@datagrok/bio 2.12.20 → 2.12.21
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- package/CHANGELOG.md +4 -0
- package/dist/package-test.js +1 -1
- package/dist/package-test.js.map +1 -1
- package/dist/package.js +1 -1
- package/dist/package.js.map +1 -1
- package/package.json +2 -2
- package/webpack.config.js +6 -2
package/dist/package-test.js
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/*! For license information please see package-test.js.LICENSE.txt */
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var bio_test;(()=>{var e={2012:(e,t,n)=>{"use strict";n.d(t,{f:()=>r});var s=n(9976);class r extends s.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(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 i{static getPalette(e="grok"){switch(e){case"grok":return r.GrokGroups;case"lesk":return r.Lesk;default:throw new Error(`ChemPalette: scheme \`${e}\` does not exist`)}}static getInnerOuter(e){let t=0,n="",s="";for(const r of e)"("==r?t++:")"==r?t--:t?n+=r:s+=r;return isNaN(parseInt(n))?[s,n]:[s,""]}static getColorAAPivot(e="",t="grok"){const n=this.getPalette(t);let[s,r]=this.getInnerOuter(e);if(s=s.length>6?`${s.slice(0,3)}...`:s,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,s,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,s,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,s,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,s,r,4]}return[this.undefinedColor,s,r,0]}}i.SemType="Aminoacids",i.SemTypeMultipleAlignment="AminoacidsMultipleAlignment",i.undefinedColor="rgb(100,100,100)",i.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"},i.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"},i.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(*)*"},i.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:(e,t,n)=>{"use strict";n.d(t,{BX:()=>i,nW:()=>l,tW:()=>c,tb:()=>u});var s=n(4469);const r="Libraries",i="System:AppData/Bio/monomer-libraries/",o={explicit:["HELMCoreLibrary.json"],exclude:[]};let a=Promise.resolve();async function l(){let e;return a=a.then((async()=>{const t=await s.dapi.userDataStorage.getValue(r,"Settings",!0);e=t?JSON.parse(t):{exclude:[],explicit:[]},e.exclude=e.exclude instanceof Array?e.exclude:[],e.explicit=e.explicit instanceof Array?e.explicit:[],console.debug(`Bio: getUserLibSettings()\n${JSON.stringify(e,void 0,2)}`)})),await a,e}async function c(e){a=a.then((async()=>{console.debug(`Bio: setUserLibSettings()\n${JSON.stringify(e,void 0,2)}`),await s.dapi.userDataStorage.postValue(r,"Settings",JSON.stringify(e),!0)})),await a}async function u(){await c(o)}},7228:(e,t,n)=>{"use strict";n.d(t,{JN:()=>a,Qx:()=>l});var s=n(976),r=n(4469),i=(n(5697),n(1047),n(6286)),o=(n(8607),n(8457));async function a(){const e=s.Func.find({package:"Bio",name:"getMonomerLibHelper"});if(0===e.length)throw new Error('Package "Bio" must be installed for MonomerLibHelper.');return(await e[0].prepare().call()).getOutputParamValue()}async function l(e,t){e instanceof s.Column&&(e=(0,o.O)(e).columns.toList());const n=(await a()).getBioLib(),l=new Array(e.length),c=e[0].length,u=new Float32Array(c);for(let o=0;o<e.length;++o){const a=t.getCanonical(o),h=n.getMonomer("PEPTIDE",a)?.smiles??"",d=e[o],m=d.getRawData(),p=d.categories,f=p.indexOf("");if(l[o]={categories:p,data:m,emptyIndex:f},void 0===a)continue;const g=s.Column.fromStrings("smiles",p.map((e=>n.getMonomer("PEPTIDE",e)?.smiles??""))),y=(s.DataFrame.fromColumns([g]),(await r.chem.getSimilarities(g,h)).getRawData());for(let e=0;e<c;++e){const t=m[e];u[e]+=a!==i.G2&&t!==f?y[t]:a===i.G2&&t===f?1:0}}for(let n=0;n<u.length;++n){let r=u[n]/t.length;for(let i=0;i<e.length;++i){const e=l[i];if(i>=t.length&&e.data[n]!==e.emptyIndex||e.data[n]===e.emptyIndex&&i<t.length){r=s.FLOAT_NULL;break}}u[n]=r}return s.Column.fromFloat32Array("Similarity",u)}},8601:(e,t,n)=>{"use strict";n.d(t,{i0:()=>d});var s=n(4469),r=n(976),i=n(6414),o=n.n(i),a=n(1821),l=n(8607);const c={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 u=n(1047);function h(e){return Math.round(c.PRECISION_FACTOR*e)/c.PRECISION_FACTOR}async function d(e,t,i){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 h=t;const d=l.g.forColumn(t);d.isHelm()&&(h=d.convert(a.r2.SEPARATOR,"."),h.name=t.name);const p=l.g.forColumn(h).alphabet;let f;if("PT"===p||"UN"===p)f="PEPTIDE";else{if("RNA"!==p&&"DNA"!==p)return{col:null,warnings:[`Unexpected column's '${h.name}' alphabet '${p}'.`]};f="RNA"}const g=function(e){const t=e.length,n=new Array(t),r=l.g.forColumn(e);let i=!1;for(let e=0;e<t;++e){const t=r.getSplitted(e);i||(i=0===t.length),n[e]=o()(t.canonicals).filter((e=>!r.isGap(e))).map((e=>e)).toArray()}return i&&s.shell.warning(`Some values in the "${e.name}" column are empty`),n}(h),y=await async function(e,t,n,r){const i=function(e,t,n){const s=new Map;for(const r of e.getMonomerSymbolsByType(t)){const i=e.getMonomer(t,r);if("RNA"===t&&("Branch"===i.monomerType||"DNA"===n&&i.symbol===c.DEOXYRIBOSE||"RNA"===n&&i.symbol===c.RIBOSE||i.symbol===c.PHOSPHATE)||"PEPTIDE"===t&&"Branch"!==i.monomerType){const e={};u.rx.forEach((t=>{e[t]=i[t]})),s.set(i.symbol,e)}}return s}(t,n,r),o=new Map,a=await s.functions.call("Chem:getRdKitModule"),l={value:null};if("RNA"===n){const e="RNA"===r?[c.RIBOSE,c.PHOSPHATE]:[c.DEOXYRIBOSE,c.PHOSPHATE];for(const t of e)m(o,t,i,a,n,l)}for(let t=0;t<e.length;++t){const s=e[t];for(const e of s)if(""!==e)try{m(o,e,i,a,n,l)}catch(t){const n=t instanceof Error?t.message:t.toString(),s=t instanceof Error?t.stack:void 0;throw console.error(`bio lib: getMonomersDictFromLib() sym='${e}', error:\n${n}\n${s}`),new Error(`Can't get monomer '${e}' from library: ${n}`)}}return o}(g,i,f,p),w=h.length,{molfileList:b,molfileWarningList:A}=await async function(e,t,s,r,i){const o=Math.max(navigator.hardwareConcurrency-2,1),a=new Array(o).fill(null).map((()=>new Worker(new URL(n.p+n.u(79),n.b)))),l=i/o;let c=[],u=[];const h=new Array(o);for(let n=0;n<o;n++){const c=Math.floor(n*l),u=n===o-1?i:Math.floor((n+1)*l);a[n].postMessage({monomerSequencesArray:e,monomersDict:t,alphabet:s,polymerType:r,start:c,end:u}),h[n]=new Promise((e=>{a[n].onmessage=({data:{molfileList:t,molfileWarningList:n}})=>{e({molfileList:t,molfileWarningList:n})}}))}return(await Promise.all(h)).forEach((e=>{c=c.concat(...e.molfileList),u=u.concat(...e.molfileWarningList)})),setTimeout((()=>{a.forEach((e=>{e.terminate()}))}),0),{molfileList:c,molfileWarningList:u}}(g,y,p,f,w);if(A.length>.05*w)throw new Error("Too many errors getting molfiles.");const C=`molfile(${h.name})`,v=e.columns.getUnusedName(C),T=r.Column.fromStrings(v,b);return T.semType=r.SEMTYPE.MOLECULE,T.setTag(r.TAGS.UNITS,r.UNITS.Molecule.MOLBLOCK),{col:T,warnings:A}}function m(e,t,n,s,r,i){if(!e.has(t)){const o=function(e,t,n,s,r){if(t.has(e)){const o=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}(o.rgroups),l=(i=o.molfile).includes("V3000")?function(e){const t=new Map,n=/M V30 (\d+) R#.+RGROUPS=\((\d+) (\d+)\).*/gm;let s;for(;null!==(s=n.exec(e));)s.index===n.lastIndex&&n.lastIndex++,t.set(parseInt(s[1]),parseInt(s[3]));return t}(i):function(e){const t=new Map;let n=e.indexOf(c.V2K_A_LINE,0),s=n;for(;-1!==n;){s=e.indexOf("\n",n);const r=parseInt(e.substring(n,s).replace(/^A\s+/,""));n=e.indexOf("R",s),s=e.indexOf("\n",n);const i=parseInt(e.substring(n,s).replace(/^R/,""));t.set(r,i),n=e.indexOf(c.V2K_A_LINE,s)}for(n=e.indexOf(c.V2K_RGP_LINE,0),s=e.indexOf("\n",n);-1!==n;){n+=c.V2K_RGP_SHIFT,s=e.indexOf("\n",n);const r=e.substring(n,s).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(c.V2K_RGP_LINE,s)}return t}(i),u=o.molfile.includes("V3000")?o.molfile:function(e,t){const n=t.get_mol(e),s=n.get_v3Kmolblock();return n.delete(),s}(function(e){let t=e.indexOf(c.V2K_A_LINE,0);-1===t&&(t=e.indexOf(c.V2K_RGP_LINE));const n=e.indexOf(c.V3K_END,t);return e.substring(0,t)+e.substring(n)}(o.molfile),n),d=function(e){let t=(e=e.replaceAll("\r","")).indexOf(c.V3K_BEGIN_COUNTS_LINE)+c.V3K_COUNTS_SHIFT,n=e.indexOf(" ",t+1);const s=parseInt(e.substring(t,n));return t=n+1,n=e.indexOf(" ",t+1),{atomCount:s,bondCount:parseInt(e.substring(t,n))}}(u),m=function(e,t){const n=new Array(t),s=new Float32Array(t),r=new Float32Array(t),i=new Array(t);let o=e.indexOf(c.V3K_BEGIN_ATOM_BLOCK);o=e.indexOf("\n",o);let a=o;for(let l=0;l<t;l++){o=e.indexOf(c.V3K_BEGIN_DATA_LINE,o)+c.V3K_IDX_SHIFT,a=e.indexOf(" ",o),o=a+1,a=e.indexOf(" ",o),n[l]=e.substring(o,a);const t=new Array(2);for(let n=0;n<2;++n)o=a+1,a=e.indexOf(" ",o),t[n]=parseFloat(e.substring(o,a));s[l]=t[0],r[l]=t[1],o=a,a=e.indexOf("\n",o)+1,i[l]=e.slice(o,a),o=a}return{atomTypes:n,x:s,y:r,kwargs:i}}(u,d.atomCount),g=function(e,t){const n=new Uint32Array(t),s=new Array(t),r=new Map,i=new Map;let o=e.indexOf(c.V3K_BEGIN_BOND_BLOCK);o=e.indexOf("\n",o);let a=o;for(let l=0;l<t;++l){const t=new Array(3);o=e.indexOf(c.V3K_BEGIN_DATA_LINE,a)+c.V3K_IDX_SHIFT,a=e.indexOf(" ",o);for(let n=0;n<3;++n)o=a+1,a=Math.min(e.indexOf("\n",o),e.indexOf(" ",o)),t[n]=parseInt(e.slice(o,a));n[l]=t[0],s[l]=t.slice(1);const u=e.indexOf("\n",o);let h=e.slice(a,u),d=h.indexOf(c.V3K_BOND_CONFIG);if(-1!==d){d=h.indexOf("=",d)+1;let e=h.indexOf(" ",d);-1===e&&(e=h.length);const t=parseInt(h.slice(d,e));r.set(l,t);const n=c.V3K_BOND_CONFIG+t.toString();h=h.replace(n,"")}h||i.set(l,h)}return{bondTypes:n,atomPairs:s,bondConfiguration:r,kwargs:i}}(u,d.bondCount),w=function(e,t,n,s){const r={backboneShift:null,branchShift:null,terminalNodes:[],rNodes:[]};return function(e,t,n){for(const[s,r]of n)e.atomTypes[s-1]=t[r-1]}(e,n,s),function(e,t){t.rNodes=Array.from(e.keys());for(let n=0;n<t.rNodes.length;n++)for(const s of[1,2])if(e.get(t.rNodes[n])===s){const e=t.rNodes[s-1];t.rNodes[s-1]=t.rNodes[n],t.rNodes[n]=e}}(s,r),p(t,r),r}(m,g,a,l),T=function(e){let t=[],n=e.indexOf("M V30 MDLV30/STEABS ATOMS=(");for(;-1!==n;){n+=28;const s=e.indexOf(")",n);t=t.concat(e.substring(n,s).split(" ").slice(1).map((e=>parseInt(e)))),n=s,n=e.indexOf("M V30 MDLV30/STEABS ATOMS=(",n)}return t}(u),S={atoms:m,bonds:g,meta:w,stereoAtoms:T};return"PEPTIDE"===s?function(e){const t=e.meta.terminalNodes[0]-1,n=e.meta.rNodes[0]-1,s=e.atoms.x,r=e.atoms.y;v(e,-s[t],-r[t]);const i=b(s[n],r[n]);A(e.atoms,-i),s[e.meta.rNodes[1]-1]<0&&function(e){C(e,!1)}(e);const o=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 s=n[e],r=n[(e+1)%2];t.has(s)?t.get(s)?.push(r):t.set(s,new Array(1).fill(r))}return t}(e);let n=0;const s=e.atoms.atomTypes.length;let r=0;for(;0===n;){const i=t.get(e.meta.terminalNodes[1])[r];if(e.atoms.atomTypes[i-1]===c.OXYGEN&&i!==e.meta.rNodes[1]&&(n=i),r++,r>s)throw new Error(`Search for double-bonded Oxygen in ${e} has exceeded the limit of ${s}`)}return n}(e);!function(e,t){e.atoms.y[e.meta.rNodes[1]-1]<0&&e.atoms.y[t-1]<0&&(function(e){C(e,!0)}(e),A(e.atoms,-function(e,t){return b(e,t)+Math.PI/2}(e.atoms.x[e.meta.terminalNodes[1]-1],e.atoms.y[e.meta.terminalNodes[1]-1])))}(e,o),function(e,t){const n=e.atoms.x;n[e.meta.rNodes[1]-1]>n[t-1]&&function(e,t,n){const s=t-1,r=n-1,i=e.atoms.x,o=e.atoms.y,a=i[s],l=o[s];i[s]=i[r],o[s]=o[r],i[r]=a,o[r]=l}(e,t,e.meta.rNodes[1])}(e,o)}(S):e===c.RIBOSE||e===c.DEOXYRIBOSE?function(e,t){const n=e.atoms.x,s=e.atoms.y;let r=e.meta.terminalNodes[0]-1;const i=e.meta.rNodes[1]-1;v(e,-n[r],-s[r]);const o=b(n[i],s[i]);A(e.atoms,3*Math.PI/2-o),t.value=function(e){const t=e.atoms.x,n=e.atoms.y,s=e.meta.rNodes[2]-1,r=e.meta.terminalNodes[2]-1,i=t[s]-t[r],o=n[s]-n[r];return Math.atan(o/i)+Math.PI/2}(e),r=e.meta.terminalNodes[0]-1,v(e,-n[r],-s[r])}(S,r):e===c.PHOSPHATE?function(e){const t=e.meta.terminalNodes[0]-1,n=e.meta.rNodes[0]-1,s=e.atoms.x,r=e.atoms.y;v(e,-s[t],-r[t]);const i=b(s[n],r[n]);A(e.atoms,Math.PI/2-i)}(S):function(e,t){const n=e.atoms.x,s=e.atoms.y,r=e.meta.terminalNodes[0]-1,i=e.meta.rNodes[0]-1;v(e,-n[r],-s[r]);const o=b(n[i],s[i]),a=t.value;if(!a)throw new Error("The value of sugarBranchToOYAngle is null");A(e.atoms,Math.PI-o+a);const l=function(e,t){return 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s=t.terminalNodes,r=e.atomPairs;let i=0,o=0;for(;i<r.length&&o<s.length;){for(let e=0;e<s.length;++e)for(let t=0;t<2;++t)r[i][t]===n[e]&&(s[e]=r[i][(t+1)%2],n.length,++o);++i}}function f(e,t){e.meta.rNodes.length>1&&(e.meta.backboneShift=g(e,e.meta.rNodes[1]-1,e.meta.terminalNodes[0]-1)),"RNA"===t&&e.meta.rNodes.length>2&&(e.meta.branchShift=g(e,e.meta.rNodes[2]-1,e.meta.terminalNodes[0]-1))}function g(e,t,n){return[h(e.atoms.x[t]-e.atoms.x[n]),h(e.atoms.y[t]-e.atoms.y[n])]}function y(e,t){if(void 0!==t){const n=t-1,s=e.atoms,r=e.bonds,i=e.meta;s.atomTypes.splice(n,1),s.x=w(Float32Array,s.x,n,1),s.y=w(Float32Array,s.y,n,1),s.kwargs.splice(n,1);for(let e=0;e<i.terminalNodes.length;++e)i.terminalNodes[e]>t?--i.terminalNodes[e]:i.terminalNodes[e]===t&&(i.terminalNodes[e]=-1);for(let e=0;e<i.rNodes.length;++e)i.rNodes[e]>t?--i.rNodes[e]:i.rNodes[e]===t&&(i.rNodes[e]=-1);let o=0;for(;o<r.atomPairs.length;){const 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r=s[t],i=this.props.monomerToShort(r,this.props.monomerLengthLimit),o=this.props.separatorWidth+i.length*this.props.monomerCharWidth;if(n[t]=Math.max(n[t]??0,o),l+=o,l>=e)break}this._updated=!0,this._processedMaxVisibleSeqLength=Math.max(this._processedMaxVisibleSeqLength,a)}return n}getPosition(e,t,n){const[s,r]=this.getCellMonomerLengths(e,n),a=o.g.forColumn(this.tableCol);return 0===i()(a.getSplitted(e).originals).toArray().length?null:c(r,t)}setMonomerLengthLimit(e){this.props.monomerLengthLimit=e,this._updated=!0}setSeparatorWidth(e){this.props.separatorWidth=e,this._updated=!0}isMsa(){return this.props.seqHandler.isMsa()}}},1047:(e,t,n)=>{"use strict";n.d(t,{$3:()=>r,pU:()=>i,rx:()=>s});const s=["symbol","molfile","rgroups","name"],r="p",i=new RegExp(`[rd]\\((\\w)\\)${r}?`,"g")},7945:(e,t,n)=>{"use strict";function s(e){return"string"==typeof e||e instanceof String?e:"StateError"===e.constructor.name?e.message:"StateError"===e.constructor.name&&"$thrownJsError"in 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t.semType=s.SEMTYPE.MACROMOLECULE,t.setTag(s.TAGS.UNITS,i.r2.FASTA),r.g.forColumn(t),[s.DataFrame.fromColumns([e,t])]}constructor(e){this._descriptionsArray=[],this._sequencesArray=[],this._fileContent=e,this.parseColumns()}}},706:(e,t,n)=>{"use strict";n.d(t,{Ug:()=>i,io:()=>o});var s=n(976),r=n(8447);function i(){const e=[];return e.push(s.Column.fromList("string","MSA",new Array(10**6).fill("meI/hHis/Aca/N/T/dE/Thr_PO3H2/Aca/D-Tyr_Et/Tyr_ab-dehydroMe/dV/E/N/D-Orn/D-aThr//Phe_4Me"))),e.push(s.Column.fromList(s.COLUMN_TYPE.FLOAT,"Activity",new Array(10**6).fill(5.30751))),e}function o(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=s.Column.fromList(s.COLUMN_TYPE.STRING,"MSA",new Array(100).fill(t));n.semType=s.SEMTYPE.MACROMOLECULE,n.setTag(s.TAGS.UNITS,r.r2.SEPARATOR),n.setTag("separator","/"),n.setTag("alphabet","UN"),n.setTag(".alphabetIsMultichar","true");const i=[];return i.push(n),i.push(s.Column.fromList(s.COLUMN_TYPE.FLOAT,"Activity",new Array(100).fill(7.30751))),i}n(6414),n(8607),n(8260)},1821:(e,t,n)=>{"use strict";n.d(t,{BM:()=>o,CI:()=>i,XS:()=>l,r2:()=>s,se:()=>a});var s,r=n(6286);!function(e){e.FASTA="fasta",e.SEPARATOR="separator",e.HELM="helm"}(s||(s={}));const i=", ",o=/(?:\[([A-Za-z0-9_\-,()]+)\])|([A-Za-z\-])/g,a=new class{constructor(){this.fasta={peptide:new Set(["G","L","Y","S","E","Q","D","N","F","A","K","R","H","C","V","P","W","I","M","T"]),dna:new Set(["A","C","G","T"]),rna:new Set(["A","C","G","U"])}}},l=[new r.LA("PT",a.fasta.peptide,.5),new r.LA("DNA",a.fasta.dna,.55),new r.LA("RNA",a.fasta.rna,.55)]},8447:(e,t,n)=>{"use strict";n.d(t,{Ar:()=>r.Ar,CI:()=>s.CI,GU:()=>r.GU,KX:()=>r.KX,XS:()=>s.XS,dQ:()=>r.dQ,gM:()=>r.gM,gP:()=>r.gP,kB:()=>r.kB,py:()=>r.py,r2:()=>s.r2,up:()=>r.up});var s=n(1821),r=n(8260)},6286:(e,t,n)=>{"use strict";n.d(t,{G2:()=>s,LA:()=>r,dJ:()=>i});const s="";class r{constructor(e,t,n){this.name=e,this.alphabet=t,this.cutoff=n}}class i extends r{constructor(e,t,n){super(e.name,e.alphabet,e.cutoff),this.freq=t,this.similarity=n}}},8260:(e,t,n)=>{"use strict";n.d(t,{wx:()=>p,w4:()=>P,gM:()=>_,KX:()=>x,py:()=>N,vU:()=>T,Ar:()=>b,jY:()=>g,GU:()=>E,dQ:()=>$,up:()=>M,kB:()=>y,FJ:()=>w,gP:()=>v});var s=n(976),r=n(6414),i=n.n(r),o=n(6286),a=n(1821),l=n(8607);class c extends Float32Array{}var u=n(850),h=n(2012),d=n(6137),m=n(7331);class p{get length(){return this.mList.length}get canonicals(){return this.mList}get originals(){return this.mList}isGap(e){return this.getOriginal(e)===this.gapOriginalMonomer}getCanonical(e){if(this.length<=e)throw new Error("Index out of bounds");return this.mList[e]}getOriginal(e){if(this.length<=e)throw new Error("Index out of bounds");return this.mList[e]}constructor(e,t){this.mList=e,this.gapOriginalMonomer=t}}class f{get length(){return this.seqS.length}get canonicals(){return this.seqS}get originals(){return this.seqS}isGap(e){return this.getOriginal(e)===l.lh[a.r2.FASTA]}getCanonical(e){if(this.length<=e)throw new Error("Index out of bounds");return this.isGap(e)?o.G2:this.seqS[e]}getOriginal(e){if(this.length<=e)throw new Error("Index out of bounds");return this.seqS[e]}constructor(e){this.seqS=e}}function g(e,t,n){const s=e.categories;return function(e,t){const n={};let s=!0,r=null;for(const i of e)if(null==r?r=i.length:i.length!==r&&(s=!1),i.length>=t)for(const e of i.canonicals)e in n||(n[e]=0),n[e]+=1;return{freq:n,sameLength:s}}(i().enumerate(e.getRawData()).map((([e,t])=>n(s[e]))),t)}const y=e=>{const t=i()(e.toString().matchAll(a.BM)).map((e=>e[2]??e[1])).toArray();return new p(t,l.lh[a.r2.FASTA])},w=e=>e?new f(e):new p([],l.lh[a.r2.FASTA]);function b(e,t=undefined){return n=>{if(n){let s;const r=new RegExp(String.raw`"-"|'-'|[^${e}]+`,"g");if(void 0!==t){r.lastIndex=0,s=new Array(Math.ceil(t));let e=null,i=0;for(;null!==(e=r.exec(n))&&i<t;)s[i++]=e[0].replace('"-"',"").replace("'-'","");s.splice(i)}else s=n.replaceAll('"-"',"").replaceAll("'-'","").split(e,t);return new p(s,l.lh[a.r2.SEPARATOR])}return new p([],l.lh[a.r2.SEPARATOR])}}const A=/(PEPTIDE1|DNA1|RNA1)\{([^}]+)}/g,C=/\[([^\[\]]+)]/g,v=e=>{A.lastIndex=0;const t=A.exec(e.toString()),n=t?t[2]:null,s=n?n.split("."):[];return new p(s.map((e=>{C.lastIndex=0;const t=C.exec(e);return t&&t.length>=2?t[1]:e})),l.lh[a.r2.HELM])};function T(e,t,n=undefined){if(e.toLowerCase().startsWith(a.r2.FASTA))return y;if(e.toLowerCase().startsWith(a.r2.SEPARATOR))return b(t,n);if(e.toLowerCase().startsWith(a.r2.HELM))return v;throw new Error(`Unexpected units ${e} .`)}const S=/([^\W_]+)/g;function E(e,t){if(e.length<=t)return e;const n=e.match(S),s=e.length>t||(n?.length??0)>1,r=n?.[0]??" ";return s?r.substring(0,t-1)+"…":r}function _(e){switch(e){case"DNA":return a.se.fasta.dna;case"RNA":return a.se.fasta.rna;case"PT":return a.se.fasta.peptide;default:throw new Error(`Unsupported alphabet '${e}'.`)}}function x(e,t,n="-"){const s=new Set([...new Set(Object.keys(e)),...t]);s.delete(n);const r=[],i=[];for(const n of s)r.push(n in e?e[n]:0),i.push(t.has(n)?1:0);const o=new c(r),a=new c(i);return(0,u.MA)(o,a)/((0,u.$G)(o)*(0,u.$G)(a))}function P(e,t,n="-"){const s=t.map((t=>{const s=x(e,t.alphabet,n);return new o.dJ(t,e,s)}));let r;const i=Math.max(...s.map((e=>e.similarity>e.cutoff?e.similarity:-1)));return r=i>0?s.find((e=>e.similarity===i)).name:"UN",r}function $(e,t=5){let n;return n=e.semType==s.SEMTYPE.MACROMOLECULE?l.g.forColumn(e).alphabet:P(g(e,t,y).freq,a.XS),N(n)}function N(e){switch(e){case"PT":return h.f.GrokGroups;case"DNA":case"RNA":return d.J.Chromatogram;default:return m.UE.Color}}function M(e){const t=e.columns.bySemTypeAll(s.SEMTYPE.MACROMOLECULE);let n=t.find((e=>{const t=e.getTag(s.TAGS.UNITS);return!!t&&-1!==t.indexOf("MSA")}))??null;return!n&&t.length>0&&(n=t[0]),n}},8607:(e,t,n)=>{"use strict";n.d(t,{g:()=>p,lh:()=>m});var s=n(976),r=n(6414),i=n.n(r),o=n(8447),a=n(6286),l=n(8260),c=n(708),u=n(7228),h=n(1047);const d=new class{constructor(){this.seqHandler="seq-handler",this.notationProvider="seq-handler.notation-provider"}},m={[o.r2.FASTA]:"-",[o.r2.SEPARATOR]:"",[o.r2.HELM]:"*"};class p{constructor(e){if(this._splitter=null,this.cached=!0,this._splitted=null,this.columnVersion=null,this._stats=null,this._maxLength=null,this._posList=null,this._joiner=void 0,e.type!==s.TYPE.STRING)throw new Error(`Unexpected column type '${e.type}', must be '${s.TYPE.STRING}'.`);this._column=e;const t=this._column.getTag(s.TAGS.UNITS);if(null==t)throw new Error("Units are not specified in column");if(this._units=t,this._notation=this.getNotation(),this._defaultGapOriginal=this.isFasta()?m[o.r2.FASTA]:this.isHelm()?m[o.r2.HELM]:m[o.r2.SEPARATOR],!this.column.tags.has("aligned")||!this.column.tags.has("alphabet")||!this.column.tags.has(".alphabetIsMultichar")&&!this.isHelm()&&"UN"===this.alphabet)if(this.isFasta())p.setUnitsToFastaColumn(this);else if(this.isSeparator()){const t=e.getTag("separator");p.setUnitsToSeparatorColumn(this,t)}else{if(!this.isHelm())throw new Error(`Unexpected units '${this.column.getTag(s.TAGS.UNITS)}'.`);p.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[d.notationProvider]??null,this.columnVersion=this.column.version}static setUnitsToFastaColumn(e){if(e.column.semType!==s.SEMTYPE.MACROMOLECULE||e.column.getTag(s.TAGS.UNITS)!==o.r2.FASTA)throw new Error(`The column of notation '${o.r2.FASTA}' must be '${s.SEMTYPE.MACROMOLECULE}'.`);e.column.setTag(s.TAGS.UNITS,o.r2.FASTA),p.setTags(e)}static setUnitsToSeparatorColumn(e,t){if(e.column.semType!==s.SEMTYPE.MACROMOLECULE||e.column.getTag(s.TAGS.UNITS)!==o.r2.SEPARATOR)throw new Error(`The column of notation '${o.r2.SEPARATOR}' must be '${s.SEMTYPE.MACROMOLECULE}'.`);if(!t)throw new Error(`The column of notation '${o.r2.SEPARATOR}' must have the separator tag.`);e.column.setTag(s.TAGS.UNITS,o.r2.SEPARATOR),e.column.setTag("separator",t),p.setTags(e)}static setUnitsToHelmColumn(e){if(e.column.semType!==s.SEMTYPE.MACROMOLECULE)throw new Error(`The column of notation '${o.r2.HELM}' must be '${s.SEMTYPE.MACROMOLECULE}'`);e.column.setTag(s.TAGS.UNITS,o.r2.HELM),p.setTags(e)}static setTags(e){const t=e.column.getTag(s.TAGS.UNITS);if([o.r2.FASTA,o.r2.SEPARATOR].includes(t)){if(!e.column.getTag("alphabet")&&0===Object.keys(e.stats.freq).length)throw new Error("Alphabet is empty and not annotated.");let t=e.column.getTag("aligned");null===t&&(t=e.stats.sameLength?"SEQ.MSA":"SEQ",e.column.setTag("aligned",t));let n=e.column.getTag("alphabet");if(null===n&&(n=(0,l.w4)(e.stats.freq,o.XS),e.column.setTag("alphabet",n)),"UN"===n){const t=Object.keys(e.stats.freq).length,n=Object.keys(e.stats.freq).some((e=>e.length>1));e.column.setTag(".alphabetSize",t.toString()),e.column.setTag(".alphabetIsMultichar",n?"true":"false")}}}get column(){return this._column}get length(){return this._column.length}get units(){return this._units}get notation(){return this._notation}get defaultGapOriginal(){return this._defaultGapOriginal}get separator(){const e=this.column.getTag("separator")??void 0;if(this.notation===o.r2.SEPARATOR&&void 0===e)throw new Error(`Separator is mandatory for column '${this.column.name}' of notation '${this.notation}'.`);return e}get aligned(){const e=this.column.getTag("aligned");if(!e&&(this.isFasta()||this.isSeparator()))throw new Error("Tag aligned not set");return e}get alphabet(){const e=this.column.getTag("alphabet");if(!e&&(this.isFasta()||this.isSeparator()))throw new Error("Tag alphabet not set");return e}get helmCompatible(){return this.column.getTag(".isHelmCompatible")}getAlphabetSize(){if(this.notation==o.r2.HELM||"UN"==this.alphabet){const e=this.column.getTag(".alphabetSize");let t;if(e)t=parseInt(e);else{const e=this.stats;t=Object.keys(e.freq).length}return t}switch(this.alphabet){case"PT":return 20;case"DNA":case"RNA":return 4;case"NT":return console.warn("Unexpected alphabet 'NT'."),4;default:throw new Error(`Unexpected alphabet '${this.alphabet}'.`)}}getAlphabetIsMultichar(){return this.notation===o.r2.HELM||"UN"===this.alphabet&&"true"===this.column.getTag(".alphabetIsMultichar")}getSplitted(e,t){if(this.cached&&void 0===t){this.column.version===this.columnVersion&&null!==this._splitted||(this.columnVersion=this.column.version,this._splitted=new Array(this.column.length));let t=this._splitted[e]?this._splitted[e].deref():void 0;if(!t){const n=this.column.get(e);t=this.splitter(n),this._splitted[e]=new WeakRef(t)}return t}{const n=this.column.get(e);return this.getSplitter(t)(n)}}get stats(){if(null===this._stats){const e={};let t=!0,n=null;const s=this.column.length;for(let r=0;r<s;++r){const s=this.getSplitted(r);null==n?n=s.length:s.length!==n&&(t=!1);for(const t of s.canonicals)t in e||(e[t]=0),e[t]+=1}this._stats={freq:e,sameLength:t}}return this._stats}get maxLength(){return null===this._maxLength&&(this._maxLength=0===this.column.length?0:Math.max(...i().count(0).take(this.column.length).map((e=>this.getSplitted(e).length)))),this._maxLength}get posList(){if(null===this._posList){const e=this.column.getTag(".positionNames");this._posList=e?e.split(o.CI).map((e=>e.trim())):i().count(1).take(this.maxLength).map((e=>e.toString())).toArray()}return this._posList}isFasta(){return this.notation===o.r2.FASTA}isSeparator(){return this.notation===o.r2.SEPARATOR}isHelm(){return this.notation===o.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(e){return!e||e===this._defaultGapOriginal}getNotation(){if(this.units.toLowerCase().startsWith(o.r2.FASTA))return o.r2.FASTA;if(this.units.toLowerCase().startsWith(o.r2.SEPARATOR))return o.r2.SEPARATOR;if(this.units.toLowerCase().startsWith(o.r2.HELM))return o.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(e,t,n,r){const i=this.column,a=e.toLowerCase()+"("+i.name+")",l=n??i.dataFrame.columns.getUnusedName(a),c=s.Column.fromList("string",l,r??new Array(this.column.length).fill(""));if(c.semType=s.SEMTYPE.MACROMOLECULE,c.setTag(s.TAGS.UNITS,e),e===o.r2.SEPARATOR){if(!t)throw new Error(`Notation '${o.r2.SEPARATOR}' requires separator value.`);c.setTag("separator",t)}c.setTag(s.TAGS.CELL_RENDERER,"sequence");const u=i.getTag("aligned");u&&c.setTag("aligned",u);let h=i.getTag("alphabet");h||this.notation!==o.r2.HELM||e===o.r2.HELM||(h="UN"),null!=h&&c.setTag("alphabet",h);let d=i.getTag(".alphabetSize");null!=h&&d&&c.setTag(".alphabetSize",d);const m=i.getTag(".alphabetIsMultichar");return null!=h&&void 0!==m&&c.setTag(".alphabetIsMultichar",m),e==o.r2.HELM&&(d=this.getAlphabetSize().toString(),c.setTag(".alphabetSize",d)),c}getNewColumnFromList(e,t){return this.getNewColumn(this.notation,this.separator,e,t)}static getNewColumn(e){const t=p.forColumn(e),n=t.notation;return t.getNewColumn(n)}static unitsStringIsValid(e){return e=e.toLowerCase(),[o.r2.FASTA,o.r2.SEPARATOR,o.r2.HELM].some((t=>e.startsWith(t.toLowerCase())))}static getNewColumnFromParams(e,t,n){if(!p.unitsStringIsValid(n))throw new Error("Invalid format of 'units' parameter");const r=s.Column.fromList("string",t,new Array(e).fill(""));return r.semType=s.SEMTYPE.MACROMOLECULE,r.setTag(s.TAGS.UNITS,n),r}getSplitter(e){let t=null;if(t=this.notationProvider?this.notationProvider.splitter:null,t)return t;if(this.units.toLowerCase().startsWith(o.r2.FASTA))return null===this.column.getTag("alphabet")||this.getAlphabetIsMultichar()?o.kB:l.FJ;if(this.units.toLowerCase().startsWith(o.r2.SEPARATOR))return(0,o.Ar)(this.separator,e);if(this.units.toLowerCase().startsWith(o.r2.HELM))return o.gP;throw new Error(`Unexpected units ${this.units} .`)}split(e){return this.splitter(e)}getDistanceFunctionName(){if(!this.isFasta())throw new Error("Only FASTA notation is supported");return this.isMsa()?c.U.HAMMING:(this.alphabet,c.U.LEVENSHTEIN)}getDistanceFunction(){return c.o[this.getDistanceFunctionName()]()}async checkHelmCompatibility(){if(this.column.tags.has(".isHelmCompatible"))return"true"===this.column.getTag(".isHelmCompatible");const e=(await(0,u.JN)()).getBioLib().getMonomerSymbolsByType("PEPTIDE"),t=new Set(e),n=((0,o.Ar)(this.separator),new Set),s=this.column.length,r=this.column.getRawData();for(let e=0;e<s;++e){const s=r[e];if(!(s in n)){n.add(s);const r=this.getSplitted(e);for(const e of r.canonicals)if(!t.has(e))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(e){return e===o.r2.FASTA}toSeparator(e){return e===o.r2.SEPARATOR}toHelm(e){return e===o.r2.HELM}convertHelmToFastaSeparator(e,t,n,s){s||(s=this.toFasta(t)?m[o.r2.FASTA]:m[o.r2.SEPARATOR]),n||(n=this.toFasta(t)?"":this.separator);const r=e.startsWith("RNA"),i=this.splitter(e),a=[];for(let e=0;e<i.length;++e){let n=i.getOriginal(e);if(r&&(n=n.replace(h.pU,"")),n===m[o.r2.HELM])a.push(s);else if(this.toFasta(t)&&n.length>1){const e="["+n+"]";a.push(e)}else a.push(n)}return a.join(n)}convert(e,t){const n=this.getJoiner({notation:e,separator:t}),s=this.getNewColumn(e,t);return s.init((e=>{const t=this.getSplitted(e);return n(t)})),s}getRegion(e,t,n){const s=this.getNewColumn(this.notation,this.separator);s.name=n;const r=e??0,i=t??this.maxLength-1,a=this.getJoiner(),c=i-r+1,u=m[this.notation];s.init((e=>{const t=this.getSplitted(e),n=new Array(c);for(let e=0;e<c;++e){const s=r+e;n[e]=s<t.length?t.getOriginal(s):u}return a(new l.wx(n,u))}));const h=e=>{const t=e.split(",").map((e=>e.trim())),n=new Array(c);for(let e=0;e<c;++e){const s=r+e;n[e]=s<t.length?t[s]:"?"}return n.join(o.CI)},d=this.column.getTag(".positionNames");d&&s.setTag(".positionNames",h(d));const p=this.column.getTag(".positionLabels");return p&&s.setTag(".positionLabels",h(p)),s}get joiner(){return this._joiner||(this._joiner=this.getJoiner()),this._joiner}getJoiner(e){const t=e?e.notation:this.notation,n=e?e.separator:this.separator;let s;const r=this;switch(t){case o.r2.FASTA:s=function(e){return r.joinToFasta(e,r.isHelm())};break;case o.r2.SEPARATOR:if(!n)throw new Error(`Separator is mandatory for notation '${t}'.`);s=function(e){return f(e,n,r.isHelm())};break;case o.r2.HELM:{const 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this.joinToFasta(n,this.isHelm())}convertToSeparator(e,t){return f(this.isHelm()?this.splitterAsHelmNucl(e):this.splitter(e),t,this.isHelm())}convertToHelm(e){const t=this.getHelmWrappers(),n=e.startsWith("DNA")||e.startsWith("RNA");return g(this.splitter(e),t,n)}splitterAsHelmNucl(e){const t=this.splitter(e),n=new Array(t.length),s=e.startsWith("DNA"),r=e.startsWith("RNA");for(let e=0;e<t.length;++e){let i=t.getOriginal(e);(s||r)&&(i=i.replace(h.pU,"$1"),i=i===h.$3?null:i),n[e]=i||null}return new l.wx(n.filter((e=>!!e)),m[o.r2.HELM])}}function f(e,t,n){const s=new Array(e.length);for(let t=0;t<e.length;++t){const r=e.getCanonical(t);let i=e.getOriginal(t);n&&(i=i.replace(h.pU,"$1")),r===a.G2?i=m[o.r2.SEPARATOR]:r===h.$3&&(i=""),s[t]=i}return s.join(t)}function g(e,t,n){const[s,r,i,l]=t,c=new Array(e.length);for(let t=0;t<e.length;++t){const s=e.getCanonical(t);let 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var bio_test;(()=>{var e={2012:(e,t,n)=>{"use strict";n.d(t,{f:()=>r});var s=n(9976);class r extends s.B{static get Lesk(){return void 0===this.lesk&&(this.lesk=this.makePalette([[["G","A","S","T"],"orange"],[["C","V","I","L","P","F","Y","M","W"],"all_green"],[["N","Q","H"],"magenta"],[["D","E"],"red"],[["K","R"],"all_blue"]],!1,r)),this.lesk}static get GrokGroups(){return void 0===this.grokGroups&&(this.grokGroups=this.makePalette([[["C","U"],"yellow"],[["G","P"],"red"],[["A","V","I","L","M","F","Y","W"],"all_green"],[["R","H","K"],"light_blue"],[["D","E"],"dark_blue"],[["S","T","N","Q"],"orange"]],!1,r)),this.grokGroups}static get RasMol(){return void 0===this.rasMol&&(this.rasMol=new r({D:"#E60A0A",E:"#E60A0A",C:"#E6E600",M:"#E6E600",K:"#145AFF",R:"#145AFF",S:"#FA9600",T:"#FA9600",F:"#3232AA",Y:"#3232AA",N:"#00DCDC",Q:"#00DCDC",G:"#EBEBEB",L:"#0F820F",V:"#0F820F",I:"#0F820F",A:"#C8C8C8",W:"#B45AB4",H:"#8282D2",P:"#DC9682",others:"#BEA06E"})),this.rasMol}get(e){const t=e in r.aaSynonyms?r.aaSynonyms[e]:e;return super.get(t)}}r.aaSynonyms={MeNle:"L",MeA:"A",MeG:"G",MeF:"F"};class i{static getPalette(e="grok"){switch(e){case"grok":return r.GrokGroups;case"lesk":return r.Lesk;default:throw new Error(`ChemPalette: scheme \`${e}\` does not exist`)}}static getInnerOuter(e){let t=0,n="",s="";for(const r of e)"("==r?t++:")"==r?t--:t?n+=r:s+=r;return isNaN(parseInt(n))?[s,n]:[s,""]}static getColorAAPivot(e="",t="grok"){const n=this.getPalette(t);let[s,r]=this.getInnerOuter(e);if(s=s.length>6?`${s.slice(0,3)}...`:s,r=r.length>6?`${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,s,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,s,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 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t=s.Color.fromHtml(e),n=s.Color.g(t),r=s.Color.r(t),i=s.Color.b(t),o=Math.sqrt(Math.pow(0-r,2)+Math.pow(0-n,2)+Math.pow(0-i,2));return o>210?`rgb(${r/o*210},${n/o*210},${i/o*210})`:s.Color.toRgb(t)}(l.palette[t])}}l.palette=l.buildPalette();class c extends r.B{static get Gray(){return void 0===this.gray&&(this.gray=new a),this.gray}static get Color(){return void 0===this.color&&(this.color=new l),this.color}}},9713:(e,t,n)=>{"use strict";n.d(t,{N:()=>o,b:()=>a});var s=n(4469),r=n(701),i=n(2997);function o(e){let t=null,n=null;try{n=e.dart?e.gridColumn:null,t=n?n.temp:null}catch{[n,t]=[null,null]}const s=e.cell.column;if(t=t??s.temp,!t)throw new Error("Grid cell renderer back store (GridColumn or Column) not found.");return[n,s,t]}class a{constructor(e,t,n){this.gridCol=e,this.tableCol=t,this.logger=n,this.subs=[],this.destroyed=!1,this.viewerId=++a.viewerCounter,this.errors=[],this._onRendered=new r.Subject,this.reset(),this.tableCol&&this.tableCol.dataFrame&&this.subs.push(this.tableCol.dataFrame.onDataChanged.subscribe((()=>{try{this.reset()}catch(e){this.logger.error(e)}}))),this.tableCol&&this.subs.push(s.events.onTableRemoved.subscribe((e=>{try{const t=e.args.dataFrame;this.tableCol?.dataFrame.id!==t.id||this.destroyed||this.destroy()}catch(e){this.logger.error(e)}}))),this.gridCol&&this.subs.push(s.events.onViewRemoving.subscribe((e=>{try{const t=e.args.view;this.gridCol?.dart&&this.gridCol.grid&&this.gridCol?.grid?.dart&&this.gridCol?.grid?.view?.id===t.id&&!this.destroyed&&this.destroy()}catch(e){this.logger.error(e)}})))}toLog(){return`${this.constructor.name}<${this.viewerId}>`}destroy(){for(const e of this.subs)e.unsubscribe();this.destroyed=!0}invalidateGrid(){this.gridCol&&this.gridCol.dart&&this.gridCol.grid?.invalidate()}get onRendered(){return this._onRendered}invalidate(e){this.invalidateGrid()}async awaitRendered(e=1e4,t=`${e} timeout`){const n=`${this.toLog()}.awaitRendered()`;if(this.logger.debug(`${n}, start, testEvent before`),await(0,i.zg)(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`)}}a.viewerCounter=-1},9611:(e,t,n)=>{"use strict";n.d(t,{A:()=>u,m:()=>c});var s=n(976),r=n(6414),i=n.n(r),o=n(8607),a=n(9713),l=n(7228);function c(e,t){let n,s=100,r=0,i=e.length-1;for(;r<=i;){if(n=Math.floor((i+r)/2),e[n]<=t&&t<e[n+1])return n;if(t<e[n]?i=n-1:r=n+1,--s<=0)throw new Error(`Get position for pointer x = ${t} searching has not converged on ${JSON.stringify(e)}. `)}return null}class u extends a.b{get updated(){return this._updated}constructor(e,t,n,r){super(e,t,n),this.propsProvider=r,this.colWidth=0,this._monomerLengthList=null,this.separatorWidth=5,this._processedMaxVisibleSeqLength=0,this._updated=!1,this._monomerLengthMap={},this._monomerStructureMap={},this.props=this.propsProvider(),this._processedRows=s.BitSet.create(this.tableCol.length),this.gridCol&&this.subs.push(this.gridCol.grid.onAfterDrawContent.subscribe((()=>{this._onRendered.next()}))),(0,l.JN)().then((e=>{if(this.destroyed)return;const t=e.getBioLib();this.subs.push(t.onChanged.subscribe((()=>{this.reset(),this.gridCol?.grid?.invalidate()})))}))}reset(){this.propsProvider&&(this.props=this.propsProvider()),this._processedRows=s.BitSet.create(this.tableCol.length),this._monomerLengthList=null,this._monomerLengthMap={},this._monomerStructureMap={}}getCellMonomerLengths(e,t){this.colWidth<t&&(this.colWidth=t,this.reset());const n=this.props.seqHandler.isMsa()?this.getCellMonomerLengthsForSeqMsa():this.getCellMonomerLengthsForSeq(e),s=new Array(n.length+1);s[0]=5;for(let e=1;e<s.length;e++)s[e]=s[e-1]+n[e-1];return[n,s]}getCellMonomerLengthsForSeq(e){null===this._monomerLengthList&&(this._monomerLengthList=new Array(this.tableCol.length).fill(null),this._updated=!0);const t=this.props.separatorWidth+1*this.props.monomerCharWidth,n=Math.ceil(this.colWidth/t),s=o.g.forColumn(this.tableCol).getSplitted(e).originals,r=Math.min(n,s.length);let i=this._monomerLengthList[e];if(null===i||i.length<r){i=this._monomerLengthList[e]=new Array(s.length);let t=0;for(let e=0;e<r;++e){const n=s[e],r=this.props.monomerToShort(n,this.props.monomerLengthLimit),o=(this.props.seqHandler.isSeparator()?this.separatorWidth:this.props.separatorWidth)+r.length*this.props.monomerCharWidth;if(i[e]=o,t+=o,t>this.colWidth)break}this._updated=!0}return i}getCellMonomerLengthsForSeqMsa(){var e;null===this._monomerLengthList&&(this._monomerLengthList=new Array(1).fill(null),this._updated=!0),(e=this._monomerLengthList)[0]??(e[0]=new Array(0));const t=this._monomerLengthList[0],{startIdx:n,endIdx:s}=(()=>{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.monomerCharWidth,i=Math.ceil(this.colWidth/r);for(let e=n;e<s;e++){if(this._processedRows.get(e)&&i<=this._processedMaxVisibleSeqLength)continue;const n=o.g.forColumn(this.tableCol).getSplitted(e,i).originals,s=Math.min(i,n.length);s>t.length&&t.push(...new Array(s-t.length).fill(r));let a=0;for(let e=0;e<s;++e){const s=n[e],r=this.props.monomerToShort(s,this.props.monomerLengthLimit),i=this.props.separatorWidth+r.length*this.props.monomerCharWidth;if(t[e]=Math.max(t[e]??0,i),a+=i,a>=this.colWidth)break}this._updated=!0,this._processedMaxVisibleSeqLength=Math.max(this._processedMaxVisibleSeqLength,i)}return t}getPosition(e,t,n){const[s,r]=this.getCellMonomerLengths(e,n),a=o.g.forColumn(this.tableCol);return 0===i()(a.getSplitted(e).originals).toArray().length?null:c(r,t)}setMonomerLengthLimit(e){this.props.monomerLengthLimit=e,this._updated=!0}setSeparatorWidth(e){this.props.separatorWidth=e,this._updated=!0}isMsa(){return this.props.seqHandler.isMsa()}}},1047:(e,t,n)=>{"use strict";n.d(t,{$3:()=>r,pU:()=>i,rx:()=>s});const s=["symbol","molfile","rgroups","name"],r="p",i=new RegExp(`[rd]\\((\\w)\\)${r}?`,"g")},7945:(e,t,n)=>{"use strict";function s(e){return"string"==typeof e||e instanceof String?e:"StateError"===e.constructor.name?e.message:"StateError"===e.constructor.name&&"$thrownJsError"in e?s(e.$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 i(e){return[s(e),r(e)]}n.d(t,{yf:()=>i})},5226:(e,t,n)=>{"use strict";n.d(t,{i:()=>o});var s=n(976),r=n(8607),i=n(1821);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 s=this._fileContent.substring(t.index+1,e.lastIndex);this._descriptionsArray.push(s),0!==n&&this._sequencesArray.push(this.parseMacromolecule(n,t.index)),n=e.lastIndex+1}this._sequencesArray.push(this.parseMacromolecule(n,-1))}importFasta(){const e=s.Column.fromStrings("description",this.descriptionsArray),t=s.Column.fromStrings("sequence",this.sequencesArray);return t.semType=s.SEMTYPE.MACROMOLECULE,t.setTag(s.TAGS.UNITS,i.r2.FASTA),r.g.forColumn(t),[s.DataFrame.fromColumns([e,t])]}constructor(e){this._descriptionsArray=[],this._sequencesArray=[],this._fileContent=e,this.parseColumns()}}},706:(e,t,n)=>{"use strict";n.d(t,{Ug:()=>i,io:()=>o});var s=n(976),r=n(8447);function i(){const e=[];return e.push(s.Column.fromList("string","MSA",new Array(10**6).fill("meI/hHis/Aca/N/T/dE/Thr_PO3H2/Aca/D-Tyr_Et/Tyr_ab-dehydroMe/dV/E/N/D-Orn/D-aThr//Phe_4Me"))),e.push(s.Column.fromList(s.COLUMN_TYPE.FLOAT,"Activity",new Array(10**6).fill(5.30751))),e}function o(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=s.Column.fromList(s.COLUMN_TYPE.STRING,"MSA",new Array(100).fill(t));n.semType=s.SEMTYPE.MACROMOLECULE,n.setTag(s.TAGS.UNITS,r.r2.SEPARATOR),n.setTag("separator","/"),n.setTag("alphabet","UN"),n.setTag(".alphabetIsMultichar","true");const i=[];return i.push(n),i.push(s.Column.fromList(s.COLUMN_TYPE.FLOAT,"Activity",new Array(100).fill(7.30751))),i}n(6414),n(8607),n(8260)},1821:(e,t,n)=>{"use strict";n.d(t,{BM:()=>o,CI:()=>i,XS:()=>l,r2:()=>s,se:()=>a});var s,r=n(6286);!function(e){e.FASTA="fasta",e.SEPARATOR="separator",e.HELM="helm"}(s||(s={}));const i=", ",o=/(?:\[([A-Za-z0-9_\-,()]+)\])|([A-Za-z\-])/g,a=new class{constructor(){this.fasta={peptide:new Set(["G","L","Y","S","E","Q","D","N","F","A","K","R","H","C","V","P","W","I","M","T"]),dna:new Set(["A","C","G","T"]),rna:new Set(["A","C","G","U"])}}},l=[new r.LA("PT",a.fasta.peptide,.5),new r.LA("DNA",a.fasta.dna,.55),new r.LA("RNA",a.fasta.rna,.55)]},8447:(e,t,n)=>{"use strict";n.d(t,{Ar:()=>r.Ar,CI:()=>s.CI,GU:()=>r.GU,KX:()=>r.KX,XS:()=>s.XS,dQ:()=>r.dQ,gM:()=>r.gM,gP:()=>r.gP,kB:()=>r.kB,py:()=>r.py,r2:()=>s.r2,up:()=>r.up});var s=n(1821),r=n(8260)},6286:(e,t,n)=>{"use strict";n.d(t,{G2:()=>s,LA:()=>r,dJ:()=>i});const s="";class r{constructor(e,t,n){this.name=e,this.alphabet=t,this.cutoff=n}}class i extends r{constructor(e,t,n){super(e.name,e.alphabet,e.cutoff),this.freq=t,this.similarity=n}}},8260:(e,t,n)=>{"use strict";n.d(t,{wx:()=>p,w4:()=>P,gM:()=>_,KX:()=>x,py:()=>N,vU:()=>T,Ar:()=>b,jY:()=>g,GU:()=>E,dQ:()=>$,up:()=>M,kB:()=>y,FJ:()=>w,gP:()=>v});var s=n(976),r=n(6414),i=n.n(r),o=n(6286),a=n(1821),l=n(8607);class c extends Float32Array{}var u=n(850),h=n(2012),d=n(6137),m=n(7331);class p{get length(){return this.mList.length}get canonicals(){return this.mList}get originals(){return this.mList}isGap(e){return this.getOriginal(e)===this.gapOriginalMonomer}getCanonical(e){if(this.length<=e)throw new Error("Index out of bounds");return this.mList[e]}getOriginal(e){if(this.length<=e)throw new Error("Index out of bounds");return this.mList[e]}constructor(e,t){this.mList=e,this.gapOriginalMonomer=t}}class f{get length(){return this.seqS.length}get canonicals(){return this.seqS}get originals(){return this.seqS}isGap(e){return this.getOriginal(e)===l.lh[a.r2.FASTA]}getCanonical(e){if(this.length<=e)throw new Error("Index out of bounds");return this.isGap(e)?o.G2:this.seqS[e]}getOriginal(e){if(this.length<=e)throw new Error("Index out of bounds");return this.seqS[e]}constructor(e){this.seqS=e}}function g(e,t,n){const s=e.categories;return function(e,t){const n={};let s=!0,r=null;for(const i of e)if(null==r?r=i.length:i.length!==r&&(s=!1),i.length>=t)for(const e of i.canonicals)e in n||(n[e]=0),n[e]+=1;return{freq:n,sameLength:s}}(i().enumerate(e.getRawData()).map((([e,t])=>n(s[e]))),t)}const y=e=>{const t=i()(e.toString().matchAll(a.BM)).map((e=>e[2]??e[1])).toArray();return new p(t,l.lh[a.r2.FASTA])},w=e=>e?new f(e):new p([],l.lh[a.r2.FASTA]);function b(e,t=undefined){return n=>{if(n){let s;const r=new RegExp(String.raw`"-"|'-'|[^${e}]+`,"g");if(void 0!==t){r.lastIndex=0,s=new Array(Math.ceil(t));let e=null,i=0;for(;null!==(e=r.exec(n))&&i<t;)s[i++]=e[0].replace('"-"',"").replace("'-'","");s.splice(i)}else s=n.replaceAll('"-"',"").replaceAll("'-'","").split(e,t);return new p(s,l.lh[a.r2.SEPARATOR])}return new p([],l.lh[a.r2.SEPARATOR])}}const A=/(PEPTIDE1|DNA1|RNA1)\{([^}]+)}/g,C=/\[([^\[\]]+)]/g,v=e=>{A.lastIndex=0;const t=A.exec(e.toString()),n=t?t[2]:null,s=n?n.split("."):[];return new p(s.map((e=>{C.lastIndex=0;const t=C.exec(e);return t&&t.length>=2?t[1]:e})),l.lh[a.r2.HELM])};function T(e,t,n=undefined){if(e.toLowerCase().startsWith(a.r2.FASTA))return y;if(e.toLowerCase().startsWith(a.r2.SEPARATOR))return b(t,n);if(e.toLowerCase().startsWith(a.r2.HELM))return v;throw new Error(`Unexpected units ${e} .`)}const S=/([^\W_]+)/g;function E(e,t){if(e.length<=t)return e;const n=e.match(S),s=e.length>t||(n?.length??0)>1,r=n?.[0]??" ";return s?r.substring(0,t-1)+"…":r}function _(e){switch(e){case"DNA":return a.se.fasta.dna;case"RNA":return a.se.fasta.rna;case"PT":return a.se.fasta.peptide;default:throw new Error(`Unsupported alphabet '${e}'.`)}}function x(e,t,n="-"){const s=new Set([...new Set(Object.keys(e)),...t]);s.delete(n);const r=[],i=[];for(const n of s)r.push(n in e?e[n]:0),i.push(t.has(n)?1:0);const o=new c(r),a=new c(i);return(0,u.MA)(o,a)/((0,u.$G)(o)*(0,u.$G)(a))}function P(e,t,n="-"){const s=t.map((t=>{const s=x(e,t.alphabet,n);return new o.dJ(t,e,s)}));let r;const i=Math.max(...s.map((e=>e.similarity>e.cutoff?e.similarity:-1)));return r=i>0?s.find((e=>e.similarity===i)).name:"UN",r}function $(e,t=5){let n;return n=e.semType==s.SEMTYPE.MACROMOLECULE?l.g.forColumn(e).alphabet:P(g(e,t,y).freq,a.XS),N(n)}function N(e){switch(e){case"PT":return h.f.GrokGroups;case"DNA":case"RNA":return d.J.Chromatogram;default:return m.UE.Color}}function M(e){const t=e.columns.bySemTypeAll(s.SEMTYPE.MACROMOLECULE);let n=t.find((e=>{const t=e.getTag(s.TAGS.UNITS);return!!t&&-1!==t.indexOf("MSA")}))??null;return!n&&t.length>0&&(n=t[0]),n}},8607:(e,t,n)=>{"use strict";n.d(t,{g:()=>p,lh:()=>m});var s=n(976),r=n(6414),i=n.n(r),o=n(8447),a=n(6286),l=n(8260),c=n(708),u=n(7228),h=n(1047);const d=new class{constructor(){this.seqHandler="seq-handler",this.notationProvider="seq-handler.notation-provider"}},m={[o.r2.FASTA]:"-",[o.r2.SEPARATOR]:"",[o.r2.HELM]:"*"};class p{constructor(e){if(this._splitter=null,this.cached=!0,this._splitted=null,this.columnVersion=null,this._stats=null,this._maxLength=null,this._posList=null,this._joiner=void 0,e.type!==s.TYPE.STRING)throw new Error(`Unexpected column type '${e.type}', must be '${s.TYPE.STRING}'.`);this._column=e;const t=this._column.getTag(s.TAGS.UNITS);if(null==t)throw new Error("Units are not specified in column");if(this._units=t,this._notation=this.getNotation(),this._defaultGapOriginal=this.isFasta()?m[o.r2.FASTA]:this.isHelm()?m[o.r2.HELM]:m[o.r2.SEPARATOR],!this.column.tags.has("aligned")||!this.column.tags.has("alphabet")||!this.column.tags.has(".alphabetIsMultichar")&&!this.isHelm()&&"UN"===this.alphabet)if(this.isFasta())p.setUnitsToFastaColumn(this);else if(this.isSeparator()){const t=e.getTag("separator");p.setUnitsToSeparatorColumn(this,t)}else{if(!this.isHelm())throw new Error(`Unexpected units '${this.column.getTag(s.TAGS.UNITS)}'.`);p.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[d.notationProvider]??null,this.columnVersion=this.column.version}static setUnitsToFastaColumn(e){if(e.column.semType!==s.SEMTYPE.MACROMOLECULE||e.column.getTag(s.TAGS.UNITS)!==o.r2.FASTA)throw new Error(`The column of notation '${o.r2.FASTA}' must be '${s.SEMTYPE.MACROMOLECULE}'.`);e.column.setTag(s.TAGS.UNITS,o.r2.FASTA),p.setTags(e)}static setUnitsToSeparatorColumn(e,t){if(e.column.semType!==s.SEMTYPE.MACROMOLECULE||e.column.getTag(s.TAGS.UNITS)!==o.r2.SEPARATOR)throw new Error(`The column of notation '${o.r2.SEPARATOR}' must be '${s.SEMTYPE.MACROMOLECULE}'.`);if(!t)throw new Error(`The column of notation '${o.r2.SEPARATOR}' must have the separator tag.`);e.column.setTag(s.TAGS.UNITS,o.r2.SEPARATOR),e.column.setTag("separator",t),p.setTags(e)}static setUnitsToHelmColumn(e){if(e.column.semType!==s.SEMTYPE.MACROMOLECULE)throw new Error(`The column of notation '${o.r2.HELM}' must be '${s.SEMTYPE.MACROMOLECULE}'`);e.column.setTag(s.TAGS.UNITS,o.r2.HELM),p.setTags(e)}static setTags(e){const t=e.column.getTag(s.TAGS.UNITS);if([o.r2.FASTA,o.r2.SEPARATOR].includes(t)){if(!e.column.getTag("alphabet")&&0===Object.keys(e.stats.freq).length)throw new Error("Alphabet is empty and not annotated.");let t=e.column.getTag("aligned");null===t&&(t=e.stats.sameLength?"SEQ.MSA":"SEQ",e.column.setTag("aligned",t));let n=e.column.getTag("alphabet");if(null===n&&(n=(0,l.w4)(e.stats.freq,o.XS),e.column.setTag("alphabet",n)),"UN"===n){const t=Object.keys(e.stats.freq).length,n=Object.keys(e.stats.freq).some((e=>e.length>1));e.column.setTag(".alphabetSize",t.toString()),e.column.setTag(".alphabetIsMultichar",n?"true":"false")}}}get column(){return this._column}get length(){return this._column.length}get units(){return this._units}get notation(){return this._notation}get defaultGapOriginal(){return this._defaultGapOriginal}get separator(){const e=this.column.getTag("separator")??void 0;if(this.notation===o.r2.SEPARATOR&&void 0===e)throw new Error(`Separator is mandatory for column '${this.column.name}' of notation '${this.notation}'.`);return e}get aligned(){const e=this.column.getTag("aligned");if(!e&&(this.isFasta()||this.isSeparator()))throw new Error("Tag aligned not set");return e}get alphabet(){const e=this.column.getTag("alphabet");if(!e&&(this.isFasta()||this.isSeparator()))throw new Error("Tag alphabet not set");return e}get helmCompatible(){return this.column.getTag(".isHelmCompatible")}getAlphabetSize(){if(this.notation==o.r2.HELM||"UN"==this.alphabet){const e=this.column.getTag(".alphabetSize");let t;if(e)t=parseInt(e);else{const e=this.stats;t=Object.keys(e.freq).length}return t}switch(this.alphabet){case"PT":return 20;case"DNA":case"RNA":return 4;case"NT":return console.warn("Unexpected alphabet 'NT'."),4;default:throw new Error(`Unexpected alphabet '${this.alphabet}'.`)}}getAlphabetIsMultichar(){return this.notation===o.r2.HELM||"UN"===this.alphabet&&"true"===this.column.getTag(".alphabetIsMultichar")}getSplitted(e,t){if(this.cached&&void 0===t){this.column.version===this.columnVersion&&null!==this._splitted||(this.columnVersion=this.column.version,this._splitted=new Array(this.column.length));let t=this._splitted[e]?this._splitted[e].deref():void 0;if(!t){const n=this.column.get(e);t=this.splitter(n),this._splitted[e]=new WeakRef(t)}return t}{const n=this.column.get(e);return this.getSplitter(t)(n)}}get stats(){if(null===this._stats){const e={};let t=!0,n=null;const s=this.column.length;for(let r=0;r<s;++r){const s=this.getSplitted(r);null==n?n=s.length:s.length!==n&&(t=!1);for(const t of s.canonicals)t in e||(e[t]=0),e[t]+=1}this._stats={freq:e,sameLength:t}}return this._stats}get maxLength(){return null===this._maxLength&&(this._maxLength=0===this.column.length?0:Math.max(...i().count(0).take(this.column.length).map((e=>this.getSplitted(e).length)))),this._maxLength}get posList(){if(null===this._posList){const e=this.column.getTag(".positionNames");this._posList=e?e.split(o.CI).map((e=>e.trim())):i().count(1).take(this.maxLength).map((e=>e.toString())).toArray()}return this._posList}isFasta(){return this.notation===o.r2.FASTA}isSeparator(){return this.notation===o.r2.SEPARATOR}isHelm(){return this.notation===o.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(e){return!e||e===this._defaultGapOriginal}getNotation(){if(this.units.toLowerCase().startsWith(o.r2.FASTA))return o.r2.FASTA;if(this.units.toLowerCase().startsWith(o.r2.SEPARATOR))return o.r2.SEPARATOR;if(this.units.toLowerCase().startsWith(o.r2.HELM))return o.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(e,t,n,r){const i=this.column,a=e.toLowerCase()+"("+i.name+")",l=n??i.dataFrame.columns.getUnusedName(a),c=s.Column.fromList("string",l,r??new Array(this.column.length).fill(""));if(c.semType=s.SEMTYPE.MACROMOLECULE,c.setTag(s.TAGS.UNITS,e),e===o.r2.SEPARATOR){if(!t)throw new Error(`Notation '${o.r2.SEPARATOR}' requires separator value.`);c.setTag("separator",t)}c.setTag(s.TAGS.CELL_RENDERER,"sequence");const u=i.getTag("aligned");u&&c.setTag("aligned",u);let h=i.getTag("alphabet");h||this.notation!==o.r2.HELM||e===o.r2.HELM||(h="UN"),null!=h&&c.setTag("alphabet",h);let d=i.getTag(".alphabetSize");null!=h&&d&&c.setTag(".alphabetSize",d);const m=i.getTag(".alphabetIsMultichar");return null!=h&&void 0!==m&&c.setTag(".alphabetIsMultichar",m),e==o.r2.HELM&&(d=this.getAlphabetSize().toString(),c.setTag(".alphabetSize",d)),c}getNewColumnFromList(e,t){return this.getNewColumn(this.notation,this.separator,e,t)}static getNewColumn(e){const t=p.forColumn(e),n=t.notation;return t.getNewColumn(n)}static unitsStringIsValid(e){return e=e.toLowerCase(),[o.r2.FASTA,o.r2.SEPARATOR,o.r2.HELM].some((t=>e.startsWith(t.toLowerCase())))}static getNewColumnFromParams(e,t,n){if(!p.unitsStringIsValid(n))throw new Error("Invalid format of 'units' parameter");const r=s.Column.fromList("string",t,new Array(e).fill(""));return r.semType=s.SEMTYPE.MACROMOLECULE,r.setTag(s.TAGS.UNITS,n),r}getSplitter(e){let t=null;if(t=this.notationProvider?this.notationProvider.splitter:null,t)return t;if(this.units.toLowerCase().startsWith(o.r2.FASTA))return null===this.column.getTag("alphabet")||this.getAlphabetIsMultichar()?o.kB:l.FJ;if(this.units.toLowerCase().startsWith(o.r2.SEPARATOR))return(0,o.Ar)(this.separator,e);if(this.units.toLowerCase().startsWith(o.r2.HELM))return o.gP;throw new Error(`Unexpected units ${this.units} .`)}split(e){return this.splitter(e)}getDistanceFunctionName(){if(!this.isFasta())throw new Error("Only FASTA notation is supported");return this.isMsa()?c.U.HAMMING:(this.alphabet,c.U.LEVENSHTEIN)}getDistanceFunction(){return c.o[this.getDistanceFunctionName()]()}async checkHelmCompatibility(){if(this.column.tags.has(".isHelmCompatible"))return"true"===this.column.getTag(".isHelmCompatible");const e=(await(0,u.JN)()).getBioLib().getMonomerSymbolsByType("PEPTIDE"),t=new Set(e),n=((0,o.Ar)(this.separator),new Set),s=this.column.length,r=this.column.getRawData();for(let e=0;e<s;++e){const s=r[e];if(!(s in n)){n.add(s);const r=this.getSplitted(e);for(const e of r.canonicals)if(!t.has(e))return 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r=e??0,i=t??this.maxLength-1,a=this.getJoiner(),c=i-r+1,u=m[this.notation];s.init((e=>{const t=this.getSplitted(e),n=new Array(c);for(let e=0;e<c;++e){const s=r+e;n[e]=s<t.length?t.getOriginal(s):u}return a(new l.wx(n,u))}));const h=e=>{const t=e.split(",").map((e=>e.trim())),n=new Array(c);for(let e=0;e<c;++e){const s=r+e;n[e]=s<t.length?t[s]:"?"}return n.join(o.CI)},d=this.column.getTag(".positionNames");d&&s.setTag(".positionNames",h(d));const p=this.column.getTag(".positionLabels");return p&&s.setTag(".positionLabels",h(p)),s}get joiner(){return this._joiner||(this._joiner=this.getJoiner()),this._joiner}getJoiner(e){const t=e?e.notation:this.notation,n=e?e.separator:this.separator;let s;const r=this;switch(t){case o.r2.FASTA:s=function(e){return r.joinToFasta(e,r.isHelm())};break;case o.r2.SEPARATOR:if(!n)throw new Error(`Separator is mandatory for notation '${t}'.`);s=function(e){return f(e,n,r.isHelm())};break;case o.r2.HELM:{const 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e={number:{type:"number",rules:[]},string:{type:"string",rules:[]},array:{type:"array",rules:[]},object:{type:"object",rules:[]}};return{types:{...e,integer:!0,boolean:!0,null:!0},rules:[{rules:[]},e.number,e.string,e.array,e.object],post:{rules:[]},all:{},keywords:{}}}},6776:(e,t,n)=>{"use strict";Object.defineProperty(t,"__esModule",{value:!0}),t.checkStrictMode=t.getErrorPath=t.Type=t.useFunc=t.setEvaluated=t.evaluatedPropsToName=t.mergeEvaluated=t.eachItem=t.unescapeJsonPointer=t.escapeJsonPointer=t.escapeFragment=t.unescapeFragment=t.schemaRefOrVal=t.schemaHasRulesButRef=t.schemaHasRules=t.checkUnknownRules=t.alwaysValidSchema=t.toHash=void 0;const s=n(3487),r=n(7023);function i(e,t=e.schema){const{opts:n,self:s}=e;if(!n.strictSchema)return;if("boolean"==typeof t)return;const r=s.RULES.keywords;for(const n in t)r[n]||p(e,`unknown keyword: "${n}"`)}function o(e,t){if("boolean"==typeof e)return!e;for(const n in e)if(t[n])return!0;return!1}function a(e){return"number"==typeof 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e)if("$ref"!==n&&t.all[n])return!0;return!1},t.schemaRefOrVal=function({topSchemaRef:e,schemaPath:t},n,r,i){if(!i){if("number"==typeof n||"boolean"==typeof n)return n;if("string"==typeof n)return s._`${n}`}return s._`${e}${t}${(0,s.getProperty)(r)}`},t.unescapeFragment=function(e){return l(decodeURIComponent(e))},t.escapeFragment=function(e){return encodeURIComponent(a(e))},t.escapeJsonPointer=a,t.unescapeJsonPointer=l,t.eachItem=function(e,t){if(Array.isArray(e))for(const n of e)t(n);else t(e)},t.mergeEvaluated={props:c({mergeNames:(e,t,n)=>e.if(s._`${n} !== true && ${t} !== undefined`,(()=>{e.if(s._`${t} === true`,(()=>e.assign(n,!0)),(()=>e.assign(n,s._`${n} || {}`).code(s._`Object.assign(${n}, ${t})`)))})),mergeToName:(e,t,n)=>e.if(s._`${n} !== true`,(()=>{!0===t?e.assign(n,!0):(e.assign(n,s._`${n} || {}`),h(e,n,t))})),mergeValues:(e,t)=>!0===e||{...e,...t},resultToName:u}),items:c({mergeNames:(e,t,n)=>e.if(s._`${n} !== true && ${t} !== undefined`,(()=>e.assign(n,s._`${t} === true 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0!==e[t.keyword]||(null===(n=t.definition.implements)||void 0===n?void 0:n.some((t=>void 0!==e[t])))}Object.defineProperty(t,"__esModule",{value:!0}),t.shouldUseRule=t.shouldUseGroup=t.schemaHasRulesForType=void 0,t.schemaHasRulesForType=function({schema:e,self:t},s){const r=t.RULES.types[s];return r&&!0!==r&&n(e,r)},t.shouldUseGroup=n,t.shouldUseRule=s},5667:(e,t,n)=>{"use strict";Object.defineProperty(t,"__esModule",{value:!0}),t.boolOrEmptySchema=t.topBoolOrEmptySchema=void 0;const s=n(4181),r=n(3487),i=n(2141),o={message:"boolean schema is false"};function a(e,t){const{gen:n,data:r}=e,i={gen:n,keyword:"false schema",data:r,schema:!1,schemaCode:!1,schemaValue:!1,params:{},it:e};(0,s.reportError)(i,o,void 0,t)}t.topBoolOrEmptySchema=function(e){const{gen:t,schema:n,validateName:s}=e;!1===n?a(e,!1):"object"==typeof n&&!0===n.$async?t.return(i.default.data):(t.assign(r._`${s}.errors`,null),t.return(!0))},t.boolOrEmptySchema=function(e,t){const{gen:n,schema:s}=e;!1===s?(n.var(t,!1),a(e)):n.var(t,!0)}},453:(e,t,n)=>{"use strict";Object.defineProperty(t,"__esModule",{value:!0}),t.reportTypeError=t.checkDataTypes=t.checkDataType=t.coerceAndCheckDataType=t.getJSONTypes=t.getSchemaTypes=t.DataType=void 0;const s=n(3141),r=n(8876),i=n(4181),o=n(3487),a=n(6776);var l;function c(e){const t=Array.isArray(e)?e:e?[e]:[];if(t.every(s.isJSONType))return t;throw new Error("type must be JSONType or JSONType[]: "+t.join(","))}!function(e){e[e.Correct=0]="Correct",e[e.Wrong=1]="Wrong"}(l=t.DataType||(t.DataType={})),t.getSchemaTypes=function(e){const t=c(e.type);if(t.includes("null")){if(!1===e.nullable)throw new Error("type: null contradicts nullable: false")}else{if(!t.length&&void 0!==e.nullable)throw new Error('"nullable" cannot be used without "type"');!0===e.nullable&&t.push("null")}return t},t.getJSONTypes=c,t.coerceAndCheckDataType=function(e,t){const{gen:n,data:s,opts:i}=e,a=function(e,t){return t?e.filter((e=>u.has(e)||"array"===t&&"array"===e)):[]}(t,i.coerceTypes),c=t.length>0&&!(0===a.length&&1===t.length&&(0,r.schemaHasRulesForType)(e,t[0]));if(c){const r=d(t,s,i.strictNumbers,l.Wrong);n.if(r,(()=>{a.length?function(e,t,n){const{gen:s,data:r,opts:i}=e,a=s.let("dataType",o._`typeof ${r}`),l=s.let("coerced",o._`undefined`);"array"===i.coerceTypes&&s.if(o._`${a} == 'object' && Array.isArray(${r}) && ${r}.length == 1`,(()=>s.assign(r,o._`${r}[0]`).assign(a,o._`typeof ${r}`).if(d(t,r,i.strictNumbers),(()=>s.assign(l,r))))),s.if(o._`${l} !== undefined`);for(const e of n)(u.has(e)||"array"===e&&"array"===i.coerceTypes)&&c(e);function c(e){switch(e){case"string":return void s.elseIf(o._`${a} == "number" || ${a} == "boolean"`).assign(l,o._`"" + ${r}`).elseIf(o._`${r} === null`).assign(l,o._`""`);case"number":return void s.elseIf(o._`${a} == "boolean" || ${r} === null
|
|
3
3
|
|| (${a} == "string" && ${r} && ${r} == +${r})`).assign(l,o._`+${r}`);case"integer":return void s.elseIf(o._`${a} === "boolean" || ${r} === null
|
|
4
4
|
|| (${a} === "string" && ${r} && ${r} == +${r} && !(${r} % 1))`).assign(l,o._`+${r}`);case"boolean":return void s.elseIf(o._`${r} === "false" || ${r} === 0 || ${r} === null`).assign(l,!1).elseIf(o._`${r} === "true" || ${r} === 1`).assign(l,!0);case"null":return s.elseIf(o._`${r} === "" || ${r} === 0 || ${r} === false`),void s.assign(l,null);case"array":s.elseIf(o._`${a} === "string" || ${a} === "number"
|
|
5
5
|
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