@datagrok/sequence-translator 1.10.16 → 1.10.18

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Files changed (27) hide show
  1. package/CHANGELOG.md +5 -0
  2. package/CLAUDE.md +274 -253
  3. package/CREDITS.md +236 -0
  4. package/detectors.js +8 -0
  5. package/dist/package-test.js +1 -1
  6. package/dist/package-test.js.map +1 -1
  7. package/dist/package.js +1 -1
  8. package/dist/package.js.map +1 -1
  9. package/package.json +3 -3
  10. package/src/apps/common/model/oligo-toolkit-package.ts +13 -1
  11. package/src/oligo-renderer/analog-cache.ts +48 -0
  12. package/src/oligo-renderer/canvas-renderer.ts +129 -15
  13. package/src/oligo-renderer/cell-renderer.ts +8 -2
  14. package/src/oligo-renderer/helm-parser.ts +3 -2
  15. package/src/oligo-renderer/legend-panel.ts +31 -6
  16. package/src/oligo-renderer/types.ts +21 -0
  17. package/src/package-api.ts +11 -0
  18. package/src/package-test.ts +1 -0
  19. package/src/package.g.ts +14 -0
  20. package/src/package.ts +60 -2
  21. package/src/polytool/pt-chem-enum-dialog.ts +50 -10
  22. package/src/polytool/pt-chem-enum.ts +76 -7
  23. package/src/polytool/pt-enumerate-seq-dialog.ts +18 -4
  24. package/src/tests/oligo-cell-editor-tests.ts +83 -0
  25. package/src/tests/oligo-renderer-tests.ts +64 -1
  26. package/test-console-output-1.log +196 -147
  27. package/test-record-1.mp4 +0 -0
package/dist/package-test.js CHANGED
@@ -1,3 +1,3 @@
1
1
  /*! For license information please see package-test.js.LICENSE.txt */
2
- var sequencetranslator_test;(()=>{var e={6717:(e,t,n)=>{"use strict";n.d(t,{j:()=>r});var o=n(6082);async function r(){const e=o.Func.find({package:"Chem",name:"getRdKitModule"});if(0===e.length)throw new Error('Package "Chem" must be installed for getRdKitModule.');return(await e[0].prepare().call()).getOutputParamValue()}},3599:(e,t,n)=>{"use strict";n.d(t,{o:()=>o.o});var o=n(6869)},9124:(e,t,n)=>{"use strict";n.d(t,{b2:()=>i});var o=n(7389),r=n(6082);async function i(){const e="Helm",t=r.Func.find({package:e,name:"getHelmHelper"});if(0===t.length)throw new Error(`Package '${e}' must be installed for HelmHelper.`);return(await t[0].prepare().call()).getOutputParamValue()}r.JsInputBase,Error,o.input.helmAsync=async function(e,t){return(await i()).createHelmInput(e,t)}},8438:(e,t,n)=>{"use strict";function o(e){return e.startsWith("[")&&e.endsWith("]")?e.slice(1,-1):e}n.d(t,{D:()=>o})},8123:(e,t,n)=>{"use strict";n.d(t,{u:()=>o});const o={V2K_RGP_SHIFT:8,V2K_RGP_LINE:"M RGP",V2K_A_LINE:"A ",V3K_COUNTS_SHIFT:14,V3K_IDX_SHIFT:7,V3K_HEADER_FIRST_LINE:"\nDatagrok macromolecule handler\n\n",V3K_HEADER_SECOND_LINE:" 0 0 0 0 0 0 999 V3000\n",V3K_BEGIN_CTAB_BLOCK:"M V30 BEGIN CTAB\n",V3K_END_CTAB_BLOCK:"M V30 END CTAB\n",V3K_BEGIN_COUNTS_LINE:"M V30 COUNTS ",V3K_COUNTS_LINE_ENDING:" 0 0 0\n",V3K_BEGIN_ATOM_BLOCK:"M V30 BEGIN ATOM\n",V3K_END_ATOM_BLOCK:"M V30 END ATOM\n",V3K_BEGIN_BOND_BLOCK:"M V30 BEGIN BOND\n",V3K_END_BOND_BLOCK:"M V30 END BOND\n",V3K_BOND_CONFIG:" CFG=",V3K_BEGIN_DATA_LINE:"M V30 ",V3K_END:"M END",PRECISION_FACTOR:1e4,DEOXYRIBOSE:{polymerType:"RNA",symbol:"d"},RIBOSE:{polymerType:"RNA",symbol:"r"},PHOSPHATE:{polymerType:"RNA",symbol:"p"},OXYGEN:"O",HYDROGEN:"H"}},6197:(e,t,n)=>{"use strict";n.d(t,{Y:()=>r});var o=n(3599);function r(e){let t;switch(e){case o.o.BASE:case o.o.SUGAR:case o.o.LINKER:case o.o.NUCLEOTIDE:case"nucleotide":t="RNA";break;case o.o.AA:t="PEPTIDE";break;case o.o.CHEM:t="CHEM";break;case o.o.BLOB:t="BLOB";break;default:t="PEPTIDE",console.warn(`Unexpected HelmType '${e}'`)}return t}},9235:(e,t,n)=>{"use strict";n.d(t,{H:()=>c,R:()=>l});var o=n(6082),r=n(1991),i=n.n(r),s=n(330),a=n(3599);async function l(e,t,r,l,c,u,h,d){const p=e.length,m=e.dataFrame,f=Math.max(navigator.hardwareConcurrency-2,1),g=new Array(f).fill(null).map((()=>new Worker(new URL(n.p+n.u(455),n.b)))),y=p/f,b=new Array(f),v=u.getSeqHandler(e),C="RNA"==l?a.o.NUCLEOTIDE:a.o.AA,x=i().count(0).take(e.length).map((e=>{const t=v.getSplitted(e);return i().count(0).take(t.length).map((e=>({position:e,symbol:t.getCanonical(e),biotype:C}))).toArray()})).toArray();for(let e=0;e<f;e++){const n=g[e],o=Math.floor(e*y),i=e===f-1?p:Math.floor((e+1)*y);b[e]=new Promise((e=>{n.onmessage=t=>{e(t.data)}})),n.postMessage({seqList:x,rolesList:d,monomersDict:t,alphabet:r,polymerType:l,start:o,end:i})}const w=[],A=[];await Promise.all(b).then((e=>{for(const t of e)w.push(...t.molfiles),A.push(...t.warnings)})),setTimeout((()=>{g.forEach((e=>{e.terminate()}))}),0);const T=(0,s.qj)(m,e.name),E=o.Column.fromType(o.COLUMN_TYPE.STRING,T,e.length).init((e=>w[e]?.molfile));return E.semType=o.SEMTYPE.MOLECULE,E.meta.units=o.UNITS.Molecule.MOLBLOCK,E.setTag(".sequence-src-col",e.name),{molCol:E,warnings:A}}function c(e,t){const n={},r={};for(const i of e){const e=t.getWebEditorMonomer(i.biotype,i.symbol).backgroundcolor,a=(0,s.vG)(e??o.Color.toRgb(o.Color.mouseOverRows))??[1,0,0,.7];for(const e of i.atoms)n[e]=a;for(const e of i.bonds)r[e]=a}return{atoms:Object.keys(n).map((e=>parseInt(e))),bonds:Object.keys(r).map((e=>parseInt(e))),highlightAtomColors:n,highlightBondColors:r}}},3561:(e,t,n)=>{"use strict";n.d(t,{Hb:()=>l,YN:()=>f,gU:()=>c});var o=n(8123),r=n(294),i=n(3151),s=n(439),a=n(6197);function l(e,t,n){const o=new Map;for(const n of e.getMonomerSymbolsByType(t)){const r=e.getMonomer(t,n);if("RNA"===t||"PEPTIDE"===t&&"Branch"!==r.monomerType){const e={};i.f6.forEach((t=>{e[t]=r[t]})),o.set(n,e)}}return o}function c(e,t,n,i,l){if(0===e.length)return r.vF.createEmpty();const c="RNA"===i&&!!l&&l.length===e.length,{atomCount:m,bondCount:g,needsCapping:y}=function(e,t,n,i,l,c){let u=0,h=0,d=0,p=!0,m=null,f=null;for(let n=0;n<e.length;++n){const o=e[n];if(o.symbol!==s._S){if("*"==o.symbol)throw new Error("Gap canonical symbol is '', not '*");m=(0,r.xb)(t,{symbol:o.symbol,polymerType:(0,a.Y)(o.biotype)}),u+=m.atoms.x.length,h+=m.bonds.bondTypes.length,d++,l&&n%3==2&&(f=m)}}if("PEPTIDE"===i)u+=1,h+=d,d>0&&((m?.meta?.rNodes?.length??0)<2||m?.terminalR2Atom?.toLowerCase()===o.u.HYDROGEN.toLowerCase())&&(p=!1,u-=1,h-=1);else if(l)h+=d,c&&c.length>0&&c[c.length-1]===r.ZN.TERMINAL_3P?p=!1:u+=1;else{const i=n===s.YI.DNA?(0,r.xb)(t,o.u.DEOXYRIBOSE):(0,r.xb)(t,o.u.RIBOSE),a=(0,r.xb)(t,o.u.PHOSPHATE);u+=(e.length-1)*a.atoms.x.length,u+=e.length*i.atoms.x.length,u+=1,h+=(e.length-1)*a.bonds.bondTypes.length,h+=e.length*i.bonds.bondTypes.length,h-=1,h+=3*e.length}return{atomCount:u,bondCount:h,needsCapping:p}}(e,t,n,i,c,l),b=new Array(m),v=new Array(g);let C,x=null,w=null;"PEPTIDE"===i?C=u:(C=d,c||(x=n===s.YI.DNA?(0,r.xb)(t,o.u.DEOXYRIBOSE):(0,r.xb)(t,o.u.RIBOSE),w=(0,r.xb)(t,o.u.PHOSPHATE)));const A={i:0,nodeShift:0,bondShift:0,backbonePositionShift:new Array(2).fill(0),branchPositionShift:new Array(2).fill(0),backboneAttachNode:0,branchAttachNode:0,flipFactor:1},T={sugar:x,phosphate:w,seqLength:c?Math.ceil(e.length/3):e.length,atomCount:m,bondCount:g},E=new r.Cg,S=[];let N,I=0;if(c)!function(e,t,n,o,i,s,l,c,u,d,m){const f=t.length>0&&t[0]===r.ZN.TERMINAL_5P,g=t.length>0&&t[t.length-1]===r.ZN.TERMINAL_3P,y=f?1:0,b=(g?t.length-1:t.length)-y,v=Math.ceil(b/3),C=b===3*v,x=(e,t)=>{const l=(0,r.xb)(n,{symbol:e.symbol,polymerType:(0,a.Y)(e.biotype)}),p=s.nodeShift,f=s.bondShift;h(l,o,i,s),l.stereoAtoms?.forEach((e=>u.push(e+m()))),d(l.atoms.x.length);const g=[];for(let e=p;e<s.nodeShift;++e)g.push(e);const y=[];for(let e=f;e<s.bondShift;++e)y.push(e);c.set(t,{biotype:e.biotype,symbol:e.symbol,atoms:g,bonds:y})};f&&(s.i=0,x(e[0],0));for(let t=0;t<v;++t){s.i=t+(f?1:0);const l=y+3*t,g=l+1,b=e[l],v=e[g],C=(0,r.xb)(n,{symbol:b.symbol,polymerType:(0,a.Y)(b.biotype)}),w=(0,r.xb)(n,{symbol:v.symbol,polymerType:(0,a.Y)(v.biotype)});if(t>=1){const n=y+3*(t-1)+2;x(e[n],n)}const A=s.nodeShift,T=s.bondShift;h(C,o,i,s),C.stereoAtoms?.forEach((e=>u.push(e+m()))),d(C.atoms.x.length);const E=[];for(let e=A;e<s.nodeShift;++e)E.push(e);const S=[];for(let e=T;e<s.bondShift;++e)S.push(e);c.set(l,{biotype:b.biotype,symbol:b.symbol,atoms:E,bonds:S});const N=s.nodeShift,I=s.bondShift;p(w,o,i,s),w.stereoAtoms?.forEach((e=>u.push(e+m()))),d(w.atoms.x.length);const M=[];for(let e=N;e<s.nodeShift;++e)M.push(e);const P=[];for(let e=I;e<s.bondShift;++e)P.push(e);c.set(g,{biotype:v.biotype,symbol:v.symbol,atoms:M,bonds:P})}if(C){const t=y+3*(v-1)+2;x(e[t],t)}g&&(s.i=v+(f?1:0),x(e[t.length-1],t.length-1))}(e,l,t,b,v,A,0,E,S,(e=>{I+=e}),(()=>I));else for(A.i=0;A.i<T.seqLength;++A.i){const n=e[A.i];if(n.symbol===s._S)continue;const o=(0,r.xb)(t,{symbol:n.symbol,polymerType:(0,a.Y)(n.biotype)});N=o.terminalR2Atom;const i=A.nodeShift,l=A.bondShift;C(o,b,v,A,T),o.stereoAtoms?.forEach((e=>S.push(e+I))),I+=o.atoms.x.length;const c=A.nodeShift-i,u=new Array(c);for(let e=0;e<c;++e)u[e]=i+e;const h=A.bondShift-l,d=new Array(h);for(let e=0;e<h;++e)d[e]=l+e;E.set(A.i,{biotype:n.biotype,symbol:n.symbol,atoms:u,bonds:d})}y&&function(e,t,n,r,i=o.u.OXYGEN){const s=n.nodeShift+1;e[r.atomCount]=o.u.V3K_BEGIN_DATA_LINE+s+" "+(i??o.u.OXYGEN)+" "+f(n.backbonePositionShift[0])+" "+n.flipFactor*f(n.backbonePositionShift[1])+" 0.000000 0\n";const a=n.backboneAttachNode,l=s;t[r.bondCount]=o.u.V3K_BEGIN_DATA_LINE+n.bondShift+" 1 "+a+" "+l+"\n"}(b,v,A,T,N??o.u.OXYGEN);const M=o.u.V3K_BEGIN_COUNTS_LINE+m+" "+g+o.u.V3K_COUNTS_LINE_ENDING;let P="";return P+=o.u.V3K_HEADER_FIRST_LINE,P+=o.u.V3K_HEADER_SECOND_LINE,P+=o.u.V3K_BEGIN_CTAB_BLOCK,P+=M,P+=o.u.V3K_BEGIN_ATOM_BLOCK,P+=b.join(""),P+=o.u.V3K_END_ATOM_BLOCK,P+=o.u.V3K_BEGIN_BOND_BLOCK,P+=v.join(""),P+=o.u.V3K_END_BOND_BLOCK,S.length>0&&(P+=function(e){const t=[];let n=`M V30 MDLV30/STEABS ATOMS=(${e.length}`;for(let o=0;o<e.length;o++){const r=`${n} ${e[o]}`;r.length>76?(t.push(`${n} -\n`),n=`M V30 ${e[o]}`):n=r,o===e.length-1&&t.push(`${n})\n`)}return`M V30 BEGIN COLLECTION\n${t.join("")}M V30 END COLLECTION\n`}(S)),P+=o.u.V3K_END_CTAB_BLOCK,P+=o.u.V3K_END,{molfile:P,monomers:E}}function u(e,t,n,o){o.flipFactor=(-1)**(o.i%2),h(e,t,n,o)}function h(e,t,n,r){!function(e,t,n){for(let r=0;r<e.atoms.atomTypes.length;++r){const i=n.nodeShift+r+1;t[n.nodeShift+r]=o.u.V3K_BEGIN_DATA_LINE+i+" "+e.atoms.atomTypes[r]+" "+f(n.backbonePositionShift[0]+e.atoms.x[r])+" "+f(n.backbonePositionShift[1]+n.flipFactor*e.atoms.y[r])+" "+e.atoms.kwargs[r]}}(e,t,r),m(e,n,r),function(e,t,n){if(0!==n.backboneAttachNode){const r=n.bondShift,i=n.backboneAttachNode,s=e.meta.terminalNodes[0]+n.nodeShift;t[n.bondShift-1]=o.u.V3K_BEGIN_DATA_LINE+r+" 1 "+i+" "+s+"\n"}}(e,n,r),null!==e.meta.branchShift&&e.meta.terminalNodes.length>2&&function(e,t){t.branchAttachNode=t.nodeShift+e.meta.terminalNodes[2];for(let n=0;n<2;++n)t.branchPositionShift[n]=t.backbonePositionShift[n]+e.meta.branchShift[n]}(e,r),function(e,t){t.backboneAttachNode=t.nodeShift+e.meta.terminalNodes[1],t.bondShift+=e.bonds.atomPairs.length+1,t.nodeShift+=e.atoms.atomTypes.length,t.backbonePositionShift[0]+=e.meta.backboneShift?.[0]??0,t.backbonePositionShift[1]+=t.flipFactor*(e.meta.backboneShift?.[1]??0)}(e,r)}function d(e,t,n,o,r){if(0===o.i)h(r.sugar,t,n,o);else for(const e of[r.phosphate,r.sugar])h(e,t,n,o);p(e,t,n,o)}function p(e,t,n,r){!function(e,t,n){for(let r=0;r<e.atoms.atomTypes.length;++r){const i=n.nodeShift+r+1;t[n.nodeShift+r]=o.u.V3K_BEGIN_DATA_LINE+i+" "+e.atoms.atomTypes[r]+" "+f(n.branchPositionShift[0]+e.atoms.x[r])+" "+f(n.branchPositionShift[1]+n.flipFactor*e.atoms.y[r])+" "+e.atoms.kwargs[r]}}(e,t,r),m(e,n,r),function(e,t,n){const r=n.bondShift,i=n.branchAttachNode,s=e.meta.terminalNodes[0]+n.nodeShift;t[r-1]=o.u.V3K_BEGIN_DATA_LINE+r+" 1 "+i+" "+s+"\n"}(e,n,r);const i=r.bondShift,s=r.branchAttachNode,a=e.meta.terminalNodes[0]+r.nodeShift;n[i-1]=o.u.V3K_BEGIN_DATA_LINE+i+" 1 "+s+" "+a+"\n",r.bondShift+=e.bonds.atomPairs.length+1,r.nodeShift+=e.atoms.atomTypes.length}function m(e,t,n){for(let r=0;r<e.bonds.atomPairs.length;++r){const i=n.bondShift+r+1,s=e.bonds.atomPairs[r][0]+n.nodeShift,a=e.bonds.atomPairs[r][1]+n.nodeShift;let l="";if(e.bonds.bondConfiguration.has(r)){let t=e.bonds.bondConfiguration.get(r);n.flipFactor<0&&(t=1===t?3:1),l=" CFG="+t}const c=e.bonds.kwargs.has(r)?" "+e.bonds.kwargs.get(r):"";t[n.bondShift+r]=o.u.V3K_BEGIN_DATA_LINE+i+" "+e.bonds.bondTypes[r]+" "+s+" "+a+l+c+"\n"}}function f(e){return Math.round(o.u.PRECISION_FACTOR*e)/o.u.PRECISION_FACTOR}},6077:(e,t,n)=>{"use strict";n.d(t,{C4:()=>f,eM:()=>y});var o=n(4328),r=n(6082),i=n(1991),s=n.n(i),a=n(439),l=n(3561),c=n(9235),u=n(294),h=n(9192),d=n(330),p=n(3599),m=n(8123);async function f(e,t,n,i,l){if(t.semType!==r.SEMTYPE.MACROMOLECULE)return{molCol:null,warnings:[`Only the ${r.SEMTYPE.MACROMOLECULE} columns can be converted to atomic level, the chosen column has semType '${t.semType}'`]};let f=t;const b=i.getSeqHandler(t),v=b.notation===a.Hi.HELM&&function(e,t){const n=t.getSeqHandler(e);if(n.notation!==a.Hi.HELM)return!1;let o=!1;for(let t=0;t<e.length;++t){const e=n.getSplitted(t);if(0===e.length)continue;const r=e.graphInfo,i=r?.polymerTypes;if(!i||i.length!==e.length)return!1;for(const e of i)if("RNA"!==e)return!1;o=!0}return o}(t,i);let C,x;v||b.notation===a.Hi.SEPARATOR||b.notation===a.Hi.BILN||(f=b.convert(a.Hi.SEPARATOR,"."),f.name=t.name);try{v?(C="RNA",x=function(e,t){const n=t.getSeqHandler(e);for(let t=0;t<e.length;++t){const e=n.getSplitted(t);for(let t=0;t<e.length;++t)if(t%3==0&&e.getCanonical(t)===m.u.DEOXYRIBOSE.symbol)return a.YI.DNA}return a.YI.RNA}(t,i)):(x=i.getSeqHandler(f).alphabet,C=(0,d.pz)(x))}catch(e){const[t,n]=(0,h.AP)(e);return{molCol:null,warnings:[t]}}const w=function(e,t){const n=e.length,r=new Array(n),i=t.getSeqHandler(e);let a=!1;const l=i.defaultBiotype;for(let e=0;e<n;++e){const t=i.getSplitted(e);a||(a=0===t.length),r[e]=s().count(0).take(t.length).filter((e=>!t.isGap(e))).map((e=>({position:e,biotype:l,symbol:t.getCanonical(e)}))).toArray()}return a&&o.shell.warning(`Some values in the "${e.name}" column are empty`),r}(f,i),A=v?function(e,t,n){const o=new Array(e.length);for(let r=0;r<e.length;++r){const i=e[r];if(0===i.length){o[r]=void 0;continue}const s=i.length>=1&&null!==g(t,n,i[0].symbol),a=i.length>=1&&!(s&&1===i.length)&&null!==g(t,n,i[i.length-1].symbol),l=i.length-(s?1:0)-(a?1:0);if(l<0||l%3!=0&&l%3!=2){o[r]=void 0;continue}const c=new Array(i.length);let h=0;for(let e=0;e<i.length;++e)0===e&&s?c[e]=u.ZN.TERMINAL_5P:e===i.length-1&&a?c[e]=u.ZN.TERMINAL_3P:(c[e]=h%3,h++);o[r]=c}return o}(w,n,C):new Array(w.length).fill(void 0);if(v)for(const e of w)for(const t of e)t.biotype=p.o.NUCLEOTIDE;const T=y(w,A,C,x,n,l),E=f.length,S=await(0,c.R)(f,T,x,C,n,i,l,A);S.warnings.length>.05*E&&o.shell.warning(`Molfile conversion resulted in ${S.warnings.length} errors`);const N=r.Func.find({name:"convertToV3KViaOCL"})[0];if(N&&S.molCol)try{const e=S.molCol.toList(),t=await N.apply({mols:e});S.molCol.init((n=>t[n]?t[n]:e[n]))}catch(e){console.error(e)}return S}function g(e,t,n){const o=e.getMonomer(t,n);if(!o||!o.rgroups||1!==o.rgroups.length)return null;if("Branch"===o.monomerType)return null;const r=o.rgroups[0].label;return"R1"===r?"r1-only":"R2"===r?"r2-only":null}function y(e,t,n,o,r,i){const s=(0,l.Hb)(r,n,o),c={},h={value:null};if("RNA"===n&&t.some((e=>void 0===e))){const e=o===a.YI.RNA?[m.u.RIBOSE,m.u.PHOSPHATE]:[m.u.DEOXYRIBOSE,m.u.PHOSPHATE];for(const t of e)b(c,t.symbol,s,i,n,h,void 0)}for(let o=0;o<e.length;++o){const r=e[o],a=t[o];for(let e=0;e<r.length;++e){const t=r[e].symbol;if(""===t)continue;const o=a?a[e]:void 0;try{if("RNA"===n&&void 0===o&&3===t.split(/\(|\)/).filter((e=>!!e)).length){const e=t.split(/\(|\)/)[1];b(c,e,s,i,n,h,u.ZN.BASE),c[n]?.[e]&&(c[n][t]=c[n][e])}else b(c,t,s,i,n,h,o)}catch(e){const n=e instanceof Error?e.message:e.toString(),o=e instanceof Error?e.stack:void 0;throw console.error(`bio lib: getMonomersDictFromLib() sym='${t}', error:\n${n}\n${o}`),new Error(`Can't get monomer '${t}' from library: ${n}`)}}}return c}function b(e,t,n,o,r,i,s){const a={polymerType:r,symbol:t};if(!(0,u.bq)(e,a)){const c=function(e,t,n,o,r,i){if(t.has(e)){const 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o="OligoNucleotide",r="helm",i=Object.freeze({r:{name:"Ribose",short:"RNA",color:"#D0D0D0",category:"sugar"},d:{name:"Deoxyribose",short:"DNA",color:"#BDBDBD",category:"sugar"},m:{name:"2'-O-Methyl",short:"2'-OMe",color:"#4A90E2",category:"sugar"},"25r":{name:"2'-O-Methyl (2,5)",short:"2'-OMe",color:"#4A90E2",category:"sugar"},fl2r:{name:"2'-Fluoro",short:"2'-F",color:"#50C878",category:"sugar"},lna:{name:"LNA",short:"LNA",color:"#E89D3C",category:"sugar"},cet:{name:"cEt",short:"cEt",color:"#E07B30",category:"sugar"},ena:{name:"ENA",short:"ENA",color:"#D26C20",category:"sugar"},moe:{name:"2'-MOE",short:"2'-MOE",color:"#66CDAA",category:"sugar"},Rgna:{name:"(R)-GNA",short:"GNA",color:"#C7A981",category:"sugar"},Sgna:{name:"(S)-GNA",short:"GNA",color:"#C7A981",category:"sugar"},una:{name:"UNA",short:"UNA",color:"#ED68B8",category:"sugar"},fana:{name:"FANA",short:"FANA",color:"#76B947",category:"sugar"},hna:{name:"HNA",short:"HNA",color:"#A4D080",category:"sugar"}}),s=Object.freeze({R:"r",dR:"d",mR:"m",fR:"fl2r",LR:"lna",L:"lna",MOE:"moe",GNA:"Sgna",UNA:"una"}),a=Object.freeze({p:{name:"Phosphate",short:"PO",color:"#888888",category:"phosphate"},sp:{name:"Phosphorothioate",short:"PS",color:"#6B46C1",category:"phosphate"},s2p:{name:"Phosphorodithioate",short:"PS₂",color:"#7E2BC4",category:"phosphate"},mp:{name:"Methylphosphonate",short:"MeP",color:"#9B5DE5",category:"phosphate"}}),l=Object.freeze({P:"p",sP:"sp"}),c=Object.freeze({GalNAc:{name:"GalNAc",short:"GalNAc",color:"#E91E63",category:"conjugate"},L3:{name:"GalNAc-L3 linker",short:"L3",color:"#E91E63",category:"conjugate"},Chol:{name:"Cholesterol",short:"Chol",color:"#B57F50",category:"conjugate"},Bio:{name:"Biotin",short:"Bio",color:"#FFC107",category:"conjugate"}}),u=Object.freeze({A:"#C1E7C5",C:"#C5DCF0",G:"#E8DCA9",U:"#F0C5C5",T:"#F0C5C5"}),h="#BCBCBC";function d(e){let t=0;for(let n=0;n<e.length;n++)t=31*t+e.charCodeAt(n)|0;return`hsl(${(t>>>0)%360}, 42%, 60%)`}function p(e){return s[e]??e}function m(e){return l[e]??e}function f(e,t){const n=p(e),o=i[n];if(o)return("r"===n||"d"===n)&&t&&u[t]?{color:u[t],meta:o}:{color:o.color,meta:o};const r=d(n);return{color:r,meta:{name:n,short:n,color:r,category:"sugar"}}}function g(e){if(!e)return{color:"#888",meta:{name:"(none)",short:"",color:"#888",category:"phosphate"}};const t=m(e),n=a[t];if(n)return{color:n.color,meta:n};const o=d(t);return{color:o,meta:{name:t,short:t,color:o,category:"phosphate"}}}function y(e){const t=c[e];return t?{color:t.color,meta:t}:{color:d(e),meta:{name:e,short:e.length>6?e.slice(0,6):e,color:d(e),category:"conjugate"}}}},9022:(e,t,n)=>{"use strict";n.d(t,{PackageFunctions:()=>Cr,_package:()=>br});var o=n(4328),r=n(6082),i=n(439),s=n(7291);const a=new class{constructor(){this.seqHandler="seq-handler",this.notationProvider="seq-handler.notation-provider"}};r.SemanticValue;var l=n(4971);class c{constructor(e,t,n=""){this.target=e,this.debugEnabled=t,this.prefix=n}error(e,t,n){return this.target.error(this.prefix+e,t,n)}warning(e,t){return this.target.warning(this.prefix+e,t)}info(e,t){return this.target.info(this.prefix+e,t)}debug(e,t){if(this.debugEnabled)return this.target.debug(this.prefix+e,t)}}const u="System:AppData/SequenceTranslator/monomers-sample",h="pattern-app-data.json",d="formats-to-helm.json",p="codes-to-symbols.json",m="linkers.json";var f=n(6686);function g(e){return e.sort(((e,t)=>t.length-e.length))}function y(e,t){const n=document.createElement("a");n.setAttribute("href","data:text/plain;charset=utf-8,"+t),n.setAttribute("download",e),n.click()}async function b(e,t,n="Oligo app"){try{return await e()}catch(e){const t=e.hasOwnProperty("message")?e.message:e.toString();throw o.shell.error(`${n} error: `+t),e}finally{t&&t()}}class v{constructor(e,t){this.sequence=e,this.th=t,this.libWrapper=this.th.monomerLibWrapper}getInvalidCodeIndex(e){if(e===f.NO.HELM)return this.sequence.length;const t=["r","d"],n=g(this.libWrapper.getCodesByFormat(e));let o=0;for(;o<this.sequence.length;){const e=n.find((e=>e===this.sequence.substring(o,o+e.length)));if(!e)break;if(o>1&&f.AL.includes(this.sequence[o])&&t.includes(this.sequence[o-2]))break;if(t.includes(this.sequence[o+1])&&f.AL.includes(this.sequence[o])){o++;break}o+=e.length}return o===this.sequence.length&&(o=-1),o}isValidSequence(e){return-1===this.getInvalidCodeIndex(e)}}class C{constructor(e,t,n,o){this.patternAppData=e,this.codesToHelmDict=t,this.codesToSymbolsDict=n,this.monomersWithPhosphate=o}}async function x(e){const t=await Promise.all([h,d,p,m].map((t=>async function(e,t){const n=e.endsWith("/")?`${e}${t}`:`${e}/${t}`;try{const e=await o.dapi.files.readAsText(n);return JSON.parse(e)}catch(e){console.error(`Error loading json from '${n}':`,e)}}(e,t))));return new C(t[0],t[1],t[2],t[3])}class w{constructor(e,t){if(this.lib=e,this.jsonData=t,null===this.lib)throw new Error("SequenceTranslator: monomer library is null");this.allMonomers=this.getAllMonomers()}formatMonomerForViewer(e){const t={};return t.name=e.symbol,t.symbol=e.symbol,t.molfile=e.molfile,this.getAllFormats().forEach((n=>{if(n===f.NO.HELM)return;const o=this.jsonData.codesToSymbolsDict[n],r=Object.keys(o).filter((t=>o[t]===e.symbol));t[n]=r.join(", ")})),t}getAllMonomers(){const e=this.lib.getPolymerTypes();let t=[];for(const n of e){const e=this.lib.getMonomerSymbolsByType(n).map((e=>this.lib.getMonomer(n,e))).filter((e=>null!==e));t=t.concat(e)}return t}getMonomer(e){const t=this.lib.getMonomer("RNA",e);if(void 0===t)throw new Error(`SequenceTranslator: no monomer with symbol ${e}`);return t}getMolfileBySymbol(e){return this.getMonomer(e).molfile}getNaturalAnalogBySymbol(e){const t=this.getMonomer(e).naturalAnalog;if(!t)throw new Error(`ST: no natural analog for ${e}`);return t}isModification(e){return!!this.getMolfileBySymbol(e).includes("MODIFICATION")}getCodeToSymbolMap(e){return new Map(Object.entries(this.jsonData.codesToSymbolsDict[e]))}getCodesByFormat(e){return Object.keys(this.jsonData.codesToSymbolsDict[e])}getAllFormats(){return Object.keys(this.jsonData.codesToSymbolsDict)}getTableForViewer(){const e=this.allMonomers.map((e=>this.formatMonomerForViewer(e)));return r.DataFrame.fromObjects(e)}getCodesToWeightsMap(){const e=new Map;return Object.entries(this.jsonData.codesToSymbolsDict).forEach((([t,n])=>{Object.entries(n).forEach((([t,n])=>{const o=this.getMonomer(n),r=o.meta?.molecularWeight;e.set(t,r)}))})),e}}var A=n(9537);const T=(e,t)=>t.length-e.length;class E{constructor(e){this.th=e,this.formats=this.getFormats()}getFormatNames(){return this.formats.sort()}getCodesByFormat(e){if(this.validateFormat(e),this.isHelm(e))throw new Error("Codes cannot be obtained for HELM");return this.getFormatCodes(e)}getHelmToFormatDict(e){return this.validateFormat(e),function(e){const t={};return Object.values(e).forEach((e=>{Object.entries(e).forEach((([e,n])=>{const o=n.replace(/\)p/g,")").replace(/\]p/g,"]");void 0===t[o]?t[o]=[e]:t[o].push(e)}))})),Object.entries(t).forEach((([e,n])=>{const o=n.sort(T);t[e]=o[0]})),t}(this.th.jsonData.codesToHelmDict[e])}getFormatToHelmDict(e){this.validateFormat(e);const t=this.th.jsonData.codesToHelmDict[e];return Object.assign({},...Object.values(t))}getTargetFormatHelmCodes(e){this.validateFormat(e);const t=this.getHelmToFormatDict(e);return Object.keys(t).sort(T)}getTargetFormatHelmCodesRegExp(e){this.validateFormat(e);const t=this.getTargetFormatHelmCodes(e);return new RegExp(S(t)+"|.","g")}getFormatRegExp(e){if(this.validateFormat(e),this.isHelm(e))throw new Error("Helm RegExp can be built for non-HELM target formats");return this.getNonHelmFormatRegExp(e)}getPhosphateHelmCodesRegExp(e){this.validateFormat(e);const t=this.th.jsonData.codesToHelmDict[e],n=S(Array.from(new Set(Object.values(t[A.ti.LINKAGE]))).sort(T));return new RegExp(`${A.q7}.(${n})`,"g")}isValidFormat(e){return this.formats.includes(e)}getFormats(){return Object.keys(this.th.jsonData.codesToHelmDict)}validateFormat(e){if(!this.isValidFormat(e))throw new Error(`Invalid format: ${e}`)}isHelm(e){return e===f.NO.HELM}getFormatCodes(e){const t=this.getFormatToHelmDict(e);return Object.keys(t).sort(T)}getNonHelmFormatRegExp(e){const t=this.getCodesByFormat(e);return new RegExp(S(t)+"|\\([^()]*\\)|.","g")}}function S(e){return e.map((e=>e.replace(/[.*+?^${}()|[\]\\]/g,"\\$&"))).map((e=>e.includes("(")||e.includes(")")?e:`(?<!\\([^()]*)${e}(?![^()]*\\))`)).join("|")}const N={LEFT:"RNA1{",RIGHT:"}$$$$"};class I{constructor(e,t,n){this.sequence=e,this.sourceFormat=t,this.th=n,this.formats=new E(this.th)}convertTo(e){const t=this.formats.getFormatNames();if(this.sourceFormat===f.NO.HELM&&t.includes(e))return this.helmToFormat(this.sequence,e);if(t.includes(this.sourceFormat)&&e===f.NO.HELM)return this.formatToHelm(this.sequence,this.sourceFormat);if([this.sourceFormat,e].every((e=>t.includes(e)))){const t=this.formatToHelm(this.sequence,this.sourceFormat);return this.helmToFormat(t,e)}throw new Error(`ST: unsupported translation direction ${this.sourceFormat} -> ${e}`)}helmToFormat(e,t){const n=new RegExp(S(Object.values(N)),"g");let o=e.replace(n,"");const r=this.formats.getHelmToFormatDict(t),i=this.formats.getTargetFormatHelmCodes(t),s=this.formats.getTargetFormatHelmCodesRegExp(t);return o=o.replace(s,(e=>i.includes(e)?r[e]:"p"===e||"."===e?e:"?")).replace(/\?+/g,A.iL).replace(/p\.|\./g,""),o=o.replace(/<empty>/g,""),o=o.replace(/\/\//g,"/"),o}formatToHelm(e,t){const n=this.formats.getFormatToHelmDict(t),o=this.formats.getCodesByFormat(t),r=this.formats.getFormatRegExp(t),i=this.formats.getPhosphateHelmCodesRegExp(t);let s=e?e.replace(r,(e=>o.includes(e)?n[e]+".":"?")):"";return s=s.replace(/\?+/g,`${A.iL}.`),s=s.slice(0,-1),s[s.length-1]===A.q7&&(s=s.slice(0,-1)),s=s.replace(i,((e,t)=>t)),s=s.replace(/<empty>/g,""),`${N.LEFT+s+N.RIGHT}`}}class M{constructor(e,t){this.sequence=e,this.th=t,this.libWrapper=this.th.monomerLibWrapper,this.formats=Object.keys(this.th.jsonData.codesToHelmDict)}getFormat(){if(this.sequence.startsWith("RNA"))return f.NO.HELM;const e=this.getListOfPossibleSynthesizersByFirstMatchedCode();if(0===e.length)return null;const t=this.th.createSequenceValidator(this.sequence),n=Array(e.length).fill(0);for(let o=0;o<e.length;++o){const r=e[o];n[o]=t.getInvalidCodeIndex(r)}const o=n.some((e=>-1===e))?-1:Math.max(...n);return e[n.indexOf(o)]}getListOfPossibleSynthesizersByFirstMatchedCode(){const e=this.sequence,t=[];for(const n of this.formats){const o=g(this.libWrapper.getCodesByFormat(n));let r=0;for(let t=0;t<e.length;t++)if(")"===e[t]&&t!==e.length-1){r=t+1;break}o.some((t=>t===e.slice(r,r+t.length)))&&t.push(n)}return t}}var P=n(7389);const _=$;var L=n.n(_);function O(e,t){let n=0;const o=t.createFormatDetector(e).getFormat();null!==o&&(n=new v(e,t).getInvalidCodeIndex(o));const r=n<0||""===e,i=P.span([]);L()(i).css("-webkit-text-fill-color","var(--grey-6)");const s=P.span([]);return L()(s).css("-webkit-text-fill-color","red"),r?i.innerHTML=e:(i.innerHTML=e.slice(0,n),s.innerHTML=e.slice(n)),[i,s]}class R extends r.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(e={debug:!1}){super(),this.highlightInvalidSubsequence=e=>O(e,this),super._logger=new c(super.logger,e.debug)}startInit(e){this._initPromise=e}completeInit(e){this._helmHelper=e}async initLibData(){return this.initLibDataPromise||(this.initLibDataPromise=(async()=>{const e=await this.getSettings();let t=e instanceof Map?e.get("MonomersPath"):e.MonomersPath;t&&await o.dapi.files.exists(t)||(this.logger.warning(`Monomers path '${t}' not found. Fallback to monomers sample path '${u}'.`),t=u),[this._jsonData,this._monomerLib]=await Promise.all([x(t),D(t)]),this._monomerLibWrapper=new w(this.monomerLib,this.jsonData)})()),this.initLibDataPromise}async getTranslationHelper(){return await o.functions.call(`${this.name}:getTranslationHelper`)}createSequenceValidator(e){return new v(e,this)}createFormatConverter(e,t){return new I(e,t,this)}createFormatDetector(e){return new M(e,this)}}async function D(e){const t=r.TaskBarProgressIndicator.create("Initializing Oligo Toolkit monomer library ...");try{const t=await(0,l.pj)(),n=(e.endsWith("/")?e:e+"/")+"monomer-lib.json";return await t.readLibraryFromFilePath(n)}finally{t.close()}}class B{constructor(e,t){this.appName=e,this.parentAppName=t}async getAppView(){const e=r.TaskBarProgressIndicator.create(`Loading ${this.appName}...`),t=o.shell.v?.root;t&&P.setUpdateIndicator(t,!0);try{return await this.constructView()}finally{e.close(),t&&P.setUpdateIndicator(t,!1)}}}class F extends B{constructor(e){super(e),this.view=r.View.create(),this.configureView()}async constructView(){await this.initView();const e=this.parentAppName?this.parentAppName+"/"+this.appName:this.appName;return this.view.path=`/apps/${br.name}/${e.replace(/\s/g,"")}/`,this.view}async initView(){const e=await this.getContent();this.view.append(e)}configureView(){this.view.box=!0,this.view.name=this.appName;const e=o.shell.windows;e.showProperties=!1,e.showToolbox=!1,e.showHelp=!1}getView(){return this.view}}const k=["SS","AS"],H={SS:"Sense strand",AS:"Anti sense"},G=["3'","5'"],U="OligoToolkit";var V,j,q,W;!function(e){e.IS_ANTISENSE_STRAND_INCLUDED="isAntisenseStrandIncluded",e.NUCLEOTIDE_SEQUENCES="nucleotideSequences",e.PHOSPHOROTHIOATE_LINKAGE_FLAGS="phosphorothioateLinkageFlags",e.STRAND_TERMINUS_MODIFICATIONS="strandTerminusModifications"}(V||(V={})),function(e){e.PATTERN_NAME="patternName",e.PATTERN_COMMENT="patternComment",e.NUCLEOTIDES_WITH_NUMERIC_LABELS="nucleotidesWithNumericLabels"}(j||(j={})),function(e){e.PATTERN_CONFIG="patternConfig",e.AUTHOR_ID="authorID",e.DATE="date"}(q||(q={})),function(e){e.CREATE="create",e.MODIFY="modify"}(W||(W={}));const z=[V.IS_ANTISENSE_STRAND_INCLUDED,V.NUCLEOTIDE_SEQUENCES,V.PHOSPHOROTHIOATE_LINKAGE_FLAGS,V.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 Q extends Error{constructor(e){super(e),this.name="PatternNameExistsError"}}class J extends Error{constructor(e){super(e),this.name="PatternExistsError"}}var X=n(4802),Z=n.n(X);class ee{constructor(e){this.th=e,this.otherUsersPatternNameToHash=new Map,this.currentUserPatternNameToHash=new Map}static async getInstance(){const e=await br.getTranslationHelper(),t=new ee(e);t.currentUserName=await t.fetchCurrentUserName(),t.currentUserId=await t.fetchCurrentUserId();const n=t.fetchPatterns();return await t.initializePatternMaps(n),t}getCurrentUserPatternNames(){return Array.from(this.currentUserPatternNameToHash.keys()).sort(((e,t)=>e.toLowerCase().localeCompare(t.toLowerCase())))}getOtherUsersPatternNames(){return Array.from(this.otherUsersPatternNameToHash.keys()).sort(((e,t)=>e.toLowerCase().localeCompare(t.toLowerCase())))}getCurrentUserName(){return this.currentUserName}validatePatternNameUniqueness(e){if(this.currentUserPatternNameToHash.has(e))throw new Q(`Pattern with name ${e} already exists`)}validatePatternUniqueness(e){if(Array.from(this.currentUserPatternNameToHash.values()).concat(Array.from(this.otherUsersPatternNameToHash.values())).includes(e))throw new J(e)}getPatternHash(e,t){const n=t?this.currentUserPatternNameToHash.get(e):this.otherUsersPatternNameToHash.get(e);if(void 0===n)throw new Error(`Pattern with name ${e} not found`);return n}async getPatternRecordByHash(e){if(null===e||""===e)return null;try{const t=o.userSettings.getValue(U,e,!1)??"null";return JSON.parse(t)}catch{return null}}async getPatternConfig(e){if(""===e||null===e)return null;const t=await this.getPatternRecordByHash(e);return null===t?null:t[q.PATTERN_CONFIG]}getDefaultPatternRecord(){const e=Y;return e[q.AUTHOR_ID]=this.currentUserId,e}getDefaultPatternConfig(){return Y[q.PATTERN_CONFIG]}getAuthorCategoryByHash(e){if(this.isCurrentUserPattern(e))return this.getCurrentUserAuthorshipCategory();if(this.isOtherUserPattern(e))return this.getOtherUsersAuthorshipCategory();throw new Error(`Pattern with hash ${e} not found`)}isCurrentUserPattern(e){return Array.from(this.currentUserPatternNameToHash.values()).includes(e)}isOtherUserPattern(e){return Array.from(this.otherUsersPatternNameToHash.values()).includes(e)}getPatternNameByHash(e){const t=[this.currentUserPatternNameToHash,this.otherUsersPatternNameToHash];for(const n of t)for(const[t,o]of n.entries())if(o===e)return t;throw new Error(`Pattern with hash ${e} not found`)}getHashOfPatternToBeLoadedAfterDeletion(){const e=this.getCurrentUserPatternNames()[0];if(!e)throw new Error("Cannot load pattern after deletion, as there are no patterns left");const t=this.currentUserPatternNameToHash.get(e);if(void 0===t)throw new Error(`Pattern with name ${e} not found`);return t}async getRecordFromPattern(e){return{[q.PATTERN_CONFIG]:e,[q.AUTHOR_ID]:await o.dapi.users.current().then((e=>e.id))}}getHash(e){const t=z.reduce(((t,n)=>(t[n]=e[n],t)),{});return Z().sha1(t)}async savePatternToUserStorage(e){const t=e.getPatternConfig();try{const n=this.getHash(t);this.validatePatternUniqueness(n);const r=t[j.PATTERN_NAME];this.validatePatternNameUniqueness(r);const i=await this.getRecordFromPattern(t),s=(new Date).toISOString();i[q.DATE]={[W.CREATE]:s,[W.MODIFY]:s};const a=JSON.stringify(i);o.userSettings.add(U,n,a,!1),this.currentUserPatternNameToHash.set(r,n),e.selectAuthor(this.getCurrentUserAuthorshipCategory()),e.updatePatternList(),e.requestPatternLoad(n),e.updateUrlState(n)}catch(e){if(e instanceof Q||e instanceof J)throw e;console.error("Error while saving pattern to user storage",e)}}async overwriteExistingPatternInUserStorage(e){const t=e.getPatternConfig(),n=t[j.PATTERN_NAME],r=this.currentUserPatternNameToHash.get(n);if(void 0===r)throw new Error("Old hash is undefined");const i=this.getHash(t),s=await this.getRecordFromPattern(t),a=(new Date).toISOString();s[q.DATE]={[W.MODIFY]:a};const l=o.userSettings.getValue(U,r,!1)??"null",c=JSON.parse(l);void 0!==c[q.DATE]&&null!=c[q.DATE][W.CREATE]&&(s[q.DATE][W.CREATE]=c[q.DATE][W.CREATE]);const u=JSON.stringify(s);o.userSettings.add(U,i,u,!1),o.userSettings.delete(U,r,!1),this.currentUserPatternNameToHash.set(n,i),e.requestPatternLoad(i),e.updateUrlState(i)}async deletePattern(e,t){const n=this.currentUserPatternNameToHash.get(e);if(e===this.getDefaultPatternName())return void o.shell.warning("Cannot delete default pattern");if(void 0===n)throw new Error(`Pattern with name ${e} not found`);o.userSettings.delete(U,n,!1),this.currentUserPatternNameToHash.delete(e),t.updatePatternList();const r=this.getHashOfPatternToBeLoadedAfterDeletion();t.requestPatternLoad(r)}fetchDefaultNucleobase(){return this.fetchAvailableNucleotideBases()[0]}fetchAvailableNucleotideBases(){const e=Object.keys(this.th.jsonData.patternAppData)[0];return Object.keys(this.th.jsonData.patternAppData[e])}async fetchCurrentUserName(){return(await o.dapi.users.current()).friendlyName}async fetchCurrentUserId(){return(await o.dapi.users.current()).id}fetchPatterns(){return o.userSettings.get(U,!1)??{}}async initializePatternMaps(e){if(!this.currentUserId)throw new Error("Current user ID is not set");const t=new Map;for(const[n,o]of Object.entries(e))await this.extractDataFromRecordToMaps(n,o,t);this.setDefaultPattern()}setDefaultPattern(){const e=Y[q.PATTERN_CONFIG];this.currentUserPatternNameToHash.set(e[j.PATTERN_NAME],"")}async extractDataFromRecordToMaps(e,t,n){const r=JSON.parse(t),i=r[q.PATTERN_CONFIG].patternName,s=r[q.AUTHOR_ID];if(this.isCurrentUserId(s))this.currentUserPatternNameToHash.set(i,e);else{if(!n.has(s)){let e="<UNKNOWN_USER>";try{e=(await o.dapi.users.find(s)).friendlyName}catch(e){}n.set(s,e)}const t=i+` (created by ${n.get(s)})`;this.otherUsersPatternNameToHash.set(t,e)}}getDefaultPatternName(){return Y[q.PATTERN_CONFIG][j.PATTERN_NAME]}getCurrentUserAuthorshipCategory(){return this.currentUserName+" (me)"}getOtherUsersAuthorshipCategory(){return"Other users"}isCurrentUserId(e){return e===this.currentUserId}}const te=rxjs,ne=rxjs.operators;function oe(e){return e.endsWith("(o)")}function re(e){const t=Object.values(e).flat().reduce(((e,t)=>(e[t]=(e[t]||0)+1,e)),{});return Object.entries(t).reduce(((e,t)=>e[1]>t[1]?e:t),["",0])[0]}var ie;function se(e){const t=Array.from(new Set(e));return Array.from(t).sort(((e,t)=>e.toLowerCase().localeCompare(t.toLowerCase())))}!function(e){e.getTruncatedStrandData=function(e,t,n){return{nucleotides:e.slice(0,n),ptoFlags:t.slice(0,n+1)}},e.getExtendedStrandData=function(e,t,n,o){const r=n-e.length,i=e.concat(new Array(n-e.length).fill(o)),s=0===e.length?n+1:r;return{nucleotides:i,ptoFlags:t.concat(new Array(s).fill(!0))}}}(ie||(ie={}));var ae=n(2543),le=n.n(ae);class ce{constructor(e,t){this.dataManager=e,this._patternListUpdated$=new te.Subject,this._patternLoadRequested$=new te.Subject,this._patternLoaded$=new te.Subject,this._uniqueNucleotides$=new te.BehaviorSubject([]),this._patternDeletionRequested$=new te.Subject,this._tableSelection$=new te.BehaviorSubject(null),this._svgSaveRequested$=new te.Subject,this._loadPatternInNewTabRequested$=new te.Subject,this._urlStateUpdated$=new te.Subject,this._patternHasUnsavedChanges$=new te.BehaviorSubject(!1),this._selectedStrandColumn=new te.BehaviorSubject(null),this._selectedIdColumn=new te.BehaviorSubject(null),this.initializeAuthorSelection(t),this.initializePatternState(t),this._lastLoadedPatternConfig=new te.BehaviorSubject(le().cloneDeep(this.getPatternConfig())),this.setupSubscriptions()}setupSubscriptions(){this._nucleotideSequences$.subscribe((()=>{this.updateUniqueNucleotides(),this.updateSequenceBase()})),this._isAntisenseStrandActive$.subscribe((e=>{e||G.forEach((e=>{this.updateTerminusModification("AS",e,"")}))})),this.patternStateChanged$.pipe((0,ne.debounceTime)(20)).subscribe((()=>{const e=this._lastLoadedPatternConfig.getValue(),t=this.getPatternConfig(),n=!le().isEqual(t,e);this._patternHasUnsavedChanges$.next(n)}))}updateUniqueNucleotides(){const e=(t=this._nucleotideSequences$.getValue(),se(Object.values(t).flat()));var t;this._uniqueNucleotides$.next(e)}updateSequenceBase(){const e=re(this._nucleotideSequences$.getValue());this._sequenceBase$.next(e)}get nucleotideSequencesChanged$(){return this._nucleotideSequences$.asObservable()}initializeAuthorSelection(e){const t=e[q.AUTHOR_ID];this.dataManager.isCurrentUserId(t)?this._patternAuthorSelection$=new te.BehaviorSubject(this.dataManager.getCurrentUserAuthorshipCategory()):this._patternAuthorSelection$=new te.BehaviorSubject(this.dataManager.getOtherUsersAuthorshipCategory())}initializePatternState(e){const t=e[q.PATTERN_CONFIG];this._patternName$=new te.BehaviorSubject(t[j.PATTERN_NAME]),this._isAntisenseStrandActive$=new te.BehaviorSubject(t[V.IS_ANTISENSE_STRAND_INCLUDED]),this._nucleotideSequences$=new te.BehaviorSubject(t[V.NUCLEOTIDE_SEQUENCES]),this._phosphorothioateLinkageFlags=new te.BehaviorSubject(t[V.PHOSPHOROTHIOATE_LINKAGE_FLAGS]),this._terminalModifications=new te.BehaviorSubject(t[V.STRAND_TERMINUS_MODIFICATIONS]),this._comment$=new te.BehaviorSubject(t[j.PATTERN_COMMENT]),this._modificationsWithNumericLabels$=new te.BehaviorSubject(t[j.NUCLEOTIDES_WITH_NUMERIC_LABELS]),this._sequenceBase$=new te.BehaviorSubject(re(t[V.NUCLEOTIDE_SEQUENCES]))}getPatternName(){return this._patternName$.getValue()}updatePatternName(e){this._patternName$.next(e)}get antisenseStrandToggled$(){return this._isAntisenseStrandActive$.asObservable()}isAntisenseStrandActive(){return this._isAntisenseStrandActive$.getValue()}toggleAntisenseStrand(e){e?this.updateStrandLength("AS",this.getNucleotideSequences().SS.length):this.updateStrandLength("AS",0),this._isAntisenseStrandActive$.next(e)}getNucleotideSequences(){return this._nucleotideSequences$.getValue()}updateNucleotideSequences(e){this._nucleotideSequences$.next(e)}updateStrandLength(e,t){const n=this.getNucleotideSequences()[e];if(n.length===t)return;const o=this.getPhosphorothioateLinkageFlags()[e];if(0===t)return void this.setNewStrandData([],[],e);if(n.length>t){const{nucleotides:r,ptoFlags:i}=ie.getTruncatedStrandData(n,o,t);return void this.setNewStrandData(r,i,e)}const r=this.getSequenceBase(),{nucleotides:i,ptoFlags:s}=ie.getExtendedStrandData(n,o,t,r);this.setNewStrandData(i,s,e)}setNewStrandData(e,t,n){this.updateNucleotideSequences({...this.getNucleotideSequences(),[n]:e}),this.updatePhosphorothioateLinkageFlags({...this.getPhosphorothioateLinkageFlags(),[n]:t})}getPhosphorothioateLinkageFlags(){return this._phosphorothioateLinkageFlags.getValue()}updatePhosphorothioateLinkageFlags(e){this._phosphorothioateLinkageFlags.next(e)}get phosphorothioateLingeFlagsChanged$(){return this._phosphorothioateLinkageFlags.asObservable()}getTerminalModifications(){return this._terminalModifications.getValue()}updateTerminalModifications(e){this._terminalModifications.next(e)}updateTerminusModification(e,t,n){const o=this.getTerminalModifications();o[e][t]=n,this.updateTerminalModifications(o)}terminalModificationsUpdated$(){return this._terminalModifications.asObservable()}getComment(){return this._comment$.getValue()}updateComment(e){this._comment$.next(e)}getModificationsWithNumericLabels(){return this._modificationsWithNumericLabels$.getValue()}updateModificationsWithNumericLabels(e){const t=function(e){return se(e).filter((e=>!oe(e)))}(e);this._modificationsWithNumericLabels$.next(t)}get patternLoadRequested$(){return this._patternLoadRequested$.asObservable()}requestPatternLoad(e){this._patternLoadRequested$.next(e)}get patternListUpdated$(){return this._patternListUpdated$.asObservable()}updatePatternList(){this._patternListUpdated$.next()}get tableSelectionChanged$(){return this._tableSelection$.asObservable()}selectTable(e){this._tableSelection$.next(e)}getTableSelection(){return this._tableSelection$.getValue()}requestPatternDeletion(e){this._patternDeletionRequested$.next(e)}get patternDeletionRequested$(){return this._patternDeletionRequested$.asObservable()}replaceSequenceBase(e){const t=this._nucleotideSequences$.getValue(),n={};k.forEach((o=>{n[o]=t[o].map((()=>e))})),this._nucleotideSequences$.next(n);const o=this._modificationsWithNumericLabels$.getValue();o.includes(e)||this.updateModificationsWithNumericLabels(o.concat(e))}get patternStateChanged$(){return te.merge(this._patternName$.pipe((0,ne.debounceTime)(300),(0,ne.map)((()=>{}))),this._isAntisenseStrandActive$,this._nucleotideSequences$,this._phosphorothioateLinkageFlags,this._terminalModifications,this._comment$.pipe((0,ne.debounceTime)(300)),this._modificationsWithNumericLabels$)}getSequenceBase(){return this._sequenceBase$.getValue()}uniqueNucleotidesChanged$(){return this.patternStateChanged$.pipe((0,ne.switchMap)((()=>this._uniqueNucleotides$)))}getUniqueNucleotides(){return this._uniqueNucleotides$.getValue()}get svgSaveRequested$(){return this._svgSaveRequested$.asObservable()}requestSvgSave(){this._svgSaveRequested$.next()}setAllPTOLinkages(e){const t=this.getPhosphorothioateLinkageFlags();k.forEach((n=>{t[n]=t[n].map((()=>e))})),this.updatePhosphorothioateLinkageFlags(t)}setPatternConfig(e){this._patternName$.next(e[j.PATTERN_NAME]),this._isAntisenseStrandActive$.next(e[V.IS_ANTISENSE_STRAND_INCLUDED]),this._nucleotideSequences$.next(e[V.NUCLEOTIDE_SEQUENCES]),this._phosphorothioateLinkageFlags.next(e[V.PHOSPHOROTHIOATE_LINKAGE_FLAGS]),this._terminalModifications.next(e[V.STRAND_TERMINUS_MODIFICATIONS]),this._comment$.next(e[j.PATTERN_COMMENT]),this._modificationsWithNumericLabels$.next(e[j.NUCLEOTIDES_WITH_NUMERIC_LABELS])}setLastLoadedPatternConfig(e){this._lastLoadedPatternConfig.next(le().cloneDeep(e))}getPatternConfig(){return{[j.PATTERN_NAME]:this.getPatternName(),[V.IS_ANTISENSE_STRAND_INCLUDED]:this.isAntisenseStrandActive(),[V.NUCLEOTIDE_SEQUENCES]:this.getNucleotideSequences(),[V.PHOSPHOROTHIOATE_LINKAGE_FLAGS]:this.getPhosphorothioateLinkageFlags(),[V.STRAND_TERMINUS_MODIFICATIONS]:this.getTerminalModifications(),[j.PATTERN_COMMENT]:this.getComment(),[j.NUCLEOTIDES_WITH_NUMERIC_LABELS]:this.getModificationsWithNumericLabels()}}setPhosphorothioateLinkageFlag(e,t,n){const o=this.getPhosphorothioateLinkageFlags();o[e][t]=n,this.updatePhosphorothioateLinkageFlags(o)}setNucleotide(e,t,n){const o=this.getNucleotideSequences();o[e][t]=n;const r=this.getModificationsWithNumericLabels();this.updateModificationsWithNumericLabels(r.concat(n)),this.updateNucleotideSequences(o)}get strandsUpdated$(){return te.merge(this._isAntisenseStrandActive$.asObservable().pipe((0,ne.map)((()=>{}))),this._nucleotideSequences$.asObservable().pipe((0,ne.map)((()=>{}))),this._patternLoaded$.asObservable().pipe((0,ne.map)((()=>{})))).pipe((0,ne.debounceTime)(10))}get strandsLinkagesAndTerminalsUpdated$(){return te.merge(this.strandsUpdated$,this._phosphorothioateLinkageFlags.asObservable().pipe((0,ne.map)((()=>{}))),this._terminalModifications.asObservable().pipe((0,ne.map)((()=>{}))))}updateControlsUponPatternLoaded(e){this._patternLoaded$.next(e)}get patternLoaded$(){return this._patternLoaded$.asObservable()}get userSelection$(){return this._patternAuthorSelection$.asObservable().pipe((0,ne.skip)(1))}selectAuthor(e){if("string"!=typeof e)throw new Error("Selected user must be defined");this._patternAuthorSelection$.next(e)}getSelectedAuthor(){return this._patternAuthorSelection$.getValue()}get loadPatternInNewTabRequested$(){return this._loadPatternInNewTabRequested$.asObservable()}requestLoadPatternInNewTab(e){this._loadPatternInNewTabRequested$.next(e)}updateUrlState(e){this._urlStateUpdated$.next(e)}get urlStateUpdated$(){return this._urlStateUpdated$.asObservable()}get patternHasUnsavedChanges$(){return this._patternHasUnsavedChanges$.asObservable()}selectStrandColumn(e,t){this._selectedStrandColumn.next({...this._selectedStrandColumn.getValue(),[e]:t})}getSelectedStrandColumn(e){const t=this._selectedStrandColumn.getValue();return t?t[e]:null}selectIdColumn(e){this._selectedIdColumn.next(e)}getSelectedIdColumn(){return this._selectedIdColumn.getValue()}get updateSvgContainer$(){return this.patternStateChanged$.pipe((0,ne.debounceTime)(100))}}const ue="pattern";class he{constructor(){this.urlSearchParams=new URLSearchParams(window.location.search)}subscribeToObservables(e){e.urlStateUpdated$.subscribe((e=>this.setPatternURL(e))),e.loadPatternInNewTabRequested$.subscribe((e=>{const t=`${window.location.origin}${window.location.pathname}?${ue}=${e}`;window.open(t,"_blank")})),window.addEventListener("popstate",(()=>{this.urlSearchParams=new URLSearchParams(window.location.search);const t=this.getPatternHash();null!==t&&e.requestPatternLoad(t)}))}getPatternHash(){return this.urlSearchParams.get(ue)}setPatternURL(e){null!==e&&""!==e?(this.urlSearchParams.set(ue,e),window.history.pushState({},"",`${window.location.pathname}?${this.urlSearchParams}`)):this.clearPatternURL()}clearPatternURL(){this.urlSearchParams.delete(ue),window.history.pushState({},"",`${window.location.pathname}`)}}var de=n(5072),pe=n.n(de),me=n(7825),fe=n.n(me),ge=n(7659),ye=n.n(ge),be=n(5056),ve=n.n(be),Ce=n(540),xe=n.n(Ce),we=n(1113),Ae=n.n(we),Te=n(9252),Ee={};Ee.styleTagTransform=Ae(),Ee.setAttributes=ve(),Ee.insert=ye().bind(null,"head"),Ee.domAPI=fe(),Ee.insertStyleElement=xe(),pe()(Te.A,Ee),Te.A&&Te.A.locals&&Te.A.locals;class Se{constructor(e){this.eventBus=e,this.columnControlsContainer=P.div([]),this.eventBus.tableSelectionChanged$.subscribe((()=>this.handleTableChoice())),this.refreshColumnControls()}getColumnControlsContainer(){return this.columnControlsContainer}get selectedTable(){return this.eventBus.getTableSelection()}handleTableChoice(){this.refreshColumnControls()}refreshColumnControls(){L()(this.columnControlsContainer).empty(),L()(this.columnControlsContainer).append(this.constructColumnControls())}constructColumnControls(){const e=this.createStrandColumnInput(),t=e.SS,n=e.AS;this.eventBus.antisenseStrandToggled$.subscribe((e=>{L()(n).toggle(e)}));const o=this.createIdColumnInput();return[t,n,o]}createStrandColumnInput(){const e=this.selectedTable?this.selectedTable.columns.names().sort(((e,t)=>e.localeCompare(t))):[];return Object.fromEntries(k.map((t=>{const n=P.input.choice(`${H[t]} column`,{value:e[0],items:e,onValueChanged:e=>this.eventBus.selectStrandColumn(t,e)});return this.eventBus.selectStrandColumn(t,e[0]),[t,n.root]})))}createIdColumnInput(){const e=this.selectedTable?this.selectedTable.columns.names():[],t=P.input.choice("ID column",{value:e[0],items:e,onValueChanged:e=>this.eventBus.selectIdColumn(e)});return this.eventBus.selectIdColumn(e[0]),t.root}}class Ne{constructor(e){this.eventBus=e,this.availableTables=[],this.tableInputContainer=P.div([]),this.subscribeToTableEvents(),this.refreshTableInput()}getTableInputContainer(){return this.tableInputContainer}subscribeToTableEvents(){o.events.onTableAdded.subscribe((e=>this.handleTableAdded(e))),o.events.onTableRemoved.subscribe((e=>this.handleTableRemoved(e))),this.eventBus.tableSelectionChanged$.subscribe((()=>this.handleTableChoice()))}getTableFromEventData(e){if(!e&&e.args&&e.args.dataFrame instanceof r.DataFrame)throw new Error("EventData does not contain a dataframe",e);return e.args.dataFrame}handleTableAdded(e){const t=this.getTableFromEventData(e);this.availableTables.some((e=>e.name===t.name))||(this.availableTables.push(t),this.eventBus.selectTable(t),this.refreshTableInput())}handleTableRemoved(e){const t=this.getTableFromEventData(e);this.availableTables=this.availableTables.filter((e=>e.name!==t.name));const n=this.availableTables[0];this.eventBus.selectTable(n||null),this.refreshTableInput()}refreshTableInput(){const e=this.createTableInput();L()(this.tableInputContainer).empty(),this.tableInputContainer.append(e.root)}createTableInput(){const e=this.eventBus.getTableSelection();return P.input.table("Tables",{value:e,items:this.availableTables,onValueChanged:e=>{null!==e&&this.eventBus.selectTable(e)}})}handleTableChoice(){const e=this.eventBus.getTableSelection();e&&(this.isTableDisplayed(e)||this.displayTable(e))}isTableDisplayed(e){return o.shell.tableNames.includes(e.name)}displayTable(e){const t=o.shell.v;o.shell.addTableView(e),o.shell.v=t}}function Ie(e,t,n,o){const r=function(e,t,n){const o=new Array(e.length+t.filter((e=>e)).length+G.length);o[0]=n["5'"],o[o.length-1]=n["3'"];let r=1;return t[0]&&(o[r]="ps",r++),e.forEach(((e,n)=>{o[n+r]=e,t[n+1]&&(o[n+r+1]="ps",r++)})),o}(e.split("").map(((e,n)=>{const o=function(e,t,n){const o=Object.keys(n.patternAppData)[0],r=n.patternAppData[o][t].substitution;return e.replace(/([AGCTU])/,r)}(e,t[n],br.jsonData);return o})),n,o);return r.join("")}class Me{constructor(e){this.eventBus=e,this.tableInputManager=new Ne(e),this.columnInputManager=new Se(e)}createControls(){const e=P.h1("Bulk convert"),t=this.tableInputManager.getTableInputContainer(),n=this.columnInputManager.getColumnControlsContainer(),o=P.bigButton("Convert",(()=>this.processConvertButtonClick()));return[e,t,n,P.buttonsInput([o])]}processConvertButtonClick(){!function(e){const t=e.getTableSelection();if(!t)return void o.shell.warning("Please select a table");const n=k.filter((t=>!("AS"===t&&!e.isAntisenseStrandActive()))).map((t=>({strand:t,column:e.getSelectedStrandColumn(t)}))).filter((e=>e.column));if(0===n.length)return void o.shell.warning("Select a sense strand column");const r=e.getSelectedIdColumn();if(!r)throw new Error("No ID column selected");t.getCol(r);const i=n.map((e=>({strand:e.strand,column:t.getCol(e.column)})));!function(e,t){const n=t.getNucleotideSequences();return e.every((e=>{const t=n[e.strand].length;return e.column.toList().every((e=>e.length===t))}))}(i,e)?o.shell.warning("Some strands in the table input do not match pattern length"):i.forEach((n=>{const o=n.column,r=n.strand,i=e.getNucleotideSequences()[r],s=e.getTerminalModifications()[r],a=e.getPhosphorothioateLinkageFlags()[r],l=`${e.getPatternName()}(${o.name})`;t.columns.addNewString(l).init((e=>Ie(o.get(e),i,a,s)))}))}(this.eventBus)}}class Pe{constructor(e,t,n){this.eventBus=e,this.initialPatternConfig=t,this.subscriptions=n}create(){return P.divV([P.h1("PTO"),P.divH([this.createAllPtoActivationInput().root,...this.createFirstPtoInputs().map((e=>e.root))],{style:{gap:"12px"}})])}areAllPtoLinkagesSet(e){return k.map((t=>e[t].filter((e=>e)).length)).reduce(((e,t)=>e+t),0)===k.map((e=>this.initialPatternConfig.nucleotideSequences[e].length)).reduce(((e,t)=>e+t),0)+k.filter((t=>e[t].length)).length}createAllPtoActivationInput(){const e=this.initialPatternConfig.phosphorothioateLinkageFlags,t=this.areAllPtoLinkagesSet(e),n=P.input.bool("All PTO",{value:t});n.onInput.subscribe((()=>{const e=n.value;this.eventBus.setAllPTOLinkages(e)}));const o=this.eventBus.phosphorothioateLingeFlagsChanged$.subscribe((()=>{const e=this.eventBus.getPatternConfig().phosphorothioateLinkageFlags,t=this.areAllPtoLinkagesSet(e);n.value=t}));return this.subscriptions.add(o),this.addStyleToPtoInput(n),P.tooltip.bind(n.captionLabel,"Activate all phosphothioates"),n}addStyleToPtoInput(e){const t=e.captionLabel;t.classList.add("ui-label-right"),Object.assign(t.style,{textAlign:"left",maxWidth:"100px",minWidth:"40px",width:"auto"})}createFirstPtoInputs(){return k.map((e=>{if(!this.eventBus.isAntisenseStrandActive()&&"AS"===e)return;const t=this.isFirstPtoActive(e),n=P.input.bool(`First ${e} PTO`,{value:t});n.onInput.subscribe((()=>{const t=n.value;this.eventBus.setPhosphorothioateLinkageFlag(e,0,t)}));const o=this.eventBus.phosphorothioateLingeFlagsChanged$.subscribe((t=>{const o=t[e][0];n.value=o}));return this.subscriptions.add(o),this.addStyleToPtoInput(n),P.tooltip.bind(n.captionLabel,`Activate first phosphothioate in ${e}`),n})).filter((e=>void 0!==e))}isFirstPtoActive(e){return this.initialPatternConfig.phosphorothioateLinkageFlags[e][0]}}class _e{constructor(e,t,n){this.eventBus=e,this.dataManager=t,this.subscriptions=n;const o=this.eventBus.nucleotideSequencesChanged$.subscribe((()=>{this.displayedInputLabels=this.computeDisplayedInputLabels()}));this.subscriptions.add(o)}create(){const e=k.map((e=>this.constructControlsPanel(e)));return P.divH(e,{style:{gap:"24px"}})}constructControlsPanel(e){if(!this.eventBus.isAntisenseStrandActive()&&"AS"===e)return P.div([]);const t=this.constructHeader(),n=this.createControls(e);return P.block([P.h1(`${H[e]}`),t,n],{style:{paddingTop:"12px"}})}constructHeader(){return P.divH([P.div([P.divText("#")],{style:{width:"20px"}}),P.block75([P.divText("Modification")]),P.div([P.divText("PTO")])])}createControls(e){const t=this.createNucleobaseInputs(e),n=this.createLabelDivs(e),o=this.createPTOFlagInputs(e);return P.div(t.map(((e,t)=>P.divH([n[t],P.block75([e.root]),o[t].root],{style:{alignItems:"center"}}))))}createNucleobaseInputs(e){const t=this.dataManager.fetchAvailableNucleotideBases().sort(((e,t)=>e.toLowerCase().localeCompare(t.toLowerCase())));return this.eventBus.getNucleotideSequences()[e].map(((n,o)=>{const r=P.input.choice("",{value:n,items:t});return r.onInput.subscribe((()=>{const t=r.value;this.eventBus.setNucleotide(e,o,t)})),r}))}createPTOFlagInputs(e){return this.eventBus.getPhosphorothioateLinkageFlags()[e].slice(1).map(((t,n)=>{const o=P.input.bool("",{value:t});o.onInput.subscribe((()=>{const t=o.value;this.eventBus.setPhosphorothioateLinkageFlag(e,n+1,t)}));const r=this.eventBus.phosphorothioateLingeFlagsChanged$.subscribe((t=>{const r=t[e][n+1];o.value=r}));return this.subscriptions.add(r),o}))}computeDisplayedInputLabels(){const e=this.eventBus.getNucleotideSequences(),t=new Map;return k.forEach((n=>{let o=1;const r=e[n].map((e=>{if(oe(e))return"";const t=String(o);return o++,t}));t.set(n,r)})),t}createLabelDivs(e){const t=this.createLabels(e).map((e=>P.div([e],{style:{width:"20px"}}))),n=this.eventBus.nucleotideSequencesChanged$.subscribe((()=>{this.createLabels(e).forEach(((e,n)=>{L()(t[n]).empty(),L()(t[n]).append(e)}))}));return this.subscriptions.add(n),t}createLabels(e){return this.eventBus.getNucleotideSequences()[e].map(((t,n)=>{const o=this.displayedInputLabels.get(e)[n];return P.label(o)}))}}class Le{constructor(){this.rxjsSubscriptions=[],this.dgSubscriptions=[]}add(e){e instanceof te.Subscription?this.rxjsSubscriptions.push(e):this.dgSubscriptions.push(e)}unsubscribeAll(){for(const e of[this.rxjsSubscriptions,this.dgSubscriptions])e.forEach((e=>e.unsubscribe())),e.length=0}}class Oe{constructor(e,t){this.eventBus=e,this.dataManager=t,this.subscriptions=new Le}static open(e,t){Oe.isDialogOpen||(Oe.instance||(Oe.instance=new Oe(e,t)),Oe.instance.openDialog())}openDialog(){this.initialPatternConfig=le().cloneDeep(this.eventBus.getPatternConfig()),Oe.isDialogOpen=!0,this.createDialog().show()}createDialog(){const e=P.divV([]);this.subscriptions.add(this.eventBus.strandsUpdated$.subscribe((()=>this.onStrandsUpdated(e))));const t=P.dialog("Edit strands").add(e).onOK((()=>{})).onCancel((()=>this.resetToInitialState()));return this.subscriptions.add(t.onClose.subscribe((()=>{Oe.isDialogOpen=!1,this.subscriptions.unsubscribeAll()}))),t}onStrandsUpdated(e){const t=new Pe(this.eventBus,this.initialPatternConfig,this.subscriptions).create(),n=new _e(this.eventBus,this.dataManager,this.subscriptions).create();L()(e).empty(),L()(e).append(t,n)}resetToInitialState(){this.eventBus.setPatternConfig(this.initialPatternConfig)}}Oe.isDialogOpen=!1;class Re{constructor(e){this.eventBus=e,this.subscriptions=new Le}static open(e){Re.isDialogOpen||(Re.instance||(Re.instance=new Re(e)),Re.instance.openDialog())}openDialog(){this.initialPatternConfig=le().cloneDeep(this.eventBus.getPatternConfig()),Re.isDialogOpen=!0,this.createDialog().show()}createDialog(){const e=P.divV([]);this.subscriptions.add(this.eventBus.strandsUpdated$.subscribe((()=>this.onStrandsUpdated(e))));const t=P.dialog("Edit terminal modifications").add(e).onOK((()=>{})).onCancel((()=>this.resetToInitialState()));return this.subscriptions.add(t.onClose.subscribe((()=>{Re.isDialogOpen=!1,this.subscriptions.unsubscribeAll()}))),t}onStrandsUpdated(e){const t=new $e(this.eventBus).create();L()(e).empty(),L()(e).append(t)}resetToInitialState(){this.eventBus.setPatternConfig(this.initialPatternConfig)}}Re.isDialogOpen=!1;class $e{constructor(e){this.eventBus=e}create(){const e=k.map((e=>this.constructControlsPanel(e)));return P.divH(e,{style:{gap:"24px"}})}constructControlsPanel(e){if(!this.eventBus.isAntisenseStrandActive()&&"AS"===e)return P.div([]);const t=this.createInputs(e);return P.block([P.h1(`${H[e]}`),t],{style:{paddingTop:"12px"}})}createInputs(e){const t=("SS"===e?[...G].reverse():G).map((t=>this.createInputForTerminus(e,t)));return P.form(t)}createInputForTerminus(e,t){const n=this.eventBus.getTerminalModifications()[e][t],o=P.input.textArea(t,{value:n});return this.applyStylingToInput(o),o.onInput.subscribe((()=>{const n=o.value;null!==n&&this.eventBus.updateTerminusModification(e,t,n)})),o}applyStylingToInput(e){const t=e.root.getElementsByTagName("textarea")[0];L()(t).css("resize","none")}}class De{constructor(e,t){this.eventBus=e,this.dataManager=t}createControls(){const e=this.createAntisenseStrandToggle(),t=this.createStrandLengthInputs(),n=t.SS.root,o=t.AS.root,r=this.createSequenceBaseInput().root,i=this.createPatternCommentInput().root,s=this.createPatternNameInputBlock(),a=this.createEditPatternButton(),l=this.createEditTerminalModificationsButton();return[P.h1("Edit"),e,n,o,r,s,i,P.buttonsInput([l,a])]}createEditPatternButton(){const e=P.button("Edit strands",(()=>Oe.open(this.eventBus,this.dataManager)));return P.tooltip.bind(e,"Edit strand modifications and PTOs"),e}createEditTerminalModificationsButton(){const e=P.button("Edit terminals",(()=>Re.open(this.eventBus)));return P.tooltip.bind(e,"Edit terminal modifications"),L()(e).css("margin-right","20px"),e}createAntisenseStrandToggle(){const e=P.input.toggle(`${H.AS} strand`,{value:this.eventBus.isAntisenseStrandActive()});return e.onInput.subscribe((()=>this.eventBus.toggleAntisenseStrand(e.value))),this.eventBus.patternLoaded$.subscribe((()=>{e.value=this.eventBus.isAntisenseStrandActive()})),e.setTooltip("Toggle antisense strand"),e.root}createStrandLengthInputs(){const e=e=>{const n=this.eventBus.getNucleotideSequences()[e].length,o=P.input.int(`${H[e]} length`,{value:n});return o.onInput.subscribe((()=>t(e,o))),this.eventBus.nucleotideSequencesChanged$.subscribe((()=>{o.value=this.eventBus.getNucleotideSequences()[e].length})),o.setTooltip(`Number of nucleotides in ${e}, including overhangs`),[e,o]},t=(e,t)=>{const n=t.value;null!==n&&(n<=0&&(o.shell.warning("Sequence length must be greater than 0"),t.value=1),n>34&&(o.shell.warning("Sequence length must be less than 35"),t.value=34),this.eventBus.updateStrandLength(e,t.value))},n=Object.fromEntries(k.map((t=>e(t))));return this.eventBus.antisenseStrandToggled$.subscribe((e=>{L()(n.AS.root).toggle(e)})),n}createSequenceBaseInput(){const e=this.dataManager.fetchAvailableNucleotideBases().sort(((e,t)=>e.toLowerCase().localeCompare(t.toLowerCase()))),t=this.dataManager.fetchDefaultNucleobase(),n=P.input.choice("Sequence basis",{value:t,items:e});return n.onInput.subscribe((()=>this.eventBus.replaceSequenceBase(n.value))),this.eventBus.nucleotideSequencesChanged$.subscribe((()=>{n.value=this.eventBus.getSequenceBase()})),n.setTooltip("Most frequent nucleobase in the strands"),n}createPatternCommentInput(){const e=P.input.textArea("Comment",{value:this.eventBus.getComment()});return L()(e.root).addClass("st-pattern-text-input"),e.onInput.subscribe((()=>this.eventBus.updateComment(e.value))),this.eventBus.patternLoaded$.subscribe((()=>{e.value=this.eventBus.getComment()})),e}createPatternNameInputBlock(){const e=P.input.textArea("Pattern name",{value:this.eventBus.getPatternName()});return L()(e.root).addClass("st-pattern-text-input"),e.onInput.subscribe((()=>this.eventBus.updatePatternName(e.value))),this.eventBus.patternLoaded$.subscribe((()=>{e.value=this.eventBus.getPatternName()})),e.setTooltip("Name under which pattern will be saved"),e.root}}class Be{constructor(e,t){this.eventBus=e,this.dataManager=t,this.subscriptions=new Le,this.authorSelectedByUser=!1,this.eventBus.patternLoadRequested$.subscribe((e=>this.handlePatternChoice(e))),this.eventBus.patternDeletionRequested$.subscribe((async e=>{await this.dataManager.deletePattern(e,this.eventBus)}))}async handlePatternChoice(e){let t=await this.dataManager.getPatternConfig(e);null===t&&(t=this.dataManager.getDefaultPatternConfig()),this.eventBus.setPatternConfig(t),this.eventBus.updateControlsUponPatternLoaded(e),this.eventBus.setLastLoadedPatternConfig(t)}isCurrentUserSelected(){return this.eventBus.getSelectedAuthor()!==this.dataManager.getOtherUsersAuthorshipCategory()}createControls(){const e=this.getPatternInputsContainer();return[P.h1("Load"),e]}getPatternInputsContainer(){const e=P.divH(this.createPatternInputs());return this.eventBus.patternListUpdated$.subscribe((()=>{this.subscriptions.unsubscribeAll(),L()(e).empty(),L()(e).append(this.createPatternInputs())})),e}createPatternInputs(){const e=this.createAuthorChoiceInput(),t=this.createPatternChoiceInputContainer(),n=this.createDeletePatternButton();return[e.root,t,n]}createPatternChoiceInputContainer(){const e=this.createPatternChoiceInput(),t=P.div([e.root]),n=this.eventBus.userSelection$.subscribe((()=>{L()(t).empty(),L()(t).append(this.createPatternChoiceInput().root)}));return this.subscriptions.add(n),t}createAuthorChoiceInput(){const e=[this.dataManager.getCurrentUserAuthorshipCategory()];this.dataManager.getOtherUsersPatternNames().length>0&&e.push(this.dataManager.getOtherUsersAuthorshipCategory());const t=P.input.choice("Author",{value:this.eventBus.getSelectedAuthor(),items:e});return t.onInput.subscribe((()=>{if(this.authorSelectedByUser=!0,null===t.value)throw new Error("author choice must be non-null");this.eventBus.selectAuthor(t.value)})),this.setAuthorChoiceInputStyle(t),t.setTooltip("Select pattern author"),t}setAuthorChoiceInputStyle(e){L()(e.input).css({"max-width":"100px","min-width":"100px"}),L()(e.root).css({"padding-right":"30px","padding-left":"30px"})}createPatternChoiceInput(){const e=this.isCurrentUserSelected()?this.dataManager.getCurrentUserPatternNames():this.dataManager.getOtherUsersPatternNames();if(this.authorSelectedByUser){const t=this.dataManager.getPatternHash(e[0],this.isCurrentUserSelected());this.eventBus.requestPatternLoad(t),this.eventBus.updateUrlState(t),this.authorSelectedByUser=!1}const t=this.getPatternName(e),n=P.input.choice("Pattern",{value:t,items:e});return n.setTooltip("Select pattern to load"),L()(n.input).css({"max-width":"100px","min-width":"100px"}),this.subscriptions.add(n.onInput.subscribe((()=>{const e=this.dataManager.getPatternHash(n.value,this.isCurrentUserSelected());this.eventBus.requestPatternLoad(e),this.eventBus.updateUrlState(e)}))),this.subscriptions.add(this.eventBus.patternLoaded$.subscribe((()=>{const t=this.eventBus.getPatternName();n.value!==t&&(n.value=this.getPatternName(e))}))),n}getPatternName(e){return e.find((e=>e.split(" (")[0]===this.eventBus.getPatternName()))??e[0]}createDeletePatternButton(){const e=P.button(P.iconFA("trash-alt"),(()=>{this.eventBus.getPatternName()!==this.dataManager.getDefaultPatternName()?this.showDeletePatternDialog():o.shell.warning("Cannot delete example pattern")}));P.tooltip.bind(e,"Delete pattern from user storage");const t=this.eventBus.userSelection$.subscribe((()=>{e.disabled=!this.isCurrentUserSelected()}));return this.subscriptions.add(t),e}showDeletePatternDialog(){const e=P.dialog("Delete pattern"),t=this.eventBus.getPatternName();e.add(P.divText(`Are you sure you want to delete pattern ${t}?`)),e.onOK((()=>this.eventBus.requestPatternDeletion(t))),e.show()}}class Fe{constructor(e,t){this.eventBus=e,this.dataManager=t}getLayout(){const e=new Be(this.eventBus,this.dataManager),t=new De(this.eventBus,this.dataManager),n=new Me(this.eventBus),o=e.createControls(),r=t.createControls(),i=n.createControls(),s=P.div(o);L()(s).css({"padding-bottom":"20px"});const a=P.div([...r,...i],"ui-form"),l=P.div([s,a]);return L()(l).css({padding:"25px"}),P.box(l,{style:{maxWidth:"450px"}})}}var ke=n(9146);class He{constructor(e,t,n){this.svgElementFactory=e,this.config=t,this.yShift=n}shiftElements(e){this.svgElements.forEach((t=>{const n=t.getAttribute("transform")||"",o=`translate(${e.x},${e.y})`;t.setAttribute("transform",`${n} ${o}`)}))}}class Ge{constructor(){}static getInstance(){return Ge.instance||(Ge.instance=new Ge,Ge.instance.canvas=document.createElement("canvas")),Ge.instance}static getTextDimensions(e,t){const n=Ge.getInstance().canvas.getContext("2d");if(!n)throw new Error("Canvas 2D context is not available");return n.font=`${t}px Arial`,{width:1.1*n.measureText(e).width,height:1.1*t}}}function Ue(e){const t=Object.keys(br.jsonData.patternAppData)[0];if(!t)throw new Error(`No format found in '${h}'`);return br.jsonData.patternAppData[t][e].color||""}class Ve extends He{constructor(e,t,n){super(e,t,n);const o=k.filter((e=>t.nucleotideSequences[e].length>0));this.strands=o.map((e=>new je(this.svgElementFactory,t,n,e))),this.terminalModifications=o.map(((e,o)=>new We(this.svgElementFactory,t,n,e,this.strands[o]))),this.labels=o.map(((e,o)=>new qe(this.svgElementFactory,t,n,e,this.terminalModifications[o])))}get svgElements(){return[...this.strands,...this.terminalModifications,...this.labels].map((e=>e.svgElements)).flat()}getContentWidth(){return Math.max(...this.labels.map((e=>e.getContentWidth())))}getContentHeight(){return this.strands.reduce(((e,t)=>e+t.getContentHeight()),0)}}class je extends He{constructor(e,t,n,o){super(e,t,n),this.svgElementFactory=e,this.config=t,this.yShift=n,this.strand=o,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 e=0;return this.config.nucleotideSequences[this.strand].map((t=>oe(t)?null:(e++,e)))}get svgElements(){return this._svgElements}getStrandCircleYShift(){return ze(this.strand,this.yShift)}createStrandCircles(){const e={x:80,y:this.getStrandCircleYShift()};return this.config.nucleotideSequences[this.strand].map(((t,n)=>this.createNucleotideElementGroup(t,n,e))).flat()}createNucleotideElementGroup(e,t,n){return[...this.createNucleotideCircleElements(e,t,n),this.config.nucleotidesWithNumericLabels.includes(e)?this.createNucleotideNumericLabel(t,n):null].filter((e=>null!==e))}createNucleotideCircleElements(e,t,n){const o=Ue(e),r={...n,x:n.x+30*t};return[this.svgElementFactory.createCircleElement(r,15,o),this.createNucleotideLetterLabel(t,n,e)]}getNucleotideCircleCenterPosition(e,t){return{x:t.x+30*e,y:t.y}}createNucleotideLetterLabel(e,t,n){if(!f.AL.includes(n))return null;const o=function(e){return!oe(e)&&f.AL.includes(e)?e:""}(n),r=function(e){const t=Ue(e),n=t.match(/\d+/g)?.map(Number);if(!n||n.length<3)return"#ffffff";const[o,r,i]=n;return.299*o+.587*r+.114*i>186?"#333333":"#ffffff"}(n),i=this.getPositionForNucleotideLabel(e,t);return this.svgElementFactory.createTextElement(o,i,17,r)}getPositionForNucleotideLabel(e,t){const n=this.getNucleotideCircleCenterPosition(e,t),o=Ge.getTextDimensions("A",17);return{x:n.x-o.width/2,y:n.y+o.height/3}}getNumericLabelYShift(e){return"SS"===this.strand?e.y-20:e.y+15+5+15}createNucleotideNumericLabel(e,t){const n=this.nucleotideNumericLabels[e];if(null===n)return null;const o=Ge.getTextDimensions(n.toString(),15).width,r={x:t.x+30*e-o/2,y:this.getNumericLabelYShift(t)};return this.svgElementFactory.createTextElement(n.toString(),r,15,"var(--grey-6)")}createPTOLinkageStars(){const e=this.config.phosphorothioateLinkageFlags[this.strand],t=this.getStrandCircleYShift()+12;return e.map(((e,n)=>{if(!e)return null;const o={x:65+30*n,y:t};return this.svgElementFactory.createStarElement(o,"red")})).filter((e=>null!==e))}getContentWidth(){return 30*this.config.nucleotideSequences[this.strand].length}getContentHeight(){return 62}}class qe extends He{constructor(e,t,n,o,r){super(e,t,n),this.svgElementFactory=e,this.config=t,this.yShift=n,this.strand=o,this.terminalModifications=r,this._svgElements=this.createSVGElements()}createSVGElements(){return[this.createLeftLabel(),this.createRightLabel()]}getLeftLabelWidth(){return 55}getRightLabelWidth(){return 20}createLeftLabel(){const e="SS"===this.strand?"5'":"3'",t=`${this.strand}: ${e} `,n=Ge.getTextDimensions(t,17),o={x:10,y:ze(this.strand,this.yShift)+n.height/3};return this.svgElementFactory.createTextElement(t,o,17,"var(--grey-6)")}createRightLabel(){const e=" "+("SS"===this.strand?"3'":"5'"),t=Ge.getTextDimensions(e,17),n={x:65+this.terminalModifications.getContentWidth()+5,y:ze(this.strand,this.yShift)+t.height/3};return this.svgElementFactory.createTextElement(e,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 We extends He{constructor(e,t,n,o,r){super(e,t,n),this.svgElementFactory=e,this.config=t,this.yShift=n,this.strand=o,this.strandSvgWrapper=r,this._svgElements=this.createSVGElements()}createSVGElements(){return this.createTerminalModifications()}getTerminalModification(e){return this.config.strandTerminusModifications[this.strand][e]}getTerminalModificationTextDimensions(e){const t=this.getTerminalModification(e);return Ge.getTextDimensions(t,17)}getLeftTerminus(){return"SS"===this.strand?"5'":"3'"}createTerminalModification(e){const t=this.getTerminalModification(e),n=this.getTerminalModificationTextDimensions(e),o=e===this.getLeftTerminus(),r={x:o?65:65+this.getTerminalModificationTextDimensions(this.getLeftTerminus()).width+this.strandSvgWrapper.getContentWidth(),y:ze(this.strand,this.yShift)+n.height/3};return o&&this.strandSvgWrapper.shiftElements({x:n.width,y:0}),this.svgElementFactory.createTextElement(t,r,17,"red")}createTerminalModifications(){return("AS"===this.strand?G:Array.from(G).reverse()).map((e=>this.createTerminalModification(e)))}get svgElements(){return this._svgElements}getContentWidth(){return this.strandSvgWrapper.getContentWidth()+G.map((e=>this.getTerminalModificationTextDimensions(e).width)).reduce(((e,t)=>e+t),0)}getContentHeight(){return this.strandSvgWrapper.getContentHeight()}}function ze(e,t){return"SS"===e?t+5+15+15:t+52+10+15}class Ye{constructor(){this.xmlNamespace="http://www.w3.org/2000/svg"}createElement(e){return document.createElementNS(this.xmlNamespace,e)}setAttributes(e,t){Object.entries(t).forEach((([t,n])=>{e.setAttribute(t,String(n))}))}createCanvas(e,t){const n=this.createElement("svg");return this.setAttributes(n,{id:"mySvg",width:e,height:t}),n}createCircleElement(e,t,n){const o=this.createElement("circle");return this.setAttributes(o,{cx:e.x,cy:e.y,r:t,fill:n}),o}createTextElement(e,t,n,o){const r=this.createElement("text");return this.setAttributes(r,{x:t.x,y:t.y,"font-size":n,"font-weight":"normal","font-family":"Arial",fill:o}),r.textContent=e,r}createStarElement(e,t){const n=this.createElement("polygon"),o=this.computeStarVertexCoordinates(e).map((e=>e.join(","))).join(" ");return this.setAttributes(n,{points:o,fill:t}),n}computeStarVertexCoordinates(e){const t=Math.PI/5,n=-t/2;return Array.from({length:10},((o,r)=>{const i=r%2==0?6:3,s=r*t+n;return[e.x+Math.cos(s)*i,e.y+Math.sin(s)*i]}))}createRectangleElement(e,t,n,o){const r=this.createElement("rect");return this.setAttributes(r,{x:e.x,y:e.y,width:t,height:n,fill:o}),r}}class Ke extends He{constructor(e,t,n){super(e,t,n),this.svgElementFactory=e,this.config=t,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 Ge.getTextDimensions(this.titleText,17).width}getContentHeight(){return Ge.getTextDimensions(this.titleText,17).height}getTitleText(){const e=`${this.config.nucleotideSequences.SS.length}`,t=this.config.isAntisenseStrandIncluded?`/${this.config.nucleotideSequences.AS.length}`:"";return`${this.config.patternName} for ${e}${t}-mer`}}class Qe extends He{constructor(e,t,n){super(e,t,n),this._svgElements=[];const{elements:o,width:r}=this.createLegendItems();this._svgElements=o,this.width=r}isPhosphorothioatePresent(){return Object.values(this.config.phosphorothioateLinkageFlags).flat().some((e=>e))}getModificationTypesList(){return[...new Set(Object.values(this.config.nucleotideSequences).flat().sort(((e,t)=>e.toLowerCase().localeCompare(t.toLowerCase()))))]}get svgElements(){return this._svgElements}createLegendItem(e,t){const n={x:t,y:this.yShift-6},o=e.includes("linkage")?this.svgElementFactory.createStarElement(n,"red"):this.svgElementFactory.createCircleElement(n,6,Ue(e));t+=12;const r={y:this.yShift,x:t};return{elements:[o,this.svgElementFactory.createTextElement(e,r,15,"var(--grey-6)")],width:12+Ge.getTextDimensions(e,15).width}}createLegendItems(){let e=10;const t=[],n=t=>e+=t+15;if(this.isPhosphorothioatePresent()){const{elements:o,width:r}=this.createLegendItem("PTO linkage",e);n(r),t.push(o)}return this.getModificationTypesList().forEach((o=>{const{elements:r,width:i}=this.createLegendItem(o,e);n(i),t.push(r)})),{elements:t.flat(),width:e}}getContentHeight(){return 20}getContentWidth(){return this.width}}class Je{constructor(e){this.svgElementFactory=new Ye;const t=le().cloneDeep(e);let n=10;this.title=new Ke(this.svgElementFactory,t,n),n+=this.title.getContentHeight(),this.strands=new Ve(this.svgElementFactory,t,n),n+=this.strands.getContentHeight()+10,this.legend=new Qe(this.svgElementFactory,t,n)}renderPattern(){const e=this.getGlobalWidth(),t=this.getGlobalHeight(),n=this.svgElementFactory.createCanvas(e,t),o=[this.title,this.strands,this.legend].map((e=>e.svgElements)).flat();return n.append(...o),n}getGlobalWidth(){const e=[this.title,this.strands,this.legend];return Math.max(...e.map((e=>e.getContentWidth())))}getGlobalHeight(){return[this.title,this.strands,this.legend].reduce(((e,t)=>e+t.getContentHeight()),10)}}class Xe{constructor(e){this.eventBus=e,this.svgDisplayDiv=P.div([]),e.updateSvgContainer$.subscribe((()=>this.updateSvgContainer())),e.svgSaveRequested$.subscribe((()=>this.saveSvgAsPng()))}static createSvgDiv(e){return new Xe(e).svgDisplayDiv}updateSvgContainer(){$(this.svgDisplayDiv).empty();const e=this.eventBus.getPatternConfig();this.svgElement=this.createSvg(e),this.svgDisplayDiv.append(this.svgElement)}createSvg(e){return new Je(e).renderPattern()}saveSvgAsPng(){const e=this.eventBus.getPatternName();ke.saveSvgAsPng(this.svgElement,e,{backgroundColor:"white"})}}class Ze{constructor(e){this.eventBus=e,this.togglesContainer=P.div([]),this.eventBus.uniqueNucleotidesChanged$().subscribe((()=>{this.updateContainer()}))}getContainer(){return this.togglesContainer}updateContainer(){L()(this.togglesContainer).empty(),L()(this.togglesContainer).append(this.createInputs())}createInputs(){const e=this.eventBus.getUniqueNucleotides().filter((e=>!oe(e))).map((e=>this.createSingleInput(e)));return e.sort(((e,t)=>e.captionLabel.textContent.localeCompare(t.captionLabel.textContent))),P.divH(e.map((e=>e.root)))}createSingleInput(e){const t=this.eventBus.getModificationsWithNumericLabels().includes(e),n=P.input.bool(e,{value:t,onValueChanged:t=>this.handleNumericLabelToggle(e,t)});return L()(n.root).css("padding-right","20px"),n.setTooltip(`Show numeric labels for ${e}`),n}handleNumericLabelToggle(e,t){const n=this.eventBus.getModificationsWithNumericLabels();if(n.includes(e)===t)return;const o=t?n.concat(e):n.filter((t=>t!==e));this.eventBus.updateModificationsWithNumericLabels(o)}}class et{constructor(e,t){this.eventBus=e,this.dataManager=t,this.subscriptions=new Le}createContainer(){return P.div([P.h1("Translation example"),this.createTranslationExamples()],{style:{paddingTop:"20px"}})}createTranslationExamples(){const e=P.divH([...this.getExampleElements()],"ui-form");return this.eventBus.antisenseStrandToggled$.subscribe((()=>{this.subscriptions.unsubscribeAll(),L()(e).empty(),L()(e).append(this.getExampleElements())})),e}getExampleElements(){return k.map((e=>new tt(e,this.eventBus,this.subscriptions).create()))}}class tt{constructor(e,t,n){this.strand=e,this.eventBus=t,this.subscriptions=n}create(){return this.eventBus.isAntisenseStrandActive()||"AS"!==this.strand?(this.inputExample=this.createInputExample(),this.outputExample=this.createOutputExample(this.inputExample.value),this.subscribeToEvents(),P.block50([P.h2(H[this.strand]),this.inputExample.root,this.outputExample.root],{style:{paddingRight:"20px"}})):P.div([])}subscribeToEvents(){const e=this.eventBus.strandsLinkagesAndTerminalsUpdated$.subscribe((()=>{const e=this.generateExampleSequence();this.inputExample.value=e,this.outputExample.value=this.computeOutputValue(e)}));"AS"===this.strand&&this.subscriptions.add(e)}createInputExample(){const e=this.createTextInputForExamples(),t=this.generateExampleSequence();return e.value=t,e.setTooltip(`Example raw nucleotides input for ${H[this.strand]}`),e}generateExampleSequence(){return this.eventBus.getNucleotideSequences()[this.strand].map(((e,t)=>f.AL[t%f.AL.length])).join("")}createOutputExample(e){const t=this.createTextInputForExamples();return t.value=this.computeOutputValue(e),t.setTooltip(`Pattern applied to the example input for ${H[this.strand]}`),t}computeOutputValue(e){const t=this.eventBus.getNucleotideSequences()[this.strand],n=this.eventBus.getTerminalModifications()[this.strand];return Ie(e,t,this.eventBus.getPhosphorothioateLinkageFlags()[this.strand],n)}createTextInputForExamples(){const e=P.input.textArea("",{value:""});return this.applyStylingToInput(e),e}applyStylingToInput(e){const t=e.root.getElementsByTagName("textarea")[0];t.setAttribute("readonly","true"),L()(t).css("resize","none"),L()(e.root).css("opacity","75%")}}class nt{constructor(e,t){this.eventBus=e,this.dataManager=t,this.svgDisplay=Xe.createSvgDiv(e)}getLayout(){const e=new Ze(this.eventBus).getContainer(),t=this.generateDownloadControls(),n=new et(this.eventBus,this.dataManager).createContainer();return P.panel([this.svgDisplay,e,t,n],{style:{overflowX:"scroll",padding:"12px 24px"}})}generateDownloadControls(){return P.divH([this.createSavePatternButton(),this.createDownloadPngButton(),this.createShareLinkButton(),this.createInfoButton()],{style:{gap:"12px",marginTop:"12px"}})}createDownloadPngButton(){const e=P.button("Get PNG",(()=>this.eventBus.requestSvgSave()));return P.tooltip.bind(e,"Download pattern as PNG"),e}createInfoButton(){const e=P.button(P.iconFA("info-circle"),(()=>this.openInfoDialog()));return this.eventBus.patternHasUnsavedChanges$.subscribe((t=>{e.disabled=t})),P.tooltip.bind(e,"View pattern metadata"),e}async openInfoDialog(){let e=this.dataManager.getCurrentUserName(),t=this.dataManager.getDefaultPatternName(),n=K,r=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[q.AUTHOR_ID];if(e=(await o.dapi.users.find(i)).friendlyName,t=s[q.PATTERN_CONFIG][j.PATTERN_NAME],void 0!==s[q.DATE]){const e=s[q.DATE][W.CREATE];void 0!==e&&(n=e);const t=s[q.DATE][W.MODIFY];void 0!==t&&(r=t)}}}const s=P.divV([P.divText(`Pattern Name: ${t}`),P.divText(`Author: ${e}`),P.divText(`Created: ${rt(new Date(n))}`),P.divText(`Modified: ${rt(new Date(r))}`)]);o.shell.info(s)}createShareLinkButton(){const e=P.button(P.iconFA("link"),(()=>navigator.clipboard.writeText(window.location.href).then((()=>o.shell.info("Link to pattern copied to clipboard")))));return this.eventBus.patternHasUnsavedChanges$.subscribe((t=>{e.disabled=t})),P.tooltip.bind(e,"Share pattern link"),e}createSavePatternButton(){const e=P.button("Save",(()=>this.processSaveButtonClick()));return this.eventBus.patternHasUnsavedChanges$.subscribe((t=>{e.disabled=!t})),P.tooltip.bind(e,"Save pattern to user storage"),e}processSaveButtonClick(){const e=this.eventBus.getPatternName();e!==this.dataManager.getDefaultPatternName()?""!==e?this.dataManager.savePatternToUserStorage(this.eventBus).then((()=>{o.shell.info(`Pattern ${e} saved`)})).catch((e=>this.handleErrorWhileSavingPattern(e))):o.shell.warning("Insert pattern name"):o.shell.warning("Cannot save default pattern")}handleErrorWhileSavingPattern(e){e instanceof Q?new ot(this.eventBus,this.dataManager).show():e instanceof J?o.shell.warning(P.div([P.divText("Pattern already exists"),P.button("Load",(()=>{const t=e.message;this.eventBus.requestLoadPatternInNewTab(t)}))])):console.error("Error while saving pattern",e)}}class ot{constructor(e,t){this.eventBus=e,this.dataManager=t}show(){const e=this.eventBus.getPatternName(),t=P.dialog(`Pattern "${e}" already exists`);t.add(P.divText(`Pattern "${e}" already exists. Do you want to overwrite it?`)),t.show(),t.onOK((()=>this.processOverwriteNamesakePattern()))}processOverwriteNamesakePattern(){const e=this.eventBus.getPatternName();this.dataManager.overwriteExistingPatternInUserStorage(this.eventBus).then((()=>{o.shell.info(`Pattern ${e} overwritten`)})).catch((e=>{console.error("Error while overwriting pattern in user storage",e),o.shell.error("Error while overwriting pattern")}))}}function rt(e){return e.toLocaleString().split(":").slice(0,-1).join(":")}class it extends F{constructor(e){super("Oligo Pattern"),this.th=e}getContent(){return async function(){const e=await ee.getInstance(),t=new he,n=await async function(e,t){const n=t.getPatternHash();if(!n)return t.clearPatternURL(),e.getDefaultPatternRecord();let o=await e.getPatternRecordByHash(n);return o||(t.clearPatternURL(),o=e.getDefaultPatternRecord()),o}(e,t),o=new ce(e,n);t.subscribeToObservables(o);const r=new Fe(o,e).getLayout(),i=new nt(o,e).getLayout();return P.splitH([r,i],{},!0)}()}}var st=n(8507),at={};function lt(e){var t;return"string"==typeof e||e instanceof String?e:("object"==typeof e||e instanceof Object)&&"$thrownJsError"in e?lt(e.$thrownJsError):e instanceof Error?null!==(t=e.stack)&&void 0!==t?t:e.message:e.toString()}at.styleTagTransform=Ae(),at.setAttributes=ve(),at.insert=ye().bind(null,"head"),at.domAPI=fe(),at.insertStyleElement=xe(),pe()(st.A,at),st.A&&st.A.locals&&st.A.locals;var ct,ut=n(2074),ht={};ht.styleTagTransform=Ae(),ht.setAttributes=ve(),ht.insert=ye().bind(null,"head"),ht.domAPI=fe(),ht.insertStyleElement=xe(),pe()(ut.A,ht),ut.A&&ut.A.locals&&ut.A.locals;class dt{constructor(e,t,n=!0){this.textInputBase=e,this.painter=t,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=P.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 e=this.painter(this.textInputBase.value);this.highlights.innerHTML="",e.forEach((e=>this.highlights.appendChild(e)))}}!function(e){e.TYPE="V2000",e[e.NUM_OF_HEADER_LINES=3]="NUM_OF_HEADER_LINES",e[e.NUM_OF_COUNTS_DIGITS=3]="NUM_OF_COUNTS_DIGITS",e[e.ATOM_TYPE_COL=4]="ATOM_TYPE_COL",e[e.FIRST_BONDED_ATOM_COL=1]="FIRST_BONDED_ATOM_COL",e[e.BOND_TYPE_COL=3]="BOND_TYPE_COL",e[e.RGP_SHIFT=8]="RGP_SHIFT",e[e.MAX_ATOM_COUNT=999]="MAX_ATOM_COUNT",e.RGP_LINE_START="M RGP",e.ATOM_ALIAS_LINE_START="A ",e.END="M END"}(ct||(ct={}));class pt{constructor(e){this.init(e)}init(e){this.fileContent=e.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 e;return null!==(e=this.xyzAtomCoordinates)&&void 0!==e||(this.xyzAtomCoordinates=this.parseAtomCoordinates()),this.xyzAtomCoordinates.x}get y(){var e;return null!==(e=this.xyzAtomCoordinates)&&void 0!==e||(this.xyzAtomCoordinates=this.parseAtomCoordinates()),this.xyzAtomCoordinates.y}get z(){var e;return null!==(e=this.xyzAtomCoordinates)&&void 0!==e||(this.xyzAtomCoordinates=this.parseAtomCoordinates()),this.xyzAtomCoordinates.z}get atomTypes(){var e;return null!==(e=this._atomTypes)&&void 0!==e||(this._atomTypes=this.parseAtomTypes()),this._atomTypes}get pairsOfBondedAtoms(){var e;return null!==(e=this._pairsOfBondedAtoms)&&void 0!==e||(this._pairsOfBondedAtoms=this.parseBondedAtomPairs()),this._pairsOfBondedAtoms}get bondTypes(){var e;return null!==(e=this._bondTypes)&&void 0!==e||(this._bondTypes=this.parseBondTypes()),this._bondTypes}setAtomAndBondCounts(){const{atomCount:e,bondCount:t}=this.parseAtomAndBondCounts();this._atomCount=e,this._bondCount=t}getNextColumnIdx(e){for(;!this.isWhitespace(e);)++e;for(;this.isWhitespace(e);)++e;return e}shiftIdxToSpecifiedColumn(e,t){let n=e;const o=this.isWhitespace(n)?t:t-1;for(let e=0;e<o;e++)n=this.getNextColumnIdx(n);return n}parseAtomTypes(){const e=this.atomCount,t=new Array(e);let n=this.getAtomBlockIdx();for(let o=0;o<e;o++)n=this.shiftIdxToAtomType(n),t[o]=this.parseAtomType(n),n=this.getNextLineIdx(n);return t}parseAtomCoordinates(){const e=new Float32Array(this.atomCount),t=new Float32Array(this.atomCount),n=new Float32Array(this.atomCount);let o=this.getAtomBlockIdx();for(let r=0;r<this.atomCount;r++){o=this.shiftIdxToXColumn(o);for(const i of[e,t,n])i[r]=this.parseFloatValue(o),o=this.getNextColumnIdx(o);o=this.getNextLineIdx(o)}return{x:e,y:t,z:n}}parseBondedAtomPairs(){const e=new Array(this.bondCount);let t=this.getBondBlockIdx();for(let n=0;n<this.bondCount;n++){t=this.shiftIdxToBondedAtomsPair(t);const o=new Uint16Array(2);o[0]=this.parseIntValue(t),t=this.getNextColumnIdx(t),o[1]=this.parseIntValue(t),e[n]=o,t=this.getNextLineIdx(t)}return e}parseBondTypes(){const e=this.bondCount,t=new Uint16Array(e);let n=this.getBondBlockIdx();for(let o=0;o<e;o++)n=this.shiftIdxToBondType(n),t[o]=this.parseIntValue(n),n=this.getNextLineIdx(n);return t}isWhitespace(e){const t=this.fileContent[e];return" "===t||"\t"===t}getNextLineIdx(e){return"\n"!==this.fileContent[e]?this.fileContent.indexOf("\n",e)+1:e+1}parseFloatValue(e){return this.parseNumericValue(parseFloat,e)}parseIntValue(e){return this.parseNumericValue(parseInt,e)}parseNumericValue(e,t){let n=t+1;for(;!this.isWhitespace(n);)++n;return e(this.fileContent.substring(t,n))}}class mt extends pt{constructor(e){super(e),this.init(e)}init(e){super.init(e)}parseAtomType(e){let t=e,n=t;return this.isQuote(t)?(n=this.getNextIdenticalChar(t),t++):n=this.fileContent.indexOf(" ",n),this.fileContent.substring(t,n)}isQuote(e){const t=this.fileContent[e].charCodeAt(0);return 39===t||34===t}getNextIdenticalChar(e){const t=this.fileContent[e];return t?this.fileContent.indexOf(t,e+1):-1}isQuery(){return this.isQueryOrFragment(((e,t)=>{return 39===e||34===e||76===e&&!((n=this.fileContent.charCodeAt(t+1))>64&&n<91||n>96&&n<123);var n}))}isFragment(){return this.isQueryOrFragment((e=>82===e||42===e))}isQueryOrFragment(e){const t=this.atomCount;let n=this.getAtomBlockIdx();for(let o=0;o<t;o++){if(n=this.shiftIdxToAtomType(n),e(this.fileContent.charCodeAt(n),n))return!0;n=this.getNextLineIdx(n)}return!1}}class ft extends mt{constructor(e){super(e)}getAtomLines(){const e=this.getAtomBlockIdx(),t=this.getBondBlockIdx();return this.fileContent.substring(e,t).split("\n").slice(0,this.atomCount)}getBondLines(){const e=this.getBondBlockIdx();return this.fileContent.substring(e).split("\n").slice(0,this.bondCount)}getRGroupIdToAtomicIdxMap(){const e=new Map,t=this.fileContent.split("\n");t.filter((e=>e.startsWith(ct.RGP_LINE_START))).forEach((t=>{const n=this.getAtomIdxToRgpIdxList(t);for(const[t,o]of n){if(e.has(t))throw new Error(`R group ${t} is already in the map`);e.set(t,o)}}));const n=t.map(((e,t)=>{if(e.startsWith(ct.ATOM_ALIAS_LINE_START))return t})).filter((e=>void 0!==e)),o=n.map((e=>t[e])),r=n.map((e=>t[e+1]));o.forEach(((t,n)=>{const o=parseInt(t.split(/\s+/)[1])-1,i=parseInt(r[n].substring(1));if(e.has(i))throw new Error(`R group ${i} is already in the map`);e.set(i,o)}));const i=this.getRGroupAtomicIndices().filter((t=>!Array.from(e.values()).includes(t)));if(0!==i.length)throw new Error(`Unaccounted R group indices: ${i}`);return e}getAtomIdxToRgpIdxList(e){const t=e.split(/\s+/).filter((e=>e)).slice(3).map((e=>parseInt(e))),n=new Array(t.length/2);for(let e=0;e<t.length;e+=2)n[e/2]=[t[e+1],t[e]-1];return n}getRGroupAtomicIndices(){return this.atomTypes.map(((e,t)=>{if(e.includes("R#"))return t})).filter((e=>void 0!==e))}static isValidMolfile(e){return-1!==e.indexOf(ct.TYPE)&&-1!==e.indexOf(ct.END)}shiftIdxToAtomType(e){return this.shiftIdxToSpecifiedColumn(e,ct.ATOM_TYPE_COL)}getCountsLineIdx(){let e=0;for(let t=0;t<ct.NUM_OF_HEADER_LINES;++t)e=this.getNextLineIdx(e);return e}getAtomBlockIdx(){let e=this.getCountsLineIdx();return e=this.getNextLineIdx(e),e}shiftIdxToXColumn(e){return this.getNextColumnIdx(e)}shiftIdxToBondedAtomsPair(e){return this.shiftIdxToSpecifiedColumn(e,ct.FIRST_BONDED_ATOM_COL)}shiftIdxToBondType(e){return this.shiftIdxToSpecifiedColumn(e,ct.BOND_TYPE_COL)}getBondBlockIdx(){let e=this.getAtomBlockIdx();for(let t=0;t<this.atomCount;t++)e=this.getNextLineIdx(e);return e}parseAtomAndBondCounts(){let e=this.getCountsLineIdx(),t=e+ct.NUM_OF_COUNTS_DIGITS;const n=parseInt(this.fileContent.substring(e,t));return e=t,t+=ct.NUM_OF_COUNTS_DIGITS,{atomCount:n,bondCount:parseInt(this.fileContent.substring(e,t))}}}class gt extends mt{constructor(e){super(e),this.init(e)}getAtomLines(){const e=this.getAtomBlockIdx(),t=this.getBondBlockIdx();return this.fileContent.substring(e,t).split("\n").slice(0,this.atomCount)}getBondLines(){const e=this.getBondBlockIdx();return this.fileContent.substring(e).split("\n").slice(0,this.bondCount)}getRGroupIdToAtomicIdxMap(){const e=new Map;return this.getAtomLines().forEach(((t,n)=>{const o=t.match(/RGROUPS=\(([\d\s]+)\)/);if(o){const t=o[1].split(/\s+/).map((e=>parseInt(e)));if(t.length>2)throw new Error(`R group data ${t} has more than 2 elements`);const r=t[1];if(e.has(r))throw new Error(`R group ${r} is already in the map`);e.set(r,n)}})),e}shiftIdxToAtomType(e){return this.shiftIdxToSpecifiedColumn(e,4)}getCountsLineIdx(){return this.fileContent.indexOf("M V30 COUNTS ")}getAtomBlockIdx(){let e=this.fileContent.indexOf("M V30 BEGIN ATOM");return e=this.getNextLineIdx(e),e}shiftIdxToXColumn(e){let t=this.shiftIdxToAtomType(e);return this.isQuote(t)?(t=this.getNextIdenticalChar(t),t=this.getNextColumnIdx(t),t):this.shiftIdxToSpecifiedColumn(e,5)}shiftIdxToBondedAtomsPair(e){return this.shiftIdxToSpecifiedColumn(e,5)}shiftIdxToBondType(e){return this.shiftIdxToSpecifiedColumn(e,4)}getBondBlockIdx(){return this.getNextLineIdx(this.fileContent.indexOf("M V30 BEGIN BOND"))}static isValidMolfile(e){return-1!==e.indexOf("V3000")&&-1!==e.indexOf("M END")}parseAtomAndBondCounts(){let e=this.fileContent.indexOf("M V30 COUNTS ")+14,t=this.fileContent.indexOf(" ",e+1);const n=parseInt(this.fileContent.substring(e,t));return e=t+1,t=this.fileContent.indexOf(" ",e+1),{atomCount:n,bondCount:parseInt(this.fileContent.substring(e,t))}}}class yt{constructor(){}static getInstance(e){if(yt.isMolfileV2K(e))return new ft(e);if(yt.isMolfileV3K(e))return new gt(e);throw new Error("Malformed molfile")}static isMolfileV2K(e){return ft.isValidMolfile(e)}static isMolfileV3K(e){return gt.isValidMolfile(e)}}const bt=class extends Error{constructor(e){super(e)}};class vt{constructor(e){this.molblock=e}get molblock(){return this._validMolBlock}set molblock(e){if(""!==e){try{this.validateMolBlock(e)}catch(t){t instanceof bt&&(e="");const n=lt(t);console.error(n)}this._validMolBlock=e}else this._validMolBlock=e}validateMolBlock(e){if(""===e)throw new bt("MoleculeImage: invalid molblock")}async drawMolBlockOnCanvas(e){try{await o.functions.call("Chem:canvasMol",{x:0,y:0,w:e.width,h:e.height,canvas:e,molString:this.molblock,scaffoldMolString:"",options:{normalizeDepiction:!1,straightenDepiction:!1}})}catch(e){const t=lt(e);console.error(t)}}getMoleculeDimensions(){const e=yt.getInstance(this.molblock),t=Math.max(...e.x)-Math.min(...e.x);return{height:Math.max(...e.y)-Math.min(...e.y),width:t}}async zoomIn(){const e=P.dialog({title:"Molecule",showFooter:!1}),t=.7*L()(window).height(),n=this.getMoleculeDimensions(),o=t/n.height,r=t,i=n.width*o,s=P.canvas(i,r);await this.drawMolBlockOnCanvas(s);const a=P.block([s],{style:{overflowX:"scroll"}});e.add(a).showModal(!0),L()(e.root).find(".d4-dialog-contents").removeClass("ui-form"),L()(e.root).find(".d4-dialog-contents").removeClass("ui-panel"),L()(e.root).find(".d4-dialog-contents").addClass("ui-box"),L()(e.root).find(".d4-dialog-contents").css("padding","0")}async drawMolecule(e,t,n){e.innerHTML="";const o=P.canvas(t*window.devicePixelRatio,n*window.devicePixelRatio);o.style.width=`${t}px`,o.style.height=`${n}px`,o.style.cursor="zoom-in",this.drawMolBlockOnCanvas(o),o.addEventListener("click",(async()=>{await this.zoomIn()})),e.append(P.tooltip.bind(o,"Click to zoom"))}}class Ct extends Error{constructor(e,t){super(e,t)}}class xt{constructor(e,t){this.sequence=e,this.codeMap=t}parseSequence(){const e=this.parseRawSequence();return this.addLinkers(e)}addLinkers(e){const t=[];return e.forEach(((n,o)=>{const r=this.getSymbolForCode(n);o>0&&function(e){return br.jsonData.monomersWithPhosphate.left.includes(e)}(r)&&t.pop(),t.push(r);const i=wt(r),s=o===e.length-1,a=o+1<e.length&&wt(this.getSymbolForCode(e[o+1]));i||function(e){return br.jsonData.monomersWithPhosphate.right.includes(e)}(r)||a||s||t.push("p")})),t}getSymbolForCode(e){let t=this.codeMap.get(e);return t??(t=e),t}parseRawSequence(){const e=this.getAllCodesOfFormat(),t=[];let n=0;for(;n<this.sequence.length;){const o=e.find((e=>e===this.sequence.substring(n,n+e.length)));if(void 0===o)throw new Ct(`Unable to match a monomer for the rest of the sequence '${this.sequence.slice(n)}'.`);t.push(o),n+=o.length}return t}getAllCodesOfFormat(){return g(Array.from(this.codeMap.keys()))}}function wt(e){return br.jsonData.monomersWithPhosphate.phosphate.includes(e)}class At{constructor(e,t=!1,n){this.invert=t,this.lib=br.monomerLibWrapper;const o=this.lib.getCodeToSymbolMap(n);this.parser=new xt(e,o)}convert(){const e=this.parser.parseSequence(),t=[];e.forEach(((e,n)=>{const o=this.getMonomerMolfile(e,n);t.push(o)}));let n=this.getPolymerMolfile(t);return this.invert&&(n=this.reflect(n),n=this.invertBondConfiguration(n)),n}invertBondConfiguration(e){const t=e.indexOf("M V30 BEGIN BOND"),n=e.indexOf("M V30 END BOND");let o=e.substring(t,n);return o=o.replace(/(CFG=)([13])/g,((e,t,n)=>"1"===n?`${t}3`:"3"===n?`${t}1`:e)),e.substring(0,t)+o+e.substring(n)}getMonomerMolfile(e,t){const n=this.lib.getMolfileBySymbol(e);return this.lib.isModification(e)?0===t?this.reflect(n):n:this.rotateNucleotidesV3000(n)}getPolymerMolfile(e){return this.linkV3000(e)}reflect(e){const t=this.extractAtomDataV3000(e),n=t.atomIndex.length,o=t.atomIndex.indexOf(1),r=t.atomIndex.indexOf(n),i=(t.x[r]+t.x[o])/2,s=(t.y[r]+t.y[o])/2;for(let e=0;e<n;e++)t.x[e]-=i,t.y[e]-=s;for(let e=0;e<n;e++)t.x[e]=-t.x[e];const a=t.x[o];for(let e=0;e<n;e++)t.x[e]-=a;let l=e.indexOf("M V30 BEGIN ATOM");l=e.indexOf("\n",l);let c=l;for(let o=0;o<n;o++)l=e.indexOf("V30",l)+4,l=e.indexOf(" ",l)+1,l=e.indexOf(" ",l)+1,c=e.indexOf(" ",l)+1,c=e.indexOf(" ",c),l=(e=e.slice(0,l)+t.x[o]+" "+t.y[o]+e.slice(c)).indexOf("\n",l)+1;return e}extractAtomDataV3000(e){const t=this.extractAtomsBondsNumbersV3000(e);let n=e.indexOf("M V30 BEGIN ATOM");n=e.indexOf("\n",n);let o=n;const r=Array(t.natom),i=Array(t.natom),s=Array(t.natom),a=Array(t.natom);for(let l=0;l<t.natom;l++)n=e.indexOf("V30",n)+4,o=e.indexOf(" ",n),r[l]=parseInt(e.substring(n,o)),n=o+1,o=e.indexOf(" ",n),i[l]=e.substring(n,o),n=o+1,o=e.indexOf(" ",n),s[l]=parseFloat(e.substring(n,o)),n=o+1,o=e.indexOf(" ",n),a[l]=parseFloat(e.substring(n,o)),n=e.indexOf("\n",n)+1;return{atomIndex:r,atomType:i,x:s,y:a}}extractAtomsBondsNumbersV3000(e){let t=(e=e.replaceAll("\r","")).indexOf("COUNTS")+7,n=e.indexOf(" ",t);const o=parseInt(e.substring(t,n));return t=n+1,n=e.indexOf(" ",t),{natom:o,nbond:parseInt(e.substring(t,n))}}rotateNucleotidesV3000(e){const t=this.extractAtomDataV3000(e),n=t.atomIndex.length,o=t.atomIndex.indexOf(1),r=t.atomIndex.indexOf(n);n>8&&this.fix5Prime(t,o,r);const i=(t.x[r]+t.x[o])/2,s=(t.y[r]+t.y[o])/2;for(let e=0;e<n;e++)t.x[e]-=i,t.y[e]-=s;let a=0;if(0===t.x[o])a=t.y[o]>t.y[r]?Math.PI/2:3*Math.PI/2;else if(0===t.y[o])a=t.x[o]>t.x[r]?Math.PI:0;else{const e=t.y[o]/t.x[o];a=e>0?t.x[o]>0?Math.PI-Math.atan(e):2*Math.PI-Math.atan(e):t.x[o]>0?-Math.PI-Math.atan(e):Math.atan(e)}const l=Math.cos(a),c=Math.sin(a);for(let e=0;e<n;e++){const n=t.x[e];t.x[e]=n*l-t.y[e]*c,t.y[e]=n*c+t.y[e]*l}const u=t.x[o];for(let e=0;e<n;e++)t.x[e]-=u;let h=e.indexOf("M V30 BEGIN ATOM");h=e.indexOf("\n",h);let d=h;for(let o=0;o<n;o++)h=e.indexOf("V30",h)+4,h=e.indexOf(" ",h)+1,h=e.indexOf(" ",h)+1,d=e.indexOf(" ",h)+1,d=e.indexOf(" ",d),h=(e=e.slice(0,h)+t.x[o]+" "+t.y[o]+e.slice(d)).indexOf("\n",h)+1;return e}linkV3000(e,t=!0){let n="\n Datagrok macromolecule handler\n\n";n+=" 0 0 0 0 0 0 999 V3000\n",n+="M V30 BEGIN CTAB\n";let o="",r="",i="";const s=[];let a=0,l=0,c=0;for(let t=0;t<e.length;t++){const n=e[t].includes("MODIFICATION")&&0===t;let i=0;n&&(i=this.extractAtomDataV3000(e[t]).atomIndex.length),e[t]=e[t].replaceAll("(-\nM V30 ","(").replaceAll("-\nM V30 ","").replaceAll(" )",")");const u=this.extractAtomsBondsNumbersV3000(e[t]),h=this.extractAtomDataV3000(e[t]);let d=e[t].indexOf("M V30 BEGIN ATOM");d=e[t].indexOf("\n",d);let p=d,m=d;for(let o=0;o<u.natom;o++)if(1!==h.atomIndex[o]||0===t){p=e[t].indexOf("V30",p)+4,m=e[t].indexOf(" ",p);let o=0;n?(o=parseInt(e[t].substring(p,m)),1===o?o=i:o===i&&(o=1),o+=a):o=parseInt(e[t].substring(p,m))+a,e[t]=e[t].slice(0,p)+o+e[t].slice(m),p=e[t].indexOf(" ",p)+1,p=e[t].indexOf(" ",p)+1,m=e[t].indexOf(" ",p);const r=c-h.x[0];let s=Math.round(1e4*(parseFloat(e[t].substring(p,m))+r))/1e4;e[t]=e[t].slice(0,p)+s+e[t].slice(m),p=e[t].indexOf(" ",p)+1,m=e[t].indexOf(" ",p),s=Math.round(1e4*parseFloat(e[t].substring(p,m)))/1e4,e[t]=e[t].slice(0,p)+s+e[t].slice(m),p=e[t].indexOf("\n",p)+1}else p=e[t].indexOf("M V30",p)-1,m=e[t].indexOf("\n",p+1),e[t]=e[t].slice(0,p)+e[t].slice(m);const f=e[t].indexOf("M V30 END ATOM");o+=e[t].substring(d+1,f);let g=e[t].indexOf("M V30 BEGIN BOND");g=e[t].indexOf("\n",g),p=g,m=g;for(let o=0;o<u.nbond;o++){p=e[t].indexOf("V30",p)+4,m=e[t].indexOf(" ",p);const o=parseInt(e[t].substring(p,m))+l;e[t]=e[t].slice(0,p)+o+e[t].slice(m),p=e[t].indexOf(" ",p)+1,p=e[t].indexOf(" ",p)+1,m=e[t].indexOf(" ",p);let r=0;n?(r=parseInt(e[t].substring(p,m)),1===r?r=i:r===i&&(r=1),r+=a):r=parseInt(e[t].substring(p,m))+a,e[t]=e[t].slice(0,p)+r+e[t].slice(m),p=e[t].indexOf(" ",p)+1,m=Math.min(e[t].indexOf("\n",p),e[t].indexOf(" ",p)),r=0,n?(r=parseInt(e[t].substring(p,m)),1===r?r=i:r===i&&(r=1),r+=a):r=parseInt(e[t].substring(p,m))+a,e[t]=e[t].slice(0,p)+r+e[t].slice(m),p=e[t].indexOf("\n",p)+1}const y=e[t].indexOf("M V30 END BOND");r+=e[t].substring(g+1,y);let b=e[t].indexOf("M V30 MDLV30/STEABS ATOMS=(");for(;-1!==b;){b+=28;const n=e[t].indexOf(")",b);e[t].substring(b,n).split(" ").slice(1).forEach((e=>{s.push(parseInt(e)+a)})),b=n,b=e[t].indexOf("M V30 MDLV30/STEABS ATOMS=(",b)}a+=u.natom-1,l+=u.nbond,c+=n?Math.max(...h.x):h.x[u.natom-1]-h.x[0]}const u=Math.ceil(s.length/4);i+="M V30 MDLV30/STEABS ATOMS=("+s.length+" -\n";for(let e=0;e<u;e++){i+="M V30 ";const t=e+1===u?s.length-4*(u-1):4;for(let n=0;n<t;n++)i+=n+1===t?e===u-1?s[4*e+n]+")\n":s[4*e+n]+" -\n":s[4*e+n]+" "}return a++,n+="M V30 COUNTS "+a+" "+l+" 0 0 0\n",n+="M V30 BEGIN ATOM\n",n+=o,n+="M V30 END ATOM\n",n+="M V30 BEGIN BOND\n",n+=r,n+="M V30 END BOND\n",t&&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(e,t,n){const o=t+1,r=e.x[o],i=e.y[o],s=e.x[n]-r,a=e.y[n]-i,l=e.x[t]-r,c=e.y[t]-i,u=l*Math.cos(2*Math.PI/3)-c*Math.sin(2*Math.PI/3),h=l*Math.sin(2*Math.PI/3)+c*Math.cos(2*Math.PI/3),d=l-s,p=c-a,m=u-s,f=h-a;Math.sqrt(f*f+m*m)>=Math.sqrt(p*p+d*d)&&(e.x[t]=u+r,e.y[t]=h+i)}}function Tt(e,t=!0){let n="\n Datagrok macromolecule handler\n\n";n+=" 0 0 0 0 0 0 999 V3000\n",n+="M V30 BEGIN CTAB\n";let o="",r="",i="";const s=[];let a=0,l=0,c=0;if(e.antiStrands.length>0)for(let t=0;t<e.antiStrands.length;t++)e.antiStrands[t]=Et(e.antiStrands[t]);let u=!1;const h=e.senseStrands.concat(e.antiStrands);let d=0;for(let t=0;t<h.length;t++){h[t]=h[t].replaceAll("(-\nM V30 ","(").replaceAll("-\nM V30 ","").replaceAll(" )",")");const n=St(h[t]),i=Nt(h[t]);if(t>=e.senseStrands.length?!1===u&&(u=!0,c=0):d=Math.min(d,Math.min(...i.y.filter((e=>e<0)))),u){const e=Math.min(...i.x)-c,t=Math.max(...i.y)+5;for(let t=0;t<i.x.length;t++)i.x[t]-=e;for(let e=0;e<i.y.length;e++)i.y[e]-=t-d}let p=h[t].indexOf("M V30 BEGIN ATOM");p=h[t].indexOf("\n",p);let m=p,f=p;for(let e=0;e<n.natom;e++){m=h[t].indexOf("V30",m)+4,f=h[t].indexOf(" ",m);const n=parseInt(h[t].substring(m,f))+a;h[t]=h[t].slice(0,m)+n+h[t].slice(f),m=h[t].indexOf(" ",m)+1,m=h[t].indexOf(" ",m)+1,f=h[t].indexOf(" ",m);let o=Math.round(1e4*i.x[e])/1e4;h[t]=h[t].slice(0,m)+o+h[t].slice(f),m=h[t].indexOf(" ",m)+1,f=h[t].indexOf(" ",m),o=Math.round(1e4*i.y[e])/1e4,h[t]=h[t].slice(0,m)+o+h[t].slice(f),m=h[t].indexOf("\n",m)+1}const g=h[t].indexOf("M V30 END ATOM");o+=h[t].substring(p+1,g);let y=h[t].indexOf("M V30 BEGIN BOND");y=h[t].indexOf("\n",y),m=y,f=y;for(let e=0;e<n.nbond;e++){m=h[t].indexOf("V30",m)+4,f=h[t].indexOf(" ",m);const e=parseInt(h[t].substring(m,f))+l;h[t]=h[t].slice(0,m)+e+h[t].slice(f),m=h[t].indexOf(" ",m)+1,m=h[t].indexOf(" ",m)+1,f=h[t].indexOf(" ",m);let n=parseInt(h[t].substring(m,f))+a;h[t]=h[t].slice(0,m)+n+h[t].slice(f),m=h[t].indexOf(" ",m)+1,f=Math.min(h[t].indexOf("\n",m),h[t].indexOf(" ",m)),n=parseInt(h[t].substring(m,f))+a,h[t]=h[t].slice(0,m)+n+h[t].slice(f),m=h[t].indexOf("\n",m)+1}const b=h[t].indexOf("M V30 END BOND");r+=h[t].substring(y+1,b);let v=h[t].indexOf("M V30 MDLV30/STEABS ATOMS=(");for(;-1!==v;){v+=28;const e=h[t].indexOf(")",v);h[t].substring(v,e).split(" ").slice(1).forEach((e=>{s.push(parseInt(e)+a)})),v=e,v=h[t].indexOf("M V30 MDLV30/STEABS ATOMS=(",v)}a+=n.natom,l+=n.nbond,c+=Math.max(...i.x)+5}const p=Math.ceil(s.length/4);i+="M V30 MDLV30/STEABS ATOMS=("+s.length+" -\n";for(let e=0;e<p;e++){i+="M V30 ";const t=e+1===p?s.length-4*(p-1):4;for(let n=0;n<t;n++)i+=n+1===t?e===p-1?s[4*e+n]+")\n":s[4*e+n]+" -\n":s[4*e+n]+" "}return n+="M V30 COUNTS "+a+" "+l+" 0 0 0\n",n+="M V30 BEGIN ATOM\n",n+=o,n+="M V30 END ATOM\n",n+="M V30 BEGIN BOND\n",n+=r,n+="M V30 END BOND\n",t&&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 Et(e){const t=Nt(e),n=t.atomIndex.length,o=(Math.max(...t.x)+Math.min(...t.x))/2,r=(Math.max(...t.y)+Math.min(...t.y))/2;for(let e=0;e<n;e++)t.x[e]-=o,t.y[e]-=r;const i=Math.PI,s=Math.cos(i),a=Math.sin(i);for(let e=0;e<n;e++){const n=t.x[e];t.x[e]=n*s-t.y[e]*a,t.y[e]=n*a+t.y[e]*s}const l=Math.max(...t.y);for(let e=0;e<n;e++)t.x[e]+=o,t.y[e]-=l;let c=e.indexOf("M V30 BEGIN ATOM");c=e.indexOf("\n",c);let u=c;for(let o=0;o<n;o++)c=e.indexOf("V30",c)+4,c=e.indexOf(" ",c)+1,c=e.indexOf(" ",c)+1,u=e.indexOf(" ",c)+1,u=e.indexOf(" ",u),c=(e=e.slice(0,c)+t.x[o]+" "+t.y[o]+e.slice(u)).indexOf("\n",c)+1;return e}function St(e){let t=(e=e.replaceAll("\r","")).indexOf("COUNTS")+7,n=e.indexOf(" ",t);const o=parseInt(e.substring(t,n));return t=n+1,n=e.indexOf(" ",t),{natom:o,nbond:parseInt(e.substring(t,n))}}function Nt(e){const t=St(e);let n=e.indexOf("M V30 BEGIN ATOM");n=e.indexOf("\n",n);let o=n;const r=Array(t.natom),i=Array(t.natom),s=Array(t.natom),a=Array(t.natom);for(let l=0;l<t.natom;l++)n=e.indexOf("V30",n)+4,o=e.indexOf(" ",n),r[l]=parseInt(e.substring(n,o)),n=o+1,o=e.indexOf(" ",n),i[l]=e.substring(n,o),n=o+1,o=e.indexOf(" ",n),s[l]=parseFloat(e.substring(n,o)),n=o+1,o=e.indexOf(" ",n),a[l]=parseFloat(e.substring(n,o)),n=e.indexOf("\n",n)+1;return{atomIndex:r,atomType:i,x:s,y:a}}function It(e,t,n){if(""===e)return"";const o=n.createFormatDetector(e).getFormat();if(!o)return"";let r="";try{r=new At(e,t,o).convert()}catch(e){const t=lt(e);console.error(t)}return r}function Mt(e,t,n,o,r){const i=[e,t,n].filter((e=>""!==e.strand));return 1===i.length?It(i[0].strand,i[0].invert,r):Tt({senseStrands:[It(e.strand,e.invert,r)],antiStrands:[It(t.strand,t.invert,r),It(n.strand,n.invert,r)].filter((e=>""!==e))},o)}const Pt=["ss","as","as2"];class _t{constructor(){this.th=br,this.onInput=new te.Subject,this.onInvalidInput=new te.Subject,this.inputBase=Object.fromEntries(Pt.map((e=>{const t=P.input.textArea(e.toUpperCase(),{value:"",onValueChanged:()=>{this.onInput.next(),L()(t.root.getElementsByTagName("div")).css("padding-left","38px")}});return[e,t]}))),this.useChiralInput=P.input.bool("Use chiral",{value:!0}),this.saveAllStrandsInput=P.input.bool("Save as one entity",{value:!0}),P.tooltip.bind(this.saveAllStrandsInput.root,"Save SDF with all strands in one molfile"),this.directionInversion=Object.fromEntries(Pt.map((e=>[e,!1]))),this.moleculeImgDiv=P.block([]),L()(this.moleculeImgDiv).addClass("st-structure-mol-img"),r.debounce(this.onInput,300).subscribe((async()=>{await this.updateMoleculeImg()})),r.debounce(this.onInvalidInput,1e3).subscribe((async()=>{o.shell.warning("Insert Sense strand")}))}async getHtmlDivElement(e){const t=this.getTableInput(e),n=this.getBoolInputsAndButton();await this.updateMoleculeImg();const o=P.divH([this.moleculeImgDiv,n]);L()(o).addClass("st-structure-bottom");const r=P.divV([t,o]);return L()(r).addClass("st-structure-body"),r}getBoolInputsAndButton(){const e=P.buttonsInput([P.bigButton("Save SDF",(()=>{const e=this.getStrandData();!function(e,t,n,r,i,s){const a=[e.strand,t.strand,n.strand].filter((e=>""!==e));if(0===a.length||1===a.length&&""===e.strand)o.shell.warning("Enter SENSE_STRAND and optionally ANTISENSE_STRAND/AS2 to save SDF");else{let l;if(i)l=Mt(e,t,n,r,s)+"\n$$$$\n";else{const h=It(e.strand,e.invert,s),d=It(t.strand,t.invert,s),p=It(n.strand,n.invert,s);l=h+"\n> <Sequence>\nSense Strand\n$$$$\n",d&&(l+=d+"\n> <Sequence>\nAnti Sense\n$$$$\n"),p&&(l+=p+"\n> <Sequence>\nAnti Sense 2\n$$$$\n")}const c=new Date;function u(e){return e>=10?e.toString():"0"+e.toString()}y(`SequenceTranslator-${c.getFullYear()+"-"+u(c.getMonth()+1)+"-"+u(c.getDate())+"_"+u(c.getHours())+"-"+u(c.getMinutes())+"-"+u(c.getSeconds())}.sdf`,encodeURIComponent(l))}}(e.ss,e.as,e.as2,this.useChiralInput.value,this.saveAllStrandsInput.value,this.th)}))]),t=[this.saveAllStrandsInput.root,this.useChiralInput.root,e],n=P.divV(t);for(const e of t)L()(e).addClass("st-structure-bool-button-block");return n}getTableInput(e){const t=Object.fromEntries(Pt.map((t=>[t,new dt(this.inputBase[t],e.highlightInvalidSubsequence)]))),n=Object.fromEntries(Pt.map(((e,t)=>{const n=0===t?"5′ → 3′":"3′ → 5′";return[e,P.input.choice(`${e.toUpperCase()} direction`,{value:n,items:["5′ → 3′","3′ → 5′"]})]})));Pt.forEach(((e,t)=>{n[e].onChanged.subscribe((n=>{let o="3′ → 5′"===n;t>0&&(o=!o),this.directionInversion[e]=o,this.onInput.next()}))}));const o=["Sense Strand","Anti Sense","Anti Sense 2"],r=new Map(Pt.map(((e,t)=>[e,o[t]]))),i=(Object.fromEntries(Pt.map((e=>[e,P.label(r.get(e))]))),Object.fromEntries(Pt.map((e=>{const n=P.icons.delete((()=>{t[e].inputBase.value=""}),"Delete"),o=P.button(n,(()=>{}));return P.tooltip.bind(o,`Clear ${e.toUpperCase()}`),[e,n]})))),s=P.form([],"st-structure-inputs"),a=P.divV([],"st-structure-clear-buttons"),l=P.form([],"st-direction-inputs");for(const e of Pt)s.append(this.inputBase[e].root),a.append(i[e]),l.append(n[e].root);return P.divH([s,a,l])}getStrandData(){return Object.fromEntries(Pt.map((e=>{const t=this.directionInversion[e];return[e,{strand:this.inputBase[e].value.replace(/\s*/g,""),invert:t}]})))}getMolfile(e,t,n){return Mt(e,t,n,this.useChiralInput.value,this.th)}async updateMoleculeImg(){let e="";try{const t=this.getStrandData();Object.values(t).some((e=>""!==e.strand))&&(e=this.getMolfile(t.ss,t.as,t.as2))}catch(e){const t=lt(e);console.error(t)}const t=new vt(e);await t.drawMolecule(this.moleculeImgDiv,650,150)}}class Lt extends F{constructor(e){super("Oligo Structure"),this.th=e,this.layout=new _t}getContent(){return this.layout.getHtmlDivElement(this.th)}}var Ot=n(2003);async function Rt(e){try{const t={overflowX:"scroll"},n=P.div([],{style:t}),r=Nt(e),i=.7*L()(window).height(),s=Math.max(...r.x)-Math.min(...r.x),a=Math.max(...r.y)-Math.min(...r.y),l=i/a,c=l*s,u=l*a,h=P.canvas(c*window.devicePixelRatio,u*window.devicePixelRatio);h.style.width=`${c}px`,h.style.height=`${u}px`,await async function(e,t){await o.functions.call("Chem:canvasMol",{x:0,y:0,w:e.width,h:e.height,canvas:e,molString:t,scaffoldMolString:"",options:{normalizeDepiction:!1,straightenDepiction:!1}})}(h,e),n.appendChild(h),P.dialog("Molecule").add(n).showModal(!0)}catch(e){const t=lt(e);console.error(t)}}class $t{static async view(){const e=br.monomerLibWrapper.getTableForViewer();e.name="Monomer Library";const t=o.shell.addTableView(e);t.grid.props.allowEdit=!1,t.grid.onCellDoubleClick.subscribe((async e=>{const t=e.cell.value;"Molecule"===e.tableColumn?.semType&&await Rt(t)}))}}var Dt=n(3480),Bt=n(5067),Ft=n(5254),kt={};kt.styleTagTransform=Ae(),kt.setAttributes=ve(),kt.insert=ye().bind(null,"head"),kt.domAPI=fe(),kt.insertStyleElement=xe(),pe()(Ft.A,kt),Ft.A&&Ft.A.locals&&Ft.A.locals;const Ht=["Sequence"];class Gt{constructor(e){this.th=e,this.inputFormats=Object.keys(br.jsonData.codesToHelmDict).concat(f.NO.HELM),this.seqHelper=br.seqHelper,this.onInput=new te.Subject,this.moleculeImgDiv=P.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=P.div([]),this.formatChoiceInput=P.input.choice("",{value:f.NO.HELM,items:this.inputFormats,onValueChanged:async(e,t)=>{this.format=e,this.updateTable(),await this.updateMolImg()}}),this.sequenceInputBase=P.input.textArea("",{value:"Afcgacsu",onValueChanged:()=>{this.onInput.next()}}),this.init(),r.debounce(this.onInput,300).subscribe((async()=>{this.init(),this.formatChoiceInput.value=this.format,this.updateTable(),await this.updateMolImg()})),this.eventBus=qt.getInstance()}async getHtmlElement(){const e=this.constructSingleSequenceControls(),t=this.constructBulkTranslationControls(),n=P.box(P.panel([e,t,P.block([P.box(this.moleculeImgDiv)])]));return this.formatChoiceInput.value=this.format,this.updateTable(),await this.updateMolImg(),n}constructBulkTranslationControls(){const e=P.h1("Bulk");P.tooltip.bind(e,"Bulk translation from table input");const t=new Ut(this.eventBus).createUIComponents(),n=P.input.choice("Input format",{value:f.NO.AXOLABS,items:this.inputFormats,onValueChanged:e=>this.eventBus.selectInputFormat(e)}),o=P.input.choice("Output format",{value:Bt.qP,items:(0,Dt.OT)(this.th),onValueChanged:e=>this.eventBus.selectOutputFormat(e)}),r=this.createConvertBulkButton(),i=P.div([...t,n,o,r],"ui-form");return P.block25([e,i])}createConvertBulkButton(){const e=P.bigButton("Convert",(()=>this.processConvertBulkButtonClick()));return P.tooltip.bind(e,"Convert sequences from table input"),L()(e).css({float:"right","margin-top":"20px"}),e}processConvertBulkButtonClick(){const e=this.eventBus.getSelectedTable();if(!e)return void o.shell.warning("No table selected");const t=this.eventBus.getSelectedInputFormat(),n=this.eventBus.getSelectedOutputFormat(),i=this.eventBus.getSelectedColumn("Sequence");if(!i)return void o.shell.warning("No sequence column selected");const s=`${i.name} (${n})`,a=r.Column.fromList(r.TYPE.STRING,s,i.toList().map((e=>(0,Dt.C6)(e,t,n,this.th))));if(n===Bt.qP||n===f.NO.HELM){a.semType=r.SEMTYPE.MACROMOLECULE;const e=n==Bt.qP?Ot.Hi.FASTA:Ot.Hi.HELM;a.meta.units=e;const t=this.seqHelper.getSeqHandler(a);(n==Bt.qP?this.seqHelper.setUnitsToFastaColumn:this.seqHelper.setUnitsToHelmColumn)(t)}e.columns.add(a),o.data.detectSemanticTypes(e),o.shell.v=o.shell.getTableView(e.name)}constructSingleSequenceControls(){const e=new dt(this.sequenceInputBase,(e=>O(e,this.th))),t=P.button("Get SDF",(()=>{this.saveMolfile()}),"Save structure as SDF"),n=P.button("Copy SMILES",(()=>{this.copySmiles()}),"Copy SMILES for the sequence"),o=P.div([this.formatChoiceInput]),r=P.button(P.icons.delete((()=>{e.inputBase.value=""}),"Delete"),(()=>{}));P.tooltip.bind(r,"Clear input");const i={format:o,textInput:e.root,clearBtn:r},s=P.table([i],(e=>[e.format,e.textInput,e.clearBtn]));s.classList.add("st-translator-input-table");const a=P.block([this.outputTableDiv,t,n]);return P.block75([P.h1("Single sequence"),s,a])}saveMolfile(){try{const e=new At(this.sequence,!1,this.formatChoiceInput.value).convert()+"\n$$$$";y(this.sequence+".sdf",encodeURIComponent(e))}catch(e){o.shell.warning("Unable to save SDF: "+e.message)}}copySmiles(){const e=r.chem.convert(this.molfile,r.chem.Notation.MolBlock,r.chem.Notation.Smiles);navigator.clipboard.writeText(e).then((()=>o.shell.info(Bt.n_)))}updateTable(){this.outputTableDiv.innerHTML="";const e=this.format?this.th.createSequenceValidator(this.sequence).getInvalidCodeIndex(this.format):0,t=(0,Dt.bD)(this.sequence,e,this.format,this.th),n=[];for(const e of Object.keys(t)){const r="indexOfFirstInvalidChar"in t?P.divH([]):P.link(t[e],(()=>navigator.clipboard.writeText(t[e]).then((()=>o.shell.info(Bt.n_)))),Bt.U_,"");n.push({format:e,sequence:r})}const r=P.table(n,(e=>[e.format,e.sequence]),["FORMAT","SEQUENCE"]);this.outputTableDiv.append(r),this.outputTableDiv.classList.add("st-translator-output-table")}async updateMolImg(){const e=new vt(this.molfile);await e.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===f.NO.HELM){const e=this.th.createFormatConverter(this.sequence,this.format).convertTo(f.NO.AXOLABS);return new At(e,!1,f.NO.AXOLABS).convert()}return new At(this.sequence,!1,this.format).convert()}}class Ut{constructor(e){this.tableInputManager=new Vt(e),this.columnInputManager=new jt(e)}createUIComponents(){return[this.tableInputManager.getTableInputContainer(),this.columnInputManager.getColumnControlsContainer()]}}class Vt{constructor(e){this.eventBus=e,this.availableTables=[],this.tableInputContainer=P.div([]),this.subscribeToTableEvents(),this.refreshTableInput()}getTableInputContainer(){return this.tableInputContainer}subscribeToTableEvents(){o.events.onTableAdded.subscribe((e=>this.handleTableAdded(e))),o.events.onTableRemoved.subscribe((e=>this.handleTableRemoved(e))),this.eventBus.tableSelected$.subscribe((()=>this.handleTableChoice()))}getTableFromEventData(e){return e.args.dataFrame}handleTableAdded(e){const t=this.getTableFromEventData(e);this.availableTables.some((e=>e.name===t.name))||(this.availableTables.push(t),this.eventBus.selectTable(t),this.refreshTableInput())}handleTableRemoved(e){const t=this.getTableFromEventData(e);this.availableTables=this.availableTables.filter((e=>e.name!==t.name));const n=this.availableTables[0];this.eventBus.selectTable(n||null),this.refreshTableInput()}refreshTableInput(){const e=this.createTableInput();L()(this.tableInputContainer).empty(),this.tableInputContainer.append(e.root)}createTableInput(){const e=this.eventBus.getSelectedTable();return P.input.table("Table",{value:e,items:this.availableTables,onValueChanged:e=>{null!==e&&this.eventBus.selectTable(e)}})}handleTableChoice(){const e=this.eventBus.getSelectedTable();e&&(this.isTableDisplayed(e)||this.displayTable(e))}isTableDisplayed(e){return o.shell.tableNames.includes(e.name)}displayTable(e){const t=o.shell.v;o.shell.addTableView(e),o.shell.v=t}}class jt{constructor(e){this.eventBus=e,this.columnControlsContainer=P.div([]),this.eventBus.tableSelected$.subscribe((()=>this.handleTableChoice())),this.refreshColumnControls()}getColumnControlsContainer(){return this.columnControlsContainer}handleTableChoice(){this.refreshColumnControls()}refreshColumnControls(){const e=this.createColumnInputs();L()(this.columnControlsContainer).empty();const t=e.map((e=>e.root));this.columnControlsContainer.append(...t)}createColumnInputs(){const e=this.eventBus.getSelectedTable(),t=null!==e?e.columns.names().sort(((e,t)=>e.localeCompare(t))):[];return Ht.map((n=>this.createColumnInput(n,t,e)))}createColumnInput(e,t,n){const o=e.toLowerCase(),r=t.find((e=>e.toLowerCase().includes(o)))||t[0];return this.selectColumnIfTableNotNull(n,r,e),P.input.choice(`${e}`,{value:r,items:t,onValueChanged:t=>this.selectColumnIfTableNotNull(n,t,e)})}selectColumnIfTableNotNull(e,t,n){if(null!==e&&t){const o=e.col(t);o&&this.eventBus.selectColumn(n,o)}}}class qt{constructor(){this._tableSelection$=new te.BehaviorSubject(null),this._columnSelection=Object.fromEntries(Ht.map((e=>[e,new te.BehaviorSubject(null)]))),this._inputFormatSelection$=new te.BehaviorSubject(f.NO.AXOLABS),this._outputFormatSelection$=new te.BehaviorSubject(Bt.qP)}static getInstance(){return void 0===qt._instance&&(qt._instance=new qt),qt._instance}get tableSelected$(){return this._tableSelection$.asObservable()}getSelectedTable(){return this._tableSelection$.getValue()}selectTable(e){this._tableSelection$.next(e)}selectColumn(e,t){this._columnSelection[e].next(t)}getSelectedColumn(e){return this._columnSelection[e].getValue()}getSelectedInputFormat(){return this._inputFormatSelection$.getValue()}selectInputFormat(e){this._inputFormatSelection$.next(e)}selectOutputFormat(e){this._outputFormatSelection$.next(e)}getSelectedOutputFormat(){return this._outputFormatSelection$.getValue()}}class Wt extends F{constructor(e){super("Oligo Translator"),this.th=e,this.th=br,this.layout=new Gt(this.th);const t=P.iconFA("book",$t.view,"View monomer library");this.topPanel=[t],this.view.setRibbonPanels([this.topPanel])}getContent(){return this.layout.getHtmlElement()}}class zt extends F{constructor(e,t){super(e),this.content=t}getContent(){return Promise.resolve(this.content)}}class Yt extends B{constructor(e,t){super("Oligo Toolkit"),this.externalViewFactories=e,this.th=t;const n=this.getViewFactories(this.th);this.multiView=new r.MultiView({viewFactories:n})}getViewFactories(e){function t(t){r.View.create();const n=new t(e);return n.initView().catch((e=>console.error(`Failed to initialize ${t.name}: ${e}`))),()=>n.getView()}let n={TRANSLATOR:t(Wt),PATTERN:t(it),STRUCTURE:t(Lt)};return this.externalViewFactories&&(n=Object.assign({},n,this.externalViewFactories)),n}getCurrentPanePath(){let e=this.multiView.tabs.currentPane.name;return e=e.charAt(0).toUpperCase()+e.substring(1).toLowerCase(),`/apps/${br.name}/OligoToolkit/${e}`}setUrl(){this.multiView.path=this.getCurrentPanePath()}async constructView(){return this.multiView.tabs.onTabChanged.subscribe((()=>this.setUrl())),this.setUrl(),this.multiView}}function Kt(e){const t=P.input.textArea("",{value:""});return{coloredInput:new dt(t,e.highlightInvalidSubsequence),codes:e.jsonData.codesToSymbolsDict}}var Qt=n(5733),Jt=n(5613),Xt=n(1536);const Zt=110,en=90;function tn(e,t,n=!1){return P.divH([P.divText(e,{style:{color:"var(--grey-4, #888)",width:"90px",flexShrink:"0"}}),P.divText(t,{style:n?{fontFamily:"ui-monospace, Menlo, monospace",wordBreak:"break-all"}:{}})],{style:{gap:"6px"}})}let nn=null;function on(e,t,n){const o=[t];"sugar"===n?o.push((0,Xt.Jy)(t)):"phosphate"===n&&o.push((0,Xt.$T)(t));const r=e.getPolymerTypes().filter((e=>"RNA"===e||"CHEM"===e)).concat(e.getPolymerTypes().filter((e=>"RNA"!==e&&"CHEM"!==e)));for(const t of o)for(const n of r){const o=e.getMonomer(n,t);if(o&&o.molfile)return o.molfile}return null}function rn(e){let t=e.symbol;return"sugar"===e.kind?t=(0,Xt.Jy)(e.symbol):"phosphate"===e.kind&&(t=(0,Xt.$T)(e.symbol)),`${e.kind}:${t}`}function sn(e){const t=P.div([],{style:{borderRadius:"4px",display:"flex",alignItems:"center",justifyContent:"center",fontSize:"10px",color:"var(--grey-4, #888)",textAlign:"center",padding:"4px"}}),n=P.divText(e,{style:{fontSize:"10px",color:"var(--grey-5, #555)",textAlign:"center",marginTop:"2px",letterSpacing:"0.04em",textTransform:"uppercase",fontWeight:"600"}});return{root:P.divV([t,n],{style:{display:"inline-flex"}}),body:t}}const an=new Map;function ln(e,t,n){try{let r=an.get(n);r||(r=o.chem.drawMolecule(t,Zt,en,!1),an.size>256&&an.clear(),an.set(n,r)),e.innerHTML="",e.appendChild(r)}catch{e.textContent="Render failed"}}const cn="OligoNucleotide";class un extends r.GridCellRenderer{constructor(){super(...arguments),this.modelCache=new Map,this.layoutCache=new Map}get name(){return cn}get cellType(){return cn}get defaultWidth(){return 320}get defaultHeight(){return 64}render(e,t,n,o,r,i,s){const a=i.cell.value;if(!a||!(0,Jt.yO)(a))return e.save(),e.beginPath(),e.rect(t,n,o,r),e.clip(),e.fillStyle="#8b949e",e.font="11px ui-monospace, Menlo, monospace",e.textBaseline="middle",e.textAlign="left",e.fillText(a??"",t+4,n+r/2),void e.restore();const l=this.getOrParse(a),c=(0,Qt.Z4)(e,t,n,o,r,l);this.layoutCache.set(this.cellKey(i),c),this.layoutCache.size>5e3&&this.layoutCache.clear()}onMouseMove(e,t){const n=e.cell.value;if(!n||!(0,Jt.yO)(n))return void P.tooltip.hide();const o=this.getOrParse(n),r=this.layoutCache.get(this.cellKey(e));if(!r)return;const i=e.bounds,s=t.offsetX-i.x,a=t.offsetY-i.y,c=(0,Qt.CB)(s,a,o,r);c?function(e,t,n){const o=function(e){const t=e.monomer,n=P.divText("",{style:{fontWeight:"600",marginBottom:"4px"}}),o=[];if(e.linkage){const t=(0,Xt.bM)(e.linkage.phosphateSymbol);n.textContent=`${t.meta.name} linkage`,o.push(tn("Strand","sense"===e.strand?"Sense":"Antisense"),tn("Between",`pos ${e.position+1} – ${e.position+2}`),tn("HELM symbol",`[${(0,Xt.$T)(e.linkage.phosphateSymbol)}]`,!0))}else if("nucleotide"===t.kind){const r=t,i=(0,Xt.xh)(r.sugar,r.base),s=(0,Xt.bM)(r.phosphate);n.textContent=`${r.base??"?"}${e.position+1} — ${i.meta.name}`,o.push(tn("Strand","sense"===e.strand?"Sense":"Antisense"),tn("Position",String(e.position+1)),tn("Base",r.base??"—"),tn("Sugar",i.meta.name),tn("3'-linkage",s.meta.name),tn("HELM",r.raw,!0))}else{const r=(0,Xt.rK)(t.symbol);n.textContent=r.meta.name,o.push(tn("Strand","sense"===e.strand?"Sense":"Antisense"),tn("Position",String(e.position+1)),tn("Type","Terminal conjugate / linker"),tn("HELM",t.raw,!0))}const r=P.div([],{style:{marginTop:"8px",display:"flex",flexDirection:"row",gap:"6px",flexWrap:"wrap"}});r.dataset.role="struct";const i=P.divText("Loading structures…",{style:{fontSize:"11px",color:"var(--grey-4, #888)"}});return r.appendChild(i),P.divV([n,...o,r],{style:{fontSize:"12px",lineHeight:"1.45",minWidth:"240px",maxWidth:"380px"}})}(e);P.tooltip.show(o,t+14,n+14),async function(e,t){const n=e.querySelector('[data-role="struct"]');if(!n)return;let o,r;if(t.linkage)o=[{label:"Linkage",symbol:t.linkage.phosphateSymbol,kind:"phosphate"}];else if("nucleotide"===t.monomer.kind){const e=t.monomer;o=[{label:"Sugar",symbol:e.sugar,kind:"sugar"}],e.base&&o.push({label:"Base",symbol:e.base,kind:"base"}),e.phosphate&&o.push({label:"3'-linkage",symbol:e.phosphate,kind:"phosphate"})}else o=[{label:"Conjugate",symbol:t.monomer.symbol,kind:"conjugate"}];try{r=await(nn||(nn=(async()=>(await(0,l.pj)()).getMonomerLib())()),nn)}catch{return n.innerHTML="",void n.appendChild(P.divText("Monomer library unavailable",{style:{fontSize:"11px",color:"var(--grey-4, #888)"}}))}n.innerHTML="";for(const e of o){const t=sn(e.label);n.appendChild(t.root);const o=on(r,e.symbol,e.kind);o?ln(t.body,o,rn(e)):t.body.textContent=`Not in HELMCore: ${e.symbol}`}}(o,e)}(c,t.clientX,t.clientY):P.tooltip.hide()}onMouseLeave(e,t){P.tooltip.hide()}getOrParse(e){let t=this.modelCache.get(e);return t||(t=(0,Jt.On)(e),this.modelCache.size>5e3&&this.modelCache.clear(),this.modelCache.set(e,t)),t}cellKey(e){return`${e.tableColumn?.name??e.gridColumn?.name??"?"}::${e.tableRowIndex??-1}`}}function hn(e,t){e.set(t,(e.get(t)??0)+1)}function dn(e,t){const n=[],o=new Map;for(const[t,n]of e.entries()){const e=(0,Xt.xh)(t,null).meta;"RNA"!==e.short&&"DNA"!==e.short&&o.set(e.short,(o.get(e.short)??0)+n)}for(const[e,t]of o.entries())n.push(`${e} ×${t}`);const r=new Map;for(const[e,n]of t.entries()){const t=(0,Xt.bM)(e).meta;"PO"!==t.short&&r.set(t.short,(r.get(t.short)??0)+n)}for(const[e,t]of r.entries())n.push(`${e} ×${t}`);return n.length?n.join(", "):"unmodified"}function pn(e,t){return P.divV([P.divText(e,{style:{fontWeight:"600",marginTop:"8px",marginBottom:"4px",color:"var(--grey-5, #555)",textTransform:"uppercase",fontSize:"10px",letterSpacing:"0.04em"}}),t])}const mn=/^(RNA|DNA|PEPTIDE|CHEM|BLOB)\d+\{/;function fn(e,t){const n=P.div([],{style:{minHeight:"60px"}});return n.appendChild(P.divText("Building structure…",{style:{fontSize:"11px",color:"var(--grey-4, #888)",padding:"4px"}})),(async()=>{try{const t=r.SemanticValue.fromTableCell(e),i=await o.functions.call("Bio:toAtomicLevelPanel",{sequence:t});n.innerHTML="",n.appendChild(i?.root??P.divText("Structure not available",{style:{fontSize:"11px",color:"var(--grey-4, #888)"}}))}catch(e){n.innerHTML="",n.appendChild(P.divText(`${t} render failed: ${e?.message??String(e)}`,{style:{fontSize:"11px",color:"var(--grey-4, #888)"}}))}})(),n}function gn(e){return e.semType=Xt.mU,e.meta.units=Xt.D2,e.setTag("cell.renderer",Xt.mU),e.setTag("quality",Xt.mU),e}function yn(e,t){return e.split("$")[0].replace(/^(RNA|DNA|PEPTIDE|CHEM|BLOB)\d+\{/,`$1${t}{`)}var bn=n(9124),vn=n(9192),Cn=n(8312),xn=n(1991),wn=n.n(xn);const An="object"==typeof performance&&performance&&"function"==typeof performance.now?performance:Date,Tn=new Set,En="object"==typeof process&&process?process:{},Sn=(e,t,n,o)=>{"function"==typeof En.emitWarning?En.emitWarning(e,t,n,o):console.error(`[${n}] ${t}: ${e}`)};let Nn=globalThis.AbortController,In=globalThis.AbortSignal;if(void 0===Nn){In=class{onabort;_onabort=[];reason;aborted=!1;addEventListener(e,t){this._onabort.push(t)}},Nn=class{constructor(){t()}signal=new In;abort(e){if(!this.signal.aborted){this.signal.reason=e,this.signal.aborted=!0;for(const t of this.signal._onabort)t(e);this.signal.onabort?.(e)}}};let e="1"!==En.env?.LRU_CACHE_IGNORE_AC_WARNING;const t=()=>{e&&(e=!1,Sn("AbortController is not defined. If using lru-cache in node 14, load an AbortController polyfill from the `node-abort-controller` package. A minimal polyfill is provided for use by LRUCache.fetch(), but it should not be relied upon in other contexts (eg, passing it to other APIs that use AbortController/AbortSignal might have undesirable effects). 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On{#t;#n;#o;#r;#i;#s;ttl;ttlResolution;ttlAutopurge;updateAgeOnGet;updateAgeOnHas;allowStale;noDisposeOnSet;noUpdateTTL;maxEntrySize;sizeCalculation;noDeleteOnFetchRejection;noDeleteOnStaleGet;allowStaleOnFetchAbort;allowStaleOnFetchRejection;ignoreFetchAbort;#a;#l;#c;#u;#h;#d;#p;#m;#f;#g;#y;#b;#v;#C;#x;#w;#A;static unsafeExposeInternals(e){return{starts:e.#v,ttls:e.#C,sizes:e.#b,keyMap:e.#c,keyList:e.#u,valList:e.#h,next:e.#d,prev:e.#p,get head(){return e.#m},get tail(){return e.#f},free:e.#g,isBackgroundFetch:t=>e.#T(t),backgroundFetch:(t,n,o,r)=>e.#E(t,n,o,r),moveToTail:t=>e.#S(t),indexes:t=>e.#N(t),rindexes:t=>e.#I(t),isStale:t=>e.#M(t)}}get max(){return this.#t}get maxSize(){return this.#n}get calculatedSize(){return this.#l}get size(){return this.#a}get fetchMethod(){return this.#i}get memoMethod(){return this.#s}get dispose(){return this.#o}get disposeAfter(){return 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c=P.divV([s,l.root]);h.appendChild(c),p.set(o,{row:c,vv:l,header:s})}})();const t=(0,io.XB)({cores:n.cores,rGroups:n.rGroupsByNum,mode:n.mode});f.innerText=t.predictedCount>0?`${t.predictedCount.toLocaleString()} molecule${1===t.predictedCount?"":"s"} will be generated`:"",g.setErrors((()=>{const e=[];n.cores.forEach(((t,n)=>{t.error&&e.push(`Core ${n+1}: ${t.error}`)}));const t=[...n.rGroupsByNum.keys()].sort(((e,t)=>e-t));for(const o of t)n.rGroupsByNum.get(o).forEach(((t,n)=>{t.error&&e.push(`R${o} group ${n+1}: ${t.error}`)}));const o=(0,io.XB)({cores:n.cores,rGroups:n.rGroupsByNum,mode:n.mode});for(const t of o.errors)/^Core "/.test(t)||e.push(t);return e})()),w&&(w.disabled=!t.ok),C&&(C.disabled=0===n.cores.length),x&&(x.disabled=0===n.rGroupsByNum.size),(()=>{P.empty(m);const e=(0,io.xD)({cores:n.cores,rGroups:n.rGroupsByNum,mode:n.mode,maxResults:Math.min(io.u8,1e3)},12);0!==e.length?e.forEach(((e,t)=>{const n=[...e.rGroupSmilesByNum.keys()].sort(((e,t)=>e-t)).map((e=>"R"+e)).join(",");m.appendChild(go({smiles:e.smiles,subtitle:`sample ${t+1} · ${n}`}))})):m.appendChild(P.divText("Preview will appear once cores and R-groups are valid.",{style:{color:"var(--grey-4)",padding:"20px 12px",fontSize:"12px"}}))})()},T=(e,t,n,o)=>{const r=[P.divText(e,{style:{fontWeight:"600",fontSize:"12px",color:"var(--grey-6)",alignSelf:"center",minWidth:"60px"}})];if(t){const n=P.button("+ Draw",t);n.style.marginLeft="4px",P.tooltip.bind(n,`${e}: open sketcher`),r.push(n)}if(n){const t=P.button("↓ Import…",n);t.style.marginLeft="4px",P.tooltip.bind(t,`${e}: pick a table + column`),r.push(t)}let i;return o&&(i=P.button("Remove all",o),i.style.marginLeft="4px",P.tooltip.bind(i,`Remove all ${e.toLowerCase()}`),r.push(i)),{root:P.divH(r,{style:{alignItems:"center",justifyContent:"flex-start",gap:"0",margin:"0 0 2px",flex:"0 0 auto"}}),clearBtn:i}},E={display:"flex",flexDirection:"column",minHeight:"150px",padding:"4px 0"},S=T("Cores",(async()=>{const t=await bo(e);t&&(n.cores.push(t),A())}),(async()=>{const t=await Co("cores",e,n.mode===io.PI.Cartesian);t?.cores&&(n.cores.push(...t.cores),A())}),(()=>{n.cores.splice(0,n.cores.length),A()}));C=S.clearBtn;const N=P.divV([S.root,P.div([a,s],{style:{padding:"0"}})],{style:E}),I=T("R-Groups",(async()=>{const t=await vo(e);if(!t)return;const o=n.rGroupsByNum.get(t.rNumber)??[];o.push(t),n.rGroupsByNum.set(t.rNumber,o),A()}),(async()=>{const t=await Co("rgroups",e,n.mode===io.PI.Cartesian);if(t?.rGroups){for(const e of t.rGroups){const t=n.rGroupsByNum.get(e.rNumber)??[];t.push(e),n.rGroupsByNum.set(e.rNumber,t)}A()}}),(()=>{n.rGroupsByNum.clear(),A()}));x=I.clearBtn;const M=P.divV([I.root,h],{style:{display:"flex",flexDirection:"column",maxHeight:"300px",padding:"4px 0"}}),_=P.divV([T("Preview").root,m],{style:{...E,width:"100%",height:"100%",overflowY:"auto",overflowX:"hidden"}}),L=P.divV([N,M],{style:{flex:"0 0 60%",width:"60%",display:"flex",flexDirection:"column",gap:"4px",paddingRight:"8px",borderRight:"1px solid var(--grey-2)"}}),O=P.divV([_],{style:{flex:"0 0 40%",width:"40%",display:"flex",flexDirection:"column",paddingLeft:"8px"}}),R=P.divH([L,O],{style:{width:"100%",alignItems:"stretch",gap:"0"}}),$=P.divH([y.root,f,g.root],{style:{alignItems:"center",gap:"16px",padding:"4px 0"}}),D=P.div([v.root],{style:{padding:"2px 0"}}),B=P.divV([R,$,D],{style:{width:"100%",padding:"4px",display:"flex",flexDirection:"column",gap:"4px"}});return A(),{root:B,state:n,execute:()=>async function(e){const t=r.TaskBarProgressIndicator.create("Enumerating...");try{t.update(10,"Building molecules...");const n=(0,io.jp)({cores:e.cores,rGroups:e.rGroupsByNum,mode:e.mode});if(!n)return void o.shell.warning("Enumeration failed — check validation messages in the dialog.");if(0===n.length)return void o.shell.warning("No molecules produced.");const i=new Set;for(const e of n)for(const t of e.rGroupSmilesByNum.keys())i.add(t);const s=[...i].sort(((e,t)=>e-t)),a=r.Column.fromStrings("Enumerated",n.map((e=>e.smiles)));a.semType=r.SEMTYPE.MOLECULE;const l=r.Column.fromStrings("Core",n.map((e=>e.coreSmiles)));l.semType=r.SEMTYPE.MOLECULE;const c=s.map((e=>r.Column.fromStrings(`R${e}`,n.map((t=>t.rGroupSmilesByNum.get(e)??"")))));for(const e of c)e.semType=r.SEMTYPE.MOLECULE;const u=r.DataFrame.fromColumns([a,l,...c]);u.name="Chem Enumeration",t.update(40,`Canonicalizing ${n.length.toLocaleString()} molecule(s)...`);try{await o.functions.call("Chem:convertNotation",{data:u,molecules:a,targetNotation:r.chem.Notation.Smiles,overwrite:!0,join:!1,kekulize:!1})}catch(e){br.logger.warning(`Canonicalization skipped: ${e?.message??e}`)}t.update(90,"Finalizing..."),await o.data.detectSemanticTypes(u),e.appendToTable?(e.appendToTable.append(u,!0),await e.appendToTable.meta.detectSemanticTypes()):o.shell.addTableView(u)}catch(e){zn(e)}finally{t.close()}}(n),bindActionButton:e=>{w=e,A()}}}var To=n(6197);class Eo extends r.InputBase{constructor(e,t){super(P.input.column(e,t).dart,t?.onValueChanged),this.options=t}setColumnInputTable(e){P.input.setColumnInputTable(this,e,this.options?.filter)}}P.input.column2=function(e,t){return new Eo(e,t)};var So=n(1296),No=n(3820);class Io extends r.JsInputBase{get inputType(){return"Positions"}get dataType(){return r.TYPE.DATA_FRAME}getInput(){return this.gridHost}getValue(){return this.grid.dataFrame}setValue(e){this.setDataFrame(e)}getStringValue(){return this.grid.dataFrame.toCsv()}setStringValue(e){this.setDataFrame(r.DataFrame.fromCsv(e))}clearInput(){const e=r.DataFrame.fromColumns([r.Column.fromType(r.COLUMN_TYPE.STRING,"Remove",0),r.Column.fromType(r.COLUMN_TYPE.INT,"Position",0),r.Column.fromType(r.COLUMN_TYPE.STRING,"Monomers",0)]);this.setDataFrame(e)}get placeholdersValue(){return function(e){const t=[];for(let n=0;n<e.rowCount;n++){if(e.getCol("Position").isNone(n))continue;const o=parseInt(e.get("Position",n))-1;if(!isNaN(o)){const r=Mo(e.get("Monomers",n));t.push({position:o,monomers:r})}}return t}(this.grid.dataFrame)}invalidateGrid(){if(this.grid){const e=this.grid.root.style.width;this.grid.root.style.width="99.9%",setTimeout((()=>{e?this.grid.root.style.width=e:this.grid.root.style.removeProperty("width")}),100)}}constructor(e,t,n){super(),this.name=e,this.onMonomerCellEdit=null,this.subs=[],this.dataFrameSubs=[],this.caption=e??"",this.root.classList.add("ui-input-polytool-pos-grid"),this.root.append(this.gridHost=P.div([],{classes:"ui-input-editor",style:{width:"100%",height:"100%",marginTop:"-8px",marginBottom:"8px",paddingBottom:"4px"}})),this.render(t,n).then((()=>{}))}detach(){for(const e of this.subs)e.unsubscribe();for(const e of this.dataFrameSubs)e.unsubscribe()}async render(e,t){let n;const o=r.DataFrame.fromColumns([n=r.Column.fromType(r.COLUMN_TYPE.STRING,"Remove",0),r.Column.fromType(r.COLUMN_TYPE.INT,"Position",0),r.Column.fromType(r.COLUMN_TYPE.STRING,"Monomers",0)]);n.setTag(r.TAGS.FRIENDLY_NAME,""),this.grid=await o.plot.fromType(r.VIEWER.GRID,t),this.grid.sort(["Position"]),this.grid.columns.byIndex(1).width=this.grid.props.rowHeight+2,this.grid.onCellRender.subscribe((e=>{const t=e.cell;t.tableColumn?.name==n.name&&(t?.tableRowIndex??-1)>=0&&(t.element=P.div(P.icons.delete((()=>{this.grid.dataFrame.rows.removeAt(t.tableRowIndex)}),"Delete"),{style:{height:`${t.grid.props.rowHeight}px`,color:"var(--grey-6)",display:"flex",flexDirection:"row",justifyContent:"center"}}))}));const i=this.grid.columns.byName("Monomers");i&&(i.editable=!1),this.subs.push(this.grid.onCellDoubleClick.subscribe((e=>{"Monomers"===e.tableColumn?.name&&null!=e.tableRowIndex&&e.tableRowIndex>=0&&this.handleMonomerCellDoubleClick(e.tableRowIndex)}))),this.updateGridHeight(e??this.grid.dataFrame.rowCount+.7),this.subs.push(P.onSizeChanged(this.grid.root).subscribe(this.gridRootOnSizeChanged.bind(this))),this.subs.push((0,te.fromEvent)(this.grid.root,"keydown").subscribe((e=>{"Enter"===e.key&&e.stopPropagation()}))),this.setDataFrame(o),this.grid.root.style.width="100%",this.gridHost.append(this.grid.root)}setDataFrame(e){for(const e of this.dataFrameSubs)e.unsubscribe();this.grid.dataFrame=e,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(e,t){const n=this.grid.dataFrame,o=n.columns.byName("Position").toList();let r=o.indexOf(e+1);-1===r&&(r=o.findIndex((e=>isNaN(e))),-1===r&&(r=n.rows.addNew(["",e+1,t??""]).idx),this.grid.cell("Monomers",r)),n.currentCell=n.cell(r,"Monomers")}setMonomersValue(e,t){const n=this.grid.dataFrame;n.rowCount<=e||n.set("Monomers",e,t)}static async create(e,t,n){return new Io(e,n,t)}updateGridHeight(e){const t=this.grid.colHeaderHeight+e*this.grid.props.rowHeight+6+2;this.grid.root.style.height=`${t}px`}async handleMonomerCellDoubleClick(e){if(!this.onMonomerCellEdit)return;const t=this.grid.dataFrame,n=parseInt(t.get("Position",e))-1;if(isNaN(n))return;const o=Mo(t.get("Monomers",e)??""),r=await this.onMonomerCellEdit(n,o);null!==r&&t.set("Monomers",e,r.join(", "))}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 Mo(e){return e.split(/,(?![^(]*\))/).map((e=>('"'===(e=e.trim()).slice(0,1)&&'"'===e.slice(-1)&&(e=e.slice(1,-1)),"'"===e.slice(0,1)&&"'"===e.slice(-1)&&(e=e.slice(1,-1)),e.trim()))).filter((e=>!!e))}class Po{constructor(e,t,n,o){this.currentMenu=null,this.menuItems=[],this.highlightedIndex=-1,this.monomerLib=e,this.polymerType=t,this.helmType=(0,s.MD)(t),this.allSymbols=e.getMonomerSymbolsByType(t),this.libHelper=o,this.selectedMonomers=n?[...n]:[],this.tagsHost=P.div([],{style:{display:"flex",flexWrap:"wrap",gap:"4px",marginTop:"4px",maxHeight:"150px",overflowY:"auto"}}),this.countLabel=P.divText("",{style:{fontSize:"11px",color:"var(--grey-4)",marginTop:"4px"}});const r=P.input.string("Search",{value:""});this.inputEl=r.input,this.inputEl.setAttribute("autocomplete","off"),this.inputEl.placeholder="Type to search monomers...",this.setupInputListeners();const i=this.createLibrarySection(),a=this.createCollectionSection(),l=P.button("Clear all",(()=>{this.selectedMonomers.length=0,this.renderTags()}));l.style.fontSize="11px",l.style.marginTop="4px",this.renderTags(),this.root=P.div([r.root,i,a,P.divH([this.countLabel,l],{style:{justifyContent:"space-between",alignItems:"center"}}),this.tagsHost],{style:{minWidth:"300px"}})}getSelectedMonomers(){return[...this.selectedMonomers]}setSelectedMonomers(e){this.selectedMonomers.length=0,this.selectedMonomers.push(...e),this.renderTags()}setPolymerType(e){this.polymerType=e,this.helmType=(0,s.MD)(e),this.allSymbols=this.monomerLib.getMonomerSymbolsByType(e)}focus(){this.inputEl.focus()}updateCountLabel(){this.countLabel.textContent=this.selectedMonomers.length>0?`${this.selectedMonomers.length} monomer(s) selected`:""}renderTags(){this.tagsHost.innerHTML="";for(const e of this.selectedMonomers){const t=P.iconFA("times",(()=>{const t=this.selectedMonomers.indexOf(e);t>=0&&(this.selectedMonomers.splice(t,1),this.renderTags(),this.updateCountLabel())}),"Remove");t.style.marginLeft="4px",t.style.cursor="pointer";const n=P.div([P.span([e]),t],{style:{display:"inline-flex",alignItems:"center",padding:"2px 6px",borderRadius:"4px",backgroundColor:"var(--grey-2)",border:"1px solid var(--grey-3)",fontSize:"12px",cursor:"default"}});n.addEventListener("mouseenter",(()=>{const t=this.monomerLib.getTooltip(this.helmType,e);P.tooltip.show(t,n.getBoundingClientRect().left,n.getBoundingClientRect().bottom+16)})),n.addEventListener("mouseleave",(()=>{P.tooltip.hide()})),this.tagsHost.appendChild(n)}this.updateCountLabel()}addMonomer(e){this.selectedMonomers.includes(e)||(this.selectedMonomers.push(e),this.renderTags()),this.inputEl.value="",this.hideMenu(),this.inputEl.focus()}addMonomers(e){let t=!1;for(const n of e)this.selectedMonomers.includes(n)||(this.selectedMonomers.push(n),t=!0);t&&this.renderTags()}hideMenu(){this.currentMenu&&(this.currentMenu.hide(),this.currentMenu=null),this.menuItems=[],this.highlightedIndex=-1}getSuggestions(e){const t=e.toLowerCase(),n=[];for(const e of this.allSymbols){if(this.selectedMonomers.includes(e))continue;const o=this.monomerLib.getMonomer(this.polymerType,e),r=e.toLowerCase(),i=o?.name?.toLowerCase()??"";r.startsWith(t)?n.push({symbol:e,monomer:o,rank:0}):r.includes(t)?n.push({symbol:e,monomer:o,rank:1}):i.includes(t)&&n.push({symbol:e,monomer:o,rank:2})}return n.sort(((e,t)=>e.rank-t.rank||e.symbol.localeCompare(t.symbol))),n.slice(0,20)}showSuggestions(){this.hideMenu();const e=this.inputEl.value.trim();if(!e)return;const t=this.getSuggestions(e);if(0===t.length)return;this.currentMenu=r.Menu.popup();const n=t.reduce(((e,t)=>{const n=t.monomer?.name?`${t.symbol} - ${t.monomer.name}`:t.symbol;return e.length<n.length?n:e}),"");this.currentMenu.item(n,(()=>{}));const o=new MouseEvent("mousemove",{clientX:this.inputEl.getBoundingClientRect().left,clientY:this.inputEl.getBoundingClientRect().bottom});this.currentMenu.show({causedBy:o,y:this.inputEl.offsetHeight+this.inputEl.offsetTop,x:this.inputEl.offsetLeft}),setTimeout((()=>{this.currentMenu?.clear();for(const e of t){const t=e.monomer?.name?`${e.symbol} - ${e.monomer.name}`:e.symbol;this.currentMenu?.item(t,(()=>{this.addMonomer(e.symbol)}))}const e=document.querySelector(".d4-menu-popup:last-of-type");e&&(this.menuItems=Array.from(e.querySelectorAll(".d4-menu-item"))),this.highlightedIndex=-1}),0)}updateHighlight(e){0!==this.menuItems.length&&(this.highlightedIndex>=0&&this.highlightedIndex<this.menuItems.length&&this.menuItems[this.highlightedIndex].classList.remove("d4-menu-item-hover"),this.highlightedIndex=e,this.highlightedIndex>=0&&this.highlightedIndex<this.menuItems.length&&(this.menuItems[this.highlightedIndex].classList.add("d4-menu-item-hover"),this.menuItems[this.highlightedIndex].scrollIntoView({block:"nearest"})))}setupInputListeners(){this.inputEl.addEventListener("input",(()=>{this.showSuggestions()})),this.inputEl.addEventListener("paste",(e=>{const t=e.clipboardData?.getData("text");if(!t)return;const n=t.split(/[\n\r]+/).map((e=>e.trim())).filter((e=>e.length>0)),o=[];for(const e of n){const t=e.split(/,(?![^(]*\))/).map((e=>('"'===(e=e.trim()).slice(0,1)&&'"'===e.slice(-1)&&(e=e.slice(1,-1)),"'"===e.slice(0,1)&&"'"===e.slice(-1)&&(e=e.slice(1,-1)),e.trim()))).filter((e=>!!e));1===t.length&&e.includes(" ")&&!e.includes(",")?o.push(...e.split(/\s+/).map((e=>e.trim())).filter((e=>e.length>0))):o.push(...t)}if(!(o.length<=1)){e.preventDefault();for(const e of o)this.selectedMonomers.includes(e)||this.selectedMonomers.push(e);this.renderTags(),this.inputEl.value="",this.hideMenu(),this.inputEl.focus()}})),this.inputEl.addEventListener("keydown",(e=>{if("ArrowDown"===e.key){if(e.preventDefault(),this.menuItems.length>0){const e=(this.highlightedIndex+1)%this.menuItems.length;this.updateHighlight(e)}}else if("ArrowUp"===e.key){if(e.preventDefault(),this.menuItems.length>0){const e=(this.highlightedIndex-1+this.menuItems.length)%this.menuItems.length;this.updateHighlight(e)}}else if("Enter"===e.key)if(e.preventDefault(),e.stopPropagation(),this.highlightedIndex>=0&&this.highlightedIndex<this.menuItems.length)this.menuItems[this.highlightedIndex].click();else{const e=this.inputEl.value.trim();e&&this.addMonomer(e)}else"Escape"===e.key&&this.hideMenu()}))}createLibrarySection(){const e=P.div([],{style:{marginTop:"8px"}});if(!this.libHelper)return e;const t=this.libHelper,n=P.input.choice("Add from library",{items:[],nullable:!0}),o=P.divText("",{style:{fontSize:"11px",color:"var(--green-2)",marginLeft:"8px",minHeight:"16px"}});return t.getAvaliableLibraryNames().then((e=>{n.items=e})),n.onChanged.subscribe((async()=>{const e=n.value;if(e){o.textContent="Loading...";try{const n=await t.readSingleLibraryByName(e);if(n){const t=n.getMonomerSymbolsByType(this.polymerType),r=this.selectedMonomers.length;this.addMonomers(t);const i=this.selectedMonomers.length-r;o.textContent=`Added ${i} monomer(s) from "${e}"`}else o.textContent=`Library "${e}" not found`}catch(e){o.textContent="Error loading library"}n.value=null,setTimeout((()=>{o.textContent=""}),4e3)}})),e.appendChild(P.divV([n.root,o])),e}createCollectionSection(){const e=P.div([],{style:{marginTop:"4px"}});if(!this.libHelper)return e;const t=this.libHelper,n=P.input.choice("Add from collection",{items:[],nullable:!0}),o=P.divText("",{style:{fontSize:"11px",color:"var(--green-2)",marginLeft:"8px",minHeight:"16px"}});return t.listMonomerCollections().then((e=>{n.items=e})),n.onChanged.subscribe((async()=>{const e=n.value;if(e){o.textContent="Loading...";try{const n=(await t.readMonomerCollection(e)).monomerSymbols??[],r=this.selectedMonomers.length;this.addMonomers(n);const i=this.selectedMonomers.length-r,s=e.replace(/\.json$/,"");o.textContent=`Added ${i} monomer(s) from "${s}"`}catch(e){o.textContent="Error loading collection"}n.value=null,setTimeout((()=>{o.textContent=""}),4e3)}})),e.appendChild(P.divV([n.root,o])),e}}async function _o(e,t,n,o){return new Promise((r=>{const i=new Po(e,t,n,o);P.dialog({title:"Select Monomers",showFooter:!0}).add(P.div([i.root],{style:{minWidth:"400px",minHeight:"250px",maxWidth:"800px"}})).onOK((()=>{r(i.getSelectedMonomers())})).onCancel((()=>{r(null)})).show({resizable:!0}),i.focus()}))}class Lo extends r.JsInputBase{get inputType(){return"Breadth"}get dataType(){return r.TYPE.DATA_FRAME}getInput(){return this.gridHost}getValue(){return this.grid.dataFrame}setValue(e){this.setDataFrame(e)}invalidateGrid(){if(this.grid){const e=this.grid.root.style.width;this.grid.root.style.width="99.9%",setTimeout((()=>{e?this.grid.root.style.width=e:this.grid.root.style.removeProperty("width")}),100)}}getStringValue(){return this.grid.dataFrame.toCsv()}setStringValue(e){this.setDataFrame(r.DataFrame.fromCsv(e))}get placeholdersBreadthValue(){return function(e){const t=[];for(let n=0;n<e.rowCount;n++){const o=parseInt(e.get("Start",n))-1,r=parseInt(e.get("End",n))-1;if(!isNaN(o)&&!isNaN(r)){const i=Mo(e.get("Monomers",n));t.push({start:o,end:r,monomers:i})}}return t}(this.grid.dataFrame)}constructor(e,t,n){super(),this.name=e,this.onMonomerCellEdit=null,this.subs=[],this.dataFrameSubs=[],this.caption=e??"",this.root.classList.add("ui-input-polytool-pos-grid"),this.root.append(this.gridHost=P.div([],{classes:"ui-input-editor",style:{width:"100%",height:"100%",marginTop:"-8px",marginBottom:"8px",paddingBottom:"4px"}})),this.render(t,n).then((()=>{}))}detach(){for(const e of this.subs)e.unsubscribe();for(const e of this.dataFrameSubs)e.unsubscribe()}clearInput(){const e=r.DataFrame.fromColumns([r.Column.fromType(r.COLUMN_TYPE.STRING,"Remove",0),r.Column.fromType(r.COLUMN_TYPE.INT,"Start",0),r.Column.fromType(r.COLUMN_TYPE.INT,"End",0),r.Column.fromType(r.COLUMN_TYPE.STRING,"Monomers",0)]);this.setDataFrame(e)}async render(e,t){let n;const o=r.DataFrame.fromColumns([n=r.Column.fromType(r.COLUMN_TYPE.STRING,"Remove",0),r.Column.fromType(r.COLUMN_TYPE.INT,"Start",0),r.Column.fromType(r.COLUMN_TYPE.INT,"End",0),r.Column.fromType(r.COLUMN_TYPE.STRING,"Monomers",0)]);n.setTag(r.TAGS.FRIENDLY_NAME,""),this.grid=await o.plot.fromType(r.VIEWER.GRID,t),this.grid.sort(["Start","End"]),this.grid.columns.byIndex(1).width=this.grid.props.rowHeight+2,this.grid.onCellRender.subscribe((e=>{const t=e.cell;t.tableColumn?.name==n.name&&(t?.tableRowIndex??-1)>=0&&(t.element=P.div(P.icons.delete((()=>{this.grid.dataFrame.rows.removeAt(t.tableRowIndex)}),"Delete"),{style:{height:`${t.grid.props.rowHeight}px`,color:"var(--grey-6)",display:"flex",flexDirection:"row",justifyContent:"center"}}))}));const i=this.grid.columns.byName("Monomers");i&&(i.editable=!1),this.subs.push(this.grid.onCellDoubleClick.subscribe((e=>{"Monomers"===e.tableColumn?.name&&null!=e.tableRowIndex&&e.tableRowIndex>=0&&this.handleMonomerCellDoubleClick(e.tableRowIndex)}))),this.updateGridHeight(e??this.grid.dataFrame.rowCount+.7),this.subs.push(P.onSizeChanged(this.grid.root).subscribe(this.gridRootOnSizeChanged.bind(this))),this.subs.push((0,te.fromEvent)(this.grid.root,"keydown").subscribe((e=>{"Enter"===e.key&&e.stopPropagation()}))),this.setDataFrame(o),this.grid.root.style.width="100%",this.gridHost.append(this.grid.root)}setDataFrame(e){for(const e of 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${t}`),this.errors.length>0){const e=this.errors[0];throw this.errors=[],e}this.logger.debug(`${n}, end`)}}Bo.viewerCounter=-1;const Fo="rgb(100,100,100)",ko="rgb(0,0,0)",Ho=s.zS;var Go,Uo,Vo;!function(e){e.maxMonomerLength=".mm.cellRenderer.maxMonomerLength"}(Go||(Go={})),function(e){e.applyToBackground=".m.cellRenderer.applyToBackground"}(Uo||(Uo={})),function(e){e.MSA="MSA",e.classic="classic"}(Vo||(Vo={}));const jo=new class{constructor(){this.color=Fo,this.pivot=0,this.left=!1,this.transparencyRate=0,this.separator="",this.last=!1,this.drawStyle=Vo.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 qo(e,t,n,o,i,s,a){var l,c,u;const h={...jo,...a};if(h.isMultiLineContext){e.textBaseline="middle",e.textAlign="center";let r=t;null!=h.maxLengthOfMonomer&&(r=Ho(r,h.maxLengthOfMonomer));const a=Math.max(.1,1-(h.transparencyRate??0));e.globalAlpha=a;const l=e.measureText(r),c=l.fontBoundingBoxAscent+l.fontBoundingBoxDescent,u=o+(s-c)/2+l.fontBoundingBoxAscent;let d=h.color??Fo;return d&&d!==Fo||(d=ko),e.fillStyle=d,h.selectedPosition===h.wordIdx+1&&(e.save(),e.fillStyle="rgba(60, 177, 115, 0.2)",e.fillRect(n,o,i,s),e.restore(),e.fillStyle=d),e.fillText(r,n+i/2,u),e.globalAlpha=1,e.textBaseline="top",e.textAlign="start",n+i}a.logger?.debug("Bio: printLeftOrCentered(), start"),e.textAlign="start";let d=t.substring(0),p=h.last?"":h.separator;h.drawStyle===Vo.MSA&&(p="");let m=!0,f=!0,g="difference";if(null!=h.gridCell&&null!=h.gridCell.cell.column&&(m=h.gridCell.cell.column.temp["color-code"]??!0,f=h.gridCell.cell.column.temp["compare-with-current"]??!0,g=h.gridCell.cell.column.temp["highlight-difference"]??"difference"),h.referenceSequence){const e=h.referenceSequence[h.wordIdx];f&&h.referenceSequence.length>0&&"difference"===g&&(h.transparencyRate=d==e?.7:h.transparencyRate),f&&h.referenceSequence.length>0&&"equal"===g&&(h.transparencyRate=d!=e?.7:h.transparencyRate)}null!=h.maxLengthOfMonomer&&(d=Ho(d,h.maxLengthOfMonomer));const y=d+p;(l=h.monomerTextSizeMap)[y]??(l[y]=e.measureText(y));let b=h.monomerTextSizeMap[y];(c=h.monomerTextSizeMap)[d]??(c[d]=e.measureText(d));let v=h.monomerTextSizeMap[d].width;const C=s/2-(b.fontBoundingBoxAscent+b.fontBoundingBoxDescent)/2+1;(u=h.monomerTextSizeMap)[p]??(u[p]=e.measureText(p));const x=h.monomerTextSizeMap[p].width;function w(t,i){let a=m?h.color:ko;h.selectedPosition===h.wordIdx+1&&(e.fillStyle="rgba(60, 177, 115, 0.2)",e.fillRect(n+t-4,o-5,h.monomerTextSizeMap[d].width+8,s+10),a=r.Color.toHtml(r.Color.setAlpha(r.Color.fromHtml(a),255))),e.fillStyle=a,e.globalAlpha=1-h.transparencyRate,h.drawStyle===Vo.classic&&(e.fillText(d,n+t,o+C),e.fillStyle="#808080",e.fillText(p,n+i,o+C)),h.drawStyle===Vo.MSA&&e.fillText(d,n+t,o+C),e.globalAlpha=1}b=b.width,h.drawStyle===Vo.MSA&&(v=h.maxWord[h.wordIdx],b=h.maxWord[h.wordIdx]);const A=(h.maxWord[h.wordIdx]??0)-(h.maxWord[0]??0);if(h.left||b>i)return w(A,A+v),n+A+v+x;{const e=(i-b)/2;return w(e,e+v),n+A+e+v}}var Wo,zo,Yo;!function(e){e.Region="region",e.Point="point",e.Motif="motif"}(Wo||(Wo={})),function(e){e.Structure="structure",e.Liability="liability",e.PTM="ptm",e.Custom="custom"}(zo||(zo={})),function(e){e.High="high",e.Medium="medium",e.Low="low",e.Info="info"}(Yo||(Yo={}));const Ko={structure:{FR:["#0095ff","#289dfd","#48adff","#3ba5fc"],CDR:["#ffdca3","#facb83","#f7a224"]},liability:{deamidation:"#E53935",isomerization:"#FF9800",oxidation:"#9C27B0",glycosylation:"#4CAF50",freeCysteine:"#607D8B"}};class Qo{constructor(e){this.tableCol=e,this._cache=null,this._rowCache=null,this._annotCol=null,this._annotColLookupVersion=-1}hasAnnotations(){return this._ensureCache(),null!==this._cache&&this._cache.annotations.length>0}getAnnotations(){return this._ensureCache(),this._cache?.annotations??[]}getRegionNameAtPosition(e,t){if(null!=t){const n=this._findRowRegionHit(t,e);if(n){const e=this._cache?.annotations.find((e=>e.id===n.annotationId));return e?.name??null}if(this._rowHasRegionData(t))return null}return this._ensureCache(),this._cache?.positionRegionNames.get(e)??null}getHitsAtPosition(e,t){if(this._ensureRowCache(),!this._rowCache)return[];const n=this._rowCache.data[e];return n?n.filter((e=>null==e.endPositionIndex&&(e.positionIndex===t||e.matchedMonomers.length>1&&t>e.positionIndex&&t<e.positionIndex+e.matchedMonomers.length))):[]}drawPositionBackground(e,t,n,o,r,i,s,a){if(this._ensureCache(),!this._cache)return;let l;this._ensureRowCache();const c=this._findRowRegionHit(s,i);if(c){const e=this._cache.annotations.find((e=>e.id===c.annotationId));l=e?.color??(e?this._getDefaultRegionColor(e):void 0)}if(l||this._rowHasRegionData(s)||(l=this._cache.positionRegionColors.get(i)),l&&(e.save(),e.globalAlpha=.25,e.fillStyle=l,e.fillRect(t,n,o,r),e.restore()),this._rowCache){const l=this._rowCache.data[s];if(l)for(const s of l)if(null==s.endPositionIndex&&i>=s.positionIndex&&i<s.positionIndex+s.matchedMonomers.length){const i=this._cache.annotations.find((e=>e.id===s.annotationId));if(i?.color){const s=null!=a?a+1:n+r-3;e.fillStyle=i.color,e.fillRect(t,s,o,3)}break}}}getTooltipInfo(e,t){this._ensureCache();const n=[];if(!this._cache)return n;this._ensureRowCache();let o=null;const r=this._findRowRegionHit(t,e);if(r){const e=this._cache.annotations.find((e=>e.id===r.annotationId));if(e){o=e.name;const t=e.sourceScheme??"";n.push(`Region: ${e.name}${t?` (${t} ${e.start}-${e.end})`:""}`)}}if(!o&&!this._rowHasRegionData(t)){const t=this._cache.positionRegionNames.get(e);if(t){const e=this._cache.annotations.find((e=>e.name===t&&e.category===zo.Structure)),o=e?.sourceScheme??"";n.push(`Region: ${t}${o?` (${o} ${e?.start}-${e?.end})`:""}`)}}if(this._rowCache){const o=this._rowCache.data[t];if(o)for(const t of o)if(null==t.endPositionIndex&&e>=t.positionIndex&&e<t.positionIndex+t.matchedMonomers.length){const e=this._cache.annotations.find((e=>e.id===t.annotationId));if(e){const t=e.severity?` - ${e.severity.charAt(0).toUpperCase()+e.severity.slice(1)}`:"";n.push(`⚠ ${e.name}${t}`)}}}return n}_findRowRegionHit(e,t){if(this._ensureRowCache(),!this._rowCache)return null;const n=this._rowCache.data[e];if(!n)return null;for(const e of n)if(null!=e.endPositionIndex&&t>=e.positionIndex&&t<=e.endPositionIndex)return e;return null}_rowHasRegionData(e){if(this._ensureRowCache(),!this._rowCache)return!1;const t=this._rowCache.data[e];return!!t&&t.some((e=>null!=e.endPositionIndex))}_ensureCache(){const e=this.tableCol.version;if(this._cache&&this._cache.colVersion===e)return;const t=this.tableCol.getTag(i.gp.annotations);if(!t)return void(this._cache=null);let n;try{n=JSON.parse(t)}catch{return void(this._cache=null)}if(!n||0===n.length)return void(this._cache=null);const o=new Map,r=new Map,s=this._getPosList();for(const e of n){if(e.category!==zo.Structure)continue;if(null==e.start||null==e.end)continue;const t=s.indexOf(e.start),n=s.indexOf(e.end);if(t<0||n<0)continue;const i=e.color??this._getDefaultRegionColor(e);for(let s=t;s<=n;s++)o.set(s,i),r.set(s,e.name)}this._cache={colVersion:e,annotations:n,positionRegionColors:o,positionRegionNames:r}}_ensureRowCache(){const e=this.tableCol.version;if(this._annotColLookupVersion!==e){this._annotColLookupVersion=e;const t=this.tableCol.getTag(i.gp.annotationColumnName);if(t)try{this._annotCol=this.tableCol.dataFrame.columns.byName(t)}catch{this._annotCol=null}else this._annotCol=null}if(!this._annotCol)return void(this._rowCache=null);const t=this._annotCol.version;if(this._rowCache&&this._rowCache.colVersion===t)return;const n=new Array(this._annotCol.length);for(let e=0;e<this._annotCol.length;e++){const t=this._annotCol.get(e);if(t)try{n[e]=JSON.parse(t)}catch{n[e]=null}else n[e]=null}this._rowCache={colVersion:t,data:n}}_getPosList(){const e=this.tableCol.getTag(i.gp.positionNames);return e?e.split(", "):[]}_getDefaultRegionColor(e){if(e.name.startsWith("CDR")){const t=parseInt(e.name.replace("CDR",""))-1;return Ko.structure.CDR[t%Ko.structure.CDR.length]}if(e.name.startsWith("FR")){const t=parseInt(e.name.replace("FR",""))-1;return Ko.structure.FR[t%Ko.structure.FR.length]}return"#90CAF9"}}var Jo=n(3599);const Xo="bio.macromolecule.highlightMonomers",Zo=r.Color.argb(255,255,220,0);r.Color.argb(255,230,140,0);const er="rgb(100,100,100)";class tr extends Bo{get separatorWidth(){return this.props?.fontCharWidth?this.props?.fontCharWidth:5}getAnnotationRenderer(){return this._annotationRenderer||(this._annotationRenderer=new Qo(this.tableCol)),this._annotationRenderer.hasAnnotations()?this._annotationRenderer:null}constructor(e,t,n,o,i){if(super(e,t,n),this.monomerLengthLimit=o,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._annotationRenderer=null,this.padding=5,this._leftThreeDotsPadding=0,this.props=this.propsProvider(),this._processedRows=r.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 e=[Ot.gp.positionShift,"renderMultiline"];this.subs.push(r.debounce(this.tableCol.dataFrame.onMetadataChanged.pipe(ne.filter((t=>t.args.source===this.tableCol&&e.includes(t.args.key)))),200).subscribe((e=>{this.reset()}))),this.subs.push(r.debounce(this.tableCol.dataFrame.onMetadataChanged.pipe(ne.filter((e=>e.args.source===this.tableCol&&e.args.key===Ot.gp.positionShift))),200).subscribe((e=>{this.reset()})))}}calculateFontBasedSpacing(e){const t=e.measureText("M");let n=12;if(this.tableCol?.temp[".mm.cellRenderer.fontSize"]){const e=this.tableCol.temp[".mm.cellRenderer.fontSize"];"number"!=typeof e||isNaN(e)||(n=Math.max(e,1))}return{lineHeight:Math.max(1.4*n,t.fontBoundingBoxAscent+t.fontBoundingBoxDescent+4),monomerSpacing:Math.max(2,.2*this.props.fontCharWidth)}}shouldUseMultilineRendering(e){return"true"===e.getTag("renderMultiline")}calculateMultiLineLayoutDynamic(e,t,n,o,r,i){if(this.dirty)try{this.reset()}catch(e){const[t,n]=(0,vn.AP)(e);this.logger.error(t,void 0,n)}const{lineHeight:s,monomerSpacing:a}=this.calculateFontBasedSpacing(e),l=t-2*this.padding;let c=0;const u=[];if(o.length>0)for(let t=r;t<o.length;t++){const n=o.getOriginal(t),r=this.props.monomerToShort(n,i);u.push({text:r,posIdx:t}),c=Math.max(c,e.measureText(r).width)}if(0===u.length)return{lineLayouts:[],lineHeight:s};const h=c;let d=Math.floor((l+a)/(h+a));d=Math.max(1,d);const p=n-2*this.padding,m=Math.max(0,Math.floor(p/s)),f=[];let g=0;for(let e=0;e<m&&g<u.length;e++){const t=[];for(let e=0;e<d&&g<u.length;e++){const n=u[g],o=this.padding+e*(h+a);t.push({posIdx:n.posIdx,x:o,width:h,om:n.text,isSeparator:!1}),g++}f.push({lineIdx:e,elements:t})}return{lineLayouts:f,lineHeight:s}}async init(){await Promise.all([(async()=>{this.seqHelper=await(0,Cn.Q)(),this.invalidateGrid()})(),(async()=>{const e=await(0,l.pj)();this.sysMonomerLib=e.getMonomerLib()})()]),this.subs.push(this.sysMonomerLib.onChanged.subscribe((()=>{this.reset()}))),this.subs.push(o.events.onCustomEvent("bio-macromolecule-monomer-highlight").subscribe((e=>this.handleHighlightEvent(e)))),this.reset()}handleHighlightEvent(e){var t;if(!e||!this.tableCol||!this.tableCol.dataFrame)return;if(e.columnName!==this.tableCol.name)return;const n=this.tableCol.dataFrame;if(e.tableId&&n.id!==e.tableId)return;if(e.tableName&&n.name!==e.tableName)return;const o=(t=this.tableCol.temp)[Xo]??(t[Xo]=new Map);null==e.monomers||0===e.monomers.length?o.delete(e.rowIdx):o.set(e.rowIdx,{monomers:e.monomers.slice(),fillColor:e.fillColor,strokeColor:e.strokeColor}),this.invalidateGrid()}getHighlightForRow(e){if(null==e)return null;const t=this.tableCol.temp[Xo];return t?.get(e)??null}drawHighlightBackground(e,t,n,o,i,s,a){const l=this.getHighlightForRow(t);if(!l||!l.monomers||0===l.monomers.length)return;if(!l.monomers.includes(n))return;const c=(u=l.fillColor??Zo,`rgba(${r.Color.r(u)},${r.Color.g(u)},${r.Color.b(u)},0.4)`);var u;e.save();try{e.fillStyle=c,e.fillRect(o,i,s,a)}finally{e.restore()}}static getFontSettings(e){let t=12;return e&&e.temp[".mm.cellRenderer.fontSize"]&&"number"==typeof e.temp[".mm.cellRenderer.fontSize"]&&!isNaN(e.temp[".mm.cellRenderer.fontSize"])&&(t=Math.max(e.temp[".mm.cellRenderer.fontSize"],1)),{font:`${t}px monospace`,fontWidth:.6*t}}toLog(){return`MonomerPlacer<${this.viewerId}>`}getMonomerLib(){return this.tableCol.temp[".mm.cellRenderer.overriddenLibrary"]??this.sysMonomerLib}reset(){this.propsProvider&&(this.props=this.propsProvider()),this._processedRows=r.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(e,t){const n=this.seqHelper.getSeqHandler(this.tableCol);if(this.colWidth<t&&(this.colWidth=t,this.dirty=!0),this.dirty)try{this.reset()}catch(e){const[t,n]=(0,vn.AP)(e);this.logger.error(t,void 0,n)}const o=n.isMsa()?this.getCellMonomerLengthsForSeqMsa():this.getCellMonomerLengthsForSeq(e);return[o,this.getSummedMonomerLengths(o)]}getSummedMonomerLengths(e){const t=new Array(e.length+1);t[0]=this.padding;for(let n=1;n<t.length;n++)t[n]=t[n-1]+e[n-1];let n=t[0];for(let e=1;e<t.length;e++)t[e]?n=t[e]:t[e]=n;return t}getCellMonomerLengthsForSeqValue(e,t){const n=this.seqHelper.getSeqHandler(this.tableCol),o=this.props.separatorWidth+1*this.props.fontCharWidth,r=this.positionShift,i=Math.ceil(t/o)+r,s=n.splitter(e),a=Math.min(i,s.length),l=new Array(a-r);let c=0;for(let e=r;e<a;++e){const o=s.getOriginal(e),i=this.props.monomerToShort(o,this.monomerLengthLimit),a=(n.isSeparator()?this.separatorWidth:this.props.separatorWidth)+i.length*this.props.fontCharWidth;if(l[e-r]=a,c+=a,c>t)break}return l}getCellMonomerLengthsForSeq(e){this.toLog(),null==this._monomerLengthList&&(this._monomerLengthList=new Array(this.tableCol.length).fill(null));const t=this.positionShift,n=this.seqHelper.getSeqHandler(this.tableCol),o=this.props.separatorWidth+1*this.props.fontCharWidth,r=Math.ceil(this.colWidth/o)+t,i=n.getSplitted(e),s=Math.min(r,i.length);let a=this._monomerLengthList[e];if(null==a||a.length!=s-t){a=this._monomerLengthList[e]=new Array(i.length);let o=0;for(let e=t;e<s;++e){const r=i.getOriginal(e),s=this.props.monomerToShort(r,this.monomerLengthLimit),l=(n.isSeparator()?this.separatorWidth:this.props.separatorWidth)+s.length*this.props.fontCharWidth;if(a[e-t]=l,o+=l,o>this.colWidth)break}}return a}getCellMonomerLengthsForSeqMsa(){var e;this.toLog(),null==this._monomerLengthList&&(this._monomerLengthList=new Array(1).fill(null)),(e=this._monomerLengthList)[0]??(e[0]=new Array(0));const t=this._monomerLengthList[0],{startIdx:n,endIdx:o}=(()=>{try{const e=this.gridCol&&this.gridCol.dart?this.gridCol.grid:null;return e&&e.dart?{startIdx:Math.max(Math.floor((e?.vertScroll.min??0)-10),0),endIdx:Math.min(Math.ceil((e?.vertScroll.max??0)+10),this.tableCol.length)}:{startIdx:0,endIdx:Math.min(this.tableCol.length,10)}}catch(e){return{startIdx:0,endIdx:Math.min(this.tableCol.length,10)}}})(),r=this.props.separatorWidth+1*this.props.fontCharWidth,i=this.positionShift,s=Math.ceil(this.colWidth/r)+i;for(let e=n;e<o;e++){if(this._processedRows.get(e)&&s<=this._processedMaxVisibleSeqLength)continue;const n=this.seqHelper.getSeqHandler(this.tableCol).getSplitted(e,s),o=Math.min(s,n.length);o-i>t.length&&t.push(...new Array(o-i-t.length).fill(r));let a=0;for(let e=i;e<o;++e){const o=n.getOriginal(e),r=this.props.monomerToShort(o,this.monomerLengthLimit),s=this.props.separatorWidth+r.length*this.props.fontCharWidth;if(t[e-i]=Math.max(t[e-i]??0,s),a+=s,a>=this.colWidth)break}this._processedMaxVisibleSeqLength=Math.max(this._processedMaxVisibleSeqLength,s),this._processedRows.set(e,!0)}return t}getPosition(e,t,n,o){const[r,i]=this.getCellMonomerLengths(e,n);return 0===this.seqHelper.getSeqHandler(this.tableCol).getSplitted(e).length?null:function(e,t,n){if((n??0)>0&&t<(e[0]??0)+n)return-1;t-=n??0;let o,r=100,i=0,s=e.length-1;for(;i<=s;){if(o=Math.floor((s+i)/2),e[o]<=t&&t<e[o+1])return o;if(t<e[o]?s=o-1:i=o+1,--r<=0)throw new Error(`Get position for pointer x = ${t} searching has not converged on ${JSON.stringify(e)}. `)}return null}(i,t,o)}setMonomerLengthLimit(e){this.monomerLengthLimit!=e&&(this.monomerLengthLimit=e,this.dirty=!0)}setSeparatorWidth(e){this.separatorWidth!=e&&(this.props.separatorWidth=e,this.dirty=!0)}get positionShift(){const e=Number.parseInt(this.tableCol?.tags[Ot.gp.positionShift]??"0")??0;return isNaN(e)?0:Math.max(e,0)}render(e,t,n,o,i,s,a){const l=s.grid?.dart&&s.grid?.canvas===e.canvas;if(!this.seqHelper)return;const c=this.tableCol,u=this.positionShift;e.save();try{const a=this.seqHelper.getSeqHandler(c);let h=this.monomerLengthLimit;if(Go.maxMonomerLength in c.tags){const e=parseInt(c.getTag(Go.maxMonomerLength));h=!isNaN(e)&&e?e:50}if(".mm.cellRenderer.maxMonomerLength"in c.temp){const e=c.temp[".mm.cellRenderer.maxMonomerLength"],t="number"==typeof e?e:parseInt(e);h=!isNaN(t)&&t?t:50}if("1"===c.temp[".mm.cellRenderer.settingsChanged"]||this.monomerLengthLimit!=h){let e=0;const t=8;e=c.temp[".mm.cellRenderer.gapLength"]??e,this.setMonomerLengthLimit(h),this.setSeparatorWidth(a.isMsa()?t:e),c.temp[".mm.cellRenderer.settingsChanged"]="0",this.dirty=!0}const d=s.cell.rowIndex,p=s.cell.value;l&&(o=function(e,t,n,o,r){return e?Math.max(Math.min(e.canvas.width/r-n,o)):Math.max(t.canvas.width/r-n,0)}(s.grid,e,t,o,window.devicePixelRatio)),e.beginPath(),e.rect(t,n,o,i),e.clip(),e.font=this.props?.font??"12px monospace",e.textBaseline="top";const m=c.meta.units,f=c.getTag(Ot.gp.aligned),g=c.getTag(Ot.gp.separator)??"",y=l?a.getSplitted(d):a.splitter(p);let b=Vo.classic;f?.includes("MSA")&&m===Ot.Hi.SEPARATOR&&(b=Vo.MSA);const v=c.temp["reference-sequence"],C=this.tableCol.temp["current-word"],x=(()=>{const e=(0,a.splitter)(null!=v&&""!==v?v:C??"");return wn().count(0).take(e.length).slice(u).map((t=>e.getCanonical(t))).toArray()})(),w=Number.parseInt(c.getTag(Ot.gp.selectedPosition)??"-200"),A=this.shouldUseMultilineRendering(c),T=this.getAnnotationRenderer();if(A){const l=[],d=this.calculateMultiLineLayoutDynamic(e,o,i,y,u,h);let p=n+this.padding;1===d.lineLayouts.length&&(p=n+(i-d.lineHeight)/2);for(const o of d.lineLayouts){const i=p+o.lineIdx*d.lineHeight;for(const h of o.elements){const p=t+h.x,m=h,f=m.posIdx,g=y.getCanonical(f);let b=er;const v=this.getMonomerLib();v&&(b=v.getMonomerTextColor(a.defaultBiotype,g));let C=0;if(s.tableRowIndex!==c.dataFrame.currentRowIdx&&x.length>0){const e=f-u;e>=0&&e<x.length&&g===x[e]&&(C=.7)}l.push({lineIdx:o.lineIdx,monomerIdx:f-u,bounds:new r.Rect(h.x,i-n,h.width,d.lineHeight),sequencePosition:f}),T&&T.drawPositionBackground(e,p,i,h.width+2,d.lineHeight,f,s.tableRowIndex),this.drawHighlightBackground(e,s.tableRowIndex,f,p,i,h.width+2,d.lineHeight),qo(e,m.om,p,i,h.width,d.lineHeight,{color:b,isMultiLineContext:!0,transparencyRate:C,selectedPosition:isNaN(w)||w<1?void 0:w,wordIdx:f})}}null!==s.tableRowIndex&&this._cellBounds.set(s.tableRowIndex,l)}else{this._leftThreeDotsPadding=this.shouldRenderShiftedThreeDots(u)?e.measureText("...").width:0;let[,r]=this.getCellMonomerLengths(s.tableRowIndex,o);l||(r=this.getSummedMonomerLengths(this.getCellMonomerLengthsForSeqValue(p,o)));const c=this.props.separatorWidth+1*this.props.fontCharWidth,d=Math.min(y.length,Math.ceil(o/c)+u);let m;const f=e.measureText("M"),v=f.fontBoundingBoxAscent+f.fontBoundingBoxDescent,C=4,A=Math.min(i,v+C),E=n+(i-A)/2;T&&(m=n+(i/2-v/2+1)+v);for(let l=u;l<d;++l){const c=l<y.length?y.getOriginal(l):a.defaultGapOriginal,d=l<y.length?y.getCanonical(l):a.defaultGapOriginal;let p=er;this.getMonomerLib()&&(p=this.getMonomerLib().getMonomerTextColor(a.defaultBiotype,d));const f=l===y.length-1,v=(y?.graphInfo?.disjointSeqStarts?.indexOf(l+1)??0)>0?"|":g,C=l-u,S=(r[C]??0)-(r[0]??0),N=(C+1<r.length?(r[C+1]??0)-(r[0]??0):S+this.props.fontCharWidth)-S,I=t+this.padding+this._leftThreeDotsPadding+S;T&&null!=s.tableRowIndex&&T.drawPositionBackground(e,I,n,N,i,l,s.tableRowIndex,m),this.drawHighlightBackground(e,s.tableRowIndex,l,I,E,N,A);const M={color:p,pivot:0,left:!0,transparencyRate:0,separator:v,last:f,drawStyle:b,maxWord:r,wordIdx:l-u,gridCell:s,referenceSequence:x,maxLengthOfMonomer:h,monomerTextSizeMap:this._monomerLengthMap,logger:this.logger,selectedPosition:isNaN(w)||w<1?void 0:w-u};qo(e,c,t+this.padding+this._leftThreeDotsPadding,n,o,i,M)}if(this.shouldRenderShiftedThreeDots(u)){const a={color:er,pivot:0,left:!0,transparencyRate:0,separator:g,last:!1,drawStyle:b,maxWord:r,wordIdx:0,gridCell:s,maxLengthOfMonomer:h,monomerTextSizeMap:this._monomerLengthMap,logger:this.logger};qo(e,"...",t+this.padding,n,o,i,a)}}}catch(e){const[t,n]=(0,vn.AP)(e);this.logger.error(t,void 0,n),this.errors.push(e)}finally{e.restore()}}shouldRenderShiftedThreeDots(e){return e>0&&(!this.gridCol||!this.gridCol.dart||!this.gridCol.grid||!this.gridCol.grid.dart||(this.gridCol.grid.props.colHeaderHeight??0)<=50)}onMouseMove(e,t){const n=`${this.toLog()}.onMouseMove()`;if(!this.seqHelper||null==e.tableRowIndex)return;const o=this.positionShift,r=e.bounds,i=t.offsetX-e.gridColumn.left+(e.gridColumn.left-r.x),s=t.offsetY-r.y;this.gridCol?.grid?.canvas&&(this.gridCol.grid.canvas.style.cursor="default");let a=null;const l=this._cellBounds.get(e.tableRowIndex);if(l){for(const e of l)if(e.bounds.contains(i,s)){a=e.monomerIdx;break}}else{const t=this.shouldRenderShiftedThreeDots(o)&&(this._leftThreeDotsPadding??0)>0?this._leftThreeDotsPadding:0;a=this.getPosition(e.tableRowIndex,i,r.width,t)}this.logger.debug(`${n}, argsX: ${i}, argsY: ${s}, left: ${a}`);const c=this.seqHelper.getSeqHandler(this.tableCol),u=c.getSplitted(e.tableRowIndex);if(null!==a&&a>=0&&a+o<u.length){const n=c.alphabet??Ot.YI.UN,r={position:a,biotype:n===Ot.YI.RNA||n===Ot.YI.DNA?Jo.o.NUCLEOTIDE:Jo.o.AA,symbol:u.getCanonical(a+o)},i=[];let s=this._monomerStructureMap[r.symbol];if(!s){const e=this.getMonomerLib();s=this._monomerStructureMap[r.symbol]=e?e.getTooltip(r.biotype,r.symbol):P.divText("Monomer library is not available")}i.push(s);const l=this.getAnnotationRenderer();if(l){const t=l.getTooltipInfo(a+o,e.tableRowIndex);if(t.length>0){const e=document.createElement("hr");e.style.margin="4px 0",e.style.border="none",e.style.borderTop="1px solid #ccc",i.push(e);for(const e of t)i.push(P.divText(e,{style:{fontSize:"12px",marginBottom:"2px"}}))}}P.tooltip.show(P.divV(i),t.x+16,t.y+16),Un(e,r)}else-1===a?P.tooltip.show(P.divText(`${Math.min(o,u.length)} hidden monomers`),t.x+16,t.y+16):P.tooltip.hide(),Un(e,null)}}class nr extends tr{constructor(e,t,n,o){super(e,t,br.logger,n,(()=>{const e=o.getSeqHandler(t),{font:n,fontWidth:r}=tr.getFontSettings(t);return{seqHandler:e,font:n,fontCharWidth:r,separatorWidth:11,monomerToShort:Ot.zS}}))}onMouseMove(e,t){super.onMouseMove(e,t)}}class or extends Ro.$G{static get notationName(){return"Harmonized Sequence"}static get implementsFromHelm(){return!1}static convertFromHelm(e,t){throw new Error("converting from helm not supported yet")}get defaultGapOriginal(){return""}constructor(e,t){super(),this.separator=e,this.helmHelper=t,this.separatorSplitter=(0,Ot.dh)(this.separator),this.splitter=this._splitter.bind(this)}setUnits(){}_splitter(e){const t=this.separatorSplitter(e);return new rr(wn().count(0).take(t.length).map((e=>t.getOriginal(e))).toArray(),i.b9[i.Hi.SEPARATOR])}getHelm(e,t){return Oo.s.fromSeparator(e,this.helmHelper).getHelm()}createCellRendererBack(e,t){const n=new nr(e,t,4,this.helmHelper.seqHelper);return n.init().then((()=>{})),n}}class rr extends s.Mu{getCanonical(e){if(this.isGap(e))return i._S;const t=this.getOriginal(e);let n=t;return t.startsWith("{")?n=t.slice(1):t.endsWith("}")?n=t.slice(0,-1):t.startsWith("(")?n=t.replace(/^\(.\d+\)/,""):t.endsWith(")")&&(n=t.replace(/\(\d+\)$/,"")),n}constructor(e,t){super(e,t)}}async function ir(e){await br.initPromise;const t=window.innerWidth,n=window.innerHeight;try{let i;function s(){if(null==i)return;const e=L()(i.root).find("div.d4-dialog-contents").get(0),t=e.clientHeight,n={0:1},o=Object.values(n).reduce(((e,t)=>e+t),0),r=t-wn().count(0).take(e.children.length).filter((e=>!(e in n))).map((t=>e.children[t])).filter((e=>e instanceof HTMLElement)).map((e=>e.offsetHeight)).reduce(((e,t)=>e+t),0)-38;for(const t of wn().count(0).take(e.children.length))if(t in n){const i=e.children[t],s=r*n[t]/o;i.style.height=`${s}px`}}i=await async function(e,t){const n="ST: PT: HelmDialog()";let i;const s=[];let c=So.aK.Single;const u=()=>{for(const e of s)e.unsubscribe();i.placeholders.detach()};try{const h=await(0,l.pj)(),d=h.getMonomerLib(),p=await(0,Cn.Q)(),m=await(0,bn.b2)(),f=m.buildMonomersFuncsFromLib(d),g=e=>{let t,n,o=null;if(e&&e.rowIndex>=0&&e?.column.semType==r.SEMTYPE.MACROMOLECULE){if(t=p.getSeqHandler(e.column).getValue(e.rowIndex),e.column.temp?.[a.notationProvider]&&!(e.column.temp[a.notationProvider]instanceof or)){let n;o=e.column.temp[a.notationProvider].getHelm(t.value,{}),r.DataFrame.fromColumns([n=r.Column.fromList(r.COLUMN_TYPE.STRING,"seq",[o])]),n.semType=r.SEMTYPE.MACROMOLECULE,n.meta.units=Ot.Hi.HELM,t=p.getSeqHandler(n).getValue(0)}n=t.tags["polytool-data-role"]??"macromolecule"}else{const e=r.Column.fromList(r.COLUMN_TYPE.STRING,"seq",[No.d]);e.semType=r.SEMTYPE.MACROMOLECULE,r.DataFrame.fromColumns([e]),e.meta.units=Ot.Hi.HELM,t=p.getSeqHandler(e).getValue(0),n="macromolecule"}return[t,n]};let y,b,[v,C]=g(e),x=null;const w=P.divText("",{style:{color:"red"}}),A=P.divText("",{style:{fontSize:"11px",color:"var(--grey-4)",marginTop:"2px",marginLeft:"4px",whiteSpace:"nowrap"}});i={macromolecule:m.createHelmInput("Macromolecule",{editable:!1,editorOptions:{drawOptions:{monomerNumbering:1,getMonomer:(t,n)=>{const o=t;if("ATOM"!==o.T)return f.getMonomer(t,n);try{if(v.isDna()||v.isRna()){const e=v.getSplittedWithSugarsAndPhosphates().getCanonical(o.bio.continuousId-1);return f.getMonomer(o.bio.type,e)}if(e?.column?.temp?.[a.notationProvider]instanceof or){const e=v.getSplitted().getCanonical(o.bio.continuousId-1);return f.getMonomer(o.bio.type,e)}{const e=o.elem;return f.getMonomer(o.bio.type,e)}}catch(e){return f.getMonomer(t,n)}}}}}),placeholders:await Io.create("Placeholders",{showAddNewRowIcon:!0,showRemoveRowIcon:!0,showRowHeader:!1,showCellTooltip:!1}),enumeratorType:P.input.choice("Enumerator type",{value:c,items:Object.values(So.aK)}),placeholdersBreadth:await Lo.create("Breadth",{showAddNewRowIcon:!0,showRemoveRowIcon:!0,showRowHeader:!1,showCellTooltip:!1}),keepOriginal:P.input.bool("Keep original",{value:!1}),toAtomicLevel:P.input.bool("To atomic level",{value:!1,onValueChanged:(e,t)=>{N()}}),generateHelm:P.input.bool(Qn,{value:!0}),chiralityEngine:P.input.bool(Jn,{value:!1}),highlightMonomers:P.input.bool(Xn,{value:!1}),rules:{header:P.inlineText([to]),form:await(b=new jn._v(jn.MU,jn.yy,".json",{onValueChanged:e=>{y=e}})).getForm()},trivialName:P.input.string("Trivial name",{value:"",onValueChanged:e=>{const t=e?.trim();x=t?{value:t,colName:"Trivial name"}:null}}),appendToTable:P.input.table("Append to table",{items:o.shell.tables,nullable:!0})};const T=()=>{const e=no[i.enumeratorType.value]??"";P.tooltip.bind(i.enumeratorType.input,e)};if(T(),e?.dataFrame){const t=P.iconFA("columns",(t=>{r.Menu.popup().singleColumnSelector(e.dataFrame,{columnFilter:t=>t.type===r.COLUMN_TYPE.STRING&&t!==e.column,onChange:(t,n,o)=>{o&&(i.trivialName.value=n.get(e.rowIndex)??"")}}).show({x:t.clientX,y:t.clientY})}),"Pick trivial name from a column");i.trivialName.addOptions(t)}i.trivialName.root.style.maxWidth="450px",i.placeholders.onMonomerCellEdit=async(e,t)=>{const n=i.macromolecule.molValue;if(e<0||e>=n.atoms.length)return null;const o=n.atoms[e].biotype(),r=(0,To.Y)(o);return _o(d,r,t,h)},i.placeholdersBreadth.onMonomerCellEdit=async(e,t,n)=>{const o=i.macromolecule.molValue;if(e<0||e>=o.atoms.length)return null;const r=o.atoms[e].biotype(),s=(0,To.Y)(r);return _o(d,s,n,h)};let E=null;i.placeholders.addValidator((e=>{E=null;const t=[];setTimeout((()=>{M()}),100);try{if(i.enumeratorType.value===So.aK.Parallel){const e=i.placeholders.placeholdersValue.filter((e=>e.monomers.length>0));if(e.length>1){const t=e[0].monomers.length,n=e.find((e=>e.monomers.length!==t));n&&(E=`Parallel mode requires all positions to have the same number of monomers. Position ${e[0].position+1} has ${t}, but position ${n.position+1} has ${n.monomers.length}.`)}}if("macromolecule"!==C)return null;const e=[];for(const n of i.placeholders.placeholdersValue){const o=n.position;if(null==o)continue;if(o>=i.macromolecule.molValue.atoms.length){t.push(`There is no monomer at position ${o+1}.`);continue}const r=i.macromolecule.molValue.atoms[o];if(r){const t=r.biotype(),o=(0,To.Y)(t);for(const t of n.monomers){const n=d.getMonomer(o,t);n&&n.lib||e.push({polymerType:o,symbol:t})}}}const n={};for(const t of e){let e=n[t.polymerType];e||(e=n[t.polymerType]=[]),e.push(t.symbol)}const o=Object.entries(n).map((([e,t])=>`${e}: ${t.join(", ")}`)).join("\n");Object.keys(o).length>0&&t.push(`Placeholders contain missed monomers: ${o}`),E=t.length>0?t.join("\n"):E}catch(e){const[t,n]=zn(e,!1);E=t}return setTimeout((()=>{M()}),0),E})),i.enumeratorType.onChanged.subscribe((e=>{c=i.enumeratorType.value,T(),i.placeholders.fireChanged()})),s.push(i.macromolecule.onMouseMove.subscribe((e=>{try{br.logger.debug(`${n}, placeholdersInput.onMouseMove()`);const t=e.offsetX,o=e.offsetY,r=i.macromolecule.molValue,s=m.getHoveredAtom(t,o,r,i.macromolecule.root.clientHeight);if(s){const t=s._parent.atoms.indexOf(s),n=i.placeholders.placeholdersValue.find((e=>e.position===t))?.monomers;if(n){const t=P.divText(n.join(", "));i.macromolecule.showTooltip(t,s),e.preventDefault(),e.stopPropagation()}}}catch(e){zn(e,!1)}}))),s.push(i.macromolecule.onClick.subscribe((e=>{try{br.logger.debug(`${n}, placeholdersInput.onClick()`);const t=e.offsetX,o=e.offsetY,r=i.macromolecule.molValue,s=m.getHoveredAtom(t,o,r,i.macromolecule.root.clientHeight);if(s){const e=s._parent.atoms.indexOf(s);i.placeholders.addPosition(e,"")}}catch(e){zn(e)}}))),s.push(i.placeholders.onChanged.subscribe((()=>{S(),_()}))),s.push(i.placeholdersBreadth.onChanged.subscribe((()=>{_()}))),s.push(i.keepOriginal.onChanged.subscribe((()=>{_()}))),s.push(P.onSizeChanged(i.placeholders.root).subscribe((()=>{t&&t()}))),s.push(o.events.onCurrentCellChanged.subscribe((()=>{const e=o.shell.tv.dataFrame.currentCell;e.column.semType===r.SEMTYPE.MACROMOLECULE&&([v,C]=g(e),O(v,C,e))}))),i.macromolecule.root.style.setProperty("min-width","250px","important");const S=()=>{const e=new Set(i.placeholders.placeholdersValue.map((e=>e.position))),t=i.macromolecule.molValue;for(let n=0;n<t.atoms.length;n++)t.atoms[n].highlighted=e.has(n);i.macromolecule.redraw()},N=()=>{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"),t&&t()};let I=null;const M=()=>{const e=E,t=w;e?(t.innerText=e,t.style.removeProperty("display"),I&&(I.disabled=!0)):(t.innerText="",t.style.setProperty("display","none"),I&&(I.disabled=!1))},_=()=>{try{const e=i.placeholders.placeholdersValue.filter((e=>e.monomers.length>0)),t=i.placeholdersBreadth.placeholdersBreadthValue.filter((e=>e.monomers.length>0&&null!=e.start&&null!=e.end));let n=0;switch(i.enumeratorType.value){case So.aK.Single:n=e.reduce(((e,t)=>e+t.monomers.length),0);break;case So.aK.Parallel:e.length>0&&(n=e.every((t=>t.monomers.length===e[0].monomers.length))?e[0].monomers.length:0);break;case So.aK.Matrix:n=e.length>0?e.reduce(((e,t)=>e*t.monomers.length),1):0}let o=0;t.length>0&&(o=t.reduce(((e,t)=>{const n=Math.abs(t.end-t.start)+1;return e*(t.monomers.length*n)}),1));let r=n+o;i.keepOriginal.value&&r>0&&(r+=1),A.textContent=r>0?`${r} sequence${1!==r?"s":""} will be generated`:""}catch(e){A.textContent=""}},L=e=>{t&&t()},O=(e,t,n)=>{i.macromolecule.value=e;const o=n?.dataFrame;L(o)};O(v,C,e),N(),_();const R=async()=>{try{const t=i.macromolecule.stringValue;if(void 0===t||""===t)o.shell.warning("PolyTool: no molecule was provided");else{if(0===Object.keys(i.placeholders.placeholdersValue).length&&0===Object.keys(i.placeholdersBreadth.placeholdersBreadthValue).length)return void o.shell.warning(`${eo}: placeholders are empty`);await(0,bn.b2)();const n=i.placeholders.placeholdersValue,r=i.enumeratorType.value;if(r===So.aK.Parallel){const e=n.filter((e=>e.monomers.length>0));if(e.length>1){const t=e[0].monomers.length;if(e.some((e=>e.monomers.length!==t)))return void o.shell.warning("Parallel mode requires all positions to have the same number of monomers")}}const s={placeholders:n,type:r,breadthPlaceholders:i.placeholdersBreadth.placeholdersBreadthValue,keepOriginal:i.keepOriginal.value};if(e?.column?.temp?.[a.notationProvider]&&!(e.column.temp[a.notationProvider]instanceof or)){const t=e.column.temp[a.notationProvider];if(t.constructor.implementsFromHelm){const e=t.constructor;s.fromHelmNotation={notationName:e.notationName,convert:t=>e.convertFromHelm(t,{})}}}const l=i.toAtomicLevel.value,c=await sr(t,C,x,s,!!l&&{generateHelm:i.generateHelm.value,chiralityEngine:i.chiralityEngine.value,highlightMonomers:i.highlightMonomers.value,rules:await b.getActive()},m),u=i.appendToTable.value;u?(u.append(c,!0),u.meta.detectSemanticTypes()):o.shell.addTableView(c)}}catch(e){zn(e)}},$=P.dialog({title:eo,showFooter:!0}).add(i.macromolecule.root).add(P.divH([P.divV([i.placeholders.root,P.divH([i.enumeratorType.root,A],{style:{alignItems:"center"}})],{style:{width:"50%"}}),P.divV([i.placeholdersBreadth.root],{style:{width:"50%"}})],{style:{width:"100%"}})).add(P.divH([P.divV([i.trivialName.root,i.keepOriginal.root,i.appendToTable.root],{style:{width:"50%"}}),P.divV([P.divH([i.toAtomicLevel.root,i.generateHelm.root]),P.divH([i.chiralityEngine.root,i.highlightMonomers.root]),i.rules.header,i.rules.form],{style:{width:"50%"}})],{style:{width:"100%"}})).add(w).onOK((()=>{if(E)return M(),void o.shell.warning("Please fix validation errors before running enumeration");R()}));return I=$.getButton("OK"),s.push($.onClose.subscribe((()=>{u()}))),$.history((()=>({description:`${i.enumeratorType.value} ${i.placeholders.placeholdersValue?.map((e=>(e.position?.toString()??"")+": "+e.monomers?.join(", "))).join("; ")}`,placeholders:i.placeholders.stringValue,enumeratorType:i.enumeratorType.value,placeholdersBreadth:i.placeholdersBreadth.stringValue,trivialName:i.trivialName.value,keepOriginal:i.keepOriginal.value,toAtomicLevel:i.toAtomicLevel.value,generateHelm:i.generateHelm.value,chiralityEngine:i.chiralityEngine.value,highlightMonomers:i.highlightMonomers.value,rules:y})),(e=>{i.enumeratorType.value=e.enumeratorType??So.aK.Single,i.placeholders.stringValue=e.placeholders,i.placeholdersBreadth.stringValue=e.placeholdersBreadth,e.trivialName&&(i.trivialName.value=e.trivialName),i.keepOriginal.value=e.keepOriginal??!1,i.toAtomicLevel.value=e.toAtomicLevel??!0,i.generateHelm.value=e.generateHelm??!0,i.chiralityEngine.value=e.chiralityEngine??!1,i.highlightMonomers.value=e.highlightMonomers??!1,b.setActive(e.rules),setTimeout((()=>{i.placeholders.invalidateGrid(),i.placeholdersBreadth.invalidateGrid(),_()}),100)})),$}catch(e){throw u(),e}}(e,s);let c=!0;P.onSizeChanged(i.root).subscribe((()=>{if(c){const e=.7*t,o=.7*n;i.root.style.width=`${Math.min(t,e)}px`,i.root.style.height=`${Math.min(n,o)}px`,i.root.style.left=`${Math.floor((t-i.root.offsetWidth)/2)}px`,i.root.style.top=`${Math.floor((n-i.root.offsetHeight)/2)}px`,c=!1}s()})),s(),br.logger.debug("PolyToolEnumerateHelmUI: dialog before show"),i.show({width:Math.max(350,.7*t),resizable:!0}),br.logger.debug("PolyToolEnumerateHelmUI: dialog after show")}catch(u){const[h,d]=(0,vn.AP)(u);br.logger.error(h,void 0,d)}}async function sr(e,t,n,i,s,a){const c=r.TaskBarProgressIndicator.create("PolyTool enumerating...");try{const c=await(0,l.pj)(),u=await(0,Vn.j)(),h=c.getMonomerLib(),d=(0,No.o)(e,n?.value??"",i);let p;switch(t){case"macromolecule":p=r.Column.fromType(r.COLUMN_TYPE.STRING,"Enumerated",d.length).init((e=>d[e][0]));break;case"template":{const e=new Array(d.length);for(let t=0;t<d.length;t++){const n=d[t][0],o=Oo.s.fromHelm(n,a);e[t]=o.getNotation()}p=r.Column.fromList(r.COLUMN_TYPE.STRING,"Enumerated",e),p.semType=r.SEMTYPE.MACROMOLECULE,p.setTag("polytool-data-role","template"),Cr.applyNotationProviderForCyclized(p,"-");break}}const m=r.DataFrame.fromColumns([p]);if("macromolecule"===t&&i.fromHelmNotation){const e=r.Column.fromType(r.COLUMN_TYPE.STRING,`${i.fromHelmNotation.notationName}(${p.name})`,m.rowCount).init((e=>p.isNone(e)?null:i.fromHelmNotation.convert(p.get(e))));m.columns.add(e)}if(await o.data.detectSemanticTypes(m),"template"==t&&Cr.applyNotationProviderForCyclized(p,"-"),s){let e;if("macromolecule"===t){e=p;const t=await a.seqHelper.helmToAtomicLevel(e,s.chiralityEngine,s.highlightMonomers);m.columns.add(t.molCol,!1);const n=t.molCol;await async function(e,t,n,o,r,i=!1){const s=o.getSeqHandler(e),a=s.alphabet==Ot.YI.RNA||s.alphabet==Ot.YI.DNA,l=s.isHelm()&&a,c=!s.isHelm()&&a,u=e=>null==e?null:l?i?e:Math.floor(e/3):c&&i?3*e+1:e,h=i?await o.getHelmToMolfileConverter(n):null,d=new On({max:100});function p(e,t){const s=e.get(t);if(null==s)return null;let a=d.get(s);return a||d.set(s,a=function(e,t){const s=o.getSeqHandler(e);if(i){const e=s.getHelm(t);return o.helmToAtomicLevelSingle(e,h,!1,!1).monomers}{const e=s.getSplitted(t),o=s.defaultBiotype,i=wn().count(0).take(e.length).map((t=>({position:t,symbol:e.getCanonical(t),biotype:o}))).toArray(),a=s.alphabet,l=a==Ot.YI.RNA||a==Ot.YI.DNA?"RNA":"PEPTIDE",c=(0,Bn.eM)([i],[void 0],l,a,n,r);return(0,Fn.gU)(i,c,a,l).monomers}}(e,t)),a}const m={targetCol:t,handler:(t,o,r)=>{const i=r.grid,s=t.tableRowIndex,a=t.gridRow,l=i.cell(r.name,a),c=Rn();if(!c||c&&(c.dataFrameId!=e.dataFrame.id||c.gridRowIdx!=a||c.seqColName!=e.name||c.seqPosition!=o?.position)){if(c&&($n(null),c.gridCell.render()),!o)return $n(null),!0;$n({gridCell:l,dataFrameId:e.dataFrame.id,gridRowIdx:a,seqColName:e.name,seqPosition:u(o?.position)??-1,getSubstruct:()=>{if(!o||"*"===o.symbol)return;const t=p(e,s);if(!t)return;const r=t.get(u(o?.position));return r?(0,kn.H)([r],n):{atoms:[],bonds:[],highlightAtomColors:[],highlightBondColors:[]}}}),l.render()}return!0},getSubstruct:o=>{if("true"!=t.getTag(".sequence-src-highlight-monomers"))return;if(null==o)return;if(!e.get(o))return;const r=p(e,o);return r?(0,kn.H)(r.values(),n):void 0}};return Gn(e.temp,m),Dn(t.temp,m),m}(e,n,h,a.seqHelper,u,!0)}else"template"===t&&(e=(await ro(p,s.generateHelm,!1,s.chiralityEngine,!1,s.rules))[0])}if(n){const e=r.Column.fromType(r.COLUMN_TYPE.STRING,n.colName,d.length).init((e=>d[e][1]));m.columns.add(e)}return m}finally{c.close()}}var ar,lr=n(3151);class cr{constructor(e){this.rawLib=e}isValid(){return this.rawLib.every((e=>"object"==typeof e&&Object.values(Yn).every((t=>t in e&&"string"==typeof e[t]))))}getJsonMonomerLib(){const e=[];return this.rawLib.forEach((t=>{const n=this.prepareMonomer(t);e.push(n)})),e}prepareMonomer(e){const t={...lr.pe};Object.entries(Yn).forEach((([n,o])=>{const r=e[o];t[n]=r}));let n="smiles";const o=e[Yn[n]],r=new ur(o),i=r.getCappedSmiles();return t[n]=i,n="rgroups",t[n]=hr.getRGroups(r.getNumberOfRGroups()),n="molfile",t[n]=new dr(r.getSmilesWithRGroups()).getMolfile(),t}}class ur{constructor(e){let t=0;this.smilesWithRGroups=e.replace(/\[R(\d+)\]/g,((e,n)=>(++t,`[${n}*]`))),this.numberOfRGroups=t}getSmilesWithRGroups(){return this.smilesWithRGroups}getCappedSmiles(){return this.capRGroups()}getNumberOfRGroups(){return this.numberOfRGroups}capRGroups(){let e=this.smilesWithRGroups.replace("[1*]","[H:1]");return e=e.replace("[2*]","[OH:2]"),e.replace("[3*]","[H:3]")}}class hr{constructor(){}static getRGroups(e){return Kn.slice(0,e)}}class dr{constructor(e){this.smilesWithRGroups=e}getMolfile(){let e=r.chem.convert(this.smilesWithRGroups,r.chem.Notation.Smiles,r.chem.Notation.MolBlock);return e=this.restoreRGPLine(e),e=this.fixRGroupSymbols(e),e}restoreRGPLine(e){return e.replace("M ISO","M RGP")}fixRGroupSymbols(e){return e.replace(/\bR\b/g,"R#")}}class pr{constructor(e,t){this.fileName=e,this.fileContent=t,this.validateFileType();const n=r.DataFrame.fromCsv(this.fileContent),o=this.toJson(n);this.polyToolMonomerLib=new cr(o),this.validateContent()}async getJson(){return this.polyToolMonomerLib.getJsonMonomerLib()}toJson(e){return Array.from({length:e.rowCount},((t,n)=>e.columns.names().reduce(((t,o)=>(t[o]=e.get(o,n),t)),{})))}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(e){e.table="table",e.seqCol="seqCol",e.generateHelm="generateHelm",e.chiralityEngine="chiralityEngine",e.rules="rules"}(ar||(ar={}));class mr{constructor(e){this.call=e,this.ruleInputs=new jn._v(jn.MU,jn.yy,".json")}async initInputs(){const e=e=>this.call.inputParams[e],t=await this.ruleInputs.getForm();this.inputs={table:(()=>{const t=e(ar.table);return P.input.table(t.property.caption,{value:t.value})})(),seqCol:(()=>{const t=e(ar.seqCol);return P.input.column(t.property.caption,{value:t.value,table:t.value.dataFrame})})(),generateHelm:P.input.forProperty(e(ar.generateHelm).property),chiralityEngine:P.input.forProperty(e(ar.chiralityEngine).property),rules:{header:P.inlineText([to]),form:t}}}static async create(e){const t=new mr(e);return await t.initInputs(),t}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 e=P.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(((t,n)=>{P.dialog({title:Zn}).add(e).onOK((async()=>{const e=await this.getParams(),n=(await this.call.func.prepare(e).call(!0)).getOutputParamValue();t(n)})).onCancel((()=>{n(new Error("Cancelled by user"))})).show()}))}widget(){throw new Error("not implemented")}}var fr=function(e,t,n,o){var r,i=arguments.length,s=i<3?t:null===o?o=Object.getOwnPropertyDescriptor(t,n):o;if("object"==typeof Reflect&&"function"==typeof Reflect.decorate)s=Reflect.decorate(e,t,n,o);else for(var a=e.length-1;a>=0;a--)(r=e[a])&&(s=(i<3?r(s):i>3?r(t,n,s):r(t,n))||s);return i>3&&s&&Object.defineProperty(t,n,s),s},gr=function(e,t){if("object"==typeof Reflect&&"function"==typeof Reflect.metadata)return Reflect.metadata(e,t)},yr=function(e,t){return function(n,o){t(n,o,e)}};o.decorators||(o.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((e=>{o.decorators[e]||(o.decorators[e]=function(e){return function(e,t,n){}})}));const br=new R({debug:!0});let vr=null;class Cr{static async oligoToolkitApp(){await br.initLibData();const e=await async function(e){const t={"Mermadesynthesis:merMadeSynthesis":{tabName:"SYNTHESIZE",parameters:Kt(e)}},n={};for(const[e,r]of Object.entries(t)){let t;try{t=await o.functions.call(e,r.parameters);const i=new zt(r.tabName,t);i.initView(),n[r.tabName]=()=>i.getView()}catch(t){console.warn(`Plugin ${e} not loaded, reason:`,t);continue}}return n}(br);if(!e)throw new Error("External app view factories not loaded");const t=new Yt(e,br);return await t.getAppView()}static async init(){return null===vr&&br.startInit(vr=async function(){const[e]=await Promise.all([(0,bn.b2)()]);br.completeInit(e)}()),vr}static async oligoTranslatorApp(){return await xr("Oligo Translator")}static async oligoPatternApp(){return await xr("Oligo Pattern")}static async oligoStructureApp(){return await xr("Oligo Structure")}static async getTranslationHelper(){return await br.initLibData(),br}static getCodeToWeightsMap(){const e=br.monomerLibWrapper.getCodesToWeightsMap();return Object.fromEntries(e)}static validateSequence(e){const t=br.createSequenceValidator(e),n=br.createFormatDetector(e).getFormat();return null!==n&&t.isValidSequence(n)}static getMolfileFromGcrsSequence(e,t){return new At(e,t,"GCRS").convert()}static linkStrands(e){return Tt(e,!0)}static async demoTranslateSequence(){await async function(){await b((async()=>{const e=await Cr.oligoTranslatorApp();o.shell.addView(e)}))}()}static async demoOligoPattern(){await async function(){await b((async()=>{const e=await Cr.oligoPatternApp();o.shell.addView(e)}))}()}static async demoOligoStructure(){await async function(){await b((async()=>{const e=await Cr.oligoStructureApp();o.shell.addView(e),["Afcgacsu","Afcgacsu","Afcgacsu"].forEach((async(e,t)=>{await async function(e,t){await r.delay(500);const n=document.querySelectorAll(".st-colored-text-input > textarea")[e];n.value=t;const o=new Event("input");n.dispatchEvent(o)}(t,e)}))}))}()}static async translateOligonucleotideSequence(e,t,n){return await br.initLibData(),br.createFormatConverter(e,t).convertTo(n)}static async polyToolConvertTopMenu(){await async function(){await br.initPromise;let e=null;try{e=await async function(){const e=[],t=()=>{for(const t of e)t.unsubscribe()};try{let n;const i=o.shell.t.columns.bySemTypeAll(r.SEMTYPE.MACROMOLECULE),s=i.filter((e=>br.seqHelper.getSeqHandler(e).notation===Ot.Hi.CUSTOM));if(!n){if(i.length<1)throw new Error("No dataframe with macromolecule columns open");if(s.length<1){const e=r.Func.find({package:"Bio",name:"toAtomicLevel"})[0];return e?(e.prepare().edit(),null):(o.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=P.input.column("Column",{table:n.dataFrame,value:n,filter:e=>s.includes(e)}),l=P.input.bool(Qn,{value:!0});P.tooltip.bind(l.root,"Add HELM column");const c=P.input.bool("Linearize",{value:!0});P.tooltip.bind(c.root,"Make representation linear if possible");const u=P.input.bool(Jn,{value:!0}),h=P.input.bool(Xn,{value:!0});let d;const p=new jn._v(jn.MU,jn.yy,".json",{onValueChanged:e=>{d=e}}),m=P.inlineText([to]);P.tooltip.bind(m,"Add or specify rules to use");const f=await p.getForm(),g=P.divV([a,l,c,u,h,m,f]),y=async()=>{try{const e=await p.getActive();await ro(a.value,l.value,c.value,u.value,h.value,e)}catch(e){zn(e)}},b=P.dialog(Zn).add(g).onOK((()=>{y()}));return e.push(b.onClose.subscribe((()=>{t()}))),b.history((()=>({generateHelm:l.value,chiralityEngine:u.value,rules:d})),(e=>{l.value=e.generateHelm,u.value=e.chiralityEngine,p.setActive(e.rules)})),b}catch(e){throw t(),e}}(),e?.show()}catch(e){const[t,n]=(0,vn.AP)(e);o.shell.warning("To run PolyTool Conversion, open a dataframe with macromolecules"),br.logger.error(t,void 0,n)}}()}static async getPolyToolConvertEditor(e){const t=await mr.create(e);return await t.showDialog()}static async polyToolConvert2(e,t,n,o,r){return(await ro(t,n,!1,o,!1,r))[0]}static async polyToolEnumerateHelmTopMenu(){await ir(o.shell.tv?.dataFrame.currentCell)}static async polyToolEnumerateChemTopMenu(){wo()}static async chemEnumerateReactionsTopMenu(){wo()}static async polyToolColumnChoice(e,t){var n;(function(e){e.semType=r.SEMTYPE.MACROMOLECULE,e.setTag("aligned","SEQ"),e.setTag("alphabet",Ot.YI.PT)})(n=t),n.meta.units=Ot.Hi.SEPARATOR,n.setTag("separator","-"),await o.data.detectSemanticTypes(e)}static async createMonomerLibraryForPolyTool(e){const t=await e.readAsString(),n=new pr(e.fileName,t),o=await n.getJson(),i=e.fileName.replace(/\.csv$/,".json"),s=JSON.stringify(o,null,2);r.Utils.download(i,s)}static async ptEnumeratorHelmApp(){await ir()}static async ptEnumeratorChemApp(){return await async function(){await br.initPromise;try{const e=Ao(await(0,Vn.j)(),null),t=P.bigButton("Enumerate",(async()=>{await e.execute()}));e.bindActionButton(t);const n=r.View.create();return n.name=so,n.box=!0,n.root.appendChild(P.divV([e.root,P.div([t],{style:{padding:"8px 4px 0"}})],{style:{height:"100%",width:"100%",padding:"8px"}})),n}catch(e){return zn(e),null}}()}static async getPtHelmEnumeratorDialog(e){return ir(e)}static async getPtChemEnumeratorDialog(e){return wo(e)}static async enumerateSingleHelmSequence(e,t,n,o=!1){return await sr(e,"macromolecule",null,{type:So.aK.Single,placeholders:t.map(((e,t)=>({position:e,monomers:n[t]})))},!!o&&{generateHelm:!0,chiralityEngine:!0,highlightMonomers:!1,rules:[]},br.helmHelper)}static async enumerateSingleHelmSequenceWithNaturalAAs(e,t=!1){const n=(0,Ot.qp)(e).length,o=Array.from({length:n},((e,t)=>t)),r=o.map((e=>["A","C","D","E","F","G","H","I","K","L","M","N","P","Q","R","S","T","V","W","Y"]));return await Cr.enumerateSingleHelmSequence(e,o,r,t)}static async getPolyToolCombineDialog(){!async function(){const e=[],t=P.divV([]),n=i=>{const s=(()=>{const e=P.divH([]),t=P.input.table("Table",{value:void 0,tooltipText:"Table with sequences"}),n=P.input.choice("Column",{items:[],value:void 0,tooltipText:"Sequence column"});return t.onChanged.subscribe((async()=>{const e=t.value;if(!e)return n.items=[],void(n.value=null);await e.meta.detectSemanticTypes(),await o.data.detectSemanticTypes(e);const i=Array.from(e.columns.categorical),s=i.map((e=>e.name));n.items=s,n.value=i.find((e=>e.semType===r.SEMTYPE.MACROMOLECULE))?.name??s.find((e=>{const t=e.toLowerCase();return t.includes("seq")||t.includes("pep")}))??s[0]})),e.appendChild(t.root),e.appendChild(n.root),e.style.alignItems="center",{root:e,getValue:()=>({table:t.value,column:n.value})}})(),a=P.icons.delete((()=>{if(!s.root.parentElement||e.length<2)return;s.root.remove();const t=e.indexOf(s);-1!==t&&e.splice(t,1)}),"Remove"),l=P.icons.add((()=>{let t=e.indexOf(s);-1===t&&(t=e.length),n(t+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 c=e[i];c?t.insertBefore(s.root,c.root):t.appendChild(s.root),e.splice(i,0,s)};n(0);const i=P.input.string("Separator",{value:"-",tooltipText:"Separator for sequences",nullable:!1});P.dialog("Combine Sequences").add(t).add(i.root).onOK((async()=>{if(!function(){const t=e.map((e=>e.getValue())),n=t.map((e=>e.table)),o=t.map((e=>e.column));return n.every((e=>!!e))&&o.every((e=>!!e))}())return void o.shell.error("Please fill all the fields");const t=e.map((e=>e.getValue())),n=t.map((e=>e.table)),s=t.map((e=>e.column)),a=i.value,l=s.map(((e,t)=>n[t].col(e).toList().filter((e=>!!e))));let c=0;const u=l.reduce(((e,t)=>e*t.length),1);if(u>1e7)return void o.shell.error("Too many combinations. Maximum allowed is 10M");const h=new Array(u).fill(null),d=(e,t)=>{if(t===l.length)return void(h[c++]=e);const n=`${e}${e?a:""}`,o=l[t];for(let e=0;e<l[t].length;e++)d(n+o[e],t+1)};d("",0);const p=r.DataFrame.fromColumns([r.Column.fromStrings("Combined Sequences",h)]);p.name="Combined Sequences",await p.meta.detectSemanticTypes(),await o.data.detectSemanticTypes(p),o.shell.addTableView(p)})).show({resizable:!0})}()}static oligoNucleotideCellRenderer(){return new un}static oligoNucleotidePanel(e){return function(e){const t=e.value??"",n=(0,Jt.On)(t),o=n.sense.monomers.filter((e=>"nucleotide"===e.kind)).length,i=n.antisense?n.antisense.monomers.filter((e=>"nucleotide"===e.kind)).length:0,s=new Map,a=new Map,l=new Map,c=[...n.sense.monomers,...n.antisense?.monomers??[]];for(const e of c)if("nucleotide"===e.kind){const t=e;hn(s,t.sugar),t.phosphate&&hn(a,t.phosphate)}else hn(l,e.symbol);const u=P.divV([],{style:{fontSize:"12px"}});return u.appendChild(pn("Summary",P.tableFromMap({"Sense length":`${o} nt`,"Antisense length":i?`${i} nt`:"single-strand","Modifications used":dn(s,a),Conjugates:l.size?Array.from(l.entries()).map((([e,t])=>`${(0,Xt.rK)(e).meta.name} ×${t}`)).join(", "):"—"}))),u.appendChild(pn("Legend",function(e,t,n){const o=[],r=new Map;for(const[t,n]of e.entries()){const e=(0,Xt.Jy)(t);"r"!==e&&"d"!==e&&r.set(e,(r.get(e)??0)+n)}for(const[e,t]of r.entries()){const n=(0,Xt.xh)(e,null).meta;o.push({label:n.name,color:n.color,count:t})}const i=new Map;for(const[e,n]of t.entries()){const t=(0,Xt.$T)(e);"p"!==t&&i.set(t,(i.get(t)??0)+n)}for(const[e,t]of i.entries()){const n=(0,Xt.bM)(e).meta;o.push({label:`${n.name} (linkage)`,color:n.color,count:t})}for(const[e,t]of n.entries()){const n=(0,Xt.rK)(e).meta;o.push({label:n.name,color:n.color,count:t})}if(0===o.length)return P.divText("No modifications. Chip color reflects the base (A/C/G/U).",{style:{fontSize:"12px",color:"var(--grey-4, #888)",lineHeight:"1.4"}});const s=o.map((({label:e,color:t,count:n})=>P.divH([P.div([],{style:{width:"14px",height:"14px",borderRadius:"3px",background:t,border:"1px solid rgba(0,0,0,0.15)",flexShrink:"0"}}),P.divText(e,{style:{fontSize:"12px",flex:"1"}}),P.divText(`×${n}`,{style:{fontSize:"11px",color:"var(--grey-4, #888)",fontVariantNumeric:"tabular-nums"}})],{style:{gap:"6px",alignItems:"center",marginBottom:"3px"}})));return P.divV(s)}(s,a,l))),r.Widget.fromRoot(u)}(e)}static oligoNucleotideStructuresPanel(e){return function(e){const t=(e.value??"").split("$")[0].split("|").map((e=>e.trim())).filter((e=>e.length>0));if(0===t.length)return r.Widget.fromRoot(P.divText("No HELM chains found",{style:{fontSize:"12px",color:"var(--grey-4, #888)"}}));const n=t.map((e=>(0,Jt.nj)(e.replace(mn,"$11{")+"$$$$"))),o=1===t.length?["Strand"]:["Sense","Antisense"],i=r.Column.fromStrings("helm",n);i.semType=r.SEMTYPE.MACROMOLECULE,i.meta.units="helm",i.setTag("aligned","SEQ"),i.setTag("alphabet","RNA"),i.setTag("cell.renderer","helm");const s=r.DataFrame.fromColumns([i]),a=P.accordion("oligo chemical structures");for(let e=0;e<s.rowCount;e++){const t=o[e],n=s.cell(e,"helm");a.addPane(t,(()=>fn(n,t)))}return r.Widget.fromRoot(a.root)}(e)}static async convertHelmToOligoNucleotide(e,t){const n=function(e,t){const n=new Array(t.length);for(let e=0;e<t.length;e++)n[e]=t.get(e)??"";const o=r.Column.fromStrings(e.columns.getUnusedName(`${t.name} (oligo)`),n);return gn(o),e.columns.add(o),o}(e,t);return await o.data.detectSemanticTypes(e),n}static async combineSenseAntisenseToOligoNucleotide(e,t,n){const i=function(e,t,n){if(t.length!==n.length)throw new Error("Sense and antisense columns must have the same length");const o=new Array(t.length);for(let e=0;e<t.length;e++){const r=t.get(e)??"",i=n.get(e)??"";if(!(0,Jt.yO)(r)){o[e]="";continue}const s=yn(r,1),a=(0,Jt.yO)(i)?yn(i,2):"",l=a?`${s}|${a}`:s;o[e]=`${l}$$$$`}const i=r.Column.fromStrings(e.columns.getUnusedName(`${t.name}+${n.name} (oligo)`),o);return gn(i),e.columns.add(i),i}(e,t,n);return await o.data.detectSemanticTypes(e),i}static applyNotationProviderForCyclized(e,t){e.setTag("aligned","SEQ"),e.setTag("alphabet","UN"),e.setTag(".alphabetIsMultichar","true"),e.meta.units=i.Hi.CUSTOM,t&&!e.tags[i.qE.separator]&&(e.tags[i.qE.separator]=t),e.tags["polytool-data-role"]="template",e.temp[a.notationProvider]=new or(t,br.helmHelper)}static async harmonizedSequenceNotationProviderConstructor(){return or}}async function xr(e){await br.initLibData();const t=function(e,t){switch(e){case"Oligo Translator":return new Wt(t);case"Oligo Pattern":return new it(t);case"Oligo Structure":return new Lt(t);default:throw new Error(`Unknown app name: ${e}`)}}(e,br);return await 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o=n(2125),r=n(8438),i=n(6694);function s(e,t){let n="";for(let e=0;e<t.length;e++){e>0&&(n+="|"),n+=`PEPTIDE${e+1}{`;for(let o=0;o<t[e].length;o++){o>0&&(n+=".");const r=t[e][o];n+=r.length>1?`[${r}]`:r}n+="}"}n+="$";for(let r=0;r<e.length;r++)r>0&&(n+="|"),n+=`PEPTIDE${e[r].fChain+1},PEPTIDE${e[r].sChain+1},`,n+=`${(0,o.M)(e[r].fMonomer-1,t)[0]+1}:R${e[r].fR}-`,n+=`${(0,o.M)(e[r].sMonomer-1,t)[0]+1}:R${e[r].sR}`;return n+="$$$V2.0",n}function a(e,t,n,o=0,r=[],i=[]){let[s,a,l,c,u]=[!1,!1,!1,-1,-1];for(let h=0;h<e.length;h++)if(e[h].includes(t)){if(s){if(l&&(n||e[h]==i[o]+t)){a=!0,u=h;break}if(l||!n&&e[h]!=r[o]+t)continue;a=!0,u=h;break}if(n)s=!0,l=!0,c=h;else if(e[h]==r[o]+t)s=!0,l=!0,c=h;else{if(e[h]!=i[o]+t)continue;s=!0,l=!!n,c=h}}return[s,a,l,c,u]}function l(e,t){const n=[];for(let o=0;o<t.length;o++){const r=`(${t[o].code})`,[s,l]=(0,i.Ln)(t[o]);if(s.length>0)for(let 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h=n(3599);function d(e,t,n){const o=n.createHelmWebEditor().editor.m;let r=0;const i=new JSDraw2.Point(0,0);for(let e=0;e<t.length;e++)for(let n=0;n<t[e].length;n++){if(t[e][n]){const s=t[e][n],a={type:h.o.AA,i:e,j:n,continuousId:r},l=new JSDraw2.Atom(i,s,a);if(o.addAtom(l),0!==n){const e=o.atoms[r-1],t=o.atoms[r],n=new JSDraw2.Bond(e,t);n.r1=2,n.r2=1,o.addBond(n)}r++,i.x+=JSDraw2.Editor.BONDLENGTH}i.y+=4*JSDraw2.Editor.BONDLENGTH}for(let t=0;t<e.length;t++){const n=o.atoms[e[t].fMonomer-1],r=o.atoms[e[t].sMonomer-1],i=new JSDraw2.Bond(n,r);i.r1=e[t].fR,i.r2=e[t].sR,o.addBond(i)}return o}class p{constructor(e,t,n){this.helmHelper=n,this.underRules=!1,this.posToPosUnderRules=[],this.linkages=t,this.monomers=e,this.mol=d(t,e,n)}static fromSeparator(e,t){const[n,o]=function(e){const t=[],n=[],o=/(\(.\d+\))?\{[^\}]*\}/g,r=[];r.push(e.replaceAll(o,""));const i=e.matchAll(o);for(const e of i){const t=e[0];t&&r.push(t)}let s=0;for(let e=0;e<r.length;e++){const o=r[e].split("-"),i=new 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function(e){const t=e.atoms,n=e.bonds,o=[],r=[];for(let e=0;e<n.length;e++)n[e].a1.bio.i!==n[e].a2.bio.i&&r.push(e);for(let e=0;e<t.length;e++){const n=t[e].bio?.i;n+1>o.length?o.push(1):o[n]++}const i=new Array(o.length);let s=0;for(let e=0;e<o.length;e++){const n=new Array(o[e]);for(let r=0;r<o[e];r++)n[r]=t[s].elem,s++;i[e]=n}let a="";for(let e=0;e<i.length;e++){let t="";for(let n=0;n<i[e].length;n++)t+=`${0==n?"":"-"}${i[e][n]}`;if(0!==e){const e=/(\(.\d+\))/,n=t.match(e);t=t.replace(n?.[0],""),t=`${n?n?.[0]:""}{${t}}`}else if(i.length>1){const e=0==n[r[0]].a1.bio.i&&0==n[r[0]].a1.bio.j,o=1==n[r[0]].a2.bio.i&&0==n[r[0]].a1.bio.j;e&&o&&(t+="-")}a+=t}return a}(this.mol)}getHelm(){return this.underRules?s(this.linkagesUnderRules,this.monomersUnderRules):s(this.linkages,this.monomers)}applyRules(e){const t=this.getNotation(),[n,o,r]=function(e,t){const n=[],o=[],r=[],i=t.heterodimerCode,s=t.homodimerCode,a=null!==i?e.split(`(${t.heterodimerCode})`):"";null!==i&&a.length>1?(r.push({fChain:0,sChain:1,fMonomer:1,sMonomer:1,fR:1,sR:1}),n.push(a[1].replaceAll("{","").replaceAll("}","")),n.push(a[2].replaceAll("{","").replaceAll("}","")),o.push(!1),o.push(!1)):(n.push(e),o.push(!1));for(let e=0;e<n.length;e++)if(null!==s&&n[e].includes(`(${s})`)){const t=n.length;r.push({fChain:e,sChain:t,fMonomer:1,sMonomer:1,fR:1,sR:1});const i=n[e].replace(`(${s})`,""),a=i.indexOf("{"),l=i.slice(0,a),c=i.replace(l,"").replaceAll("{","").replaceAll("}","");n[e]=l+c,n.push(c),o.push(!0)}return[r,n,o]}(t,e),i=new Array(o.length);let s=0;for(let e=0;e<o.length;e++)if(i[e]=o[e].split("-"),r[e]){const t=this.posToPosUnderRules.length-i[e].length;for(let n=0;n<i[e].length;n++)this.posToPosUnderRules[t+n].push(s),s++}else for(let t=0;t<i[e].length;t++)this.posToPosUnderRules.push([s]),s++;!function(e,t,n){for(let o=0;o<e.length;o++){const r=e[o],i=l(r,n.linkRules),[s,a,u,h]=c(n.linkRules,r,i);for(let e=0;e<s.length;e++)t.push({fChain:o,sChain:o,fMonomer:s[e],sMonomer:a[e],fR:u[e],sR:h[e]});e[o]=r}}(i,n,e),function(e,t,n){for(let o=0;o<e.length;o++){const r=l(e[o],n.reactionRules),[i,s,a]=u(n.reactionRules,e[o],r);i.length>=1&&(t.push({fChain:o,sChain:e.length,fMonomer:i[0],sMonomer:1,fR:3,sR:1}),t.push({fChain:o,sChain:e.length,fMonomer:s[0],sMonomer:1,fR:3,sR:2}),e.push([n.reactionRules[a[0]].name]))}}(i,n,e),this.underRules=!0,this.linkagesUnderRules=n,this.monomersUnderRules=i,this.molUnderRules=d(n,i,this.helmHelper)}check(e=!1){const t=[],n=this.monomers.map((e=>e.length)).reduce(((e,t)=>e+t),0);this.mol.atoms.length!==n&&t.push(`The mol atoms count ${this.mol.atoms.length} does not match the total number ${n} of chains' monomers.`);const o=this.monomers.map((e=>e.length-1)).reduce(((e,t)=>e+t),0)+this.linkages.length;this.mol.bonds.length!==o&&t.push(`The mol bonds count ${this.mol.bonds.length} does not match the total number ${o} in- and inter-chain linkages.`);let r=0;for(let e=0;e<this.monomers.length;++e){const n=this.monomers[e];for(let e=0;e<n.length;++e)try{const o=n[e],i=this.mol.atoms[r];i.bio.continuousId!==r&&t.push(`Atom #${r} has incorrect .bio.continuousId: ${i.bio.continuousId}.`),i.elem!==o&&t.push(`Atom #${r} elem: '${i.elem}' does not match chain monomer: '${o}'.`)}finally{r++}}if(e&&t.length>0)throw new Error(`Chain errors:\n${t.map((e=>` ${e}`)).join("\n")}`);return t}}},4229:(e,t,n)=>{"use strict";n.d(t,{b:()=>s});var o=n(9192),r=n(6307),i=n(9022);function s(e,t,n){const s=new Array(e.length),a=new Array(e.length),l=new Array(e.length);for(let c=0;c<e.length;c++)try{if(null==e[c])s[c]="";else{const o=r.s.fromSeparator(e[c],n);o.applyRules(t),a[c]=!(o.monomersUnderRules.length>1||o.linkagesUnderRules.length>0),s[c]=o.getHelm(),l[c]=o.posToPosUnderRules}}catch(e){const[t,n]=(0,o.AP)(e);i._package.logger.error(t,void 0,n),s[c]=""}return[s,a,l]}},2125:(e,t,n)=>{"use strict";function o(e,t){let n,o=e;for(n=0;n<t.length&&o>=t[n].length;++n)o-=t[n].length;return[o,n]}function r(e,t,n){let o=0;for(let e=0;e<t;++e)o+=n[e].length;return o+e}n.d(t,{M:()=>o,j:()=>r})},6694:(e,t,n)=>{"use strict";n.d(t,{MU:()=>V,yy:()=>j,_v:()=>J,Ln:()=>te,Q4:()=>ee});var o=n(6082),r=n(4328),i=n(7389),s=n(1991),a=n.n(s),l=function(e,t,n,o){return new(n||(n=Promise))((function(r,i){function s(e){try{l(o.next(e))}catch(e){i(e)}}function a(e){try{l(o.throw(e))}catch(e){i(e)}}function l(e){var t;e.done?r(e.value):(t=e.value,t instanceof n?t:new n((function(e){e(t)}))).then(s,a)}l((o=o.apply(e,t||[])).next())}))};class c{constructor(e,t,n=".csv",o){this.path=e,this.userStorageName=t,this.ext=n,this.options=o,this.inputs=null,"/"!==this.path[this.path.length-1]&&(this.path+="/"),"."!==this.ext[0]&&(this.ext="."+this.ext)}getUserSettings(){return l(this,void 0,void 0,(function*(){if(this.settings)return this.settings;const e=r.userSettings.getValue(this.userStorageName,"Settings"),t=e?JSON.parse(e):{excluded:[],explicit:[]};return t.explicit=t.explicit instanceof Array?t.explicit:[],t.excluded=t.excluded instanceof Array?t.excluded:[],this.settings=t}))}setUserSettings(e){this.settings=e,r.userSettings.add(this.userStorageName,"Settings",JSON.stringify(e))}getAllAvailable(){return l(this,void 0,void 0,(function*(){return(yield r.dapi.files.list(this.path)).map((e=>e.fullPath.replace(`${this.path}`,"")))}))}getActive(){return l(this,void 0,void 0,(function*(){const e=yield this.getUserSettings();return e.explicit.length>0?e.explicit:(yield this.getAllAvailable()).filter((t=>!e.excluded.includes(t)))}))}setActive(e){const t=new Set(e);for(const[e,n]of this.inputs.entries())n.value=t.has(e)}createInput(e,t){const n=i.input.bool(e,{value:t,onValueChanged:t=>this.updateSelectionStatus(e,t)});return n.addOptions(i.button(i.iconFA("trash"),(()=>{i.dialog({title:"Warning"}).add(i.divText(`Delete file '${e}'?`)).onOK((()=>{n.root.remove(),this.availableRemove(e)})).show()}),`Delete ${e}`)),n}getInputs(){return l(this,void 0,void 0,(function*(){this.inputs=new Map;const e=yield this.getAllAvailable(),t=yield this.getActive(),n=new Array(e.length);for(let o=0;o<e.length;o++){const r=t.includes(e[o]);n[o]=this.createInput(e[o],r),this.inputs.set(e[o],n[o])}return this.fireOnValueChanged(),n}))}getForm(){return l(this,void 0,void 0,(function*(){const e=yield this.getInputs(),t=i.divV(e);return i.divV([t,i.button("ADD",(()=>l(this,void 0,void 0,(function*(){let e="";if(e=yield this.getNewAvailable(),""!==e){const n=this.createInput(e,!0);t.append(n.root),this.inputs.set(e,n),this.fireOnValueChanged()}}))))])}))}fireOnValueChanged(){var e;null===(e=this.options)||void 0===e||e.onValueChanged(a()(this.inputs.entries()).filter((([e,t])=>t.value)).map((([e,t])=>e)).toArray())}updateSelectionStatus(e,t){return l(this,void 0,void 0,(function*(){const n=yield this.getUserSettings();if(!n.excluded.includes(e)!==t){if(t){const t=n.excluded.indexOf(e);t>-1&&n.excluded.splice(t,1)}else n.excluded.push(e);this.fireOnValueChanged(),this.setUserSettings(n)}}))}availableRemove(e){return l(this,void 0,void 0,(function*(){this.inputs.delete(e),this.fireOnValueChanged();const t=yield this.getUserSettings(),n=t.excluded.indexOf(e);n>-1&&t.excluded.splice(n,1),this.setUserSettings(t),yield r.dapi.files.delete(this.path+e),r.shell.info(`File ${e} successfully deleted`)}))}getNewAvailable(){return l(this,void 0,void 0,(function*(){return new Promise(((e,t)=>{o.Utils.openFile({accept:this.ext,open:t=>l(this,void 0,void 0,(function*(){const n=t.name,o=yield t.arrayBuffer();yield r.dapi.files.write(this.path+`${t.name}`,new Uint8Array(o)),e(n)}))})}))}))}}var u=n(9022),h=n(9124),d=n(4229),p=n(439),m=n(5174),f=n(5412),g=n(6717),y=n(8312);function b(e){let t=e.replaceAll(/\[R[1-9]\]/g,(e=>`[*:${e[2]}]`));return t=t.replaceAll(/\[\d\*\]/g,(e=>`[*:${e[1]}]`)),t.replaceAll(/\[\d\*\:\d\]/g,(e=>`[*:${e[1]}]`))}function v(e){return e.replaceAll(/\[\*\:\d\]/g,(e=>`[C:${e[3]}]`))}function C(e){return e.replaceAll(/\[C\:\d\]/g,(e=>`[*:${e[3]}]`))}function x(e,t){const n=t?.firstReactantSmiles?C(t.firstReactantSmiles):"[*:1]C",o=t?.secondReactantSmiles?C(t.secondReactantSmiles):"[*:2]C",s=t?.productSmiles?C(t.productSmiles):"[*:1]CC[*:2]",a=t?.code,l=t?.firstMonomers??[],c=t?.secondMonomers??[],u=t?.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"}),p=i.input.string("Second monomers",{value:c.join(","),nullable:!1,tooltipText:"Comma-separated list of monomers for the second reactant"}),m=i.input.string("Result monomer name",{value:u,nullable:!1,tooltipText:"Name of the resulting pseudo-monomer generated by the reaction of the two reactants"}),f=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:o,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(!f||!g||!y)return"Inputs not initialized yet";const e=v(b(r.chem.convert(f.value??"",r.chem.Notation.Unknown,r.chem.Notation.Smiles))),t=v(b(r.chem.convert(g.value??"",r.chem.Notation.Unknown,r.chem.Notation.Smiles))),n=v(b(r.chem.convert(y.value??"",r.chem.Notation.Unknown,r.chem.Notation.Smiles)));return e&&t&&n?-1==e.indexOf("[C:1]")?"First Reactant must contain R1-group":-1==t.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"};f.addValidator(x),g.addValidator(x),y.addValidator(x);const w=i.dialog(t?"Edit Reaction Rule":"Add Reaction Rule").add(h).add(m).add(d).add(p).add(f).add(g).add(y);w.addButton("Save",(()=>{const n=x();if(null!=n)return void r.shell.warning(n);const o=v(b(r.chem.convert(f.value??"",r.chem.Notation.Unknown,r.chem.Notation.Smiles))),i=v(b(r.chem.convert(g.value??"",r.chem.Notation.Unknown,r.chem.Notation.Smiles))),s=v(b(r.chem.convert(y.value??"",r.chem.Notation.Unknown,r.chem.Notation.Smiles)));e({code:h.value,resultMonomerName:m.value,firstMonomers:d.value.split(",").map((e=>e.trim())).filter((e=>e.length>0)),secondMonomers:p.value.split(",").map((e=>e.trim())).filter((e=>e.length>0)),firstReactantSmiles:o,secondReactantSmiles:i,productSmiles:s,rowIndex:t?.rowIndex}),w.close()})),w.show()}const w="Links",A="Reactions";class T{constructor(e,t){this.v=null,this.substituteReactionGridDataFrame=null,this.rules=e;const n=this.rules.getLinkRulesDf();this.linkRuleDataFrame=n.res,this.addLinkRulesFunc=n.addNewRow;const o=this.rules.getSynthesisRulesDf();this.addSynthRulesFunc=e=>{o.addNewRow(e),this.rules.setSynthesisRules(o.df),this.synthRuleDataFrame=o.df,this.substituteReactionGridDataFrame?.(),this.save()},this.synthRuleDataFrame=o.df,this.fileName=t;const r=this.rules.homodimerCode?this.rules.homodimerCode:"",s=this.rules.heterodimerCode?this.rules.heterodimerCode:"";this.homoDimerInput=i.input.string("Homo dimer",{value:r,onValueChanged:()=>{},nullable:!1}),this.heteroDimerInput=i.input.string("Hetero dimer",{value:s,onValueChanged:()=>{},nullable:!1})}async getAndAddView(){if(this.v)try{const e=Array.from(r.shell.views).find((e=>e.name===this.v.name));if(!e)throw this.v.detach(),this.v.close(),new Error("View is closed, making it null in catch statement");r.shell.v=e}catch(e){this.v=null}return this.v||(this.v=o.View.create(),this.v.name=`Manage Polytool Rules - ${this.fileName}`,this.v.append(await this.getForm()),this.v=r.shell.addView(this.v),r.shell.v=this.v),this.v}static async getInstance(e){if(!this.instances[e]){const t=await ee([e]);this.instances[e]=new T(t,e)}return this.instances[e]}save(){this.rules.homodimerCode=this.homoDimerInput.value,this.rules.heterodimerCode=this.heteroDimerInput.value,this.rules.setLinkRules(this.linkRuleDataFrame),this.rules.setSynthesisRules(this.synthRuleDataFrame);const e={homodimerCode:this.rules.homodimerCode,heterodimerCode:this.rules.heterodimerCode,linkRules:this.rules.linkRules,reactionRules:this.rules.reactionRules},t=JSON.stringify(e,void 0,2);u._package.files.writeAsText(`polytool-rules/${this.fileName}`,t),r.shell.info(`Polytool rules at ${this.fileName} was updated`)}createGridDiv(e,t,n){const o=i.h1(e,"polytool-grid-header");i.tooltip.bind(o,n),o.style.marginTop="10px",o.style.marginRight="10px",t.root.style.height="100%";const r=i.splitV([i.box(o,{style:{maxHeight:"60px"}}),t.root]);return r.style.height="100%",r}async getLinkExamplesGrid(){const e=[];for(let t=0;t<this.rules.linkRules.length;t++){const n=this.rules.linkRules[t].code,[o,r]=te(this.rules.linkRules[t]);for(let t=0;t<o.length;t++){const i=`${o[t]}(${n})-A-A-A-A-${r[t]}(${n})`;e.push(i)}}const t=await(0,h.b2)(),[n,r,i]=(0,d.b)(e,this.rules,t),s=o.Column.fromStrings("Monomers",e),a=o.Column.fromStrings("Helm",n);return u.PackageFunctions.applyNotationProviderForCyclized(s,"-"),s.semType=o.SEMTYPE.MACROMOLECULE,a.semType=o.SEMTYPE.MACROMOLECULE,a.meta.units=p.Hi.HELM,a.setTag(o.TAGS.CELL_RENDERER,"helm"),o.DataFrame.fromColumns([s,a]).plot.grid()}async getReactionExamplesGrid(){const e=[];for(let t=0;t<this.rules.reactionRules.length;t++){const n=this.rules.reactionRules[t].code,[o,r]=te(this.rules.reactionRules[t]);for(let t=0;t<o.length;t++){const i=`${o[t]}(${n})-A-A-A-A-${r[t]}(${n})`;e.push(i)}}const t=await(0,h.b2)(),[n,r,i]=(0,d.b)(e,this.rules,t),s=o.Column.fromStrings("Monomers",e),a=o.Column.fromStrings("Helm",n),l=o.DataFrame.fromColumns([s,a]);s.semType=o.SEMTYPE.MACROMOLECULE;const c=await(0,g.j)(),b=await(0,y.Q)();u.PackageFunctions.applyNotationProviderForCyclized(s,"-"),s.tags[o.TAGS.CELL_RENDERER]="Sequence",a.semType=o.SEMTYPE.MACROMOLECULE,a.meta.units=p.Hi.HELM,a.setTag(o.TAGS.CELL_RENDERER,"helm");const v=await(0,m.A)(this.rules),C=a.temp;C[".mm.cellRenderer.overriddenLibrary"]=v,a.temp=C;const x=await(0,f.m)(a,e,r,!0,!1,!1,v,c,b);return x.name="molfile(sequence)",x.semType=o.SEMTYPE.MOLECULE,l.columns.add(x),l.plot.grid()}async getForm(){const e=this.linkRuleDataFrame.plot.grid({showAddNewRowIcon:!1,allowEdit:!1,rowHeight:60});e.onCellDoubleClick.subscribe((()=>{if(!e.dataFrame||-1==e.dataFrame.currentRowIdx||null==e.dataFrame.currentRowIdx)return;const t=e.dataFrame.currentRowIdx,n={row:t,code:this.linkRuleDataFrame.get("code",t),firstMonomers:this.linkRuleDataFrame.get("firstMonomers",t),secondMonomers:this.linkRuleDataFrame.get("secondMonomers",t),firstLinkingGroup:this.linkRuleDataFrame.get("firstLinkingGroup",t),secondLinkingGroup:this.linkRuleDataFrame.get("secondLinkingGroup",t)};this.getAddNewLinkRuleDialog(n)}));const t=this.createGridDiv("Rules",e,"specification for monomers to link and linking positions"),n=this.createGridDiv("Examples",await this.getLinkExamplesGrid(),"specification for monomers to link and linking positions");t.style.width="50%",n.style.width="50%";const o=i.h1("Monomers","polytool-grid-header");i.tooltip.bind(o,"Click different cobination to see how monomers will link"),this.linkCards=await this.rules.getLinkCards();const r=i.splitV([i.box(o,{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 e=this.linkRuleDataFrame.currentRowIdx;-1!==e&&null!=e&&(i.empty(r),r.append(i.splitV([i.box(o,{style:{maxHeight:"30px"}}),this.linkCards[e].root])),this.linkCards[e].render(),await this.linkCards[e].reset())}));const s=i.splitH([t,r],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 e=a.dataFrame.currentRowIdx;x((e=>this.addSynthRulesFunc(e)),{rowIndex:e,code:this.synthRuleDataFrame.get("code",e),firstMonomers:this.synthRuleDataFrame.get("firstMonomers",e).split(",").map((e=>e.trim())).filter((e=>e)),secondMonomers:this.synthRuleDataFrame.get("secondMonomers",e).split(",").map((e=>e.trim())).filter((e=>e)),resultMonomerName:this.synthRuleDataFrame.get("name",e),firstReactantSmiles:this.synthRuleDataFrame.get("firstReactant",e),secondReactantSmiles:this.synthRuleDataFrame.get("secondReactant",e),productSmiles:this.synthRuleDataFrame.get("product",e)})}));const l=this.createGridDiv("Rules",a),c=await this.getReactionExamplesGrid(),u=this.createGridDiv("Examples",c);this.substituteReactionGridDataFrame=async()=>{const e=await this.getReactionExamplesGrid();c.dataFrame=e.dataFrame},l.style.width="50%",u.style.width="50%";const h=i.divH([l,u]),d=i.divV([this.homoDimerInput,this.heteroDimerInput]),p=i.tabControl({Links:s,Reactions:h,Dimers:d},!1);i.tooltip.bind(p.getPane(w).header,"Specify rules to link monomers based on HELM notation"),i.tooltip.bind(p.getPane(A).header,"Specify rules to perform reactions within monomers"),i.tooltip.bind(p.getPane("Dimers").header,"Specify symbols for homodimeric and heterodimeric codes"),p.root.style.height="100%",p.root.style.width="100%",p.root.classList.add("rules-manager-form-tab-control"),p.header.style.marginBottom="10px";const m=i.divV([p.root]),f=[i.bigButton("Save",(()=>{this.save()})),i.button("Add rule",(()=>{const e=p.currentPane.name;e==w?this.getAddNewLinkRuleDialog():e==A&&x((e=>this.addSynthRulesFunc(e)))})),i.button("Remove rule",(()=>{const t=p.currentPane.name;if(t==w){if(null==this.linkRuleDataFrame||-1==this.linkRuleDataFrame.currentRowIdx||null==this.linkRuleDataFrame.currentRowIdx)return;const t=e.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(t),this.rules.setLinkRules(this.linkRuleDataFrame),this.save()})).show()}else if(t==A){if(null==this.synthRuleDataFrame||-1==this.synthRuleDataFrame.currentRowIdx||null==this.synthRuleDataFrame.currentRowIdx)return;const e=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(e),this.rules.setSynthesisRules(this.synthRuleDataFrame),this.substituteReactionGridDataFrame?.(),this.save()})).show()}}))];return this.v.setRibbonPanels([f]),m.style.height="100%",m.style.alignItems="center",p.root}getAddNewLinkRuleDialog(e){const t=i.input.int("Code",{nullable:!1,value:e?.code}),n=i.input.string("First monomers",{placeholder:"E.g. C,D,E",value:e?.firstMonomers,tooltipText:"Comma separated list of first monomers applicable for the rule. If left empty, all monomers will be considered",nullable:!0}),o=i.input.string("Second monomers",{placeholder:"E.g. C,D,E",value:e?.secondMonomers,tooltipText:"Comma separated list of second monomers applicable for the rule. If left empty, all monomers will be considered",nullable:!0}),r=e?.firstLinkingGroup?`R${e.firstLinkingGroup}`:"R3",s=e?.secondLinkingGroup?`R${e.secondLinkingGroup}`:"R3",a=i.input.choice("First linking group",{value:r,items:["R1","R2","R3","R4"],tooltipText:"Specifies which R-group of the first monomer will be used for linking",nullable:!1}),l=i.input.choice("Second linking group",{value:s,items:["R1","R2","R3","R4"],tooltipText:"Specifies which R-group of the second monomer will be used for linking",nullable:!1});i.dialog("Add new link rule").add(t).add(n).add(o).add(a).add(l).onOK((async()=>{const r=t.value,i=(n.value??"").split(",").map((e=>e.trim())).filter((e=>e)).join(","),s=(o.value??"").split(",").map((e=>e.trim())).filter((e=>e)).join(","),c=parseInt(a.value.substring(1)),u=parseInt(l.value.substring(1));this.addLinkRulesFunc({code:r,firstMonomers:i??"",secondMonomers:s??"",firstLinkingGroup:c,secondLinkingGroup:u,row:e?.row}),this.rules.setLinkRules(this.linkRuleDataFrame),this.linkCards=await this.rules.getLinkCards(),this.save()})).show()}}T.instances={};var E=n(5072),S=n.n(E),N=n(7825),I=n.n(N),M=n(7659),P=n.n(M),_=n(5056),L=n.n(_),O=n(540),R=n.n(O),$=n(1113),D=n.n($),B=n(890),F={};F.styleTagTransform=D(),F.setAttributes=L(),F.insert=P().bind(null,"head"),F.domAPI=I(),F.insertStyleElement=R(),S()(B.A,F),B.A&&B.A.locals&&B.A.locals;var k=n(2003);class H{get selected(){return this._selected}set selected(e){this._selected=e,this.root.style.border=e?"2px solid var(--green-2)":"2px solid var(--grey-2)"}constructor(e,t){this.monomer=e,this.monomerSymbol=t,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 e=this.monomer.smiles&&r.chem.checkSmiles(this.monomer.smiles)?r.chem.drawMolecule(this.monomer.smiles,150,120):r.chem.drawMolecule(this.monomer.molfile??"",150,120);this.root.appendChild(e);const t=i.divH([i.divText("Monomer Name: "),i.divText(this.monomer.name)],{classes:"monomer-card-info-rules"});if(this.root.appendChild(t),i.tooltip.bind(t,this.monomer.name),this.monomer.lib?.source){const e=i.divH([i.divText("Source: "),i.divText(this.monomer.lib.source)],{classes:"monomer-card-info-rules"});this.root.appendChild(e),i.tooltip.bind(e,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 ${this.monomerSymbol} not found in libraries`],{style:{textAlign:"center",height:"100%"}}))}}class G{constructor(e,t,n,o,r){this.firstMonomers=e,this.secondMonomers=t,this.code=o,this.rules=r,this.root=i.divH([],{style:{width:"100%",overflow:"hidden",visibility:"visible"},classes:"monomer-cards"});const s=!e?.length,a=!t?.length;s&&(this.firstMonomers=e=["C","D","E","F","G"]),a&&(this.secondMonomers=t=["D","C","E","F","G"]),this.actionable=!0;const l=i.divH([],{style:{overflowX:"auto",width:"100%"}}),c=i.divH([],{style:{overflowX:"auto",width:"100%"}});this.resulting=i.divH([],{style:{overflowX:"auto",width:"100%",minHeight:"150px"}});const u=i.h2("First Monomer"+(s?" (Applied to all monomers, example list shown)":""),{style:{width:"100%"}}),h=i.h2("Second Monomer"+(a?" (Applied to all monomers, example list shown)":""),{style:{width:"100%"}}),d=i.divV([u,l,h,c,this.resulting]);this.cardsFirst=e.map((e=>new H(n.getMonomer("PEPTIDE",e),e))),this.cardsSecond=t.map((e=>new H(n.getMonomer("PEPTIDE",e),e))),this.cardsFirst.forEach((e=>{e.root.onclick=()=>{this.cardsFirst.forEach((e=>e.selected=!1)),e.selected=!0,this.firstCard=e,this.reset()},l.appendChild(e.root)})),this.cardsSecond.forEach((e=>{e.root.onclick=()=>{this.cardsSecond.forEach((e=>e.selected=!1)),e.selected=!0,this.secondCard=e,this.reset()},c.appendChild(e.root)})),this.cardsFirst[0].selected=!0,this.cardsSecond[0].selected=!0,this.firstCard=this.cardsFirst[0],this.secondCard=this.cardsSecond[0],this.root.appendChild(d)}async reset(){if(this.actionable){const e=[`${this.firstCard.monomer?.symbol}(${this.code})-A-A-A-A-${this.secondCard.monomer?.symbol}(${this.code})`],t=await(0,h.b2)(),[n,s,a]=(0,d.b)(e,this.rules,t),l=o.Column.fromType(o.COLUMN_TYPE.STRING,"helm",n.length).init((e=>n[e]));l.semType=o.SEMTYPE.MACROMOLECULE,l.meta.units=k.Hi.HELM,l.setTag(o.TAGS.CELL_RENDERER,"helm");const c=await(0,g.j)(),u=await(0,y.Q)(),p=await(0,m.A)(this.rules),b=l.temp;l.temp=b;const v=(await(0,f.m)(l,n,s,!0,!1,!1,p,c,u)).get(0),C=v&&r.chem.checkSmiles(v)?r.chem.drawMolecule(v,200,200):r.chem.drawMolecule(v??"",200,200);v&&(C.style.cursor="pointer",C.onclick=()=>{const e=window.innerWidth-200,t=window.innerHeight-200,n=r.chem.checkSmiles(v)?r.chem.drawMolecule(v,e,t):r.chem.drawMolecule(v??"",e,t);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(e[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((e=>e.render())),this.cardsSecond.forEach((e=>e.render())))}}var U=n(4971);const V="System:AppData/SequenceTranslator/polytool-rules/",j="Polytool",q="code",W="firstMonomers",z="secondMonomers",Y="name",K="firstLinkingGroup",Q="secondLinkingGroup";class J extends c{constructor(e,t,n,o){super(e,t,n,o)}createInput(e,t){const n=super.createInput(e,t),r=i.icons.edit((async()=>{const t=await T.getInstance(e);o.Dialog.getOpenDialogs()?.filter((e=>e.root.contains(r))).forEach((e=>e.close())),await t.getAndAddView()}),"Edit rules");return n.addOptions(r),n}async getForm(){const e=await super.getForm();return this.processRulesForm(e),e}async processRulesForm(e){const t=Array.from(e.getElementsByTagName("label")??[]).filter((e=>e.textContent?.endsWith(".json")&&null!=e.parentElement));for(const e of t){const t=e.textContent.trim(),n=e.parentElement.getElementsByTagName("input")[0];i.tooltip.bind(n,i.wait((async()=>{var e;return(e=J.ruleDescriptions)[t]??(e[t]=(async()=>{try{const e=JSON.parse(await r.dapi.files.readAsText(`${V}/${t}`)),n=i.divV([i.h1(t)]),o=e.linkRules??[];if(o.length>0){n.appendChild(i.h3("Linkage Rules"));const e=i.table(o,(e=>[e.code?.toString()??"",X((e.firstMonomers??[]).join(", ")),X((e.secondMonomers??[]).join(", ")),e.firstLinkingGroup?.toString()??"",e.secondLinkingGroup?.toString()??""]),["Code","M1","M2","L1","L2"]);n.appendChild(e)}const s=e.reactionRules??[];if(s.length>0){n.appendChild(i.h3("Synthesis Rules"));const e=i.table(s,(e=>[e.code?.toString()??"",X((e.firstMonomers??[]).join(", ")),X((e.secondMonomers??[]).join(", ")),X(e.name??""),r.chem.drawMolecule(e.reaction?.split(">>")[1]??"",70,70)]),["Code","M1","M2","Name","Product"]);n.appendChild(e)}return n}catch(e){return u._package.logger.error(`Failed to load rule ${t}: ${e?.toString?.()}`),console.error(e),i.divText(`Failed to load rule ${t}`)}})()),await J.ruleDescriptions[t]})))}}}function X(e,t=30){return e.length<=t?e:`${e.substring(0,t)}...`}J.ruleDescriptions={};class Z{constructor(e,t,n,o){this.homodimerCode=e,this.heterodimerCode=t,this.linkRules=n,this.reactionRules=o}set homodimer(e){this.homodimerCode=e}set heterodimer(e){this.heterodimerCode=e}addLinkRules(e){for(let t=0;t<e.length;t++)this.linkRules.push(e[t])}addSynthesisRules(e){for(let t=0;t<e.length;t++)this.reactionRules.push(e[t])}getLinkRulesDf(){const e=this.linkRules.length,t=o.Column.int(q,e);t.setTag("friendlyName","Code");const n=o.Column.string(W,e);n.temp[".mm.cellRenderer.fontSize"]=16,n.setTag("friendlyName","First monomers"),n.semType=o.SEMTYPE.MACROMOLECULE,u.PackageFunctions.applyNotationProviderForCyclized(n,",");const r=o.Column.string(z,e);r.setTag("friendlyName","Second monomers"),r.temp[".mm.cellRenderer.fontSize"]=16,r.semType=o.SEMTYPE.MACROMOLECULE,u.PackageFunctions.applyNotationProviderForCyclized(r,",");const i=o.Column.int(K,e);i.setTag("friendlyName","First group");const s=o.Column.int(Q,e);s.setTag("friendlyName","Second group");for(let o=0;o<e;o++)t.set(o,this.linkRules[o].code),n.set(o,this.linkRules[o].firstMonomers.toString()),r.set(o,this.linkRules[o].secondMonomers.toString()),i.set(o,this.linkRules[o].firstLinkingGroup),s.set(o,this.linkRules[o].secondLinkingGroup);const a=o.DataFrame.fromColumns([t,n,r,i,s]);return{res:a,addNewRow:e=>{if(null!=e.row&&e.row<a.rowCount&&e.row>=0)t.set(e.row,e.code),n.set(e.row,e.firstMonomers),r.set(e.row,e.secondMonomers),i.set(e.row,e.firstLinkingGroup),s.set(e.row,e.secondLinkingGroup);else{const{code:t,firstMonomers:n,secondMonomers:o,firstLinkingGroup:r,secondLinkingGroup:i}=e;a.rows.addNew([t,n??"",o??"",r??1,i??2])}}}}async getLinkCards(){const e=this.linkRules.length,t=new Array(e),n=(await(0,U.pj)()).getMonomerLib();for(let o=0;o<e;o++)t[o]=new G(this.linkRules[o].firstMonomers,this.linkRules[o].secondMonomers,n,this.linkRules[o].code,this);return t}getSynthesisRulesDf(){const e=this.reactionRules.length,t=o.Column.int(q,e);t.setTag("friendlyName","Code");const n=o.Column.string(W,e);n.setTag("friendlyName","First monomers");const r=o.Column.string(z,e);r.setTag("friendlyName","Second monomers"),n.semType=o.SEMTYPE.MACROMOLECULE,n.temp[".mm.cellRenderer.fontSize"]=16,u.PackageFunctions.applyNotationProviderForCyclized(n,","),r.semType=o.SEMTYPE.MACROMOLECULE,r.temp[".mm.cellRenderer.fontSize"]=16,u.PackageFunctions.applyNotationProviderForCyclized(r,","),r.setTag(o.TAGS.CELL_RENDERER,"Sequence"),n.setTag(o.TAGS.CELL_RENDERER,"Sequence");const i=o.Column.string(Y,e);i.setTag("friendlyName","Name");const s=o.Column.string("firstReactant",e);s.setTag("friendlyName","First reactant");const a=o.Column.string("secondReactant",e);a.setTag("friendlyName","Second reactant");const l=o.Column.string("product",e);l.setTag("friendlyName","Product");for(let o=0;o<e;o++){t.set(o,this.reactionRules[o].code),n.set(o,this.reactionRules[o].firstMonomers.toString()),r.set(o,this.reactionRules[o].secondMonomers.toString()),i.set(o,this.reactionRules[o].name);const e=this.reactionRules[o].reaction.split(">>"),c=e[0].split(".");s.set(o,c[0]),a.set(o,c[1]),l.set(o,e[1])}s.semType=o.SEMTYPE.MOLECULE,a.semType=o.SEMTYPE.MOLECULE,l.semType=o.SEMTYPE.MOLECULE;const c=o.DataFrame.fromColumns([i,s,a,l,t,n,r]);return{df:c,addNewRow:e=>{if(null!=e.rowIndex&&e.rowIndex<c.rowCount&&e.rowIndex>=0)i.set(e.rowIndex,e.resultMonomerName),t.set(e.rowIndex,e.code),n.set(e.rowIndex,e.firstMonomers.join(",")),r.set(e.rowIndex,e.secondMonomers.join(",")),s.set(e.rowIndex,e.firstReactantSmiles),a.set(e.rowIndex,e.secondReactantSmiles),l.set(e.rowIndex,e.productSmiles);else{const{resultMonomerName:t,code:n,firstMonomers:o,secondMonomers:r,firstReactantSmiles:i,secondReactantSmiles:s,productSmiles:a}=e;c.rows.addNew([t,i,s,a,n,o.join(","),r.join(",")])}}}}setLinkRules(e){const t=e.rowCount,n=new Array(t),o=e.columns.byName(q),r=e.columns.byName(W),i=e.columns.byName(z),s=e.columns.byName(K),a=e.columns.byName(Q);for(let e=0;e<t;e++){const t=r.get(e).split(","),l=i.get(e).split(","),c={code:o.get(e),firstMonomers:""!==t[0]?t:[],secondMonomers:""!==l[0]?l:[],firstLinkingGroup:s.get(e),secondLinkingGroup:a.get(e)};n[e]=c}this.linkRules=n}setSynthesisRules(e){const t=e.rowCount,n=new Array(t),o=e.columns.byName(q),r=e.columns.byName(W),i=e.columns.byName(z),s=e.columns.byName(Y),a=e.columns.byName("firstReactant"),l=e.columns.byName("secondReactant"),c=e.columns.byName("product");for(let e=0;e<t;e++){const t=`${a.get(e)}.${l.get(e)}>>${c.get(e)}`,u=r.get(e).split(","),h=i.get(e).split(","),d={code:o.get(e),firstMonomers:""!==u[0]?u:[],secondMonomers:""!==h[0]?h:[],reaction:t,name:s.get(e)};n[e]=d}this.reactionRules=n}}async function ee(e){const t=new o.FileSource(V),n=new Z(null,null,[],[]);for(let o=0;o<e.length;o++){const r=await t.readAsText(e[o].replace(V,"")),i=JSON.parse(r);n.homodimer=i.homodimerCode,n.heterodimer=i.heterodimerCode,n.addLinkRules(i.linkRules),n.addSynthesisRules(i.reactionRules)}return n}function te(e){const t=e.firstMonomers.length*e.secondMonomers.length,n=new Array(t),o=new Array(t);let r=0;for(let t=0;t<e.firstMonomers.length;t++)for(let i=0;i<e.secondMonomers.length;i++)n[r]=e.firstMonomers[t],o[r]=e.secondMonomers[i],r++;return[n,o]}},5174:(e,t,n)=>{"use strict";n.d(t,{A:()=>u,T:()=>h});var o=n(6717),r=n(1296),i=n(9192),s=n(4328),a=n(1991),l=n.n(a),c=n(4971);async function u(e){const t=(await(0,c.pj)()).getMonomerLib(),n=await(0,o.j)(),r={};let i=[],a=[];for(let o=0;o<e.reactionRules.length;o++)try{[i,a]=h(n,t,e.reactionRules[o])}catch(e){i=[],a=[],console.error(e),s.shell.warning(e)}finally{for(let e=0;e<i.length;e++)null!=i[e]&&null!=a[e]&&(r[i[e]]=a[e])}const u={PEPTIDE:r};return t.override(u,"ST-PT-reactions."+l().repeat(1).map((()=>Math.floor(36*Math.random()).toString(36))).take(4).toArray().join(""))}function h(e,t,n){const o=n.reaction,r=n.name,s=n.firstMonomers.length+n.secondMonomers.length+1,a=n.reaction.split(">>"),l=a[0].split("."),c=new Array(s),u=new Array(s),h=new Array(s),f=p(e,o),g=`${l[0]}>>[C:1]C`,y=`${l[1]}>>[C:2]C`,b=p(e,g),v=p(e,y);let C=0;for(let o=0;o<n.firstMonomers.length;o++){const i=t.getMonomer("PEPTIDE",n.firstMonomers[o]);if(i&&i.molfile)try{const t=d(e,i.molfile,b,i.name);h[C]=t,c[C]=`${i.symbol}_${r}`}catch(e){console.error(e)}C++}for(let o=0;o<n.secondMonomers.length;o++){const i=t.getMonomer("PEPTIDE",n.secondMonomers[o]);if(i&&i.molfile)try{const t=d(e,i.molfile,v,i.name);h[C]=t,c[C]=`${i.symbol}_${r}`}catch(e){console.error(e)}C++}let x=null;a[1]=a[1].replace("[C:1]","[1*]").replace("[C:2]","[2*]").replace("[C:3]","[3*]");let w="";try{x=e.get_mol(a[1]),w=x?.get_molblock()}catch(e){const[t,n]=(0,i.AP)(e);throw console.error(`Can not assemble monomer '${r}': ${t}.`),e}finally{x?.delete()}h[C]=w,c[C]=r;for(let e=0;e<s-1;e++)h[e]&&(h[e]=h[e].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(e){const t=e.replace("M RAD","M RGP").replace("M ISO","M RGP").split("\n"),n=t.findIndex((e=>e.startsWith("M RGP"))),o=Number(t[n].substring(9,13)),r=Number(t[n].substring(17,21)),i=Number(t[n].substring(13,17)),s=Number(t[n].substring(21,25));t[n]=t[n].substring(0,13)+` ${i}`+t[n].substring(17,21)+` ${s}`,t[3+o]=t[3+o].substring(0,30)+" R# 0 0 0 0 0 0 0 0 0 0 0 0",t[3+r]=t[3+r].substring(0,30)+" R# 0 0 0 0 0 0 0 0 0 0 0 0";let a="";for(let e=0;e<t.length;e++)a+=t[e]+"\n";return a}(h[s-1]);for(let e=0;e<s;e++){const t=e==s-1;if(!h[e]||!c[e])continue;const n={symbol:c[e],name:c[e],molfile:h[e],author:"",id:0,rgroups:m(t),smiles:"",polymerType:"PEPTIDE",monomerType:"Backbone",createDate:null};n.meta=Object.assign(n.meta??{},{colors:{default:{line:"#2083D5",text:"#2083D5",background:"#F2F2F5"}}}),c[e]=c[e],u[e]=n}return f.delete(),b.delete(),v.delete(),[c,u]}function d(e,t,n,o){let r=null,s=null,a=null,l=null,c="";try{r=new e.MolList,s=e.get_mol(t),r.append(s),a=n.run_reactants(r,1),l=a.get(0).next(),c=l?.get_molblock()}catch(e){const[t,n]=(0,i.AP)(e);throw console.error(`Can not assemble monomer '${o}': ${t}.`),e}finally{r?.delete(),s?.delete(),a?.delete(),l?.delete()}return c}function p(e,t){let n=null;try{if(n=e.get_rxn(t),!n)throw new r.J5(t)}catch(e){n?.delete();const[o,r]=(0,i.AP)(e);throw console.error(`Can not assemble monomer '${t}': ${o}.`),e}return n}function m(e){if(e){const e=new Array(2),t={capGroupSMILES:"[*:1][H]",alternateId:"R1-H",capGroupName:"H",label:"R1"},n={capGroupSMILES:"[*:2][H]",alternateId:"R2-H",capGroupName:"H",label:"R2"};return e[0]=t,e[1]=n,e}return[{capGroupSMILES:"[*:3][H]",alternateId:"R3-H",capGroupName:"H",label:"R3"}]}},3309:(e,t,n)=>{"use strict";n.d(t,{BG:()=>y,HL:()=>A,Ii:()=>C,KS:()=>h,PI:()=>r,Qk:()=>c,XB:()=>f,ah:()=>d,aj:()=>u,j7:()=>l,jp:()=>T,k5:()=>m,u8:()=>o,xD:()=>E,yw:()=>v,z9:()=>b});const 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we.getTranslationHelper()}));for(const t of Object.keys(G))for(const[n,o]of Object.entries(G[t]))x(`${t} to HELM`,(async()=>{const r=o;w(k(n,t,e),r)}))})),S("HELM to Formats",(()=>{let e;N((async()=>{e=await we.getTranslationHelper()}));for(const t of Object.keys(G))for(const[n,o]of Object.entries(G[t]))x(`${t} to HELM`,(async()=>{const r=n;w(H(o,t,e),r)}))}));var V=n(3480);S("HELM to Nucleotides",(()=>{let e;N((async()=>{e=await we.getTranslationHelper()})),Object.entries(U).forEach((([t,n],o)=>{x(`Sequence ${o+1} to nucleotides`,(async()=>{const o=n;w((0,V.Hs)(t,e.monomerLibWrapper),o)}))}))}));const j={[B.NO.AXOLABS]:"Afcgacsu",[B.NO.HELM]:"RNA1{[fR](A)p.[25r](C)p.[25r](G)p.[25r](A)p.[25r](C)[sp].[25r](U)}$$$$"};S("Formats support",(()=>{let e;N((async()=>{e=await we.getTranslationHelper()})),Object.entries(j).forEach((([t,n])=>{x(`All formats for ${t}`,(async()=>{const o=function(e,t,n){const o=n.createSequenceValidator(e).getInvalidCodeIndex(t);return(0,V.bD)(e,o,t,n)}(n,t,e),r=Object.keys(o).length;w(!0,Object.keys(G).length+1<=r)}))}))}));var q=n(9192);S("files",(()=>{let t;N((async()=>{t=await we.getTranslationHelper()})),x("list",(async()=>{let n;const o=e.DataFrame.fromColumns([e.Column.string("subTest"),n=e.Column.bool("success"),e.Column.string("format"),e.Column.string("src"),e.Column.string("res"),e.Column.string("tgt"),e.Column.string("error"),e.Column.string("stack")]),r=await we.files.list("tests",!0,".csv");for(const n of r){const r=e.DataFrame.fromCsv(await n.readAsString()),i=r.columns.byIndex(0),s=i.name,a=r.columns.byIndex(1),l=r.rowCount;for(let e=0;e<l;++e){const r=o.rows.addNew();r.subTest=`${n.name}, row: ${e}`;try{const n=i.get(e),o=a.get(e);r.format=s,r.src=n,r.tgt=o,w(r.res=k(n,s,t),o),r.success=!0}catch(e){const[t,n]=(0,q.AP)(e);r.error=t,r.stack=n,r.success=!1}}}0==o.rowCount&&o.rows.addNew(["empty",!0,"",""]);const 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Object.entries(n))x(`innerIdx-${e}`,(async()=>{const[e,n]=(0,ge.M)(r,i);w(e,t),w(n,o)}));for(const[e,{inIdx:t,spIdx:o,outIdx:r,monomers:i}]of Object.entries(n))x(`outerIdx-${e}`,(async()=>{w((0,ge.j)(t,o,i),r)}))})),S("PolyTool: Chain",(()=>{let e;N((async()=>{e=await(0,ae.b2)()}));const t={cyclized:{data:{templateSeq:"R-F-C(1)-T-G-H-F-Y-P-C(1)-meI",templateHelm:"PEPTIDE1{R.F.[C(1)].T.G.H.F.Y.P.[C(1)].[meI]}$$$$V2.0",mmHelm:"PEPTIDE1{R.F.C.T.G.H.F.Y.P.C.[meI]}$PEPTIDE1,PEPTIDE1,3:R3-10:R3$$$V2.0"},tgt:{templateChain:{monomerCount:[11],linkageCount:0},mmChain:{monomerCount:[11],linkageCount:0}}},dimerized1:{data:{templateSeq:"(#3)Succ-{A(CHOL)-F-C(1)-T-G-H-Y-P-C(1)-NH2}",templateHelm:"PEPTIDE1{[(#3)Succ]}|PEPTIDE2{[A(CHOL)].F.[C(1)].T.G.H.Y.P.[C(1)].[NH2]}$PEPTIDE1,PEPTIDE2,1:R1-1:R1$$$V2.0",mmHelm:"PEPTIDE1{[(#3)Succ].[{A(CHOL)].F.C.T.G.H.Y.P.C.[NH2}]}$PEPTIDE1,PEPTIDE1,4:R3-10:R3$$$V2.0"},tgt:{templateChain:{monomerCount:[1,10],linkageCount:1},mmChain:{monomerCount:[11],linkageCount:1}}},dimerized2:{data:{templateSeq:"($3)Succ-{R-F-C(1)-T-G-H-F-P-C(1)-NH2}($3){A(CHOL)-F-C(1)-Y-H-G-D-N-C(1)-meI}",templateHelm:"PEPTIDE1{[($3)Succ]}|PEPTIDE2{R.F.[C(1)].T.G.H.F.P.[C(1)].[NH2]}|PEPTIDE3{[($3)A(CHOL)].F.[C(1)].Y.H.G.D.N.[C(1)].[meI]}$PEPTIDE1,PEPTIDE2,1:R1-1:R1$$$V2.0",mmHelm:"PEPTIDE1{[($3)Succ].[{R].F.C.T.G.H.F.P.C.[NH2}($3){A(CHOL)].F.[C(1)].Y.H.G.D.N.[C(1)].[meI}]}$PEPTIDE1,PEPTIDE1,4:R3-10:R3$$$V2.0"},tgt:{templateChain:{monomerCount:[1,10,10],linkageCount:1},mmChain:{monomerCount:[20],linkageCount:1}}}};for(const[n,{data:o,tgt:r}]of Object.entries(t))x(`fromNotation-${n}`,(async()=>{const t=await(0,ue.Q4)(["rules_example.json"]),n=fe.s.fromSeparator(o.templateSeq,e);n.applyRules(t),n.check(!0),E(n.monomers.map((e=>e.length)),r.mmChain.monomerCount),w(n.linkages.length,r.mmChain.linkageCount),w(n.getHelm(),o.mmHelm)}),{skipReason:"3157"});for(const[n,{data:o,tgt:r}]of Object.entries(t))x(`parseNotation-${n}`,(async()=>{await(0,ue.Q4)(["rules_example.json"]);const t=fe.s.fromSeparator(o.templateSeq,e);t.check(!0),E(t.monomers.map((e=>e.length)),r.templateChain.monomerCount),w(t.linkages.length,r.templateChain.linkageCount),w(t.getHelm(),o.templateHelm),w(t.getNotation(),o.templateSeq)}));for(const[n,{data:o,tgt:r}]of Object.entries(t))x(`parseHelm-${n}`,(async()=>{await(0,ue.Q4)(["rules_example.json"]);const t=fe.s.fromHelm(o.templateHelm,e);t.check(!0),E(t.monomers.map((e=>e.length)),r.templateChain.monomerCount),w(t.linkages.length,r.templateChain.linkageCount),w(t.getHelm(),o.templateHelm),w(t.getNotation(),o.templateSeq)}));for(const[n,{data:o,tgt:r}]of Object.entries(t))x(`applyRules-${n}`,(async()=>{const t=await(0,ue.Q4)(["rules_example.json"]),n=fe.s.fromSeparator(o.templateSeq,e);n.applyRules(t),n.check(!0),E(n.monomers.map((e=>e.length)),r.mmChain.monomerCount),w(n.linkages.length,r.mmChain.linkageCount),w(n.getHelm(),o.mmHelm)}),{skipReason:"applyRules is not implemented"})})),S("toAtomicLevel",(()=>{let t,n,o;N((async()=>{n=await(0,J.pj)(),t=await re(),o=await(0,se.j)(),await n.loadMonomerLibForTests()})),I((async()=>{await ie(t),await n.loadMonomerLib(!0)})),x("override",(async()=>{const t=n.getMonomerLib(),r=await we.files.readAsText("tests/polytool-reaction-lib.json"),i=JSON.parse(r).find((e=>"GGaz"===e.symbol));w(null!=i,!0,"Monomer 'GGaz' not found.");const s={PEPTIDE:{GGaz:i}},a=t.override(s,"test"),l=await(0,W.Q)(),c=e.Column.fromList(e.COLUMN_TYPE.STRING,"helm",["PEPTIDE1{F.P.Y.[GGaz].H.A.A.G.G.A.C}|PEPTIDE2{A.A.A}$PEPTIDE1,PEPTIDE2,4:R4-1:R1|PEPTIDE1,PEPTIDE1,11:R2-4:R3$$$V2.0"]);c.semType=e.SEMTYPE.MACROMOLECULE,c.meta.units=z.Hi.HELM;const u=await l.helmToAtomicLevel(c,!1,!1,a);w(null!=u.molCol,!0,"Result molCol is null");const h=u.molCol.get(0);w(!!h,!0,"Molfile is empty");const d=o.get_mol(h);try{const e=d.get_inchi(),t=o.get_inchikey_for_inchi(e);w(d.get_num_bonds(),103),w(d.get_num_atoms(),98),w(t,"XPQUTLNSNIMERR-WKBTUBAPSA-N")}finally{d.delete()}})),x("getNewMonomer",(async()=>{const e=await(0,se.j)(),t=n.getMonomerLib(),o=(await(0,ue.Q4)(["rules_example.json"])).reactionRules.find((e=>"GGaz"==e.name)),[r,i]=(0,ce.T)(e,t,o);w(r?.[0],"azG_GGaz");const s=e.get_mol(i[0].molfile);try{const t=s.get_inchi();e.get_inchikey_for_inchi(t),w(s.get_num_bonds(),7),w(s.get_num_atoms(),8)}finally{s.delete()}}))}));var ye=n(5613),be=n(5733),ve=n(1536);const Ce="RNA1{m(G)[sp].m(A)[sp].[fl2r](C)p.[fl2r](U)p.r(G)p.r(A)p.r(A)p.r(U)p.r(A)p.r(U)p.r(A)p.r(A)p.r(A)p.r(C)p.r(U)p.r(U)p.m(G)p.m(U)[sp].m(G)[sp].[L3]}|RNA2{[fl2r](C)[sp].m(A)[sp].m(A)p.m(G)p.r(U)p.r(U)p.r(U)p.r(A)p.r(U)p.r(A)p.r(U)p.r(U)p.r(C)p.r(A)p.r(U)p.m(C)p.m(A)[sp].m(G)[sp].r(U)}$$$$",xe="RNA1{[lna](C)[sp].[lna](A)[sp].[lna](G)[sp].d(T)[sp].d(C)[sp].d(A)[sp]}$$$$";S("OligoRenderer: parser",(()=>{x("looksLikeHelm — positive",(async()=>{w((0,ye.yO)(Ce),!0),w((0,ye.yO)("RNA1{R(A)P}"),!0),w((0,ye.yO)("PEPTIDE1{A.C.G}"),!0)})),x("looksLikeHelm — negative",(async()=>{w((0,ye.yO)(""),!1),w((0,ye.yO)("AUCGUACGUAGCUAGCAU"),!1),w((0,ye.yO)("Af Cf Gf Uf"),!1)})),x("parses two-strand duplex",(async()=>{const e=(0,ye.On)(Ce);w(e.sense.type,"RNA"),w(e.sense.monomers.length,20),w(null!==e.antisense,!0),w(e.antisense.monomers.length,19)})),x("parses single-strand",(async()=>{const e=(0,ye.On)(xe);w(e.sense.monomers.length,6),w(e.antisense,null);const t=e.sense.monomers[0];w(t.kind,"nucleotide"),"nucleotide"===t.kind&&(w(t.sugar,"lna"),w(t.base,"C"),w(t.phosphate,"sp"))})),x("single-char unbracketed deoxyribose `d` parses correctly",(async()=>{const e=(0,ye.On)("RNA1{d(T)p.d(C)p.d(G)}$$$$");w(e.sense.monomers.length,3);const t=e.sense.monomers[0];"nucleotide"===t.kind&&(w(t.sugar,"d"),w(t.base,"T"),w(t.phosphate,"p"))})),x("parses bracketed conjugate",(async()=>{const e=(0,ye.On)(Ce),t=e.sense.monomers[e.sense.monomers.length-1];w(t.kind,"conjugate"),"conjugate"===t.kind&&w(t.symbol,"L3")})),x("handles empty / malformed without throwing",(async()=>{const e=(0,ye.On)("");w(e.sense.monomers.length,0),w(e.antisense,null),w((0,ye.On)("not a helm string").sense.monomers.length,0)})),x("passes through unknown sugar/phosphate symbols",(async()=>{const e=(0,ye.On)("RNA1{[xr](A)[zp].[yr](C)p}$$$$").sense.monomers[0];"nucleotide"===e.kind&&(w(e.sugar,"xr"),w(e.phosphate,"zp"))}))})),S("OligoRenderer: modification dictionary",(()=>{x("resolves 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e=(0,ye.On)(Ce),t=(0,be.aA)(800,70,e),n=t.antiChips[0],o=(0,be.CB)(n.x+n.w/2,t.antiY+t.chipH/2,e,t);w(null!==o,!0),w(o.strand,"antisense"),w(o.position,e.antisense.monomers.length-1,"leftmost AS chip in pair-aligned display = last monomer in data")})),x("hovering between two chips with PS linkage returns the linkage",(async()=>{const e=(0,ye.On)("RNA1{m(G)[sp].m(A)p.m(C)p}$$$$"),t=(0,be.aA)(600,70,e),n=t.senseChips[0],o=t.senseChips[1],r=(n.x+n.w+o.x)/2,i=(0,be.CB)(r,t.senseY+t.chipH/2,e,t);w(null!==i,!0),w(void 0!==i.linkage,!0),w(i.linkage.phosphateSymbol,"sp")}))})),S("OligoRenderer: drawing smoke",(()=>{x("draws without error on offscreen canvas",(async()=>{const e=document.createElement("canvas");e.width=500,e.height=70;const t=e.getContext("2d"),n=(0,ye.On)(Ce);w((0,be.Z4)(t,0,0,500,70,n).textOnlyFallback,!1)})),x("handles unknown modifications without throwing",(async()=>{const e=document.createElement("canvas");e.width=200,e.height=50;const t=e.getContext("2d"),n=(0,ye.On)("RNA1{[xr](A)[zp].[yr](C)p}$$$$");(0,be.Z4)(t,0,0,200,50,n),w(!0,!0)})),x("renders legacy uppercase symbols via alias map",(async()=>{const e=document.createElement("canvas");e.width=400,e.height=50;const t=e.getContext("2d"),n=(0,ye.On)("RNA1{[mR](G)[sP].[mR](A)[sP].[fR](C)P.R(U)P}|RNA2{[mR](C)[sP].R(A)P.R(U)P.R(G)P}$$$$");(0,be.Z4)(t,0,0,400,50,n),w(n.sense.monomers.length,4),w(null!==n.antisense,!0)}))}));const we=new F;async function Ae(t,n,o){const d=await function(e){var t,n,o;return r(this,void 0,void 0,(function*(){const d=(null==e?void 0:e.nodeOptions)?e.nodeOptions.package:grok.functions.getCurrentCall().func.package;if(!d)throw new Error("Can't run tests outside of the package");const p=null===(t=d.packageOwner)||void 0===t?void 0:t.match(/<([^>]*)>/),m=p?p[1]:"";null!=d&&(yield P(d));const f=[];console.log("Running tests..."),console.log(e),null!=e||(e={}),null!==(n=(o=e).testContext)&&void 0!==n||(o.testContext=new 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2
+ var sequencetranslator_test;(()=>{var e={6717:(e,t,n)=>{"use strict";n.d(t,{j:()=>r});var o=n(6082);async function r(){const e=o.Func.find({package:"Chem",name:"getRdKitModule"});if(0===e.length)throw new Error('Package "Chem" must be installed for getRdKitModule.');return(await e[0].prepare().call()).getOutputParamValue()}},3599:(e,t,n)=>{"use strict";n.d(t,{o:()=>o.o});var o=n(6869)},9124:(e,t,n)=>{"use strict";n.d(t,{b2:()=>i});var o=n(7389),r=n(6082);async function i(){const e="Helm",t=r.Func.find({package:e,name:"getHelmHelper"});if(0===t.length)throw new Error(`Package '${e}' must be installed for HelmHelper.`);return(await t[0].prepare().call()).getOutputParamValue()}r.JsInputBase,Error,o.input.helmAsync=async function(e,t){return(await i()).createHelmInput(e,t)}},8438:(e,t,n)=>{"use strict";function o(e){return e.startsWith("[")&&e.endsWith("]")?e.slice(1,-1):e}n.d(t,{D:()=>o})},8123:(e,t,n)=>{"use strict";n.d(t,{u:()=>o});const o={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:(e,t,n)=>{"use strict";n.d(t,{Y:()=>r});var o=n(3599);function r(e){let t;switch(e){case o.o.BASE:case o.o.SUGAR:case o.o.LINKER:case o.o.NUCLEOTIDE:case"nucleotide":t="RNA";break;case o.o.AA:t="PEPTIDE";break;case o.o.CHEM:t="CHEM";break;case o.o.BLOB:t="BLOB";break;default:t="PEPTIDE",console.warn(`Unexpected HelmType '${e}'`)}return t}},9235:(e,t,n)=>{"use strict";n.d(t,{H:()=>c,R:()=>l});var o=n(6082),r=n(1991),i=n.n(r),s=n(330),a=n(3599);async function l(e,t,r,l,c,u,h,d){const p=e.length,m=e.dataFrame,f=Math.max(navigator.hardwareConcurrency-2,1),g=new Array(f).fill(null).map((()=>new Worker(new URL(n.p+n.u(455),n.b)))),y=p/f,b=new Array(f),v=u.getSeqHandler(e),C="RNA"==l?a.o.NUCLEOTIDE:a.o.AA,x=i().count(0).take(e.length).map((e=>{const t=v.getSplitted(e);return i().count(0).take(t.length).map((e=>({position:e,symbol:t.getCanonical(e),biotype:C}))).toArray()})).toArray();for(let e=0;e<f;e++){const n=g[e],o=Math.floor(e*y),i=e===f-1?p:Math.floor((e+1)*y);b[e]=new Promise((e=>{n.onmessage=t=>{e(t.data)}})),n.postMessage({seqList:x,rolesList:d,monomersDict:t,alphabet:r,polymerType:l,start:o,end:i})}const w=[],A=[];await Promise.all(b).then((e=>{for(const t of e)w.push(...t.molfiles),A.push(...t.warnings)})),setTimeout((()=>{g.forEach((e=>{e.terminate()}))}),0);const T=(0,s.qj)(m,e.name),E=o.Column.fromType(o.COLUMN_TYPE.STRING,T,e.length).init((e=>w[e]?.molfile));return E.semType=o.SEMTYPE.MOLECULE,E.meta.units=o.UNITS.Molecule.MOLBLOCK,E.setTag(".sequence-src-col",e.name),{molCol:E,warnings:A}}function c(e,t){const n={},r={};for(const i of e){const e=t.getWebEditorMonomer(i.biotype,i.symbol).backgroundcolor,a=(0,s.vG)(e??o.Color.toRgb(o.Color.mouseOverRows))??[1,0,0,.7];for(const e of i.atoms)n[e]=a;for(const e of i.bonds)r[e]=a}return{atoms:Object.keys(n).map((e=>parseInt(e))),bonds:Object.keys(r).map((e=>parseInt(e))),highlightAtomColors:n,highlightBondColors:r}}},3561:(e,t,n)=>{"use strict";n.d(t,{Hb:()=>l,YN:()=>f,gU:()=>c});var o=n(8123),r=n(294),i=n(3151),s=n(439),a=n(6197);function l(e,t,n){const o=new Map;for(const n of e.getMonomerSymbolsByType(t)){const r=e.getMonomer(t,n);if("RNA"===t||"PEPTIDE"===t&&"Branch"!==r.monomerType){const e={};i.f6.forEach((t=>{e[t]=r[t]})),o.set(n,e)}}return o}function c(e,t,n,i,l){if(0===e.length)return r.vF.createEmpty();const c="RNA"===i&&!!l&&l.length===e.length,{atomCount:m,bondCount:g,needsCapping:y}=function(e,t,n,i,l,c){let u=0,h=0,d=0,p=!0,m=null,f=null;for(let n=0;n<e.length;++n){const o=e[n];if(o.symbol!==s._S){if("*"==o.symbol)throw new Error("Gap canonical symbol is '', not '*");m=(0,r.xb)(t,{symbol:o.symbol,polymerType:(0,a.Y)(o.biotype)}),u+=m.atoms.x.length,h+=m.bonds.bondTypes.length,d++,l&&n%3==2&&(f=m)}}if("PEPTIDE"===i)u+=1,h+=d,d>0&&((m?.meta?.rNodes?.length??0)<2||m?.terminalR2Atom?.toLowerCase()===o.u.HYDROGEN.toLowerCase())&&(p=!1,u-=1,h-=1);else if(l)h+=d,c&&c.length>0&&c[c.length-1]===r.ZN.TERMINAL_3P?p=!1:u+=1;else{const i=n===s.YI.DNA?(0,r.xb)(t,o.u.DEOXYRIBOSE):(0,r.xb)(t,o.u.RIBOSE),a=(0,r.xb)(t,o.u.PHOSPHATE);u+=(e.length-1)*a.atoms.x.length,u+=e.length*i.atoms.x.length,u+=1,h+=(e.length-1)*a.bonds.bondTypes.length,h+=e.length*i.bonds.bondTypes.length,h-=1,h+=3*e.length}return{atomCount:u,bondCount:h,needsCapping:p}}(e,t,n,i,c,l),b=new Array(m),v=new Array(g);let C,x=null,w=null;"PEPTIDE"===i?C=u:(C=d,c||(x=n===s.YI.DNA?(0,r.xb)(t,o.u.DEOXYRIBOSE):(0,r.xb)(t,o.u.RIBOSE),w=(0,r.xb)(t,o.u.PHOSPHATE)));const A={i:0,nodeShift:0,bondShift:0,backbonePositionShift:new Array(2).fill(0),branchPositionShift:new Array(2).fill(0),backboneAttachNode:0,branchAttachNode:0,flipFactor:1},T={sugar:x,phosphate:w,seqLength:c?Math.ceil(e.length/3):e.length,atomCount:m,bondCount:g},E=new r.Cg,S=[];let N,I=0;if(c)!function(e,t,n,o,i,s,l,c,u,d,m){const f=t.length>0&&t[0]===r.ZN.TERMINAL_5P,g=t.length>0&&t[t.length-1]===r.ZN.TERMINAL_3P,y=f?1:0,b=(g?t.length-1:t.length)-y,v=Math.ceil(b/3),C=b===3*v,x=(e,t)=>{const l=(0,r.xb)(n,{symbol:e.symbol,polymerType:(0,a.Y)(e.biotype)}),p=s.nodeShift,f=s.bondShift;h(l,o,i,s),l.stereoAtoms?.forEach((e=>u.push(e+m()))),d(l.atoms.x.length);const g=[];for(let e=p;e<s.nodeShift;++e)g.push(e);const y=[];for(let e=f;e<s.bondShift;++e)y.push(e);c.set(t,{biotype:e.biotype,symbol:e.symbol,atoms:g,bonds:y})};f&&(s.i=0,x(e[0],0));for(let t=0;t<v;++t){s.i=t+(f?1:0);const l=y+3*t,g=l+1,b=e[l],v=e[g],C=(0,r.xb)(n,{symbol:b.symbol,polymerType:(0,a.Y)(b.biotype)}),w=(0,r.xb)(n,{symbol:v.symbol,polymerType:(0,a.Y)(v.biotype)});if(t>=1){const n=y+3*(t-1)+2;x(e[n],n)}const A=s.nodeShift,T=s.bondShift;h(C,o,i,s),C.stereoAtoms?.forEach((e=>u.push(e+m()))),d(C.atoms.x.length);const E=[];for(let e=A;e<s.nodeShift;++e)E.push(e);const S=[];for(let e=T;e<s.bondShift;++e)S.push(e);c.set(l,{biotype:b.biotype,symbol:b.symbol,atoms:E,bonds:S});const N=s.nodeShift,I=s.bondShift;p(w,o,i,s),w.stereoAtoms?.forEach((e=>u.push(e+m()))),d(w.atoms.x.length);const M=[];for(let e=N;e<s.nodeShift;++e)M.push(e);const P=[];for(let e=I;e<s.bondShift;++e)P.push(e);c.set(g,{biotype:v.biotype,symbol:v.symbol,atoms:M,bonds:P})}if(C){const t=y+3*(v-1)+2;x(e[t],t)}g&&(s.i=v+(f?1:0),x(e[t.length-1],t.length-1))}(e,l,t,b,v,A,0,E,S,(e=>{I+=e}),(()=>I));else for(A.i=0;A.i<T.seqLength;++A.i){const n=e[A.i];if(n.symbol===s._S)continue;const o=(0,r.xb)(t,{symbol:n.symbol,polymerType:(0,a.Y)(n.biotype)});N=o.terminalR2Atom;const i=A.nodeShift,l=A.bondShift;C(o,b,v,A,T),o.stereoAtoms?.forEach((e=>S.push(e+I))),I+=o.atoms.x.length;const c=A.nodeShift-i,u=new Array(c);for(let e=0;e<c;++e)u[e]=i+e;const h=A.bondShift-l,d=new Array(h);for(let e=0;e<h;++e)d[e]=l+e;E.set(A.i,{biotype:n.biotype,symbol:n.symbol,atoms:u,bonds:d})}y&&function(e,t,n,r,i=o.u.OXYGEN){const s=n.nodeShift+1;e[r.atomCount]=o.u.V3K_BEGIN_DATA_LINE+s+" "+(i??o.u.OXYGEN)+" "+f(n.backbonePositionShift[0])+" "+n.flipFactor*f(n.backbonePositionShift[1])+" 0.000000 0\n";const a=n.backboneAttachNode,l=s;t[r.bondCount]=o.u.V3K_BEGIN_DATA_LINE+n.bondShift+" 1 "+a+" "+l+"\n"}(b,v,A,T,N??o.u.OXYGEN);const M=o.u.V3K_BEGIN_COUNTS_LINE+m+" "+g+o.u.V3K_COUNTS_LINE_ENDING;let P="";return P+=o.u.V3K_HEADER_FIRST_LINE,P+=o.u.V3K_HEADER_SECOND_LINE,P+=o.u.V3K_BEGIN_CTAB_BLOCK,P+=M,P+=o.u.V3K_BEGIN_ATOM_BLOCK,P+=b.join(""),P+=o.u.V3K_END_ATOM_BLOCK,P+=o.u.V3K_BEGIN_BOND_BLOCK,P+=v.join(""),P+=o.u.V3K_END_BOND_BLOCK,S.length>0&&(P+=function(e){const t=[];let n=`M V30 MDLV30/STEABS ATOMS=(${e.length}`;for(let o=0;o<e.length;o++){const r=`${n} ${e[o]}`;r.length>76?(t.push(`${n} -\n`),n=`M V30 ${e[o]}`):n=r,o===e.length-1&&t.push(`${n})\n`)}return`M V30 BEGIN COLLECTION\n${t.join("")}M V30 END COLLECTION\n`}(S)),P+=o.u.V3K_END_CTAB_BLOCK,P+=o.u.V3K_END,{molfile:P,monomers:E}}function u(e,t,n,o){o.flipFactor=(-1)**(o.i%2),h(e,t,n,o)}function h(e,t,n,r){!function(e,t,n){for(let r=0;r<e.atoms.atomTypes.length;++r){const i=n.nodeShift+r+1;t[n.nodeShift+r]=o.u.V3K_BEGIN_DATA_LINE+i+" "+e.atoms.atomTypes[r]+" "+f(n.backbonePositionShift[0]+e.atoms.x[r])+" "+f(n.backbonePositionShift[1]+n.flipFactor*e.atoms.y[r])+" "+e.atoms.kwargs[r]}}(e,t,r),m(e,n,r),function(e,t,n){if(0!==n.backboneAttachNode){const r=n.bondShift,i=n.backboneAttachNode,s=e.meta.terminalNodes[0]+n.nodeShift;t[n.bondShift-1]=o.u.V3K_BEGIN_DATA_LINE+r+" 1 "+i+" "+s+"\n"}}(e,n,r),null!==e.meta.branchShift&&e.meta.terminalNodes.length>2&&function(e,t){t.branchAttachNode=t.nodeShift+e.meta.terminalNodes[2];for(let n=0;n<2;++n)t.branchPositionShift[n]=t.backbonePositionShift[n]+e.meta.branchShift[n]}(e,r),function(e,t){t.backboneAttachNode=t.nodeShift+e.meta.terminalNodes[1],t.bondShift+=e.bonds.atomPairs.length+1,t.nodeShift+=e.atoms.atomTypes.length,t.backbonePositionShift[0]+=e.meta.backboneShift?.[0]??0,t.backbonePositionShift[1]+=t.flipFactor*(e.meta.backboneShift?.[1]??0)}(e,r)}function d(e,t,n,o,r){if(0===o.i)h(r.sugar,t,n,o);else 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t=e.bonds.bondConfiguration.get(r);n.flipFactor<0&&(t=1===t?3:1),l=" CFG="+t}const c=e.bonds.kwargs.has(r)?" 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C,x;v||b.notation===a.Hi.SEPARATOR||b.notation===a.Hi.BILN||(f=b.convert(a.Hi.SEPARATOR,"."),f.name=t.name);try{v?(C="RNA",x=function(e,t){const n=t.getSeqHandler(e);for(let t=0;t<e.length;++t){const e=n.getSplitted(t);for(let t=0;t<e.length;++t)if(t%3==0&&e.getCanonical(t)===m.u.DEOXYRIBOSE.symbol)return a.YI.DNA}return a.YI.RNA}(t,i)):(x=i.getSeqHandler(f).alphabet,C=(0,d.pz)(x))}catch(e){const[t,n]=(0,h.AP)(e);return{molCol:null,warnings:[t]}}const w=function(e,t){const n=e.length,r=new Array(n),i=t.getSeqHandler(e);let a=!1;const l=i.defaultBiotype;for(let e=0;e<n;++e){const t=i.getSplitted(e);a||(a=0===t.length),r[e]=s().count(0).take(t.length).filter((e=>!t.isGap(e))).map((e=>({position:e,biotype:l,symbol:t.getCanonical(e)}))).toArray()}return a&&o.shell.warning(`Some values in the "${e.name}" column are empty`),r}(f,i),A=v?function(e,t,n){const o=new Array(e.length);for(let r=0;r<e.length;++r){const i=e[r];if(0===i.length){o[r]=void 0;continue}const 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a(e){const t=[];let n=0,o="",r=0;for(const i of e){if("["===i||"("===i)n++;else if("]"===i||")"===i)n--;else if("."===i&&0===n){o&&t.push(l(o,r++)),o="";continue}o+=i}return o&&t.push(l(o,r)),t}function l(e,t){let n=0,r="",i=null,s="";const a=e;if("["===e[0]){const t=e.indexOf("]");r=e.substring(1,t),n=t+1}else r=e[0]??"",n=1;if("("===e[n]){const t=e.indexOf(")",n);i=(0,o.D)(e.substring(n+1,t)),n=t+1}if(n<e.length)if("["===e[n]){const t=e.indexOf("]",n);s=e.substring(n+1,t),n=t+1}else s=e.substring(n);return null===i?{kind:"conjugate",position:t,symbol:r,raw:a}:{kind:"nucleotide",position:t,sugar:r,base:i,phosphate:s,raw:a}}function c(e){return/^\s*(?:RNA|DNA|PEPTIDE|CHEM|BLOB)\d+\s*\{/.test(e??"")}function u(e){if("conjugate"===e.kind)return`[${e.symbol}]`;const t=e,n=(0,r.Jy)(t.sugar),o=(0,r.$T)(t.phosphate),i=1===n.length?n:`[${n}]`,s=o?1===o.length?o:`[${o}]`:"";return`${i}${t.base?1===t.base.length?`(${t.base})`:`([${t.base}])`:""}${s}`}function h(e){return`${(e??"").split("$")[0].split("|").map((e=>e.trim())).filter(Boolean).map((e=>{const t=e.match(/^((?:RNA|DNA|PEPTIDE|CHEM|BLOB)\d+)\{(.*)\}$/);if(!t)return e;const[,n,o]=t;return`${n}{${function(e){return a(e).map(u).join(".")}(o)}}`})).join("|")}$$$$`}},1536:(e,t,n)=>{"use strict";n.d(t,{$T:()=>y,Av:()=>m,D2:()=>r,FN:()=>d,Jy:()=>g,L1:()=>u,P4:()=>a,bM:()=>v,e8:()=>f,kT:()=>p,mU:()=>o,pt:()=>c,rK:()=>C,xh:()=>b});const o="OligoNucleotide",r="helm",i=Object.freeze({r:{name:"Ribose",short:"RNA",color:"#D0D0D0",category:"sugar"},d:{name:"Deoxyribose",short:"DNA",color:"#BDBDBD",category:"sugar"},m:{name:"2'-O-Methyl",short:"2'-OMe",color:"#4A90E2",category:"sugar"},"25r":{name:"2'-O-Methyl (2,5)",short:"2'-OMe",color:"#4A90E2",category:"sugar"},fl2r:{name:"2'-Fluoro",short:"2'-F",color:"#50C878",category:"sugar"},lna:{name:"LNA",short:"LNA",color:"#E89D3C",category:"sugar"},cet:{name:"cEt",short:"cEt",color:"#E07B30",category:"sugar"},ena:{name:"ENA",short:"ENA",color:"#D26C20",category:"sugar"},moe:{name:"2'-MOE",short:"2'-MOE",color:"#66CDAA",category:"sugar"},Rgna:{name:"(R)-GNA",short:"GNA",color:"#C7A981",category:"sugar"},Sgna:{name:"(S)-GNA",short:"GNA",color:"#C7A981",category:"sugar"},una:{name:"UNA",short:"UNA",color:"#ED68B8",category:"sugar"},fana:{name:"FANA",short:"FANA",color:"#76B947",category:"sugar"},hna:{name:"HNA",short:"HNA",color:"#A4D080",category:"sugar"}}),s=Object.freeze({R:"r",dR:"d",mR:"m",fR:"fl2r",LR:"lna",L:"lna",MOE:"moe",GNA:"Sgna",UNA:"una"}),a=Object.freeze({p:{name:"Phosphate",short:"PO",color:"#888888",category:"phosphate"},sp:{name:"Phosphorothioate",short:"PS",color:"#6B46C1",category:"phosphate"},s2p:{name:"Phosphorodithioate",short:"PS₂",color:"#7E2BC4",category:"phosphate"},mp:{name:"Methylphosphonate",short:"MeP",color:"#9B5DE5",category:"phosphate"}}),l=Object.freeze({P:"p",sP:"sp"}),c=Object.freeze({GalNAc:{name:"GalNAc",short:"GalNAc",color:"#E91E63",category:"conjugate"},L3:{name:"GalNAc-L3 linker",short:"L3",color:"#E91E63",category:"conjugate"},Chol:{name:"Cholesterol",short:"Chol",color:"#B57F50",category:"conjugate"},Bio:{name:"Biotin",short:"Bio",color:"#FFC107",category:"conjugate"}}),u=Object.freeze({A:"#C1E7C5",C:"#C5DCF0",G:"#E8DCA9",U:"#F0C5C5",T:"#F0C5C5"}),h=new Set(["A","C","G","U","T"]),d="#BCBCBC";function p(e){return!!e&&h.has(e)}function m(e){return e?e.length<=2?e:e[0]+"…":""}function f(e){let t=0;for(let n=0;n<e.length;n++)t=31*t+e.charCodeAt(n)|0;return`hsl(${(t>>>0)%360}, 42%, 60%)`}function g(e){return s[e]??e}function y(e){return l[e]??e}function b(e,t){const n=g(e),o=i[n];if(o)return("r"===n||"d"===n)&&t&&u[t]?{color:u[t],meta:o}:{color:o.color,meta:o};const r=f(n);return{color:r,meta:{name:n,short:n,color:r,category:"sugar"}}}function v(e){if(!e)return{color:"#888",meta:{name:"(none)",short:"",color:"#888",category:"phosphate"}};const t=y(e),n=a[t];if(n)return{color:n.color,meta:n};const o=f(t);return{color:o,meta:{name:t,short:t,color:o,category:"phosphate"}}}function C(e){const t=c[e];return t?{color:t.color,meta:t}:{color:f(e),meta:{name:e,short:e.length>6?e.slice(0,6):e,color:f(e),category:"conjugate"}}}},6345:(e,t,n)=>{"use strict";n.d(t,{PackageFunctions:()=>Cr,_package:()=>br});var o=n(4328),r=n(7389),i=n(6082),s=n(439),a=n(7291);const l=new class{constructor(){this.seqHandler="seq-handler",this.notationProvider="seq-handler.notation-provider"}};i.SemanticValue;var c=n(4971);class u{constructor(e,t,n=""){this.target=e,this.debugEnabled=t,this.prefix=n}error(e,t,n){return this.target.error(this.prefix+e,t,n)}warning(e,t){return this.target.warning(this.prefix+e,t)}info(e,t){return this.target.info(this.prefix+e,t)}debug(e,t){if(this.debugEnabled)return this.target.debug(this.prefix+e,t)}}const h="System:AppData/SequenceTranslator/monomers-sample",d="pattern-app-data.json",p="formats-to-helm.json",m="codes-to-symbols.json",f="linkers.json";var g=n(6686);function y(e){return e.sort(((e,t)=>t.length-e.length))}function b(e,t){const n=document.createElement("a");n.setAttribute("href","data:text/plain;charset=utf-8,"+t),n.setAttribute("download",e),n.click()}async function v(e,t,n="Oligo app"){try{return await e()}catch(e){const t=e.hasOwnProperty("message")?e.message:e.toString();throw o.shell.error(`${n} error: `+t),e}finally{t&&t()}}class C{constructor(e,t){this.sequence=e,this.th=t,this.libWrapper=this.th.monomerLibWrapper}getInvalidCodeIndex(e){if(e===g.NO.HELM)return this.sequence.length;const t=["r","d"],n=y(this.libWrapper.getCodesByFormat(e));let o=0;for(;o<this.sequence.length;){const e=n.find((e=>e===this.sequence.substring(o,o+e.length)));if(!e)break;if(o>1&&g.AL.includes(this.sequence[o])&&t.includes(this.sequence[o-2]))break;if(t.includes(this.sequence[o+1])&&g.AL.includes(this.sequence[o])){o++;break}o+=e.length}return o===this.sequence.length&&(o=-1),o}isValidSequence(e){return-1===this.getInvalidCodeIndex(e)}}class x{constructor(e,t,n,o){this.patternAppData=e,this.codesToHelmDict=t,this.codesToSymbolsDict=n,this.monomersWithPhosphate=o}}async function w(e){const t=await Promise.all([d,p,m,f].map((t=>async function(e,t){const n=e.endsWith("/")?`${e}${t}`:`${e}/${t}`;try{const e=await o.dapi.files.readAsText(n);return JSON.parse(e)}catch(e){console.error(`Error loading json from '${n}':`,e)}}(e,t))));return new x(t[0],t[1],t[2],t[3])}class A{constructor(e,t){if(this.lib=e,this.jsonData=t,null===this.lib)throw new Error("SequenceTranslator: monomer library is null");this.allMonomers=this.getAllMonomers()}formatMonomerForViewer(e){const t={};return t.name=e.symbol,t.symbol=e.symbol,t.molfile=e.molfile,this.getAllFormats().forEach((n=>{if(n===g.NO.HELM)return;const o=this.jsonData.codesToSymbolsDict[n],r=Object.keys(o).filter((t=>o[t]===e.symbol));t[n]=r.join(", ")})),t}getAllMonomers(){const e=this.lib.getPolymerTypes();let t=[];for(const n of e){const e=this.lib.getMonomerSymbolsByType(n).map((e=>this.lib.getMonomer(n,e))).filter((e=>null!==e));t=t.concat(e)}return t}getMonomer(e){const t=this.lib.getMonomer("RNA",e);if(void 0===t)throw new Error(`SequenceTranslator: no monomer with symbol ${e}`);return t}getMolfileBySymbol(e){return this.getMonomer(e).molfile}getNaturalAnalogBySymbol(e){const t=this.getMonomer(e).naturalAnalog;if(!t)throw new Error(`ST: no natural analog for ${e}`);return t}isModification(e){return!!this.getMolfileBySymbol(e).includes("MODIFICATION")}getCodeToSymbolMap(e){return new Map(Object.entries(this.jsonData.codesToSymbolsDict[e]))}getCodesByFormat(e){return Object.keys(this.jsonData.codesToSymbolsDict[e])}getAllFormats(){return Object.keys(this.jsonData.codesToSymbolsDict)}getTableForViewer(){const e=this.allMonomers.map((e=>this.formatMonomerForViewer(e)));return i.DataFrame.fromObjects(e)}getCodesToWeightsMap(){const e=new Map;return Object.entries(this.jsonData.codesToSymbolsDict).forEach((([t,n])=>{Object.entries(n).forEach((([t,n])=>{const o=this.getMonomer(n),r=o.meta?.molecularWeight;e.set(t,r)}))})),e}}var T=n(9537);const E=(e,t)=>t.length-e.length;class S{constructor(e){this.th=e,this.formats=this.getFormats()}getFormatNames(){return this.formats.sort()}getCodesByFormat(e){if(this.validateFormat(e),this.isHelm(e))throw new Error("Codes cannot be obtained for HELM");return this.getFormatCodes(e)}getHelmToFormatDict(e){return this.validateFormat(e),function(e){const t={};return Object.values(e).forEach((e=>{Object.entries(e).forEach((([e,n])=>{const o=n.replace(/\)p/g,")").replace(/\]p/g,"]");void 0===t[o]?t[o]=[e]:t[o].push(e)}))})),Object.entries(t).forEach((([e,n])=>{const o=n.sort(E);t[e]=o[0]})),t}(this.th.jsonData.codesToHelmDict[e])}getFormatToHelmDict(e){this.validateFormat(e);const t=this.th.jsonData.codesToHelmDict[e];return Object.assign({},...Object.values(t))}getTargetFormatHelmCodes(e){this.validateFormat(e);const t=this.getHelmToFormatDict(e);return Object.keys(t).sort(E)}getTargetFormatHelmCodesRegExp(e){this.validateFormat(e);const t=this.getTargetFormatHelmCodes(e);return new RegExp(N(t)+"|.","g")}getFormatRegExp(e){if(this.validateFormat(e),this.isHelm(e))throw new Error("Helm RegExp can be built for non-HELM target formats");return this.getNonHelmFormatRegExp(e)}getPhosphateHelmCodesRegExp(e){this.validateFormat(e);const t=this.th.jsonData.codesToHelmDict[e],n=N(Array.from(new Set(Object.values(t[T.ti.LINKAGE]))).sort(E));return new RegExp(`${T.q7}.(${n})`,"g")}isValidFormat(e){return this.formats.includes(e)}getFormats(){return Object.keys(this.th.jsonData.codesToHelmDict)}validateFormat(e){if(!this.isValidFormat(e))throw new Error(`Invalid format: ${e}`)}isHelm(e){return e===g.NO.HELM}getFormatCodes(e){const t=this.getFormatToHelmDict(e);return Object.keys(t).sort(E)}getNonHelmFormatRegExp(e){const t=this.getCodesByFormat(e);return new RegExp(N(t)+"|\\([^()]*\\)|.","g")}}function N(e){return e.map((e=>e.replace(/[.*+?^${}()|[\]\\]/g,"\\$&"))).map((e=>e.includes("(")||e.includes(")")?e:`(?<!\\([^()]*)${e}(?![^()]*\\))`)).join("|")}const I={LEFT:"RNA1{",RIGHT:"}$$$$"};class M{constructor(e,t,n){this.sequence=e,this.sourceFormat=t,this.th=n,this.formats=new S(this.th)}convertTo(e){const t=this.formats.getFormatNames();if(this.sourceFormat===g.NO.HELM&&t.includes(e))return this.helmToFormat(this.sequence,e);if(t.includes(this.sourceFormat)&&e===g.NO.HELM)return this.formatToHelm(this.sequence,this.sourceFormat);if([this.sourceFormat,e].every((e=>t.includes(e)))){const t=this.formatToHelm(this.sequence,this.sourceFormat);return this.helmToFormat(t,e)}throw new Error(`ST: unsupported translation direction ${this.sourceFormat} -> ${e}`)}helmToFormat(e,t){const n=new RegExp(N(Object.values(I)),"g");let o=e.replace(n,"");const r=this.formats.getHelmToFormatDict(t),i=this.formats.getTargetFormatHelmCodes(t),s=this.formats.getTargetFormatHelmCodesRegExp(t);return o=o.replace(s,(e=>i.includes(e)?r[e]:"p"===e||"."===e?e:"?")).replace(/\?+/g,T.iL).replace(/p\.|\./g,""),o=o.replace(/<empty>/g,""),o=o.replace(/\/\//g,"/"),o}formatToHelm(e,t){const n=this.formats.getFormatToHelmDict(t),o=this.formats.getCodesByFormat(t),r=this.formats.getFormatRegExp(t),i=this.formats.getPhosphateHelmCodesRegExp(t);let s=e?e.replace(r,(e=>o.includes(e)?n[e]+".":"?")):"";return s=s.replace(/\?+/g,`${T.iL}.`),s=s.slice(0,-1),s[s.length-1]===T.q7&&(s=s.slice(0,-1)),s=s.replace(i,((e,t)=>t)),s=s.replace(/<empty>/g,""),`${I.LEFT+s+I.RIGHT}`}}class P{constructor(e,t){this.sequence=e,this.th=t,this.libWrapper=this.th.monomerLibWrapper,this.formats=Object.keys(this.th.jsonData.codesToHelmDict)}getFormat(){if(this.sequence.startsWith("RNA"))return g.NO.HELM;const e=this.getListOfPossibleSynthesizersByFirstMatchedCode();if(0===e.length)return null;const t=this.th.createSequenceValidator(this.sequence),n=Array(e.length).fill(0);for(let o=0;o<e.length;++o){const r=e[o];n[o]=t.getInvalidCodeIndex(r)}const o=n.some((e=>-1===e))?-1:Math.max(...n);return e[n.indexOf(o)]}getListOfPossibleSynthesizersByFirstMatchedCode(){const e=this.sequence,t=[];for(const n of this.formats){const o=y(this.libWrapper.getCodesByFormat(n));let r=0;for(let t=0;t<e.length;t++)if(")"===e[t]&&t!==e.length-1){r=t+1;break}o.some((t=>t===e.slice(r,r+t.length)))&&t.push(n)}return t}}var _=n(1757),L=n.n(_);function O(e,t){let n=0;const o=t.createFormatDetector(e).getFormat();null!==o&&(n=new C(e,t).getInvalidCodeIndex(o));const i=n<0||""===e,s=r.span([]);L()(s).css("-webkit-text-fill-color","var(--grey-6)");const a=r.span([]);return L()(a).css("-webkit-text-fill-color","red"),i?s.innerHTML=e:(s.innerHTML=e.slice(0,n),a.innerHTML=e.slice(n)),[s,a]}class R extends i.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 bioMonomerLib(){if(!this._bioMonomerLib)throw new Error("Package SequenceTranslator .bioMonomerLib is not initialized");return this._bioMonomerLib}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(e={debug:!1}){super(),this.highlightInvalidSubsequence=e=>O(e,this),super._logger=new u(super.logger,e.debug)}startInit(e){this._initPromise=e}completeInit(e,t){this._helmHelper=e,this._bioMonomerLib=t}async initLibData(){return this.initLibDataPromise||(this.initLibDataPromise=(async()=>{const e=await this.getSettings();let t=e instanceof Map?e.get("MonomersPath"):e.MonomersPath;t&&await o.dapi.files.exists(t)||(this.logger.warning(`Monomers path '${t}' not found. Fallback to monomers sample path '${h}'.`),t=h),[this._jsonData,this._monomerLib]=await Promise.all([w(t),D(t)]),this._monomerLibWrapper=new A(this.monomerLib,this.jsonData)})()),this.initLibDataPromise}async getTranslationHelper(){return await o.functions.call(`${this.name}:getTranslationHelper`)}createSequenceValidator(e){return new C(e,this)}createFormatConverter(e,t){return new M(e,t,this)}createFormatDetector(e){return new P(e,this)}}async function D(e){const t=i.TaskBarProgressIndicator.create("Initializing Oligo Toolkit monomer library ...");try{const t=await(0,c.pj)(),n=(e.endsWith("/")?e:e+"/")+"monomer-lib.json";return await t.readLibraryFromFilePath(n)}finally{t.close()}}class B{constructor(e,t){this.appName=e,this.parentAppName=t}async getAppView(){const e=i.TaskBarProgressIndicator.create(`Loading ${this.appName}...`),t=o.shell.v?.root;t&&r.setUpdateIndicator(t,!0);try{return await this.constructView()}finally{e.close(),t&&r.setUpdateIndicator(t,!1)}}}class F extends B{constructor(e){super(e),this.view=i.View.create(),this.configureView()}async constructView(){await this.initView();const e=this.parentAppName?this.parentAppName+"/"+this.appName:this.appName;return this.view.path=`/apps/${br.name}/${e.replace(/\s/g,"")}/`,this.view}async initView(){const e=await this.getContent();this.view.append(e)}configureView(){this.view.box=!0,this.view.name=this.appName;const e=o.shell.windows;e.showProperties=!1,e.showToolbox=!1,e.showHelp=!1}getView(){return this.view}}const k=["SS","AS"],H={SS:"Sense strand",AS:"Anti sense"},G=["3'","5'"],U="OligoToolkit";var V,j,q,W;!function(e){e.IS_ANTISENSE_STRAND_INCLUDED="isAntisenseStrandIncluded",e.NUCLEOTIDE_SEQUENCES="nucleotideSequences",e.PHOSPHOROTHIOATE_LINKAGE_FLAGS="phosphorothioateLinkageFlags",e.STRAND_TERMINUS_MODIFICATIONS="strandTerminusModifications"}(V||(V={})),function(e){e.PATTERN_NAME="patternName",e.PATTERN_COMMENT="patternComment",e.NUCLEOTIDES_WITH_NUMERIC_LABELS="nucleotidesWithNumericLabels"}(j||(j={})),function(e){e.PATTERN_CONFIG="patternConfig",e.AUTHOR_ID="authorID",e.DATE="date"}(q||(q={})),function(e){e.CREATE="create",e.MODIFY="modify"}(W||(W={}));const z=[V.IS_ANTISENSE_STRAND_INCLUDED,V.NUCLEOTIDE_SEQUENCES,V.PHOSPHOROTHIOATE_LINKAGE_FLAGS,V.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 Q extends Error{constructor(e){super(e),this.name="PatternNameExistsError"}}class J extends Error{constructor(e){super(e),this.name="PatternExistsError"}}var X=n(4802),Z=n.n(X);class ee{constructor(e){this.th=e,this.otherUsersPatternNameToHash=new Map,this.currentUserPatternNameToHash=new Map}static async getInstance(){const e=await br.getTranslationHelper(),t=new ee(e);t.currentUserName=await t.fetchCurrentUserName(),t.currentUserId=await t.fetchCurrentUserId();const n=t.fetchPatterns();return await t.initializePatternMaps(n),t}getCurrentUserPatternNames(){return Array.from(this.currentUserPatternNameToHash.keys()).sort(((e,t)=>e.toLowerCase().localeCompare(t.toLowerCase())))}getOtherUsersPatternNames(){return Array.from(this.otherUsersPatternNameToHash.keys()).sort(((e,t)=>e.toLowerCase().localeCompare(t.toLowerCase())))}getCurrentUserName(){return this.currentUserName}validatePatternNameUniqueness(e){if(this.currentUserPatternNameToHash.has(e))throw new Q(`Pattern with name ${e} already exists`)}validatePatternUniqueness(e){if(Array.from(this.currentUserPatternNameToHash.values()).concat(Array.from(this.otherUsersPatternNameToHash.values())).includes(e))throw new J(e)}getPatternHash(e,t){const n=t?this.currentUserPatternNameToHash.get(e):this.otherUsersPatternNameToHash.get(e);if(void 0===n)throw new Error(`Pattern with name ${e} not found`);return n}async getPatternRecordByHash(e){if(null===e||""===e)return null;try{const t=o.userSettings.getValue(U,e,!1)??"null";return JSON.parse(t)}catch{return null}}async getPatternConfig(e){if(""===e||null===e)return null;const t=await this.getPatternRecordByHash(e);return null===t?null:t[q.PATTERN_CONFIG]}getDefaultPatternRecord(){const e=Y;return e[q.AUTHOR_ID]=this.currentUserId,e}getDefaultPatternConfig(){return Y[q.PATTERN_CONFIG]}getAuthorCategoryByHash(e){if(this.isCurrentUserPattern(e))return this.getCurrentUserAuthorshipCategory();if(this.isOtherUserPattern(e))return this.getOtherUsersAuthorshipCategory();throw new Error(`Pattern with hash ${e} not found`)}isCurrentUserPattern(e){return Array.from(this.currentUserPatternNameToHash.values()).includes(e)}isOtherUserPattern(e){return Array.from(this.otherUsersPatternNameToHash.values()).includes(e)}getPatternNameByHash(e){const t=[this.currentUserPatternNameToHash,this.otherUsersPatternNameToHash];for(const n of t)for(const[t,o]of n.entries())if(o===e)return t;throw new Error(`Pattern with hash ${e} not found`)}getHashOfPatternToBeLoadedAfterDeletion(){const e=this.getCurrentUserPatternNames()[0];if(!e)throw new Error("Cannot load pattern after deletion, as there are no patterns left");const t=this.currentUserPatternNameToHash.get(e);if(void 0===t)throw new Error(`Pattern with name ${e} not found`);return t}async getRecordFromPattern(e){return{[q.PATTERN_CONFIG]:e,[q.AUTHOR_ID]:await o.dapi.users.current().then((e=>e.id))}}getHash(e){const t=z.reduce(((t,n)=>(t[n]=e[n],t)),{});return Z().sha1(t)}async savePatternToUserStorage(e){const t=e.getPatternConfig();try{const n=this.getHash(t);this.validatePatternUniqueness(n);const r=t[j.PATTERN_NAME];this.validatePatternNameUniqueness(r);const i=await this.getRecordFromPattern(t),s=(new Date).toISOString();i[q.DATE]={[W.CREATE]:s,[W.MODIFY]:s};const a=JSON.stringify(i);o.userSettings.add(U,n,a,!1),this.currentUserPatternNameToHash.set(r,n),e.selectAuthor(this.getCurrentUserAuthorshipCategory()),e.updatePatternList(),e.requestPatternLoad(n),e.updateUrlState(n)}catch(e){if(e instanceof Q||e instanceof J)throw e;console.error("Error while saving pattern to user storage",e)}}async overwriteExistingPatternInUserStorage(e){const t=e.getPatternConfig(),n=t[j.PATTERN_NAME],r=this.currentUserPatternNameToHash.get(n);if(void 0===r)throw new Error("Old hash is undefined");const i=this.getHash(t),s=await this.getRecordFromPattern(t),a=(new Date).toISOString();s[q.DATE]={[W.MODIFY]:a};const l=o.userSettings.getValue(U,r,!1)??"null",c=JSON.parse(l);void 0!==c[q.DATE]&&null!=c[q.DATE][W.CREATE]&&(s[q.DATE][W.CREATE]=c[q.DATE][W.CREATE]);const u=JSON.stringify(s);o.userSettings.add(U,i,u,!1),o.userSettings.delete(U,r,!1),this.currentUserPatternNameToHash.set(n,i),e.requestPatternLoad(i),e.updateUrlState(i)}async deletePattern(e,t){const n=this.currentUserPatternNameToHash.get(e);if(e===this.getDefaultPatternName())return void o.shell.warning("Cannot delete default pattern");if(void 0===n)throw new Error(`Pattern with name ${e} not found`);o.userSettings.delete(U,n,!1),this.currentUserPatternNameToHash.delete(e),t.updatePatternList();const r=this.getHashOfPatternToBeLoadedAfterDeletion();t.requestPatternLoad(r)}fetchDefaultNucleobase(){return this.fetchAvailableNucleotideBases()[0]}fetchAvailableNucleotideBases(){const e=Object.keys(this.th.jsonData.patternAppData)[0];return Object.keys(this.th.jsonData.patternAppData[e])}async fetchCurrentUserName(){return(await o.dapi.users.current()).friendlyName}async fetchCurrentUserId(){return(await o.dapi.users.current()).id}fetchPatterns(){return o.userSettings.get(U,!1)??{}}async initializePatternMaps(e){if(!this.currentUserId)throw new Error("Current user ID is not set");const t=new Map;for(const[n,o]of Object.entries(e))await this.extractDataFromRecordToMaps(n,o,t);this.setDefaultPattern()}setDefaultPattern(){const e=Y[q.PATTERN_CONFIG];this.currentUserPatternNameToHash.set(e[j.PATTERN_NAME],"")}async extractDataFromRecordToMaps(e,t,n){const r=JSON.parse(t),i=r[q.PATTERN_CONFIG].patternName,s=r[q.AUTHOR_ID];if(this.isCurrentUserId(s))this.currentUserPatternNameToHash.set(i,e);else{if(!n.has(s)){let e="<UNKNOWN_USER>";try{e=(await o.dapi.users.find(s)).friendlyName}catch(e){}n.set(s,e)}const t=i+` (created by ${n.get(s)})`;this.otherUsersPatternNameToHash.set(t,e)}}getDefaultPatternName(){return Y[q.PATTERN_CONFIG][j.PATTERN_NAME]}getCurrentUserAuthorshipCategory(){return this.currentUserName+" (me)"}getOtherUsersAuthorshipCategory(){return"Other users"}isCurrentUserId(e){return e===this.currentUserId}}const te=rxjs,ne=rxjs.operators;function oe(e){return e.endsWith("(o)")}function re(e){const t=Object.values(e).flat().reduce(((e,t)=>(e[t]=(e[t]||0)+1,e)),{});return Object.entries(t).reduce(((e,t)=>e[1]>t[1]?e:t),["",0])[0]}var ie;function se(e){const t=Array.from(new Set(e));return Array.from(t).sort(((e,t)=>e.toLowerCase().localeCompare(t.toLowerCase())))}!function(e){e.getTruncatedStrandData=function(e,t,n){return{nucleotides:e.slice(0,n),ptoFlags:t.slice(0,n+1)}},e.getExtendedStrandData=function(e,t,n,o){const r=n-e.length,i=e.concat(new Array(n-e.length).fill(o)),s=0===e.length?n+1:r;return{nucleotides:i,ptoFlags:t.concat(new Array(s).fill(!0))}}}(ie||(ie={}));var ae=n(2543),le=n.n(ae);class ce{constructor(e,t){this.dataManager=e,this._patternListUpdated$=new te.Subject,this._patternLoadRequested$=new te.Subject,this._patternLoaded$=new te.Subject,this._uniqueNucleotides$=new te.BehaviorSubject([]),this._patternDeletionRequested$=new te.Subject,this._tableSelection$=new te.BehaviorSubject(null),this._svgSaveRequested$=new te.Subject,this._loadPatternInNewTabRequested$=new te.Subject,this._urlStateUpdated$=new te.Subject,this._patternHasUnsavedChanges$=new te.BehaviorSubject(!1),this._selectedStrandColumn=new te.BehaviorSubject(null),this._selectedIdColumn=new te.BehaviorSubject(null),this.initializeAuthorSelection(t),this.initializePatternState(t),this._lastLoadedPatternConfig=new te.BehaviorSubject(le().cloneDeep(this.getPatternConfig())),this.setupSubscriptions()}setupSubscriptions(){this._nucleotideSequences$.subscribe((()=>{this.updateUniqueNucleotides(),this.updateSequenceBase()})),this._isAntisenseStrandActive$.subscribe((e=>{e||G.forEach((e=>{this.updateTerminusModification("AS",e,"")}))})),this.patternStateChanged$.pipe((0,ne.debounceTime)(20)).subscribe((()=>{const e=this._lastLoadedPatternConfig.getValue(),t=this.getPatternConfig(),n=!le().isEqual(t,e);this._patternHasUnsavedChanges$.next(n)}))}updateUniqueNucleotides(){const e=(t=this._nucleotideSequences$.getValue(),se(Object.values(t).flat()));var t;this._uniqueNucleotides$.next(e)}updateSequenceBase(){const e=re(this._nucleotideSequences$.getValue());this._sequenceBase$.next(e)}get nucleotideSequencesChanged$(){return this._nucleotideSequences$.asObservable()}initializeAuthorSelection(e){const t=e[q.AUTHOR_ID];this.dataManager.isCurrentUserId(t)?this._patternAuthorSelection$=new te.BehaviorSubject(this.dataManager.getCurrentUserAuthorshipCategory()):this._patternAuthorSelection$=new te.BehaviorSubject(this.dataManager.getOtherUsersAuthorshipCategory())}initializePatternState(e){const t=e[q.PATTERN_CONFIG];this._patternName$=new te.BehaviorSubject(t[j.PATTERN_NAME]),this._isAntisenseStrandActive$=new te.BehaviorSubject(t[V.IS_ANTISENSE_STRAND_INCLUDED]),this._nucleotideSequences$=new te.BehaviorSubject(t[V.NUCLEOTIDE_SEQUENCES]),this._phosphorothioateLinkageFlags=new te.BehaviorSubject(t[V.PHOSPHOROTHIOATE_LINKAGE_FLAGS]),this._terminalModifications=new te.BehaviorSubject(t[V.STRAND_TERMINUS_MODIFICATIONS]),this._comment$=new te.BehaviorSubject(t[j.PATTERN_COMMENT]),this._modificationsWithNumericLabels$=new te.BehaviorSubject(t[j.NUCLEOTIDES_WITH_NUMERIC_LABELS]),this._sequenceBase$=new te.BehaviorSubject(re(t[V.NUCLEOTIDE_SEQUENCES]))}getPatternName(){return this._patternName$.getValue()}updatePatternName(e){this._patternName$.next(e)}get antisenseStrandToggled$(){return this._isAntisenseStrandActive$.asObservable()}isAntisenseStrandActive(){return this._isAntisenseStrandActive$.getValue()}toggleAntisenseStrand(e){e?this.updateStrandLength("AS",this.getNucleotideSequences().SS.length):this.updateStrandLength("AS",0),this._isAntisenseStrandActive$.next(e)}getNucleotideSequences(){return this._nucleotideSequences$.getValue()}updateNucleotideSequences(e){this._nucleotideSequences$.next(e)}updateStrandLength(e,t){const n=this.getNucleotideSequences()[e];if(n.length===t)return;const o=this.getPhosphorothioateLinkageFlags()[e];if(0===t)return void this.setNewStrandData([],[],e);if(n.length>t){const{nucleotides:r,ptoFlags:i}=ie.getTruncatedStrandData(n,o,t);return void this.setNewStrandData(r,i,e)}const r=this.getSequenceBase(),{nucleotides:i,ptoFlags:s}=ie.getExtendedStrandData(n,o,t,r);this.setNewStrandData(i,s,e)}setNewStrandData(e,t,n){this.updateNucleotideSequences({...this.getNucleotideSequences(),[n]:e}),this.updatePhosphorothioateLinkageFlags({...this.getPhosphorothioateLinkageFlags(),[n]:t})}getPhosphorothioateLinkageFlags(){return this._phosphorothioateLinkageFlags.getValue()}updatePhosphorothioateLinkageFlags(e){this._phosphorothioateLinkageFlags.next(e)}get phosphorothioateLingeFlagsChanged$(){return this._phosphorothioateLinkageFlags.asObservable()}getTerminalModifications(){return this._terminalModifications.getValue()}updateTerminalModifications(e){this._terminalModifications.next(e)}updateTerminusModification(e,t,n){const o=this.getTerminalModifications();o[e][t]=n,this.updateTerminalModifications(o)}terminalModificationsUpdated$(){return this._terminalModifications.asObservable()}getComment(){return this._comment$.getValue()}updateComment(e){this._comment$.next(e)}getModificationsWithNumericLabels(){return this._modificationsWithNumericLabels$.getValue()}updateModificationsWithNumericLabels(e){const t=function(e){return se(e).filter((e=>!oe(e)))}(e);this._modificationsWithNumericLabels$.next(t)}get patternLoadRequested$(){return this._patternLoadRequested$.asObservable()}requestPatternLoad(e){this._patternLoadRequested$.next(e)}get patternListUpdated$(){return this._patternListUpdated$.asObservable()}updatePatternList(){this._patternListUpdated$.next()}get tableSelectionChanged$(){return this._tableSelection$.asObservable()}selectTable(e){this._tableSelection$.next(e)}getTableSelection(){return this._tableSelection$.getValue()}requestPatternDeletion(e){this._patternDeletionRequested$.next(e)}get patternDeletionRequested$(){return this._patternDeletionRequested$.asObservable()}replaceSequenceBase(e){const t=this._nucleotideSequences$.getValue(),n={};k.forEach((o=>{n[o]=t[o].map((()=>e))})),this._nucleotideSequences$.next(n);const o=this._modificationsWithNumericLabels$.getValue();o.includes(e)||this.updateModificationsWithNumericLabels(o.concat(e))}get patternStateChanged$(){return te.merge(this._patternName$.pipe((0,ne.debounceTime)(300),(0,ne.map)((()=>{}))),this._isAntisenseStrandActive$,this._nucleotideSequences$,this._phosphorothioateLinkageFlags,this._terminalModifications,this._comment$.pipe((0,ne.debounceTime)(300)),this._modificationsWithNumericLabels$)}getSequenceBase(){return this._sequenceBase$.getValue()}uniqueNucleotidesChanged$(){return this.patternStateChanged$.pipe((0,ne.switchMap)((()=>this._uniqueNucleotides$)))}getUniqueNucleotides(){return this._uniqueNucleotides$.getValue()}get svgSaveRequested$(){return this._svgSaveRequested$.asObservable()}requestSvgSave(){this._svgSaveRequested$.next()}setAllPTOLinkages(e){const t=this.getPhosphorothioateLinkageFlags();k.forEach((n=>{t[n]=t[n].map((()=>e))})),this.updatePhosphorothioateLinkageFlags(t)}setPatternConfig(e){this._patternName$.next(e[j.PATTERN_NAME]),this._isAntisenseStrandActive$.next(e[V.IS_ANTISENSE_STRAND_INCLUDED]),this._nucleotideSequences$.next(e[V.NUCLEOTIDE_SEQUENCES]),this._phosphorothioateLinkageFlags.next(e[V.PHOSPHOROTHIOATE_LINKAGE_FLAGS]),this._terminalModifications.next(e[V.STRAND_TERMINUS_MODIFICATIONS]),this._comment$.next(e[j.PATTERN_COMMENT]),this._modificationsWithNumericLabels$.next(e[j.NUCLEOTIDES_WITH_NUMERIC_LABELS])}setLastLoadedPatternConfig(e){this._lastLoadedPatternConfig.next(le().cloneDeep(e))}getPatternConfig(){return{[j.PATTERN_NAME]:this.getPatternName(),[V.IS_ANTISENSE_STRAND_INCLUDED]:this.isAntisenseStrandActive(),[V.NUCLEOTIDE_SEQUENCES]:this.getNucleotideSequences(),[V.PHOSPHOROTHIOATE_LINKAGE_FLAGS]:this.getPhosphorothioateLinkageFlags(),[V.STRAND_TERMINUS_MODIFICATIONS]:this.getTerminalModifications(),[j.PATTERN_COMMENT]:this.getComment(),[j.NUCLEOTIDES_WITH_NUMERIC_LABELS]:this.getModificationsWithNumericLabels()}}setPhosphorothioateLinkageFlag(e,t,n){const o=this.getPhosphorothioateLinkageFlags();o[e][t]=n,this.updatePhosphorothioateLinkageFlags(o)}setNucleotide(e,t,n){const o=this.getNucleotideSequences();o[e][t]=n;const r=this.getModificationsWithNumericLabels();this.updateModificationsWithNumericLabels(r.concat(n)),this.updateNucleotideSequences(o)}get strandsUpdated$(){return te.merge(this._isAntisenseStrandActive$.asObservable().pipe((0,ne.map)((()=>{}))),this._nucleotideSequences$.asObservable().pipe((0,ne.map)((()=>{}))),this._patternLoaded$.asObservable().pipe((0,ne.map)((()=>{})))).pipe((0,ne.debounceTime)(10))}get strandsLinkagesAndTerminalsUpdated$(){return te.merge(this.strandsUpdated$,this._phosphorothioateLinkageFlags.asObservable().pipe((0,ne.map)((()=>{}))),this._terminalModifications.asObservable().pipe((0,ne.map)((()=>{}))))}updateControlsUponPatternLoaded(e){this._patternLoaded$.next(e)}get patternLoaded$(){return this._patternLoaded$.asObservable()}get userSelection$(){return this._patternAuthorSelection$.asObservable().pipe((0,ne.skip)(1))}selectAuthor(e){if("string"!=typeof e)throw new Error("Selected user must be defined");this._patternAuthorSelection$.next(e)}getSelectedAuthor(){return this._patternAuthorSelection$.getValue()}get loadPatternInNewTabRequested$(){return this._loadPatternInNewTabRequested$.asObservable()}requestLoadPatternInNewTab(e){this._loadPatternInNewTabRequested$.next(e)}updateUrlState(e){this._urlStateUpdated$.next(e)}get urlStateUpdated$(){return this._urlStateUpdated$.asObservable()}get patternHasUnsavedChanges$(){return this._patternHasUnsavedChanges$.asObservable()}selectStrandColumn(e,t){this._selectedStrandColumn.next({...this._selectedStrandColumn.getValue(),[e]:t})}getSelectedStrandColumn(e){const t=this._selectedStrandColumn.getValue();return t?t[e]:null}selectIdColumn(e){this._selectedIdColumn.next(e)}getSelectedIdColumn(){return this._selectedIdColumn.getValue()}get updateSvgContainer$(){return this.patternStateChanged$.pipe((0,ne.debounceTime)(100))}}const ue="pattern";class he{constructor(){this.urlSearchParams=new URLSearchParams(window.location.search)}subscribeToObservables(e){e.urlStateUpdated$.subscribe((e=>this.setPatternURL(e))),e.loadPatternInNewTabRequested$.subscribe((e=>{const t=`${window.location.origin}${window.location.pathname}?${ue}=${e}`;window.open(t,"_blank")})),window.addEventListener("popstate",(()=>{this.urlSearchParams=new URLSearchParams(window.location.search);const t=this.getPatternHash();null!==t&&e.requestPatternLoad(t)}))}getPatternHash(){return this.urlSearchParams.get(ue)}setPatternURL(e){null!==e&&""!==e?(this.urlSearchParams.set(ue,e),window.history.pushState({},"",`${window.location.pathname}?${this.urlSearchParams}`)):this.clearPatternURL()}clearPatternURL(){this.urlSearchParams.delete(ue),window.history.pushState({},"",`${window.location.pathname}`)}}var de=n(5072),pe=n.n(de),me=n(7825),fe=n.n(me),ge=n(7659),ye=n.n(ge),be=n(5056),ve=n.n(be),Ce=n(540),xe=n.n(Ce),we=n(1113),Ae=n.n(we),Te=n(9252),Ee={};Ee.styleTagTransform=Ae(),Ee.setAttributes=ve(),Ee.insert=ye().bind(null,"head"),Ee.domAPI=fe(),Ee.insertStyleElement=xe(),pe()(Te.A,Ee),Te.A&&Te.A.locals&&Te.A.locals;class Se{constructor(e){this.eventBus=e,this.columnControlsContainer=r.div([]),this.eventBus.tableSelectionChanged$.subscribe((()=>this.handleTableChoice())),this.refreshColumnControls()}getColumnControlsContainer(){return this.columnControlsContainer}get selectedTable(){return this.eventBus.getTableSelection()}handleTableChoice(){this.refreshColumnControls()}refreshColumnControls(){L()(this.columnControlsContainer).empty(),L()(this.columnControlsContainer).append(this.constructColumnControls())}constructColumnControls(){const e=this.createStrandColumnInput(),t=e.SS,n=e.AS;this.eventBus.antisenseStrandToggled$.subscribe((e=>{L()(n).toggle(e)}));const o=this.createIdColumnInput();return[t,n,o]}createStrandColumnInput(){const e=this.selectedTable?this.selectedTable.columns.names().sort(((e,t)=>e.localeCompare(t))):[];return Object.fromEntries(k.map((t=>{const n=r.input.choice(`${H[t]} column`,{value:e[0],items:e,onValueChanged:e=>this.eventBus.selectStrandColumn(t,e)});return this.eventBus.selectStrandColumn(t,e[0]),[t,n.root]})))}createIdColumnInput(){const e=this.selectedTable?this.selectedTable.columns.names():[],t=r.input.choice("ID column",{value:e[0],items:e,onValueChanged:e=>this.eventBus.selectIdColumn(e)});return this.eventBus.selectIdColumn(e[0]),t.root}}class Ne{constructor(e){this.eventBus=e,this.availableTables=[],this.tableInputContainer=r.div([]),this.subscribeToTableEvents(),this.refreshTableInput()}getTableInputContainer(){return this.tableInputContainer}subscribeToTableEvents(){o.events.onTableAdded.subscribe((e=>this.handleTableAdded(e))),o.events.onTableRemoved.subscribe((e=>this.handleTableRemoved(e))),this.eventBus.tableSelectionChanged$.subscribe((()=>this.handleTableChoice()))}getTableFromEventData(e){if(!e&&e.args&&e.args.dataFrame instanceof i.DataFrame)throw new Error("EventData does not contain a dataframe",e);return e.args.dataFrame}handleTableAdded(e){const t=this.getTableFromEventData(e);this.availableTables.some((e=>e.name===t.name))||(this.availableTables.push(t),this.eventBus.selectTable(t),this.refreshTableInput())}handleTableRemoved(e){const t=this.getTableFromEventData(e);this.availableTables=this.availableTables.filter((e=>e.name!==t.name));const n=this.availableTables[0];this.eventBus.selectTable(n||null),this.refreshTableInput()}refreshTableInput(){const e=this.createTableInput();L()(this.tableInputContainer).empty(),this.tableInputContainer.append(e.root)}createTableInput(){const e=this.eventBus.getTableSelection();return r.input.table("Tables",{value:e,items:this.availableTables,onValueChanged:e=>{null!==e&&this.eventBus.selectTable(e)}})}handleTableChoice(){const e=this.eventBus.getTableSelection();e&&(this.isTableDisplayed(e)||this.displayTable(e))}isTableDisplayed(e){return o.shell.tableNames.includes(e.name)}displayTable(e){const t=o.shell.v;o.shell.addTableView(e),o.shell.v=t}}function Ie(e,t,n,o){const r=function(e,t,n){const o=new Array(e.length+t.filter((e=>e)).length+G.length);o[0]=n["5'"],o[o.length-1]=n["3'"];let r=1;return t[0]&&(o[r]="ps",r++),e.forEach(((e,n)=>{o[n+r]=e,t[n+1]&&(o[n+r+1]="ps",r++)})),o}(e.split("").map(((e,n)=>{const o=function(e,t,n){const o=Object.keys(n.patternAppData)[0],r=n.patternAppData[o][t].substitution;return e.replace(/([AGCTU])/,r)}(e,t[n],br.jsonData);return o})),n,o);return r.join("")}class Me{constructor(e){this.eventBus=e,this.tableInputManager=new Ne(e),this.columnInputManager=new Se(e)}createControls(){const e=r.h1("Bulk convert"),t=this.tableInputManager.getTableInputContainer(),n=this.columnInputManager.getColumnControlsContainer(),o=r.bigButton("Convert",(()=>this.processConvertButtonClick()));return[e,t,n,r.buttonsInput([o])]}processConvertButtonClick(){!function(e){const t=e.getTableSelection();if(!t)return void o.shell.warning("Please select a table");const n=k.filter((t=>!("AS"===t&&!e.isAntisenseStrandActive()))).map((t=>({strand:t,column:e.getSelectedStrandColumn(t)}))).filter((e=>e.column));if(0===n.length)return void o.shell.warning("Select a sense strand column");const r=e.getSelectedIdColumn();if(!r)throw new Error("No ID column selected");t.getCol(r);const i=n.map((e=>({strand:e.strand,column:t.getCol(e.column)})));!function(e,t){const n=t.getNucleotideSequences();return e.every((e=>{const t=n[e.strand].length;return e.column.toList().every((e=>e.length===t))}))}(i,e)?o.shell.warning("Some strands in the table input do not match pattern length"):i.forEach((n=>{const o=n.column,r=n.strand,i=e.getNucleotideSequences()[r],s=e.getTerminalModifications()[r],a=e.getPhosphorothioateLinkageFlags()[r],l=`${e.getPatternName()}(${o.name})`;t.columns.addNewString(l).init((e=>Ie(o.get(e),i,a,s)))}))}(this.eventBus)}}class Pe{constructor(e,t,n){this.eventBus=e,this.initialPatternConfig=t,this.subscriptions=n}create(){return r.divV([r.h1("PTO"),r.divH([this.createAllPtoActivationInput().root,...this.createFirstPtoInputs().map((e=>e.root))],{style:{gap:"12px"}})])}areAllPtoLinkagesSet(e){return k.map((t=>e[t].filter((e=>e)).length)).reduce(((e,t)=>e+t),0)===k.map((e=>this.initialPatternConfig.nucleotideSequences[e].length)).reduce(((e,t)=>e+t),0)+k.filter((t=>e[t].length)).length}createAllPtoActivationInput(){const e=this.initialPatternConfig.phosphorothioateLinkageFlags,t=this.areAllPtoLinkagesSet(e),n=r.input.bool("All PTO",{value:t});n.onInput.subscribe((()=>{const e=n.value;this.eventBus.setAllPTOLinkages(e)}));const o=this.eventBus.phosphorothioateLingeFlagsChanged$.subscribe((()=>{const e=this.eventBus.getPatternConfig().phosphorothioateLinkageFlags,t=this.areAllPtoLinkagesSet(e);n.value=t}));return this.subscriptions.add(o),this.addStyleToPtoInput(n),r.tooltip.bind(n.captionLabel,"Activate all phosphothioates"),n}addStyleToPtoInput(e){const t=e.captionLabel;t.classList.add("ui-label-right"),Object.assign(t.style,{textAlign:"left",maxWidth:"100px",minWidth:"40px",width:"auto"})}createFirstPtoInputs(){return k.map((e=>{if(!this.eventBus.isAntisenseStrandActive()&&"AS"===e)return;const t=this.isFirstPtoActive(e),n=r.input.bool(`First ${e} PTO`,{value:t});n.onInput.subscribe((()=>{const t=n.value;this.eventBus.setPhosphorothioateLinkageFlag(e,0,t)}));const o=this.eventBus.phosphorothioateLingeFlagsChanged$.subscribe((t=>{const o=t[e][0];n.value=o}));return this.subscriptions.add(o),this.addStyleToPtoInput(n),r.tooltip.bind(n.captionLabel,`Activate first phosphothioate in ${e}`),n})).filter((e=>void 0!==e))}isFirstPtoActive(e){return this.initialPatternConfig.phosphorothioateLinkageFlags[e][0]}}class _e{constructor(e,t,n){this.eventBus=e,this.dataManager=t,this.subscriptions=n;const o=this.eventBus.nucleotideSequencesChanged$.subscribe((()=>{this.displayedInputLabels=this.computeDisplayedInputLabels()}));this.subscriptions.add(o)}create(){const e=k.map((e=>this.constructControlsPanel(e)));return r.divH(e,{style:{gap:"24px"}})}constructControlsPanel(e){if(!this.eventBus.isAntisenseStrandActive()&&"AS"===e)return r.div([]);const t=this.constructHeader(),n=this.createControls(e);return r.block([r.h1(`${H[e]}`),t,n],{style:{paddingTop:"12px"}})}constructHeader(){return r.divH([r.div([r.divText("#")],{style:{width:"20px"}}),r.block75([r.divText("Modification")]),r.div([r.divText("PTO")])])}createControls(e){const t=this.createNucleobaseInputs(e),n=this.createLabelDivs(e),o=this.createPTOFlagInputs(e);return r.div(t.map(((e,t)=>r.divH([n[t],r.block75([e.root]),o[t].root],{style:{alignItems:"center"}}))))}createNucleobaseInputs(e){const t=this.dataManager.fetchAvailableNucleotideBases().sort(((e,t)=>e.toLowerCase().localeCompare(t.toLowerCase())));return this.eventBus.getNucleotideSequences()[e].map(((n,o)=>{const i=r.input.choice("",{value:n,items:t});return i.onInput.subscribe((()=>{const t=i.value;this.eventBus.setNucleotide(e,o,t)})),i}))}createPTOFlagInputs(e){return this.eventBus.getPhosphorothioateLinkageFlags()[e].slice(1).map(((t,n)=>{const o=r.input.bool("",{value:t});o.onInput.subscribe((()=>{const t=o.value;this.eventBus.setPhosphorothioateLinkageFlag(e,n+1,t)}));const i=this.eventBus.phosphorothioateLingeFlagsChanged$.subscribe((t=>{const r=t[e][n+1];o.value=r}));return this.subscriptions.add(i),o}))}computeDisplayedInputLabels(){const e=this.eventBus.getNucleotideSequences(),t=new Map;return k.forEach((n=>{let o=1;const r=e[n].map((e=>{if(oe(e))return"";const t=String(o);return o++,t}));t.set(n,r)})),t}createLabelDivs(e){const t=this.createLabels(e).map((e=>r.div([e],{style:{width:"20px"}}))),n=this.eventBus.nucleotideSequencesChanged$.subscribe((()=>{this.createLabels(e).forEach(((e,n)=>{L()(t[n]).empty(),L()(t[n]).append(e)}))}));return this.subscriptions.add(n),t}createLabels(e){return this.eventBus.getNucleotideSequences()[e].map(((t,n)=>{const o=this.displayedInputLabels.get(e)[n];return r.label(o)}))}}class Le{constructor(){this.rxjsSubscriptions=[],this.dgSubscriptions=[]}add(e){e instanceof te.Subscription?this.rxjsSubscriptions.push(e):this.dgSubscriptions.push(e)}unsubscribeAll(){for(const e of[this.rxjsSubscriptions,this.dgSubscriptions])e.forEach((e=>e.unsubscribe())),e.length=0}}class Oe{constructor(e,t){this.eventBus=e,this.dataManager=t,this.subscriptions=new Le}static open(e,t){Oe.isDialogOpen||(Oe.instance||(Oe.instance=new Oe(e,t)),Oe.instance.openDialog())}openDialog(){this.initialPatternConfig=le().cloneDeep(this.eventBus.getPatternConfig()),Oe.isDialogOpen=!0,this.createDialog().show()}createDialog(){const e=r.divV([]);this.subscriptions.add(this.eventBus.strandsUpdated$.subscribe((()=>this.onStrandsUpdated(e))));const t=r.dialog("Edit strands").add(e).onOK((()=>{})).onCancel((()=>this.resetToInitialState()));return this.subscriptions.add(t.onClose.subscribe((()=>{Oe.isDialogOpen=!1,this.subscriptions.unsubscribeAll()}))),t}onStrandsUpdated(e){const t=new Pe(this.eventBus,this.initialPatternConfig,this.subscriptions).create(),n=new _e(this.eventBus,this.dataManager,this.subscriptions).create();L()(e).empty(),L()(e).append(t,n)}resetToInitialState(){this.eventBus.setPatternConfig(this.initialPatternConfig)}}Oe.isDialogOpen=!1;class Re{constructor(e){this.eventBus=e,this.subscriptions=new Le}static open(e){Re.isDialogOpen||(Re.instance||(Re.instance=new Re(e)),Re.instance.openDialog())}openDialog(){this.initialPatternConfig=le().cloneDeep(this.eventBus.getPatternConfig()),Re.isDialogOpen=!0,this.createDialog().show()}createDialog(){const e=r.divV([]);this.subscriptions.add(this.eventBus.strandsUpdated$.subscribe((()=>this.onStrandsUpdated(e))));const t=r.dialog("Edit terminal modifications").add(e).onOK((()=>{})).onCancel((()=>this.resetToInitialState()));return this.subscriptions.add(t.onClose.subscribe((()=>{Re.isDialogOpen=!1,this.subscriptions.unsubscribeAll()}))),t}onStrandsUpdated(e){const t=new $e(this.eventBus).create();L()(e).empty(),L()(e).append(t)}resetToInitialState(){this.eventBus.setPatternConfig(this.initialPatternConfig)}}Re.isDialogOpen=!1;class $e{constructor(e){this.eventBus=e}create(){const e=k.map((e=>this.constructControlsPanel(e)));return r.divH(e,{style:{gap:"24px"}})}constructControlsPanel(e){if(!this.eventBus.isAntisenseStrandActive()&&"AS"===e)return r.div([]);const t=this.createInputs(e);return r.block([r.h1(`${H[e]}`),t],{style:{paddingTop:"12px"}})}createInputs(e){const t=("SS"===e?[...G].reverse():G).map((t=>this.createInputForTerminus(e,t)));return r.form(t)}createInputForTerminus(e,t){const n=this.eventBus.getTerminalModifications()[e][t],o=r.input.textArea(t,{value:n});return this.applyStylingToInput(o),o.onInput.subscribe((()=>{const n=o.value;null!==n&&this.eventBus.updateTerminusModification(e,t,n)})),o}applyStylingToInput(e){const t=e.root.getElementsByTagName("textarea")[0];L()(t).css("resize","none")}}class De{constructor(e,t){this.eventBus=e,this.dataManager=t}createControls(){const e=this.createAntisenseStrandToggle(),t=this.createStrandLengthInputs(),n=t.SS.root,o=t.AS.root,i=this.createSequenceBaseInput().root,s=this.createPatternCommentInput().root,a=this.createPatternNameInputBlock(),l=this.createEditPatternButton(),c=this.createEditTerminalModificationsButton();return[r.h1("Edit"),e,n,o,i,a,s,r.buttonsInput([c,l])]}createEditPatternButton(){const e=r.button("Edit strands",(()=>Oe.open(this.eventBus,this.dataManager)));return r.tooltip.bind(e,"Edit strand modifications and PTOs"),e}createEditTerminalModificationsButton(){const e=r.button("Edit terminals",(()=>Re.open(this.eventBus)));return r.tooltip.bind(e,"Edit terminal modifications"),L()(e).css("margin-right","20px"),e}createAntisenseStrandToggle(){const e=r.input.toggle(`${H.AS} strand`,{value:this.eventBus.isAntisenseStrandActive()});return e.onInput.subscribe((()=>this.eventBus.toggleAntisenseStrand(e.value))),this.eventBus.patternLoaded$.subscribe((()=>{e.value=this.eventBus.isAntisenseStrandActive()})),e.setTooltip("Toggle antisense strand"),e.root}createStrandLengthInputs(){const e=e=>{const n=this.eventBus.getNucleotideSequences()[e].length,o=r.input.int(`${H[e]} length`,{value:n});return o.onInput.subscribe((()=>t(e,o))),this.eventBus.nucleotideSequencesChanged$.subscribe((()=>{o.value=this.eventBus.getNucleotideSequences()[e].length})),o.setTooltip(`Number of nucleotides in ${e}, including overhangs`),[e,o]},t=(e,t)=>{const n=t.value;null!==n&&(n<=0&&(o.shell.warning("Sequence length must be greater than 0"),t.value=1),n>34&&(o.shell.warning("Sequence length must be less than 35"),t.value=34),this.eventBus.updateStrandLength(e,t.value))},n=Object.fromEntries(k.map((t=>e(t))));return this.eventBus.antisenseStrandToggled$.subscribe((e=>{L()(n.AS.root).toggle(e)})),n}createSequenceBaseInput(){const e=this.dataManager.fetchAvailableNucleotideBases().sort(((e,t)=>e.toLowerCase().localeCompare(t.toLowerCase()))),t=this.dataManager.fetchDefaultNucleobase(),n=r.input.choice("Sequence basis",{value:t,items:e});return n.onInput.subscribe((()=>this.eventBus.replaceSequenceBase(n.value))),this.eventBus.nucleotideSequencesChanged$.subscribe((()=>{n.value=this.eventBus.getSequenceBase()})),n.setTooltip("Most frequent nucleobase in the strands"),n}createPatternCommentInput(){const e=r.input.textArea("Comment",{value:this.eventBus.getComment()});return L()(e.root).addClass("st-pattern-text-input"),e.onInput.subscribe((()=>this.eventBus.updateComment(e.value))),this.eventBus.patternLoaded$.subscribe((()=>{e.value=this.eventBus.getComment()})),e}createPatternNameInputBlock(){const e=r.input.textArea("Pattern name",{value:this.eventBus.getPatternName()});return L()(e.root).addClass("st-pattern-text-input"),e.onInput.subscribe((()=>this.eventBus.updatePatternName(e.value))),this.eventBus.patternLoaded$.subscribe((()=>{e.value=this.eventBus.getPatternName()})),e.setTooltip("Name under which pattern will be saved"),e.root}}class Be{constructor(e,t){this.eventBus=e,this.dataManager=t,this.subscriptions=new Le,this.authorSelectedByUser=!1,this.eventBus.patternLoadRequested$.subscribe((e=>this.handlePatternChoice(e))),this.eventBus.patternDeletionRequested$.subscribe((async e=>{await this.dataManager.deletePattern(e,this.eventBus)}))}async handlePatternChoice(e){let t=await this.dataManager.getPatternConfig(e);null===t&&(t=this.dataManager.getDefaultPatternConfig()),this.eventBus.setPatternConfig(t),this.eventBus.updateControlsUponPatternLoaded(e),this.eventBus.setLastLoadedPatternConfig(t)}isCurrentUserSelected(){return this.eventBus.getSelectedAuthor()!==this.dataManager.getOtherUsersAuthorshipCategory()}createControls(){const e=this.getPatternInputsContainer();return[r.h1("Load"),e]}getPatternInputsContainer(){const e=r.divH(this.createPatternInputs());return this.eventBus.patternListUpdated$.subscribe((()=>{this.subscriptions.unsubscribeAll(),L()(e).empty(),L()(e).append(this.createPatternInputs())})),e}createPatternInputs(){const e=this.createAuthorChoiceInput(),t=this.createPatternChoiceInputContainer(),n=this.createDeletePatternButton();return[e.root,t,n]}createPatternChoiceInputContainer(){const e=this.createPatternChoiceInput(),t=r.div([e.root]),n=this.eventBus.userSelection$.subscribe((()=>{L()(t).empty(),L()(t).append(this.createPatternChoiceInput().root)}));return this.subscriptions.add(n),t}createAuthorChoiceInput(){const e=[this.dataManager.getCurrentUserAuthorshipCategory()];this.dataManager.getOtherUsersPatternNames().length>0&&e.push(this.dataManager.getOtherUsersAuthorshipCategory());const t=r.input.choice("Author",{value:this.eventBus.getSelectedAuthor(),items:e});return t.onInput.subscribe((()=>{if(this.authorSelectedByUser=!0,null===t.value)throw new Error("author choice must be non-null");this.eventBus.selectAuthor(t.value)})),this.setAuthorChoiceInputStyle(t),t.setTooltip("Select pattern author"),t}setAuthorChoiceInputStyle(e){L()(e.input).css({"max-width":"100px","min-width":"100px"}),L()(e.root).css({"padding-right":"30px","padding-left":"30px"})}createPatternChoiceInput(){const e=this.isCurrentUserSelected()?this.dataManager.getCurrentUserPatternNames():this.dataManager.getOtherUsersPatternNames();if(this.authorSelectedByUser){const t=this.dataManager.getPatternHash(e[0],this.isCurrentUserSelected());this.eventBus.requestPatternLoad(t),this.eventBus.updateUrlState(t),this.authorSelectedByUser=!1}const t=this.getPatternName(e),n=r.input.choice("Pattern",{value:t,items:e});return n.setTooltip("Select pattern to load"),L()(n.input).css({"max-width":"100px","min-width":"100px"}),this.subscriptions.add(n.onInput.subscribe((()=>{const e=this.dataManager.getPatternHash(n.value,this.isCurrentUserSelected());this.eventBus.requestPatternLoad(e),this.eventBus.updateUrlState(e)}))),this.subscriptions.add(this.eventBus.patternLoaded$.subscribe((()=>{const t=this.eventBus.getPatternName();n.value!==t&&(n.value=this.getPatternName(e))}))),n}getPatternName(e){return e.find((e=>e.split(" (")[0]===this.eventBus.getPatternName()))??e[0]}createDeletePatternButton(){const e=r.button(r.iconFA("trash-alt"),(()=>{this.eventBus.getPatternName()!==this.dataManager.getDefaultPatternName()?this.showDeletePatternDialog():o.shell.warning("Cannot delete example pattern")}));r.tooltip.bind(e,"Delete pattern from user storage");const t=this.eventBus.userSelection$.subscribe((()=>{e.disabled=!this.isCurrentUserSelected()}));return this.subscriptions.add(t),e}showDeletePatternDialog(){const e=r.dialog("Delete pattern"),t=this.eventBus.getPatternName();e.add(r.divText(`Are you sure you want to delete pattern ${t}?`)),e.onOK((()=>this.eventBus.requestPatternDeletion(t))),e.show()}}class Fe{constructor(e,t){this.eventBus=e,this.dataManager=t}getLayout(){const e=new Be(this.eventBus,this.dataManager),t=new De(this.eventBus,this.dataManager),n=new Me(this.eventBus),o=e.createControls(),i=t.createControls(),s=n.createControls(),a=r.div(o);L()(a).css({"padding-bottom":"20px"});const l=r.div([...i,...s],"ui-form"),c=r.div([a,l]);return L()(c).css({padding:"25px"}),r.box(c,{style:{maxWidth:"450px"}})}}var ke=n(9146);class He{constructor(e,t,n){this.svgElementFactory=e,this.config=t,this.yShift=n}shiftElements(e){this.svgElements.forEach((t=>{const n=t.getAttribute("transform")||"",o=`translate(${e.x},${e.y})`;t.setAttribute("transform",`${n} ${o}`)}))}}class Ge{constructor(){}static getInstance(){return Ge.instance||(Ge.instance=new Ge,Ge.instance.canvas=document.createElement("canvas")),Ge.instance}static getTextDimensions(e,t){const n=Ge.getInstance().canvas.getContext("2d");if(!n)throw new Error("Canvas 2D context is not available");return n.font=`${t}px Arial`,{width:1.1*n.measureText(e).width,height:1.1*t}}}function Ue(e){const t=Object.keys(br.jsonData.patternAppData)[0];if(!t)throw new Error(`No format found in '${d}'`);return br.jsonData.patternAppData[t][e].color||""}class Ve extends He{constructor(e,t,n){super(e,t,n);const o=k.filter((e=>t.nucleotideSequences[e].length>0));this.strands=o.map((e=>new je(this.svgElementFactory,t,n,e))),this.terminalModifications=o.map(((e,o)=>new We(this.svgElementFactory,t,n,e,this.strands[o]))),this.labels=o.map(((e,o)=>new qe(this.svgElementFactory,t,n,e,this.terminalModifications[o])))}get svgElements(){return[...this.strands,...this.terminalModifications,...this.labels].map((e=>e.svgElements)).flat()}getContentWidth(){return Math.max(...this.labels.map((e=>e.getContentWidth())))}getContentHeight(){return this.strands.reduce(((e,t)=>e+t.getContentHeight()),0)}}class je extends He{constructor(e,t,n,o){super(e,t,n),this.svgElementFactory=e,this.config=t,this.yShift=n,this.strand=o,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 e=0;return this.config.nucleotideSequences[this.strand].map((t=>oe(t)?null:(e++,e)))}get svgElements(){return this._svgElements}getStrandCircleYShift(){return ze(this.strand,this.yShift)}createStrandCircles(){const e={x:80,y:this.getStrandCircleYShift()};return this.config.nucleotideSequences[this.strand].map(((t,n)=>this.createNucleotideElementGroup(t,n,e))).flat()}createNucleotideElementGroup(e,t,n){return[...this.createNucleotideCircleElements(e,t,n),this.config.nucleotidesWithNumericLabels.includes(e)?this.createNucleotideNumericLabel(t,n):null].filter((e=>null!==e))}createNucleotideCircleElements(e,t,n){const o=Ue(e),r={...n,x:n.x+30*t};return[this.svgElementFactory.createCircleElement(r,15,o),this.createNucleotideLetterLabel(t,n,e)]}getNucleotideCircleCenterPosition(e,t){return{x:t.x+30*e,y:t.y}}createNucleotideLetterLabel(e,t,n){if(!g.AL.includes(n))return null;const o=function(e){return!oe(e)&&g.AL.includes(e)?e:""}(n),r=function(e){const t=Ue(e),n=t.match(/\d+/g)?.map(Number);if(!n||n.length<3)return"#ffffff";const[o,r,i]=n;return.299*o+.587*r+.114*i>186?"#333333":"#ffffff"}(n),i=this.getPositionForNucleotideLabel(e,t);return this.svgElementFactory.createTextElement(o,i,17,r)}getPositionForNucleotideLabel(e,t){const n=this.getNucleotideCircleCenterPosition(e,t),o=Ge.getTextDimensions("A",17);return{x:n.x-o.width/2,y:n.y+o.height/3}}getNumericLabelYShift(e){return"SS"===this.strand?e.y-20:e.y+15+5+15}createNucleotideNumericLabel(e,t){const n=this.nucleotideNumericLabels[e];if(null===n)return null;const o=Ge.getTextDimensions(n.toString(),15).width,r={x:t.x+30*e-o/2,y:this.getNumericLabelYShift(t)};return this.svgElementFactory.createTextElement(n.toString(),r,15,"var(--grey-6)")}createPTOLinkageStars(){const e=this.config.phosphorothioateLinkageFlags[this.strand],t=this.getStrandCircleYShift()+12;return e.map(((e,n)=>{if(!e)return null;const o={x:65+30*n,y:t};return this.svgElementFactory.createStarElement(o,"red")})).filter((e=>null!==e))}getContentWidth(){return 30*this.config.nucleotideSequences[this.strand].length}getContentHeight(){return 62}}class qe extends He{constructor(e,t,n,o,r){super(e,t,n),this.svgElementFactory=e,this.config=t,this.yShift=n,this.strand=o,this.terminalModifications=r,this._svgElements=this.createSVGElements()}createSVGElements(){return[this.createLeftLabel(),this.createRightLabel()]}getLeftLabelWidth(){return 55}getRightLabelWidth(){return 20}createLeftLabel(){const e="SS"===this.strand?"5'":"3'",t=`${this.strand}: ${e} `,n=Ge.getTextDimensions(t,17),o={x:10,y:ze(this.strand,this.yShift)+n.height/3};return this.svgElementFactory.createTextElement(t,o,17,"var(--grey-6)")}createRightLabel(){const e=" "+("SS"===this.strand?"3'":"5'"),t=Ge.getTextDimensions(e,17),n={x:65+this.terminalModifications.getContentWidth()+5,y:ze(this.strand,this.yShift)+t.height/3};return this.svgElementFactory.createTextElement(e,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 We extends He{constructor(e,t,n,o,r){super(e,t,n),this.svgElementFactory=e,this.config=t,this.yShift=n,this.strand=o,this.strandSvgWrapper=r,this._svgElements=this.createSVGElements()}createSVGElements(){return this.createTerminalModifications()}getTerminalModification(e){return this.config.strandTerminusModifications[this.strand][e]}getTerminalModificationTextDimensions(e){const t=this.getTerminalModification(e);return Ge.getTextDimensions(t,17)}getLeftTerminus(){return"SS"===this.strand?"5'":"3'"}createTerminalModification(e){const t=this.getTerminalModification(e),n=this.getTerminalModificationTextDimensions(e),o=e===this.getLeftTerminus(),r={x:o?65:65+this.getTerminalModificationTextDimensions(this.getLeftTerminus()).width+this.strandSvgWrapper.getContentWidth(),y:ze(this.strand,this.yShift)+n.height/3};return o&&this.strandSvgWrapper.shiftElements({x:n.width,y:0}),this.svgElementFactory.createTextElement(t,r,17,"red")}createTerminalModifications(){return("AS"===this.strand?G:Array.from(G).reverse()).map((e=>this.createTerminalModification(e)))}get svgElements(){return this._svgElements}getContentWidth(){return this.strandSvgWrapper.getContentWidth()+G.map((e=>this.getTerminalModificationTextDimensions(e).width)).reduce(((e,t)=>e+t),0)}getContentHeight(){return this.strandSvgWrapper.getContentHeight()}}function ze(e,t){return"SS"===e?t+5+15+15:t+52+10+15}class Ye{constructor(){this.xmlNamespace="http://www.w3.org/2000/svg"}createElement(e){return document.createElementNS(this.xmlNamespace,e)}setAttributes(e,t){Object.entries(t).forEach((([t,n])=>{e.setAttribute(t,String(n))}))}createCanvas(e,t){const n=this.createElement("svg");return this.setAttributes(n,{id:"mySvg",width:e,height:t}),n}createCircleElement(e,t,n){const o=this.createElement("circle");return this.setAttributes(o,{cx:e.x,cy:e.y,r:t,fill:n}),o}createTextElement(e,t,n,o){const r=this.createElement("text");return this.setAttributes(r,{x:t.x,y:t.y,"font-size":n,"font-weight":"normal","font-family":"Arial",fill:o}),r.textContent=e,r}createStarElement(e,t){const n=this.createElement("polygon"),o=this.computeStarVertexCoordinates(e).map((e=>e.join(","))).join(" ");return this.setAttributes(n,{points:o,fill:t}),n}computeStarVertexCoordinates(e){const t=Math.PI/5,n=-t/2;return Array.from({length:10},((o,r)=>{const i=r%2==0?6:3,s=r*t+n;return[e.x+Math.cos(s)*i,e.y+Math.sin(s)*i]}))}createRectangleElement(e,t,n,o){const r=this.createElement("rect");return this.setAttributes(r,{x:e.x,y:e.y,width:t,height:n,fill:o}),r}}class Ke extends He{constructor(e,t,n){super(e,t,n),this.svgElementFactory=e,this.config=t,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 Ge.getTextDimensions(this.titleText,17).width}getContentHeight(){return Ge.getTextDimensions(this.titleText,17).height}getTitleText(){const e=`${this.config.nucleotideSequences.SS.length}`,t=this.config.isAntisenseStrandIncluded?`/${this.config.nucleotideSequences.AS.length}`:"";return`${this.config.patternName} for ${e}${t}-mer`}}class Qe extends He{constructor(e,t,n){super(e,t,n),this._svgElements=[];const{elements:o,width:r}=this.createLegendItems();this._svgElements=o,this.width=r}isPhosphorothioatePresent(){return Object.values(this.config.phosphorothioateLinkageFlags).flat().some((e=>e))}getModificationTypesList(){return[...new Set(Object.values(this.config.nucleotideSequences).flat().sort(((e,t)=>e.toLowerCase().localeCompare(t.toLowerCase()))))]}get svgElements(){return this._svgElements}createLegendItem(e,t){const n={x:t,y:this.yShift-6},o=e.includes("linkage")?this.svgElementFactory.createStarElement(n,"red"):this.svgElementFactory.createCircleElement(n,6,Ue(e));t+=12;const r={y:this.yShift,x:t};return{elements:[o,this.svgElementFactory.createTextElement(e,r,15,"var(--grey-6)")],width:12+Ge.getTextDimensions(e,15).width}}createLegendItems(){let e=10;const t=[],n=t=>e+=t+15;if(this.isPhosphorothioatePresent()){const{elements:o,width:r}=this.createLegendItem("PTO linkage",e);n(r),t.push(o)}return this.getModificationTypesList().forEach((o=>{const{elements:r,width:i}=this.createLegendItem(o,e);n(i),t.push(r)})),{elements:t.flat(),width:e}}getContentHeight(){return 20}getContentWidth(){return this.width}}class Je{constructor(e){this.svgElementFactory=new Ye;const t=le().cloneDeep(e);let n=10;this.title=new Ke(this.svgElementFactory,t,n),n+=this.title.getContentHeight(),this.strands=new Ve(this.svgElementFactory,t,n),n+=this.strands.getContentHeight()+10,this.legend=new Qe(this.svgElementFactory,t,n)}renderPattern(){const e=this.getGlobalWidth(),t=this.getGlobalHeight(),n=this.svgElementFactory.createCanvas(e,t),o=[this.title,this.strands,this.legend].map((e=>e.svgElements)).flat();return n.append(...o),n}getGlobalWidth(){const e=[this.title,this.strands,this.legend];return Math.max(...e.map((e=>e.getContentWidth())))}getGlobalHeight(){return[this.title,this.strands,this.legend].reduce(((e,t)=>e+t.getContentHeight()),10)}}class Xe{constructor(e){this.eventBus=e,this.svgDisplayDiv=r.div([]),e.updateSvgContainer$.subscribe((()=>this.updateSvgContainer())),e.svgSaveRequested$.subscribe((()=>this.saveSvgAsPng()))}static createSvgDiv(e){return new Xe(e).svgDisplayDiv}updateSvgContainer(){$(this.svgDisplayDiv).empty();const e=this.eventBus.getPatternConfig();this.svgElement=this.createSvg(e),this.svgDisplayDiv.append(this.svgElement)}createSvg(e){return new Je(e).renderPattern()}saveSvgAsPng(){const e=this.eventBus.getPatternName();ke.saveSvgAsPng(this.svgElement,e,{backgroundColor:"white"})}}class Ze{constructor(e){this.eventBus=e,this.togglesContainer=r.div([]),this.eventBus.uniqueNucleotidesChanged$().subscribe((()=>{this.updateContainer()}))}getContainer(){return this.togglesContainer}updateContainer(){L()(this.togglesContainer).empty(),L()(this.togglesContainer).append(this.createInputs())}createInputs(){const e=this.eventBus.getUniqueNucleotides().filter((e=>!oe(e))).map((e=>this.createSingleInput(e)));return e.sort(((e,t)=>e.captionLabel.textContent.localeCompare(t.captionLabel.textContent))),r.divH(e.map((e=>e.root)))}createSingleInput(e){const t=this.eventBus.getModificationsWithNumericLabels().includes(e),n=r.input.bool(e,{value:t,onValueChanged:t=>this.handleNumericLabelToggle(e,t)});return L()(n.root).css("padding-right","20px"),n.setTooltip(`Show numeric labels for ${e}`),n}handleNumericLabelToggle(e,t){const n=this.eventBus.getModificationsWithNumericLabels();if(n.includes(e)===t)return;const o=t?n.concat(e):n.filter((t=>t!==e));this.eventBus.updateModificationsWithNumericLabels(o)}}class et{constructor(e,t){this.eventBus=e,this.dataManager=t,this.subscriptions=new Le}createContainer(){return r.div([r.h1("Translation example"),this.createTranslationExamples()],{style:{paddingTop:"20px"}})}createTranslationExamples(){const e=r.divH([...this.getExampleElements()],"ui-form");return this.eventBus.antisenseStrandToggled$.subscribe((()=>{this.subscriptions.unsubscribeAll(),L()(e).empty(),L()(e).append(this.getExampleElements())})),e}getExampleElements(){return k.map((e=>new tt(e,this.eventBus,this.subscriptions).create()))}}class tt{constructor(e,t,n){this.strand=e,this.eventBus=t,this.subscriptions=n}create(){return this.eventBus.isAntisenseStrandActive()||"AS"!==this.strand?(this.inputExample=this.createInputExample(),this.outputExample=this.createOutputExample(this.inputExample.value),this.subscribeToEvents(),r.block50([r.h2(H[this.strand]),this.inputExample.root,this.outputExample.root],{style:{paddingRight:"20px"}})):r.div([])}subscribeToEvents(){const e=this.eventBus.strandsLinkagesAndTerminalsUpdated$.subscribe((()=>{const e=this.generateExampleSequence();this.inputExample.value=e,this.outputExample.value=this.computeOutputValue(e)}));"AS"===this.strand&&this.subscriptions.add(e)}createInputExample(){const e=this.createTextInputForExamples(),t=this.generateExampleSequence();return e.value=t,e.setTooltip(`Example raw nucleotides input for ${H[this.strand]}`),e}generateExampleSequence(){return this.eventBus.getNucleotideSequences()[this.strand].map(((e,t)=>g.AL[t%g.AL.length])).join("")}createOutputExample(e){const t=this.createTextInputForExamples();return t.value=this.computeOutputValue(e),t.setTooltip(`Pattern applied to the example input for ${H[this.strand]}`),t}computeOutputValue(e){const t=this.eventBus.getNucleotideSequences()[this.strand],n=this.eventBus.getTerminalModifications()[this.strand];return Ie(e,t,this.eventBus.getPhosphorothioateLinkageFlags()[this.strand],n)}createTextInputForExamples(){const e=r.input.textArea("",{value:""});return this.applyStylingToInput(e),e}applyStylingToInput(e){const t=e.root.getElementsByTagName("textarea")[0];t.setAttribute("readonly","true"),L()(t).css("resize","none"),L()(e.root).css("opacity","75%")}}class nt{constructor(e,t){this.eventBus=e,this.dataManager=t,this.svgDisplay=Xe.createSvgDiv(e)}getLayout(){const e=new Ze(this.eventBus).getContainer(),t=this.generateDownloadControls(),n=new et(this.eventBus,this.dataManager).createContainer();return r.panel([this.svgDisplay,e,t,n],{style:{overflowX:"scroll",padding:"12px 24px"}})}generateDownloadControls(){return r.divH([this.createSavePatternButton(),this.createDownloadPngButton(),this.createShareLinkButton(),this.createInfoButton()],{style:{gap:"12px",marginTop:"12px"}})}createDownloadPngButton(){const e=r.button("Get PNG",(()=>this.eventBus.requestSvgSave()));return r.tooltip.bind(e,"Download pattern as PNG"),e}createInfoButton(){const e=r.button(r.iconFA("info-circle"),(()=>this.openInfoDialog()));return this.eventBus.patternHasUnsavedChanges$.subscribe((t=>{e.disabled=t})),r.tooltip.bind(e,"View pattern metadata"),e}async openInfoDialog(){let e=this.dataManager.getCurrentUserName(),t=this.dataManager.getDefaultPatternName(),n=K,i=K;const s=new URLSearchParams(window.location.search).get("pattern");if(null!==s){const r=await this.dataManager.getPatternRecordByHash(s);if(null!==r){const s=r[q.AUTHOR_ID];if(e=(await o.dapi.users.find(s)).friendlyName,t=r[q.PATTERN_CONFIG][j.PATTERN_NAME],void 0!==r[q.DATE]){const e=r[q.DATE][W.CREATE];void 0!==e&&(n=e);const t=r[q.DATE][W.MODIFY];void 0!==t&&(i=t)}}}const a=r.divV([r.divText(`Pattern Name: ${t}`),r.divText(`Author: ${e}`),r.divText(`Created: ${rt(new Date(n))}`),r.divText(`Modified: ${rt(new Date(i))}`)]);o.shell.info(a)}createShareLinkButton(){const e=r.button(r.iconFA("link"),(()=>navigator.clipboard.writeText(window.location.href).then((()=>o.shell.info("Link to pattern copied to clipboard")))));return this.eventBus.patternHasUnsavedChanges$.subscribe((t=>{e.disabled=t})),r.tooltip.bind(e,"Share pattern link"),e}createSavePatternButton(){const e=r.button("Save",(()=>this.processSaveButtonClick()));return this.eventBus.patternHasUnsavedChanges$.subscribe((t=>{e.disabled=!t})),r.tooltip.bind(e,"Save pattern to user storage"),e}processSaveButtonClick(){const e=this.eventBus.getPatternName();e!==this.dataManager.getDefaultPatternName()?""!==e?this.dataManager.savePatternToUserStorage(this.eventBus).then((()=>{o.shell.info(`Pattern ${e} saved`)})).catch((e=>this.handleErrorWhileSavingPattern(e))):o.shell.warning("Insert pattern name"):o.shell.warning("Cannot save default pattern")}handleErrorWhileSavingPattern(e){e instanceof Q?new ot(this.eventBus,this.dataManager).show():e instanceof J?o.shell.warning(r.div([r.divText("Pattern already exists"),r.button("Load",(()=>{const t=e.message;this.eventBus.requestLoadPatternInNewTab(t)}))])):console.error("Error while saving pattern",e)}}class ot{constructor(e,t){this.eventBus=e,this.dataManager=t}show(){const e=this.eventBus.getPatternName(),t=r.dialog(`Pattern "${e}" already exists`);t.add(r.divText(`Pattern "${e}" already exists. Do you want to overwrite it?`)),t.show(),t.onOK((()=>this.processOverwriteNamesakePattern()))}processOverwriteNamesakePattern(){const e=this.eventBus.getPatternName();this.dataManager.overwriteExistingPatternInUserStorage(this.eventBus).then((()=>{o.shell.info(`Pattern ${e} overwritten`)})).catch((e=>{console.error("Error while overwriting pattern in user storage",e),o.shell.error("Error while overwriting pattern")}))}}function rt(e){return e.toLocaleString().split(":").slice(0,-1).join(":")}class it extends F{constructor(e){super("Oligo Pattern"),this.th=e}getContent(){return async function(){const e=await ee.getInstance(),t=new he,n=await async function(e,t){const n=t.getPatternHash();if(!n)return t.clearPatternURL(),e.getDefaultPatternRecord();let o=await e.getPatternRecordByHash(n);return o||(t.clearPatternURL(),o=e.getDefaultPatternRecord()),o}(e,t),o=new ce(e,n);t.subscribeToObservables(o);const i=new Fe(o,e).getLayout(),s=new nt(o,e).getLayout();return r.splitH([i,s],{},!0)}()}}var st=n(8507),at={};function lt(e){var t;return"string"==typeof e||e instanceof String?e:("object"==typeof e||e instanceof Object)&&"$thrownJsError"in e?lt(e.$thrownJsError):e instanceof Error?null!==(t=e.stack)&&void 0!==t?t:e.message:e.toString()}at.styleTagTransform=Ae(),at.setAttributes=ve(),at.insert=ye().bind(null,"head"),at.domAPI=fe(),at.insertStyleElement=xe(),pe()(st.A,at),st.A&&st.A.locals&&st.A.locals;var ct,ut=n(2074),ht={};ht.styleTagTransform=Ae(),ht.setAttributes=ve(),ht.insert=ye().bind(null,"head"),ht.domAPI=fe(),ht.insertStyleElement=xe(),pe()(ut.A,ht),ut.A&&ut.A.locals&&ut.A.locals;class dt{constructor(e,t,n=!0){this.textInputBase=e,this.painter=t,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=r.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 e=this.painter(this.textInputBase.value);this.highlights.innerHTML="",e.forEach((e=>this.highlights.appendChild(e)))}}!function(e){e.TYPE="V2000",e[e.NUM_OF_HEADER_LINES=3]="NUM_OF_HEADER_LINES",e[e.NUM_OF_COUNTS_DIGITS=3]="NUM_OF_COUNTS_DIGITS",e[e.ATOM_TYPE_COL=4]="ATOM_TYPE_COL",e[e.FIRST_BONDED_ATOM_COL=1]="FIRST_BONDED_ATOM_COL",e[e.BOND_TYPE_COL=3]="BOND_TYPE_COL",e[e.RGP_SHIFT=8]="RGP_SHIFT",e[e.MAX_ATOM_COUNT=999]="MAX_ATOM_COUNT",e.RGP_LINE_START="M RGP",e.ATOM_ALIAS_LINE_START="A ",e.END="M END"}(ct||(ct={}));class pt{constructor(e){this.init(e)}init(e){this.fileContent=e.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 e;return null!==(e=this.xyzAtomCoordinates)&&void 0!==e||(this.xyzAtomCoordinates=this.parseAtomCoordinates()),this.xyzAtomCoordinates.x}get y(){var e;return null!==(e=this.xyzAtomCoordinates)&&void 0!==e||(this.xyzAtomCoordinates=this.parseAtomCoordinates()),this.xyzAtomCoordinates.y}get z(){var e;return null!==(e=this.xyzAtomCoordinates)&&void 0!==e||(this.xyzAtomCoordinates=this.parseAtomCoordinates()),this.xyzAtomCoordinates.z}get atomTypes(){var e;return null!==(e=this._atomTypes)&&void 0!==e||(this._atomTypes=this.parseAtomTypes()),this._atomTypes}get pairsOfBondedAtoms(){var e;return null!==(e=this._pairsOfBondedAtoms)&&void 0!==e||(this._pairsOfBondedAtoms=this.parseBondedAtomPairs()),this._pairsOfBondedAtoms}get bondTypes(){var e;return null!==(e=this._bondTypes)&&void 0!==e||(this._bondTypes=this.parseBondTypes()),this._bondTypes}setAtomAndBondCounts(){const{atomCount:e,bondCount:t}=this.parseAtomAndBondCounts();this._atomCount=e,this._bondCount=t}getNextColumnIdx(e){for(;!this.isWhitespace(e);)++e;for(;this.isWhitespace(e);)++e;return e}shiftIdxToSpecifiedColumn(e,t){let n=e;const o=this.isWhitespace(n)?t:t-1;for(let e=0;e<o;e++)n=this.getNextColumnIdx(n);return n}parseAtomTypes(){const e=this.atomCount,t=new Array(e);let n=this.getAtomBlockIdx();for(let o=0;o<e;o++)n=this.shiftIdxToAtomType(n),t[o]=this.parseAtomType(n),n=this.getNextLineIdx(n);return t}parseAtomCoordinates(){const e=new Float32Array(this.atomCount),t=new Float32Array(this.atomCount),n=new Float32Array(this.atomCount);let o=this.getAtomBlockIdx();for(let r=0;r<this.atomCount;r++){o=this.shiftIdxToXColumn(o);for(const i of[e,t,n])i[r]=this.parseFloatValue(o),o=this.getNextColumnIdx(o);o=this.getNextLineIdx(o)}return{x:e,y:t,z:n}}parseBondedAtomPairs(){const e=new Array(this.bondCount);let t=this.getBondBlockIdx();for(let n=0;n<this.bondCount;n++){t=this.shiftIdxToBondedAtomsPair(t);const o=new Uint16Array(2);o[0]=this.parseIntValue(t),t=this.getNextColumnIdx(t),o[1]=this.parseIntValue(t),e[n]=o,t=this.getNextLineIdx(t)}return e}parseBondTypes(){const e=this.bondCount,t=new Uint16Array(e);let n=this.getBondBlockIdx();for(let o=0;o<e;o++)n=this.shiftIdxToBondType(n),t[o]=this.parseIntValue(n),n=this.getNextLineIdx(n);return t}isWhitespace(e){const t=this.fileContent[e];return" "===t||"\t"===t}getNextLineIdx(e){return"\n"!==this.fileContent[e]?this.fileContent.indexOf("\n",e)+1:e+1}parseFloatValue(e){return this.parseNumericValue(parseFloat,e)}parseIntValue(e){return this.parseNumericValue(parseInt,e)}parseNumericValue(e,t){let n=t+1;for(;!this.isWhitespace(n);)++n;return e(this.fileContent.substring(t,n))}}class mt extends pt{constructor(e){super(e),this.init(e)}init(e){super.init(e)}parseAtomType(e){let t=e,n=t;return this.isQuote(t)?(n=this.getNextIdenticalChar(t),t++):n=this.fileContent.indexOf(" ",n),this.fileContent.substring(t,n)}isQuote(e){const t=this.fileContent[e].charCodeAt(0);return 39===t||34===t}getNextIdenticalChar(e){const t=this.fileContent[e];return t?this.fileContent.indexOf(t,e+1):-1}isQuery(){return this.isQueryOrFragment(((e,t)=>{return 39===e||34===e||76===e&&!((n=this.fileContent.charCodeAt(t+1))>64&&n<91||n>96&&n<123);var n}))}isFragment(){return this.isQueryOrFragment((e=>82===e||42===e))}isQueryOrFragment(e){const t=this.atomCount;let n=this.getAtomBlockIdx();for(let o=0;o<t;o++){if(n=this.shiftIdxToAtomType(n),e(this.fileContent.charCodeAt(n),n))return!0;n=this.getNextLineIdx(n)}return!1}}class ft extends mt{constructor(e){super(e)}getAtomLines(){const e=this.getAtomBlockIdx(),t=this.getBondBlockIdx();return this.fileContent.substring(e,t).split("\n").slice(0,this.atomCount)}getBondLines(){const e=this.getBondBlockIdx();return this.fileContent.substring(e).split("\n").slice(0,this.bondCount)}getRGroupIdToAtomicIdxMap(){const e=new Map,t=this.fileContent.split("\n");t.filter((e=>e.startsWith(ct.RGP_LINE_START))).forEach((t=>{const n=this.getAtomIdxToRgpIdxList(t);for(const[t,o]of n){if(e.has(t))throw new Error(`R group ${t} is already in the map`);e.set(t,o)}}));const n=t.map(((e,t)=>{if(e.startsWith(ct.ATOM_ALIAS_LINE_START))return t})).filter((e=>void 0!==e)),o=n.map((e=>t[e])),r=n.map((e=>t[e+1]));o.forEach(((t,n)=>{const o=parseInt(t.split(/\s+/)[1])-1,i=parseInt(r[n].substring(1));if(e.has(i))throw new Error(`R group ${i} is already in the map`);e.set(i,o)}));const i=this.getRGroupAtomicIndices().filter((t=>!Array.from(e.values()).includes(t)));if(0!==i.length)throw new Error(`Unaccounted R group indices: ${i}`);return e}getAtomIdxToRgpIdxList(e){const t=e.split(/\s+/).filter((e=>e)).slice(3).map((e=>parseInt(e))),n=new Array(t.length/2);for(let e=0;e<t.length;e+=2)n[e/2]=[t[e+1],t[e]-1];return n}getRGroupAtomicIndices(){return this.atomTypes.map(((e,t)=>{if(e.includes("R#"))return t})).filter((e=>void 0!==e))}static isValidMolfile(e){return-1!==e.indexOf(ct.TYPE)&&-1!==e.indexOf(ct.END)}shiftIdxToAtomType(e){return this.shiftIdxToSpecifiedColumn(e,ct.ATOM_TYPE_COL)}getCountsLineIdx(){let e=0;for(let t=0;t<ct.NUM_OF_HEADER_LINES;++t)e=this.getNextLineIdx(e);return e}getAtomBlockIdx(){let e=this.getCountsLineIdx();return e=this.getNextLineIdx(e),e}shiftIdxToXColumn(e){return this.getNextColumnIdx(e)}shiftIdxToBondedAtomsPair(e){return this.shiftIdxToSpecifiedColumn(e,ct.FIRST_BONDED_ATOM_COL)}shiftIdxToBondType(e){return this.shiftIdxToSpecifiedColumn(e,ct.BOND_TYPE_COL)}getBondBlockIdx(){let e=this.getAtomBlockIdx();for(let t=0;t<this.atomCount;t++)e=this.getNextLineIdx(e);return e}parseAtomAndBondCounts(){let e=this.getCountsLineIdx(),t=e+ct.NUM_OF_COUNTS_DIGITS;const n=parseInt(this.fileContent.substring(e,t));return e=t,t+=ct.NUM_OF_COUNTS_DIGITS,{atomCount:n,bondCount:parseInt(this.fileContent.substring(e,t))}}}class gt extends mt{constructor(e){super(e),this.init(e)}getAtomLines(){const e=this.getAtomBlockIdx(),t=this.getBondBlockIdx();return this.fileContent.substring(e,t).split("\n").slice(0,this.atomCount)}getBondLines(){const e=this.getBondBlockIdx();return this.fileContent.substring(e).split("\n").slice(0,this.bondCount)}getRGroupIdToAtomicIdxMap(){const e=new Map;return this.getAtomLines().forEach(((t,n)=>{const o=t.match(/RGROUPS=\(([\d\s]+)\)/);if(o){const t=o[1].split(/\s+/).map((e=>parseInt(e)));if(t.length>2)throw new Error(`R group data ${t} has more than 2 elements`);const r=t[1];if(e.has(r))throw new Error(`R group ${r} is already in the map`);e.set(r,n)}})),e}shiftIdxToAtomType(e){return this.shiftIdxToSpecifiedColumn(e,4)}getCountsLineIdx(){return this.fileContent.indexOf("M V30 COUNTS ")}getAtomBlockIdx(){let e=this.fileContent.indexOf("M V30 BEGIN ATOM");return e=this.getNextLineIdx(e),e}shiftIdxToXColumn(e){let t=this.shiftIdxToAtomType(e);return this.isQuote(t)?(t=this.getNextIdenticalChar(t),t=this.getNextColumnIdx(t),t):this.shiftIdxToSpecifiedColumn(e,5)}shiftIdxToBondedAtomsPair(e){return this.shiftIdxToSpecifiedColumn(e,5)}shiftIdxToBondType(e){return this.shiftIdxToSpecifiedColumn(e,4)}getBondBlockIdx(){return this.getNextLineIdx(this.fileContent.indexOf("M V30 BEGIN BOND"))}static isValidMolfile(e){return-1!==e.indexOf("V3000")&&-1!==e.indexOf("M END")}parseAtomAndBondCounts(){let e=this.fileContent.indexOf("M V30 COUNTS ")+14,t=this.fileContent.indexOf(" ",e+1);const n=parseInt(this.fileContent.substring(e,t));return e=t+1,t=this.fileContent.indexOf(" ",e+1),{atomCount:n,bondCount:parseInt(this.fileContent.substring(e,t))}}}class yt{constructor(){}static getInstance(e){if(yt.isMolfileV2K(e))return new ft(e);if(yt.isMolfileV3K(e))return new gt(e);throw new Error("Malformed molfile")}static isMolfileV2K(e){return ft.isValidMolfile(e)}static isMolfileV3K(e){return gt.isValidMolfile(e)}}const bt=class extends Error{constructor(e){super(e)}};class vt{constructor(e){this.molblock=e}get molblock(){return this._validMolBlock}set molblock(e){if(""!==e){try{this.validateMolBlock(e)}catch(t){t instanceof bt&&(e="");const n=lt(t);console.error(n)}this._validMolBlock=e}else this._validMolBlock=e}validateMolBlock(e){if(""===e)throw new bt("MoleculeImage: invalid molblock")}async drawMolBlockOnCanvas(e){try{await o.functions.call("Chem:canvasMol",{x:0,y:0,w:e.width,h:e.height,canvas:e,molString:this.molblock,scaffoldMolString:"",options:{normalizeDepiction:!1,straightenDepiction:!1}})}catch(e){const t=lt(e);console.error(t)}}getMoleculeDimensions(){const e=yt.getInstance(this.molblock),t=Math.max(...e.x)-Math.min(...e.x);return{height:Math.max(...e.y)-Math.min(...e.y),width:t}}async zoomIn(){const e=r.dialog({title:"Molecule",showFooter:!1}),t=.7*L()(window).height(),n=this.getMoleculeDimensions(),o=t/n.height,i=t,s=n.width*o,a=r.canvas(s,i);await this.drawMolBlockOnCanvas(a);const l=r.block([a],{style:{overflowX:"scroll"}});e.add(l).showModal(!0),L()(e.root).find(".d4-dialog-contents").removeClass("ui-form"),L()(e.root).find(".d4-dialog-contents").removeClass("ui-panel"),L()(e.root).find(".d4-dialog-contents").addClass("ui-box"),L()(e.root).find(".d4-dialog-contents").css("padding","0")}async drawMolecule(e,t,n){e.innerHTML="";const o=r.canvas(t*window.devicePixelRatio,n*window.devicePixelRatio);o.style.width=`${t}px`,o.style.height=`${n}px`,o.style.cursor="zoom-in",this.drawMolBlockOnCanvas(o),o.addEventListener("click",(async()=>{await this.zoomIn()})),e.append(r.tooltip.bind(o,"Click to zoom"))}}class Ct extends Error{constructor(e,t){super(e,t)}}class xt{constructor(e,t){this.sequence=e,this.codeMap=t}parseSequence(){const e=this.parseRawSequence();return this.addLinkers(e)}addLinkers(e){const t=[];return e.forEach(((n,o)=>{const r=this.getSymbolForCode(n);o>0&&function(e){return br.jsonData.monomersWithPhosphate.left.includes(e)}(r)&&t.pop(),t.push(r);const i=wt(r),s=o===e.length-1,a=o+1<e.length&&wt(this.getSymbolForCode(e[o+1]));i||function(e){return br.jsonData.monomersWithPhosphate.right.includes(e)}(r)||a||s||t.push("p")})),t}getSymbolForCode(e){let t=this.codeMap.get(e);return t??(t=e),t}parseRawSequence(){const e=this.getAllCodesOfFormat(),t=[];let n=0;for(;n<this.sequence.length;){const o=e.find((e=>e===this.sequence.substring(n,n+e.length)));if(void 0===o)throw new Ct(`Unable to match a monomer for the rest of the sequence '${this.sequence.slice(n)}'.`);t.push(o),n+=o.length}return t}getAllCodesOfFormat(){return y(Array.from(this.codeMap.keys()))}}function wt(e){return br.jsonData.monomersWithPhosphate.phosphate.includes(e)}class At{constructor(e,t=!1,n){this.invert=t,this.lib=br.monomerLibWrapper;const o=this.lib.getCodeToSymbolMap(n);this.parser=new xt(e,o)}convert(){const e=this.parser.parseSequence(),t=[];e.forEach(((e,n)=>{const o=this.getMonomerMolfile(e,n);t.push(o)}));let n=this.getPolymerMolfile(t);return this.invert&&(n=this.reflect(n),n=this.invertBondConfiguration(n)),n}invertBondConfiguration(e){const t=e.indexOf("M V30 BEGIN BOND"),n=e.indexOf("M V30 END BOND");let o=e.substring(t,n);return o=o.replace(/(CFG=)([13])/g,((e,t,n)=>"1"===n?`${t}3`:"3"===n?`${t}1`:e)),e.substring(0,t)+o+e.substring(n)}getMonomerMolfile(e,t){const n=this.lib.getMolfileBySymbol(e);return this.lib.isModification(e)?0===t?this.reflect(n):n:this.rotateNucleotidesV3000(n)}getPolymerMolfile(e){return this.linkV3000(e)}reflect(e){const t=this.extractAtomDataV3000(e),n=t.atomIndex.length,o=t.atomIndex.indexOf(1),r=t.atomIndex.indexOf(n),i=(t.x[r]+t.x[o])/2,s=(t.y[r]+t.y[o])/2;for(let e=0;e<n;e++)t.x[e]-=i,t.y[e]-=s;for(let e=0;e<n;e++)t.x[e]=-t.x[e];const a=t.x[o];for(let e=0;e<n;e++)t.x[e]-=a;let l=e.indexOf("M V30 BEGIN ATOM");l=e.indexOf("\n",l);let c=l;for(let o=0;o<n;o++)l=e.indexOf("V30",l)+4,l=e.indexOf(" ",l)+1,l=e.indexOf(" ",l)+1,c=e.indexOf(" ",l)+1,c=e.indexOf(" ",c),l=(e=e.slice(0,l)+t.x[o]+" "+t.y[o]+e.slice(c)).indexOf("\n",l)+1;return e}extractAtomDataV3000(e){const t=this.extractAtomsBondsNumbersV3000(e);let n=e.indexOf("M V30 BEGIN ATOM");n=e.indexOf("\n",n);let o=n;const r=Array(t.natom),i=Array(t.natom),s=Array(t.natom),a=Array(t.natom);for(let l=0;l<t.natom;l++)n=e.indexOf("V30",n)+4,o=e.indexOf(" ",n),r[l]=parseInt(e.substring(n,o)),n=o+1,o=e.indexOf(" ",n),i[l]=e.substring(n,o),n=o+1,o=e.indexOf(" ",n),s[l]=parseFloat(e.substring(n,o)),n=o+1,o=e.indexOf(" ",n),a[l]=parseFloat(e.substring(n,o)),n=e.indexOf("\n",n)+1;return{atomIndex:r,atomType:i,x:s,y:a}}extractAtomsBondsNumbersV3000(e){let t=(e=e.replaceAll("\r","")).indexOf("COUNTS")+7,n=e.indexOf(" ",t);const o=parseInt(e.substring(t,n));return t=n+1,n=e.indexOf(" ",t),{natom:o,nbond:parseInt(e.substring(t,n))}}rotateNucleotidesV3000(e){const t=this.extractAtomDataV3000(e),n=t.atomIndex.length,o=t.atomIndex.indexOf(1),r=t.atomIndex.indexOf(n);n>8&&this.fix5Prime(t,o,r);const i=(t.x[r]+t.x[o])/2,s=(t.y[r]+t.y[o])/2;for(let e=0;e<n;e++)t.x[e]-=i,t.y[e]-=s;let a=0;if(0===t.x[o])a=t.y[o]>t.y[r]?Math.PI/2:3*Math.PI/2;else if(0===t.y[o])a=t.x[o]>t.x[r]?Math.PI:0;else{const e=t.y[o]/t.x[o];a=e>0?t.x[o]>0?Math.PI-Math.atan(e):2*Math.PI-Math.atan(e):t.x[o]>0?-Math.PI-Math.atan(e):Math.atan(e)}const l=Math.cos(a),c=Math.sin(a);for(let e=0;e<n;e++){const n=t.x[e];t.x[e]=n*l-t.y[e]*c,t.y[e]=n*c+t.y[e]*l}const u=t.x[o];for(let e=0;e<n;e++)t.x[e]-=u;let h=e.indexOf("M V30 BEGIN ATOM");h=e.indexOf("\n",h);let d=h;for(let o=0;o<n;o++)h=e.indexOf("V30",h)+4,h=e.indexOf(" ",h)+1,h=e.indexOf(" ",h)+1,d=e.indexOf(" ",h)+1,d=e.indexOf(" ",d),h=(e=e.slice(0,h)+t.x[o]+" "+t.y[o]+e.slice(d)).indexOf("\n",h)+1;return e}linkV3000(e,t=!0){let n="\n Datagrok macromolecule handler\n\n";n+=" 0 0 0 0 0 0 999 V3000\n",n+="M V30 BEGIN CTAB\n";let o="",r="",i="";const s=[];let a=0,l=0,c=0;for(let t=0;t<e.length;t++){const n=e[t].includes("MODIFICATION")&&0===t;let i=0;n&&(i=this.extractAtomDataV3000(e[t]).atomIndex.length),e[t]=e[t].replaceAll("(-\nM V30 ","(").replaceAll("-\nM V30 ","").replaceAll(" )",")");const u=this.extractAtomsBondsNumbersV3000(e[t]),h=this.extractAtomDataV3000(e[t]);let d=e[t].indexOf("M V30 BEGIN ATOM");d=e[t].indexOf("\n",d);let p=d,m=d;for(let o=0;o<u.natom;o++)if(1!==h.atomIndex[o]||0===t){p=e[t].indexOf("V30",p)+4,m=e[t].indexOf(" ",p);let o=0;n?(o=parseInt(e[t].substring(p,m)),1===o?o=i:o===i&&(o=1),o+=a):o=parseInt(e[t].substring(p,m))+a,e[t]=e[t].slice(0,p)+o+e[t].slice(m),p=e[t].indexOf(" ",p)+1,p=e[t].indexOf(" ",p)+1,m=e[t].indexOf(" ",p);const r=c-h.x[0];let s=Math.round(1e4*(parseFloat(e[t].substring(p,m))+r))/1e4;e[t]=e[t].slice(0,p)+s+e[t].slice(m),p=e[t].indexOf(" ",p)+1,m=e[t].indexOf(" ",p),s=Math.round(1e4*parseFloat(e[t].substring(p,m)))/1e4,e[t]=e[t].slice(0,p)+s+e[t].slice(m),p=e[t].indexOf("\n",p)+1}else p=e[t].indexOf("M V30",p)-1,m=e[t].indexOf("\n",p+1),e[t]=e[t].slice(0,p)+e[t].slice(m);const f=e[t].indexOf("M V30 END ATOM");o+=e[t].substring(d+1,f);let g=e[t].indexOf("M V30 BEGIN BOND");g=e[t].indexOf("\n",g),p=g,m=g;for(let o=0;o<u.nbond;o++){p=e[t].indexOf("V30",p)+4,m=e[t].indexOf(" ",p);const o=parseInt(e[t].substring(p,m))+l;e[t]=e[t].slice(0,p)+o+e[t].slice(m),p=e[t].indexOf(" ",p)+1,p=e[t].indexOf(" ",p)+1,m=e[t].indexOf(" ",p);let r=0;n?(r=parseInt(e[t].substring(p,m)),1===r?r=i:r===i&&(r=1),r+=a):r=parseInt(e[t].substring(p,m))+a,e[t]=e[t].slice(0,p)+r+e[t].slice(m),p=e[t].indexOf(" ",p)+1,m=Math.min(e[t].indexOf("\n",p),e[t].indexOf(" ",p)),r=0,n?(r=parseInt(e[t].substring(p,m)),1===r?r=i:r===i&&(r=1),r+=a):r=parseInt(e[t].substring(p,m))+a,e[t]=e[t].slice(0,p)+r+e[t].slice(m),p=e[t].indexOf("\n",p)+1}const y=e[t].indexOf("M V30 END BOND");r+=e[t].substring(g+1,y);let b=e[t].indexOf("M V30 MDLV30/STEABS ATOMS=(");for(;-1!==b;){b+=28;const n=e[t].indexOf(")",b);e[t].substring(b,n).split(" ").slice(1).forEach((e=>{s.push(parseInt(e)+a)})),b=n,b=e[t].indexOf("M V30 MDLV30/STEABS ATOMS=(",b)}a+=u.natom-1,l+=u.nbond,c+=n?Math.max(...h.x):h.x[u.natom-1]-h.x[0]}const u=Math.ceil(s.length/4);i+="M V30 MDLV30/STEABS ATOMS=("+s.length+" -\n";for(let e=0;e<u;e++){i+="M V30 ";const t=e+1===u?s.length-4*(u-1):4;for(let n=0;n<t;n++)i+=n+1===t?e===u-1?s[4*e+n]+")\n":s[4*e+n]+" -\n":s[4*e+n]+" "}return a++,n+="M V30 COUNTS "+a+" "+l+" 0 0 0\n",n+="M V30 BEGIN ATOM\n",n+=o,n+="M V30 END ATOM\n",n+="M V30 BEGIN BOND\n",n+=r,n+="M V30 END BOND\n",t&&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(e,t,n){const o=t+1,r=e.x[o],i=e.y[o],s=e.x[n]-r,a=e.y[n]-i,l=e.x[t]-r,c=e.y[t]-i,u=l*Math.cos(2*Math.PI/3)-c*Math.sin(2*Math.PI/3),h=l*Math.sin(2*Math.PI/3)+c*Math.cos(2*Math.PI/3),d=l-s,p=c-a,m=u-s,f=h-a;Math.sqrt(f*f+m*m)>=Math.sqrt(p*p+d*d)&&(e.x[t]=u+r,e.y[t]=h+i)}}function Tt(e,t=!0){let n="\n Datagrok macromolecule handler\n\n";n+=" 0 0 0 0 0 0 999 V3000\n",n+="M V30 BEGIN CTAB\n";let o="",r="",i="";const s=[];let a=0,l=0,c=0;if(e.antiStrands.length>0)for(let t=0;t<e.antiStrands.length;t++)e.antiStrands[t]=Et(e.antiStrands[t]);let u=!1;const h=e.senseStrands.concat(e.antiStrands);let d=0;for(let t=0;t<h.length;t++){h[t]=h[t].replaceAll("(-\nM V30 ","(").replaceAll("-\nM V30 ","").replaceAll(" )",")");const n=St(h[t]),i=Nt(h[t]);if(t>=e.senseStrands.length?!1===u&&(u=!0,c=0):d=Math.min(d,Math.min(...i.y.filter((e=>e<0)))),u){const e=Math.min(...i.x)-c,t=Math.max(...i.y)+5;for(let t=0;t<i.x.length;t++)i.x[t]-=e;for(let e=0;e<i.y.length;e++)i.y[e]-=t-d}let p=h[t].indexOf("M V30 BEGIN ATOM");p=h[t].indexOf("\n",p);let m=p,f=p;for(let e=0;e<n.natom;e++){m=h[t].indexOf("V30",m)+4,f=h[t].indexOf(" ",m);const n=parseInt(h[t].substring(m,f))+a;h[t]=h[t].slice(0,m)+n+h[t].slice(f),m=h[t].indexOf(" ",m)+1,m=h[t].indexOf(" ",m)+1,f=h[t].indexOf(" ",m);let o=Math.round(1e4*i.x[e])/1e4;h[t]=h[t].slice(0,m)+o+h[t].slice(f),m=h[t].indexOf(" ",m)+1,f=h[t].indexOf(" ",m),o=Math.round(1e4*i.y[e])/1e4,h[t]=h[t].slice(0,m)+o+h[t].slice(f),m=h[t].indexOf("\n",m)+1}const g=h[t].indexOf("M V30 END ATOM");o+=h[t].substring(p+1,g);let y=h[t].indexOf("M V30 BEGIN BOND");y=h[t].indexOf("\n",y),m=y,f=y;for(let e=0;e<n.nbond;e++){m=h[t].indexOf("V30",m)+4,f=h[t].indexOf(" ",m);const e=parseInt(h[t].substring(m,f))+l;h[t]=h[t].slice(0,m)+e+h[t].slice(f),m=h[t].indexOf(" ",m)+1,m=h[t].indexOf(" ",m)+1,f=h[t].indexOf(" ",m);let n=parseInt(h[t].substring(m,f))+a;h[t]=h[t].slice(0,m)+n+h[t].slice(f),m=h[t].indexOf(" ",m)+1,f=Math.min(h[t].indexOf("\n",m),h[t].indexOf(" ",m)),n=parseInt(h[t].substring(m,f))+a,h[t]=h[t].slice(0,m)+n+h[t].slice(f),m=h[t].indexOf("\n",m)+1}const b=h[t].indexOf("M V30 END BOND");r+=h[t].substring(y+1,b);let v=h[t].indexOf("M V30 MDLV30/STEABS ATOMS=(");for(;-1!==v;){v+=28;const e=h[t].indexOf(")",v);h[t].substring(v,e).split(" ").slice(1).forEach((e=>{s.push(parseInt(e)+a)})),v=e,v=h[t].indexOf("M V30 MDLV30/STEABS ATOMS=(",v)}a+=n.natom,l+=n.nbond,c+=Math.max(...i.x)+5}const p=Math.ceil(s.length/4);i+="M V30 MDLV30/STEABS ATOMS=("+s.length+" -\n";for(let e=0;e<p;e++){i+="M V30 ";const t=e+1===p?s.length-4*(p-1):4;for(let n=0;n<t;n++)i+=n+1===t?e===p-1?s[4*e+n]+")\n":s[4*e+n]+" -\n":s[4*e+n]+" "}return n+="M V30 COUNTS "+a+" "+l+" 0 0 0\n",n+="M V30 BEGIN ATOM\n",n+=o,n+="M V30 END ATOM\n",n+="M V30 BEGIN BOND\n",n+=r,n+="M V30 END BOND\n",t&&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 Et(e){const t=Nt(e),n=t.atomIndex.length,o=(Math.max(...t.x)+Math.min(...t.x))/2,r=(Math.max(...t.y)+Math.min(...t.y))/2;for(let e=0;e<n;e++)t.x[e]-=o,t.y[e]-=r;const i=Math.PI,s=Math.cos(i),a=Math.sin(i);for(let e=0;e<n;e++){const n=t.x[e];t.x[e]=n*s-t.y[e]*a,t.y[e]=n*a+t.y[e]*s}const l=Math.max(...t.y);for(let e=0;e<n;e++)t.x[e]+=o,t.y[e]-=l;let c=e.indexOf("M V30 BEGIN ATOM");c=e.indexOf("\n",c);let u=c;for(let o=0;o<n;o++)c=e.indexOf("V30",c)+4,c=e.indexOf(" ",c)+1,c=e.indexOf(" ",c)+1,u=e.indexOf(" ",c)+1,u=e.indexOf(" ",u),c=(e=e.slice(0,c)+t.x[o]+" "+t.y[o]+e.slice(u)).indexOf("\n",c)+1;return e}function St(e){let t=(e=e.replaceAll("\r","")).indexOf("COUNTS")+7,n=e.indexOf(" ",t);const o=parseInt(e.substring(t,n));return t=n+1,n=e.indexOf(" ",t),{natom:o,nbond:parseInt(e.substring(t,n))}}function Nt(e){const t=St(e);let n=e.indexOf("M V30 BEGIN ATOM");n=e.indexOf("\n",n);let o=n;const r=Array(t.natom),i=Array(t.natom),s=Array(t.natom),a=Array(t.natom);for(let l=0;l<t.natom;l++)n=e.indexOf("V30",n)+4,o=e.indexOf(" ",n),r[l]=parseInt(e.substring(n,o)),n=o+1,o=e.indexOf(" ",n),i[l]=e.substring(n,o),n=o+1,o=e.indexOf(" ",n),s[l]=parseFloat(e.substring(n,o)),n=o+1,o=e.indexOf(" ",n),a[l]=parseFloat(e.substring(n,o)),n=e.indexOf("\n",n)+1;return{atomIndex:r,atomType:i,x:s,y:a}}function It(e,t,n){if(""===e)return"";const o=n.createFormatDetector(e).getFormat();if(!o)return"";let r="";try{r=new At(e,t,o).convert()}catch(e){const t=lt(e);console.error(t)}return r}function Mt(e,t,n,o,r){const i=[e,t,n].filter((e=>""!==e.strand));return 1===i.length?It(i[0].strand,i[0].invert,r):Tt({senseStrands:[It(e.strand,e.invert,r)],antiStrands:[It(t.strand,t.invert,r),It(n.strand,n.invert,r)].filter((e=>""!==e))},o)}const Pt=["ss","as","as2"];class _t{constructor(){this.th=br,this.onInput=new te.Subject,this.onInvalidInput=new te.Subject,this.inputBase=Object.fromEntries(Pt.map((e=>{const t=r.input.textArea(e.toUpperCase(),{value:"",onValueChanged:()=>{this.onInput.next(),L()(t.root.getElementsByTagName("div")).css("padding-left","38px")}});return[e,t]}))),this.useChiralInput=r.input.bool("Use chiral",{value:!0}),this.saveAllStrandsInput=r.input.bool("Save as one entity",{value:!0}),r.tooltip.bind(this.saveAllStrandsInput.root,"Save SDF with all strands in one molfile"),this.directionInversion=Object.fromEntries(Pt.map((e=>[e,!1]))),this.moleculeImgDiv=r.block([]),L()(this.moleculeImgDiv).addClass("st-structure-mol-img"),i.debounce(this.onInput,300).subscribe((async()=>{await this.updateMoleculeImg()})),i.debounce(this.onInvalidInput,1e3).subscribe((async()=>{o.shell.warning("Insert Sense strand")}))}async getHtmlDivElement(e){const t=this.getTableInput(e),n=this.getBoolInputsAndButton();await this.updateMoleculeImg();const o=r.divH([this.moleculeImgDiv,n]);L()(o).addClass("st-structure-bottom");const i=r.divV([t,o]);return L()(i).addClass("st-structure-body"),i}getBoolInputsAndButton(){const e=r.buttonsInput([r.bigButton("Save SDF",(()=>{const e=this.getStrandData();!function(e,t,n,r,i,s){const a=[e.strand,t.strand,n.strand].filter((e=>""!==e));if(0===a.length||1===a.length&&""===e.strand)o.shell.warning("Enter SENSE_STRAND and optionally ANTISENSE_STRAND/AS2 to save SDF");else{let l;if(i)l=Mt(e,t,n,r,s)+"\n$$$$\n";else{const h=It(e.strand,e.invert,s),d=It(t.strand,t.invert,s),p=It(n.strand,n.invert,s);l=h+"\n> <Sequence>\nSense Strand\n$$$$\n",d&&(l+=d+"\n> <Sequence>\nAnti Sense\n$$$$\n"),p&&(l+=p+"\n> <Sequence>\nAnti Sense 2\n$$$$\n")}const c=new Date;function u(e){return e>=10?e.toString():"0"+e.toString()}b(`SequenceTranslator-${c.getFullYear()+"-"+u(c.getMonth()+1)+"-"+u(c.getDate())+"_"+u(c.getHours())+"-"+u(c.getMinutes())+"-"+u(c.getSeconds())}.sdf`,encodeURIComponent(l))}}(e.ss,e.as,e.as2,this.useChiralInput.value,this.saveAllStrandsInput.value,this.th)}))]),t=[this.saveAllStrandsInput.root,this.useChiralInput.root,e],n=r.divV(t);for(const e of t)L()(e).addClass("st-structure-bool-button-block");return n}getTableInput(e){const t=Object.fromEntries(Pt.map((t=>[t,new dt(this.inputBase[t],e.highlightInvalidSubsequence)]))),n=Object.fromEntries(Pt.map(((e,t)=>{const n=0===t?"5′ → 3′":"3′ → 5′";return[e,r.input.choice(`${e.toUpperCase()} direction`,{value:n,items:["5′ → 3′","3′ → 5′"]})]})));Pt.forEach(((e,t)=>{n[e].onChanged.subscribe((n=>{let o="3′ → 5′"===n;t>0&&(o=!o),this.directionInversion[e]=o,this.onInput.next()}))}));const o=["Sense Strand","Anti Sense","Anti Sense 2"],i=new Map(Pt.map(((e,t)=>[e,o[t]]))),s=(Object.fromEntries(Pt.map((e=>[e,r.label(i.get(e))]))),Object.fromEntries(Pt.map((e=>{const n=r.icons.delete((()=>{t[e].inputBase.value=""}),"Delete"),o=r.button(n,(()=>{}));return r.tooltip.bind(o,`Clear ${e.toUpperCase()}`),[e,n]})))),a=r.form([],"st-structure-inputs"),l=r.divV([],"st-structure-clear-buttons"),c=r.form([],"st-direction-inputs");for(const e of Pt)a.append(this.inputBase[e].root),l.append(s[e]),c.append(n[e].root);return r.divH([a,l,c])}getStrandData(){return Object.fromEntries(Pt.map((e=>{const t=this.directionInversion[e];return[e,{strand:this.inputBase[e].value.replace(/\s*/g,""),invert:t}]})))}getMolfile(e,t,n){return Mt(e,t,n,this.useChiralInput.value,this.th)}async updateMoleculeImg(){let e="";try{const t=this.getStrandData();Object.values(t).some((e=>""!==e.strand))&&(e=this.getMolfile(t.ss,t.as,t.as2))}catch(e){const t=lt(e);console.error(t)}const t=new vt(e);await t.drawMolecule(this.moleculeImgDiv,650,150)}}class Lt extends F{constructor(e){super("Oligo Structure"),this.th=e,this.layout=new _t}getContent(){return this.layout.getHtmlDivElement(this.th)}}var Ot=n(2003);async function Rt(e){try{const t={overflowX:"scroll"},n=r.div([],{style:t}),i=Nt(e),s=.7*L()(window).height(),a=Math.max(...i.x)-Math.min(...i.x),l=Math.max(...i.y)-Math.min(...i.y),c=s/l,u=c*a,h=c*l,d=r.canvas(u*window.devicePixelRatio,h*window.devicePixelRatio);d.style.width=`${u}px`,d.style.height=`${h}px`,await async function(e,t){await o.functions.call("Chem:canvasMol",{x:0,y:0,w:e.width,h:e.height,canvas:e,molString:t,scaffoldMolString:"",options:{normalizeDepiction:!1,straightenDepiction:!1}})}(d,e),n.appendChild(d),r.dialog("Molecule").add(n).showModal(!0)}catch(e){const t=lt(e);console.error(t)}}class $t{static async view(){const e=br.monomerLibWrapper.getTableForViewer();e.name="Monomer Library";const t=o.shell.addTableView(e);t.grid.props.allowEdit=!1,t.grid.onCellDoubleClick.subscribe((async e=>{const t=e.cell.value;"Molecule"===e.tableColumn?.semType&&await Rt(t)}))}}var Dt=n(3480),Bt=n(5067),Ft=n(5254),kt={};kt.styleTagTransform=Ae(),kt.setAttributes=ve(),kt.insert=ye().bind(null,"head"),kt.domAPI=fe(),kt.insertStyleElement=xe(),pe()(Ft.A,kt),Ft.A&&Ft.A.locals&&Ft.A.locals;const Ht=["Sequence"];class Gt{constructor(e){this.th=e,this.inputFormats=Object.keys(br.jsonData.codesToHelmDict).concat(g.NO.HELM),this.seqHelper=br.seqHelper,this.onInput=new te.Subject,this.moleculeImgDiv=r.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=r.div([]),this.formatChoiceInput=r.input.choice("",{value:g.NO.HELM,items:this.inputFormats,onValueChanged:async(e,t)=>{this.format=e,this.updateTable(),await this.updateMolImg()}}),this.sequenceInputBase=r.input.textArea("",{value:"Afcgacsu",onValueChanged:()=>{this.onInput.next()}}),this.init(),i.debounce(this.onInput,300).subscribe((async()=>{this.init(),this.formatChoiceInput.value=this.format,this.updateTable(),await this.updateMolImg()})),this.eventBus=qt.getInstance()}async getHtmlElement(){const e=this.constructSingleSequenceControls(),t=this.constructBulkTranslationControls(),n=r.box(r.panel([e,t,r.block([r.box(this.moleculeImgDiv)])]));return this.formatChoiceInput.value=this.format,this.updateTable(),await this.updateMolImg(),n}constructBulkTranslationControls(){const e=r.h1("Bulk");r.tooltip.bind(e,"Bulk translation from table input");const t=new Ut(this.eventBus).createUIComponents(),n=r.input.choice("Input format",{value:g.NO.AXOLABS,items:this.inputFormats,onValueChanged:e=>this.eventBus.selectInputFormat(e)}),o=r.input.choice("Output format",{value:Bt.qP,items:(0,Dt.OT)(this.th),onValueChanged:e=>this.eventBus.selectOutputFormat(e)}),i=this.createConvertBulkButton(),s=r.div([...t,n,o,i],"ui-form");return r.block25([e,s])}createConvertBulkButton(){const e=r.bigButton("Convert",(()=>this.processConvertBulkButtonClick()));return r.tooltip.bind(e,"Convert sequences from table input"),L()(e).css({float:"right","margin-top":"20px"}),e}processConvertBulkButtonClick(){const e=this.eventBus.getSelectedTable();if(!e)return void o.shell.warning("No table selected");const t=this.eventBus.getSelectedInputFormat(),n=this.eventBus.getSelectedOutputFormat(),r=this.eventBus.getSelectedColumn("Sequence");if(!r)return void o.shell.warning("No sequence column selected");const s=`${r.name} (${n})`,a=i.Column.fromList(i.TYPE.STRING,s,r.toList().map((e=>(0,Dt.C6)(e,t,n,this.th))));if(n===Bt.qP||n===g.NO.HELM){a.semType=i.SEMTYPE.MACROMOLECULE;const e=n==Bt.qP?Ot.Hi.FASTA:Ot.Hi.HELM;a.meta.units=e;const t=this.seqHelper.getSeqHandler(a);(n==Bt.qP?this.seqHelper.setUnitsToFastaColumn:this.seqHelper.setUnitsToHelmColumn)(t)}e.columns.add(a),o.data.detectSemanticTypes(e),o.shell.v=o.shell.getTableView(e.name)}constructSingleSequenceControls(){const e=new dt(this.sequenceInputBase,(e=>O(e,this.th))),t=r.button("Get SDF",(()=>{this.saveMolfile()}),"Save structure as SDF"),n=r.button("Copy SMILES",(()=>{this.copySmiles()}),"Copy SMILES for the sequence"),o=r.div([this.formatChoiceInput]),i=r.button(r.icons.delete((()=>{e.inputBase.value=""}),"Delete"),(()=>{}));r.tooltip.bind(i,"Clear input");const s={format:o,textInput:e.root,clearBtn:i},a=r.table([s],(e=>[e.format,e.textInput,e.clearBtn]));a.classList.add("st-translator-input-table");const l=r.block([this.outputTableDiv,t,n]);return r.block75([r.h1("Single sequence"),a,l])}saveMolfile(){try{const e=new At(this.sequence,!1,this.formatChoiceInput.value).convert()+"\n$$$$";b(this.sequence+".sdf",encodeURIComponent(e))}catch(e){o.shell.warning("Unable to save SDF: "+e.message)}}copySmiles(){const e=i.chem.convert(this.molfile,i.chem.Notation.MolBlock,i.chem.Notation.Smiles);navigator.clipboard.writeText(e).then((()=>o.shell.info(Bt.n_)))}updateTable(){this.outputTableDiv.innerHTML="";const e=this.format?this.th.createSequenceValidator(this.sequence).getInvalidCodeIndex(this.format):0,t=(0,Dt.bD)(this.sequence,e,this.format,this.th),n=[];for(const e of Object.keys(t)){const i="indexOfFirstInvalidChar"in t?r.divH([]):r.link(t[e],(()=>navigator.clipboard.writeText(t[e]).then((()=>o.shell.info(Bt.n_)))),Bt.U_,"");n.push({format:e,sequence:i})}const i=r.table(n,(e=>[e.format,e.sequence]),["FORMAT","SEQUENCE"]);this.outputTableDiv.append(i),this.outputTableDiv.classList.add("st-translator-output-table")}async updateMolImg(){const e=new vt(this.molfile);await e.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===g.NO.HELM){const e=this.th.createFormatConverter(this.sequence,this.format).convertTo(g.NO.AXOLABS);return new At(e,!1,g.NO.AXOLABS).convert()}return new At(this.sequence,!1,this.format).convert()}}class Ut{constructor(e){this.tableInputManager=new Vt(e),this.columnInputManager=new jt(e)}createUIComponents(){return[this.tableInputManager.getTableInputContainer(),this.columnInputManager.getColumnControlsContainer()]}}class Vt{constructor(e){this.eventBus=e,this.availableTables=[],this.tableInputContainer=r.div([]),this.subscribeToTableEvents(),this.refreshTableInput()}getTableInputContainer(){return this.tableInputContainer}subscribeToTableEvents(){o.events.onTableAdded.subscribe((e=>this.handleTableAdded(e))),o.events.onTableRemoved.subscribe((e=>this.handleTableRemoved(e))),this.eventBus.tableSelected$.subscribe((()=>this.handleTableChoice()))}getTableFromEventData(e){return e.args.dataFrame}handleTableAdded(e){const t=this.getTableFromEventData(e);this.availableTables.some((e=>e.name===t.name))||(this.availableTables.push(t),this.eventBus.selectTable(t),this.refreshTableInput())}handleTableRemoved(e){const t=this.getTableFromEventData(e);this.availableTables=this.availableTables.filter((e=>e.name!==t.name));const n=this.availableTables[0];this.eventBus.selectTable(n||null),this.refreshTableInput()}refreshTableInput(){const e=this.createTableInput();L()(this.tableInputContainer).empty(),this.tableInputContainer.append(e.root)}createTableInput(){const e=this.eventBus.getSelectedTable();return r.input.table("Table",{value:e,items:this.availableTables,onValueChanged:e=>{null!==e&&this.eventBus.selectTable(e)}})}handleTableChoice(){const e=this.eventBus.getSelectedTable();e&&(this.isTableDisplayed(e)||this.displayTable(e))}isTableDisplayed(e){return o.shell.tableNames.includes(e.name)}displayTable(e){const t=o.shell.v;o.shell.addTableView(e),o.shell.v=t}}class jt{constructor(e){this.eventBus=e,this.columnControlsContainer=r.div([]),this.eventBus.tableSelected$.subscribe((()=>this.handleTableChoice())),this.refreshColumnControls()}getColumnControlsContainer(){return this.columnControlsContainer}handleTableChoice(){this.refreshColumnControls()}refreshColumnControls(){const e=this.createColumnInputs();L()(this.columnControlsContainer).empty();const t=e.map((e=>e.root));this.columnControlsContainer.append(...t)}createColumnInputs(){const e=this.eventBus.getSelectedTable(),t=null!==e?e.columns.names().sort(((e,t)=>e.localeCompare(t))):[];return Ht.map((n=>this.createColumnInput(n,t,e)))}createColumnInput(e,t,n){const o=e.toLowerCase(),i=t.find((e=>e.toLowerCase().includes(o)))||t[0];return this.selectColumnIfTableNotNull(n,i,e),r.input.choice(`${e}`,{value:i,items:t,onValueChanged:t=>this.selectColumnIfTableNotNull(n,t,e)})}selectColumnIfTableNotNull(e,t,n){if(null!==e&&t){const o=e.col(t);o&&this.eventBus.selectColumn(n,o)}}}class qt{constructor(){this._tableSelection$=new te.BehaviorSubject(null),this._columnSelection=Object.fromEntries(Ht.map((e=>[e,new te.BehaviorSubject(null)]))),this._inputFormatSelection$=new te.BehaviorSubject(g.NO.AXOLABS),this._outputFormatSelection$=new te.BehaviorSubject(Bt.qP)}static getInstance(){return void 0===qt._instance&&(qt._instance=new qt),qt._instance}get tableSelected$(){return this._tableSelection$.asObservable()}getSelectedTable(){return this._tableSelection$.getValue()}selectTable(e){this._tableSelection$.next(e)}selectColumn(e,t){this._columnSelection[e].next(t)}getSelectedColumn(e){return this._columnSelection[e].getValue()}getSelectedInputFormat(){return this._inputFormatSelection$.getValue()}selectInputFormat(e){this._inputFormatSelection$.next(e)}selectOutputFormat(e){this._outputFormatSelection$.next(e)}getSelectedOutputFormat(){return this._outputFormatSelection$.getValue()}}class Wt extends F{constructor(e){super("Oligo Translator"),this.th=e,this.th=br,this.layout=new Gt(this.th);const t=r.iconFA("book",$t.view,"View monomer library");this.topPanel=[t],this.view.setRibbonPanels([this.topPanel])}getContent(){return this.layout.getHtmlElement()}}class zt extends F{constructor(e,t){super(e),this.content=t}getContent(){return Promise.resolve(this.content)}}class Yt extends B{constructor(e,t){super("Oligo Toolkit"),this.externalViewFactories=e,this.th=t;const n=this.getViewFactories(this.th);this.multiView=new i.MultiView({viewFactories:n})}getViewFactories(e){function t(t){i.View.create();const n=new t(e);return n.initView().catch((e=>console.error(`Failed to initialize ${t.name}: ${e}`))),()=>n.getView()}let n={TRANSLATOR:t(Wt),PATTERN:t(it),STRUCTURE:t(Lt)};return this.externalViewFactories&&(n=Object.assign({},n,this.externalViewFactories)),n}getCurrentPanePath(){let e=this.multiView.tabs.currentPane.name;return e=e.charAt(0).toUpperCase()+e.substring(1).toLowerCase(),`/apps/${br.name}/OligoToolkit/${e}`}setUrl(){this.multiView.path=this.getCurrentPanePath()}async constructView(){return this.multiView.tabs.onTabChanged.subscribe((()=>this.setUrl())),this.setUrl(),this.multiView}}function Kt(e){const t=r.input.textArea("",{value:""});return{coloredInput:new dt(t,e.highlightInvalidSubsequence),codes:e.jsonData.codesToSymbolsDict}}var Qt=n(5733),Jt=n(5613),Xt=n(1536);const Zt=110,en=90;function tn(e,t,n=!1){return r.divH([r.divText(e,{style:{color:"var(--grey-4, #888)",width:"90px",flexShrink:"0"}}),r.divText(t,{style:n?{fontFamily:"ui-monospace, Menlo, monospace",wordBreak:"break-all"}:{}})],{style:{gap:"6px"}})}let nn=null;function on(e,t,n){const o=[t];"sugar"===n?o.push((0,Xt.Jy)(t)):"phosphate"===n&&o.push((0,Xt.$T)(t));const r=e.getPolymerTypes().filter((e=>"RNA"===e||"CHEM"===e)).concat(e.getPolymerTypes().filter((e=>"RNA"!==e&&"CHEM"!==e)));for(const t of o)for(const n of r){const o=e.getMonomer(n,t);if(o&&o.molfile)return o.molfile}return null}function rn(e){let t=e.symbol;return"sugar"===e.kind?t=(0,Xt.Jy)(e.symbol):"phosphate"===e.kind&&(t=(0,Xt.$T)(e.symbol)),`${e.kind}:${t}`}function sn(e){const t=r.div([],{style:{borderRadius:"4px",display:"flex",alignItems:"center",justifyContent:"center",fontSize:"10px",color:"var(--grey-4, #888)",textAlign:"center",padding:"4px"}}),n=r.divText(e,{style:{fontSize:"10px",color:"var(--grey-5, #555)",textAlign:"center",marginTop:"2px",letterSpacing:"0.04em",textTransform:"uppercase",fontWeight:"600"}});return{root:r.divV([t,n],{style:{display:"inline-flex"}}),body:t}}const an=new Map;function ln(e,t,n){try{let r=an.get(n);r||(r=o.chem.drawMolecule(t,Zt,en,!1),an.size>256&&an.clear(),an.set(n,r)),e.innerHTML="",e.appendChild(r)}catch{e.textContent="Render failed"}}const cn="OligoNucleotide";class un extends i.GridCellRenderer{constructor(){super(...arguments),this.modelCache=new Map,this.layoutCache=new Map}get name(){return cn}get cellType(){return cn}get defaultWidth(){return 320}get defaultHeight(){return 64}render(e,t,n,o,r,i,s){const a=i.cell.value;if(!a||!(0,Jt.yO)(a))return e.save(),e.beginPath(),e.rect(t,n,o,r),e.clip(),e.fillStyle="#8b949e",e.font="11px ui-monospace, Menlo, monospace",e.textBaseline="middle",e.textAlign="left",e.fillText(a??"",t+4,n+r/2),void e.restore();const l=this.getOrParse(a),c=(0,Qt.Z4)(e,t,n,o,r,l);this.layoutCache.set(this.cellKey(i),c),this.layoutCache.size>5e3&&this.layoutCache.clear()}onMouseMove(e,t){const n=e.cell.value;if(!n||!(0,Jt.yO)(n))return void r.tooltip.hide();const o=this.getOrParse(n),i=this.layoutCache.get(this.cellKey(e));if(!i)return;const s=e.bounds,a=t.offsetX-s.x,l=t.offsetY-s.y,u=(0,Qt.CB)(a,l,o,i);u?function(e,t,n){const o=function(e){const t=e.monomer,n=r.divText("",{style:{fontWeight:"600",marginBottom:"4px"}}),o=[];if(e.linkage){const t=(0,Xt.bM)(e.linkage.phosphateSymbol);n.textContent=`${t.meta.name} linkage`,o.push(tn("Strand","sense"===e.strand?"Sense":"Antisense"),tn("Between",`pos ${e.position+1} – ${e.position+2}`),tn("HELM symbol",`[${(0,Xt.$T)(e.linkage.phosphateSymbol)}]`,!0))}else if("nucleotide"===t.kind){const r=t,i=(0,Xt.xh)(r.sugar,r.base),s=(0,Xt.bM)(r.phosphate);n.textContent=`${r.base??"?"}${e.position+1} — ${i.meta.name}`,o.push(tn("Strand","sense"===e.strand?"Sense":"Antisense"),tn("Position",String(e.position+1)),tn("Base",r.base??"—"),tn("Sugar",i.meta.name),tn("3'-linkage",s.meta.name),tn("HELM",r.raw,!0))}else{const r=(0,Xt.rK)(t.symbol);n.textContent=r.meta.name,o.push(tn("Strand","sense"===e.strand?"Sense":"Antisense"),tn("Position",String(e.position+1)),tn("Type","Terminal conjugate / linker"),tn("HELM",t.raw,!0))}const i=r.div([],{style:{marginTop:"8px",display:"flex",flexDirection:"row",gap:"6px",flexWrap:"wrap"}});i.dataset.role="struct";const s=r.divText("Loading structures…",{style:{fontSize:"11px",color:"var(--grey-4, #888)"}});return i.appendChild(s),r.divV([n,...o,i],{style:{fontSize:"12px",lineHeight:"1.45",minWidth:"240px",maxWidth:"380px"}})}(e);r.tooltip.show(o,t+14,n+14),async function(e,t){const n=e.querySelector('[data-role="struct"]');if(!n)return;let o,i;if(t.linkage)o=[{label:"Linkage",symbol:t.linkage.phosphateSymbol,kind:"phosphate"}];else 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e=o.error?`err:${o.originalSmiles}`:o.smiles;t.has(e)?r++:(t.add(e),n.push(o))}}g.cores=n,n.forEach(((e,t)=>{e.error&&a.push(`Core ${t+1}: ${e.error}`),s.push({smi:e.error?"":e.smiles,err:e.error,subtitle:e.error?"invalid":e.rNumbers.map((e=>"R"+e)).join(", ")})})),m.innerText=`${n.length} core${1===n.length?"":"s"}`+(i&&r?` (${r} duplicate${1===r?"":"s"} skipped)`:"")+"."}else{const e=u.value??1,n=o.map((n=>(0,io.ah)(n,e,"",t)));let r=n,l=0;if(i){const e=new Set;r=[];for(const t of n){const n=t.error?`err:${t.originalSmiles}`:t.smiles;e.has(n)?l++:(e.add(n),r.push(t))}}g.rGroups=r,r.forEach(((e,t)=>{e.error&&a.push(`R-group ${t+1}: ${e.error}`);const n=e.error?"invalid":e.isSingleAtom?`R${e.rNumber} · atom`:`R${e.rNumber}${null!=e.sourceRNumber&&e.sourceRNumber!==e.rNumber?` (from R${e.sourceRNumber})`:""}`;s.push({smi:e.error?"":e.smiles,err:e.error,subtitle:n})})),m.innerText=`${r.length} R-group${1===r.length?"":"s"} for R${e}`+(i&&l?` (${l} duplicate${1===l?"":"s"} skipped)`:"")+"."}f.setErrors(a),b?b.setData(s.length,(e=>go({smiles:s[e].smi,subtitle:s[e].subtitle,error:s[e].err}))):(b=r.virtualView(s.length,(e=>go({smiles:s[e].smi,subtitle:s[e].subtitle,error:s[e].err})),!1,1),b.root.style.height=`${co+12}px`,b.root.style.width="100%",p.appendChild(b.root)),y&&(y.disabled=0===o.length)};l.onChanged.subscribe((async()=>{const e=l.value;e&&(await e.meta.detectSemanticTypes(),await o.data.detectSemanticTypes(e)),d(!0),v()})),c.onChanged.subscribe((()=>{if("rgroups"===e&&c.value){const e=function(e){const t=e.match(/r[\s_\-:]*(\d+)/i);return t?parseInt(t[1],10):null}(c.value);null!=e&&(u.value=e)}v()})),u&&u.onChanged.subscribe((()=>v())),h.onChanged.subscribe((()=>v()));const C=r.divV([l.root,c.root,...u?[u.root]:[],h.root,r.divH([m,f.root],{style:{alignItems:"center",gap:"8px"}}),p]),x=r.dialog({title:"cores"===e?"Import Cores":"Import R-Groups"}).add(C).onOK((()=>s(g))).onCancel((()=>s(null)));x.show({resizable:!0,width:640}),y=x.getButton("OK"),y.disabled=!0,l.value&&l.value.meta.detectSemanticTypes().then((()=>{d(!0),v()}))}))}function xo(){const e=r.div([],{style:{display:"none",alignItems:"center",gap:"4px",padding:"2px 8px",borderRadius:"10px",background:"var(--red-2)",color:"var(--red-3)",fontSize:"11px",fontWeight:"600",cursor:"help"}});return{root:e,setErrors(t){0!==t.length?(e.style.display="inline-flex",e.innerText=`⚠ ${t.length} issue${1===t.length?"":"s"}`,r.tooltip.bind(e,t.join("\n"))):e.style.display="none"}}}async function wo(e){await br.initPromise;try{const t=await(0,Vn.j)();let n=null;if(e){const r=await async function(e){try{if(!e||e.rowIndex<0||e.column?.semType!==i.SEMTYPE.MOLECULE)return null;const t=e.value;return t?i.chem.isMolBlock(t)?t:await o.functions.call("Chem:convertMolNotation",{molecule:t,sourceNotation:e.column.getTag(i.TAGS.UNITS)??i.chem.Notation.Unknown,targetNotation:i.chem.Notation.MolBlock})??null:null}catch{return null}}(e);if(r){const e=await o.functions.call("Chem:convertMolNotation",{molecule:r,sourceNotation:i.chem.Notation.MolBlock,targetNotation:i.chem.Notation.Smiles});if(e){const r=(0,io.KS)(e,"",t);r.error?o.shell.info("Selected molecule has no R-group — add at least one R-label to use it as a core."):n=r}}}const s=Ao(t,n),a=r.dialog({title:so}).add(s.root).onOK((async()=>{await s.execute()}));s.bindActionButton(a.getButton("OK")),a.show({resizable:!0,width:960})}catch(e){zn(e)}}function Ao(e,t){const n={cores:t?[t]:[],rGroupsByNum:new Map,mode:io.PI.Cartesian,appendToTable:null},s=co+16,a=r.divText("No cores — draw or import at least one.",{style:{color:"var(--grey-4)",padding:"20px 12px",fontSize:"12px"}}),l=r.div([],{style:{width:"100%",height:`${s}px`,overflow:"hidden"}});let c=null;const u=t=>{const o=n.cores[t];return go({smiles:o.error?"":o.smiles,subtitle:o.error?"invalid":`core ${t+1} · ${o.rNumbers.map((e=>"R"+e)).join(", ")}`,error:o.error,onEdit:async()=>{const r=await bo(e,o.smiles);r&&(n.cores[t]=r,T())},onDuplicate:async()=>{const t=await bo(e,o.smiles);t&&(n.cores.push(t),T())},onRemove:()=>{n.cores.splice(t,1),T()}})};function h(e){e.style.width="100%",e.style.height=`${s}px`,e.style.setProperty("overflow-y","hidden","important"),e.style.setProperty("overflow-x","auto","important");const t=e.firstElementChild;t&&(t.style.setProperty("overflow-y","hidden","important"),t.style.setProperty("overflow-x","auto","important"),t.style.height=`${s}px`)}const d=r.div([],{style:{width:"100%",padding:"2px 0",flex:"1 1 auto",minHeight:"0",overflowY:"auto",overflowX:"hidden"}}),p=r.divText("No R-groups — draw or import for each R number used by your cores.",{style:{color:"var(--grey-4)",padding:"12px",fontSize:"12px"}}),m=new Map,f=r.div([],{style:{width:"100%",display:"flex",flexWrap:"wrap",gap:"6px",alignContent:"flex-start",padding:"2px 0",maxHeight:"450px",overflow:"scroll"}}),g=r.divText("",{style:{fontSize:"12px",color:"var(--grey-6)"}}),y=xo(),b=r.input.choice("Enumerator type",{value:n.mode,items:Object.values(io.PI),onValueChanged:e=>{n.mode=e,v(),T()}}),v=()=>r.tooltip.bind(b.input,ao[n.mode]??"");v();const C=r.input.table("Append to table",{items:o.shell.tables,nullable:!0,onValueChanged:e=>{n.appendToTable=e}});let x,w,A=null;const T=()=>{(()=>{if(0===n.cores.length)return l.firstChild&&r.empty(l),c=null,a.parentElement!==l.parentElement&&l.parentElement?.insertBefore(a,l.nextSibling),l.style.display="none",void(a.style.display="block");l.style.display="block",a.style.display="none",c?c.setData(n.cores.length,u):(c=r.virtualView(n.cores.length,u,!1,1),h(c.root),l.appendChild(c.root))})(),(()=>{if(r.empty(d),m.clear(),0===n.rGroupsByNum.size)return void d.appendChild(p);const t=[...n.rGroupsByNum.keys()].sort(((e,t)=>e-t));for(const o of t){const t=n.rGroupsByNum.get(o),i=r.divText(`R${o} (${t.length})`,{style:{fontWeight:"600",fontSize:"12px",color:"var(--grey-6)",alignSelf:"center"}}),s=r.button("Remove all",(()=>{n.rGroupsByNum.delete(o),T()}));s.style.marginLeft="4px",r.tooltip.bind(s,`Remove all R${o} groups`);const a=r.divH([i,s],{style:{alignItems:"center",justifyContent:"flex-start",gap:"0",margin:"6px 0 2px"}}),l=r=>{const i=t[r],s=null!=i.sourceRNumber&&i.sourceRNumber!==i.rNumber?` (from R${i.sourceRNumber})`:"",a=i.error?"invalid":i.isSingleAtom?`r group ${r+1} · R${i.rNumber} · atom`:`r group ${r+1} · R${i.rNumber}${s}`;return go({smiles:i.error?"":i.smiles,subtitle:a,error:i.error,onEdit:async()=>{const o=await vo(e,i.smiles,i.rNumber);if(o){if(o.rNumber!==i.rNumber){t.splice(r,1),0===t.length&&n.rGroupsByNum.delete(i.rNumber);const e=n.rGroupsByNum.get(o.rNumber)??[];e.push(o),n.rGroupsByNum.set(o.rNumber,e)}else t[r]=o;T()}},onDuplicate:async()=>{const t=await vo(e,i.smiles,i.rNumber);if(!t)return;const o=n.rGroupsByNum.get(t.rNumber)??[];o.push(t),n.rGroupsByNum.set(t.rNumber,o),T()},onRemove:()=>{t.splice(r,1),0===t.length&&n.rGroupsByNum.delete(o),T()}})},c=r.virtualView(t.length,l,!1,1);h(c.root);const u=r.divV([a,c.root]);d.appendChild(u),m.set(o,{row:u,vv:c,header:a})}})();const t=(0,io.XB)({cores:n.cores,rGroups:n.rGroupsByNum,mode:n.mode});g.innerText=t.predictedCount>0?`${t.predictedCount.toLocaleString()} molecule${1===t.predictedCount?"":"s"} will be generated`:"",y.setErrors((()=>{const e=[];n.cores.forEach(((t,n)=>{t.error&&e.push(`Core ${n+1}: ${t.error}`)}));const t=[...n.rGroupsByNum.keys()].sort(((e,t)=>e-t));for(const o of t)n.rGroupsByNum.get(o).forEach(((t,n)=>{t.error&&e.push(`R${o} group ${n+1}: ${t.error}`)}));const o=(0,io.XB)({cores:n.cores,rGroups:n.rGroupsByNum,mode:n.mode});for(const t of o.errors)/^Core "/.test(t)||e.push(t);return e})()),A&&(A.disabled=!t.ok),x&&(x.disabled=0===n.cores.length),w&&(w.disabled=0===n.rGroupsByNum.size),(()=>{r.empty(f);const e=(0,io.xD)({cores:n.cores,rGroups:n.rGroupsByNum,mode:n.mode,maxResults:Math.min(io.u8,1e3)},12);0!==e.length?e.forEach(((e,t)=>{const n=[...e.rGroupSmilesByNum.keys()].sort(((e,t)=>e-t)).map((e=>"R"+e)).join(",");f.appendChild(go({smiles:e.smiles,subtitle:`sample ${t+1} · ${n}`}))})):f.appendChild(r.divText("Preview will appear once cores and R-groups are valid.",{style:{color:"var(--grey-4)",padding:"20px 12px",fontSize:"12px"}}))})()},E=(e,t,n,o)=>{const i=[r.divText(e,{style:{fontWeight:"600",fontSize:"12px",color:"var(--grey-6)",alignSelf:"center",minWidth:"60px"}})];if(t){const n=r.button("+ Draw",t);n.style.marginLeft="4px",r.tooltip.bind(n,`${e}: open sketcher`),i.push(n)}if(n){const t=r.button("↓ Import…",n);t.style.marginLeft="4px",r.tooltip.bind(t,`${e}: pick a table + column`),i.push(t)}let s;return o&&(s=r.button("Remove all",o),s.style.marginLeft="4px",r.tooltip.bind(s,`Remove all ${e.toLowerCase()}`),i.push(s)),{root:r.divH(i,{style:{alignItems:"center",justifyContent:"flex-start",gap:"0",margin:"0 0 2px",flex:"0 0 auto"}}),clearBtn:s}},S={display:"flex",flexDirection:"column",minHeight:"150px",padding:"4px 0"},N=E("Cores",(async()=>{const t=await bo(e);t&&(n.cores.push(t),T())}),(async()=>{const t=await Co("cores",e,n.mode===io.PI.Cartesian);t?.cores&&(n.cores.push(...t.cores),T())}),(()=>{n.cores.splice(0,n.cores.length),T()}));x=N.clearBtn;const I=r.divV([N.root,r.div([l,a],{style:{padding:"0"}})],{style:S}),M=E("R-Groups",(async()=>{const t=await vo(e);if(!t)return;const o=n.rGroupsByNum.get(t.rNumber)??[];o.push(t),n.rGroupsByNum.set(t.rNumber,o),T()}),(async()=>{const t=await Co("rgroups",e,n.mode===io.PI.Cartesian);if(t?.rGroups){for(const e of t.rGroups){const t=n.rGroupsByNum.get(e.rNumber)??[];t.push(e),n.rGroupsByNum.set(e.rNumber,t)}T()}}),(()=>{n.rGroupsByNum.clear(),T()}));w=M.clearBtn;const P=r.divV([M.root,d],{style:{display:"flex",flexDirection:"column",maxHeight:"300px",padding:"4px 0"}}),_=r.divV([E("Preview").root,f],{style:{...S,width:"100%",height:"100%",overflowY:"auto",overflowX:"hidden"}}),L=r.divV([I,P],{style:{flex:"0 0 60%",width:"60%",display:"flex",flexDirection:"column",gap:"4px",paddingRight:"8px",borderRight:"1px solid var(--grey-2)"}}),O=r.divV([_],{style:{flex:"0 0 40%",width:"40%",display:"flex",flexDirection:"column",paddingLeft:"8px"}}),R=r.divH([L,O],{style:{width:"100%",alignItems:"stretch",gap:"0"}}),$=r.divH([b.root,g,y.root],{style:{alignItems:"center",gap:"16px",padding:"4px 0"}}),D=r.div([C.root],{style:{padding:"2px 0"}}),B=r.divV([R,$,D],{style:{width:"100%",padding:"4px",display:"flex",flexDirection:"column",gap:"4px"}});return T(),{root:B,state:n,execute:()=>async function(e){const t=i.TaskBarProgressIndicator.create("Enumerating...");try{t.update(10,"Building molecules...");const n=(0,io.jp)({cores:e.cores,rGroups:e.rGroupsByNum,mode:e.mode});if(!n)return void o.shell.warning("Enumeration failed — check validation messages in the dialog.");if(0===n.length)return void o.shell.warning("No molecules produced.");const r=new Set;for(const e of n)for(const t of e.rGroupSmilesByNum.keys())r.add(t);const s=[...r].sort(((e,t)=>e-t)),a=i.Column.fromStrings("Enumerated",n.map((e=>e.smiles)));a.semType=i.SEMTYPE.MOLECULE;const l=i.Column.fromStrings("Core",n.map((e=>e.coreSmiles)));l.semType=i.SEMTYPE.MOLECULE;const c=s.map((e=>i.Column.fromStrings(`R${e}`,n.map((t=>t.rGroupSmilesByNum.get(e)??"")))));for(const e of c)e.semType=i.SEMTYPE.MOLECULE;const u=i.DataFrame.fromColumns([a,l,...c]);u.name="Chem Enumeration",t.update(40,`Canonicalizing ${n.length.toLocaleString()} molecule(s)...`);try{await o.functions.call("Chem:convertNotation",{data:u,molecules:a,targetNotation:i.chem.Notation.Smiles,overwrite:!0,join:!1,kekulize:!1})}catch(e){br.logger.warning(`Canonicalization skipped: ${e?.message??e}`)}t.update(90,"Finalizing..."),await o.data.detectSemanticTypes(u),e.appendToTable?(e.appendToTable.append(u,!0),await e.appendToTable.meta.detectSemanticTypes()):o.shell.addTableView(u)}catch(e){zn(e)}finally{t.close()}}(n),bindActionButton:e=>{A=e,T()}}}var To=n(6197);class Eo extends i.InputBase{constructor(e,t){super(r.input.column(e,t).dart,t?.onValueChanged),this.options=t}setColumnInputTable(e){r.input.setColumnInputTable(this,e,this.options?.filter)}}r.input.column2=function(e,t){return new Eo(e,t)};var So=n(1296),No=n(3820);class Io extends i.JsInputBase{get inputType(){return"Positions"}get dataType(){return i.TYPE.DATA_FRAME}getInput(){return this.gridHost}getValue(){return this.grid.dataFrame}setValue(e){this.setDataFrame(e)}getStringValue(){return this.grid.dataFrame.toCsv()}setStringValue(e){this.setDataFrame(i.DataFrame.fromCsv(e))}clearInput(){const e=i.DataFrame.fromColumns([i.Column.fromType(i.COLUMN_TYPE.STRING,"Remove",0),i.Column.fromType(i.COLUMN_TYPE.INT,"Position",0),i.Column.fromType(i.COLUMN_TYPE.STRING,"Monomers",0)]);this.setDataFrame(e)}get placeholdersValue(){return function(e){const t=[];for(let n=0;n<e.rowCount;n++){if(e.getCol("Position").isNone(n))continue;const o=parseInt(e.get("Position",n))-1;if(!isNaN(o)){const r=Mo(e.get("Monomers",n));t.push({position:o,monomers:r})}}return t}(this.grid.dataFrame)}invalidateGrid(){if(this.grid){const e=this.grid.root.style.width;this.grid.root.style.width="99.9%",setTimeout((()=>{e?this.grid.root.style.width=e:this.grid.root.style.removeProperty("width")}),100)}}constructor(e,t,n){super(),this.name=e,this.onMonomerCellEdit=null,this.subs=[],this.dataFrameSubs=[],this.caption=e??"",this.root.classList.add("ui-input-polytool-pos-grid"),this.root.append(this.gridHost=r.div([],{classes:"ui-input-editor",style:{width:"100%",height:"100%",marginTop:"-8px",marginBottom:"8px",paddingBottom:"4px"}})),this.render(t,n).then((()=>{}))}detach(){for(const e of this.subs)e.unsubscribe();for(const e of this.dataFrameSubs)e.unsubscribe()}async render(e,t){let n;const o=i.DataFrame.fromColumns([n=i.Column.fromType(i.COLUMN_TYPE.STRING,"Remove",0),i.Column.fromType(i.COLUMN_TYPE.INT,"Position",0),i.Column.fromType(i.COLUMN_TYPE.STRING,"Monomers",0)]);n.setTag(i.TAGS.FRIENDLY_NAME,""),this.grid=await o.plot.fromType(i.VIEWER.GRID,t),this.grid.sort(["Position"]),this.grid.columns.byIndex(1).width=this.grid.props.rowHeight+2,this.grid.onCellRender.subscribe((e=>{const t=e.cell;t.tableColumn?.name==n.name&&(t?.tableRowIndex??-1)>=0&&(t.element=r.div(r.icons.delete((()=>{this.grid.dataFrame.rows.removeAt(t.tableRowIndex)}),"Delete"),{style:{height:`${t.grid.props.rowHeight}px`,color:"var(--grey-6)",display:"flex",flexDirection:"row",justifyContent:"center"}}))}));const s=this.grid.columns.byName("Monomers");s&&(s.editable=!1),this.subs.push(this.grid.onCellDoubleClick.subscribe((e=>{"Monomers"===e.tableColumn?.name&&null!=e.tableRowIndex&&e.tableRowIndex>=0&&this.handleMonomerCellDoubleClick(e.tableRowIndex)}))),this.updateGridHeight(e??this.grid.dataFrame.rowCount+.7),this.subs.push(r.onSizeChanged(this.grid.root).subscribe(this.gridRootOnSizeChanged.bind(this))),this.subs.push((0,te.fromEvent)(this.grid.root,"keydown").subscribe((e=>{"Enter"===e.key&&e.stopPropagation()}))),this.setDataFrame(o),this.grid.root.style.width="100%",this.gridHost.append(this.grid.root)}setDataFrame(e){for(const e of this.dataFrameSubs)e.unsubscribe();this.grid.dataFrame=e,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(e,t){const n=this.grid.dataFrame,o=n.columns.byName("Position").toList();let r=o.indexOf(e+1);-1===r&&(r=o.findIndex((e=>isNaN(e))),-1===r&&(r=n.rows.addNew(["",e+1,t??""]).idx),this.grid.cell("Monomers",r)),n.currentCell=n.cell(r,"Monomers")}setMonomersValue(e,t){const n=this.grid.dataFrame;n.rowCount<=e||n.set("Monomers",e,t)}static async create(e,t,n){return new Io(e,n,t)}updateGridHeight(e){const t=this.grid.colHeaderHeight+e*this.grid.props.rowHeight+6+2;this.grid.root.style.height=`${t}px`}async handleMonomerCellDoubleClick(e){if(!this.onMonomerCellEdit)return;const t=this.grid.dataFrame,n=parseInt(t.get("Position",e))-1;if(isNaN(n))return;const o=Mo(t.get("Monomers",e)??""),r=await this.onMonomerCellEdit(n,o);null!==r&&t.set("Monomers",e,r.join(", "))}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 Mo(e){return e.split(/,(?![^(]*\))/).map((e=>('"'===(e=e.trim()).slice(0,1)&&'"'===e.slice(-1)&&(e=e.slice(1,-1)),"'"===e.slice(0,1)&&"'"===e.slice(-1)&&(e=e.slice(1,-1)),e.trim()))).filter((e=>!!e))}class Po{constructor(e,t,n,o){this.currentMenu=null,this.menuItems=[],this.highlightedIndex=-1,this.monomerLib=e,this.polymerType=t,this.helmType=(0,a.MD)(t),this.allSymbols=e.getMonomerSymbolsByType(t),this.libHelper=o,this.selectedMonomers=n?[...n]:[],this.tagsHost=r.div([],{style:{display:"flex",flexWrap:"wrap",gap:"4px",marginTop:"4px",maxHeight:"150px",overflowY:"auto"}}),this.countLabel=r.divText("",{style:{fontSize:"11px",color:"var(--grey-4)",marginTop:"4px"}});const i=r.input.string("Search",{value:""});this.inputEl=i.input,this.inputEl.setAttribute("autocomplete","off"),this.inputEl.placeholder="Type to search monomers...",this.setupInputListeners();const s=this.createLibrarySection(),l=this.createCollectionSection(),c=r.button("Clear all",(()=>{this.selectedMonomers.length=0,this.renderTags()}));c.style.fontSize="11px",c.style.marginTop="4px",this.renderTags(),this.root=r.div([i.root,s,l,r.divH([this.countLabel,c],{style:{justifyContent:"space-between",alignItems:"center"}}),this.tagsHost],{style:{minWidth:"300px"}})}getSelectedMonomers(){return[...this.selectedMonomers]}setSelectedMonomers(e){this.selectedMonomers.length=0,this.selectedMonomers.push(...e),this.renderTags()}setPolymerType(e){this.polymerType=e,this.helmType=(0,a.MD)(e),this.allSymbols=this.monomerLib.getMonomerSymbolsByType(e)}focus(){this.inputEl.focus()}updateCountLabel(){this.countLabel.textContent=this.selectedMonomers.length>0?`${this.selectedMonomers.length} monomer(s) selected`:""}renderTags(){this.tagsHost.innerHTML="";for(const e of this.selectedMonomers){const t=r.iconFA("times",(()=>{const t=this.selectedMonomers.indexOf(e);t>=0&&(this.selectedMonomers.splice(t,1),this.renderTags(),this.updateCountLabel())}),"Remove");t.style.marginLeft="4px",t.style.cursor="pointer";const n=r.div([r.span([e]),t],{style:{display:"inline-flex",alignItems:"center",padding:"2px 6px",borderRadius:"4px",backgroundColor:"var(--grey-2)",border:"1px solid var(--grey-3)",fontSize:"12px",cursor:"default"}});n.addEventListener("mouseenter",(()=>{const t=this.monomerLib.getTooltip(this.helmType,e);r.tooltip.show(t,n.getBoundingClientRect().left,n.getBoundingClientRect().bottom+16)})),n.addEventListener("mouseleave",(()=>{r.tooltip.hide()})),this.tagsHost.appendChild(n)}this.updateCountLabel()}addMonomer(e){this.selectedMonomers.includes(e)||(this.selectedMonomers.push(e),this.renderTags()),this.inputEl.value="",this.hideMenu(),this.inputEl.focus()}addMonomers(e){let t=!1;for(const n of e)this.selectedMonomers.includes(n)||(this.selectedMonomers.push(n),t=!0);t&&this.renderTags()}hideMenu(){this.currentMenu&&(this.currentMenu.hide(),this.currentMenu=null),this.menuItems=[],this.highlightedIndex=-1}getSuggestions(e){const t=e.toLowerCase(),n=[];for(const e of this.allSymbols){if(this.selectedMonomers.includes(e))continue;const o=this.monomerLib.getMonomer(this.polymerType,e),r=e.toLowerCase(),i=o?.name?.toLowerCase()??"";r.startsWith(t)?n.push({symbol:e,monomer:o,rank:0}):r.includes(t)?n.push({symbol:e,monomer:o,rank:1}):i.includes(t)&&n.push({symbol:e,monomer:o,rank:2})}return n.sort(((e,t)=>e.rank-t.rank||e.symbol.localeCompare(t.symbol))),n.slice(0,20)}showSuggestions(){this.hideMenu();const e=this.inputEl.value.trim();if(!e)return;const t=this.getSuggestions(e);if(0===t.length)return;this.currentMenu=i.Menu.popup();const n=t.reduce(((e,t)=>{const n=t.monomer?.name?`${t.symbol} - ${t.monomer.name}`:t.symbol;return e.length<n.length?n:e}),"");this.currentMenu.item(n,(()=>{}));const o=new MouseEvent("mousemove",{clientX:this.inputEl.getBoundingClientRect().left,clientY:this.inputEl.getBoundingClientRect().bottom});this.currentMenu.show({causedBy:o,y:this.inputEl.offsetHeight+this.inputEl.offsetTop,x:this.inputEl.offsetLeft}),setTimeout((()=>{this.currentMenu?.clear();for(const e of t){const t=e.monomer?.name?`${e.symbol} - ${e.monomer.name}`:e.symbol;this.currentMenu?.item(t,(()=>{this.addMonomer(e.symbol)}))}const e=document.querySelector(".d4-menu-popup:last-of-type");e&&(this.menuItems=Array.from(e.querySelectorAll(".d4-menu-item"))),this.highlightedIndex=-1}),0)}updateHighlight(e){0!==this.menuItems.length&&(this.highlightedIndex>=0&&this.highlightedIndex<this.menuItems.length&&this.menuItems[this.highlightedIndex].classList.remove("d4-menu-item-hover"),this.highlightedIndex=e,this.highlightedIndex>=0&&this.highlightedIndex<this.menuItems.length&&(this.menuItems[this.highlightedIndex].classList.add("d4-menu-item-hover"),this.menuItems[this.highlightedIndex].scrollIntoView({block:"nearest"})))}setupInputListeners(){this.inputEl.addEventListener("input",(()=>{this.showSuggestions()})),this.inputEl.addEventListener("paste",(e=>{const t=e.clipboardData?.getData("text");if(!t)return;const n=t.split(/[\n\r]+/).map((e=>e.trim())).filter((e=>e.length>0)),o=[];for(const e of n){const t=e.split(/,(?![^(]*\))/).map((e=>('"'===(e=e.trim()).slice(0,1)&&'"'===e.slice(-1)&&(e=e.slice(1,-1)),"'"===e.slice(0,1)&&"'"===e.slice(-1)&&(e=e.slice(1,-1)),e.trim()))).filter((e=>!!e));1===t.length&&e.includes(" ")&&!e.includes(",")?o.push(...e.split(/\s+/).map((e=>e.trim())).filter((e=>e.length>0))):o.push(...t)}if(!(o.length<=1)){e.preventDefault();for(const e of o)this.selectedMonomers.includes(e)||this.selectedMonomers.push(e);this.renderTags(),this.inputEl.value="",this.hideMenu(),this.inputEl.focus()}})),this.inputEl.addEventListener("keydown",(e=>{if("ArrowDown"===e.key){if(e.preventDefault(),this.menuItems.length>0){const e=(this.highlightedIndex+1)%this.menuItems.length;this.updateHighlight(e)}}else if("ArrowUp"===e.key){if(e.preventDefault(),this.menuItems.length>0){const e=(this.highlightedIndex-1+this.menuItems.length)%this.menuItems.length;this.updateHighlight(e)}}else if("Enter"===e.key)if(e.preventDefault(),e.stopPropagation(),this.highlightedIndex>=0&&this.highlightedIndex<this.menuItems.length)this.menuItems[this.highlightedIndex].click();else{const e=this.inputEl.value.trim();e&&this.addMonomer(e)}else"Escape"===e.key&&this.hideMenu()}))}createLibrarySection(){const e=r.div([],{style:{marginTop:"8px"}});if(!this.libHelper)return e;const t=this.libHelper,n=r.input.choice("Add from library",{items:[],nullable:!0}),o=r.divText("",{style:{fontSize:"11px",color:"var(--green-2)",marginLeft:"8px",minHeight:"16px"}});return t.getAvaliableLibraryNames().then((e=>{n.items=e})),n.onChanged.subscribe((async()=>{const e=n.value;if(e){o.textContent="Loading...";try{const n=await t.readSingleLibraryByName(e);if(n){const t=n.getMonomerSymbolsByType(this.polymerType),r=this.selectedMonomers.length;this.addMonomers(t);const i=this.selectedMonomers.length-r;o.textContent=`Added ${i} monomer(s) from "${e}"`}else o.textContent=`Library "${e}" not found`}catch(e){o.textContent="Error loading library"}n.value=null,setTimeout((()=>{o.textContent=""}),4e3)}})),e.appendChild(r.divV([n.root,o])),e}createCollectionSection(){const e=r.div([],{style:{marginTop:"4px"}});if(!this.libHelper)return e;const t=this.libHelper,n=r.input.choice("Add from collection",{items:[],nullable:!0}),o=r.divText("",{style:{fontSize:"11px",color:"var(--green-2)",marginLeft:"8px",minHeight:"16px"}});return t.listMonomerCollections().then((e=>{n.items=e})),n.onChanged.subscribe((async()=>{const e=n.value;if(e){o.textContent="Loading...";try{const n=(await t.readMonomerCollection(e)).monomerSymbols??[],r=this.selectedMonomers.length;this.addMonomers(n);const i=this.selectedMonomers.length-r,s=e.replace(/\.json$/,"");o.textContent=`Added ${i} monomer(s) from "${s}"`}catch(e){o.textContent="Error loading collection"}n.value=null,setTimeout((()=>{o.textContent=""}),4e3)}})),e.appendChild(r.divV([n.root,o])),e}}async function _o(e,t,n,o){return new Promise((i=>{const s=new Po(e,t,n,o);r.dialog({title:"Select Monomers",showFooter:!0}).add(r.div([s.root],{style:{minWidth:"400px",minHeight:"250px",maxWidth:"800px"}})).onOK((()=>{i(s.getSelectedMonomers())})).onCancel((()=>{i(null)})).show({resizable:!0}),s.focus()}))}class Lo extends i.JsInputBase{get inputType(){return"Breadth"}get dataType(){return i.TYPE.DATA_FRAME}getInput(){return this.gridHost}getValue(){return this.grid.dataFrame}setValue(e){this.setDataFrame(e)}invalidateGrid(){if(this.grid){const e=this.grid.root.style.width;this.grid.root.style.width="99.9%",setTimeout((()=>{e?this.grid.root.style.width=e:this.grid.root.style.removeProperty("width")}),100)}}getStringValue(){return this.grid.dataFrame.toCsv()}setStringValue(e){this.setDataFrame(i.DataFrame.fromCsv(e))}get placeholdersBreadthValue(){return function(e){const t=[];for(let n=0;n<e.rowCount;n++){const o=parseInt(e.get("Start",n))-1,r=parseInt(e.get("End",n))-1;if(!isNaN(o)&&!isNaN(r)){const i=Mo(e.get("Monomers",n));t.push({start:o,end:r,monomers:i})}}return t}(this.grid.dataFrame)}constructor(e,t,n){super(),this.name=e,this.onMonomerCellEdit=null,this.subs=[],this.dataFrameSubs=[],this.caption=e??"",this.root.classList.add("ui-input-polytool-pos-grid"),this.root.append(this.gridHost=r.div([],{classes:"ui-input-editor",style:{width:"100%",height:"100%",marginTop:"-8px",marginBottom:"8px",paddingBottom:"4px"}})),this.render(t,n).then((()=>{}))}detach(){for(const e of this.subs)e.unsubscribe();for(const e of this.dataFrameSubs)e.unsubscribe()}clearInput(){const e=i.DataFrame.fromColumns([i.Column.fromType(i.COLUMN_TYPE.STRING,"Remove",0),i.Column.fromType(i.COLUMN_TYPE.INT,"Start",0),i.Column.fromType(i.COLUMN_TYPE.INT,"End",0),i.Column.fromType(i.COLUMN_TYPE.STRING,"Monomers",0)]);this.setDataFrame(e)}async render(e,t){let n;const o=i.DataFrame.fromColumns([n=i.Column.fromType(i.COLUMN_TYPE.STRING,"Remove",0),i.Column.fromType(i.COLUMN_TYPE.INT,"Start",0),i.Column.fromType(i.COLUMN_TYPE.INT,"End",0),i.Column.fromType(i.COLUMN_TYPE.STRING,"Monomers",0)]);n.setTag(i.TAGS.FRIENDLY_NAME,""),this.grid=await o.plot.fromType(i.VIEWER.GRID,t),this.grid.sort(["Start","End"]),this.grid.columns.byIndex(1).width=this.grid.props.rowHeight+2,this.grid.onCellRender.subscribe((e=>{const t=e.cell;t.tableColumn?.name==n.name&&(t?.tableRowIndex??-1)>=0&&(t.element=r.div(r.icons.delete((()=>{this.grid.dataFrame.rows.removeAt(t.tableRowIndex)}),"Delete"),{style:{height:`${t.grid.props.rowHeight}px`,color:"var(--grey-6)",display:"flex",flexDirection:"row",justifyContent:"center"}}))}));const s=this.grid.columns.byName("Monomers");s&&(s.editable=!1),this.subs.push(this.grid.onCellDoubleClick.subscribe((e=>{"Monomers"===e.tableColumn?.name&&null!=e.tableRowIndex&&e.tableRowIndex>=0&&this.handleMonomerCellDoubleClick(e.tableRowIndex)}))),this.updateGridHeight(e??this.grid.dataFrame.rowCount+.7),this.subs.push(r.onSizeChanged(this.grid.root).subscribe(this.gridRootOnSizeChanged.bind(this))),this.subs.push((0,te.fromEvent)(this.grid.root,"keydown").subscribe((e=>{"Enter"===e.key&&e.stopPropagation()}))),this.setDataFrame(o),this.grid.root.style.width="100%",this.gridHost.append(this.grid.root)}setDataFrame(e){for(const e of this.dataFrameSubs)e.unsubscribe();this.grid.dataFrame=e,this.dataFrameSubs.push(this.grid.dataFrame.onRowsRemoved.subscribe((()=>{this.updateGridHeight(this.grid.dataFrame.rowCount+.7),this.fireChanged()}))),this.dataFrameSubs.push(this.grid.dataFrame.onRowsAdded.subscribe((()=>{this.updateGridHeight(this.grid.dataFrame.rowCount+.7)}))),this.dataFrameSubs.push(this.grid.dataFrame.onDataChanged.subscribe((()=>{this.fireChanged()}))),this.updateGridHeight(this.grid.dataFrame.rowCount+.7),this.fireChanged()}static async create(e,t,n){return new Lo(e,n,t)}updateGridHeight(e){const t=this.grid.colHeaderHeight+e*this.grid.props.rowHeight+6+2;this.grid.root.style.height=`${t}px`}async handleMonomerCellDoubleClick(e){if(!this.onMonomerCellEdit)return;const t=this.grid.dataFrame,n=parseInt(t.get("Start",e))-1,o=parseInt(t.get("End",e))-1;if(isNaN(n)||isNaN(o))return;const r=Mo(t.get("Monomers",e)??""),i=await this.onMonomerCellEdit(n,o,r);null!==i&&t.set("Monomers",e,i.join(", 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0.13277988512492753],""points"":[{""x"":0.10000000149011612,""y"":3.0498509407043457},{""x"":0.6000000238418579,""y"":2.805217742919922},{""x"":1.100000023841858,""y"":3.3415253162384033},{""x"":1.600000023841858,""y"":3.0549843311309814},{""x"":2.0999999046325684,""y"":3.250074863433838},{""x"":2.5999999046325684,""y"":3.0432586669921875},{""x"":3.0999999046325684,""y"":3.265852451324463},{""x"":3.5999999046325684,""y"":2.9475724697113037},{""x"":4.099999904632568,""y"":3.1929898262023926},{""x"":4.599999904632568,""y"":2.7460060119628906},{""x"":5.099999904632568,""y"":1.6175861358642578},{""x"":5.599999904632568,""y"":0.3006608486175537},{""x"":6.099999904632568,""y"":0.3444803059101105},{""x"":6.599999904632568,""y"":0.015537971630692482},{""x"":7.099999904632568,""y"":0.5527358055114746}]}],""chartOptions"":{""xAxisName"":""Conc."",""yAxisName"":""Activity"",""title"":""Dose-Response curves""}}",text,,\n,,,,,,,,,,,,,,,,,,,,,').columns.add(DG.Column.fromList(DG.TYPE.BYTE_ARRAY,"BinaryImage",Array.from(new Uint8Array(11))));var $o;console.log.bind(console),console.info.bind(console),console.warn.bind(console),console.error.bind(console),function(e){e.notNull=function(e,t){if(null==e)throw new Error(`${null==t?"Value":t} not defined`)}}($o||($o={})),DG.DataFrame.fromColumns([DG.Column.fromStrings("col",["val1","val2","val3"])]);class Do{onKeyDown(e,t){}onKeyPress(e,t){}onMouseEnter(e,t){}onMouseLeave(e,t){}onMouseDown(e,t){}onMouseUp(e,t){}onMouseMove(e,t){}onClick(e,t){}onDoubleClick(e,t){}}class Bo extends Do{constructor(e,t,n){super(),this.gridCol=e,this.tableCol=t,this.logger=n,this.subs=[],this.dirty=!0,this.destroyed=!1,this.viewerId=++Bo.viewerCounter,this.errors=[],this._onRendered=new te.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((e=>{try{this.destroyed||!this.tableCol||this.tableCol.dataFrame||this.destroy()}catch(e){this.logger.error(e)}})))),this.tableCol&&this.subs.push(o.events.onTableRemoved.subscribe((e=>{try{const t=e.args.dataFrame;this.tableCol?.dataFrame.id!==t.id||this.destroyed||this.destroy()}catch(e){this.logger.error(e)}}))),this.gridCol&&this.subs.push(o.events.onViewRemoving.subscribe((e=>{try{const t=e.args.view;this.gridCol?.dart&&this.gridCol.grid&&this.gridCol?.grid?.dart&&this.gridCol?.grid?.view?.id===t.id&&!this.destroyed&&this.destroy()}catch(e){this.logger.error(e)}})))}toLog(){return`${this.constructor.name}<${this.viewerId}>`}destroy(){for(const e of this.subs)e.unsubscribe();this.destroyed=!0}invalidateGrid(){this.gridCol&&this.gridCol.dart&&this.gridCol.grid?.invalidate()}reset(){this.dirty=!1}get onRendered(){return this._onRendered}invalidate(e){this.invalidateGrid()}async awaitRendered(e=1e4,t=`${e} timeout`){const n=`${this.toLog()}.awaitRendered()`;if(this.logger.debug(`${n}, start, testEvent before`),await function(e,t,n,o=0,r="timeout"){return function(e,t,n,o){return new(n||(n=Promise))((function(r,i){function s(e){try{l(o.next(e))}catch(e){i(e)}}function a(e){try{l(o.throw(e))}catch(e){i(e)}}function l(e){var t;e.done?r(e.value):(t=e.value,t instanceof n?t:new n((function(e){e(t)}))).then(s,a)}l((o=o.apply(e,t||[])).next())}))}(this,void 0,void 0,(function*(){return new Promise(((i,s)=>{const a=e.subscribe((e=>{try{t(e),i("OK")}catch(e){s(e)}finally{a.unsubscribe(),clearTimeout(l)}})),l=setTimeout((()=>{a.unsubscribe(),s(r)}),o);n()}))}))}(this._onRendered,(()=>{}),(()=>{this.invalidate()}),e,`${n}, ${t}`),this.errors.length>0){const e=this.errors[0];throw this.errors=[],e}this.logger.debug(`${n}, end`)}}Bo.viewerCounter=-1;const Fo="rgb(100,100,100)",ko="rgb(0,0,0)",Ho=a.zS;var Go,Uo,Vo;!function(e){e.maxMonomerLength=".mm.cellRenderer.maxMonomerLength"}(Go||(Go={})),function(e){e.applyToBackground=".m.cellRenderer.applyToBackground"}(Uo||(Uo={})),function(e){e.MSA="MSA",e.classic="classic"}(Vo||(Vo={}));const jo=new class{constructor(){this.color=Fo,this.pivot=0,this.left=!1,this.transparencyRate=0,this.separator="",this.last=!1,this.drawStyle=Vo.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 qo(e,t,n,o,r,s,a){var l,c,u;const h={...jo,...a};if(h.isMultiLineContext){e.textBaseline="middle",e.textAlign="center";let i=t;null!=h.maxLengthOfMonomer&&(i=Ho(i,h.maxLengthOfMonomer));const a=Math.max(.1,1-(h.transparencyRate??0));e.globalAlpha=a;const l=e.measureText(i),c=l.fontBoundingBoxAscent+l.fontBoundingBoxDescent,u=o+(s-c)/2+l.fontBoundingBoxAscent;let d=h.color??Fo;return d&&d!==Fo||(d=ko),e.fillStyle=d,h.selectedPosition===h.wordIdx+1&&(e.save(),e.fillStyle="rgba(60, 177, 115, 0.2)",e.fillRect(n,o,r,s),e.restore(),e.fillStyle=d),e.fillText(i,n+r/2,u),e.globalAlpha=1,e.textBaseline="top",e.textAlign="start",n+r}a.logger?.debug("Bio: printLeftOrCentered(), start"),e.textAlign="start";let d=t.substring(0),p=h.last?"":h.separator;h.drawStyle===Vo.MSA&&(p="");let m=!0,f=!0,g="difference";if(null!=h.gridCell&&null!=h.gridCell.cell.column&&(m=h.gridCell.cell.column.temp["color-code"]??!0,f=h.gridCell.cell.column.temp["compare-with-current"]??!0,g=h.gridCell.cell.column.temp["highlight-difference"]??"difference"),h.referenceSequence){const e=h.referenceSequence[h.wordIdx];f&&h.referenceSequence.length>0&&"difference"===g&&(h.transparencyRate=d==e?.7:h.transparencyRate),f&&h.referenceSequence.length>0&&"equal"===g&&(h.transparencyRate=d!=e?.7:h.transparencyRate)}null!=h.maxLengthOfMonomer&&(d=Ho(d,h.maxLengthOfMonomer));const y=d+p;(l=h.monomerTextSizeMap)[y]??(l[y]=e.measureText(y));let b=h.monomerTextSizeMap[y];(c=h.monomerTextSizeMap)[d]??(c[d]=e.measureText(d));let v=h.monomerTextSizeMap[d].width;const C=s/2-(b.fontBoundingBoxAscent+b.fontBoundingBoxDescent)/2+1;(u=h.monomerTextSizeMap)[p]??(u[p]=e.measureText(p));const x=h.monomerTextSizeMap[p].width;function w(t,r){let a=m?h.color:ko;h.selectedPosition===h.wordIdx+1&&(e.fillStyle="rgba(60, 177, 115, 0.2)",e.fillRect(n+t-4,o-5,h.monomerTextSizeMap[d].width+8,s+10),a=i.Color.toHtml(i.Color.setAlpha(i.Color.fromHtml(a),255))),e.fillStyle=a,e.globalAlpha=1-h.transparencyRate,h.drawStyle===Vo.classic&&(e.fillText(d,n+t,o+C),e.fillStyle="#808080",e.fillText(p,n+r,o+C)),h.drawStyle===Vo.MSA&&e.fillText(d,n+t,o+C),e.globalAlpha=1}b=b.width,h.drawStyle===Vo.MSA&&(v=h.maxWord[h.wordIdx],b=h.maxWord[h.wordIdx]);const A=(h.maxWord[h.wordIdx]??0)-(h.maxWord[0]??0);if(h.left||b>r)return w(A,A+v),n+A+v+x;{const e=(r-b)/2;return w(e,e+v),n+A+e+v}}var Wo,zo,Yo;!function(e){e.Region="region",e.Point="point",e.Motif="motif"}(Wo||(Wo={})),function(e){e.Structure="structure",e.Liability="liability",e.PTM="ptm",e.Custom="custom"}(zo||(zo={})),function(e){e.High="high",e.Medium="medium",e.Low="low",e.Info="info"}(Yo||(Yo={}));const Ko={structure:{FR:["#0095ff","#289dfd","#48adff","#3ba5fc"],CDR:["#ffdca3","#facb83","#f7a224"]},liability:{deamidation:"#E53935",isomerization:"#FF9800",oxidation:"#9C27B0",glycosylation:"#4CAF50",freeCysteine:"#607D8B"}};class Qo{constructor(e){this.tableCol=e,this._cache=null,this._rowCache=null,this._annotCol=null,this._annotColLookupVersion=-1}hasAnnotations(){return this._ensureCache(),null!==this._cache&&this._cache.annotations.length>0}getAnnotations(){return this._ensureCache(),this._cache?.annotations??[]}getRegionNameAtPosition(e,t){if(null!=t){const n=this._findRowRegionHit(t,e);if(n){const e=this._cache?.annotations.find((e=>e.id===n.annotationId));return e?.name??null}if(this._rowHasRegionData(t))return null}return this._ensureCache(),this._cache?.positionRegionNames.get(e)??null}getHitsAtPosition(e,t){if(this._ensureRowCache(),!this._rowCache)return[];const n=this._rowCache.data[e];return n?n.filter((e=>null==e.endPositionIndex&&(e.positionIndex===t||e.matchedMonomers.length>1&&t>e.positionIndex&&t<e.positionIndex+e.matchedMonomers.length))):[]}drawPositionBackground(e,t,n,o,r,i,s,a){if(this._ensureCache(),!this._cache)return;let l;this._ensureRowCache();const c=this._findRowRegionHit(s,i);if(c){const e=this._cache.annotations.find((e=>e.id===c.annotationId));l=e?.color??(e?this._getDefaultRegionColor(e):void 0)}if(l||this._rowHasRegionData(s)||(l=this._cache.positionRegionColors.get(i)),l&&(e.save(),e.globalAlpha=.25,e.fillStyle=l,e.fillRect(t,n,o,r),e.restore()),this._rowCache){const l=this._rowCache.data[s];if(l)for(const s of l)if(null==s.endPositionIndex&&i>=s.positionIndex&&i<s.positionIndex+s.matchedMonomers.length){const i=this._cache.annotations.find((e=>e.id===s.annotationId));if(i?.color){const s=null!=a?a+1:n+r-3;e.fillStyle=i.color,e.fillRect(t,s,o,3)}break}}}getTooltipInfo(e,t){this._ensureCache();const n=[];if(!this._cache)return n;this._ensureRowCache();let o=null;const r=this._findRowRegionHit(t,e);if(r){const e=this._cache.annotations.find((e=>e.id===r.annotationId));if(e){o=e.name;const t=e.sourceScheme??"";n.push(`Region: ${e.name}${t?` (${t} ${e.start}-${e.end})`:""}`)}}if(!o&&!this._rowHasRegionData(t)){const t=this._cache.positionRegionNames.get(e);if(t){const e=this._cache.annotations.find((e=>e.name===t&&e.category===zo.Structure)),o=e?.sourceScheme??"";n.push(`Region: ${t}${o?` (${o} ${e?.start}-${e?.end})`:""}`)}}if(this._rowCache){const o=this._rowCache.data[t];if(o)for(const t of o)if(null==t.endPositionIndex&&e>=t.positionIndex&&e<t.positionIndex+t.matchedMonomers.length){const e=this._cache.annotations.find((e=>e.id===t.annotationId));if(e){const t=e.severity?` - ${e.severity.charAt(0).toUpperCase()+e.severity.slice(1)}`:"";n.push(`⚠ ${e.name}${t}`)}}}return n}_findRowRegionHit(e,t){if(this._ensureRowCache(),!this._rowCache)return null;const n=this._rowCache.data[e];if(!n)return null;for(const e of n)if(null!=e.endPositionIndex&&t>=e.positionIndex&&t<=e.endPositionIndex)return e;return null}_rowHasRegionData(e){if(this._ensureRowCache(),!this._rowCache)return!1;const t=this._rowCache.data[e];return!!t&&t.some((e=>null!=e.endPositionIndex))}_ensureCache(){const e=this.tableCol.version;if(this._cache&&this._cache.colVersion===e)return;const t=this.tableCol.getTag(s.gp.annotations);if(!t)return void(this._cache=null);let n;try{n=JSON.parse(t)}catch{return void(this._cache=null)}if(!n||0===n.length)return void(this._cache=null);const o=new Map,r=new Map,i=this._getPosList();for(const e of n){if(e.category!==zo.Structure)continue;if(null==e.start||null==e.end)continue;const t=i.indexOf(e.start),n=i.indexOf(e.end);if(t<0||n<0)continue;const s=e.color??this._getDefaultRegionColor(e);for(let i=t;i<=n;i++)o.set(i,s),r.set(i,e.name)}this._cache={colVersion:e,annotations:n,positionRegionColors:o,positionRegionNames:r}}_ensureRowCache(){const e=this.tableCol.version;if(this._annotColLookupVersion!==e){this._annotColLookupVersion=e;const t=this.tableCol.getTag(s.gp.annotationColumnName);if(t)try{this._annotCol=this.tableCol.dataFrame.columns.byName(t)}catch{this._annotCol=null}else this._annotCol=null}if(!this._annotCol)return void(this._rowCache=null);const t=this._annotCol.version;if(this._rowCache&&this._rowCache.colVersion===t)return;const n=new Array(this._annotCol.length);for(let e=0;e<this._annotCol.length;e++){const t=this._annotCol.get(e);if(t)try{n[e]=JSON.parse(t)}catch{n[e]=null}else n[e]=null}this._rowCache={colVersion:t,data:n}}_getPosList(){const e=this.tableCol.getTag(s.gp.positionNames);return e?e.split(", "):[]}_getDefaultRegionColor(e){if(e.name.startsWith("CDR")){const t=parseInt(e.name.replace("CDR",""))-1;return Ko.structure.CDR[t%Ko.structure.CDR.length]}if(e.name.startsWith("FR")){const t=parseInt(e.name.replace("FR",""))-1;return Ko.structure.FR[t%Ko.structure.FR.length]}return"#90CAF9"}}var Jo=n(3599);const Xo="bio.macromolecule.highlightMonomers",Zo=i.Color.argb(255,255,220,0);i.Color.argb(255,230,140,0);const er="rgb(100,100,100)";class tr extends Bo{get separatorWidth(){return this.props?.fontCharWidth?this.props?.fontCharWidth:5}getAnnotationRenderer(){return this._annotationRenderer||(this._annotationRenderer=new Qo(this.tableCol)),this._annotationRenderer.hasAnnotations()?this._annotationRenderer:null}constructor(e,t,n,o,r){if(super(e,t,n),this.monomerLengthLimit=o,this.propsProvider=r,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._annotationRenderer=null,this.padding=5,this._leftThreeDotsPadding=0,this.props=this.propsProvider(),this._processedRows=i.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 e=[Ot.gp.positionShift,"renderMultiline"];this.subs.push(i.debounce(this.tableCol.dataFrame.onMetadataChanged.pipe(ne.filter((t=>t.args.source===this.tableCol&&e.includes(t.args.key)))),200).subscribe((e=>{this.reset()}))),this.subs.push(i.debounce(this.tableCol.dataFrame.onMetadataChanged.pipe(ne.filter((e=>e.args.source===this.tableCol&&e.args.key===Ot.gp.positionShift))),200).subscribe((e=>{this.reset()})))}}calculateFontBasedSpacing(e){const t=e.measureText("M");let n=12;if(this.tableCol?.temp[".mm.cellRenderer.fontSize"]){const e=this.tableCol.temp[".mm.cellRenderer.fontSize"];"number"!=typeof e||isNaN(e)||(n=Math.max(e,1))}return{lineHeight:Math.max(1.4*n,t.fontBoundingBoxAscent+t.fontBoundingBoxDescent+4),monomerSpacing:Math.max(2,.2*this.props.fontCharWidth)}}shouldUseMultilineRendering(e){return"true"===e.getTag("renderMultiline")}calculateMultiLineLayoutDynamic(e,t,n,o,r,i){if(this.dirty)try{this.reset()}catch(e){const[t,n]=(0,vn.AP)(e);this.logger.error(t,void 0,n)}const{lineHeight:s,monomerSpacing:a}=this.calculateFontBasedSpacing(e),l=t-2*this.padding;let c=0;const u=[];if(o.length>0)for(let t=r;t<o.length;t++){const n=o.getOriginal(t),r=this.props.monomerToShort(n,i);u.push({text:r,posIdx:t}),c=Math.max(c,e.measureText(r).width)}if(0===u.length)return{lineLayouts:[],lineHeight:s};const h=c;let d=Math.floor((l+a)/(h+a));d=Math.max(1,d);const p=n-2*this.padding,m=Math.max(0,Math.floor(p/s)),f=[];let g=0;for(let e=0;e<m&&g<u.length;e++){const t=[];for(let e=0;e<d&&g<u.length;e++){const n=u[g],o=this.padding+e*(h+a);t.push({posIdx:n.posIdx,x:o,width:h,om:n.text,isSeparator:!1}),g++}f.push({lineIdx:e,elements:t})}return{lineLayouts:f,lineHeight:s}}async init(){await Promise.all([(async()=>{this.seqHelper=await(0,Cn.Q)(),this.invalidateGrid()})(),(async()=>{const e=await(0,c.pj)();this.sysMonomerLib=e.getMonomerLib()})()]),this.subs.push(this.sysMonomerLib.onChanged.subscribe((()=>{this.reset()}))),this.subs.push(o.events.onCustomEvent("bio-macromolecule-monomer-highlight").subscribe((e=>this.handleHighlightEvent(e)))),this.reset()}handleHighlightEvent(e){var t;if(!e||!this.tableCol||!this.tableCol.dataFrame)return;if(e.columnName!==this.tableCol.name)return;const n=this.tableCol.dataFrame;if(e.tableId&&n.id!==e.tableId)return;if(e.tableName&&n.name!==e.tableName)return;const o=(t=this.tableCol.temp)[Xo]??(t[Xo]=new Map);null==e.monomers||0===e.monomers.length?o.delete(e.rowIdx):o.set(e.rowIdx,{monomers:e.monomers.slice(),fillColor:e.fillColor,strokeColor:e.strokeColor}),this.invalidateGrid()}getHighlightForRow(e){if(null==e)return null;const t=this.tableCol.temp[Xo];return t?.get(e)??null}drawHighlightBackground(e,t,n,o,r,s,a){const l=this.getHighlightForRow(t);if(!l||!l.monomers||0===l.monomers.length)return;if(!l.monomers.includes(n))return;const c=(u=l.fillColor??Zo,`rgba(${i.Color.r(u)},${i.Color.g(u)},${i.Color.b(u)},0.4)`);var u;e.save();try{e.fillStyle=c,e.fillRect(o,r,s,a)}finally{e.restore()}}static getFontSettings(e){let t=12;return e&&e.temp[".mm.cellRenderer.fontSize"]&&"number"==typeof e.temp[".mm.cellRenderer.fontSize"]&&!isNaN(e.temp[".mm.cellRenderer.fontSize"])&&(t=Math.max(e.temp[".mm.cellRenderer.fontSize"],1)),{font:`${t}px monospace`,fontWidth:.6*t}}toLog(){return`MonomerPlacer<${this.viewerId}>`}getMonomerLib(){return this.tableCol.temp[".mm.cellRenderer.overriddenLibrary"]??this.sysMonomerLib}reset(){this.propsProvider&&(this.props=this.propsProvider()),this._processedRows=i.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(e,t){const n=this.seqHelper.getSeqHandler(this.tableCol);if(this.colWidth<t&&(this.colWidth=t,this.dirty=!0),this.dirty)try{this.reset()}catch(e){const[t,n]=(0,vn.AP)(e);this.logger.error(t,void 0,n)}const o=n.isMsa()?this.getCellMonomerLengthsForSeqMsa():this.getCellMonomerLengthsForSeq(e);return[o,this.getSummedMonomerLengths(o)]}getSummedMonomerLengths(e){const t=new Array(e.length+1);t[0]=this.padding;for(let n=1;n<t.length;n++)t[n]=t[n-1]+e[n-1];let n=t[0];for(let e=1;e<t.length;e++)t[e]?n=t[e]:t[e]=n;return t}getCellMonomerLengthsForSeqValue(e,t){const n=this.seqHelper.getSeqHandler(this.tableCol),o=this.props.separatorWidth+1*this.props.fontCharWidth,r=this.positionShift,i=Math.ceil(t/o)+r,s=n.splitter(e),a=Math.min(i,s.length),l=new Array(a-r);let c=0;for(let e=r;e<a;++e){const o=s.getOriginal(e),i=this.props.monomerToShort(o,this.monomerLengthLimit),a=(n.isSeparator()?this.separatorWidth:this.props.separatorWidth)+i.length*this.props.fontCharWidth;if(l[e-r]=a,c+=a,c>t)break}return l}getCellMonomerLengthsForSeq(e){this.toLog(),null==this._monomerLengthList&&(this._monomerLengthList=new Array(this.tableCol.length).fill(null));const t=this.positionShift,n=this.seqHelper.getSeqHandler(this.tableCol),o=this.props.separatorWidth+1*this.props.fontCharWidth,r=Math.ceil(this.colWidth/o)+t,i=n.getSplitted(e),s=Math.min(r,i.length);let a=this._monomerLengthList[e];if(null==a||a.length!=s-t){a=this._monomerLengthList[e]=new Array(i.length);let o=0;for(let e=t;e<s;++e){const r=i.getOriginal(e),s=this.props.monomerToShort(r,this.monomerLengthLimit),l=(n.isSeparator()?this.separatorWidth:this.props.separatorWidth)+s.length*this.props.fontCharWidth;if(a[e-t]=l,o+=l,o>this.colWidth)break}}return a}getCellMonomerLengthsForSeqMsa(){var e;this.toLog(),null==this._monomerLengthList&&(this._monomerLengthList=new Array(1).fill(null)),(e=this._monomerLengthList)[0]??(e[0]=new Array(0));const t=this._monomerLengthList[0],{startIdx:n,endIdx:o}=(()=>{try{const e=this.gridCol&&this.gridCol.dart?this.gridCol.grid:null;return e&&e.dart?{startIdx:Math.max(Math.floor((e?.vertScroll.min??0)-10),0),endIdx:Math.min(Math.ceil((e?.vertScroll.max??0)+10),this.tableCol.length)}:{startIdx:0,endIdx:Math.min(this.tableCol.length,10)}}catch(e){return{startIdx:0,endIdx:Math.min(this.tableCol.length,10)}}})(),r=this.props.separatorWidth+1*this.props.fontCharWidth,i=this.positionShift,s=Math.ceil(this.colWidth/r)+i;for(let e=n;e<o;e++){if(this._processedRows.get(e)&&s<=this._processedMaxVisibleSeqLength)continue;const n=this.seqHelper.getSeqHandler(this.tableCol).getSplitted(e,s),o=Math.min(s,n.length);o-i>t.length&&t.push(...new Array(o-i-t.length).fill(r));let a=0;for(let e=i;e<o;++e){const o=n.getOriginal(e),r=this.props.monomerToShort(o,this.monomerLengthLimit),s=this.props.separatorWidth+r.length*this.props.fontCharWidth;if(t[e-i]=Math.max(t[e-i]??0,s),a+=s,a>=this.colWidth)break}this._processedMaxVisibleSeqLength=Math.max(this._processedMaxVisibleSeqLength,s),this._processedRows.set(e,!0)}return t}getPosition(e,t,n,o){const[r,i]=this.getCellMonomerLengths(e,n);return 0===this.seqHelper.getSeqHandler(this.tableCol).getSplitted(e).length?null:function(e,t,n){if((n??0)>0&&t<(e[0]??0)+n)return-1;t-=n??0;let o,r=100,i=0,s=e.length-1;for(;i<=s;){if(o=Math.floor((s+i)/2),e[o]<=t&&t<e[o+1])return o;if(t<e[o]?s=o-1:i=o+1,--r<=0)throw new Error(`Get position for pointer x = ${t} searching has not converged on ${JSON.stringify(e)}. `)}return null}(i,t,o)}setMonomerLengthLimit(e){this.monomerLengthLimit!=e&&(this.monomerLengthLimit=e,this.dirty=!0)}setSeparatorWidth(e){this.separatorWidth!=e&&(this.props.separatorWidth=e,this.dirty=!0)}get positionShift(){const e=Number.parseInt(this.tableCol?.tags[Ot.gp.positionShift]??"0")??0;return isNaN(e)?0:Math.max(e,0)}render(e,t,n,o,r,s,a){const l=s.grid?.dart&&s.grid?.canvas===e.canvas;if(!this.seqHelper)return;const c=this.tableCol,u=this.positionShift;e.save();try{const a=this.seqHelper.getSeqHandler(c);let h=this.monomerLengthLimit;if(Go.maxMonomerLength in c.tags){const e=parseInt(c.getTag(Go.maxMonomerLength));h=!isNaN(e)&&e?e:50}if(".mm.cellRenderer.maxMonomerLength"in c.temp){const e=c.temp[".mm.cellRenderer.maxMonomerLength"],t="number"==typeof e?e:parseInt(e);h=!isNaN(t)&&t?t:50}if("1"===c.temp[".mm.cellRenderer.settingsChanged"]||this.monomerLengthLimit!=h){let e=0;const t=8;e=c.temp[".mm.cellRenderer.gapLength"]??e,this.setMonomerLengthLimit(h),this.setSeparatorWidth(a.isMsa()?t:e),c.temp[".mm.cellRenderer.settingsChanged"]="0",this.dirty=!0}const d=s.cell.rowIndex,p=s.cell.value;l&&(o=function(e,t,n,o,r){return e?Math.max(Math.min(e.canvas.width/r-n,o)):Math.max(t.canvas.width/r-n,0)}(s.grid,e,t,o,window.devicePixelRatio)),e.beginPath(),e.rect(t,n,o,r),e.clip(),e.font=this.props?.font??"12px monospace",e.textBaseline="top";const m=c.meta.units,f=c.getTag(Ot.gp.aligned),g=c.getTag(Ot.gp.separator)??"",y=l?a.getSplitted(d):a.splitter(p);let b=Vo.classic;f?.includes("MSA")&&m===Ot.Hi.SEPARATOR&&(b=Vo.MSA);const v=c.temp["reference-sequence"],C=this.tableCol.temp["current-word"],x=(()=>{const e=(0,a.splitter)(null!=v&&""!==v?v:C??"");return wn().count(0).take(e.length).slice(u).map((t=>e.getCanonical(t))).toArray()})(),w=Number.parseInt(c.getTag(Ot.gp.selectedPosition)??"-200"),A=this.shouldUseMultilineRendering(c),T=this.getAnnotationRenderer();if(A){const l=[],d=this.calculateMultiLineLayoutDynamic(e,o,r,y,u,h);let p=n+this.padding;1===d.lineLayouts.length&&(p=n+(r-d.lineHeight)/2);for(const o of d.lineLayouts){const r=p+o.lineIdx*d.lineHeight;for(const h of o.elements){const p=t+h.x,m=h,f=m.posIdx,g=y.getCanonical(f);let b=er;const v=this.getMonomerLib();v&&(b=v.getMonomerTextColor(a.defaultBiotype,g));let C=0;if(s.tableRowIndex!==c.dataFrame.currentRowIdx&&x.length>0){const e=f-u;e>=0&&e<x.length&&g===x[e]&&(C=.7)}l.push({lineIdx:o.lineIdx,monomerIdx:f-u,bounds:new i.Rect(h.x,r-n,h.width,d.lineHeight),sequencePosition:f}),T&&T.drawPositionBackground(e,p,r,h.width+2,d.lineHeight,f,s.tableRowIndex),this.drawHighlightBackground(e,s.tableRowIndex,f,p,r,h.width+2,d.lineHeight),qo(e,m.om,p,r,h.width,d.lineHeight,{color:b,isMultiLineContext:!0,transparencyRate:C,selectedPosition:isNaN(w)||w<1?void 0:w,wordIdx:f})}}null!==s.tableRowIndex&&this._cellBounds.set(s.tableRowIndex,l)}else{this._leftThreeDotsPadding=this.shouldRenderShiftedThreeDots(u)?e.measureText("...").width:0;let[,i]=this.getCellMonomerLengths(s.tableRowIndex,o);l||(i=this.getSummedMonomerLengths(this.getCellMonomerLengthsForSeqValue(p,o)));const c=this.props.separatorWidth+1*this.props.fontCharWidth,d=Math.min(y.length,Math.ceil(o/c)+u);let m;const f=e.measureText("M"),v=f.fontBoundingBoxAscent+f.fontBoundingBoxDescent,C=4,A=Math.min(r,v+C),E=n+(r-A)/2;T&&(m=n+(r/2-v/2+1)+v);for(let l=u;l<d;++l){const c=l<y.length?y.getOriginal(l):a.defaultGapOriginal,d=l<y.length?y.getCanonical(l):a.defaultGapOriginal;let p=er;this.getMonomerLib()&&(p=this.getMonomerLib().getMonomerTextColor(a.defaultBiotype,d));const f=l===y.length-1,v=(y?.graphInfo?.disjointSeqStarts?.indexOf(l+1)??0)>0?"|":g,C=l-u,S=(i[C]??0)-(i[0]??0),N=(C+1<i.length?(i[C+1]??0)-(i[0]??0):S+this.props.fontCharWidth)-S,I=t+this.padding+this._leftThreeDotsPadding+S;T&&null!=s.tableRowIndex&&T.drawPositionBackground(e,I,n,N,r,l,s.tableRowIndex,m),this.drawHighlightBackground(e,s.tableRowIndex,l,I,E,N,A);const M={color:p,pivot:0,left:!0,transparencyRate:0,separator:v,last:f,drawStyle:b,maxWord:i,wordIdx:l-u,gridCell:s,referenceSequence:x,maxLengthOfMonomer:h,monomerTextSizeMap:this._monomerLengthMap,logger:this.logger,selectedPosition:isNaN(w)||w<1?void 0:w-u};qo(e,c,t+this.padding+this._leftThreeDotsPadding,n,o,r,M)}if(this.shouldRenderShiftedThreeDots(u)){const a={color:er,pivot:0,left:!0,transparencyRate:0,separator:g,last:!1,drawStyle:b,maxWord:i,wordIdx:0,gridCell:s,maxLengthOfMonomer:h,monomerTextSizeMap:this._monomerLengthMap,logger:this.logger};qo(e,"...",t+this.padding,n,o,r,a)}}}catch(e){const[t,n]=(0,vn.AP)(e);this.logger.error(t,void 0,n),this.errors.push(e)}finally{e.restore()}}shouldRenderShiftedThreeDots(e){return e>0&&(!this.gridCol||!this.gridCol.dart||!this.gridCol.grid||!this.gridCol.grid.dart||(this.gridCol.grid.props.colHeaderHeight??0)<=50)}onMouseMove(e,t){const n=`${this.toLog()}.onMouseMove()`;if(!this.seqHelper||null==e.tableRowIndex)return;const o=this.positionShift,i=e.bounds,s=t.offsetX-e.gridColumn.left+(e.gridColumn.left-i.x),a=t.offsetY-i.y;this.gridCol?.grid?.canvas&&(this.gridCol.grid.canvas.style.cursor="default");let l=null;const c=this._cellBounds.get(e.tableRowIndex);if(c){for(const e of c)if(e.bounds.contains(s,a)){l=e.monomerIdx;break}}else{const t=this.shouldRenderShiftedThreeDots(o)&&(this._leftThreeDotsPadding??0)>0?this._leftThreeDotsPadding:0;l=this.getPosition(e.tableRowIndex,s,i.width,t)}this.logger.debug(`${n}, argsX: ${s}, argsY: ${a}, left: ${l}`);const u=this.seqHelper.getSeqHandler(this.tableCol),h=u.getSplitted(e.tableRowIndex);if(null!==l&&l>=0&&l+o<h.length){const n=u.alphabet??Ot.YI.UN,i={position:l,biotype:n===Ot.YI.RNA||n===Ot.YI.DNA?Jo.o.NUCLEOTIDE:Jo.o.AA,symbol:h.getCanonical(l+o)},s=[];let a=this._monomerStructureMap[i.symbol];if(!a){const e=this.getMonomerLib();a=this._monomerStructureMap[i.symbol]=e?e.getTooltip(i.biotype,i.symbol):r.divText("Monomer library is not available")}s.push(a);const c=this.getAnnotationRenderer();if(c){const t=c.getTooltipInfo(l+o,e.tableRowIndex);if(t.length>0){const e=document.createElement("hr");e.style.margin="4px 0",e.style.border="none",e.style.borderTop="1px solid #ccc",s.push(e);for(const e of t)s.push(r.divText(e,{style:{fontSize:"12px",marginBottom:"2px"}}))}}r.tooltip.show(r.divV(s),t.x+16,t.y+16),Un(e,i)}else-1===l?r.tooltip.show(r.divText(`${Math.min(o,h.length)} hidden monomers`),t.x+16,t.y+16):r.tooltip.hide(),Un(e,null)}}class nr extends tr{constructor(e,t,n,o){super(e,t,br.logger,n,(()=>{const e=o.getSeqHandler(t),{font:n,fontWidth:r}=tr.getFontSettings(t);return{seqHandler:e,font:n,fontCharWidth:r,separatorWidth:11,monomerToShort:Ot.zS}}))}onMouseMove(e,t){super.onMouseMove(e,t)}}class or extends Ro.$G{static get notationName(){return"Harmonized Sequence"}static get implementsFromHelm(){return!1}static convertFromHelm(e,t){throw new Error("converting from helm not supported yet")}get defaultGapOriginal(){return""}constructor(e,t){super(),this.separator=e,this.helmHelper=t,this.separatorSplitter=(0,Ot.dh)(this.separator),this.splitter=this._splitter.bind(this)}setUnits(){}_splitter(e){const t=this.separatorSplitter(e);return new rr(wn().count(0).take(t.length).map((e=>t.getOriginal(e))).toArray(),s.b9[s.Hi.SEPARATOR])}getHelm(e,t){return Oo.s.fromSeparator(e,this.helmHelper).getHelm()}createCellRendererBack(e,t){const n=new nr(e,t,4,this.helmHelper.seqHelper);return n.init().then((()=>{})),n}}class rr extends a.Mu{getCanonical(e){if(this.isGap(e))return s._S;const t=this.getOriginal(e);let n=t;return t.startsWith("{")?n=t.slice(1):t.endsWith("}")?n=t.slice(0,-1):t.startsWith("(")?n=t.replace(/^\(.\d+\)/,""):t.endsWith(")")&&(n=t.replace(/\(\d+\)$/,"")),n}constructor(e,t){super(e,t)}}async function ir(e,t=!1){await br.initPromise;const n=window.innerWidth,s=window.innerHeight;try{let a;function u(){if(null==a)return;const e=L()(a.root).find("div.d4-dialog-contents").get(0),t=e.clientHeight,n={0:1},o=Object.values(n).reduce(((e,t)=>e+t),0),r=t-wn().count(0).take(e.children.length).filter((e=>!(e in n))).map((t=>e.children[t])).filter((e=>e instanceof HTMLElement)).map((e=>e.offsetHeight)).reduce(((e,t)=>e+t),0)-38;for(const t of wn().count(0).take(e.children.length))if(t in n){const i=e.children[t],s=r*n[t]/o;i.style.height=`${s}px`}}a=await async function(e,t,n=!1){const s="ST: PT: HelmDialog()";let a;const u=[];let h=So.aK.Single;const d=()=>{for(const e of u)e.unsubscribe();a.placeholders.detach()};try{const p=await(0,c.pj)(),m=p.getMonomerLib(),f=await(0,Cn.Q)(),g=await(0,bn.b2)(),y=g.buildMonomersFuncsFromLib(m),b=e=>{let t,n,o=null;if(e&&e.rowIndex>=0&&e?.column.semType==i.SEMTYPE.MACROMOLECULE){if(t=f.getSeqHandler(e.column).getValue(e.rowIndex),e.column.temp?.[l.notationProvider]&&!(e.column.temp[l.notationProvider]instanceof or)){let n;o=e.column.temp[l.notationProvider].getHelm(t.value,{}),i.DataFrame.fromColumns([n=i.Column.fromList(i.COLUMN_TYPE.STRING,"seq",[o])]),n.semType=i.SEMTYPE.MACROMOLECULE,n.meta.units=Ot.Hi.HELM,t=f.getSeqHandler(n).getValue(0)}n=t.tags["polytool-data-role"]??"macromolecule"}else{const e=i.Column.fromList(i.COLUMN_TYPE.STRING,"seq",[No.d]);e.semType=i.SEMTYPE.MACROMOLECULE,i.DataFrame.fromColumns([e]),e.meta.units=Ot.Hi.HELM,t=f.getSeqHandler(e).getValue(0),n="macromolecule"}return[t,n]};let v,C,[x,w]=b(e),A=null;const T=r.divText("",{style:{color:"red"}}),E=r.divText("",{style:{fontSize:"11px",color:"var(--grey-4)",marginTop:"2px",marginLeft:"4px",whiteSpace:"nowrap"}});a={macromolecule:g.createHelmInput("Macromolecule",{editable:!1,editorOptions:{drawOptions:{monomerNumbering:1,getMonomer:(t,n)=>{const o=t;if("ATOM"!==o.T)return y.getMonomer(t,n);try{if(x.isDna()||x.isRna()){const e=x.getSplittedWithSugarsAndPhosphates().getCanonical(o.bio.continuousId-1);return y.getMonomer(o.bio.type,e)}if(e?.column?.temp?.[l.notationProvider]instanceof or){const e=x.getSplitted().getCanonical(o.bio.continuousId-1);return y.getMonomer(o.bio.type,e)}{const e=o.elem;return y.getMonomer(o.bio.type,e)}}catch(e){return y.getMonomer(t,n)}}}}}),placeholders:await Io.create("Placeholders",{showAddNewRowIcon:!0,showRemoveRowIcon:!0,showRowHeader:!1,showCellTooltip:!1}),enumeratorType:r.input.choice("Enumerator type",{value:h,items:Object.values(So.aK)}),placeholdersBreadth:await Lo.create("Breadth",{showAddNewRowIcon:!0,showRemoveRowIcon:!0,showRowHeader:!1,showCellTooltip:!1}),keepOriginal:r.input.bool("Keep original",{value:!1}),toAtomicLevel:r.input.bool("To atomic level",{value:!1,onValueChanged:(e,t)=>{M()}}),generateHelm:r.input.bool(Qn,{value:!0}),chiralityEngine:r.input.bool(Jn,{value:!1}),highlightMonomers:r.input.bool(Xn,{value:!1}),rules:{header:r.inlineText([to]),form:await(C=new jn._v(jn.MU,jn.yy,".json",{onValueChanged:e=>{v=e}})).getForm()},trivialName:r.input.string("Trivial name",{value:"",onValueChanged:e=>{const t=e?.trim();A=t?{value:t,colName:"Trivial name"}:null}}),appendToTable:r.input.table("Append to table",{items:o.shell.tables,nullable:!0})};const S=()=>{const e=no[a.enumeratorType.value]??"";r.tooltip.bind(a.enumeratorType.input,e)};if(S(),e?.dataFrame){const t=r.iconFA("columns",(t=>{i.Menu.popup().singleColumnSelector(e.dataFrame,{columnFilter:t=>t.type===i.COLUMN_TYPE.STRING&&t!==e.column,onChange:(t,n,o)=>{o&&(a.trivialName.value=n.get(e.rowIndex)??"")}}).show({x:t.clientX,y:t.clientY})}),"Pick trivial name from a column");a.trivialName.addOptions(t)}a.trivialName.root.style.maxWidth="450px",a.placeholders.onMonomerCellEdit=async(e,t)=>{const n=a.macromolecule.molValue;if(e<0||e>=n.atoms.length)return null;const o=n.atoms[e].biotype(),r=(0,To.Y)(o);return _o(m,r,t,p)},a.placeholdersBreadth.onMonomerCellEdit=async(e,t,n)=>{const o=a.macromolecule.molValue;if(e<0||e>=o.atoms.length)return null;const r=o.atoms[e].biotype(),i=(0,To.Y)(r);return _o(m,i,n,p)};let N=null;a.placeholders.addValidator((e=>{N=null;const t=[];setTimeout((()=>{_()}),100);try{if(a.enumeratorType.value===So.aK.Parallel){const e=a.placeholders.placeholdersValue.filter((e=>e.monomers.length>0));if(e.length>1){const t=e[0].monomers.length,n=e.find((e=>e.monomers.length!==t));n&&(N=`Parallel mode requires all positions to have the same number of monomers. Position ${e[0].position+1} has ${t}, but position ${n.position+1} has ${n.monomers.length}.`)}}if("macromolecule"!==w)return null;const e=[];for(const n of a.placeholders.placeholdersValue){const o=n.position;if(null==o)continue;if(o>=a.macromolecule.molValue.atoms.length){t.push(`There is no monomer at position ${o+1}.`);continue}const r=a.macromolecule.molValue.atoms[o];if(r){const t=r.biotype(),o=(0,To.Y)(t);for(const t of n.monomers){const n=m.getMonomer(o,t);n&&n.lib||e.push({polymerType:o,symbol:t})}}}const n={};for(const t of e){let e=n[t.polymerType];e||(e=n[t.polymerType]=[]),e.push(t.symbol)}const o=Object.entries(n).map((([e,t])=>`${e}: ${t.join(", ")}`)).join("\n");Object.keys(o).length>0&&t.push(`Placeholders contain missed monomers: ${o}`),N=t.length>0?t.join("\n"):N}catch(e){const[t,n]=zn(e,!1);N=t}return setTimeout((()=>{_()}),0),N})),a.enumeratorType.onChanged.subscribe((e=>{h=a.enumeratorType.value,S(),a.placeholders.fireChanged()})),u.push(a.macromolecule.onMouseMove.subscribe((e=>{try{br.logger.debug(`${s}, placeholdersInput.onMouseMove()`);const t=e.offsetX,n=e.offsetY,o=a.macromolecule.molValue,i=g.getHoveredAtom(t,n,o,a.macromolecule.root.clientHeight);if(i){const t=i._parent.atoms.indexOf(i),n=a.placeholders.placeholdersValue.find((e=>e.position===t))?.monomers;if(n){const t=r.divText(n.join(", "));a.macromolecule.showTooltip(t,i),e.preventDefault(),e.stopPropagation()}}}catch(e){zn(e,!1)}}))),u.push(a.macromolecule.onClick.subscribe((e=>{try{br.logger.debug(`${s}, placeholdersInput.onClick()`);const t=e.offsetX,n=e.offsetY,o=a.macromolecule.molValue,r=g.getHoveredAtom(t,n,o,a.macromolecule.root.clientHeight);if(r){const e=r._parent.atoms.indexOf(r);a.placeholders.addPosition(e,"")}}catch(e){zn(e)}}))),u.push(a.placeholders.onChanged.subscribe((()=>{I(),L()}))),u.push(a.placeholdersBreadth.onChanged.subscribe((()=>{L()}))),u.push(a.keepOriginal.onChanged.subscribe((()=>{L()}))),u.push(r.onSizeChanged(a.placeholders.root).subscribe((()=>{t&&t()}))),u.push(o.events.onCurrentCellChanged.subscribe((()=>{const e=o.shell.tv.dataFrame.currentCell;e.column.semType===i.SEMTYPE.MACROMOLECULE&&([x,w]=b(e),R(x,w,e))}))),a.macromolecule.root.style.setProperty("min-width","250px","important");const I=()=>{const e=new Set(a.placeholders.placeholdersValue.map((e=>e.position))),t=a.macromolecule.molValue;for(let n=0;n<t.atoms.length;n++)t.atoms[n].highlighted=e.has(n);a.macromolecule.redraw()},M=()=>{a.toAtomicLevel.value&&"template"===w?(a.generateHelm.root.style.removeProperty("display"),a.chiralityEngine.root.style.removeProperty("display"),a.highlightMonomers.root.style.removeProperty("display"),a.rules.header.style.removeProperty("display"),a.rules.form.style.removeProperty("display")):(a.generateHelm.root.style.display=a.chiralityEngine.root.style.display=a.highlightMonomers.root.style.display="none",a.rules.header.style.display=a.rules.form.style.display="none"),t&&t()};let P=null;const _=()=>{const e=N,t=T;e?(t.innerText=e,t.style.removeProperty("display"),P&&(P.disabled=!0)):(t.innerText="",t.style.setProperty("display","none"),P&&(P.disabled=!1))},L=()=>{try{const e=a.placeholders.placeholdersValue.filter((e=>e.monomers.length>0)),t=a.placeholdersBreadth.placeholdersBreadthValue.filter((e=>e.monomers.length>0&&null!=e.start&&null!=e.end));let n=0;switch(a.enumeratorType.value){case So.aK.Single:n=e.reduce(((e,t)=>e+t.monomers.length),0);break;case So.aK.Parallel:e.length>0&&(n=e.every((t=>t.monomers.length===e[0].monomers.length))?e[0].monomers.length:0);break;case So.aK.Matrix:n=e.length>0?e.reduce(((e,t)=>e*t.monomers.length),1):0}let o=0;t.length>0&&(o=t.reduce(((e,t)=>{const n=Math.abs(t.end-t.start)+1;return e*(t.monomers.length*n)}),1));let r=n+o;a.keepOriginal.value&&r>0&&(r+=1),E.textContent=r>0?`${r} sequence${1!==r?"s":""} will be generated`:""}catch(e){E.textContent=""}},O=e=>{t&&t()},R=(e,t,n)=>{a.macromolecule.value=e;const o=n?.dataFrame;O(o)};R(x,w,e),M(),L();const $=async()=>{try{const t=a.macromolecule.stringValue;if(void 0===t||""===t)o.shell.warning("PolyTool: no molecule was provided");else{if(0===Object.keys(a.placeholders.placeholdersValue).length&&0===Object.keys(a.placeholdersBreadth.placeholdersBreadthValue).length)return void o.shell.warning(`${eo}: placeholders are empty`);await(0,bn.b2)();const r=a.placeholders.placeholdersValue,s=a.enumeratorType.value;if(s===So.aK.Parallel){const e=r.filter((e=>e.monomers.length>0));if(e.length>1){const t=e[0].monomers.length;if(e.some((e=>e.monomers.length!==t)))return void o.shell.warning("Parallel mode requires all positions to have the same number of monomers")}}const c={placeholders:r,type:s,breadthPlaceholders:a.placeholdersBreadth.placeholdersBreadthValue,keepOriginal:a.keepOriginal.value};if(e?.column?.temp?.[l.notationProvider]&&!(e.column.temp[l.notationProvider]instanceof or)){const t=e.column.temp[l.notationProvider];if(t.constructor.implementsFromHelm){const e=t.constructor;c.fromHelmNotation={notationName:e.notationName,convert:t=>e.convertFromHelm(t,{})}}}const u=a.toAtomicLevel.value,h=await sr(t,w,A,c,!!u&&{generateHelm:a.generateHelm.value,chiralityEngine:a.chiralityEngine.value,highlightMonomers:a.highlightMonomers.value,rules:await C.getActive()},g);if(n){const e=h.col("Enumerated");e&&e.type===i.COLUMN_TYPE.STRING&&(0,yn.P)(e)}const d=a.appendToTable.value;d?(d.append(h,!0),d.meta.detectSemanticTypes()):o.shell.addTableView(h)}}catch(e){zn(e)}},D=r.dialog({title:eo,showFooter:!0}).add(a.macromolecule.root).add(r.divH([r.divV([a.placeholders.root,r.divH([a.enumeratorType.root,E],{style:{alignItems:"center"}})],{style:{width:"50%"}}),r.divV([a.placeholdersBreadth.root],{style:{width:"50%"}})],{style:{width:"100%"}})).add(r.divH([r.divV([a.trivialName.root,a.keepOriginal.root,a.appendToTable.root],{style:{width:"50%"}}),r.divV([r.divH([a.toAtomicLevel.root,a.generateHelm.root]),r.divH([a.chiralityEngine.root,a.highlightMonomers.root]),a.rules.header,a.rules.form],{style:{width:"50%"}})],{style:{width:"100%"}})).add(T).onOK((()=>{if(N)return _(),void o.shell.warning("Please fix validation errors before running enumeration");$()}));return P=D.getButton("OK"),u.push(D.onClose.subscribe((()=>{d()}))),D.history((()=>({description:`${a.enumeratorType.value} ${a.placeholders.placeholdersValue?.map((e=>(e.position?.toString()??"")+": "+e.monomers?.join(", "))).join("; ")}`,placeholders:a.placeholders.stringValue,enumeratorType:a.enumeratorType.value,placeholdersBreadth:a.placeholdersBreadth.stringValue,trivialName:a.trivialName.value,keepOriginal:a.keepOriginal.value,toAtomicLevel:a.toAtomicLevel.value,generateHelm:a.generateHelm.value,chiralityEngine:a.chiralityEngine.value,highlightMonomers:a.highlightMonomers.value,rules:v})),(e=>{a.enumeratorType.value=e.enumeratorType??So.aK.Single,a.placeholders.stringValue=e.placeholders,a.placeholdersBreadth.stringValue=e.placeholdersBreadth,e.trivialName&&(a.trivialName.value=e.trivialName),a.keepOriginal.value=e.keepOriginal??!1,a.toAtomicLevel.value=e.toAtomicLevel??!0,a.generateHelm.value=e.generateHelm??!0,a.chiralityEngine.value=e.chiralityEngine??!1,a.highlightMonomers.value=e.highlightMonomers??!1,C.setActive(e.rules),setTimeout((()=>{a.placeholders.invalidateGrid(),a.placeholdersBreadth.invalidateGrid(),L()}),100)})),D}catch(e){throw d(),e}}(e,u,t);let h=!0;r.onSizeChanged(a.root).subscribe((()=>{if(h){const e=.7*n,t=.7*s;a.root.style.width=`${Math.min(n,e)}px`,a.root.style.height=`${Math.min(s,t)}px`,a.root.style.left=`${Math.floor((n-a.root.offsetWidth)/2)}px`,a.root.style.top=`${Math.floor((s-a.root.offsetHeight)/2)}px`,h=!1}u()})),u(),br.logger.debug("PolyToolEnumerateHelmUI: dialog before show"),a.show({width:Math.max(350,.7*n),resizable:!0}),br.logger.debug("PolyToolEnumerateHelmUI: dialog after show")}catch(d){const[p,m]=(0,vn.AP)(d);br.logger.error(p,void 0,m)}}async function sr(e,t,n,r,s,a){const l=i.TaskBarProgressIndicator.create("PolyTool enumerating...");try{const l=await(0,c.pj)(),u=await(0,Vn.j)(),h=l.getMonomerLib(),d=(0,No.o)(e,n?.value??"",r);let p;switch(t){case"macromolecule":p=i.Column.fromType(i.COLUMN_TYPE.STRING,"Enumerated",d.length).init((e=>d[e][0]));break;case"template":{const e=new Array(d.length);for(let t=0;t<d.length;t++){const n=d[t][0],o=Oo.s.fromHelm(n,a);e[t]=o.getNotation()}p=i.Column.fromList(i.COLUMN_TYPE.STRING,"Enumerated",e),p.semType=i.SEMTYPE.MACROMOLECULE,p.setTag("polytool-data-role","template"),Cr.applyNotationProviderForCyclized(p,"-");break}}const m=i.DataFrame.fromColumns([p]);if("macromolecule"===t&&r.fromHelmNotation){const e=i.Column.fromType(i.COLUMN_TYPE.STRING,`${r.fromHelmNotation.notationName}(${p.name})`,m.rowCount).init((e=>p.isNone(e)?null:r.fromHelmNotation.convert(p.get(e))));m.columns.add(e)}if(await o.data.detectSemanticTypes(m),"template"==t&&Cr.applyNotationProviderForCyclized(p,"-"),s){let e;if("macromolecule"===t){e=p;const t=await a.seqHelper.helmToAtomicLevel(e,s.chiralityEngine,s.highlightMonomers);m.columns.add(t.molCol,!1);const n=t.molCol;await async function(e,t,n,o,r,i=!1){const s=o.getSeqHandler(e),a=s.alphabet==Ot.YI.RNA||s.alphabet==Ot.YI.DNA,l=s.isHelm()&&a,c=!s.isHelm()&&a,u=e=>null==e?null:l?i?e:Math.floor(e/3):c&&i?3*e+1:e,h=i?await o.getHelmToMolfileConverter(n):null,d=new On({max:100});function p(e,t){const s=e.get(t);if(null==s)return null;let a=d.get(s);return a||d.set(s,a=function(e,t){const s=o.getSeqHandler(e);if(i){const e=s.getHelm(t);return o.helmToAtomicLevelSingle(e,h,!1,!1).monomers}{const e=s.getSplitted(t),o=s.defaultBiotype,i=wn().count(0).take(e.length).map((t=>({position:t,symbol:e.getCanonical(t),biotype:o}))).toArray(),a=s.alphabet,l=a==Ot.YI.RNA||a==Ot.YI.DNA?"RNA":"PEPTIDE",c=(0,Bn.eM)([i],[void 0],l,a,n,r);return(0,Fn.gU)(i,c,a,l).monomers}}(e,t)),a}const m={targetCol:t,handler:(t,o,r)=>{const i=r.grid,s=t.tableRowIndex,a=t.gridRow,l=i.cell(r.name,a),c=Rn();if(!c||c&&(c.dataFrameId!=e.dataFrame.id||c.gridRowIdx!=a||c.seqColName!=e.name||c.seqPosition!=o?.position)){if(c&&($n(null),c.gridCell.render()),!o)return $n(null),!0;$n({gridCell:l,dataFrameId:e.dataFrame.id,gridRowIdx:a,seqColName:e.name,seqPosition:u(o?.position)??-1,getSubstruct:()=>{if(!o||"*"===o.symbol)return;const t=p(e,s);if(!t)return;const r=t.get(u(o?.position));return r?(0,kn.H)([r],n):{atoms:[],bonds:[],highlightAtomColors:[],highlightBondColors:[]}}}),l.render()}return!0},getSubstruct:o=>{if("true"!=t.getTag(".sequence-src-highlight-monomers"))return;if(null==o)return;if(!e.get(o))return;const r=p(e,o);return r?(0,kn.H)(r.values(),n):void 0}};return Gn(e.temp,m),Dn(t.temp,m),m}(e,n,h,a.seqHelper,u,!0)}else"template"===t&&(e=(await ro(p,s.generateHelm,!1,s.chiralityEngine,!1,s.rules))[0])}if(n){const e=i.Column.fromType(i.COLUMN_TYPE.STRING,n.colName,d.length).init((e=>d[e][1]));m.columns.add(e)}return m}finally{l.close()}}var ar,lr=n(3151);class cr{constructor(e){this.rawLib=e}isValid(){return this.rawLib.every((e=>"object"==typeof e&&Object.values(Yn).every((t=>t in e&&"string"==typeof e[t]))))}getJsonMonomerLib(){const e=[];return this.rawLib.forEach((t=>{const n=this.prepareMonomer(t);e.push(n)})),e}prepareMonomer(e){const t={...lr.pe};Object.entries(Yn).forEach((([n,o])=>{const r=e[o];t[n]=r}));let n="smiles";const o=e[Yn[n]],r=new ur(o),i=r.getCappedSmiles();return t[n]=i,n="rgroups",t[n]=hr.getRGroups(r.getNumberOfRGroups()),n="molfile",t[n]=new dr(r.getSmilesWithRGroups()).getMolfile(),t}}class ur{constructor(e){let t=0;this.smilesWithRGroups=e.replace(/\[R(\d+)\]/g,((e,n)=>(++t,`[${n}*]`))),this.numberOfRGroups=t}getSmilesWithRGroups(){return this.smilesWithRGroups}getCappedSmiles(){return this.capRGroups()}getNumberOfRGroups(){return this.numberOfRGroups}capRGroups(){let e=this.smilesWithRGroups.replace("[1*]","[H:1]");return e=e.replace("[2*]","[OH:2]"),e.replace("[3*]","[H:3]")}}class hr{constructor(){}static getRGroups(e){return Kn.slice(0,e)}}class dr{constructor(e){this.smilesWithRGroups=e}getMolfile(){let e=i.chem.convert(this.smilesWithRGroups,i.chem.Notation.Smiles,i.chem.Notation.MolBlock);return e=this.restoreRGPLine(e),e=this.fixRGroupSymbols(e),e}restoreRGPLine(e){return e.replace("M ISO","M RGP")}fixRGroupSymbols(e){return e.replace(/\bR\b/g,"R#")}}class pr{constructor(e,t){this.fileName=e,this.fileContent=t,this.validateFileType();const n=i.DataFrame.fromCsv(this.fileContent),o=this.toJson(n);this.polyToolMonomerLib=new cr(o),this.validateContent()}async getJson(){return this.polyToolMonomerLib.getJsonMonomerLib()}toJson(e){return Array.from({length:e.rowCount},((t,n)=>e.columns.names().reduce(((t,o)=>(t[o]=e.get(o,n),t)),{})))}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(e){e.table="table",e.seqCol="seqCol",e.generateHelm="generateHelm",e.chiralityEngine="chiralityEngine",e.rules="rules"}(ar||(ar={}));class mr{constructor(e){this.call=e,this.ruleInputs=new jn._v(jn.MU,jn.yy,".json")}async initInputs(){const e=e=>this.call.inputParams[e],t=await this.ruleInputs.getForm();this.inputs={table:(()=>{const t=e(ar.table);return r.input.table(t.property.caption,{value:t.value})})(),seqCol:(()=>{const t=e(ar.seqCol);return r.input.column(t.property.caption,{value:t.value,table:t.value.dataFrame})})(),generateHelm:r.input.forProperty(e(ar.generateHelm).property),chiralityEngine:r.input.forProperty(e(ar.chiralityEngine).property),rules:{header:r.inlineText([to]),form:t}}}static async create(e){const t=new mr(e);return await t.initInputs(),t}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 e=r.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(((t,n)=>{r.dialog({title:Zn}).add(e).onOK((async()=>{const e=await this.getParams(),n=(await this.call.func.prepare(e).call(!0)).getOutputParamValue();t(n)})).onCancel((()=>{n(new Error("Cancelled by user"))})).show()}))}widget(){throw new Error("not implemented")}}var fr=function(e,t,n,o){var r,i=arguments.length,s=i<3?t:null===o?o=Object.getOwnPropertyDescriptor(t,n):o;if("object"==typeof Reflect&&"function"==typeof Reflect.decorate)s=Reflect.decorate(e,t,n,o);else for(var a=e.length-1;a>=0;a--)(r=e[a])&&(s=(i<3?r(s):i>3?r(t,n,s):r(t,n))||s);return i>3&&s&&Object.defineProperty(t,n,s),s},gr=function(e,t){if("object"==typeof Reflect&&"function"==typeof Reflect.metadata)return Reflect.metadata(e,t)},yr=function(e,t){return function(n,o){t(n,o,e)}};o.decorators||(o.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((e=>{o.decorators[e]||(o.decorators[e]=function(e){return function(e,t,n){}})}));const br=new R({debug:!0});let vr=null;class Cr{static async oligoToolkitApp(){await br.initLibData();const e=await async function(e){const t={"Mermadesynthesis:merMadeSynthesis":{tabName:"SYNTHESIZE",parameters:Kt(e)}},n={};for(const[e,r]of Object.entries(t)){let t;try{t=await o.functions.call(e,r.parameters);const i=new zt(r.tabName,t);i.initView(),n[r.tabName]=()=>i.getView()}catch(t){console.warn(`Plugin ${e} not loaded, reason:`,t);continue}}return n}(br);if(!e)throw new Error("External app view factories not loaded");const t=new Yt(e,br);return await t.getAppView()}static async init(){return null===vr&&br.startInit(vr=async function(){const[e,t]=await Promise.all([(0,bn.b2)(),(0,c.pj)()]);br.completeInit(e,t.getMonomerLib())}()),vr}static async oligoTranslatorApp(){return await xr("Oligo Translator")}static async oligoPatternApp(){return await xr("Oligo Pattern")}static async oligoStructureApp(){return await xr("Oligo Structure")}static async getTranslationHelper(){return await br.initLibData(),br}static getCodeToWeightsMap(){const e=br.monomerLibWrapper.getCodesToWeightsMap();return Object.fromEntries(e)}static validateSequence(e){const t=br.createSequenceValidator(e),n=br.createFormatDetector(e).getFormat();return null!==n&&t.isValidSequence(n)}static getMolfileFromGcrsSequence(e,t){return new At(e,t,"GCRS").convert()}static linkStrands(e){return Tt(e,!0)}static async demoTranslateSequence(){await async function(){await v((async()=>{const e=await Cr.oligoTranslatorApp();o.shell.addView(e)}))}()}static async demoOligoPattern(){await async function(){await v((async()=>{const e=await Cr.oligoPatternApp();o.shell.addView(e)}))}()}static async demoOligoStructure(){await async function(){await v((async()=>{const e=await Cr.oligoStructureApp();o.shell.addView(e),["Afcgacsu","Afcgacsu","Afcgacsu"].forEach((async(e,t)=>{await async function(e,t){await i.delay(500);const n=document.querySelectorAll(".st-colored-text-input > textarea")[e];n.value=t;const o=new Event("input");n.dispatchEvent(o)}(t,e)}))}))}()}static async translateOligonucleotideSequence(e,t,n){return await br.initLibData(),br.createFormatConverter(e,t).convertTo(n)}static async polyToolConvertTopMenu(){await async function(){await br.initPromise;let e=null;try{e=await async function(){const e=[],t=()=>{for(const t of e)t.unsubscribe()};try{let n;const s=o.shell.t.columns.bySemTypeAll(i.SEMTYPE.MACROMOLECULE),a=s.filter((e=>br.seqHelper.getSeqHandler(e).notation===Ot.Hi.CUSTOM));if(!n){if(s.length<1)throw new Error("No dataframe with macromolecule columns open");if(a.length<1){const e=i.Func.find({package:"Bio",name:"toAtomicLevel"})[0];return e?(e.prepare().edit(),null):(o.shell.warning("Polytool requires a macromolecule column with custom notation. \n\nUse Top menu | Bio | Transform | To Atomic Level."),null)}n=s[0]}const l=r.input.column("Column",{table:n.dataFrame,value:n,filter:e=>a.includes(e)}),c=r.input.bool(Qn,{value:!0});r.tooltip.bind(c.root,"Add HELM column");const u=r.input.bool("Linearize",{value:!0});r.tooltip.bind(u.root,"Make representation linear if possible");const h=r.input.bool(Jn,{value:!0}),d=r.input.bool(Xn,{value:!0});let p;const m=new jn._v(jn.MU,jn.yy,".json",{onValueChanged:e=>{p=e}}),f=r.inlineText([to]);r.tooltip.bind(f,"Add or specify rules to use");const g=await m.getForm(),y=r.divV([l,c,u,h,d,f,g]),b=async()=>{try{const e=await m.getActive();await ro(l.value,c.value,u.value,h.value,d.value,e)}catch(e){zn(e)}},v=r.dialog(Zn).add(y).onOK((()=>{b()}));return e.push(v.onClose.subscribe((()=>{t()}))),v.history((()=>({generateHelm:c.value,chiralityEngine:h.value,rules:p})),(e=>{c.value=e.generateHelm,h.value=e.chiralityEngine,m.setActive(e.rules)})),v}catch(e){throw t(),e}}(),e?.show()}catch(e){const[t,n]=(0,vn.AP)(e);o.shell.warning("To run PolyTool Conversion, open a dataframe with macromolecules"),br.logger.error(t,void 0,n)}}()}static async getPolyToolConvertEditor(e){const t=await mr.create(e);return await t.showDialog()}static async polyToolConvert2(e,t,n,o,r){return(await ro(t,n,!1,o,!1,r))[0]}static async polyToolEnumerateHelmTopMenu(){await ir(o.shell.tv?.dataFrame.currentCell)}static async polyToolEnumerateChemTopMenu(){wo()}static async chemEnumerateReactionsTopMenu(){wo()}static async polyToolColumnChoice(e,t){var n;(function(e){e.semType=i.SEMTYPE.MACROMOLECULE,e.setTag("aligned","SEQ"),e.setTag("alphabet",Ot.YI.PT)})(n=t),n.meta.units=Ot.Hi.SEPARATOR,n.setTag("separator","-"),await o.data.detectSemanticTypes(e)}static async createMonomerLibraryForPolyTool(e){const t=await e.readAsString(),n=new pr(e.fileName,t),o=await n.getJson(),r=e.fileName.replace(/\.csv$/,".json"),s=JSON.stringify(o,null,2);i.Utils.download(r,s)}static async ptEnumeratorHelmApp(){await ir()}static async ptEnumeratorChemApp(){return await async function(){await br.initPromise;try{const e=Ao(await(0,Vn.j)(),null),t=r.bigButton("Enumerate",(async()=>{await e.execute()}));e.bindActionButton(t);const n=i.View.create();return n.name=so,n.box=!0,n.root.appendChild(r.divV([e.root,r.div([t],{style:{padding:"8px 4px 0"}})],{style:{height:"100%",width:"100%",padding:"8px"}})),n}catch(e){return zn(e),null}}()}static async getPtHelmEnumeratorDialog(e){return ir(e)}static async getPtChemEnumeratorDialog(e){return wo(e)}static async getPtOligoEnumeratorDialog(e){if(!e||null==e.value)return ir(void 0,!0);const t=String(e.value),n=i.Column.fromStrings("helm",[t]);return n.semType=i.SEMTYPE.MACROMOLECULE,n.meta.units="helm",n.setTag("aligned","SEQ"),n.setTag("alphabet","RNA"),n.setTag("cell.renderer","helm"),ir(i.DataFrame.fromColumns([n]).cell(0,"helm"),!0)}static async enumerateSingleHelmSequence(e,t,n,o=!1){return await sr(e,"macromolecule",null,{type:So.aK.Single,placeholders:t.map(((e,t)=>({position:e,monomers:n[t]})))},!!o&&{generateHelm:!0,chiralityEngine:!0,highlightMonomers:!1,rules:[]},br.helmHelper)}static async enumerateSingleHelmSequenceWithNaturalAAs(e,t=!1){const n=(0,Ot.qp)(e).length,o=Array.from({length:n},((e,t)=>t)),r=o.map((e=>["A","C","D","E","F","G","H","I","K","L","M","N","P","Q","R","S","T","V","W","Y"]));return await Cr.enumerateSingleHelmSequence(e,o,r,t)}static async getPolyToolCombineDialog(){!async function(){const e=[],t=r.divV([]),n=s=>{const a=(()=>{const e=r.divH([]),t=r.input.table("Table",{value:void 0,tooltipText:"Table with sequences"}),n=r.input.choice("Column",{items:[],value:void 0,tooltipText:"Sequence 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u=e[s];u?t.insertBefore(a.root,u.root):t.appendChild(a.root),e.splice(s,0,a)};n(0);const s=r.input.string("Separator",{value:"-",tooltipText:"Separator for sequences",nullable:!1});r.dialog("Combine Sequences").add(t).add(s.root).onOK((async()=>{if(!function(){const t=e.map((e=>e.getValue())),n=t.map((e=>e.table)),o=t.map((e=>e.column));return n.every((e=>!!e))&&o.every((e=>!!e))}())return void o.shell.error("Please fill all the fields");const t=e.map((e=>e.getValue())),n=t.map((e=>e.table)),r=t.map((e=>e.column)),a=s.value,l=r.map(((e,t)=>n[t].col(e).toList().filter((e=>!!e))));let c=0;const u=l.reduce(((e,t)=>e*t.length),1);if(u>1e7)return void o.shell.error("Too many combinations. Maximum allowed is 10M");const h=new Array(u).fill(null),d=(e,t)=>{if(t===l.length)return void(h[c++]=e);const n=`${e}${e?a:""}`,o=l[t];for(let e=0;e<l[t].length;e++)d(n+o[e],t+1)};d("",0);const p=i.DataFrame.fromColumns([i.Column.fromStrings("Combined Sequences",h)]);p.name="Combined Sequences",await p.meta.detectSemanticTypes(),await o.data.detectSemanticTypes(p),o.shell.addTableView(p)})).show({resizable:!0})}()}static oligoNucleotideCellRenderer(){return new un}static async editOligoNucleotideCell(e){const t=await(0,bn.b2)(),n=r.div(),o=t.createWebEditorApp(n,e.cell.value??"");r.dialog({showHeader:!1,showFooter:!0}).add(n).onOK((()=>{const t=o.canvas.getHelm(!0).replace(/<\/span>/g,"").replace(/<span style='background:#bbf;'>/g,"");e.setValue(t)})).show({modal:!0,fullScreen:!0})}static oligoNucleotidePanel(e){return function(e){const t=e.value??"",n=(0,Jt.On)(t),o=n.sense.monomers.filter((e=>"nucleotide"===e.kind)).length,s=n.antisense?n.antisense.monomers.filter((e=>"nucleotide"===e.kind)).length:0,a=new Map,l=new Map,c=new Map,u=new Map,h=[...n.sense.monomers,...n.antisense?.monomers??[]];for(const e of h)if("nucleotide"===e.kind){const t=e;dn(a,t.sugar),t.phosphate&&dn(l,t.phosphate),t.base&&!(0,Xt.kT)(t.base)&&dn(u,t.base)}else dn(c,e.symbol);const d=r.divV([],{style:{fontSize:"12px"}});return d.appendChild(mn("Summary",r.tableFromMap({"Sense length":`${o} nt`,"Antisense length":s?`${s} nt`:"single-strand","Modifications used":pn(a,l,u),Conjugates:c.size?Array.from(c.entries()).map((([e,t])=>`${(0,Xt.rK)(e).meta.name} ×${t}`)).join(", "):"—"}))),d.appendChild(mn("Legend",function(e,t,n,o){const i=[],s=new Map;for(const[t,n]of e.entries()){const e=(0,Xt.Jy)(t);"r"!==e&&"d"!==e&&s.set(e,(s.get(e)??0)+n)}for(const[e,t]of s.entries()){const n=(0,Xt.xh)(e,null).meta;i.push({label:n.name,color:n.color,count:t})}const a=new Map;for(const[e,n]of t.entries()){const t=(0,Xt.$T)(e);"p"!==t&&a.set(t,(a.get(t)??0)+n)}for(const[e,t]of a.entries()){const n=(0,Xt.bM)(e).meta;i.push({label:`${n.name} (linkage)`,color:n.color,count:t})}for(const[e,t]of o.entries()){const n=(0,hn.Y)(e),o=n&&Xt.L1[n]?Xt.L1[n]:Xt.FN,r=n?`${e} (base, analog ${n})`:`${e} (base)`;i.push({label:r,color:o,count:t})}for(const[e,t]of n.entries()){const n=(0,Xt.rK)(e).meta;i.push({label:n.name,color:n.color,count:t})}if(0===i.length)return r.divText("No modifications. Chip color reflects the base (A/C/G/U).",{style:{fontSize:"12px",color:"var(--grey-4, #888)",lineHeight:"1.4"}});const l=i.map((({label:e,color:t,count:n})=>r.divH([r.div([],{style:{width:"14px",height:"14px",borderRadius:"3px",background:t,border:"1px solid rgba(0,0,0,0.15)",flexShrink:"0"}}),r.divText(e,{style:{fontSize:"12px",flex:"1"}}),r.divText(`×${n}`,{style:{fontSize:"11px",color:"var(--grey-4, #888)",fontVariantNumeric:"tabular-nums"}})],{style:{gap:"6px",alignItems:"center",marginBottom:"3px"}})));return r.divV(l)}(a,l,c,u))),i.Widget.fromRoot(d)}(e)}static oligoNucleotideStructuresPanel(e){return function(e){const t=(e.value??"").split("$")[0].split("|").map((e=>e.trim())).filter((e=>e.length>0));if(0===t.length)return i.Widget.fromRoot(r.divText("No HELM chains found",{style:{fontSize:"12px",color:"var(--grey-4, #888)"}}));const n=t.map((e=>(0,Jt.nj)(e.replace(fn,"$11{")+"$$$$"))),o=1===t.length?["Strand"]:["Sense","Antisense"],s=i.Column.fromStrings("helm",n);s.semType=i.SEMTYPE.MACROMOLECULE,s.meta.units="helm",s.setTag("aligned","SEQ"),s.setTag("alphabet","RNA"),s.setTag("cell.renderer","helm");const a=i.DataFrame.fromColumns([s]),l=r.accordion("oligo chemical structures");for(let e=0;e<a.rowCount;e++){const t=o[e],n=a.cell(e,"helm");l.addPane(t,(()=>gn(n,t)))}return i.Widget.fromRoot(l.root)}(e)}static async convertHelmToOligoNucleotide(e,t){const n=(0,yn.zZ)(e,t);return await o.data.detectSemanticTypes(e),n}static async combineSenseAntisenseToOligoNucleotide(e,t,n){const r=(0,yn.xE)(e,t,n);return await o.data.detectSemanticTypes(e),r}static applyNotationProviderForCyclized(e,t){e.setTag("aligned","SEQ"),e.setTag("alphabet","UN"),e.setTag(".alphabetIsMultichar","true"),e.meta.units=s.Hi.CUSTOM,t&&!e.tags[s.qE.separator]&&(e.tags[s.qE.separator]=t),e.tags["polytool-data-role"]="template",e.temp[l.notationProvider]=new or(t,br.helmHelper)}static async harmonizedSequenceNotationProviderConstructor(){return or}}async function xr(e){await br.initLibData();const t=function(e,t){switch(e){case"Oligo Translator":return new Wt(t);case"Oligo Pattern":return new it(t);case"Oligo Structure":return new Lt(t);default:throw new Error(`Unknown app name: ${e}`)}}(e,br);return await t.getAppView()}fr([o.decorators.app({icon:"img/icons/toolkit.png",browsePath:"Peptides | Oligo Toolkit",name:"Oligo 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h=0;h<e.length;h++)if(e[h].includes(t)){if(s){if(l&&(n||e[h]==i[o]+t)){a=!0,u=h;break}if(l||!n&&e[h]!=r[o]+t)continue;a=!0,u=h;break}if(n)s=!0,l=!0,c=h;else if(e[h]==r[o]+t)s=!0,l=!0,c=h;else{if(e[h]!=i[o]+t)continue;s=!0,l=!!n,c=h}}return[s,a,l,c,u]}function l(e,t){const n=[];for(let o=0;o<t.length;o++){const r=`(${t[o].code})`,[s,l]=(0,i.Ln)(t[o]);if(s.length>0)for(let t=0;t<s.length;t++){const[i,c,u,h,d]=a(e,r,!1,t,s,l);i&&c&&(u?n.push({firstIdx:h,secondIdx:d,ruleIdx:o}):n.push({firstIdx:d,secondIdx:h,ruleIdx:o}))}else{const[t,i,s,l,c]=a(e,r,!0);if(!t||!i)continue;s?n.push({firstIdx:l,secondIdx:c,ruleIdx:o}):n.push({firstIdx:c,secondIdx:l,ruleIdx:o})}}return n}function c(e,t,n){const o=[],r=[],i=[],s=[],a=n.length;for(let l=0;l<a;l++){if(-1==n[l].firstIdx)continue;const a=n[l].ruleIdx,c=e[a].code;t[n[l].firstIdx]=t[n[l].firstIdx].replace(`(${c})`,""),t[n[l].secondIdx]=t[n[l].secondIdx].replace(`(${c})`,""),o.push(n[l].firstIdx+1),r.push(n[l].secondIdx+1),i.push(e[a].firstLinkingGroup),s.push(e[a].secondLinkingGroup)}return[o,r,i,s]}function u(e,t,n){const o=[],r=[],i=[],s=n.length;for(let a=0;a<s;a++){if(-1==n[a].firstIdx)continue;const s=n[a].firstIdx,l=n[a].secondIdx,c=n[a].ruleIdx,u=e[c].code;t[s]=t[s].replace(`(${u})`,"")+`_${e[c].name}`,t[l]=t[l].replace(`(${u})`,"")+`_${e[c].name}`,o.push(s+1),r.push(l+1),i.push(n[a].ruleIdx)}return[o,r,i]}var h=n(3599);function d(e,t,n){const o=n.createHelmWebEditor().editor.m;let r=0;const i=new JSDraw2.Point(0,0);for(let e=0;e<t.length;e++)for(let n=0;n<t[e].length;n++){if(t[e][n]){const s=t[e][n],a={type:h.o.AA,i:e,j:n,continuousId:r},l=new JSDraw2.Atom(i,s,a);if(o.addAtom(l),0!==n){const e=o.atoms[r-1],t=o.atoms[r],n=new JSDraw2.Bond(e,t);n.r1=2,n.r2=1,o.addBond(n)}r++,i.x+=JSDraw2.Editor.BONDLENGTH}i.y+=4*JSDraw2.Editor.BONDLENGTH}for(let t=0;t<e.length;t++){const n=o.atoms[e[t].fMonomer-1],r=o.atoms[e[t].sMonomer-1],i=new JSDraw2.Bond(n,r);i.r1=e[t].fR,i.r2=e[t].sR,o.addBond(i)}return o}class p{constructor(e,t,n){this.helmHelper=n,this.underRules=!1,this.posToPosUnderRules=[],this.linkages=t,this.monomers=e,this.mol=d(t,e,n)}static fromSeparator(e,t){const[n,o]=function(e){const t=[],n=[],o=/(\(.\d+\))?\{[^\}]*\}/g,r=[];r.push(e.replaceAll(o,""));const i=e.matchAll(o);for(const e of i){const t=e[0];t&&r.push(t)}let s=0;for(let e=0;e<r.length;e++){const o=r[e].split("-"),i=new Array(o.length);let a=0;for(let t=0;t<o.length;t++){const r=o[t].replace("{","").replace("}","");""!==r?(i[t]=r,s++,a++):n.push({fChain:e,sChain:e+1,fMonomer:s,sMonomer:s+1,fR:1,sR:1})}t.push(i.slice(0,a))}return[n,t]}(e);return new p(o,n,t)}static fromHelm(e,t){const[n,i]=function(e){const t=/(\w+\{.*\})\$(.*)\$(.*)\$(.*)\$/g.exec(e),n=[t[1],t[2],t[3],t[4]],i=n[0].split("|"),s=n[1].split("|"),a=new Array(i.length),l=[];for(let e=0;e<i.length;e++){const t=i[e].indexOf("{"),n=i[e].indexOf("}");a[e]=i[e].slice(t+1,n).split(".").map((e=>(0,r.D)(e)))}for(let e=0;e<s.length;e++)if(""!==s[e]&&"V2.0"!==s[e]){const t=s[e].split(","),n=parseInt(t[0].replace("PEPTIDE",""))-1,r=parseInt(t[1].replace("PEPTIDE",""))-1,i=t[2].split("-"),c=i[0].split(":"),u=i[1].split(":");l.push({fChain:n,sChain:r,fMonomer:(0,o.j)(parseInt(c[0]),n,a),sMonomer:(0,o.j)(parseInt(u[0]),r,a),fR:parseInt(c[1].replace("R","")),sR:parseInt(u[1].replace("R",""))})}return[l,a]}(e);return new p(i,n,t)}getNotation(){return function(e){const t=e.atoms,n=e.bonds,o=[],r=[];for(let e=0;e<n.length;e++)n[e].a1.bio.i!==n[e].a2.bio.i&&r.push(e);for(let e=0;e<t.length;e++){const n=t[e].bio?.i;n+1>o.length?o.push(1):o[n]++}const i=new Array(o.length);let s=0;for(let e=0;e<o.length;e++){const n=new Array(o[e]);for(let r=0;r<o[e];r++)n[r]=t[s].elem,s++;i[e]=n}let a="";for(let e=0;e<i.length;e++){let t="";for(let n=0;n<i[e].length;n++)t+=`${0==n?"":"-"}${i[e][n]}`;if(0!==e){const e=/(\(.\d+\))/,n=t.match(e);t=t.replace(n?.[0],""),t=`${n?n?.[0]:""}{${t}}`}else if(i.length>1){const e=0==n[r[0]].a1.bio.i&&0==n[r[0]].a1.bio.j,o=1==n[r[0]].a2.bio.i&&0==n[r[0]].a1.bio.j;e&&o&&(t+="-")}a+=t}return a}(this.mol)}getHelm(){return this.underRules?s(this.linkagesUnderRules,this.monomersUnderRules):s(this.linkages,this.monomers)}applyRules(e){const t=this.getNotation(),[n,o,r]=function(e,t){const n=[],o=[],r=[],i=t.heterodimerCode,s=t.homodimerCode,a=null!==i?e.split(`(${t.heterodimerCode})`):"";null!==i&&a.length>1?(r.push({fChain:0,sChain:1,fMonomer:1,sMonomer:1,fR:1,sR:1}),n.push(a[1].replaceAll("{","").replaceAll("}","")),n.push(a[2].replaceAll("{","").replaceAll("}","")),o.push(!1),o.push(!1)):(n.push(e),o.push(!1));for(let e=0;e<n.length;e++)if(null!==s&&n[e].includes(`(${s})`)){const t=n.length;r.push({fChain:e,sChain:t,fMonomer:1,sMonomer:1,fR:1,sR:1});const i=n[e].replace(`(${s})`,""),a=i.indexOf("{"),l=i.slice(0,a),c=i.replace(l,"").replaceAll("{","").replaceAll("}","");n[e]=l+c,n.push(c),o.push(!0)}return[r,n,o]}(t,e),i=new Array(o.length);let s=0;for(let e=0;e<o.length;e++)if(i[e]=o[e].split("-"),r[e]){const t=this.posToPosUnderRules.length-i[e].length;for(let n=0;n<i[e].length;n++)this.posToPosUnderRules[t+n].push(s),s++}else for(let t=0;t<i[e].length;t++)this.posToPosUnderRules.push([s]),s++;!function(e,t,n){for(let o=0;o<e.length;o++){const r=e[o],i=l(r,n.linkRules),[s,a,u,h]=c(n.linkRules,r,i);for(let e=0;e<s.length;e++)t.push({fChain:o,sChain:o,fMonomer:s[e],sMonomer:a[e],fR:u[e],sR:h[e]});e[o]=r}}(i,n,e),function(e,t,n){for(let o=0;o<e.length;o++){const r=l(e[o],n.reactionRules),[i,s,a]=u(n.reactionRules,e[o],r);i.length>=1&&(t.push({fChain:o,sChain:e.length,fMonomer:i[0],sMonomer:1,fR:3,sR:1}),t.push({fChain:o,sChain:e.length,fMonomer:s[0],sMonomer:1,fR:3,sR:2}),e.push([n.reactionRules[a[0]].name]))}}(i,n,e),this.underRules=!0,this.linkagesUnderRules=n,this.monomersUnderRules=i,this.molUnderRules=d(n,i,this.helmHelper)}check(e=!1){const t=[],n=this.monomers.map((e=>e.length)).reduce(((e,t)=>e+t),0);this.mol.atoms.length!==n&&t.push(`The mol atoms count ${this.mol.atoms.length} does not match the total number ${n} of chains' monomers.`);const o=this.monomers.map((e=>e.length-1)).reduce(((e,t)=>e+t),0)+this.linkages.length;this.mol.bonds.length!==o&&t.push(`The mol bonds count ${this.mol.bonds.length} does not match the total number ${o} in- and inter-chain linkages.`);let r=0;for(let e=0;e<this.monomers.length;++e){const n=this.monomers[e];for(let e=0;e<n.length;++e)try{const o=n[e],i=this.mol.atoms[r];i.bio.continuousId!==r&&t.push(`Atom #${r} has incorrect .bio.continuousId: ${i.bio.continuousId}.`),i.elem!==o&&t.push(`Atom #${r} elem: '${i.elem}' does not match chain monomer: '${o}'.`)}finally{r++}}if(e&&t.length>0)throw new Error(`Chain errors:\n${t.map((e=>` ${e}`)).join("\n")}`);return t}}},4229:(e,t,n)=>{"use strict";n.d(t,{b:()=>s});var o=n(9192),r=n(6307),i=n(6345);function s(e,t,n){const s=new Array(e.length),a=new Array(e.length),l=new Array(e.length);for(let c=0;c<e.length;c++)try{if(null==e[c])s[c]="";else{const o=r.s.fromSeparator(e[c],n);o.applyRules(t),a[c]=!(o.monomersUnderRules.length>1||o.linkagesUnderRules.length>0),s[c]=o.getHelm(),l[c]=o.posToPosUnderRules}}catch(e){const[t,n]=(0,o.AP)(e);i._package.logger.error(t,void 0,n),s[c]=""}return[s,a,l]}},2125:(e,t,n)=>{"use strict";function o(e,t){let n,o=e;for(n=0;n<t.length&&o>=t[n].length;++n)o-=t[n].length;return[o,n]}function r(e,t,n){let o=0;for(let e=0;e<t;++e)o+=n[e].length;return o+e}n.d(t,{M:()=>o,j:()=>r})},6694:(e,t,n)=>{"use strict";n.d(t,{MU:()=>V,yy:()=>j,_v:()=>J,Ln:()=>te,Q4:()=>ee});var o=n(6082),r=n(4328),i=n(7389),s=n(1991),a=n.n(s),l=function(e,t,n,o){return new(n||(n=Promise))((function(r,i){function s(e){try{l(o.next(e))}catch(e){i(e)}}function a(e){try{l(o.throw(e))}catch(e){i(e)}}function l(e){var t;e.done?r(e.value):(t=e.value,t instanceof n?t:new n((function(e){e(t)}))).then(s,a)}l((o=o.apply(e,t||[])).next())}))};class c{constructor(e,t,n=".csv",o){this.path=e,this.userStorageName=t,this.ext=n,this.options=o,this.inputs=null,"/"!==this.path[this.path.length-1]&&(this.path+="/"),"."!==this.ext[0]&&(this.ext="."+this.ext)}getUserSettings(){return l(this,void 0,void 0,(function*(){if(this.settings)return this.settings;const e=r.userSettings.getValue(this.userStorageName,"Settings"),t=e?JSON.parse(e):{excluded:[],explicit:[]};return t.explicit=t.explicit instanceof Array?t.explicit:[],t.excluded=t.excluded instanceof Array?t.excluded:[],this.settings=t}))}setUserSettings(e){this.settings=e,r.userSettings.add(this.userStorageName,"Settings",JSON.stringify(e))}getAllAvailable(){return l(this,void 0,void 0,(function*(){return(yield r.dapi.files.list(this.path)).map((e=>e.fullPath.replace(`${this.path}`,"")))}))}getActive(){return l(this,void 0,void 0,(function*(){const e=yield this.getUserSettings();return e.explicit.length>0?e.explicit:(yield this.getAllAvailable()).filter((t=>!e.excluded.includes(t)))}))}setActive(e){const t=new Set(e);for(const[e,n]of this.inputs.entries())n.value=t.has(e)}createInput(e,t){const n=i.input.bool(e,{value:t,onValueChanged:t=>this.updateSelectionStatus(e,t)});return n.addOptions(i.button(i.iconFA("trash"),(()=>{i.dialog({title:"Warning"}).add(i.divText(`Delete file '${e}'?`)).onOK((()=>{n.root.remove(),this.availableRemove(e)})).show()}),`Delete ${e}`)),n}getInputs(){return l(this,void 0,void 0,(function*(){this.inputs=new Map;const e=yield this.getAllAvailable(),t=yield this.getActive(),n=new Array(e.length);for(let o=0;o<e.length;o++){const r=t.includes(e[o]);n[o]=this.createInput(e[o],r),this.inputs.set(e[o],n[o])}return this.fireOnValueChanged(),n}))}getForm(){return l(this,void 0,void 0,(function*(){const e=yield this.getInputs(),t=i.divV(e);return i.divV([t,i.button("ADD",(()=>l(this,void 0,void 0,(function*(){let e="";if(e=yield this.getNewAvailable(),""!==e){const n=this.createInput(e,!0);t.append(n.root),this.inputs.set(e,n),this.fireOnValueChanged()}}))))])}))}fireOnValueChanged(){var e;null===(e=this.options)||void 0===e||e.onValueChanged(a()(this.inputs.entries()).filter((([e,t])=>t.value)).map((([e,t])=>e)).toArray())}updateSelectionStatus(e,t){return l(this,void 0,void 0,(function*(){const n=yield this.getUserSettings();if(!n.excluded.includes(e)!==t){if(t){const t=n.excluded.indexOf(e);t>-1&&n.excluded.splice(t,1)}else n.excluded.push(e);this.fireOnValueChanged(),this.setUserSettings(n)}}))}availableRemove(e){return l(this,void 0,void 0,(function*(){this.inputs.delete(e),this.fireOnValueChanged();const t=yield this.getUserSettings(),n=t.excluded.indexOf(e);n>-1&&t.excluded.splice(n,1),this.setUserSettings(t),yield r.dapi.files.delete(this.path+e),r.shell.info(`File ${e} successfully deleted`)}))}getNewAvailable(){return l(this,void 0,void 0,(function*(){return new Promise(((e,t)=>{o.Utils.openFile({accept:this.ext,open:t=>l(this,void 0,void 0,(function*(){const n=t.name,o=yield t.arrayBuffer();yield r.dapi.files.write(this.path+`${t.name}`,new Uint8Array(o)),e(n)}))})}))}))}}var u=n(6345),h=n(9124),d=n(4229),p=n(439),m=n(5174),f=n(5412),g=n(6717),y=n(8312);function b(e){let t=e.replaceAll(/\[R[1-9]\]/g,(e=>`[*:${e[2]}]`));return t=t.replaceAll(/\[\d\*\]/g,(e=>`[*:${e[1]}]`)),t.replaceAll(/\[\d\*\:\d\]/g,(e=>`[*:${e[1]}]`))}function v(e){return e.replaceAll(/\[\*\:\d\]/g,(e=>`[C:${e[3]}]`))}function C(e){return e.replaceAll(/\[C\:\d\]/g,(e=>`[*:${e[3]}]`))}function x(e,t){const n=t?.firstReactantSmiles?C(t.firstReactantSmiles):"[*:1]C",o=t?.secondReactantSmiles?C(t.secondReactantSmiles):"[*:2]C",s=t?.productSmiles?C(t.productSmiles):"[*:1]CC[*:2]",a=t?.code,l=t?.firstMonomers??[],c=t?.secondMonomers??[],u=t?.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"}),p=i.input.string("Second monomers",{value:c.join(","),nullable:!1,tooltipText:"Comma-separated list of monomers for the second reactant"}),m=i.input.string("Result monomer name",{value:u,nullable:!1,tooltipText:"Name of the resulting pseudo-monomer generated by the reaction of the two reactants"}),f=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:o,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(!f||!g||!y)return"Inputs not initialized yet";const e=v(b(r.chem.convert(f.value??"",r.chem.Notation.Unknown,r.chem.Notation.Smiles))),t=v(b(r.chem.convert(g.value??"",r.chem.Notation.Unknown,r.chem.Notation.Smiles))),n=v(b(r.chem.convert(y.value??"",r.chem.Notation.Unknown,r.chem.Notation.Smiles)));return e&&t&&n?-1==e.indexOf("[C:1]")?"First Reactant must contain R1-group":-1==t.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"};f.addValidator(x),g.addValidator(x),y.addValidator(x);const w=i.dialog(t?"Edit Reaction Rule":"Add Reaction Rule").add(h).add(m).add(d).add(p).add(f).add(g).add(y);w.addButton("Save",(()=>{const n=x();if(null!=n)return void r.shell.warning(n);const o=v(b(r.chem.convert(f.value??"",r.chem.Notation.Unknown,r.chem.Notation.Smiles))),i=v(b(r.chem.convert(g.value??"",r.chem.Notation.Unknown,r.chem.Notation.Smiles))),s=v(b(r.chem.convert(y.value??"",r.chem.Notation.Unknown,r.chem.Notation.Smiles)));e({code:h.value,resultMonomerName:m.value,firstMonomers:d.value.split(",").map((e=>e.trim())).filter((e=>e.length>0)),secondMonomers:p.value.split(",").map((e=>e.trim())).filter((e=>e.length>0)),firstReactantSmiles:o,secondReactantSmiles:i,productSmiles:s,rowIndex:t?.rowIndex}),w.close()})),w.show()}const w="Links",A="Reactions";class T{constructor(e,t){this.v=null,this.substituteReactionGridDataFrame=null,this.rules=e;const n=this.rules.getLinkRulesDf();this.linkRuleDataFrame=n.res,this.addLinkRulesFunc=n.addNewRow;const o=this.rules.getSynthesisRulesDf();this.addSynthRulesFunc=e=>{o.addNewRow(e),this.rules.setSynthesisRules(o.df),this.synthRuleDataFrame=o.df,this.substituteReactionGridDataFrame?.(),this.save()},this.synthRuleDataFrame=o.df,this.fileName=t;const r=this.rules.homodimerCode?this.rules.homodimerCode:"",s=this.rules.heterodimerCode?this.rules.heterodimerCode:"";this.homoDimerInput=i.input.string("Homo dimer",{value:r,onValueChanged:()=>{},nullable:!1}),this.heteroDimerInput=i.input.string("Hetero dimer",{value:s,onValueChanged:()=>{},nullable:!1})}async getAndAddView(){if(this.v)try{const e=Array.from(r.shell.views).find((e=>e.name===this.v.name));if(!e)throw this.v.detach(),this.v.close(),new Error("View is closed, making it null in catch statement");r.shell.v=e}catch(e){this.v=null}return this.v||(this.v=o.View.create(),this.v.name=`Manage Polytool Rules - ${this.fileName}`,this.v.append(await this.getForm()),this.v=r.shell.addView(this.v),r.shell.v=this.v),this.v}static async getInstance(e){if(!this.instances[e]){const t=await ee([e]);this.instances[e]=new T(t,e)}return this.instances[e]}save(){this.rules.homodimerCode=this.homoDimerInput.value,this.rules.heterodimerCode=this.heteroDimerInput.value,this.rules.setLinkRules(this.linkRuleDataFrame),this.rules.setSynthesisRules(this.synthRuleDataFrame);const e={homodimerCode:this.rules.homodimerCode,heterodimerCode:this.rules.heterodimerCode,linkRules:this.rules.linkRules,reactionRules:this.rules.reactionRules},t=JSON.stringify(e,void 0,2);u._package.files.writeAsText(`polytool-rules/${this.fileName}`,t),r.shell.info(`Polytool rules at ${this.fileName} was updated`)}createGridDiv(e,t,n){const o=i.h1(e,"polytool-grid-header");i.tooltip.bind(o,n),o.style.marginTop="10px",o.style.marginRight="10px",t.root.style.height="100%";const r=i.splitV([i.box(o,{style:{maxHeight:"60px"}}),t.root]);return r.style.height="100%",r}async getLinkExamplesGrid(){const e=[];for(let t=0;t<this.rules.linkRules.length;t++){const n=this.rules.linkRules[t].code,[o,r]=te(this.rules.linkRules[t]);for(let t=0;t<o.length;t++){const i=`${o[t]}(${n})-A-A-A-A-${r[t]}(${n})`;e.push(i)}}const t=await(0,h.b2)(),[n,r,i]=(0,d.b)(e,this.rules,t),s=o.Column.fromStrings("Monomers",e),a=o.Column.fromStrings("Helm",n);return u.PackageFunctions.applyNotationProviderForCyclized(s,"-"),s.semType=o.SEMTYPE.MACROMOLECULE,a.semType=o.SEMTYPE.MACROMOLECULE,a.meta.units=p.Hi.HELM,a.setTag(o.TAGS.CELL_RENDERER,"helm"),o.DataFrame.fromColumns([s,a]).plot.grid()}async getReactionExamplesGrid(){const e=[];for(let t=0;t<this.rules.reactionRules.length;t++){const n=this.rules.reactionRules[t].code,[o,r]=te(this.rules.reactionRules[t]);for(let t=0;t<o.length;t++){const i=`${o[t]}(${n})-A-A-A-A-${r[t]}(${n})`;e.push(i)}}const t=await(0,h.b2)(),[n,r,i]=(0,d.b)(e,this.rules,t),s=o.Column.fromStrings("Monomers",e),a=o.Column.fromStrings("Helm",n),l=o.DataFrame.fromColumns([s,a]);s.semType=o.SEMTYPE.MACROMOLECULE;const c=await(0,g.j)(),b=await(0,y.Q)();u.PackageFunctions.applyNotationProviderForCyclized(s,"-"),s.tags[o.TAGS.CELL_RENDERER]="Sequence",a.semType=o.SEMTYPE.MACROMOLECULE,a.meta.units=p.Hi.HELM,a.setTag(o.TAGS.CELL_RENDERER,"helm");const v=await(0,m.A)(this.rules),C=a.temp;C[".mm.cellRenderer.overriddenLibrary"]=v,a.temp=C;const x=await(0,f.m)(a,e,r,!0,!1,!1,v,c,b);return x.name="molfile(sequence)",x.semType=o.SEMTYPE.MOLECULE,l.columns.add(x),l.plot.grid()}async getForm(){const e=this.linkRuleDataFrame.plot.grid({showAddNewRowIcon:!1,allowEdit:!1,rowHeight:60});e.onCellDoubleClick.subscribe((()=>{if(!e.dataFrame||-1==e.dataFrame.currentRowIdx||null==e.dataFrame.currentRowIdx)return;const t=e.dataFrame.currentRowIdx,n={row:t,code:this.linkRuleDataFrame.get("code",t),firstMonomers:this.linkRuleDataFrame.get("firstMonomers",t),secondMonomers:this.linkRuleDataFrame.get("secondMonomers",t),firstLinkingGroup:this.linkRuleDataFrame.get("firstLinkingGroup",t),secondLinkingGroup:this.linkRuleDataFrame.get("secondLinkingGroup",t)};this.getAddNewLinkRuleDialog(n)}));const t=this.createGridDiv("Rules",e,"specification for monomers to link and linking positions"),n=this.createGridDiv("Examples",await this.getLinkExamplesGrid(),"specification for monomers to link and linking positions");t.style.width="50%",n.style.width="50%";const o=i.h1("Monomers","polytool-grid-header");i.tooltip.bind(o,"Click different cobination to see how monomers will link"),this.linkCards=await this.rules.getLinkCards();const r=i.splitV([i.box(o,{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 e=this.linkRuleDataFrame.currentRowIdx;-1!==e&&null!=e&&(i.empty(r),r.append(i.splitV([i.box(o,{style:{maxHeight:"30px"}}),this.linkCards[e].root])),this.linkCards[e].render(),await this.linkCards[e].reset())}));const s=i.splitH([t,r],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 e=a.dataFrame.currentRowIdx;x((e=>this.addSynthRulesFunc(e)),{rowIndex:e,code:this.synthRuleDataFrame.get("code",e),firstMonomers:this.synthRuleDataFrame.get("firstMonomers",e).split(",").map((e=>e.trim())).filter((e=>e)),secondMonomers:this.synthRuleDataFrame.get("secondMonomers",e).split(",").map((e=>e.trim())).filter((e=>e)),resultMonomerName:this.synthRuleDataFrame.get("name",e),firstReactantSmiles:this.synthRuleDataFrame.get("firstReactant",e),secondReactantSmiles:this.synthRuleDataFrame.get("secondReactant",e),productSmiles:this.synthRuleDataFrame.get("product",e)})}));const l=this.createGridDiv("Rules",a),c=await this.getReactionExamplesGrid(),u=this.createGridDiv("Examples",c);this.substituteReactionGridDataFrame=async()=>{const e=await this.getReactionExamplesGrid();c.dataFrame=e.dataFrame},l.style.width="50%",u.style.width="50%";const h=i.divH([l,u]),d=i.divV([this.homoDimerInput,this.heteroDimerInput]),p=i.tabControl({Links:s,Reactions:h,Dimers:d},!1);i.tooltip.bind(p.getPane(w).header,"Specify rules to link monomers based on HELM notation"),i.tooltip.bind(p.getPane(A).header,"Specify rules to perform reactions within monomers"),i.tooltip.bind(p.getPane("Dimers").header,"Specify symbols for homodimeric and heterodimeric codes"),p.root.style.height="100%",p.root.style.width="100%",p.root.classList.add("rules-manager-form-tab-control"),p.header.style.marginBottom="10px";const m=i.divV([p.root]),f=[i.bigButton("Save",(()=>{this.save()})),i.button("Add rule",(()=>{const e=p.currentPane.name;e==w?this.getAddNewLinkRuleDialog():e==A&&x((e=>this.addSynthRulesFunc(e)))})),i.button("Remove rule",(()=>{const t=p.currentPane.name;if(t==w){if(null==this.linkRuleDataFrame||-1==this.linkRuleDataFrame.currentRowIdx||null==this.linkRuleDataFrame.currentRowIdx)return;const t=e.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(t),this.rules.setLinkRules(this.linkRuleDataFrame),this.save()})).show()}else if(t==A){if(null==this.synthRuleDataFrame||-1==this.synthRuleDataFrame.currentRowIdx||null==this.synthRuleDataFrame.currentRowIdx)return;const e=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(e),this.rules.setSynthesisRules(this.synthRuleDataFrame),this.substituteReactionGridDataFrame?.(),this.save()})).show()}}))];return this.v.setRibbonPanels([f]),m.style.height="100%",m.style.alignItems="center",p.root}getAddNewLinkRuleDialog(e){const t=i.input.int("Code",{nullable:!1,value:e?.code}),n=i.input.string("First monomers",{placeholder:"E.g. C,D,E",value:e?.firstMonomers,tooltipText:"Comma separated list of first monomers applicable for the rule. If left empty, all monomers will be considered",nullable:!0}),o=i.input.string("Second monomers",{placeholder:"E.g. C,D,E",value:e?.secondMonomers,tooltipText:"Comma separated list of second monomers applicable for the rule. If left empty, all monomers will be considered",nullable:!0}),r=e?.firstLinkingGroup?`R${e.firstLinkingGroup}`:"R3",s=e?.secondLinkingGroup?`R${e.secondLinkingGroup}`:"R3",a=i.input.choice("First linking group",{value:r,items:["R1","R2","R3","R4"],tooltipText:"Specifies which R-group of the first monomer will be used for linking",nullable:!1}),l=i.input.choice("Second linking group",{value:s,items:["R1","R2","R3","R4"],tooltipText:"Specifies which R-group of the second monomer will be used for linking",nullable:!1});i.dialog("Add new link rule").add(t).add(n).add(o).add(a).add(l).onOK((async()=>{const r=t.value,i=(n.value??"").split(",").map((e=>e.trim())).filter((e=>e)).join(","),s=(o.value??"").split(",").map((e=>e.trim())).filter((e=>e)).join(","),c=parseInt(a.value.substring(1)),u=parseInt(l.value.substring(1));this.addLinkRulesFunc({code:r,firstMonomers:i??"",secondMonomers:s??"",firstLinkingGroup:c,secondLinkingGroup:u,row:e?.row}),this.rules.setLinkRules(this.linkRuleDataFrame),this.linkCards=await this.rules.getLinkCards(),this.save()})).show()}}T.instances={};var E=n(5072),S=n.n(E),N=n(7825),I=n.n(N),M=n(7659),P=n.n(M),_=n(5056),L=n.n(_),O=n(540),R=n.n(O),$=n(1113),D=n.n($),B=n(890),F={};F.styleTagTransform=D(),F.setAttributes=L(),F.insert=P().bind(null,"head"),F.domAPI=I(),F.insertStyleElement=R(),S()(B.A,F),B.A&&B.A.locals&&B.A.locals;var k=n(2003);class H{get selected(){return this._selected}set selected(e){this._selected=e,this.root.style.border=e?"2px solid var(--green-2)":"2px solid var(--grey-2)"}constructor(e,t){this.monomer=e,this.monomerSymbol=t,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 e=this.monomer.smiles&&r.chem.checkSmiles(this.monomer.smiles)?r.chem.drawMolecule(this.monomer.smiles,150,120):r.chem.drawMolecule(this.monomer.molfile??"",150,120);this.root.appendChild(e);const t=i.divH([i.divText("Monomer Name: "),i.divText(this.monomer.name)],{classes:"monomer-card-info-rules"});if(this.root.appendChild(t),i.tooltip.bind(t,this.monomer.name),this.monomer.lib?.source){const e=i.divH([i.divText("Source: "),i.divText(this.monomer.lib.source)],{classes:"monomer-card-info-rules"});this.root.appendChild(e),i.tooltip.bind(e,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 ${this.monomerSymbol} not found in libraries`],{style:{textAlign:"center",height:"100%"}}))}}class G{constructor(e,t,n,o,r){this.firstMonomers=e,this.secondMonomers=t,this.code=o,this.rules=r,this.root=i.divH([],{style:{width:"100%",overflow:"hidden",visibility:"visible"},classes:"monomer-cards"});const s=!e?.length,a=!t?.length;s&&(this.firstMonomers=e=["C","D","E","F","G"]),a&&(this.secondMonomers=t=["D","C","E","F","G"]),this.actionable=!0;const l=i.divH([],{style:{overflowX:"auto",width:"100%"}}),c=i.divH([],{style:{overflowX:"auto",width:"100%"}});this.resulting=i.divH([],{style:{overflowX:"auto",width:"100%",minHeight:"150px"}});const u=i.h2("First Monomer"+(s?" (Applied to all monomers, example list shown)":""),{style:{width:"100%"}}),h=i.h2("Second Monomer"+(a?" (Applied to all monomers, example list shown)":""),{style:{width:"100%"}}),d=i.divV([u,l,h,c,this.resulting]);this.cardsFirst=e.map((e=>new H(n.getMonomer("PEPTIDE",e),e))),this.cardsSecond=t.map((e=>new H(n.getMonomer("PEPTIDE",e),e))),this.cardsFirst.forEach((e=>{e.root.onclick=()=>{this.cardsFirst.forEach((e=>e.selected=!1)),e.selected=!0,this.firstCard=e,this.reset()},l.appendChild(e.root)})),this.cardsSecond.forEach((e=>{e.root.onclick=()=>{this.cardsSecond.forEach((e=>e.selected=!1)),e.selected=!0,this.secondCard=e,this.reset()},c.appendChild(e.root)})),this.cardsFirst[0].selected=!0,this.cardsSecond[0].selected=!0,this.firstCard=this.cardsFirst[0],this.secondCard=this.cardsSecond[0],this.root.appendChild(d)}async reset(){if(this.actionable){const e=[`${this.firstCard.monomer?.symbol}(${this.code})-A-A-A-A-${this.secondCard.monomer?.symbol}(${this.code})`],t=await(0,h.b2)(),[n,s,a]=(0,d.b)(e,this.rules,t),l=o.Column.fromType(o.COLUMN_TYPE.STRING,"helm",n.length).init((e=>n[e]));l.semType=o.SEMTYPE.MACROMOLECULE,l.meta.units=k.Hi.HELM,l.setTag(o.TAGS.CELL_RENDERER,"helm");const c=await(0,g.j)(),u=await(0,y.Q)(),p=await(0,m.A)(this.rules),b=l.temp;l.temp=b;const v=(await(0,f.m)(l,n,s,!0,!1,!1,p,c,u)).get(0),C=v&&r.chem.checkSmiles(v)?r.chem.drawMolecule(v,200,200):r.chem.drawMolecule(v??"",200,200);v&&(C.style.cursor="pointer",C.onclick=()=>{const e=window.innerWidth-200,t=window.innerHeight-200,n=r.chem.checkSmiles(v)?r.chem.drawMolecule(v,e,t):r.chem.drawMolecule(v??"",e,t);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(e[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((e=>e.render())),this.cardsSecond.forEach((e=>e.render())))}}var U=n(4971);const V="System:AppData/SequenceTranslator/polytool-rules/",j="Polytool",q="code",W="firstMonomers",z="secondMonomers",Y="name",K="firstLinkingGroup",Q="secondLinkingGroup";class J extends c{constructor(e,t,n,o){super(e,t,n,o)}createInput(e,t){const n=super.createInput(e,t),r=i.icons.edit((async()=>{const t=await T.getInstance(e);o.Dialog.getOpenDialogs()?.filter((e=>e.root.contains(r))).forEach((e=>e.close())),await t.getAndAddView()}),"Edit rules");return n.addOptions(r),n}async getForm(){const e=await super.getForm();return this.processRulesForm(e),e}async processRulesForm(e){const t=Array.from(e.getElementsByTagName("label")??[]).filter((e=>e.textContent?.endsWith(".json")&&null!=e.parentElement));for(const e of t){const t=e.textContent.trim(),n=e.parentElement.getElementsByTagName("input")[0];i.tooltip.bind(n,i.wait((async()=>{var e;return(e=J.ruleDescriptions)[t]??(e[t]=(async()=>{try{const e=JSON.parse(await r.dapi.files.readAsText(`${V}/${t}`)),n=i.divV([i.h1(t)]),o=e.linkRules??[];if(o.length>0){n.appendChild(i.h3("Linkage Rules"));const e=i.table(o,(e=>[e.code?.toString()??"",X((e.firstMonomers??[]).join(", ")),X((e.secondMonomers??[]).join(", ")),e.firstLinkingGroup?.toString()??"",e.secondLinkingGroup?.toString()??""]),["Code","M1","M2","L1","L2"]);n.appendChild(e)}const s=e.reactionRules??[];if(s.length>0){n.appendChild(i.h3("Synthesis Rules"));const e=i.table(s,(e=>[e.code?.toString()??"",X((e.firstMonomers??[]).join(", ")),X((e.secondMonomers??[]).join(", ")),X(e.name??""),r.chem.drawMolecule(e.reaction?.split(">>")[1]??"",70,70)]),["Code","M1","M2","Name","Product"]);n.appendChild(e)}return n}catch(e){return u._package.logger.error(`Failed to load rule ${t}: ${e?.toString?.()}`),console.error(e),i.divText(`Failed to load rule ${t}`)}})()),await J.ruleDescriptions[t]})))}}}function X(e,t=30){return e.length<=t?e:`${e.substring(0,t)}...`}J.ruleDescriptions={};class Z{constructor(e,t,n,o){this.homodimerCode=e,this.heterodimerCode=t,this.linkRules=n,this.reactionRules=o}set homodimer(e){this.homodimerCode=e}set heterodimer(e){this.heterodimerCode=e}addLinkRules(e){for(let t=0;t<e.length;t++)this.linkRules.push(e[t])}addSynthesisRules(e){for(let t=0;t<e.length;t++)this.reactionRules.push(e[t])}getLinkRulesDf(){const e=this.linkRules.length,t=o.Column.int(q,e);t.setTag("friendlyName","Code");const n=o.Column.string(W,e);n.temp[".mm.cellRenderer.fontSize"]=16,n.setTag("friendlyName","First monomers"),n.semType=o.SEMTYPE.MACROMOLECULE,u.PackageFunctions.applyNotationProviderForCyclized(n,",");const r=o.Column.string(z,e);r.setTag("friendlyName","Second monomers"),r.temp[".mm.cellRenderer.fontSize"]=16,r.semType=o.SEMTYPE.MACROMOLECULE,u.PackageFunctions.applyNotationProviderForCyclized(r,",");const i=o.Column.int(K,e);i.setTag("friendlyName","First group");const s=o.Column.int(Q,e);s.setTag("friendlyName","Second group");for(let o=0;o<e;o++)t.set(o,this.linkRules[o].code),n.set(o,this.linkRules[o].firstMonomers.toString()),r.set(o,this.linkRules[o].secondMonomers.toString()),i.set(o,this.linkRules[o].firstLinkingGroup),s.set(o,this.linkRules[o].secondLinkingGroup);const a=o.DataFrame.fromColumns([t,n,r,i,s]);return{res:a,addNewRow:e=>{if(null!=e.row&&e.row<a.rowCount&&e.row>=0)t.set(e.row,e.code),n.set(e.row,e.firstMonomers),r.set(e.row,e.secondMonomers),i.set(e.row,e.firstLinkingGroup),s.set(e.row,e.secondLinkingGroup);else{const{code:t,firstMonomers:n,secondMonomers:o,firstLinkingGroup:r,secondLinkingGroup:i}=e;a.rows.addNew([t,n??"",o??"",r??1,i??2])}}}}async getLinkCards(){const e=this.linkRules.length,t=new Array(e),n=(await(0,U.pj)()).getMonomerLib();for(let o=0;o<e;o++)t[o]=new G(this.linkRules[o].firstMonomers,this.linkRules[o].secondMonomers,n,this.linkRules[o].code,this);return t}getSynthesisRulesDf(){const e=this.reactionRules.length,t=o.Column.int(q,e);t.setTag("friendlyName","Code");const n=o.Column.string(W,e);n.setTag("friendlyName","First monomers");const r=o.Column.string(z,e);r.setTag("friendlyName","Second monomers"),n.semType=o.SEMTYPE.MACROMOLECULE,n.temp[".mm.cellRenderer.fontSize"]=16,u.PackageFunctions.applyNotationProviderForCyclized(n,","),r.semType=o.SEMTYPE.MACROMOLECULE,r.temp[".mm.cellRenderer.fontSize"]=16,u.PackageFunctions.applyNotationProviderForCyclized(r,","),r.setTag(o.TAGS.CELL_RENDERER,"Sequence"),n.setTag(o.TAGS.CELL_RENDERER,"Sequence");const i=o.Column.string(Y,e);i.setTag("friendlyName","Name");const s=o.Column.string("firstReactant",e);s.setTag("friendlyName","First reactant");const a=o.Column.string("secondReactant",e);a.setTag("friendlyName","Second reactant");const l=o.Column.string("product",e);l.setTag("friendlyName","Product");for(let o=0;o<e;o++){t.set(o,this.reactionRules[o].code),n.set(o,this.reactionRules[o].firstMonomers.toString()),r.set(o,this.reactionRules[o].secondMonomers.toString()),i.set(o,this.reactionRules[o].name);const e=this.reactionRules[o].reaction.split(">>"),c=e[0].split(".");s.set(o,c[0]),a.set(o,c[1]),l.set(o,e[1])}s.semType=o.SEMTYPE.MOLECULE,a.semType=o.SEMTYPE.MOLECULE,l.semType=o.SEMTYPE.MOLECULE;const c=o.DataFrame.fromColumns([i,s,a,l,t,n,r]);return{df:c,addNewRow:e=>{if(null!=e.rowIndex&&e.rowIndex<c.rowCount&&e.rowIndex>=0)i.set(e.rowIndex,e.resultMonomerName),t.set(e.rowIndex,e.code),n.set(e.rowIndex,e.firstMonomers.join(",")),r.set(e.rowIndex,e.secondMonomers.join(",")),s.set(e.rowIndex,e.firstReactantSmiles),a.set(e.rowIndex,e.secondReactantSmiles),l.set(e.rowIndex,e.productSmiles);else{const{resultMonomerName:t,code:n,firstMonomers:o,secondMonomers:r,firstReactantSmiles:i,secondReactantSmiles:s,productSmiles:a}=e;c.rows.addNew([t,i,s,a,n,o.join(","),r.join(",")])}}}}setLinkRules(e){const t=e.rowCount,n=new Array(t),o=e.columns.byName(q),r=e.columns.byName(W),i=e.columns.byName(z),s=e.columns.byName(K),a=e.columns.byName(Q);for(let e=0;e<t;e++){const t=r.get(e).split(","),l=i.get(e).split(","),c={code:o.get(e),firstMonomers:""!==t[0]?t:[],secondMonomers:""!==l[0]?l:[],firstLinkingGroup:s.get(e),secondLinkingGroup:a.get(e)};n[e]=c}this.linkRules=n}setSynthesisRules(e){const t=e.rowCount,n=new Array(t),o=e.columns.byName(q),r=e.columns.byName(W),i=e.columns.byName(z),s=e.columns.byName(Y),a=e.columns.byName("firstReactant"),l=e.columns.byName("secondReactant"),c=e.columns.byName("product");for(let e=0;e<t;e++){const t=`${a.get(e)}.${l.get(e)}>>${c.get(e)}`,u=r.get(e).split(","),h=i.get(e).split(","),d={code:o.get(e),firstMonomers:""!==u[0]?u:[],secondMonomers:""!==h[0]?h:[],reaction:t,name:s.get(e)};n[e]=d}this.reactionRules=n}}async function ee(e){const t=new o.FileSource(V),n=new Z(null,null,[],[]);for(let o=0;o<e.length;o++){const r=await t.readAsText(e[o].replace(V,"")),i=JSON.parse(r);n.homodimer=i.homodimerCode,n.heterodimer=i.heterodimerCode,n.addLinkRules(i.linkRules),n.addSynthesisRules(i.reactionRules)}return n}function te(e){const t=e.firstMonomers.length*e.secondMonomers.length,n=new Array(t),o=new Array(t);let r=0;for(let t=0;t<e.firstMonomers.length;t++)for(let i=0;i<e.secondMonomers.length;i++)n[r]=e.firstMonomers[t],o[r]=e.secondMonomers[i],r++;return[n,o]}},5174:(e,t,n)=>{"use strict";n.d(t,{A:()=>u,T:()=>h});var o=n(6717),r=n(1296),i=n(9192),s=n(4328),a=n(1991),l=n.n(a),c=n(4971);async function u(e){const t=(await(0,c.pj)()).getMonomerLib(),n=await(0,o.j)(),r={};let i=[],a=[];for(let o=0;o<e.reactionRules.length;o++)try{[i,a]=h(n,t,e.reactionRules[o])}catch(e){i=[],a=[],console.error(e),s.shell.warning(e)}finally{for(let e=0;e<i.length;e++)null!=i[e]&&null!=a[e]&&(r[i[e]]=a[e])}const u={PEPTIDE:r};return t.override(u,"ST-PT-reactions."+l().repeat(1).map((()=>Math.floor(36*Math.random()).toString(36))).take(4).toArray().join(""))}function h(e,t,n){const o=n.reaction,r=n.name,s=n.firstMonomers.length+n.secondMonomers.length+1,a=n.reaction.split(">>"),l=a[0].split("."),c=new Array(s),u=new Array(s),h=new Array(s),f=p(e,o),g=`${l[0]}>>[C:1]C`,y=`${l[1]}>>[C:2]C`,b=p(e,g),v=p(e,y);let C=0;for(let o=0;o<n.firstMonomers.length;o++){const i=t.getMonomer("PEPTIDE",n.firstMonomers[o]);if(i&&i.molfile)try{const t=d(e,i.molfile,b,i.name);h[C]=t,c[C]=`${i.symbol}_${r}`}catch(e){console.error(e)}C++}for(let o=0;o<n.secondMonomers.length;o++){const i=t.getMonomer("PEPTIDE",n.secondMonomers[o]);if(i&&i.molfile)try{const t=d(e,i.molfile,v,i.name);h[C]=t,c[C]=`${i.symbol}_${r}`}catch(e){console.error(e)}C++}let x=null;a[1]=a[1].replace("[C:1]","[1*]").replace("[C:2]","[2*]").replace("[C:3]","[3*]");let w="";try{x=e.get_mol(a[1]),w=x?.get_molblock()}catch(e){const[t,n]=(0,i.AP)(e);throw console.error(`Can not assemble monomer '${r}': ${t}.`),e}finally{x?.delete()}h[C]=w,c[C]=r;for(let e=0;e<s-1;e++)h[e]&&(h[e]=h[e].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(e){const t=e.replace("M RAD","M RGP").replace("M ISO","M RGP").split("\n"),n=t.findIndex((e=>e.startsWith("M RGP"))),o=Number(t[n].substring(9,13)),r=Number(t[n].substring(17,21)),i=Number(t[n].substring(13,17)),s=Number(t[n].substring(21,25));t[n]=t[n].substring(0,13)+` ${i}`+t[n].substring(17,21)+` ${s}`,t[3+o]=t[3+o].substring(0,30)+" R# 0 0 0 0 0 0 0 0 0 0 0 0",t[3+r]=t[3+r].substring(0,30)+" R# 0 0 0 0 0 0 0 0 0 0 0 0";let a="";for(let e=0;e<t.length;e++)a+=t[e]+"\n";return a}(h[s-1]);for(let e=0;e<s;e++){const t=e==s-1;if(!h[e]||!c[e])continue;const n={symbol:c[e],name:c[e],molfile:h[e],author:"",id:0,rgroups:m(t),smiles:"",polymerType:"PEPTIDE",monomerType:"Backbone",createDate:null};n.meta=Object.assign(n.meta??{},{colors:{default:{line:"#2083D5",text:"#2083D5",background:"#F2F2F5"}}}),c[e]=c[e],u[e]=n}return f.delete(),b.delete(),v.delete(),[c,u]}function d(e,t,n,o){let r=null,s=null,a=null,l=null,c="";try{r=new e.MolList,s=e.get_mol(t),r.append(s),a=n.run_reactants(r,1),l=a.get(0).next(),c=l?.get_molblock()}catch(e){const[t,n]=(0,i.AP)(e);throw console.error(`Can not assemble monomer '${o}': ${t}.`),e}finally{r?.delete(),s?.delete(),a?.delete(),l?.delete()}return c}function p(e,t){let n=null;try{if(n=e.get_rxn(t),!n)throw new r.J5(t)}catch(e){n?.delete();const[o,r]=(0,i.AP)(e);throw console.error(`Can not assemble monomer '${t}': ${o}.`),e}return n}function m(e){if(e){const e=new Array(2),t={capGroupSMILES:"[*:1][H]",alternateId:"R1-H",capGroupName:"H",label:"R1"},n={capGroupSMILES:"[*:2][H]",alternateId:"R2-H",capGroupName:"H",label:"R2"};return e[0]=t,e[1]=n,e}return[{capGroupSMILES:"[*:3][H]",alternateId:"R3-H",capGroupName:"H",label:"R3"}]}},3309:(e,t,n)=>{"use strict";n.d(t,{BG:()=>b,HL:()=>T,Ii:()=>x,KS:()=>h,PI:()=>r,Qk:()=>c,XB:()=>f,ah:()=>d,aj:()=>u,j7:()=>l,jp:()=>E,k5:()=>m,u8:()=>o,xD:()=>S,yw:()=>C,z9:()=>v});const 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r=(e??"").trim();if(""===r)return{smiles:"",originalSmiles:e,rNumber:t,id:n,error:"Empty SMILES"};const i=l(r),s=c(i);if(0===s.length){if(o){const r=function(e,t){let n=null;try{if(n=t.get_mol(e),!n||!n.is_valid())return null;if(1!==n.get_num_atoms(!0))return null;n.remove_hs_in_place();const o=n.get_smiles();return o&&o.length>0?o:null}catch{return null}finally{n?.delete()}}(i,o);if(r)return{smiles:r,originalSmiles:e,rNumber:t,id:n,isSingleAtom:!0}}return{smiles:i,originalSmiles:e,rNumber:t,id:n,error:"R-group must contain exactly one R label, or be a single atom (e.g. N, O, Cl)"}}if(s.length>1)return{smiles:i,originalSmiles:e,rNumber:t,id:n,sourceRNumber:s[0],error:`R-group must contain exactly one R label (found ${s.length}: ${s.map((e=>"R"+e)).join(", ")})`};const a=s[0],h=u(i,t);if(o){const r=p(h,o);if(r)return{smiles:h,originalSmiles:e,rNumber:t,id:n,sourceRNumber:a,error:`Invalid SMILES: ${r}`}}return{smiles:h,originalSmiles:e,rNumber:t,id:n,sourceRNumber:a}}function p(e,t){let n=null;try{return n=t.get_mol(e),n&&n.is_valid()?null:"failed to parse"}catch(e){return(e?.message??String(e)).toString().slice(0,120)}finally{n?.delete()}}function m(e,t,n){const o=[],i=[];for(const n of e.rNumbers){const e=t.get(n);e&&0!==e.length?i.push(e.filter((e=>!e.error)).length):o.push(n)}if(o.length>0)return{count:0,uncovered:o};if(i.some((e=>0===e)))return{count:0,uncovered:o};if(n===r.Zip){if(0===i.length)return{count:0,uncovered:o};const e=i[0];return{count:i.every((t=>t===e))?e:-1,uncovered:o}}return{count:i.reduce(((e,t)=>e*t),1),uncovered:o}}function f(e){const t=e.maxResults??o,n=[];let i=0;const s=e.cores.filter((e=>!e.error));0===s.length&&n.push("No valid cores provided.");const a=new Set;for(const e of s)for(const t of e.rNumbers)a.add(t);const l=new Map;for(const t of a){const o=(e.rGroups.get(t)??[]).filter((e=>!e.error)).length;l.set(t,o),0===o&&n.push(`No valid R-group provided for R${t}.`)}if(e.mode===r.Zip){const e=[...l.values()].filter((e=>e>0));e.length>1&&!e.every((t=>t===e[0]))&&n.push(`Zip mode requires every R-group list to have the same number of entries. 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o=[];let r=0;for(const{core:i,assignment:s}of A(e)){const e=new Map;for(const[t,n]of s)e.set(t,n.smiles);const a=g(i.smiles,e);if(!a)continue;const l=new Map;for(const[e,t]of s)l.set(e,t.originalSmiles);const c={smiles:a,coreSmiles:i.originalSmiles,rGroupSmilesByNum:l};if(o.length<t)o.push(c);else{const e=Math.floor(n()*(r+1));e<t&&(o[e]=c)}r++}return o}},3820:(e,t,n)=>{"use strict";n.d(t,{d:()=>r,o:()=>s});var o=n(1296);const r="PEPTIDE1{R.[Aca].T.G.H.F.G.A.A.Y.P.E.[meI]}$$$$";function i(e,t,n,o){const r=new Array(o.length*(n-t+1));for(let i=0;i<o.length;++i){const s=n-t+1;for(let n=0;n<s;++n){const a=t+n,l=o[i],c=r[i*s+n]=e.clone(),u=c.atoms[a].elem;c.atoms[a].elem=l;const h=u?.length>1?`[${u}]`:u,d=l?.length>1?`[${l}]`:l;c.name=`${e.name}-${h}${a+1}${d}`}}return r}function s(e,t,n){const r=new JSDraw2.MolHandler,s=new org.helm.webeditor.Plugin(r);org.helm.webeditor.IO.parseHelm(s,e,new JSDraw2.Point(0,0),void 0);const a=r.m;a.name=t;let l=[];if(n.placeholders)switch(n.type){case 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e=(0,Ce.xh)("r","A"),t=(0,Ce.xh)("r","C");w(e.color!==t.color,!0,`Unmodified A and C must use distinct canonical colors, got ${e.color} for both`)})),x("falls back to hash color for unknown sugar",(async()=>{const e=(0,Ce.xh)("zzz","A");w(e.color.startsWith("hsl("),!0),w(e.meta.name,"zzz")})),x("hashColor is deterministic",(async()=>{w((0,Ce.e8)("foo"),(0,Ce.e8)("foo")),w((0,Ce.e8)("foo")!==(0,Ce.e8)("bar"),!0)})),x("PS phosphate (canonical and legacy) resolve to same color",(async()=>{w((0,Ce.bM)("sp").color,Ce.P4.sp.color),w((0,Ce.bM)("sP").color,Ce.P4.sp.color)})),x("GalNAc / L3 / Chol resolve as conjugates",(async()=>{w((0,Ce.rK)("GalNAc").meta.category,"conjugate"),w((0,Ce.rK)("L3").meta.category,"conjugate"),w((0,Ce.rK)("Chol").meta.color,Ce.pt.Chol.color)}))})),S("OligoRenderer: layout",(()=>{x("comfortable cell — chips fit width and height",(async()=>{const e=(0,be.On)(xe),t=(0,ve.aA)(500,70,e);w(t.textOnlyFallback,!1),w(t.chipW>5,!0,"chip width should be larger than minimum"),w(t.chipW<=17,!0,"chip width should respect max (17)"),w(t.antiY>t.senseY,!0),w(t.senseChips.length>0,!0),w(t.antiChips.length>0,!0)})),x("compact cell — both strands still fit in 28px row",(async()=>{const e=(0,be.On)(xe),t=(0,ve.aA)(300,28,e);w(t.antiY>0,!0),w(2*t.chipH+t.strandGap<=28,!0,"two strands must fit within 28px row")})),x("very narrow cell triggers text-only fallback",(async()=>{const e=(0,be.On)(xe),t=(0,ve.aA)(60,30,e);w(t.textOnlyFallback,!0),w(t.senseChips.length,0)})),x("aspect ratio is preserved across sizes",(async()=>{const e=(0,be.On)(xe);for(const[t,n]of[[300,50],[500,70],[800,90]]){const o=(0,ve.aA)(t,n,e),r=o.chipH/o.chipW;w(Math.abs(r-1.25)<.01,!0,`aspect ratio drifted at ${t}x${n}: got ${r.toFixed(3)}`)}})),x("single-strand layout",(async()=>{const e=(0,be.On)(we),t=(0,ve.aA)(400,50,e);w(t.antiY,-1),w(t.antiChips.length,0)})),x("antisense reversed by default for pair-alignment",(async()=>{const e=(0,be.On)(xe),t=(0,ve.aA)(800,70,e);w(t.antiReversed,!0);const n=e.antisense.monomers[e.antisense.monomers.length-1];w(t.antiChips[0].monomer===n,!0)})),x("pairAlign: false leaves antisense in data order",(async()=>{const e=(0,be.On)(xe),t=(0,ve.aA)(800,70,e,{pairAlign:!1});w(t.antiReversed,!1),w(t.antiChips[0].monomer===e.antisense.monomers[0],!0)})),x("conjugate occupies a wider position; following chip does not overlap",(async()=>{const e=(0,be.On)("RNA1{m(G)p.m(A)p.m(C)p.[L3]}|RNA2{m(C)p.m(A)p.m(A)p.r(G)}$$$$"),t=(0,ve.aA)(600,70,e),n=t.senseChips[3];w(n.monomer.kind,"conjugate"),w(n.w>=t.chipW,!0,"conjugate must be at least chip-wide")}))})),S("OligoRenderer: hit testing",(()=>{x("hits each chip via stored positions",(async()=>{const e=(0,be.On)(xe),t=(0,ve.aA)(800,70,e),n=t.senseChips[0],o=(0,ve.CB)(n.x+n.w/2,t.senseY+t.chipH/2,e,t);w(null!==o,!0),w(o.strand,"sense"),w(o.position,0);const r=e.sense.monomers[0],i="nucleotide"===r.kind&&"sp"===r.phosphate,s=n.x+n.w+.1*t.chipGap,a=(0,ve.CB)(s,t.senseY+t.chipH/2,e,t);i?(w(null!==a,!0),w(void 0!==a.linkage,!0)):w(a,null)})),x("antisense hit returns original position despite reversed display",(async()=>{const e=(0,be.On)(xe),t=(0,ve.aA)(800,70,e),n=t.antiChips[0],o=(0,ve.CB)(n.x+n.w/2,t.antiY+t.chipH/2,e,t);w(null!==o,!0),w(o.strand,"antisense"),w(o.position,e.antisense.monomers.length-1,"leftmost AS chip in pair-aligned display = last monomer in data")})),x("hovering between two chips with PS linkage returns the linkage",(async()=>{const e=(0,be.On)("RNA1{m(G)[sp].m(A)p.m(C)p}$$$$"),t=(0,ve.aA)(600,70,e),n=t.senseChips[0],o=t.senseChips[1],r=(n.x+n.w+o.x)/2,i=(0,ve.CB)(r,t.senseY+t.chipH/2,e,t);w(null!==i,!0),w(void 0!==i.linkage,!0),w(i.linkage.phosphateSymbol,"sp")}))})),S("OligoRenderer: drawing smoke",(()=>{x("draws without error on offscreen canvas",(async()=>{const e=document.createElement("canvas");e.width=500,e.height=70;const t=e.getContext("2d"),n=(0,be.On)(xe);w((0,ve.Z4)(t,0,0,500,70,n).textOnlyFallback,!1)})),x("handles unknown modifications without throwing",(async()=>{const e=document.createElement("canvas");e.width=200,e.height=50;const t=e.getContext("2d"),n=(0,be.On)("RNA1{[xr](A)[zp].[yr](C)p}$$$$");(0,ve.Z4)(t,0,0,200,50,n),w(!0,!0)})),x("renders legacy uppercase symbols via alias map",(async()=>{const e=document.createElement("canvas");e.width=400,e.height=50;const t=e.getContext("2d"),n=(0,be.On)("RNA1{[mR](G)[sP].[mR](A)[sP].[fR](C)P.R(U)P}|RNA2{[mR](C)[sP].R(A)P.R(U)P.R(G)P}$$$$");(0,ve.Z4)(t,0,0,400,50,n),w(n.sense.monomers.length,4),w(null!==n.antisense,!0)}))}));var Ae=n(1757),Te=n.n(Ae),Ee=n(4900);const Se="RNA1{r(A)p.r(C)p.r(G)p.r(U)p}|RNA2{r(U)p.r(C)p.r(G)p.r(A)p}$$$$";function Ne(){return Te()(".d4-dialog").length}S("OligoCellEditor",(()=>{I((async()=>{Te()(".d4-dialog .ui-btn-cancel, .d4-dialog .d4-dialog-header 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button.ui-btn.ui-btn-ok").first();w(a.length>0,!0,"OK button not found in dialog"),a.trigger("click"),await $((()=>Ne()<=s),"Dialog did not close after OK",5e3);const l=i.cell.value;w("string"==typeof l&&l.includes("RNA1{")&&l.includes("RNA2{")&&l.includes("$$$$"),!0,`Expected cell value to remain valid HELM after OK; got: ${l}`)}))}));const Ie=new k;async function Me(t,n,o){const d=await function(e){var t,n,o;return r(this,void 0,void 0,(function*(){const d=(null==e?void 0:e.nodeOptions)?e.nodeOptions.package:grok.functions.getCurrentCall().func.package;if(!d)throw new Error("Can't run tests outside of the package");const p=null===(t=d.packageOwner)||void 0===t?void 0:t.match(/<([^>]*)>/),m=p?p[1]:"";null!=d&&(yield P(d));const f=[];console.log("Running tests..."),console.log(e),null!=e||(e={}),null!==(n=(o=e).testContext)&&void 0!==n||(o.testContext=new v),grok.shell.clearLastError();const g=function(){const e=[];return console.log=(...t)=>{e.push(...t),a(...t)},console.info=(...t)=>{e.push(...t),l(...t)},console.warn=(...t)=>{e.push(...t),c(...t)},console.error=(...t)=>{e.push(...t),u(...t)},e}();yield function(e,t){var n,o,i,s,h,p;return r(this,void 0,void 0,(function*(){try{let l=null!=(null==t?void 0:t.skipToCategory),c=!1;for(const[u,g]of Object.entries(e)){if(null===(n=t.exclude)||void 0===n?void 0:n.some((e=>u.startsWith(e))))continue;if(null!=(null==t?void 0:t.category)&&!u.toLowerCase().startsWith(null==t?void 0:t.category.toLowerCase().trim()))continue;if(l)if(c)l=!1;else{if(null==(null==t?void 0:t.skipToCategory)||u.toLowerCase().trim()!==(null==t?void 0:t.skipToCategory.toLowerCase().trim()))continue;c=!0}const e=null===(o=g.tests)||void 0===o?void 0:o.every((e=>{var n;return(null===(n=e.options)||void 0===n?void 0:n.skipReason)||null!=(null==t?void 0:t.test)&&t.test.toLowerCase()!==e.name.toLowerCase()}));if(!e){const e=(null!==(i=g.tests)&&void 0!==i?i:[]).filter((e=>{var 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grok.shell.reportTest("package",e)}))))):v=yield b(g,t,l);const x=v.filter((e=>"skipped"!=e.result));if(e||(g.afterStatus=yield y(g.after,u)),g.afterStatus&&(a(`Package testing: Category after() {{${u}}} failed`),a(`Package testing: Result for {{${u}}} after: ${g.afterStatus}`),x.push({date:(new Date).toISOString(),category:u,name:"after",success:!1,result:g.afterStatus,ms:0,skipped:!1,logs:"",owner:m,package:d.name,widgetsDifference:0,flaking:DG.Test.isReproducing})),g.beforeStatus&&(a(`Package testing: Category before() {{${u}}} failed`),a(`Package testing: Result for {{${u}}} before: ${g.beforeStatus}`),x.push({date:(new Date).toISOString(),category:u,name:"before",success:!1,result:g.beforeStatus,ms:0,skipped:!1,logs:"",owner:m,package:d.name,widgetsDifference:0,flaking:DG.Test.isReproducing})),f.push(...x),t.returnOnFail&&x.some((e=>!e.success&&!e.skipped&&e.name!==t.skipToTest)))break}}finally{console.log=a,console.info=l,console.warn=c,console.error=u}if(t.testContext.catchUnhandled&&!DG.Test.isInBenchmark){yield R(1e3);const e=yield grok.shell.lastError;if(null!=e){const t={logs:"",date:(new Date).toISOString(),category:"Unhandled exceptions",name:"Exception",result:null!=e?e:"",success:!e,ms:0,skipped:!1,owner:null!=m?m:"",package:d.name,widgetsDifference:0};a(`Package testing: Unhandled Exception: ${e}`),f.push(Object.assign(Object.assign({},t),{flaking:DG.Test.isReproducing&&!e})),t.package=d.name,yield grok.shell.reportTest("package",t)}}}))}(h,e);for(let e of f)e.result=e.result.toString().replace(/"/g,"'"),null!=e.logs&&(e.logs=e.logs.toString().replace(/"/g,"'"));return f;function y(e,t){return r(this,void 0,void 0,(function*(){let n;try{void 0!==e&&(yield D((()=>r(this,void 0,void 0,(function*(){yield e()}))),1e5,`before ${t}: timeout error`))}catch(e){n=yield _(e)}return n}))}function b(e,t,n){var o,a,l,c,u,h,p,f,y,b,v,x,w,A,T,E,S,N;return r(this,void 0,void 0,(function*(){let r=null!==(o=e.tests)&&void 0!==o?o:[];const I=[],M=C();if(e.clear){let o=n&&null!=t.skipToTest;for(let n=0;n<r.length;n++){r[n].options&&void 0===(null===(a=r[n].options)||void 0===a?void 0:a.benchmark)&&(r[n].options||(r[n].options={}),r[n].options.benchmark=null!==(l=e.benchmarks)&&void 0!==l&&l);let x=r[n];if(t.test&&t.test.toLowerCase()!==x.name.toLowerCase())continue;if(o){if(null==(null==t?void 0:t.skipToTest)||x.name.toLowerCase().trim()!==(null==t?void 0:t.skipToTest.toLowerCase().trim()))continue;o=!1}(null==x?void 0:x.options)&&(x.options.owner=null!==(p=null!==(h=null!==(u=null===(c=r[n].options)||void 0===c?void 0:c.owner)&&void 0!==u?u:null==e?void 0:e.owner)&&void 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