,this.inputFormats=Object.keys(Xr.jsonData.codesToHelmDict).concat(m.NO.HELM),this.seqHelper=Xr.seqHelper,this.onInput=new et.Subject,this.moleculeImgDiv=M.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=M.div([]),this.formatChoiceInput=M.input.choice("",{value:m.NO.HELM,items:this.inputFormats,onValueChanged:async(t,e)=>{this.format=t,this.updateTable(),await this.updateMolImg()}}),L()(this.formatChoiceInput.root.getElementsByTagName("select")[0]).css("width","20%"),this.sequenceInputBase=M.input.textArea("",{value:"Afcgacsu",onValueChanged:()=>{this.onInput.next()}}),this.init(),o.debounce(this.onInput,300).subscribe((async()=>{this.init(),this.formatChoiceInput.value=this.format,this.updateTable(),await this.updateMolImg()})),this.eventBus=Ge.getInstance()}async getHtmlElement(){const t=this.constructSingleSequenceControls(),e=this.constructBulkTranslationControls(),n=M.box(M.panel([t,e,M.block([M.box(this.moleculeImgDiv)])]));return this.formatChoiceInput.value=this.format,this.updateTable(),await this.updateMolImg(),n}constructBulkTranslationControls(){const t=M.h1("Bulk");M.tooltip.bind(t,"Bulk translation from table input");const e=new Ve(this.eventBus).createUIComponents(),n=M.input.choice("Input format",{value:m.NO.AXOLABS,items:this.inputFormats,onValueChanged:t=>this.eventBus.selectInputFormat(t)}),r=M.input.choice("Output format",{value:Fe.qP,items:(0,De.OT)(this.th),onValueChanged:t=>this.eventBus.selectOutputFormat(t)}),o=this.createConvertBulkButton(),i=M.div([...e,n,r,o],"ui-form");return M.block25([t,i])}createConvertBulkButton(){const t=M.bigButton("Convert",(()=>this.processConvertBulkButtonClick()));return M.tooltip.bind(t,"Convert sequences from table input"),L()(t).css({float:"right","margin-top":"20px"}),t}processConvertBulkButtonClick(){const t=this.eventBus.getSelectedTable();if(!t)return void r.shell.warning("No table selected");const e=this.eventBus.getSelectedInputFormat(),n=this.eventBus.getSelectedOutputFormat(),i=this.eventBus.getSelectedColumn("Sequence");if(!i)return void r.shell.warning("No sequence column selected");const s=`${i.name} (${n})`,a=o.Column.fromList(o.TYPE.STRING,s,i.toList().map((t=>(0,De.C6)(t,e,n,this.th))));if(n===Fe.qP||n===m.NO.HELM){a.semType=o.SEMTYPE.MACROMOLECULE;const t=n==Fe.qP?Re.Hi.FASTA:Re.Hi.HELM;a.meta.units=t;const e=this.seqHelper.getSeqHandler(a);(n==Fe.qP?this.seqHelper.setUnitsToFastaColumn:this.seqHelper.setUnitsToHelmColumn)(e)}t.columns.add(a),r.data.detectSemanticTypes(t),r.shell.v=r.shell.getTableView(t.name)}constructSingleSequenceControls(){const t=new de(this.sequenceInputBase,(t=>R(t,this.th))),e=M.button("Get SDF",(()=>{this.saveMolfile()}),"Save structure as SDF"),n=M.button("Copy SMILES",(()=>{this.copySmiles()}),"Copy SMILES for the sequence"),r=M.div([this.formatChoiceInput]),o=M.button(M.icons.delete((()=>{t.inputBase.value=""})),(()=>{}));M.tooltip.bind(o,"Clear input");const i={format:r,textInput:t.root,clearBtn:o},s=M.table([i],(t=>[t.format,t.textInput,t.clearBtn]));s.classList.add("st-translator-input-table");const a=M.block([this.outputTableDiv,e,n]);return M.block75([M.h1("Single sequence"),s,a])}saveMolfile(){const t=new xe(this.sequence,!1,this.formatChoiceInput.value).convert()+"\n$$$$";y(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(Fe.n_)))}updateTable(){this.outputTableDiv.innerHTML="";const t=this.format?this.th.createSequenceValidator(this.sequence).getInvalidCodeIndex(this.format):0,e=(0,De.bD)(this.sequence,t,this.format,this.th),n=[];for(const t of Object.keys(e)){const o="indexOfFirstInvalidChar"in e?M.divH([]):M.link(e[t],(()=>navigator.clipboard.writeText(e[t]).then((()=>r.shell.info(Fe.n_)))),Fe.U_,"");n.push({format:t,sequence:o})}const o=M.table(n,(t=>[t.format,t.sequence]),["FORMAT","SEQUENCE"]);this.outputTableDiv.append(o),this.outputTableDiv.classList.add("st-translator-output-table")}async updateMolImg(){const t=new ve(this.molfile);await t.drawMolecule(this.moleculeImgDiv,500,170)}init(){this.sequence=this.getFormattedSequence(),this.format=this.th.createFormatDetector(this.sequence).getFormat(),this.molfile=this.getMolfile()}getFormattedSequence(){return this.sequenceInputBase.value.replace(/\s/g,"")}getMolfile(){if(!this.format)return"";if(this.format===m.NO.HELM){const t=this.th.createFormatConverter(this.sequence,this.format).convertTo(m.NO.AXOLABS);return new xe(t,!1,m.NO.AXOLABS).convert()}return new xe(this.sequence,!1,this.format).convert()}}class Ve{constructor(t){this.tableInputManager=new qe(t),this.columnInputManager=new je(t)}createUIComponents(){return[this.tableInputManager.getTableInputContainer(),this.columnInputManager.getColumnControlsContainer()]}}class qe{constructor(t){this.eventBus=t,this.availableTables=[],this.tableInputContainer=M.div([]),this.subscribeToTableEvents(),this.refreshTableInput()}getTableInputContainer(){return this.tableInputContainer}subscribeToTableEvents(){r.events.onTableAdded.subscribe((t=>this.handleTableAdded(t))),r.events.onTableRemoved.subscribe((t=>this.handleTableRemoved(t))),this.eventBus.tableSelected$.subscribe((()=>this.handleTableChoice()))}getTableFromEventData(t){return t.args.dataFrame}handleTableAdded(t){const e=this.getTableFromEventData(t);this.availableTables.some((t=>t.name===e.name))||(this.availableTables.push(e),this.eventBus.selectTable(e),this.refreshTableInput())}handleTableRemoved(t){const e=this.getTableFromEventData(t);this.availableTables=this.availableTables.filter((t=>t.name!==e.name));const n=this.availableTables[0];this.eventBus.selectTable(n||null),this.refreshTableInput()}refreshTableInput(){const t=this.createTableInput();L()(this.tableInputContainer).empty(),this.tableInputContainer.append(t.root)}createTableInput(){const t=this.eventBus.getSelectedTable();return M.input.table("Table",{value:t,items:this.availableTables,onValueChanged:t=>{null!==t&&this.eventBus.selectTable(t)}})}handleTableChoice(){const t=this.eventBus.getSelectedTable();t&&(this.isTableDisplayed(t)||this.displayTable(t))}isTableDisplayed(t){return r.shell.tableNames.includes(t.name)}displayTable(t){const e=r.shell.v;r.shell.addTableView(t),r.shell.v=e}}class je{constructor(t){this.eventBus=t,this.columnControlsContainer=M.div([]),this.eventBus.tableSelected$.subscribe((()=>this.handleTableChoice())),this.refreshColumnControls()}getColumnControlsContainer(){return this.columnControlsContainer}handleTableChoice(){this.refreshColumnControls()}refreshColumnControls(){const t=this.createColumnInputs();L()(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 Ue.map((n=>this.createColumnInput(n,e,t)))}createColumnInput(t,e,n){const r=t.toLowerCase(),o=e.find((t=>t.toLowerCase().includes(r)))||e[0];return this.selectColumnIfTableNotNull(n,o,t),M.input.choice(`${t}`,{value:o,items:e,onValueChanged:e=>this.selectColumnIfTableNotNull(n,e,t)})}selectColumnIfTableNotNull(t,e,n){if(null!==t&&e){const r=t.col(e);r&&this.eventBus.selectColumn(n,r)}}}class Ge{constructor(){this._tableSelection$=new et.BehaviorSubject(null),this._columnSelection=Object.fromEntries(Ue.map((t=>[t,new et.BehaviorSubject(null)]))),this._inputFormatSelection$=new et.BehaviorSubject(m.NO.AXOLABS),this._outputFormatSelection$=new et.BehaviorSubject(Fe.qP)}static getInstance(){return void 0===Ge._instance&&(Ge._instance=new Ge),Ge._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 ze extends F{constructor(t){super("Oligo Translator"),this.th=t,this.th=Xr,this.layout=new $e(this.th);const e=M.iconFA("book",Be.view,"View monomer library");this.topPanel=[e],this.view.setRibbonPanels([this.topPanel])}getContent(){return this.layout.getHtmlElement()}}class We extends F{constructor(t,e){super(t),this.content=e}getContent(){return Promise.resolve(this.content)}}class Ye extends D{constructor(t,e){super("Oligo Toolkit"),this.externalViewFactories=t,this.th=e;const n=this.getViewFactories(this.th);this.multiView=new o.MultiView({viewFactories:n})}getViewFactories(t){function e(e){o.View.create();const n=new e(t);return n.initView().catch((t=>console.error(`Failed to initialize ${e.name}: ${t}`))),()=>n.getView()}let n={TRANSLATOR:e(ze),PATTERN:e(ie),STRUCTURE:e(Le)};return this.externalViewFactories&&(n=Object.assign({},n,this.externalViewFactories)),n}getCurrentPanePath(){let t=this.multiView.tabs.currentPane.name;return t=t.charAt(0).toUpperCase()+t.substring(1).toLowerCase(),`/apps/${Xr.name}/OligoToolkit/${t}`}setUrl(){this.multiView.path=this.getCurrentPanePath()}async constructView(){return this.multiView.tabs.onTabChanged.subscribe((()=>this.setUrl())),this.setUrl(),this.multiView}}var Ke=n(8070);function Je(t){const e=M.input.textArea("",{value:""});return{coloredInput:new de(e,t.highlightInvalidSubsequence),codes:t.jsonData.codesToSymbolsDict}}var Qe=n(9124),Xe=n(9192),Ze=n(8312),tn=n(1991),en=n.n(tn);const nn="object"==typeof performance&&performance&&"function"==typeof performance.now?performance:Date,rn=new Set,on="object"==typeof process&&process?process:{},sn=(t,e,n,r)=>{"function"==typeof on.emitWarning?on.emitWarning(t,e,n,r):console.error(`[${n}] ${e}: ${t}`)};let an=globalThis.AbortController,ln=globalThis.AbortSignal;if(void 0===an){ln=class{onabort;_onabort=[];reason;aborted=!1;addEventListener(t,e){this._onabort.push(e)}},an=class{constructor(){e()}signal=new ln;abort(t){if(!this.signal.aborted){this.signal.reason=t,this.signal.aborted=!0;for(const e of this.signal._onabort)e(t);this.signal.onabort?.(t)}}};let t="1"!==on.env?.LRU_CACHE_IGNORE_AC_WARNING;const e=()=>{t&&(t=!1,sn("AbortController is not defined. If using lru-cache in node 14, load an AbortController polyfill from the `node-abort-controller` package. A minimal polyfill is provided for use by LRUCache.fetch(), but it should not be relied upon in other contexts (eg, passing it to other APIs that use AbortController/AbortSignal might have undesirable effects). You may disable this with LRU_CACHE_IGNORE_AC_WARNING=1 in the env.","NO_ABORT_CONTROLLER","ENOTSUP",e))}}Symbol("type");const un=t=>t&&t===Math.floor(t)&&t>0&&isFinite(t),cn=t=>un(t)?t<=Math.pow(2,8)?Uint8Array:t<=Math.pow(2,16)?Uint16Array:t<=Math.pow(2,32)?Uint32Array:t<=Number.MAX_SAFE_INTEGER?hn:null:null;class hn extends Array{constructor(t){super(t),this.fill(0)}}class dn{heap;length;static#t=!1;static create(t){const e=cn(t);if(!e)return[];dn.#t=!0;const n=new dn(t,e);return dn.#t=!1,n}constructor(t,e){if(!dn.#t)throw new TypeError("instantiate Stack using Stack.create(n)");this.heap=new e(t),this.length=0}push(t){this.heap[this.length++]=t}pop(){return this.heap[--this.length]}}class fn{#e;#n;#r;#o;#i;#s;ttl;ttlResolution;ttlAutopurge;updateAgeOnGet;updateAgeOnHas;allowStale;noDisposeOnSet;noUpdateTTL;maxEntrySize;sizeCalculation;noDeleteOnFetchRejection;noDeleteOnStaleGet;allowStaleOnFetchAbort;allowStaleOnFetchRejection;ignoreFetchAbort;#a;#l;#u;#c;#h;#d;#f;#p;#m;#g;#y;#b;#v;#w;#C;#A;#x;static unsafeExposeInternals(t){return{starts:t.#v,ttls:t.#w,sizes:t.#b,keyMap:t.#u,keyList:t.#c,valList:t.#h,next:t.#d,prev:t.#f,get head(){return t.#p},get tail(){return t.#m},free:t.#g,isBackgroundFetch:e=>t.#S(e),backgroundFetch:(e,n,r,o)=>t.#T(e,n,r,o),moveToTail:e=>t.#E(e),indexes:e=>t.#_(e),rindexes:e=>t.#I(e),isStale:e=>t.#N(e)}}get max(){return this.#e}get maxSize(){return this.#n}get calculatedSize(){return this.#l}get size(){return this.#a}get fetchMethod(){return this.#i}get memoMethod(){return this.#s}get dispose(){return this.#r}get disposeAfter(){return this.#o}constructor(t){const{max:e=0,ttl:n,ttlResolution:r=1,ttlAutopurge:o,updateAgeOnGet:i,updateAgeOnHas:s,allowStale:a,dispose:l,disposeAfter:u,noDisposeOnSet:c,noUpdateTTL:h,maxSize:d=0,maxEntrySize:f=0,sizeCalculation:p,fetchMethod:m,memoMethod:g,noDeleteOnFetchRejection:y,noDeleteOnStaleGet:b,allowStaleOnFetchRejection:v,allowStaleOnFetchAbort:w,ignoreFetchAbort:C}=t;if(0!==e&&!un(e))throw new TypeError("max option must be a nonnegative integer");const A=e?cn(e):Array;if(!A)throw new Error("invalid max value: "+e);if(this.#e=e,this.#n=d,this.maxEntrySize=f||this.#n,this.sizeCalculation=p,this.sizeCalculation){if(!this.#n&&!this.maxEntrySize)throw new TypeError("cannot set sizeCalculation without setting maxSize or maxEntrySize");if("function"!=typeof this.sizeCalculation)throw new TypeError("sizeCalculation set to non-function")}if(void 0!==g&&"function"!=typeof g)throw new TypeError("memoMethod must be a function if defined");if(this.#s=g,void 0!==m&&"function"!=typeof m)throw 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n=t[wn];n||(n=t[wn]=[]),n.push(e),t[wn]=n}function An(t,e){try{const n=t.tableColumn;if(!n)return;const r=function(t){return t.temp[wn]??[]}(n);for(let n=r.length-1;n>=0;--n){const o=r[n],i=t.grid.col(o.targetCol.name);if(i&&!o.handler(t,e,i))break}}catch(t){console.error(t)}}var xn=n(6717),Sn=n(6694),Tn=n(4229),En=n(5174);function _n(t,e=!0){const[n,o]=(0,Xe.AP)(t);return Xr.logger.error(n,void 0,o),e&&r.shell.error(n),[n,o]}async function In(){return(await(0,l.pj)()).getAvaliableLibraryNames()}const Nn={symbol:"Short Name",name:"Medium Name",smiles:"SMILES"},Mn=[{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"}],On="Get HELM",Ln="Chirality engine",Rn="Highlight monomers",Pn="Poly Tool Conversion",Bn="Poly Tool Enumeration",Dn="Rules used";var Fn=n(5412);async function kn(t){await Xr.initPromise;try{const e=await async function(t){const e=[],n=()=>{for(const t of e)t.unsubscribe()};try{const[i,s]=await Promise.all([In(),(0,Qe.b2)()]),a=t&&t.rowIndex>=0?t.value:"\n\n\n 22 24 0 0 0 0 0 0 0 0999 V2000\n 0.3128 -0.7509 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n 0.3128 0.0740 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n -0.4054 -1.1623 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n -1.1081 -0.7509 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n -0.4054 0.4877 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0\n -1.1081 0.0740 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n -1.8175 -1.1623 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n 1.0222 0.4877 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n -1.8175 0.4877 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n -2.5292 -0.7509 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n 1.0222 1.3127 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n 1.7227 1.7263 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n -0.4054 -1.9896 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0\n -2.5292 0.0740 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n 2.4544 1.3127 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n 1.7406 0.0740 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n 1.0222 -1.1623 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0\n 2.4544 0.4877 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n -1.8175 -1.9896 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0\n -3.2453 0.4877 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0\n 3.1670 1.7285 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0\n 1.7149 2.5513 0.0000 R# 0 0 0 0 0 0 0 0 0 0 0 0\n 2 1 2 0 0 0 0\n 3 1 1 0 0 0 0\n 4 3 1 0 0 0 0\n 5 2 1 0 0 0 0\n 6 5 1 0 0 0 0\n 7 4 1 0 0 0 0\n 8 2 1 0 0 0 0\n 9 6 1 0 0 0 0\n 10 7 2 0 0 0 0\n 11 8 2 0 0 0 0\n 12 11 1 0 0 0 0\n 13 3 2 0 0 0 0\n 14 9 2 0 0 0 0\n 15 18 1 0 0 0 0\n 16 8 1 0 0 0 0\n 17 1 1 0 0 0 0\n 18 16 2 0 0 0 0\n 19 7 1 0 0 0 0\n 20 14 1 0 0 0 0\n 6 4 2 0 0 0 0\n 15 12 2 0 0 0 0\n 14 10 1 0 0 0 0\n 15 21 1 0 0 0 0\n 12 22 1 0 0 0 0\nM RGP 1 22 1\nM END";let u=await(async()=>o.chem.isMolBlock(a)?a:await r.functions.call("Chem:convertMolNotation",{molecule:a,sourceNotation:t?.column.getTag(o.TAGS.UNITS)??o.chem.Notation.Unknown,targetNotation:o.chem.Notation.MolBlock}))();const c=new o.chem.Sketcher(o.chem.SKETCHER_MODE.EXTERNAL);c.syncCurrentObject=!1,c.onChanged.subscribe((t=>{u=c.getMolFile()})),c.root.classList.add("ui-input-editor"),c.root.style.marginTop="3px",c.setMolFile(u);const h=M.input.choice("Library to use",{value:null,items:i});c.root.setAttribute("style","min-width:250px!important;"),c.root.setAttribute("style","max-width:250px!important;"),h.input.setAttribute("style","min-width:250px!important;");const d=M.div([c.root,h.root]);e.push(r.events.onCurrentCellChanged.subscribe((()=>{const t=r.shell.tv.dataFrame.currentCell;t.column.semType===o.SEMTYPE.MOLECULE&&c.setValue(t.value)})));const f=async()=>{try{const t=c.getMolFile();if(void 0===t||""===t)r.shell.warning("PolyTool: no molecule was provided");else if(t.includes("R#")){const e=await async function(t,e){const n=await async function(t){const e=await(0,l.pj)(),n=await e.readSingleLibraryByName(t);return n?n.getMonomerSymbolsByType("PEPTIDE"):(Xr.logger.error(`Monomer library '${t}' not found.`),[])}(e),o=await async function(t){const e=await(0,l.pj)(),n=await e.readSingleLibraryByName(t);if(!n)return Xr.logger.error(`Monomer library '${t}' not found.`),{};const r=n.getMonomerSymbolsByType("PEPTIDE");return new Array(r.length),n.getMonomerMolsByPolymerType("PEPTIDE")}(e),i=new Array(n.length),s=await r.functions.call("Chem:getRdKitModule"),a=s.get_mol(t),u=a.get_smiles();a.delete();const c=new Array(n.length);for(let t=0;t<n.length;t++){const e=o[n[t]],r=s.get_mol(e);c[t]=r.get_smiles(),r.delete()}for(let t=0;t<n.length;t++){let e=null;try{const n=`${`${u}.${c[t]}`.replaceAll("[1*]C","C([1*])").replaceAll("[1*]c","c([1*])").replaceAll("[1*]O","O([1*])").replaceAll("[1*]N","N([1*])")}`.replaceAll("([1*])","9").replaceAll("[1*]","9");e=s.get_mol(n,JSON.stringify({mappedDummiesAreRGroups:!0}));const r=e.get_v3Kmolblock();i[t]=r}catch(e){i[t]=""}finally{e?.delete()}}return i}(t,h.value),n=o.Column.fromStrings("Enumerated",e),i=o.DataFrame.fromColumns([n]);r.shell.addTableView(i)}else r.shell.warning("PolyTool: no R group was provided")}catch(t){_n(t)}},p=M.dialog(Bn).add(d).onOK((()=>{f().finally((()=>{n()}))})).onCancel((()=>{n()}));return e.push(p.onClose.subscribe((()=>{n()}))),p.history((()=>({mol:c.getMolFile(),screenLibrary:h.value})),(t=>{c.setMolFile(t.mol),h.value=t.screenLibrary})),p}catch(t){throw n(),t}}(t);e.show({resizable:!0})}catch(t){r.shell.warning("To run PolyTool Enumeration, sketch the molecule and specify the R group to vary")}}async function Hn(t,e,n,i,s,a){const l=o.TaskBarProgressIndicator.create("PolyTool converting...");try{const l=(t,e)=>t?t.columns.getUnusedName(e):e,u=await(0,Qe.b2)(),c=t.dataFrame,h=await(0,Sn.Q4)(a),[d,f,p]=(0,Tn.b)(t.toList(),h,u),m=l(c,`transformed(${t.name})`),g=o.Column.fromType(o.COLUMN_TYPE.STRING,m,d.length).init((t=>d[t]));g.semType=o.SEMTYPE.MACROMOLECULE,g.meta.units=Re.Hi.HELM,g.setTag(o.TAGS.CELL_RENDERER,"helm"),e&&c&&c.columns.add(g,!0);const y=await(0,xn.j)(),b=await(0,Ze.Q)(),v=await(0,En.A)(h),w=g.temp;w[".mm.cellRenderer.overriddenLibrary"]=v,g.temp=w;const C=await(0,Fn.m)(g,d,f,i,s,n,v,y,b);return C.name=l(c,`molfile(${t.name})`),C.semType=o.SEMTYPE.MOLECULE,c&&(c.columns.add(C,!0),await r.data.detectSemanticTypes(c)),function(t,e,n,r,o,i,s){const a=new fn({max:100});function l(t,e){const n=t.get(e);if(null==n)return null;let s=a.get(n);return s||a.set(n,s=function(t,e){const n=o.getSeqHandler(t),s=n.getSplitted(e),a=n.defaultBiotype,l=en().count(0).take(s.length).map((t=>({position:t,symbol:s.getCanonical(t),biotype:a}))).toArray(),u=n.alphabet,c=u==Re.YI.RNA||u==Re.YI.DNA?"RNA":"PEPTIDE",h=(0,yn.eM)([l],c,u,r,i);return(0,bn.gU)(l,h,u,c).monomers}(t,e)),s}const u={targetCol:n,handler:(t,n,o)=>{if(!t||!o.grid||!e.dataFrame)return!0;const i=o.grid,a=t.tableRowIndex,u=t.gridRow,c=i.cell(o.name,u),h=s[u],d=pn();if(!d||d&&(d.dataFrameId!=e.dataFrame?.id||d.gridRowIdx!=u||d.seqColName!=e.name||d.seqPosition!=n?.position)){if(d&&(mn(null),d.gridCell.render()),!n)return mn(null),!0;mn({gridCell:c,dataFrameId:e.dataFrame.id,gridRowIdx:u,seqColName:e.name,seqPosition:n?n.position:-1,getSubstruct:()=>{if(!n||"*"===n.symbol)return;const t=l(e,a);if(!t)return;const o=[],i=h[n.position];for(const e of i){const n=t.get(e);if(!n)return{atoms:[],bonds:[],highlightAtomColors:[],highlightBondColors:[]};o.push((0,vn.H)([n],r))}return function(t){var e,n,r,o;const i={atoms:[],bonds:[],highlightAtomColors:{},highlightBondColors:{}};for(const s of t)i.atoms=[...null!==(e=i.atoms)&&void 0!==e?e:[],...null!==(n=s.atoms)&&void 0!==n?n:[]],i.bonds=[...null!==(r=i.bonds)&&void 0!==r?r:[],...null!==(o=s.bonds)&&void 0!==o?o:[]],i.highlightAtomColors=Object.assign(Object.assign({},i.highlightAtomColors),s.highlightAtomColors),i.highlightBondColors=Object.assign(Object.assign({},i.highlightBondColors),s.highlightBondColors);return i}(o)}}),c.render()}return!0},getSubstruct:t=>{if("true"!=n.getTag(".sequence-src-highlight-monomers"))return;if(null==t)return;if(!e.get(t))return;const o=l(e,t);return o?(0,vn.H)(o.values(),r):void 0}};Cn(t.temp,u),gn(n.temp,u)}(t,g,C,v,b,y,p),[g,C]}finally{l.close()}}var Un=n(6197);class $n extends o.InputBase{constructor(t,e){super(M.input.column(t,e).dart,e?.onValueChanged),this.options=e}setColumnInputTable(t){M.input.setColumnInputTable(this,t,this.options?.filter)}}M.input.column2=function(t,e){return new $n(t,e)};var Vn=n(1296),qn=n(3820);class jn extends o.JsInputBase{get inputType(){return"Positions"}get dataType(){return o.TYPE.DATA_FRAME}getInput(){return this.gridHost}getValue(){return this.grid.dataFrame}setValue(t){this.setDataFrame(t)}getStringValue(){return this.grid.dataFrame.toCsv()}setStringValue(t){this.setDataFrame(o.DataFrame.fromCsv(t))}clearInput(){const t=o.DataFrame.fromColumns([o.Column.fromType(o.COLUMN_TYPE.STRING,"Remove",0),o.Column.fromType(o.COLUMN_TYPE.INT,"Position",0),o.Column.fromType(o.COLUMN_TYPE.STRING,"Monomers",0)]);this.setDataFrame(t)}get placeholdersValue(){return function(t){const e=[];for(let n=0;n<t.rowCount;n++){if(t.getCol("Position").isNone(n))continue;const r=parseInt(t.get("Position",n))-1;if(!isNaN(r)){const o=Gn(t.get("Monomers",n));e.push({position:r,monomers:o})}}return e}(this.grid.dataFrame)}constructor(t,e,n){super(),this.name=t,this.subs=[],this.dataFrameSubs=[],this.caption=t??"",this.root.classList.add("ui-input-polytool-pos-grid"),this.root.append(this.gridHost=M.div([],{classes:"ui-input-editor",style:{width:"100%",height:"100%",marginTop:"-8px",marginBottom:"8px",paddingBottom:"4px"}})),this.render(e,n).then((()=>{}))}detach(){for(const t of this.subs)t.unsubscribe();for(const t of this.dataFrameSubs)t.unsubscribe()}async render(t,e){let n;const r=o.DataFrame.fromColumns([n=o.Column.fromType(o.COLUMN_TYPE.STRING,"Remove",0),o.Column.fromType(o.COLUMN_TYPE.INT,"Position",0),o.Column.fromType(o.COLUMN_TYPE.STRING,"Monomers",0)]);n.setTag(o.TAGS.FRIENDLY_NAME,""),this.grid=await r.plot.fromType(o.VIEWER.GRID,e),this.grid.sort(["Position"]),this.grid.columns.byIndex(1).width=this.grid.props.rowHeight+2,this.grid.onCellRender.subscribe((t=>{const e=t.cell;e.tableColumn?.name==n.name&&(e?.tableRowIndex??-1)>=0&&(e.element=M.div(M.icons.delete((()=>{this.grid.dataFrame.rows.removeAt(e.tableRowIndex)}),"Delete"),{style:{height:`${e.grid.props.rowHeight}px`,color:"var(--grey-6)",display:"flex",flexDirection:"row",justifyContent:"center"}}))})),this.updateGridHeight(t??this.grid.dataFrame.rowCount+.7),this.subs.push(M.onSizeChanged(this.grid.root).subscribe(this.gridRootOnSizeChanged.bind(this))),this.subs.push((0,et.fromEvent)(this.grid.root,"keydown").subscribe((t=>{"Enter"===t.key&&t.stopPropagation()}))),this.setDataFrame(r),this.grid.root.style.width="100%",this.gridHost.append(this.grid.root)}setDataFrame(t){for(const t of this.dataFrameSubs)t.unsubscribe();this.grid.dataFrame=t,this.dataFrameSubs.push(this.grid.dataFrame.onRowsRemoved.subscribe((()=>{this.updateGridHeight(this.grid.dataFrame.rowCount+.7),this.fireChanged()}))),this.dataFrameSubs.push(this.grid.dataFrame.onRowsAdded.subscribe((()=>{this.updateGridHeight(this.grid.dataFrame.rowCount+.7)}))),this.dataFrameSubs.push(this.grid.dataFrame.onDataChanged.subscribe((()=>{this.fireChanged()}))),this.updateGridHeight(this.grid.dataFrame.rowCount+.7),this.fireChanged()}addPosition(t,e){const n=this.grid.dataFrame,r=n.columns.byName("Position").toList();let o=r.indexOf(t+1);-1===o&&(o=r.findIndex((t=>isNaN(t))),-1===o&&(o=n.rows.addNew(["",t+1,e??""]).idx),this.grid.cell("Monomers",o)),n.currentCell=n.cell(o,"Monomers")}setMonomersValue(t,e){const n=this.grid.dataFrame;n.rowCount<=t||n.set("Monomers",t,e)}static async create(t,e,n){return new jn(t,n,e)}updateGridHeight(t){const e=this.grid.colHeaderHeight+t*this.grid.props.rowHeight+6+2;this.grid.root.style.height=`${e}px`}gridRootOnSizeChanged(){this.grid.columns.byIndex(3).width=this.grid.root.clientWidth-this.grid.horzScroll.root.offsetWidth-this.grid.columns.byIndex(0).width-this.grid.columns.byIndex(1).width-this.grid.columns.byIndex(2).width-10}}function Gn(t){return t.split(/,(?![^(]*\))/).map((t=>('"'===(t=t.trim()).slice(0,1)&&'"'===t.slice(-1)&&(t=t.slice(1,-1)),"'"===t.slice(0,1)&&"'"===t.slice(-1)&&(t=t.slice(1,-1)),t.trim()))).filter((t=>!!t))}class zn extends o.JsInputBase{get inputType(){return"Breadth"}get dataType(){return o.TYPE.DATA_FRAME}getInput(){return this.gridHost}getValue(){return this.grid.dataFrame}setValue(t){this.setDataFrame(t)}getStringValue(){return this.grid.dataFrame.toCsv()}setStringValue(t){this.setDataFrame(o.DataFrame.fromCsv(t))}get placeholdersBreadthValue(){return function(t){const e=[];for(let n=0;n<t.rowCount;n++){const r=parseInt(t.get("Start",n))-1,o=parseInt(t.get("End",n))-1;if(!isNaN(r)&&!isNaN(o)){const i=Gn(t.get("Monomers",n));e.push({start:r,end:o,monomers:i})}}return e}(this.grid.dataFrame)}constructor(t,e,n){super(),this.name=t,this.subs=[],this.dataFrameSubs=[],this.caption=t??"",this.root.classList.add("ui-input-polytool-pos-grid"),this.root.append(this.gridHost=M.div([],{classes:"ui-input-editor",style:{width:"100%",height:"100%",marginTop:"-8px",marginBottom:"8px",paddingBottom:"4px"}})),this.render(e,n).then((()=>{}))}detach(){for(const t of this.subs)t.unsubscribe();for(const t of this.dataFrameSubs)t.unsubscribe()}clearInput(){const t=o.DataFrame.fromColumns([o.Column.fromType(o.COLUMN_TYPE.STRING,"Remove",0),o.Column.fromType(o.COLUMN_TYPE.INT,"Start",0),o.Column.fromType(o.COLUMN_TYPE.INT,"End",0),o.Column.fromType(o.COLUMN_TYPE.STRING,"Monomers",0)]);this.setDataFrame(t)}async render(t,e){let n;const r=o.DataFrame.fromColumns([n=o.Column.fromType(o.COLUMN_TYPE.STRING,"Remove",0),o.Column.fromType(o.COLUMN_TYPE.INT,"Start",0),o.Column.fromType(o.COLUMN_TYPE.INT,"End",0),o.Column.fromType(o.COLUMN_TYPE.STRING,"Monomers",0)]);n.setTag(o.TAGS.FRIENDLY_NAME,""),this.grid=await r.plot.fromType(o.VIEWER.GRID,e),this.grid.sort(["Start","End"]),this.grid.columns.byIndex(1).width=this.grid.props.rowHeight+2,this.grid.onCellRender.subscribe((t=>{const e=t.cell;e.tableColumn?.name==n.name&&(e?.tableRowIndex??-1)>=0&&(e.element=M.div(M.icons.delete((()=>{this.grid.dataFrame.rows.removeAt(e.tableRowIndex)}),"Delete"),{style:{height:`${e.grid.props.rowHeight}px`,color:"var(--grey-6)",display:"flex",flexDirection:"row",justifyContent:"center"}}))})),this.updateGridHeight(t??this.grid.dataFrame.rowCount+.7),this.subs.push(M.onSizeChanged(this.grid.root).subscribe(this.gridRootOnSizeChanged.bind(this))),this.subs.push((0,et.fromEvent)(this.grid.root,"keydown").subscribe((t=>{"Enter"===t.key&&t.stopPropagation()}))),this.setDataFrame(r),this.grid.root.style.width="100%",this.gridHost.append(this.grid.root)}setDataFrame(t){for(const t of this.dataFrameSubs)t.unsubscribe();this.grid.dataFrame=t,this.dataFrameSubs.push(this.grid.dataFrame.onRowsRemoved.subscribe((()=>{this.updateGridHeight(this.grid.dataFrame.rowCount+.7),this.fireChanged()}))),this.dataFrameSubs.push(this.grid.dataFrame.onRowsAdded.subscribe((()=>{this.updateGridHeight(this.grid.dataFrame.rowCount+.7)}))),this.dataFrameSubs.push(this.grid.dataFrame.onDataChanged.subscribe((()=>{this.fireChanged()}))),this.updateGridHeight(this.grid.dataFrame.rowCount+.7),this.fireChanged()}static async create(t,e,n){return new zn(t,n,e)}updateGridHeight(t){const e=this.grid.colHeaderHeight+t*this.grid.props.rowHeight+6+2;this.grid.root.style.height=`${e}px`}gridRootOnSizeChanged(){this.grid.columns.byIndex(4).width=this.grid.root.clientWidth-this.grid.horzScroll.root.offsetWidth-this.grid.columns.byIndex(0).width-this.grid.columns.byIndex(1).width-this.grid.columns.byIndex(2).width-this.grid.columns.byIndex(3).width-10}}var Wn=n(6307);async function Yn(t){await Xr.initPromise;const e=window.innerWidth,n=window.innerHeight;try{let i;function s(){if(null==i)return;const t=L()(i.root).find("div.d4-dialog-contents").get(0),e=t.clientHeight,n={0:1},r=Object.values(n).reduce(((t,e)=>t+e),0),o=e-en().count(0).take(t.children.length).filter((t=>!(t in n))).map((e=>t.children[e])).filter((t=>t instanceof HTMLElement)).map((t=>t.offsetHeight)).reduce(((t,e)=>t+e),0)-38;for(const e of en().count(0).take(t.children.length))if(e in n){const i=t.children[e],s=o*n[e]/r;i.style.height=`${s}px`}}i=await async function(t,e){const n="ST: PT: HelmDialog()";let i;const s=[];let a=Vn.aK.Single;const u=()=>{for(const t of s)t.unsubscribe();i.placeholders.detach()};try{const c=await(0,l.pj)(),h=c.getMonomerLib(),d=await(0,Ze.Q)(),f=o.DataFrame.fromColumns([]),[p,m]=await Promise.all([In(),(0,Qe.b2)()]),g=m.buildMonomersFuncsFromLib(h),y=t=>{let e,n;if(t&&t.rowIndex>=0&&t?.column.semType==o.SEMTYPE.MACROMOLECULE)e=d.getSeqHandler(t.column).getValue(t.rowIndex),n=e.tags["polytool-data-role"]??"macromolecule";else{const t=o.Column.fromList(o.COLUMN_TYPE.STRING,"seq",[qn.d]);t.semType=o.SEMTYPE.MACROMOLECULE,o.DataFrame.fromColumns([t]),t.meta.units=Re.Hi.HELM,e=d.getSeqHandler(t).getValue(0),n="macromolecule"}return[e,n]};let b,v,[w,C]=y(t),A=null;const x=M.divText("",{style:{marginLeft:"8px",marginTop:"2px"}}),S=M.divText("",{style:{color:"red"}});i={macromolecule:m.createHelmInput("Macromolecule",{editable:!1,editorOptions:{drawOptions:{monomerNumbering:1,getMonomer:(t,e)=>{const n=t;if("ATOM"!==n.T)return g.getMonomer(t,e);try{if(w.isDna()||w.isRna()){const t=w.getSplittedWithSugarsAndPhosphates().getCanonical(n.bio.continuousId-1);return g.getMonomer(n.bio.type,t)}{const t=w.getSplitted().getCanonical(n.bio.continuousId-1);return g.getMonomer(n.bio.type,t)}}catch(n){return g.getMonomer(t,e)}}}}}),placeholders:await jn.create("Placeholders",{showAddNewRowIcon:!0,showRemoveRowIcon:!0,showRowHeader:!1,showCellTooltip:!1}),enumeratorType:M.input.choice("Enumerator type",{value:a,items:Object.values(Vn.aK)}),placeholdersBreadth:await zn.create("Breadth",{showAddNewRowIcon:!0,showRemoveRowIcon:!0,showRowHeader:!1,showCellTooltip:!1}),keepOriginal:M.input.bool("Keep original",{value:!1}),toAtomicLevel:M.input.bool("To atomic level",{value:!1,onValueChanged:(t,e)=>{_()}}),generateHelm:M.input.bool(On,{value:!0}),chiralityEngine:M.input.bool(Ln,{value:!1}),highlightMonomers:M.input.bool(Rn,{value:!1}),rules:{header:M.inlineText([Dn]),form:await(v=new Sn._v(Sn.MU,Sn.yy,".json",{onValueChanged:t=>{b=t}})).getForm()},trivialNameCol:M.input.column2("Trivial name",{table:t?.dataFrame,filter:e=>e.type===o.COLUMN_TYPE.STRING&&e!=t?.column,onValueChanged:()=>{const e=i.trivialNameCol.value;let n=null;t&&e&&(n={value:e.get(t.rowIndex),colName:e.name}),A=n,x.textContent=A?`Original ID: ${A.value}`:""},nullable:!0}),library:M.input.choice("Monomer Library",{items:p,value:p[0],nullable:!0})},i.library.root.style.setProperty("display","none"),i.trivialNameCol.addOptions(x);let T=null;i.placeholders.addValidator((t=>{const e=[];try{if(i.enumeratorType.value===Vn.aK.Library){setTimeout((()=>{I()}),10);const t=i.placeholders.placeholdersValue;if(t.length>1)return"Only one placeholder is allowed for Library mode";if(1===t.length){if(null==t[0].position)return"Position is required for Library mode";if(t[0].position>i.macromolecule.molValue.atoms.length)return`There is no monomer at position ${t[0].position+1}.`}return null}if("macromolecule"!==C)return null;const t=[];for(const n of i.placeholders.placeholdersValue){const r=n.position;if(null==r)continue;if(r>=i.macromolecule.molValue.atoms.length){e.push(`There is no monomer at position ${r+1}.`);continue}const o=i.macromolecule.molValue.atoms[r];if(o){const e=o.biotype(),r=(0,Un.Y)(e);for(const e of n.monomers){const n=h.getMonomer(r,e);n&&n.lib||t.push({polymerType:r,symbol:e})}}}const n={};for(const e of t){let t=n[e.polymerType];t||(t=n[e.polymerType]=[]),t.push(e.symbol)}const r=Object.entries(n).map((([t,e])=>`${t}: ${e.join(", ")}`)).join("\n");Object.keys(r).length>0&&e.push(`Placeholders contain missed monomers: ${r}`),T=e.length>0?e.join("\n"):null}catch(t){const[e,n]=_n(t,!1);T=e}return setTimeout((()=>{I()}),0),T})),i.library.addValidator((t=>i.enumeratorType.value!==Vn.aK.Library||i.library.value?null:"Monomer Library is required for this enumerator type")),i.library.onChanged.subscribe((()=>{i.enumeratorType.value===Vn.aK.Library&&i.placeholders.setMonomersValue(0,i.library.value??"")})),i.enumeratorType.onChanged.subscribe((t=>{const e=i.enumeratorType.value===Vn.aK.Library;i.library.root.style.setProperty("display",e?"flex":"none");try{if(a!==Vn.aK.Library&&e||a===Vn.aK.Library&&!e){const t=1===i.placeholders.placeholdersValue.length?i.placeholders.placeholdersValue[0].position:null;i.placeholders.clearInput(),i.placeholdersBreadth.clearInput(),e&&null!=t&&i.placeholders.addPosition(t,i.library.value??"")}}catch(t){_n(t,!1)}a=i.enumeratorType.value})),s.push(i.macromolecule.onMouseMove.subscribe((t=>{try{Xr.logger.debug(`${n}, placeholdersInput.onMouseMove()`);const e=t.offsetX,r=t.offsetY,o=i.macromolecule.molValue,s=m.getHoveredAtom(e,r,o,i.macromolecule.root.clientHeight);if(s){const e=s._parent.atoms.indexOf(s),n=i.placeholders.placeholdersValue.find((t=>t.position===e))?.monomers;if(n){const e=M.divText(n.join(", "));i.macromolecule.showTooltip(e,s),t.preventDefault(),t.stopPropagation()}}}catch(t){_n(t,!1)}}))),s.push(i.macromolecule.onClick.subscribe((t=>{try{Xr.logger.debug(`${n}, placeholdersInput.onClick()`);const e=t.offsetX,r=t.offsetY,o=i.macromolecule.molValue,s=m.getHoveredAtom(e,r,o,i.macromolecule.root.clientHeight);if(s){const t=s._parent.atoms.indexOf(s);String(t+1);let e="";i.enumeratorType.value===Vn.aK.Library&&(i.placeholders.clearInput(),e=i.library.value??""),i.placeholders.addPosition(t,e)}}catch(t){_n(t)}}))),s.push(i.placeholders.onChanged.subscribe((()=>{E()}))),s.push(M.onSizeChanged(i.placeholders.root).subscribe((()=>{e&&e()}))),s.push(r.events.onCurrentCellChanged.subscribe((()=>{const t=r.shell.tv.dataFrame.currentCell;t.column.semType===o.SEMTYPE.MACROMOLECULE&&([w,C]=y(),O(w,C,t))}))),i.macromolecule.root.style.setProperty("min-width","250px","important");const E=()=>{const t=new Set(i.placeholders.placeholdersValue.map((t=>t.position))),e=i.macromolecule.molValue;for(let n=0;n<e.atoms.length;n++)e.atoms[n].highlighted=t.has(n);i.macromolecule.redraw()},_=()=>{i.toAtomicLevel.value&&"template"===C?(i.generateHelm.root.style.removeProperty("display"),i.chiralityEngine.root.style.removeProperty("display"),i.highlightMonomers.root.style.removeProperty("display"),i.rules.header.style.removeProperty("display"),i.rules.form.style.removeProperty("display")):(i.generateHelm.root.style.display=i.chiralityEngine.root.style.display=i.highlightMonomers.root.style.display="none",i.rules.header.style.display=i.rules.form.style.display="none"),e&&e()},I=()=>{const t=T,e=S;t?(e.innerText=t,e.style.removeProperty("display")):(e.innerText="",e.style.setProperty("display","none"))},N=t=>{t?(i.trivialNameCol.setColumnInputTable(t),i.trivialNameCol.root.style.removeProperty("display")):(i.trivialNameCol.setColumnInputTable(f),i.trivialNameCol.root.style.setProperty("display","none")),e&&e()},O=(t,e,n)=>{i.macromolecule.value=t;const r=n?.dataFrame;N(r)};O(w,C,t),_();const L=async()=>{try{const t=i.macromolecule.stringValue,e=en().enumerate(i.macromolecule.molValue.atoms).filter((([t,e])=>t.highlighted)).map((([t,e])=>e)).toArray();if(i.enumeratorType.value===Vn.aK.Library){if(0===e.length)return void r.shell.warning("PolyTool: position for enumeration was not selected");if(!i.library.value)return void r.shell.warning("PolyTool: No monomer library was selected")}if(void 0===t||""===t)r.shell.warning("PolyTool: no molecule was provided");else{if(0===Object.keys(i.placeholders.placeholdersValue).length&&0===Object.keys(i.placeholdersBreadth.placeholdersBreadthValue).length)return void r.shell.warning(`${Bn}: placeholders are empty`);await(0,Qe.b2)();const e=i.placeholders.placeholdersValue;let n=i.enumeratorType.value;if(n===Vn.aK.Library){if(1!==e.length)return void r.shell.warning("Only one placeholder is allowed for Library mode");if(!e[0].monomers||!p.includes(e[0].monomers[0]))return void r.shell.warning("Valid Monomer Library is required for this enumerator type");const t=e[0].monomers[0],o=await c.readSingleLibraryByName(t);if(!o)return void r.shell.warning(`Monomer Library '${t}' was not found`);const i=o.getMonomerSymbolsByType("PEPTIDE");e[0].monomers=i,n=Vn.aK.Single}const o={placeholders:e,type:n,breadthPlaceholders:i.placeholdersBreadth.placeholdersBreadthValue,keepOriginal:i.keepOriginal.value},s=i.toAtomicLevel.value,a=await Kn(t,C,A,o,!!s&&{generateHelm:i.generateHelm.value,chiralityEngine:i.chiralityEngine.value,highlightMonomers:i.highlightMonomers.value,rules:await v.getActive()},m);r.shell.addTableView(a)}}catch(t){_n(t)}},R=M.dialog({title:Bn,showFooter:!0}).add(i.macromolecule.root).add(M.divH([M.divV([i.placeholders.root,i.enumeratorType.root,i.library.root],{style:{width:"50%"}}),M.divV([i.placeholdersBreadth.root],{style:{width:"50%"}})],{style:{width:"100%"}})).add(M.divH([M.divV([i.trivialNameCol.root,i.keepOriginal.root],{style:{width:"50%"}}),M.divV([M.divH([i.toAtomicLevel.root,i.generateHelm.root]),M.divH([i.chiralityEngine.root,i.highlightMonomers.root]),i.rules.header,i.rules.form],{style:{width:"50%"}})],{style:{width:"100%"}})).add(S).onOK((()=>{L()}));return s.push(R.onClose.subscribe((()=>{u()}))),R.history((()=>({description:`${i.enumeratorType.value} ${i.placeholders.placeholdersValue?.map((t=>(t.position?.toString()??"")+": "+t.monomers?.join(", "))).join("; ")}`,placeholders:i.placeholders.stringValue,enumeratorType:i.enumeratorType.value,placeholdersBreadth:i.placeholdersBreadth.stringValue,trivialNameCol:i.trivialNameCol.stringValue,keepOriginal:i.keepOriginal.value,toAtomicLevel:i.toAtomicLevel.value,generateHelm:i.generateHelm.value,chiralityEngine:i.chiralityEngine.value,highlightMonomers:i.highlightMonomers.value,rules:b,library:i.library.value})),(t=>{i.enumeratorType.value=t.enumeratorType??Vn.aK.Single,i.placeholders.stringValue=t.placeholders,i.placeholdersBreadth.stringValue=t.placeholdersBreadth,i.trivialNameCol.stringValue=t.trivialNameCol,i.keepOriginal.value=t.keepOriginal??!1,i.toAtomicLevel.value=t.toAtomicLevel??!0,i.generateHelm.value=t.generateHelm??!0,i.chiralityEngine.value=t.chiralityEngine??!1,i.highlightMonomers.value=t.highlightMonomers??!1,v.setActive(t.rules),i.library.value=t.library})),R}catch(t){throw u(),t}}(t,s);let a=!0;M.onSizeChanged(i.root).subscribe((()=>{if(a){const t=.7*e,r=.7*n;i.root.style.width=`${Math.min(e,t)}px`,i.root.style.height=`${Math.min(n,r)}px`,i.root.style.left=`${Math.floor((e-i.root.offsetWidth)/2)}px`,i.root.style.top=`${Math.floor((n-i.root.offsetHeight)/2)}px`,a=!1}s()})),s(),Xr.logger.debug("PolyToolEnumerateHelmUI: dialog before show"),i.show({width:Math.max(350,.7*e),resizable:!0}),Xr.logger.debug("PolyToolEnumerateHelmUI: dialog after show")}catch(u){const[c,h]=(0,Xe.AP)(u);Xr.logger.error(c,void 0,h)}}async function Kn(t,e,n,i,s,a){const u=o.TaskBarProgressIndicator.create("PolyTool enumerating...");try{const u=await(0,l.pj)(),c=await(0,xn.j)(),h=u.getMonomerLib(),d=(0,qn.o)(t,n?.value??"",i);let f;switch(e){case"macromolecule":f=o.Column.fromType(o.COLUMN_TYPE.STRING,"Enumerated",d.length).init((t=>d[t][0]));break;case"template":{const t=new Array(d.length);for(let e=0;e<d.length;e++){const n=d[e][0],r=Wn.s.fromHelm(n,a);t[e]=r.getNotation()}f=o.Column.fromList(o.COLUMN_TYPE.STRING,"Enumerated",t),f.semType=o.SEMTYPE.MACROMOLECULE,f.setTag("polytool-data-role","template"),to.applyNotationProviderForCyclized(f,"-");break}}const p=o.DataFrame.fromColumns([f]);if(await r.data.detectSemanticTypes(p),"template"==e&&to.applyNotationProviderForCyclized(f,"-"),s){let t;if("macromolecule"===e){t=f;const e=await a.seqHelper.helmToAtomicLevel(t,s.chiralityEngine,s.highlightMonomers);p.columns.add(e.molCol,!1);const n=e.molCol;await async function(t,e,n,r,o,i=!1){const s=r.getSeqHandler(t),a=s.alphabet==Re.YI.RNA||s.alphabet==Re.YI.DNA,l=s.isHelm()&&a,u=!s.isHelm()&&a,c=t=>null==t?null:l?i?t:Math.floor(t/3):u&&i?3*t+1:t,h=i?await r.getHelmToMolfileConverter(n):null,d=new fn({max:100});function f(t,e){const s=t.get(e);if(null==s)return null;let a=d.get(s);return a||d.set(s,a=function(t,e){const s=r.getSeqHandler(t);if(i){const t=s.getHelm(e);return r.helmToAtomicLevelSingle(t,h,!1,!1).monomers}{const t=s.getSplitted(e),r=s.defaultBiotype,i=en().count(0).take(t.length).map((e=>({position:e,symbol:t.getCanonical(e),biotype:r}))).toArray(),a=s.alphabet,l=a==Re.YI.RNA||a==Re.YI.DNA?"RNA":"PEPTIDE",u=(0,yn.eM)([i],l,a,n,o);return(0,bn.gU)(i,u,a,l).monomers}}(t,e)),a}const p={targetCol:e,handler:(e,r,o)=>{const i=o.grid,s=e.tableRowIndex,a=e.gridRow,l=i.cell(o.name,a),u=pn();if(!u||u&&(u.dataFrameId!=t.dataFrame.id||u.gridRowIdx!=a||u.seqColName!=t.name||u.seqPosition!=r?.position)){if(u&&(mn(null),u.gridCell.render()),!r)return mn(null),!0;mn({gridCell:l,dataFrameId:t.dataFrame.id,gridRowIdx:a,seqColName:t.name,seqPosition:c(r?.position)??-1,getSubstruct:()=>{if(!r||"*"===r.symbol)return;const e=f(t,s);if(!e)return;const o=e.get(c(r?.position));return o?(0,vn.H)([o],n):{atoms:[],bonds:[],highlightAtomColors:[],highlightBondColors:[]}}}),l.render()}return!0},getSubstruct:r=>{if("true"!=e.getTag(".sequence-src-highlight-monomers"))return;if(null==r)return;if(!t.get(r))return;const o=f(t,r);return o?(0,vn.H)(o.values(),n):void 0}};return Cn(t.temp,p),gn(e.temp,p),p}(t,n,h,a.seqHelper,c,!0)}else"template"===e&&(t=(await Hn(f,s.generateHelm,!1,s.chiralityEngine,!1,s.rules))[0])}if(n){const t=o.Column.fromType(o.COLUMN_TYPE.STRING,n.colName,d.length).init((t=>d[t][1]));p.columns.add(t)}return p}finally{u.close()}}var Jn,Qn=n(3151);class Xn{constructor(t){this.rawLib=t}isValid(){return this.rawLib.every((t=>"object"==typeof t&&Object.values(Nn).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={...Qn.pe};Object.entries(Nn).forEach((([n,r])=>{const o=t[r];e[n]=o}));let n="smiles";const r=t[Nn[n]],o=new Zn(r),i=o.getCappedSmiles();return e[n]=i,n="rgroups",e[n]=tr.getRGroups(o.getNumberOfRGroups()),n="molfile",e[n]=new er(o.getSmilesWithRGroups()).getMolfile(),e}}class Zn{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 tr{constructor(){}static getRGroups(t){return Mn.slice(0,t)}}class er{constructor(t){this.smilesWithRGroups=t}getMolfile(){let t=o.chem.convert(this.smilesWithRGroups,o.chem.Notation.Smiles,o.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 nr{constructor(t,e){this.fileName=t,this.fileContent=e,this.validateFileType();const n=o.DataFrame.fromCsv(this.fileContent),r=this.toJson(n);this.polyToolMonomerLib=new Xn(r),this.validateContent()}async getJson(){return this.polyToolMonomerLib.getJsonMonomerLib()}toJson(t){return Array.from({length:t.rowCount},((e,n)=>t.columns.names().reduce(((e,r)=>(e[r]=t.get(r,n),e)),{})))}validateFileType(){if(!this.fileName.endsWith(".csv"))throw new Error(`File ${this.fileName} is not an CSV file`)}validateContent(){if(!this.polyToolMonomerLib.isValid())throw new Error("Invalid format of CSV monomer lib")}}!function(t){t.table="table",t.seqCol="seqCol",t.generateHelm="generateHelm",t.chiralityEngine="chiralityEngine",t.rules="rules"}(Jn||(Jn={}));class rr{constructor(t){this.call=t,this.ruleInputs=new Sn._v(Sn.MU,Sn.yy,".json")}async initInputs(){const t=t=>this.call.inputParams[t],e=await this.ruleInputs.getForm();this.inputs={table:(()=>{const e=t(Jn.table);return M.input.table(e.property.caption,{value:e.value})})(),seqCol:(()=>{const e=t(Jn.seqCol);return M.input.column(e.property.caption,{value:e.value,table:e.value.dataFrame})})(),generateHelm:M.input.forProperty(t(Jn.generateHelm).property),chiralityEngine:M.input.forProperty(t(Jn.chiralityEngine).property),rules:{header:M.inlineText([Dn]),form:e}}}static async create(t){const e=new rr(t);return await e.initInputs(),e}async getParams(){return{table:this.inputs.table.value,seqCol:this.inputs.seqCol.value,generateHelm:this.inputs.generateHelm.value,chiralityEngine:this.inputs.chiralityEngine.value,rules:await this.ruleInputs.getActive()}}async showDialog(){const t=M.div([this.inputs.table,this.inputs.seqCol,this.inputs.generateHelm,this.inputs.chiralityEngine,this.inputs.rules.header,this.inputs.rules.form],{style:{minWidth:"320px"}});return new Promise(((e,n)=>{M.dialog({title:Pn}).add(t).onOK((async()=>{const t=await this.getParams(),n=(await this.call.func.prepare(t).call(!0)).getOutputParamValue();e(n)})).onCancel((()=>{n(new Error("Cancelled by user"))})).show()}))}widget(){throw new Error("not implemented")}}class or{onKeyDown(t,e){}onKeyPress(t,e){}onMouseEnter(t,e){}onMouseLeave(t,e){}onMouseDown(t,e){}onMouseUp(t,e){}onMouseMove(t,e){}onClick(t,e){}onDoubleClick(t,e){}}class ir extends or{constructor(t,e,n){super(),this.gridCol=t,this.tableCol=e,this.logger=n,this.subs=[],this.dirty=!0,this.destroyed=!1,this.viewerId=++ir.viewerCounter,this.errors=[],this._onRendered=new et.Subject,this.tableCol&&this.tableCol.dataFrame&&(this.subs.push(this.tableCol.dataFrame.onDataChanged.subscribe((()=>{this.dirty=!0}))),this.subs.push(this.tableCol.dataFrame.onColumnsRemoved.subscribe((t=>{try{this.destroyed||!this.tableCol||this.tableCol.dataFrame||this.destroy()}catch(t){this.logger.error(t)}})))),this.tableCol&&this.subs.push(r.events.onTableRemoved.subscribe((t=>{try{const e=t.args.dataFrame;this.tableCol?.dataFrame.id!==e.id||this.destroyed||this.destroy()}catch(t){this.logger.error(t)}}))),this.gridCol&&this.subs.push(r.events.onViewRemoving.subscribe((t=>{try{const e=t.args.view;this.gridCol?.dart&&this.gridCol.grid&&this.gridCol?.grid?.dart&&this.gridCol?.grid?.view?.id===e.id&&!this.destroyed&&this.destroy()}catch(t){this.logger.error(t)}})))}toLog(){return`${this.constructor.name}<${this.viewerId}>`}destroy(){for(const t of this.subs)t.unsubscribe();this.destroyed=!0}invalidateGrid(){this.gridCol&&this.gridCol.dart&&this.gridCol.grid?.invalidate()}reset(){this.dirty=!1}get onRendered(){return this._onRendered}invalidate(t){this.invalidateGrid()}async awaitRendered(t=1e4,e=`${t} timeout`){const n=`${this.toLog()}.awaitRendered()`;if(this.logger.debug(`${n}, start, testEvent before`),await(0,Ke.PE)(this._onRendered,(()=>{}),(()=>{this.invalidate()}),t,`${n}, ${e}`),this.errors.length>0){const t=this.errors[0];throw this.errors=[],t}this.logger.debug(`${n}, end`)}}ir.viewerCounter=-1;const sr="rgb(100,100,100)",ar="rgb(0,0,0)",lr=s.zS;var ur,cr,hr;!function(t){t.maxMonomerLength=".mm.cellRenderer.maxMonomerLength"}(ur||(ur={})),function(t){t.applyToBackground=".m.cellRenderer.applyToBackground"}(cr||(cr={})),function(t){t.MSA="MSA",t.classic="classic"}(hr||(hr={}));const dr=new class{constructor(){this.color=sr,this.pivot=0,this.left=!1,this.transparencyRate=0,this.separator="",this.last=!1,this.drawStyle=hr.classic,this.maxWord=[],this.wordIdx=0,this.gridCell=null,this.referenceSequence=null,this.maxLengthOfMonomer=null,this.monomerTextSizeMap={},this.logger=void 0,this.selectedPosition=void 0,this.isMultiLineContext=!1,this.lineNumber=0}};function fr(t,e,n,r,i,s,a){var l,u,c;const h={...dr,...a};if(h.isMultiLineContext){t.textBaseline="middle",t.textAlign="center";let o=e;null!=h.maxLengthOfMonomer&&(o=lr(o,h.maxLengthOfMonomer));const a=Math.max(.1,1-(h.transparencyRate??0));t.globalAlpha=a;const l=t.measureText(o),u=l.fontBoundingBoxAscent+l.fontBoundingBoxDescent,c=r+(s-u)/2+l.fontBoundingBoxAscent;let d=h.color??sr;return d&&d!==sr||(d=ar),t.fillStyle=d,h.selectedPosition===h.wordIdx+1&&(t.save(),t.fillStyle="rgba(60, 177, 115, 0.2)",t.fillRect(n,r,i,s),t.restore(),t.fillStyle=d),t.fillText(o,n+i/2,c),t.globalAlpha=1,t.textBaseline="top",t.textAlign="start",n+i}a.logger?.debug("Bio: printLeftOrCentered(), start"),t.textAlign="start";let d=e.substring(0),f=h.last?"":h.separator;h.drawStyle===hr.MSA&&(f="");let p=!0,m=!0,g="difference";if(null!=h.gridCell&&null!=h.gridCell.cell.column&&(p=h.gridCell.cell.column.temp["color-code"]??!0,m=h.gridCell.cell.column.temp["compare-with-current"]??!0,g=h.gridCell.cell.column.temp["highlight-difference"]??"difference"),h.referenceSequence){const t=h.referenceSequence[h.wordIdx];m&&h.referenceSequence.length>0&&"difference"===g&&(h.transparencyRate=d==t?.7:h.transparencyRate),m&&h.referenceSequence.length>0&&"equal"===g&&(h.transparencyRate=d!=t?.7:h.transparencyRate)}null!=h.maxLengthOfMonomer&&(d=lr(d,h.maxLengthOfMonomer));const y=d+f;(l=h.monomerTextSizeMap)[y]??(l[y]=t.measureText(y));let b=h.monomerTextSizeMap[y];(u=h.monomerTextSizeMap)[d]??(u[d]=t.measureText(d));let v=h.monomerTextSizeMap[d].width;const w=s/2-(b.fontBoundingBoxAscent+b.fontBoundingBoxDescent)/2+1;(c=h.monomerTextSizeMap)[f]??(c[f]=t.measureText(f));const C=h.monomerTextSizeMap[f].width;function A(e,i){let a=p?h.color:ar;h.selectedPosition===h.wordIdx+1&&(t.fillStyle="rgba(60, 177, 115, 0.2)",t.fillRect(n+e-4,r-5,h.monomerTextSizeMap[d].width+8,s+10),a=o.Color.toHtml(o.Color.setAlpha(o.Color.fromHtml(a),255))),t.fillStyle=a,t.globalAlpha=1-h.transparencyRate,h.drawStyle===hr.classic&&(t.fillText(d,n+e,r+w),t.fillStyle="#808080",t.fillText(f,n+i,r+w)),h.drawStyle===hr.MSA&&t.fillText(d,n+e,r+w),t.globalAlpha=1}b=b.width,h.drawStyle===hr.MSA&&(v=h.maxWord[h.wordIdx],b=h.maxWord[h.wordIdx]);const x=(h.maxWord[h.wordIdx]??0)-(h.maxWord[0]??0);if(h.left||b>i)return A(x,x+v),n+x+v+C;{const t=(i-b)/2;return A(t,t+v),n+x+t+v}}var pr=n(3599);const mr="rgb(100,100,100)";class gr extends ir{get separatorWidth(){return this.props?.fontCharWidth?this.props?.fontCharWidth:5}constructor(t,e,n,r,i){if(super(t,e,n),this.monomerLengthLimit=r,this.propsProvider=i,this.colWidth=0,this._monomerLengthList=null,this._processedMaxVisibleSeqLength=0,this._monomerLengthMap={},this._monomerStructureMap={},this._ellipsisBounds=void 0,this._totalLinesNeeded=0,this._lineHeight=20,this._cellBounds=new Map,this.sysMonomerLib=null,this.padding=5,this._leftThreeDotsPadding=0,this.props=this.propsProvider(),this._processedRows=o.BitSet.create(this.tableCol.length),this.gridCol&&this.subs.push(this.gridCol.grid.onAfterDrawContent.subscribe((()=>{this._onRendered.next()}))),this.tableCol&&this.gridCol){this.subs.push(this.tableCol.dataFrame.onCurrentRowChanged.subscribe((()=>{-1===this.tableCol.dataFrame.currentRowIdx&&(this.tableCol.temp["reference-sequence"]=null,this.tableCol.temp["current-word"]=null,this.invalidateGrid())})));const t=[Re.gp.positionShift,"renderMultiline"];this.subs.push(o.debounce(this.tableCol.dataFrame.onMetadataChanged.pipe(nt.filter((e=>e.args.source===this.tableCol&&t.includes(e.args.key)))),200).subscribe((t=>{this.reset()}))),this.subs.push(o.debounce(this.tableCol.dataFrame.onMetadataChanged.pipe(nt.filter((t=>t.args.source===this.tableCol&&t.args.key===Re.gp.positionShift))),200).subscribe((t=>{this.reset()})))}}calculateFontBasedSpacing(t){const e=t.measureText("M");let n=12;if(this.tableCol?.temp[".mm.cellRenderer.fontSize"]){const t=this.tableCol.temp[".mm.cellRenderer.fontSize"];"number"!=typeof t||isNaN(t)||(n=Math.max(t,1))}return{lineHeight:Math.max(1.4*n,e.fontBoundingBoxAscent+e.fontBoundingBoxDescent+4),monomerSpacing:Math.max(2,.2*this.props.fontCharWidth)}}shouldUseMultilineRendering(t){return"true"===t.getTag("renderMultiline")}calculateMultiLineLayoutDynamic(t,e,n,r,o,i){if(this.dirty)try{this.reset()}catch(t){const[e,n]=(0,Xe.AP)(t);this.logger.error(e,void 0,n)}const{lineHeight:s,monomerSpacing:a}=this.calculateFontBasedSpacing(t),l=e-2*this.padding;let u=0;const c=[];if(r.length>0)for(let e=o;e<r.length;e++){const n=r.getOriginal(e),o=this.props.monomerToShort(n,i);c.push({text:o,posIdx:e}),u=Math.max(u,t.measureText(o).width)}if(0===c.length)return{lineLayouts:[],lineHeight:s};const h=u;let d=Math.floor((l+a)/(h+a));d=Math.max(1,d);const f=n-2*this.padding,p=Math.max(0,Math.floor(f/s)),m=[];let g=0;for(let t=0;t<p&&g<c.length;t++){const e=[];for(let t=0;t<d&&g<c.length;t++){const n=c[g],r=this.padding+t*(h+a);e.push({posIdx:n.posIdx,x:r,width:h,om:n.text,isSeparator:!1}),g++}m.push({lineIdx:t,elements:e})}return{lineLayouts:m,lineHeight:s}}async init(){await Promise.all([(async()=>{this.seqHelper=await(0,Ze.Q)(),this.invalidateGrid()})(),(async()=>{const t=await(0,l.pj)();this.sysMonomerLib=t.getMonomerLib()})()]),this.subs.push(this.sysMonomerLib.onChanged.subscribe((()=>{this.reset()}))),this.reset()}static getFontSettings(t){let e=12;return t&&t.temp[".mm.cellRenderer.fontSize"]&&"number"==typeof t.temp[".mm.cellRenderer.fontSize"]&&!isNaN(t.temp[".mm.cellRenderer.fontSize"])&&(e=Math.max(t.temp[".mm.cellRenderer.fontSize"],1)),{font:`${e}px monospace`,fontWidth:.6*e}}toLog(){return`MonomerPlacer<${this.viewerId}>`}getMonomerLib(){return this.tableCol.temp[".mm.cellRenderer.overriddenLibrary"]??this.sysMonomerLib}reset(){this.propsProvider&&(this.props=this.propsProvider()),this._processedRows=o.BitSet.create(this.tableCol.length),this._monomerLengthList=null,this._monomerLengthMap={},this._monomerStructureMap={},this._cellBounds.clear(),super.reset(),this.invalidateGrid()}invalidateGrid(){this.gridCol&&this.gridCol.dart&&this.gridCol.grid?.invalidate()}getCellMonomerLengths(t,e){const n=this.seqHelper.getSeqHandler(this.tableCol);if(this.colWidth<e&&(this.colWidth=e,this.dirty=!0),this.dirty)try{this.reset()}catch(t){const[e,n]=(0,Xe.AP)(t);this.logger.error(e,void 0,n)}const r=n.isMsa()?this.getCellMonomerLengthsForSeqMsa():this.getCellMonomerLengthsForSeq(t);return[r,this.getSummedMonomerLengths(r)]}getSummedMonomerLengths(t){const e=new Array(t.length+1);e[0]=this.padding;for(let n=1;n<e.length;n++)e[n]=e[n-1]+t[n-1];let n=e[0];for(let t=1;t<e.length;t++)e[t]?n=e[t]:e[t]=n;return e}getCellMonomerLengthsForSeqValue(t,e){const n=this.seqHelper.getSeqHandler(this.tableCol),r=this.props.separatorWidth+1*this.props.fontCharWidth,o=this.positionShift,i=Math.ceil(e/r)+o,s=n.splitter(t),a=Math.min(i,s.length),l=new Array(a-o);let u=0;for(let t=o;t<a;++t){const r=s.getOriginal(t),i=this.props.monomerToShort(r,this.monomerLengthLimit),a=(n.isSeparator()?this.separatorWidth:this.props.separatorWidth)+i.length*this.props.fontCharWidth;if(l[t-o]=a,u+=a,u>e)break}return l}getCellMonomerLengthsForSeq(t){this.toLog(),null===this._monomerLengthList&&(this._monomerLengthList=new Array(this.tableCol.length).fill(null));const e=this.positionShift,n=this.seqHelper.getSeqHandler(this.tableCol),r=this.props.separatorWidth+1*this.props.fontCharWidth,o=Math.ceil(this.colWidth/r)+e,i=n.getSplitted(t),s=Math.min(o,i.length);let a=this._monomerLengthList[t];if(null===a||a.length!=s-e){a=this._monomerLengthList[t]=new Array(i.length);let r=0;for(let t=e;t<s;++t){const o=i.getOriginal(t),s=this.props.monomerToShort(o,this.monomerLengthLimit),l=(n.isSeparator()?this.separatorWidth:this.props.separatorWidth)+s.length*this.props.fontCharWidth;if(a[t-e]=l,r+=l,r>this.colWidth)break}}return a}getCellMonomerLengthsForSeqMsa(){var t;this.toLog(),null===this._monomerLengthList&&(this._monomerLengthList=new Array(1).fill(null)),(t=this._monomerLengthList)[0]??(t[0]=new Array(0));const e=this._monomerLengthList[0],{startIdx:n,endIdx:r}=(()=>{try{const t=this.gridCol&&this.gridCol.dart?this.gridCol.grid:null;return t&&t.dart?{startIdx:Math.max(Math.floor((t?.vertScroll.min??0)-10),0),endIdx:Math.min(Math.ceil((t?.vertScroll.max??0)+10),this.tableCol.length)}:{startIdx:0,endIdx:Math.min(this.tableCol.length,10)}}catch(t){return{startIdx:0,endIdx:Math.min(this.tableCol.length,10)}}})(),o=this.props.separatorWidth+1*this.props.fontCharWidth,i=this.positionShift,s=Math.ceil(this.colWidth/o)+i;for(let t=n;t<r;t++){if(this._processedRows.get(t)&&s<=this._processedMaxVisibleSeqLength)continue;const n=this.seqHelper.getSeqHandler(this.tableCol).getSplitted(t,s),r=Math.min(s,n.length);r-i>e.length&&e.push(...new Array(r-i-e.length).fill(o));let a=0;for(let t=i;t<r;++t){const r=n.getOriginal(t),o=this.props.monomerToShort(r,this.monomerLengthLimit),s=this.props.separatorWidth+o.length*this.props.fontCharWidth;if(e[t-i]=Math.max(e[t-i]??0,s),a+=s,a>=this.colWidth)break}this._processedMaxVisibleSeqLength=Math.max(this._processedMaxVisibleSeqLength,s),this._processedRows.set(t,!0)}return e}getPosition(t,e,n,r){const[o,i]=this.getCellMonomerLengths(t,n);return 0===this.seqHelper.getSeqHandler(this.tableCol).getSplitted(t).length?null:function(t,e,n){if((n??0)>0&&e<(t[0]??0)+n)return-1;e-=n??0;let r,o=100,i=0,s=t.length-1;for(;i<=s;){if(r=Math.floor((s+i)/2),t[r]<=e&&e<t[r+1])return r;if(e<t[r]?s=r-1:i=r+1,--o<=0)throw new Error(`Get position for pointer x = ${e} searching has not converged on ${JSON.stringify(t)}. `)}return null}(i,e,r)}setMonomerLengthLimit(t){this.monomerLengthLimit!=t&&(this.monomerLengthLimit=t,this.dirty=!0)}setSeparatorWidth(t){this.separatorWidth!=t&&(this.props.separatorWidth=t,this.dirty=!0)}get positionShift(){const t=Number.parseInt(this.tableCol?.tags[Re.gp.positionShift]??"0")??0;return isNaN(t)?0:Math.max(t,0)}render(t,e,n,r,i,s,a){const l=s.grid?.dart&&s.grid?.canvas===t.canvas;if(!this.seqHelper)return;const u=this.tableCol,c=this.positionShift;t.save();try{const a=this.seqHelper.getSeqHandler(u);let h=this.monomerLengthLimit;if(ur.maxMonomerLength in u.tags){const t=parseInt(u.getTag(ur.maxMonomerLength));h=!isNaN(t)&&t?t:50}if(".mm.cellRenderer.maxMonomerLength"in u.temp){const t=u.temp[".mm.cellRenderer.maxMonomerLength"],e="number"==typeof t?t:parseInt(t);h=!isNaN(e)&&e?e:50}if("1"===u.temp[".mm.cellRenderer.settingsChanged"]||this.monomerLengthLimit!=h){let t=0;const e=8;t=u.temp[".mm.cellRenderer.gapLength"]??t,this.setMonomerLengthLimit(h),this.setSeparatorWidth(a.isMsa()?e:t),u.temp[".mm.cellRenderer.settingsChanged"]="0",this.dirty=!0}const d=s.cell.rowIndex,f=s.cell.value;l&&(r=function(t,e,n,r,o){return t?Math.max(Math.min(t.canvas.width/o-n,r)):Math.max(e.canvas.width/o-n,0)}(s.grid,t,e,r,window.devicePixelRatio)),t.beginPath(),t.rect(e,n,r,i),t.clip(),t.font=this.props?.font??"12px monospace",t.textBaseline="top";const p=u.meta.units,m=u.getTag(Re.gp.aligned),g=u.getTag(Re.gp.separator)??"",y=l?a.getSplitted(d):a.splitter(f);let b=hr.classic;m?.includes("MSA")&&p===Re.Hi.SEPARATOR&&(b=hr.MSA);const v=u.temp["reference-sequence"],w=this.tableCol.temp["current-word"],C=(()=>{const t=(0,a.splitter)(null!=v&&""!==v?v:w??"");return en().count(0).take(t.length).slice(c).map((e=>t.getCanonical(e))).toArray()})(),A=Number.parseInt(u.getTag(Re.gp.selectedPosition)??"-200");if(this.shouldUseMultilineRendering(u)){const l=[],d=this.calculateMultiLineLayoutDynamic(t,r,i,y,c,h);let f=n+this.padding;1===d.lineLayouts.length&&(f=n+(i-d.lineHeight)/2);for(const r of d.lineLayouts){const i=f+r.lineIdx*d.lineHeight;for(const h of r.elements){const f=e+h.x,p=h,m=p.posIdx,g=y.getCanonical(m);let b=mr;const v=this.getMonomerLib();v&&(b=v.getMonomerTextColor(a.defaultBiotype,g));let w=0;if(s.tableRowIndex!==u.dataFrame.currentRowIdx&&C.length>0){const t=m-c;t>=0&&t<C.length&&g===C[t]&&(w=.7)}l.push({lineIdx:r.lineIdx,monomerIdx:m-c,bounds:new o.Rect(h.x,i-n,h.width,d.lineHeight),sequencePosition:m}),fr(t,p.om,f,i,h.width,d.lineHeight,{color:b,isMultiLineContext:!0,transparencyRate:w,selectedPosition:isNaN(A)||A<1?void 0:A,wordIdx:m})}}null!==s.tableRowIndex&&this._cellBounds.set(s.tableRowIndex,l)}else{this._leftThreeDotsPadding=this.shouldRenderShiftedThreeDots(c)?t.measureText("...").width:0;let[,o]=this.getCellMonomerLengths(s.tableRowIndex,r);l||(o=this.getSummedMonomerLengths(this.getCellMonomerLengthsForSeqValue(f,r)));const u=this.props.separatorWidth+1*this.props.fontCharWidth,d=Math.min(y.length,Math.ceil(r/u)+c);for(let l=c;l<d;++l){const u=l<y.length?y.getOriginal(l):a.defaultGapOriginal,d=l<y.length?y.getCanonical(l):a.defaultGapOriginal;let f=mr;this.getMonomerLib()&&(f=this.getMonomerLib().getMonomerTextColor(a.defaultBiotype,d));const p=l===y.length-1,m={color:f,pivot:0,left:!0,transparencyRate:0,separator:(y?.graphInfo?.disjointSeqStarts?.indexOf(l+1)??0)>0?"|":g,last:p,drawStyle:b,maxWord:o,wordIdx:l-c,gridCell:s,referenceSequence:C,maxLengthOfMonomer:h,monomerTextSizeMap:this._monomerLengthMap,logger:this.logger,selectedPosition:isNaN(A)||A<1?void 0:A-c};fr(t,u,e+this.padding+this._leftThreeDotsPadding,n,r,i,m)}if(this.shouldRenderShiftedThreeDots(c)){const a={color:mr,pivot:0,left:!0,transparencyRate:0,separator:g,last:!1,drawStyle:b,maxWord:o,wordIdx:0,gridCell:s,maxLengthOfMonomer:h,monomerTextSizeMap:this._monomerLengthMap,logger:this.logger};fr(t,"...",e+this.padding,n,r,i,a)}}}catch(t){const[e,n]=(0,Xe.AP)(t);this.logger.error(e,void 0,n),this.errors.push(t)}finally{t.restore()}}shouldRenderShiftedThreeDots(t){return t>0&&(!this.gridCol||!this.gridCol.dart||!this.gridCol.grid||!this.gridCol.grid.dart||(this.gridCol.grid.props.colHeaderHeight??0)<=50)}onMouseMove(t,e){const n=`${this.toLog()}.onMouseMove()`;if(!this.seqHelper||null==t.tableRowIndex)return;const r=this.positionShift,o=t.bounds,i=e.offsetX-t.gridColumn.left+(t.gridColumn.left-o.x),s=e.offsetY-o.y;this.gridCol?.grid?.canvas&&(this.gridCol.grid.canvas.style.cursor="default");let a=null;const l=this._cellBounds.get(t.tableRowIndex);if(l){for(const t of l)if(t.bounds.contains(i,s)){a=t.monomerIdx;break}}else{const e=this.shouldRenderShiftedThreeDots(r)&&(this._leftThreeDotsPadding??0)>0?this._leftThreeDotsPadding:0;a=this.getPosition(t.tableRowIndex,i,o.width,e)}this.logger.debug(`${n}, argsX: ${i}, argsY: ${s}, left: ${a}`);const u=this.seqHelper.getSeqHandler(this.tableCol),c=u.getSplitted(t.tableRowIndex);if(null!==a&&a>=0&&a+r<c.length){const n=u.alphabet??Re.YI.UN,o={position:a,biotype:n===Re.YI.RNA||n===Re.YI.DNA?pr.o.NUCLEOTIDE:pr.o.AA,symbol:c.getCanonical(a+r)},i=[];let s=this._monomerStructureMap[o.symbol];if(!s){const t=this.getMonomerLib();s=this._monomerStructureMap[o.symbol]=t?t.getTooltip(o.biotype,o.symbol):M.divText("Monomer library is not available")}i.push(s),M.tooltip.show(M.divV(i),e.x+16,e.y+16),An(t,o)}else-1===a?M.tooltip.show(M.divText(`${Math.min(r,c.length)} hidden monomers`),e.x+16,e.y+16):M.tooltip.hide(),An(t,null)}}class yr extends gr{constructor(t,e,n,r){super(t,e,Xr.logger,n,(()=>{const t=r.getSeqHandler(e),{font:n,fontWidth:o}=gr.getFontSettings(e);return{seqHandler:t,font:n,fontCharWidth:o,separatorWidth:11,monomerToShort:Re.zS}}))}onMouseMove(t,e){super.onMouseMove(t,e)}}class br{get defaultGapOriginal(){return""}constructor(t,e){this.separator=t,this.helmHelper=e,this.separatorSplitter=(0,Re.dh)(this.separator),this.splitter=this._splitter.bind(this)}setUnits(){}_splitter(t){const e=this.separatorSplitter(t);return new vr(en().count(0).take(e.length).map((t=>e.getOriginal(t))).toArray(),i.b9[i.Hi.SEPARATOR])}getHelm(t,e){return Wn.s.fromSeparator(t,this.helmHelper).getHelm()}createCellRendererBack(t,e){const n=new yr(t,e,4,this.helmHelper.seqHelper);return n.init().then((()=>{})),n}}class vr extends s.Mu{getCanonical(t){if(this.isGap(t))return i._S;const e=this.getOriginal(t);let n=e;return e.startsWith("{")?n=e.slice(1):e.endsWith("}")?n=e.slice(0,-1):e.startsWith("(")?n=e.replace(/^\(.\d+\)/,""):e.endsWith(")")&&(n=e.replace(/\(\d+\)$/,"")),n}constructor(t,e){super(t,e)}}async function wr(){return await to.oligoToolkitApp()}async function Cr(){await to.init()}async function Ar(){return await to.oligoTranslatorApp()}async function xr(){return await to.oligoPatternApp()}async function Sr(){return await to.oligoStructureApp()}async function Tr(){return await to.getTranslationHelper()}function Er(){return to.getCodeToWeightsMap()}function _r(t){return to.validateSequence(t)}function Ir(t,e){return to.getMolfileFromGcrsSequence(t,e)}function Nr(t){return to.linkStrands(t)}async function Mr(){await to.demoTranslateSequence()}async function Or(){await to.demoOligoPattern()}async function Lr(){await to.demoOligoStructure()}async function Rr(t,e,n){return await to.translateOligonucleotideSequence(t,e,n)}async function Pr(){await to.polyToolConvertTopMenu()}async function Br(t){return await to.getPolyToolConvertEditor(t)}async function Dr(t,e,n,r,o){return await to.polyToolConvert2(t,e,n,r,o)}async function Fr(){await to.polyToolEnumerateHelmTopMenu()}async function kr(){await to.polyToolEnumerateChemTopMenu()}async function Hr(t,e){await to.polyToolColumnChoice(t,e)}async function Ur(t){await to.createMonomerLibraryForPolyTool(t)}async function $r(){await to.ptEnumeratorHelmApp()}async function Vr(){await to.ptEnumeratorChemApp()}async function qr(t){await to.getPtHelmEnumeratorDialog(t)}async function jr(t){await to.getPtChemEnumeratorDialog(t)}async function Gr(t,e,n,r){return await to.enumerateSingleHelmSequence(t,e,n,r)}async function zr(t,e){return await to.enumerateSingleHelmSequenceWithNaturalAAs(t,e)}async function Wr(){await to.getPolyToolCombineDialog()}function Yr(t,e){to.applyNotationProviderForCyclized(t,e)}var Kr=function(t,e,n,r){var o,i=arguments.length,s=i<3?e:null===r?r=Object.getOwnPropertyDescriptor(e,n):r;if("object"==typeof Reflect&&"function"==typeof Reflect.decorate)s=Reflect.decorate(t,e,n,r);else for(var a=t.length-1;a>=0;a--)(o=t[a])&&(s=(i<3?o(s):i>3?o(e,n,s):o(e,n))||s);return i>3&&s&&Object.defineProperty(e,n,s),s},Jr=function(t,e){if("object"==typeof Reflect&&"function"==typeof Reflect.metadata)return Reflect.metadata(t,e)},Qr=function(t,e){return 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Ye(t,Xr);return await e.getAppView()}static async init(){return null===Zr&&Xr.startInit(Zr=async function(){const[t]=await Promise.all([(0,Qe.b2)()]);Xr.completeInit(t)}()),Zr}static async oligoTranslatorApp(){return await eo("Oligo Translator")}static async oligoPatternApp(){return await eo("Oligo Pattern")}static async oligoStructureApp(){return await eo("Oligo Structure")}static async getTranslationHelper(){return await Xr.initLibData(),Xr}static getCodeToWeightsMap(){const t=Xr.monomerLibWrapper.getCodesToWeightsMap();return Object.fromEntries(t)}static validateSequence(t){const e=Xr.createSequenceValidator(t),n=Xr.createFormatDetector(t).getFormat();return null!==n&&e.isValidSequence(n)}static getMolfileFromGcrsSequence(t,e){return new xe(t,e,"GCRS").convert()}static linkStrands(t){return Se(t,!0)}static async demoTranslateSequence(){await async function(){await b((async()=>{const t=await to.oligoTranslatorApp();r.shell.addView(t)}))}()}static async demoOligoPattern(){await async function(){await b((async()=>{const t=await to.oligoPatternApp();r.shell.addView(t)}))}()}static async demoOligoStructure(){await async function(){await b((async()=>{const t=await to.oligoStructureApp();r.shell.addView(t),["Afcgacsu","Afcgacsu","Afcgacsu"].forEach((async(t,e)=>{await async function(t,e){await(0,Ke.cb)(500);const n=document.querySelectorAll(".st-colored-text-input > textarea")[t];n.value=e;const r=new Event("input");n.dispatchEvent(r)}(e,t)}))}))}()}static async translateOligonucleotideSequence(t,e,n){return await Xr.initLibData(),Xr.createFormatConverter(t,e).convertTo(n)}static async polyToolConvertTopMenu(){await async function(){await Xr.initPromise;let t=null;try{t=await async function(){const t=[],e=()=>{for(const e of t)e.unsubscribe()};try{let n;const i=r.shell.t.columns.bySemTypeAll(o.SEMTYPE.MACROMOLECULE),s=i.filter((t=>Xr.seqHelper.getSeqHandler(t).notation===Re.Hi.CUSTOM));if(!n){if(i.length<1)throw new Error("No dataframe with macromolecule columns open");if(s.length<1){const t=o.Func.find({package:"Bio",name:"toAtomicLevel"})[0];return t?(t.prepare().edit(),null):(r.shell.warning("Polytool requires a macromolecule column with custom notation. \n\nUse Top menu | Bio | Transform | To Atomic Level."),null)}n=i[0]}const a=M.input.column("Column",{table:n.dataFrame,value:n,filter:t=>s.includes(t)}),l=M.input.bool(On,{value:!0});M.tooltip.bind(l.root,"Add HELM column");const u=M.input.bool("Linearize",{value:!0});M.tooltip.bind(u.root,"Make representation linear if possible");const c=M.input.bool(Ln,{value:!0}),h=M.input.bool(Rn,{value:!0});let d;const f=new Sn._v(Sn.MU,Sn.yy,".json",{onValueChanged:t=>{d=t}}),p=M.inlineText([Dn]);M.tooltip.bind(p,"Add or specify rules to use");const m=await f.getForm(),g=M.divV([a,l,u,c,h,p,m]),y=async()=>{try{const t=await f.getActive();await Hn(a.value,l.value,u.value,c.value,h.value,t)}catch(t){_n(t)}},b=M.dialog(Pn).add(g).onOK((()=>{y()}));return t.push(b.onClose.subscribe((()=>{e()}))),b.history((()=>({generateHelm:l.value,chiralityEngine:c.value,rules:d})),(t=>{l.value=t.generateHelm,c.value=t.chiralityEngine,f.setActive(t.rules)})),b}catch(t){throw e(),t}}(),t?.show()}catch(t){const[e,n]=(0,Xe.AP)(t);r.shell.warning("To run PolyTool Conversion, open a dataframe with macromolecules"),Xr.logger.error(e,void 0,n)}}()}static async getPolyToolConvertEditor(t){const e=await rr.create(t);return await e.showDialog()}static async polyToolConvert2(t,e,n,r,o){return(await Hn(e,n,!1,r,!1,o))[0]}static async polyToolEnumerateHelmTopMenu(){await Yn(r.shell.tv?.dataFrame.currentCell)}static async polyToolEnumerateChemTopMenu(){kn()}static async polyToolColumnChoice(t,e){var n;(function(t){t.semType=o.SEMTYPE.MACROMOLECULE,t.setTag("aligned","SEQ"),t.setTag("alphabet",Re.YI.PT)})(n=e),n.meta.units=Re.Hi.SEPARATOR,n.setTag("separator","-"),await r.data.detectSemanticTypes(t)}static async createMonomerLibraryForPolyTool(t){const e=await t.readAsString(),n=new nr(t.fileName,e),r=await n.getJson(),i=t.fileName.replace(/\.csv$/,".json"),s=JSON.stringify(r,null,2);o.Utils.download(i,s)}static async ptEnumeratorHelmApp(){await Yn()}static async ptEnumeratorChemApp(){kn()}static async getPtHelmEnumeratorDialog(t){return Yn(t)}static async getPtChemEnumeratorDialog(t){return kn(t)}static async enumerateSingleHelmSequence(t,e,n,r=!1){return await Kn(t,"macromolecule",null,{type:Vn.aK.Single,placeholders:e.map(((t,e)=>({position:t,monomers:n[e]})))},!!r&&{generateHelm:!0,chiralityEngine:!0,highlightMonomers:!1,rules:[]},Xr.helmHelper)}static async enumerateSingleHelmSequenceWithNaturalAAs(t,e=!1){const n=(0,Re.qp)(t).length,r=Array.from({length:n},((t,e)=>e)),o=r.map((t=>["A","C","D","E","F","G","H","I","K","L","M","N","P","Q","R","S","T","V","W","Y"]));return await to.enumerateSingleHelmSequence(t,r,o,e)}static async getPolyToolCombineDialog(){!async function(){const t=[],e=M.divV([]),n=i=>{const s=(()=>{const t=M.divH([]),e=M.input.table("Table",{value:void 0,tooltipText:"Table with sequences"}),n=M.input.choice("Column",{items:[],value:void 0,tooltipText:"Sequence column"});return e.onChanged.subscribe((async()=>{const t=e.value;if(!t)return n.items=[],void(n.value=null);await t.meta.detectSemanticTypes(),await r.data.detectSemanticTypes(t);const i=Array.from(t.columns.categorical),s=i.map((t=>t.name));n.items=s,n.value=i.find((t=>t.semType===o.SEMTYPE.MACROMOLECULE))?.name??s.find((t=>{const e=t.toLowerCase();return e.includes("seq")||e.includes("pep")}))??s[0]})),t.appendChild(e.root),t.appendChild(n.root),t.style.alignItems="center",{root:t,getValue:()=>({table:e.value,column:n.value})}})(),a=M.icons.delete((()=>{if(!s.root.parentElement||t.length<2)return;s.root.remove();const e=t.indexOf(s);-1!==e&&t.splice(e,1)}),"Remove"),l=M.icons.add((()=>{let e=t.indexOf(s);-1===e&&(e=t.length),n(e+1)}),"Add");s.root.appendChild(a),s.root.appendChild(l),a.style.marginLeft="8px",a.style.marginRight="8px",a.style.color="var(--blue-1)",l.style.color="var(--blue-1)";const u=t[i];u?e.insertBefore(s.root,u.root):e.appendChild(s.root),t.splice(i,0,s)};n(0);const i=M.input.string("Separator",{value:"-",tooltipText:"Separator for sequences",nullable:!1});M.dialog("Combine Sequences").add(e).add(i.root).onOK((async()=>{if(!function(){const e=t.map((t=>t.getValue())),n=e.map((t=>t.table)),r=e.map((t=>t.column));return n.every((t=>!!t))&&r.every((t=>!!t))}())return void r.shell.error("Please fill all the fields");const e=t.map((t=>t.getValue())),n=e.map((t=>t.table)),s=e.map((t=>t.column)),a=i.value,l=s.map(((t,e)=>n[e].col(t).toList().filter((t=>!!t))));let u=0;const c=l.reduce(((t,e)=>t*e.length),1);if(c>1e7)return void r.shell.error("Too many combinations. Maximum allowed is 10M");const h=new Array(c).fill(null),d=(t,e)=>{if(e===l.length)return void(h[u++]=t);const n=`${t}${t?a:""}`,r=l[e];for(let t=0;t<l[e].length;t++)d(n+r[t],e+1)};d("",0);const f=o.DataFrame.fromColumns([o.Column.fromStrings("Combined Sequences",h)]);f.name="Combined Sequences",await f.meta.detectSemanticTypes(),await r.data.detectSemanticTypes(f),r.shell.addTableView(f)})).show({resizable:!0})}()}static applyNotationProviderForCyclized(t,e){t.setTag("aligned","SEQ"),t.setTag("alphabet","UN"),t.setTag(".alphabetIsMultichar","true"),t.meta.units=i.Hi.CUSTOM,t.tags["polytool-data-role"]="template",t.temp[a.notationProvider]=new br(e,Xr.helmHelper)}}async function eo(t){await Xr.initLibData();const e=function(t,e){switch(t){case"Oligo Translator":return new ze(e);case"Oligo Pattern":return new ie(e);case"Oligo Structure":return new Le(e);default:throw new Error(`Unknown app name: ${t}`)}}(t,Xr);return await e.getAppView()}Kr([r.decorators.app({icon:"img/icons/toolkit.png",browsePath:"Peptides | Oligo Toolkit",name:"Oligo Toolkit"}),Jr("design:type",Function),Jr("design:paramtypes",[]),Jr("design:returntype",Promise)],to,"oligoToolkitApp",null),Kr([r.decorators.init(),Jr("design:type",Function),Jr("design:paramtypes",[]),Jr("design:returntype",Promise)],to,"init",null),Kr([r.decorators.app({icon:"img/icons/translator.png",browsePath:"Peptides | Oligo Toolkit",name:"Oligo Translator"}),Jr("design:type",Function),Jr("design:paramtypes",[]),Jr("design:returntype",Promise)],to,"oligoTranslatorApp",null),Kr([r.decorators.app({icon:"img/icons/pattern.png",browsePath:"Peptides | Oligo Toolkit",name:"Oligo Pattern"}),Jr("design:type",Function),Jr("design:paramtypes",[]),Jr("design:returntype",Promise)],to,"oligoPatternApp",null),Kr([r.decorators.app({icon:"img/icons/structure.png",browsePath:"Peptides | Oligo Toolkit",name:"Oligo 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| Oligo Toolkit | Translator",path:"/apps/Tutorials/Demo/Bioinformatics/Oligonucleotide%20Sequence:%20Translate",demoSkip:"GROK-14320"},name:"demoOligoTranslator",description:"Translate oligonucleotide sequences across various formats accepted by different synthesizers"}),Jr("design:type",Function),Jr("design:paramtypes",[]),Jr("design:returntype",Promise)],to,"demoTranslateSequence",null),Kr([r.decorators.func({meta:{demoPath:"Bioinformatics | Oligo Toolkit | Pattern",path:"%20/apps/Tutorials/Demo/Bioinformatics/Oligonucleotide%20Sequence:%20Visualize%20duplex"},description:"Design a modification pattern for an oligonucleotide sequence"}),Jr("design:type",Function),Jr("design:paramtypes",[]),Jr("design:returntype",Promise)],to,"demoOligoPattern",null),Kr([r.decorators.func({meta:{demoPath:"Bioinformatics | Oligo Toolkit | Structure",path:"%20/apps/Tutorials/Demo/Bioinformatics/Oligonucleotide%20Sequence:%20Visualize%20duplex"},description:"Visualize duplex and save 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molfiles"}),Jr("design:type",Function),Jr("design:paramtypes",[]),Jr("design:returntype",Promise)],to,"polyToolConvertTopMenu",null),Kr([r.decorators.editor(),Jr("design:type",Function),Jr("design:paramtypes",[o.FuncCall]),Jr("design:returntype",Promise)],to,"getPolyToolConvertEditor",null),Kr([r.decorators.func({editor:"SequenceTranslator:getPolyToolConvertEditor"}),Qr(1,r.decorators.param({options:{caption:"Sequence"}})),Qr(2,r.decorators.param({options:{initialValue:"true"}})),Qr(3,r.decorators.param({options:{initialValue:"true"}})),Qr(4,r.decorators.param({type:"object"})),Jr("design:type",Function),Jr("design:paramtypes",[o.DataFrame,o.Column,Boolean,Boolean,Array]),Jr("design:returntype",Promise)],to,"polyToolConvert2",null),Kr([r.decorators.func({"top-menu":"Bio | PolyTool | Enumerate HELM...",name:"polyToolEnumerateHelm",description:"Dialog for configuring enumeration of a HELM sequence"}),Jr("design:type",Function),Jr("design:paramtypes",[]),Jr("design:returntype",Promise)],to,"polyToolEnumerateHelmTopMenu",null),Kr([r.decorators.func({"top-menu":"Bio | PolyTool | Enumerate Chem...",name:"polyToolEnumerateChem",description:"Perform enumeration of a molecule using different fragments at specified positions"}),Jr("design:type",Function),Jr("design:paramtypes",[]),Jr("design:returntype",Promise)],to,"polyToolEnumerateChemTopMenu",null),Kr([r.decorators.func(),Qr(0,r.decorators.param({options:{description:"Input data table"}})),Jr("design:type",Function),Jr("design:paramtypes",[o.DataFrame,o.Column]),Jr("design:returntype",Promise)],to,"polyToolColumnChoice",null),Kr([r.decorators.func(),Jr("design:type",Function),Jr("design:paramtypes",[o.FileInfo]),Jr("design:returntype",Promise)],to,"createMonomerLibraryForPolyTool",null),Kr([r.decorators.func({meta:{icon:"img/icons/structure.png",browsePath:"Peptides | PolyTool"},tags:["app"],name:"HELM 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r=n(2125),o=n(8438),i=n(6694);function s(t,e){let n="";for(let t=0;t<e.length;t++){t>0&&(n+="|"),n+=`PEPTIDE${t+1}{`;for(let r=0;r<e[t].length;r++){r>0&&(n+=".");const o=e[t][r];n+=o.length>1?`[${o}]`:o}n+="}"}n+="$";for(let o=0;o<t.length;o++)o>0&&(n+="|"),n+=`PEPTIDE${t[o].fChain+1},PEPTIDE${t[o].sChain+1},`,n+=`${(0,r.M)(t[o].fMonomer-1,e)[0]+1}:R${t[o].fR}-`,n+=`${(0,r.M)(t[o].sMonomer-1,e)[0]+1}:R${t[o].sR}`;return n+="$$$V2.0",n}function a(t,e,n,r=0,o=[],i=[]){let[s,a,l,u,c]=[!1,!1,!1,-1,-1];for(let h=0;h<t.length;h++)if(t[h].includes(e)){if(s){if(l&&(n||t[h]==i[r]+e)){a=!0,c=h;break}if(l||!n&&t[h]!=o[r]+e)continue;a=!0,c=h;break}if(n)s=!0,l=!0,u=h;else if(t[h]==o[r]+e)s=!0,l=!0,u=h;else{if(t[h]!=i[r]+e)continue;s=!0,l=!!n,u=h}}return[s,a,l,u,c]}function l(t,e){const n=[];for(let r=0;r<e.length;r++){const o=`(${e[r].code})`,[s,l]=(0,i.Ln)(e[r]);if(s.length>0)for(let 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h=n(3599);function d(t,e,n){const r=n.createHelmWebEditor().editor.m;let o=0;const i=new JSDraw2.Point(0,0);for(let t=0;t<e.length;t++)for(let n=0;n<e[t].length;n++){if(e[t][n]){const s=e[t][n],a={type:h.o.AA,i:t,j:n,continuousId:o},l=new JSDraw2.Atom(i,s,a);if(r.addAtom(l),0!==n){const t=r.atoms[o-1],e=r.atoms[o],n=new JSDraw2.Bond(t,e);n.r1=2,n.r2=1,r.addBond(n)}o++,i.x+=JSDraw2.Editor.BONDLENGTH}i.y+=4*JSDraw2.Editor.BONDLENGTH}for(let e=0;e<t.length;e++){const n=r.atoms[t[e].fMonomer-1],o=r.atoms[t[e].sMonomer-1],i=new JSDraw2.Bond(n,o);i.r1=t[e].fR,i.r2=t[e].sR,r.addBond(i)}return r}class f{constructor(t,e,n){this.helmHelper=n,this.underRules=!1,this.posToPosUnderRules=[],this.linkages=e,this.monomers=t,this.mol=d(e,t,n)}static fromSeparator(t,e){const[n,r]=function(t){const e=[],n=[],r=/(\(.\d+\))?\{[^\}]*\}/g,o=[];o.push(t.replaceAll(r,""));const i=t.matchAll(r);for(const t of i){const e=t[0];e&&o.push(e)}let s=0;for(let t=0;t<o.length;t++){const r=o[t].split("-"),i=new Array(r.length);let a=0;for(let e=0;e<r.length;e++){const o=r[e].replace("{","").replace("}","");""!==o?(i[e]=o,s++,a++):n.push({fChain:t,sChain:t+1,fMonomer:s,sMonomer:s+1,fR:1,sR:1})}e.push(i.slice(0,a))}return[n,e]}(t);return new f(r,n,e)}static fromHelm(t,e){const[n,i]=function(t){const e=/(\w+\{.*\})\$(.*)\$(.*)\$(.*)\$/g.exec(t),n=[e[1],e[2],e[3],e[4]],i=n[0].split("|"),s=n[1].split("|"),a=new Array(i.length),l=[];for(let t=0;t<i.length;t++){const e=i[t].indexOf("{"),n=i[t].indexOf("}");a[t]=i[t].slice(e+1,n).split(".").map((t=>(0,o.D)(t)))}for(let t=0;t<s.length;t++)if(""!==s[t]&&"V2.0"!==s[t]){const e=s[t].split(","),n=parseInt(e[0].replace("PEPTIDE",""))-1,o=parseInt(e[1].replace("PEPTIDE",""))-1,i=e[2].split("-"),u=i[0].split(":"),c=i[1].split(":");l.push({fChain:n,sChain:o,fMonomer:(0,r.j)(parseInt(u[0]),n,a),sMonomer:(0,r.j)(parseInt(c[0]),o,a),fR:parseInt(u[1].replace("R","")),sR:parseInt(c[1].replace("R",""))})}return[l,a]}(t);return new f(i,n,e)}getNotation(){return function(t){const e=t.atoms,n=t.bonds,r=[],o=[];for(let t=0;t<n.length;t++)n[t].a1.bio.i!==n[t].a2.bio.i&&o.push(t);for(let t=0;t<e.length;t++){const n=e[t].bio?.i;n+1>r.length?r.push(1):r[n]++}const i=new Array(r.length);let s=0;for(let t=0;t<r.length;t++){const n=new Array(r[t]);for(let o=0;o<r[t];o++)n[o]=e[s].elem,s++;i[t]=n}let a="";for(let t=0;t<i.length;t++){let e="";for(let n=0;n<i[t].length;n++)e+=`${0==n?"":"-"}${i[t][n]}`;if(0!==t){const t=/(\(.\d+\))/,n=e.match(t);e=e.replace(n?.[0],""),e=`${n?n?.[0]:""}{${e}}`}else if(i.length>1){const t=0==n[o[0]].a1.bio.i&&0==n[o[0]].a1.bio.j,r=1==n[o[0]].a2.bio.i&&0==n[o[0]].a1.bio.j;t&&r&&(e+="-")}a+=e}return a}(this.mol)}getHelm(){return this.underRules?s(this.linkagesUnderRules,this.monomersUnderRules):s(this.linkages,this.monomers)}applyRules(t){const e=this.getNotation(),[n,r,o]=function(t,e){const n=[],r=[],o=[],i=e.heterodimerCode,s=e.homodimerCode,a=null!==i?t.split(`(${e.heterodimerCode})`):"";null!==i&&a.length>1?(o.push({fChain:0,sChain:1,fMonomer:1,sMonomer:1,fR:1,sR:1}),n.push(a[1].replaceAll("{","").replaceAll("}","")),n.push(a[2].replaceAll("{","").replaceAll("}","")),r.push(!1),r.push(!1)):(n.push(t),r.push(!1));for(let t=0;t<n.length;t++)if(null!==s&&n[t].includes(`(${s})`)){const e=n.length;o.push({fChain:t,sChain:e,fMonomer:1,sMonomer:1,fR:1,sR:1});const i=n[t].replace(`(${s})`,""),a=i.indexOf("{"),l=i.slice(0,a),u=i.replace(l,"").replaceAll("{","").replaceAll("}","");n[t]=l+u,n.push(u),r.push(!0)}return[o,n,r]}(e,t),i=new Array(r.length);let s=0;for(let t=0;t<r.length;t++)if(i[t]=r[t].split("-"),o[t]){const e=this.posToPosUnderRules.length-i[t].length;for(let n=0;n<i[t].length;n++)this.posToPosUnderRules[e+n].push(s),s++}else for(let e=0;e<i[t].length;e++)this.posToPosUnderRules.push([s]),s++;!function(t,e,n){for(let r=0;r<t.length;r++){const o=t[r],i=l(o,n.linkRules),[s,a,c,h]=u(n.linkRules,o,i);for(let t=0;t<s.length;t++)e.push({fChain:r,sChain:r,fMonomer:s[t],sMonomer:a[t],fR:c[t],sR:h[t]});t[r]=o}}(i,n,t),function(t,e,n){for(let r=0;r<t.length;r++){const o=l(t[r],n.reactionRules),[i,s,a]=c(n.reactionRules,t[r],o);i.length>=1&&(e.push({fChain:r,sChain:t.length,fMonomer:i[0],sMonomer:1,fR:3,sR:1}),e.push({fChain:r,sChain:t.length,fMonomer:s[0],sMonomer:1,fR:3,sR:2}),t.push([n.reactionRules[a[0]].name]))}}(i,n,t),this.underRules=!0,this.linkagesUnderRules=n,this.monomersUnderRules=i,this.molUnderRules=d(n,i,this.helmHelper)}check(t=!1){const e=[],n=this.monomers.map((t=>t.length)).reduce(((t,e)=>t+e),0);this.mol.atoms.length!==n&&e.push(`The mol atoms count ${this.mol.atoms.length} does not match the total number ${n} of chains' monomers.`);const r=this.monomers.map((t=>t.length-1)).reduce(((t,e)=>t+e),0)+this.linkages.length;this.mol.bonds.length!==r&&e.push(`The mol bonds count ${this.mol.bonds.length} does not match the total number ${r} in- and inter-chain linkages.`);let o=0;for(let t=0;t<this.monomers.length;++t){const n=this.monomers[t];for(let t=0;t<n.length;++t)try{const r=n[t],i=this.mol.atoms[o];i.bio.continuousId!==o&&e.push(`Atom #${o} has incorrect .bio.continuousId: ${i.bio.continuousId}.`),i.elem!==r&&e.push(`Atom #${o} elem: '${i.elem}' does not match chain monomer: '${r}'.`)}finally{o++}}if(t&&e.length>0)throw new Error(`Chain errors:\n${e.map((t=>` ${t}`)).join("\n")}`);return e}}},4229:(t,e,n)=>{"use strict";n.d(e,{b:()=>s});var r=n(9192),o=n(6307),i=n(9788);function s(t,e,n){const s=new Array(t.length),a=new Array(t.length),l=new Array(t.length);for(let u=0;u<t.length;u++)try{if(null==t[u])s[u]="";else{const r=o.s.fromSeparator(t[u],n);r.applyRules(e),a[u]=!(r.monomersUnderRules.length>1||r.linkagesUnderRules.length>0),s[u]=r.getHelm(),l[u]=r.posToPosUnderRules}}catch(t){const[e,n]=(0,r.AP)(t);i._package.logger.error(e,void 0,n),s[u]=""}return[s,a,l]}},2125:(t,e,n)=>{"use strict";function r(t,e){let n,r=t;for(n=0;n<e.length&&r>=e[n].length;++n)r-=e[n].length;return[r,n]}function o(t,e,n){let r=0;for(let t=0;t<e;++t)r+=n[t].length;return r+t}n.d(e,{M:()=>r,j:()=>o})},6694:(t,e,n)=>{"use strict";n.d(e,{MU:()=>q,yy:()=>j,_v:()=>Q,Ln:()=>et,Q4:()=>tt});var r=n(6082),o=n(4328),i=n(7389),s=n(1991),a=n.n(s),l=function(t,e,n,r){return new(n||(n=Promise))((function(o,i){function s(t){try{l(r.next(t))}catch(t){i(t)}}function a(t){try{l(r.throw(t))}catch(t){i(t)}}function l(t){var e;t.done?o(t.value):(e=t.value,e instanceof n?e:new n((function(t){t(e)}))).then(s,a)}l((r=r.apply(t,e||[])).next())}))};class u{constructor(t,e,n=".csv",r){this.path=t,this.userStorageName=e,this.ext=n,this.options=r,this.inputs=null,"/"!==this.path[this.path.length-1]&&(this.path+="/"),"."!==this.ext[0]&&(this.ext="."+this.ext)}getUserSettings(){return l(this,void 0,void 0,(function*(){if(this.settings)return this.settings;const t=o.userSettings.getValue(this.userStorageName,"Settings"),e=t?JSON.parse(t):{excluded:[],explicit:[]};return e.explicit=e.explicit instanceof Array?e.explicit:[],e.excluded=e.excluded instanceof Array?e.excluded:[],this.settings=e}))}setUserSettings(t){this.settings=t,o.userSettings.add(this.userStorageName,"Settings",JSON.stringify(t))}getAllAvailable(){return l(this,void 0,void 0,(function*(){return(yield o.dapi.files.list(this.path)).map((t=>t.fullPath.replace(`${this.path}`,"")))}))}getActive(){return l(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)))}))}setActive(t){const e=new Set(t);for(const[t,n]of this.inputs.entries())n.value=e.has(t)}createInput(t,e){const n=i.input.bool(t,{value:e,onValueChanged:e=>this.updateSelectionStatus(t,e)});return n.addOptions(i.button(i.iconFA("trash"),(()=>{i.dialog({title:"Warning"}).add(i.divText(`Delete file '${t}'?`)).onOK((()=>{n.root.remove(),this.availableRemove(t)})).show()}),`Delete ${t}`)),n}getInputs(){return l(this,void 0,void 0,(function*(){this.inputs=new Map;const t=yield this.getAllAvailable(),e=yield this.getActive(),n=new Array(t.length);for(let r=0;r<t.length;r++){const o=e.includes(t[r]);n[r]=this.createInput(t[r],o),this.inputs.set(t[r],n[r])}return this.fireOnValueChanged(),n}))}getForm(){return l(this,void 0,void 0,(function*(){const t=yield this.getInputs(),e=i.divV(t);return i.divV([e,i.button("ADD",(()=>l(this,void 0,void 0,(function*(){let t="";if(t=yield this.getNewAvailable(),""!==t){const n=this.createInput(t,!0);e.append(n.root),this.inputs.set(t,n),this.fireOnValueChanged()}}))))])}))}fireOnValueChanged(){var t;null===(t=this.options)||void 0===t||t.onValueChanged(a()(this.inputs.entries()).filter((([t,e])=>e.value)).map((([t,e])=>t)).toArray())}updateSelectionStatus(t,e){return l(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.fireOnValueChanged(),this.setUserSettings(n)}}))}availableRemove(t){return l(this,void 0,void 0,(function*(){this.inputs.delete(t),this.fireOnValueChanged();const e=yield this.getUserSettings(),n=e.excluded.indexOf(t);n>-1&&e.excluded.splice(n,1),this.setUserSettings(e),yield o.dapi.files.delete(this.path+t),o.shell.info(`File ${t} successfully deleted`)}))}getNewAvailable(){return l(this,void 0,void 0,(function*(){return new Promise(((t,e)=>{r.Utils.openFile({accept:this.ext,open:e=>l(this,void 0,void 0,(function*(){const n=e.name,r=yield e.arrayBuffer();yield o.dapi.files.write(this.path+`${e.name}`,new Uint8Array(r)),t(n)}))})}))}))}}var c=n(9788),h=n(9124),d=n(4229),f=n(439),p=n(5174),m=n(5412),g=n(6717),y=n(8312);function b(t){let e=t.replaceAll(/\[R[1-9]\]/g,(t=>`[*:${t[2]}]`));return e=e.replaceAll(/\[\d\*\]/g,(t=>`[*:${t[1]}]`)),e.replaceAll(/\[\d\*\:\d\]/g,(t=>`[*:${t[1]}]`))}function v(t){return t.replaceAll(/\[\*\:\d\]/g,(t=>`[C:${t[3]}]`))}function w(t){return t.replaceAll(/\[C\:\d\]/g,(t=>`[*:${t[3]}]`))}function C(t,e){const n=e?.firstReactantSmiles?w(e.firstReactantSmiles):"[*:1]C",r=e?.secondReactantSmiles?w(e.secondReactantSmiles):"[*:2]C",s=e?.productSmiles?w(e.productSmiles):"[*:1]CC[*:2]",a=e?.code,l=e?.firstMonomers??[],u=e?.secondMonomers??[],c=e?.resultMonomerName??"",h=i.input.int("Code",{value:a,nullable:!1,showPlusMinus:!1,showSlider:!1,tooltipText:"Reaction code"}),d=i.input.string("First monomers",{value:l.join(","),nullable:!1,tooltipText:"Comma-separated list of monomers for the first reactant"}),f=i.input.string("Second monomers",{value:u.join(","),nullable:!1,tooltipText:"Comma-separated list of monomers for the second reactant"}),p=i.input.string("Result monomer name",{value:c,nullable:!1,tooltipText:"Name of the resulting pseudo-monomer generated by the reaction of the two reactants"}),m=i.input.molecule("First reactant",{value:n,nullable:!1,tooltipText:"Reactant fragment of first monomer(s). Use numbered R groups in correspondence with the rest of the molecule."}),g=i.input.molecule("Second reactant",{value:r,nullable:!1,tooltipText:"Reactant fragment of second monomer(s). Use numbered R groups in correspondence with the rest of the molecule."}),y=i.input.molecule("Product",{value:s,nullable:!1,tooltipText:"Product fragment of the resulting monomer from the reaction of the two reactants. Use numbered R groups in correspondence with the reactants."}),C=()=>{if(!m||!g||!y)return"Inputs not initialized yet";const t=v(b(o.chem.convert(m.value??"",o.chem.Notation.Unknown,o.chem.Notation.Smiles))),e=v(b(o.chem.convert(g.value??"",o.chem.Notation.Unknown,o.chem.Notation.Smiles))),n=v(b(o.chem.convert(y.value??"",o.chem.Notation.Unknown,o.chem.Notation.Smiles)));return t&&e&&n?-1==t.indexOf("[C:1]")?"First Reactant must contain R1-group":-1==e.indexOf("[C:2]")?"Second Reactant must contain R2-group":-1==n.indexOf("[C:1]")||-1==n.indexOf("[C:2]")?"Product must contain R1- and R2-groups":null:"First/Second Reactants and Product must all be set"};m.addValidator(C),g.addValidator(C),y.addValidator(C);const A=i.dialog(e?"Edit Reaction Rule":"Add Reaction Rule").add(h).add(p).add(d).add(f).add(m).add(g).add(y);A.addButton("Save",(()=>{const n=C();if(null!=n)return void o.shell.warning(n);const r=v(b(o.chem.convert(m.value??"",o.chem.Notation.Unknown,o.chem.Notation.Smiles))),i=v(b(o.chem.convert(g.value??"",o.chem.Notation.Unknown,o.chem.Notation.Smiles))),s=v(b(o.chem.convert(y.value??"",o.chem.Notation.Unknown,o.chem.Notation.Smiles)));t({code:h.value,resultMonomerName:p.value,firstMonomers:d.value.split(",").map((t=>t.trim())).filter((t=>t.length>0)),secondMonomers:f.value.split(",").map((t=>t.trim())).filter((t=>t.length>0)),firstReactantSmiles:r,secondReactantSmiles:i,productSmiles:s,rowIndex:e?.rowIndex}),A.close()})),A.show()}const A="Links",x="Reactions";class S{constructor(t,e){this.v=null,this.substituteReactionGridDataFrame=null,this.rules=t;const n=this.rules.getLinkRulesDf();this.linkRuleDataFrame=n.res,this.addLinkRulesFunc=n.addNewRow;const r=this.rules.getSynthesisRulesDf();this.addSynthRulesFunc=t=>{r.addNewRow(t),this.rules.setSynthesisRules(r.df),this.synthRuleDataFrame=r.df,this.substituteReactionGridDataFrame?.(),this.save()},this.synthRuleDataFrame=r.df,this.fileName=e;const o=this.rules.homodimerCode?this.rules.homodimerCode:"",s=this.rules.heterodimerCode?this.rules.heterodimerCode:"";this.homoDimerInput=i.input.string("Homo dimer",{value:o,onValueChanged:()=>{},nullable:!1}),this.heteroDimerInput=i.input.string("Hetero dimer",{value:s,onValueChanged:()=>{},nullable:!1})}async getAndAddView(){if(this.v)try{const t=Array.from(o.shell.views).find((t=>t.name===this.v.name));if(!t)throw this.v.detach(),this.v.close(),new Error("View is closed, making it null in catch statement");o.shell.v=t}catch(t){this.v=null}return this.v||(this.v=r.View.create(),this.v.name=`Manage Polytool Rules - ${this.fileName}`,this.v.append(await this.getForm()),this.v=o.shell.addView(this.v),o.shell.v=this.v),this.v}static async getInstance(t){if(!this.instances[t]){const e=await tt([t]);this.instances[t]=new S(e,t)}return this.instances[t]}save(){this.rules.homodimerCode=this.homoDimerInput.value,this.rules.heterodimerCode=this.heteroDimerInput.value,this.rules.setLinkRules(this.linkRuleDataFrame),this.rules.setSynthesisRules(this.synthRuleDataFrame);const t={homodimerCode:this.rules.homodimerCode,heterodimerCode:this.rules.heterodimerCode,linkRules:this.rules.linkRules,reactionRules:this.rules.reactionRules},e=JSON.stringify(t,void 0,2);c._package.files.writeAsText(`polytool-rules/${this.fileName}`,e),o.shell.info(`Polytool rules at ${this.fileName} was updated`)}createGridDiv(t,e,n){const r=i.h1(t,"polytool-grid-header");i.tooltip.bind(r,n),r.style.marginTop="10px",r.style.marginRight="10px",e.root.style.height="100%";const o=i.splitV([i.box(r,{style:{maxHeight:"60px"}}),e.root]);return o.style.height="100%",o}async getLinkExamplesGrid(){const t=[];for(let e=0;e<this.rules.linkRules.length;e++){const n=this.rules.linkRules[e].code,[r,o]=et(this.rules.linkRules[e]);for(let e=0;e<r.length;e++){const i=`${r[e]}(${n})-A-A-A-A-${o[e]}(${n})`;t.push(i)}}const e=await(0,h.b2)(),[n,o,i]=(0,d.b)(t,this.rules,e),s=r.Column.fromStrings("Monomers",t),a=r.Column.fromStrings("Helm",n);return c.PackageFunctions.applyNotationProviderForCyclized(s,"-"),s.semType=r.SEMTYPE.MACROMOLECULE,a.semType=r.SEMTYPE.MACROMOLECULE,a.meta.units=f.Hi.HELM,a.setTag(r.TAGS.CELL_RENDERER,"helm"),r.DataFrame.fromColumns([s,a]).plot.grid()}async getReactionExamplesGrid(){const t=[];for(let e=0;e<this.rules.reactionRules.length;e++){const n=this.rules.reactionRules[e].code,[r,o]=et(this.rules.reactionRules[e]);for(let e=0;e<r.length;e++){const i=`${r[e]}(${n})-A-A-A-A-${o[e]}(${n})`;t.push(i)}}const e=await(0,h.b2)(),[n,o,i]=(0,d.b)(t,this.rules,e),s=r.Column.fromStrings("Monomers",t),a=r.Column.fromStrings("Helm",n),l=r.DataFrame.fromColumns([s,a]);s.semType=r.SEMTYPE.MACROMOLECULE;const u=await(0,g.j)(),b=await(0,y.Q)();c.PackageFunctions.applyNotationProviderForCyclized(s,"-"),s.tags[r.TAGS.CELL_RENDERER]="Sequence",a.semType=r.SEMTYPE.MACROMOLECULE,a.meta.units=f.Hi.HELM,a.setTag(r.TAGS.CELL_RENDERER,"helm");const v=await(0,p.A)(this.rules),w=a.temp;w[".mm.cellRenderer.overriddenLibrary"]=v,a.temp=w;const C=await(0,m.m)(a,t,o,!0,!1,!1,v,u,b);return C.name="molfile(sequence)",C.semType=r.SEMTYPE.MOLECULE,l.columns.add(C),l.plot.grid()}async getForm(){const t=this.linkRuleDataFrame.plot.grid({showAddNewRowIcon:!1,allowEdit:!1,rowHeight:60});t.onCellDoubleClick.subscribe((()=>{if(!t.dataFrame||-1==t.dataFrame.currentRowIdx||null==t.dataFrame.currentRowIdx)return;const e=t.dataFrame.currentRowIdx,n={row:e,code:this.linkRuleDataFrame.get("code",e),firstMonomers:this.linkRuleDataFrame.get("firstMonomers",e),secondMonomers:this.linkRuleDataFrame.get("secondMonomers",e),firstLinkingGroup:this.linkRuleDataFrame.get("firstLinkingGroup",e),secondLinkingGroup:this.linkRuleDataFrame.get("secondLinkingGroup",e)};this.getAddNewLinkRuleDialog(n)}));const e=this.createGridDiv("Rules",t,"specification for monomers to link and linking positions"),n=this.createGridDiv("Examples",await this.getLinkExamplesGrid(),"specification for monomers to link and linking positions");e.style.width="50%",n.style.width="50%";const r=i.h1("Monomers","polytool-grid-header");i.tooltip.bind(r,"Click different cobination to see how monomers will link"),this.linkCards=await this.rules.getLinkCards();const o=i.splitV([i.box(r,{style:{maxHeight:"30px"}}),this.linkCards[0].root]);this.linkCards[0].render(),await this.linkCards[0].reset(),this.linkRuleDataFrame.currentRowIdx=0,this.linkRuleDataFrame.onCurrentRowChanged.subscribe((async()=>{const t=this.linkRuleDataFrame.currentRowIdx;-1!==t&&null!=t&&(i.empty(o),o.append(i.splitV([i.box(r,{style:{maxHeight:"30px"}}),this.linkCards[t].root])),this.linkCards[t].render(),await this.linkCards[t].reset())}));const s=i.splitH([e,o],null,!0),a=this.synthRuleDataFrame.plot.grid({showAddNewRowIcon:!1,allowEdit:!1,rowHeight:130});a.onCellDoubleClick.subscribe((()=>{if(!a.dataFrame||-1==a.dataFrame.currentRowIdx||null==a.dataFrame.currentRowIdx)return;const t=a.dataFrame.currentRowIdx;C((t=>this.addSynthRulesFunc(t)),{rowIndex:t,code:this.synthRuleDataFrame.get("code",t),firstMonomers:this.synthRuleDataFrame.get("firstMonomers",t).split(",").map((t=>t.trim())).filter((t=>t)),secondMonomers:this.synthRuleDataFrame.get("secondMonomers",t).split(",").map((t=>t.trim())).filter((t=>t)),resultMonomerName:this.synthRuleDataFrame.get("name",t),firstReactantSmiles:this.synthRuleDataFrame.get("firstReactant",t),secondReactantSmiles:this.synthRuleDataFrame.get("secondReactant",t),productSmiles:this.synthRuleDataFrame.get("product",t)})}));const l=this.createGridDiv("Rules",a),u=await this.getReactionExamplesGrid(),c=this.createGridDiv("Examples",u);this.substituteReactionGridDataFrame=async()=>{const t=await this.getReactionExamplesGrid();u.dataFrame=t.dataFrame},l.style.width="50%",c.style.width="50%";const h=i.divH([l,c]),d=i.divV([this.homoDimerInput,this.heteroDimerInput]),f=i.tabControl({Links:s,Reactions:h,Dimers:d},!1);i.tooltip.bind(f.getPane(A).header,"Specify rules to link monomers based on HELM notation"),i.tooltip.bind(f.getPane(x).header,"Specify rules to perform reactions within monomers"),i.tooltip.bind(f.getPane("Dimers").header,"Specify symbols for homodimeric and heterodimeric codes"),f.root.style.height="100%",f.root.style.width="100%",f.root.classList.add("rules-manager-form-tab-control"),f.header.style.marginBottom="10px";const p=i.divV([f.root]),m=[i.bigButton("Save",(()=>{this.save()})),i.button("Add rule",(()=>{const t=f.currentPane.name;t==A?this.getAddNewLinkRuleDialog():t==x&&C((t=>this.addSynthRulesFunc(t)))})),i.button("Remove rule",(()=>{const e=f.currentPane.name;if(e==A){if(null==this.linkRuleDataFrame||-1==this.linkRuleDataFrame.currentRowIdx||null==this.linkRuleDataFrame.currentRowIdx)return;const e=t.dataFrame.currentRowIdx;i.dialog("Are you sure you want to remove the rule?").add(i.divText("This action is irreversible!")).onOK((()=>{this.linkRuleDataFrame.rows.removeAt(e),this.rules.setLinkRules(this.linkRuleDataFrame),this.save()})).show()}else if(e==x){if(null==this.synthRuleDataFrame||-1==this.synthRuleDataFrame.currentRowIdx||null==this.synthRuleDataFrame.currentRowIdx)return;const t=a.dataFrame.currentRowIdx;i.dialog("Are you sure you want to remove the rule?").add(i.divText("This action is irreversible!")).onOK((()=>{this.synthRuleDataFrame.rows.removeAt(t),this.rules.setSynthesisRules(this.synthRuleDataFrame),this.substituteReactionGridDataFrame?.(),this.save()})).show()}}))];return this.v.setRibbonPanels([m]),p.style.height="100%",p.style.alignItems="center",f.root}getAddNewLinkRuleDialog(t){const e=i.input.int("Code",{nullable:!1,value:t?.code}),n=i.input.string("First monomers",{placeholder:"E.g. C,D,E",value:t?.firstMonomers,tooltipText:"Comma separated list of first monomers applicable for the rule. If left empty, all monomers will be considered",nullable:!0}),r=i.input.string("Second monomers",{placeholder:"E.g. C,D,E",value:t?.secondMonomers,tooltipText:"Comma separated list of second monomers applicable for the rule. If left empty, all monomers will be considered",nullable:!0}),o=t?.firstLinkingGroup?`R${t.firstLinkingGroup}`:"R3",s=t?.secondLinkingGroup?`R${t.secondLinkingGroup}`:"R3",a=i.input.choice("First linking group",{value:o,items:["R1","R2","R3","R4"],tooltipText:"Specifies which R-group of the first monomer will be used for linking",nullable:!1}),l=i.input.choice("Second linking group",{value:s,items:["R1","R2","R3","R4"],tooltipText:"Specifies which R-group of the second monomer will be used for linking",nullable:!1});i.dialog("Add new link rule").add(e).add(n).add(r).add(a).add(l).onOK((async()=>{const o=e.value,i=(n.value??"").split(",").map((t=>t.trim())).filter((t=>t)).join(","),s=(r.value??"").split(",").map((t=>t.trim())).filter((t=>t)).join(","),u=parseInt(a.value.substring(1)),c=parseInt(l.value.substring(1));this.addLinkRulesFunc({code:o,firstMonomers:i??"",secondMonomers:s??"",firstLinkingGroup:u,secondLinkingGroup:c,row:t?.row}),this.rules.setLinkRules(this.linkRuleDataFrame),this.linkCards=await this.rules.getLinkCards(),this.save()})).show()}}S.instances={};var T=n(5072),E=n.n(T),_=n(7825),I=n.n(_),N=n(7659),M=n.n(N),O=n(5056),L=n.n(O),R=n(540),P=n.n(R),B=n(1113),D=n.n(B),F=n(890),k={};k.styleTagTransform=D(),k.setAttributes=L(),k.insert=M().bind(null,"head"),k.domAPI=I(),k.insertStyleElement=P(),E()(F.A,k),F.A&&F.A.locals&&F.A.locals;var H=n(2003);class U{get selected(){return this._selected}set selected(t){this._selected=t,this.root.style.border=t?"2px solid var(--green-2)":"2px solid var(--grey-2)"}constructor(t,e){this.monomer=t,this.monomerSymbol=e,this.root=i.divV([],{classes:"monomer-card-rule-root"}),this._selected=!1}render(){if(i.empty(this.root),this.root.appendChild(i.h2(this.monomerSymbol,{style:{textAlign:"center"}})),this.monomer){const t=this.monomer.smiles&&o.chem.checkSmiles(this.monomer.smiles)?o.chem.drawMolecule(this.monomer.smiles,150,120):o.chem.drawMolecule(this.monomer.molfile??"",150,120);this.root.appendChild(t);const e=i.divH([i.divText("Monomer Name: "),i.divText(this.monomer.name)],{classes:"monomer-card-info-rules"});if(this.root.appendChild(e),i.tooltip.bind(e,this.monomer.name),this.monomer.lib?.source){const t=i.divH([i.divText("Source: "),i.divText(this.monomer.lib.source)],{classes:"monomer-card-info-rules"});this.root.appendChild(t),i.tooltip.bind(t,this.monomer.lib.source)}const n=i.divH([i.divText("Polymer Type: "),i.divText(this.monomer.polymerType)],{classes:"monomer-card-info-rules"});this.root.appendChild(n),i.tooltip.bind(n,this.monomer.polymerType),i.tooltip.bind(this.root,"Select Monomer")}else this.root.appendChild(i.divV([`Monomer ${this.monomerSymbol} not found in libraries`],{style:{textAlign:"center",height:"100%"}}))}}class ${constructor(t,e,n,r,o){this.firstMonomers=t,this.secondMonomers=e,this.code=r,this.rules=o,this.root=i.divH([],{style:{width:"100%",overflow:"hidden",visibility:"visible"},classes:"monomer-cards"});const s=!t?.length,a=!e?.length;s&&(this.firstMonomers=t=["C","D","E","F","G"]),a&&(this.secondMonomers=e=["D","C","E","F","G"]),this.actionable=!0;const l=i.divH([],{style:{overflowX:"auto",width:"100%"}}),u=i.divH([],{style:{overflowX:"auto",width:"100%"}});this.resulting=i.divH([],{style:{overflowX:"auto",width:"100%",minHeight:"150px"}});const c=i.h2("First Monomer"+(s?" (Applied to all monomers, example list shown)":""),{style:{width:"100%"}}),h=i.h2("Second Monomer"+(a?" (Applied to all monomers, example list shown)":""),{style:{width:"100%"}}),d=i.divV([c,l,h,u,this.resulting]);this.cardsFirst=t.map((t=>new U(n.getMonomer("PEPTIDE",t),t))),this.cardsSecond=e.map((t=>new U(n.getMonomer("PEPTIDE",t),t))),this.cardsFirst.forEach((t=>{t.root.onclick=()=>{this.cardsFirst.forEach((t=>t.selected=!1)),t.selected=!0,this.firstCard=t,this.reset()},l.appendChild(t.root)})),this.cardsSecond.forEach((t=>{t.root.onclick=()=>{this.cardsSecond.forEach((t=>t.selected=!1)),t.selected=!0,this.secondCard=t,this.reset()},u.appendChild(t.root)})),this.cardsFirst[0].selected=!0,this.cardsSecond[0].selected=!0,this.firstCard=this.cardsFirst[0],this.secondCard=this.cardsSecond[0],this.root.appendChild(d)}async reset(){if(this.actionable){const t=[`${this.firstCard.monomer?.symbol}(${this.code})-A-A-A-A-${this.secondCard.monomer?.symbol}(${this.code})`],e=await(0,h.b2)(),[n,s,a]=(0,d.b)(t,this.rules,e),l=r.Column.fromType(r.COLUMN_TYPE.STRING,"helm",n.length).init((t=>n[t]));l.semType=r.SEMTYPE.MACROMOLECULE,l.meta.units=H.Hi.HELM,l.setTag(r.TAGS.CELL_RENDERER,"helm");const u=await(0,g.j)(),c=await(0,y.Q)(),f=await(0,p.A)(this.rules),b=l.temp;l.temp=b;const v=(await(0,m.m)(l,n,s,!0,!1,!1,f,u,c)).get(0),w=v&&o.chem.checkSmiles(v)?o.chem.drawMolecule(v,200,200):o.chem.drawMolecule(v??"",200,200);v&&(w.style.cursor="pointer",w.onclick=()=>{const t=window.innerWidth-200,e=window.innerHeight-200,n=o.chem.checkSmiles(v)?o.chem.drawMolecule(v,t,e):o.chem.drawMolecule(v??"",t,e);i.dialog({title:"Molecule"}).add(n).showModal(!0)},i.tooltip.bind(w,"Click to expand"));const C=i.divV([i.h2("Example Result:"),i.h2(t[0])],{style:{width:"200px"}});i.empty(this.resulting),this.resulting.append(i.divH([C,w],{style:{overflowX:"auto",width:"100%",minHeight:"150px"}}))}}render(){this.actionable&&(this.cardsFirst.forEach((t=>t.render())),this.cardsSecond.forEach((t=>t.render())))}}var V=n(4971);const q="System:AppData/SequenceTranslator/polytool-rules/",j="Polytool",G="code",z="firstMonomers",W="secondMonomers",Y="name",K="firstLinkingGroup",J="secondLinkingGroup";class Q extends u{constructor(t,e,n,r){super(t,e,n,r)}createInput(t,e){const n=super.createInput(t,e),o=i.icons.edit((async()=>{const e=await S.getInstance(t);r.Dialog.getOpenDialogs()?.filter((t=>t.root.contains(o))).forEach((t=>t.close())),await e.getAndAddView()}),"Edit rules");return n.addOptions(o),n}async getForm(){const t=await super.getForm();return this.processRulesForm(t),t}async processRulesForm(t){const e=Array.from(t.getElementsByTagName("label")??[]).filter((t=>t.textContent?.endsWith(".json")&&null!=t.parentElement));for(const t of e){const e=t.textContent.trim(),n=t.parentElement.getElementsByTagName("input")[0];i.tooltip.bind(n,i.wait((async()=>{var t;return(t=Q.ruleDescriptions)[e]??(t[e]=(async()=>{try{const t=JSON.parse(await o.dapi.files.readAsText(`${q}/${e}`)),n=i.divV([i.h1(e)]),r=t.linkRules??[];if(r.length>0){n.appendChild(i.h3("Linkage Rules"));const t=i.table(r,(t=>[t.code?.toString()??"",X((t.firstMonomers??[]).join(", ")),X((t.secondMonomers??[]).join(", ")),t.firstLinkingGroup?.toString()??"",t.secondLinkingGroup?.toString()??""]),["Code","M1","M2","L1","L2"]);n.appendChild(t)}const s=t.reactionRules??[];if(s.length>0){n.appendChild(i.h3("Synthesis Rules"));const t=i.table(s,(t=>[t.code?.toString()??"",X((t.firstMonomers??[]).join(", ")),X((t.secondMonomers??[]).join(", ")),X(t.name??""),o.chem.drawMolecule(t.reaction?.split(">>")[1]??"",70,70)]),["Code","M1","M2","Name","Product"]);n.appendChild(t)}return n}catch(t){return c._package.logger.error(`Failed to load rule ${e}: ${t?.toString?.()}`),console.error(t),i.divText(`Failed to load rule ${e}`)}})()),await Q.ruleDescriptions[e]})))}}}function X(t,e=30){return t.length<=e?t:`${t.substring(0,e)}...`}Q.ruleDescriptions={};class Z{constructor(t,e,n,r){this.homodimerCode=t,this.heterodimerCode=e,this.linkRules=n,this.reactionRules=r}set homodimer(t){this.homodimerCode=t}set heterodimer(t){this.heterodimerCode=t}addLinkRules(t){for(let e=0;e<t.length;e++)this.linkRules.push(t[e])}addSynthesisRules(t){for(let e=0;e<t.length;e++)this.reactionRules.push(t[e])}getLinkRulesDf(){const t=this.linkRules.length,e=r.Column.int(G,t);e.setTag("friendlyName","Code");const n=r.Column.string(z,t);n.temp[".mm.cellRenderer.fontSize"]=16,n.setTag("friendlyName","First monomers"),n.semType=r.SEMTYPE.MACROMOLECULE,c.PackageFunctions.applyNotationProviderForCyclized(n,",");const o=r.Column.string(W,t);o.setTag("friendlyName","Second monomers"),o.temp[".mm.cellRenderer.fontSize"]=16,o.semType=r.SEMTYPE.MACROMOLECULE,c.PackageFunctions.applyNotationProviderForCyclized(o,",");const i=r.Column.int(K,t);i.setTag("friendlyName","First group");const s=r.Column.int(J,t);s.setTag("friendlyName","Second group");for(let r=0;r<t;r++)e.set(r,this.linkRules[r].code),n.set(r,this.linkRules[r].firstMonomers.toString()),o.set(r,this.linkRules[r].secondMonomers.toString()),i.set(r,this.linkRules[r].firstLinkingGroup),s.set(r,this.linkRules[r].secondLinkingGroup);const a=r.DataFrame.fromColumns([e,n,o,i,s]);return{res:a,addNewRow:t=>{if(null!=t.row&&t.row<a.rowCount&&t.row>=0)e.set(t.row,t.code),n.set(t.row,t.firstMonomers),o.set(t.row,t.secondMonomers),i.set(t.row,t.firstLinkingGroup),s.set(t.row,t.secondLinkingGroup);else{const{code:e,firstMonomers:n,secondMonomers:r,firstLinkingGroup:o,secondLinkingGroup:i}=t;a.rows.addNew([e,n??"",r??"",o??1,i??2])}}}}async getLinkCards(){const t=this.linkRules.length,e=new Array(t),n=(await(0,V.pj)()).getMonomerLib();for(let r=0;r<t;r++)e[r]=new $(this.linkRules[r].firstMonomers,this.linkRules[r].secondMonomers,n,this.linkRules[r].code,this);return e}getSynthesisRulesDf(){const t=this.reactionRules.length,e=r.Column.int(G,t);e.setTag("friendlyName","Code");const n=r.Column.string(z,t);n.setTag("friendlyName","First monomers");const o=r.Column.string(W,t);o.setTag("friendlyName","Second monomers"),n.semType=r.SEMTYPE.MACROMOLECULE,n.temp[".mm.cellRenderer.fontSize"]=16,c.PackageFunctions.applyNotationProviderForCyclized(n,","),o.semType=r.SEMTYPE.MACROMOLECULE,o.temp[".mm.cellRenderer.fontSize"]=16,c.PackageFunctions.applyNotationProviderForCyclized(o,","),o.setTag(r.TAGS.CELL_RENDERER,"Sequence"),n.setTag(r.TAGS.CELL_RENDERER,"Sequence");const i=r.Column.string(Y,t);i.setTag("friendlyName","Name");const s=r.Column.string("firstReactant",t);s.setTag("friendlyName","First reactant");const a=r.Column.string("secondReactant",t);a.setTag("friendlyName","Second reactant");const l=r.Column.string("product",t);l.setTag("friendlyName","Product");for(let r=0;r<t;r++){e.set(r,this.reactionRules[r].code),n.set(r,this.reactionRules[r].firstMonomers.toString()),o.set(r,this.reactionRules[r].secondMonomers.toString()),i.set(r,this.reactionRules[r].name);const t=this.reactionRules[r].reaction.split(">>"),u=t[0].split(".");s.set(r,u[0]),a.set(r,u[1]),l.set(r,t[1])}s.semType=r.SEMTYPE.MOLECULE,a.semType=r.SEMTYPE.MOLECULE,l.semType=r.SEMTYPE.MOLECULE;const u=r.DataFrame.fromColumns([i,s,a,l,e,n,o]);return{df:u,addNewRow:t=>{if(null!=t.rowIndex&&t.rowIndex<u.rowCount&&t.rowIndex>=0)i.set(t.rowIndex,t.resultMonomerName),e.set(t.rowIndex,t.code),n.set(t.rowIndex,t.firstMonomers.join(",")),o.set(t.rowIndex,t.secondMonomers.join(",")),s.set(t.rowIndex,t.firstReactantSmiles),a.set(t.rowIndex,t.secondReactantSmiles),l.set(t.rowIndex,t.productSmiles);else{const{resultMonomerName:e,code:n,firstMonomers:r,secondMonomers:o,firstReactantSmiles:i,secondReactantSmiles:s,productSmiles:a}=t;u.rows.addNew([e,i,s,a,n,r.join(","),o.join(",")])}}}}setLinkRules(t){const e=t.rowCount,n=new Array(e),r=t.columns.byName(G),o=t.columns.byName(z),i=t.columns.byName(W),s=t.columns.byName(K),a=t.columns.byName(J);for(let t=0;t<e;t++){const e=o.get(t).split(","),l=i.get(t).split(","),u={code:r.get(t),firstMonomers:""!==e[0]?e:[],secondMonomers:""!==l[0]?l:[],firstLinkingGroup:s.get(t),secondLinkingGroup:a.get(t)};n[t]=u}this.linkRules=n}setSynthesisRules(t){const e=t.rowCount,n=new Array(e),r=t.columns.byName(G),o=t.columns.byName(z),i=t.columns.byName(W),s=t.columns.byName(Y),a=t.columns.byName("firstReactant"),l=t.columns.byName("secondReactant"),u=t.columns.byName("product");for(let t=0;t<e;t++){const e=`${a.get(t)}.${l.get(t)}>>${u.get(t)}`,c=o.get(t).split(","),h=i.get(t).split(","),d={code:r.get(t),firstMonomers:""!==c[0]?c:[],secondMonomers:""!==h[0]?h:[],reaction:e,name:s.get(t)};n[t]=d}this.reactionRules=n}}async function tt(t){const e=new r.FileSource(q),n=new Z(null,null,[],[]);for(let r=0;r<t.length;r++){const o=await e.readAsText(t[r].replace(q,"")),i=JSON.parse(o);n.homodimer=i.homodimerCode,n.heterodimer=i.heterodimerCode,n.addLinkRules(i.linkRules),n.addSynthesisRules(i.reactionRules)}return n}function et(t){const e=t.firstMonomers.length*t.secondMonomers.length,n=new Array(e),r=new Array(e);let o=0;for(let e=0;e<t.firstMonomers.length;e++)for(let i=0;i<t.secondMonomers.length;i++)n[o]=t.firstMonomers[e],r[o]=t.secondMonomers[i],o++;return[n,r]}},5174:(t,e,n)=>{"use strict";n.d(e,{A:()=>c});var r=n(6717),o=n(1296),i=n(9192),s=n(4328),a=n(1991),l=n.n(a),u=n(4971);async function c(t){const e=(await(0,u.pj)()).getMonomerLib(),n=await(0,r.j)(),o={};let i=[],a=[];for(let r=0;r<t.reactionRules.length;r++)try{[i,a]=h(n,e,t.reactionRules[r])}catch(t){i=[],a=[],console.error(t),s.shell.warning(t)}finally{for(let t=0;t<i.length;t++)null!=i[t]&&null!=a[t]&&(o[i[t]]=a[t])}const c={PEPTIDE:o};return e.override(c,"ST-PT-reactions."+l().repeat(1).map((()=>Math.floor(36*Math.random()).toString(36))).take(4).toArray().join(""))}function h(t,e,n){const r=n.reaction,o=n.name,s=n.firstMonomers.length+n.secondMonomers.length+1,a=n.reaction.split(">>"),l=a[0].split("."),u=new Array(s),c=new Array(s),h=new Array(s),m=f(t,r),g=`${l[0]}>>[C:1]C`,y=`${l[1]}>>[C:2]C`,b=f(t,g),v=f(t,y);let w=0;for(let r=0;r<n.firstMonomers.length;r++){const i=e.getMonomer("PEPTIDE",n.firstMonomers[r]);if(i&&i.molfile)try{const e=d(t,i.molfile,b,i.name);h[w]=e,u[w]=`${i.symbol}_${o}`}catch(t){console.error(t)}w++}for(let r=0;r<n.secondMonomers.length;r++){const i=e.getMonomer("PEPTIDE",n.secondMonomers[r]);if(i&&i.molfile)try{const e=d(t,i.molfile,v,i.name);h[w]=e,u[w]=`${i.symbol}_${o}`}catch(t){console.error(t)}w++}let C=null;a[1]=a[1].replace("[C:1]","[1*]").replace("[C:2]","[2*]").replace("[C:3]","[3*]");let A="";try{C=t.get_mol(a[1]),A=C?.get_molblock()}catch(t){const[e,n]=(0,i.AP)(t);throw console.error(`Can not assemble monomer '${o}': ${e}.`),t}finally{C?.delete()}h[w]=A,u[w]=o;for(let t=0;t<s-1;t++)h[t]&&(h[t]=h[t].replace(" 0.0000 0.0000 0.0000 C "," 0.0000 0.0000 0.0000 R# ").replace("M RGP 2","M RGP 3 2 3"));h[s-1]=function(t){const e=t.replace("M RAD","M RGP").replace("M ISO","M RGP").split("\n"),n=e.findIndex((t=>t.startsWith("M RGP"))),r=Number(e[n].substring(9,13)),o=Number(e[n].substring(17,21)),i=Number(e[n].substring(13,17)),s=Number(e[n].substring(21,25));e[n]=e[n].substring(0,13)+` ${i}`+e[n].substring(17,21)+` ${s}`,e[3+r]=e[3+r].substring(0,30)+" R# 0 0 0 0 0 0 0 0 0 0 0 0",e[3+o]=e[3+o].substring(0,30)+" R# 0 0 0 0 0 0 0 0 0 0 0 0";let a="";for(let t=0;t<e.length;t++)a+=e[t]+"\n";return a}(h[s-1]);for(let t=0;t<s;t++){const e=t==s-1;if(!h[t]||!u[t])continue;const n={symbol:u[t],name:u[t],molfile:h[t],author:"",id:0,rgroups:p(e),smiles:"",polymerType:"PEPTIDE",monomerType:"Backbone",createDate:null};n.meta=Object.assign(n.meta??{},{colors:{default:{line:"#2083D5",text:"#2083D5",background:"#F2F2F5"}}}),u[t]=u[t],c[t]=n}return m.delete(),b.delete(),v.delete(),[u,c]}function d(t,e,n,r){let o=null,s=null,a=null,l=null,u="";try{o=new t.MolList,s=t.get_mol(e),o.append(s),a=n.run_reactants(o,1),l=a.get(0).next(),u=l?.get_molblock()}catch(t){const[e,n]=(0,i.AP)(t);throw console.error(`Can not assemble monomer '${r}': ${e}.`),t}finally{o?.delete(),s?.delete(),a?.delete(),l?.delete()}return u}function f(t,e){let n=null;try{if(n=t.get_rxn(e),!n)throw new o.J5(e)}catch(t){n?.delete();const[r,o]=(0,i.AP)(t);throw console.error(`Can not assemble monomer '${e}': ${r}.`),t}return n}function p(t){if(t){const t=new Array(2),e={capGroupSMILES:"[*:1][H]",alternateId:"R1-H",capGroupName:"H",label:"R1"},n={capGroupSMILES:"[*:2][H]",alternateId:"R2-H",capGroupName:"H",label:"R2"};return t[0]=e,t[1]=n,t}return[{capGroupSMILES:"[*:3][H]",alternateId:"R3-H",capGroupName:"H",label:"R3"}]}},3820:(t,e,n)=>{"use strict";n.d(e,{d:()=>o,o:()=>s});var r=n(1296);const o="PEPTIDE1{R.[Aca].T.G.H.F.G.A.A.Y.P.E.[meI]}$$$$";function i(t,e,n,r){const o=new Array(r.length*(n-e+1));for(let i=0;i<r.length;++i){const s=n-e+1;for(let n=0;n<s;++n){const a=e+n,l=r[i],u=o[i*s+n]=t.clone(),c=u.atoms[a].elem;u.atoms[a].elem=l;const h=c?.length>1?`[${c}]`:c,d=l?.length>1?`[${l}]`:l;u.name=`${t.name}-${h}${a+1}${d}`}}return o}function s(t,e,n){const o=new JSDraw2.MolHandler,s=new org.helm.webeditor.Plugin(o);org.helm.webeditor.IO.parseHelm(s,t,new JSDraw2.Point(0,0),void 0);const a=o.m;a.name=e;let l=[];if(n.placeholders)switch(n.type){case r.aK.Single:l=function(t,e){return e.map((e=>i(t,e.position,e.position,e.monomers))).reduce(((t,e)=>t.concat(e)),[])}(o.m,n.placeholders);break;case r.aK.Matrix:l=function(t,e){let n=[t];for(const t of e){const e=n.map((e=>i(e,t.position,t.position,t.monomers)));n=e.reduce(((t,e)=>t.concat(e)),[])}return n}(o.m,n.placeholders)}let u=[];n.breadthPlaceholders&&(u=function(t,e){if(0==e.length)return[];let n=[t];for(const t of e){const e=n.map((e=>i(e,t.start,t.end,t.monomers)));n=e.reduce(((t,e)=>t.concat(e)),[])}return n}(o.m,n.breadthPlaceholders)),l=l.concat(u),n.keepOriginal&&(l=[a,...l]);const c=l.map((t=>[org.helm.webeditor.IO.getHelm(t),t.name]));return c}},1296:(t,e,n)=>{"use strict";var r;n.d(e,{J5:()=>o,aK:()=>r}),function(t){t.Single="single",t.Matrix="matrix",t.Library="library"}(r||(r={})),Error;class o extends Error{constructor(t,e){super(`Invalid reaction '${t}'.`),this.type="InvalidReactionError"}}},6082:t=>{"use strict";t.exports=DG},4328:t=>{"use strict";t.exports=grok},7389:t=>{"use strict";t.exports=ui},1991:t=>{"use strict";t.exports=wu}},e={};function n(r){var o=e[r];if(void 0!==o)return o.exports;var i=e[r]={id:r,loaded:!1,exports:{}};return t[r].call(i.exports,i,i.exports,n),i.loaded=!0,i.exports}n.m=t,n.n=t=>{var e=t&&t.__esModule?()=>t.default:()=>t;return n.d(e,{a:e}),e},n.d=(t,e)=>{for(var r in e)n.o(e,r)&&!n.o(t,r)&&Object.defineProperty(t,r,{enumerable:!0,get:e[r]})},n.u=t=>t+".js",n.g=function(){if("object"==typeof globalThis)return globalThis;try{return this||new Function("return this")()}catch(t){if("object"==typeof window)return 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