@datagrok/bio 2.12.8 → 2.12.9

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Files changed (6) hide show
  1. package/CHANGELOG.md +6 -0
  2. package/dist/79.js.map +1 -1
  3. package/dist/package-test.js.map +1 -1
  4. package/dist/package.js +1 -1
  5. package/dist/package.js.map +1 -1
  6. package/package.json +2 -2
package/dist/package.js CHANGED
@@ -1,5 +1,5 @@
1
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  /*! For license information please see package.js.LICENSE.txt */
2
- var bio;(()=>{var n={2012:(n,t,e)=>{"use strict";e.d(t,{f:()=>r});var i=e(9976);class r extends i.B{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(n){const t=n in r.aaSynonyms?r.aaSynonyms[n]:n;return super.get(t)}}r.aaSynonyms={MeNle:"L",MeA:"A",MeG:"G",MeF:"F"};class a{static getPalette(n="grok"){switch(n){case"grok":return r.GrokGroups;case"lesk":return r.Lesk;default:throw new Error(`ChemPalette: scheme \`${n}\` does not exist`)}}static getInnerOuter(n){let t=0,e="",i="";for(const r of n)"("==r?t++:")"==r?t--:t?e+=r:i+=r;return isNaN(parseInt(e))?[i,e]:[i,""]}static getColorAAPivot(n="",t="grok"){const e=this.getPalette(t);let[i,r]=this.getInnerOuter(n);if(i=i.length>6?`${i.slice(0,3)}...`:i,r=r.length>6?`${r.slice(0,3)}...`:r,1==n.length||"("==n[1]){const t=n[0]?.toUpperCase();return t in e?[e.get(t),t,r,1]:[this.undefinedColor,i,r,1]}if("d"==n[0]&&n[1]in e&&(2==n.length||"("==n[2])){const t=n[1]?.toUpperCase();return t in e?[e.get(t),t,r,2]:[this.undefinedColor,i,r,2]}if(n.substring(0,3)in this.AAFullNames&&(3==n.length||"("==n[3])){const t=this.AAFullNames[n.substring(0,3)];return t in e?[e.get(t),t,r,3]:[this.undefinedColor,i,r,3]}if(n[0]?.toLowerCase()==n[0]&&n.substring(1,3)in this.AAFullNames&&(4==n.length||"("==n[4])){const t=this.AAFullNames[n.substring(1,3)];return t in e?[e.get(t),t,r,4]:[this.undefinedColor,i,r,4]}return[this.undefinedColor,i,r,0]}}a.SemType="Aminoacids",a.SemTypeMultipleAlignment="AminoacidsMultipleAlignment",a.undefinedColor="rgb(100,100,100)",a.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"},a.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"},a.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(*)*"},a.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"}},6584:(n,t,e)=>{"use strict";e.d(t,{BX:()=>a,nW:()=>o,tW:()=>f});var i=e(4469);const r="Libraries",a="System:AppData/Bio/monomer-libraries/";let s=Promise.resolve();async function o(){let n;return s=s.then((async()=>{const t=await i.dapi.userDataStorage.getValue(r,"Settings",!0);n=t?JSON.parse(t):{exclude:[],explicit:[]},n.exclude=n.exclude instanceof Array?n.exclude:[],n.explicit=n.explicit instanceof Array?n.explicit:[],console.debug(`Bio: getUserLibSettings()\n${JSON.stringify(n,void 0,2)}`)})),await s,n}async function f(n){s=s.then((async()=>{console.debug(`Bio: setUserLibSettings()\n${JSON.stringify(n,void 0,2)}`),await i.dapi.userDataStorage.postValue(r,"Settings",JSON.stringify(n),!0)})),await s}},7228:(n,t,e)=>{"use strict";e.d(t,{GR:()=>b,JN:()=>h,Qx:()=>u,Xk:()=>d});var i=e(976),r=e(4469),a=e(1047),s=e(6286),o=(e(8260),e(8457)),f=e(5697);function d(n){const t=[];for(let e=0;e<n.rowCount;e++){const i={};Object.keys(a.K4).forEach((t=>{if("symbol"===t){const r=n.get(a.K4[t],e);i[t]="."===r?n.get(a.At,e):r}else if("rgroups"===t){const r=n.get(a.K4[t],e).split("\n"),s=[];r.forEach((n=>{const t={},e=n.substring(n.lastIndexOf("]")+1),i=n.match(/\[R(\d+)\]/)[1];t.capGroupSMILES="H"===e?`[*:${i}][H]`:`O[*:${i}]`,t.alternateId="H"===e?`R${i}-H`:`R${i}-OH`,t.capGroupName="H"===e?"H":"OH",t.label=`R${i}`,s.push(t)})),i[t]=s}else a.K4[t]&&(i[t]=n.get(a.K4[t],e))})),t.push(i)}return t}async function h(){const n=i.Func.find({package:"Bio",name:"getMonomerLibHelper"});if(0===n.length)throw new Error('Package "Bio" must be installed for MonomerLibHelper.');return(await n[0].prepare().call()).getOutputParamValue()}async function u(n,t){n instanceof i.Column&&(n=(0,o.O)(n).columns.toList());const e=(await h()).getBioLib(),a=new Array(n.length),f=n[0].length,d=new Float32Array(f);for(let o=0;o<n.length;++o){const h=t.getCanonical(o),u=e.getMonomer("PEPTIDE",h)?.smiles??"",c=n[o],b=c.getRawData(),l=c.categories,g=l.indexOf("");if(a[o]={categories:l,data:b,emptyIndex:g},void 0===h)continue;const D=i.Column.fromStrings("smiles",l.map((n=>e.getMonomer("PEPTIDE",n)?.smiles??""))),j=(i.DataFrame.fromColumns([D]),(await r.chem.getSimilarities(D,u)).getRawData());for(let n=0;n<f;++n){const t=b[n];d[n]+=h!==s.G2&&t!==g?j[t]:h===s.G2&&t===g?1:0}}for(let e=0;e<d.length;++e){let r=d[e]/t.length;for(let s=0;s<n.length;++s){const n=a[s];if(s>=t.length&&n.data[e]!==n.emptyIndex||n.data[e]===n.emptyIndex&&s<t.length){r=i.FLOAT_NULL;break}}d[e]=r}return i.Column.fromFloat32Array("Similarity",d)}async function c(n){const t=(await h()).getBioLib(),e=[],a={},s=n.map((n=>t.getMonomer("PEPTIDE",n)?.smiles??"")),o=i.Column.fromStrings("smiles",s);for(let t=0;t<s.length;++t){a[n[t]]=t;const i=s[t],f=""===i?new Array(s.length).fill(0):(await r.chem.getSimilarities(o,i)).getRawData();f[t]=1,e[t]=Array.from(f)}return{scoringMatrix:e,alphabetIndexes:a}}async function b(n,t="Morgan"){const e=(await h()).getBioLib(),r=new Array(n.length).fill(0).map((()=>new Array(n.length).fill(0))),a={},s=n.map((n=>e.getMonomer("PEPTIDE",n)?.smiles??"")),o=i.Func.find({package:"Chem",name:"getFingerprints"})[0];if(!o)return console.warn('Function "Chem:getFingerprints" is not found in chem package. falling back to Morgan fingerprints'),await c(n);const d=i.Column.fromStrings("smiles",s),u=(i.DataFrame.fromColumns([d]),(await o.apply({col:d,fingerprintType:t}))?.entries);if(!u)return console.warn(`${t} Fingerprints could not be calculated for monomers from chem package.\n falling back to Morgan fingerprints`),await c(n);for(let t=0;t<u.length;++t)if(r[t][t]=1,a[n[t]]=t,u[t])for(let n=t+1;n<u.length;++n)u[n]&&(r[t][n]=r[n][t]=(0,f.Z3)(u[t],u[n]));return{scoringMatrix:r,alphabetIndexes:a}}},8601:(n,t,e)=>{"use strict";e.d(t,{i0:()=>c});var i=e(4469),r=e(976),a=e(6414),s=e.n(a),o=e(1821),f=e(8260);const d={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:"d",RIBOSE:"r",PHOSPHATE:"p",OXYGEN:"O",HYDROGEN:"H"};var h=e(1047);function u(n){return Math.round(d.PRECISION_FACTOR*n)/d.PRECISION_FACTOR}async function c(n,t,a){if(0===r.Func.find({package:"Chem",name:"getRdKitModule"}).length)return{col:null,warnings:['Transformation to atomic level requires the package "Chem" installed.']};if(t.semType!==r.SEMTYPE.MACROMOLECULE)return{col:null,warnings:[`Only the ${r.SEMTYPE.MACROMOLECULE} columns can be converted to atomic level, the chosen column has semType '${t.semType}'`]};let u=t;const c=f.g.forColumn(t);c.isHelm()&&(u=c.convert(o.r2.SEPARATOR,"."),u.name=t.name);const l=f.g.forColumn(u).alphabet;let g;if("PT"===l||"UN"===l)g="PEPTIDE";else{if("RNA"!==l&&"DNA"!==l)return{col:null,warnings:[`Unexpected column's '${u.name}' alphabet '${l}'.`]};g="RNA"}const D=function(n){const t=n.length,e=new Array(t),r=f.g.forColumn(n);let a=!1;for(let n=0;n<t;++n){const t=r.getSplitted(n);a||(a=0===t.length),e[n]=s()(t.canonicals).filter((n=>!r.isGap(n))).map((n=>n)).toArray()}return a&&i.shell.warning(`Some values in the "${n.name}" column are empty`),e}(u),j=await async function(n,t,e,r){const a=function(n,t,e){const i=new Map;for(const r of n.getMonomerSymbolsByType(t)){const a=n.getMonomer(t,r);if("RNA"===t&&("Branch"===a.monomerType||"DNA"===e&&a.symbol===d.DEOXYRIBOSE||"RNA"===e&&a.symbol===d.RIBOSE||a.symbol===d.PHOSPHATE)||"PEPTIDE"===t&&"Branch"!==a.monomerType){const n={};h.rx.forEach((t=>{n[t]=a[t]})),i.set(a.symbol,n)}}return i}(t,e,r),s=new Map,o=await i.functions.call("Chem:getRdKitModule"),f={value:null};if("RNA"===e){const n="RNA"===r?[d.RIBOSE,d.PHOSPHATE]:[d.DEOXYRIBOSE,d.PHOSPHATE];for(const t of n)b(s,t,a,o,e,f)}for(let t=0;t<n.length;++t){const i=n[t];for(const n of i)if(""!==n)try{b(s,n,a,o,e,f)}catch(t){const e=t instanceof Error?t.message:t.toString(),i=t instanceof Error?t.stack:void 0;throw console.error(`bio lib: getMonomersDictFromLib() sym='${n}', error:\n${e}\n${i}`),new Error(`Can't get monomer '${n}' from library: ${e}`)}}return s}(D,a,g,l),H=u.length,{molfileList:A,molfileWarningList:p}=await async function(n,t,i,r,a){const s=Math.max(navigator.hardwareConcurrency-2,1),o=new Array(s).fill(null).map((()=>new Worker(new URL(e.p+e.u(79),e.b)))),f=a/s;let d=[],h=[];const u=new Array(s);for(let e=0;e<s;e++){const d=Math.floor(e*f),h=e===s-1?a:Math.floor((e+1)*f);o[e].postMessage({monomerSequencesArray:n,monomersDict:t,alphabet:i,polymerType:r,start:d,end:h}),u[e]=new Promise((n=>{o[e].onmessage=({data:{molfileList:t,molfileWarningList:e}})=>{n({molfileList:t,molfileWarningList:e})}}))}return(await Promise.all(u)).forEach((n=>{d=d.concat(...n.molfileList),h=h.concat(...n.molfileWarningList)})),setTimeout((()=>{o.forEach((n=>{n.terminate()}))}),0),{molfileList:d,molfileWarningList:h}}(D,j,l,g,H);if(p.length>.05*H)throw new Error("Too many errors getting molfiles.");const I=`molfile(${u.name})`,M=n.columns.getUnusedName(I),T=r.Column.fromStrings(M,A);return T.semType=r.SEMTYPE.MOLECULE,T.setTag(r.TAGS.UNITS,r.UNITS.Molecule.MOLBLOCK),{col:T,warnings:p}}function b(n,t,e,i,r,a){if(!n.has(t)){const s=function(n,t,e,i,r){if(t.has(n)){const s=t.get(n),o=function(n){const t=[];for(const e of n){let n=e.capGroupSMILES;n||(n=e.capGroupSMILES),n=n.replace(/(\[|\]|\*|:|\d)/g,""),t.push(n)}return t}(s.rgroups),f=(a=s.molfile).includes("V3000")?function(n){const t=new Map,e=/M V30 (\d+) R#.+RGROUPS=\((\d+) (\d+)\).*/gm;let i;for(;null!==(i=e.exec(n));)i.index===e.lastIndex&&e.lastIndex++,t.set(parseInt(i[1]),parseInt(i[3]));return t}(a):function(n){const t=new Map;let e=n.indexOf(d.V2K_A_LINE,0),i=e;for(;-1!==e;){i=n.indexOf("\n",e);const r=parseInt(n.substring(e,i).replace(/^A\s+/,""));e=n.indexOf("R",i),i=n.indexOf("\n",e);const a=parseInt(n.substring(e,i).replace(/^R/,""));t.set(r,a),e=n.indexOf(d.V2K_A_LINE,i)}for(e=n.indexOf(d.V2K_RGP_LINE,0),i=n.indexOf("\n",e);-1!==e;){e+=d.V2K_RGP_SHIFT,i=n.indexOf("\n",e);const r=n.substring(e,i).replaceAll(/\s+/g," ").split(" ").map((n=>parseInt(n))).slice(1);for(let n=0;n<r.length;n+=2){if(t.has(r[n])&&t.get(r[n])!==r[n+1])throw new Error(`r-group index ${r[n]} has already been added with a different value`);t.set(r[n],r[n+1])}e=n.indexOf(d.V2K_RGP_LINE,i)}return t}(a),h=s.molfile.includes("V3000")?s.molfile:function(n,t){const e=t.get_mol(n),i=e.get_v3Kmolblock();return e.delete(),i}(function(n){let t=n.indexOf(d.V2K_A_LINE,0);-1===t&&(t=n.indexOf(d.V2K_RGP_LINE));const e=n.indexOf(d.V3K_END,t);return n.substring(0,t)+n.substring(e)}(s.molfile),e),c=function(n){let t=(n=n.replaceAll("\r","")).indexOf(d.V3K_BEGIN_COUNTS_LINE)+d.V3K_COUNTS_SHIFT,e=n.indexOf(" ",t+1);const i=parseInt(n.substring(t,e));return t=e+1,e=n.indexOf(" ",t+1),{atomCount:i,bondCount:parseInt(n.substring(t,e))}}(h),b=function(n,t){const e=new Array(t),i=new Float32Array(t),r=new Float32Array(t),a=new Array(t);let s=n.indexOf(d.V3K_BEGIN_ATOM_BLOCK);s=n.indexOf("\n",s);let o=s;for(let f=0;f<t;f++){s=n.indexOf(d.V3K_BEGIN_DATA_LINE,s)+d.V3K_IDX_SHIFT,o=n.indexOf(" ",s),s=o+1,o=n.indexOf(" ",s),e[f]=n.substring(s,o);const t=new Array(2);for(let e=0;e<2;++e)s=o+1,o=n.indexOf(" ",s),t[e]=parseFloat(n.substring(s,o));i[f]=t[0],r[f]=t[1],s=o,o=n.indexOf("\n",s)+1,a[f]=n.slice(s,o),s=o}return{atomTypes:e,x:i,y:r,kwargs:a}}(h,c.atomCount),D=function(n,t){const e=new Uint32Array(t),i=new Array(t),r=new Map,a=new Map;let s=n.indexOf(d.V3K_BEGIN_BOND_BLOCK);s=n.indexOf("\n",s);let o=s;for(let f=0;f<t;++f){const t=new Array(3);s=n.indexOf(d.V3K_BEGIN_DATA_LINE,o)+d.V3K_IDX_SHIFT,o=n.indexOf(" ",s);for(let e=0;e<3;++e)s=o+1,o=Math.min(n.indexOf("\n",s),n.indexOf(" ",s)),t[e]=parseInt(n.slice(s,o));e[f]=t[0],i[f]=t.slice(1);const h=n.indexOf("\n",s);let u=n.slice(o,h),c=u.indexOf(d.V3K_BOND_CONFIG);if(-1!==c){c=u.indexOf("=",c)+1;let n=u.indexOf(" ",c);-1===n&&(n=u.length);const t=parseInt(u.slice(c,n));r.set(f,t);const e=d.V3K_BOND_CONFIG+t.toString();u=u.replace(e,"")}u||a.set(f,u)}return{bondTypes:e,atomPairs:i,bondConfiguration:r,kwargs:a}}(h,c.bondCount),H=function(n,t,e,i){const r={backboneShift:null,branchShift:null,terminalNodes:[],rNodes:[]};return function(n,t,e){for(const[i,r]of e)n.atomTypes[i-1]=t[r-1]}(n,e,i),function(n,t){t.rNodes=Array.from(n.keys());for(let e=0;e<t.rNodes.length;e++)for(const i of[1,2])if(n.get(t.rNodes[e])===i){const n=t.rNodes[i-1];t.rNodes[i-1]=t.rNodes[e],t.rNodes[e]=n}}(i,r),l(t,r),r}(b,D,o,f),T=function(n){let t=[],e=n.indexOf("M V30 MDLV30/STEABS ATOMS=(");for(;-1!==e;){e+=28;const i=n.indexOf(")",e);t=t.concat(n.substring(e,i).split(" ").slice(1).map((n=>parseInt(n)))),e=i,e=n.indexOf("M V30 MDLV30/STEABS ATOMS=(",e)}return t}(h),m={atoms:b,bonds:D,meta:H,stereoAtoms:T};return"PEPTIDE"===i?function(n){const t=n.meta.terminalNodes[0]-1,e=n.meta.rNodes[0]-1,i=n.atoms.x,r=n.atoms.y;M(n,-i[t],-r[t]);const a=A(i[e],r[e]);p(n.atoms,-a),i[n.meta.rNodes[1]-1]<0&&function(n){I(n,!1)}(n);const s=function(n){const t=function(n){const t=new Map;for(const e of n.bonds.atomPairs)for(let n=0;n<2;n++){const i=e[n],r=e[(n+1)%2];t.has(i)?t.get(i)?.push(r):t.set(i,new Array(1).fill(r))}return t}(n);let e=0;const 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i,r=e(6286);!function(n){n.FASTA="fasta",n.SEPARATOR="separator",n.HELM="helm"}(i||(i={}));const a=", ",s=/(?:\[([A-Za-z0-9_\-,()]+)\])|([A-Za-z\-])/g,o=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"])}}},f=[new r.LA("PT",o.fasta.peptide,.5),new r.LA("DNA",o.fasta.dna,.55),new r.LA("RNA",o.fasta.rna,.55)]},8447:(n,t,e)=>{"use strict";e.d(t,{Ar:()=>r.Ar,CI:()=>i.CI,GU:()=>r.GU,XS:()=>i.XS,dQ:()=>r.dQ,gP:()=>r.gP,kB:()=>r.kB,py:()=>r.py,r2:()=>i.r2,up:()=>r.up});var i=e(1821),r=e(2583)},6286:(n,t,e)=>{"use strict";e.d(t,{G2:()=>i,LA:()=>r,dJ:()=>a});const i="";class r{constructor(n,t,e){this.name=n,this.alphabet=t,this.cutoff=e}}class a extends r{constructor(n,t,e){super(n.name,n.alphabet,n.cutoff),this.freq=t,this.similarity=e}}},2583:(n,t,e)=>{"use strict";e.d(t,{wx:()=>l,w4:()=>J,py:()=>N,vU:()=>M,Ar:()=>H,GU:()=>m,dQ:()=>P,up:()=>w,kB:()=>D,FJ:()=>j,gP:()=>I});var i=e(976),r=e(6414),a=e.n(r),s=e(6286),o=e(1821),f=e(8260);class d extends Float32Array{}var h=e(850),u=e(2012),c=e(6137),b=e(7331);class l{get length(){return this.mList.length}get canonicals(){return this.mList}get originals(){return this.mList}isGap(n){return this.getOriginal(n)===this.gapOriginalMonomer}getCanonical(n){if(this.length<=n)throw new Error("Index out of bounds");return this.mList[n]}getOriginal(n){if(this.length<=n)throw new Error("Index out of bounds");return this.mList[n]}constructor(n,t){this.mList=n,this.gapOriginalMonomer=t}}class g{get length(){return this.seqS.length}get canonicals(){return this.seqS}get originals(){return this.seqS}isGap(n){return this.getOriginal(n)===f.lh[o.r2.FASTA]}getCanonical(n){if(this.length<=n)throw new Error("Index out of bounds");return this.isGap(n)?s.G2:this.seqS[n]}getOriginal(n){if(this.length<=n)throw new Error("Index out of bounds");return this.seqS[n]}constructor(n){this.seqS=n}}const D=n=>{const t=a()(n.toString().matchAll(o.BM)).map((n=>n[2]??n[1])).toArray();return new l(t,f.lh[o.r2.FASTA])},j=n=>n?new g(n):new l([],f.lh[o.r2.FASTA]);function H(n,t=undefined){return e=>{if(e){const i=e.replaceAll('"-"',"").replaceAll("'-'","").split(n,t);return new l(i,f.lh[o.r2.SEPARATOR])}return new l([],f.lh[o.r2.SEPARATOR])}}const A=/(PEPTIDE1|DNA1|RNA1)\{([^}]+)}/g,p=/\[([^\[\]]+)]/g,I=n=>{A.lastIndex=0;const t=A.exec(n.toString()),e=t?t[2]:null,i=e?e.split("."):[];return new l(i.map((n=>{p.lastIndex=0;const t=p.exec(n);return t&&t.length>=2?t[1]:n})),f.lh[o.r2.HELM])};function M(n,t,e=undefined){if(n.toLowerCase().startsWith(o.r2.FASTA))return D;if(n.toLowerCase().startsWith(o.r2.SEPARATOR))return H(t,e);if(n.toLowerCase().startsWith(o.r2.HELM))return I;throw new Error(`Unexpected units ${n} .`)}const T=/([^\W_]+)/g;function m(n,t){if(n.length<=t)return n;const e=n.match(T),i=n.length>t||(e?.length??0)>1,r=e?.[0]??" ";return i?r.substring(0,t-1)+"…":r}function J(n,t,e="-"){const i=t.map((t=>{const i=function(n,t,e="-"){const i=new Set([...new Set(Object.keys(n)),...t]);i.delete(e);const r=[],a=[];for(const e of i)r.push(e in n?n[e]:0),a.push(t.has(e)?1:0);const s=new d(r),o=new d(a);return(0,h.MA)(s,o)/((0,h.$G)(s)*(0,h.$G)(o))}(n,t.alphabet,e);return new s.dJ(t,n,i)}));let r;const a=Math.max(...i.map((n=>n.similarity>n.cutoff?n.similarity:-1)));return r=a>0?i.find((n=>n.similarity===a)).name:"UN",r}function P(n,t=5){let e;if(n.semType==i.SEMTYPE.MACROMOLECULE)e=f.g.forColumn(n).alphabet;else{const i=function(n,t,e){const i=n.categories;return function(n,t){const e={};let i=!0,r=null;for(const a of n)if(null==r?r=a.length:a.length!==r&&(i=!1),a.length>=t)for(const n of a.canonicals)n in e||(e[n]=0),e[n]+=1;return{freq:e,sameLength:i}}(a().enumerate(n.getRawData()).map((([n,t])=>e(i[n]))),t)}(n,t,D);e=J(i.freq,o.XS)}return N(e)}function N(n){switch(n){case"PT":return u.f.GrokGroups;case"DNA":case"RNA":return c.J.Chromatogram;default:return b.UE.Color}}function w(n){const t=n.columns.bySemTypeAll(i.SEMTYPE.MACROMOLECULE);let e=t.find((n=>{const t=n.getTag(i.TAGS.UNITS);return!!t&&-1!==t.indexOf("MSA")}))??null;return!e&&t.length>0&&(e=t[0]),e}},8260:(n,t,e)=>{"use strict";e.d(t,{dm:()=>c,g:()=>l,lh:()=>b});var i=e(976),r=e(6414),a=e.n(r),s=e(8447),o=e(6286),f=e(2583),d=e(708),h=e(7228),u=e(1047);const c=new class{constructor(){this.seqHandler="seq-handler",this.notationProvider="seq-handler.notation-provider"}},b={[s.r2.FASTA]:"-",[s.r2.SEPARATOR]:"",[s.r2.HELM]:"*"};class l{constructor(n){if(this._splitter=null,this.cached=!0,this._splitted=null,this.columnVersion=null,this._stats=null,this._maxLength=null,this._posList=null,this._joiner=void 0,n.type!==i.TYPE.STRING)throw new Error(`Unexpected column type '${n.type}', must be '${i.TYPE.STRING}'.`);this._column=n;const t=this._column.getTag(i.TAGS.UNITS);if(null==t)throw new Error("Units are not specified in column");if(this._units=t,this._notation=this.getNotation(),this._defaultGapOriginal=this.isFasta()?b[s.r2.FASTA]:this.isHelm()?b[s.r2.HELM]:b[s.r2.SEPARATOR],!this.column.tags.has("aligned")||!this.column.tags.has("alphabet")||!this.column.tags.has(".alphabetIsMultichar")&&!this.isHelm()&&"UN"===this.alphabet)if(this.isFasta())l.setUnitsToFastaColumn(this);else if(this.isSeparator()){const t=n.getTag("separator");l.setUnitsToSeparatorColumn(this,t)}else{if(!this.isHelm())throw new Error(`Unexpected units '${this.column.getTag(i.TAGS.UNITS)}'.`);l.setUnitsToHelmColumn(this)}if(!this.column.tags.has(".alphabetIsMultichar"))if(this.isHelm())this.column.setTag(".alphabetIsMultichar","true");else if(["UN"].includes(this.alphabet))throw new Error(`For column '${this.column.name}' of alphabet '${this.alphabet}' tag '.alphabetIsMultichar' is mandatory.`);this.notationProvider=this.column.temp[c.notationProvider]??null,this.columnVersion=this.column.version}static setUnitsToFastaColumn(n){if(n.column.semType!==i.SEMTYPE.MACROMOLECULE||n.column.getTag(i.TAGS.UNITS)!==s.r2.FASTA)throw new Error(`The column of notation '${s.r2.FASTA}' must be '${i.SEMTYPE.MACROMOLECULE}'.`);n.column.setTag(i.TAGS.UNITS,s.r2.FASTA),l.setTags(n)}static setUnitsToSeparatorColumn(n,t){if(n.column.semType!==i.SEMTYPE.MACROMOLECULE||n.column.getTag(i.TAGS.UNITS)!==s.r2.SEPARATOR)throw new Error(`The column of notation '${s.r2.SEPARATOR}' must be '${i.SEMTYPE.MACROMOLECULE}'.`);if(!t)throw new Error(`The column of notation '${s.r2.SEPARATOR}' must have the separator tag.`);n.column.setTag(i.TAGS.UNITS,s.r2.SEPARATOR),n.column.setTag("separator",t),l.setTags(n)}static setUnitsToHelmColumn(n){if(n.column.semType!==i.SEMTYPE.MACROMOLECULE)throw new Error(`The column of notation '${s.r2.HELM}' must be '${i.SEMTYPE.MACROMOLECULE}'`);n.column.setTag(i.TAGS.UNITS,s.r2.HELM),l.setTags(n)}static setTags(n){const t=n.column.getTag(i.TAGS.UNITS),e=n.stats;if(Object.keys(e.freq).some((n=>n.length>1)),[s.r2.FASTA,s.r2.SEPARATOR].includes(t)){if(!n.column.getTag("alphabet")&&0===Object.keys(e.freq).length)throw new Error("Alphabet is empty and not annotated.");let t=n.column.getTag("aligned");null===t&&(t=e.sameLength?"SEQ.MSA":"SEQ",n.column.setTag("aligned",t));let i=n.column.getTag("alphabet");if(null===i&&(i=(0,f.w4)(e.freq,s.XS),n.column.setTag("alphabet",i)),"UN"===i){const t=Object.keys(e.freq).length,i=Object.keys(e.freq).some((n=>n.length>1));n.column.setTag(".alphabetSize",t.toString()),n.column.setTag(".alphabetIsMultichar",i?"true":"false")}}}get column(){return this._column}get length(){return this._column.length}get units(){return this._units}get notation(){return this._notation}get defaultGapOriginal(){return this._defaultGapOriginal}get separator(){const n=this.column.getTag("separator")??void 0;if(this.notation===s.r2.SEPARATOR&&void 0===n)throw new Error(`Separator is mandatory for column '${this.column.name}' of notation '${this.notation}'.`);return n}get aligned(){const n=this.column.getTag("aligned");if(!n&&(this.isFasta()||this.isSeparator()))throw new Error("Tag aligned not set");return n}get alphabet(){const n=this.column.getTag("alphabet");if(!n&&(this.isFasta()||this.isSeparator()))throw new Error("Tag alphabet not set");return n}get helmCompatible(){return this.column.getTag(".isHelmCompatible")}getAlphabetSize(){if(this.notation==s.r2.HELM||"UN"==this.alphabet){const n=this.column.getTag(".alphabetSize");let t;if(n)t=parseInt(n);else{const n=this.stats;t=Object.keys(n.freq).length}return t}switch(this.alphabet){case"PT":return 20;case"DNA":case"RNA":return 4;case"NT":return console.warn("Unexpected alphabet 'NT'."),4;default:throw new Error(`Unexpected alphabet '${this.alphabet}'.`)}}getAlphabetIsMultichar(){return this.notation===s.r2.HELM||"UN"===this.alphabet&&"true"===this.column.getTag(".alphabetIsMultichar")}getSplitted(n){if(this.cached){this.column.version===this.columnVersion&&null!==this._splitted||(this.columnVersion=this.column.version,this._splitted=new Array(this.column.length));let t=this._splitted[n]?this._splitted[n].deref():void 0;if(!t){const e=this.column.get(n);t=this.splitter(e),this._splitted[n]=new WeakRef(t)}return t}{const t=this.column.get(n);return this.splitter(t)}}get stats(){if(null===this._stats){const n={};let t=!0,e=null;const i=this.column.length;for(let r=0;r<i;++r){const i=this.getSplitted(r);null==e?e=i.length:i.length!==e&&(t=!1);for(const t of i.canonicals)t in n||(n[t]=0),n[t]+=1}this._stats={freq:n,sameLength:t}}return this._stats}get maxLength(){return null===this._maxLength&&(this._maxLength=0===this.column.length?0:Math.max(...a().count(0).take(this.column.length).map((n=>this.getSplitted(n).length)))),this._maxLength}get posList(){if(null===this._posList){const n=this.column.getTag(".positionNames");this._posList=n?n.split(s.CI).map((n=>n.trim())):a().count(1).take(this.maxLength).map((n=>n.toString())).toArray()}return this._posList}isFasta(){return this.notation===s.r2.FASTA}isSeparator(){return this.notation===s.r2.SEPARATOR}isHelm(){return this.notation===s.r2.HELM}isRna(){return"RNA"===this.alphabet}isDna(){return"DNA"===this.alphabet}isPeptide(){return"PT"===this.alphabet}isMsa(){return!!this.aligned&&this.aligned.toUpperCase().includes("MSA")}isHelmCompatible(){return"true"===this.helmCompatible}isGap(n){return!n||n===this._defaultGapOriginal}getNotation(){if(this.units.toLowerCase().startsWith(s.r2.FASTA))return s.r2.FASTA;if(this.units.toLowerCase().startsWith(s.r2.SEPARATOR))return s.r2.SEPARATOR;if(this.units.toLowerCase().startsWith(s.r2.HELM))return s.r2.HELM;throw new Error(`Column '${this.column.name}' has unexpected notation '${this.units}'.`)}getHelmWrappers(){return[this.isDna()||this.isRna()||this.isHelmCompatible()?"RNA1{":"PEPTIDE1{",this.isDna()?"d(":this.isRna()?"r(":"",this.isDna()||this.isRna()?")p":"","}$$$$"]}getNewColumn(n,t,e,r){const a=this.column,o=n.toLowerCase()+"("+a.name+")",f=e??a.dataFrame.columns.getUnusedName(o),d=i.Column.fromList("string",f,r??new Array(this.column.length).fill(""));if(d.semType=i.SEMTYPE.MACROMOLECULE,d.setTag(i.TAGS.UNITS,n),n===s.r2.SEPARATOR){if(!t)throw new Error(`Notation '${s.r2.SEPARATOR}' requires separator value.`);d.setTag("separator",t)}d.setTag(i.TAGS.CELL_RENDERER,"sequence");const h=a.getTag("aligned");h&&d.setTag("aligned",h);let u=a.getTag("alphabet");u||this.notation!==s.r2.HELM||n===s.r2.HELM||(u="UN"),null!=u&&d.setTag("alphabet",u);let c=a.getTag(".alphabetSize");null!=u&&c&&d.setTag(".alphabetSize",c);const b=a.getTag(".alphabetIsMultichar");return null!=u&&void 0!==b&&d.setTag(".alphabetIsMultichar",b),n==s.r2.HELM&&(c=this.getAlphabetSize().toString(),d.setTag(".alphabetSize",c)),d}getNewColumnFromList(n,t){return this.getNewColumn(this.notation,this.separator,n,t)}static getNewColumn(n){const t=l.forColumn(n),e=t.notation;return t.getNewColumn(e)}static unitsStringIsValid(n){return n=n.toLowerCase(),[s.r2.FASTA,s.r2.SEPARATOR,s.r2.HELM].some((t=>n.startsWith(t.toLowerCase())))}static getNewColumnFromParams(n,t,e){if(!l.unitsStringIsValid(e))throw new Error("Invalid format of 'units' parameter");const r=i.Column.fromList("string",t,new Array(n).fill(""));return r.semType=i.SEMTYPE.MACROMOLECULE,r.setTag(i.TAGS.UNITS,e),r}getSplitter(n){let t=null;if(t=this.notationProvider?this.notationProvider.splitter:null,t)return t;if(this.units.toLowerCase().startsWith(s.r2.FASTA))return null===this.column.getTag("alphabet")||this.getAlphabetIsMultichar()?s.kB:f.FJ;if(this.units.toLowerCase().startsWith(s.r2.SEPARATOR))return(0,s.Ar)(this.separator,n);if(this.units.toLowerCase().startsWith(s.r2.HELM))return s.gP;throw new Error(`Unexpected units ${this.units} .`)}split(n){return this.splitter(n)}getDistanceFunctionName(){if(!this.isFasta())throw new Error("Only FASTA notation is supported");return this.isMsa()?d.U.HAMMING:(this.alphabet,d.U.LEVENSHTEIN)}getDistanceFunction(){return d.o[this.getDistanceFunctionName()]()}async checkHelmCompatibility(){if(this.column.tags.has(".isHelmCompatible"))return"true"===this.column.getTag(".isHelmCompatible");const n=(await(0,h.JN)()).getBioLib().getMonomerSymbolsByType("PEPTIDE".toString()),t=new Set(n),e=((0,s.Ar)(this.separator),new Set),i=this.column.length,r=this.column.getRawData();for(let n=0;n<i;++n){const i=r[n];if(!(i in e)){e.add(i);const r=this.getSplitted(n);for(const n of r.canonicals)if(!t.has(n))return this.column.setTag(".isHelmCompatible","false"),!1}}return this.column.setTag(".isHelmCompatible","true"),!0}get splitter(){return null===this._splitter&&(this._splitter=this.getSplitter()),this._splitter}toFasta(n){return n===s.r2.FASTA}toSeparator(n){return n===s.r2.SEPARATOR}toHelm(n){return n===s.r2.HELM}convertHelmToFastaSeparator(n,t,e,i){i||(i=this.toFasta(t)?b[s.r2.FASTA]:b[s.r2.SEPARATOR]),e||(e=this.toFasta(t)?"":this.separator);const r=n.startsWith("RNA"),a=this.splitter(n),o=[];for(let n=0;n<a.length;++n){let e=a.getOriginal(n);if(r&&(e=e.replace(u.pU,"")),e===b[s.r2.HELM])o.push(i);else if(this.toFasta(t)&&e.length>1){const n="["+e+"]";o.push(n)}else o.push(e)}return o.join(e)}convert(n,t){const e=this.getJoiner({notation:n,separator:t}),i=this.getNewColumn(n,t);return i.init((n=>{const t=this.getSplitted(n);return e(t)})),i}getRegion(n,t,e){const i=this.getNewColumn(this.notation,this.separator);i.name=e;const r=n??0,a=t??this.maxLength-1,o=this.getJoiner(),d=a-r+1,h=b[this.notation];i.init((n=>{const t=this.getSplitted(n),e=new Array(d);for(let n=0;n<d;++n){const i=r+n;e[n]=i<t.length?t.getOriginal(i):h}return o(new f.wx(e,h))}));const u=n=>{const t=n.split(",").map((n=>n.trim())),e=new Array(d);for(let n=0;n<d;++n){const i=r+n;e[n]=i<t.length?t[i]:"?"}return e.join(s.CI)},c=this.column.getTag(".positionNames");c&&i.setTag(".positionNames",u(c));const l=this.column.getTag(".positionLabels");return l&&i.setTag(".positionLabels",u(l)),i}get joiner(){return this._joiner||(this._joiner=this.getJoiner()),this._joiner}getJoiner(n){const t=n?n.notation:this.notation,e=n?n.separator:this.separator;let i;const r=this;switch(t){case s.r2.FASTA:i=function(n){return r.joinToFasta(n,r.isHelm())};break;case s.r2.SEPARATOR:if(!e)throw new Error(`Separator is mandatory for notation '${t}'.`);i=function(n){return g(n,e,r.isHelm())};break;case s.r2.HELM:{const n="DNA"===r.alphabet||"RNA"===r.alphabet,t=r.getHelmWrappers();i=function(e){return D(e,t,n)};break}default:throw new Error(`Unexpected notation '${t}'.`)}return i}getConverter(n,t=undefined){if(n===s.r2.SEPARATOR&&!t)throw new Error(`Target separator is not specified for target units '${s.r2.SEPARATOR}'.`);const e=this;if(n===s.r2.FASTA)return function(n){return e.convertToFasta(n)};if(n===s.r2.HELM)return function(n){return e.convertToHelm(n)};if(n===s.r2.SEPARATOR)return function(n){return e.convertToSeparator(n,t)};throw new Error}static forColumn(n){let t=n.temp[c.seqHandler];return t&&t.columnVersion===n.version||(t=n.temp[c.seqHandler]=new l(n)),t}joinToFasta(n,t){const e=new Array(n.length);for(let i=0;i<n.length;++i){const r=n.getOriginal(i);let a=n.getOriginal(i);t&&(a=a.replace(u.pU,"$1")),r===o.G2?a=b[s.r2.FASTA]:r===u.$3?a="":a.length>1&&(a="["+a+"]"),e[i]=a}return e.join("")}convertToFasta(n){const t=this.splitter,e=this.isHelm()?this.splitterAsHelmNucl(n):t(n);return this.joinToFasta(e,this.isHelm())}convertToSeparator(n,t){return g(this.isHelm()?this.splitterAsHelmNucl(n):this.splitter(n),t,this.isHelm())}convertToHelm(n){const t=this.getHelmWrappers(),e=n.startsWith("DNA")||n.startsWith("RNA");return D(this.splitter(n),t,e)}splitterAsHelmNucl(n){const t=this.splitter(n),e=new Array(t.length),i=n.startsWith("DNA"),r=n.startsWith("RNA");for(let n=0;n<t.length;++n){let a=t.getOriginal(n);(i||r)&&(a=a.replace(u.pU,"$1"),a=a===u.$3?null:a),e[n]=a||null}return new f.wx(e.filter((n=>!!n)),b[s.r2.HELM])}}function g(n,t,e){const i=new Array(n.length);for(let t=0;t<n.length;++t){const r=n.getCanonical(t);let a=n.getOriginal(t);e&&(a=a.replace(u.pU,"$1")),r===o.G2?a=b[s.r2.SEPARATOR]:r===u.$3&&(a=""),i[t]=a}return i.join(t)}function D(n,t,e){const[i,r,a,f]=t,d=new Array(n.length);for(let t=0;t<n.length;++t){const i=n.getCanonical(t);let 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r.aaSynonyms?r.aaSynonyms[n]:n;return super.get(t)}}r.aaSynonyms={MeNle:"L",MeA:"A",MeG:"G",MeF:"F"};class a{static getPalette(n="grok"){switch(n){case"grok":return r.GrokGroups;case"lesk":return r.Lesk;default:throw new Error(`ChemPalette: scheme \`${n}\` does not exist`)}}static getInnerOuter(n){let t=0,e="",i="";for(const r of n)"("==r?t++:")"==r?t--:t?e+=r:i+=r;return isNaN(parseInt(e))?[i,e]:[i,""]}static getColorAAPivot(n="",t="grok"){const e=this.getPalette(t);let[i,r]=this.getInnerOuter(n);if(i=i.length>6?`${i.slice(0,3)}...`:i,r=r.length>6?`${r.slice(0,3)}...`:r,1==n.length||"("==n[1]){const t=n[0]?.toUpperCase();return t in e?[e.get(t),t,r,1]:[this.undefinedColor,i,r,1]}if("d"==n[0]&&n[1]in e&&(2==n.length||"("==n[2])){const t=n[1]?.toUpperCase();return t in e?[e.get(t),t,r,2]:[this.undefinedColor,i,r,2]}if(n.substring(0,3)in this.AAFullNames&&(3==n.length||"("==n[3])){const t=this.AAFullNames[n.substring(0,3)];return t in e?[e.get(t),t,r,3]:[this.undefinedColor,i,r,3]}if(n[0]?.toLowerCase()==n[0]&&n.substring(1,3)in this.AAFullNames&&(4==n.length||"("==n[4])){const t=this.AAFullNames[n.substring(1,3)];return t in e?[e.get(t),t,r,4]:[this.undefinedColor,i,r,4]}return[this.undefinedColor,i,r,0]}}a.SemType="Aminoacids",a.SemTypeMultipleAlignment="AminoacidsMultipleAlignment",a.undefinedColor="rgb(100,100,100)",a.Names={G:"Glycine",L:"Leucine",Y:"Tyrosine",S:"Serine",E:"Glutamic acid",Q:"Glutamine",D:"Aspartic 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r=n.get(a.K4[t],e);i[t]="."===r?n.get(a.At,e):r}else if("rgroups"===t){const r=n.get(a.K4[t],e).split("\n"),s=[];r.forEach((n=>{const t={},e=n.substring(n.lastIndexOf("]")+1),i=n.match(/\[R(\d+)\]/)[1];t.capGroupSMILES="H"===e?`[*:${i}][H]`:`O[*:${i}]`,t.alternateId="H"===e?`R${i}-H`:`R${i}-OH`,t.capGroupName="H"===e?"H":"OH",t.label=`R${i}`,s.push(t)})),i[t]=s}else a.K4[t]&&(i[t]=n.get(a.K4[t],e))})),i.author??(i.author=""),i.id??(i.id=0),i.smiles??(i.smiles=""),i.monomerType??(i.monomerType="Backbone"),i.createDate??(i.createDate=null),t.push(i)}return t}async function h(){const n=i.Func.find({package:"Bio",name:"getMonomerLibHelper"});if(0===n.length)throw new Error('Package "Bio" must be installed for MonomerLibHelper.');return(await n[0].prepare().call()).getOutputParamValue()}async function u(n,t){n instanceof i.Column&&(n=(0,o.O)(n).columns.toList());const e=(await h()).getBioLib(),a=new Array(n.length),f=n[0].length,d=new Float32Array(f);for(let o=0;o<n.length;++o){const 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e=n.match(T),i=n.length>t||(e?.length??0)>1,r=e?.[0]??" ";return i?r.substring(0,t-1)+"…":r}function J(n,t,e="-"){const i=t.map((t=>{const i=function(n,t,e="-"){const i=new Set([...new Set(Object.keys(n)),...t]);i.delete(e);const r=[],a=[];for(const e of i)r.push(e in n?n[e]:0),a.push(t.has(e)?1:0);const s=new d(r),o=new d(a);return(0,h.MA)(s,o)/((0,h.$G)(s)*(0,h.$G)(o))}(n,t.alphabet,e);return new s.dJ(t,n,i)}));let r;const a=Math.max(...i.map((n=>n.similarity>n.cutoff?n.similarity:-1)));return r=a>0?i.find((n=>n.similarity===a)).name:"UN",r}function P(n,t=5){let e;if(n.semType==i.SEMTYPE.MACROMOLECULE)e=f.g.forColumn(n).alphabet;else{const i=function(n,t,e){const i=n.categories;return function(n,t){const e={};let i=!0,r=null;for(const a of n)if(null==r?r=a.length:a.length!==r&&(i=!1),a.length>=t)for(const n of a.canonicals)n in e||(e[n]=0),e[n]+=1;return{freq:e,sameLength:i}}(a().enumerate(n.getRawData()).map((([n,t])=>e(i[n]))),t)}(n,t,D);e=J(i.freq,o.XS)}return N(e)}function N(n){switch(n){case"PT":return u.f.GrokGroups;case"DNA":case"RNA":return c.J.Chromatogram;default:return b.UE.Color}}function w(n){const t=n.columns.bySemTypeAll(i.SEMTYPE.MACROMOLECULE);let e=t.find((n=>{const t=n.getTag(i.TAGS.UNITS);return!!t&&-1!==t.indexOf("MSA")}))??null;return!e&&t.length>0&&(e=t[0]),e}},8260:(n,t,e)=>{"use strict";e.d(t,{dm:()=>c,g:()=>l,lh:()=>b});var i=e(976),r=e(6414),a=e.n(r),s=e(8447),o=e(6286),f=e(2583),d=e(708),h=e(7228),u=e(1047);const c=new class{constructor(){this.seqHandler="seq-handler",this.notationProvider="seq-handler.notation-provider"}},b={[s.r2.FASTA]:"-",[s.r2.SEPARATOR]:"",[s.r2.HELM]:"*"};class l{constructor(n){if(this._splitter=null,this.cached=!0,this._splitted=null,this.columnVersion=null,this._stats=null,this._maxLength=null,this._posList=null,this._joiner=void 0,n.type!==i.TYPE.STRING)throw new Error(`Unexpected column type '${n.type}', must be '${i.TYPE.STRING}'.`);this._column=n;const t=this._column.getTag(i.TAGS.UNITS);if(null==t)throw new Error("Units are not specified in column");if(this._units=t,this._notation=this.getNotation(),this._defaultGapOriginal=this.isFasta()?b[s.r2.FASTA]:this.isHelm()?b[s.r2.HELM]:b[s.r2.SEPARATOR],!this.column.tags.has("aligned")||!this.column.tags.has("alphabet")||!this.column.tags.has(".alphabetIsMultichar")&&!this.isHelm()&&"UN"===this.alphabet)if(this.isFasta())l.setUnitsToFastaColumn(this);else if(this.isSeparator()){const t=n.getTag("separator");l.setUnitsToSeparatorColumn(this,t)}else{if(!this.isHelm())throw new Error(`Unexpected units '${this.column.getTag(i.TAGS.UNITS)}'.`);l.setUnitsToHelmColumn(this)}if(!this.column.tags.has(".alphabetIsMultichar"))if(this.isHelm())this.column.setTag(".alphabetIsMultichar","true");else if(["UN"].includes(this.alphabet))throw new Error(`For column '${this.column.name}' of alphabet '${this.alphabet}' tag '.alphabetIsMultichar' is mandatory.`);this.notationProvider=this.column.temp[c.notationProvider]??null,this.columnVersion=this.column.version}static setUnitsToFastaColumn(n){if(n.column.semType!==i.SEMTYPE.MACROMOLECULE||n.column.getTag(i.TAGS.UNITS)!==s.r2.FASTA)throw new Error(`The column of notation '${s.r2.FASTA}' must be '${i.SEMTYPE.MACROMOLECULE}'.`);n.column.setTag(i.TAGS.UNITS,s.r2.FASTA),l.setTags(n)}static setUnitsToSeparatorColumn(n,t){if(n.column.semType!==i.SEMTYPE.MACROMOLECULE||n.column.getTag(i.TAGS.UNITS)!==s.r2.SEPARATOR)throw new Error(`The column of notation '${s.r2.SEPARATOR}' must be '${i.SEMTYPE.MACROMOLECULE}'.`);if(!t)throw new Error(`The column of notation '${s.r2.SEPARATOR}' must have the separator tag.`);n.column.setTag(i.TAGS.UNITS,s.r2.SEPARATOR),n.column.setTag("separator",t),l.setTags(n)}static setUnitsToHelmColumn(n){if(n.column.semType!==i.SEMTYPE.MACROMOLECULE)throw new Error(`The column of notation '${s.r2.HELM}' must be '${i.SEMTYPE.MACROMOLECULE}'`);n.column.setTag(i.TAGS.UNITS,s.r2.HELM),l.setTags(n)}static setTags(n){const t=n.column.getTag(i.TAGS.UNITS),e=n.stats;if(Object.keys(e.freq).some((n=>n.length>1)),[s.r2.FASTA,s.r2.SEPARATOR].includes(t)){if(!n.column.getTag("alphabet")&&0===Object.keys(e.freq).length)throw new Error("Alphabet is empty and not annotated.");let t=n.column.getTag("aligned");null===t&&(t=e.sameLength?"SEQ.MSA":"SEQ",n.column.setTag("aligned",t));let i=n.column.getTag("alphabet");if(null===i&&(i=(0,f.w4)(e.freq,s.XS),n.column.setTag("alphabet",i)),"UN"===i){const t=Object.keys(e.freq).length,i=Object.keys(e.freq).some((n=>n.length>1));n.column.setTag(".alphabetSize",t.toString()),n.column.setTag(".alphabetIsMultichar",i?"true":"false")}}}get column(){return this._column}get length(){return this._column.length}get units(){return this._units}get notation(){return this._notation}get defaultGapOriginal(){return this._defaultGapOriginal}get separator(){const n=this.column.getTag("separator")??void 0;if(this.notation===s.r2.SEPARATOR&&void 0===n)throw new Error(`Separator is mandatory for column '${this.column.name}' of notation '${this.notation}'.`);return n}get aligned(){const n=this.column.getTag("aligned");if(!n&&(this.isFasta()||this.isSeparator()))throw new Error("Tag aligned not set");return n}get alphabet(){const n=this.column.getTag("alphabet");if(!n&&(this.isFasta()||this.isSeparator()))throw new Error("Tag alphabet not set");return n}get helmCompatible(){return this.column.getTag(".isHelmCompatible")}getAlphabetSize(){if(this.notation==s.r2.HELM||"UN"==this.alphabet){const n=this.column.getTag(".alphabetSize");let t;if(n)t=parseInt(n);else{const n=this.stats;t=Object.keys(n.freq).length}return t}switch(this.alphabet){case"PT":return 20;case"DNA":case"RNA":return 4;case"NT":return console.warn("Unexpected alphabet 'NT'."),4;default:throw new Error(`Unexpected alphabet '${this.alphabet}'.`)}}getAlphabetIsMultichar(){return this.notation===s.r2.HELM||"UN"===this.alphabet&&"true"===this.column.getTag(".alphabetIsMultichar")}getSplitted(n){if(this.cached){this.column.version===this.columnVersion&&null!==this._splitted||(this.columnVersion=this.column.version,this._splitted=new Array(this.column.length));let t=this._splitted[n]?this._splitted[n].deref():void 0;if(!t){const e=this.column.get(n);t=this.splitter(e),this._splitted[n]=new WeakRef(t)}return t}{const t=this.column.get(n);return this.splitter(t)}}get stats(){if(null===this._stats){const n={};let t=!0,e=null;const i=this.column.length;for(let r=0;r<i;++r){const i=this.getSplitted(r);null==e?e=i.length:i.length!==e&&(t=!1);for(const t of i.canonicals)t in n||(n[t]=0),n[t]+=1}this._stats={freq:n,sameLength:t}}return this._stats}get maxLength(){return null===this._maxLength&&(this._maxLength=0===this.column.length?0:Math.max(...a().count(0).take(this.column.length).map((n=>this.getSplitted(n).length)))),this._maxLength}get posList(){if(null===this._posList){const n=this.column.getTag(".positionNames");this._posList=n?n.split(s.CI).map((n=>n.trim())):a().count(1).take(this.maxLength).map((n=>n.toString())).toArray()}return this._posList}isFasta(){return this.notation===s.r2.FASTA}isSeparator(){return this.notation===s.r2.SEPARATOR}isHelm(){return this.notation===s.r2.HELM}isRna(){return"RNA"===this.alphabet}isDna(){return"DNA"===this.alphabet}isPeptide(){return"PT"===this.alphabet}isMsa(){return!!this.aligned&&this.aligned.toUpperCase().includes("MSA")}isHelmCompatible(){return"true"===this.helmCompatible}isGap(n){return!n||n===this._defaultGapOriginal}getNotation(){if(this.units.toLowerCase().startsWith(s.r2.FASTA))return s.r2.FASTA;if(this.units.toLowerCase().startsWith(s.r2.SEPARATOR))return s.r2.SEPARATOR;if(this.units.toLowerCase().startsWith(s.r2.HELM))return s.r2.HELM;throw new Error(`Column '${this.column.name}' has unexpected notation '${this.units}'.`)}getHelmWrappers(){return[this.isDna()||this.isRna()||this.isHelmCompatible()?"RNA1{":"PEPTIDE1{",this.isDna()?"d(":this.isRna()?"r(":"",this.isDna()||this.isRna()?")p":"","}$$$$"]}getNewColumn(n,t,e,r){const a=this.column,o=n.toLowerCase()+"("+a.name+")",f=e??a.dataFrame.columns.getUnusedName(o),d=i.Column.fromList("string",f,r??new Array(this.column.length).fill(""));if(d.semType=i.SEMTYPE.MACROMOLECULE,d.setTag(i.TAGS.UNITS,n),n===s.r2.SEPARATOR){if(!t)throw new Error(`Notation '${s.r2.SEPARATOR}' requires separator value.`);d.setTag("separator",t)}d.setTag(i.TAGS.CELL_RENDERER,"sequence");const h=a.getTag("aligned");h&&d.setTag("aligned",h);let u=a.getTag("alphabet");u||this.notation!==s.r2.HELM||n===s.r2.HELM||(u="UN"),null!=u&&d.setTag("alphabet",u);let c=a.getTag(".alphabetSize");null!=u&&c&&d.setTag(".alphabetSize",c);const b=a.getTag(".alphabetIsMultichar");return null!=u&&void 0!==b&&d.setTag(".alphabetIsMultichar",b),n==s.r2.HELM&&(c=this.getAlphabetSize().toString(),d.setTag(".alphabetSize",c)),d}getNewColumnFromList(n,t){return this.getNewColumn(this.notation,this.separator,n,t)}static getNewColumn(n){const t=l.forColumn(n),e=t.notation;return t.getNewColumn(e)}static unitsStringIsValid(n){return n=n.toLowerCase(),[s.r2.FASTA,s.r2.SEPARATOR,s.r2.HELM].some((t=>n.startsWith(t.toLowerCase())))}static getNewColumnFromParams(n,t,e){if(!l.unitsStringIsValid(e))throw new Error("Invalid format of 'units' parameter");const r=i.Column.fromList("string",t,new Array(n).fill(""));return r.semType=i.SEMTYPE.MACROMOLECULE,r.setTag(i.TAGS.UNITS,e),r}getSplitter(n){let t=null;if(t=this.notationProvider?this.notationProvider.splitter:null,t)return t;if(this.units.toLowerCase().startsWith(s.r2.FASTA))return null===this.column.getTag("alphabet")||this.getAlphabetIsMultichar()?s.kB:f.FJ;if(this.units.toLowerCase().startsWith(s.r2.SEPARATOR))return(0,s.Ar)(this.separator,n);if(this.units.toLowerCase().startsWith(s.r2.HELM))return s.gP;throw new Error(`Unexpected units ${this.units} .`)}split(n){return this.splitter(n)}getDistanceFunctionName(){if(!this.isFasta())throw new Error("Only FASTA notation is supported");return this.isMsa()?d.U.HAMMING:(this.alphabet,d.U.LEVENSHTEIN)}getDistanceFunction(){return d.o[this.getDistanceFunctionName()]()}async checkHelmCompatibility(){if(this.column.tags.has(".isHelmCompatible"))return"true"===this.column.getTag(".isHelmCompatible");const n=(await(0,h.JN)()).getBioLib().getMonomerSymbolsByType("PEPTIDE".toString()),t=new Set(n),e=((0,s.Ar)(this.separator),new Set),i=this.column.length,r=this.column.getRawData();for(let n=0;n<i;++n){const i=r[n];if(!(i in e)){e.add(i);const r=this.getSplitted(n);for(const n of r.canonicals)if(!t.has(n))return this.column.setTag(".isHelmCompatible","false"),!1}}return this.column.setTag(".isHelmCompatible","true"),!0}get splitter(){return null===this._splitter&&(this._splitter=this.getSplitter()),this._splitter}toFasta(n){return n===s.r2.FASTA}toSeparator(n){return n===s.r2.SEPARATOR}toHelm(n){return n===s.r2.HELM}convertHelmToFastaSeparator(n,t,e,i){i||(i=this.toFasta(t)?b[s.r2.FASTA]:b[s.r2.SEPARATOR]),e||(e=this.toFasta(t)?"":this.separator);const r=n.startsWith("RNA"),a=this.splitter(n),o=[];for(let n=0;n<a.length;++n){let e=a.getOriginal(n);if(r&&(e=e.replace(u.pU,"")),e===b[s.r2.HELM])o.push(i);else if(this.toFasta(t)&&e.length>1){const n="["+e+"]";o.push(n)}else o.push(e)}return o.join(e)}convert(n,t){const e=this.getJoiner({notation:n,separator:t}),i=this.getNewColumn(n,t);return i.init((n=>{const t=this.getSplitted(n);return e(t)})),i}getRegion(n,t,e){const i=this.getNewColumn(this.notation,this.separator);i.name=e;const r=n??0,a=t??this.maxLength-1,o=this.getJoiner(),d=a-r+1,h=b[this.notation];i.init((n=>{const t=this.getSplitted(n),e=new Array(d);for(let n=0;n<d;++n){const i=r+n;e[n]=i<t.length?t.getOriginal(i):h}return o(new f.wx(e,h))}));const u=n=>{const t=n.split(",").map((n=>n.trim())),e=new Array(d);for(let n=0;n<d;++n){const i=r+n;e[n]=i<t.length?t[i]:"?"}return e.join(s.CI)},c=this.column.getTag(".positionNames");c&&i.setTag(".positionNames",u(c));const l=this.column.getTag(".positionLabels");return l&&i.setTag(".positionLabels",u(l)),i}get joiner(){return this._joiner||(this._joiner=this.getJoiner()),this._joiner}getJoiner(n){const t=n?n.notation:this.notation,e=n?n.separator:this.separator;let i;const r=this;switch(t){case s.r2.FASTA:i=function(n){return r.joinToFasta(n,r.isHelm())};break;case s.r2.SEPARATOR:if(!e)throw new Error(`Separator is mandatory for notation '${t}'.`);i=function(n){return g(n,e,r.isHelm())};break;case s.r2.HELM:{const n="DNA"===r.alphabet||"RNA"===r.alphabet,t=r.getHelmWrappers();i=function(e){return D(e,t,n)};break}default:throw new Error(`Unexpected notation '${t}'.`)}return i}getConverter(n,t=undefined){if(n===s.r2.SEPARATOR&&!t)throw new Error(`Target separator is not specified for target units '${s.r2.SEPARATOR}'.`);const e=this;if(n===s.r2.FASTA)return function(n){return e.convertToFasta(n)};if(n===s.r2.HELM)return function(n){return e.convertToHelm(n)};if(n===s.r2.SEPARATOR)return function(n){return e.convertToSeparator(n,t)};throw new Error}static forColumn(n){let t=n.temp[c.seqHandler];return t&&t.columnVersion===n.version||(t=n.temp[c.seqHandler]=new l(n)),t}joinToFasta(n,t){const e=new Array(n.length);for(let i=0;i<n.length;++i){const r=n.getOriginal(i);let a=n.getOriginal(i);t&&(a=a.replace(u.pU,"$1")),r===o.G2?a=b[s.r2.FASTA]:r===u.$3?a="":a.length>1&&(a="["+a+"]"),e[i]=a}return e.join("")}convertToFasta(n){const t=this.splitter,e=this.isHelm()?this.splitterAsHelmNucl(n):t(n);return this.joinToFasta(e,this.isHelm())}convertToSeparator(n,t){return g(this.isHelm()?this.splitterAsHelmNucl(n):this.splitter(n),t,this.isHelm())}convertToHelm(n){const t=this.getHelmWrappers(),e=n.startsWith("DNA")||n.startsWith("RNA");return D(this.splitter(n),t,e)}splitterAsHelmNucl(n){const t=this.splitter(n),e=new Array(t.length),i=n.startsWith("DNA"),r=n.startsWith("RNA");for(let n=0;n<t.length;++n){let a=t.getOriginal(n);(i||r)&&(a=a.replace(u.pU,"$1"),a=a===u.$3?null:a),e[n]=a||null}return new f.wx(e.filter((n=>!!n)),b[s.r2.HELM])}}function g(n,t,e){const i=new Array(n.length);for(let t=0;t<n.length;++t){const r=n.getCanonical(t);let a=n.getOriginal(t);e&&(a=a.replace(u.pU,"$1")),r===o.G2?a=b[s.r2.SEPARATOR]:r===u.$3&&(a=""),i[t]=a}return i.join(t)}function D(n,t,e){const[i,r,a,f]=t,d=new Array(n.length);for(let t=0;t<n.length;++t){const i=n.getCanonical(t);let f=n.getOriginal(t);i===o.G2?f=b[s.r2.HELM]:(e&&(f=f.replace(u.pU,"$1")),f=1===f.length?`${r}${f}${a}`:`${r}[${f}]${a}`),d[t]=f}return`${i}${d.join(".")}${f}`}},8457:(n,t,e)=>{"use strict";e.d(t,{O:()=>a});var i=e(976),r=e(8260);function a(n){const t=n=>{const t=s.columns.addNewString((n+1).toString());return e.push(t),t},e=[],a=n.length,s=i.DataFrame.create(a),o=r.g.forColumn(n);for(let n=0;n<a;++n){const i=o.getSplitted(n);for(let r=0;r<i.length;++r){const a=i.getOriginal(r);((e[r]??null)||t(r)).set(n,a,!1)}}return s}},172:(n,t,e)=>{"use strict";e.d(t,{c:()=>a});var i,r=e(7945);!function(n){n[n.error=0]="error",n[n.warning=1]="warning",n[n.info=2]="info",n[n.debug=3]="debug"}(i||(i={}));class a{constructor(n){this.logger=n,this.promise=Promise.resolve(),this.errors=[],this.syncCounter=0}sync(n,t){const e=++this.syncCounter;this.logger.debug(`${n}, SYNC syncId = ${e}, IN `),this.promise=this.promise.then((async()=>{this.logger.debug(`${n}, SYNC syncId = ${e}, START `),await t(),this.logger.debug(`${n}, SYNC syncId = ${e}, END `)})).catch((t=>{const[i,a]=(0,r.yf)(t);this.logger.error(`${n}, SYNC syncId = ${e}, ERROR:\n${i}`,void 0,a),this.errors.push(t)}))}resetErrors(){const n=this.errors;return this.errors=[],n}}},9298:(n,t,e)=>{"use strict";e.d(t,{Ct:()=>f,DX:()=>i,ES:()=>r,dE:()=>o,iD:()=>s,vS:()=>h,vw:()=>a});var i,r,a,s,o,f,d=e(976);!function(n){n.tooltipWebLogo=".tooltipWebLogo"}(i||(i={})),function(n){n.Entropy="Entropy",n.full="100%"}(r||(r={})),function(n){n.TOP="top",n.MIDDLE="middle",n.BOTTOM="bottom"}(a||(a={})),function(n){n.LEFT="left",n.CENTER="center",n.RIGHT="right"}(s||(s={})),function(n){n.AUTO="auto",n.ON="on",n.OFF="off"}(o||(o={})),function(n){n.Filtered="Filtered",n.Selected="Selected"}(f||(f={}));const h=new class{constructor(){this.sequenceColumnName=null,this.valueAggrType=d.AGG.TOTAL_COUNT,this.valueColumnName="Activity",this.startPositionName=null,this.endPositionName=null,this.skipEmptySequences=!0,this.skipEmptyPositions=!1,this.shrinkEmptyTail=!0,this.backgroundColor=4294967295,this.positionHeight=r.Entropy,this.positionWidth=16,this.verticalAlignment=a.MIDDLE,this.horizontalAlignment=s.CENTER,this.fixWidth=!1,this.fitArea=!0,this.minHeight=50,this.maxHeight=100,this.showPositionLabels=!0,this.positionMarginState=o.AUTO,this.positionMargin=0,this.filterSource=f.Filtered}}},922:(n,t,e)=>{"use strict";e.d(t,{_:()=>f});class i{constructor(n){this.init(n)}init(n){this.fileContent=n.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 n;return null!==(n=this.xyzAtomCoordinates)&&void 0!==n||(this.xyzAtomCoordinates=this.parseAtomCoordinates()),this.xyzAtomCoordinates.x}get y(){var n;return null!==(n=this.xyzAtomCoordinates)&&void 0!==n||(this.xyzAtomCoordinates=this.parseAtomCoordinates()),this.xyzAtomCoordinates.y}get z(){var n;return null!==(n=this.xyzAtomCoordinates)&&void 0!==n||(this.xyzAtomCoordinates=this.parseAtomCoordinates()),this.xyzAtomCoordinates.z}get atomTypes(){var n;return null!==(n=this._atomTypes)&&void 0!==n||(this._atomTypes=this.parseAtomTypes()),this._atomTypes}get pairsOfBondedAtoms(){var n;return null!==(n=this._pairsOfBondedAtoms)&&void 0!==n||(this._pairsOfBondedAtoms=this.parseBondedAtomPairs()),this._pairsOfBondedAtoms}get bondTypes(){var n;return null!==(n=this._bondTypes)&&void 0!==n||(this._bondTypes=this.parseBondTypes()),this._bondTypes}setAtomAndBondCounts(){const{atomCount:n,bondCount:t}=this.parseAtomAndBondCounts();this._atomCount=n,this._bondCount=t}getNextColumnIdx(n){for(;!this.isWhitespace(n);)++n;for(;this.isWhitespace(n);)++n;return n}shiftIdxToSpecifiedColumn(n,t){let e=n;const i=this.isWhitespace(e)?t:t-1;for(let n=0;n<i;n++)e=this.getNextColumnIdx(e);return e}parseAtomTypes(){const n=this.atomCount,t=new Array(n);let e=this.getAtomBlockIdx();for(let i=0;i<n;i++)e=this.shiftIdxToAtomType(e),t[i]=this.parseAtomType(e),e=this.getNextLineIdx(e);return t}parseAtomCoordinates(){const n=new Float32Array(this.atomCount),t=new Float32Array(this.atomCount),e=new Float32Array(this.atomCount);let i=this.getAtomBlockIdx();for(let r=0;r<this.atomCount;r++){i=this.shiftIdxToXColumn(i);for(const a of[n,t,e])a[r]=this.parseFloatValue(i),i=this.getNextColumnIdx(i);i=this.getNextLineIdx(i)}return{x:n,y:t,z:e}}parseBondedAtomPairs(){const n=new 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