@datagrok/bio 2.20.3 → 2.20.4

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Files changed (10) hide show
  1. package/CHANGELOG.md +4 -0
  2. package/dist/455.js +1 -1
  3. package/dist/455.js.map +1 -1
  4. package/dist/package-test.js +1 -1
  5. package/dist/package-test.js.map +1 -1
  6. package/dist/package.js +1 -1
  7. package/dist/package.js.map +1 -1
  8. package/package.json +2 -2
  9. package/test-console-output-1.log +333 -387
  10. package/test-record-1.mp4 +0 -0
package/dist/package.js CHANGED
@@ -1,4 +1,4 @@
1
- var bio;(()=>{var e={8924:(e,t,n)=>{"use strict";var i=n(7362);class r extends i.e{static get Lesk(){return void 0===this.lesk&&(this.lesk=this.makePalette([[["G","A","S","T"],"orange"],[["C","V","I","L","P","F","Y","M","W"],"all_green"],[["N","Q","H"],"magenta"],[["D","E"],"red"],[["K","R"],"all_blue"]],!1,r)),this.lesk}static get GrokGroups(){return void 0===this.grokGroups&&(this.grokGroups=this.makePalette([[["C","U"],"yellow"],[["G","P"],"red"],[["A","V","I","L","M","F","Y","W"],"all_green"],[["R","H","K"],"light_blue"],[["D","E"],"dark_blue"],[["S","T","N","Q"],"orange"]],!1,r)),this.grokGroups}static get RasMol(){return void 0===this.rasMol&&(this.rasMol=new r({D:"#E60A0A",E:"#E60A0A",C:"#E6E600",M:"#E6E600",K:"#145AFF",R:"#145AFF",S:"#FA9600",T:"#FA9600",F:"#3232AA",Y:"#3232AA",N:"#00DCDC",Q:"#00DCDC",G:"#EBEBEB",L:"#0F820F",V:"#0F820F",I:"#0F820F",A:"#C8C8C8",W:"#B45AB4",H:"#8282D2",P:"#DC9682",others:"#BEA06E"})),this.rasMol}get(e){const t=e in r.aaSynonyms?r.aaSynonyms[e]:e;return super.get(t)}}r.aaSynonyms={MeNle:"L",MeA:"A",MeG:"G",MeF:"F"};class o{static getPalette(e="grok"){switch(e){case"grok":return r.GrokGroups;case"lesk":return r.Lesk;default:throw new Error(`ChemPalette: scheme \`${e}\` does not exist`)}}static getInnerOuter(e){let t=0,n="",i="";for(const r of e)"("==r?t++:")"==r?t--:t?n+=r:i+=r;return isNaN(parseInt(n))?[i,n]:[i,""]}static getColorAAPivot(e="",t="grok"){const n=this.getPalette(t);let[i,r]=this.getInnerOuter(e);if(i=i.length>6?`${i.slice(0,3)}...`:i,r=r.length>6?`${r.slice(0,3)}...`:r,1==e.length||"("==e[1]){const t=e[0]?.toUpperCase();return t in n?[n.get(t),t,r,1]:[this.undefinedColor,i,r,1]}if("d"==e[0]&&e[1]in n&&(2==e.length||"("==e[2])){const t=e[1]?.toUpperCase();return t in n?[n.get(t),t,r,2]:[this.undefinedColor,i,r,2]}if(e.substring(0,3)in this.AAFullNames&&(3==e.length||"("==e[3])){const t=this.AAFullNames[e.substring(0,3)];return t in n?[n.get(t),t,r,3]:[this.undefinedColor,i,r,3]}if(e[0]?.toLowerCase()==e[0]&&e.substring(1,3)in this.AAFullNames&&(4==e.length||"("==e[4])){const t=this.AAFullNames[e.substring(1,3)];return t in n?[n.get(t),t,r,4]:[this.undefinedColor,i,r,4]}return[this.undefinedColor,i,r,0]}}o.SemType="Aminoacids",o.SemTypeMultipleAlignment="AminoacidsMultipleAlignment",o.undefinedColor="rgb(100,100,100)",o.Names={G:"Glycine",L:"Leucine",Y:"Tyrosine",S:"Serine",E:"Glutamic acid",Q:"Glutamine",D:"Aspartic acid",N:"Asparagine",F:"Phenylalanine",A:"Alanine",K:"Lysine",R:"Arginine",H:"Histidine",C:"Cysteine",V:"Valine",P:"Proline",W:"Tryptophan",I:"Isoleucine",M:"Methionine",T:"Threonine"},o.AASmiles={G:"NCC(=O)O",L:"N[C@H](CC(C)C)C(=O)O",Y:"NC(CC1=CC=C(O)C=C1)C(=O)O",S:"NC(CO)C(=O)O",E:"N[C@@H](CCC(O)=O)C(=O)O",Q:"N[C@@H](CCC(N)=O)C(=O)O",D:"N[C@@H](CC(O)=O)C(=O)O",N:"N[C@@H](CC(N)=O)C(=O)O",F:"NC(CC1=CC=CC=C1)C(=O)O",A:"N[C@H](C)C(=O)O",K:"NC(CCCCN)C(=O)O",R:"N[C@H](CCCNC(=N)C)C(=O)O",H:"NC(CC1=CN=C[N]1)C(=O)O",C:"N[C@@H](CS)C(=O)O",V:"NC(C(C)C)C(=O)O",P:"N(CCC1)C1C(=O)O",W:"N[C@@H](Cc1c2ccccc2n([H])c1)C(=O)O",I:"N[C@H]([C@H](C)CC)C(=O)O",M:"NC(CCSC)C(=O)O",T:"NC(C(O)C)C(=O)O"},o.AASmilesTruncated={G:"*C*",L:"CC(C)C[C@H](*)*",Y:"C1=CC(=CC=C1CC(*)*)O",S:"OCC(*)C*",E:"*[C@@H](CCC(O)=O)*",Q:"*N[C@@H](CCC(N)=O)*",D:"*[C@@H](CC(O)=O)*",N:"*[C@@H](CC(N)=O)*",F:"C1=CC=C(C=C1)CC(*)*",A:"C[C@H](*)*",K:"C(CCN)CC(*)*",R:"*[C@H](CCCNC(=N)C)*",H:"C1=C(NC=N1)CC(*)*",C:"C([C@@H](*)*)S",V:"CC(C)C(*)*",P:"C1CCN(*)C1*",W:"*[C@@H](Cc1c2ccccc2n([H])c1)*",I:"CC[C@H](C)[C@H](*)*",M:"CSCCC(*)*",T:"CC(O)C(*)*"},o.AAFullNames={Ala:"A",Arg:"R",Asn:"N",Asp:"D",Cys:"C",Gln:"Q",Glu:"E",Gly:"G",His:"H",Ile:"I",Leu:"L",Lys:"K",Met:"M",Phe:"F",Pro:"P",Ser:"S",Thr:"T",Trp:"W",Tyr:"Y",Val:"V"}},6717:(e,t,n)=>{"use strict";n.d(t,{j:()=>r});var i=n(6082);async function r(){const e=i.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:()=>i.o});var i=n(6869)},9124:(e,t,n)=>{"use strict";n.d(t,{b2:()=>o,fA:()=>s});var i=n(7389),r=n(6082);async function o(){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()}function s(e,t){if(!e)throw new Error("Argument 'a' of type Atom or HelmType is mandatory.");let n,i;const r=e;return"ATOM"===r.T?(n=r.biotype(),i=r.elem):(n=e,i=t),[n,i]}r.JsInputBase,Error,i.input.helmAsync=async function(e,t){return(await o()).createHelmInput(e,t)}},8438:(e,t,n)=>{"use strict";function i(e){return e.startsWith("[")&&e.endsWith("]")?e.slice(1,-1):e}n.d(t,{D:()=>i})},8123:(e,t,n)=>{"use strict";n.d(t,{u:()=>i});const i={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"}},4356:(e,t,n)=>{"use strict";n.d(t,{Eu:()=>a,ub:()=>s});var i=n(4328);const r="Libraries";let o=Promise.resolve();async function s(){let e;return o=o.then((async()=>{const t=i.userSettings.getValue(r,"Settings",!0);e=t?JSON.parse(t):{exclude:[],explicit:[],duplicateMonomerPreferences:{}},e.exclude=e.exclude instanceof Array?e.exclude:[],e.explicit=e.explicit instanceof Array?e.explicit:[],e.duplicateMonomerPreferences=e.duplicateMonomerPreferences instanceof Object?e.duplicateMonomerPreferences:{},console.debug(`Bio: getUserLibSettings()\n${JSON.stringify(e,void 0,2)}`)})),await o,e}async function a(e){o=o.then((async()=>{console.debug(`Bio: setUserLibSettings()\n${JSON.stringify(e,void 0,2)}`),i.userSettings.add(r,"Settings",JSON.stringify(e),!0)})),await o}},5553:(e,t,n)=>{"use strict";n.d(t,{Qc:()=>A,WN:()=>S});var i=n(1991),r=n.n(i);const o="object"==typeof performance&&performance&&"function"==typeof performance.now?performance:Date,s=new Set,a="object"==typeof process&&process?process:{},l=(e,t,n,i)=>{"function"==typeof a.emitWarning?a.emitWarning(e,t,n,i):console.error(`[${n}] ${t}: ${e}`)};let c=globalThis.AbortController,h=globalThis.AbortSignal;if(void 0===c){h=class{onabort;_onabort=[];reason;aborted=!1;addEventListener(e,t){this._onabort.push(t)}},c=class{constructor(){t()}signal=new h;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"!==a.env?.LRU_CACHE_IGNORE_AC_WARNING;const t=()=>{e&&(e=!1,l("AbortController is not defined. If using lru-cache in node 14, load an AbortController polyfill from the `node-abort-controller` package. A minimal polyfill is provided for use by LRUCache.fetch(), but it should not be relied upon in other contexts (eg, passing it to other APIs that use AbortController/AbortSignal might have undesirable effects). You may disable this with LRU_CACHE_IGNORE_AC_WARNING=1 in the env.","NO_ABORT_CONTROLLER","ENOTSUP",t))}}Symbol("type");const u=e=>e&&e===Math.floor(e)&&e>0&&isFinite(e),d=e=>u(e)?e<=Math.pow(2,8)?Uint8Array:e<=Math.pow(2,16)?Uint16Array:e<=Math.pow(2,32)?Uint32Array:e<=Number.MAX_SAFE_INTEGER?p:null:null;class p extends Array{constructor(e){super(e),this.fill(0)}}class m{heap;length;static#e=!1;static create(e){const t=d(e);if(!t)return[];m.#e=!0;const n=new m(e,t);return m.#e=!1,n}constructor(e,t){if(!m.#e)throw new TypeError("instantiate Stack using Stack.create(n)");this.heap=new t(e),this.length=0}push(e){this.heap[this.length++]=e}pop(){return this.heap[--this.length]}}class 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o().count(0).take(t.length).map((e=>({position:e,symbol:t.getCanonical(e),biotype:v}))).toArray()})).toArray();for(let e=0;e<m;e++){const n=f[e],i=Math.floor(e*g),o=e===m-1?d:Math.floor((e+1)*g);y[e]=new Promise((e=>{n.onmessage=t=>{e(t.data)}})),n.postMessage({seqList:w,monomersDict:t,alphabet:r,polymerType:l,start:i,end:o})}const C=[],A=[];await Promise.all(y).then((e=>{for(const t of e)C.push(...t.molfiles),A.push(...t.warnings)})),setTimeout((()=>{f.forEach((e=>{e.terminate()}))}),0);const S=(0,s.qj)(p,e.name),x=i.Column.fromType(i.COLUMN_TYPE.STRING,S,e.length).init((e=>C[e]?.molfile));return x.semType=i.SEMTYPE.MOLECULE,x.meta.units=i.UNITS.Molecule.MOLBLOCK,x.setTag(".sequence-src-col",e.name),{molCol:x,warnings:A}}function c(e,t){const n={},r={};for(const o of e){const e=t.getWebEditorMonomer(o.biotype,o.symbol).backgroundcolor,a=(0,s.vG)(e??i.Color.toRgb(i.Color.mouseOverRows))??[1,0,0,.7];for(const e of o.atoms)n[e]=a;for(const e of 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Array(2).fill(0),branchPositionShift:new Array(2).fill(0),backboneAttachNode:0,branchAttachNode:0,flipFactor:1},C={sugar:b,phosphate:v,seqLength:e.length,atomCount:c,bondCount:u},A=new r.Cg,S=[];let x=0;for(w.i=0;w.i<C.seqLength;++w.i){const n=e[w.i];if(n.symbol===s._S)continue;const i=(0,r.xb)(t,{symbol:n.symbol,polymerType:(0,a.Y)(n.biotype)}),o=w.nodeShift,l=w.bondShift;y(i,p,g,w,C),i.stereoAtoms?.forEach((e=>S.push(e+x))),x+=i.atoms.x.length;const c=w.nodeShift-o,h=new Array(c);for(let e=0;e<c;++e)h[e]=o+e;const u=w.bondShift-l,d=new Array(u);for(let e=0;e<u;++e)d[e]=l+e;A.set(w.i,{biotype:n.biotype,symbol:n.symbol,atoms:h,bonds:d})}!function(e,t,n,r){const o=n.nodeShift+1;e[r.atomCount]=i.u.V3K_BEGIN_DATA_LINE+o+" "+i.u.OXYGEN+" "+f(n.backbonePositionShift[0])+" "+n.flipFactor*f(n.backbonePositionShift[1])+" 0.000000 0\n";const s=n.backboneAttachNode,a=o;t[r.bondCount]=i.u.V3K_BEGIN_DATA_LINE+n.bondShift+" 1 "+s+" "+a+"\n"}(p,g,w,C);const E=i.u.V3K_BEGIN_COUNTS_LINE+c+" 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m(e,t,n,o,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 h=t;const p=o.getSeqHandler(t);let m,g;p.notation!==a.Hi.SEPARATOR&&(h=p.convert(a.Hi.SEPARATOR,"."),h.name=t.name);try{g=o.getSeqHandler(h).alphabet,m=(0,d.pz)(g)}catch(e){const[t,n]=(0,u.AP)(e);return{molCol:null,warnings:[t]}}const y=function(e,t){const n=e.length,r=new Array(n),o=t.getSeqHandler(e);let a=!1;const l=o.defaultBiotype;for(let e=0;e<n;++e){const t=o.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&&i.shell.warning(`Some values in the "${e.name}" column are empty`),r}(h,o),b=f(y,m,g,n,l),v=h.length,w=await(0,c.R)(h,b,g,m,n,o,l);return w.warnings.length>.05*v&&i.shell.warning(`Molfile conversion resulted in ${w.warnings.length} errors`),w}function f(e,t,n,i,r){const o=(0,l.Hb)(i,t,n),s={},c={value:null};if("RNA"===t){const e=n===a.YI.RNA?[p.u.RIBOSE,p.u.PHOSPHATE]:[p.u.DEOXYRIBOSE,p.u.PHOSPHATE];for(const n of e)g(s,n.symbol,o,r,t,c)}for(let n=0;n<e.length;++n){const i=e[n];for(const e of i){const n=e.symbol;if(""!==n)try{if("RNA"===t&&3===n.split(/\(|\)/).filter((e=>!!e)).length){const e=n.split(/\(|\)/)[1];g(s,e,o,r,t,c),s[t]?.[e]&&(s[t][n]=s[t][e])}else g(s,n,o,r,t,c)}catch(e){const t=e instanceof Error?e.message:e.toString(),i=e instanceof Error?e.stack:void 0;throw console.error(`bio lib: getMonomersDictFromLib() sym='${n}', error:\n${t}\n${i}`),new Error(`Can't get monomer '${n}' from library: ${t}`)}}}return s}function g(e,t,n,i,r,o){const s={polymerType:r,symbol:t};if(!(0,h.bq)(e,s)){const a=function(e,t,n,i,r){if(t.has(e)){const s=t.get(e),a=function(e){const t=[];for(const n of e){let e=n.capGroupSmiles;e||(e=n.capGroupSMILES),e=e.replace(/(\[|\]|\*|:|\d)/g,""),t.push(e)}return t}(s.rgroups),c=(o=s.molfile).includes("V3000")?function(e){const t=new Map,n=/M V30 (\d+) R#.+RGROUPS=\((\d+) (\d+)\).*/gm;let i;for(;null!==(i=n.exec(e));)i.index===n.lastIndex&&n.lastIndex++,t.set(parseInt(i[1]),parseInt(i[3]));return t}(o):function(e){const t=new Map;let n=e.indexOf(p.u.V2K_A_LINE,0),i=n;for(;-1!==n;){i=e.indexOf("\n",n);const r=parseInt(e.substring(n,i).replace(/^A\s+/,""));n=e.indexOf("R",i),i=e.indexOf("\n",n);const o=parseInt(e.substring(n,i).replace(/^R/,""));t.set(r,o),n=e.indexOf(p.u.V2K_A_LINE,i)}for(n=e.indexOf(p.u.V2K_RGP_LINE,0),i=e.indexOf("\n",n);-1!==n;){n+=p.u.V2K_RGP_SHIFT,i=e.indexOf("\n",n);const r=e.substring(n,i).replaceAll(/\s+/g," ").split(" ").map((e=>parseInt(e))).slice(1);for(let e=0;e<r.length;e+=2){if(t.has(r[e])&&t.get(r[e])!==r[e+1])throw new Error(`r-group index ${r[e]} has already been added with a different value`);t.set(r[e],r[e+1])}n=e.indexOf(p.u.V2K_RGP_LINE,i)}return t}(o),h=s.molfile.includes("V3000")?s.molfile:function(e,t){const n=t.get_mol(e),i=n.get_v3Kmolblock();return n.delete(),i}(function(e){let t=e.indexOf(p.u.V2K_A_LINE,0);-1===t&&(t=e.indexOf(p.u.V2K_RGP_LINE));const n=e.indexOf(p.u.V3K_END,t);return e.substring(0,t)+e.substring(n)}(s.molfile),n),u=function(e){let t=(e=e.replaceAll("\r","")).indexOf(p.u.V3K_BEGIN_COUNTS_LINE)+p.u.V3K_COUNTS_SHIFT,n=e.indexOf(" ",t+1);const i=parseInt(e.substring(t,n));return t=n+1,n=e.indexOf(" ",t+1),{atomCount:i,bondCount:parseInt(e.substring(t,n))}}(h),d=function(e,t){const n=new Array(t),i=new Float32Array(t),r=new Float32Array(t),o=new Array(t);let s=e.indexOf(p.u.V3K_BEGIN_ATOM_BLOCK);s=e.indexOf("\n",s);let a=s;for(let l=0;l<t;l++){s=e.indexOf(p.u.V3K_BEGIN_DATA_LINE,s)+p.u.V3K_IDX_SHIFT,a=e.indexOf(" ",s),s=a+1,a=e.indexOf(" ",s),n[l]=e.substring(s,a);const t=new Array(2);for(let n=0;n<2;++n)s=a+1,a=e.indexOf(" 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function(e,t,n){for(const[i,r]of n)e.atomTypes[i-1]=t[r-1]}(e,n,i),function(e,t){t.rNodes=Array.from(e.keys());for(let n=0;n<t.rNodes.length;n++)for(const i of[1,2])if(e.get(t.rNodes[n])===i){const e=t.rNodes[i-1];t.rNodes[i-1]=t.rNodes[n],t.rNodes[n]=e}}(i,r),y(t,r),r}(d,m,a,c),g=function(e){let t=[],n=e.indexOf("M V30 MDLV30/STEABS ATOMS=(");for(;-1!==n;){n+=28;const i=e.indexOf(")",n);t=t.concat(e.substring(n,i).split(" ").slice(1).map((e=>parseInt(e)))),n=i,n=e.indexOf("M V30 MDLV30/STEABS ATOMS=(",n)}return t}(h),v={atoms:d,bonds:m,meta:f,stereoAtoms:g};return"PEPTIDE"===i?function(e){const t=e.meta.terminalNodes[0]-1,n=e.meta.rNodes[0]-1,i=e.atoms.x,r=e.atoms.y;_(e,-i[t],-r[t]);const o=A(i[n],r[n]);S(e.atoms,-o),i[e.meta.rNodes[1]-1]<0&&x(e);const s=function(e){const t=function(e){const t=new Map;for(const n of e.bonds.atomPairs)for(let e=0;e<2;e++){const i=n[e],r=n[(e+1)%2];t.has(i)?t.get(i)?.push(r):t.set(i,new Array(1).fill(r))}return t}(e);let n=0;const i=e.atoms.atomTypes.length;let r=0;if(e.meta.terminalNodes.length<2)return null;for(;0===n;){const o=t.get(e.meta.terminalNodes[1])[r];if(e.atoms.atomTypes[o-1]===p.u.OXYGEN&&o!==e.meta.rNodes[1]&&(n=o),r++,r>i)return null}return n}(e);null!=s&&(function(e,t){e.atoms.y[e.meta.rNodes[1]-1]<0&&e.atoms.y[t-1]<0&&(function(e){E(e,!0)}(e),S(e.atoms,-function(e,t){return A(e,t)+Math.PI/2}(e.atoms.x[e.meta.terminalNodes[1]-1],e.atoms.y[e.meta.terminalNodes[1]-1])))}(e,s),function(e,t){const n=e.atoms.x;n[e.meta.rNodes[1]-1]>n[t-1]&&function(e,t,n){const i=t-1,r=n-1,o=e.atoms.x,s=e.atoms.y,a=o[i],l=s[i];o[i]=o[r],s[i]=s[r],o[r]=a,s[r]=l}(e,t,e.meta.rNodes[1])}(e,s))}(v):e===p.u.RIBOSE.symbol||e===p.u.DEOXYRIBOSE.symbol?function(e,t){const n=e.atoms.x,i=e.atoms.y;let r=e.meta.terminalNodes[0]-1;const o=e.meta.rNodes[1]-1;_(e,-n[r],-i[r]);const s=A(n[e.meta.rNodes[2]-1],i[e.meta.rNodes[2]-1]);S(e.atoms,-s),n[e.meta.rNodes[0]-1]>n[e.meta.rNodes[1]-1]&&x(e);const a=A(n[o],i[o]);S(e.atoms,3*Math.PI/2-a),t.value=function(e){const t=e.atoms.x,n=e.atoms.y,i=e.meta.rNodes[2]-1,r=e.meta.terminalNodes[2]-1,o=t[i]-t[r],s=n[i]-n[r];return Math.atan2(o,s)}(e),r=e.meta.terminalNodes[0]-1,_(e,-n[r],-i[r])}(v,r):e===p.u.PHOSPHATE.symbol?function(e){const t=e.meta.rNodes[1]-1,n=e.meta.rNodes[0]-1,i=e.atoms.x,r=e.atoms.y;_(e,-i[t],-r[t]);const o=A(i[n],r[n]);S(e.atoms,Math.PI/2-o)}(v):function(e,t){const n=e.atoms.x,i=e.atoms.y,r=e.meta.terminalNodes[0]-1,o=e.meta.rNodes[0]-1;_(e,-n[r],-i[r]);const s=A(n[o],i[o]),a=t.value;if(!a)throw new Error("The value of sugarBranchToOYAngle is null");S(e.atoms,Math.PI-s+a);const c=function(e,t){return(0,l.YN)(Math.sqrt((e.x-t.x)**2+(e.y-t.y)**2))}({x:n[e.meta.rNodes[0]-1],y:i[e.meta.rNodes[0]-1]},{x:n[e.meta.terminalNodes[0]-1],y:i[e.meta.terminalNodes[0]-1]});if(1!=c)for(let e=0;e<n.length;++e)n[e]=(0,l.YN)(n[e]/c),i[e]=(0,l.YN)(i[e]/c)}(v,r),function(e,t,n){"PEPTIDE"===e?(b(t,e),w(t,t.meta.rNodes[1])):n===p.u.RIBOSE.symbol||n===p.u.DEOXYRIBOSE.symbol?(w(t,t.meta.rNodes[1]),t.meta.rNodes[1]=t.meta.terminalNodes[1],y(t.bonds,t.meta),b(t,e),w(t,t.meta.rNodes[1]),w(t,t.meta.rNodes[0]),w(t,t.meta.rNodes[2])):n===p.u.PHOSPHATE.symbol&&(t.meta.terminalNodes[0]=t.meta.rNodes[0],_(t,-t.atoms.x[t.meta.terminalNodes[0]-1],-t.atoms.y[t.meta.terminalNodes[0]-1]),b(t,e),w(t,t.meta.rNodes[1]))}(i,v,e),function(e){let t=0;for(;t<e.atoms.atomTypes.length;)e.atoms.atomTypes[t]===p.u.HYDROGEN&&(w(e,t+1),--t),++t}(v),function(e){const t=" RGROUPS=(1 1)";for(let n=0;n<(e.atoms.kwargs?.length??0);n++){const i=e.atoms.kwargs[n];i&&i.includes(t)&&(e.atoms.kwargs[n]=i.replace(t,""))}}(v),v}var o;return null}(t,n,i,r,o);if(!a)throw new Error(`Monomer with symbol '${t}' is absent the monomer library`);(0,h.LQ)(e,s,a)}}function y(e,t){const n=t.rNodes;t.terminalNodes=new Array(n.length).fill(0);const i=t.terminalNodes,r=e.atomPairs;let o=0,s=0;for(;o<r.length&&s<i.length;){for(let e=0;e<i.length;++e)for(let t=0;t<2;++t)r[o][t]===n[e]&&(i[e]=r[o][(t+1)%2],n.length,++s);++o}}function b(e,t){e.meta.rNodes.length>1&&(e.meta.backboneShift=v(e,e.meta.rNodes[1]-1,e.meta.terminalNodes[0]-1)),"RNA"===t&&e.meta.rNodes.length>2&&(e.meta.branchShift=v(e,e.meta.rNodes[2]-1,e.meta.terminalNodes[0]-1))}function v(e,t,n){return[(0,l.YN)(e.atoms.x[t]-e.atoms.x[n]),(0,l.YN)(e.atoms.y[t]-e.atoms.y[n])]}function w(e,t){if(void 0!==t){const n=t-1,i=e.atoms,r=e.bonds,o=e.meta;i.atomTypes.splice(n,1),i.x=C(Float32Array,i.x,n,1),i.y=C(Float32Array,i.y,n,1),i.kwargs.splice(n,1);for(let e=0;e<o.terminalNodes.length;++e)o.terminalNodes[e]>t?--o.terminalNodes[e]:o.terminalNodes[e]===t&&(o.terminalNodes[e]=-1);for(let e=0;e<o.rNodes.length;++e)o.rNodes[e]>t?--o.rNodes[e]:o.rNodes[e]===t&&(o.rNodes[e]=-1);let s=0;for(;s<r.atomPairs.length;){const 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get palette(){return c._pallete||(c._pallete=c.buildPalette()),c._pallete}static buildPalette(){return(0,o.pj)().then((e=>{e.awaitLoaded(1/0).then((()=>{const t=e.getMonomerLib();t.onChanged.subscribe((()=>{c.customMonomerColors={},c.polymerTypes=t.getPolymerTypes();for(const e of this.polymerTypes){const n=t.getMonomerSymbolsByType(e);for(const i of n){const n=t.getMonomer(e,i);n?.meta?.colors?.default?.background&&(this.customMonomerColors[i]||(this.customMonomerColors[i]={}),this.customMonomerColors[i][e]=s(n.meta.colors.default.background))}}}))}))})),[].concat(...Object.values(r.e.colourPalette))}get(e,t){const n=c.palette.length,i=c.customMonomerColors[e],r=t??"PEPTIDE";if(i&&i[r])return i[r];const o=a.hashCode(e)%n;return s(c.palette[o])}}c._pallete=null,c.customMonomerColors={},c.polymerTypes=[]},6642:(e,t,n)=>{"use strict";n.d(t,{BG:()=>s,sD:()=>l});var i=n(4328),r=n(1858),o=n(8070);function s(e){let 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this.errors=[],e}this.logger.debug(`${n}, end`)}}l.viewerCounter=-1},673:(e,t,n)=>{"use strict";n.d(t,{s:()=>i});const i={true:"1",false:"0"}},6882:(e,t,n)=>{"use strict";n.d(t,{Jy:()=>y,S$:()=>g,U0:()=>b});var i=n(7389),r=n(6082),o=n(1991),s=n.n(o),a=n(8312),l=n(2003),c=n(6642),h=n(6718),u=n(9192),d=n(3856),p=n(673),m=n(3599),f=n(5553);const g="rgb(100,100,100)";class y extends c.sD{get separatorWidth(){return this.props?.fontCharWidth?this.props?.fontCharWidth:5}constructor(e,t,n,i,o){super(e,t,n),this.monomerLengthLimit=i,this.propsProvider=o,this.colWidth=0,this._monomerLengthList=null,this._processedMaxVisibleSeqLength=0,this._monomerLengthMap={},this._monomerStructureMap={},this.sysMonomerLib=null,this.padding=5,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((()=>{const e=this.tableCol.dataFrame;this.gridCol.grid,-1===e.currentRowIdx&&(this.tableCol.temp["reference-sequence"]=null,this.tableCol.temp["current-word"]=null,this.invalidateGrid())})))}async init(){await Promise.all([(async()=>{this.seqHelper=await(0,a.Q)(),this.invalidateGrid()})(),(async()=>{const e=await(0,h.pj)();this.sysMonomerLib=e.getMonomerLib()})()]),this.subs.push(this.sysMonomerLib.onChanged.subscribe((()=>{this.reset()}))),this.reset()}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={},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,u.AP)(e);this.logger.error(t,void 0,n)}const i=n.isMsa()?this.getCellMonomerLengthsForSeqMsa():this.getCellMonomerLengthsForSeq(e);return[i,this.getSummedMonomerLengths(i)]}getSummedMonomerLengths(e){const t=new Array(e.length+1);t[0]=5;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}getCellMonomerLengthsForSeq(e){this.toLog(),null===this._monomerLengthList&&(this._monomerLengthList=new Array(this.tableCol.length).fill(null));const t=this.seqHelper.getSeqHandler(this.tableCol),n=this.props.separatorWidth+1*this.props.fontCharWidth,i=Math.ceil(this.colWidth/n),r=t.getSplitted(e),o=Math.min(i,r.length);let s=this._monomerLengthList[e];if(null===s||s.length<o){s=this._monomerLengthList[e]=new Array(r.length);let n=0;for(let e=0;e<o;++e){const i=r.getOriginal(e),o=this.props.monomerToShort(i,this.monomerLengthLimit),a=(t.isSeparator()?this.separatorWidth:this.props.separatorWidth)+o.length*this.props.fontCharWidth;if(s[e]=a,n+=a,n>this.colWidth)break}}return s}getCellMonomerLengthsForSeqValue(e,t){const n=this.seqHelper.getSeqHandler(this.tableCol),i=this.props.separatorWidth+1*this.props.fontCharWidth,r=Math.ceil(t/i),o=n.splitter(e),s=Math.min(r,o.length),a=new Array(s);let l=0;for(let e=0;e<s;++e){const i=o.getOriginal(e),r=this.props.monomerToShort(i,this.monomerLengthLimit),s=(n.isSeparator()?this.separatorWidth:this.props.separatorWidth)+r.length*this.props.fontCharWidth;if(a[e]=s,l+=s,l>t)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:i}=(()=>{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,o=Math.ceil(this.colWidth/r);for(let e=n;e<i;e++){if(this._processedRows.get(e)&&o<=this._processedMaxVisibleSeqLength)continue;const n=this.seqHelper.getSeqHandler(this.tableCol).getSplitted(e,o),i=Math.min(o,n.length);i>t.length&&t.push(...new Array(i-t.length).fill(r));let s=0;for(let e=0;e<i;++e){const i=n.getOriginal(e),r=this.props.monomerToShort(i,this.monomerLengthLimit),o=this.props.separatorWidth+r.length*this.props.fontCharWidth;if(t[e]=Math.max(t[e]??0,o),s+=o,s>=this.colWidth)break}this._processedMaxVisibleSeqLength=Math.max(this._processedMaxVisibleSeqLength,o)}return t}getPosition(e,t,n){const[i,r]=this.getCellMonomerLengths(e,n);return 0===this.seqHelper.getSeqHandler(this.tableCol).getSplitted(e).length?null:function(e,t){let n,i=100,r=0,o=e.length-1;for(;r<=o;){if(n=Math.floor((o+r)/2),e[n]<=t&&t<e[n+1])return n;if(t<e[n]?o=n-1:r=n+1,--i<=0)throw new Error(`Get position for pointer x = ${t} searching has not converged on ${JSON.stringify(e)}. `)}return null}(r,t)}setMonomerLengthLimit(e){this.monomerLengthLimit!=e&&(this.monomerLengthLimit=e,this.dirty=!0)}setSeparatorWidth(e){this.separatorWidth!=e&&(this.props.separatorWidth=e,this.dirty=!0)}render(e,t,n,i,r,o,a){const c=o.grid?.canvas===e.canvas;if(!this.seqHelper)return;const h=this.gridCol,m=this.tableCol,f=window.devicePixelRatio,y=`${this.toLog()}.render()`;this.logger.debug(`${y}, start`);let v=this.monomerLengthLimit;if(d.gp.maxMonomerLength in m.tags){const e=parseInt(m.getTag(d.gp.maxMonomerLength));v=!isNaN(e)&&e?e:50}if(".mm.cellRenderer.maxMonomerLength"in m.temp){const 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S=m.meta.units,x=m.getTag(l.gp.aligned),E=m.getTag(l.gp.separator)??"",_=this.props.separatorWidth+1*this.props.fontCharWidth,M=Math.ceil(i/_),I=m.temp["reference-sequence"],T=this.tableCol.temp["current-word"];T&&-1===m?.dataFrame?.currentRowIdx&&(this.tableCol.temp["current-word"]=null);const L=(()=>{const e=a.getSplitter(M)(null!=I&&""!=I?I:T??"");return s().count(0).take(e.length).map((t=>e.getOriginal(t))).toArray()})(),N=c?a.getSplitted(C):a.splitter(w);c||(y=this.getSummedMonomerLengths(this.getCellMonomerLengthsForSeqValue(w,i)));let $=d.yg.classic;x&&x.includes("MSA")&&S==l.Hi.SEPARATOR&&($=d.yg.MSA);const P=Math.min(N.length,M);for(let s=0;s<P;++s){const l=N.getOriginal(s),c=N.getCanonical(s);let h=g;const u=this.getMonomerLib();if(u){const e=a.defaultBiotype;h=u.getMonomerTextColor(e,c)}e.fillStyle=g;const p={color:h,pivot:0,left:!0,transparencyRate:1,separator:E,last:s===N.length-1,drawStyle:$,maxWord:y,wordIdx:s,gridCell:o,referenceSequence:L,maxLengthOfMonomer:v,monomerTextSizeMap:this._monomerLengthMap,logger:this.logger};if((0,d.oZ)(e,l,t+this.padding,n,i,r,p),A>i)break}}catch(e){const[t,n]=(0,u.AP)(e);this.logger.error(t,void 0,n),this.errors.push(e)}finally{e.restore()}}onMouseMove(e,t){const n=`${this.toLog()}.onMouseMove()`;if(!this.seqHelper||null==e.tableRowIndex)return;const r=e.bounds,o=t.offsetX-e.gridColumn.left+(e.gridColumn.left-r.x),s=this.getPosition(e.tableRowIndex,o,r.width);this.logger.debug(`${n}, start, argsX: ${o}, left: ${s}`);const a=this.seqHelper.getSeqHandler(this.tableCol),c=a.getSplitted(e.tableRowIndex);if(null!==s&&s<c.length){const n=a.alphabet??l.YI.UN,r={position:s,biotype:n===l.YI.RNA||n===l.YI.DNA?m.o.NUCLEOTIDE:m.o.AA,symbol:c.getCanonical(s)},o=[];let h=this._monomerStructureMap[r.symbol];{const e=this.getMonomerLib();h=this._monomerStructureMap[r.symbol]=e?e.getTooltip(r.biotype,r.symbol):i.divText("Monomer library is not available")}o.push(h),i.tooltip.show(i.divV(o),t.x+16,t.y+16),(0,f.WN)(e,r)}else i.tooltip.hide(),(0,f.WN)(e,null)}}function b(e,t,n,i,r){return e?Math.max(Math.min(e.canvas.width/r-n,i)):Math.max(t.canvas.width/r-n,0)}},3856:(e,t,n)=>{"use strict";n.d(t,{Mn:()=>l,gp:()=>a,oZ:()=>u,yg:()=>c});var i=n(7278);const r="#808080",o="rgb(0,0,0)",s=i.zS;var a,l,c;!function(e){e.maxMonomerLength=".mm.cellRenderer.maxMonomerLength"}(a||(a={})),function(e){e.applyToBackground=".m.cellRenderer.applyToBackground"}(l||(l={})),function(e){e.MSA="MSA",e.classic="classic"}(c||(c={}));const h=new class{constructor(){this.color="rgb(100,100,100)",this.pivot=0,this.left=!1,this.transparencyRate=1,this.separator="",this.last=!1,this.drawStyle=c.classic,this.maxWord=[],this.wordIdx=0,this.gridCell=null,this.referenceSequence=null,this.maxLengthOfMonomer=null,this.monomerTextSizeMap={},this.logger=void 0}};function u(e,t,n,i,a,l,u){var d,p,m;const f=Object.assign(Object.assign({},h),u);u.logger?.debug("Bio: printLeftOrCentered(), start"),e.textAlign="start";let g=t.substring(0),y=f.last?"":f.separator;f.drawStyle===c.MSA&&(y="");let b=!0,v=!0,w="difference";if(null!=f.gridCell&&null!=f.gridCell.cell.column&&(b=f.gridCell.cell.column.temp["color-code"]??!0,v=f.gridCell.cell.column.temp["compare-with-current"]??!0,w=f.gridCell.cell.column.temp["highlight-difference"]??"difference"),f.referenceSequence){const e=f.referenceSequence[f.wordIdx];v&&f.referenceSequence.length>0&&"difference"===w&&(f.transparencyRate=g==e?.3:f.transparencyRate),v&&f.referenceSequence.length>0&&"equal"===w&&(f.transparencyRate=g!=e?.3:f.transparencyRate)}null!=f.maxLengthOfMonomer&&(g=s(g,f.maxLengthOfMonomer));const C=g+y;(d=f.monomerTextSizeMap)[C]??(d[C]=e.measureText(C));let A=f.monomerTextSizeMap[C];(p=f.monomerTextSizeMap)[g]??(p[g]=e.measureText(g));let S=f.monomerTextSizeMap[g].width;const x=l/2-(A.fontBoundingBoxAscent+A.fontBoundingBoxDescent)/2+1;(m=f.monomerTextSizeMap)[y]??(m[y]=e.measureText(y));const E=f.monomerTextSizeMap[y].width;function _(t,s){const a=b?f.color:o;e.fillStyle=a,e.globalAlpha=f.transparencyRate,f.drawStyle===c.classic&&(e.fillText(g,n+t,i+x),e.fillStyle=r,e.fillText(y,n+s,i+x)),f.drawStyle===c.MSA&&e.fillText(g,n+t,i+x)}A=A.width,f.drawStyle===c.MSA&&(S=f.maxWord[f.wordIdx],A=f.maxWord[f.wordIdx]);const M=(f.maxWord[f.wordIdx]??0)-(f.maxWord[0]??0);if(f.left||A>a)return _(M,M+S),n+M+S+E;{const e=(a-A)/2;return _(e,e+S),n+M+e+S}}},3151:(e,t,n)=>{"use strict";n.d(t,{EK:()=>l,Ec:()=>o,f6:()=>i,pe:()=>s,q7:()=>a,yw:()=>r});const i=["symbol","molfile","rgroups","name"],r="MonomerName",o={monomerType:null,smiles:null,name:"Name",author:null,molfile:"molecule",naturalAnalog:"MonomerNaturalAnalogCode",rgroups:"MonomerCaps",createDate:null,id:null,polymerType:"MonomerType",symbol:"MonomerName"},s={monomerType:"Backbone",smiles:"",name:"",author:"Datagrok",molfile:"",naturalAnalog:"",rgroups:[],createDate:null,id:0,polymerType:"PEPTIDE",symbol:""},a="p",l=new RegExp(`[rd]\\((\\w)\\)${a}?`,"g")},9192:(e,t,n)=>{"use strict";function i(e){return"string"==typeof e||e instanceof String?e:"StateError"===e.constructor.name?e.message:"StateError"===e.constructor.name&&"$thrownJsError"in e?i(e.$thrownJsError):e instanceof Error?e.message:e.toString()}function r(e){return e instanceof Error?e.stack:"StateError"===e.constructor.name&&"$thrownJsError"in e?r(e.$thrownJsError):void 0}function o(e){return[i(e),r(e)]}n.d(t,{AP:()=>o})},3516:(e,t,n)=>{"use strict";n.d(t,{m:()=>o});var i=n(6082),r=n(439);class o{get descriptionsArray(){return this._descriptionsArray}get sequencesArray(){return this._sequencesArray}parseMacromolecule(e,t){return this._fileContent.slice(e,t).split(/\s/).join("")}parseColumns(){const e=/^>(.*)$/gm;let t,n=0;for(;t=e.exec(this._fileContent);){const i=this._fileContent.substring(t.index+1,e.lastIndex);this._descriptionsArray.push(i),0!==n&&this._sequencesArray.push(this.parseMacromolecule(n,t.index)),n=e.lastIndex+1}this._sequencesArray.push(this.parseMacromolecule(n,-1))}importFasta(){const e=i.Column.fromStrings("description",this.descriptionsArray),t=i.Column.fromStrings("sequence",this.sequencesArray);return t.semType=i.SEMTYPE.MACROMOLECULE,t.meta.units=r.Hi.FASTA,[i.DataFrame.fromColumns([e,t])]}constructor(e){this._descriptionsArray=[],this._sequencesArray=[],this._fileContent=e,this.parseColumns()}}},6873:(e,t,n)=>{"use strict";n.d(t,{Hx:()=>h,dW:()=>c});var i=n(6082),r=n(1991),o=n.n(r),s=n(2003),a=n(7278),l=n(439);function c(e=10**5){const t="meI/hHis/Aca/N//dE/Thr_PO3H2/Aca/D-Tyr_Et/Tyr_ab-dehydroMe".repeat(Math.ceil(e/10)).slice(0,-1),n=i.Column.fromList(i.COLUMN_TYPE.STRING,"MSA",new Array(100).fill(t));n.semType=i.SEMTYPE.MACROMOLECULE,n.meta.units=s.Hi.SEPARATOR,n.setTag(s.gp.separator,"/"),n.setTag(s.gp.alphabet,s.YI.UN),n.setTag(s.gp.alphabetIsMultichar,"true");const r=[];return r.push(n),r.push(i.Column.fromList(i.COLUMN_TYPE.FLOAT,"Activity",new Array(100).fill(7.30751))),r}function h(e,t=s.Hi.SEPARATOR,n=s.YI.PT,r=(t===s.Hi.SEPARATOR?"-":void 0),c=void 0,h="seq",u=100,d=10**6){const p=n===s.YI.UN?c?.getMonomerSymbolsByType("PEPTIDE")??[]:Array.from((0,s.Qf)(n)),m=p.length,f=i.Column.fromType(i.COLUMN_TYPE.STRING,h,u);f.semType=i.SEMTYPE.MACROMOLECULE,f.meta.units=t,f.setTag(s.gp.alphabet,n),t==s.Hi.SEPARATOR&&f.setTag(s.gp.separator,r);const g=e.getSeqHandler(f);for(let e=0;e<u;e++){const n=o().count(0).take(d).map((e=>p[Math.floor(Math.random()*m)])).toArray(),i=g.joiner(new a.Mu(n,l.b9[t]));f.set(e,i)}return f}},439:(e,t,n)=>{"use strict";n.d(t,{B5:()=>l,Hi:()=>i,Vl:()=>c,YI:()=>r,_S:()=>u,b9:()=>d,gp:()=>o,q7:()=>h,z1:()=>a});var i,r,o,s=n(2738);!function(e){e.FASTA="fasta",e.SEPARATOR="separator",e.HELM="helm",e.CUSTOM="custom"}(i||(i={})),function(e){e.DNA="DNA",e.RNA="RNA",e.PT="PT",e.UN="UN"}(r||(r={})),function(e){e.aligned="aligned",e.alphabet="alphabet",e.alphabetSize=".alphabetSize",e.alphabetIsMultichar=".alphabetIsMultichar",e.separator="separator",e.isHelmCompatible=".isHelmCompatible",e.positionNames=".positionNames",e.positionLabels=".positionLabels",e.regions=".regions"}(o||(o={}));const a=", ",l=/(?:\[([A-Za-z0-9_\-,()]+)\])|([A-Za-z\-])/g,c=new class{constructor(){this.fasta={peptide:new Set(["G","L","Y","S","E","Q","D","N","F","A","K","R","H","C","V","P","W","I","M","T"]),dna:new Set(["A","C","G","T"]),rna:new Set(["A","C","G","U"])}}},h=[new s.a(r.PT,c.fasta.peptide,.5),new s.a(r.DNA,c.fasta.dna,.55),new s.a(r.RNA,c.fasta.rna,.55)],u="",d={[i.FASTA]:"-",[i.SEPARATOR]:"",[i.HELM]:"*"}},2003:(e,t,n)=>{"use 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this.mList[e]}constructor(e,t){this.mList=e,this.gapOriginalMonomer=t}}class d{get length(){return this.seqS.length}isGap(e){return this.getOriginal(e)===c.b9[c.Hi.FASTA]}getCanonical(e){if(this.length<=e)throw new Error("Index out of bounds");return this.isGap(e)?c._S:this.seqS[e]}getOriginal(e){if(this.length<=e)throw new Error("Index out of bounds");return this.seqS[e]}constructor(e){this.seqS=e}}const p=e=>{const t=o()(e.toString().matchAll(c.B5)).map((e=>e[2]??e[1])).toArray();return new u(t,c.b9[c.Hi.FASTA])},m=e=>e?new d(e):new u([],c.b9[c.Hi.FASTA]);function f(e,t=void 0){return n=>{if(n){let i;const r=new RegExp(`(?<=^|\\${e})("-"|'-'|[^\\${e}]*)(?=\\${e}|$)`,"g");return void 0!==t?(r.lastIndex=0,i=o()(n.matchAll(r)).take(t).map((e=>e[0])).toArray()):i=n.replaceAll('"-"',"").replaceAll("'-'","").split(e,t),new u(i,c.b9[c.Hi.SEPARATOR])}return new u([],c.b9[c.Hi.SEPARATOR])}}const g=e=>{const t=e.split("$")[0].split("|"),n=o()(t.map((e=>(e.match(/(?<=\{).+(?=})/)?.[0]?.split(".")??[]).map((e=>(0,h.D)(e)))))).flatten().toArray();return new u(n,c.b9[c.Hi.HELM])};function y(e,t,n=void 0){if(e.toLowerCase().startsWith(c.Hi.FASTA))return p;if(e.toLowerCase().startsWith(c.Hi.SEPARATOR))return f(t,n);if(e.toLowerCase().startsWith(c.Hi.HELM))return g;throw new Error(`Unexpected units ${e} .`)}const b=/([^\W_]+)/g;function v(e,t){if(e.length<=t)return e;const n=e.match(b),i=e.length>t||(n?.length??0)>1,r=n?.[0]??" 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n=t.find((e=>{const t=e.meta.units;return!!t&&-1!==t.indexOf("MSA")}))??null;return!n&&t.length>0&&(n=t[0]),n}},8312:(e,t,n)=>{"use strict";n.d(t,{Q:()=>r});var i=n(6082);async function r(){const e=i.Func.find({package:"Bio",name:"getSeqHelper"});if(0===e.length)throw new Error("Package 'Bio' must be installed for SeqHelper.");return(await e[0].prepare().call()).getOutputParamValue()}},3077:(e,t,n)=>{"use strict";n.d(t,{R:()=>r});var i=n(6082);function r(e,t){const n=e=>{const t=s.columns.addNewString((e+1).toString());return r.push(t),t},r=[],o=e.length,s=i.DataFrame.create(o),a=t.getSeqHandler(e);for(let e=0;e<o;++e){const t=a.getSplitted(e);for(let i=0;i<t.length;++i){const o=t.getCanonical(i);((r[i]??null)||n(i)).set(e,o,!1)}}return s}},7602:(e,t,n)=>{"use strict";n.d(t,{g:()=>o});var i,r=n(9192);!function(e){e[e.error=0]="error",e[e.warning=1]="warning",e[e.info=2]="info",e[e.debug=3]="debug"}(i||(i={}));class 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e=0;e<i.length;++e)i[e]=(0,l.YN)(i[e]+t),void 0!==n&&(r[e]=(0,l.YN)(r[e]+n))}},294:(e,t,n)=>{"use strict";function i(e,t){return e[t.polymerType]?.[t.symbol]}function r(e,t){return!!e[t.polymerType]?.[t.symbol]}function o(e,t,n){let i=e[t.polymerType];i||(i=e[t.polymerType]={}),i[t.symbol]=n}n.d(t,{Cg:()=>s,LQ:()=>o,bq:()=>r,vF:()=>a,xb:()=>i});class s extends Map{constructor(e){super(e)}}class a{constructor(e,t){this.molfile=e,this.monomers=t}static createEmpty(){return new a("",new s(null))}}},330:(e,t,n)=>{"use strict";n.d(t,{kA:()=>r,pz:()=>s,qj:()=>o,vG:()=>a});var i=n(2003);function r(e,t){return e?e.columns.getUnusedName(t):t}function o(e,t){return r(e,`molfile(${t})`)}function s(e){let t;if(e===i.YI.PT||e===i.YI.UN)t="PEPTIDE";else{if(e!==i.YI.RNA&&e!==i.YI.DNA)throw new Error(`Unexpected alphabet '${e}'.`);t="RNA"}return t}function a(e){const t=7===e.length?/^#?([a-f\d]{2})([a-f\d]{2})([a-f\d]{2})$/i.exec(e):/^#?([a-f\d]{2})([a-f\d]{2})([a-f\d]{2})([a-f\d]{2})$/i.exec(e);return t?[parseInt(t[1],16)/256,parseInt(t[2],16)/256,parseInt(t[3],16)/256,t.length>4?parseInt(t[4],16)/256:.3]:null}},1093:(e,t,n)=>{"use strict";n(7362);class i{}i.SemType="Nucleotides",i.SemTypeMultipleAlignment="NucleotidesMultipleAlignment",i.Names={A:"Adenine",C:"Cytosine",G:"Guanine",T:"Thymine",U:"Uracil"}},7362:(e,t,n)=>{"use strict";n.d(t,{e:()=>i});class i{static makePalette(e,t=!1,n=i){const r={};return e.forEach((e=>{const n=e[0],i=e[1];n.forEach(((e,n)=>{r[e]=this.colourPalette[i][t?0:n]}))})),new n(r)}constructor(e){this._palette=e}get(e,t){return this._palette[e]}}i.undefinedColor="rgb(100,100,100)",i.colourPalette={orange:["rgb(255,187,120)","rgb(245,167,100)","rgb(235,137,70)","rgb(205, 111, 71)"],all_green:["rgb(44,160,44)","rgb(74,160,74)","rgb(23,103,57)","rgb(30,110,96)","rgb(60,131,95)","rgb(24,110,79)","rgb(152,223,138)","rgb(182, 223, 138)","rgb(152, 193, 138)"],all_blue:["rgb(31,119,180)","rgb(23,190,207)","rgb(122, 102, 189)","rgb(158,218,229)","rgb(141, 124, 217)","rgb(31, 120, 150)"],magenta:["rgb(162,106,192)","rgb(197,165,224)","rgb(208,113,218)"],red:["rgb(214,39,40)","rgb(255,152,150)"],st_blue:["rgb(23,190,207)","rgb(158,218,229)","rgb(31,119,180)"],dark_blue:["rgb(31,119,180)","rgb(31, 120, 150)"],light_blue:["rgb(23,190,207)","rgb(158,218,229)","rgb(108, 218, 229)","rgb(23,190,227)"],lilac_blue:["rgb(124,102,211)","rgb(149,134,217)","rgb(97, 81, 150)"],dark_green:["rgb(23,103,57)","rgb(30,110,96)","rgb(60,131,95)","rgb(24,110,79)"],green:["rgb(44,160,44)","rgb(74,160,74)"],light_green:["rgb(152,223,138)","rgb(182, 223, 138)","rgb(152, 193, 138)"],st_green:["rgb(44,160,44)","rgb(152,223,138)","rgb(39, 174, 96)","rgb(74,160,74)"],pink:["rgb(247,182,210)"],brown:["rgb(140,86,75)","rgb(102, 62, 54)"],gray:["rgb(127,127,127)","rgb(199,199,199)","rgb(196,156,148)","rgb(222, 222, 180)"],yellow:["rgb(188,189,34)"],white:["rgb(230,230,230)"]}},4574:(e,t,n)=>{"use strict";n.d(t,{O:()=>o,n:()=>r});var i=n(1858);class r{constructor(e,t=!0,n){return this.substructure=e,this.readOnly=t,this.logger=n,new Proxy(this,{set:(e,t,n)=>{if(this.logger?.debug(`BioFilterProps.set ${t.toString()}( '${n}' )`),this.readOnly)throw new Error("Properties are immutable.");return e[t]=n,!0}})}}class o{constructor(){this.onChanged=new i.Subject,this._props=null,this._propsChanging=!1}get props(){return this._props||(this._props=this.emptyProps),this._props}set props(e){this._propsChanging=!0;try{this._props=e,this.applyProps(),this.onChanged.next()}finally{this._propsChanging=!1}}saveProps(){const e={};for(const[t,n]of Object.entries(this.props))"_onChanged"!==t&&"logger"!==t&&(e[t]=this.props[t]);return e}async detach(){}get filterSummary(){return this.props.substructure}get isFiltering(){return""!==this.props.substructure}resetFilter(){this.props=this.emptyProps,this.onChanged.next()}}},4152:(e,t,n)=>{"use strict";var i=n(6082),r=n(7362),o=n(6718);function s(e,t=!0){if(null==e)return"rgb(100,100,100)";const n=i.Color.fromHtml(e);if(t){const e=i.Color.g(n),t=i.Color.r(n),r=i.Color.b(n),o=Math.sqrt(Math.pow(0-t,2)+Math.pow(0-e,2)+Math.pow(0-r,2));if(o>210)return`rgb(${t/o*210},${e/o*210},${r/o*210})`}return i.Color.toRgb(n)}class a{static hashCode(e){let t=0;if(0===e.length)return t;for(let n=0;n<e.length;n++)t=(t<<5)-t+e.charCodeAt(n),t|=0;return t}}class l{}class c extends l{static get palette(){return c._pallete||(c._pallete=c.buildPalette()),c._pallete}static buildPalette(){return(0,o.pj)().then((e=>{e.awaitLoaded(1/0).then((()=>{const t=e.getMonomerLib();t.onChanged.subscribe((()=>{c.customMonomerColors={},c.polymerTypes=t.getPolymerTypes();for(const e of this.polymerTypes){const n=t.getMonomerSymbolsByType(e);for(const i of n){const n=t.getMonomer(e,i);n?.meta?.colors?.default?.background&&(this.customMonomerColors[i]||(this.customMonomerColors[i]={}),this.customMonomerColors[i][e]=s(n.meta.colors.default.background))}}}))}))})),[].concat(...Object.values(r.e.colourPalette))}get(e,t){const n=c.palette.length,i=c.customMonomerColors[e],r=t??"PEPTIDE";if(i&&i[r])return i[r];const o=a.hashCode(e)%n;return s(c.palette[o])}}c._pallete=null,c.customMonomerColors={},c.polymerTypes=[]},6642:(e,t,n)=>{"use strict";n.d(t,{BG:()=>s,sD:()=>l});var i=n(4328),r=n(1858),o=n(8070);function s(e){let t=null,n=null;try{n=e.dart?e.gridColumn:null,t=n?n.temp:null}catch{[n,t]=[null,null]}const i=e.cell.column;if(t=t??(i?i.temp:null),!t)throw new Error("Grid cell renderer back store (GridColumn or Column) not found.");return[n,i,t]}class a{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 l extends a{constructor(e,t,n){super(),this.gridCol=e,this.tableCol=t,this.logger=n,this.subs=[],this.dirty=!0,this.destroyed=!1,this.viewerId=++l.viewerCounter,this.errors=[],this._onRendered=new r.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(i.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(i.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(0,o.PE)(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`)}}l.viewerCounter=-1},673:(e,t,n)=>{"use strict";n.d(t,{s:()=>i});const i={true:"1",false:"0"}},6882:(e,t,n)=>{"use strict";n.d(t,{Jy:()=>y,S$:()=>g,U0:()=>b});var i=n(7389),r=n(6082),o=n(1991),s=n.n(o),a=n(8312),l=n(2003),c=n(6642),h=n(6718),u=n(9192),d=n(3856),p=n(673),m=n(3599),f=n(5553);const g="rgb(100,100,100)";class y extends c.sD{get separatorWidth(){return this.props?.fontCharWidth?this.props?.fontCharWidth:5}constructor(e,t,n,i,o){super(e,t,n),this.monomerLengthLimit=i,this.propsProvider=o,this.colWidth=0,this._monomerLengthList=null,this._processedMaxVisibleSeqLength=0,this._monomerLengthMap={},this._monomerStructureMap={},this.sysMonomerLib=null,this.padding=5,this.props=this.propsProvider(),this._processedRows=r.BitSet.create(this.tableCol.length),this.gridCol&&this.subs.push(this.gridCol.grid.onAfterDrawContent.subscribe((()=>{this._onRendered.next()}))),this.tableCol&&this.gridCol&&this.subs.push(this.tableCol.dataFrame.onCurrentRowChanged.subscribe((()=>{const e=this.tableCol.dataFrame;this.gridCol.grid,-1===e.currentRowIdx&&(this.tableCol.temp["reference-sequence"]=null,this.tableCol.temp["current-word"]=null,this.invalidateGrid())})))}async init(){await Promise.all([(async()=>{this.seqHelper=await(0,a.Q)(),this.invalidateGrid()})(),(async()=>{const e=await(0,h.pj)();this.sysMonomerLib=e.getMonomerLib()})()]),this.subs.push(this.sysMonomerLib.onChanged.subscribe((()=>{this.reset()}))),this.reset()}static getFontSettings(e){let t=12;return e&&e.temp[".mm.cellRenderer.fontSize"]&&"number"==typeof e.temp[".mm.cellRenderer.fontSize"]&&!isNaN(e.temp[".mm.cellRenderer.fontSize"])&&(t=Math.max(e.temp[".mm.cellRenderer.fontSize"],1)),{font:`${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={},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,u.AP)(e);this.logger.error(t,void 0,n)}const i=n.isMsa()?this.getCellMonomerLengthsForSeqMsa():this.getCellMonomerLengthsForSeq(e);return[i,this.getSummedMonomerLengths(i)]}getSummedMonomerLengths(e){const t=new Array(e.length+1);t[0]=5;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}getCellMonomerLengthsForSeq(e){this.toLog(),null===this._monomerLengthList&&(this._monomerLengthList=new Array(this.tableCol.length).fill(null));const t=this.seqHelper.getSeqHandler(this.tableCol),n=this.props.separatorWidth+1*this.props.fontCharWidth,i=Math.ceil(this.colWidth/n),r=t.getSplitted(e),o=Math.min(i,r.length);let s=this._monomerLengthList[e];if(null===s||s.length<o){s=this._monomerLengthList[e]=new Array(r.length);let n=0;for(let e=0;e<o;++e){const i=r.getOriginal(e),o=this.props.monomerToShort(i,this.monomerLengthLimit),a=(t.isSeparator()?this.separatorWidth:this.props.separatorWidth)+o.length*this.props.fontCharWidth;if(s[e]=a,n+=a,n>this.colWidth)break}}return s}getCellMonomerLengthsForSeqValue(e,t){const n=this.seqHelper.getSeqHandler(this.tableCol),i=this.props.separatorWidth+1*this.props.fontCharWidth,r=Math.ceil(t/i),o=n.splitter(e),s=Math.min(r,o.length),a=new Array(s);let l=0;for(let e=0;e<s;++e){const i=o.getOriginal(e),r=this.props.monomerToShort(i,this.monomerLengthLimit),s=(n.isSeparator()?this.separatorWidth:this.props.separatorWidth)+r.length*this.props.fontCharWidth;if(a[e]=s,l+=s,l>t)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:i}=(()=>{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,o=Math.ceil(this.colWidth/r);for(let e=n;e<i;e++){if(this._processedRows.get(e)&&o<=this._processedMaxVisibleSeqLength)continue;const n=this.seqHelper.getSeqHandler(this.tableCol).getSplitted(e,o),i=Math.min(o,n.length);i>t.length&&t.push(...new Array(i-t.length).fill(r));let s=0;for(let e=0;e<i;++e){const i=n.getOriginal(e),r=this.props.monomerToShort(i,this.monomerLengthLimit),o=this.props.separatorWidth+r.length*this.props.fontCharWidth;if(t[e]=Math.max(t[e]??0,o),s+=o,s>=this.colWidth)break}this._processedMaxVisibleSeqLength=Math.max(this._processedMaxVisibleSeqLength,o)}return t}getPosition(e,t,n){const[i,r]=this.getCellMonomerLengths(e,n);return 0===this.seqHelper.getSeqHandler(this.tableCol).getSplitted(e).length?null:function(e,t){let n,i=100,r=0,o=e.length-1;for(;r<=o;){if(n=Math.floor((o+r)/2),e[n]<=t&&t<e[n+1])return n;if(t<e[n]?o=n-1:r=n+1,--i<=0)throw new Error(`Get position for pointer x = ${t} searching has not converged on ${JSON.stringify(e)}. `)}return null}(r,t)}setMonomerLengthLimit(e){this.monomerLengthLimit!=e&&(this.monomerLengthLimit=e,this.dirty=!0)}setSeparatorWidth(e){this.separatorWidth!=e&&(this.props.separatorWidth=e,this.dirty=!0)}render(e,t,n,i,r,o,a){const c=o.grid?.canvas===e.canvas;if(!this.seqHelper)return;const h=this.gridCol,m=this.tableCol,f=window.devicePixelRatio,y=`${this.toLog()}.render()`;this.logger.debug(`${y}, start`);let v=this.monomerLengthLimit;if(d.gp.maxMonomerLength in m.tags){const e=parseInt(m.getTag(d.gp.maxMonomerLength));v=!isNaN(e)&&e?e:50}if(".mm.cellRenderer.maxMonomerLength"in m.temp){const e=m.temp[".mm.cellRenderer.maxMonomerLength"];v=!isNaN(e)&&e?e:50}e.save();try{const a=this.seqHelper.getSeqHandler(m);if(m.temp[".mm.cellRenderer.settingsChanged"]===p.s.true||this.monomerLengthLimit!=v){let e=0;const t=8;e=m.temp[".mm.cellRenderer.gapLength"]??e,this.setMonomerLengthLimit(v),this.setSeparatorWidth(a.isMsa()?t:e),m.temp[".mm.cellRenderer.settingsChanged"]=p.s.false}let[u,y]=this.getCellMonomerLengths(o.tableRowIndex,i);u.length;const w=o.cell.value,C=o.cell.rowIndex,A=(m.getTag(l.gp.alphabet),50);c&&(i=b(h?.grid,e,t,i,f)),e.beginPath(),e.rect(t+this.padding,n+this.padding,i-this.padding-1,r-2*this.padding),e.clip(),e.font=this.props?.font??"12px monospace",e.textBaseline="top";const S=m.meta.units,x=m.getTag(l.gp.aligned),E=m.getTag(l.gp.separator)??"",_=this.props.separatorWidth+1*this.props.fontCharWidth,M=Math.ceil(i/_),I=m.temp["reference-sequence"],T=this.tableCol.temp["current-word"];T&&-1===m?.dataFrame?.currentRowIdx&&(this.tableCol.temp["current-word"]=null);const L=(()=>{const e=a.getSplitter(M)(null!=I&&""!=I?I:T??"");return s().count(0).take(e.length).map((t=>e.getOriginal(t))).toArray()})(),N=c?a.getSplitted(C):a.splitter(w);c||(y=this.getSummedMonomerLengths(this.getCellMonomerLengthsForSeqValue(w,i)));let $=d.yg.classic;x&&x.includes("MSA")&&S==l.Hi.SEPARATOR&&($=d.yg.MSA);const P=Math.min(N.length,M);for(let s=0;s<P;++s){const l=N.getOriginal(s),c=N.getCanonical(s);let h=g;const u=this.getMonomerLib();if(u){const e=a.defaultBiotype;h=u.getMonomerTextColor(e,c)}e.fillStyle=g;const p={color:h,pivot:0,left:!0,transparencyRate:1,separator:E,last:s===N.length-1,drawStyle:$,maxWord:y,wordIdx:s,gridCell:o,referenceSequence:L,maxLengthOfMonomer:v,monomerTextSizeMap:this._monomerLengthMap,logger:this.logger};if((0,d.oZ)(e,l,t+this.padding,n,i,r,p),A>i)break}}catch(e){const[t,n]=(0,u.AP)(e);this.logger.error(t,void 0,n),this.errors.push(e)}finally{e.restore()}}onMouseMove(e,t){const n=`${this.toLog()}.onMouseMove()`;if(!this.seqHelper||null==e.tableRowIndex)return;const r=e.bounds,o=t.offsetX-e.gridColumn.left+(e.gridColumn.left-r.x),s=this.getPosition(e.tableRowIndex,o,r.width);this.logger.debug(`${n}, start, argsX: ${o}, left: ${s}`);const a=this.seqHelper.getSeqHandler(this.tableCol),c=a.getSplitted(e.tableRowIndex);if(null!==s&&s<c.length){const n=a.alphabet??l.YI.UN,r={position:s,biotype:n===l.YI.RNA||n===l.YI.DNA?m.o.NUCLEOTIDE:m.o.AA,symbol:c.getCanonical(s)},o=[];let h=this._monomerStructureMap[r.symbol];{const e=this.getMonomerLib();h=this._monomerStructureMap[r.symbol]=e?e.getTooltip(r.biotype,r.symbol):i.divText("Monomer library is not available")}o.push(h),i.tooltip.show(i.divV(o),t.x+16,t.y+16),(0,f.WN)(e,r)}else i.tooltip.hide(),(0,f.WN)(e,null)}}function b(e,t,n,i,r){return e?Math.max(Math.min(e.canvas.width/r-n,i)):Math.max(t.canvas.width/r-n,0)}},3856:(e,t,n)=>{"use strict";n.d(t,{Mn:()=>l,gp:()=>a,oZ:()=>u,yg:()=>c});var i=n(7278);const r="#808080",o="rgb(0,0,0)",s=i.zS;var 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i.if(t,(()=>this.mergeEvaluated(e,h.Name))),!0}}function M(e,t,n,i){const r=new _(e,n,t);"code"in n?n.code(r,i):r.$data&&n.validate?(0,l.funcKeywordCode)(r,n):"macro"in n?(0,l.macroKeywordCode)(r,n):(n.compile||n.validate)&&(0,l.funcKeywordCode)(r,n)}t.KeywordCxt=_;const I=/^\/(?:[^~]|~0|~1)*$/,T=/^([0-9]+)(#|\/(?:[^~]|~0|~1)*)?$/;function L(e,{dataLevel:t,dataNames:n,dataPathArr:i}){let r,o;if(""===e)return u.default.rootData;if("/"===e[0]){if(!I.test(e))throw new Error(`Invalid JSON-pointer: ${e}`);r=e,o=u.default.rootData}else{const s=T.exec(e);if(!s)throw new Error(`Invalid JSON-pointer: ${e}`);const a=+s[1];if(r=s[2],"#"===r){if(a>=t)throw new Error(l("property/index",a));return i[t-a]}if(a>t)throw new Error(l("data",a));if(o=n[t-a],!r)return o}let s=o;const a=r.split("/");for(const e of a)e&&(o=h._`${o}${(0,h.getProperty)((0,p.unescapeJsonPointer)(e))}`,s=h._`${s} && ${o}`);return s;function l(e,n){return`Cannot access ${e} ${n} levels up, current level is 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n;const{gen:c,keyword:h,schema:u,parentSchema:d,$data:p,it:m}=e;!function({schemaEnv:e},t){if(t.async&&!e.$async)throw new Error("async keyword in sync schema")}(m,t);const f=!p&&t.compile?t.compile.call(m.self,u,d,m):t.validate,g=l(c,h,f),y=c.let("valid");function b(n=(t.async?i._`await `:i.nil)){const s=m.opts.passContext?r.default.this:r.default.self,a=!("compile"in t&&!p||!1===t.schema);c.assign(y,i._`${n}${(0,o.callValidateCode)(e,g,s,a)}`,t.modifying)}function v(e){var n;c.if((0,i.not)(null!==(n=t.valid)&&void 0!==n?n:y),e)}e.block$data(y,(function(){if(!1===t.errors)b(),t.modifying&&a(e),v((()=>e.error()));else{const n=t.async?function(){const e=c.let("ruleErrs",null);return c.try((()=>b(i._`await `)),(t=>c.assign(y,!1).if(i._`${t} instanceof ${m.ValidationError}`,(()=>c.assign(e,i._`${t}.errors`)),(()=>c.throw(t))))),e}():function(){const e=i._`${g}.errors`;return c.assign(e,null),b(i.nil),e}();t.modifying&&a(e),v((()=>function(e,t){const{gen:n}=e;n.if(i._`Array.isArray(${t})`,(()=>{n.assign(r.default.vErrors,i._`${r.default.vErrors} === null ? ${t} : ${r.default.vErrors}.concat(${t})`).assign(r.default.errors,i._`${r.default.vErrors}.length`),(0,s.extendErrors)(e)}),(()=>e.error()))}(e,n)))}})),e.ok(null!==(n=t.valid)&&void 0!==n?n:y)},t.validSchemaType=function(e,t,n=!1){return!t.length||t.some((t=>"array"===t?Array.isArray(e):"object"===t?e&&"object"==typeof e&&!Array.isArray(e):typeof e==t||n&&void 0===e))},t.validateKeywordUsage=function({schema:e,opts:t,self:n,errSchemaPath:i},r,o){if(Array.isArray(r.keyword)?!r.keyword.includes(o):r.keyword!==o)throw new Error("ajv implementation error");const s=r.dependencies;if(null==s?void 0:s.some((t=>!Object.prototype.hasOwnProperty.call(e,t))))throw new Error(`parent schema must have dependencies of ${o}: ${s.join(",")}`);if(r.validateSchema&&!r.validateSchema(e[o])){const e=`keyword "${o}" value is 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0!==i&&(e.compositeRule=i),void 0!==r&&(e.createErrors=r),void 0!==o&&(e.allErrors=o),e.jtdDiscriminator=t,e.jtdMetadata=n}},4042:(e,t,n)=>{"use strict";Object.defineProperty(t,"__esModule",{value:!0}),t.CodeGen=t.Name=t.nil=t.stringify=t.str=t._=t.KeywordCxt=void 0;var i=n(2586);Object.defineProperty(t,"KeywordCxt",{enumerable:!0,get:function(){return i.KeywordCxt}});var r=n(9029);Object.defineProperty(t,"_",{enumerable:!0,get:function(){return r._}}),Object.defineProperty(t,"str",{enumerable:!0,get:function(){return r.str}}),Object.defineProperty(t,"stringify",{enumerable:!0,get:function(){return r.stringify}}),Object.defineProperty(t,"nil",{enumerable:!0,get:function(){return r.nil}}),Object.defineProperty(t,"Name",{enumerable:!0,get:function(){return r.Name}}),Object.defineProperty(t,"CodeGen",{enumerable:!0,get:function(){return r.CodeGen}});const o=n(3558),s=n(4551),a=n(396),l=n(3835),c=n(9029),h=n(6939),u=n(208),d=n(4227),p=n(3837),m=n(5944),f=(e,t)=>new RegExp(e,t);f.code="new RegExp";const g=["removeAdditional","useDefaults","coerceTypes"],y=new Set(["validate","serialize","parse","wrapper","root","schema","keyword","pattern","formats","validate$data","func","obj","Error"]),b={errorDataPath:"",format:"`validateFormats: false` can be used instead.",nullable:'"nullable" keyword is supported by default.',jsonPointers:"Deprecated jsPropertySyntax can be used instead.",extendRefs:"Deprecated ignoreKeywordsWithRef can be used instead.",missingRefs:"Pass empty schema with $id that should be ignored to ajv.addSchema.",processCode:"Use option `code: {process: (code, schemaEnv: object) => string}`",sourceCode:"Use option `code: {source: true}`",strictDefaults:"It is default now, see option `strict`.",strictKeywords:"It is default now, see option `strict`.",uniqueItems:'"uniqueItems" keyword is always validated.',unknownFormats:"Disable strict mode or pass `true` to `ajv.addFormat` (or `formats` option).",cache:"Map is used as cache, schema object as 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console;if(e.log&&e.warn&&e.error)return e;throw new Error("logger must implement log, warn and error methods")}(e.logger);const i=e.validateFormats;e.validateFormats=!1,this.RULES=(0,a.getRules)(),A.call(this,b,e,"NOT SUPPORTED"),A.call(this,v,e,"DEPRECATED","warn"),this._metaOpts=M.call(this),e.formats&&E.call(this),this._addVocabularies(),this._addDefaultMetaSchema(),e.keywords&&_.call(this,e.keywords),"object"==typeof e.meta&&this.addMetaSchema(e.meta),x.call(this),e.validateFormats=i}_addVocabularies(){this.addKeyword("$async")}_addDefaultMetaSchema(){const{$data:e,meta:t,schemaId:n}=this.opts;let i=p;"id"===n&&(i={...p},i.id=i.$id,delete i.$id),t&&e&&this.addMetaSchema(i,i[n],!1)}defaultMeta(){const{meta:e,schemaId:t}=this.opts;return this.opts.defaultMeta="object"==typeof e?e[t]||e:void 0}validate(e,t){let n;if("string"==typeof e){if(n=this.getSchema(e),!n)throw new Error(`no schema with key or ref "${e}"`)}else n=this.compile(e);const i=n(t);return"$async"in 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t;for(;"string"==typeof(t=S.call(this,e));)e=t;if(void 0===t){const{schemaId:n}=this.opts,i=new l.SchemaEnv({schema:{},schemaId:n});if(t=l.resolveSchema.call(this,i,e),!t)return;this.refs[e]=t}return t.validate||this._compileSchemaEnv(t)}removeSchema(e){if(e instanceof RegExp)return this._removeAllSchemas(this.schemas,e),this._removeAllSchemas(this.refs,e),this;switch(typeof e){case"undefined":return this._removeAllSchemas(this.schemas),this._removeAllSchemas(this.refs),this._cache.clear(),this;case"string":{const t=S.call(this,e);return"object"==typeof t&&this._cache.delete(t.schema),delete this.schemas[e],delete this.refs[e],this}case"object":{const t=e;this._cache.delete(t);let n=e[this.opts.schemaId];return n&&(n=(0,h.normalizeId)(n),delete this.schemas[n],delete this.refs[n]),this}default:throw new Error("ajv.removeSchema: invalid parameter")}}addVocabulary(e){for(const t of e)this.addKeyword(t);return this}addKeyword(e,t){let n;if("string"==typeof e)n=e,"object"==typeof 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