@datagrok/sequence-translator 1.10.4 → 1.10.6

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Files changed (32) hide show
  1. package/CHANGELOG.md +4 -0
  2. package/detectors.js +3 -1
  3. package/dist/package-test.js +1 -1
  4. package/dist/package-test.js.map +1 -1
  5. package/dist/package.js +1 -1
  6. package/dist/package.js.map +1 -1
  7. package/package.json +9 -5
  8. package/scripts/build-monomer-lib.py +0 -1
  9. package/src/apps/common/view/components/colored-input/input-painters.ts +1 -1
  10. package/src/apps/structure/model/monomer-code-parser.ts +1 -1
  11. package/src/apps/translator/model/conversion-utils.ts +1 -1
  12. package/src/demo/demo-st-ui.ts +1 -1
  13. package/src/package-test.ts +1 -1
  14. package/src/package.g.ts +8 -0
  15. package/src/package.ts +18 -12
  16. package/src/polytool/conversion/pt-synthetic.ts +16 -8
  17. package/src/polytool/pt-enumerate-seq-dialog.ts +29 -7
  18. package/src/tests/files-tests.ts +1 -1
  19. package/src/tests/formats-support.ts +1 -1
  20. package/src/tests/formats-to-helm.ts +1 -1
  21. package/src/tests/helm-to-nucleotides.ts +1 -1
  22. package/src/tests/polytool-chain-from-notation-tests.ts +1 -1
  23. package/src/tests/polytool-chain-parse-notation-tests.ts +1 -1
  24. package/src/tests/polytool-convert-tests.ts +1 -1
  25. package/src/tests/polytool-detectors-custom-notation-test.ts +1 -1
  26. package/src/tests/polytool-enumerate-breadth-tests.ts +1 -1
  27. package/src/tests/polytool-enumerate-tests.ts +1 -1
  28. package/src/tests/polytool-unrule-tests.ts +1 -1
  29. package/src/tests/toAtomicLevel-tests.ts +1 -1
  30. package/src/tests/utils/detect-macromolecule-utils.ts +1 -1
  31. package/test-console-output-1.log +253 -1496
  32. 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 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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 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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 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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 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 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 Xr=new P({debug:!0});let Zr=null;class to{static async oligoToolkitApp(){await Xr.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}(Xr);if(!t)throw new Error("External app view factories not loaded");const e=new 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 Structure"}),Jr("design:type",Function),Jr("design:paramtypes",[]),Jr("design:returntype",Promise)],to,"oligoStructureApp",null),Kr([r.decorators.func({outputs:[{type:"object",name:"result"}]}),Jr("design:type",Function),Jr("design:paramtypes",[]),Jr("design:returntype",Promise)],to,"getTranslationHelper",null),Kr([r.decorators.func({outputs:[{type:"object",name:"result"}]}),Jr("design:type",Function),Jr("design:paramtypes",[]),Jr("design:returntype",Object)],to,"getCodeToWeightsMap",null),Kr([r.decorators.func(),Jr("design:type",Function),Jr("design:paramtypes",[String]),Jr("design:returntype",Boolean)],to,"validateSequence",null),Kr([r.decorators.func({name:"validateSequence"}),Jr("design:type",Function),Jr("design:paramtypes",[String,Boolean]),Jr("design:returntype",String)],to,"getMolfileFromGcrsSequence",null),Kr([r.decorators.func(),Qr(0,r.decorators.param({type:"object"})),Jr("design:type",Function),Jr("design:paramtypes",[Object]),Jr("design:returntype",String)],to,"linkStrands",null),Kr([r.decorators.func({meta:{demoPath:"Bioinformatics | 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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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){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,C=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:C,monomersDict:e,alphabet:o,polymerType:l,start:r,end:i})}const x=[],w=[];await Promise.all(y).then((t=>{for(const e of t)x.push(...e.molfiles),w.push(...e.warnings)})),setTimeout((()=>{m.forEach((t=>{t.terminate()}))}),0);const A=(0,s.qj)(f,t.name),S=r.Column.fromType(r.COLUMN_TYPE.STRING,A,t.length).init((t=>x[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:w}}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,C=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),C=(0,o.xb)(e,r.u.PHOSPHATE));const x={i:0,nodeShift:0,bondShift:0,backbonePositionShift:new Array(2).fill(0),branchPositionShift:new Array(2).fill(0),backboneAttachNode:0,branchAttachNode:0,flipFactor:1},w={sugar:v,phosphate:C,seqLength:t.length,atomCount:u,bondCount:h},A=new o.Cg,S=[];let T,E=0;for(x.i=0;x.i<w.seqLength;++x.i){const n=t[x.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=x.nodeShift,l=x.bondShift;b(r,g,y,x,w),r.stereoAtoms?.forEach((t=>S.push(t+E))),E+=r.atoms.x.length;const u=x.nodeShift-i,c=new Array(u);for(let t=0;t<u;++t)c[t]=i+t;const h=x.bondShift-l,d=new Array(h);for(let t=0;t<h;++t)d[t]=l+t;A.set(x.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,x,w,T??r.u.OXYGEN);const _=r.u.V3K_BEGIN_COUNTS_LINE+u+" "+h+r.u.V3K_COUNTS_LINE_ENDING;let N="";return N+=r.u.V3K_HEADER_FIRST_LINE,N+=r.u.V3K_HEADER_SECOND_LINE,N+=r.u.V3K_BEGIN_CTAB_BLOCK,N+=_,N+=r.u.V3K_BEGIN_ATOM_BLOCK,N+=g.join(""),N+=r.u.V3K_END_ATOM_BLOCK,N+=r.u.V3K_BEGIN_BOND_BLOCK,N+=y.join(""),N+=r.u.V3K_END_BOND_BLOCK,S.length>0&&(N+=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)),N+=r.u.V3K_END_CTAB_BLOCK,N+=r.u.V3K_END,{molfile:N,monomers:A}}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,C=await(0,u.R)(c,b,g,p,n,i,l);C.warnings.length>.05*v&&r.shell.warning(`Molfile conversion resulted in ${C.warnings.length} errors`);const x=o.Func.find({name:"convertToV3KViaOCL"})[0];if(x&&C.molCol)try{const t=C.molCol.toList(),e=await x.apply({mols:t});C.molCol.init((n=>e[n]?e[n]:t[n]))}catch(t){console.error(t)}return C}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 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c=t.x.reduce(((e,n,r)=>{if(r===s)return e;if(r===u)return e;const o=t.y[r];return Math.sqrt((n-a)**2+(o-l)**2)>Math.sqrt((t.x[e]-a)**2+(t.y[e]-l)**2)?r:e}),-1);if(-1===c&&(c=t.x.length,t.x=new Float32Array([...t.x,-a]),t.y=new Float32Array([...t.y,-l]),t.atomTypes=[...t.atomTypes,"H"],t.kwargs=[...t.kwargs,""],e.atomPairs.push([u+1,c+1]),e.bondTypes=new Uint32Array([...e.bondTypes,1]),e.kwargs.set(e.atomPairs.length-1,"")),r.set(c+1,o),1===o)n.unshift(t.atomTypes[c]);else{if(2!==o)throw new Error(`Unexpected missing R-group: ${o}`);n.splice(1,0,t.atomTypes[c])}}return function(t,e,n){for(const[r,o]of n)t.atomTypes[r-1]=e[o-1]}(t,n,r),function(t,e){e.rNodes=Array.from(t.keys());for(let n=0;n<e.rNodes.length;n++)for(const r of[1,2])if(t.get(e.rNodes[n])===r){const t=e.rNodes[r-1];e.rNodes[r-1]=e.rNodes[n],e.rNodes[n]=t}}(r,o),y(e,o),o}(d,p,a,u),g=function(t){let e=[],n=t.indexOf("M V30 MDLV30/STEABS ATOMS=(");for(;-1!==n;){n+=28;const r=t.indexOf(")",n);e=e.concat(t.substring(n,r).split(" ").slice(1).map((t=>parseInt(t)))),n=r,n=t.indexOf("M V30 MDLV30/STEABS ATOMS=(",n)}return e}(c),v={atoms:d,bonds:p,meta:m,stereoAtoms:g};return"PEPTIDE"===r?function(t){const e=t.meta.terminalNodes[0]-1,n=t.meta.rNodes[0]-1,r=t.atoms.x,o=t.atoms.y;E(t,-r[e],-o[e]);const i=w(r[n],o[n]);A(t.atoms,-i),r[t.meta.rNodes[1]-1]<0&&S(t);const s=function(t){const e=function(t){const e=new Map;for(const n of t.bonds.atomPairs)for(let t=0;t<2;t++){const r=n[t],o=n[(t+1)%2];e.has(r)?e.get(r)?.push(o):e.set(r,new Array(1).fill(o))}return e}(t);let n=0;const r=t.atoms.atomTypes.length;let o=0;if(t.meta.terminalNodes.length<2)return null;for(;0===n;){const i=e.get(t.meta.terminalNodes[1])[o];if(t.atoms.atomTypes[i-1]===f.u.OXYGEN&&i!==t.meta.rNodes[1]&&(n=i),o++,o>r)return null}return n}(t);null!=s&&(function(t,e){t.atoms.y[t.meta.rNodes[1]-1]<0&&t.atoms.y[e-1]<0&&(function(t){T(t,!0)}(t),A(t.atoms,-function(t,e){return w(t,e)+Math.PI/2}(t.atoms.x[t.meta.terminalNodes[1]-1],t.atoms.y[t.meta.terminalNodes[1]-1])))}(t,s),function(t,e){const n=t.atoms.x;n[t.meta.rNodes[1]-1]>n[e-1]&&function(t,e,n){const r=e-1,o=n-1,i=t.atoms.x,s=t.atoms.y,a=i[r],l=s[r];i[r]=i[o],s[r]=s[o],i[o]=a,s[o]=l}(t,e,t.meta.rNodes[1])}(t,s))}(v):t===f.u.RIBOSE.symbol||t===f.u.DEOXYRIBOSE.symbol?function(t,e){const n=t.atoms.x,r=t.atoms.y;let o=t.meta.terminalNodes[0]-1;const i=t.meta.rNodes[1]-1;E(t,-n[o],-r[o]);const s=w(n[t.meta.rNodes[2]-1],r[t.meta.rNodes[2]-1]);A(t.atoms,-s),n[t.meta.rNodes[0]-1]>n[t.meta.rNodes[1]-1]&&S(t);const a=w(n[i],r[i]);A(t.atoms,3*Math.PI/2-a),e.value=function(t){const e=t.atoms.x,n=t.atoms.y,r=t.meta.rNodes[2]-1,o=t.meta.terminalNodes[2]-1,i=e[r]-e[o],s=n[r]-n[o];return Math.atan2(i,s)}(t),o=t.meta.terminalNodes[0]-1,E(t,-n[o],-r[o])}(v,o):t===f.u.PHOSPHATE.symbol?function(t){const e=t.meta.rNodes[1]-1,n=t.meta.rNodes[0]-1,r=t.atoms.x,o=t.atoms.y;E(t,-r[e],-o[e]);const i=w(r[n],o[n]);A(t.atoms,Math.PI/2-i)}(v):function(t,e){const n=t.atoms.x,r=t.atoms.y,o=t.meta.terminalNodes[0]-1,i=t.meta.rNodes[0]-1;E(t,-n[o],-r[o]);const s=w(n[i],r[i]),a=e.value;if(!a)throw new Error("The value of sugarBranchToOYAngle is null");A(t.atoms,Math.PI-s+a);const u=function(t,e){return(0,l.YN)(Math.sqrt((t.x-e.x)**2+(t.y-e.y)**2))}({x:n[t.meta.rNodes[0]-1],y:r[t.meta.rNodes[0]-1]},{x:n[t.meta.terminalNodes[0]-1],y:r[t.meta.terminalNodes[0]-1]});if(1!=u)for(let t=0;t<n.length;++t)n[t]=(0,l.YN)(n[t]/u),r[t]=(0,l.YN)(r[t]/u)}(v,o),function(t,e,n){if("PEPTIDE"===t){b(e,t);const n=C(e,e.meta.rNodes[1]);n?.removedAtom&&(e.terminalR2Atom=n.removedAtom)}else 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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},${o/i*210})`}return r.Color.toRgb(n)}class f{static hashCode(t){let e=0;if(0===t.length)return e;for(let n=0;n<t.length;n++)e=(e<<5)-e+t.charCodeAt(n),e|=0;return e}}class p{}class m extends p{static get palette(){return m._pallete||(m._pallete=m.buildPalette()),m._pallete}static buildPalette(){return(0,h.pj)().then((t=>{t.awaitLoaded(1/0).then((()=>{const e=t.getMonomerLib();e.onChanged.subscribe((()=>{m.customMonomerColors={},m.polymerTypes=e.getPolymerTypes();for(const t of this.polymerTypes){const n=e.getMonomerSymbolsByType(t);for(const r of n){const n=e.getMonomer(t,r);n?.meta?.colors?.default?.background&&(this.customMonomerColors[r]||(this.customMonomerColors[r]={}),this.customMonomerColors[r][t]=d(n.meta.colors.default.background))}}}))}))})),[].concat(...Object.values(a.colourPalette))}get(t,e){const n=m.palette.length,r=m.customMonomerColors[t],o=e??"PEPTIDE";if(r&&r[o])return r[o];const i=f.hashCode(t)%n;return d(m.palette[i])}}m._pallete=null,m.customMonomerColors={},m.polymerTypes=[];var g=n(8438);n(3599);class y{get length(){return this.mList.length}get graphInfo(){}isGap(t){return this.getOriginal(t)===this.gapOriginalMonomer}getCanonical(t){if(this.length<=t)throw new Error("Index out of bounds");const e=this.mList[t];return e!==this.gapOriginalMonomer?e:s._S}getOriginal(t){if(this.length<=t)throw new Error("Index out of bounds");return this.mList[t]}getCanonicalRegion(t,e){const n=Math.min(Math.max(0,t),this.length),r=Math.max(Math.min(this.length,e),0)-n,o=this.gapOriginalMonomer;return new 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r.dapi.files.readAsText(n);return JSON.parse(t)}catch(t){console.error(`Error loading json from '${n}':`,t)}}(t,e))));return new C(e[0],e[1],e[2],e[3])}class w{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 A=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[A.ti.LINKAGE]))).sort(S));return new RegExp(`${A.q7}.(${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 N{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} -> ${t}`)}helmToFormat(t,e){const n=new RegExp(E(Object.values(_)),"g");let r=t.replace(n,"");const o=this.formats.getHelmToFormatDict(e),i=this.formats.getTargetFormatHelmCodes(e),s=this.formats.getTargetFormatHelmCodesRegExp(e);return r=r.replace(s,(t=>i.includes(t)?o[t]:"p"===t||"."===t?t:"?")).replace(/\?+/g,A.iL).replace(/p\.|\./g,""),r=r.replace(/<empty>/g,""),r=r.replace(/\/\//g,"/"),r}formatToHelm(t,e){const n=this.formats.getFormatToHelmDict(e),r=this.formats.getCodesByFormat(e),o=this.formats.getFormatRegExp(e),i=this.formats.getPhosphateHelmCodesRegExp(e);let s=t?t.replace(o,(t=>r.includes(t)?n[t]+".":"?")):"";return s=s.replace(/\?+/g,`${A.iL}.`),s=s.slice(0,-1),s[s.length-1]===A.q7&&(s=s.slice(0,-1)),s=s.replace(i,((t,e)=>e)),s=s.replace(/<empty>/g,""),`${_.LEFT+s+_.RIGHT}`}}class I{constructor(t,e){this.sequence=t,this.th=e,this.libWrapper=this.th.monomerLibWrapper,this.formats=Object.keys(this.th.jsonData.codesToHelmDict)}getFormat(){if(this.sequence.startsWith("RNA"))return m.NO.HELM;const t=this.getListOfPossibleSynthesizersByFirstMatchedCode();if(0===t.length)return null;const e=this.th.createSequenceValidator(this.sequence),n=Array(t.length).fill(0);for(let r=0;r<t.length;++r){const o=t[r];n[r]=e.getInvalidCodeIndex(o)}const r=n.some((t=>-1===t))?-1:Math.max(...n);return t[n.indexOf(r)]}getListOfPossibleSynthesizersByFirstMatchedCode(){const t=this.sequence,e=[];for(const n of this.formats){const r=g(this.libWrapper.getCodesByFormat(n));let o=0;for(let e=0;e<t.length;e++)if(")"===t[e]&&e!==t.length-1){o=e+1;break}r.some((e=>e===t.slice(o,o+e.length)))&&e.push(n)}return e}}var M=n(7389);const O=$;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([x(e),B(e)]),this._monomerLibWrapper=new w(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 N(t,e,this)}createFormatDetector(t){return new I(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 ${this.appName}...`),e=r.shell.v?.root;e&&M.setUpdateIndicator(e,!0);try{return await this.constructView()}finally{t.close(),e&&M.setUpdateIndicator(e,!1)}}}class F extends D{constructor(t){super(t),this.view=o.View.create(),this.configureView()}async constructView(){await this.initView();const t=this.parentAppName?this.parentAppName+"/"+this.appName:this.appName;return this.view.path=`/apps/${Zr.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,G,j,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"}(G||(G={})),function(t){t.PATTERN_CONFIG="patternConfig",t.AUTHOR_ID="authorID",t.DATE="date"}(j||(j={})),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=(G.PATTERN_NAME,G.PATTERN_COMMENT,G.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 Q extends Error{constructor(t){super(t),this.name="PatternNameExistsError"}}class J 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 Zr.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 Q(`Pattern with name ${t} already exists`)}validatePatternUniqueness(t){if(Array.from(this.currentUserPatternNameToHash.values()).concat(Array.from(this.otherUsersPatternNameToHash.values())).includes(t))throw new J(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[j.PATTERN_CONFIG]}getDefaultPatternRecord(){const t=Y;return t[j.AUTHOR_ID]=this.currentUserId,t}getDefaultPatternConfig(){return Y[j.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{[j.PATTERN_CONFIG]:t,[j.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[G.PATTERN_NAME];this.validatePatternNameUniqueness(o);const i=await this.getRecordFromPattern(e),s=(new Date).toISOString();i[j.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 Q||t instanceof J)throw t;console.error("Error while saving pattern to user storage",t)}}async overwriteExistingPatternInUserStorage(t){const e=t.getPatternConfig(),n=e[G.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[j.DATE]={[z.MODIFY]:a};const l=r.userSettings.getValue(V,o,!1)??"null",u=JSON.parse(l);void 0!==u[j.DATE]&&null!=u[j.DATE][z.CREATE]&&(s[j.DATE][z.CREATE]=u[j.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[j.PATTERN_CONFIG];this.currentUserPatternNameToHash.set(t[G.PATTERN_NAME],"")}async extractDataFromRecordToMaps(t,e,n){const o=JSON.parse(e),i=o[j.PATTERN_CONFIG].patternName,s=o[j.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 ${n.get(s)})`;this.otherUsersPatternNameToHash.set(e,t)}}getDefaultPatternName(){return Y[j.PATTERN_CONFIG][G.PATTERN_NAME]}getCurrentUserAuthorshipCategory(){return this.currentUserName+" (me)"}getOtherUsersAuthorshipCategory(){return"Other users"}isCurrentUserId(t){return t===this.currentUserId}}const et=rxjs,nt=rxjs.operators;function rt(t){return t.endsWith("(o)")}function ot(t){const e=Object.values(t).flat().reduce(((t,e)=>(t[e]=(t[e]||0)+1,t)),{});return Object.entries(e).reduce(((t,e)=>t[1]>e[1]?t:e),["",0])[0]}var it;function st(t){const e=Array.from(new Set(t));return Array.from(e).sort(((t,e)=>t.toLowerCase().localeCompare(e.toLowerCase())))}!function(t){t.getTruncatedStrandData=function(t,e,n){return{nucleotides:t.slice(0,n),ptoFlags:e.slice(0,n+1)}},t.getExtendedStrandData=function(t,e,n,r){const o=n-t.length,i=t.concat(new Array(n-t.length).fill(r)),s=0===t.length?n+1:o;return{nucleotides:i,ptoFlags:e.concat(new Array(s).fill(!0))}}}(it||(it={}));var at=n(2543),lt=n.n(at);class ut{constructor(t,e){this.dataManager=t,this._patternListUpdated$=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$.asObservable()}initializeAuthorSelection(t){const e=t[j.AUTHOR_ID];this.dataManager.isCurrentUserId(e)?this._patternAuthorSelection$=new et.BehaviorSubject(this.dataManager.getCurrentUserAuthorshipCategory()):this._patternAuthorSelection$=new et.BehaviorSubject(this.dataManager.getOtherUsersAuthorshipCategory())}initializePatternState(t){const e=t[j.PATTERN_CONFIG];this._patternName$=new et.BehaviorSubject(e[G.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$=new et.BehaviorSubject(e[G.PATTERN_COMMENT]),this._modificationsWithNumericLabels$=new et.BehaviorSubject(e[G.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[G.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$.next(t[G.PATTERN_COMMENT]),this._modificationsWithNumericLabels$.next(t[G.NUCLEOTIDES_WITH_NUMERIC_LABELS])}setLastLoadedPatternConfig(t){this._lastLoadedPatternConfig.next(lt().cloneDeep(t))}getPatternConfig(){return{[G.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(),[G.PATTERN_COMMENT]:this.getComment(),[G.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),Ct=n(540),xt=n.n(Ct),wt=n(1113),At=n.n(wt),St=n(9252),Tt={};Tt.styleTagTransform=At(),Tt.setAttributes=vt(),Tt.insert=yt().bind(null,"head"),Tt.domAPI=mt(),Tt.insertStyleElement=xt(),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 Nt(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],Zr.jsonData);return r})),n,r);return o.join("")}class It{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=>Nt(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 ${e}?`)),t.onOK((()=>this.eventBus.requestPatternDeletion(e))),t.show()}}class kt{constructor(t,e){this.eventBus=t,this.dataManager=e}getLayout(){const t=new Ft(this.eventBus,this.dataManager),e=new Dt(this.eventBus,this.dataManager),n=new It(this.eventBus),r=t.createControls(),o=e.createControls(),i=n.createControls(),s=M.div(r);L()(s).css({"padding-bottom":"20px"});const a=M.div([...o,...i],"ui-form"),l=M.div([s,a]);return L()(l).css({padding:"25px"}),M.box(l,{style:{maxWidth:"450px"}})}}var Ht=n(9146);class Ut{constructor(t,e,n){this.svgElementFactory=t,this.config=e,this.yShift=n}shiftElements(t){this.svgElements.forEach((e=>{const n=e.getAttribute("transform")||"",r=`translate(${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=`${e}px Arial`,{width:1.1*n.measureText(t).width,height:1.1*e}}}function Vt(t){const e=Object.keys(Zr.jsonData.patternAppData)[0];if(!e)throw new Error(`No format found in '${h}'`);return Zr.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 Gt(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 jt(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 Gt 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 jt 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 Qt 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+$t.getTextDimensions(t,15).width}}createLegendItems(){let t=10;const e=[],n=e=>t+=e+15;if(this.isPhosphorothioatePresent()){const{elements:r,width:o}=this.createLegendItem("PTO linkage",t);n(o),e.push(r)}return this.getModificationTypesList().forEach((r=>{const{elements:o,width:i}=this.createLegendItem(r,t);n(i),e.push(o)})),{elements:e.flat(),width:t}}getContentHeight(){return 20}getContentWidth(){return this.width}}class Jt{constructor(t){this.svgElementFactory=new Yt;const e=lt().cloneDeep(t);let n=10;this.title=new Kt(this.svgElementFactory,e,n),n+=this.title.getContentHeight(),this.strands=new qt(this.svgElementFactory,e,n),n+=this.strands.getContentHeight()+10,this.legend=new Qt(this.svgElementFactory,e,n)}renderPattern(){const t=this.getGlobalWidth(),e=this.getGlobalHeight(),n=this.svgElementFactory.createCanvas(t,e),r=[this.title,this.strands,this.legend].map((t=>t.svgElements)).flat();return n.append(...r),n}getGlobalWidth(){const t=[this.title,this.strands,this.legend];return Math.max(...t.map((t=>t.getContentWidth())))}getGlobalHeight(){return[this.title,this.strands,this.legend].reduce(((t,e)=>t+e.getContentHeight()),10)}}class Xt{constructor(t){this.eventBus=t,this.svgDisplayDiv=M.div([]),t.updateSvgContainer$.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 Jt(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 ${H[this.strand]}`),e}computeOutputValue(t){const e=this.eventBus.getNucleotideSequences()[this.strand],n=this.eventBus.getTerminalModifications()[this.strand];return Nt(t,e,this.eventBus.getPhosphorothioateLinkageFlags()[this.strand],n)}createTextInputForExamples(){const t=M.input.textArea("",{value:""});return this.applyStylingToInput(t),t}applyStylingToInput(t){const e=t.root.getElementsByTagName("textarea")[0];e.setAttribute("readonly","true"),L()(e).css("resize","none"),L()(t.root).css("opacity","75%")}}class ne{constructor(t,e){this.eventBus=t,this.dataManager=e,this.svgDisplay=Xt.createSvgDiv(t)}getLayout(){const t=new Zt(this.eventBus).getContainer(),e=this.generateDownloadControls(),n=new te(this.eventBus,this.dataManager).createContainer();return M.panel([this.svgDisplay,t,e,n],{style:{overflowX:"scroll",padding:"12px 24px"}})}generateDownloadControls(){return M.divH([this.createSavePatternButton(),this.createDownloadPngButton(),this.createShareLinkButton(),this.createInfoButton()],{style:{gap:"12px",marginTop:"12px"}})}createDownloadPngButton(){const t=M.button("Get PNG",(()=>this.eventBus.requestSvgSave()));return M.tooltip.bind(t,"Download pattern as PNG"),t}createInfoButton(){const t=M.button(M.iconFA("info-circle"),(()=>this.openInfoDialog()));return this.eventBus.patternHasUnsavedChanges$.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[j.AUTHOR_ID];if(t=(await r.dapi.users.find(i)).friendlyName,e=s[j.PATTERN_CONFIG][G.PATTERN_NAME],void 0!==s[j.DATE]){const t=s[j.DATE][z.CREATE];void 0!==t&&(n=t);const e=s[j.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 ${t} saved`)})).catch((t=>this.handleErrorWhileSavingPattern(t))):r.shell.warning("Insert pattern name"):r.shell.warning("Cannot save default pattern")}handleErrorWhileSavingPattern(t){t instanceof Q?new re(this.eventBus,this.dataManager).show():t instanceof J?r.shell.warning(M.div([M.divText("Pattern already exists"),M.button("Load",(()=>{const e=t.message;this.eventBus.requestLoadPatternInNewTab(e)}))])):console.error("Error while saving pattern",t)}}class re{constructor(t,e){this.eventBus=t,this.dataManager=e}show(){const t=this.eventBus.getPatternName(),e=M.dialog(`Pattern "${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=At(),ae.setAttributes=vt(),ae.insert=yt().bind(null,"head"),ae.domAPI=mt(),ae.insertStyleElement=xt(),ft()(se.A,ae),se.A&&se.A.locals&&se.A.locals;var ue,ce=n(2074),he={};he.styleTagTransform=At(),he.setAttributes=vt(),he.insert=yt().bind(null,"head"),he.domAPI=mt(),he.insertStyleElement=xt(),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=`${n}px`,r.style.cursor="zoom-in",this.drawMolBlockOnCanvas(r),r.addEventListener("click",(async()=>{await this.zoomIn()})),t.append(M.tooltip.bind(r,"Click to zoom"))}}class Ce extends Error{constructor(t,e){super(t,e)}}class xe{constructor(t,e){this.sequence=t,this.codeMap=e}parseSequence(){const t=this.parseRawSequence();return this.addLinkers(t)}addLinkers(t){const e=[];return t.forEach(((n,r)=>{const o=this.getSymbolForCode(n);r>0&&function(t){return Zr.jsonData.monomersWithPhosphate.left.includes(t)}(o)&&e.pop(),e.push(o);const i=we(o),s=r===t.length-1,a=r+1<t.length&&we(this.getSymbolForCode(t[r+1]));i||function(t){return Zr.jsonData.monomersWithPhosphate.right.includes(t)}(o)||a||s||e.push("p")})),e}getSymbolForCode(t){let e=this.codeMap.get(t);return e??(e=t),e}parseRawSequence(){const t=this.getAllCodesOfFormat(),e=[];let n=0;for(;n<this.sequence.length;){const r=t.find((t=>t===this.sequence.substring(n,n+t.length)));if(void 0===r)throw new Ce(`Unable to match a monomer for the rest of the sequence '${this.sequence.slice(n)}'.`);e.push(r),n+=r.length}return e}getAllCodesOfFormat(){return g(Array.from(this.codeMap.keys()))}}function we(t){return Zr.jsonData.monomersWithPhosphate.phosphate.includes(t)}class Ae{constructor(t,e=!1,n){this.invert=e,this.lib=Zr.monomerLibWrapper;const r=this.lib.getCodeToSymbolMap(n);this.parser=new xe(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 Ne(t,e,n){if(""===t)return"";const r=n.createFormatDetector(t).getFormat();if(!r)return"";let o="";try{o=new Ae(t,e,r).convert()}catch(t){const e=le(t);console.error(e)}return o}function Ie(t,e,n,r,o){const i=[t,e,n].filter((t=>""!==t.strand));return 1===i.length?Ne(i[0].strand,i[0].invert,o):Se({senseStrands:[Ne(t.strand,t.invert,o)],antiStrands:[Ne(e.strand,e.invert,o),Ne(n.strand,n.invert,o)].filter((t=>""!==t))},r)}const Me=["ss","as","as2"];class Oe{constructor(){this.th=Zr,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=Ie(t,e,n,o,s)+"\n$$$$\n";else{const h=Ne(t.strand,t.invert,s),d=Ne(e.strand,e.invert,s),f=Ne(n.strand,n.invert,s);l=h+"\n> <Sequence>\nSense Strand\n$$$$\n",d&&(l+=d+"\n> <Sequence>\nAnti Sense\n$$$$\n"),f&&(l+=f+"\n> <Sequence>\nAnti Sense 2\n$$$$\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 Ie(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=Zr.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=At(),He.setAttributes=vt(),He.insert=yt().bind(null,"head"),He.domAPI=mt(),He.insertStyleElement=xt(),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(Zr.jsonData.codesToHelmDict).concat(m.NO.HELM),this.seqHelper=Zr.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=je.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 Ae(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 Ae(t,!1,m.NO.AXOLABS).convert()}return new Ae(this.sequence,!1,this.format).convert()}}class Ve{constructor(t){this.tableInputManager=new qe(t),this.columnInputManager=new Ge(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$.subscribe((()=>this.handleTableChoice()))}getTableFromEventData(t){return t.args.dataFrame}handleTableAdded(t){const e=this.getTableFromEventData(t);this.availableTables.some((t=>t.name===e.name))||(this.availableTables.push(e),this.eventBus.selectTable(e),this.refreshTableInput())}handleTableRemoved(t){const e=this.getTableFromEventData(t);this.availableTables=this.availableTables.filter((t=>t.name!==e.name));const n=this.availableTables[0];this.eventBus.selectTable(n||null),this.refreshTableInput()}refreshTableInput(){const t=this.createTableInput();L()(this.tableInputContainer).empty(),this.tableInputContainer.append(t.root)}createTableInput(){const t=this.eventBus.getSelectedTable();return M.input.table("Table",{value:t,items:this.availableTables,onValueChanged:t=>{null!==t&&this.eventBus.selectTable(t)}})}handleTableChoice(){const t=this.eventBus.getSelectedTable();t&&(this.isTableDisplayed(t)||this.displayTable(t))}isTableDisplayed(t){return r.shell.tableNames.includes(t.name)}displayTable(t){const e=r.shell.v;r.shell.addTableView(t),r.shell.v=e}}class Ge{constructor(t){this.eventBus=t,this.columnControlsContainer=M.div([]),this.eventBus.tableSelected$.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(`${t}`,{value:o,items:e,onValueChanged:e=>this.selectColumnIfTableNotNull(n,e,t)})}selectColumnIfTableNotNull(t,e,n){if(null!==t&&e){const r=t.col(e);r&&this.eventBus.selectColumn(n,r)}}}class je{constructor(){this._tableSelection$=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===je._instance&&(je._instance=new je),je._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=Zr,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}: ${t}`))),()=>n.getView()}let n={TRANSLATOR:e(ze),PATTERN:e(ie),STRUCTURE:e(Le)};return this.externalViewFactories&&(n=Object.assign({},n,this.externalViewFactories)),n}getCurrentPanePath(){let t=this.multiView.tabs.currentPane.name;return t=t.charAt(0).toUpperCase()+t.substring(1).toLowerCase(),`/apps/${Zr.name}/OligoToolkit/${t}`}setUrl(){this.multiView.path=this.getCurrentPanePath()}async constructView(){return this.multiView.tabs.onTabChanged.subscribe((()=>this.setUrl())),this.setUrl(),this.multiView}}var Ke=n(5749);function Qe(t){const e=M.input.textArea("",{value:""});return{coloredInput:new de(e,t.highlightInvalidSubsequence),codes:t.jsonData.codesToSymbolsDict}}var Je=n(9124),Xe=n(9192),Ze=n(8312),tn=n(1991),en=n.n(tn);const nn="object"==typeof performance&&performance&&"function"==typeof performance.now?performance:Date,rn=new Set,on="object"==typeof process&&process?process:{},sn=(t,e,n,r)=>{"function"==typeof on.emitWarning?on.emitWarning(t,e,n,r):console.error(`[${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;#C;#x;#w;#A;static unsafeExposeInternals(t){return{starts:t.#v,ttls:t.#C,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.#N(e),isStale:e=>t.#I(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:C,ignoreFetchAbort:x}=t;if(0!==e&&!un(e))throw new TypeError("max option must be a nonnegative integer");const w=e?cn(e):Array;if(!w)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[Cn];n||(n=t[Cn]=[]),n.push(e),t[Cn]=n}function wn(t,e){try{const n=t.tableColumn;if(!n)return;const r=function(t){return t.temp[Cn]??[]}(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 An=n(6717),Sn=n(6694),Tn=n(4229),En=n(5174);function _n(t,e=!0){const[n,o]=(0,Xe.AP)(t);return Zr.logger.error(n,void 0,o),e&&r.shell.error(n),[n,o]}async function Nn(){return(await(0,l.pj)()).getAvaliableLibraryNames()}const In={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 Zr.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([Nn(),(0,Je.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"):(Zr.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 Zr.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,Je.b2)(),c=t.dataFrame,h=await(0,Sn.Q4)(a),[d,f,p]=(0,Tn.b)(t.toList(),h,u),m=l(c,`transformed(${t.name})`),g=o.Column.fromType(o.COLUMN_TYPE.STRING,m,d.length).init((t=>d[t]));g.semType=o.SEMTYPE.MACROMOLECULE,g.meta.units=Re.Hi.HELM,g.setTag(o.TAGS.CELL_RENDERER,"helm"),e&&c&&c.columns.add(g,!0);const y=await(0,An.j)(),b=await(0,Ze.Q)(),v=await(0,En.A)(h),C=g.temp;C[".mm.cellRenderer.overriddenLibrary"]=v,g.temp=C;const x=await(0,Fn.m)(g,d,f,i,s,n,v,y,b);return x.name=l(c,`molfile(${t.name})`),x.semType=o.SEMTYPE.MOLECULE,c&&(c.columns.add(x,!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}};xn(t.temp,u),gn(n.temp,u)}(t,g,x,v,b,y,p),[g,x]}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 $n(t,e)};var Vn=n(1296),qn=n(3820);class Gn extends o.JsInputBase{get inputType(){return"Positions"}get dataType(){return o.TYPE.DATA_FRAME}getInput(){return this.gridHost}getValue(){return this.grid.dataFrame}setValue(t){this.setDataFrame(t)}getStringValue(){return this.grid.dataFrame.toCsv()}setStringValue(t){this.setDataFrame(o.DataFrame.fromCsv(t))}clearInput(){const t=o.DataFrame.fromColumns([o.Column.fromType(o.COLUMN_TYPE.STRING,"Remove",0),o.Column.fromType(o.COLUMN_TYPE.INT,"Position",0),o.Column.fromType(o.COLUMN_TYPE.STRING,"Monomers",0)]);this.setDataFrame(t)}get placeholdersValue(){return function(t){const e=[];for(let n=0;n<t.rowCount;n++){if(t.getCol("Position").isNone(n))continue;const r=parseInt(t.get("Position",n))-1;if(!isNaN(r)){const o=jn(t.get("Monomers",n));e.push({position:r,monomers:o})}}return e}(this.grid.dataFrame)}constructor(t,e,n){super(),this.name=t,this.subs=[],this.dataFrameSubs=[],this.caption=t??"",this.root.classList.add("ui-input-polytool-pos-grid"),this.root.append(this.gridHost=M.div([],{classes:"ui-input-editor",style:{width:"100%",height:"100%",marginTop:"-8px",marginBottom:"8px",paddingBottom:"4px"}})),this.render(e,n).then((()=>{}))}detach(){for(const t of this.subs)t.unsubscribe();for(const t of this.dataFrameSubs)t.unsubscribe()}async render(t,e){let n;const r=o.DataFrame.fromColumns([n=o.Column.fromType(o.COLUMN_TYPE.STRING,"Remove",0),o.Column.fromType(o.COLUMN_TYPE.INT,"Position",0),o.Column.fromType(o.COLUMN_TYPE.STRING,"Monomers",0)]);n.setTag(o.TAGS.FRIENDLY_NAME,""),this.grid=await r.plot.fromType(o.VIEWER.GRID,e),this.grid.sort(["Position"]),this.grid.columns.byIndex(1).width=this.grid.props.rowHeight+2,this.grid.onCellRender.subscribe((t=>{const e=t.cell;e.tableColumn?.name==n.name&&(e?.tableRowIndex??-1)>=0&&(e.element=M.div(M.icons.delete((()=>{this.grid.dataFrame.rows.removeAt(e.tableRowIndex)}),"Delete"),{style:{height:`${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 Gn(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 jn(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=jn(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 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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(tr.maxMonomerLength in u.tags){const t=parseInt(u.getTag(tr.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=nr.classic;m?.includes("MSA")&&p===Re.Hi.SEPARATOR&&(b=nr.MSA);const v=u.temp["reference-sequence"],C=this.tableCol.temp["current-word"],x=(()=>{const t=(0,a.splitter)(null!=v&&""!==v?v:C??"");return en().count(0).take(t.length).slice(c).map((e=>t.getCanonical(e))).toArray()})(),w=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=sr;const v=this.getMonomerLib();v&&(b=v.getMonomerTextColor(a.defaultBiotype,g));let C=0;if(s.tableRowIndex!==u.dataFrame.currentRowIdx&&x.length>0){const t=m-c;t>=0&&t<x.length&&g===x[t]&&(C=.7)}l.push({lineIdx:r.lineIdx,monomerIdx:m-c,bounds:new o.Rect(h.x,i-n,h.width,d.lineHeight),sequencePosition:m}),or(t,p.om,f,i,h.width,d.lineHeight,{color:b,isMultiLineContext:!0,transparencyRate:C,selectedPosition:isNaN(w)||w<1?void 0:w,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=sr;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:x,maxLengthOfMonomer:h,monomerTextSizeMap:this._monomerLengthMap,logger:this.logger,selectedPosition:isNaN(w)||w<1?void 0:w-c};or(t,u,e+this.padding+this._leftThreeDotsPadding,n,r,i,m)}if(this.shouldRenderShiftedThreeDots(c)){const a={color:sr,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};or(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: ${a}`);const u=this.seqHelper.getSeqHandler(this.tableCol),c=u.getSplitted(t.tableRowIndex);if(null!==a&&a>=0&&a+r<c.length){const n=u.alphabet??Re.YI.UN,o={position:a,biotype:n===Re.YI.RNA||n===Re.YI.DNA?ir.o.NUCLEOTIDE:ir.o.AA,symbol:c.getCanonical(a+r)},i=[];let s=this._monomerStructureMap[o.symbol];if(!s){const t=this.getMonomerLib();s=this._monomerStructureMap[o.symbol]=t?t.getTooltip(o.biotype,o.symbol):M.divText("Monomer library is not available")}i.push(s),M.tooltip.show(M.divV(i),e.x+16,e.y+16),wn(t,o)}else-1===a?M.tooltip.show(M.divText(`${Math.min(r,c.length)} hidden monomers`),e.x+16,e.y+16):M.tooltip.hide(),wn(t,null)}}class lr extends ar{constructor(t,e,n,r){super(t,e,Zr.logger,n,(()=>{const t=r.getSeqHandler(e),{font:n,fontWidth:o}=ar.getFontSettings(e);return{seqHandler:t,font:n,fontCharWidth:o,separatorWidth:11,monomerToShort:Re.zS}}))}onMouseMove(t,e){super.onMouseMove(t,e)}}class ur{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 cr(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 lr(t,e,4,this.helmHelper.seqHelper);return n.init().then((()=>{})),n}}class cr 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(/\(\d+\)$/,"")),n}constructor(t,e){super(t,e)}}async function hr(t){await Zr.initPromise;const e=window.innerWidth,n=window.innerHeight;try{let i;function s(){if(null==i)return;const t=L()(i.root).find("div.d4-dialog-contents").get(0),e=t.clientHeight,n={0:1},r=Object.values(n).reduce(((t,e)=>t+e),0),o=e-en().count(0).take(t.children.length).filter((t=>!(t in n))).map((e=>t.children[e])).filter((t=>t instanceof HTMLElement)).map((t=>t.offsetHeight)).reduce(((t,e)=>t+e),0)-38;for(const e of en().count(0).take(t.children.length))if(e in n){const i=t.children[e],s=o*n[e]/r;i.style.height=`${s}px`}}i=await async function(t,e){const n="ST: PT: HelmDialog()";let i;const s=[];let u=Vn.aK.Single;const c=()=>{for(const t of s)t.unsubscribe();i.placeholders.detach()};try{const h=await(0,l.pj)(),d=h.getMonomerLib(),f=await(0,Ze.Q)(),p=o.DataFrame.fromColumns([]),[m,g]=await Promise.all([Nn(),(0,Je.b2)()]),y=g.buildMonomersFuncsFromLib(d),b=t=>{let e,n,r=null;if(t&&t.rowIndex>=0&&t?.column.semType==o.SEMTYPE.MACROMOLECULE){if(e=f.getSeqHandler(t.column).getValue(t.rowIndex),t.column.temp?.[a.notationProvider]&&!(t.column.temp[a.notationProvider]instanceof ur)){let n;r=t.column.temp[a.notationProvider].getHelm(e.value,{}),o.DataFrame.fromColumns([n=o.Column.fromList(o.COLUMN_TYPE.STRING,"seq",[r])]),n.semType=o.SEMTYPE.MACROMOLECULE,n.meta.units=Re.Hi.HELM,e=f.getSeqHandler(n).getValue(0)}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=f.getSeqHandler(t).getValue(0),n="macromolecule"}return[e,n]};let v,C,[x,w]=b(t),A=null;const S=M.divText("",{style:{marginLeft:"8px",marginTop:"2px"}}),T=M.divText("",{style:{color:"red"}});i={macromolecule:g.createHelmInput("Macromolecule",{editable:!1,editorOptions:{drawOptions:{monomerNumbering:1,getMonomer:(e,n)=>{const r=e;if("ATOM"!==r.T)return y.getMonomer(e,n);try{if(x.isDna()||x.isRna()){const t=x.getSplittedWithSugarsAndPhosphates().getCanonical(r.bio.continuousId-1);return y.getMonomer(r.bio.type,t)}if(t?.column?.temp?.[a.notationProvider]instanceof ur){const t=x.getSplitted().getCanonical(r.bio.continuousId-1);return y.getMonomer(r.bio.type,t)}{const t=r.elem;return y.getMonomer(r.bio.type,t)}}catch(t){return y.getMonomer(e,n)}}}}}),placeholders:await Gn.create("Placeholders",{showAddNewRowIcon:!0,showRemoveRowIcon:!0,showRowHeader:!1,showCellTooltip:!1}),enumeratorType:M.input.choice("Enumerator type",{value:u,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)=>{N()}}),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(C=new Sn._v(Sn.MU,Sn.yy,".json",{onValueChanged:t=>{v=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,S.textContent=A?`Original ID: ${A.value}`:""},nullable:!0}),library:M.input.choice("Monomer Library",{items:m,value:m[0],nullable:!0})},i.library.root.style.setProperty("display","none"),i.trivialNameCol.addOptions(S);let E=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"!==w)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 ${r+1}.`);continue}const o=i.macromolecule.molValue.atoms[r];if(o){const e=o.biotype(),r=(0,Un.Y)(e);for(const e of n.monomers){const n=d.getMonomer(r,e);n&&n.lib||t.push({polymerType:r,symbol:e})}}}const n={};for(const e of t){let t=n[e.polymerType];t||(t=n[e.polymerType]=[]),t.push(e.symbol)}const r=Object.entries(n).map((([t,e])=>`${t}: ${e.join(", ")}`)).join("\n");Object.keys(r).length>0&&e.push(`Placeholders contain missed monomers: ${r}`),E=e.length>0?e.join("\n"):null}catch(t){const[e,n]=_n(t,!1);E=e}return setTimeout((()=>{I()}),0),E})),i.library.addValidator((t=>i.enumeratorType.value!==Vn.aK.Library||i.library.value?null:"Monomer Library is required for this enumerator type")),i.library.onChanged.subscribe((()=>{i.enumeratorType.value===Vn.aK.Library&&i.placeholders.setMonomersValue(0,i.library.value??"")})),i.enumeratorType.onChanged.subscribe((t=>{const e=i.enumeratorType.value===Vn.aK.Library;i.library.root.style.setProperty("display",e?"flex":"none");try{if(u!==Vn.aK.Library&&e||u===Vn.aK.Library&&!e){const t=1===i.placeholders.placeholdersValue.length?i.placeholders.placeholdersValue[0].position:null;i.placeholders.clearInput(),i.placeholdersBreadth.clearInput(),e&&null!=t&&i.placeholders.addPosition(t,i.library.value??"")}}catch(t){_n(t,!1)}u=i.enumeratorType.value})),s.push(i.macromolecule.onMouseMove.subscribe((t=>{try{Zr.logger.debug(`${n}, placeholdersInput.onMouseMove()`);const e=t.offsetX,r=t.offsetY,o=i.macromolecule.molValue,s=g.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{Zr.logger.debug(`${n}, placeholdersInput.onClick()`);const e=t.offsetX,r=t.offsetY,o=i.macromolecule.molValue,s=g.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((()=>{_()}))),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&&([x,w]=b(t),L(x,w,t))}))),i.macromolecule.root.style.setProperty("min-width","250px","important");const _=()=>{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()},N=()=>{i.toAtomicLevel.value&&"template"===w?(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=E,e=T;t?(e.innerText=t,e.style.removeProperty("display")):(e.innerText="",e.style.setProperty("display","none"))},O=t=>{t?(i.trivialNameCol.setColumnInputTable(t),i.trivialNameCol.root.style.removeProperty("display")):(i.trivialNameCol.setColumnInputTable(p),i.trivialNameCol.root.style.setProperty("display","none")),e&&e()},L=(t,e,n)=>{i.macromolecule.value=t;const r=n?.dataFrame;O(r)};L(x,w,t),N();const R=async()=>{try{const t=i.macromolecule.stringValue,e=en().enumerate(i.macromolecule.molValue.atoms).filter((([t,e])=>t.highlighted)).map((([t,e])=>t)).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,Je.b2)();const n=i.placeholders.placeholdersValue;let o=i.enumeratorType.value;if(o===Vn.aK.Library){if(1!==n.length)return void r.shell.warning("Only one placeholder is allowed for Library mode");if(!n[0].monomers||!m.includes(n[0].monomers[0]))return void r.shell.warning("Valid Monomer Library is required for this enumerator type");const t=n[0].monomers[0],i=await h.readSingleLibraryByName(t);if(!i)return void r.shell.warning(`Monomer Library '${t}' was not found`);const s=(0,Un.Y)(e[0].biotype()??"HELM_AA"),a=i.getMonomerSymbolsByType(s);n[0].monomers=a,o=Vn.aK.Single}const s={placeholders:n,type:o,breadthPlaceholders:i.placeholdersBreadth.placeholdersBreadthValue,keepOriginal:i.keepOriginal.value},a=i.toAtomicLevel.value,l=await dr(t,w,A,s,!!a&&{generateHelm:i.generateHelm.value,chiralityEngine:i.chiralityEngine.value,highlightMonomers:i.highlightMonomers.value,rules:await C.getActive()},g);r.shell.addTableView(l)}}catch(t){_n(t)}},P=M.dialog({title:Bn,showFooter:!0}).add(i.macromolecule.root).add(M.divH([M.divV([i.placeholders.root,i.enumeratorType.root,i.library.root],{style:{width:"50%"}}),M.divV([i.placeholdersBreadth.root],{style:{width:"50%"}})],{style:{width:"100%"}})).add(M.divH([M.divV([i.trivialNameCol.root,i.keepOriginal.root],{style:{width:"50%"}}),M.divV([M.divH([i.toAtomicLevel.root,i.generateHelm.root]),M.divH([i.chiralityEngine.root,i.highlightMonomers.root]),i.rules.header,i.rules.form],{style:{width:"50%"}})],{style:{width:"100%"}})).add(T).onOK((()=>{R()}));return s.push(P.onClose.subscribe((()=>{c()}))),P.history((()=>({description:`${i.enumeratorType.value} ${i.placeholders.placeholdersValue?.map((t=>(t.position?.toString()??"")+": "+t.monomers?.join(", "))).join("; ")}`,placeholders:i.placeholders.stringValue,enumeratorType:i.enumeratorType.value,placeholdersBreadth:i.placeholdersBreadth.stringValue,trivialNameCol:i.trivialNameCol.stringValue,keepOriginal:i.keepOriginal.value,toAtomicLevel:i.toAtomicLevel.value,generateHelm:i.generateHelm.value,chiralityEngine:i.chiralityEngine.value,highlightMonomers:i.highlightMonomers.value,rules:v,library:i.library.value})),(t=>{i.enumeratorType.value=t.enumeratorType??Vn.aK.Single,i.placeholders.stringValue=t.placeholders,i.placeholdersBreadth.stringValue=t.placeholdersBreadth,i.trivialNameCol.stringValue=t.trivialNameCol,i.keepOriginal.value=t.keepOriginal??!1,i.toAtomicLevel.value=t.toAtomicLevel??!0,i.generateHelm.value=t.generateHelm??!0,i.chiralityEngine.value=t.chiralityEngine??!1,i.highlightMonomers.value=t.highlightMonomers??!1,C.setActive(t.rules),i.library.value=t.library})),P}catch(t){throw c(),t}}(t,s);let u=!0;M.onSizeChanged(i.root).subscribe((()=>{if(u){const t=.7*e,r=.7*n;i.root.style.width=`${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`,u=!1}s()})),s(),Zr.logger.debug("PolyToolEnumerateHelmUI: dialog before show"),i.show({width:Math.max(350,.7*e),resizable:!0}),Zr.logger.debug("PolyToolEnumerateHelmUI: dialog after show")}catch(c){const[h,d]=(0,Xe.AP)(c);Zr.logger.error(h,void 0,d)}}async function dr(t,e,n,i,s,a){const u=o.TaskBarProgressIndicator.create("PolyTool enumerating...");try{const u=await(0,l.pj)(),c=await(0,An.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"),eo.applyNotationProviderForCyclized(f,"-");break}}const p=o.DataFrame.fromColumns([f]);if(await r.data.detectSemanticTypes(p),"template"==e&&eo.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 xn(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 fr,pr=n(3151);class mr{constructor(t){this.rawLib=t}isValid(){return this.rawLib.every((t=>"object"==typeof t&&Object.values(In).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={...pr.pe};Object.entries(In).forEach((([n,r])=>{const o=t[r];e[n]=o}));let n="smiles";const r=t[In[n]],o=new gr(r),i=o.getCappedSmiles();return e[n]=i,n="rgroups",e[n]=yr.getRGroups(o.getNumberOfRGroups()),n="molfile",e[n]=new br(o.getSmilesWithRGroups()).getMolfile(),e}}class gr{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 yr{constructor(){}static getRGroups(t){return Mn.slice(0,t)}}class br{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 vr{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 mr(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"}(fr||(fr={}));class Cr{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(fr.table);return M.input.table(e.property.caption,{value:e.value})})(),seqCol:(()=>{const e=t(fr.seqCol);return M.input.column(e.property.caption,{value:e.value,table:e.value.dataFrame})})(),generateHelm:M.input.forProperty(t(fr.generateHelm).property),chiralityEngine:M.input.forProperty(t(fr.chiralityEngine).property),rules:{header:M.inlineText([Dn]),form:e}}}static async create(t){const e=new Cr(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")}}async function xr(){return await eo.oligoToolkitApp()}async function wr(){await eo.init()}async function Ar(){return await eo.oligoTranslatorApp()}async function Sr(){return await eo.oligoPatternApp()}async function Tr(){return await eo.oligoStructureApp()}async function Er(){return await eo.getTranslationHelper()}function _r(){return eo.getCodeToWeightsMap()}function Nr(t){return eo.validateSequence(t)}function Ir(t,e){return eo.getMolfileFromGcrsSequence(t,e)}function Mr(t){return eo.linkStrands(t)}async function Or(){await eo.demoTranslateSequence()}async function Lr(){await eo.demoOligoPattern()}async function Rr(){await eo.demoOligoStructure()}async function Pr(t,e,n){return await eo.translateOligonucleotideSequence(t,e,n)}async function Br(){await eo.polyToolConvertTopMenu()}async function Dr(t){return await eo.getPolyToolConvertEditor(t)}async function Fr(t,e,n,r,o){return await eo.polyToolConvert2(t,e,n,r,o)}async function kr(){await eo.polyToolEnumerateHelmTopMenu()}async function Hr(){await eo.polyToolEnumerateChemTopMenu()}async function Ur(t,e){await eo.polyToolColumnChoice(t,e)}async function $r(t){await eo.createMonomerLibraryForPolyTool(t)}async function Vr(){await eo.ptEnumeratorHelmApp()}async function qr(){await eo.ptEnumeratorChemApp()}async function Gr(t){await eo.getPtHelmEnumeratorDialog(t)}async function jr(t){await eo.getPtChemEnumeratorDialog(t)}async function zr(t,e,n,r){return await eo.enumerateSingleHelmSequence(t,e,n,r)}async function Wr(t,e){return await eo.enumerateSingleHelmSequenceWithNaturalAAs(t,e)}async function Yr(){await eo.getPolyToolCombineDialog()}function Kr(t,e){eo.applyNotationProviderForCyclized(t,e)}var Qr=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)},Xr=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 Zr=new P({debug:!0});let to=null;class eo{static async oligoToolkitApp(){await Zr.initLibData();const t=await async function(t){const e={"Mermadesynthesis:merMadeSynthesis":{tabName:"SYNTHESIZE",parameters:Qe(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}(Zr);if(!t)throw new Error("External app view factories not loaded");const e=new Ye(t,Zr);return await e.getAppView()}static async init(){return null===to&&Zr.startInit(to=async function(){const[t]=await Promise.all([(0,Je.b2)()]);Zr.completeInit(t)}()),to}static async oligoTranslatorApp(){return await no("Oligo Translator")}static async oligoPatternApp(){return await no("Oligo Pattern")}static async oligoStructureApp(){return await no("Oligo Structure")}static async getTranslationHelper(){return await Zr.initLibData(),Zr}static getCodeToWeightsMap(){const t=Zr.monomerLibWrapper.getCodesToWeightsMap();return Object.fromEntries(t)}static validateSequence(t){const e=Zr.createSequenceValidator(t),n=Zr.createFormatDetector(t).getFormat();return null!==n&&e.isValidSequence(n)}static getMolfileFromGcrsSequence(t,e){return new Ae(t,e,"GCRS").convert()}static linkStrands(t){return Se(t,!0)}static async demoTranslateSequence(){await async function(){await b((async()=>{const t=await eo.oligoTranslatorApp();r.shell.addView(t)}))}()}static async demoOligoPattern(){await async function(){await b((async()=>{const t=await eo.oligoPatternApp();r.shell.addView(t)}))}()}static async demoOligoStructure(){await async function(){await b((async()=>{const t=await eo.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 Zr.initLibData(),Zr.createFormatConverter(t,e).convertTo(n)}static async polyToolConvertTopMenu(){await async function(){await Zr.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=>Zr.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"),Zr.logger.error(e,void 0,n)}}()}static async getPolyToolConvertEditor(t){const e=await Cr.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 hr(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 vr(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 hr()}static async ptEnumeratorChemApp(){kn()}static async getPtHelmEnumeratorDialog(t){return hr(t)}static async getPtChemEnumeratorDialog(t){return kn(t)}static async enumerateSingleHelmSequence(t,e,n,r=!1){return await dr(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:[]},Zr.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 eo.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 ur(e,Zr.helmHelper)}}async function no(t){await Zr.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,Zr);return await e.getAppView()}Qr([r.decorators.app({icon:"img/icons/toolkit.png",browsePath:"Peptides | Oligo Toolkit",name:"Oligo Toolkit",tags:["app"]}),Jr("design:type",Function),Jr("design:paramtypes",[]),Jr("design:returntype",Promise)],eo,"oligoToolkitApp",null),Qr([r.decorators.init({tags:["init"]}),Jr("design:type",Function),Jr("design:paramtypes",[]),Jr("design:returntype",Promise)],eo,"init",null),Qr([r.decorators.app({icon:"img/icons/translator.png",browsePath:"Peptides | Oligo Toolkit",name:"Oligo Translator",tags:["app"]}),Jr("design:type",Function),Jr("design:paramtypes",[]),Jr("design:returntype",Promise)],eo,"oligoTranslatorApp",null),Qr([r.decorators.app({icon:"img/icons/pattern.png",browsePath:"Peptides | Oligo Toolkit",name:"Oligo Pattern",tags:["app"]}),Jr("design:type",Function),Jr("design:paramtypes",[]),Jr("design:returntype",Promise)],eo,"oligoPatternApp",null),Qr([r.decorators.app({icon:"img/icons/structure.png",browsePath:"Peptides | Oligo Toolkit",name:"Oligo Structure",tags:["app"]}),Jr("design:type",Function),Jr("design:paramtypes",[]),Jr("design:returntype",Promise)],eo,"oligoStructureApp",null),Qr([r.decorators.func({outputs:[{type:"object",name:"result"}]}),Jr("design:type",Function),Jr("design:paramtypes",[]),Jr("design:returntype",Promise)],eo,"getTranslationHelper",null),Qr([r.decorators.func({outputs:[{type:"object",name:"result"}]}),Jr("design:type",Function),Jr("design:paramtypes",[]),Jr("design:returntype",Object)],eo,"getCodeToWeightsMap",null),Qr([r.decorators.func(),Jr("design:type",Function),Jr("design:paramtypes",[String]),Jr("design:returntype",Boolean)],eo,"validateSequence",null),Qr([r.decorators.func({name:"validateSequence"}),Jr("design:type",Function),Jr("design:paramtypes",[String,Boolean]),Jr("design:returntype",String)],eo,"getMolfileFromGcrsSequence",null),Qr([r.decorators.func(),Xr(0,r.decorators.param({type:"object"})),Jr("design:type",Function),Jr("design:paramtypes",[Object]),Jr("design:returntype",String)],eo,"linkStrands",null),Qr([r.decorators.func({meta:{demoPath:"Bioinformatics | 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)],eo,"demoTranslateSequence",null),Qr([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)],eo,"demoOligoPattern",null),Qr([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)],eo,"polyToolConvertTopMenu",null),Qr([r.decorators.editor({tags:["editor"]}),Jr("design:type",Function),Jr("design:paramtypes",[o.FuncCall]),Jr("design:returntype",Promise)],eo,"getPolyToolConvertEditor",null),Qr([r.decorators.func({editor:"SequenceTranslator:getPolyToolConvertEditor"}),Xr(1,r.decorators.param({options:{caption:"Sequence"}})),Xr(2,r.decorators.param({options:{initialValue:"true"}})),Xr(3,r.decorators.param({options:{initialValue:"true"}})),Xr(4,r.decorators.param({type:"object"})),Jr("design:type",Function),Jr("design:paramtypes",[o.DataFrame,o.Column,Boolean,Boolean,Array]),Jr("design:returntype",Promise)],eo,"polyToolConvert2",null),Qr([r.decorators.func({"top-menu":"Bio | PolyTool | Enumerate HELM...",name:"polyToolEnumerateHelm",description:"Dialog for configuring enumeration of a HELM 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Generated table has sequence column called "Enumerated", and molecule column called "Molfile(Enumerated) if toAtomicLevel is set to true. Keywords: Optimize, enumerate, HELM optimization, Maximize Minimize property. When you want to optimize certain peptide using for example logS, set toAtomicLevel to true and use generated molecule column to calculate given property using chem package functions.',outputs:[{type:"dataframe",name:"result"}]}),Jr("design:type",Function),Jr("design:paramtypes",[String,Boolean]),Jr("design:returntype",Promise)],eo,"enumerateSingleHelmSequenceWithNaturalAAs",null),Qr([r.decorators.func({name:"Combine Sequences","top-menu":"Bio | PolyTool | Combine Sequences..."}),Jr("design:type",Function),Jr("design:paramtypes",[]),Jr("design:returntype",Promise)],eo,"getPolyToolCombineDialog",null),Qr([r.decorators.func({name:"applyNotationProviderForHarmonizedSequence"}),Xr(0,r.decorators.param({type:"column"})),Jr("design:type",Function),Jr("design:paramtypes",[o.Column,String]),Jr("design:returntype",void 0)],eo,"applyNotationProviderForCyclized",null)},5412:(t,e,n)=>{"use strict";n.d(e,{m:()=>l});var r=n(6082),o=n(4328),i=n(4971),s=n(6077),a=n(2003);async function l(t,e,n,l,u,c,h,d,f){const p=(await f.helmToAtomicLevel(t,l,u,h)).molCol,m=n.filter((t=>t)).length;if(c&&m>0){const t=new Array(m);let l=0;for(let r=0;r<n.length;r++)n[r]&&(t[l]=e[r],l++);const u=r.Column.fromStrings("helm",t);u.semType=r.SEMTYPE.MACROMOLECULE,u.meta.units=a.Hi.HELM,u.setTag(r.TAGS.CELL_RENDERER,"helm");const c=(await(0,i.pj)()).getMonomerLib();try{const t=await(0,s.C4)(r.DataFrame.create(0),u,c,f,d);l=0;for(let e=0;e<n.length;e++)n[e]&&(p.set(e,t.molCol.get(l)),l++)}catch(t){o.shell.warning("PolyTool was not able to linearize sequences")}}return function(t){for(let e=0;e<t.length;e++)t.set(e,t.get(e).replaceAll("undefined","H")),t.set(e,t.get(e).replaceAll("Oh","O").replaceAll("OH","O")),t.set(e,t.get(e).replaceAll("0.000000 3","0.000000 0")),t.set(e,t.get(e).replaceAll("?","O")),t.set(e,t.get(e).replaceAll(" 0 3\n"," 0 0\n")),t.set(e,t.get(e).replaceAll("RGROUPS=(1 1)",""))}(p),p}},6307:(t,e,n)=>{"use strict";n.d(e,{s:()=>f});var 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=>` ${t}`)).join("\n")}`);return e}}},4229:(t,e,n)=>{"use strict";n.d(e,{b:()=>s});var r=n(9192),o=n(6307),i=n(4822);function s(t,e,n){const s=new Array(t.length),a=new Array(t.length),l=new Array(t.length);for(let u=0;u<t.length;u++)try{if(null==t[u])s[u]="";else{const r=o.s.fromSeparator(t[u],n);r.applyRules(e),a[u]=!(r.monomersUnderRules.length>1||r.linkagesUnderRules.length>0),s[u]=r.getHelm(),l[u]=r.posToPosUnderRules}}catch(t){const[e,n]=(0,r.AP)(t);i._package.logger.error(e,void 0,n),s[u]=""}return[s,a,l]}},2125:(t,e,n)=>{"use strict";function r(t,e){let n,r=t;for(n=0;n<e.length&&r>=e[n].length;++n)r-=e[n].length;return[r,n]}function o(t,e,n){let r=0;for(let t=0;t<e;++t)r+=n[t].length;return r+t}n.d(e,{M:()=>r,j:()=>o})},6694:(t,e,n)=>{"use strict";n.d(e,{MU:()=>q,yy:()=>G,_v:()=>J,Ln:()=>et,Q4:()=>tt});var r=n(6082),o=n(4328),i=n(7389),s=n(1991),a=n.n(s),l=function(t,e,n,r){return new(n||(n=Promise))((function(o,i){function s(t){try{l(r.next(t))}catch(t){i(t)}}function a(t){try{l(r.throw(t))}catch(t){i(t)}}function l(t){var e;t.done?o(t.value):(e=t.value,e instanceof n?e:new n((function(t){t(e)}))).then(s,a)}l((r=r.apply(t,e||[])).next())}))};class u{constructor(t,e,n=".csv",r){this.path=t,this.userStorageName=e,this.ext=n,this.options=r,this.inputs=null,"/"!==this.path[this.path.length-1]&&(this.path+="/"),"."!==this.ext[0]&&(this.ext="."+this.ext)}getUserSettings(){return l(this,void 0,void 0,(function*(){if(this.settings)return this.settings;const t=o.userSettings.getValue(this.userStorageName,"Settings"),e=t?JSON.parse(t):{excluded:[],explicit:[]};return e.explicit=e.explicit instanceof Array?e.explicit:[],e.excluded=e.excluded instanceof Array?e.excluded:[],this.settings=e}))}setUserSettings(t){this.settings=t,o.userSettings.add(this.userStorageName,"Settings",JSON.stringify(t))}getAllAvailable(){return l(this,void 0,void 0,(function*(){return(yield o.dapi.files.list(this.path)).map((t=>t.fullPath.replace(`${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(4822),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 C(t){return t.replaceAll(/\[C\:\d\]/g,(t=>`[*:${t[3]}]`))}function x(t,e){const n=e?.firstReactantSmiles?C(e.firstReactantSmiles):"[*:1]C",r=e?.secondReactantSmiles?C(e.secondReactantSmiles):"[*:2]C",s=e?.productSmiles?C(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."}),x=()=>{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(x),g.addValidator(x),y.addValidator(x);const w=i.dialog(e?"Edit Reaction Rule":"Add Reaction Rule").add(h).add(p).add(d).add(f).add(m).add(g).add(y);w.addButton("Save",(()=>{const n=x();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}),w.close()})),w.show()}const w="Links",A="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),C=a.temp;C[".mm.cellRenderer.overriddenLibrary"]=v,a.temp=C;const x=await(0,m.m)(a,t,o,!0,!1,!1,v,u,b);return x.name="molfile(sequence)",x.semType=r.SEMTYPE.MOLECULE,l.columns.add(x),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;x((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(w).header,"Specify rules to link monomers based on HELM notation"),i.tooltip.bind(f.getPane(A).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==w?this.getAddNewLinkRuleDialog():t==A&&x((t=>this.addSynthRulesFunc(t)))})),i.button("Remove rule",(()=>{const e=f.currentPane.name;if(e==w){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==A){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),N=n.n(_),I=n(7659),M=n.n(I),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=N(),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),C=v&&o.chem.checkSmiles(v)?o.chem.drawMolecule(v,200,200):o.chem.drawMolecule(v??"",200,200);v&&(C.style.cursor="pointer",C.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(C,"Click to expand"));const x=i.divV([i.h2("Example Result:"),i.h2(t[0])],{style:{width:"200px"}});i.empty(this.resulting),this.resulting.append(i.divH([x,C],{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/",G="Polytool",j="code",z="firstMonomers",W="secondMonomers",Y="name",K="firstLinkingGroup",Q="secondLinkingGroup";class J 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=J.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 ${e}`)}})()),await J.ruleDescriptions[e]})))}}}function X(t,e=30){return t.length<=e?t:`${t.substring(0,e)}...`}J.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(j,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(Q,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(j,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(j),o=t.columns.byName(z),i=t.columns.byName(W),s=t.columns.byName(K),a=t.columns.byName(Q);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(j),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 C=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[C]=e,u[C]=`${i.symbol}_${o}`}catch(t){console.error(t)}C++}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[C]=e,u[C]=`${i.symbol}_${o}`}catch(t){console.error(t)}C++}let x=null;a[1]=a[1].replace("[C:1]","[1*]").replace("[C:2]","[2*]").replace("[C:3]","[3*]");let w="";try{x=t.get_mol(a[1]),w=x?.get_molblock()}catch(t){const[e,n]=(0,i.AP)(t);throw console.error(`Can not assemble monomer '${o}': ${e}.`),t}finally{x?.delete()}h[C]=w,u[C]=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 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