@datagrok/bio 2.13.5 → 2.13.6

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Files changed (6) hide show
  1. package/CHANGELOG.md +4 -0
  2. package/dist/package-test.js +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-test.js CHANGED
@@ -1,4 +1,4 @@
1
- var bio_test;(()=>{var e={8924:(e,t,n)=>{"use strict";n.d(t,{X:()=>s});var r=n(7362);class s extends r.e{static get Lesk(){return void 0===this.lesk&&(this.lesk=this.makePalette([[["G","A","S","T"],"orange"],[["C","V","I","L","P","F","Y","M","W"],"all_green"],[["N","Q","H"],"magenta"],[["D","E"],"red"],[["K","R"],"all_blue"]],!1,s)),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,s)),this.grokGroups}static get RasMol(){return void 0===this.rasMol&&(this.rasMol=new s({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 s.aaSynonyms?s.aaSynonyms[e]:e;return super.get(t)}}s.aaSynonyms={MeNle:"L",MeA:"A",MeG:"G",MeF:"F"};class o{static getPalette(e="grok"){switch(e){case"grok":return s.GrokGroups;case"lesk":return s.Lesk;default:throw new Error(`ChemPalette: scheme \`${e}\` does not exist`)}}static getInnerOuter(e){let t=0,n="",r="";for(const s of e)"("==s?t++:")"==s?t--:t?n+=s:r+=s;return isNaN(parseInt(n))?[r,n]:[r,""]}static getColorAAPivot(e="",t="grok"){const n=this.getPalette(t);let[r,s]=this.getInnerOuter(e);if(r=r.length>6?`${r.slice(0,3)}...`:r,s=s.length>6?`${s.slice(0,3)}...`:s,1==e.length||"("==e[1]){const t=e[0]?.toUpperCase();return t in n?[n.get(t),t,s,1]:[this.undefinedColor,r,s,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,s,2]:[this.undefinedColor,r,s,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,s,3]:[this.undefinedColor,r,s,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,s,4]:[this.undefinedColor,r,s,4]}return[this.undefinedColor,r,s,0]}}o.SemType="Aminoacids",o.SemTypeMultipleAlignment="AminoacidsMultipleAlignment",o.undefinedColor="rgb(100,100,100)",o.Names={G:"Glycine",L:"Leucine",Y:"Tyrosine",S:"Serine",E:"Glutamic acid",Q:"Glutamine",D:"Aspartic acid",N:"Asparagine",F:"Phenylalanine",A:"Alanine",K:"Lysine",R:"Arginine",H:"Histidine",C:"Cysteine",V:"Valine",P:"Proline",W:"Tryptophan",I:"Isoleucine",M:"Methionine",T:"Threonine"},o.AASmiles={G:"NCC(=O)O",L:"N[C@H](CC(C)C)C(=O)O",Y:"NC(CC1=CC=C(O)C=C1)C(=O)O",S:"NC(CO)C(=O)O",E:"N[C@@H](CCC(O)=O)C(=O)O",Q:"N[C@@H](CCC(N)=O)C(=O)O",D:"N[C@@H](CC(O)=O)C(=O)O",N:"N[C@@H](CC(N)=O)C(=O)O",F:"NC(CC1=CC=CC=C1)C(=O)O",A:"N[C@H](C)C(=O)O",K:"NC(CCCCN)C(=O)O",R:"N[C@H](CCCNC(=N)C)C(=O)O",H:"NC(CC1=CN=C[N]1)C(=O)O",C:"N[C@@H](CS)C(=O)O",V:"NC(C(C)C)C(=O)O",P:"N(CCC1)C1C(=O)O",W:"N[C@@H](Cc1c2ccccc2n([H])c1)C(=O)O",I:"N[C@H]([C@H](C)CC)C(=O)O",M:"NC(CCSC)C(=O)O",T:"NC(C(O)C)C(=O)O"},o.AASmilesTruncated={G:"*C*",L:"CC(C)C[C@H](*)*",Y:"C1=CC(=CC=C1CC(*)*)O",S:"OCC(*)C*",E:"*[C@@H](CCC(O)=O)*",Q:"*N[C@@H](CCC(N)=O)*",D:"*[C@@H](CC(O)=O)*",N:"*[C@@H](CC(N)=O)*",F:"C1=CC=C(C=C1)CC(*)*",A:"C[C@H](*)*",K:"C(CCN)CC(*)*",R:"*[C@H](CCCNC(=N)C)*",H:"C1=C(NC=N1)CC(*)*",C:"C([C@@H](*)*)S",V:"CC(C)C(*)*",P:"C1CCN(*)C1*",W:"*[C@@H](Cc1c2ccccc2n([H])c1)*",I:"CC[C@H](C)[C@H](*)*",M:"CSCCC(*)*",T:"CC(O)C(*)*"},o.AAFullNames={Ala:"A",Arg:"R",Asn:"N",Asp:"D",Cys:"C",Gln:"Q",Glu:"E",Gly:"G",His:"H",Ile:"I",Leu:"L",Lys:"K",Met:"M",Phe:"F",Pro:"P",Ser:"S",Thr:"T",Trp:"W",Tyr:"Y",Val:"V"}},9124:(e,t,n)=>{"use strict";n.d(t,{b:()=>o});var r=n(7389),s=n(6082);async function o(){const e="Helm",t=s.Func.find({package:e,name:"getHelmHelper"});if(0===t.length)throw new Error(`Package '${e}' must be installed for HelmHelper.`);return(await t[0].prepare().call()).getOutputParamValue()}r.input.helmAsync=async function(e,t){return(await o()).createHelmInput(e,t)}},4356:(e,t,n)=>{"use strict";n.d(t,{Eu:()=>l,so:()=>o,ub:()=>c,yZ:()=>u});var r=n(4328);const s="Libraries",o="System:AppData/Bio/monomer-libraries/",a={explicit:["HELMCoreLibrary.json"],exclude:[]};let i=Promise.resolve();async function c(){let e;return i=i.then((async()=>{const t=await r.dapi.userDataStorage.getValue(s,"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${JSON.stringify(e,void 0,2)}`)})),await i,e}async function l(e){i=i.then((async()=>{console.debug(`Bio: setUserLibSettings()\n${JSON.stringify(e,void 0,2)}`),await r.dapi.userDataStorage.postValue(s,"Settings",JSON.stringify(e),!0)})),await i}async function u(){await l(a)}},6718:(e,t,n)=>{"use strict";n.d(t,{A7:()=>d,pj:()=>c,uL:()=>l});var r=n(6082),s=n(4328),o=n(6295),a=(n(3151),n(2738)),i=(n(826),n(3077));async function c(){const e=r.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 r.Column&&(e=(0,i.R)(e).columns.toList());const n=(await c()).getBioLib(),o=new Array(e.length),l=e[0].length,u=new Float32Array(l);for(let i=0;i<e.length;++i){const c=i<t.length?t.getCanonical(i):a._S,d=n.getMonomer("PEPTIDE",c)?.smiles??"",h=e[i],m=h.getRawData(),p=h.categories,f=p.indexOf("");if(o[i]={categories:p,data:m,emptyIndex:f},void 0===c)continue;const g=r.Column.fromStrings("smiles",p.map((e=>n.getMonomer("PEPTIDE",e)?.smiles??""))),y=(r.DataFrame.fromColumns([g]),await s.chem.getSimilarities(g,d)),w=y?y.getRawData():null;for(let e=0;e<l;++e){const t=m[e];c!==a._S&&t!==f?u[e]+=w[t]:c===a._S&&t===f&&(u[e]+=1)}}for(let n=0;n<u.length;++n){let s=u[n]/t.length;for(let a=0;a<e.length;++a){const e=o[a];if(a>=t.length&&e.data[n]!==e.emptyIndex||e.data[n]===e.emptyIndex&&a<t.length){s=r.FLOAT_NULL;break}}u[n]=s}return r.Column.fromFloat32Array("Similarity",u)}async function u(e){const t=(await c()).getBioLib(),n=[],o={},a=e.map((e=>t.getMonomer("PEPTIDE",e)?.smiles??"")),i=r.Column.fromStrings("smiles",a);for(let t=0;t<a.length;++t){o[e[t]]=t;const r=a[t],c=""===r?new Array(a.length).fill(0):(await s.chem.getSimilarities(i,r)).getRawData();c[t]=1,n[t]=Array.from(c)}return{scoringMatrix:n,alphabetIndexes:o}}async function d(e,t="Morgan"){const n=(await c()).getBioLib(),s=new Array(e.length).fill(0).map((()=>new Array(e.length).fill(0))),a={},i=e.map((e=>n.getMonomer("PEPTIDE",e)?.smiles??"")),l=r.Func.find({package:"Chem",name:"getFingerprints"})[0];if(!l)return console.warn('Function "Chem:getFingerprints" is not found in chem package. falling back to Morgan fingerprints'),await u(e);const d=r.Column.fromStrings("smiles",i),h=(r.DataFrame.fromColumns([d]),(await l.apply({col:d,fingerprintType:t}))?.entries);if(!h)return console.warn(`${t} Fingerprints could not be calculated for monomers from chem package.\n falling back to Morgan fingerprints`),await u(e);for(let t=0;t<h.length;++t)if(s[t][t]=1,a[e[t]]=t,h[t])for(let e=t+1;e<h.length;++e)h[e]&&(s[t][e]=s[e][t]=(0,o.$1)(h[t],h[e]));return{scoringMatrix:s,alphabetIndexes:a}}},7384:(e,t,n)=>{"use strict";n.d(t,{C4:()=>h});var r=n(4328),s=n(6082),o=n(1991),a=n.n(o),i=n(439),c=n(826);const l={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(3151);function d(e){return Math.round(l.PRECISION_FACTOR*e)/l.PRECISION_FACTOR}async function h(e,t,o){if(0===s.Func.find({package:"Chem",name:"getRdKitModule"}).length)return{col:null,warnings:['Transformation to atomic level requires the package "Chem" installed.']};if(t.semType!==s.SEMTYPE.MACROMOLECULE)return{col:null,warnings:[`Only the ${s.SEMTYPE.MACROMOLECULE} columns can be converted to atomic level, the chosen column has semType '${t.semType}'`]};let d=t;const h=c.GO.forColumn(t);h.isHelm()&&(d=h.convert(i.Hi.SEPARATOR,"."),d.name=t.name);const p=c.GO.forColumn(d).alphabet;let f;if(p===i.YI.PT||p===i.YI.UN)f="PEPTIDE";else{if(p!==i.YI.RNA&&p!==i.YI.DNA)return{col:null,warnings:[`Unexpected column's '${d.name}' alphabet '${p}'.`]};f="RNA"}const g=function(e){const t=e.length,n=new Array(t),s=c.GO.forColumn(e);let o=!1;for(let e=0;e<t;++e){const t=s.getSplitted(e);o||(o=0===t.length),n[e]=a()(t.canonicals).filter((e=>!s.isGap(e))).map((e=>e)).toArray()}return o&&r.shell.warning(`Some values in the "${e.name}" column are empty`),n}(d),y=await async function(e,t,n,s){const o=function(e,t,n){const r=new Map;for(const s of e.getMonomerSymbolsByType(t)){const o=e.getMonomer(t,s);if("RNA"===t&&("Branch"===o.monomerType||n===i.YI.DNA&&o.symbol===l.DEOXYRIBOSE||n===i.YI.RNA&&o.symbol===l.RIBOSE||o.symbol===l.PHOSPHATE)||"PEPTIDE"===t&&"Branch"!==o.monomerType){const e={};u.f6.forEach((t=>{e[t]=o[t]})),r.set(o.symbol,e)}}return r}(t,n,s),a=new Map,c=await r.functions.call("Chem:getRdKitModule"),d={value:null};if("RNA"===n){const e=s===i.YI.RNA?[l.RIBOSE,l.PHOSPHATE]:[l.DEOXYRIBOSE,l.PHOSPHATE];for(const t of e)m(a,t,o,c,n,d)}for(let t=0;t<e.length;++t){const r=e[t];for(const e of r)if(""!==e)try{m(a,e,o,c,n,d)}catch(t){const n=t instanceof Error?t.message:t.toString(),r=t instanceof Error?t.stack:void 0;throw console.error(`bio lib: getMonomersDictFromLib() sym='${e}', error:\n${n}\n${r}`),new Error(`Can't get monomer '${e}' from library: ${n}`)}}return a}(g,o,f,p),w=d.length,{molfileList:b,molfileWarningList:A}=await async function(e,t,r,s,o){const a=Math.max(navigator.hardwareConcurrency-2,1),i=new Array(a).fill(null).map((()=>new Worker(new URL(n.p+n.u(248),n.b)))),c=o/a;let l=[],u=[];const d=new Array(a);for(let n=0;n<a;n++){const l=Math.floor(n*c),u=n===a-1?o:Math.floor((n+1)*c);i[n].postMessage({monomerSequencesArray:e,monomersDict:t,alphabet:r,polymerType:s,start:l,end:u}),d[n]=new Promise((e=>{i[n].onmessage=({data:{molfileList:t,molfileWarningList:n}})=>{e({molfileList:t,molfileWarningList:n})}}))}return(await Promise.all(d)).forEach((e=>{l=l.concat(...e.molfileList),u=u.concat(...e.molfileWarningList)})),setTimeout((()=>{i.forEach((e=>{e.terminate()}))}),0),{molfileList:l,molfileWarningList:u}}(g,y,p,f,w);if(A.length>.05*w)throw new Error("Too many errors getting molfiles.");const C=`molfile(${d.name})`,T=e.columns.getUnusedName(C),v=s.Column.fromStrings(T,b);return v.semType=s.SEMTYPE.MOLECULE,v.meta.units=s.UNITS.Molecule.MOLBLOCK,{col:v,warnings:A}}function m(e,t,n,r,s,o){if(!e.has(t)){const a=function(e,t,n,r,s){if(t.has(e)){const a=t.get(e),i=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}(a.rgroups),c=(o=a.molfile).includes("V3000")?function(e){const t=new Map,n=/M V30 (\d+) R#.+RGROUPS=\((\d+) (\d+)\).*/gm;let r;for(;null!==(r=n.exec(e));)r.index===n.lastIndex&&n.lastIndex++,t.set(parseInt(r[1]),parseInt(r[3]));return t}(o):function(e){const t=new Map;let n=e.indexOf(l.V2K_A_LINE,0),r=n;for(;-1!==n;){r=e.indexOf("\n",n);const s=parseInt(e.substring(n,r).replace(/^A\s+/,""));n=e.indexOf("R",r),r=e.indexOf("\n",n);const o=parseInt(e.substring(n,r).replace(/^R/,""));t.set(s,o),n=e.indexOf(l.V2K_A_LINE,r)}for(n=e.indexOf(l.V2K_RGP_LINE,0),r=e.indexOf("\n",n);-1!==n;){n+=l.V2K_RGP_SHIFT,r=e.indexOf("\n",n);const s=e.substring(n,r).replaceAll(/\s+/g," ").split(" ").map((e=>parseInt(e))).slice(1);for(let e=0;e<s.length;e+=2){if(t.has(s[e])&&t.get(s[e])!==s[e+1])throw new Error(`r-group index ${s[e]} has already been added with a different value`);t.set(s[e],s[e+1])}n=e.indexOf(l.V2K_RGP_LINE,r)}return t}(o),u=a.molfile.includes("V3000")?a.molfile:function(e,t){const n=t.get_mol(e),r=n.get_v3Kmolblock();return n.delete(),r}(function(e){let t=e.indexOf(l.V2K_A_LINE,0);-1===t&&(t=e.indexOf(l.V2K_RGP_LINE));const n=e.indexOf(l.V3K_END,t);return e.substring(0,t)+e.substring(n)}(a.molfile),n),h=function(e){let t=(e=e.replaceAll("\r","")).indexOf(l.V3K_BEGIN_COUNTS_LINE)+l.V3K_COUNTS_SHIFT,n=e.indexOf(" ",t+1);const r=parseInt(e.substring(t,n));return t=n+1,n=e.indexOf(" ",t+1),{atomCount:r,bondCount:parseInt(e.substring(t,n))}}(u),m=function(e,t){const n=new Array(t),r=new Float32Array(t),s=new Float32Array(t),o=new Array(t);let a=e.indexOf(l.V3K_BEGIN_ATOM_BLOCK);a=e.indexOf("\n",a);let i=a;for(let c=0;c<t;c++){a=e.indexOf(l.V3K_BEGIN_DATA_LINE,a)+l.V3K_IDX_SHIFT,i=e.indexOf(" ",a),a=i+1,i=e.indexOf(" ",a),n[c]=e.substring(a,i);const t=new Array(2);for(let n=0;n<2;++n)a=i+1,i=e.indexOf(" ",a),t[n]=parseFloat(e.substring(a,i));r[c]=t[0],s[c]=t[1],a=i,i=e.indexOf("\n",a)+1,o[c]=e.slice(a,i),a=i}return{atomTypes:n,x:r,y:s,kwargs:o}}(u,h.atomCount),g=function(e,t){const n=new Uint32Array(t),r=new Array(t),s=new Map,o=new Map;let a=e.indexOf(l.V3K_BEGIN_BOND_BLOCK);a=e.indexOf("\n",a);let i=a;for(let c=0;c<t;++c){const t=new Array(3);a=e.indexOf(l.V3K_BEGIN_DATA_LINE,i)+l.V3K_IDX_SHIFT,i=e.indexOf(" ",a);for(let n=0;n<3;++n)a=i+1,i=Math.min(e.indexOf("\n",a),e.indexOf(" ",a)),t[n]=parseInt(e.slice(a,i));n[c]=t[0],r[c]=t.slice(1);const u=e.indexOf("\n",a);let d=e.slice(i,u),h=d.indexOf(l.V3K_BOND_CONFIG);if(-1!==h){h=d.indexOf("=",h)+1;let e=d.indexOf(" ",h);-1===e&&(e=d.length);const t=parseInt(d.slice(h,e));s.set(c,t);const n=l.V3K_BOND_CONFIG+t.toString();d=d.replace(n,"")}d||o.set(c,d)}return{bondTypes:n,atomPairs:r,bondConfiguration:s,kwargs:o}}(u,h.bondCount),w=function(e,t,n,r){const s={backboneShift:null,branchShift:null,terminalNodes:[],rNodes:[]};return function(e,t,n){for(const[r,s]of n)e.atomTypes[r-1]=t[s-1]}(e,n,r),function(e,t){t.rNodes=Array.from(e.keys());for(let n=0;n<t.rNodes.length;n++)for(const r of[1,2])if(e.get(t.rNodes[n])===r){const e=t.rNodes[r-1];t.rNodes[r-1]=t.rNodes[n],t.rNodes[n]=e}}(r,s),p(t,s),s}(m,g,i,c),v=function(e){let t=[],n=e.indexOf("M V30 MDLV30/STEABS ATOMS=(");for(;-1!==n;){n+=28;const r=e.indexOf(")",n);t=t.concat(e.substring(n,r).split(" ").slice(1).map((e=>parseInt(e)))),n=r,n=e.indexOf("M V30 MDLV30/STEABS ATOMS=(",n)}return t}(u),E={atoms:m,bonds:g,meta:w,stereoAtoms:v};return"PEPTIDE"===r?function(e){const t=e.meta.terminalNodes[0]-1,n=e.meta.rNodes[0]-1,r=e.atoms.x,s=e.atoms.y;T(e,-r[t],-s[t]);const o=b(r[n],s[n]);A(e.atoms,-o),r[e.meta.rNodes[1]-1]<0&&function(e){C(e,!1)}(e);const a=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 r=n[e],s=n[(e+1)%2];t.has(r)?t.get(r)?.push(s):t.set(r,new Array(1).fill(s))}return t}(e);let n=0;const r=e.atoms.atomTypes.length;let s=0;for(;0===n;){const o=t.get(e.meta.terminalNodes[1])[s];if(e.atoms.atomTypes[o-1]===l.OXYGEN&&o!==e.meta.rNodes[1]&&(n=o),s++,s>r)throw new Error(`Search for double-bonded Oxygen in ${e} has exceeded the limit of ${r}`)}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,a),function(e,t){const n=e.atoms.x;n[e.meta.rNodes[1]-1]>n[t-1]&&function(e,t,n){const r=t-1,s=n-1,o=e.atoms.x,a=e.atoms.y,i=o[r],c=a[r];o[r]=o[s],a[r]=a[s],o[s]=i,a[s]=c}(e,t,e.meta.rNodes[1])}(e,a)}(E):e===l.RIBOSE||e===l.DEOXYRIBOSE?function(e,t){const n=e.atoms.x,r=e.atoms.y;let s=e.meta.terminalNodes[0]-1;const o=e.meta.rNodes[1]-1;T(e,-n[s],-r[s]);const a=b(n[o],r[o]);A(e.atoms,3*Math.PI/2-a),t.value=function(e){const t=e.atoms.x,n=e.atoms.y,r=e.meta.rNodes[2]-1,s=e.meta.terminalNodes[2]-1,o=t[r]-t[s],a=n[r]-n[s];return Math.atan(a/o)+Math.PI/2}(e),s=e.meta.terminalNodes[0]-1,T(e,-n[s],-r[s])}(E,s):e===l.PHOSPHATE?function(e){const t=e.meta.terminalNodes[0]-1,n=e.meta.rNodes[0]-1,r=e.atoms.x,s=e.atoms.y;T(e,-r[t],-s[t]);const o=b(r[n],s[n]);A(e.atoms,Math.PI/2-o)}(E):function(e,t){const n=e.atoms.x,r=e.atoms.y,s=e.meta.terminalNodes[0]-1,o=e.meta.rNodes[0]-1;T(e,-n[s],-r[s]);const a=b(n[o],r[o]),i=t.value;if(!i)throw new Error("The value of sugarBranchToOYAngle is null");A(e.atoms,Math.PI-a+i);const c=function(e,t){return d(Math.sqrt((e.x-t.x)**2+(e.y-t.y)**2))}({x:n[e.meta.rNodes[0]-1],y:r[e.meta.rNodes[0]-1]},{x:n[e.meta.terminalNodes[0]-1],y:r[e.meta.terminalNodes[0]-1]});if(1!=c)for(let 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i.s{constructor(e,t,n,s,o){super(e,t,n),this.monomerLengthLimit=s,this.propsProvider=o,this.colWidth=0,this._monomerLengthList=null,this.separatorWidth=5,this._processedMaxVisibleSeqLength=0,this._monomerLengthMap={},this._monomerStructureMap={},this.props=this.propsProvider(),this._processedRows=r.BitSet.create(this.tableCol.length),this.gridCol&&this.subs.push(this.gridCol.grid.onAfterDrawContent.subscribe((()=>{this._onRendered.next()}))),(0,c.pj)().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=r.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),r=new Array(n.length+1);r[0]=5;for(let e=1;e<r.length;e++)r[e]=r[e-1]+n[e-1];return[n,r]}getCellMonomerLengthsForSeq(e){this.toLog(),null===this._monomerLengthList&&(this._monomerLengthList=new Array(this.tableCol.length).fill(null));const t=this.props.separatorWidth+1*this.props.monomerCharWidth,n=Math.ceil(this.colWidth/t),r=a.GO.forColumn(this.tableCol).getSplitted(e).originals,s=Math.min(n,r.length);let o=this._monomerLengthList[e];if(null===o||o.length<s){o=this._monomerLengthList[e]=new Array(r.length);let t=0;for(let e=0;e<s;++e){const n=r[e],s=this.props.monomerToShort(n,this.monomerLengthLimit),a=(this.props.seqHandler.isSeparator()?this.separatorWidth:this.props.separatorWidth)+s.length*this.props.monomerCharWidth;if(o[e]=a,t+=a,t>this.colWidth)break}}return o}getCellMonomerLengthsForSeqMsa(){var e;this.toLog(),null===this._monomerLengthList&&(this._monomerLengthList=new 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t.semType=r.SEMTYPE.MACROMOLECULE,t.meta.units=o.Hi.FASTA,s.GO.forColumn(t),[r.DataFrame.fromColumns([e,t])]}constructor(e){this._descriptionsArray=[],this._sequencesArray=[],this._fileContent=e,this.parseColumns()}}},6873:(e,t,n)=>{"use strict";n.d(t,{dW:()=>a,fD:()=>o});var r=n(6082),s=(n(1991),n(2003));function o(){const e=[];return e.push(r.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(r.Column.fromList(r.COLUMN_TYPE.FLOAT,"Activity",new Array(10**6).fill(5.30751))),e}function a(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=r.Column.fromList(r.COLUMN_TYPE.STRING,"MSA",new Array(100).fill(t));n.semType=r.SEMTYPE.MACROMOLECULE,n.meta.units=s.Hi.SEPARATOR,n.setTag(s.gp.separator,"/"),n.setTag(s.gp.alphabet,s.YI.UN),n.setTag(s.gp.alphabetIsMultichar,"true");const o=[];return o.push(n),o.push(r.Column.fromList(r.COLUMN_TYPE.FLOAT,"Activity",new Array(100).fill(7.30751))),o}n(826),n(9322)},439:(e,t,n)=>{"use strict";n.d(t,{B5:()=>c,Hi:()=>r,Vl:()=>l,YI:()=>s,gp:()=>o,q7:()=>u,z1:()=>i});var r,s,o,a=n(2738);!function(e){e.FASTA="fasta",e.SEPARATOR="separator",e.HELM="helm"}(r||(r={})),function(e){e.DNA="DNA",e.RNA="RNA",e.PT="PT",e.UN="UN"}(s||(s={})),function(e){e.aligned="aligned",e.alphabet="alphabet",e.alphabetSize=".alphabetSize",e.alphabetIsMultichar=".alphabetIsMultichar",e.separator="separator",e.isHelmCompatible=".isHelmCompatible",e.positionNames=".positionNames",e.positionLabels=".positionLabels",e.regions=".regions"}(o||(o={}));const i=", ",c=/(?:\[([A-Za-z0-9_\-,()]+)\])|([A-Za-z\-])/g,l=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"])}}},u=[new a.aD(s.PT,l.fasta.peptide,.5),new a.aD(s.DNA,l.fasta.dna,.55),new a.aD(s.RNA,l.fasta.rna,.55)]},2003:(e,t,n)=>{"use strict";n.d(t,{Hi:()=>r.Hi,J9:()=>s.J9,Qf:()=>s.Qf,SM:()=>s.SM,YI:()=>r.YI,dh:()=>s.dh,gp:()=>r.gp,mn:()=>s.mn,nq:()=>s.nq,ny:()=>s.ny,q7:()=>r.q7,qp:()=>s.qp,z1:()=>r.z1,zS:()=>s.zS});var r=n(439),s=n(9322)},2738:(e,t,n)=>{"use strict";n.d(t,{XN:()=>o,_S:()=>r,aD:()=>s});const r="";class s{constructor(e,t,n){this.name=e,this.alphabet=t,this.cutoff=n}}class o extends s{constructor(e,t,n){super(e.name,e.alphabet,e.cutoff),this.freq=t,this.similarity=n}}},9322:(e,t,n)=>{"use strict";n.d(t,{Mu:()=>p,pc:()=>x,Qf:()=>_,nq:()=>P,ny:()=>M,Iv:()=>v,dh:()=>b,vZ:()=>g,zS:()=>S,SM:()=>$,mn:()=>N,J9:()=>y,tm:()=>w,qp:()=>T});var r=n(6082),s=n(1991),o=n.n(s),a=n(2738),i=n(439),c=n(826);class l extends Float32Array{}var u=n(3629),d=n(8924),h=n(1093),m=n(4152);class p{get length(){return this.mList.length}get canonicals(){return this.mList}get originals(){return this.mList}isGap(e){return this.getOriginal(e)===this.gapOriginalMonomer}getCanonical(e){if(this.length<=e)throw new Error("Index out of bounds");return this.mList[e]}getOriginal(e){if(this.length<=e)throw new Error("Index out of bounds");return this.mList[e]}constructor(e,t){this.mList=e,this.gapOriginalMonomer=t}}class f{get length(){return this.seqS.length}get canonicals(){return this.seqS}get originals(){return this.seqS}isGap(e){return this.getOriginal(e)===c.b9[i.Hi.FASTA]}getCanonical(e){if(this.length<=e)throw new Error("Index out of bounds");return this.isGap(e)?a._S:this.seqS[e]}getOriginal(e){if(this.length<=e)throw new Error("Index out of bounds");return this.seqS[e]}constructor(e){this.seqS=e}}function g(e,t,n){const r=e.categories;return function(e,t){const n={};let r=!0,s=null;for(const o of e)if(null==s?s=o.length:o.length!==s&&(r=!1),o.length>=t)for(const e of o.canonicals)e in n||(n[e]=0),n[e]+=1;return{freq:n,sameLength:r}}(o().enumerate(e.getRawData()).map((([e,t])=>n(r[e]))),t)}const y=e=>{const t=o()(e.toString().matchAll(i.B5)).map((e=>e[2]??e[1])).toArray();return new p(t,c.b9[i.Hi.FASTA])},w=e=>e?new f(e):new p([],c.b9[i.Hi.FASTA]);function b(e,t=void 0){return n=>{if(n){let r;const s=new RegExp(String.raw`"-"|'-'|[^${e}]+`,"g");if(void 0!==t){s.lastIndex=0,r=new Array(Math.ceil(t));let e=null,o=0;for(;null!==(e=s.exec(n))&&o<t;)r[o++]=e[0].replace('"-"',"").replace("'-'","");r.splice(o)}else r=n.replaceAll('"-"',"").replaceAll("'-'","").split(e,t);return new p(r,c.b9[i.Hi.SEPARATOR])}return new p([],c.b9[i.Hi.SEPARATOR])}}const A=/(PEPTIDE1|DNA1|RNA1)\{([^}]+)}/g,C=/\[([^\[\]]+)]/g,T=e=>{A.lastIndex=0;const t=A.exec(e.toString()),n=t?t[2]:null,r=n?n.split("."):[];return new p(r.map((e=>{C.lastIndex=0;const t=C.exec(e);return t&&t.length>=2?t[1]:e})),c.b9[i.Hi.HELM])};function v(e,t,n=void 0){if(e.toLowerCase().startsWith(i.Hi.FASTA))return y;if(e.toLowerCase().startsWith(i.Hi.SEPARATOR))return b(t,n);if(e.toLowerCase().startsWith(i.Hi.HELM))return T;throw new Error(`Unexpected units ${e} .`)}const E=/([^\W_]+)/g;function S(e,t){if(e.length<=t)return e;const n=e.match(E),r=e.length>t||(n?.length??0)>1,s=n?.[0]??" ";return r?s.substring(0,t-1)+"…":s}function _(e){switch(e){case i.YI.DNA:return i.Vl.fasta.dna;case i.YI.RNA:return i.Vl.fasta.rna;case i.YI.PT:return i.Vl.fasta.peptide;default:throw new Error(`Unsupported alphabet '${e}'.`)}}function P(e,t,n="-"){const r=new Set([...new Set(Object.keys(e)),...t]);r.delete(n);const s=[],o=[];for(const n of r)s.push(n in e?e[n]:0),o.push(t.has(n)?1:0);const a=new l(s),i=new l(o);return(0,u.KE)(a,i)/((0,u.wQ)(a)*(0,u.wQ)(i))}function x(e,t,n="-"){const r=t.map((t=>{const r=P(e,t.alphabet,n);return new a.XN(t,e,r)}));let s;const o=Math.max(...r.map((e=>e.similarity>e.cutoff?e.similarity:-1)));return s=o>0?r.find((e=>e.similarity===o)).name:i.YI.UN,s}function $(e,t=5){let n;return n=e.semType==r.SEMTYPE.MACROMOLECULE?c.GO.forColumn(e).alphabet:x(g(e,t,y).freq,i.q7),M(n)}function M(e){switch(e){case i.YI.PT:return d.X.GrokGroups;case i.YI.DNA:case i.YI.RNA:return h.A.Chromatogram;default:return m.oT.Color}}function N(e){const t=e.columns.bySemTypeAll(r.SEMTYPE.MACROMOLECULE);let n=t.find((e=>{const t=e.meta.units;return!!t&&-1!==t.indexOf("MSA")}))??null;return!n&&t.length>0&&(n=t[0]),n}},826:(e,t,n)=>{"use strict";n.d(t,{GO:()=>p,b9:()=>m});var r=n(6082),s=n(1991),o=n.n(s),a=n(2003),i=n(2738),c=n(9322),l=n(6863),u=n(6718),d=n(3151);const h=new class{constructor(){this.seqHandler="seq-handler",this.notationProvider="seq-handler.notation-provider"}},m={[a.Hi.FASTA]:"-",[a.Hi.SEPARATOR]:"",[a.Hi.HELM]:"*"};class p{constructor(e){if(this._splitter=null,this.cached=!0,this._splitted=null,this.columnVersion=null,this._stats=null,this._maxLength=null,this._posList=null,this._joiner=void 0,e.type!==r.TYPE.STRING)throw new Error(`Unexpected column type '${e.type}', must be '${r.TYPE.STRING}'.`);this._column=e;const t=this._column.meta.units;if(null==t)throw new Error("Units are not specified in column");if(this._units=t,this._notation=this.getNotation(),this._defaultGapOriginal=this.isFasta()?m[a.Hi.FASTA]:this.isHelm()?m[a.Hi.HELM]:m[a.Hi.SEPARATOR],!this.column.tags.has(a.gp.aligned)||!this.column.tags.has(a.gp.alphabet)||!this.column.tags.has(a.gp.alphabetIsMultichar)&&!this.isHelm()&&this.alphabet===a.YI.UN)if(this.isFasta())p.setUnitsToFastaColumn(this);else if(this.isSeparator()){const t=e.getTag(a.gp.separator);p.setUnitsToSeparatorColumn(this,t)}else{if(!this.isHelm())throw new Error(`Unexpected units '${this.column.meta.units}'.`);p.setUnitsToHelmColumn(this)}if(!this.column.tags.has(a.gp.alphabetIsMultichar))if(this.isHelm())this.column.setTag(a.gp.alphabetIsMultichar,"true");else if(["UN"].includes(this.alphabet))throw new Error(`For column '${this.column.name}' of alphabet '${this.alphabet}' tag '${a.gp.alphabetIsMultichar}' is mandatory.`);this.notationProvider=this.column.temp[h.notationProvider]??null,this.columnVersion=this.column.version}static setUnitsToFastaColumn(e){if(e.column.semType!==r.SEMTYPE.MACROMOLECULE||e.column.meta.units!==a.Hi.FASTA)throw new Error(`The column of notation '${a.Hi.FASTA}' must be '${r.SEMTYPE.MACROMOLECULE}'.`);e.column.meta.units=a.Hi.FASTA,p.setTags(e)}static setUnitsToSeparatorColumn(e,t){if(e.column.semType!==r.SEMTYPE.MACROMOLECULE||e.column.meta.units!==a.Hi.SEPARATOR)throw new Error(`The column of notation '${a.Hi.SEPARATOR}' must be '${r.SEMTYPE.MACROMOLECULE}'.`);if(!t)throw new Error(`The column of notation '${a.Hi.SEPARATOR}' must have the separator tag.`);e.column.meta.units=a.Hi.SEPARATOR,e.column.setTag(a.gp.separator,t),p.setTags(e)}static setUnitsToHelmColumn(e){if(e.column.semType!==r.SEMTYPE.MACROMOLECULE)throw new Error(`The column of notation '${a.Hi.HELM}' must be '${r.SEMTYPE.MACROMOLECULE}'`);e.column.meta.units=a.Hi.HELM,p.setTags(e)}static setTags(e){const t=e.column.meta.units;if([a.Hi.FASTA,a.Hi.SEPARATOR].includes(t)){if(!e.column.getTag(a.gp.alphabet)&&0===Object.keys(e.stats.freq).length)throw new Error("Alphabet is empty and not annotated.");let t=e.column.getTag(a.gp.aligned);null===t&&(t=e.stats.sameLength?"SEQ.MSA":"SEQ",e.column.setTag(a.gp.aligned,t));let n=e.column.getTag(a.gp.alphabet);if(null===n&&(n=(0,c.pc)(e.stats.freq,a.q7),e.column.setTag(a.gp.alphabet,n)),n===a.YI.UN){const t=Object.keys(e.stats.freq).length,n=Object.keys(e.stats.freq).some((e=>e.length>1));e.column.setTag(a.gp.alphabetSize,t.toString()),e.column.setTag(a.gp.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(a.gp.separator)??void 0;if(this.notation===a.Hi.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(a.gp.aligned);if(!e&&(this.isFasta()||this.isSeparator()))throw new Error("Tag aligned not set");return e}get alphabet(){const e=this.column.getTag(a.gp.alphabet);if(!e&&(this.isFasta()||this.isSeparator()))throw new Error("Tag alphabet not set");return e}get helmCompatible(){return this.column.getTag(a.gp.isHelmCompatible)}getAlphabetSize(){if(this.notation==a.Hi.HELM||this.alphabet==a.YI.UN){const e=this.column.getTag(a.gp.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 a.YI.PT:return 20;case a.YI.DNA:case a.YI.RNA:return 4;case"NT":return console.warn("Unexpected alphabet 'NT'."),4;default:throw new Error(`Unexpected alphabet '${this.alphabet}'.`)}}getAlphabetIsMultichar(){return this.notation===a.Hi.HELM||this.alphabet===a.YI.UN&&"true"===this.column.getTag(a.gp.alphabetIsMultichar)}getSplitted(e,t){if(this.cached&&void 0===t){this.column.version===this.columnVersion&&null!==this._splitted||(this.columnVersion=this.column.version,this._splitted=new Array(this.column.length));let t=this._splitted[e]?this._splitted[e].deref():void 0;if(!t){const n=this.column.get(e);t=this.splitter(n),this._splitted[e]=new WeakRef(t)}return t}{const n=this.column.get(e);return this.getSplitter(t)(n)}}get stats(){if(null===this._stats){const e={};let t=!0,n=null;const r=this.column.length;for(let s=0;s<r;++s){const r=this.getSplitted(s);null==n?n=r.length:r.length!==n&&(t=!1);for(const t of r.canonicals)t in e||(e[t]=0),e[t]+=1}this._stats={freq:e,sameLength:t}}return this._stats}get maxLength(){return null===this._maxLength&&(this._maxLength=0===this.column.length?0:Math.max(...o().count(0).take(this.column.length).map((e=>this.getSplitted(e).length)))),this._maxLength}get posList(){if(null===this._posList){const e=this.column.getTag(a.gp.positionNames);this._posList=e?e.split(a.z1).map((e=>e.trim())):o().count(1).take(this.maxLength).map((e=>e.toString())).toArray()}return this._posList}isFasta(){return this.notation===a.Hi.FASTA}isSeparator(){return this.notation===a.Hi.SEPARATOR}isHelm(){return this.notation===a.Hi.HELM}isRna(){return this.alphabet===a.YI.RNA}isDna(){return this.alphabet===a.YI.DNA}isPeptide(){return this.alphabet===a.YI.PT}isMsa(){return!!this.aligned&&this.aligned.toUpperCase().includes("MSA")}isHelmCompatible(){return"true"===this.helmCompatible}isGap(e){return!e||e===this._defaultGapOriginal}getNotation(){if(this.units.toLowerCase().startsWith(a.Hi.FASTA))return a.Hi.FASTA;if(this.units.toLowerCase().startsWith(a.Hi.SEPARATOR))return a.Hi.SEPARATOR;if(this.units.toLowerCase().startsWith(a.Hi.HELM))return a.Hi.HELM;throw new Error(`Column '${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,s){const o=this.column,i=e.toLowerCase()+"("+o.name+")",c=n??o.dataFrame.columns.getUnusedName(i),l=r.Column.fromList("string",c,s??new Array(this.column.length).fill(""));if(l.semType=r.SEMTYPE.MACROMOLECULE,l.meta.units=e,e===a.Hi.SEPARATOR){if(!t)throw new Error(`Notation '${a.Hi.SEPARATOR}' requires separator value.`);l.setTag(a.gp.separator,t)}l.setTag(r.TAGS.CELL_RENDERER,e===a.Hi.HELM?"helm":"sequence");const u=o.getTag(a.gp.aligned);u&&l.setTag(a.gp.aligned,u);let d=o.getTag(a.gp.alphabet);d||this.notation!==a.Hi.HELM||e===a.Hi.HELM||(d=a.YI.UN),null!=d&&l.setTag(a.gp.alphabet,d);let h=o.getTag(a.gp.alphabetSize);null!=d&&h&&l.setTag(a.gp.alphabetSize,h);const m=o.getTag(a.gp.alphabetIsMultichar);return null!=d&&void 0!==m&&l.setTag(a.gp.alphabetIsMultichar,m),e==a.Hi.HELM&&(h=this.getAlphabetSize().toString(),l.setTag(a.gp.alphabetSize,h)),l}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(),[a.Hi.FASTA,a.Hi.SEPARATOR,a.Hi.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 s=r.Column.fromList("string",t,new Array(e).fill(""));return s.semType=r.SEMTYPE.MACROMOLECULE,s.meta.units=n,s}getSplitter(e){let t=null;if(t=this.notationProvider?this.notationProvider.splitter:null,t)return t;if(this.units.toLowerCase().startsWith(a.Hi.FASTA))return null===this.column.getTag(a.gp.alphabet)||this.getAlphabetIsMultichar()?a.J9:c.tm;if(this.units.toLowerCase().startsWith(a.Hi.SEPARATOR))return(0,a.dh)(this.separator,e);if(this.units.toLowerCase().startsWith(a.Hi.HELM))return a.qp;throw new Error(`Unexpected units ${this.units} .`)}split(e){return this.splitter(e)}getDistanceFunctionName(){if(!this.isFasta())throw new Error("Only FASTA notation is supported");if(this.isMsa())return l.Z.HAMMING;switch(this.alphabet){case a.YI.DNA:case a.YI.RNA:case a.YI.PT:}return l.Z.LEVENSHTEIN}getDistanceFunction(){return l.V[this.getDistanceFunctionName()]()}async checkHelmCompatibility(){if(this.column.tags.has(a.gp.isHelmCompatible))return"true"===this.column.getTag(a.gp.isHelmCompatible);const e=(await(0,u.pj)()).getBioLib().getMonomerSymbolsByType("PEPTIDE"),t=new Set(e),n=((0,a.dh)(this.separator),new Set),r=this.column.length,s=this.column.getRawData();for(let e=0;e<r;++e){const r=s[e];if(!(r in n)){n.add(r);const s=this.getSplitted(e);for(const e of s.canonicals)if(!t.has(e))return this.column.setTag(a.gp.isHelmCompatible,"false"),!1}}return this.column.setTag(a.gp.isHelmCompatible,"true"),!0}get splitter(){return null===this._splitter&&(this._splitter=this.getSplitter()),this._splitter}toFasta(e){return e===a.Hi.FASTA}toSeparator(e){return e===a.Hi.SEPARATOR}toHelm(e){return e===a.Hi.HELM}convertHelmToFastaSeparator(e,t,n,r){r||(r=this.toFasta(t)?m[a.Hi.FASTA]:m[a.Hi.SEPARATOR]),n||(n=this.toFasta(t)?"":this.separator);const s=e.startsWith("RNA"),o=this.splitter(e),i=[];for(let e=0;e<o.length;++e){let n=o.getOriginal(e);if(s&&(n=n.replace(d.EK,"")),n===m[a.Hi.HELM])i.push(r);else if(this.toFasta(t)&&n.length>1){const e="["+n+"]";i.push(e)}else i.push(n)}return i.join(n)}convert(e,t){const n=this.getJoiner({notation:e,separator:t}),r=this.getNewColumn(e,t);return r.init((e=>{const t=this.getSplitted(e);return n(t)})),r}getRegion(e,t,n){const 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f(e,n,s.isHelm())};break;case a.Hi.HELM:{const e=s.alphabet===a.YI.DNA||s.alphabet===a.YI.RNA,t=s.getHelmWrappers();r=function(n){return g(n,t,e)};break}default:throw new Error(`Unexpected notation '${t}'.`)}return r}getConverter(e,t=void 0){if(e===a.Hi.SEPARATOR&&!t)throw new Error(`Target separator is not specified for target units '${a.Hi.SEPARATOR}'.`);const n=this;if(e===a.Hi.FASTA)return function(e){return n.convertToFasta(e)};if(e===a.Hi.HELM)return function(e){return n.convertToHelm(e)};if(e===a.Hi.SEPARATOR)return function(e){return n.convertToSeparator(e,t)};throw new Error}static forColumn(e){let t=e.temp[h.seqHandler];return t&&t.columnVersion===e.version||(t=e.temp[h.seqHandler]=new p(e)),t}joinToFasta(e,t){const n=new Array(e.length);for(let r=0;r<e.length;++r){const s=e.getOriginal(r);let o=e.getOriginal(r);t&&(o=o.replace(d.EK,"$1")),s===i._S?o=m[a.Hi.FASTA]:s===d.q7?o="":o.length>1&&(o="["+o+"]"),n[r]=o}return n.join("")}convertToFasta(e){const 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t=r.Color.fromHtml(e),n=r.Color.g(t),s=r.Color.r(t),o=r.Color.b(t),a=Math.sqrt(Math.pow(0-s,2)+Math.pow(0-n,2)+Math.pow(0-o,2));return a>210?`rgb(${s/a*210},${n/a*210},${o/a*210})`:r.Color.toRgb(t)}(c.palette[t])}}c.palette=c.buildPalette();class l extends s.e{static get Gray(){return void 0===this.gray&&(this.gray=new i),this.gray}static get Color(){return void 0===this.color&&(this.color=new c),this.color}}},6642:(e,t,n)=>{"use strict";n.d(t,{h:()=>a,s:()=>i});var r=n(4328),s=n(1858),o=n(8070);function a(e){let t=null,n=null;try{n=e.dart?e.gridColumn:null,t=n?n.temp:null}catch{[n,t]=[null,null]}const r=e.cell.column;if(t=t??r.temp,!t)throw new Error("Grid cell renderer back store (GridColumn or Column) not found.");return[n,r,t]}class i{constructor(e,t,n){this.gridCol=e,this.tableCol=t,this.logger=n,this.subs=[],this.destroyed=!1,this.viewerId=++i.viewerCounter,this.errors=[],this._onRendered=new s.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(r.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(r.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(`${n}, start, testEvent before`),await(0,o.PE)(this._onRendered,(()=>{}),(()=>{this.invalidate()}),e,`${n}, ${t}`),this.errors.length>0){const e=this.errors[0];throw this.errors=[],e}this.logger.debug(`${n}, end`)}}i.viewerCounter=-1},6882:(e,t,n)=>{"use strict";n.d(t,{B:()=>l,J:()=>u});var r=n(6082),s=n(1991),o=n.n(s),a=n(826),i=n(6642),c=n(6718);function l(e,t){let n,r=100,s=0,o=e.length-1;for(;s<=o;){if(n=Math.floor((o+s)/2),e[n]<=t&&t<e[n+1])return n;if(t<e[n]?o=n-1:s=n+1,--r<=0)throw new Error(`Get position for pointer x = ${t} searching has not converged on ${JSON.stringify(e)}. `)}return null}class u extends i.s{constructor(e,t,n,s,o){super(e,t,n),this.monomerLengthLimit=s,this.propsProvider=o,this.colWidth=0,this._monomerLengthList=null,this.separatorWidth=5,this._processedMaxVisibleSeqLength=0,this._monomerLengthMap={},this._monomerStructureMap={},this.props=this.propsProvider(),this._processedRows=r.BitSet.create(this.tableCol.length),this.gridCol&&this.subs.push(this.gridCol.grid.onAfterDrawContent.subscribe((()=>{this._onRendered.next()}))),(0,c.pj)().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=r.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),r=new Array(n.length+1);r[0]=5;for(let e=1;e<r.length;e++)r[e]=r[e-1]+n[e-1];return[n,r]}getCellMonomerLengthsForSeq(e){this.toLog(),null===this._monomerLengthList&&(this._monomerLengthList=new Array(this.tableCol.length).fill(null));const t=this.props.separatorWidth+1*this.props.monomerCharWidth,n=Math.ceil(this.colWidth/t),r=a.GO.forColumn(this.tableCol).getSplitted(e).originals,s=Math.min(n,r.length);let o=this._monomerLengthList[e];if(null===o||o.length<s){o=this._monomerLengthList[e]=new Array(r.length);let t=0;for(let e=0;e<s;++e){const n=r[e],s=this.props.monomerToShort(n,this.monomerLengthLimit),a=(this.props.seqHandler.isSeparator()?this.separatorWidth:this.props.separatorWidth)+s.length*this.props.monomerCharWidth;if(o[e]=a,t+=a,t>this.colWidth)break}}return o}getCellMonomerLengthsForSeqMsa(){var e;this.toLog(),null===this._monomerLengthList&&(this._monomerLengthList=new Array(1).fill(null)),(e=this._monomerLengthList)[0]??(e[0]=new Array(0));const t=this._monomerLengthList[0],{startIdx:n,endIdx:r}=(()=>{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)}}})(),s=this.props.separatorWidth+1*this.props.monomerCharWidth,o=Math.ceil(this.colWidth/s);for(let e=n;e<r;e++){if(this._processedRows.get(e)&&o<=this._processedMaxVisibleSeqLength)continue;const n=a.GO.forColumn(this.tableCol).getSplitted(e,o).originals,r=Math.min(o,n.length);r>t.length&&t.push(...new Array(r-t.length).fill(s));let i=0;for(let e=0;e<r;++e){const r=n[e],s=this.props.monomerToShort(r,this.monomerLengthLimit),o=this.props.separatorWidth+s.length*this.props.monomerCharWidth;if(t[e]=Math.max(t[e]??0,o),i+=o,i>=this.colWidth)break}this._processedMaxVisibleSeqLength=Math.max(this._processedMaxVisibleSeqLength,o)}return t}getPosition(e,t,n){const[r,s]=this.getCellMonomerLengths(e,n),i=a.GO.forColumn(this.tableCol);return 0===o()(i.getSplitted(e).originals).toArray().length?null:l(s,t)}setMonomerLengthLimit(e){this.monomerLengthLimit=e,this.reset()}setSeparatorWidth(e){this.props.separatorWidth=e,this.reset()}isMsa(){return this.props.seqHandler.isMsa()}}},3151:(e,t,n)=>{"use strict";n.d(t,{EK:()=>o,f6:()=>r,q7:()=>s});const r=["symbol","molfile","rgroups","name"],s="p",o=new RegExp(`[rd]\\((\\w)\\)${s}?`,"g")},9192:(e,t,n)=>{"use strict";function r(e){return"string"==typeof e||e instanceof String?e:"StateError"===e.constructor.name?e.message:"StateError"===e.constructor.name&&"$thrownJsError"in e?r(e.$thrownJsError):e instanceof Error?e.message:e.toString()}function s(e){return e instanceof Error?e.stack:"StateError"===e.constructor.name&&"$thrownJsError"in e?s(e.$thrownJsError):void 0}function o(e){return[r(e),s(e)]}n.d(t,{AP:()=>o})},3516:(e,t,n)=>{"use strict";n.d(t,{m:()=>a});var r=n(6082),s=n(826),o=n(439);class a{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 r=this._fileContent.substring(t.index+1,e.lastIndex);this._descriptionsArray.push(r),0!==n&&this._sequencesArray.push(this.parseMacromolecule(n,t.index)),n=e.lastIndex+1}this._sequencesArray.push(this.parseMacromolecule(n,-1))}importFasta(){const e=r.Column.fromStrings("description",this.descriptionsArray),t=r.Column.fromStrings("sequence",this.sequencesArray);return t.semType=r.SEMTYPE.MACROMOLECULE,t.meta.units=o.Hi.FASTA,s.GO.forColumn(t),[r.DataFrame.fromColumns([e,t])]}constructor(e){this._descriptionsArray=[],this._sequencesArray=[],this._fileContent=e,this.parseColumns()}}},6873:(e,t,n)=>{"use strict";n.d(t,{dW:()=>a,fD:()=>o});var r=n(6082),s=(n(1991),n(2003));function o(){const e=[];return e.push(r.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(r.Column.fromList(r.COLUMN_TYPE.FLOAT,"Activity",new Array(10**6).fill(5.30751))),e}function a(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=r.Column.fromList(r.COLUMN_TYPE.STRING,"MSA",new Array(100).fill(t));n.semType=r.SEMTYPE.MACROMOLECULE,n.meta.units=s.Hi.SEPARATOR,n.setTag(s.gp.separator,"/"),n.setTag(s.gp.alphabet,s.YI.UN),n.setTag(s.gp.alphabetIsMultichar,"true");const o=[];return o.push(n),o.push(r.Column.fromList(r.COLUMN_TYPE.FLOAT,"Activity",new Array(100).fill(7.30751))),o}n(826),n(9322)},439:(e,t,n)=>{"use strict";n.d(t,{B5:()=>c,Hi:()=>r,Vl:()=>l,YI:()=>s,gp:()=>o,q7:()=>u,z1:()=>i});var r,s,o,a=n(2738);!function(e){e.FASTA="fasta",e.SEPARATOR="separator",e.HELM="helm"}(r||(r={})),function(e){e.DNA="DNA",e.RNA="RNA",e.PT="PT",e.UN="UN"}(s||(s={})),function(e){e.aligned="aligned",e.alphabet="alphabet",e.alphabetSize=".alphabetSize",e.alphabetIsMultichar=".alphabetIsMultichar",e.separator="separator",e.isHelmCompatible=".isHelmCompatible",e.positionNames=".positionNames",e.positionLabels=".positionLabels",e.regions=".regions"}(o||(o={}));const i=", ",c=/(?:\[([A-Za-z0-9_\-,()]+)\])|([A-Za-z\-])/g,l=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"])}}},u=[new a.aD(s.PT,l.fasta.peptide,.5),new a.aD(s.DNA,l.fasta.dna,.55),new a.aD(s.RNA,l.fasta.rna,.55)]},2003:(e,t,n)=>{"use strict";n.d(t,{Hi:()=>r.Hi,J9:()=>s.J9,Qf:()=>s.Qf,SM:()=>s.SM,YI:()=>r.YI,dh:()=>s.dh,gp:()=>r.gp,mn:()=>s.mn,nq:()=>s.nq,ny:()=>s.ny,q7:()=>r.q7,qp:()=>s.qp,z1:()=>r.z1,zS:()=>s.zS});var r=n(439),s=n(9322)},2738:(e,t,n)=>{"use strict";n.d(t,{XN:()=>o,_S:()=>r,aD:()=>s});const r="";class s{constructor(e,t,n){this.name=e,this.alphabet=t,this.cutoff=n}}class o extends s{constructor(e,t,n){super(e.name,e.alphabet,e.cutoff),this.freq=t,this.similarity=n}}},9322:(e,t,n)=>{"use strict";n.d(t,{Mu:()=>p,pc:()=>x,Qf:()=>_,nq:()=>P,ny:()=>M,Iv:()=>v,dh:()=>b,vZ:()=>g,zS:()=>S,SM:()=>$,mn:()=>N,J9:()=>y,tm:()=>w,qp:()=>T});var r=n(6082),s=n(1991),o=n.n(s),a=n(2738),i=n(439),c=n(826);class l extends Float32Array{}var u=n(3629),d=n(8924),h=n(1093),m=n(4152);class p{get length(){return this.mList.length}get canonicals(){return this.mList}get originals(){return this.mList}isGap(e){return this.getOriginal(e)===this.gapOriginalMonomer}getCanonical(e){if(this.length<=e)throw new Error("Index out of bounds");return this.mList[e]}getOriginal(e){if(this.length<=e)throw new Error("Index out of bounds");return this.mList[e]}constructor(e,t){this.mList=e,this.gapOriginalMonomer=t}}class f{get length(){return this.seqS.length}get canonicals(){return this.seqS}get originals(){return this.seqS}isGap(e){return this.getOriginal(e)===c.b9[i.Hi.FASTA]}getCanonical(e){if(this.length<=e)throw new Error("Index out of bounds");return this.isGap(e)?a._S:this.seqS[e]}getOriginal(e){if(this.length<=e)throw new Error("Index out of bounds");return this.seqS[e]}constructor(e){this.seqS=e}}function g(e,t,n){const r=e.categories;return function(e,t){const n={};let r=!0,s=null;for(const o of e)if(null==s?s=o.length:o.length!==s&&(r=!1),o.length>=t)for(const e of o.canonicals)e in n||(n[e]=0),n[e]+=1;return{freq:n,sameLength:r}}(o().enumerate(e.getRawData()).map((([e,t])=>n(r[e]))),t)}const y=e=>{const t=o()(e.toString().matchAll(i.B5)).map((e=>e[2]??e[1])).toArray();return new p(t,c.b9[i.Hi.FASTA])},w=e=>e?new f(e):new p([],c.b9[i.Hi.FASTA]);function b(e,t=void 0){return n=>{if(n){let r;const s=new RegExp(String.raw`"-"|'-'|[^${e}]+`,"g");if(void 0!==t){s.lastIndex=0,r=new Array(Math.ceil(t));let e=null,o=0;for(;null!==(e=s.exec(n))&&o<t;)r[o++]=e[0].replace('"-"',"").replace("'-'","");r.splice(o)}else r=n.replaceAll('"-"',"").replaceAll("'-'","").split(e,t);return new p(r,c.b9[i.Hi.SEPARATOR])}return new p([],c.b9[i.Hi.SEPARATOR])}}const A=/(PEPTIDE1|DNA1|RNA1)\{([^}]+)}/g,C=/\[([^\[\]]+)]/g,T=e=>{A.lastIndex=0;const t=A.exec(e.toString()),n=t?t[2]:null,r=n?n.split("."):[];return new p(r.map((e=>{C.lastIndex=0;const t=C.exec(e);return t&&t.length>=2?t[1]:e})),c.b9[i.Hi.HELM])};function v(e,t,n=void 0){if(e.toLowerCase().startsWith(i.Hi.FASTA))return y;if(e.toLowerCase().startsWith(i.Hi.SEPARATOR))return b(t,n);if(e.toLowerCase().startsWith(i.Hi.HELM))return T;throw new Error(`Unexpected units ${e} .`)}const E=/([^\W_]+)/g;function S(e,t){if(e.length<=t)return e;const n=e.match(E),r=e.length>t||(n?.length??0)>1,s=n?.[0]??" ";return r?s.substring(0,t-1)+"…":s}function _(e){switch(e){case i.YI.DNA:return i.Vl.fasta.dna;case i.YI.RNA:return i.Vl.fasta.rna;case i.YI.PT:return i.Vl.fasta.peptide;default:throw new Error(`Unsupported alphabet '${e}'.`)}}function P(e,t,n="-"){const r=new Set([...new Set(Object.keys(e)),...t]);r.delete(n);const s=[],o=[];for(const n of r)s.push(n in e?e[n]:0),o.push(t.has(n)?1:0);const a=new l(s),i=new l(o);return(0,u.KE)(a,i)/((0,u.wQ)(a)*(0,u.wQ)(i))}function x(e,t,n="-"){const r=t.map((t=>{const r=P(e,t.alphabet,n);return new a.XN(t,e,r)}));let s;const o=Math.max(...r.map((e=>e.similarity>e.cutoff?e.similarity:-1)));return s=o>0?r.find((e=>e.similarity===o)).name:i.YI.UN,s}function $(e,t=5){let n;return n=e.semType==r.SEMTYPE.MACROMOLECULE?c.GO.forColumn(e).alphabet:x(g(e,t,y).freq,i.q7),M(n)}function M(e){switch(e){case i.YI.PT:return d.X.GrokGroups;case i.YI.DNA:case i.YI.RNA:return h.A.Chromatogram;default:return m.oT.Color}}function N(e){const t=e.columns.bySemTypeAll(r.SEMTYPE.MACROMOLECULE);let n=t.find((e=>{const t=e.meta.units;return!!t&&-1!==t.indexOf("MSA")}))??null;return!n&&t.length>0&&(n=t[0]),n}},826:(e,t,n)=>{"use strict";n.d(t,{GO:()=>p,b9:()=>m});var r=n(6082),s=n(1991),o=n.n(s),a=n(2003),i=n(2738),c=n(9322),l=n(6863),u=n(6718),d=n(3151);const h=new class{constructor(){this.seqHandler="seq-handler",this.notationProvider="seq-handler.notation-provider"}},m={[a.Hi.FASTA]:"-",[a.Hi.SEPARATOR]:"",[a.Hi.HELM]:"*"};class p{constructor(e){if(this._splitter=null,this.cached=!0,this._splitted=null,this.columnVersion=null,this._stats=null,this._maxLength=null,this._posList=null,this._joiner=void 0,e.type!==r.TYPE.STRING)throw new Error(`Unexpected column type '${e.type}', must be '${r.TYPE.STRING}'.`);this._column=e;const t=this._column.meta.units;if(null==t)throw new Error("Units are not specified in column");if(this._units=t,this._notation=this.getNotation(),this._defaultGapOriginal=this.isFasta()?m[a.Hi.FASTA]:this.isHelm()?m[a.Hi.HELM]:m[a.Hi.SEPARATOR],!this.column.tags.has(a.gp.aligned)||!this.column.tags.has(a.gp.alphabet)||!this.column.tags.has(a.gp.alphabetIsMultichar)&&!this.isHelm()&&this.alphabet===a.YI.UN)if(this.isFasta())p.setUnitsToFastaColumn(this);else if(this.isSeparator()){const t=e.getTag(a.gp.separator);p.setUnitsToSeparatorColumn(this,t)}else{if(!this.isHelm())throw new Error(`Unexpected units '${this.column.meta.units}'.`);p.setUnitsToHelmColumn(this)}if(!this.column.tags.has(a.gp.alphabetIsMultichar))if(this.isHelm())this.column.setTag(a.gp.alphabetIsMultichar,"true");else if(["UN"].includes(this.alphabet))throw new Error(`For column '${this.column.name}' of alphabet '${this.alphabet}' tag '${a.gp.alphabetIsMultichar}' is mandatory.`);this.notationProvider=this.column.temp[h.notationProvider]??null,this.columnVersion=this.column.version}static setUnitsToFastaColumn(e){if(e.column.semType!==r.SEMTYPE.MACROMOLECULE||e.column.meta.units!==a.Hi.FASTA)throw new Error(`The column of notation '${a.Hi.FASTA}' must be '${r.SEMTYPE.MACROMOLECULE}'.`);e.column.meta.units=a.Hi.FASTA,p.setTags(e)}static setUnitsToSeparatorColumn(e,t){if(e.column.semType!==r.SEMTYPE.MACROMOLECULE||e.column.meta.units!==a.Hi.SEPARATOR)throw new Error(`The column of notation '${a.Hi.SEPARATOR}' must be '${r.SEMTYPE.MACROMOLECULE}'.`);if(!t)throw new Error(`The column of notation '${a.Hi.SEPARATOR}' must have the separator tag.`);e.column.meta.units=a.Hi.SEPARATOR,e.column.setTag(a.gp.separator,t),p.setTags(e)}static setUnitsToHelmColumn(e){if(e.column.semType!==r.SEMTYPE.MACROMOLECULE)throw new Error(`The column of notation '${a.Hi.HELM}' must be '${r.SEMTYPE.MACROMOLECULE}'`);e.column.meta.units=a.Hi.HELM,p.setTags(e)}static setTags(e){const t=e.column.meta.units;if([a.Hi.FASTA,a.Hi.SEPARATOR].includes(t)){if(!e.column.getTag(a.gp.alphabet)&&0===Object.keys(e.stats.freq).length)throw new Error("Alphabet is empty and not annotated.");let t=e.column.getTag(a.gp.aligned);null===t&&(t=e.stats.sameLength?"SEQ.MSA":"SEQ",e.column.setTag(a.gp.aligned,t));let n=e.column.getTag(a.gp.alphabet);if(null===n&&(n=(0,c.pc)(e.stats.freq,a.q7),e.column.setTag(a.gp.alphabet,n)),n===a.YI.UN){const t=Object.keys(e.stats.freq).length,n=Object.keys(e.stats.freq).some((e=>e.length>1));e.column.setTag(a.gp.alphabetSize,t.toString()),e.column.setTag(a.gp.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(a.gp.separator)??void 0;if(this.notation===a.Hi.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(a.gp.aligned);if(!e&&(this.isFasta()||this.isSeparator()))throw new Error("Tag aligned not set");return e}get alphabet(){const e=this.column.getTag(a.gp.alphabet);if(!e&&(this.isFasta()||this.isSeparator()))throw new Error("Tag alphabet not set");return e}get helmCompatible(){return this.column.getTag(a.gp.isHelmCompatible)}getAlphabetSize(){if(this.notation==a.Hi.HELM||this.alphabet==a.YI.UN){const e=this.column.getTag(a.gp.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 a.YI.PT:return 20;case a.YI.DNA:case a.YI.RNA:return 4;case"NT":return console.warn("Unexpected alphabet 'NT'."),4;default:throw new Error(`Unexpected alphabet '${this.alphabet}'.`)}}getAlphabetIsMultichar(){return this.notation===a.Hi.HELM||this.alphabet===a.YI.UN&&"true"===this.column.getTag(a.gp.alphabetIsMultichar)}getSplitted(e,t){if(this.cached&&void 0===t){this.column.version===this.columnVersion&&null!==this._splitted||(this.columnVersion=this.column.version,this._splitted=new Array(this.column.length));let t=this._splitted[e]?this._splitted[e].deref():void 0;if(!t){const n=this.column.get(e);t=this.splitter(n),this._splitted[e]=new WeakRef(t)}return t}{const n=this.column.get(e);return this.getSplitter(t)(n)}}get stats(){if(null===this._stats){const e={};let t=!0,n=null;const r=this.column.length;for(let s=0;s<r;++s){const r=this.getSplitted(s);null==n?n=r.length:r.length!==n&&(t=!1);for(const t of r.canonicals)t in e||(e[t]=0),e[t]+=1}this._stats={freq:e,sameLength:t}}return this._stats}get maxLength(){return null===this._maxLength&&(this._maxLength=0===this.column.length?0:Math.max(...o().count(0).take(this.column.length).map((e=>this.getSplitted(e).length)))),this._maxLength}get posList(){if(null===this._posList){const e=this.column.getTag(a.gp.positionNames);this._posList=e?e.split(a.z1).map((e=>e.trim())):o().count(1).take(this.maxLength).map((e=>e.toString())).toArray()}return this._posList}isFasta(){return this.notation===a.Hi.FASTA}isSeparator(){return this.notation===a.Hi.SEPARATOR}isHelm(){return this.notation===a.Hi.HELM}isRna(){return this.alphabet===a.YI.RNA}isDna(){return this.alphabet===a.YI.DNA}isPeptide(){return this.alphabet===a.YI.PT}isMsa(){return!!this.aligned&&this.aligned.toUpperCase().includes("MSA")}isHelmCompatible(){return"true"===this.helmCompatible}isGap(e){return!e||e===this._defaultGapOriginal}getNotation(){if(this.units.toLowerCase().startsWith(a.Hi.FASTA))return a.Hi.FASTA;if(this.units.toLowerCase().startsWith(a.Hi.SEPARATOR))return a.Hi.SEPARATOR;if(this.units.toLowerCase().startsWith(a.Hi.HELM))return a.Hi.HELM;throw new Error(`Column '${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,s){const o=this.column,i=e.toLowerCase()+"("+o.name+")",c=n??o.dataFrame.columns.getUnusedName(i),l=r.Column.fromList("string",c,s??new Array(this.column.length).fill(""));if(l.semType=r.SEMTYPE.MACROMOLECULE,l.meta.units=e,e===a.Hi.SEPARATOR){if(!t)throw new Error(`Notation '${a.Hi.SEPARATOR}' requires separator value.`);l.setTag(a.gp.separator,t)}l.setTag(r.TAGS.CELL_RENDERER,e===a.Hi.HELM?"helm":"sequence");const u=o.getTag(a.gp.aligned);u&&l.setTag(a.gp.aligned,u);let d=o.getTag(a.gp.alphabet);d||this.notation!==a.Hi.HELM||e===a.Hi.HELM||(d=a.YI.UN),null!=d&&l.setTag(a.gp.alphabet,d);let h=o.getTag(a.gp.alphabetSize);null!=d&&h&&l.setTag(a.gp.alphabetSize,h);const m=o.getTag(a.gp.alphabetIsMultichar);return null!=d&&void 0!==m&&l.setTag(a.gp.alphabetIsMultichar,m),e==a.Hi.HELM&&(h=this.getAlphabetSize().toString(),l.setTag(a.gp.alphabetSize,h)),l}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(),[a.Hi.FASTA,a.Hi.SEPARATOR,a.Hi.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 s=r.Column.fromList("string",t,new Array(e).fill(""));return s.semType=r.SEMTYPE.MACROMOLECULE,s.meta.units=n,s}getSplitter(e){let t=null;if(t=this.notationProvider?this.notationProvider.splitter:null,t)return t;if(this.units.toLowerCase().startsWith(a.Hi.FASTA))return null===this.column.getTag(a.gp.alphabet)||this.getAlphabetIsMultichar()?a.J9:c.tm;if(this.units.toLowerCase().startsWith(a.Hi.SEPARATOR))return(0,a.dh)(this.separator,e);if(this.units.toLowerCase().startsWith(a.Hi.HELM))return a.qp;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");if(this.isMsa())return l.Z.HAMMING;switch(this.alphabet){case a.YI.DNA:case a.YI.RNA:case a.YI.PT:}return l.Z.LEVENSHTEIN}getDistanceFunction(){return l.V[this.getDistanceFunctionName()]()}async checkHelmCompatibility(){if(this.column.tags.has(a.gp.isHelmCompatible))return"true"===this.column.getTag(a.gp.isHelmCompatible);const e=(await(0,u.pj)()).getBioLib().getMonomerSymbolsByType("PEPTIDE"),t=new Set(e),n=((0,a.dh)(this.separator),new Set),r=this.column.length,s=this.column.getRawData();for(let e=0;e<r;++e){const r=s[e];if(!(r in n)){n.add(r);const s=this.getSplitted(e);for(const e of s.canonicals)if(!t.has(e))return this.column.setTag(a.gp.isHelmCompatible,"false"),!1}}return this.column.setTag(a.gp.isHelmCompatible,"true"),!0}get splitter(){return null===this._splitter&&(this._splitter=this.getSplitter()),this._splitter}toFasta(e){return e===a.Hi.FASTA}toSeparator(e){return e===a.Hi.SEPARATOR}toHelm(e){return e===a.Hi.HELM}convertHelmToFastaSeparator(e,t,n,r){r||(r=this.toFasta(t)?m[a.Hi.FASTA]:m[a.Hi.SEPARATOR]),n||(n=this.toFasta(t)?"":this.separator);const s=e.startsWith("RNA"),o=this.splitter(e),i=[];for(let e=0;e<o.length;++e){let n=o.getOriginal(e);if(s&&(n=n.replace(d.EK,"")),n===m[a.Hi.HELM])i.push(r);else if(this.toFasta(t)&&n.length>1){const e="["+n+"]";i.push(e)}else i.push(n)}return i.join(n)}convert(e,t){const n=this.getJoiner({notation:e,separator:t}),r=this.getNewColumn(e,t);return r.init((e=>{const t=this.getSplitted(e);return n(t)})),r}getRegion(e,t,n){const r=this.getNewColumn(this.notation,this.separator);r.name=n;const s=e??0,o=t??this.maxLength-1,i=this.getJoiner(),l=o-s+1,u=m[this.notation];r.init((e=>{const t=this.getSplitted(e),n=new Array(l);for(let e=0;e<l;++e){const r=s+e;n[e]=r<t.length?t.getOriginal(r):u}return i(new c.Mu(n,u))}));const d=e=>{const t=e.split(",").map((e=>e.trim())),n=new Array(l);for(let e=0;e<l;++e){const r=s+e;n[e]=r<t.length?t[r]:"?"}return n.join(a.z1)},h=this.column.getTag(a.gp.positionNames);h&&r.setTag(a.gp.positionNames,d(h));const p=this.column.getTag(a.gp.positionLabels);return p&&r.setTag(a.gp.positionLabels,d(p)),r}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 r;const s=this;switch(t){case a.Hi.FASTA:r=function(e){return s.joinToFasta(e,s.isHelm())};break;case a.Hi.SEPARATOR:if(!n)throw new Error(`Separator is mandatory for notation '${t}'.`);r=function(e){return f(e,n,s.isHelm())};break;case a.Hi.HELM:{const e=s.alphabet===a.YI.DNA||s.alphabet===a.YI.RNA,t=s.getHelmWrappers();r=function(n){return g(n,t,e)};break}default:throw new Error(`Unexpected notation '${t}'.`)}return r}getConverter(e,t=void 0){if(e===a.Hi.SEPARATOR&&!t)throw new Error(`Target separator is not specified for target units '${a.Hi.SEPARATOR}'.`);const n=this;if(e===a.Hi.FASTA)return function(e){return n.convertToFasta(e)};if(e===a.Hi.HELM)return function(e){return n.convertToHelm(e)};if(e===a.Hi.SEPARATOR)return function(e){return n.convertToSeparator(e,t)};throw new Error}static forColumn(e){let t=e.temp[h.seqHandler];return t&&t.columnVersion===e.version||(t=e.temp[h.seqHandler]=new p(e)),t}joinToFasta(e,t){const n=new Array(e.length);for(let r=0;r<e.length;++r){const s=e.getOriginal(r);let o=e.getOriginal(r);t&&(o=o.replace(d.EK,"$1")),s===i._S?o=m[a.Hi.FASTA]:s===d.q7?o="":o.length>1&&(o="["+o+"]"),n[r]=o}return n.join("")}convertToFasta(e){const 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