@datagrok/peptides 1.18.2 → 1.18.3

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.
Files changed (7) 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 +1 -1
  7. package/src/viewers/sar-viewer.ts +49 -26
package/dist/package-test.js CHANGED
@@ -1,2 +1,2 @@
1
- var peptides_test;(()=>{var t={9135:(t,e,n)=>{"use strict";n.d(e,{pj:()=>m,uL:()=>g});var i,r,o,s,a,l,u,c=n(6082),h=n(4328);n(8774),function(t){t.Levenshtein="Levenshtein",t.JaroWinkler="Jaro-Winkler",t.Manhattan="Manhattan",t.Onehot="One-Hot"}(i||(i={})),function(t){t.Euclidean="Euclidean"}(r||(r={})),function(t){t.Tanimoto="Tanimoto",t.Dice="Dice",t.Asymmetric="Asymmetric",t.BraunBlanquet="Braun-Blanquet",t.Cosine="Cosine",t.Kulczynski="Kulczynski",t.McConnaughey="Mc-Connaughey",t.RogotGoldberg="Rogot-Goldberg",t.Russel="Russel",t.Sokal="Sokal",t.Hamming="Hamming",t.Euclidean="Euclidean"}(o||(o={})),function(t){t.TanimotoIntArray="TanimotoIntArray"}(s||(s={})),function(t){t.Vector="Vector",t.String="String",t.BitArray="BitArray",t.MacroMolecule="MacroMolecule",t.Number="Number",t.IntArray="IntArray",t.NumberArray="NumberArray"}(a||(a={})),function(t){t.Difference="Difference"}(l||(l={})),function(t){t.CommonItems="Common Items"}(u||(u={}));var d=n(4572);o.Tanimoto,o.Dice,o.Asymmetric,o.BraunBlanquet,o.Cosine,o.Kulczynski,o.McConnaughey,o.RogotGoldberg,o.Russel,o.Sokal,o.Hamming,o.Euclidean,o.Tanimoto,o.Dice,o.Asymmetric,o.BraunBlanquet,o.Cosine,o.Kulczynski,o.McConnaughey,o.RogotGoldberg,o.Russel,o.Sokal,o.Hamming,o.Euclidean,o.Tanimoto,o.Dice,o.Cosine,o.Tanimoto,o.Asymmetric,o.Cosine,o.Sokal,d.Z.HAMMING,d.Z.LEVENSHTEIN,d.Z.MONOMER_CHEMICAL_DISTANCE,d.Z.NEEDLEMANN_WUNSCH,n(3151);var f=n(2738),p=(n(826),n(3077));async function m(){const t=c.Func.find({package:"Bio",name:"getMonomerLibHelper"});if(0===t.length)throw new Error('Package "Bio" must be installed for MonomerLibHelper.');return(await t[0].prepare().call()).getOutputParamValue()}async function g(t,e){t instanceof c.Column&&(t=(0,p.R)(t).columns.toList());const n=(await m()).getMonomerLib(),i=new Array(t.length),r=t[0].length,o=new Float32Array(r);for(let s=0;s<t.length;++s){const a=s<e.length?e.getCanonical(s):f._S,l=n.getMonomer("PEPTIDE",a)?.smiles??"",u=t[s],d=u.getRawData(),p=u.categories,m=p.indexOf("");if(i[s]={categories:p,data:d,emptyIndex:m},void 0===a)continue;const g=c.Column.fromStrings("smiles",p.map((t=>n.getMonomer("PEPTIDE",t)?.smiles??""))),v=(c.DataFrame.fromColumns([g]),await h.chem.getSimilarities(g,l)),y=v?v.getRawData():null;for(let t=0;t<r;++t){const e=d[t];a!==f._S&&e!==m?o[t]+=y[e]:a===f._S&&e===m&&(o[t]+=1)}}for(let n=0;n<o.length;++n){let r=o[n]/e.length;for(let o=0;o<t.length;++o){const t=i[o];if(o>=e.length&&t.data[n]!==t.emptyIndex||t.data[n]===t.emptyIndex&&o<e.length){r=c.FLOAT_NULL;break}}o[n]=r}return c.Column.fromFloat32Array("Similarity",o)}},3151:(t,e,n)=>{"use strict";n.d(e,{EK:()=>r,q7:()=>i});const i="p",r=new RegExp(`[rd]\\((\\w)\\)${i}?`,"g")},439:(t,e,n)=>{"use strict";n.d(e,{B5:()=>l,Hi:()=>i,YI:()=>r,gp:()=>o,q7:()=>c,z1:()=>a});var i,r,o,s=n(2738);!function(t){t.FASTA="fasta",t.SEPARATOR="separator",t.HELM="helm"}(i||(i={})),function(t){t.DNA="DNA",t.RNA="RNA",t.PT="PT",t.UN="UN"}(r||(r={})),function(t){t.aligned="aligned",t.alphabet="alphabet",t.alphabetSize=".alphabetSize",t.alphabetIsMultichar=".alphabetIsMultichar",t.separator="separator",t.isHelmCompatible=".isHelmCompatible",t.positionNames=".positionNames",t.positionLabels=".positionLabels",t.regions=".regions"}(o||(o={}));const a=", ",l=/(?:\[([A-Za-z0-9_\-,()]+)\])|([A-Za-z\-])/g,u=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"])}}},c=[new s.aD(r.PT,u.fasta.peptide,.5),new s.aD(r.DNA,u.fasta.dna,.55),new s.aD(r.RNA,u.fasta.rna,.55)]},2003:(t,e,n)=>{"use strict";n.d(e,{Hi:()=>i.Hi,J9:()=>r.J9,SM:()=>r.SM,YI:()=>i.YI,dh:()=>r.dh,gp:()=>i.gp,q7:()=>i.q7,qp:()=>r.qp,z1:()=>i.z1,zS:()=>r.zS});var i=n(439),r=n(9634)},2738:(t,e,n)=>{"use strict";n.d(e,{XN:()=>o,_S:()=>i,aD:()=>r});const i="";class r{constructor(t,e,n){this.name=t,this.alphabet=e,this.cutoff=n}}class o extends r{constructor(t,e,n){super(t.name,t.alphabet,t.cutoff),this.freq=e,this.similarity=n}}},9634:(t,e,n)=>{"use strict";n.d(e,{Mu:()=>E,pc:()=>R,dh:()=>_,zS:()=>I,SM:()=>P,J9:()=>T,tm:()=>x,qp:()=>O});var i=n(6082),r=n(144),o=n.n(r),s=n(2738),a=n(439),l=n(826);class u extends Float32Array{}function c(t){let e=0;for(let n=0;n<t.length;n++)e+=t[n]*t[n];return Math.sqrt(e)}class h{static makePalette(t,e=!1,n=h){const i={};return t.forEach((t=>{const n=t[0],r=t[1];n.forEach(((t,n)=>{i[t]=this.colourPalette[r][e?0:n]}))})),new n(i)}constructor(t){this._palette=t}get(t,e){return this._palette[t]}}h.undefinedColor="rgb(100,100,100)",h.colourPalette={orange:["rgb(255,187,120)","rgb(245,167,100)","rgb(235,137,70)","rgb(205, 111, 71)"],all_green:["rgb(44,160,44)","rgb(74,160,74)","rgb(23,103,57)","rgb(30,110,96)","rgb(60,131,95)","rgb(24,110,79)","rgb(152,223,138)","rgb(182, 223, 138)","rgb(152, 193, 138)"],all_blue:["rgb(31,119,180)","rgb(23,190,207)","rgb(122, 102, 189)","rgb(158,218,229)","rgb(141, 124, 217)","rgb(31, 120, 150)"],magenta:["rgb(162,106,192)","rgb(197,165,224)","rgb(208,113,218)"],red:["rgb(214,39,40)","rgb(255,152,150)"],st_blue:["rgb(23,190,207)","rgb(158,218,229)","rgb(31,119,180)"],dark_blue:["rgb(31,119,180)","rgb(31, 120, 150)"],light_blue:["rgb(23,190,207)","rgb(158,218,229)","rgb(108, 218, 229)","rgb(23,190,227)"],lilac_blue:["rgb(124,102,211)","rgb(149,134,217)","rgb(97, 81, 150)"],dark_green:["rgb(23,103,57)","rgb(30,110,96)","rgb(60,131,95)","rgb(24,110,79)"],green:["rgb(44,160,44)","rgb(74,160,74)"],light_green:["rgb(152,223,138)","rgb(182, 223, 138)","rgb(152, 193, 138)"],st_green:["rgb(44,160,44)","rgb(152,223,138)","rgb(39, 174, 96)","rgb(74,160,74)"],pink:["rgb(247,182,210)"],brown:["rgb(140,86,75)","rgb(102, 62, 54)"],gray:["rgb(127,127,127)","rgb(199,199,199)","rgb(196,156,148)","rgb(222, 222, 180)"],yellow:["rgb(188,189,34)"],white:["rgb(230,230,230)"]};class d extends h{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,d)),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,d)),this.grokGroups}static get RasMol(){return void 0===this.rasMol&&(this.rasMol=new d({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(t){const e=t in d.aaSynonyms?d.aaSynonyms[t]:t;return super.get(e)}}d.aaSynonyms={MeNle:"L",MeA:"A",MeG:"G",MeF:"F"};class f{static getPalette(t="grok"){switch(t){case"grok":return d.GrokGroups;case"lesk":return d.Lesk;default:throw new Error(`ChemPalette: scheme \`${t}\` does not exist`)}}static getInnerOuter(t){let e=0,n="",i="";for(const r of t)"("==r?e++:")"==r?e--:e?n+=r:i+=r;return isNaN(parseInt(n))?[i,n]:[i,""]}static getColorAAPivot(t="",e="grok"){const n=this.getPalette(e);let[i,r]=this.getInnerOuter(t);if(i=i.length>6?`${i.slice(0,3)}...`:i,r=r.length>6?`${r.slice(0,3)}...`:r,1==t.length||"("==t[1]){const e=t[0]?.toUpperCase();return e in n?[n.get(e),e,r,1]:[this.undefinedColor,i,r,1]}if("d"==t[0]&&t[1]in n&&(2==t.length||"("==t[2])){const e=t[1]?.toUpperCase();return e in n?[n.get(e),e,r,2]:[this.undefinedColor,i,r,2]}if(t.substring(0,3)in this.AAFullNames&&(3==t.length||"("==t[3])){const e=this.AAFullNames[t.substring(0,3)];return e in n?[n.get(e),e,r,3]:[this.undefinedColor,i,r,3]}if(t[0]?.toLowerCase()==t[0]&&t.substring(1,3)in this.AAFullNames&&(4==t.length||"("==t[4])){const e=this.AAFullNames[t.substring(1,3)];return e in n?[n.get(e),e,r,4]:[this.undefinedColor,i,r,4]}return[this.undefinedColor,i,r,0]}}f.SemType="Aminoacids",f.SemTypeMultipleAlignment="AminoacidsMultipleAlignment",f.undefinedColor="rgb(100,100,100)",f.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"},f.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"},f.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(*)*"},f.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"};class p extends h{static get Chromatogram(){return void 0===this.chromatogram&&(this.chromatogram=new p({A:"green",C:"blue",G:"black",T:"red",U:"red",others:"gray"})),this.chromatogram}}class m{}m.SemType="Nucleotides",m.SemTypeMultipleAlignment="NucleotidesMultipleAlignment",m.Names={A:"Adenine",C:"Cytosine",G:"Guanine",T:"Thymine",U:"Uracil"};var g=n(9135);function v(t,e=!0){if(null==t)return"rgb(100,100,100)";const n=i.Color.fromHtml(t);if(e){const t=i.Color.g(n),e=i.Color.r(n),r=i.Color.b(n),o=Math.sqrt(Math.pow(0-e,2)+Math.pow(0-t,2)+Math.pow(0-r,2));if(o>210)return`rgb(${e/o*210},${t/o*210},${r/o*210})`}return i.Color.toRgb(n)}class y{static hashCode(t){let e=0;if(0===t.length)return e;for(let n=0;n<t.length;n++)e=(e<<5)-e+t.charCodeAt(n),e|=0;return e}}class C{}class w extends C{get(t,e){return"#666666"}}class b extends C{static buildPalette(){return(0,g.pj)().then((t=>{t.awaitLoaded().then((()=>{const e=t.getMonomerLib();e.onChanged.subscribe((()=>{b.customMonomerColors={},b.polymerTypes=e.getPolymerTypes();for(const t of this.polymerTypes){const n=e.getMonomerSymbolsByType(t);for(const i of n){const n=e.getMonomer(t,i);n?.meta?.colors?.default?.background&&(this.customMonomerColors[i]||(this.customMonomerColors[i]={}),this.customMonomerColors[i][t]=v(n.meta.colors.default.background,!1))}}}))}))})),[].concat(...Object.values(h.colourPalette))}get(t,e){const n=b.customMonomerColors[t],i=e??"PEPTIDE";if(n&&n[i])return n[i];const r=y.hashCode(t)%b.palette.length;return v(b.palette[r])}}b.palette=b.buildPalette(),b.customMonomerColors={},b.polymerTypes=[];class A extends h{static get Gray(){return void 0===this.gray&&(this.gray=new w),this.gray}static get Color(){return void 0===this.color&&(this.color=new b),this.color}}class E{get length(){return this.mList.length}get canonicals(){return this.mList}get originals(){return this.mList}isGap(t){return this.getOriginal(t)===this.gapOriginalMonomer}getCanonical(t){if(this.length<=t)throw new Error("Index out of bounds");return this.mList[t]}getOriginal(t){if(this.length<=t)throw new Error("Index out of bounds");return this.mList[t]}constructor(t,e){this.mList=t,this.gapOriginalMonomer=e}}class S{get length(){return this.seqS.length}get canonicals(){return this.seqS}get originals(){return this.seqS}isGap(t){return this.getOriginal(t)===l.b9[a.Hi.FASTA]}getCanonical(t){if(this.length<=t)throw new Error("Index out of bounds");return this.isGap(t)?s._S:this.seqS[t]}getOriginal(t){if(this.length<=t)throw new Error("Index out of bounds");return this.seqS[t]}constructor(t){this.seqS=t}}const T=t=>{const e=o()(t.toString().matchAll(a.B5)).map((t=>t[2]??t[1])).toArray();return new E(e,l.b9[a.Hi.FASTA])},x=t=>t?new S(t):new E([],l.b9[a.Hi.FASTA]);function _(t,e=void 0){return n=>{if(n){let i;const r=new RegExp(String.raw`"-"|'-'|[^${t}]+`,"g");if(void 0!==e){r.lastIndex=0,i=new Array(Math.ceil(e));let t=null,o=0;for(;null!==(t=r.exec(n))&&o<e;)i[o++]=t[0].replace('"-"',"").replace("'-'","");i.splice(o)}else i=n.replaceAll('"-"',"").replaceAll("'-'","").split(t,e);return new E(i,l.b9[a.Hi.SEPARATOR])}return new E([],l.b9[a.Hi.SEPARATOR])}}const N=/(PEPTIDE1|DNA1|RNA1)\{([^}]+)}/g,M=/\[([^\[\]]+)]/g,O=t=>{N.lastIndex=0;const e=N.exec(t.toString()),n=e?e[2]:null,i=n?n.split("."):[];return new E(i.map((t=>{M.lastIndex=0;const e=M.exec(t);return e&&e.length>=2?e[1]:t})),l.b9[a.Hi.HELM])},L=/([^\W_]+)/g;function I(t,e){if(t.length<=e)return t;const n=t.match(L),i=t.length>e||(n?.length??0)>1,r=n?.[0]??" ";return i?r.substring(0,e-1)+"…":r}function R(t,e,n="-"){const i=e.map((e=>{const i=function(t,e,n="-"){const i=new Set([...new Set(Object.keys(t)),...e]);i.delete(n);const r=[],o=[];for(const n of i)r.push(n in t?t[n]:0),o.push(e.has(n)?1:0);const s=new u(r),a=new u(o);return function(t,e){if(t.length!=e.length)throw new Error("The dimensionality of the vectors must match");let n=0;for(let i=0;i<t.length;i++)n+=t[i]*e[i];return n}(s,a)/(c(s)*c(a))}(t,e.alphabet,n);return new s.XN(e,t,i)}));let r;const o=Math.max(...i.map((t=>t.similarity>t.cutoff?t.similarity:-1)));return r=o>0?i.find((t=>t.similarity===o)).name:a.YI.UN,r}function P(t,e=5){let n;if(t.semType==i.SEMTYPE.MACROMOLECULE)n=l.GO.forColumn(t).alphabet;else{const i=function(t,e,n){const i=t.categories;return function(t,e){const n={};let i=!0,r=null;for(const o of t)if(null==r?r=o.length:o.length!==r&&(i=!1),o.length>=e)for(const t of o.canonicals)t in n||(n[t]=0),n[t]+=1;return{freq:n,sameLength:i}}(o().enumerate(t.getRawData()).map((([t,e])=>n(i[t]))),e)}(t,e,T);n=R(i.freq,a.q7)}return function(t){switch(t){case a.YI.PT:return d.GrokGroups;case a.YI.DNA:case a.YI.RNA:return p.Chromatogram;default:return A.Color}}(n)}},826:(t,e,n)=>{"use strict";n.d(e,{GO:()=>p,b9:()=>f});var i=n(6082),r=n(144),o=n.n(r),s=n(2003),a=n(2738),l=n(9634),u=n(4572),c=n(9135),h=n(3151);const d=new class{constructor(){this.seqHandler="seq-handler",this.notationProvider="seq-handler.notation-provider"}},f={[s.Hi.FASTA]:"-",[s.Hi.SEPARATOR]:"",[s.Hi.HELM]:"*"};class p{constructor(t){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,t.type!==i.TYPE.STRING)throw new Error(`Unexpected column type '${t.type}', must be '${i.TYPE.STRING}'.`);this._column=t;const e=this._column.meta.units;if(null==e)throw new Error("Units are not specified in column");if(this._units=e,this._notation=this.getNotation(),this._defaultGapOriginal=this.isFasta()?f[s.Hi.FASTA]:this.isHelm()?f[s.Hi.HELM]:f[s.Hi.SEPARATOR],!this.column.tags.has(s.gp.aligned)||!this.column.tags.has(s.gp.alphabet)||!this.column.tags.has(s.gp.alphabetIsMultichar)&&!this.isHelm()&&this.alphabet===s.YI.UN)if(this.isFasta())p.setUnitsToFastaColumn(this);else if(this.isSeparator()){const e=t.getTag(s.gp.separator);p.setUnitsToSeparatorColumn(this,e)}else{if(!this.isHelm())throw new Error(`Unexpected units '${this.column.meta.units}'.`);p.setUnitsToHelmColumn(this)}if(!this.column.tags.has(s.gp.alphabetIsMultichar))if(this.isHelm())this.column.setTag(s.gp.alphabetIsMultichar,"true");else if(["UN"].includes(this.alphabet))throw new Error(`For column '${this.column.name}' of alphabet '${this.alphabet}' tag '${s.gp.alphabetIsMultichar}' is mandatory.`);this.notationProvider=this.column.temp[d.notationProvider]??null,this.columnVersion=this.column.version}static setUnitsToFastaColumn(t){if(t.column.semType!==i.SEMTYPE.MACROMOLECULE||t.column.meta.units!==s.Hi.FASTA)throw new Error(`The column of notation '${s.Hi.FASTA}' must be '${i.SEMTYPE.MACROMOLECULE}'.`);t.column.meta.units=s.Hi.FASTA,p.setTags(t)}static setUnitsToSeparatorColumn(t,e){if(t.column.semType!==i.SEMTYPE.MACROMOLECULE||t.column.meta.units!==s.Hi.SEPARATOR)throw new Error(`The column of notation '${s.Hi.SEPARATOR}' must be '${i.SEMTYPE.MACROMOLECULE}'.`);if(!e)throw new Error(`The column of notation '${s.Hi.SEPARATOR}' must have the separator tag.`);t.column.meta.units=s.Hi.SEPARATOR,t.column.setTag(s.gp.separator,e),p.setTags(t)}static setUnitsToHelmColumn(t){if(t.column.semType!==i.SEMTYPE.MACROMOLECULE)throw new Error(`The column of notation '${s.Hi.HELM}' must be '${i.SEMTYPE.MACROMOLECULE}'`);t.column.meta.units=s.Hi.HELM,p.setTags(t)}static setTags(t){const e=t.column.meta.units;if([s.Hi.FASTA,s.Hi.SEPARATOR].includes(e)){if(!t.column.getTag(s.gp.alphabet)&&0===Object.keys(t.stats.freq).length)throw new Error("Alphabet is empty and not annotated.");let e=t.column.getTag(s.gp.aligned);null===e&&(e=t.stats.sameLength?"SEQ.MSA":"SEQ",t.column.setTag(s.gp.aligned,e));let n=t.column.getTag(s.gp.alphabet);if(null===n&&(n=(0,l.pc)(t.stats.freq,s.q7),t.column.setTag(s.gp.alphabet,n)),n===s.YI.UN){const e=Object.keys(t.stats.freq).length,n=Object.keys(t.stats.freq).some((t=>t.length>1));t.column.setTag(s.gp.alphabetSize,e.toString()),t.column.setTag(s.gp.alphabetIsMultichar,n?"true":"false")}}}get column(){return this._column}get length(){return this._column.length}get units(){return this._units}get notation(){return this._notation}get defaultGapOriginal(){return this._defaultGapOriginal}get separator(){const t=this.column.getTag(s.gp.separator)??void 0;if(this.notation===s.Hi.SEPARATOR&&void 0===t)throw new Error(`Separator is mandatory for column '${this.column.name}' of notation '${this.notation}'.`);return t}get aligned(){const t=this.column.getTag(s.gp.aligned);if(!t&&(this.isFasta()||this.isSeparator()))throw new Error("Tag aligned not set");return t}get alphabet(){const t=this.column.getTag(s.gp.alphabet);if(!t&&(this.isFasta()||this.isSeparator()))throw new Error("Tag alphabet not set");return t}get helmCompatible(){return this.column.getTag(s.gp.isHelmCompatible)}getAlphabetSize(){if(this.notation==s.Hi.HELM||this.alphabet==s.YI.UN){const t=this.column.getTag(s.gp.alphabetSize);let e;if(t)e=parseInt(t);else{const t=this.stats;e=Object.keys(t.freq).length}return e}switch(this.alphabet){case s.YI.PT:return 20;case s.YI.DNA:case s.YI.RNA:return 4;case"NT":return console.warn("Unexpected alphabet 'NT'."),4;default:throw new Error(`Unexpected alphabet '${this.alphabet}'.`)}}getAlphabetIsMultichar(){return this.notation===s.Hi.HELM||this.alphabet===s.YI.UN&&"true"===this.column.getTag(s.gp.alphabetIsMultichar)}getSplitted(t,e){if(this.cached&&void 0===e){this.column.version===this.columnVersion&&null!==this._splitted||(this.columnVersion=this.column.version,this._splitted=new Array(this.column.length));let e=this._splitted[t]?this._splitted[t].deref():void 0;if(!e){const n=this.column.get(t);e=this.splitter(n),this._splitted[t]=new WeakRef(e)}return e}{const n=this.column.get(t);return this.getSplitter(e)(n)}}async getHelm(t,e){const n=this.column.get(t);return this.notationProvider?(await this.notationProvider.getHelm(this.column,e)).get(t):this.convertToHelm(n)}get stats(){if(null===this._stats){const t={};let e=!0,n=null;const i=this.column.length;for(let r=0;r<i;++r){const i=this.getSplitted(r);null==n?n=i.length:i.length!==n&&(e=!1);for(const e of i.canonicals)e in t||(t[e]=0),t[e]+=1}this._stats={freq:t,sameLength:e}}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((t=>this.getSplitted(t).length)))),this._maxLength}get posList(){if(null===this._posList){const t=this.column.getTag(s.gp.positionNames);this._posList=t?t.split(s.z1).map((t=>t.trim())):o().count(1).take(this.maxLength).map((t=>t.toString())).toArray()}return this._posList}isFasta(){return this.notation===s.Hi.FASTA}isSeparator(){return this.notation===s.Hi.SEPARATOR}isHelm(){return this.notation===s.Hi.HELM}isRna(){return this.alphabet===s.YI.RNA}isDna(){return this.alphabet===s.YI.DNA}isPeptide(){return this.alphabet===s.YI.PT}isMsa(){return!!this.aligned&&this.aligned.toUpperCase().includes("MSA")}isHelmCompatible(){return"true"===this.helmCompatible}isGap(t){return!t||t===this._defaultGapOriginal}getNotation(){if(this.units.toLowerCase().startsWith(s.Hi.FASTA))return s.Hi.FASTA;if(this.units.toLowerCase().startsWith(s.Hi.SEPARATOR))return s.Hi.SEPARATOR;if(this.units.toLowerCase().startsWith(s.Hi.HELM))return s.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(t,e,n,r){const o=this.column,a=t.toLowerCase()+"("+o.name+")",l=n??o.dataFrame.columns.getUnusedName(a),u=i.Column.fromList("string",l,r??new Array(this.column.length).fill(""));if(u.semType=i.SEMTYPE.MACROMOLECULE,u.meta.units=t,t===s.Hi.SEPARATOR){if(!e)throw new Error(`Notation '${s.Hi.SEPARATOR}' requires separator value.`);u.setTag(s.gp.separator,e)}u.setTag(i.TAGS.CELL_RENDERER,t===s.Hi.HELM?"helm":"sequence");const c=o.getTag(s.gp.aligned);c&&u.setTag(s.gp.aligned,c);let h=o.getTag(s.gp.alphabet);h||this.notation!==s.Hi.HELM||t===s.Hi.HELM||(h=s.YI.UN),null!=h&&u.setTag(s.gp.alphabet,h);let d=o.getTag(s.gp.alphabetSize);null!=h&&d&&u.setTag(s.gp.alphabetSize,d);const f=o.getTag(s.gp.alphabetIsMultichar);return null!=h&&void 0!==f&&u.setTag(s.gp.alphabetIsMultichar,f),t==s.Hi.HELM&&(d=this.getAlphabetSize().toString(),u.setTag(s.gp.alphabetSize,d)),u}getNewColumnFromList(t,e){return this.getNewColumn(this.notation,this.separator,t,e)}static getNewColumn(t){const e=p.forColumn(t),n=e.notation;return e.getNewColumn(n)}static unitsStringIsValid(t){return t=t.toLowerCase(),[s.Hi.FASTA,s.Hi.SEPARATOR,s.Hi.HELM].some((e=>t.startsWith(e.toLowerCase())))}static getNewColumnFromParams(t,e,n){if(!p.unitsStringIsValid(n))throw new Error("Invalid format of 'units' parameter");const r=i.Column.fromList("string",e,new Array(t).fill(""));return r.semType=i.SEMTYPE.MACROMOLECULE,r.meta.units=n,r}getSplitter(t){let e=null;if(e=this.notationProvider?this.notationProvider.splitter:null,e)return e;if(this.units.toLowerCase().startsWith(s.Hi.FASTA))return null===this.column.getTag(s.gp.alphabet)||this.getAlphabetIsMultichar()?s.J9:l.tm;if(this.units.toLowerCase().startsWith(s.Hi.SEPARATOR))return(0,s.dh)(this.separator,t);if(this.units.toLowerCase().startsWith(s.Hi.HELM))return s.qp;throw new Error(`Unexpected units ${this.units} .`)}split(t){return this.splitter(t)}getDistanceFunctionName(){if(!this.isFasta())throw new Error("Only FASTA notation is supported");if(this.isMsa())return u.Z.HAMMING;switch(this.alphabet){case s.YI.DNA:case s.YI.RNA:case s.YI.PT:}return u.Z.LEVENSHTEIN}getDistanceFunction(){return u.V[this.getDistanceFunctionName()]()}async checkHelmCompatibility(){if(this.column.tags.has(s.gp.isHelmCompatible))return"true"===this.column.getTag(s.gp.isHelmCompatible);const t=(await(0,c.pj)()).getMonomerLib().getMonomerSymbolsByType("PEPTIDE"),e=new Set(t),n=((0,s.dh)(this.separator),new Set),i=this.column.length,r=this.column.getRawData();for(let t=0;t<i;++t){const i=r[t];if(!(i in n)){n.add(i);const r=this.getSplitted(t);for(const t of r.canonicals)if(!e.has(t))return this.column.setTag(s.gp.isHelmCompatible,"false"),!1}}return this.column.setTag(s.gp.isHelmCompatible,"true"),!0}get splitter(){return null===this._splitter&&(this._splitter=this.getSplitter()),this._splitter}toFasta(t){return t===s.Hi.FASTA}toSeparator(t){return t===s.Hi.SEPARATOR}toHelm(t){return t===s.Hi.HELM}convertHelmToFastaSeparator(t,e,n,i){i||(i=this.toFasta(e)?f[s.Hi.FASTA]:f[s.Hi.SEPARATOR]),n||(n=this.toFasta(e)?"":this.separator);const r=t.startsWith("RNA"),o=this.splitter(t),a=[];for(let t=0;t<o.length;++t){let n=o.getOriginal(t);if(r&&(n=n.replace(h.EK,"")),n===f[s.Hi.HELM])a.push(i);else if(this.toFasta(e)&&n.length>1){const t="["+n+"]";a.push(t)}else a.push(n)}return a.join(n)}convert(t,e){const n=this.getJoiner({notation:t,separator:e}),i=this.getNewColumn(t,e);return i.init((t=>{const e=this.getSplitted(t);return n(e)})),i}getRegion(t,e,n){const i=this.getNewColumn(this.notation,this.separator);i.name=n;const r=t??0,o=e??this.maxLength-1,a=this.getJoiner(),u=o-r+1,c=f[this.notation];i.init((t=>{const e=this.getSplitted(t),n=new Array(u);for(let t=0;t<u;++t){const i=r+t;n[t]=i<e.length?e.getOriginal(i):c}return a(new l.Mu(n,c))}));const h=t=>{const e=t.split(",").map((t=>t.trim())),n=new Array(u);for(let t=0;t<u;++t){const i=r+t;n[t]=i<e.length?e[i]:"?"}return n.join(s.z1)},d=this.column.getTag(s.gp.positionNames);d&&i.setTag(s.gp.positionNames,h(d));const p=this.column.getTag(s.gp.positionLabels);return p&&i.setTag(s.gp.positionLabels,h(p)),i}get joiner(){return this._joiner||(this._joiner=this.getJoiner()),this._joiner}getJoiner(t){const e=t?t.notation:this.notation,n=t?t.separator:this.separator;let i;const r=this;switch(e){case s.Hi.FASTA:i=function(t){return r.joinToFasta(t,r.isHelm())};break;case s.Hi.SEPARATOR:if(!n)throw new Error(`Separator is mandatory for notation '${e}'.`);i=function(t){return m(t,n,r.isHelm())};break;case s.Hi.HELM:{const t=r.alphabet===s.YI.DNA||r.alphabet===s.YI.RNA,e=r.getHelmWrappers();i=function(n){return g(n,e,t)};break}default:throw new Error(`Unexpected notation '${e}'.`)}return i}getConverter(t,e=void 0){if(t===s.Hi.SEPARATOR&&!e)throw new Error(`Target separator is not specified for target units '${s.Hi.SEPARATOR}'.`);const n=this;if(t===s.Hi.FASTA)return function(t){return n.convertToFasta(t)};if(t===s.Hi.HELM)return function(t){return n.convertToHelm(t)};if(t===s.Hi.SEPARATOR)return function(t){return n.convertToSeparator(t,e)};throw new Error}static forColumn(t){let e=t.temp[d.seqHandler];return e&&e.columnVersion===t.version||(e=t.temp[d.seqHandler]=new p(t)),e}joinToFasta(t,e){const n=new Array(t.length);for(let i=0;i<t.length;++i){const r=t.getOriginal(i);let o=t.getOriginal(i);e&&(o=o.replace(h.EK,"$1")),r===a._S?o=f[s.Hi.FASTA]:r===h.q7?o="":o.length>1&&(o="["+o+"]"),n[i]=o}return n.join("")}convertToFasta(t){const e=this.splitter,n=this.isHelm()?this.splitterAsHelmNucl(t):e(t);return this.joinToFasta(n,this.isHelm())}convertToSeparator(t,e){return m(this.isHelm()?this.splitterAsHelmNucl(t):this.splitter(t),e,this.isHelm())}convertToHelm(t){if(this.notation==s.Hi.HELM)return t;const e=this.getHelmWrappers(),n=t.startsWith("DNA")||t.startsWith("RNA");return g(this.splitter(t),e,n)}splitterAsHelmNucl(t){const e=this.splitter(t),n=new Array(e.length),i=t.startsWith("DNA"),r=t.startsWith("RNA");for(let t=0;t<e.length;++t){let o=e.getOriginal(t);(i||r)&&(o=o.replace(h.EK,"$1"),o=o===h.q7?null:o),n[t]=o||null}return new l.Mu(n.filter((t=>!!t)),f[s.Hi.HELM])}}function m(t,e,n){const i=new Array(t.length);for(let e=0;e<t.length;++e){const r=t.getCanonical(e);let o=t.getOriginal(e);n&&(o=o.replace(h.EK,"$1")),r===a._S?o=f[s.Hi.SEPARATOR]:r===h.q7&&(o=""),i[e]=o}return i.join(e)}function g(t,e,n){const[i,r,o,l]=e,u=new Array(t.length);for(let e=0;e<t.length;++e){const i=t.getCanonical(e);let 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infer the one you want information about."));var o=""+t,s=""+i;if(i=arguments[2],!(r=l(this,o,s,n)))throw new B("Graph.".concat(e,': could not find an edge for the given path ("').concat(o,'" - "').concat(s,'").'))}else{if("mixed"!==n)throw new q("Graph.".concat(e,": calling this method with only a key (vs. a source and target) does not make sense since an edge with this key could have the other type."));if(t=""+t,!(r=this._edges.get(t)))throw new B("Graph.".concat(e,': could not find the "').concat(t,'" edge in the graph.'))}if("function"!=typeof i)throw new H("Graph.".concat(e,": provided updater is not a function."));return r.attributes=i(r.attributes),this.emit("edgeAttributesUpdated",{key:r.key,type:"update",attributes:r.attributes}),this}}}],X=L,J=D,Z=function(){var t=arguments,e=null,n=-1;return new X((function(){for(var i=null;;){if(null===e){if(++n>=t.length)return{done:!0};e=J(t[n])}if(!0!==(i=e.next()).done)break;e=null}return i}))},tt=[{name:"edges",type:"mixed"},{name:"inEdges",type:"directed",direction:"in"},{name:"outEdges",type:"directed",direction:"out"},{name:"inboundEdges",type:"mixed",direction:"in"},{name:"outboundEdges",type:"mixed",direction:"out"},{name:"directedEdges",type:"directed"},{name:"undirectedEdges",type:"undirected"}];function et(t,e,n,i){var r=!1;for(var o in e)if(o!==i){var s=e[o];if(r=n(s.key,s.attributes,s.source.key,s.target.key,s.source.attributes,s.target.attributes,s.undirected),t&&r)return s.key}}function nt(t,e,n,i){var r,o,s,a=!1;for(var l in e)if(l!==i){r=e[l];do{if(o=r.source,s=r.target,a=n(r.key,r.attributes,o.key,s.key,o.attributes,s.attributes,r.undirected),t&&a)return r.key;r=r.next}while(void 0!==r)}}function it(t,e){var n,i=Object.keys(t),r=i.length,o=0;return new L((function(){do{if(n)n=n.next;else{if(o>=r)return{done:!0};var s=i[o++];if(s===e){n=void 0;continue}n=t[s]}}while(!n);return{done:!1,value:{edge:n.key,attributes:n.attributes,source:n.source.key,target:n.target.key,sourceAttributes:n.source.attributes,targetAttributes:n.target.attributes,undirected:n.undirected}}}))}function rt(t,e,n,i){var r=e[n];if(r){var o=r.source,s=r.target;return i(r.key,r.attributes,o.key,s.key,o.attributes,s.attributes,r.undirected)&&t?r.key:void 0}}function ot(t,e,n,i){var r=e[n];if(r){var o=!1;do{if(o=i(r.key,r.attributes,r.source.key,r.target.key,r.source.attributes,r.target.attributes,r.undirected),t&&o)return r.key;r=r.next}while(void 0!==r)}}function st(t,e){var n=t[e];return void 0!==n.next?new L((function(){if(!n)return{done:!0};var t={edge:n.key,attributes:n.attributes,source:n.source.key,target:n.target.key,sourceAttributes:n.source.attributes,targetAttributes:n.target.attributes,undirected:n.undirected};return n=n.next,{done:!1,value:t}})):L.of({edge:n.key,attributes:n.attributes,source:n.source.key,target:n.target.key,sourceAttributes:n.source.attributes,targetAttributes:n.target.attributes,undirected:n.undirected})}function at(t,e,n,i){if(0!==e.size)for(var r,o,s="mixed"!==n&&n!==e.type,a="undirected"===n,l=!1,u=e._edges.values();!0!==(r=u.next()).done;)if(o=r.value,!s||o.undirected===a){var c=o,h=c.key,d=c.attributes,f=c.source,p=c.target;if(l=i(h,d,f.key,p.key,f.attributes,p.attributes,o.undirected),t&&l)return h}}function lt(t,e,n,i,r,o){var s,a=e?nt:et;if("undirected"!==n){if("out"!==i&&(s=a(t,r.in,o),t&&s))return s;if("in"!==i&&(s=a(t,r.out,o,i?void 0:r.key),t&&s))return s}if("directed"!==n&&(s=a(t,r.undirected,o),t&&s))return s}function ut(t,e,n,i,r,o,s){var a,l=n?ot:rt;if("undirected"!==e){if(void 0!==r.in&&"out"!==i&&(a=l(t,r.in,o,s),t&&a))return a;if(void 0!==r.out&&"in"!==i&&(i||r.key!==o)&&(a=l(t,r.out,o,s),t&&a))return a}if("directed"!==e&&void 0!==r.undirected&&(a=l(t,r.undirected,o,s),t&&a))return a}var ct=[{name:"neighbors",type:"mixed"},{name:"inNeighbors",type:"directed",direction:"in"},{name:"outNeighbors",type:"directed",direction:"out"},{name:"inboundNeighbors",type:"mixed",direction:"in"},{name:"outboundNeighbors",type:"mixed",direction:"out"},{name:"directedNeighbors",type:"directed"},{name:"undirectedNeighbors",type:"undirected"}];function ht(){this.A=null,this.B=null}function dt(t,e,n,i,r){for(var o in i){var s=i[o],a=s.source,l=s.target,u=a===n?l:a;if(!e||!e.has(u.key)){var c=r(u.key,u.attributes);if(t&&c)return u.key}}}function ft(t,e,n,i,r){if("mixed"!==e){if("undirected"===e)return dt(t,null,i,i.undirected,r);if("string"==typeof n)return dt(t,null,i,i[n],r)}var o,s=new ht;if("undirected"!==e){if("out"!==n){if(o=dt(t,null,i,i.in,r),t&&o)return o;s.wrap(i.in)}if("in"!==n){if(o=dt(t,s,i,i.out,r),t&&o)return o;s.wrap(i.out)}}if("directed"!==e&&(o=dt(t,s,i,i.undirected,r),t&&o))return o}function pt(t,e,n){var i=Object.keys(n),r=i.length,o=0;return new L((function(){var s=null;do{if(o>=r)return t&&t.wrap(n),{done:!0};var a=n[i[o++]],l=a.source,u=a.target;s=l===e?u:l,t&&t.has(s.key)&&(s=null)}while(null===s);return{done:!1,value:{neighbor:s.key,attributes:s.attributes}}}))}function mt(t,e,n,i,r){for(var o,s,a,l,u,c,h,d=i._nodes.values(),f=i.type;!0!==(o=d.next()).done;){var p=!1;if(s=o.value,"undirected"!==f)for(a in l=s.out){u=l[a];do{if(c=u.target,p=!0,h=r(s.key,c.key,s.attributes,c.attributes,u.key,u.attributes,u.undirected),t&&h)return u;u=u.next}while(u)}if("directed"!==f)for(a in l=s.undirected)if(!(e&&s.key>a)){u=l[a];do{if((c=u.target).key!==a&&(c=u.source),p=!0,h=r(s.key,c.key,s.attributes,c.attributes,u.key,u.attributes,u.undirected),t&&h)return u;u=u.next}while(u)}if(n&&!p&&(h=r(s.key,null,s.attributes,null,null,null,null),t&&h))return null}}function gt(t){if(!u(t))throw new H('Graph.import: invalid serialized node. A serialized node should be a plain object with at least a "key" property.');if(!("key"in t))throw new H("Graph.import: serialized node is missing its key.");if("attributes"in t&&(!u(t.attributes)||null===t.attributes))throw new H("Graph.import: invalid attributes. Attributes should be a plain object, null or omitted.")}function vt(t){if(!u(t))throw new H('Graph.import: invalid serialized edge. A serialized edge should be a plain object with at least a "source" & "target" property.');if(!("source"in t))throw new H("Graph.import: serialized edge is missing its source.");if(!("target"in t))throw new H("Graph.import: serialized edge is missing its target.");if("attributes"in t&&(!u(t.attributes)||null===t.attributes))throw new H("Graph.import: invalid attributes. Attributes should be a plain object, null or omitted.");if("undirected"in t&&"boolean"!=typeof t.undirected)throw new H("Graph.import: invalid undirectedness information. Undirected should be boolean or omitted.")}ht.prototype.wrap=function(t){null===this.A?this.A=t:null===this.B&&(this.B=t)},ht.prototype.has=function(t){return null!==this.A&&t in this.A||null!==this.B&&t in this.B};var yt,Ct=(yt=255&Math.floor(256*Math.random()),function(){return yt++}),wt=new Set(["directed","undirected","mixed"]),bt=new Set(["domain","_events","_eventsCount","_maxListeners"]),At={allowSelfLoops:!0,multi:!1,type:"mixed"};function Et(t,e,n){var i=new t.NodeDataClass(e,n);return t._nodes.set(e,i),t.emit("nodeAdded",{key:e,attributes:n}),i}function St(t,e,n,i,r,o,s,a){if(!i&&"undirected"===t.type)throw new q("Graph.".concat(e,": you cannot add a directed edge to an undirected graph. Use the #.addEdge or #.addUndirectedEdge instead."));if(i&&"directed"===t.type)throw new q("Graph.".concat(e,": you cannot add an undirected edge to a directed graph. Use the #.addEdge or #.addDirectedEdge instead."));if(a&&!u(a))throw new H("Graph.".concat(e,': invalid attributes. Expecting an object but got "').concat(a,'"'));if(o=""+o,s=""+s,a=a||{},!t.allowSelfLoops&&o===s)throw new q("Graph.".concat(e,': source & target are the same ("').concat(o,"\"), thus creating a loop explicitly forbidden by this graph 'allowSelfLoops' option set to false."));var l=t._nodes.get(o),c=t._nodes.get(s);if(!l)throw new B("Graph.".concat(e,': source node "').concat(o,'" not found.'));if(!c)throw new B("Graph.".concat(e,': target node "').concat(s,'" not found.'));var h={key:null,undirected:i,source:o,target:s,attributes:a};if(n)r=t._edgeKeyGenerator();else if(r=""+r,t._edges.has(r))throw new q("Graph.".concat(e,': the "').concat(r,'" edge already exists in the graph.'));if(!t.multi&&(i?void 0!==l.undirected[s]:void 0!==l.out[s]))throw new q("Graph.".concat(e,': an edge linking "').concat(o,'" to "').concat(s,"\" already exists. If you really want to add multiple edges linking those nodes, you should create a multi graph by using the 'multi' option."));var d=new W(i,r,l,c,a);t._edges.set(r,d);var f=o===s;return i?(l.undirectedDegree++,c.undirectedDegree++,f&&(l.undirectedLoops++,t._undirectedSelfLoopCount++)):(l.outDegree++,c.inDegree++,f&&(l.directedLoops++,t._directedSelfLoopCount++)),t.multi?d.attachMulti():d.attach(),i?t._undirectedSize++:t._directedSize++,h.key=r,t.emit("edgeAdded",h),r}function Tt(t,e,n,i,r,o,s,l,c){if(!i&&"undirected"===t.type)throw new q("Graph.".concat(e,": you cannot merge/update a directed edge to an undirected graph. Use the #.mergeEdge/#.updateEdge or #.addUndirectedEdge instead."));if(i&&"directed"===t.type)throw new q("Graph.".concat(e,": you cannot merge/update an undirected edge to a directed graph. Use the #.mergeEdge/#.updateEdge or #.addDirectedEdge instead."));if(l)if(c){if("function"!=typeof l)throw new H("Graph.".concat(e,': invalid updater function. Expecting a function but got "').concat(l,'"'))}else if(!u(l))throw new H("Graph.".concat(e,': invalid attributes. Expecting an object but got "').concat(l,'"'));var h;if(o=""+o,s=""+s,c&&(h=l,l=void 0),!t.allowSelfLoops&&o===s)throw new q("Graph.".concat(e,': source & target are the same ("').concat(o,"\"), thus creating a loop explicitly forbidden by this graph 'allowSelfLoops' option set to false."));var d,f,p=t._nodes.get(o),m=t._nodes.get(s);if(!n&&(d=t._edges.get(r))){if(!(d.source.key===o&&d.target.key===s||i&&d.source.key===s&&d.target.key===o))throw new q("Graph.".concat(e,': inconsistency detected when attempting to merge the "').concat(r,'" edge with "').concat(o,'" source & "').concat(s,'" target vs. ("').concat(d.source.key,'", "').concat(d.target.key,'").'));f=d}if(f||t.multi||!p||(f=i?p.undirected[s]:p.out[s]),f){var g=[f.key,!1,!1,!1];if(c?!h:!l)return g;if(c){var v=f.attributes;f.attributes=h(v),t.emit("edgeAttributesUpdated",{type:"replace",key:f.key,attributes:f.attributes})}else a(f.attributes,l),t.emit("edgeAttributesUpdated",{type:"merge",key:f.key,attributes:f.attributes,data:l});return g}l=l||{},c&&h&&(l=h(l));var y={key:null,undirected:i,source:o,target:s,attributes:l};if(n)r=t._edgeKeyGenerator();else if(r=""+r,t._edges.has(r))throw new q("Graph.".concat(e,': the "').concat(r,'" edge already exists in the graph.'));var C=!1,w=!1;p||(p=Et(t,o,{}),C=!0,o===s&&(m=p,w=!0)),m||(m=Et(t,s,{}),w=!0),d=new W(i,r,p,m,l),t._edges.set(r,d);var b=o===s;return i?(p.undirectedDegree++,m.undirectedDegree++,b&&(p.undirectedLoops++,t._undirectedSelfLoopCount++)):(p.outDegree++,m.inDegree++,b&&(p.directedLoops++,t._directedSelfLoopCount++)),t.multi?d.attachMulti():d.attach(),i?t._undirectedSize++:t._directedSize++,y.key=r,t.emit("edgeAdded",y),[r,!0,C,w]}function xt(t,e){t._edges.delete(e.key);var n=e.source,i=e.target,r=e.attributes,o=e.undirected,s=n===i;o?(n.undirectedDegree--,i.undirectedDegree--,s&&(n.undirectedLoops--,t._undirectedSelfLoopCount--)):(n.outDegree--,i.inDegree--,s&&(n.directedLoops--,t._directedSelfLoopCount--)),t.multi?e.detachMulti():e.detach(),o?t._undirectedSize--:t._directedSize--,t.emit("edgeDropped",{key:e.key,attributes:r,source:n.key,target:i.key,undirected:o})}var _t=function(n){function i(t){var e;if(e=n.call(this)||this,"boolean"!=typeof(t=a({},At,t)).multi)throw new H("Graph.constructor: invalid 'multi' option. Expecting a boolean but got \"".concat(t.multi,'".'));if(!wt.has(t.type))throw new H('Graph.constructor: invalid \'type\' option. Should be one of "mixed", "directed" or "undirected" but got "'.concat(t.type,'".'));if("boolean"!=typeof t.allowSelfLoops)throw new H("Graph.constructor: invalid 'allowSelfLoops' option. Expecting a boolean but got \"".concat(t.allowSelfLoops,'".'));var i="mixed"===t.type?Y:"directed"===t.type?$:j;h(s(e),"NodeDataClass",i);var r="geid_"+Ct()+"_",o=0;return h(s(e),"_attributes",{}),h(s(e),"_nodes",new Map),h(s(e),"_edges",new Map),h(s(e),"_directedSize",0),h(s(e),"_undirectedSize",0),h(s(e),"_directedSelfLoopCount",0),h(s(e),"_undirectedSelfLoopCount",0),h(s(e),"_edgeKeyGenerator",(function(){var t;do{t=r+o++}while(e._edges.has(t));return t})),h(s(e),"_options",t),bt.forEach((function(t){return h(s(e),t,e[t])})),d(s(e),"order",(function(){return e._nodes.size})),d(s(e),"size",(function(){return e._edges.size})),d(s(e),"directedSize",(function(){return e._directedSize})),d(s(e),"undirectedSize",(function(){return e._undirectedSize})),d(s(e),"selfLoopCount",(function(){return e._directedSelfLoopCount+e._undirectedSelfLoopCount})),d(s(e),"directedSelfLoopCount",(function(){return e._directedSelfLoopCount})),d(s(e),"undirectedSelfLoopCount",(function(){return e._undirectedSelfLoopCount})),d(s(e),"multi",e._options.multi),d(s(e),"type",e._options.type),d(s(e),"allowSelfLoops",e._options.allowSelfLoops),d(s(e),"implementation",(function(){return"graphology"})),e}e(i,n);var r=i.prototype;return r._resetInstanceCounters=function(){this._directedSize=0,this._undirectedSize=0,this._directedSelfLoopCount=0,this._undirectedSelfLoopCount=0},r.hasNode=function(t){return this._nodes.has(""+t)},r.hasDirectedEdge=function(t,e){if("undirected"===this.type)return!1;if(1===arguments.length){var n=""+t,i=this._edges.get(n);return!!i&&!i.undirected}if(2===arguments.length){t=""+t,e=""+e;var r=this._nodes.get(t);return!!r&&r.out.hasOwnProperty(e)}throw new H("Graph.hasDirectedEdge: invalid arity (".concat(arguments.length,", instead of 1 or 2). You can either ask for an edge id or for the existence of an edge between a source & a target."))},r.hasUndirectedEdge=function(t,e){if("directed"===this.type)return!1;if(1===arguments.length){var n=""+t,i=this._edges.get(n);return!!i&&i.undirected}if(2===arguments.length){t=""+t,e=""+e;var r=this._nodes.get(t);return!!r&&r.undirected.hasOwnProperty(e)}throw new H("Graph.hasDirectedEdge: invalid arity (".concat(arguments.length,", instead of 1 or 2). You can either ask for an edge id or for the existence of an edge between a source & a target."))},r.hasEdge=function(t,e){if(1===arguments.length){var n=""+t;return this._edges.has(n)}if(2===arguments.length){t=""+t,e=""+e;var i=this._nodes.get(t);return!!i&&(void 0!==i.out&&i.out.hasOwnProperty(e)||void 0!==i.undirected&&i.undirected.hasOwnProperty(e))}throw new H("Graph.hasEdge: invalid arity (".concat(arguments.length,", instead of 1 or 2). You can either ask for an edge id or for the existence of an edge between a source & a target."))},r.directedEdge=function(t,e){if("undirected"!==this.type){if(t=""+t,e=""+e,this.multi)throw new q("Graph.directedEdge: this method is irrelevant with multigraphs since there might be multiple edges between source & target. See #.directedEdges instead.");var n=this._nodes.get(t);if(!n)throw new B('Graph.directedEdge: could not find the "'.concat(t,'" source node in the graph.'));if(!this._nodes.has(e))throw new B('Graph.directedEdge: could not find the "'.concat(e,'" target node in the graph.'));var i=n.out&&n.out[e]||void 0;return i?i.key:void 0}},r.undirectedEdge=function(t,e){if("directed"!==this.type){if(t=""+t,e=""+e,this.multi)throw new q("Graph.undirectedEdge: this method is irrelevant with multigraphs since there might be multiple edges between source & target. See #.undirectedEdges instead.");var n=this._nodes.get(t);if(!n)throw new B('Graph.undirectedEdge: could not find the "'.concat(t,'" source node in the graph.'));if(!this._nodes.has(e))throw new B('Graph.undirectedEdge: could not find the "'.concat(e,'" target node in the graph.'));var i=n.undirected&&n.undirected[e]||void 0;return i?i.key:void 0}},r.edge=function(t,e){if(this.multi)throw new q("Graph.edge: this method is irrelevant with multigraphs since there might be multiple edges between source & target. See #.edges instead.");t=""+t,e=""+e;var n=this._nodes.get(t);if(!n)throw new B('Graph.edge: could not find the "'.concat(t,'" source node in the graph.'));if(!this._nodes.has(e))throw new B('Graph.edge: could not find the "'.concat(e,'" target node in the graph.'));var i=n.out&&n.out[e]||n.undirected&&n.undirected[e]||void 0;if(i)return i.key},r.areDirectedNeighbors=function(t,e){t=""+t,e=""+e;var n=this._nodes.get(t);if(!n)throw new B('Graph.areDirectedNeighbors: could not find the "'.concat(t,'" node in the graph.'));return"undirected"!==this.type&&(e in n.in||e in n.out)},r.areOutNeighbors=function(t,e){t=""+t,e=""+e;var n=this._nodes.get(t);if(!n)throw new B('Graph.areOutNeighbors: could not find the "'.concat(t,'" node in the graph.'));return"undirected"!==this.type&&e in n.out},r.areInNeighbors=function(t,e){t=""+t,e=""+e;var n=this._nodes.get(t);if(!n)throw new B('Graph.areInNeighbors: could not find the "'.concat(t,'" node in the graph.'));return"undirected"!==this.type&&e in n.in},r.areUndirectedNeighbors=function(t,e){t=""+t,e=""+e;var n=this._nodes.get(t);if(!n)throw new B('Graph.areUndirectedNeighbors: could not find the "'.concat(t,'" node in the graph.'));return"directed"!==this.type&&e in n.undirected},r.areNeighbors=function(t,e){t=""+t,e=""+e;var n=this._nodes.get(t);if(!n)throw new B('Graph.areNeighbors: could not find the "'.concat(t,'" node in the graph.'));return"undirected"!==this.type&&(e in n.in||e in n.out)||"directed"!==this.type&&e in n.undirected},r.areInboundNeighbors=function(t,e){t=""+t,e=""+e;var n=this._nodes.get(t);if(!n)throw new B('Graph.areInboundNeighbors: could not find the "'.concat(t,'" node in the graph.'));return"undirected"!==this.type&&e in n.in||"directed"!==this.type&&e in n.undirected},r.areOutboundNeighbors=function(t,e){t=""+t,e=""+e;var n=this._nodes.get(t);if(!n)throw new B('Graph.areOutboundNeighbors: could not find the "'.concat(t,'" node in the graph.'));return"undirected"!==this.type&&e in n.out||"directed"!==this.type&&e in n.undirected},r.inDegree=function(t){t=""+t;var e=this._nodes.get(t);if(!e)throw new B('Graph.inDegree: could not find the "'.concat(t,'" node in the graph.'));return"undirected"===this.type?0:e.inDegree},r.outDegree=function(t){t=""+t;var e=this._nodes.get(t);if(!e)throw new B('Graph.outDegree: could not find the "'.concat(t,'" node in the graph.'));return"undirected"===this.type?0:e.outDegree},r.directedDegree=function(t){t=""+t;var e=this._nodes.get(t);if(!e)throw new B('Graph.directedDegree: could not find the "'.concat(t,'" node in the graph.'));return"undirected"===this.type?0:e.inDegree+e.outDegree},r.undirectedDegree=function(t){t=""+t;var e=this._nodes.get(t);if(!e)throw new B('Graph.undirectedDegree: could not find the "'.concat(t,'" node in the graph.'));return"directed"===this.type?0:e.undirectedDegree},r.inboundDegree=function(t){t=""+t;var e=this._nodes.get(t);if(!e)throw new B('Graph.inboundDegree: could not find the "'.concat(t,'" node in the graph.'));var n=0;return"directed"!==this.type&&(n+=e.undirectedDegree),"undirected"!==this.type&&(n+=e.inDegree),n},r.outboundDegree=function(t){t=""+t;var e=this._nodes.get(t);if(!e)throw new B('Graph.outboundDegree: could not find the "'.concat(t,'" node in the graph.'));var n=0;return"directed"!==this.type&&(n+=e.undirectedDegree),"undirected"!==this.type&&(n+=e.outDegree),n},r.degree=function(t){t=""+t;var e=this._nodes.get(t);if(!e)throw new B('Graph.degree: could not find the "'.concat(t,'" node in the graph.'));var n=0;return"directed"!==this.type&&(n+=e.undirectedDegree),"undirected"!==this.type&&(n+=e.inDegree+e.outDegree),n},r.inDegreeWithoutSelfLoops=function(t){t=""+t;var e=this._nodes.get(t);if(!e)throw new B('Graph.inDegreeWithoutSelfLoops: could not find the "'.concat(t,'" node in the graph.'));return"undirected"===this.type?0:e.inDegree-e.directedLoops},r.outDegreeWithoutSelfLoops=function(t){t=""+t;var e=this._nodes.get(t);if(!e)throw new B('Graph.outDegreeWithoutSelfLoops: could not find the "'.concat(t,'" node in the graph.'));return"undirected"===this.type?0:e.outDegree-e.directedLoops},r.directedDegreeWithoutSelfLoops=function(t){t=""+t;var e=this._nodes.get(t);if(!e)throw new B('Graph.directedDegreeWithoutSelfLoops: could not find the "'.concat(t,'" node in the graph.'));return"undirected"===this.type?0:e.inDegree+e.outDegree-2*e.directedLoops},r.undirectedDegreeWithoutSelfLoops=function(t){t=""+t;var e=this._nodes.get(t);if(!e)throw new B('Graph.undirectedDegreeWithoutSelfLoops: could not find the "'.concat(t,'" node in the graph.'));return"directed"===this.type?0:e.undirectedDegree-2*e.undirectedLoops},r.inboundDegreeWithoutSelfLoops=function(t){t=""+t;var e=this._nodes.get(t);if(!e)throw new B('Graph.inboundDegreeWithoutSelfLoops: could not find the "'.concat(t,'" node in the graph.'));var n=0,i=0;return"directed"!==this.type&&(n+=e.undirectedDegree,i+=2*e.undirectedLoops),"undirected"!==this.type&&(n+=e.inDegree,i+=e.directedLoops),n-i},r.outboundDegreeWithoutSelfLoops=function(t){t=""+t;var e=this._nodes.get(t);if(!e)throw new B('Graph.outboundDegreeWithoutSelfLoops: could not find the "'.concat(t,'" node in the graph.'));var n=0,i=0;return"directed"!==this.type&&(n+=e.undirectedDegree,i+=2*e.undirectedLoops),"undirected"!==this.type&&(n+=e.outDegree,i+=e.directedLoops),n-i},r.degreeWithoutSelfLoops=function(t){t=""+t;var e=this._nodes.get(t);if(!e)throw new B('Graph.degreeWithoutSelfLoops: could not find the "'.concat(t,'" node in the graph.'));var n=0,i=0;return"directed"!==this.type&&(n+=e.undirectedDegree,i+=2*e.undirectedLoops),"undirected"!==this.type&&(n+=e.inDegree+e.outDegree,i+=2*e.directedLoops),n-i},r.source=function(t){t=""+t;var e=this._edges.get(t);if(!e)throw new B('Graph.source: could not find the "'.concat(t,'" edge in the graph.'));return e.source.key},r.target=function(t){t=""+t;var e=this._edges.get(t);if(!e)throw new B('Graph.target: could not find the "'.concat(t,'" edge in the graph.'));return e.target.key},r.extremities=function(t){t=""+t;var e=this._edges.get(t);if(!e)throw new B('Graph.extremities: could not find the "'.concat(t,'" edge in the graph.'));return[e.source.key,e.target.key]},r.opposite=function(t,e){t=""+t,e=""+e;var n=this._edges.get(e);if(!n)throw new B('Graph.opposite: could not find the "'.concat(e,'" edge in the graph.'));var i=n.source.key,r=n.target.key;if(t===i)return r;if(t===r)return i;throw new B('Graph.opposite: the "'.concat(t,'" node is not attached to the "').concat(e,'" edge (').concat(i,", ").concat(r,")."))},r.hasExtremity=function(t,e){t=""+t,e=""+e;var n=this._edges.get(t);if(!n)throw new B('Graph.hasExtremity: could not find the "'.concat(t,'" edge in the graph.'));return n.source.key===e||n.target.key===e},r.isUndirected=function(t){t=""+t;var e=this._edges.get(t);if(!e)throw new B('Graph.isUndirected: could not find the "'.concat(t,'" edge in the graph.'));return e.undirected},r.isDirected=function(t){t=""+t;var e=this._edges.get(t);if(!e)throw new B('Graph.isDirected: could not find the "'.concat(t,'" edge in the graph.'));return!e.undirected},r.isSelfLoop=function(t){t=""+t;var e=this._edges.get(t);if(!e)throw new B('Graph.isSelfLoop: could not find the "'.concat(t,'" edge in the graph.'));return e.source===e.target},r.addNode=function(t,e){var n=function(t,e,n){if(n&&!u(n))throw new H('Graph.addNode: invalid attributes. Expecting an object but got "'.concat(n,'"'));if(e=""+e,n=n||{},t._nodes.has(e))throw new q('Graph.addNode: the "'.concat(e,'" node already exist in the graph.'));var i=new t.NodeDataClass(e,n);return t._nodes.set(e,i),t.emit("nodeAdded",{key:e,attributes:n}),i}(this,t,e);return n.key},r.mergeNode=function(t,e){if(e&&!u(e))throw new H('Graph.mergeNode: invalid attributes. Expecting an object but got "'.concat(e,'"'));t=""+t,e=e||{};var n=this._nodes.get(t);return n?(e&&(a(n.attributes,e),this.emit("nodeAttributesUpdated",{type:"merge",key:t,attributes:n.attributes,data:e})),[t,!1]):(n=new this.NodeDataClass(t,e),this._nodes.set(t,n),this.emit("nodeAdded",{key:t,attributes:e}),[t,!0])},r.updateNode=function(t,e){if(e&&"function"!=typeof e)throw new H('Graph.updateNode: invalid updater function. Expecting a function but got "'.concat(e,'"'));t=""+t;var n=this._nodes.get(t);if(n){if(e){var i=n.attributes;n.attributes=e(i),this.emit("nodeAttributesUpdated",{type:"replace",key:t,attributes:n.attributes})}return[t,!1]}var r=e?e({}):{};return n=new this.NodeDataClass(t,r),this._nodes.set(t,n),this.emit("nodeAdded",{key:t,attributes:r}),[t,!0]},r.dropNode=function(t){t=""+t;var e,n=this._nodes.get(t);if(!n)throw new B('Graph.dropNode: could not find the "'.concat(t,'" node in the graph.'));if("undirected"!==this.type){for(var i in n.out){e=n.out[i];do{xt(this,e),e=e.next}while(e)}for(var r in n.in){e=n.in[r];do{xt(this,e),e=e.next}while(e)}}if("directed"!==this.type)for(var o in n.undirected){e=n.undirected[o];do{xt(this,e),e=e.next}while(e)}this._nodes.delete(t),this.emit("nodeDropped",{key:t,attributes:n.attributes})},r.dropEdge=function(t){var e;if(arguments.length>1){var n=""+arguments[0],i=""+arguments[1];if(!(e=l(this,n,i,this.type)))throw new B('Graph.dropEdge: could not find the "'.concat(n,'" -> "').concat(i,'" edge in the graph.'))}else if(t=""+t,!(e=this._edges.get(t)))throw new B('Graph.dropEdge: could not find the "'.concat(t,'" edge in the graph.'));return xt(this,e),this},r.dropDirectedEdge=function(t,e){if(arguments.length<2)throw new q("Graph.dropDirectedEdge: it does not make sense to try and drop a directed edge by key. What if the edge with this key is undirected? Use #.dropEdge for this purpose instead.");if(this.multi)throw new q("Graph.dropDirectedEdge: cannot use a {source,target} combo when dropping an edge in a MultiGraph since we cannot infer the one you want to delete as there could be multiple ones.");var n=l(this,t=""+t,e=""+e,"directed");if(!n)throw new B('Graph.dropDirectedEdge: could not find a "'.concat(t,'" -> "').concat(e,'" edge in the graph.'));return xt(this,n),this},r.dropUndirectedEdge=function(t,e){if(arguments.length<2)throw new q("Graph.dropUndirectedEdge: it does not make sense to drop a directed edge by key. What if the edge with this key is undirected? Use #.dropEdge for this purpose instead.");if(this.multi)throw new q("Graph.dropUndirectedEdge: cannot use a {source,target} combo when dropping an edge in a MultiGraph since we cannot infer the one you want to delete as there could be multiple ones.");var n=l(this,t,e,"undirected");if(!n)throw new B('Graph.dropUndirectedEdge: could not find a "'.concat(t,'" -> "').concat(e,'" edge in the graph.'));return xt(this,n),this},r.clear=function(){this._edges.clear(),this._nodes.clear(),this._resetInstanceCounters(),this.emit("cleared")},r.clearEdges=function(){for(var t,e=this._nodes.values();!0!==(t=e.next()).done;)t.value.clear();this._edges.clear(),this._resetInstanceCounters(),this.emit("edgesCleared")},r.getAttribute=function(t){return this._attributes[t]},r.getAttributes=function(){return this._attributes},r.hasAttribute=function(t){return this._attributes.hasOwnProperty(t)},r.setAttribute=function(t,e){return this._attributes[t]=e,this.emit("attributesUpdated",{type:"set",attributes:this._attributes,name:t}),this},r.updateAttribute=function(t,e){if("function"!=typeof e)throw new H("Graph.updateAttribute: updater should be a function.");var n=this._attributes[t];return this._attributes[t]=e(n),this.emit("attributesUpdated",{type:"set",attributes:this._attributes,name:t}),this},r.removeAttribute=function(t){return delete this._attributes[t],this.emit("attributesUpdated",{type:"remove",attributes:this._attributes,name:t}),this},r.replaceAttributes=function(t){if(!u(t))throw new H("Graph.replaceAttributes: provided attributes are not a plain object.");return this._attributes=t,this.emit("attributesUpdated",{type:"replace",attributes:this._attributes}),this},r.mergeAttributes=function(t){if(!u(t))throw new H("Graph.mergeAttributes: provided attributes are not a plain object.");return a(this._attributes,t),this.emit("attributesUpdated",{type:"merge",attributes:this._attributes,data:t}),this},r.updateAttributes=function(t){if("function"!=typeof t)throw new H("Graph.updateAttributes: provided updater is not a function.");return this._attributes=t(this._attributes),this.emit("attributesUpdated",{type:"update",attributes:this._attributes}),this},r.updateEachNodeAttributes=function(t,e){if("function"!=typeof t)throw new H("Graph.updateEachNodeAttributes: expecting an updater function.");if(e&&!f(e))throw new H("Graph.updateEachNodeAttributes: invalid hints. Expecting an object having the following shape: {attributes?: [string]}");for(var n,i,r=this._nodes.values();!0!==(n=r.next()).done;)(i=n.value).attributes=t(i.key,i.attributes);this.emit("eachNodeAttributesUpdated",{hints:e||null})},r.updateEachEdgeAttributes=function(t,e){if("function"!=typeof t)throw new H("Graph.updateEachEdgeAttributes: expecting an updater function.");if(e&&!f(e))throw new H("Graph.updateEachEdgeAttributes: invalid hints. Expecting an object having the following shape: {attributes?: [string]}");for(var n,i,r,o,s=this._edges.values();!0!==(n=s.next()).done;)r=(i=n.value).source,o=i.target,i.attributes=t(i.key,i.attributes,r.key,o.key,r.attributes,o.attributes,i.undirected);this.emit("eachEdgeAttributesUpdated",{hints:e||null})},r.forEachAdjacencyEntry=function(t){if("function"!=typeof t)throw new H("Graph.forEachAdjacencyEntry: expecting a callback.");mt(!1,!1,!1,this,t)},r.forEachAdjacencyEntryWithOrphans=function(t){if("function"!=typeof t)throw new H("Graph.forEachAdjacencyEntryWithOrphans: expecting a callback.");mt(!1,!1,!0,this,t)},r.forEachAssymetricAdjacencyEntry=function(t){if("function"!=typeof t)throw new H("Graph.forEachAssymetricAdjacencyEntry: expecting a callback.");mt(!1,!0,!1,this,t)},r.forEachAssymetricAdjacencyEntryWithOrphans=function(t){if("function"!=typeof t)throw new H("Graph.forEachAssymetricAdjacencyEntryWithOrphans: expecting a callback.");mt(!1,!0,!0,this,t)},r.nodes=function(){return"function"==typeof Array.from?Array.from(this._nodes.keys()):V(this._nodes.keys(),this._nodes.size)},r.forEachNode=function(t){if("function"!=typeof t)throw new H("Graph.forEachNode: expecting a callback.");for(var e,n,i=this._nodes.values();!0!==(e=i.next()).done;)t((n=e.value).key,n.attributes)},r.findNode=function(t){if("function"!=typeof t)throw new H("Graph.findNode: expecting a callback.");for(var e,n,i=this._nodes.values();!0!==(e=i.next()).done;)if(t((n=e.value).key,n.attributes))return n.key},r.mapNodes=function(t){if("function"!=typeof t)throw new H("Graph.mapNode: expecting a callback.");for(var e,n,i=this._nodes.values(),r=new Array(this.order),o=0;!0!==(e=i.next()).done;)n=e.value,r[o++]=t(n.key,n.attributes);return r},r.someNode=function(t){if("function"!=typeof t)throw new H("Graph.someNode: expecting a callback.");for(var e,n,i=this._nodes.values();!0!==(e=i.next()).done;)if(t((n=e.value).key,n.attributes))return!0;return!1},r.everyNode=function(t){if("function"!=typeof t)throw new H("Graph.everyNode: expecting a callback.");for(var e,n,i=this._nodes.values();!0!==(e=i.next()).done;)if(!t((n=e.value).key,n.attributes))return!1;return!0},r.filterNodes=function(t){if("function"!=typeof t)throw new H("Graph.filterNodes: expecting a callback.");for(var e,n,i=this._nodes.values(),r=[];!0!==(e=i.next()).done;)t((n=e.value).key,n.attributes)&&r.push(n.key);return r},r.reduceNodes=function(t,e){if("function"!=typeof t)throw new H("Graph.reduceNodes: expecting a callback.");if(arguments.length<2)throw new H("Graph.reduceNodes: missing initial value. You must provide it because the callback takes more than one argument and we cannot infer the initial value from the first iteration, as you could with a simple array.");for(var n,i,r=e,o=this._nodes.values();!0!==(n=o.next()).done;)r=t(r,(i=n.value).key,i.attributes);return r},r.nodeEntries=function(){var t=this._nodes.values();return new L((function(){var e=t.next();if(e.done)return e;var n=e.value;return{value:{node:n.key,attributes:n.attributes},done:!1}}))},r.export=function(){var t=this,e=new Array(this._nodes.size),n=0;this._nodes.forEach((function(t,i){e[n++]=function(t,e){var n={key:t};return c(e.attributes)||(n.attributes=a({},e.attributes)),n}(i,t)}));var i=new Array(this._edges.size);return n=0,this._edges.forEach((function(e,r){i[n++]=function(t,e,n){var i={key:e,source:n.source.key,target:n.target.key};return c(n.attributes)||(i.attributes=a({},n.attributes)),"mixed"===t&&n.undirected&&(i.undirected=!0),i}(t.type,r,e)})),{options:{type:this.type,multi:this.multi,allowSelfLoops:this.allowSelfLoops},attributes:this.getAttributes(),nodes:e,edges:i}},r.import=function(t){var e,n,r,o,s,a=this,l=arguments.length>1&&void 0!==arguments[1]&&arguments[1];if(t instanceof i)return t.forEachNode((function(t,e){l?a.mergeNode(t,e):a.addNode(t,e)})),t.forEachEdge((function(t,e,n,i,r,o,s){l?s?a.mergeUndirectedEdgeWithKey(t,n,i,e):a.mergeDirectedEdgeWithKey(t,n,i,e):s?a.addUndirectedEdgeWithKey(t,n,i,e):a.addDirectedEdgeWithKey(t,n,i,e)})),this;if(!u(t))throw new H("Graph.import: invalid argument. Expecting a serialized graph or, alternatively, a Graph instance.");if(t.attributes){if(!u(t.attributes))throw new H("Graph.import: invalid attributes. Expecting a plain object.");l?this.mergeAttributes(t.attributes):this.replaceAttributes(t.attributes)}if(t.nodes){if(r=t.nodes,!Array.isArray(r))throw new H("Graph.import: invalid nodes. Expecting an array.");for(e=0,n=r.length;e<n;e++){gt(o=r[e]);var c=o,h=c.key,d=c.attributes;l?this.mergeNode(h,d):this.addNode(h,d)}}if(t.edges){var f=!1;if("undirected"===this.type&&(f=!0),r=t.edges,!Array.isArray(r))throw new H("Graph.import: invalid edges. Expecting an array.");for(e=0,n=r.length;e<n;e++){vt(s=r[e]);var p=s,m=p.source,g=p.target,v=p.attributes,y=p.undirected,C=void 0===y?f:y;"key"in s?(l?C?this.mergeUndirectedEdgeWithKey:this.mergeDirectedEdgeWithKey:C?this.addUndirectedEdgeWithKey:this.addDirectedEdgeWithKey).call(this,s.key,m,g,v):(l?C?this.mergeUndirectedEdge:this.mergeDirectedEdge:C?this.addUndirectedEdge:this.addDirectedEdge).call(this,m,g,v)}}return this},r.nullCopy=function(t){var e=new i(a({},this._options,t));return e.replaceAttributes(a({},this.getAttributes())),e},r.emptyCopy=function(t){var e=this.nullCopy(t);return this._nodes.forEach((function(t,n){var i=a({},t.attributes);t=new e.NodeDataClass(n,i),e._nodes.set(n,t)})),e},r.copy=function(t){if("string"==typeof(t=t||{}).type&&t.type!==this.type&&"mixed"!==t.type)throw new q('Graph.copy: cannot create an incompatible copy from "'.concat(this.type,'" type to "').concat(t.type,'" because this would mean losing information about the current graph.'));if("boolean"==typeof t.multi&&t.multi!==this.multi&&!0!==t.multi)throw new q("Graph.copy: cannot create an incompatible copy by downgrading a multi graph to a simple one because this would mean losing information about the current graph.");if("boolean"==typeof t.allowSelfLoops&&t.allowSelfLoops!==this.allowSelfLoops&&!0!==t.allowSelfLoops)throw new q("Graph.copy: cannot create an incompatible copy from a graph allowing self loops to one that does not because this would mean losing information about the current graph.");for(var e,n,i=this.emptyCopy(t),r=this._edges.values();!0!==(e=r.next()).done;)St(i,"copy",!1,(n=e.value).undirected,n.key,n.source.key,n.target.key,a({},n.attributes));return i},r.toJSON=function(){return this.export()},r.toString=function(){return"[object Graph]"},r.inspect=function(){var e=this,n={};this._nodes.forEach((function(t,e){n[e]=t.attributes}));var i={},r={};this._edges.forEach((function(t,n){var o,s=t.undirected?"--":"->",a="",l=t.source.key,u=t.target.key;t.undirected&&l>u&&(o=l,l=u,u=o);var c="(".concat(l,")").concat(s,"(").concat(u,")");n.startsWith("geid_")?e.multi&&(void 0===r[c]?r[c]=0:r[c]++,a+="".concat(r[c],". 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O,L,I,R,P,k,G,D=n(912);n(5540),n(4329),(L=O||(O={})).EUCLIDEAN="EUCLIDEAN",L.MANHATTAN="MANHATTAN",O.EUCLIDEAN,O.MANHATTAN,(R=I||(I={})).HAMMING="Hamming",R.EUCLIDEAN="Euclidean",R.MANHATTAN="Manhattan",R.TANIMOTO="Tanimoto",R.LEVENSTEIN="Levenshtein",R.NEEDLEMAN_WUNSCH="Needlemann-Wunsch",R.MONOMER_CHEMICAL_DISTANCE="Monomer chemical distance",R.SOKAL="Sokal",R.COSINE="Cosine",R.ASYMMETRIC="Asymmetric",R.Difference="Difference",R.OneHot="One-Hot",I.HAMMING,I.EUCLIDEAN,I.MANHATTAN,I.TANIMOTO,I.LEVENSTEIN,I.NEEDLEMAN_WUNSCH,I.MONOMER_CHEMICAL_DISTANCE,I.SOKAL,I.COSINE,I.ASYMMETRIC,I.Difference,I.OneHot,I.HAMMING,I.EUCLIDEAN,I.MANHATTAN,I.TANIMOTO,I.SOKAL,I.COSINE,I.ASYMMETRIC,I.LEVENSTEIN,I.NEEDLEMAN_WUNSCH,I.MONOMER_CHEMICAL_DISTANCE,I.Difference,I.OneHot,new Set([I.HAMMING,I.LEVENSTEIN,I.NEEDLEMAN_WUNSCH,I.MONOMER_CHEMICAL_DISTANCE,I.OneHot]),new Set([I.HAMMING,I.EUCLIDEAN,I.MANHATTAN,I.MONOMER_CHEMICAL_DISTANCE,I.LEVENSTEIN,I.NEEDLEMAN_WUNSCH,I.TANIMOTO,I.COSINE,I.SOKAL,I.ASYMMETRIC,I.OneHot,I.Difference]),new Set([I.EUCLIDEAN,I.MANHATTAN,I.OneHot,I.Difference]),new Set([I.EUCLIDEAN,I.MANHATTAN,I.Difference]),new Set([I.EUCLIDEAN,I.MANHATTAN,I.Difference]),new Set([I.TANIMOTO,I.COSINE,I.SOKAL,I.ASYMMETRIC]),function(t){t.ADD="ADD",t.SUB="SUB",t.MULT="MULT"}(P||(P={})),function(t){t.SQUARE="SQUARE",t.INVERSE="INVERSE",t.TRANSPOSE="TRANSPOSE",t.NORM="NORM",t.COLUMN_NORM="COLUMN_NORM"}(k||(k={})),function(t){t.SCALARMULT="SCALARMULT",t.SCALARADD="SCALARADD",t.SCALARPOW="SCALARPOW"}(G||(G={})),Object.prototype.toString,Promise.resolve(),n(934),n(8903);var U,V,F=n(1858);!function(t){t.none="none",t.bold="bold",t.dashed="dashed"}(U||(U={}));class H{get currentLineId(){return this._currentLineIdx}set currentLineId(t){t!==this._currentLineIdx&&(this._currentLineIdx=t,this.sp.render(this.ctx))}set linesToRender(t){this.updateLines(t),this.sp.render(this.ctx)}set linesVisibility(t){this.visibility=t,this.sp.render(this.ctx)}constructor(t,e,n,i,r=U.none){var o;this._currentLineIdx=-1,this.lineClicked=new F.Subject,this.lineHover=new F.Subject,this.mouseOverLineId=-1,this.arrowWidth=15,this.sp=t,this.xAxisCol=this.sp.dataFrame.columns.byName(e),this.yAxisCol=this.sp.dataFrame.columns.byName(n),this.canvas=this.sp.getInfo().canvas,this.ctx=this.canvas.getContext("2d"),this.currentLineStyle=r,this.updateLines(i),this.visibility=null!==(o=i.visibility)&&void 0!==o?o:new p.A(this.lines.from.length),i.visibility||this.visibility.setAll(!0,!1),i.arrowSize&&(this.arrowWidth=i.arrowSize),this.canvas.onmousedown=t=>{var e;(null===(e=this.lines)||void 0===e?void 0:e.skipMouseOverDetection)&&(this.mouseOverLineId=this.checkCoordsOnLine(t.offsetX,t.offsetY)),-1!==this.mouseOverLineId&&this.lineClicked.next({x:t.clientX,y:t.clientY,id:this.mouseOverLineId,event:t})},this.canvas.onmousemove=t=>{var e;this.mouseOverLineId=(null===(e=this.lines)||void 0===e?void 0:e.skipMouseOverDetection)?-1:this.checkCoordsOnLine(t.offsetX,t.offsetY),-1!==this.mouseOverLineId&&this.lineHover.next({x:t.clientX,y:t.clientY,id:this.mouseOverLineId,event:t})},t.onEvent("d4-before-draw-scene").subscribe((t=>{this.renderLines()}))}updateLines(t){this.lines=t,this.multipleLinesCounts=new Uint8Array(this.lines.from.length),t.skipMultiLineCalculation?this.multipleLinesCounts.fill(0):this.createMultiLinesIndices()}renderLines(){var t,e,n,i,r,o,s,a,l,u,c,h,d,f,p,m,g;const v=this.sp.getOptions().look,y=this.lines.colors||this.lines.widths||this.lines.opacities||this.lines.drawArrowsArr;y||(this.ctx.lineWidth=null!==(t=this.lines.width)&&void 0!==t?t:1,this.ctx.strokeStyle=`rgba(${null!==(e=this.lines.color)&&void 0!==e?e:"0,128,0"},${null!==(n=this.lines.opacity)&&void 0!==n?n:1})`);const C=v.sizeColumnName?this.sp.dataFrame.col(v.sizeColumnName):null,w=this.sp.dataFrame.filter,b=Math.pow(null!==(i=this.lines.shortLineThreshold)&&void 0!==i?i:5,2);for(let t=0;t<this.lines.from.length;t++)if(w.get(this.lines.from[t])&&w.get(this.lines.to[t])&&this.visibility.getBit(t)){let e=0;const{sizeFrom:n,sizeTo:i}=this.getMarkersSizes(v,C,t),w=this.sp.worldToScreen(this.xAxisCol.get(this.lines.from[t]),this.yAxisCol.get(this.lines.from[t]));let A=null==w?void 0:w.x,E=null==w?void 0:w.y;const S=this.sp.worldToScreen(this.xAxisCol.get(this.lines.to[t]),this.yAxisCol.get(this.lines.to[t]));let T=null==S?void 0:S.x,x=null==S?void 0:S.y;const _=Math.min(this.sp.viewBox.width,this.sp.viewBox.height);if(this.ctx.beginPath(),A&&E&&T&&x&&Math.hypot(T-A,x-E)/_>.01){if(y){const e=(null===(r=this.lines.colors)||void 0===r?void 0:r[t])?null===(o=this.lines.colors)||void 0===o?void 0:o[t]:null!==(s=this.lines.color)&&void 0!==s?s:"0,128,0",n=(null===(a=this.lines.opacities)||void 0===a?void 0:a[t])?null===(l=this.lines.opacities)||void 0===l?void 0:l[t]:null!==(u=this.lines.opacity)&&void 0!==u?u:1;this.ctx.strokeStyle=`rgba(${e},${n})`,this.ctx.lineWidth=(null===(c=this.lines.widths)||void 0===c?void 0:c[t])?null===(h=this.lines.widths)||void 0===h?void 0:h[t]:null!==(d=this.lines.width)&&void 0!==d?d:1}t===this._currentLineIdx&&this.toggleCurrentLineStyle(!0);const v=this.multipleLinesCounts[t];let C=null;if(v){e=this.getLineLength(A,E,T,x);const r=this.getPointOnDistance(A,E,T,x,i,e),o=this.getPointOnDistance(T,x,A,E,n,e);A=r.x,E=r.y,T=o.x,x=o.y,C=this.lines.from[t]>this.lines.to[t]?this.findControlPoint(v,A,E,T,x,t):this.findControlPoint(v,T,x,A,E,t),this.ctx.moveTo(A,E),this.ctx.quadraticCurveTo(C.x,C.y,T,x)}else(!this.lines.skipShortLines||Math.pow(T-A,2)+Math.pow(x-E,2)>b)&&(this.ctx.moveTo(A,E),this.ctx.lineTo(T,x));if((null!==(f=this.lines.drawArrows)&&void 0!==f?f:null===(p=this.lines.drawArrowsArr)||void 0===p?void 0:p.getBit(t))&&(e||(e=this.getLineLength(A,E,T,x)),e>this.arrowWidth)){const t=v?null:this.getPointOnDistance(A,E,T,x,i,e),n=v?C.x:A,r=v?C.y:E;this.canvasArrow(this.ctx,null!==(m=null==t?void 0:t.x)&&void 0!==m?m:A,null!==(g=null==t?void 0:t.y)&&void 0!==g?g:E,n,r)}this.ctx.stroke(),this.ctx.closePath(),t===this._currentLineIdx&&this.toggleCurrentLineStyle(!1)}}this.fillLeftBottomRect()}toggleCurrentLineStyle(t){switch(this.currentLineStyle){case U.bold:t?this.ctx.lineWidth+=2:this.ctx.lineWidth-=2;break;case U.dashed:t?this.ctx.setLineDash([5,5]):this.ctx.setLineDash([]);break;default:return}}getMarkersSizes(t,e,n){let i=3,r=3;return e?(i=(t.markerMinSize+(t.markerMaxSize-t.markerMinSize)*e.scale(this.lines.from[n]))/2,r=(t.markerMinSize+(t.markerMaxSize-t.markerMinSize)*e.scale(this.lines.to[n]))/2):t.markerDefaultSize&&(i=t.markerDefaultSize/2,r=t.markerDefaultSize/2),{sizeFrom:i,sizeTo:r}}fillLeftBottomRect(){const t=new Path2D;t.rect(this.sp.yAxisBox.minX,this.sp.yAxisBox.maxY,this.sp.yAxisBox.width,this.sp.xAxisBox.height),this.ctx.fillStyle="white",this.ctx.beginPath(),this.ctx.fill(t),this.ctx.closePath()}createMultiLinesIndices(){const t={};for(let e=0;e<this.lines.from.length;e++){let n=0,i=0;this.lines.from[e]<this.lines.to[e]?(n=this.lines.from[e],i=this.lines.to[e]):(n=this.lines.to[e],i=this.lines.from[e]),t[`${n}|${i}`]?(1===t[`${n}|${i}`].length&&(this.multipleLinesCounts[t[`${n}|${i}`][0]]=1,t[`${n}|${i}`].push(1)),this.multipleLinesCounts[e]=++t[`${n}|${i}`][1]):t[`${n}|${i}`]=[e]}}checkCoordsOnLine(t,e){let n=-1,i=null,r=null;const o=this.sp.getOptions().look,s=o.sizeColumnName?this.sp.dataFrame.col(o.sizeColumnName):null,a=this.sp.dataFrame.filter;for(let l=0;l<this.lines.from.length;l++)if(a.get(this.lines.from[l])&&a.get(this.lines.to[l])&&this.visibility.getBit(l)){const{sizeFrom:a,sizeTo:u}=this.getMarkersSizes(o,s,l),c=this.sp.worldToScreen(this.xAxisCol.get(this.lines.from[l]),this.yAxisCol.get(this.lines.from[l])),h=this.sp.worldToScreen(this.xAxisCol.get(this.lines.to[l]),this.yAxisCol.get(this.lines.to[l]));if(this.multipleLinesCounts[l]){const n=this.getLineLength(c.x,c.y,h.x,h.y),i=this.getPointOnDistance(c.x,c.y,h.x,h.y,u,n),o=this.getPointOnDistance(h.x,h.y,null==c?void 0:c.x,null==c?void 0:c.y,a,n),s=this.lines.from[l]>this.lines.to[l]?this.findControlPoint(this.multipleLinesCounts[l],i.x,i.y,o.x,o.y,l):this.findControlPoint(this.multipleLinesCounts[l],o.x,o.y,i.x,i.y,l);r=this.calculateDistToCurveLine(l,t,e,i,o,s)}else r=this.calculateDistToStraightLine(t,e,c,h);(!i&&null!==r&&r<5||i&&null!==r&&r<i)&&(i=r,n=l)}return n}calculateDistToStraightLine(t,e,n,i){const r=Math.min(n.x,i.x),o=Math.max(n.x,i.x),s=Math.min(n.y,i.y),a=Math.max(n.y,i.y);return t>=r-2&&t<=o+2&&e>=s-2&&e<=a+2?this.distToStraightLineSegment(t,e,n,i):null}distToStraightLineSegment(t,e,n,i){const r=(t,e,n,i)=>Math.pow(t-n,2)+Math.pow(e-i,2),o=r(n.x,n.y,i.x,i.y);if(0==o)return r(t,e,n.x,n.y);let s=((t-n.x)*(i.x-n.x)+(e-n.y)*(i.y-n.y))/o;return s=Math.max(0,Math.min(1,s)),r(t,e,n.x+s*(i.x-n.x),n.y+s*(i.y-n.y))}calculateDistToCurveLine(t,e,n,i,r,o){const s=Math.min(i.x,r.x,o.x),a=Math.max(i.x,r.x,o.x),l=Math.min(i.y,r.y,o.y),u=Math.max(i.y,r.y,o.y);if(e>=s-2&&e<=a+2&&n>=l-2&&n<=u+2){const t=a-s,c=u-l;return this.calculateDistToCurveInRect(e,n,i,o,r,t,c)}return null}calculateDistToCurveInRect(t,e,n,i,r,o,s){const a=Math.floor((o+s)/3),l=1/a,u=new Uint32Array(a),c=new Uint32Array(a),h=new Uint32Array(a);let d=null;const f=new p.A(a);for(let o=0;o<u.length;o++){const s=o*l,a=Math.pow(1-s,2)*n.x+2*s*(1-s)*i.x+Math.pow(s,2)*r.x,f=Math.pow(1-s,2)*n.y+2*s*(1-s)*i.y+Math.pow(s,2)*r.y,p=Math.abs(t-a),m=Math.abs(e-f),g=p+m;(!d||d>g)&&(d=g),h[o]=Math.max(p,m),u[o]=a,c[o]=f}for(let t=0;t<u.length;t++)h[t]<d&&f.setBit(t,!0,!1);let m=null;for(let n=-1;-1!==(n=f.findNext(n));){const i=Math.hypot(u[n]-t,c[n]-e);(!m||m>i)&&(m=i)}return m}getLineLength(t,e,n,i){return Math.sqrt(Math.pow(n-t,2)+Math.pow(i-e,2))}getPointOnDistance(t,e,n,i,r,o){const a=n-r*((n-t)/o),l=i-r*((i-e)/o);return new s.Point(a,l)}findControlPoint(t,e,n,i,r,o){const a=e+(i-e)/2,l=n+(r-n)/2;let u=a-e,c=l-n;const h=Math.sqrt(u*u+c*c);u/=h,c/=h;const d=50*Math.ceil(t/2);return t%2==0?new s.Point(a+d/2*c,l-d/2*u):new s.Point(a-d/2*c,l+d/2*u)}canvasArrow(t,e,n,i,r){const o=Math.atan2(i-e,r-n)+Math.PI;t.moveTo(e-this.arrowWidth*Math.sin(o-Math.PI/10),n-this.arrowWidth*Math.cos(o-Math.PI/10)),t.lineTo(e,n),t.lineTo(e-this.arrowWidth*Math.sin(o+Math.PI/10),n-this.arrowWidth*Math.cos(o+Math.PI/10))}}!function(t){t.EUCLIDEAN="EUCLIDEAN",t.MANHATTAN="MANHATTAN"}(V||(V={}));var B,q=function(t,e,n,i){return new(n||(n=Promise))((function(r,o){function s(t){try{l(i.next(t))}catch(t){o(t)}}function a(t){try{l(i.throw(t))}catch(t){o(t)}}function l(t){var e;t.done?r(t.value):(e=t.value,e instanceof n?e:new n((function(t){t(e)}))).then(s,a)}l((i=i.apply(t,e||[])).next())}))};!function(t){t.SEQUENCE_VARIABILITY_MAP="Sequence Variability Map",t.MOST_POTENT_RESIDUES="Most Potent Residues",t.LOGO_SUMMARY_TABLE="Logo Summary Table",t.DENDROGRAM="Dendrogram",t.CLUSTER_MAX_ACTIVITY="Active peptide selection"}(B||(B={}));class Y{constructor(t){this.isBitsetChangedInitialized=!1,this.isUserChangedSelection=!0,this._dm=null,this.isInitialized=!1,this.isRibbonSet=!1,this.webLogoSelectedMonomers={},this.webLogoBounds={},this.cachedWebLogoTooltip={bar:"",tooltip:null},this._layoutEventInitialized=!1,this.subs=[],this.isHighlighting=!1,this.controlFire=!1,this.accordionSource=null,this._sequenceSpaceViewer=null,this._mclViewer=null,this._monomerPositionStats=null,this._settings=null,this._sequenceSpaceCols=[],this._mclCols=[],this._webLogoSelection=null,this.df=t}get monomerPositionStats(){var t;if(null!==this._monomerPositionStats)return this._monomerPositionStats;const e=this.getScaledActivityColumn();return null===this.positionColumns||null===e?null:(null!==(t=this._monomerPositionStats)&&void 0!==t||(this._monomerPositionStats=(0,M.Ej)(e,this.df.filter,this.positionColumns)),this._monomerPositionStats)}get analysisView(){return void 0===this._analysisView&&(this._analysisView=g()(o.shell.tableViews).find((({dataFrame:t})=>(null==t?void 0:t.getTag(s.TAGS.ID))===this.id)),void 0===this._analysisView&&(this._analysisView=o.shell.addTableView(this.df))),"1"===this.df.getTag(C.gp.MULTIPLE_VIEWS)||this._layoutEventInitialized||o.shell.isInDemo||(o.shell.v=this._analysisView),this._analysisView.grid.invalidate(),this._analysisView}get settings(){var t;const e=this.df.getTag(C.gp.SETTINGS);return null==e?null:(null!==(t=this._settings)&&void 0!==t||(this._settings=JSON.parse(e)),this._settings)}set settings(t){var e,n,i;const r=Object.entries(t),o=Object.assign({},null!==(n=null===(e=this.settings)||void 0===e?void 0:e.sequenceSpaceParams)&&void 0!==n?n:{}),s=new Set;for(const[t,e]of r)switch(this.settings[t]=e,t){case"activityColumnName":case"activityScaling":s.add("activity"),s.add("stats");break;case"showDendrogram":s.add("dendrogram");break;case"showClusterMaxActivity":s.add("clusterMaxActivity");break;case"showSequenceSpace":s.add("showSequenceSpace");break;case"showLogoSummaryTable":s.add("logoSummaryTable");break;case"showMonomerPosition":s.add("monomerPosition");break;case"showMostPotentResidues":s.add("mostPotentResidues");break;case"columns":s.add("columns");break;case"sequenceSpaceParams":s.add("sequenceSpaceParams");break;case"mclSettings":s.add("mclSettings")}if(this.df.setTag("settings",JSON.stringify(this._settings)),this.isInitialized){if(s.has("sequenceSpaceParams")){const t=this.settings.sequenceSpaceParams;Object.entries(t).some((([t,e])=>o[t]!==e&&"epsilon"!==t&&"minPts"!==t&&"clusterEmbeddings"!==t))||(s.delete("sequenceSpaceParams"),this.settings.sequenceSpaceParams.clusterEmbeddings&&s.add("clusterParams"))}s.has("sequenceSpaceParams")&&s.delete("clusterParams");for(const t of s)switch(t){case"activity":this.createScaledCol();break;case"stats":this.webLogoSelection=(0,b.ZR)(this.positionColumns),this.webLogoBounds={},this.cachedWebLogoTooltip={bar:"",tooltip:null},this._monomerPositionStats=null;break;case"dendrogram":this.settings.showDendrogram?this.addDendrogram():this.closeViewer(B.DENDROGRAM);break;case"clusterMaxActivity":this.settings.showClusterMaxActivity?this.addClusterMaxActivityViewer():this.closeViewer(B.CLUSTER_MAX_ACTIVITY);break;case"logoSummaryTable":this.settings.showLogoSummaryTable?this.addLogoSummaryTable():this.closeViewer(B.LOGO_SUMMARY_TABLE);break;case"monomerPosition":this.settings.showMonomerPosition?this.addMonomerPosition():this.closeViewer(B.SEQUENCE_VARIABILITY_MAP);break;case"mostPotentResidues":this.settings.showMostPotentResidues?this.addMostPotentResidues():this.closeViewer(B.MOST_POTENT_RESIDUES);break;case"columns":const t=this.findViewer(B.LOGO_SUMMARY_TABLE);t._viewerGrid=null,t._logoSummaryTable=null,t.render();const e=this.findViewer(B.MOST_POTENT_RESIDUES);e._viewerGrid=null,e.render();break;case"sequenceSpaceParams":case"showSequenceSpace":this.settings.showSequenceSpace&&this.addSequenceSpace({clusterEmbeddings:null===(i=this.settings.sequenceSpaceParams)||void 0===i?void 0:i.clusterEmbeddings});break;case"clusterParams":this.clusterEmbeddings();break;case"mclSettings":this.addMCLClusters()}}}get webLogoSelection(){var t;const e=this.df.getTag(`${C.YX.WL}${C.gp.INVARIANT_MAP_SELECTION}`);return null!==(t=this._webLogoSelection)&&void 0!==t||(this._webLogoSelection=null===e&&null!==this.positionColumns?(0,b.ZR)(this.positionColumns):JSON.parse(null!=e?e:"{}")),this._webLogoSelection}set webLogoSelection(t){this._webLogoSelection=t,this.df.setTag(`${C.YX.WL}${C.gp.INVARIANT_MAP_SELECTION}`,JSON.stringify(t)),this.fireBitsetChanged(null),this.analysisView.grid.invalidate()}get positionColumns(){const t=g()(this.df.columns.byTags({[C.gp.POSITION_COL]:"true"})).toArray();return 0===t.length?null:t}get id(){return this.df.getTag(s.TAGS.ID)}get alphabet(){return this.df.getCol(this.settings.sequenceColumnName).getTag(a.gp.alphabet)}static getInstance(t){var e,n,i;return t.columns.contains(C.$2.ACTIVITY_SCALED)&&!t.columns.contains(C.$2.ACTIVITY)&&(t.getCol(C.$2.ACTIVITY_SCALED).name=C.$2.ACTIVITY),null!==(e=(n=t.temp)[i=Y.modelName])&&void 0!==e||(n[i]=new Y(t)),t.temp[Y.modelName]}modifyWebLogoSelection(t,e={shiftPressed:!1,ctrlPressed:!1},n=!0){n?this.webLogoSelection=(0,b.vW)(this.webLogoSelection,t,e):this._webLogoSelection=(0,b.vW)(this.webLogoSelection,t,e)}getVisibleSelection(){return this.df.selection.clone().and(this.df.filter)}createAccordion(){var t,e,n,i,l,u;const c=null===(t=o.shell.t)||void 0===t?void 0:t.temp[Y.modelName];if(!c)return null;const h=r.accordion("Peptides analysis panel");h.root.style.width="100%";const d=c.getVisibleSelection(),f=c.df.filter.anyFalse?` among ${c.df.filter.trueCount} filtered`:"",p=t=>{const e=[];for(const[n,i]of Object.entries(t))for(const t of i)e.push(`${n}:${t}`);return e.join(", ")},m=c.findViewer(B.LOGO_SUMMARY_TABLE),v=[],C=(null===m?[]:m.clusterSelection[x.W.ORIGINAL].concat(m.clusterSelection[x.W.CUSTOM])).join(", ");0!==C.length&&(v.push(r.h1("Logo summary table selection")),v.push(r.divText(`Selected clusters: ${C}`)));const w=c.findViewer(B.SEQUENCE_VARIABILITY_MAP),_=p(null!==(e=null==w?void 0:w.invariantMapSelection)&&void 0!==e?e:{}),N=p(null!==(n=null==w?void 0:w.mutationCliffsSelection)&&void 0!==n?n:{});0===_.length&&0===N.length||v.push(r.h1("Sequence Variabily Map viewer selection")),0!==_.length&&v.push(r.divText(`Selected monomer-positions: ${_}`)),0!==N.length&&v.push(r.divText(`Selected mutation cliffs pairs: ${N}`));const O=c.findViewer(B.MOST_POTENT_RESIDUES),L=p(null!==(i=null==O?void 0:O.mutationCliffsSelection)&&void 0!==i?i:{});0!==L.length&&(v.push(r.h1("Most Potent Residues viewer selection")),v.push(r.divText(`Selected monomer-positions: ${L}`)));const I=p(c.webLogoSelection);0!==I.length&&(v.push(r.h1("WebLogo selection")),v.push(r.divText(`Selected monomers: ${I}`)));const R=r.div(r.divV(v));h.addTitle(r.divV([r.h1(`${d.trueCount} selected rows${f}`),R],"css-gap-small")),d.anyTrue&&h.addPane("Actions",(()=>{try{const t=r.label("New view");if(y()(t).addClass("d4-link-action"),t.onclick=()=>c.createNewView(),t.onmouseover=t=>r.tooltip.show("Creates a new view from current selection",t.clientX+5,t.clientY+5),null===m)return r.divV([t]);const e=r.label("New cluster");y()(e).addClass("d4-link-action"),e.onclick=()=>{if(null===m)throw new Error("Logo summary table viewer is not found");m.clusterFromSelection()},e.onmouseover=t=>r.tooltip.show("Creates a new cluster from selection",t.clientX+5,t.clientY+5);const n=r.label("Remove cluster");return y()(n).addClass("d4-link-action"),n.onclick=()=>{const t=c.findViewer(B.LOGO_SUMMARY_TABLE);if(null===t)throw new Error("Logo summary table viewer is not found");t.removeCluster()},n.onmouseover=t=>r.tooltip.show("Removes currently selected custom cluster",t.clientX+5,t.clientY+5),n.style.visibility=0===m.clusterSelection[x.W.CUSTOM].length?"hidden":"visible",r.divV([t,e,n])}catch(t){const e=r.divText("Error in Actions");return r.tooltip.bind(e,String(t)),e}}),!0);let P=c.settings;const k=[w,O,m].filter((t=>null!==t&&(t.type!==this.accordionSource||(P=t,!1))));if(null===P)throw new Error("PeptidesError: Model is the source of accordion but is not initialized");P!==c.settings&&k.push(c.settings);const G=k.filter((t=>null!==t&&(0,b.$s)(P,t)&&(t!==c.settings||c.isInitialized)));G.push(P);const D=s.BitSet.create(c.df.rowCount);for(const t of G){const e=t===this.settings?(0,b.KT)(this.webLogoSelection,this.monomerPositionStats):t instanceof x.s?(0,b.KT)(t.clusterSelection,t.clusterStats):t instanceof A.xN?(0,b.KT)(t.mutationCliffsSelection,(0,b.qI)(null!==(l=t.mutationCliffs)&&void 0!==l?l:new Map,c.df.rowCount)):null;if(null!==e&&D.or(e),t instanceof A.J){const e=(0,b.KT)(t.invariantMapSelection,t.monomerPositionStats);null!==e&&D.or(e)}}const U=P;P===c.settings||U instanceof x.s||null==U.mutationCliffs||h.addPane("Mutation Cliffs pairs",(()=>(0,S.F)(c.df,{mutationCliffs:U.mutationCliffs,mutationCliffsSelection:U.mutationCliffsSelection,gridColumns:c.analysisView.grid.columns,sequenceColumnName:U.sequenceColumnName,positionColumns:U.positionColumns,activityCol:U.getScaledActivityColumn()}).root),!0);const V=P===c.settings,F=V?this.webLogoSelection:P instanceof A.J?P.invariantMapSelection:{},H=P instanceof x.s?P.clusterSelection:null!==(u=null==m?void 0:m.clusterSelection)&&void 0!==u?u:{};h.addPane("Distribution",(()=>{var t;try{return(0,T.HV)(c.df,{peptideSelection:D,columns:V?null!==(t=c.settings.columns)&&void 0!==t?t:{}:P.getAggregationColumns(),activityCol:V?c.getScaledActivityColumn():P.getScaledActivityColumn(),monomerPositionSelection:F,clusterSelection:H,clusterColName:null==m?void 0:m.clustersColumnName})}catch(t){const e=r.divText("Error in Distribution");return r.tooltip.bind(e,String(t)),e}}),!0);const q=(t,e)=>{if(null==t||null==e)return!1;for(const[n,i]of Object.entries(t))if(i!==e[n])return!1;return!0};return h.addPane("Selection",(()=>{var t;try{return function(t,e){var n,i;if(0===e.tableSelection.trueCount)return r.divText("No compounds selected");const o=s.DataFrame.create(t.rowCount);o.name="Selected compounds",o.filter.copyFrom(e.tableSelection);const a=g()(t.columns.numerical);let l=null;for(let t=1;t<e.gridColumns.length;t++){const r=e.gridColumns.byIndex(t);if(!r.visible)continue;const u=r.column;if(u.type===s.COLUMN_TYPE.BOOL)continue;null===l&&r.grid&&(null===(n=r.grid.sortByColumns)||void 0===n?void 0:n.length)>0&&(null===(i=r.grid.sortTypes)||void 0===i?void 0:i.length)===r.grid.sortByColumns.length&&(l={cols:r.grid.sortByColumns,types:r.grid.sortTypes});let c=null,h=null;try{c=u.getRawData(),h=u.categories}catch(t){}const d=c&&h?a.some((t=>t.name===u.name))?t=>c[t]:t=>h[c[t]]:t=>u.get(t),f=u.name===e.activityColumn.name?o.columns.addNewFloat(r.name).init((t=>d(t))):o.columns.addNewVirtual(r.name,(t=>d(t)),u.type);for(const[t,e]of u.tags)f.setTag(t,e)}const u=o.plot.grid();u.props.showRowHeader=!1,u.root.style.maxWidth="100%",s.debounce(r.onSizeChanged(u.root),50).subscribe((t=>{var e;const n=u.root.parentElement;(null===(e=null==n?void 0:n.parentElement)||void 0===e?void 0:e.classList.contains("panel-content"))&&(u.root.style.height="calc(100% - 20px)",u.root.style.width="calc(100% - 20px)",u.root.style.position="absolute",u.root.style.right="10px",u.root.style.top="10px")})),(0,b.zz)(u);const c=r.box(u.root);c.style.marginLeft="0px",setTimeout((()=>{null!==l&&u.sort(l.cols,l.types);for(let t=1;t<e.gridColumns.length;t++){const n=e.gridColumns.byIndex(t);n.visible&&u.col(n.name)&&(u.col(n.name).width=n.width)}}),500);const h=(0,M.Ej)(e.activityColumn,o.filter,e.positionColumns,{isFiltered:o.filter.anyTrue||o.filter.anyFalse}),d={isSelectionTable:!0,cachedWebLogoTooltip:()=>({bar:"",tooltip:null}),webLogoBounds:()=>({}),colorPalette:()=>e.colorPalette},f={x:0,y:0,monomerPosition:{},mpStats:h};return e.isAnalysis&&(0,E.FZ)(u,h,e.positionColumns,e.activityColumn,d,f),c}(c.df,{positionColumns:V?c.positionColumns:P.positionColumns,columns:V?null!==(t=c.settings.columns)&&void 0!==t?t:{}:P.getAggregationColumns(),activityColumn:V?c.getScaledActivityColumn():P.getScaledActivityColumn(),gridColumns:c.analysisView.grid.columns,colorPalette:(0,a.SM)(c.df.getCol(V?c.settings.sequenceColumnName:P.sequenceColumnName)),tableSelection:c.getCombinedSelection(),isAnalysis:null!==c.settings&&(V||q(c.settings.columns,P.getAggregationColumns()))})}catch(t){const e=r.divText("Error in Selection");return r.tooltip.bind(e,String(t)),e}}),!0),h}getScaledActivityColumn(t=!1){const e=this.df.col(C.$2.ACTIVITY);return t&&null!==e?s.DataFrame.fromColumns([e]).clone(this.df.filter).getCol(e.name):e}updateGrid(){this.joinDataFrames(),this.createScaledCol(),this.webLogoBounds={};const t={selectionCallback:(t,e)=>this.modifyWebLogoSelection(t,e),unhighlightCallback:()=>this.unhighlight(),colorPalette:()=>(0,a.SM)(this.df.getCol(this.settings.sequenceColumnName)),webLogoBounds:()=>this.webLogoBounds,cachedWebLogoTooltip:()=>this.cachedWebLogoTooltip,highlightCallback:(t,e,n)=>(0,b.dl)(t,e,n),isSelectionTable:!1,headerSelectedMonomers:()=>this.webLogoSelectedMonomers};if(null===this.monomerPositionStats||null===this.positionColumns)throw new Error("PeptidesError: Could not updage grid: monomerPositionStats or positionColumns are null");E.FZ(this.analysisView.grid,this.monomerPositionStats,this.positionColumns,this.getScaledActivityColumn(),t),this._layoutEventInitialized||(o.events.onViewLayoutApplied.subscribe((t=>{t.view.id===this.analysisView.id&&this.updateGrid()})),this._layoutEventInitialized=!0),this.setTooltips(),this.setBitsetCallback(),this.setGridProperties()}joinDataFrames(){const t=this.df.name,e=this.df.columns,n=(0,c.R)(this.df.getCol(this.settings.sequenceColumnName)),i=n.columns.names();for(const t of i){let i=this.df.col(t);const r=n.getCol(t);null!==i&&e.remove(t);const o=r.categories,s=r.getRawData();i=e.addNew(r.name,r.type).init((t=>o[s[t]])),i.setTag(C.gp.ANALYSIS_COL,"true"),i.setTag(C.gp.POSITION_COL,"true"),E.rI(i,this.alphabet)}this.df.name=t}createScaledCol(){const t=this.analysisView.grid,e=(0,b.Y1)(this.df.getCol(this.settings.activityColumnName),this.settings.activityScaling);this.df.columns.replace(C.$2.ACTIVITY,e),t.columns.setOrder([e.name])}unhighlight(){this.isHighlighting&&(this.df.rows.highlight(null),this.isHighlighting=!1)}setTooltips(){this.analysisView.grid.onCellTooltip(((t,e,n)=>{var i,r;return!(!t.isColHeader||(null===(i=t.tableColumn)||void 0===i?void 0:i.semType)!==C.uF.MONOMER)||!(!t.isTableCell||(null===(r=t.tableColumn)||void 0===r?void 0:r.semType)!==C.uF.MONOMER)&&((0,D.cr)(t.cell.value,e,n),!0)}))}getCombinedSelection(){var t,e,n,i,r,o,a,l;const u=new p.A(this.df.rowCount,!1),c=(t,e)=>{for(const[n,i]of Object.entries(t))for(const t of i){const i=null==e?void 0:e[n];if(void 0===i)continue;const r=i[t];void 0!==r&&u.or(r.mask)}};c(this.webLogoSelection,this.monomerPositionStats);const h=this.findViewer(B.SEQUENCE_VARIABILITY_MAP);c(null!==(t=null==h?void 0:h.invariantMapSelection)&&void 0!==t?t:{},null!==(e=null==h?void 0:h.monomerPositionStats)&&void 0!==e?e:null);const d=(t,e)=>{var n,i;for(const[r,o]of Object.entries(t))for(const t of o){const o=null!==(i=null===(n=null==e?void 0:e.get(t))||void 0===n?void 0:n.get(r))&&void 0!==i?i:null;if(null!==o)for(const[t,e]of o.entries()){u.setTrue(t);for(const t of e)u.setTrue(t)}}};d(null!==(n=null==h?void 0:h.mutationCliffsSelection)&&void 0!==n?n:{},null!==(i=null==h?void 0:h.mutationCliffs)&&void 0!==i?i:null);const f=this.findViewer(B.MOST_POTENT_RESIDUES);d(null!==(r=null==f?void 0:f.mutationCliffsSelection)&&void 0!==r?r:{},null!==(o=null==f?void 0:f.mutationCliffs)&&void 0!==o?o:null);const m=this.findViewer(B.LOGO_SUMMARY_TABLE);for(const t of Object.keys(null!==(a=null==m?void 0:m.clusterSelection)&&void 0!==a?a:{}))for(const e of null!==(l=m.clusterSelection[t])&&void 0!==l?l:[]){const n=m.clusterStats[t][e];u.or(n.mask)}return s.BitSet.fromBytes(u.buffer.buffer,u.length)}setBitsetCallback(){if(this.isBitsetChangedInitialized)return;const t=this.df.selection,e=this.df.filter,n=()=>{try{const t=this.createAccordion();if(null===t)return;o.shell.o=t.root}catch(t){console.error(t)}};t.onChanged.subscribe((()=>{if(this.controlFire)this.controlFire=!1;else try{this.isUserChangedSelection||t.copyFrom(this.getCombinedSelection(),!1)}catch(t){N._package.logger.debug("Peptides: Error on selection changed"),N._package.logger.debug(t)}finally{n()}})),e.onChanged.subscribe((()=>{var t,e;try{if(this.controlFire)return void(this.controlFire=!1);const n=this.findViewer(B.LOGO_SUMMARY_TABLE);null!==n&&void 0!==n.model&&(n._logoSummaryTable=null!==(t=n.createLogoSummaryTable())&&void 0!==t?t:n._logoSummaryTable,n._viewerGrid=null!==(e=n.createLogoSummaryTableGrid())&&void 0!==e?e:n._viewerGrid,n.render())}catch(t){N._package.logger.debug("Peptides: Error on filter changed"),N._package.logger.debug(t)}finally{n()}})),this.isBitsetChangedInitialized=!0}fireBitsetChanged(t,e=!1){this.accordionSource=t,this.isBitsetChangedInitialized||this.setBitsetCallback(),this.isUserChangedSelection=!1,this.df.selection.fireChanged(),e&&this.df.filter.fireChanged(),this.controlFire=!0,this.df.selection.fireChanged(),e&&this.df.filter.fireChanged(),this.isUserChangedSelection=!0,this.webLogoSelectedMonomers=(0,b.qx)(this.df)}setGridProperties(t){var e,n,i,r;const o=this.analysisView.grid,s=o.props;s.allowColSelection=null!==(e=null==t?void 0:t.allowColSelection)&&void 0!==e&&e,s.allowEdit=null!==(n=null==t?void 0:t.allowEdit)&&void 0!==n&&n,s.showReadOnlyNotifications=null!==(i=null==t?void 0:t.showReadOnlyNotifications)&&void 0!==i&&i,s.showCurrentRowIndicator=null!==(r=null==t?void 0:t.showCurrentRowIndicator)&&void 0!==r&&r;const l=this.positionColumns;if(null===l)throw new Error("PeptidesError: Could not set grid properties: positionColumns are null");let u=10;const c=o.canvas.getContext("2d");if(null===c)throw new Error("PeptidesError: Could not set grid properties: canvas context is null");for(const t of l){const e=(0,a.zS)(t.categories.reduce(((t,e)=>t.length>e.length?t:e)),6),n=Math.ceil(c.measureText(e).width);u=Math.max(u,n)}const h=l.map((t=>t.name));for(let t=1;t<this.analysisView.grid.columns.length;++t){const e=this.analysisView.grid.columns.byIndex(t);if(null===e)throw new Error(`PeptidesError: Could not get analysis view: grid column with index '${t}' is null`);if(null===e.column)throw new Error(`PeptidesError: Could not get analysis view: grid column with index '${t}' has null column`);e.visible=h.includes(e.column.name)||e.column.name===C.$2.ACTIVITY}setTimeout((()=>{for(const t of l){const e=o.col(t.name);if(null===e)throw new Error(`PeptidesError: Could not set column width: grid column '${t.name}' is null`);e.width=u+15}}),100)}closeViewer(t){const e=this.findViewer(t);null==e||e.detach(),null==e||e.close()}findViewerNode(t){for(const e of this.analysisView.dockManager.rootNode.children)if(e.container.containerElement.innerHTML.includes(t))return e;return null}addDendrogram(){return q(this,void 0,void 0,(function*(){const t=s.TaskBarProgressIndicator.create("Calculating distance matrix...");try{const t=s.Func.find({package:"Dendrogram",name:"hierarchicalClustering"})[0];if(!t||4!==t.inputs.length)throw new Error("Correct dendrogram function is not found");yield t.apply({df:this.df,colNameList:[this.settings.sequenceColumnName],distance:"euclidean",linkage:"complete"})}catch(t){N._package.logger.error(t)}finally{t.close()}}))}init(t){if(!this.isInitialized){if(this.settings=t,this.isInitialized=!0,!this.isRibbonSet&&"1"!==this.df.getTag(C.gp.MULTIPLE_VIEWS)){const t=r.iconFA("wrench",(()=>(0,_.OH)(this)),"Peptides analysis settings");this.analysisView.setRibbonPanels([[t]],!1),this.isRibbonSet=!0,this.updateGrid()}this.subs.push(o.events.onAccordionConstructed.subscribe((t=>{if(!(o.shell.o instanceof s.SemanticValue||o.shell.o instanceof s.Column&&this.df.columns.toList().includes(o.shell.o)))return;const e=t.getPane("Actions"),n=y()(e.root).find(".d4-flex-col"),a=r.label("Calculate identity");a.classList.add("d4-link-action"),r.tooltip.bind(a,"Adds a column with fractions of matching monomers against sequence in the current row"),a.onclick=()=>{const t=this.df.getCol(this.settings.sequenceColumnName);d(this.df,t,t.get(this.df.currentRowIdx),i.IDENTITY).then((e=>e.setTag(C.gp.IDENTITY_TEMPLATE,t.get(this.df.currentRowIdx)))).catch((t=>N._package.logger.debug(t)))},n.append(r.span([a],"d4-markdown-row"));const l=r.label("Calculate similarity");l.classList.add("d4-link-action"),r.tooltip.bind(l,"Adds a column with sequence similarity scores against sequence in the current row"),l.onclick=()=>{const t=this.df.getCol(this.settings.sequenceColumnName);d(this.df,t,t.get(this.df.currentRowIdx),i.SIMILARITY).then((e=>e.setTag(C.gp.SIMILARITY_TEMPLATE,t.get(this.df.currentRowIdx)))).catch((t=>N._package.logger.debug(t)))},n.append(r.span([l],"d4-markdown-row"))}))),this.subs.push(o.events.onViewRemoved.subscribe((t=>{t.id===this.analysisView.id&&this.subs.forEach((t=>t.unsubscribe())),o.log.debug(`Peptides: view ${t.name} removed`)}))),this.subs.push(o.events.onTableRemoved.subscribe((t=>{t.id===this.df.id&&this.subs.forEach((t=>t.unsubscribe())),o.log.debug(`Peptides: table ${t.name} removed`)}))),this.subs.push(o.events.onProjectClosed.subscribe((t=>{t.id===o.shell.project.id&&this.subs.forEach((t=>t.unsubscribe())),o.log.debug(`Peptides: project ${t.name} closed`)}))),this.fireBitsetChanged(null,!0),this.analysisView.grid.invalidate()}}findViewer(t){return g()(this.analysisView.viewers).find((e=>e.type===t))||null}addLogoSummaryTable(t){return q(this,void 0,void 0,(function*(){null!=t||(t={sequenceColumnName:this.settings.sequenceColumnName,clustersColumnName:g()(this.df.columns.categorical).next().value,activityColumnName:this.settings.activityColumnName,activityScaling:this.settings.activityScaling});const e=yield this.df.plot.fromType(B.LOGO_SUMMARY_TABLE,t);this.analysisView.dockManager.dock(e,s.DOCK_TYPE.RIGHT,null,B.LOGO_SUMMARY_TABLE),e.viewerGrid.invalidate()}))}addClusterMaxActivityViewer(t){return q(this,void 0,void 0,(function*(){var e,n,i,r,o,a,l;const u=null!==(r=null!==(n=null===(e=this._mclCols)||void 0===e?void 0:e.find((t=>t.toLowerCase().startsWith("cluster (mcl)"))))&&void 0!==n?n:null===(i=this.findViewer(B.LOGO_SUMMARY_TABLE))||void 0===i?void 0:i.clustersColumnName)&&void 0!==r?r:null===(o=this._sequenceSpaceCols)||void 0===o?void 0:o.find((t=>t.toLowerCase().startsWith("cluster")));null!=t||(t={activityColumnName:this.settings.activityColumnName,clusterColumnName:null!=u?u:null===(a=g()(this.df.columns.categorical).next().value)||void 0===a?void 0:a.name,activityTarget:C.wf.HIGH,connectivityColumnName:this._mclCols.find((t=>t.toLowerCase().startsWith("connectivity"))),clusterSizeThreshold:20,activityThreshold:1e3});const c=yield this.df.plot.fromType(B.CLUSTER_MAX_ACTIVITY,t),h=null!==(l=this.findViewerNode(B.LOGO_SUMMARY_TABLE))&&void 0!==l?l:null;this.analysisView.dockManager.dock(c,h?s.DOCK_TYPE.DOWN:s.DOCK_TYPE.RIGHT,h,B.CLUSTER_MAX_ACTIVITY)}))}addMonomerPosition(t){return q(this,void 0,void 0,(function*(){null!=t||(t={maxMutations:1,activityScaling:this.settings.activityScaling,activityColumnName:this.settings.activityColumnName,sequenceColumnName:this.settings.sequenceColumnName,minActivityDelta:0,activityTarget:C.wf.HIGH});const e=yield this.df.plot.fromType(B.SEQUENCE_VARIABILITY_MAP,t),n=this.findViewer(B.MOST_POTENT_RESIDUES),i=this.analysisView.dockManager,[r,o,a]=null===n?[s.DOCK_TYPE.DOWN,null,void 0]:[s.DOCK_TYPE.LEFT,this.findViewerNode(B.MOST_POTENT_RESIDUES),.7];i.dock(e,r,o,B.SEQUENCE_VARIABILITY_MAP,a)}))}addMostPotentResidues(t){return q(this,void 0,void 0,(function*(){null!=t||(t={activityScaling:this.settings.activityScaling,activityColumnName:this.settings.activityColumnName,sequenceColumnName:this.settings.sequenceColumnName,minActivityDelta:0,maxMutations:1,activityTarget:C.wf.HIGH});const e=yield this.df.plot.fromType(B.MOST_POTENT_RESIDUES,t),n=this.findViewer(B.SEQUENCE_VARIABILITY_MAP),i=this.analysisView.dockManager,[r,o,a]=null===n?[s.DOCK_TYPE.DOWN,null,void 0]:[s.DOCK_TYPE.RIGHT,this.findViewerNode(B.SEQUENCE_VARIABILITY_MAP),.3];i.dock(e,r,o,B.MOST_POTENT_RESIDUES,a)}))}createNewView(){const t=this.getVisibleSelection(),e=this.df.clone(t);for(const[t,n]of e.tags)e.setTag(t,t===C.gp.SETTINGS?n:"");e.name="Peptides Multiple Views",e.setTag(C.gp.MULTIPLE_VIEWS,"1");const n=o.shell.addTableView(e),i=this.findViewer(B.LOGO_SUMMARY_TABLE);return null!=i&&n.addViewer(B.LOGO_SUMMARY_TABLE,{[`sequence${C.To}`]:i.sequenceColumnName,[`activity${C.To}`]:i.activityColumnName,activityScaling:i.activityScaling,webLogoMode:i.webLogoMode,membersRatioThreshold:i.membersRatioThreshold,[`clusters${C.To}`]:i.clustersColumnName}),e.getTag(s.TAGS.ID)}clusterEmbeddings(){return q(this,void 0,void 0,(function*(){var t,e;if(!this._sequenceSpaceCols||0===this._sequenceSpaceCols.length)return void o.shell.warning("Embeddings columns are not initialized");const i=this._sequenceSpaceCols.filter((t=>t.toLowerCase().startsWith("embed_")));if(2!==i.length)return void o.shell.warning(`Found ${i.length} embeddings columns, expected 2`);const r=this._sequenceSpaceCols.filter((t=>t.toLowerCase().startsWith("cluster")));r.length>0&&this.df.columns.remove(r[0]);const s=this.df.getCol(i[0]).getRawData(),a=this.df.getCol(i[1]).getRawData(),l=null!==(t=this.settings.sequenceSpaceParams.epsilon)&&void 0!==t?t:.01,u=null!==(e=this.settings.sequenceSpaceParams.minPts)&&void 0!==e?e:4,c=yield function(t,e,i,r){return o=this,s=void 0,l=function*(){return new Promise((function(o,s){const a=new Worker(new URL(n.p+n.u(682),n.b));a.postMessage({embedX:t,embedY:e,minPts:r,epsilon:i}),a.onmessage=({data:{error:t,clusters:e}})=>{a.terminate(),t?s(t):o(e)}}))},new((a=void 0)||(a=Promise))((function(t,e){function n(t){try{r(l.next(t))}catch(t){e(t)}}function i(t){try{r(l.throw(t))}catch(t){e(t)}}function r(e){var r;e.done?t(e.value):(r=e.value,r instanceof a?r:new a((function(t){t(r)}))).then(n,i)}r((l=l.apply(o,s||[])).next())}));var o,s,a,l}(s,a,l,u),h=this.df.columns.getUnusedName("Cluster (DBSCAN)"),d=this.df.columns.addNewString(h);d.init((t=>c[t].toString())),null!==this._sequenceSpaceViewer&&(this._sequenceSpaceViewer.props.colorColumnName=d.name),this._sequenceSpaceCols=[i[0],i[1],d.name];const f=this.analysisView.grid.col(d.name);f&&(f.visible=!1)}))}addMCLClusters(){return q(this,void 0,void 0,(function*(){var t,e,i,a,l;if(null!==this._mclViewer)try{null===(t=this._mclViewer)||void 0===t||t.detach(),null===(e=this._mclViewer)||void 0===e||e.close()}catch(t){}0!==this._mclCols.length&&this._mclCols.forEach((t=>this.df.columns.remove(t))),this._mclCols=[];const u=this.df.getCol(this.settings.sequenceColumnName);null!==(i=(l=this.settings).mclSettings)&&void 0!==i||(l.mclSettings=new w.av);const c=this.settings.mclSettings;let h=0;const d=this.df.onColumnsAdded.subscribe((t=>{for(const e of t.columns)if((e.name.toLowerCase().startsWith("embed")||e.name.toLowerCase().startsWith("cluster")||e.name.toLowerCase().startsWith("connectivity"))&&e.name.toLowerCase().includes("mcl")){const t=this.analysisView.grid.col(e.name);if(null==t||this._mclCols.includes(e.name))continue;t.visible=!1,this._mclCols.push(e.name),h++}5===h&&d.unsubscribe()})),f=o.events.onViewerAdded.subscribe((t=>{try{const e=t.args.viewer;if(e.type===s.VIEWER.SCATTER_PLOT){if(this._sequenceSpaceViewer&&this.analysisView.dockManager.findNode(this._sequenceSpaceViewer.root)){const t=this.analysisView.dockManager.findNode(this._sequenceSpaceViewer.root);setTimeout((()=>{this.analysisView.dockManager.dock(e,s.DOCK_TYPE.FILL,t)}))}f.unsubscribe()}}catch(t){console.error(t)}})),p=s.Func.find({package:"Bio",name:"macromoleculePreprocessingFunction"})[0],m=yield async function(t,e,i,a,l,u,c,h=80,d=10,f=!1,p=2,m=5,g){const v=o.shell.tableView(t.name)??o.shell.addTableView(t),y=g??v.scatterPlot({showXAxis:!1,showYAxis:!1,showXSelector:!1,showYSelector:!1,title:"MCL"});r.setUpdateIndicator(y.root,!0);const C=[],w=[];for(let t=0;t<u.length;++t){const n=u[t];if(n){const r=n.inputs[0].name,o=n.inputs[1].name,{entries:s,options:a}=await n.apply({[r]:e[t],[o]:i[t],...c[t]??{}});w.push({entries:s,options:a}),C.push(a??{})}else{const n=e[t].toList(),i={};w.push({entries:n,options:i}),C.push(i)}}const b=function(t,e,i,r,o,s,a=10,l=!1,u=2){const c=new Worker(new URL(n.p+n.u(51),n.b));let h;return c.postMessage({data:t,threshold:e,weights:i,aggregationMethod:r,distanceFns:o,distanceFnArgs:s,maxIterations:a,useWebGPU:l,inflate:u}),{promise:new Promise(((t,e)=>{h=t,c.onmessage=e=>{setTimeout((()=>c.terminate()),100),t(e.data.res)},c.onerror=t=>{setTimeout((()=>c.terminate()),100),e(t)}})),terminate:()=>{try{h(null),c.terminate()}catch(t){console.error(t)}}}}(w.map((t=>t.entries)),h,a,l,i,C,d,f,p),A=o.events.onViewerClosed.subscribe((t=>{t.args.viewer?.props?.title===y.props.title&&y.type===t.args?.viewer?.type&&(A.unsubscribe(),b.terminate())})),E=await b.promise;if(!E)return;const S=t.columns.getUnusedName("Cluster (MCL)"),T=t.columns.getUnusedName("EmbedX (MCL)"),x=t.columns.getUnusedName("EmbedY (MCL)"),_={};E.clusters.forEach((t=>{_[t]||(_[t]=0),_[t]++}));const N=new Uint32Array(E.embedX.length);for(let t=0;t<E.is.length;t++)N[E.is[t]]++,N[E.js[t]]++;const M=t.columns.getUnusedName("Cluster size (MCL)"),O=t.columns.getUnusedName("Connectivity (MCL)"),L=t.columns.addNewFloat(T);L.init((t=>E.embedX[t]));const I=t.columns.addNewFloat(x);I.init((t=>E.embedY[t]));const R=t.columns.addNewString(S);R.init((t=>_[E.clusters[t]]>=m?E.clusters[t].toString():"-1"));const P={"-1":s.Color.setAlpha(s.Color.lightBlue,100)};R.setTag(s.TAGS.COLOR_CODING_CATEGORICAL,JSON.stringify(P)),R.temp[s.TAGS.COLOR_CODING_CATEGORICAL]=P;const k=t.columns.addNewInt(M);k.init((t=>_[E.clusters[t]]));const G=t.columns.addNewInt(O);G.init((t=>N[t])),y.props.xColumnName=T,y.props.yColumnName=x,y.props.colorColumnName=S,y.props.markerDefaultSize=6,A.unsubscribe();const D=[],V=[],F=new Map;for(let t=0;t<E.is.length;t++){let e=E.clusters[E.is[t]],n=E.clusters[E.js[t]];if(e===n){D.push(E.is[t]),V.push(E.js[t]);continue}if(e>n){const t=e;e=n,n=t}let i=F.get(e);i||(i=new Map,F.set(e,i));let r=i.get(n);r||(r=0),r>=20||(r++,i.set(n,r),D.push(E.is[t]),V.push(E.js[t]))}return new H(y,T,x,{from:new Uint32Array(D),to:new Uint32Array(V),drawArrows:!1,opacity:.3,skipMultiLineCalculation:!0,skipShortLines:!0,skipMouseOverDetection:!0,shortLineThreshold:6,width:.75,color:"128,128,128"},U.none),r.setUpdateIndicator(y.root,!1),{sc:y,embedXCol:L,embedYCol:I,clusterCol:R,clusterCounterCol:k,connectivityCol:G}}(this.df,[u],[c.distanceF],[1],V.MANHATTAN,[p],[{gapOpen:c.gapOpen,gapExtend:c.gapExtend,fingerprintType:c.fingerprintType}],c.threshold,c.maxIterations,c.useWebGPU,c.inflation,c.minClusterSize);f.unsubscribe();const g=this.findViewer(B.LOGO_SUMMARY_TABLE);if(g&&(g._clusterStats=null,g._clusterSelection=null,g._viewerGrid=null,g._logoSummaryTable=null,g.render()),null==m?void 0:m.sc){const t=JSON.stringify({cols:[u].map((t=>t.name)),metrics:[c.distanceF],weights:[1],aggregationMethod:V.MANHATTAN,preprocessingFuncs:[p].map((t=>{var e;return null!==(e=null==t?void 0:t.name)&&void 0!==e?e:null})),preprocessingFuncArgs:[{gapOpen:c.gapOpen,gapExtend:c.gapExtend,fingerprintType:c.fingerprintType}],threshold:c.threshold,maxIterations:c.maxIterations,useWebGPU:c.useWebGPU,inflate:c.inflation,minClusterSize:c.minClusterSize});this.df.setTag("MCL_OPTIONS",t),m.sc.props.initializationFunction="EDA:MCLInitializationFunction",this._mclViewer=null!==(a=null==m?void 0:m.sc)&&void 0!==a?a:null}}))}addSequenceSpace(){return q(this,arguments,void 0,(function*(t={}){var e,n,i,r;if(null!==this._sequenceSpaceViewer)try{null===(e=this._sequenceSpaceViewer)||void 0===e||e.detach(),null===(n=this._sequenceSpaceViewer)||void 0===n||n.close()}catch(t){}0!==this._sequenceSpaceCols.length&&this._sequenceSpaceCols.forEach((t=>this.df.columns.remove(t))),this._sequenceSpaceCols=[];let l=this.df.getCol(this.settings.sequenceColumnName);const u=h.GO.forColumn(l);if(u.isHelm())try{o.shell.warning("Column is in HELM notation. Sequences space will linearize sequences from position 0 prior to analysis");const t=u.convert(a.Hi.SEPARATOR,"/"),e=this.df.columns.getUnusedName(`Separator(${l.name})`);t.name=e,this.df.columns.add(t,!0),this.analysisView.grid.col(e).visible=!1,l=t}catch(t){return o.shell.error("Error on converting HELM notation to linear notation"),void o.shell.error(t)}const c=!t.clusterCol&&!!t.clusterEmbeddings,d=null!==(r=null===(i=this.settings)||void 0===i?void 0:i.sequenceSpaceParams)&&void 0!==r?r:new w.GI(c);d.clusterEmbeddings=c;const p={table:this.df,molecules:l,methodName:f.UMAP,similarityMetric:d.distanceF,plotEmbeddings:!0,options:{bypassLargeDataWarning:!0,dbScanEpsilon:d.epsilon,dbScanMinPts:d.minPts,randomSeed:"1",preprocessingFuncArgs:{gapOpen:d.gapOpen,gapExtend:d.gapExtend,fingerprintType:d.fingerprintType}},clusterEmbeddings:d.clusterEmbeddings};let m=0;const g=d.clusterEmbeddings?3:2,v=this.df.onColumnsAdded.subscribe((t=>{for(const e of t.columns)if(e.name.toLowerCase().startsWith("embed_")||d.clusterEmbeddings&&e.name.toLowerCase().startsWith("cluster")){const t=this.analysisView.grid.col(e.name);if(null==t||this._sequenceSpaceCols.includes(e.name))continue;t.visible=!1,this._sequenceSpaceCols.push(e.name),m++}m===g&&v.unsubscribe()})),y=o.events.onViewerAdded.subscribe((t=>{try{const e=t.args.viewer;if(e.type===s.VIEWER.SCATTER_PLOT){if(this._mclViewer&&this.analysisView.dockManager.findNode(this._mclViewer.root)){const t=this.analysisView.dockManager.findNode(this._mclViewer.root);setTimeout((()=>{this.analysisView.dockManager.dock(e,s.DOCK_TYPE.FILL,t)}))}y.unsubscribe()}}catch(t){console.error(t)}})),C=yield o.functions.call("Bio:sequenceSpaceTopMenu",p);y.unsubscribe(),C instanceof s.ScatterPlotViewer&&(d.clusterEmbeddings||t.clusterCol||(C.props.colorColumnName=this.getScaledActivityColumn().name),C.props.showXSelector=!1,C.props.showYSelector=!1,t.clusterCol&&(C.props.colorColumnName=t.clusterCol.name),this._sequenceSpaceViewer=C,C.onContextMenu.subscribe((t=>{try{t.item("Modify Sequence space parameters",(()=>{(0,_.OH)(this)}))}catch(t){}})))}))}}Y.modelName="peptidesModel"},3273:(t,e,n)=>{"use strict";n.d(e,{_package:()=>R,getMonomerWorksInstance:()=>P,getTreeHelperInstance:()=>k});var i,r,o=n(4328),s=n(7389),a=n(6082),l=(n(5082),n(7233)),u=n.n(l),c=(n(4788),n(9484));n(826),n(3541),n(5480),(r=i||(i={})).BASE="HELM_BASE",r.SUGAR="HELM_SUGAR",r.LINKER="HELM_LINKER",r.AA="HELM_AA",r.CHEM="HELM_CHEM",r.BLOB="HELM_BLOB",r.NUCLEOTIDE="HELM_NUCLETIDE";var h=n(4139);n(8608),n(2003),n(8070);var d=n(5072),f=n.n(d),p=n(7825),m=n.n(p),g=n(7659),v=n.n(g),y=n(5056),C=n.n(y),w=n(540),b=n.n(w),A=n(1113),E=n.n(A),S=n(6677),T={};T.styleTagTransform=E(),T.setAttributes=C(),T.insert=v().bind(null,"head"),T.domAPI=m(),T.insertStyleElement=b(),f()(S.A,T),S.A&&S.A.locals&&S.A.locals;var x;!function(t){let e,n;!function(t){t.vert=function(t){return s.divV(t.map((t=>s.render(t))),{classes:"u2-panel"})},t.horz=function(t){return s.divH(t.map((t=>s.render(t))),{classes:"u2-panel"})}}(e=t.panels||(t.panels={})),t.appHeader=function(t){const n=s.iconImage("",t.iconPath);return u()(n).addClass("ui-app-header-icon").css("margin-right","20px"),e.horz([n,e.vert([s.markdown(t.description),t.learnMoreUrl?s.link("Learn more",t.learnMoreUrl):null])])},function(t){t.runAsync=function(t,e){return n=this,i=void 0,a=function*(){s.setUpdateIndicator(t,!0);try{return yield e()}catch(t){o.log.error(t)}finally{s.setUpdateIndicator(t,!1)}},new((r=void 0)||(r=Promise))((function(t,e){function o(t){try{l(a.next(t))}catch(t){e(t)}}function s(t){try{l(a.throw(t))}catch(t){e(t)}}function l(e){var n;e.done?t(e.value):(n=e.value,n instanceof r?n:new r((function(t){t(n)}))).then(o,s)}l((a=a.apply(n,i||[])).next())}));var n,i,r,a}}(n=t.tools||(t.tools={}))}(x||(x={}));var _=n(144),N=n.n(_);const M=rxjs.operators;class O extends a.JsViewer{get scViewer(){return this._scViewer||(this._scViewer=this.createSCViewer()),this._scViewer}constructor(){super(),this._titleHost=s.divText(c.q.CLUSTER_MAX_ACTIVITY,{id:"pep-viewer-title",style:{marginRight:"auto"}}),this._selsectIcon=s.div(),this.activityTarget=h.wf.HIGH,this.viewerError="",this.renderTimeout=null,this.renderDebounceTime=500,this.scFilterQuery=`\${${O.maxActivityInClusterColName}} == 1`,this.selectionSubscription=null,this.linesDrawSubscription=null,this.clusterColumnName=this.column("cluster",{nullable:!1}),this.activityColumnName=this.column("activity",{nullable:!1}),this.colorColumnName=this.column("color",{nullable:!0,defaultValue:null}),this.activityTarget=this.string("activityTarget",h.wf.HIGH,{choices:[h.wf.HIGH,h.wf.LOW]}),this.clusterSizeThreshold=this.int("clusterSizeThreshold",20),this.activityThreshold=this.int("activityThreshold",1e3),this.connectivityColumnName=this.column("connectivity",{nullable:!0})}get model(){return c.i.getInstance(this.dataFrame)}createSCViewer(){var t;const e={showXAxis:!0,showYAxis:!0,showXSelector:!1,showYSelector:!1,showColorSelector:!1,xAxisType:a.AxisType.logarithmic,yAxisType:a.AxisType.logarithmic,invertYAxis:this.activityTarget===h.wf.LOW,xColumnName:O.clusterSizeColName,markerType:"circle",markerDefaultSize:10,showSizeSelector:!1};if(null==this.clusterColumnName||null==this.activityColumnName||!this.dataFrame.columns.contains(this.clusterColumnName)||!this.dataFrame.columns.contains(this.activityColumnName))return this.viewerError="Please set valid cluster and activity columns",null;const n=this.dataFrame.columns.byName(this.activityColumnName),i=this.dataFrame.columns.byName(this.clusterColumnName),r=null!=this.connectivityColumnName?this.dataFrame.columns.byName(this.connectivityColumnName):null;if(![a.COLUMN_TYPE.FLOAT,a.COLUMN_TYPE.INT,a.COLUMN_TYPE.BIG_INT,a.COLUMN_TYPE.QNUM].includes(n.type))return this.viewerError="Activity column should be numeric",null;const o=this.dataFrame.columns.getOrCreate(O.clusterSizeColName,a.TYPE.INT,this.dataFrame.rowCount),l={};for(let e=0;e<this.dataFrame.rowCount;e++){const n=i.get(e);null!=n&&"-1"!=n&&(l[n]=(null!==(t=l[n])&&void 0!==t?t:0)+1)}o.init((t=>{var e;return i.isNone(t)?null:null!==(e=l[i.get(t)])&&void 0!==e?e:null})),n.stats.min<=0&&(e.yAxisType=a.AxisType.linear);const u={},c={};for(let t=0;t<this.dataFrame.rowCount;t++){const e=i.get(t);if(null==e||i.isNone(t)||n.isNone(t))continue;const o=n.get(t),s=u[e];if((null==s||null==s||o>n.get(s)&&this.activityTarget===h.wf.HIGH||o<n.get(s)&&this.activityTarget===h.wf.LOW)&&(u[e]=t),r){const n=r.get(t),i=c[e];(null==i||null==i||n>r.get(i))&&(c[e]=t)}}const d=this.dataFrame.columns.getOrCreate(O.maxActivityInClusterColName,a.COLUMN_TYPE.INT,this.dataFrame.rowCount);d.init((t=>i.isNone(t)?0:t===u[i.get(t)]?1:0)),this.dataFrame.columns.getOrCreate(O.maxConnectivityInClusterColName,a.COLUMN_TYPE.INT,this.dataFrame.rowCount).init((t=>i.isNone(t)?0:t===c[i.get(t)]?1:0)),this.dataFrame.columns.getOrCreate(O.synSelectionColName,a.TYPE.STRING,this.dataFrame.rowCount).init((t=>{if(i.isNone(t))return null;let e=null;return t===u[i.get(t)]&&(e=O.maxActivityLabel),r&&t===c[i.get(t)]&&(e=e?`${e}, ${O.maxConnectivityLabel}`:O.maxConnectivityLabel),e})),e.xColumnName=O.clusterSizeColName,e.yColumnName=this.activityColumnName,e.filter=this.scFilterQuery,this.viewerError="";const f=a.Viewer.scatterPlot(this.dataFrame,e);this.selectionSubscription&&this.selectionSubscription.unsubscribe(),this.selectionSubscription=f.onDataEvent.pipe((0,M.filter)((t=>"d4-select"==t.type))).subscribe((t=>{var e,n;const r=null!==(n=null===(e=t.bitset)||void 0===e?void 0:e.getSelectedIndexes())&&void 0!==n?n:[],o=this.dataFrame.selection,s=a.BitSet.create(this.dataFrame.rowCount,(t=>1==d.get(t)));s.and(o);for(let t=0;t<r.length;t++){const e=r[t],n=i.get(e);i.isNone(e)||(s.set(e,!0),null!=c[n]&&s.set(c[n],!0))}s.fireChanged();const l=s.getSelectedIndexes();for(const t of l){const e=i.get(t);null!=e&&null!=c[e]&&s.set(c[e],!0)}setTimeout((()=>{this.dataFrame.selection.copyFrom(s,!0),setTimeout((()=>{this.model&&this.model.createAccordion()}),200)}),200)}));const p=()=>{const t=a.BitSet.create(this.dataFrame.rowCount);Object.entries(u).forEach((([e,i])=>{var r;if(null==e||null==i)return;const o=parseInt(e),s=n.get(i),a=null!==(r=l[o])&&void 0!==r?r:l[e];s<this.activityThreshold&&a<this.clusterSizeThreshold||(t.set(i,!0,!1),null!=c[o]&&t.set(c[o],!0,!1))})),t.fireChanged(),this.dataFrame.selection.copyFrom(t,!0)};return this._selsectIcon=s.iconSvg("select-all",(()=>{p()}),"Select 3 Active 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Size",{style:{alignSelf:"center",color:"var(--grey-6)",marginBottom:"5px"}}),r=s.div(this.activityTarget===h.wf.HIGH?"Maximum Activity":"Minimum Activity",{style:{color:"var(--grey-6)",alignSelf:"center",textOrientation:"mixed",writingMode:"tb",transform:"rotate(180deg)",marginLeft:"5px"}});n.props.colorColumnName=null!==(e=this.colorColumnName)&&void 0!==e?e:null,this.root.appendChild(s.divH([r,s.divV([s.divH([this._titleHost,this._selsectIcon],{style:{alignSelf:"center",lineHeight:"normal",width:"100%"}}),n.root,i],{style:{flexGrow:"1"}})])),n.root.style.width="100%",setTimeout((()=>{n.props.filter=this.scFilterQuery,n.invalidateCanvas()}),100)}),this.renderDebounceTime)}onPropertyChanged(t){super.onPropertyChanged(t),(null==t?void 0:t.name)!==`color${h.To}`&&(this._scViewer=null),this.render()}}O.clusterSizeColName="~cluster.size",O.maxActivityInClusterColName="~max.activity.for.cluster",O.maxConnectivityInClusterColName="~max.connectivity.for.cluster",O.synSelectionColName="Syn 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i=0;i<this._workerCount;i++)u[i]=new Promise(((r,o)=>{const s=Math.floor(i*h),l=i===this._workerCount-1?c:Math.floor((i+1)*h);this._workers[i].postMessage({startIdx:s,endIdx:l,activityArray:t,monomerInfoArray:e,settings:n,currentTargetIdx:a}),this._workers[i].onmessage=({data:{pos:t,seq1Idxs:e,seq2Idxs:n,error:s}})=>{var a;s?(null===(a=this._workers[i])||void 0===a||a.terminate(),o(s)):(this._workers[i].terminate(),r({pos:t,seq1Idxs:e,seq2Idxs:n}))}}));const d=yield Promise.all(u),f=new Map;e.forEach(((t,e)=>{f.set(t.name,e)})),d.filter(Boolean).forEach((t=>{for(let n=0;n<t.pos.length;n++){const i=f.get(t.pos[n]),r=e[i].rawData[t.seq1Idxs[n]],o=e[i].cat[r],a=e[i].rawData[t.seq2Idxs[n]],l=e[i].cat[a];s.has(o)||s.set(o,new Map),s.has(l)||s.set(l,new Map);const u=s.get(o),c=s.get(l);u.has(t.pos[n])||u.set(t.pos[n],new Map),c.has(t.pos[n])||c.set(t.pos[n],new Map);const h=u.get(t.pos[n]),d=c.get(t.pos[n]);h.has(t.seq1Idxs[n])||h.set(t.seq1Idxs[n],[]),d.has(t.seq2Idxs[n])||d.set(t.seq2Idxs[n],[]);const p=h.get(t.seq1Idxs[n]),m=d.get(t.seq2Idxs[n]);p.push(t.seq2Idxs[n]),m.push(t.seq1Idxs[n])}}))}catch(t){this.terminate(),console.error(t)}return s},new((r=void 0)||(r=Promise))((function(t,e){function s(t){try{l(o.next(t))}catch(t){e(t)}}function a(t){try{l(o.throw(t))}catch(t){e(t)}}function l(e){var n;e.done?t(e.value):(n=e.value,n instanceof r?n:new r((function(t){t(n)}))).then(s,a)}l((o=o.apply(n,i||[])).next())}));var n,i,r,o}terminate(){var t;null===(t=this._workers)||void 0===t||t.forEach((t=>{try{null==t||t.terminate()}catch(t){console.error(t)}}))}}var s=n(5480),a=n(8774),l=n(5070),u=function(t,e,n,i){return new(n||(n=Promise))((function(r,o){function s(t){try{l(i.next(t))}catch(t){o(t)}}function a(t){try{l(i.throw(t))}catch(t){o(t)}}function l(t){var e;t.done?r(t.value):(e=t.value,e instanceof n?e:new n((function(t){t(e)}))).then(s,a)}l((i=i.apply(t,e||[])).next())}))};function c(t,e){return u(this,arguments,void 0,(function*(t,e,n={}){var i,s;if(0===e.length)throw new Error(`PepAlgorithmError: Couldn't find any column of semType '${r.uF.MONOMER}'`);null!==(i=n.minActivityDelta)&&void 0!==i||(n.minActivityDelta=0),null!==(s=n.maxMutations)&&void 0!==s||(n.maxMutations=1);const a=new o,l=yield a.calc(t,e,n);return a.terminate(),l}))}function h(t,e){const n=new Map;let i=999999,r=-999999,o=2,s=2;for(const u of t.keys()){const c=new Map;n.set(u,c);const h=t.get(u);for(const t of h.keys()){const n=h.get(t),u=new a.A(e.length,!1);if(0===n.size)continue;for(const t of n.keys())u.setFast(t,!0),n.get(t).forEach((t=>u.setFast(t,!0)));const d=(0,l.GT)(e,u);i=Math.min(i,d.meanDifference),r=Math.max(r,d.meanDifference),o=Math.min(o,d.count),s=Math.max(s,d.count),c.set(t,d)}}return{stats:n,minDiff:i,maxDiff:r,minCount:o,maxCount:s}}function d(t,e,n,r={}){var o,s,u,c,h,d;null!==(o=r.isFiltered)&&void 0!==o||(r.isFiltered=!1);const p={general:{}};let m=t.getRawData(),g=t.length;if(r.isFiltered){g=e.trueCount;const t=new Float64Array(g),o=e.getSelectedIndexes();for(let e=0;e<g;++e)t[e]=m[o[e]];m=t,n=i.DataFrame.fromColumns(n).clone(e).columns.toList(),r.target&&(r.target.col=r.target.col.clone(e)),r.aggValue&&(r.aggValue.col=r.aggValue.col.clone(e))}null!==(s=r.columns)&&void 0!==s||(r.columns=n.map((t=>t.name)));const v=null===(c=null===(u=r.target)||void 0===u?void 0:u.col)||void 0===c?void 0:c.getRawData(),y=null===(h=r.target)||void 0===h?void 0:h.col.categories,C=(null===(d=r.target)||void 0===d?void 0:d.cat)?null==y?void 0:y.indexOf(r.target.cat):-1;for(const t of n){if(!r.columns.includes(t.name))continue;const e=t.getRawData(),n=t.categories,i={general:{}};for(let t=0;t<n.length;++t){const o=n[t];if(""===o)continue;const s=new Array(g).fill(!1);for(let n=0;n<g;++n)e[n]!==t||v&&-1!==C&&v[n]!==C||(s[n]=!0);const u=a.A.fromValues(s);if(u.allFalse)continue;const c=(0,l.GT)(m,u,r.aggValue);i[o]=c,f(i.general,c)}p[t.name]=i,f(p.general,null,i.general)}return p}function f(t,e=null,n=null){var i,r,o,s,a,l,u,c,h,d,f,p,m,g,v,y,C;if(null===e&&null===n)throw new Error("MonomerPositionStatsError: either stats or summaryStats must be present");const w=null!==(i=null==e?void 0:e.count)&&void 0!==i?i:n.maxCount;null!==(r=t.maxCount)&&void 0!==r||(t.maxCount=w),t.maxCount<w&&(t.maxCount=w);const b=null!==(o=null==e?void 0:e.count)&&void 0!==o?o:n.minCount;null!==(s=t.minCount)&&void 0!==s||(t.minCount=b),t.minCount>b&&(t.minCount=b);const A=null!==(a=null==e?void 0:e.meanDifference)&&void 0!==a?a:n.maxMeanDifference;null!==(l=t.maxMeanDifference)&&void 0!==l||(t.maxMeanDifference=A),t.maxMeanDifference<A&&(t.maxMeanDifference=A);const E=null!==(u=null==e?void 0:e.meanDifference)&&void 0!==u?u:n.minMeanDifference;if(null!==(c=t.minMeanDifference)&&void 0!==c||(t.minMeanDifference=E),t.minMeanDifference>E&&(t.minMeanDifference=E),!isNaN(null!==(h=null==e?void 0:e.pValue)&&void 0!==h?h:NaN)){const i=null!==(d=null==e?void 0:e.pValue)&&void 0!==d?d:n.maxPValue;null!==(f=t.maxPValue)&&void 0!==f||(t.maxPValue=i),t.maxPValue<i&&(t.maxPValue=i);const r=null!==(p=null==e?void 0:e.pValue)&&void 0!==p?p:n.minPValue;null!==(m=t.minPValue)&&void 0!==m||(t.minPValue=r),t.minPValue>r&&(t.minPValue=r)}const S=null!==(g=null==e?void 0:e.ratio)&&void 0!==g?g:n.maxRatio;null!==(v=t.maxRatio)&&void 0!==v||(t.maxRatio=S),t.maxRatio<S&&(t.maxRatio=S);const T=null!==(y=null==e?void 0:e.ratio)&&void 0!==y?y:n.minRatio;null!==(C=t.minRatio)&&void 0!==C||(t.minRatio=T),t.minRatio>T&&(t.minRatio=T)}function p(t,e,n,i){const r=t.rowCount,o=t.getCol(e),u=o.getRawData(),c=o.categories,h=Array.from({length:c.length},(()=>new a.A(r,!1)));for(let t=0;t<r;++t)h[u[t]].setTrue(t);const d=n.map((t=>a.A.fromUint32Array(r,t.getRawData()))),f=n.map((t=>t.name)),p=i.getRawData(),m={},g={};for(const t of Object.values(s.W)){const e=t===s.W.ORIGINAL?h:d,n=t===s.W.ORIGINAL?c:f,r=t===s.W.ORIGINAL?m:g;for(let t=0;t<e.length;++t){const o=e[t];r[n[t]]=o.allTrue||o.allFalse?{count:o.length,meanDifference:0,ratio:1,pValue:null,mask:o,mean:i.stats.avg}:(0,l.GT)(p,o)}}const v={};return v[s.W.ORIGINAL]=m,v[s.W.CUSTOM]=g,v}},2935:(t,e,n)=>{"use strict";n.d(e,{X5:()=>m,rW:()=>y,k8:()=>C,Yd:()=>v,rI:()=>g,FZ:()=>w});var i,r,o,s=n(7389),a=n(6082),l=n(4139),u=n(2003),c=n(3657),h=n(1858),d=n(912),f=n(5480),p=n(3541);function m(t,e){t.strokeStyle=a.Color.toHtml(a.Color.selectedRows),t.lineWidth=3,t.strokeRect(e.x+1,e.y+1,e.width-1,e.height-1)}function g(t,e,n){t.semType=l.uF.MONOMER,t.setTag(a.TAGS.CELL_RENDERER,l.uF.MONOMER),t.setTag(l.gp.ALPHABET,e),n&&t.setTag(r.applyToBackground,"true")}function v(t,e,n,i,r){var o,s,l,u,c,h,d;const f=r.width/2,g=Math.ceil(r.x+1+f),v=Math.ceil(r.y+1+r.height/2),y=.9*f/2;if(i instanceof p.UJ){const r=i.monomerPositionStats[n],o=r[e].pValue,s=r[e].meanDifference,l=1-r.general.maxPValue,u=1-r.general.minPValue,c=Math.min(l,u),h=l-c,d=u-c,p=Math.max(h,d),m=null===o?0:1-o-c,C=s>=0?m:-m,w=a.Color.toHtml(null===o?a.Color.lightLightGray:a.Color.scaleColor(C,-p,p,255)),b=Math.max(Math.abs(i.monomerPositionStats.general.minMeanDifference),i.monomerPositionStats.general.maxMeanDifference),A=Math.abs(s)/b,E=Math.floor(y*A);t.beginPath(),t.fillStyle=w,t.arc(g-f/2,v,E<3||null===o?3:E,0,2*Math.PI,!0),t.closePath(),t.fill()}else if(i instanceof p.J&&i.mutationCliffs&&i.cliffStats){const r=i.cliffStats.maxCount,u=i.cliffStats.minDiff,c=i.cliffStats.maxDiff,h=null===(l=null===(s=null===(o=i.cliffStats)||void 0===o?void 0:o.stats)||void 0===s?void 0:s.get(e))||void 0===l?void 0:l.get(n);if(h){const e=h.count,n=h.meanDifference,i=Math.floor(Math.abs(e/Math.max(r,2))*y),o=Math.max(Math.abs(u),Math.abs(c)),s=a.Color.toHtml(null===n?a.Color.lightLightGray:a.Color.scaleColor(n,-o,o,255));t.beginPath(),t.fillStyle=s,t.arc(g-f/2,v,i<3||0==e?3:i,0,2*Math.PI,!0),t.closePath(),t.fill()}}t.textBaseline="middle",t.textAlign="end",t.fillStyle="#606060",t.font="13px Roboto, Roboto Local, sans-serif",t.shadowBlur=5,t.shadowColor=a.Color.toHtml(a.Color.white);const C=new Set,w=null!==(d=null===(h=null===(c=null===(u=i.mutationCliffs)||void 0===u?void 0:u.get(e))||void 0===c?void 0:c.get(n))||void 0===h?void 0:h.entries())&&void 0!==d?d:null;if(null!==w)for(const[t,e]of w){C.add(t);for(const t of e)C.add(t)}0!==C.size&&t.fillText(C.size.toString(),g+f-5,v,f-5);const b=i.mutationCliffsSelection[n];b&&b.includes(e)&&m(t,r)}function y(t,e,n,i,r,o,s){s=a.Color.fromHtml(a.Color.toHtml(function(t,e){return(16777215&t|255<<24)>>>0}(s)));let l=r.toFixed(2);l.endsWith(".00")&&(l=r.toFixed(0)),l.endsWith("0")&&l.includes(".")&&(l=r.toFixed(1));const u=Math.min(13,Math.floor(o.width/40/l.length*6*13));t.fillStyle=a.Color.toHtml(s),t.fillRect(o.x,o.y,o.width,o.height),t.font=`${u}px Roboto, Roboto Local, sans-serif`,t.textAlign="center",t.textBaseline="middle",t.fillStyle=a.Color.toHtml(a.Color.getContrastColor(s)),t.fillText(l,o.x+o.width/2,o.y+o.height/2,o.width);const c=i[n];c&&c.includes(e)&&m(t,o)}function C(t,e,n,i){t.font="13px Roboto, Roboto Local, sans-serif",t.textAlign="center",t.textBaseline="middle",t.fillStyle="#000",t.fillText(e.toString(),i.x+i.width/2,i.y+i.height/2,i.width),(n[f.W.CUSTOM].includes(e)||n[f.W.ORIGINAL].includes(e))&&m(t,i)}function w(t,e,n,i,r,o={x:0,y:0,mpStats:{},monomerPosition:{}}){var f;if(null!==(f=r.isSelectionTable)&&void 0!==f||(r.isSelectionTable=!1),0==Object.keys(o.mpStats).length&&(o.mpStats=e),r.isSelectionTable&&(!r.webLogoBounds||!r.cachedWebLogoTooltip))throw new Error("Peptides: Cannot set WebLogo renderer for selection table without `headerSelectedMonomers`, `webLogoBounds` and `cachedWebLogoTooltip` options.");const p=t.dataFrame;t.setOptions({colHeaderHeight:130});t.onCellRender.subscribe((t=>(t=>{var o;const s=t.g,h=t.bounds,d=t.cell.tableColumn;s.save();try{if(s.beginPath(),s.rect(h.x,h.y,h.width,h.height),s.clip(),t.cell.isColHeader&&(null==d?void 0:d.semType)===l.uF.MONOMER){let f;if(p.filter.anyFalse){const t=null!==(o=p.temp[l.gp.M_P_STATS_CACHE])&&void 0!==o?o:{},e=null==t?void 0:t[d.name],r=p.filter.getBuffer();if(t&&e&&e.filter.length===r.length&&e.filter.every(((t,e)=>t===r[e])))f=e.stats[d.name];else{const e=(0,c.Ej)(i,p.filter,n,{isFiltered:!0,columns:[d.name]});f=e[d.name],t[d.name]={filter:p.filter.getBuffer(),stats:e,selection:p.selection.getBuffer()}}p.temp[l.gp.M_P_STATS_CACHE]=t}else f=r.isSelectionTable?(0,c.Ej)(i,p.filter,n,{isFiltered:!0,columns:[d.name]})[d.name]:e[d.name];if(!f)return;const m=Object.keys(f).sort(((t,e)=>""===t||"-"===t?1:""===e||"-"===e?-1:0)).filter((t=>"general"!==t));r.webLogoBounds()[d.name]=function(t,e,n,i,r,o,s,l={},c={}){var h,d,f,p,m,g,v,y,C,w;const b=window.devicePixelRatio;null!==(h=c.symbolStyle)&&void 0!==h||(c.symbolStyle="16px Roboto, Roboto Local, sans-serif"),null!==(d=c.upperLetterHeight)&&void 0!==d||(c.upperLetterHeight=12.2),null!==(f=c.upperLetterAscent)&&void 0!==f||(c.upperLetterAscent=.25),null!==(p=c.marginVertical)&&void 0!==p||(c.marginVertical=1),null!==(m=c.marginHorizontal)&&void 0!==m||(c.marginHorizontal=1),null!==(g=c.selectionWidth)&&void 0!==g||(c.selectionWidth=2),null!==(v=c.textHeight)&&void 0!==v||(c.textHeight=13),null!==(y=c.headerStyle)&&void 0!==y||(c.headerStyle=`bold ${c.textHeight*b}px Roboto, Roboto Local, sans-serif`);const A=(r.length-1)*c.upperLetterAscent;let E=(e.y+c.marginVertical)*b;const S=(e.height-2*c.marginVertical-A-1.25*c.textHeight)*b,T=(e.x+c.marginHorizontal)*b,x=Math.max(c.selectionWidth*b,.05*e.width*b),_=2*c.marginHorizontal+c.selectionWidth,N=(e.width-(_+c.marginHorizontal))*b,M=(e.x+_)*b,O={};for(const e of r){const i=S*(n[e].count/o),r=S*((null!==(C=l[e])&&void 0!==C?C:0)/o);if(O[e]=new a.Rect(M/b,E/b,N/b,i/b),t.resetTransform(),"-"!==e&&""!==e){const n=(0,u.zS)(e,5),o=t.measureText(n);r>0&&(t.lineWidth=x,t.line(T,E,T,E+r,a.Color.rowSelection)),t.fillStyle=null!==(w=s.get(e))&&void 0!==w?w:s.get("other"),t.textAlign="left",t.textBaseline="top",t.font=c.symbolStyle;const l=N/o.width,h=i/c.upperLetterHeight;t.setTransform(l,0,0,h,M,E),t.fillText(n,0,0,o.width)}E+=i+c.upperLetterAscent*b}return t.resetTransform(),t.fillStyle=a.Color.toHtml(a.Color.black),t.textAlign="center",t.textBaseline="top",t.font=c.headerStyle,t.fillText(i,(e.x+e.width/2)*b,(e.y+e.height-c.textHeight)*b),O}(s,h,f,d.name,m,p.filter.trueCount,r.colorPalette(),r.headerSelectedMonomers?r.headerSelectedMonomers()[d.name]:{}),t.preventDefault()}}catch(t){console.warn(`PeptidesHeaderLogoError: couldn't render WebLogo for column \`${d.name}\`. 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class{constructor(){this.color="rgb(100,100,100)",this.pivot=0,this.left=!1,this.transparencyRate=1,this.separator="",this.last=!1,this.drawStyle=o.classic,this.maxWord=[],this.wordIdx=0,this.gridCell=null,this.referenceSequence=null,this.maxLengthOfMonomer=null,this.monomerTextSizeMap={},this.logger=void 0}},a.GridCellRenderer},4139:(t,e,n)=>{"use strict";n.d(e,{$2:()=>i,To:()=>l,V5:()=>d,YX:()=>h,gp:()=>o,i6:()=>r,rg:()=>u,uF:()=>s,wf:()=>c,zW:()=>f});var i,r,o,s,a=n(6082);!function(t){t.SPLIT_COL="~split",t.ACTIVITY="Activity",t.ACTIVITY_SCALED="Scaled activity",t.MONOMER="AAR",t.POSITION="Pos",t.P_VALUE="pValue",t.MEAN_DIFFERENCE="Mean difference",t.COUNT="Count",t.RATIO="Ratio",t.MEAN="Mean"}(i||(i={})),function(t){t.MEMBERS="Members",t.WEB_LOGO="WebLogo",t.DISTRIBUTION="Distribution",t.MEAN_DIFFERENCE="Mean difference",t.P_VALUE="P-Value",t.RATIO="Ratio",t.CLUSTER="Cluster"}(r||(r={})),function(t){t.MONOMER="monomer",t.POSITION="pos",t.SEPARATOR="separator",t.SELECTION="selection",t.MUTATION_CLIFFS_SELECTION="mutationCliffsSelection",t.ALPHABET="alphabet",t.FILTER="filter",t.INVARIANT_MAP_SELECTION="invariantMapSelection",t.SAR_MODE="sarMode",t.CLUSTER_SELECTION="clusterSelection",t.VISIBLE="visible",t.SETTINGS="settings",t.CUSTOM_CLUSTER="customCluster",t.MONOMER_POSITION_MODE="monomerPositionMode",t.MULTIPLE_VIEWS="isMultipleViews",t.IDENTITY_TEMPLATE="Identity template",t.SIMILARITY_TEMPLATE="Similarity template",t.ANALYSIS_COL="isAnalysisCol",t.POSITION_COL="isPositionCol",t.M_P_STATS_CACHE=".MPStatsCache",t.INVARIANT_MAP_COLOR_CACHE=".InvariantMapColorCache",t.INVARIANT_MAP_COLOR_MAX_CACHE=".InvariantMapColorMaxCache",t.INVARIANT_MAP_COLOR_MIN_CACHE=".InvariantMapColorMinCache"}(o||(o={})),function(t){t.MONOMER="Monomer",t.MACROMOLECULE_DIFFERENCE="MacromoleculeDifference"}(s||(s={}));const l="ColumnName";var u,c,h;!function(t){t.NONE="none",t.LG="lg",t.MINUS_LG="-lg"}(u||(u={})),function(t){t.HIGH="High",t.LOW="Low"}(c||(c={})),function(t){t.LST="lst-",t.MP="mp-",t.MPR="mpr-",t.WL="wl-"}(h||(h={}));const d=Object.values(a.AGG).filter((t=>![a.AGG.FIRST,a.AGG.KEY,a.AGG.PIVOT,a.AGG.SELECTED_ROWS_COUNT].includes(t))),f={[a.AGG.TOTAL_COUNT]:"totalCount",[a.AGG.VALUE_COUNT]:"valueCount",[a.AGG.UNIQUE_COUNT]:"uniqueCount",[a.AGG.MISSING_VALUE_COUNT]:"missingValueCount",[a.AGG.MIN]:"min",[a.AGG.MAX]:"max",[a.AGG.SUM]:"sum",[a.AGG.MED]:"med",[a.AGG.AVG]:"avg",[a.AGG.STDEV]:"stdev",[a.AGG.VARIANCE]:"variance",[a.AGG.SKEW]:"skew",[a.AGG.KURT]:"kurt",[a.AGG.Q1]:"q1",[a.AGG.Q2]:"q2",[a.AGG.Q3]:"q3"}},8608:(t,e,n)=>{"use strict";n.d(e,{$s:()=>T,AN:()=>i,AY:()=>h,B2:()=>N,BE:()=>y,CD:()=>w,F2:()=>m,FZ:()=>g,KT:()=>S,Y1:()=>d,ZR:()=>E,dl:()=>A,eY:()=>p,qI:()=>x,qx:()=>f,sg:()=>M,vW:()=>b,vY:()=>C,zm:()=>_,zz:()=>v});var i,r=n(7389),o=n(6082),s=n(4139),a=n(8774),l=n(144),u=n.n(l),c=function(t,e,n,i){return new(n||(n=Promise))((function(r,o){function s(t){try{l(i.next(t))}catch(t){o(t)}}function a(t){try{l(i.throw(t))}catch(t){o(t)}}function l(t){var e;t.done?r(t.value):(e=t.value,e instanceof n?e:new n((function(t){t(e)}))).then(s,a)}l((i=i.apply(t,e||[])).next())}))};function h(t){var e;return null!==(e=t.getTag(s.gp.SEPARATOR))&&void 0!==e?e:""}function d(t,e=s.rg.NONE){let n=t=>t;switch(e){case s.rg.NONE:break;case s.rg.LG:n=t=>Math.log10(t);break;case s.rg.MINUS_LG:n=t=>-Math.log10(t);break;default:throw new Error(`ScalingError: method \`${e}\` is not available.`)}const i=t.getRawData(),r=o.Column.float(s.$2.ACTIVITY,t.length).init((t=>{const e=i[t];return e===o.FLOAT_NULL||e===o.INT_NULL?e:n(e)}));return r.setTag(s.gp.ANALYSIS_COL,"true"),r.setTag(o.TAGS.FORMULA,e),r}function f(t){var e,n,i,r;const o=t.columns.bySemTypeAll(s.uF.MONOMER),a={},l=t.filter.clone().and(t.selection).getSelectedIndexes();for(const t of l)for(const s of o){const o=s.get(t);o&&(null!==(e=a[i=s.name])&&void 0!==e||(a[i]={}),null!==(n=(r=a[s.name])[o])&&void 0!==n||(r[o]=0),a[s.name][o]+=1)}return a}function p(t){return{name:t.name,cat:t.categories,rawData:t.getRawData()}}function m(t,e,n={}){var a;const l=t.dataFrame.getCol(s.$2.SPLIT_COL),u=[],c=l.categories,h=l.getRawData();for(let t=0;t<c.length;++t){if(!Object.values(i).includes(c[t]))continue;const e=o.Color.toHtml(l.meta.colors.getColor(h.indexOf(t))),s=r.label(null!==(a=n[c[t]])&&void 0!==a?a:c[t],{style:{color:e}});u.push(s)}const d=r.divV([r.divV(u),t.root,r.tableFromMap(e)]);return t.root.style.maxHeight="75px",d}function g(t,e,n){var r,a;const l=null!==(r=null==n?void 0:n.clone().xor(e).anyTrue)&&void 0!==r&&r,u=t.length,c=t.getRawData(),h=new Float32Array(u+e.trueCount+(l&&null!==(a=null==n?void 0:n.trueCount)&&void 0!==a?a:0)),d=new Array(h.length);for(let t=0,r=0,o=0;t<u;++t){const s=e.get(t);h[t]=c[t],d[t]=s?i.SELECTION:i.ALL,s&&(h[u+r]=c[t],d[u+r]=i.ALL,++r),l&&(null==n?void 0:n.get(t))&&(h[u+e.trueCount+o]=c[t],d[u+e.trueCount+o]=i.PEPTIDES_SELECTION,++o)}const f=o.Column.fromStrings(s.$2.SPLIT_COL,d),p=[i.ALL,i.SELECTION];return l&&p.push(i.PEPTIDES_SELECTION),f.setCategoryOrder(p),f.meta.colors.setCategorical(),o.DataFrame.fromColumns([o.Column.fromFloat32Array(s.$2.ACTIVITY,h),f])}function v(t){const e=r.iconFA("expand-alt",(()=>{const e=t.dataFrame.plot.grid();C(e,!1),e.root.style.height="100%";const n=r.dialog(t.dataFrame.name);n.add(e.root),n.showModal(!0),e.invalidate()}));t.root.appendChild(e),e.style.position="absolute",e.style.right="0px",e.style.top="0px",e.style.visibility="hidden",t.root.addEventListener("mouseenter",(t=>{e.style.visibility="visible"})),t.root.addEventListener("mouseleave",(t=>{e.style.visibility="hidden"}))}function y(t,e,n,i){const o=r.iconFA("expand-alt",(()=>{const e=i(),n=r.dialog(t);n.add(e),n.showModal(!0)}),"Expand to full screen");o.style.marginLeft="auto",o.style.marginRight="15px",n.addEventListener("mouseenter",(()=>{o.style.visibility="visible"})),n.addEventListener("mouseleave",(()=>{o.style.visibility="hidden"})),e.appendChild(o)}function C(t,e=!0){t.props.allowEdit=!1,t.props.showReadOnlyNotifications=!1,t.props.allowRowSelection=!1,t.props.allowBlockSelection=!1,t.props.allowColSelection=!1,t.props.showRowHeader=!1,t.props.showCurrentRowIndicator=!1,t.root.style.width="100%",t.root.style.maxWidth="100%",e&&t.autoSize(1e3,175,0,0,!0)}function w(t){for(const e of Object.values(t))if(0!==e.length)return!1;return!0}function b(t,e,n){const i=t[e.positionOrClusterType],r=i.indexOf(e.monomerOrCluster);if(n.shiftPressed&&n.ctrlPressed)-1!==r&&i.splice(r,1);else if(n.ctrlPressed)-1===r?i.push(e.monomerOrCluster):i.splice(r,1);else if(n.shiftPressed)-1===r&&i.push(e.monomerOrCluster);else{const n=Object.keys(t);t={};for(const i of n)t[i]=[],i===e.positionOrClusterType&&t[i].push(e.monomerOrCluster)}return t}function A(t,e,n){if(!e)return;const i=new a.A(e.rowCount);if(t.positionOrClusterType===s.$2.MONOMER){const e=Object.values(n);for(const n of e){const e=n[t.monomerOrCluster];void 0!==e&&i.or(e.mask)}}else{const 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r.concat(o).filter((e=>t.columns.contains(e[0])&&t.col(e[0]).matches("numerical")))}function N(t,e=2){return t.columns.bySemTypeAll(o.SEMTYPE.MACROMOLECULE).length>0&&u()(t.columns.numerical).toArray().length>0&&t.rowCount>=e}function M(t,e=500){let n;return(...i)=>c(this,void 0,void 0,(function*(){return new Promise((r=>{clearTimeout(n),n=setTimeout((()=>r(t(...i))),e)}))}))}!function(t){t.SELECTION="Selection",t.ALL="All",t.PEPTIDES_SELECTION="Peptides selection"}(i||(i={}))},5070:(t,e,n)=>{"use strict";n.d(e,{hX:()=>s,I_:()=>u,m2:()=>c,lh:()=>l,GT:()=>a,J1:()=>h});var i=n(6082),r=n(6572),o=n(4139);const s=(t,e)=>`${t}(${e})`;function a(t,e,n){var o;if(t.length!==e.length&&t.some(((t,n)=>n>=e.length&&0!==t)))throw new Error("PeptidesError: Data and bit array have different lengths");const s=new Float32Array(e.trueCount()),a=new Float32Array(e.falseCount());let l;if(n)try{l=null===(o=i.DataFrame.fromColumns([n.col]).clone(i.BitSet.fromBytes(e.buffer.buffer,e.length)).col(n.col.name))||void 0===o?void 0:o.aggregate(n.type)}catch(t){console.error(t)}let u=0,c=0;for(let n=0;n<e.length;++n)e.getBit(n)?s[u++]=t[n]:a[c++]=t[n];const h=s.reduce(((t,e)=>t+e),0)/Math.max(s.length,1);if(s.length<2||a.length<2){const t=a.reduce(((t,e)=>t+e),0)/Math.max(a.length,1);return{count:s.length,pValue:null,mean:h,meanDifference:h-t,ratio:s.length/e.length,mask:e,aggValue:l}}const d=function(t,e,n=!1,i=!1){if(t.length<=1||e.length<=1)throw new Error(`StatisticsError: Wrong sample size; expected at least 2, got ${Math.min(t.length,e.length)})`);const o=r.mean(t),s=r.mean(e),a=r.variance(t),l=r.variance(e),u=t.length,c=e.length;let h,d,f;if(n){const t=a/u,e=l/c,n=(o-s)/Math.sqrt(t+e);d=r.normal.pdf(n,0,1),h=1-d,f=2*(d<h?d:h)}else if(i){const t=u+c-2,e=(a*(u-1)+l*(c-1))/t,n=Math.sqrt(u*c/(u+c))*(o-s)/e;h=1-r.studentt.cdf(n,t),d=r.studentt.cdf(n,t),f=2*(d<h?d:h)}else{const t=a/u,e=l/c,n=(o-s)/Math.sqrt(t+e),i=Math.pow(t+e,2)/(Math.pow(t,2)/(u-1)+Math.pow(e,2)/(c-1));d=r.studentt.cdf(n,i),h=1-d,f=2*(d<h?d:h)}return{"p-value":f,"Mean difference":o-s,"p-value more":h,"p-value less":d}}(s,a),f=d["Mean difference"];return{count:s.length,pValue:d[f>=0?"p-value more":"p-value less"],mean:h,meanDifference:f,ratio:s.length/e.length,mask:e,aggValue:l}}function l(t,e,n){const r=o.zW[e],s=i.Stats.fromColumn(t,n);if(!(r in s))throw new Error(`Aggregation type ${r} is not supported`);return s[r]}function u(t,e,n={}){var i,r;null!==(i=n.filterDf)&&void 0!==i||(n.filterDf=!1),null!==(r=n.fractionDigits)&&void 0!==r||(n.fractionDigits=3);const o=n.filterDf&&t.filter.anyFalse?t.clone(t.filter):t,a={};for(const[t,i]of e){const e=s(i,t),r=l(o.getCol(t),i,n.mask);a[e]=r.toFixed(n.fractionDigits)}return a}function c(t,e,n,i){var r;null!==(r=i.fractionDigits)&&void 0!==r||(i.fractionDigits=3);const o={};for(const[r,a]of n){const n=s(a,r),l=t.get(n,e);o[n]=l.toFixed(i.fractionDigits)}return o}function h(t,e,n){var r;const o=t.col(e.substring(5,e.length-1));if(!o||!o.matches("categorical"))return"{}";null!=n||(n=i.BitSet.create(t.rowCount,(()=>!0)));const s=o.getRawData(),a=new Map;for(let t=-1;-1!==(t=n.findNext(t,!0));)a.set(s[t],(null!==(r=a.get(s[t]))&&void 0!==r?r:0)+1);const l={};for(const[t,e]of a)l[o.categories[t]]=e;return JSON.stringify(l)}},912:(t,e,n)=>{"use strict";n.d(e,{DK:()=>d,YE:()=>f,cr:()=>h});var i=n(7389),r=n(4328),o=n(6082),s=n(4139),a=n(7654),l=n(8608),u=n(3273),c=n(5070);function h(t,e,n){const o=[],s=t.toLowerCase(),a=(0,u.getMonomerWorksInstance)(),l=null==a?void 0:a.getCappedRotatedMonomer("PEPTIDE",t);if(l){o.push(i.div(s));const t={autoCrop:!0,autoCropMargin:0,suppressChiralText:!0};o.push(r.chem.svgMol(l,void 0,void 0,t))}else{if(""===t)return!0;o.push(i.div(t))}return i.tooltip.show(i.divV(o),e,n),!0}function d(t,e,n,i){var r,o,a;return null!==(r=i.fromViewer)&&void 0!==r||(i.fromViewer=!1),null!==(o=i.isMutationCliffs)&&void 0!==o||(i.isMutationCliffs=!1),null!==(a=i.isMostPotentResidues)&&void 0!==a||(i.isMostPotentResidues=!1),i.monomerPosition.positionOrClusterType===s.$2.MONOMER?h(i.monomerPosition.monomerOrCluster,i.x,i.y):f(t,e,n,i),!0}function f(t,e,n,r){var s,u,h,d,f,p,m;if(null!==(s=r.fromViewer)&&void 0!==s||(r.fromViewer=!1),null!==(u=r.isMutationCliffs)&&void 0!==u||(r.isMutationCliffs=!1),null!==(h=r.isMostPotentResidues)&&void 0!==h||(r.isMostPotentResidues=!1),r.cliffStats&&r.isMutationCliffs){const s=null===(p=null===(f=r.cliffStats)||void 0===f?void 0:f.get(r.monomerPosition.monomerOrCluster))||void 0===p?void 0:p.get(r.monomerPosition.positionOrClusterType);if(!s)return null;const u=o.BitSet.fromBytes(s.mask.buffer.buffer,e.length),h=(0,a.M1)((0,l.FZ)(e,u),!0),d=(0,a.QD)(s);r.fromViewer&&(d["Mean difference"]=`${d["Mean difference"]} (Color)`,d.Count&&(d.Count=`${d.Count} (Size)`));const g=null!==(m=r.aggrColValues)&&void 0!==m?m:(0,c.I_)(t,n,{mask:u}),v=Object.assign(Object.assign({},d),g),y=(0,l.F2)(h,v);return i.tooltip.show(y,r.x,r.y),y}{const s=r.mpStats[r.monomerPosition.positionOrClusterType][r.monomerPosition.monomerOrCluster];if(!(null==s?void 0:s.count))return null;const u=o.BitSet.fromBytes(s.mask.buffer.buffer,e.length),h=(0,a.M1)((0,l.FZ)(e,u),!0),f=(0,a.QD)(s);r.fromViewer&&(f["Mean difference"]=`${f["Mean difference"]}${r.isMostPotentResidues?" (size)":""}`,f["p-value"]&&(f["p-value"]=`${f["p-value"]}${r.isMostPotentResidues?" (color)":""}`));const p=null!==(d=r.aggrColValues)&&void 0!==d?d:(0,c.I_)(t,n,{mask:u}),m=Object.assign(Object.assign({},f),p),g=(0,l.F2)(h,m);return i.tooltip.show(g,r.x,r.y),g}}},115:(t,e,n)=>{"use strict";n.d(e,{GI:()=>a,Ku:()=>o,av:()=>s});var i=n(4572),r=n(4329);const o="WebGPU is not supported on this device";class s{constructor(){this.maxIterations=16,this.inflation=1.4,this.threshold=70,this.distanceF=i.Z.NEEDLEMANN_WUNSCH,this.gapOpen=1.5,this.gapExtend=.2,this.fingerprintType="Morgan",this.useWebGPU=!1,this.minClusterSize=5,this.webGPUDescription=o,this.webGPUDescriptionPromise=(0,r._)().then((t=>{t&&(this.webGPUDescription=t)}))}}class a{constructor(t){this.distanceF=i.Z.NEEDLEMANN_WUNSCH,this.gapOpen=1.5,this.gapExtend=.2,this.clusterEmbeddings=!0,this.epsilon=.01,this.minPts=4,this.fingerprintType="Morgan",this.clusterEmbeddings=!!t}}},5480:(t,e,n)=>{"use strict";n.d(e,{W:()=>A,s:()=>S});var i=n(7389),r=n(4328),o=n(6082),s=n(7233),a=n.n(s),l=n(9484),u=n(4139),c=n(2935),h=n(4326),d=n(5070),f=n(144),p=n.n(f),m=n(7654),g=n(8608),v=n(8774),y=n(3273),C=n(3657),w=n(3077);const b=(t,e)=>`${t}(${e})`;var A,E;!function(t){t.ORIGINAL="original",t.CUSTOM="custom"}(A||(A={})),function(t){t.GENERAL="General",t.STYLE="WebLogo",t.AGGREGATION="Aggregation"}(E||(E={}));class S extends o.JsViewer{constructor(){super(),this._titleHost=i.divText(l.q.LOGO_SUMMARY_TABLE,{id:"pep-viewer-title"}),this.bitsets=[],this.keyPress=!1,this.currentRowIndex=null,this._scaledActivityColumn=null,this._viewerGrid=null,this._clusterStats=null,this._clusterSelection=null,this._logoSummaryTable=null,this._positionColumns=null,this.sequenceColumnName=this.column("sequence",{category:E.GENERAL,nullable:!1}),this.clustersColumnName=this.column("clusters",{category:E.GENERAL,nullable:!1,columnTypeFilter:o.TYPE.CATEGORICAL}),this.activityColumnName=this.column("activity",{category:E.GENERAL,nullable:!1,columnTypeFilter:o.TYPE.NUMERICAL}),this.activityScaling=this.string("activityScaling",u.rg.NONE,{category:E.GENERAL,choices:Object.values(u.rg)}),this.webLogoMode=this.string("webLogoMode",h.fH.Entropy,{choices:[h.fH.full,h.fH.Entropy],category:E.STYLE}),this.membersRatioThreshold=this.float("membersRatioThreshold",.1,{min:0,max:1,category:E.STYLE}),this.columns=this.columnList("columns",[],{category:E.AGGREGATION}),this.aggregation=this.string("aggregation",o.AGG.AVG,{category:E.AGGREGATION,choices:u.V5})}get model(){return l.i.getInstance(this.dataFrame)}get viewerGrid(){var t;return null!==(t=this._viewerGrid)&&void 0!==t||(this._viewerGrid=this.createLogoSummaryTableGrid()),this._viewerGrid}get clusterStats(){var t;return null!==(t=this._clusterStats)&&void 0!==t||(this._clusterStats=(0,C.eW)(this.dataFrame,this.clustersColumnName,this.customClusters.toArray(),this.getScaledActivityColumn())),this._clusterStats}get clusterSelection(){var t;const e=this.dataFrame.getTag(u.gp.CLUSTER_SELECTION);return null!==(t=this._clusterSelection)&&void 0!==t||(this._clusterSelection=null===e?this.initClusterSelection({notify:!1}):JSON.parse(e)),this._clusterSelection}set clusterSelection(t){this._clusterSelection=t,this.dataFrame.setTag(u.gp.CLUSTER_SELECTION,JSON.stringify(t)),this.model.fireBitsetChanged(l.q.LOGO_SUMMARY_TABLE),this.model.analysisView.grid.invalidate()}get logoSummaryTable(){var t;return null!==(t=this._logoSummaryTable)&&void 0!==t||(this._logoSummaryTable=this.createLogoSummaryTable()),this._logoSummaryTable}set logoSummaryTable(t){this._logoSummaryTable=t}get positionColumns(){var t,e,n,i;if(null!=this._positionColumns)return this._positionColumns;const r=t=>{const e=this.model.findViewer(t);return this.sequenceColumnName===(null==e?void 0:e.sequenceColumnName)?e._positionColumns:null};return null!=this.model.positionColumns&&this.sequenceColumnName===(null===(t=this.model.settings)||void 0===t?void 0:t.sequenceColumnName)&&(this._positionColumns=this.model.positionColumns),null!==(e=this._positionColumns)&&void 0!==e||(this._positionColumns=null!==(i=null!==(n=r(l.q.SEQUENCE_VARIABILITY_MAP))&&void 0!==n?n:r(l.q.MOST_POTENT_RESIDUES))&&void 0!==i?i:(0,w.R)(this.dataFrame.getCol(this.sequenceColumnName)).columns.toList()),this._positionColumns}get isClusterSelectionEmpty(){return 0===this.clusterSelection[A.ORIGINAL].length+this.clusterSelection[A.CUSTOM].length}get customClusters(){const t={};return t[u.gp.CUSTOM_CLUSTER]="1",p()(this.dataFrame.columns.byTags(t))}getScaledActivityColumn(t=!1){var e,n,i;return(null===(e=this.model.settings)||void 0===e?void 0:e.activityColumnName)===this.activityColumnName&&(null===(n=this.model.settings)||void 0===n?void 0:n.activityScaling)===this.activityScaling&&(this._scaledActivityColumn=this.model.getScaledActivityColumn(t)),null!==(i=this._scaledActivityColumn)&&void 0!==i||(this._scaledActivityColumn=(0,g.Y1)(this.dataFrame.getCol(this.activityColumnName),this.activityScaling)),t?o.DataFrame.fromColumns([this._scaledActivityColumn]).clone(this.dataFrame.filter).getCol(this._scaledActivityColumn.name):this._scaledActivityColumn}getAggregationColumns(){return Object.fromEntries(this.columns.map((t=>[t,this.aggregation])).filter((([t,e])=>this.model.df.columns.contains(t)&&this.model.df.col(t).matches("numerical"))))}onTableAttached(){var t,e,n;if(super.onTableAttached(),(0,g.B2)(this.dataFrame))null===(t=this.getProperty(`sequence${u.To}`))||void 0===t||t.set(this,this.dataFrame.columns.bySemType(o.SEMTYPE.MACROMOLECULE).name),null===(e=this.getProperty(`activity${u.To}`))||void 0===e||e.set(this,p()(this.dataFrame.columns.numerical).next().value.name),null===(n=this.getProperty(`clusters${u.To}`))||void 0===n||n.set(this,p()(this.dataFrame.columns.categorical).next().value.name);else{const t="PeptidesError: dataframe is missing Macromolecule or numeric columns";r.log.error(t),r.shell.warning(t)}this.render()}detach(){this.subs.forEach((t=>t.unsubscribe()))}render(){if(a()(this.root).empty(),null==this.clustersColumnName||null==this.sequenceColumnName||null==this.activityColumnName)return void this.root.appendChild(i.divText("Please, select a sequence, cluster and activity columns in the viewer properties"));if(!this.logoSummaryTable.filter.anyTrue){const t=i.divText("No clusters to satisfy the threshold. Please, lower the threshold in viewer proeperties to include clusters");return void this.root.appendChild(i.divV([this._titleHost,t]))}const t=i.iconFA("expand-alt",(()=>{const t=i.dialog("Logo Summary Table");t.add(this.viewerGrid.root),t.onCancel((()=>this.render())),t.showModal(!0),this.viewerGrid.invalidate()}),"Show Logo Summary Table in full screen");a()(t).addClass("pep-help-icon"),this.viewerGrid.root.style.width="auto",this.root.appendChild(i.divV([i.divH([this._titleHost,t],{style:{alignSelf:"center",lineHeight:"normal"}}),this.viewerGrid.root])),this.viewerGrid.invalidate()}onPropertyChanged(t){super.onPropertyChanged(t);let e=!1;switch(t.name){case"membersRatioThreshold":this.logoSummaryTable.filter.anyTrue||(e=!0),this.updateFilter();break;case`sequence${u.To}`:this._viewerGrid=null,this._logoSummaryTable=null,e=!0;break;case`clusters${u.To}`:this._clusterStats=null,this._clusterSelection=null,this._viewerGrid=null,this._logoSummaryTable=null,e=!0;break;case`activity${u.To}`:case"activityScaling":this._scaledActivityColumn=null,this._viewerGrid=null,this._clusterStats=null,this._logoSummaryTable=null,e=!0;break;case"columns":case"aggregation":this._viewerGrid=null,this._logoSummaryTable=null,e=!0;break;case"webLogoMode":this.viewerGrid.invalidate()}e&&this.render()}initClusterSelection(t={}){var e;null!==(e=t.notify)&&void 0!==e||(t.notify=!0);const n={};return n[A.ORIGINAL]=[],n[A.CUSTOM]=[],t.notify?this.clusterSelection=n:this._clusterSelection=n,this.clusterSelection}getTotalViewerAggColumns(){var t,e;const n=this.getAggregationColumns();return(0,g.zm)(this.model.df,this.columns,n,null===(e=null===(t=this.model)||void 0===t?void 0:t.settings)||void 0===e?void 0:e.columns)}getStringAggregatedColumns(){return this.columns.filter((t=>this.model.df.columns.contains(t)&&this.model.df.col(t).matches("categorical"))).map((t=>`dist(${t})`))}createLogoSummaryTable(){var t,e,n;const i=this.clustersColumnName,r=this.dataFrame.filter.anyFalse,s=r?this.dataFrame.clone(this.dataFrame.filter):this.dataFrame,a=s.columns,l=s.rowCount,c=this.getScaledActivityColumn(r).getRawData(),h=s.getCol(i),f=h.getRawData(),m=h.categories,g={};g[u.gp.CUSTOM_CLUSTER]="1";const y=p()(a.byTags(g)).filter((t=>t.max>0)).toArray(),C=o.DataFrame.create(y.length),w=C.columns,E=w.addNewString(u.i6.CLUSTER),S=w.addNewInt(u.i6.MEMBERS).getRawData(),T=w.addNewString(u.i6.WEB_LOGO),x=w.addNewString(u.i6.DISTRIBUTION),_=w.addNewFloat(u.i6.MEAN_DIFFERENCE).getRawData(),N=w.addNewFloat(u.i6.P_VALUE).getRawData(),M=w.addNewFloat(u.i6.RATIO).getRawData();let O=s.groupBy([i]);const L=this.getTotalViewerAggColumns(),I=this.getStringAggregatedColumns(),R=I.map((t=>w.addNewString(t))),P=L.map((([t,e])=>b(e,t))),k=new Array(P.length+I.length),G=L.map((([t,e])=>[s.getCol(t),e]));for(let t=0;t<L.length;++t){const[e,n]=L[t];O=O.add(n,e,P[t]);const i=w.addNewFloat(P[t]);k[t]=i.getRawData()}const D=new Array(y.length);for(let e=0;e<y.length;++e){const n=y[e];E.set(e,n.name);const i=v.A.fromUint32Array(l,n.getRawData());if(i.allFalse)continue;const a=o.BitSet.fromBytes(i.buffer.buffer,l),u=r?(0,d.GT)(c,i):this.clusterStats[A.CUSTOM][n.name];S[e]=u.count,D[e]=a,_[e]=u.meanDifference,N[e]=null!==(t=u.pValue)&&void 0!==t?t:o.FLOAT_NULL,M[e]=u.ratio;for(let t=0;t<P.length;++t){const[n,i]=G[t];k[t][e]=(0,d.lh)(n,i,a)}for(let t=P.length;t<k.length;++t){const n=I[t-P.length];R[t-P.length].set(e,(0,d.J1)(s,n,a))}}T.setTag(o.TAGS.CELL_RENDERER,"html"),x.setTag(o.TAGS.CELL_RENDERER,"html");const U=O.aggregate(),V=U.rowCount,F=U.columns;let H=U.getCol(i);H.name=u.i6.CLUSTER,H.type!==o.COLUMN_TYPE.STRING&&(U.columns.replace(H,H.convertTo(o.COLUMN_TYPE.STRING)),H=U.getCol(H.name));const B=H.categories,q=F.addNewInt(u.i6.MEMBERS).getRawData(),Y=F.addNewString(u.i6.WEB_LOGO),$=F.addNewString(u.i6.DISTRIBUTION),j=F.addNewFloat(u.i6.MEAN_DIFFERENCE).getRawData(),W=F.addNewFloat(u.i6.P_VALUE).getRawData(),z=F.addNewFloat(u.i6.RATIO).getRawData(),K=I.map((t=>F.addNewString(t))),Q=new Array(V),X=Array.from({length:V},(()=>new v.A(l,!1)));for(let t=0;t<l;++t){const n=m[f[t]];null===(e=X[B.indexOf(n)])||void 0===e||e.setTrue(t)}for(let t=0;t<V;++t){const e=X[t];if(e.allFalse)continue;const i=o.BitSet.fromBytes(e.buffer.buffer,l),a=r?(0,d.GT)(c,e):this.clusterStats[A.ORIGINAL][B[t]];for(let e=0;e<I.length;++e){const n=I[e];K[e].set(t,(0,d.J1)(s,n,i))}q[t]=a.count,Q[t]=i,j[t]=a.meanDifference,W[t]=null!==(n=a.pValue)&&void 0!==n?n:o.FLOAT_NULL,z[t]=a.ratio}Y.setTag(o.TAGS.CELL_RENDERER,"html"),$.setTag(o.TAGS.CELL_RENDERER,"html");const J=U.append(C);return this.bitsets=Q.concat(D),I.forEach((t=>J.col(t).semType="lst-pie-chart")),J}createLogoSummaryTableGrid(){const t=this.dataFrame.filter.anyFalse,e=t?this.dataFrame.clone(this.dataFrame.filter):this.dataFrame,n=this.getTotalViewerAggColumns().map((([t,e])=>b(e,t))),s=this.logoSummaryTable.plot.grid();s.sort([u.i6.MEMBERS],[!1]),this.updateFilter(),s.col(u.i6.CLUSTER).visible=!0,s.columns.setOrder([u.i6.CLUSTER,u.i6.MEMBERS,u.i6.WEB_LOGO,...this.getStringAggregatedColumns(),u.i6.DISTRIBUTION,u.i6.MEAN_DIFFERENCE,u.i6.P_VALUE,u.i6.RATIO,...n]),s.columns.rowHeader.visible=!1,s.props.rowHeight=55;const d=new o.LruCache,f=new o.LruCache,p=this.positionColumns.length,m=s.columns.byName(u.i6.WEB_LOGO);m.cellType="html",m.width=350;const v=this.getScaledActivityColumn(t),C=e.getCol(this.sequenceColumnName);s.onCellRender.subscribe((t=>{return e=this,n=void 0,r=function*(){var e,n,i;const r=t.cell,s=r.tableRowIndex;if(!r.isTableCell||null==s||-1===s)return;const l=t.g,m=t.bounds;l.save(),l.beginPath(),l.rect(m.x,m.y,m.width,m.height),l.clip();try{const y=Math.max(r.bounds.height-2,0),w=this.bitsets[s];if((null===(e=r.tableColumn)||void 0===e?void 0:e.name)===u.i6.CLUSTER)c.k8(l,r.cell.value,this.clusterSelection,m),t.preventDefault();else if((null===(n=r.tableColumn)||void 0===n?void 0:n.name)===u.i6.WEB_LOGO){const e=Math.floor((r.bounds.width-2-4*(p-1))/p);let n=d.get(s);if(void 0!==n){const t=n.getProperties();for(const i of t)"positionHeight"===i.name&&i.get(n)!==this.webLogoMode?i.set(n,this.webLogoMode):"positionWidth"===i.name&&i.get(n)!==e?i.set(n,e):"minHeight"===i.name&&i.get(n)!==y&&i.set(n,y);a()(n.root).css("height",`${y}px`).children().first().css("overflow-y","hidden !important")}else{const t=this.createWebLogoDf(C,w);n=yield t.plot.fromType("WebLogo",{positionHeight:this.webLogoMode,horizontalAlignment:h.P4.LEFT,maxHeight:1e3,minHeight:y,positionWidth:e,showPositionLabels:!1}),d.set(s,n)}n.root.style.height=`${y}px`,r.element=n.root,t.preventDefault()}else if((null===(i=r.tableColumn)||void 0===i?void 0:i.name)===u.i6.DISTRIBUTION){let e=f.get(s);void 0===e&&(e=(0,g.FZ)(v,w).plot.histogram({filteringEnabled:!1,valueColumnName:v.name,splitColumnName:u.$2.SPLIT_COL,legendVisibility:"Never",showXAxis:!1,showColumnSelector:!1,showRangeSlider:!1,showBinSelector:!1,backColor:o.Color.toHtml(o.Color.white),xAxisHeight:1,showSplitSelector:!1}),e.root.style.width="auto",f.set(s,e)),e.root.style.height=`${y}px`,r.element=e.root,t.preventDefault()}}finally{l.restore()}},new((i=void 0)||(i=Promise))((function(t,o){function s(t){try{l(r.next(t))}catch(t){o(t)}}function a(t){try{l(r.throw(t))}catch(t){o(t)}}function l(e){var n;e.done?t(e.value):(n=e.value,n instanceof i?n:new i((function(t){t(n)}))).then(s,a)}l((r=r.apply(e,n||[])).next())}));var e,n,i,r})),s.root.addEventListener("mouseleave",(t=>this.model.unhighlight())),o.debounce(s.onCurrentCellChanged,500).subscribe((t=>{var e;if(t.isTableCell)try{if(!this.keyPress||(null===(e=t.tableColumn)||void 0===e?void 0:e.name)!==u.i6.CLUSTER)return;null!==this.currentRowIndex&&-1!==this.currentRowIndex&&this.modifyClusterSelection(this.getCluster(s.cell(u.i6.CLUSTER,this.currentRowIndex)),{shiftPressed:!0,ctrlPressed:!0},!1),this.modifyClusterSelection(this.getCluster(t),{shiftPressed:!0,ctrlPressed:!1}),s.invalidate()}finally{this.keyPress=!1,this.currentRowIndex=t.gridRow}})),s.root.addEventListener("keydown",(t=>{if(this.keyPress=t.key.startsWith("Arrow"),!this.keyPress){if("Escape"===t.key||"KeyA"===t.code&&t.shiftKey&&t.ctrlKey)this.initClusterSelection({notify:!1});else if("KeyA"===t.code&&t.ctrlKey)for(let t=0;t<this.logoSummaryTable.rowCount;++t)this.modifyClusterSelection(this.getCluster(s.cell(u.i6.CLUSTER,t)),{shiftPressed:!0,ctrlPressed:!1},!1);this.model.fireBitsetChanged(l.q.LOGO_SUMMARY_TABLE),s.invalidate()}})),s.root.addEventListener("click",(t=>{var e;const n=s.hitTest(t.offsetX,t.offsetY);if(!n||!n.isTableCell||(null===(e=n.tableColumn)||void 0===e?void 0:e.name)!==u.i6.CLUSTER)return;const o=this.getCluster(n);this.modifyClusterSelection(o,{shiftPressed:t.shiftKey,ctrlPressed:t.ctrlKey}),s.invalidate(),y._package.files.readAsText("help/logo-summary-table.md").then((t=>{r.shell.windows.help.showHelp(i.markdown(t))})).catch((t=>r.log.error(t)))})),s.onCellTooltip(((t,e,n)=>{var i;if(!t.isTableCell)return this.model.unhighlight(),!0;const r=this.getCluster(t);return this.highlightCluster(r),(null===(i=t.tableColumn)||void 0===i?void 0:i.name)===u.i6.CLUSTER&&this.showTooltip(r,e,n),!0}));const w=s.props;return w.allowEdit=!1,w.allowRowSelection=!1,w.allowBlockSelection=!1,w.allowColSelection=!1,w.showCurrentRowIndicator=!1,w.showReadOnlyNotifications=!1,s}highlightCluster(t){const e=this.clusterStats[t.positionOrClusterType][t.monomerOrCluster].mask;this.dataFrame.rows.highlight((t=>e.getBit(t))),this.model.isHighlighting=!0}getCluster(t){const e=this.logoSummaryTable.get(u.i6.CLUSTER,t.tableRowIndex);return{positionOrClusterType:this.dataFrame.getCol(this.clustersColumnName).categories.includes(e)?A.ORIGINAL:A.CUSTOM,monomerOrCluster:e}}updateFilter(){const t=this.logoSummaryTable.getCol(u.i6.MEMBERS),e=this.logoSummaryTable.getCol(u.i6.CLUSTER),n=e.getRawData(),i=e.categories,r=i.indexOf("-1"),o=t.getRawData();let s=0;o.forEach(((t,e)=>{"-1"!==i[n[e]]&&(s=Math.max(s,o[e]))}));const a=Math.ceil(s*this.membersRatioThreshold);this.logoSummaryTable.filter.init((t=>o[t]>a&&(-1===r||"-1"!==i[n[t]])))}clusterFromSelection(){const t=this.model.getVisibleSelection(),e=this.logoSummaryTable.columns,n=e.length,i=new Array(e.length),r=this.getScaledActivityColumn(),o=v.A.fromString(t.toBinaryString()),s=(0,d.GT)(r.getRawData(),o);this.bitsets.push(t.clone());const a=this.dataFrame.columns.getUnusedName("New Cluster"),l={},c={},h=this.getTotalViewerAggColumns(),f=this.getStringAggregatedColumns();for(const[e,n]of h){const i=b(n,e),r=this.dataFrame.getCol(e);l[i]=(0,d.lh)(r,n,t)}for(const e of f)c[e]=(0,d.J1)(this.dataFrame,e,t);for(let r=0;r<n;++r){const n=e.byIndex(r);i[r]=n.name===u.i6.CLUSTER?a:n.name===u.i6.MEMBERS?t.trueCount:n.name===u.i6.WEB_LOGO||n.name===u.i6.DISTRIBUTION?null:n.name===u.i6.MEAN_DIFFERENCE?s.meanDifference:n.name===u.i6.P_VALUE?s.pValue:n.name===u.i6.RATIO?s.ratio:n.name in l?l[n.name]:n.name in c?c[n.name]:void 0,void 0===i[r]&&y._package.logger.warning(`PeptidesLSTWarn: value for column ${n.name} is undefined`)}this.logoSummaryTable.rows.addNew(i),this.clusterStats[A.CUSTOM][a]=s,this.addNewCluster(a)}removeCluster(){const t=this.clusterSelection[A.CUSTOM];if(0===t.length)return void r.shell.warning("No custom clusters selected to be removed");const e=this.logoSummaryTable.rows,n=this.logoSummaryTable.getCol(u.i6.CLUSTER),i=n.categories,o=this.dataFrame.columns;for(const n of t){t.splice(t.indexOf(n),1),o.remove(n),delete this.clusterStats[A.CUSTOM][n];const r=i.indexOf(n);e.removeAt(r),this.bitsets.splice(r,1)}n.compact(),this.clusterSelection[A.CUSTOM]=t,this.render()}addNewCluster(t){const e=o.Column.fromBitSet(t,this.model.getVisibleSelection());e.setTag(u.gp.CUSTOM_CLUSTER,"1"),e.setTag(u.gp.ANALYSIS_COL,"true"),this.dataFrame.columns.add(e),this.model.analysisView.grid.col(e.name).visible=!1}modifyClusterSelection(t,e={shiftPressed:!1,ctrlPressed:!1},n=!0){n?this.clusterSelection=(0,g.vW)(this.clusterSelection,t,e):this._clusterSelection=(0,g.vW)(this.clusterSelection,t,e)}showTooltip(t,e,n){const r=this.dataFrame.filter,s=r.anyFalse?this.dataFrame.clone(r):this.dataFrame,a=s.rowCount,l=new v.A(a,!1),u=this.getScaledActivityColumn(r.anyFalse),c=u.getRawData();if(t.positionOrClusterType===A.ORIGINAL){const e=s.getCol(this.clustersColumnName),n=e.getRawData(),i=e.categories.indexOf(t.monomerOrCluster);for(let t=0;t<a;++t)n[t]===i&&l.setTrue(t);l.incrementVersion()}else{const e=s.getCol(t.monomerOrCluster);l.buffer=e.getRawData()}const h=r.anyFalse?(0,d.GT)(c,l):this.clusterStats[t.positionOrClusterType][t.monomerOrCluster];if(!h.count)return null;const f=o.BitSet.fromBytes(l.buffer.buffer,a),p=(0,g.FZ)(u,f),y=(0,m.M1)(p,!0),C=(0,m.QD)(h),w=(0,d.I_)(this.dataFrame,this.getTotalViewerAggColumns(),{filterDf:!0,mask:f}),b=Object.assign(Object.assign({},C),w),E=(0,g.F2)(y,b);return i.tooltip.show(E,e,n),E}createWebLogoDf(t,e){const n=o.DataFrame.fromColumns([t]);return n.filter.copyFrom(e),n}}},3541:(t,e,n)=>{"use strict";n.d(e,{J:()=>_,UJ:()=>N,ds:()=>i,xN:()=>x});var i,r,o,s,a=n(4328),l=n(7389),u=n(6082),c=n(7233),h=n.n(c),d=n(4139),f=n(2935),p=n(9484),m=n(144),g=n.n(m),v=n(5070),y=n(3273),C=n(912),w=n(3657),b=n(8608),A=n(3077),E=n(439),S=n(2003),T=function(t,e,n,i){return new(n||(n=Promise))((function(r,o){function s(t){try{l(i.next(t))}catch(t){o(t)}}function a(t){try{l(i.throw(t))}catch(t){o(t)}}function l(t){var e;t.done?r(t.value):(e=t.value,e instanceof n?e:new n((function(t){t(e)}))).then(s,a)}l((i=i.apply(t,e||[])).next())}))};!function(t){t.MUTATION_CLIFFS="Mutation Cliffs",t.INVARIANT_MAP="Invariant Map"}(i||(i={})),function(t){t.SEQUENCE="sequence",t.ACTIVITY="activity",t.ACTIVITY_SCALING="activityScaling",t.TARGET="target",t.TARGET_CATEGORY="targetCategory",t.MIN_ACTIVITY_DELTA="minActivityDelta",t.MAX_MUTATIONS="maxMutations",t.COLUMNS="columns",t.AGGREGATION="aggregation",t.ACTIVITY_TARGET="activityTarget",t.VALUE_INVARIANT_MAP="value",t.AGGREGATION_INVARIANT_MAP_VALUE="valueAggregation"}(r||(r={})),function(t){t.COLOR="color",t.COLOR_AGGREGATION="colorAggregation",t.CUSTOM_COLOR_RANGE="customColorRange",t.MIN_COLOR_VALUE="minColorValue",t.MAX_COLOR_VALUE="maxColorValue",t.LOWER_BOUND_COLOR="lowerBoundColor",t.MIDDLE_COLOR="middleColor",t.UPPER_BOUND_COLOR="upperBoundColor",t.LOG_SCALE_COLOR="logScaleColor"}(o||(o={})),function(t){t.GENERAL="General",t.INVARIANT_MAP="Invariant Map",t.MUTATION_CLIFFS="Mutation Cliffs",t.AGGREGATION="Aggregation"}(s||(s={}));class x extends u.JsViewer{constructor(){super(),this.keyPressed=!1,this._scaledActivityColumn=null,this.doRender=!0,this._viewerGrid=null,this._positionColumns=null,this._monomerPositionStats=null,this._mutationCliffs=null,this._mutationCliffStats=null,this._invariantMapSelection=null,this._mutationCliffsSelection=null,this.sequenceColumnName=this.column(r.SEQUENCE,{category:s.GENERAL,semType:u.SEMTYPE.MACROMOLECULE,nullable:!1}),this.activityColumnName=this.column(r.ACTIVITY,{category:s.GENERAL,nullable:!1}),this.activityScaling=this.string(r.ACTIVITY_SCALING,d.rg.NONE,{category:s.GENERAL,choices:Object.values(d.rg),nullable:!1}),this.activityTarget=this.string(r.ACTIVITY_TARGET,d.wf.HIGH,{category:s.GENERAL,choices:Object.values(d.wf),nullable:!1}),this.targetColumnName=this.column(r.TARGET,{category:s.GENERAL,nullable:!0,columnTypeFilter:"categorical",userEditable:!0}),this.minActivityDelta=this.float(r.MIN_ACTIVITY_DELTA,0,{category:s.MUTATION_CLIFFS,min:0,max:100}),this.maxMutations=this.int(r.MAX_MUTATIONS,1,{category:s.MUTATION_CLIFFS,min:1,max:20}),this.columns=this.columnList(r.COLUMNS,[],{category:s.AGGREGATION}),this.aggregation=this.string(r.AGGREGATION,u.AGG.AVG,{category:s.AGGREGATION,choices:d.V5}),this.valueColumnName=this.column(r.VALUE_INVARIANT_MAP,{category:s.INVARIANT_MAP,userEditable:!0,nullable:!1,columnTypeFilter:"numerical"}),this.valueAggregation=this.string(r.AGGREGATION_INVARIANT_MAP_VALUE,u.AGG.TOTAL_COUNT,{category:s.INVARIANT_MAP,choices:d.V5,userEditable:!0,nullable:!1}),this.mutationCliffsDebouncer=(0,b.sg)(((t,e,n)=>T(this,void 0,void 0,(function*(){return yield(0,w.uz)(t,e,n)})))),this.targetCategoryInput=l.input.choice("Category",{value:null,items:[],nullable:!0,onValueChanged:()=>{var t;this._mutationCliffs=null,this._mutationCliffStats=null,this._mutationCliffsSelection=null,this._invariantMapSelection=null,this.doRender=!1,this._monomerPositionStats=null,null===(t=this.positionColumns)||void 0===t||t.forEach((t=>{t.temp[d.gp.INVARIANT_MAP_COLOR_CACHE]=null})),this.sequenceColumnName&&this.activityColumnName&&this.calculateMutationCliffs().then((t=>{this.mutationCliffs=t.cliffs,this.cliffStats=t.cliffStats})),this.viewerGrid.invalidate()}}),this.targetCategoryInput.root.style.display="none",this.targetCategoryInput.root.style.width="50%",this.targetCategoryInput.root.style.marginLeft="8px"}get viewerGrid(){var t;return null!==(t=this._viewerGrid)&&void 0!==t||(this._viewerGrid=this.createViewerGrid()),this._viewerGrid}get alphabet(){var t;return null!==(t=this.dataFrame.getCol(this.sequenceColumnName).getTag(E.gp.alphabet))&&void 0!==t?t:S.YI.UN}get model(){return p.i.getInstance(this.dataFrame)}get positionColumns(){var t,e,n;if(null!=this._positionColumns)return this._positionColumns;const i=t=>{const e=this.model.findViewer(t);return this.sequenceColumnName===(null==e?void 0:e.sequenceColumnName)?e._positionColumns:null};return null!=this.model.positionColumns&&this.sequenceColumnName===(null===(t=this.model.settings)||void 0===t?void 0:t.sequenceColumnName)?this._positionColumns=this.model.positionColumns:this instanceof _?this._positionColumns=i(p.q.MOST_POTENT_RESIDUES):this instanceof N&&(this._positionColumns=i(p.q.SEQUENCE_VARIABILITY_MAP)),null!==(e=this._positionColumns)&&void 0!==e||(this._positionColumns=null!==(n=i(p.q.LOGO_SUMMARY_TABLE))&&void 0!==n?n:(0,A.R)(this.dataFrame.getCol(this.sequenceColumnName)).columns.toList()),this._positionColumns}get monomerPositionStats(){var t;if(null!=this._monomerPositionStats)return this._monomerPositionStats;const e=t=>{var e,n,i;return!(this.sequenceColumnName!==(null==t?void 0:t.sequenceColumnName)||this.activityColumnName!==(null==t?void 0:t.activityColumnName)||this.activityScaling!==(null==t?void 0:t.activityScaling)||!(t instanceof x&&this.targetColumnName==(null==t?void 0:t.targetColumnName)&&(null===(e=this.targetCategoryInput)||void 0===e?void 0:e.value)===(null===(n=null==t?void 0:t.targetCategoryInput)||void 0===n?void 0:n.value))&&(t instanceof x||null!=this.targetColumnName&&null!=(null===(i=this.targetCategoryInput)||void 0===i?void 0:i.value))||!(t instanceof x&&this.valueColumnName==(null==t?void 0:t.valueColumnName)&&this.valueAggregation==(null==t?void 0:t.valueAggregation))&&(t instanceof x||this.valueColumnName&&this.valueAggregation&&this.valueAggregation!=u.AGG.VALUE_COUNT&&this.valueAggregation!=u.AGG.TOTAL_COUNT))},n=t=>{const n=this.model.findViewer(t);return e(n)?n._monomerPositionStats:null};null!==this.model.monomerPositionStats&&e(this.model.settings)?this._monomerPositionStats=this.model.monomerPositionStats:this instanceof _?this._monomerPositionStats=n(p.q.MOST_POTENT_RESIDUES):this instanceof N&&(this._monomerPositionStats=n(p.q.SEQUENCE_VARIABILITY_MAP));const i=this.targetColumnName?this.dataFrame.col(this.targetColumnName):null,r=this.targetCategoryInput.value,o=this.dataFrame.col(this.valueColumnName),s=this.valueAggregation;return null!==(t=this._monomerPositionStats)&&void 0!==t||(this._monomerPositionStats=(0,w.Ej)(this.getScaledActivityColumn(),this.dataFrame.filter,this.positionColumns,{target:i&&r?{col:i,cat:r}:void 0,aggValue:s&&o?{col:o,type:s}:void 0})),this._monomerPositionStats}get mutationCliffs(){if(null!=this._mutationCliffs)return this._mutationCliffs;const t=t=>{const e=this.model.findViewer(t);return i=e,(n=this).sequenceColumnName===(null==i?void 0:i.sequenceColumnName)&&n.activityColumnName===i.activityColumnName&&n.activityScaling===i.activityScaling&&n.targetColumnName===(null==i?void 0:i.targetColumnName)&&(null===(r=n.targetCategoryInput)||void 0===r?void 0:r.value)===(null===(o=null==i?void 0:i.targetCategoryInput)||void 0===o?void 0:o.value)&&n.minActivityDelta===(null==i?void 0:i.minActivityDelta)&&n.maxMutations===(null==i?void 0:i.maxMutations)?e._mutationCliffs:null;var n,i,r,o};return this instanceof _?this._mutationCliffs=t(p.q.MOST_POTENT_RESIDUES):this instanceof N&&(this._mutationCliffs=t(p.q.SEQUENCE_VARIABILITY_MAP)),this._mutationCliffs}set mutationCliffs(t){this._mutationCliffs=t,this.viewerGrid.invalidate()}get cliffStats(){if(!this._mutationCliffStats&&this.mutationCliffs&&this.activityColumnName&&this.sequenceColumnName&&this.dataFrame.col(this.activityColumnName)){const t=this.dataFrame.col(this.activityColumnName).getRawData();this._mutationCliffStats=(0,w.Lw)(this.mutationCliffs,t)}return this._mutationCliffStats}set cliffStats(t){this._mutationCliffStats=t,this.viewerGrid.invalidate}get mutationCliffsSelection(){var t;const e=this instanceof _?d.YX.MP:d.YX.MPR,n=this.dataFrame.getTag(`${e}${d.gp.MUTATION_CLIFFS_SELECTION}`);return null!==(t=this._mutationCliffsSelection)&&void 0!==t||(this._mutationCliffsSelection=null===n?(0,b.ZR)(this.positionColumns):JSON.parse(n)),this._mutationCliffsSelection}set mutationCliffsSelection(t){this._mutationCliffsSelection=t;const e=this instanceof _?d.YX.MP:d.YX.MPR;this.dataFrame.setTag(`${e}${d.gp.MUTATION_CLIFFS_SELECTION}`,JSON.stringify(t)),this.model.fireBitsetChanged(this instanceof _?p.q.SEQUENCE_VARIABILITY_MAP:p.q.MOST_POTENT_RESIDUES);const n=this.model.findViewer(p.q.SEQUENCE_VARIABILITY_MAP);null==n||n.viewerGrid.invalidate();const i=this.model.findViewer(p.q.MOST_POTENT_RESIDUES);null==i||i.viewerGrid.invalidate(),this.model.analysisView.grid.invalidate()}getScaledActivityColumn(t=!1){var e,n,i;return(null===(e=this.model.settings)||void 0===e?void 0:e.activityColumnName)===this.activityColumnName&&(null===(n=this.model.settings)||void 0===n?void 0:n.activityScaling)===this.activityScaling&&(this._scaledActivityColumn=this.model.getScaledActivityColumn(t)),null!==(i=this._scaledActivityColumn)&&void 0!==i||(this._scaledActivityColumn=(0,b.Y1)(this.dataFrame.getCol(this.activityColumnName),this.activityScaling)),t?u.DataFrame.fromColumns([this._scaledActivityColumn]).clone(this.dataFrame.filter).getCol(this._scaledActivityColumn.name):this._scaledActivityColumn}modifyMutationCliffsSelection(t,e={shiftPressed:!1,ctrlPressed:!1},n=!0){n?this.mutationCliffsSelection=(0,b.vW)(this.mutationCliffsSelection,t,e):this._mutationCliffsSelection=(0,b.vW)(this.mutationCliffsSelection,t,e)}resetTargetCategoryValue(){var t;const e=this.targetColumnName,n=this.dataFrame.col(e);this.targetCategoryInput.items=null!==(t=null==n?void 0:n.categories)&&void 0!==t?t:[],this.targetCategoryInput.value=null,this.targetCategoryInput.root.style.display=e?"flex":"none"}onPropertyChanged(t){switch(super.onPropertyChanged(t),this.doRender=!0,t.name){case`${r.SEQUENCE}${d.To}`:this._positionColumns=null,this._monomerPositionStats=null,this._mutationCliffs=null,this._mutationCliffStats=null,this._mutationCliffsSelection=null,this._viewerGrid=null;break;case`${r.ACTIVITY}${d.To}`:case r.ACTIVITY_SCALING:this._monomerPositionStats=null,this._mutationCliffs=null,this._mutationCliffStats=null,this._mutationCliffsSelection=null,this._viewerGrid=null,this._scaledActivityColumn=null;break;case`${r.VALUE_INVARIANT_MAP}${d.To}`:case r.AGGREGATION_INVARIANT_MAP_VALUE:this._monomerPositionStats=null,this._viewerGrid=null,this._invariantMapSelection=null;break;case r.MIN_ACTIVITY_DELTA:case r.MAX_MUTATIONS:this._mutationCliffs=null,this._mutationCliffStats=null,this._mutationCliffsSelection=null,this.doRender=!1;break;case r.COLUMNS:case r.AGGREGATION:this instanceof N&&(this._viewerGrid=null);break;case r.ACTIVITY_TARGET:(this instanceof N||this instanceof _)&&(this._viewerGrid=null)}null===this._mutationCliffs&&this.sequenceColumnName&&this.activityColumnName&&this.calculateMutationCliffs().then((t=>{this.mutationCliffs=t.cliffs,this.cliffStats=t.cliffStats})),t.name===`${r.TARGET}${d.To}`&&this.targetColumnInput&&(this.targetColumnInput.value=this.targetColumnName?this.dataFrame.col(this.targetColumnName):null,this.resetTargetCategoryValue())}getAggregationColumns(){return Object.fromEntries(this.columns.map((t=>[t,this.aggregation])).filter((([t,e])=>this.model.df.columns.contains(t)&&this.model.df.col(t).matches("numerical"))))}getTotalViewerAggColumns(){var t,e;const n=this.getAggregationColumns();return(0,b.zm)(this.model.df,this.columns,n,null===(e=null===(t=this.model)||void 0===t?void 0:t.settings)||void 0===e?void 0:e.columns)}createViewerGrid(){throw new Error("Not implemented")}detach(){this.subs.forEach((t=>t.unsubscribe()))}onTableAttached(){var t,e,n;if(super.onTableAttached(),this.helpUrl="https://datagrok.ai/help/datagrok/solutions/domains/bio/peptides-sar",(0,b.B2)(this.dataFrame))null===(t=this.getProperty(`${r.SEQUENCE}${d.To}`))||void 0===t||t.set(this,this.dataFrame.columns.bySemType(u.SEMTYPE.MACROMOLECULE).name),null===(e=this.getProperty(`${r.ACTIVITY}${d.To}`))||void 0===e||e.set(this,g()(this.dataFrame.columns.numerical).next().value.name),null===(n=this.getProperty(`${r.VALUE_INVARIANT_MAP}${d.To}`))||void 0===n||n.set(this,g()(this.dataFrame.columns.numerical).next().value.name),null===this.mutationCliffs&&this.sequenceColumnName&&this.activityColumnName&&this.calculateMutationCliffs().then((t=>{this.mutationCliffs=t.cliffs,this.cliffStats=t.cliffStats}));else{const t="PeptidesError: dataframe is missing Macromolecule or numeric columns";a.log.error(t),a.shell.warning(t)}}calculateMutationCliffs(){return T(this,void 0,void 0,(function*(){const t=this.dataFrame.getCol(this.activityColumnName),e=this.positionColumns.map(b.eY),n=this.targetColumnName?(0,b.eY)(this.dataFrame.getCol(this.targetColumnName)):null,i={maxMutations:this.maxMutations,minActivityDelta:this.minActivityDelta,targetCol:n,currentTarget:this.targetCategoryInput.value},r=t.getRawData(),o=yield this.mutationCliffsDebouncer(r,e,i);return{cliffs:o,cliffStats:(0,w.Lw)(o,r)}}))}}class _ extends x{constructor(){super(),this.currentGridCell=null,this.customColorRange=!1,this.minColorValue=0,this.maxColorValue=0,this.logScaleColor=!1,this.colorColumnName=this.column(o.COLOR,{category:s.INVARIANT_MAP,nullable:!1,columnTypeFilter:"numerical"}),this.colorAggregation=this.string(o.COLOR_AGGREGATION,u.AGG.AVG,{category:s.INVARIANT_MAP,choices:d.V5}),this.lowerBoundColor=this.int(o.LOWER_BOUND_COLOR,4278190335,{category:s.INVARIANT_MAP,editor:"color"}),this.middleColor=this.int(o.MIDDLE_COLOR,4294967295,{category:s.INVARIANT_MAP,editor:"color"}),this.upperBoundColor=this.int(o.UPPER_BOUND_COLOR,4294901760,{category:s.INVARIANT_MAP,editor:"color"}),this.logScaleColor=this.bool(o.LOG_SCALE_COLOR,!1,{category:s.INVARIANT_MAP}),this.customColorRange=this.bool(o.CUSTOM_COLOR_RANGE,!1,{category:s.INVARIANT_MAP}),this.minColorValue=this.float(o.MIN_COLOR_VALUE,0,{category:s.INVARIANT_MAP}),this.maxColorValue=this.float(o.MAX_COLOR_VALUE,0,{category:s.INVARIANT_MAP})}get name(){return p.q.SEQUENCE_VARIABILITY_MAP}get mode(){var t;return null!==(t=this.dataFrame.getTag(d.gp.MONOMER_POSITION_MODE))&&void 0!==t?t:i.MUTATION_CLIFFS}set mode(t){this.dataFrame.setTag(d.gp.MONOMER_POSITION_MODE,t),this.viewerGrid.invalidate()}get invariantMapSelection(){var t;const e=this.dataFrame.getTag(`${d.YX.MP}${d.gp.INVARIANT_MAP_SELECTION}`);return null!==(t=this._invariantMapSelection)&&void 0!==t||(this._invariantMapSelection=null===e?(0,b.ZR)(this.positionColumns):JSON.parse(e)),this._invariantMapSelection}set invariantMapSelection(t){this._invariantMapSelection=t,this.dataFrame.setTag(`${d.YX.MP}${d.gp.INVARIANT_MAP_SELECTION}`,JSON.stringify(t)),this.model.fireBitsetChanged(p.q.SEQUENCE_VARIABILITY_MAP),this.model.analysisView.grid.invalidate()}onTableAttached(){var t;if(super.onTableAttached(),(0,b.B2)(this.dataFrame))null===(t=this.getProperty(`${o.COLOR}${d.To}`))||void 0===t||t.set(this,this.activityColumnName),this.targetColumnInput=l.input.column("Target",{value:void 0,nullable:!0,table:this.dataFrame,onValueChanged:t=>{var e;const n=this.getProperty(`${r.TARGET}${d.To}`);n&&n.get(this)!==t.name&&(null==n||n.set(this,null!==(e=t.name)&&void 0!==e?e:null))}});else{const t="PeptidesError: dataframe is missing Macromolecule or numeric columns";a.log.error(t),a.shell.warning(t)}this.render()}modifyInvariantMapSelection(t,e={shiftPressed:!1,ctrlPressed:!1},n=!0){n?this.invariantMapSelection=(0,b.vW)(this.invariantMapSelection,t,e):this._invariantMapSelection=(0,b.vW)(this.invariantMapSelection,t,e)}onPropertyChanged(t){var e;super.onPropertyChanged(t),t.name===r.SEQUENCE&&(this._invariantMapSelection=null),null===(e=this.positionColumns)||void 0===e||e.forEach((t=>{t.temp[d.gp.INVARIANT_MAP_COLOR_CACHE]=null})),this.doRender?this.render():this.viewerGrid.invalidate()}createMonomerPositionDf(){const t=new Set,e=this.positionColumns;for(const n of e){const e=n.categories;for(const n of e)""!==n&&t.add(n)}const n=u.Column.fromStrings(d.$2.MONOMER,Array.from(t)),i=u.DataFrame.fromColumns([n]);i.name="SAR";for(const t of e)i.columns.addNewBool(t.name);return i}cacheInvariantMapColors(){if(this.colorColumnName&&this.dataFrame.col(this.colorColumnName)){const t=this.dataFrame.getCol(this.colorColumnName).getRawData();let e=9999999,n=-9999999;const i=this.targetColumnName?this.dataFrame.col(this.targetColumnName):null,r=null==i?void 0:i.getRawData(),o=this.targetCategoryInput.value,s=null==o?null:null==i?void 0:i.categories.indexOf(o);for(const i of this.positionColumns){i.temp[d.gp.INVARIANT_MAP_COLOR_CACHE]={};const o=i.temp[d.gp.INVARIANT_MAP_COLOR_CACHE],a=i.name,l=i.getRawData(),c=i.categories;if(!this.monomerPositionStats[a])continue;const h=this.monomerPositionStats[a];for(const a of Object.keys(h)){if("general"===a)continue;const h=[];for(let t=0;t<i.length;++t){const e=c[l[t]]===a,n=!r||null==s||-1==s||r[t]===s;e&&n&&h.push(t)}const d=u.Column.float("color",h.length).init((e=>t[h[e]])).aggregate(this.colorAggregation);o[a]=d,e=Math.min(e,d),n=Math.max(n,d)}i.temp[d.gp.INVARIANT_MAP_COLOR_CACHE]=o}const a=this.customColorRange&&null!=this.minColorValue&&null!=this.maxColorValue;let l=a?this.minColorValue:e,c=a?this.maxColorValue:n;const h=this.logScaleColor&&l>1e-30&&c>1e-30&&e>1e-30&&n>1e-30;h&&(l=Math.log(l),c=Math.log(c));for(const t of this.positionColumns){const i=t.temp[d.gp.INVARIANT_MAP_COLOR_CACHE];if(i){for(const t of Object.keys(i))this.activityTarget===d.wf.LOW&&(i[t]=c-i[t]+l),i[t]=u.Color.scaleColor(h?Math.log(i[t]):i[t],l,c,void 0,[this.lowerBoundColor,this.middleColor,this.upperBoundColor]);t.temp[d.gp.INVARIANT_MAP_COLOR_CACHE]=i,t.temp[d.gp.INVARIANT_MAP_COLOR_MIN_CACHE]=e,t.temp[d.gp.INVARIANT_MAP_COLOR_MAX_CACHE]=n}}}}createViewerGrid(){const t=this.createMonomerPositionDf(),e=t.plot.grid();e.sort([d.$2.MONOMER]);const n=this.positionColumns.map((t=>t.name));e.columns.setOrder([d.$2.MONOMER,...n]);const r=t.getCol(d.$2.MONOMER);f.rI(r,this.alphabet,!0),this.cacheInvariantMapColors(),e.onCellRender.subscribe((t=>M(t,this,this.mode===i.INVARIANT_MAP,this.dataFrame.getCol(this.colorColumnName),this.colorAggregation))),e.onCellTooltip(((t,e,n)=>{var r,o;if(!t.isTableCell)return this.model.unhighlight(),!0;const s=this.getMonomerPosition(t);(0,b.dl)(s,this.dataFrame,this.monomerPositionStats),this.model.isHighlighting=!0;const a=this.getTotalViewerAggColumns();return this.mode===i.INVARIANT_MAP&&(this.colorColumnName&&this.colorAggregation&&a.unshift([this.colorColumnName,this.colorAggregation]),this.valueColumnName&&this.valueAggregation&&this.valueAggregation!==u.AGG.VALUE_COUNT&&this.valueAggregation!==u.AGG.TOTAL_COUNT&&a.unshift([this.valueColumnName,this.valueAggregation])),(0,C.DK)(this.model.df,this.getScaledActivityColumn(),a,{fromViewer:!0,isMutationCliffs:this.mode===i.MUTATION_CLIFFS,monomerPosition:s,x:e,y:n,mpStats:this.monomerPositionStats,cliffStats:null!==(o=null===(r=this.cliffStats)||void 0===r?void 0:r.stats)&&void 0!==o?o:void 0})})),e.root.addEventListener("mouseleave",(t=>this.model.unhighlight())),u.debounce(e.onCurrentCellChanged,500).subscribe((t=>{var n,r,o,s,a,l;try{if(!this.keyPressed)return;if(null!==this.currentGridCell){const t=this.getMonomerPosition(this.currentGridCell);this.mode===i.INVARIANT_MAP?this.modifyInvariantMapSelection(t,{shiftPressed:!0,ctrlPressed:!0},!1):(null===(o=null===(r=null===(n=this.mutationCliffs)||void 0===n?void 0:n.get(t.monomerOrCluster))||void 0===r?void 0:r.get(t.positionOrClusterType))||void 0===o?void 0:o.size)&&this.modifyMutationCliffsSelection(t,{shiftPressed:!0,ctrlPressed:!0},!1)}const u=this.getMonomerPosition(t);this.mode===i.INVARIANT_MAP?this.modifyInvariantMapSelection(u,{shiftPressed:!0,ctrlPressed:!1},!0):(null===(l=null===(a=null===(s=this.mutationCliffs)||void 0===s?void 0:s.get(u.monomerOrCluster))||void 0===a?void 0:a.get(u.positionOrClusterType))||void 0===l?void 0:l.size)&&this.modifyMutationCliffsSelection(u,{shiftPressed:!0,ctrlPressed:!1},!0),e.invalidate(),setTimeout((()=>null==e?void 0:e.invalidate()),300)}finally{this.keyPressed=!1,this.currentGridCell=t}})),e.root.addEventListener("keydown",(t=>{if(this.keyPressed=t.key.startsWith("Arrow"),!this.keyPressed){if("Escape"===t.key||"KeyA"===t.code&&t.ctrlKey&&t.shiftKey)this.mode===i.INVARIANT_MAP?this._invariantMapSelection=(0,b.ZR)(this.positionColumns):this._mutationCliffsSelection=(0,b.ZR)(this.positionColumns);else{if("KeyA"!==t.code||!t.ctrlKey)return;{const t=Object.keys(this.monomerPositionStats).filter((t=>"general"!==t));for(const e of t){const t=Object.keys(this.monomerPositionStats[e]).filter((t=>"general"!==t));for(const n of t){const t={monomerOrCluster:n,positionOrClusterType:e};this.mode===i.INVARIANT_MAP?this.modifyInvariantMapSelection(t,{shiftPressed:!0,ctrlPressed:!1},!1):this.modifyMutationCliffsSelection(t,{shiftPressed:!0,ctrlPressed:!1},!1)}}}}this.model.fireBitsetChanged(p.q.SEQUENCE_VARIABILITY_MAP),e.invalidate()}})),e.root.addEventListener("click",(n=>{var r,o,s,a;const l=e.hitTest(n.offsetX,n.offsetY);if(!(null==l?void 0:l.isTableCell)||(null===(r=null==l?void 0:l.tableColumn)||void 0===r?void 0:r.name)===d.$2.MONOMER)return;const u=this.getMonomerPosition(l);this.mode===i.INVARIANT_MAP?(this.modifyInvariantMapSelection(u,{shiftPressed:n.shiftKey,ctrlPressed:n.ctrlKey}),(0,b.CD)(this.invariantMapSelection)&&(t.currentRowIdx=-1)):(null===(a=null===(s=null===(o=this.mutationCliffs)||void 0===o?void 0:o.get(u.monomerOrCluster))||void 0===s?void 0:s.get(u.positionOrClusterType))||void 0===a?void 0:a.size)&&this.modifyMutationCliffsSelection(u,{shiftPressed:n.shiftKey,ctrlPressed:n.ctrlKey}),e.invalidate(),this.showHelp()})),O(e);const o=e.onAfterDrawContent.subscribe((()=>{const t=e.col(d.$2.MONOMER);if(40!==t.width){t.width=40;for(const t of n)e.col(t).width=40}else o.unsubscribe()}));return e}showHelp(){y._package.files.readAsText("help/monomer-position.md").then((t=>{a.shell.windows.help.showHelp(l.markdown(t))})).catch((t=>a.log.error(t)))}getMonomerPosition(t){return{monomerOrCluster:t.cell.dataFrame.get(d.$2.MONOMER,t.tableRowIndex),positionOrClusterType:t.tableColumn.name}}render(){var t,e,n;if(h()(this.root).empty(),!this.activityColumnName||!this.sequenceColumnName)return void this.root.appendChild(l.divText("Please, select a sequence and activity columns in the viewer properties"));const r=this.getProperty(o.COLOR);r&&(r.choices=g()(a.shell.t.columns.numerical).toArray().map((t=>t.name)),r.get(this)===d.$2.ACTIVITY_SCALED&&r.set(this,d.$2.ACTIVITY)),h()(this.root).empty();let s=l.divText(p.q.MOST_POTENT_RESIDUES,{id:"pep-viewer-title"});if(this.name===p.q.SEQUENCE_VARIABILITY_MAP){const t=l.input.bool(i.MUTATION_CLIFFS,{value:this.mode===i.MUTATION_CLIFFS});t.root.addEventListener("click",(()=>{e.value=!1,t.value=!0,this.mode=i.MUTATION_CLIFFS,this.showHelp()})),t.setTooltip("Statistically significant changes in activity");const e=l.input.bool(i.INVARIANT_MAP,{value:this.mode===i.INVARIANT_MAP});e.root.addEventListener("click",(()=>{t.value=!1,e.value=!0,this.mode=i.INVARIANT_MAP,this.showHelp()})),e.setTooltip("Number of sequences having monomer-position");const n=t=>{h()(t.root).find(".ui-input-editor").css("margin","0px").attr("type","radio"),h()(t.root).find(".ui-input-description").css("padding","0px").css("padding-right","16px"),h()(t.captionLabel).addClass("ui-label-right")};n(t),n(e),s=l.divH([t.root,e.root],{id:"pep-viewer-title"}),h()(s).css("width","auto").css("align-self","center")}const u=this.viewerGrid.root;u.style.width="auto";const c=l.iconFA("expand-alt",(()=>{const t=l.dialog();t.add(l.divV([s,u],{style:{height:"100%"}})),t.onCancel((()=>this.render())),t.showModal(!0),this.viewerGrid.invalidate()}),"Show Sequence Variability Map Table in full screen");h()(c).addClass("pep-help-icon"),this.targetColumnInput&&(this.targetColumnInput.root.style.width="50%");const f=l.divH([null!==(e=null===(t=this.targetColumnInput)||void 0===t?void 0:t.root)&&void 0!==e?e:l.div(),this.targetCategoryInput.root],{style:{alignSelf:"center",justifyContent:"center"}}),m=l.divH([c,s,f],{style:{alignSelf:"center",lineHeight:"normal",flexDirection:"column"}});this.root.appendChild(l.divV([m,u])),null===(n=this.viewerGrid)||void 0===n||n.invalidate()}}class N extends x{constructor(){super(),this.currentGridRowIdx=null}get name(){return p.q.MOST_POTENT_RESIDUES}onTableAttached(){super.onTableAttached(),this.helpUrl="https://datagrok.ai/help/datagrok/solutions/domains/bio/peptides-sar",this.render()}onPropertyChanged(t){super.onPropertyChanged(t),this.doRender&&this.render()}createMostPotentResiduesDf(){var t;const e=Object.entries(this.monomerPositionStats),n=new Array(e.length-1),i=new Array(n.length),r=new Array(n.length),o=new Array(n.length),s=new Array(n.length),a=new Array(n.length),l=new Array(n.length),c=this.getTotalViewerAggColumns(),h=c.map((([t,e])=>(0,v.hX)(e,t))),f=new Array(h.length);h.forEach(((t,e)=>f[e]=new Array(n.length)));let p=0;for(const[m,g]of e){const e=g.general;if(!e)continue;if(1===Object.entries(g).length)continue;const y=[];for(const[n,i]of Object.entries(g))"general"!==n&&(i.count>1&&(null==i.pValue||(null!==(t=i.pValue)&&void 0!==t?t:1)<=.05)&&y.push([n,i]),i.pValue===e.minPValue&&y.push([n,i]));if(0===y.length)continue;let C=null;for(const[t,e]of y)(null===C||this.activityTarget===d.wf.HIGH&&C[1].meanDifference<e.meanDifference||this.activityTarget===d.wf.LOW&&C[1].meanDifference>e.meanDifference)&&(C=[t,e]);if(null===C)continue;n[p]=parseInt(m),i[p]=C[0],r[p]=C[1].meanDifference,o[p]=C[1].pValue,s[p]=C[1].count,a[p]=C[1].ratio,l[p]=C[1].mean;const w=this.monomerPositionStats[m][C[0]],b=u.BitSet.fromBytes(w.mask.buffer.buffer,this.model.df.col(this.activityColumnName).length);for(let t=0;t<h.length;t++){const[e,n]=c[t];f[t][p]=(0,v.lh)(this.model.df.getCol(e),n,b)}++p}n.length=p,i.length=p,r.length=p,o.length=p,s.length=p,a.length=p,l.length=p;const m=u.DataFrame.create(p),g=m.columns;return g.add(u.Column.fromList(u.TYPE.INT,d.$2.POSITION,n)),g.add(u.Column.fromList(u.TYPE.STRING,d.$2.MONOMER,i)),g.add(u.Column.fromList(u.TYPE.FLOAT,d.$2.MEAN_DIFFERENCE,r)),g.add(u.Column.fromList(u.TYPE.FLOAT,d.$2.MEAN,l)),g.add(u.Column.fromList(u.TYPE.FLOAT,d.$2.P_VALUE,o)),g.add(u.Column.fromList(u.TYPE.INT,d.$2.COUNT,s)),g.add(u.Column.fromList(u.TYPE.FLOAT,d.$2.RATIO,a)),h.forEach(((t,e)=>g.add(u.Column.fromList(u.TYPE.FLOAT,t,f[e])))),m}createViewerGrid(){const t=this.createMostPotentResiduesDf(),e=t.plot.grid();e.sort([d.$2.POSITION]);const n=e.col(d.$2.P_VALUE);n.format="#.000",n.name="P-value";const i=t.getCol(d.$2.MONOMER);f.rI(i,this.alphabet,!0),e.onCellRender.subscribe((t=>M(t,this,!1))),e.onCellTooltip(((t,e,n)=>{var i,r;if(!t.isTableCell)return this.model.unhighlight(),!0;const o=this.getMonomerPosition(t);if((0,b.dl)(o,this.dataFrame,this.monomerPositionStats),this.model.isHighlighting=!0,(null===(i=t.tableColumn)||void 0===i?void 0:i.name)===d.$2.MONOMER)o.positionOrClusterType=d.$2.MONOMER;else if((null===(r=t.tableColumn)||void 0===r?void 0:r.name)!==d.$2.MEAN_DIFFERENCE)return!1;const s=this.getTotalViewerAggColumns(),a=null==t.tableRowIndex?void 0:(0,v.m2)(t.grid.dataFrame,t.tableRowIndex,s,{});return(0,C.DK)(this.model.df,this.getScaledActivityColumn(),s,{fromViewer:!0,isMostPotentResidues:!0,monomerPosition:o,x:e,y:n,mpStats:this.monomerPositionStats,aggrColValues:a})})),u.debounce(e.onCurrentCellChanged,500).subscribe((n=>{var i,r,o;try{if(this.keyPressed&&t.currentCol.name!==d.$2.MEAN_DIFFERENCE||!this.keyPressed)return;const s=this.getMonomerPosition(n);if(null!==this.currentGridRowIdx){const t=this.getMonomerPosition(e.cell("Diff",this.currentGridRowIdx));this.modifyMutationCliffsSelection(t,{shiftPressed:!0,ctrlPressed:!0},!1)}(null===(o=null===(r=null===(i=this.mutationCliffs)||void 0===i?void 0:i.get(s.monomerOrCluster))||void 0===r?void 0:r.get(s.positionOrClusterType))||void 0===o?void 0:o.size)&&this.modifyMutationCliffsSelection(s,{shiftPressed:!0,ctrlPressed:!1}),e.invalidate()}finally{this.keyPressed=!1,this.currentGridRowIdx=n.gridRow}})),e.root.addEventListener("keydown",(n=>{if(this.keyPressed=n.key.startsWith("Arrow"),!this.keyPressed){if("Escape"===n.key||"KeyA"===n.code&&n.ctrlKey&&n.shiftKey)this._mutationCliffsSelection=(0,b.ZR)(this.positionColumns);else{if("KeyA"!==n.code||!n.ctrlKey)return;for(let n=0;n<t.rowCount;++n){const t=this.getMonomerPosition(e.cell("Diff",n));this.modifyMutationCliffsSelection(t,{shiftPressed:!0,ctrlPressed:!1},!1)}}this.model.fireBitsetChanged(p.q.MOST_POTENT_RESIDUES),e.invalidate()}})),e.root.addEventListener("mouseleave",(t=>this.model.unhighlight())),e.root.addEventListener("click",(t=>{var n,i,r;const o=e.hitTest(t.offsetX,t.offsetY);if(!(null==o?void 0:o.isTableCell)||o.tableColumn.name!==d.$2.MEAN_DIFFERENCE)return;const s=this.getMonomerPosition(o);(null===(r=null===(i=null===(n=this.mutationCliffs)||void 0===n?void 0:n.get(s.monomerOrCluster))||void 0===i?void 0:i.get(s.positionOrClusterType))||void 0===r?void 0:r.size)&&(this.modifyMutationCliffsSelection(s,{shiftPressed:t.shiftKey,ctrlPressed:t.ctrlKey}),e.invalidate(),y._package.files.readAsText("help/most-potent-residues.md").then((t=>{a.shell.windows.help.showHelp(l.markdown(t))})).catch((t=>a.log.error(t))))})),O(e);const r=e.col(d.$2.MEAN_DIFFERENCE);r.name="Diff";const o=e.onAfterDrawContent.subscribe((()=>{const t=e.col(d.$2.MONOMER);40!==t.width?(t.width=40,r.width=40):o.unsubscribe()}));return e}getMonomerPosition(t){return{monomerOrCluster:t.cell.dataFrame.get(d.$2.MONOMER,t.tableRowIndex),positionOrClusterType:`${t.cell.dataFrame.get(d.$2.POSITION,t.tableRowIndex)}`}}render(){var t;if(h()(this.root).empty(),!this.activityColumnName||!this.sequenceColumnName)return void this.root.appendChild(l.divText("Please, select a sequence and activity columns in the viewer properties"));const e=l.divText(p.q.MOST_POTENT_RESIDUES,{id:"pep-viewer-title"}),n=this.viewerGrid.root;n.style.width="auto";const i=l.divH([e],{style:{alignSelf:"center",lineHeight:"normal"}});this.root.appendChild(l.divV([i,n])),null===(t=this.viewerGrid)||void 0===t||t.invalidate()}}function M(t,e,n,i,r){var o,s,a,l,c;const h=[...e.positionColumns.map((t=>t.name)),d.$2.MEAN_DIFFERENCE],p=t.g,m=t.bounds;p.save(),p.beginPath(),p.rect(m.x,m.y,m.width,m.height),p.clip();const g=t.cell;if(g.isRowHeader&&g.gridColumn.visible)return g.gridColumn.visible=!1,t.preventDefault(),void p.restore();const v=null===(o=g.tableColumn)||void 0===o?void 0:o.name,y=g.tableRowIndex;if(!g.isTableCell||-1===h.indexOf(v))return void p.restore();const C=g.grid.table,w=C.get(d.$2.MONOMER,y),b=v!==d.$2.MEAN_DIFFERENCE?v:C.get(d.$2.POSITION,y).toFixed(),A=e.monomerPositionStats[b];if(!A[w])return t.preventDefault(),void p.restore();if(n){const t=null!==(s=A[w].aggValue)&&void 0!==s?s:A[w].count,n=e.positionColumns.find((t=>t.name===b)),i=null!==(a=n.temp[d.gp.INVARIANT_MAP_COLOR_CACHE])&&void 0!==a?a:{};let r=u.Color.white;null!=i[w]?r=i[w]:e instanceof _&&(e.cacheInvariantMapColors(),r=null!==(c=(null!==(l=n.temp[d.gp.INVARIANT_MAP_COLOR_CACHE])&&void 0!==l?l:{})[w])&&void 0!==c?c:u.Color.white),f.rW(p,w,b,e.invariantMapSelection,t,m,r)}else f.Yd(p,w,b,e,m);t.preventDefault(),p.restore()}function O(t){const e=t.props;e.allowEdit=!1,e.allowRowSelection=!1,e.allowBlockSelection=!1,e.allowColSelection=!1,e.showRowHeader=!1,e.showCurrentRowIndicator=!1,e.showReadOnlyNotifications=!1,e.rowHeight=20}},7654:(t,e,n)=>{"use strict";n.d(e,{HV:()=>m,M1:()=>g,QD:()=>v});var i,r=n(7389),o=n(6082),s=n(7233),a=n.n(s),l=n(4139),u=n(5070),c=n(8608),h=n(5480),d=n(8774);!function(t){t.SEPARATE_MONOMERS="separateMonomers",t.SEPARATE_POSITIONS="separatePositions",t.SEPARATE_CLUSTERS="separateClusters"}(i||(i={}));const f="general",p=t=>t===f?"General":t.substring(8);function m(t,e){if(!t.selection.anyTrue)return r.divText("No distribution");const n=()=>{const n=[C(f,t,e)];for(const r of Object.values(i))"true"!==t.getTag(r)||r===i.SEPARATE_CLUSTERS&&!e.clusterColName||n.push(C(r,t,e));return 1===n.length?n[0]:r.div(n)},o=r.div(n()),s=Object.values(i),l=new Array(s.length);for(let u=0;u<s.length;u++){const c=s[u].substring(8);l[u]=r.input.bool(c,{value:"true"===t.getTag(s[u]),onValueChanged:e=>{t.setTag(s[u],`${e}`),a()(o).empty(),o.append(n())}}),a()(l[u].captionLabel).addClass("ui-label-right").css("text-align","left"),a()(l[u].root).find(".ui-input-editor").css("margin","0px"),a()(l[u].root).find(".ui-input-description").css("margin","0px"),l[u].setTooltip(`Show distribution for each ${c}`),c===i.SEPARATE_CLUSTERS?l[u].enabled=!(!e.clusterColName||!e.clusterSelection[h.W.ORIGINAL]):c!==i.SEPARATE_MONOMERS&&c!==i.SEPARATE_POSITIONS||(l[u].enabled=0!==Object.entries(e.monomerPositionSelection).length)}const u=r.form(l);return r.divV([u,o])}function g(t,e=!1){const n=t.plot.histogram({filteringEnabled:!1,valueColumnName:l.$2.ACTIVITY,splitColumnName:l.$2.SPLIT_COL,legendVisibility:"Never",showXAxis:!0,showColumnSelector:!1,showRangeSlider:!1,showBinSelector:!1,backColor:e?"#fdffe5":"#fffff"});return n.root.style.width="auto",n}function v(t,e={}){var n;null!==(n=e.fractionDigits)&&void 0!==n||(e.fractionDigits=3);const i={Count:`${t.count} (${(100*t.ratio).toFixed(e.fractionDigits)}%)`,"Mean difference":t.meanDifference.toFixed(e.fractionDigits),"Mean activity":t.mean.toFixed(e.fractionDigits)};return null!=t.pValue&&(i["p-value"]=t.pValue<.01?"<0.01":t.pValue.toFixed(e.fractionDigits)),i}function y(t,e,n,i={}){const r=g((0,c.FZ)(n.activityCol,t.selection,n.peptideSelection)),s=(0,u.I_)(t,Object.entries(n.columns),{filterDf:!0,mask:o.BitSet.fromBytes(e.mask.buffer.buffer,e.mask.length)}),l=v(e),h=Object.assign(Object.assign({},l),s),d=(0,c.F2)(r,h,i);return a()(d).addClass("d4-flex-col"),d}function C(t,e,n){let o=r.divText("No distribution");switch(t){case f:const t=d.A.fromSeq(e.selection.length,(t=>e.selection.get(t))),s=e.selection.anyTrue&&e.selection.anyFalse?(0,u.GT)(n.activityCol.getRawData(),t):{count:n.activityCol.length,pValue:null,meanDifference:0,ratio:1,mask:t,mean:n.activityCol.stats.avg};o=y(e,s,n);break;case i.SEPARATE_CLUSTERS:o=function(t,e,n){const i=t.rowCount,o=[],s=e.activityCol.getRawData(),a=t.getCol(e.clusterColName),l=a.categories,f=a.getRawData(),p=n[h.W.ORIGINAL].map((t=>l.indexOf(t))),m=new Array(p.length).fill(new d.A(i));for(let t=0;t<i;t++){const e=f[t],n=p.indexOf(e);-1!==n&&m[n].setTrue(t)}for(let n=0;n<p.length;n++){const i=p[n],r=(0,u.GT)(s,m[n]);o.push(y(t,r,e,{[c.AN.SELECTION]:l[i]}))}const g=n[h.W.CUSTOM];for(const n of g){const r=t.getCol(n),a=d.A.fromUint32Array(i,r.getRawData()),l=(0,u.GT)(s,a);o.push(y(t,l,e,{[c.AN.SELECTION]:n}))}return r.div(o,"d4-flex-wrap")}(e,n,n.clusterSelection);break;case i.SEPARATE_MONOMERS:const a=function(t){const e={},n=Object.keys(t);for(const i of n)for(const n of t[i])e.hasOwnProperty(n)?e[n].includes(i)||e[n].push(i):e[n]=[i];return e}(n.monomerPositionSelection);o=function(t,e,n){var i,o,s;const a=Object.keys(n),l=t.rowCount,h=[],f=[],p=[],m=[],g=e.activityCol.getRawData();for(const r of a){const a=n[r],v=new d.A(l);for(let e=0;e<a.length;e++){const n=a[e];null!==(i=f[e])&&void 0!==i||(f[e]=t.getCol(n)),null!==(o=p[e])&&void 0!==o||(p[e]=f[e].categories),null!==(s=m[e])&&void 0!==s||(m[e]=f[e].getRawData());const u=p[e].indexOf(r);for(let t=0;t<l;t++)m[e][t]===u&&v.setTrue(t)}const C=(0,u.GT)(g,v);h.push(y(t,C,e,{[c.AN.SELECTION]:r}))}return r.div(h,"d4-flex-wrap")}(e,n,a);break;case i.SEPARATE_POSITIONS:o=function(t,e,n){var i,o,s;const a=Object.keys(n),l=t.rowCount,h=[],f=e.activityCol.getRawData(),p=[],m=[],g=[];for(let r=0;r<a.length;r++){const v=a[r],C=n[v];if(0===C.length)continue;null!==(i=p[r])&&void 0!==i||(p[r]=t.getCol(v)),null!==(o=m[r])&&void 0!==o||(m[r]=p[r].categories),null!==(s=g[r])&&void 0!==s||(g[r]=p[r].getRawData());const w=new d.A(t.rowCount);for(let t=0;t<C.length;t++){const e=C[t],n=m[r].indexOf(e);for(let t=0;t<l;t++)g[r][t]===n&&w.setTrue(t)}const b=(0,u.GT)(f,w);h.push(y(t,b,e,{[c.AN.SELECTION]:v}))}return r.div(h,"d4-flex-wrap")}(e,n,n.monomerPositionSelection)}return r.divV([r.h1(p(t)),o])}},7923:(t,e,n)=>{"use strict";n.d(e,{F:()=>l});var i=n(7389),r=n(6082),o=n(4139),s=n(8608),a=n(2935);function l(t,e,n=!0){const o=u(t,e);if(!o)return new r.Widget(i.label("No mutations table generated"));const{pairsGrid:a,uniqueSequencesGrid:l,aminoToInput:c}=o,h=[a,l],d=i.divV([c.root,...h.map((t=>t.root))],{style:{width:"100%"}});return n&&(0,s.BE)("Mutation Cliffs pairs",c.root,d,(()=>{const n=u(t,e);return i.divV([n.aminoToInput.root,n.pairsGrid.root,n.uniqueSequencesGrid.root],{style:{width:"100%",height:"100%"}})})),new r.Widget(d)}function u(t,e){var n,l;const u=t.filter.getSelectedIndexes(),c=Object.keys(e.mutationCliffsSelection);if(!c.length||null===e.mutationCliffs)return null;const h=[],d=[],f=[],p=[],m=[],g=t.getCol(e.sequenceColumnName),v=g.categories,y=g.getRawData(),C=e.activityCol.getRawData(),w=new Map,b=r.BitSet.create(t.rowCount),A=Object.fromEntries(e.positionColumns.map((t=>[t.name,t])));for(const t of c){const i=A[t],r=i.categories,o=i.getRawData();for(const i of e.mutationCliffsSelection[t]){const s=null===(n=e.mutationCliffs.get(i))||void 0===n?void 0:n.get(t);if(void 0!==s)for(const[t,e]of s.entries()){if(!u.includes(t))continue;const n=null!==(l=w.get(t))&&void 0!==l?l:[],i=v[y[t]],s=C[t];for(const a of e){if(n.includes(a)||!u.includes(a))continue;w.has(a)||w.set(a,[]);const e=v[y[a]];w.get(a).push(t),h.push(`${i}#${e}`),d.push(s-C[a]),f.push(r[o[a]]),p.push(t),m.push(a),b.set(t,!0),b.set(a,!0)}}}}if(0===h.length)return null;const E=r.Column.fromStrings("Mutation",h),S=r.Column.fromList("double","Delta",d),T=r.Column.fromStrings("~to",f),x=r.Column.fromList(r.COLUMN_TYPE.INT,"~toIdx",m),_=r.Column.fromList(r.COLUMN_TYPE.INT,"~fromIdx",p),N=r.DataFrame.fromColumns([E,S,T,x,_]);N.name="Mutation Cliff pairs";const M=i.input.string("Mutated to:",{value:"",onValueChanged:t=>{const e=t;""!==e?N.filter.init((t=>T.get(t)===e)):N.filter.setAll(!0)}});M.setTooltip("Filter the rows by the monomer that the mutation was substituted to");const O=N.plot.grid();(0,s.vY)(O,!0),E.semType=o.uF.MACROMOLECULE_DIFFERENCE,E.tags[o.gp.SEPARATOR]=(0,s.AY)(g),E.tags[r.TAGS.UNITS]=g.tags[r.TAGS.UNITS],E.tags[r.TAGS.CELL_RENDERER]="MacromoleculeDifference";let L=!1,I=null;const R=[];O.onCurrentCellChanged.subscribe((t=>{try{if(!t||!t.dart)return R.length=0,void H();const e=t.tableRowIndex;if(!L)return;if(null===e)return R.length=0,void H();null!==I&&R.splice(R.indexOf(I),1),R.includes(e)||(R.push(e),O.invalidate()),H()}finally{L=!1,I=t&&t.dart?t.tableRowIndex:null}})),O.root.addEventListener("keydown",(t=>{L=t.key.startsWith("Arrow")})),O.root.addEventListener("click",(t=>{const e=O.hitTest(t.offsetX,t.offsetY);if(!e||null===e.tableRowIndex)return;const n=e.tableRowIndex;if(t.shiftKey){const t=R.indexOf(n);-1===t?R.push(n):R.splice(t,1)}else R.length=0,R.push(n);H(),O.invalidate(),F.invalidate()})),O.onCellRender.subscribe((t=>{var e;(null===(e=t.cell.tableColumn)||void 0===e?void 0:e.name)===E.name&&R.includes(t.cell.tableRowIndex)&&(0,a.X5)(t.g,t.bounds)}));const P=e.gridColumns.length,k=[];for(let t=1;t<P;t++){const n=e.gridColumns.byIndex(t);((null==n?void 0:n.name)===e.sequenceColumnName||!0===(null==n?void 0:n.visible)&&!Object.hasOwn(A,n.name))&&k.push(n.name)}const G=t.clone(b,k);G.name="Unique sequences that form Mutation Cliffs pairs";const D=G.columns.addNewInt("~seqIdx"),U=D.getRawData(),V=b.getSelectedIndexes();D.init((t=>V[t]));const F=G.plot.grid();function H(){const t=[];for(const e of R)t.push(_.get(e)),t.push(x.get(e));G.filter.init((e=>0===R.length||t.includes(U[e])),!0),O.invalidate(),F.invalidate()}return(0,s.vY)(F,!0),F.props.rowHeight=20,O.root.style.width="100% !important",F.root.style.width="100% !important",setTimeout((()=>{O.root.style.removeProperty("width"),O.root.style.setProperty("width","100%"),F.root.style.removeProperty("width"),F.root.style.setProperty("width","100%"),O.root.style.minHeight="250px",F.root.style.minHeight="250px"}),200),{pairsGrid:O,uniqueSequencesGrid:F,aminoToInput:M}}},5082:(t,e,n)=>{"use strict";n.d(e,{n:()=>u});var i=n(4328),r=(n(7389),n(6082)),o=(n(4788),n(4139)),s=n(115),a=n(9484),l=(n(7233),n(8608),n(2003),n(4572),n(5429),function(t,e,n,i){return new(n||(n=Promise))((function(r,o){function s(t){try{l(i.next(t))}catch(t){o(t)}}function a(t){try{l(i.throw(t))}catch(t){o(t)}}function l(t){var e;t.done?r(t.value):(e=t.value,e instanceof n?e:new n((function(t){t(e)}))).then(s,a)}l((i=i.apply(t,e||[])).next())}))});function u(t,e,n,u,c,h){return l(this,arguments,void 0,(function*(t,e,n,l,u,c,h={}){var d,f,p,m,g;let v=null;if(t.type!==r.COLUMN_TYPE.FLOAT&&t.type!==r.COLUMN_TYPE.INT&&t.type!==r.COLUMN_TYPE.QNUM)return i.shell.error("The activity column must be of numeric type!"),v;const y=r.TaskBarProgressIndicator.create("Loading SAR..."),C=r.DataFrame.create(l.rowCount);C.name="Peptides analysis";const w=C.columns;w.add(u);for(const t of l.columns)"true"!==t.getTag(o.gp.ANALYSIS_COL)&&(t.name.toLowerCase()===u.name.toLowerCase()&&(t.name=l.columns.getUnusedName(t.name)),w.add(t));const b={sequenceColumnName:e.name,activityColumnName:t.name,activityScaling:c,columns:{},showDendrogram:!1,showSequenceSpace:!1,sequenceSpaceParams:new s.GI(!!h.useEmbeddingsClusters&&!n),mclSettings:null!==(d=h.mclSettings)&&void 0!==d?d:new s.av};if(n){const t=C.getCol(n.name);t.type!==r.COLUMN_TYPE.STRING&&w.replace(t,t.convertTo(r.COLUMN_TYPE.STRING))}C.setTag(o.gp.SETTINGS,JSON.stringify(b));const A=r.BitSet.create(l.rowCount,(n=>!t.isNone(n)&&!e.isNone(n)&&l.filter.get(n)));if(v=a.i.getInstance(C.clone(A)),v.init(b),n){const i={clustersColumnName:n.name,sequenceColumnName:e.name,activityScaling:c,activityColumnName:t.name};yield v.addLogoSummaryTable(i)}if(yield v.addMonomerPosition(),yield v.addMostPotentResidues(),null!==(f=h.addSequenceSpace)&&void 0!==f&&f){if(yield v.addSequenceSpace({clusterCol:n,clusterEmbeddings:h.useEmbeddingsClusters}),!n&&null!==(p=h.useEmbeddingsClusters)&&void 0!==p&&p){const n=v._sequenceSpaceCols.find((t=>{var e;return v.df.col(t)&&(null===(e=v.df.col(t))||void 0===e?void 0:e.type)===r.COLUMN_TYPE.STRING}));if(n){const i={clustersColumnName:n,sequenceColumnName:e.name,activityScaling:c,activityColumnName:t.name};yield v.addLogoSummaryTable(i),setTimeout((()=>{var t,e;v&&(null===(t=null==v?void 0:v.findViewer(a.q.LOGO_SUMMARY_TABLE))||void 0===t?void 0:t.render)&&(null===(e=null==v?void 0:v.findViewer(a.q.LOGO_SUMMARY_TABLE))||void 0===e||e.render())}),100)}}}else if(null!==(m=h.addMCL)&&void 0!==m&&m&&(yield v.addMCLClusters(),!n&&null!==(g=h.useEmbeddingsClusters)&&void 0!==g&&g)){const n=v._mclCols.find((t=>(null==v?void 0:v.df.col(t))&&t.toLowerCase().startsWith("cluster")&&!t.toLowerCase().includes("size")));if(n){const i={clustersColumnName:n,sequenceColumnName:e.name,activityScaling:c,activityColumnName:t.name};yield v.addLogoSummaryTable(i),setTimeout((()=>{var t,e;v&&(null===(t=null==v?void 0:v.findViewer(a.q.LOGO_SUMMARY_TABLE))||void 0===t?void 0:t.render)&&(null===(e=null==v?void 0:v.findViewer(a.q.LOGO_SUMMARY_TABLE))||void 0===e||e.render())}),100)}}return y.close(),v}))}},5429:(t,e,n)=>{"use strict";n.d(e,{Av:()=>b,OH:()=>A,OO:()=>i});var i,r,o,s,a,l,u=n(7389),c=n(4328),h=n(6082),d=n(115),f=n(4139),p=n(9484),m=n(7233),g=n.n(m),v=n(144),y=n.n(v),C=n(3273),w=n(4572);!function(t){t.GENERAL="General",t.VIEWERS="Viewers",t.COLUMNS="Columns",t.SEQUENCE_SPACE="Sequence space",t.MCL="MCL"}(i||(i={})),function(t){t.ACTIVITY="Activity",t.ACTIVITY_SCALING="Activity scaling"}(r||(r={})),function(t){t.DENDROGRAM="Dendrogram"}(o||(o={})),function(t){t.IS_INCLUDED="",t.AGGREGATION="Aggregation"}(s||(s={})),function(t){t.DISTANCE_FUNCTION="Distance Function",t.GAP_OPEN="Gap Open Penalty",t.GAP_EXTEND="Gap Extend Penalty",t.CLUSTER_EMBEDDINGS="Cluster Embeddings",t.EPSILON="Epsilon",t.MIN_PTS="Minimum Points",t.FINGERPRINT_TYPE="Fingerprint Type"}(a||(a={})),function(t){t.DISTANCE_FUNCTION="Distance Function",t.GAP_OPEN="Gap Open Penalty",t.GAP_EXTEND="Gap Extend Penalty",t.FINGERPRINT_TYPE="Fingerprint Type",t.THRESHOLD="Similarity Threshold",t.INFLATION="Inflation Factor",t.MAX_ITERATIONS="Max Iterations",t.USE_WEBGPU="Use WebGPU",t.MIN_CLUSTER_SIZE="Min Cluster Size"}(l||(l={}));const b={[i.GENERAL]:r,[i.VIEWERS]:o,[i.COLUMNS]:s,[i.SEQUENCE_SPACE]:a,[i.MCL]:l};function A(t){var e,n,o,m,v,b,A,E,S,T;null==t.settings&&c.log.error("PeptidesError: Settings are not initialized");const x=u.accordion(),_=t.settings,N=null!==(e=null==_?void 0:_.activityScaling)&&void 0!==e?e:f.rg.NONE,M=null!==(n=null==_?void 0:_.columns)&&void 0!==n?n:{},O={},L={},I=null!==(o=null==_?void 0:_.sequenceSpaceParams)&&void 0!==o?o:new d.GI,R=null!==(m=null==_?void 0:_.mclSettings)&&void 0!==m?m:new d.av,P=u.input.column(r.ACTIVITY,{table:t.df,value:t.df.getCol(t.settings.activityColumnName),onValueChanged:t=>{O.activityColumnName=t.name},filter:t=>(t.type===h.TYPE.FLOAT||t.type===h.TYPE.INT)&&t.name!==f.$2.ACTIVITY&&0===t.stats.missingValueCount});P.setTooltip("Numeric activity column");const k=u.input.choice(r.ACTIVITY_SCALING,{value:N,items:Object.values(f.rg),onValueChanged:t=>O.activityScaling=t});k.setTooltip("Activity column transformation method"),x.addPane(i.GENERAL,(()=>u.inputs([P,k])),!0),L[i.GENERAL]=[P,k];const G=y()(t.analysisView.viewers).some((t=>t.type===p.q.DENDROGRAM)),D=u.input.bool(p.q.DENDROGRAM,{value:null!=G&&G,onValueChanged:t=>O.showDendrogram=t}),U=u.input.bool(p.q.CLUSTER_MAX_ACTIVITY,{value:!!(null==_?void 0:_.showClusterMaxActivity),onValueChanged:t=>{O.showClusterMaxActivity=null!=t?t:void 0}}),V=u.input.bool("Sequence space",{value:!!(null==_?void 0:_.showSequenceSpace),onValueChanged:t=>{O.showSequenceSpace=null!=t?t:void 0,t?(ft.root.style.display="flex",(null==_?void 0:_.showSequenceSpace)||(O.sequenceSpaceParams=I)):(ft.root.style.display="none",delete O.sequenceSpaceParams),O.showSequenceSpace===(null==_?void 0:_.showSequenceSpace)&&delete O.showSequenceSpace}});U.setTooltip("Show cluster max activity viewer"),D.setTooltip("Show dendrogram viewer"),D.enabled=null!==(0,C.getTreeHelperInstance)(),x.addPane(i.VIEWERS,(()=>u.inputs([D,V,U])),!0),L[i.VIEWERS]=[D,V,U];const F=[],H=[];for(const e of t.df.columns.numerical){const t=e.name;if(t===_.activityColumnName||t===f.$2.ACTIVITY)continue;const n=u.input.bool(s.IS_INCLUDED,{value:void 0!==M[t],onValueChanged:e=>{var n;null!==(n=O.columns)&&void 0!==n||(O.columns={}),e?O.columns[t]=i.value:(delete O.columns[t],Object.keys(O.columns).length===Object.keys(M).length&&delete O.columns)}});n.setTooltip("Include aggregated column value in tooltips, Logo Summary Table and Distribution panel");const i=u.input.choice(s.AGGREGATION,{value:null!==(v=M[t])&&void 0!==v?v:h.AGG.AVG,items:Object.values(h.STATS),onValueChanged:i=>{var r;null!==(r=O.columns)&&void 0!==r||(O.columns={}),n.value?O.columns[t]=i:(delete O.columns[e.name],Object.keys(O.columns).length===Object.keys(M).length&&delete O.columns)}});i.setTooltip("Aggregation method"),g()(i.root).find("label").css("width","auto");const 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m,g=n(3541),v=n(5480),y=n(4326);!function(t){t.SEQUENCE="sequence",t.ACTIVITY="activity",t.CLUSTER="cluster"}(m||(m={}));var C=n(912),w=function(t,e,n,i){return new(n||(n=Promise))((function(r,o){function s(t){try{l(i.next(t))}catch(t){o(t)}}function a(t){try{l(i.throw(t))}catch(t){o(t)}}function l(t){var e;t.done?r(t.value):(e=t.value,e instanceof n?e:new n((function(t){t(e)}))).then(s,a)}l((i=i.apply(t,e||[])).next())}))};(0,e.L1)("Viewers: Basic",(()=>{let n;(0,e.gM)((()=>w(void 0,void 0,void 0,(function*(){n=t.DataFrame.fromCsv(yield I.files.readAsText("tests/HELM_small.csv")),yield(0,e.cb)(500)}))));const i=t.Func.find({package:"Peptides",tags:["viewer"]}).map((t=>t.friendlyName));for(const t of i)(0,e.t6)(t,(()=>w(void 0,void 0,void 0,(function*(){yield(0,e.Bl)(t,n.clone(),{detectSemanticTypes:!0,arbitraryDfTest:!1,readOnly:!0}),yield(0,e.cb)(1e3)}))))})),(0,e.L1)("Viewers: Monomer-Position",(()=>{let n,i,r,c,h,d,f;(0,e.gM)((()=>w(void 0,void 0,void 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c=u.temp[s.i.modelName].findViewer(s.q.LOGO_SUMMARY_TABLE);(0,e.E3)(null!==c,!0,"New view is expected to have Logo Summary Table viewer attached")})))),(0,e.t6)("Custom clusters",(()=>x(void 0,void 0,void 0,(function*(){const t=i.df.filter;t.setAll(!1,!1),t.set(0,!0,!1),t.set(1,!0,!1),i.df.selection.set(0,!0,!1);const n=i.findViewer(s.q.LOGO_SUMMARY_TABLE);if(null===n)throw new Error("Logo summary table viewer is not found");(0,e.E3)(T()(n.customClusters).toArray().length,0,"Expected to have 0 custom clusters before creating one"),n.clusterFromSelection();const r=T()(n.customClusters).toArray();(0,e.E3)(r.length,1,"Expected to have 1 custom cluster");const o=r[0].name;(0,e.E3)(null!==i.df.col(o),!0,"Expected to have custom cluster column in the table"),(0,e.E3)(-1!==n.viewerGrid.table.getCol(a.i6.CLUSTER).categories.indexOf(o),!0,"Expected to have custom cluster in the Logo Summary 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f="none",p={monomerOrCluster:"Aze",positionOrClusterType:"10",mcCount:3,imCount:1},g={monomerOrCluster:"meI",positionOrClusterType:"1",mcCount:2,imCount:10},y={monomerOrCluster:"0",positionOrClusterType:v.W.ORIGINAL,count:3},w={monomerOrCluster:"1",positionOrClusterType:v.W.ORIGINAL,count:3};(0,e.gM)((()=>_(void 0,void 0,void 0,(function*(){n=t.DataFrame.fromCsv(yield I.files.readAsText("tests/HELM_small.csv")),r=n.getCol(m.ACTIVITY),c=n.getCol(m.SEQUENCE),c.semType=t.SEMTYPE.MACROMOLECULE,c.setTag(t.TAGS.UNITS,u.Hi.HELM),d=(0,l.Y1)(r,f),h=n.getCol(m.CLUSTER);const s=yield(0,o.n)(r,c,h,n,d,f);if(null===s)throw new Error("Model is null");i=s,yield(0,e.cb)(500)})))),(0,e.Pl)((()=>_(void 0,void 0,void 0,(function*(){return yield(0,e.cb)(3e3)})))),(0,e.t6)("Tooltip",(()=>_(void 0,void 0,void 0,(function*(){(0,e.E3)((0,C.cr)(p.monomerOrCluster,0,0),!0,`Couldn't structure for monomer ${p.monomerOrCluster}`)}))),{skipReason:"Need to find a way to replace _package variable to call for Bio 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${p.positionOrClusterType}`),n.mutationCliffsSelection=(0,l.ZR)(n.positionColumns);for(const[t,i]of Object.entries(n.mutationCliffsSelection))(0,e.E3)(i.length,0,`Selection is not empty for position ${t} after clearing monomer-position selection`);(0,e.E3)(t.trueCount,0,"Selection count is not equal to 0 after clearing monomer-position selection");const r=i.findViewer(s.q.LOGO_SUMMARY_TABLE);(0,e.E3)(null!==r,!0,"Couldn't find Logo Summary Table viewer"),r.modifyClusterSelection(y),(0,e.E3)(r.clusterSelection[y.positionOrClusterType].includes(y.monomerOrCluster),!0,`Cluster ${y.monomerOrCluster} is not selected`),(0,e.E3)(t.trueCount,y.count,`Selection count is not equal to ${y.count} for cluster ${y.monomerOrCluster}`),r.modifyClusterSelection(w,{shiftPressed:!0,ctrlPressed:!1}),(0,e.E3)(r.clusterSelection[w.positionOrClusterType].includes(w.monomerOrCluster),!0,`Cluster ${w.monomerOrCluster} is not selected`),(0,e.E3)(t.trueCount,y.count+w.count,`Selection count is not equal to ${y.count+w.count} for cluster ${y.monomerOrCluster} and cluster \n ${w.monomerOrCluster}`),r.modifyClusterSelection(y,{shiftPressed:!0,ctrlPressed:!0}),(0,e.E3)(r.clusterSelection[y.positionOrClusterType].includes(y.monomerOrCluster),!1,`Cluster ${y.monomerOrCluster} is still selected after deselection`),(0,e.E3)(t.trueCount,w.count,`Selection count is not equal to ${w.count} for cluster ${w.monomerOrCluster} after deselection of cluster ${y.monomerOrCluster}`),r.initClusterSelection(),(0,e.E3)(r.isClusterSelectionEmpty,!0,"Selection is not empty after clearing cluster selection"),(0,e.E3)(t.trueCount,0,"Selection count is not equal to 0 after clearing cluster selection")})))),(0,e.t6)("Invariant Map selection",(()=>_(void 0,void 0,void 0,(function*(){const t=i.df.selection;for(const[t,n]of Object.entries(i.webLogoSelection))(0,e.E3)(n.length,0,`Filter is not empty for position ${t} after initialization`);i.modifyWebLogoSelection(g),(0,e.E3)(i.webLogoSelection[g.positionOrClusterType].includes(g.monomerOrCluster),!0,`Monomer ${g.monomerOrCluster} is not filtered at position ${g.positionOrClusterType}`),(0,e.E3)(t.trueCount,g.imCount,`Filter count is not equal to ${g.imCount} for monomer ${g.monomerOrCluster} at position ${g.positionOrClusterType}`),i.modifyWebLogoSelection(p,{shiftPressed:!0,ctrlPressed:!1}),(0,e.E3)(i.webLogoSelection[p.positionOrClusterType].includes(p.monomerOrCluster),!0,`Monomer ${p.monomerOrCluster} is not filtered at position ${p.positionOrClusterType}`),(0,e.E3)(t.trueCount,g.imCount,`Filter count is not equal to ${g.imCount} for monomer ${p.monomerOrCluster} at position ${p.positionOrClusterType}`),i.modifyWebLogoSelection(g,{shiftPressed:!0,ctrlPressed:!0}),(0,e.E3)(i.webLogoSelection[g.positionOrClusterType].includes(g.monomerOrCluster),!1,`Monomer ${g.monomerOrCluster} is still filtered at position \n ${g.positionOrClusterType} after deselection`),(0,e.E3)(t.trueCount,p.imCount,`Filter count is not equal to ${p.imCount} for monomer ${p.monomerOrCluster} at position ${p.positionOrClusterType} after deselection of monomer ${g.monomerOrCluster} at position ${g.positionOrClusterType}`),(0,e.E3)(null!==i.positionColumns,!0,"Position columns are not initialized"),i.webLogoSelection=(0,l.ZR)(i.positionColumns),(0,e.E3)(t.trueCount,0,"Filter count is not equal to 0 after clearing monomer-position filter");for(const[t,n]of Object.entries(i.webLogoSelection))(0,e.E3)(n.length,0,`Filter is not empty for position ${t} after clearing monomer-position filter`)}))))}),{clear:!1});var N=n(5070),M=function(t,e,n,i){return new(n||(n=Promise))((function(r,o){function s(t){try{l(i.next(t))}catch(t){o(t)}}function a(t){try{l(i.throw(t))}catch(t){o(t)}}function l(t){var e;t.done?r(t.value):(e=t.value,e instanceof n?e:new n((function(t){t(e)}))).then(s,a)}l((i=i.apply(t,e||[])).next())}))};(0,e.L1)("Model: Settings",(()=>{let n,i,r,c,h,d;(0,e.gM)((()=>M(void 0,void 0,void 0,(function*(){n=t.DataFrame.fromCsv(yield I.files.readAsText("tests/HELM_small.csv")),r=n.getCol(m.ACTIVITY),c=n.getCol(m.SEQUENCE),c.semType=t.SEMTYPE.MACROMOLECULE,c.setTag(t.TAGS.UNITS,u.Hi.HELM),d=(0,l.Y1)(r,a.rg.NONE),h=n.getCol(m.CLUSTER);const s=yield(0,o.n)(r,c,h,n,d,a.rg.NONE);if(null===s)throw new Error("Model is null");i=s,yield(0,e.cb)(500)})))),(0,e.Pl)((()=>M(void 0,void 0,void 0,(function*(){return yield(0,e.cb)(3e3)})))),(0,e.t6)("Activity scaling",(()=>M(void 0,void 0,void 0,(function*(){var t;const n=(t,e)=>`Activity mismatch at row ${t} for scaling method '${e}'`,o=1e-4,s=i.df.getCol(null===(t=i.settings)||void 0===t?void 0:t.activityColumnName).getRawData(),u=i.df.getCol(a.$2.ACTIVITY),c=i.df.rowCount;let h=u.getRawData();for(let t=0;t<c;t++)(0,e.Wj)(h[t],s[t],o,n(t,a.rg.NONE));h=(0,l.Y1)(r,a.rg.LG).getRawData();for(let t=0;t<c;t++)(0,e.Wj)(h[t],Math.log10(s[t]),o,n(t,a.rg.LG));h=(0,l.Y1)(r,a.rg.MINUS_LG).getRawData();for(let t=0;t<c;t++)(0,e.Wj)(h[t],-Math.log10(s[t]),o,n(t,a.rg.MINUS_LG));h=d.getRawData();for(let t=0;t<c;t++)(0,e.Wj)(h[t],s[t],o,n(t,a.rg.NONE))})))),(0,e.t6)("Mutation Cliffs",(()=>M(void 0,void 0,void 0,(function*(){const t=i.findViewer(s.q.SEQUENCE_VARIABILITY_MAP);(0,e.E3)(t.maxMutations,1,`Max mutations mismatch: expected 1, actual ${t.maxMutations}`),(0,e.E3)(t.minActivityDelta,0,`Min activity delta mismatch: expected 0, actual ${t.minActivityDelta}`),t.maxMutations=2,t.minActivityDelta=.5,(0,e.E3)(t.maxMutations,2,`Max mutations mismatch: expected 2, actual ${t.maxMutations}`),(0,e.E3)(t.minActivityDelta,.5,`Min activity delta mismatch: expected 0.5, actual ${t.minActivityDelta}`)})))),(0,e.t6)("Include columns",(()=>M(void 0,void 0,void 0,(function*(){var n,r;const o="rank",a={[o]:t.AGG.AVG};i.settings={columns:a};const l=i.findViewer(s.q.LOGO_SUMMARY_TABLE),u=(0,N.hX)(t.AGG.AVG,o);(0,e.E3)(null!==l.viewerGrid.col(u),!0,`Expected to include column '${o}' in ${s.q.LOGO_SUMMARY_TABLE} but it is absent`),i.settings={columns:{}},(0,e.E3)(Object.keys(null===(n=i.settings)||void 0===n?void 0:n.columns).length,0,`Expected to remove all column aggregations but columns {${Object.keys(null===(r=i.settings)||void 0===r?void 0:r.columns).join(" & ")}} are still included`),(0,e.E3)(null===l.viewerGrid.col(u),!0,`Expected to remove column '${o}' from ${s.q.LOGO_SUMMARY_TABLE} but it is still present`)})))),(0,e.t6)("Dendrogram",(()=>M(void 0,void 0,void 0,(function*(){var t,n;i.settings={showDendrogram:!0},(0,e.E3)(null===(t=i.settings)||void 0===t?void 0:t.showDendrogram,!0,"Dendrogram is disabled after enabling"),yield(0,e.bk)((()=>null!==i.findViewer(s.q.DENDROGRAM)),"Dendrogram is not present in the view after 5s delay",5e3),i.settings={showDendrogram:!1},(0,e.E3)(null===(n=i.settings)||void 0===n?void 0:n.showDendrogram,!1,"Dendrogram is enabled after disabling"),(0,e.E3)(null===i.findViewer(s.q.DENDROGRAM),!0,"Dendrogram is present in the view after disabling")}))),{skipReason:"Need to find a way to replace _package variable to call for Bio function with tests"})}),{clear:!1});var O=function(t,e,n,i){return new(n||(n=Promise))((function(r,o){function s(t){try{l(i.next(t))}catch(t){o(t)}}function a(t){try{l(i.throw(t))}catch(t){o(t)}}function l(t){var e;t.done?r(t.value):(e=t.value,e instanceof n?e:new n((function(t){t(e)}))).then(s,a)}l((i=i.apply(t,e||[])).next())}))};(0,e.L1)("Algorithms",(()=>{let n,i,r,o;(0,e.gM)((()=>O(void 0,void 0,void 0,(function*(){n=t.Column.fromList("int","test",[1,2,5]).getRawData(),i=[t.Column.fromList("string","1","AAA".split("")),t.Column.fromList("string","2","BCC".split("")),t.Column.fromList("string","3","CCD".split(""))].map((t=>({name:t.name,rawData:t.getRawData(),cat:t.categories}))),o=(0,l.eY)(t.Column.fromList("string","target",["1","2","2"])),r={maxMutations:1,minActivityDelta:2}})))),(0,e.t6)("MutationCliffs",(()=>O(void 0,void 0,void 0,(function*(){let t=yield(0,h.uz)(n,i,r);(0,e.E3)(t.has("C"),!0,"MutationCliffsInfo should have key 'C'"),(0,e.E3)(t.has("D"),!0,"MutationCliffsInfo should have key 'D'"),(0,e.E3)(t.has("A"),!1,"MutationCliffsInfo should not have key 'A'");const s=t.get("C"),a=t.get("D");(0,e.E3)(s.has("3"),!0,"MutationCliffsInfo['C'] should have key '3'"),(0,e.E3)(a.has("3"),!0,"MutationCliffsInfo['D'] should have key '3'");const l=s.get("3"),u=a.get("3");(0,e.E3)(l.has(1),!0,"MutationCliffsInfo['C']['3'] should have key 1"),(0,e.E3)(u.has(2),!0,"MutationCliffsInfo['D']['3'] should have key 2");const c=l.get(1),d=u.get(2);(0,e.E3)(c[0],2,"MutationCliffsInfo['C']['3'][1] should have value 2"),(0,e.E3)(d[0],1,"MutationCliffsInfo['D']['3'][2] should have value 1"),r.targetCol=o,r.currentTarget="1",t=yield(0,h.uz)(n,i,r),(0,e.E3)(t.size,0,"MutationCliffsInfo should be empty for target '1'")}))))}));var L=function(t,e,n,i){return new(n||(n=Promise))((function(r,o){function s(t){try{l(i.next(t))}catch(t){o(t)}}function a(t){try{l(i.throw(t))}catch(t){o(t)}}function l(t){var e;t.done?r(t.value):(e=t.value,e instanceof n?e:new n((function(t){t(e)}))).then(s,a)}l((i=i.apply(t,e||[])).next())}))};const I=new t.Package;function R(n,i,r){return L(this,void 0,void 0,(function*(){r.catchUnhandled=!1;const o=yield(0,e.N$)({category:n,test:i,testContext:r});return t.DataFrame.fromObjects(o)}))}function P(){return L(this,void 0,void 0,(function*(){yield(0,e.Xb)(I,I.getModule("package-test.js"))}))}})(),peptides_test=i})();
1
+ var peptides_test;(()=>{var t={9135:(t,e,n)=>{"use strict";n.d(e,{pj:()=>m,uL:()=>g});var i,r,o,s,a,l,u,c=n(6082),h=n(4328);n(8774),function(t){t.Levenshtein="Levenshtein",t.JaroWinkler="Jaro-Winkler",t.Manhattan="Manhattan",t.Onehot="One-Hot"}(i||(i={})),function(t){t.Euclidean="Euclidean"}(r||(r={})),function(t){t.Tanimoto="Tanimoto",t.Dice="Dice",t.Asymmetric="Asymmetric",t.BraunBlanquet="Braun-Blanquet",t.Cosine="Cosine",t.Kulczynski="Kulczynski",t.McConnaughey="Mc-Connaughey",t.RogotGoldberg="Rogot-Goldberg",t.Russel="Russel",t.Sokal="Sokal",t.Hamming="Hamming",t.Euclidean="Euclidean"}(o||(o={})),function(t){t.TanimotoIntArray="TanimotoIntArray"}(s||(s={})),function(t){t.Vector="Vector",t.String="String",t.BitArray="BitArray",t.MacroMolecule="MacroMolecule",t.Number="Number",t.IntArray="IntArray",t.NumberArray="NumberArray"}(a||(a={})),function(t){t.Difference="Difference"}(l||(l={})),function(t){t.CommonItems="Common Items"}(u||(u={}));var d=n(4572);o.Tanimoto,o.Dice,o.Asymmetric,o.BraunBlanquet,o.Cosine,o.Kulczynski,o.McConnaughey,o.RogotGoldberg,o.Russel,o.Sokal,o.Hamming,o.Euclidean,o.Tanimoto,o.Dice,o.Asymmetric,o.BraunBlanquet,o.Cosine,o.Kulczynski,o.McConnaughey,o.RogotGoldberg,o.Russel,o.Sokal,o.Hamming,o.Euclidean,o.Tanimoto,o.Dice,o.Cosine,o.Tanimoto,o.Asymmetric,o.Cosine,o.Sokal,d.Z.HAMMING,d.Z.LEVENSHTEIN,d.Z.MONOMER_CHEMICAL_DISTANCE,d.Z.NEEDLEMANN_WUNSCH,n(3151);var f=n(2738),p=(n(826),n(3077));async function m(){const t=c.Func.find({package:"Bio",name:"getMonomerLibHelper"});if(0===t.length)throw new Error('Package "Bio" must be installed for MonomerLibHelper.');return(await t[0].prepare().call()).getOutputParamValue()}async function g(t,e){t instanceof c.Column&&(t=(0,p.R)(t).columns.toList());const n=(await m()).getMonomerLib(),i=new Array(t.length),r=t[0].length,o=new Float32Array(r);for(let s=0;s<t.length;++s){const a=s<e.length?e.getCanonical(s):f._S,l=n.getMonomer("PEPTIDE",a)?.smiles??"",u=t[s],d=u.getRawData(),p=u.categories,m=p.indexOf("");if(i[s]={categories:p,data:d,emptyIndex:m},void 0===a)continue;const g=c.Column.fromStrings("smiles",p.map((t=>n.getMonomer("PEPTIDE",t)?.smiles??""))),v=(c.DataFrame.fromColumns([g]),await h.chem.getSimilarities(g,l)),y=v?v.getRawData():null;for(let t=0;t<r;++t){const e=d[t];a!==f._S&&e!==m?o[t]+=y[e]:a===f._S&&e===m&&(o[t]+=1)}}for(let n=0;n<o.length;++n){let r=o[n]/e.length;for(let o=0;o<t.length;++o){const t=i[o];if(o>=e.length&&t.data[n]!==t.emptyIndex||t.data[n]===t.emptyIndex&&o<e.length){r=c.FLOAT_NULL;break}}o[n]=r}return c.Column.fromFloat32Array("Similarity",o)}},3151:(t,e,n)=>{"use strict";n.d(e,{EK:()=>r,q7:()=>i});const i="p",r=new RegExp(`[rd]\\((\\w)\\)${i}?`,"g")},439:(t,e,n)=>{"use strict";n.d(e,{B5:()=>l,Hi:()=>i,YI:()=>r,gp:()=>o,q7:()=>c,z1:()=>a});var i,r,o,s=n(2738);!function(t){t.FASTA="fasta",t.SEPARATOR="separator",t.HELM="helm"}(i||(i={})),function(t){t.DNA="DNA",t.RNA="RNA",t.PT="PT",t.UN="UN"}(r||(r={})),function(t){t.aligned="aligned",t.alphabet="alphabet",t.alphabetSize=".alphabetSize",t.alphabetIsMultichar=".alphabetIsMultichar",t.separator="separator",t.isHelmCompatible=".isHelmCompatible",t.positionNames=".positionNames",t.positionLabels=".positionLabels",t.regions=".regions"}(o||(o={}));const a=", ",l=/(?:\[([A-Za-z0-9_\-,()]+)\])|([A-Za-z\-])/g,u=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"])}}},c=[new s.aD(r.PT,u.fasta.peptide,.5),new s.aD(r.DNA,u.fasta.dna,.55),new s.aD(r.RNA,u.fasta.rna,.55)]},2003:(t,e,n)=>{"use strict";n.d(e,{Hi:()=>i.Hi,J9:()=>r.J9,SM:()=>r.SM,YI:()=>i.YI,dh:()=>r.dh,gp:()=>i.gp,q7:()=>i.q7,qp:()=>r.qp,z1:()=>i.z1,zS:()=>r.zS});var i=n(439),r=n(9634)},2738:(t,e,n)=>{"use strict";n.d(e,{XN:()=>o,_S:()=>i,aD:()=>r});const i="";class r{constructor(t,e,n){this.name=t,this.alphabet=e,this.cutoff=n}}class o extends r{constructor(t,e,n){super(t.name,t.alphabet,t.cutoff),this.freq=e,this.similarity=n}}},9634:(t,e,n)=>{"use strict";n.d(e,{Mu:()=>E,pc:()=>R,dh:()=>_,zS:()=>I,SM:()=>P,J9:()=>T,tm:()=>x,qp:()=>O});var i=n(6082),r=n(144),o=n.n(r),s=n(2738),a=n(439),l=n(826);class u extends Float32Array{}function c(t){let e=0;for(let n=0;n<t.length;n++)e+=t[n]*t[n];return Math.sqrt(e)}class h{static makePalette(t,e=!1,n=h){const i={};return t.forEach((t=>{const n=t[0],r=t[1];n.forEach(((t,n)=>{i[t]=this.colourPalette[r][e?0:n]}))})),new n(i)}constructor(t){this._palette=t}get(t,e){return this._palette[t]}}h.undefinedColor="rgb(100,100,100)",h.colourPalette={orange:["rgb(255,187,120)","rgb(245,167,100)","rgb(235,137,70)","rgb(205, 111, 71)"],all_green:["rgb(44,160,44)","rgb(74,160,74)","rgb(23,103,57)","rgb(30,110,96)","rgb(60,131,95)","rgb(24,110,79)","rgb(152,223,138)","rgb(182, 223, 138)","rgb(152, 193, 138)"],all_blue:["rgb(31,119,180)","rgb(23,190,207)","rgb(122, 102, 189)","rgb(158,218,229)","rgb(141, 124, 217)","rgb(31, 120, 150)"],magenta:["rgb(162,106,192)","rgb(197,165,224)","rgb(208,113,218)"],red:["rgb(214,39,40)","rgb(255,152,150)"],st_blue:["rgb(23,190,207)","rgb(158,218,229)","rgb(31,119,180)"],dark_blue:["rgb(31,119,180)","rgb(31, 120, 150)"],light_blue:["rgb(23,190,207)","rgb(158,218,229)","rgb(108, 218, 229)","rgb(23,190,227)"],lilac_blue:["rgb(124,102,211)","rgb(149,134,217)","rgb(97, 81, 150)"],dark_green:["rgb(23,103,57)","rgb(30,110,96)","rgb(60,131,95)","rgb(24,110,79)"],green:["rgb(44,160,44)","rgb(74,160,74)"],light_green:["rgb(152,223,138)","rgb(182, 223, 138)","rgb(152, 193, 138)"],st_green:["rgb(44,160,44)","rgb(152,223,138)","rgb(39, 174, 96)","rgb(74,160,74)"],pink:["rgb(247,182,210)"],brown:["rgb(140,86,75)","rgb(102, 62, 54)"],gray:["rgb(127,127,127)","rgb(199,199,199)","rgb(196,156,148)","rgb(222, 222, 180)"],yellow:["rgb(188,189,34)"],white:["rgb(230,230,230)"]};class d extends h{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,d)),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,d)),this.grokGroups}static get RasMol(){return void 0===this.rasMol&&(this.rasMol=new d({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(t){const e=t in d.aaSynonyms?d.aaSynonyms[t]:t;return super.get(e)}}d.aaSynonyms={MeNle:"L",MeA:"A",MeG:"G",MeF:"F"};class f{static getPalette(t="grok"){switch(t){case"grok":return d.GrokGroups;case"lesk":return d.Lesk;default:throw new Error(`ChemPalette: scheme \`${t}\` does not exist`)}}static getInnerOuter(t){let e=0,n="",i="";for(const r of t)"("==r?e++:")"==r?e--:e?n+=r:i+=r;return isNaN(parseInt(n))?[i,n]:[i,""]}static getColorAAPivot(t="",e="grok"){const n=this.getPalette(e);let[i,r]=this.getInnerOuter(t);if(i=i.length>6?`${i.slice(0,3)}...`:i,r=r.length>6?`${r.slice(0,3)}...`:r,1==t.length||"("==t[1]){const e=t[0]?.toUpperCase();return e in n?[n.get(e),e,r,1]:[this.undefinedColor,i,r,1]}if("d"==t[0]&&t[1]in n&&(2==t.length||"("==t[2])){const e=t[1]?.toUpperCase();return e in n?[n.get(e),e,r,2]:[this.undefinedColor,i,r,2]}if(t.substring(0,3)in this.AAFullNames&&(3==t.length||"("==t[3])){const e=this.AAFullNames[t.substring(0,3)];return e in n?[n.get(e),e,r,3]:[this.undefinedColor,i,r,3]}if(t[0]?.toLowerCase()==t[0]&&t.substring(1,3)in this.AAFullNames&&(4==t.length||"("==t[4])){const e=this.AAFullNames[t.substring(1,3)];return e in n?[n.get(e),e,r,4]:[this.undefinedColor,i,r,4]}return[this.undefinedColor,i,r,0]}}f.SemType="Aminoacids",f.SemTypeMultipleAlignment="AminoacidsMultipleAlignment",f.undefinedColor="rgb(100,100,100)",f.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"},f.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"},f.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(*)*"},f.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"};class p extends h{static get Chromatogram(){return void 0===this.chromatogram&&(this.chromatogram=new p({A:"green",C:"blue",G:"black",T:"red",U:"red",others:"gray"})),this.chromatogram}}class m{}m.SemType="Nucleotides",m.SemTypeMultipleAlignment="NucleotidesMultipleAlignment",m.Names={A:"Adenine",C:"Cytosine",G:"Guanine",T:"Thymine",U:"Uracil"};var g=n(9135);function v(t,e=!0){if(null==t)return"rgb(100,100,100)";const n=i.Color.fromHtml(t);if(e){const t=i.Color.g(n),e=i.Color.r(n),r=i.Color.b(n),o=Math.sqrt(Math.pow(0-e,2)+Math.pow(0-t,2)+Math.pow(0-r,2));if(o>210)return`rgb(${e/o*210},${t/o*210},${r/o*210})`}return i.Color.toRgb(n)}class y{static hashCode(t){let e=0;if(0===t.length)return e;for(let n=0;n<t.length;n++)e=(e<<5)-e+t.charCodeAt(n),e|=0;return e}}class C{}class w extends C{get(t,e){return"#666666"}}class b extends C{static buildPalette(){return(0,g.pj)().then((t=>{t.awaitLoaded().then((()=>{const e=t.getMonomerLib();e.onChanged.subscribe((()=>{b.customMonomerColors={},b.polymerTypes=e.getPolymerTypes();for(const t of this.polymerTypes){const n=e.getMonomerSymbolsByType(t);for(const i of n){const n=e.getMonomer(t,i);n?.meta?.colors?.default?.background&&(this.customMonomerColors[i]||(this.customMonomerColors[i]={}),this.customMonomerColors[i][t]=v(n.meta.colors.default.background,!1))}}}))}))})),[].concat(...Object.values(h.colourPalette))}get(t,e){const n=b.customMonomerColors[t],i=e??"PEPTIDE";if(n&&n[i])return n[i];const r=y.hashCode(t)%b.palette.length;return v(b.palette[r])}}b.palette=b.buildPalette(),b.customMonomerColors={},b.polymerTypes=[];class A extends h{static get Gray(){return void 0===this.gray&&(this.gray=new w),this.gray}static get Color(){return void 0===this.color&&(this.color=new b),this.color}}class E{get length(){return this.mList.length}get canonicals(){return this.mList}get originals(){return this.mList}isGap(t){return this.getOriginal(t)===this.gapOriginalMonomer}getCanonical(t){if(this.length<=t)throw new Error("Index out of bounds");return this.mList[t]}getOriginal(t){if(this.length<=t)throw new Error("Index out of bounds");return this.mList[t]}constructor(t,e){this.mList=t,this.gapOriginalMonomer=e}}class S{get length(){return this.seqS.length}get canonicals(){return this.seqS}get originals(){return this.seqS}isGap(t){return this.getOriginal(t)===l.b9[a.Hi.FASTA]}getCanonical(t){if(this.length<=t)throw new Error("Index out of bounds");return this.isGap(t)?s._S:this.seqS[t]}getOriginal(t){if(this.length<=t)throw new Error("Index out of bounds");return this.seqS[t]}constructor(t){this.seqS=t}}const T=t=>{const e=o()(t.toString().matchAll(a.B5)).map((t=>t[2]??t[1])).toArray();return new E(e,l.b9[a.Hi.FASTA])},x=t=>t?new S(t):new E([],l.b9[a.Hi.FASTA]);function _(t,e=void 0){return n=>{if(n){let i;const r=new RegExp(String.raw`"-"|'-'|[^${t}]+`,"g");if(void 0!==e){r.lastIndex=0,i=new Array(Math.ceil(e));let t=null,o=0;for(;null!==(t=r.exec(n))&&o<e;)i[o++]=t[0].replace('"-"',"").replace("'-'","");i.splice(o)}else i=n.replaceAll('"-"',"").replaceAll("'-'","").split(t,e);return new E(i,l.b9[a.Hi.SEPARATOR])}return new E([],l.b9[a.Hi.SEPARATOR])}}const N=/(PEPTIDE1|DNA1|RNA1)\{([^}]+)}/g,M=/\[([^\[\]]+)]/g,O=t=>{N.lastIndex=0;const e=N.exec(t.toString()),n=e?e[2]:null,i=n?n.split("."):[];return new E(i.map((t=>{M.lastIndex=0;const e=M.exec(t);return e&&e.length>=2?e[1]:t})),l.b9[a.Hi.HELM])},L=/([^\W_]+)/g;function I(t,e){if(t.length<=e)return t;const n=t.match(L),i=t.length>e||(n?.length??0)>1,r=n?.[0]??" ";return i?r.substring(0,e-1)+"…":r}function R(t,e,n="-"){const i=e.map((e=>{const i=function(t,e,n="-"){const i=new Set([...new Set(Object.keys(t)),...e]);i.delete(n);const r=[],o=[];for(const n of i)r.push(n in t?t[n]:0),o.push(e.has(n)?1:0);const s=new u(r),a=new u(o);return function(t,e){if(t.length!=e.length)throw new Error("The dimensionality of the vectors must match");let n=0;for(let i=0;i<t.length;i++)n+=t[i]*e[i];return n}(s,a)/(c(s)*c(a))}(t,e.alphabet,n);return new s.XN(e,t,i)}));let r;const o=Math.max(...i.map((t=>t.similarity>t.cutoff?t.similarity:-1)));return r=o>0?i.find((t=>t.similarity===o)).name:a.YI.UN,r}function P(t,e=5){let n;if(t.semType==i.SEMTYPE.MACROMOLECULE)n=l.GO.forColumn(t).alphabet;else{const i=function(t,e,n){const i=t.categories;return function(t,e){const n={};let i=!0,r=null;for(const o of t)if(null==r?r=o.length:o.length!==r&&(i=!1),o.length>=e)for(const t of o.canonicals)t in n||(n[t]=0),n[t]+=1;return{freq:n,sameLength:i}}(o().enumerate(t.getRawData()).map((([t,e])=>n(i[t]))),e)}(t,e,T);n=R(i.freq,a.q7)}return function(t){switch(t){case a.YI.PT:return d.GrokGroups;case a.YI.DNA:case a.YI.RNA:return p.Chromatogram;default:return A.Color}}(n)}},826:(t,e,n)=>{"use strict";n.d(e,{GO:()=>p,b9:()=>f});var i=n(6082),r=n(144),o=n.n(r),s=n(2003),a=n(2738),l=n(9634),u=n(4572),c=n(9135),h=n(3151);const d=new class{constructor(){this.seqHandler="seq-handler",this.notationProvider="seq-handler.notation-provider"}},f={[s.Hi.FASTA]:"-",[s.Hi.SEPARATOR]:"",[s.Hi.HELM]:"*"};class p{constructor(t){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,t.type!==i.TYPE.STRING)throw new Error(`Unexpected column type '${t.type}', must be '${i.TYPE.STRING}'.`);this._column=t;const e=this._column.meta.units;if(null==e)throw new Error("Units are not specified in column");if(this._units=e,this._notation=this.getNotation(),this._defaultGapOriginal=this.isFasta()?f[s.Hi.FASTA]:this.isHelm()?f[s.Hi.HELM]:f[s.Hi.SEPARATOR],!this.column.tags.has(s.gp.aligned)||!this.column.tags.has(s.gp.alphabet)||!this.column.tags.has(s.gp.alphabetIsMultichar)&&!this.isHelm()&&this.alphabet===s.YI.UN)if(this.isFasta())p.setUnitsToFastaColumn(this);else if(this.isSeparator()){const e=t.getTag(s.gp.separator);p.setUnitsToSeparatorColumn(this,e)}else{if(!this.isHelm())throw new Error(`Unexpected units '${this.column.meta.units}'.`);p.setUnitsToHelmColumn(this)}if(!this.column.tags.has(s.gp.alphabetIsMultichar))if(this.isHelm())this.column.setTag(s.gp.alphabetIsMultichar,"true");else if(["UN"].includes(this.alphabet))throw new Error(`For column '${this.column.name}' of alphabet '${this.alphabet}' tag '${s.gp.alphabetIsMultichar}' is mandatory.`);this.notationProvider=this.column.temp[d.notationProvider]??null,this.columnVersion=this.column.version}static setUnitsToFastaColumn(t){if(t.column.semType!==i.SEMTYPE.MACROMOLECULE||t.column.meta.units!==s.Hi.FASTA)throw new Error(`The column of notation '${s.Hi.FASTA}' must be '${i.SEMTYPE.MACROMOLECULE}'.`);t.column.meta.units=s.Hi.FASTA,p.setTags(t)}static setUnitsToSeparatorColumn(t,e){if(t.column.semType!==i.SEMTYPE.MACROMOLECULE||t.column.meta.units!==s.Hi.SEPARATOR)throw new Error(`The column of notation '${s.Hi.SEPARATOR}' must be '${i.SEMTYPE.MACROMOLECULE}'.`);if(!e)throw new Error(`The column of notation '${s.Hi.SEPARATOR}' must have the separator tag.`);t.column.meta.units=s.Hi.SEPARATOR,t.column.setTag(s.gp.separator,e),p.setTags(t)}static setUnitsToHelmColumn(t){if(t.column.semType!==i.SEMTYPE.MACROMOLECULE)throw new Error(`The column of notation '${s.Hi.HELM}' must be '${i.SEMTYPE.MACROMOLECULE}'`);t.column.meta.units=s.Hi.HELM,p.setTags(t)}static setTags(t){const e=t.column.meta.units;if([s.Hi.FASTA,s.Hi.SEPARATOR].includes(e)){if(!t.column.getTag(s.gp.alphabet)&&0===Object.keys(t.stats.freq).length)throw new Error("Alphabet is empty and not annotated.");let e=t.column.getTag(s.gp.aligned);null===e&&(e=t.stats.sameLength?"SEQ.MSA":"SEQ",t.column.setTag(s.gp.aligned,e));let n=t.column.getTag(s.gp.alphabet);if(null===n&&(n=(0,l.pc)(t.stats.freq,s.q7),t.column.setTag(s.gp.alphabet,n)),n===s.YI.UN){const e=Object.keys(t.stats.freq).length,n=Object.keys(t.stats.freq).some((t=>t.length>1));t.column.setTag(s.gp.alphabetSize,e.toString()),t.column.setTag(s.gp.alphabetIsMultichar,n?"true":"false")}}}get column(){return this._column}get length(){return this._column.length}get units(){return this._units}get notation(){return this._notation}get defaultGapOriginal(){return this._defaultGapOriginal}get separator(){const t=this.column.getTag(s.gp.separator)??void 0;if(this.notation===s.Hi.SEPARATOR&&void 0===t)throw new Error(`Separator is mandatory for column '${this.column.name}' of notation '${this.notation}'.`);return t}get aligned(){const t=this.column.getTag(s.gp.aligned);if(!t&&(this.isFasta()||this.isSeparator()))throw new Error("Tag aligned not set");return t}get alphabet(){const t=this.column.getTag(s.gp.alphabet);if(!t&&(this.isFasta()||this.isSeparator()))throw new Error("Tag alphabet not set");return t}get helmCompatible(){return this.column.getTag(s.gp.isHelmCompatible)}getAlphabetSize(){if(this.notation==s.Hi.HELM||this.alphabet==s.YI.UN){const t=this.column.getTag(s.gp.alphabetSize);let e;if(t)e=parseInt(t);else{const t=this.stats;e=Object.keys(t.freq).length}return e}switch(this.alphabet){case s.YI.PT:return 20;case s.YI.DNA:case s.YI.RNA:return 4;case"NT":return console.warn("Unexpected alphabet 'NT'."),4;default:throw new Error(`Unexpected alphabet '${this.alphabet}'.`)}}getAlphabetIsMultichar(){return this.notation===s.Hi.HELM||this.alphabet===s.YI.UN&&"true"===this.column.getTag(s.gp.alphabetIsMultichar)}getSplitted(t,e){if(this.cached&&void 0===e){this.column.version===this.columnVersion&&null!==this._splitted||(this.columnVersion=this.column.version,this._splitted=new Array(this.column.length));let e=this._splitted[t]?this._splitted[t].deref():void 0;if(!e){const n=this.column.get(t);e=this.splitter(n),this._splitted[t]=new WeakRef(e)}return e}{const n=this.column.get(t);return this.getSplitter(e)(n)}}async getHelm(t,e){const n=this.column.get(t);return this.notationProvider?(await this.notationProvider.getHelm(this.column,e)).get(t):this.convertToHelm(n)}get stats(){if(null===this._stats){const t={};let e=!0,n=null;const i=this.column.length;for(let r=0;r<i;++r){const i=this.getSplitted(r);null==n?n=i.length:i.length!==n&&(e=!1);for(const e of i.canonicals)e in t||(t[e]=0),t[e]+=1}this._stats={freq:t,sameLength:e}}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((t=>this.getSplitted(t).length)))),this._maxLength}get posList(){if(null===this._posList){const t=this.column.getTag(s.gp.positionNames);this._posList=t?t.split(s.z1).map((t=>t.trim())):o().count(1).take(this.maxLength).map((t=>t.toString())).toArray()}return this._posList}isFasta(){return this.notation===s.Hi.FASTA}isSeparator(){return this.notation===s.Hi.SEPARATOR}isHelm(){return this.notation===s.Hi.HELM}isRna(){return this.alphabet===s.YI.RNA}isDna(){return this.alphabet===s.YI.DNA}isPeptide(){return this.alphabet===s.YI.PT}isMsa(){return!!this.aligned&&this.aligned.toUpperCase().includes("MSA")}isHelmCompatible(){return"true"===this.helmCompatible}isGap(t){return!t||t===this._defaultGapOriginal}getNotation(){if(this.units.toLowerCase().startsWith(s.Hi.FASTA))return s.Hi.FASTA;if(this.units.toLowerCase().startsWith(s.Hi.SEPARATOR))return s.Hi.SEPARATOR;if(this.units.toLowerCase().startsWith(s.Hi.HELM))return s.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(t,e,n,r){const o=this.column,a=t.toLowerCase()+"("+o.name+")",l=n??o.dataFrame.columns.getUnusedName(a),u=i.Column.fromList("string",l,r??new Array(this.column.length).fill(""));if(u.semType=i.SEMTYPE.MACROMOLECULE,u.meta.units=t,t===s.Hi.SEPARATOR){if(!e)throw new Error(`Notation '${s.Hi.SEPARATOR}' requires separator value.`);u.setTag(s.gp.separator,e)}u.setTag(i.TAGS.CELL_RENDERER,t===s.Hi.HELM?"helm":"sequence");const c=o.getTag(s.gp.aligned);c&&u.setTag(s.gp.aligned,c);let h=o.getTag(s.gp.alphabet);h||this.notation!==s.Hi.HELM||t===s.Hi.HELM||(h=s.YI.UN),null!=h&&u.setTag(s.gp.alphabet,h);let d=o.getTag(s.gp.alphabetSize);null!=h&&d&&u.setTag(s.gp.alphabetSize,d);const f=o.getTag(s.gp.alphabetIsMultichar);return null!=h&&void 0!==f&&u.setTag(s.gp.alphabetIsMultichar,f),t==s.Hi.HELM&&(d=this.getAlphabetSize().toString(),u.setTag(s.gp.alphabetSize,d)),u}getNewColumnFromList(t,e){return this.getNewColumn(this.notation,this.separator,t,e)}static getNewColumn(t){const e=p.forColumn(t),n=e.notation;return e.getNewColumn(n)}static unitsStringIsValid(t){return t=t.toLowerCase(),[s.Hi.FASTA,s.Hi.SEPARATOR,s.Hi.HELM].some((e=>t.startsWith(e.toLowerCase())))}static getNewColumnFromParams(t,e,n){if(!p.unitsStringIsValid(n))throw new Error("Invalid format of 'units' parameter");const r=i.Column.fromList("string",e,new Array(t).fill(""));return r.semType=i.SEMTYPE.MACROMOLECULE,r.meta.units=n,r}getSplitter(t){let e=null;if(e=this.notationProvider?this.notationProvider.splitter:null,e)return e;if(this.units.toLowerCase().startsWith(s.Hi.FASTA))return null===this.column.getTag(s.gp.alphabet)||this.getAlphabetIsMultichar()?s.J9:l.tm;if(this.units.toLowerCase().startsWith(s.Hi.SEPARATOR))return(0,s.dh)(this.separator,t);if(this.units.toLowerCase().startsWith(s.Hi.HELM))return s.qp;throw new Error(`Unexpected units ${this.units} .`)}split(t){return this.splitter(t)}getDistanceFunctionName(){if(!this.isFasta())throw new Error("Only FASTA notation is supported");if(this.isMsa())return u.Z.HAMMING;switch(this.alphabet){case s.YI.DNA:case s.YI.RNA:case s.YI.PT:}return u.Z.LEVENSHTEIN}getDistanceFunction(){return u.V[this.getDistanceFunctionName()]()}async checkHelmCompatibility(){if(this.column.tags.has(s.gp.isHelmCompatible))return"true"===this.column.getTag(s.gp.isHelmCompatible);const t=(await(0,c.pj)()).getMonomerLib().getMonomerSymbolsByType("PEPTIDE"),e=new Set(t),n=((0,s.dh)(this.separator),new Set),i=this.column.length,r=this.column.getRawData();for(let t=0;t<i;++t){const i=r[t];if(!(i in n)){n.add(i);const r=this.getSplitted(t);for(const t of r.canonicals)if(!e.has(t))return this.column.setTag(s.gp.isHelmCompatible,"false"),!1}}return this.column.setTag(s.gp.isHelmCompatible,"true"),!0}get splitter(){return null===this._splitter&&(this._splitter=this.getSplitter()),this._splitter}toFasta(t){return t===s.Hi.FASTA}toSeparator(t){return t===s.Hi.SEPARATOR}toHelm(t){return t===s.Hi.HELM}convertHelmToFastaSeparator(t,e,n,i){i||(i=this.toFasta(e)?f[s.Hi.FASTA]:f[s.Hi.SEPARATOR]),n||(n=this.toFasta(e)?"":this.separator);const r=t.startsWith("RNA"),o=this.splitter(t),a=[];for(let t=0;t<o.length;++t){let n=o.getOriginal(t);if(r&&(n=n.replace(h.EK,"")),n===f[s.Hi.HELM])a.push(i);else if(this.toFasta(e)&&n.length>1){const t="["+n+"]";a.push(t)}else a.push(n)}return a.join(n)}convert(t,e){const n=this.getJoiner({notation:t,separator:e}),i=this.getNewColumn(t,e);return i.init((t=>{const e=this.getSplitted(t);return n(e)})),i}getRegion(t,e,n){const 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i}))},tt=[{name:"edges",type:"mixed"},{name:"inEdges",type:"directed",direction:"in"},{name:"outEdges",type:"directed",direction:"out"},{name:"inboundEdges",type:"mixed",direction:"in"},{name:"outboundEdges",type:"mixed",direction:"out"},{name:"directedEdges",type:"directed"},{name:"undirectedEdges",type:"undirected"}];function et(t,e,n,i){var r=!1;for(var o in e)if(o!==i){var s=e[o];if(r=n(s.key,s.attributes,s.source.key,s.target.key,s.source.attributes,s.target.attributes,s.undirected),t&&r)return s.key}}function nt(t,e,n,i){var r,o,s,a=!1;for(var l in e)if(l!==i){r=e[l];do{if(o=r.source,s=r.target,a=n(r.key,r.attributes,o.key,s.key,o.attributes,s.attributes,r.undirected),t&&a)return r.key;r=r.next}while(void 0!==r)}}function it(t,e){var n,i=Object.keys(t),r=i.length,o=0;return new L((function(){do{if(n)n=n.next;else{if(o>=r)return{done:!0};var s=i[o++];if(s===e){n=void 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n=n.next,{done:!1,value:t}})):L.of({edge:n.key,attributes:n.attributes,source:n.source.key,target:n.target.key,sourceAttributes:n.source.attributes,targetAttributes:n.target.attributes,undirected:n.undirected})}function at(t,e,n,i){if(0!==e.size)for(var r,o,s="mixed"!==n&&n!==e.type,a="undirected"===n,l=!1,u=e._edges.values();!0!==(r=u.next()).done;)if(o=r.value,!s||o.undirected===a){var c=o,h=c.key,d=c.attributes,f=c.source,p=c.target;if(l=i(h,d,f.key,p.key,f.attributes,p.attributes,o.undirected),t&&l)return h}}function lt(t,e,n,i,r,o){var s,a=e?nt:et;if("undirected"!==n){if("out"!==i&&(s=a(t,r.in,o),t&&s))return s;if("in"!==i&&(s=a(t,r.out,o,i?void 0:r.key),t&&s))return s}if("directed"!==n&&(s=a(t,r.undirected,o),t&&s))return s}function ut(t,e,n,i,r,o,s){var a,l=n?ot:rt;if("undirected"!==e){if(void 0!==r.in&&"out"!==i&&(a=l(t,r.in,o,s),t&&a))return a;if(void 0!==r.out&&"in"!==i&&(i||r.key!==o)&&(a=l(t,r.out,o,s),t&&a))return a}if("directed"!==e&&void 0!==r.undirected&&(a=l(t,r.undirected,o,s),t&&a))return a}var ct=[{name:"neighbors",type:"mixed"},{name:"inNeighbors",type:"directed",direction:"in"},{name:"outNeighbors",type:"directed",direction:"out"},{name:"inboundNeighbors",type:"mixed",direction:"in"},{name:"outboundNeighbors",type:"mixed",direction:"out"},{name:"directedNeighbors",type:"directed"},{name:"undirectedNeighbors",type:"undirected"}];function ht(){this.A=null,this.B=null}function dt(t,e,n,i,r){for(var o in i){var s=i[o],a=s.source,l=s.target,u=a===n?l:a;if(!e||!e.has(u.key)){var c=r(u.key,u.attributes);if(t&&c)return u.key}}}function ft(t,e,n,i,r){if("mixed"!==e){if("undirected"===e)return dt(t,null,i,i.undirected,r);if("string"==typeof n)return dt(t,null,i,i[n],r)}var o,s=new ht;if("undirected"!==e){if("out"!==n){if(o=dt(t,null,i,i.in,r),t&&o)return o;s.wrap(i.in)}if("in"!==n){if(o=dt(t,s,i,i.out,r),t&&o)return o;s.wrap(i.out)}}if("directed"!==e&&(o=dt(t,s,i,i.undirected,r),t&&o))return o}function pt(t,e,n){var i=Object.keys(n),r=i.length,o=0;return new L((function(){var s=null;do{if(o>=r)return t&&t.wrap(n),{done:!0};var a=n[i[o++]],l=a.source,u=a.target;s=l===e?u:l,t&&t.has(s.key)&&(s=null)}while(null===s);return{done:!1,value:{neighbor:s.key,attributes:s.attributes}}}))}function mt(t,e,n,i,r){for(var o,s,a,l,u,c,h,d=i._nodes.values(),f=i.type;!0!==(o=d.next()).done;){var p=!1;if(s=o.value,"undirected"!==f)for(a in l=s.out){u=l[a];do{if(c=u.target,p=!0,h=r(s.key,c.key,s.attributes,c.attributes,u.key,u.attributes,u.undirected),t&&h)return u;u=u.next}while(u)}if("directed"!==f)for(a in l=s.undirected)if(!(e&&s.key>a)){u=l[a];do{if((c=u.target).key!==a&&(c=u.source),p=!0,h=r(s.key,c.key,s.attributes,c.attributes,u.key,u.attributes,u.undirected),t&&h)return u;u=u.next}while(u)}if(n&&!p&&(h=r(s.key,null,s.attributes,null,null,null,null),t&&h))return null}}function gt(t){if(!u(t))throw new H('Graph.import: invalid serialized node. A serialized node should be a plain object with at least a "key" property.');if(!("key"in t))throw new H("Graph.import: serialized node is missing its key.");if("attributes"in t&&(!u(t.attributes)||null===t.attributes))throw new H("Graph.import: invalid attributes. Attributes should be a plain object, null or omitted.")}function vt(t){if(!u(t))throw new H('Graph.import: invalid serialized edge. A serialized edge should be a plain object with at least a "source" & "target" property.');if(!("source"in t))throw new H("Graph.import: serialized edge is missing its source.");if(!("target"in t))throw new H("Graph.import: serialized edge is missing its target.");if("attributes"in t&&(!u(t.attributes)||null===t.attributes))throw new H("Graph.import: invalid attributes. Attributes should be a plain object, null or omitted.");if("undirected"in t&&"boolean"!=typeof t.undirected)throw new H("Graph.import: invalid undirectedness information. Undirected should be boolean or omitted.")}ht.prototype.wrap=function(t){null===this.A?this.A=t:null===this.B&&(this.B=t)},ht.prototype.has=function(t){return null!==this.A&&t in this.A||null!==this.B&&t in this.B};var yt,Ct=(yt=255&Math.floor(256*Math.random()),function(){return yt++}),wt=new Set(["directed","undirected","mixed"]),bt=new Set(["domain","_events","_eventsCount","_maxListeners"]),At={allowSelfLoops:!0,multi:!1,type:"mixed"};function Et(t,e,n){var i=new t.NodeDataClass(e,n);return t._nodes.set(e,i),t.emit("nodeAdded",{key:e,attributes:n}),i}function St(t,e,n,i,r,o,s,a){if(!i&&"undirected"===t.type)throw new q("Graph.".concat(e,": you cannot add a directed edge to an undirected graph. Use the #.addEdge or #.addUndirectedEdge instead."));if(i&&"directed"===t.type)throw new q("Graph.".concat(e,": you cannot add an undirected edge to a directed graph. Use the #.addEdge or #.addDirectedEdge instead."));if(a&&!u(a))throw new H("Graph.".concat(e,': invalid attributes. Expecting an object but got "').concat(a,'"'));if(o=""+o,s=""+s,a=a||{},!t.allowSelfLoops&&o===s)throw new q("Graph.".concat(e,': source & target are the same ("').concat(o,"\"), thus creating a loop explicitly forbidden by this graph 'allowSelfLoops' option set to false."));var l=t._nodes.get(o),c=t._nodes.get(s);if(!l)throw new B("Graph.".concat(e,': source node "').concat(o,'" not found.'));if(!c)throw new B("Graph.".concat(e,': target node "').concat(s,'" not found.'));var h={key:null,undirected:i,source:o,target:s,attributes:a};if(n)r=t._edgeKeyGenerator();else if(r=""+r,t._edges.has(r))throw new q("Graph.".concat(e,': the "').concat(r,'" edge already exists in the graph.'));if(!t.multi&&(i?void 0!==l.undirected[s]:void 0!==l.out[s]))throw new q("Graph.".concat(e,': an edge linking "').concat(o,'" to "').concat(s,"\" already exists. If you really want to add multiple edges linking those nodes, you should create a multi graph by using the 'multi' option."));var d=new W(i,r,l,c,a);t._edges.set(r,d);var f=o===s;return i?(l.undirectedDegree++,c.undirectedDegree++,f&&(l.undirectedLoops++,t._undirectedSelfLoopCount++)):(l.outDegree++,c.inDegree++,f&&(l.directedLoops++,t._directedSelfLoopCount++)),t.multi?d.attachMulti():d.attach(),i?t._undirectedSize++:t._directedSize++,h.key=r,t.emit("edgeAdded",h),r}function Tt(t,e,n,i,r,o,s,l,c){if(!i&&"undirected"===t.type)throw new q("Graph.".concat(e,": you cannot merge/update a directed edge to an undirected graph. Use the #.mergeEdge/#.updateEdge or #.addUndirectedEdge instead."));if(i&&"directed"===t.type)throw new q("Graph.".concat(e,": you cannot merge/update an undirected edge to a directed graph. Use the #.mergeEdge/#.updateEdge or #.addDirectedEdge instead."));if(l)if(c){if("function"!=typeof l)throw new H("Graph.".concat(e,': invalid updater function. Expecting a function but got "').concat(l,'"'))}else if(!u(l))throw new H("Graph.".concat(e,': invalid attributes. Expecting an object but got "').concat(l,'"'));var h;if(o=""+o,s=""+s,c&&(h=l,l=void 0),!t.allowSelfLoops&&o===s)throw new q("Graph.".concat(e,': source & target are the same ("').concat(o,"\"), thus creating a loop explicitly forbidden by this graph 'allowSelfLoops' option set to false."));var d,f,p=t._nodes.get(o),m=t._nodes.get(s);if(!n&&(d=t._edges.get(r))){if(!(d.source.key===o&&d.target.key===s||i&&d.source.key===s&&d.target.key===o))throw new q("Graph.".concat(e,': inconsistency detected when attempting to merge the "').concat(r,'" edge with "').concat(o,'" source & "').concat(s,'" target vs. ("').concat(d.source.key,'", "').concat(d.target.key,'").'));f=d}if(f||t.multi||!p||(f=i?p.undirected[s]:p.out[s]),f){var g=[f.key,!1,!1,!1];if(c?!h:!l)return g;if(c){var v=f.attributes;f.attributes=h(v),t.emit("edgeAttributesUpdated",{type:"replace",key:f.key,attributes:f.attributes})}else a(f.attributes,l),t.emit("edgeAttributesUpdated",{type:"merge",key:f.key,attributes:f.attributes,data:l});return g}l=l||{},c&&h&&(l=h(l));var y={key:null,undirected:i,source:o,target:s,attributes:l};if(n)r=t._edgeKeyGenerator();else if(r=""+r,t._edges.has(r))throw new q("Graph.".concat(e,': the "').concat(r,'" edge already exists in the graph.'));var C=!1,w=!1;p||(p=Et(t,o,{}),C=!0,o===s&&(m=p,w=!0)),m||(m=Et(t,s,{}),w=!0),d=new W(i,r,p,m,l),t._edges.set(r,d);var b=o===s;return i?(p.undirectedDegree++,m.undirectedDegree++,b&&(p.undirectedLoops++,t._undirectedSelfLoopCount++)):(p.outDegree++,m.inDegree++,b&&(p.directedLoops++,t._directedSelfLoopCount++)),t.multi?d.attachMulti():d.attach(),i?t._undirectedSize++:t._directedSize++,y.key=r,t.emit("edgeAdded",y),[r,!0,C,w]}function xt(t,e){t._edges.delete(e.key);var n=e.source,i=e.target,r=e.attributes,o=e.undirected,s=n===i;o?(n.undirectedDegree--,i.undirectedDegree--,s&&(n.undirectedLoops--,t._undirectedSelfLoopCount--)):(n.outDegree--,i.inDegree--,s&&(n.directedLoops--,t._directedSelfLoopCount--)),t.multi?e.detachMulti():e.detach(),o?t._undirectedSize--:t._directedSize--,t.emit("edgeDropped",{key:e.key,attributes:r,source:n.key,target:i.key,undirected:o})}var _t=function(n){function i(t){var e;if(e=n.call(this)||this,"boolean"!=typeof(t=a({},At,t)).multi)throw new H("Graph.constructor: invalid 'multi' option. Expecting a boolean but got \"".concat(t.multi,'".'));if(!wt.has(t.type))throw new H('Graph.constructor: invalid \'type\' option. Should be one of "mixed", "directed" or "undirected" but got "'.concat(t.type,'".'));if("boolean"!=typeof t.allowSelfLoops)throw new H("Graph.constructor: invalid 'allowSelfLoops' option. Expecting a boolean but got \"".concat(t.allowSelfLoops,'".'));var i="mixed"===t.type?Y:"directed"===t.type?$:j;h(s(e),"NodeDataClass",i);var r="geid_"+Ct()+"_",o=0;return h(s(e),"_attributes",{}),h(s(e),"_nodes",new Map),h(s(e),"_edges",new Map),h(s(e),"_directedSize",0),h(s(e),"_undirectedSize",0),h(s(e),"_directedSelfLoopCount",0),h(s(e),"_undirectedSelfLoopCount",0),h(s(e),"_edgeKeyGenerator",(function(){var t;do{t=r+o++}while(e._edges.has(t));return t})),h(s(e),"_options",t),bt.forEach((function(t){return h(s(e),t,e[t])})),d(s(e),"order",(function(){return e._nodes.size})),d(s(e),"size",(function(){return e._edges.size})),d(s(e),"directedSize",(function(){return e._directedSize})),d(s(e),"undirectedSize",(function(){return e._undirectedSize})),d(s(e),"selfLoopCount",(function(){return e._directedSelfLoopCount+e._undirectedSelfLoopCount})),d(s(e),"directedSelfLoopCount",(function(){return e._directedSelfLoopCount})),d(s(e),"undirectedSelfLoopCount",(function(){return e._undirectedSelfLoopCount})),d(s(e),"multi",e._options.multi),d(s(e),"type",e._options.type),d(s(e),"allowSelfLoops",e._options.allowSelfLoops),d(s(e),"implementation",(function(){return"graphology"})),e}e(i,n);var r=i.prototype;return r._resetInstanceCounters=function(){this._directedSize=0,this._undirectedSize=0,this._directedSelfLoopCount=0,this._undirectedSelfLoopCount=0},r.hasNode=function(t){return this._nodes.has(""+t)},r.hasDirectedEdge=function(t,e){if("undirected"===this.type)return!1;if(1===arguments.length){var n=""+t,i=this._edges.get(n);return!!i&&!i.undirected}if(2===arguments.length){t=""+t,e=""+e;var r=this._nodes.get(t);return!!r&&r.out.hasOwnProperty(e)}throw new H("Graph.hasDirectedEdge: invalid arity (".concat(arguments.length,", instead of 1 or 2). You can either ask for an edge id or for the existence of an edge between a source & a target."))},r.hasUndirectedEdge=function(t,e){if("directed"===this.type)return!1;if(1===arguments.length){var n=""+t,i=this._edges.get(n);return!!i&&i.undirected}if(2===arguments.length){t=""+t,e=""+e;var r=this._nodes.get(t);return!!r&&r.undirected.hasOwnProperty(e)}throw new H("Graph.hasDirectedEdge: invalid arity (".concat(arguments.length,", instead of 1 or 2). You can either ask for an edge id or for the existence of an edge between a source & a target."))},r.hasEdge=function(t,e){if(1===arguments.length){var n=""+t;return this._edges.has(n)}if(2===arguments.length){t=""+t,e=""+e;var i=this._nodes.get(t);return!!i&&(void 0!==i.out&&i.out.hasOwnProperty(e)||void 0!==i.undirected&&i.undirected.hasOwnProperty(e))}throw new H("Graph.hasEdge: invalid arity (".concat(arguments.length,", instead of 1 or 2). You can either ask for an edge id or for the existence of an edge between a source & a target."))},r.directedEdge=function(t,e){if("undirected"!==this.type){if(t=""+t,e=""+e,this.multi)throw new q("Graph.directedEdge: this method is irrelevant with multigraphs since there might be multiple edges between source & target. See #.directedEdges instead.");var n=this._nodes.get(t);if(!n)throw new B('Graph.directedEdge: could not find the "'.concat(t,'" source node in the graph.'));if(!this._nodes.has(e))throw new B('Graph.directedEdge: could not find the "'.concat(e,'" target node in the graph.'));var i=n.out&&n.out[e]||void 0;return i?i.key:void 0}},r.undirectedEdge=function(t,e){if("directed"!==this.type){if(t=""+t,e=""+e,this.multi)throw new q("Graph.undirectedEdge: this method is irrelevant with multigraphs since there might be multiple edges between source & target. See #.undirectedEdges instead.");var n=this._nodes.get(t);if(!n)throw new B('Graph.undirectedEdge: could not find the "'.concat(t,'" source node in the graph.'));if(!this._nodes.has(e))throw new B('Graph.undirectedEdge: could not find the "'.concat(e,'" target node in the graph.'));var i=n.undirected&&n.undirected[e]||void 0;return i?i.key:void 0}},r.edge=function(t,e){if(this.multi)throw new q("Graph.edge: this method is irrelevant with multigraphs since there might be multiple edges between source & target. See #.edges instead.");t=""+t,e=""+e;var n=this._nodes.get(t);if(!n)throw new B('Graph.edge: could not find the "'.concat(t,'" source node in the graph.'));if(!this._nodes.has(e))throw new B('Graph.edge: could not find the "'.concat(e,'" target node in the graph.'));var i=n.out&&n.out[e]||n.undirected&&n.undirected[e]||void 0;if(i)return i.key},r.areDirectedNeighbors=function(t,e){t=""+t,e=""+e;var n=this._nodes.get(t);if(!n)throw new B('Graph.areDirectedNeighbors: could not find the "'.concat(t,'" node in the graph.'));return"undirected"!==this.type&&(e in n.in||e in n.out)},r.areOutNeighbors=function(t,e){t=""+t,e=""+e;var n=this._nodes.get(t);if(!n)throw new B('Graph.areOutNeighbors: could not find the "'.concat(t,'" node in the graph.'));return"undirected"!==this.type&&e in n.out},r.areInNeighbors=function(t,e){t=""+t,e=""+e;var n=this._nodes.get(t);if(!n)throw new B('Graph.areInNeighbors: could not find the "'.concat(t,'" node in the graph.'));return"undirected"!==this.type&&e in n.in},r.areUndirectedNeighbors=function(t,e){t=""+t,e=""+e;var n=this._nodes.get(t);if(!n)throw new B('Graph.areUndirectedNeighbors: could not find the "'.concat(t,'" node in the graph.'));return"directed"!==this.type&&e in n.undirected},r.areNeighbors=function(t,e){t=""+t,e=""+e;var n=this._nodes.get(t);if(!n)throw new B('Graph.areNeighbors: could not find the "'.concat(t,'" node in the graph.'));return"undirected"!==this.type&&(e in n.in||e in n.out)||"directed"!==this.type&&e in n.undirected},r.areInboundNeighbors=function(t,e){t=""+t,e=""+e;var n=this._nodes.get(t);if(!n)throw new B('Graph.areInboundNeighbors: could not find the "'.concat(t,'" node in the graph.'));return"undirected"!==this.type&&e in n.in||"directed"!==this.type&&e in n.undirected},r.areOutboundNeighbors=function(t,e){t=""+t,e=""+e;var n=this._nodes.get(t);if(!n)throw new B('Graph.areOutboundNeighbors: could not find the "'.concat(t,'" node in the graph.'));return"undirected"!==this.type&&e in n.out||"directed"!==this.type&&e in n.undirected},r.inDegree=function(t){t=""+t;var e=this._nodes.get(t);if(!e)throw new B('Graph.inDegree: could not find the "'.concat(t,'" node in the graph.'));return"undirected"===this.type?0:e.inDegree},r.outDegree=function(t){t=""+t;var e=this._nodes.get(t);if(!e)throw new B('Graph.outDegree: could not find the "'.concat(t,'" node in the graph.'));return"undirected"===this.type?0:e.outDegree},r.directedDegree=function(t){t=""+t;var e=this._nodes.get(t);if(!e)throw new B('Graph.directedDegree: could not find the "'.concat(t,'" node in the graph.'));return"undirected"===this.type?0:e.inDegree+e.outDegree},r.undirectedDegree=function(t){t=""+t;var e=this._nodes.get(t);if(!e)throw new B('Graph.undirectedDegree: could not find the "'.concat(t,'" node in the graph.'));return"directed"===this.type?0:e.undirectedDegree},r.inboundDegree=function(t){t=""+t;var e=this._nodes.get(t);if(!e)throw new B('Graph.inboundDegree: could not find the "'.concat(t,'" node in the graph.'));var n=0;return"directed"!==this.type&&(n+=e.undirectedDegree),"undirected"!==this.type&&(n+=e.inDegree),n},r.outboundDegree=function(t){t=""+t;var e=this._nodes.get(t);if(!e)throw new B('Graph.outboundDegree: could not find the "'.concat(t,'" node in the graph.'));var n=0;return"directed"!==this.type&&(n+=e.undirectedDegree),"undirected"!==this.type&&(n+=e.outDegree),n},r.degree=function(t){t=""+t;var e=this._nodes.get(t);if(!e)throw new B('Graph.degree: could not find the "'.concat(t,'" node in the graph.'));var n=0;return"directed"!==this.type&&(n+=e.undirectedDegree),"undirected"!==this.type&&(n+=e.inDegree+e.outDegree),n},r.inDegreeWithoutSelfLoops=function(t){t=""+t;var e=this._nodes.get(t);if(!e)throw new B('Graph.inDegreeWithoutSelfLoops: could not find the "'.concat(t,'" node in the graph.'));return"undirected"===this.type?0:e.inDegree-e.directedLoops},r.outDegreeWithoutSelfLoops=function(t){t=""+t;var e=this._nodes.get(t);if(!e)throw new B('Graph.outDegreeWithoutSelfLoops: could not find the "'.concat(t,'" node in the graph.'));return"undirected"===this.type?0:e.outDegree-e.directedLoops},r.directedDegreeWithoutSelfLoops=function(t){t=""+t;var e=this._nodes.get(t);if(!e)throw new B('Graph.directedDegreeWithoutSelfLoops: could not find the "'.concat(t,'" node in the graph.'));return"undirected"===this.type?0:e.inDegree+e.outDegree-2*e.directedLoops},r.undirectedDegreeWithoutSelfLoops=function(t){t=""+t;var e=this._nodes.get(t);if(!e)throw new B('Graph.undirectedDegreeWithoutSelfLoops: could not find the "'.concat(t,'" node in the graph.'));return"directed"===this.type?0:e.undirectedDegree-2*e.undirectedLoops},r.inboundDegreeWithoutSelfLoops=function(t){t=""+t;var e=this._nodes.get(t);if(!e)throw new B('Graph.inboundDegreeWithoutSelfLoops: could not find the "'.concat(t,'" node in the graph.'));var n=0,i=0;return"directed"!==this.type&&(n+=e.undirectedDegree,i+=2*e.undirectedLoops),"undirected"!==this.type&&(n+=e.inDegree,i+=e.directedLoops),n-i},r.outboundDegreeWithoutSelfLoops=function(t){t=""+t;var e=this._nodes.get(t);if(!e)throw new B('Graph.outboundDegreeWithoutSelfLoops: could not find the "'.concat(t,'" node in the graph.'));var n=0,i=0;return"directed"!==this.type&&(n+=e.undirectedDegree,i+=2*e.undirectedLoops),"undirected"!==this.type&&(n+=e.outDegree,i+=e.directedLoops),n-i},r.degreeWithoutSelfLoops=function(t){t=""+t;var e=this._nodes.get(t);if(!e)throw new B('Graph.degreeWithoutSelfLoops: could not find the "'.concat(t,'" node in the graph.'));var n=0,i=0;return"directed"!==this.type&&(n+=e.undirectedDegree,i+=2*e.undirectedLoops),"undirected"!==this.type&&(n+=e.inDegree+e.outDegree,i+=2*e.directedLoops),n-i},r.source=function(t){t=""+t;var e=this._edges.get(t);if(!e)throw new B('Graph.source: could not find the "'.concat(t,'" edge in the graph.'));return e.source.key},r.target=function(t){t=""+t;var e=this._edges.get(t);if(!e)throw new B('Graph.target: could not find the "'.concat(t,'" edge in the graph.'));return e.target.key},r.extremities=function(t){t=""+t;var e=this._edges.get(t);if(!e)throw new B('Graph.extremities: could not find the "'.concat(t,'" edge in the graph.'));return[e.source.key,e.target.key]},r.opposite=function(t,e){t=""+t,e=""+e;var n=this._edges.get(e);if(!n)throw new B('Graph.opposite: could not find the "'.concat(e,'" edge in the graph.'));var i=n.source.key,r=n.target.key;if(t===i)return r;if(t===r)return i;throw new B('Graph.opposite: the "'.concat(t,'" node is not attached to the "').concat(e,'" edge (').concat(i,", ").concat(r,")."))},r.hasExtremity=function(t,e){t=""+t,e=""+e;var n=this._edges.get(t);if(!n)throw new B('Graph.hasExtremity: could not find the "'.concat(t,'" edge in the graph.'));return n.source.key===e||n.target.key===e},r.isUndirected=function(t){t=""+t;var e=this._edges.get(t);if(!e)throw new B('Graph.isUndirected: could not find the "'.concat(t,'" edge in the graph.'));return e.undirected},r.isDirected=function(t){t=""+t;var e=this._edges.get(t);if(!e)throw new B('Graph.isDirected: could not find the "'.concat(t,'" edge in the graph.'));return!e.undirected},r.isSelfLoop=function(t){t=""+t;var e=this._edges.get(t);if(!e)throw new B('Graph.isSelfLoop: could not find the "'.concat(t,'" edge in the graph.'));return e.source===e.target},r.addNode=function(t,e){var n=function(t,e,n){if(n&&!u(n))throw new H('Graph.addNode: invalid attributes. Expecting an object but got "'.concat(n,'"'));if(e=""+e,n=n||{},t._nodes.has(e))throw new q('Graph.addNode: the "'.concat(e,'" node already exist in the graph.'));var i=new t.NodeDataClass(e,n);return t._nodes.set(e,i),t.emit("nodeAdded",{key:e,attributes:n}),i}(this,t,e);return n.key},r.mergeNode=function(t,e){if(e&&!u(e))throw new H('Graph.mergeNode: invalid attributes. Expecting an object but got "'.concat(e,'"'));t=""+t,e=e||{};var n=this._nodes.get(t);return n?(e&&(a(n.attributes,e),this.emit("nodeAttributesUpdated",{type:"merge",key:t,attributes:n.attributes,data:e})),[t,!1]):(n=new this.NodeDataClass(t,e),this._nodes.set(t,n),this.emit("nodeAdded",{key:t,attributes:e}),[t,!0])},r.updateNode=function(t,e){if(e&&"function"!=typeof e)throw new H('Graph.updateNode: invalid updater function. Expecting a function but got "'.concat(e,'"'));t=""+t;var n=this._nodes.get(t);if(n){if(e){var i=n.attributes;n.attributes=e(i),this.emit("nodeAttributesUpdated",{type:"replace",key:t,attributes:n.attributes})}return[t,!1]}var r=e?e({}):{};return n=new this.NodeDataClass(t,r),this._nodes.set(t,n),this.emit("nodeAdded",{key:t,attributes:r}),[t,!0]},r.dropNode=function(t){t=""+t;var e,n=this._nodes.get(t);if(!n)throw new B('Graph.dropNode: could not find the "'.concat(t,'" node in the graph.'));if("undirected"!==this.type){for(var i in n.out){e=n.out[i];do{xt(this,e),e=e.next}while(e)}for(var r in n.in){e=n.in[r];do{xt(this,e),e=e.next}while(e)}}if("directed"!==this.type)for(var o in n.undirected){e=n.undirected[o];do{xt(this,e),e=e.next}while(e)}this._nodes.delete(t),this.emit("nodeDropped",{key:t,attributes:n.attributes})},r.dropEdge=function(t){var e;if(arguments.length>1){var n=""+arguments[0],i=""+arguments[1];if(!(e=l(this,n,i,this.type)))throw new B('Graph.dropEdge: could not find the "'.concat(n,'" -> "').concat(i,'" edge in the graph.'))}else if(t=""+t,!(e=this._edges.get(t)))throw new B('Graph.dropEdge: could not find the "'.concat(t,'" edge in the graph.'));return xt(this,e),this},r.dropDirectedEdge=function(t,e){if(arguments.length<2)throw new q("Graph.dropDirectedEdge: it does not make sense to try and drop a directed edge by key. What if the edge with this key is undirected? Use #.dropEdge for this purpose instead.");if(this.multi)throw new q("Graph.dropDirectedEdge: cannot use a {source,target} combo when dropping an edge in a MultiGraph since we cannot infer the one you want to delete as there could be multiple ones.");var n=l(this,t=""+t,e=""+e,"directed");if(!n)throw new B('Graph.dropDirectedEdge: could not find a "'.concat(t,'" -> "').concat(e,'" edge in the graph.'));return xt(this,n),this},r.dropUndirectedEdge=function(t,e){if(arguments.length<2)throw new q("Graph.dropUndirectedEdge: it does not make sense to drop a directed edge by key. What if the edge with this key is undirected? Use #.dropEdge for this purpose instead.");if(this.multi)throw new q("Graph.dropUndirectedEdge: cannot use a {source,target} combo when dropping an edge in a MultiGraph since we cannot infer the one you want to delete as there could be multiple ones.");var n=l(this,t,e,"undirected");if(!n)throw new B('Graph.dropUndirectedEdge: could not find a "'.concat(t,'" -> "').concat(e,'" edge in the graph.'));return xt(this,n),this},r.clear=function(){this._edges.clear(),this._nodes.clear(),this._resetInstanceCounters(),this.emit("cleared")},r.clearEdges=function(){for(var t,e=this._nodes.values();!0!==(t=e.next()).done;)t.value.clear();this._edges.clear(),this._resetInstanceCounters(),this.emit("edgesCleared")},r.getAttribute=function(t){return this._attributes[t]},r.getAttributes=function(){return this._attributes},r.hasAttribute=function(t){return this._attributes.hasOwnProperty(t)},r.setAttribute=function(t,e){return this._attributes[t]=e,this.emit("attributesUpdated",{type:"set",attributes:this._attributes,name:t}),this},r.updateAttribute=function(t,e){if("function"!=typeof e)throw new H("Graph.updateAttribute: updater should be a function.");var n=this._attributes[t];return this._attributes[t]=e(n),this.emit("attributesUpdated",{type:"set",attributes:this._attributes,name:t}),this},r.removeAttribute=function(t){return delete this._attributes[t],this.emit("attributesUpdated",{type:"remove",attributes:this._attributes,name:t}),this},r.replaceAttributes=function(t){if(!u(t))throw new H("Graph.replaceAttributes: provided attributes are not a plain object.");return this._attributes=t,this.emit("attributesUpdated",{type:"replace",attributes:this._attributes}),this},r.mergeAttributes=function(t){if(!u(t))throw new H("Graph.mergeAttributes: provided attributes are not a plain object.");return a(this._attributes,t),this.emit("attributesUpdated",{type:"merge",attributes:this._attributes,data:t}),this},r.updateAttributes=function(t){if("function"!=typeof t)throw new H("Graph.updateAttributes: provided updater is not a function.");return this._attributes=t(this._attributes),this.emit("attributesUpdated",{type:"update",attributes:this._attributes}),this},r.updateEachNodeAttributes=function(t,e){if("function"!=typeof t)throw new H("Graph.updateEachNodeAttributes: expecting an updater function.");if(e&&!f(e))throw new H("Graph.updateEachNodeAttributes: invalid hints. Expecting an object having the following shape: {attributes?: [string]}");for(var n,i,r=this._nodes.values();!0!==(n=r.next()).done;)(i=n.value).attributes=t(i.key,i.attributes);this.emit("eachNodeAttributesUpdated",{hints:e||null})},r.updateEachEdgeAttributes=function(t,e){if("function"!=typeof t)throw new H("Graph.updateEachEdgeAttributes: expecting an updater function.");if(e&&!f(e))throw new H("Graph.updateEachEdgeAttributes: invalid hints. Expecting an object having the following shape: {attributes?: [string]}");for(var n,i,r,o,s=this._edges.values();!0!==(n=s.next()).done;)r=(i=n.value).source,o=i.target,i.attributes=t(i.key,i.attributes,r.key,o.key,r.attributes,o.attributes,i.undirected);this.emit("eachEdgeAttributesUpdated",{hints:e||null})},r.forEachAdjacencyEntry=function(t){if("function"!=typeof t)throw new H("Graph.forEachAdjacencyEntry: expecting a callback.");mt(!1,!1,!1,this,t)},r.forEachAdjacencyEntryWithOrphans=function(t){if("function"!=typeof t)throw new H("Graph.forEachAdjacencyEntryWithOrphans: expecting a callback.");mt(!1,!1,!0,this,t)},r.forEachAssymetricAdjacencyEntry=function(t){if("function"!=typeof t)throw new H("Graph.forEachAssymetricAdjacencyEntry: expecting a callback.");mt(!1,!0,!1,this,t)},r.forEachAssymetricAdjacencyEntryWithOrphans=function(t){if("function"!=typeof t)throw new H("Graph.forEachAssymetricAdjacencyEntryWithOrphans: expecting a callback.");mt(!1,!0,!0,this,t)},r.nodes=function(){return"function"==typeof Array.from?Array.from(this._nodes.keys()):V(this._nodes.keys(),this._nodes.size)},r.forEachNode=function(t){if("function"!=typeof t)throw new H("Graph.forEachNode: expecting a callback.");for(var e,n,i=this._nodes.values();!0!==(e=i.next()).done;)t((n=e.value).key,n.attributes)},r.findNode=function(t){if("function"!=typeof t)throw new H("Graph.findNode: expecting a callback.");for(var e,n,i=this._nodes.values();!0!==(e=i.next()).done;)if(t((n=e.value).key,n.attributes))return n.key},r.mapNodes=function(t){if("function"!=typeof t)throw new H("Graph.mapNode: expecting a callback.");for(var e,n,i=this._nodes.values(),r=new Array(this.order),o=0;!0!==(e=i.next()).done;)n=e.value,r[o++]=t(n.key,n.attributes);return r},r.someNode=function(t){if("function"!=typeof t)throw new H("Graph.someNode: expecting a callback.");for(var e,n,i=this._nodes.values();!0!==(e=i.next()).done;)if(t((n=e.value).key,n.attributes))return!0;return!1},r.everyNode=function(t){if("function"!=typeof t)throw new H("Graph.everyNode: expecting a callback.");for(var e,n,i=this._nodes.values();!0!==(e=i.next()).done;)if(!t((n=e.value).key,n.attributes))return!1;return!0},r.filterNodes=function(t){if("function"!=typeof t)throw new H("Graph.filterNodes: expecting a callback.");for(var e,n,i=this._nodes.values(),r=[];!0!==(e=i.next()).done;)t((n=e.value).key,n.attributes)&&r.push(n.key);return r},r.reduceNodes=function(t,e){if("function"!=typeof t)throw new H("Graph.reduceNodes: expecting a callback.");if(arguments.length<2)throw new H("Graph.reduceNodes: missing initial value. You must provide it because the callback takes more than one argument and we cannot infer the initial value from the first iteration, as you could with a simple array.");for(var n,i,r=e,o=this._nodes.values();!0!==(n=o.next()).done;)r=t(r,(i=n.value).key,i.attributes);return r},r.nodeEntries=function(){var t=this._nodes.values();return new L((function(){var e=t.next();if(e.done)return e;var n=e.value;return{value:{node:n.key,attributes:n.attributes},done:!1}}))},r.export=function(){var t=this,e=new Array(this._nodes.size),n=0;this._nodes.forEach((function(t,i){e[n++]=function(t,e){var n={key:t};return c(e.attributes)||(n.attributes=a({},e.attributes)),n}(i,t)}));var i=new Array(this._edges.size);return n=0,this._edges.forEach((function(e,r){i[n++]=function(t,e,n){var i={key:e,source:n.source.key,target:n.target.key};return c(n.attributes)||(i.attributes=a({},n.attributes)),"mixed"===t&&n.undirected&&(i.undirected=!0),i}(t.type,r,e)})),{options:{type:this.type,multi:this.multi,allowSelfLoops:this.allowSelfLoops},attributes:this.getAttributes(),nodes:e,edges:i}},r.import=function(t){var e,n,r,o,s,a=this,l=arguments.length>1&&void 0!==arguments[1]&&arguments[1];if(t instanceof i)return t.forEachNode((function(t,e){l?a.mergeNode(t,e):a.addNode(t,e)})),t.forEachEdge((function(t,e,n,i,r,o,s){l?s?a.mergeUndirectedEdgeWithKey(t,n,i,e):a.mergeDirectedEdgeWithKey(t,n,i,e):s?a.addUndirectedEdgeWithKey(t,n,i,e):a.addDirectedEdgeWithKey(t,n,i,e)})),this;if(!u(t))throw new H("Graph.import: invalid argument. Expecting a serialized graph or, alternatively, a Graph instance.");if(t.attributes){if(!u(t.attributes))throw new H("Graph.import: invalid attributes. Expecting a plain object.");l?this.mergeAttributes(t.attributes):this.replaceAttributes(t.attributes)}if(t.nodes){if(r=t.nodes,!Array.isArray(r))throw new H("Graph.import: invalid nodes. Expecting an array.");for(e=0,n=r.length;e<n;e++){gt(o=r[e]);var c=o,h=c.key,d=c.attributes;l?this.mergeNode(h,d):this.addNode(h,d)}}if(t.edges){var f=!1;if("undirected"===this.type&&(f=!0),r=t.edges,!Array.isArray(r))throw new H("Graph.import: invalid edges. Expecting an array.");for(e=0,n=r.length;e<n;e++){vt(s=r[e]);var p=s,m=p.source,g=p.target,v=p.attributes,y=p.undirected,C=void 0===y?f:y;"key"in s?(l?C?this.mergeUndirectedEdgeWithKey:this.mergeDirectedEdgeWithKey:C?this.addUndirectedEdgeWithKey:this.addDirectedEdgeWithKey).call(this,s.key,m,g,v):(l?C?this.mergeUndirectedEdge:this.mergeDirectedEdge:C?this.addUndirectedEdge:this.addDirectedEdge).call(this,m,g,v)}}return this},r.nullCopy=function(t){var e=new i(a({},this._options,t));return e.replaceAttributes(a({},this.getAttributes())),e},r.emptyCopy=function(t){var e=this.nullCopy(t);return this._nodes.forEach((function(t,n){var i=a({},t.attributes);t=new e.NodeDataClass(n,i),e._nodes.set(n,t)})),e},r.copy=function(t){if("string"==typeof(t=t||{}).type&&t.type!==this.type&&"mixed"!==t.type)throw new q('Graph.copy: cannot create an incompatible copy from "'.concat(this.type,'" type to "').concat(t.type,'" because this would mean losing information about the current graph.'));if("boolean"==typeof t.multi&&t.multi!==this.multi&&!0!==t.multi)throw new q("Graph.copy: cannot create an incompatible copy by downgrading a multi graph to a simple one because this would mean losing information about the current graph.");if("boolean"==typeof t.allowSelfLoops&&t.allowSelfLoops!==this.allowSelfLoops&&!0!==t.allowSelfLoops)throw new q("Graph.copy: cannot create an incompatible copy from a graph allowing self loops to one that does not because this would mean losing information about the current graph.");for(var e,n,i=this.emptyCopy(t),r=this._edges.values();!0!==(e=r.next()).done;)St(i,"copy",!1,(n=e.value).undirected,n.key,n.source.key,n.target.key,a({},n.attributes));return i},r.toJSON=function(){return this.export()},r.toString=function(){return"[object Graph]"},r.inspect=function(){var e=this,n={};this._nodes.forEach((function(t,e){n[e]=t.attributes}));var i={},r={};this._edges.forEach((function(t,n){var o,s=t.undirected?"--":"->",a="",l=t.source.key,u=t.target.key;t.undirected&&l>u&&(o=l,l=u,u=o);var c="(".concat(l,")").concat(s,"(").concat(u,")");n.startsWith("geid_")?e.multi&&(void 0===r[c]?r[c]=0:r[c]++,a+="".concat(r[c],". ")):a+="[".concat(n,"]: "),i[a+=c]=t.attributes}));var o={};for(var s in this)this.hasOwnProperty(s)&&!bt.has(s)&&"function"!=typeof this[s]&&"symbol"!==t(s)&&(o[s]=this[s]);return o.attributes=this._attributes,o.nodes=n,o.edges=i,h(o,"constructor",this.constructor),o},i}(m.exports.EventEmitter);"undefined"!=typeof Symbol&&(_t.prototype[Symbol.for("nodejs.util.inspect.custom")]=_t.prototype.inspect),[{name:function(t){return"".concat(t,"Edge")},generateKey:!0},{name:function(t){return"".concat(t,"DirectedEdge")},generateKey:!0,type:"directed"},{name:function(t){return"".concat(t,"UndirectedEdge")},generateKey:!0,type:"undirected"},{name:function(t){return"".concat(t,"EdgeWithKey")}},{name:function(t){return"".concat(t,"DirectedEdgeWithKey")},type:"directed"},{name:function(t){return"".concat(t,"UndirectedEdgeWithKey")},type:"undirected"}].forEach((function(t){["add","merge","update"].forEach((function(e){var n=t.name(e),i="add"===e?St:Tt;t.generateKey?_t.prototype[n]=function(r,o,s){return i(this,n,!0,"undirected"===(t.type||this.type),null,r,o,s,"update"===e)}:_t.prototype[n]=function(r,o,s,a){return i(this,n,!1,"undirected"===(t.type||this.type),r,o,s,a,"update"===e)}}))})),function(t){K.forEach((function(e){var n=e.name,i=e.attacher;i(t,n("Node"),0),i(t,n("Source"),1),i(t,n("Target"),2),i(t,n("Opposite"),3)}))}(_t),function(t){Q.forEach((function(e){var n=e.name,i=e.attacher;i(t,n("Edge"),"mixed"),i(t,n("DirectedEdge"),"directed"),i(t,n("UndirectedEdge"),"undirected")}))}(_t),function(t){tt.forEach((function(e){!function(t,e){var n=e.name,i=e.type,r=e.direction;t.prototype[n]=function(t,e){if("mixed"!==i&&"mixed"!==this.type&&i!==this.type)return[];if(!arguments.length)return function(t,e){if(0===t.size)return[];if("mixed"===e||e===t.type)return"function"==typeof Array.from?Array.from(t._edges.keys()):V(t._edges.keys(),t._edges.size);for(var n,i,r="undirected"===e?t.undirectedSize:t.directedSize,o=new Array(r),s="undirected"===e,a=t._edges.values(),l=0;!0!==(n=a.next()).done;)(i=n.value).undirected===s&&(o[l++]=i.key);return o}(this,i);if(1===arguments.length){t=""+t;var o=this._nodes.get(t);if(void 0===o)throw new B("Graph.".concat(n,': could not find the "').concat(t,'" node in the graph.'));return function(t,e,n,i){var r=[];return lt(!1,t,e,n,i,(function(t){r.push(t)})),r}(this.multi,"mixed"===i?this.type:i,r,o)}if(2===arguments.length){t=""+t,e=""+e;var s=this._nodes.get(t);if(!s)throw new B("Graph.".concat(n,': could not find the "').concat(t,'" source node in the graph.'));if(!this._nodes.has(e))throw new B("Graph.".concat(n,': could not find the "').concat(e,'" target node in the graph.'));return function(t,e,n,i,r){var o=[];return ut(!1,t,e,n,i,r,(function(t){o.push(t)})),o}(i,this.multi,r,s,e)}throw new H("Graph.".concat(n,": too many arguments (expecting 0, 1 or 2 and got ").concat(arguments.length,")."))}}(t,e),function(t,e){var n=e.name,i=e.type,r=e.direction,o="forEach"+n[0].toUpperCase()+n.slice(1,-1);t.prototype[o]=function(t,e,n){if("mixed"===i||"mixed"===this.type||i===this.type){if(1===arguments.length)return at(!1,this,i,n=t);if(2===arguments.length){t=""+t,n=e;var s=this._nodes.get(t);if(void 0===s)throw new B("Graph.".concat(o,': could not find the "').concat(t,'" node in the graph.'));return lt(!1,this.multi,"mixed"===i?this.type:i,r,s,n)}if(3===arguments.length){t=""+t,e=""+e;var a=this._nodes.get(t);if(!a)throw new B("Graph.".concat(o,': could not find the "').concat(t,'" source node in the graph.'));if(!this._nodes.has(e))throw new B("Graph.".concat(o,': could not find the "').concat(e,'" target node in the graph.'));return ut(!1,i,this.multi,r,a,e,n)}throw new H("Graph.".concat(o,": too many arguments (expecting 1, 2 or 3 and got ").concat(arguments.length,")."))}};var s="map"+n[0].toUpperCase()+n.slice(1);t.prototype[s]=function(){var t,e=Array.prototype.slice.call(arguments),n=e.pop();if(0===e.length){var r=0;"directed"!==i&&(r+=this.undirectedSize),"undirected"!==i&&(r+=this.directedSize),t=new Array(r);var s=0;e.push((function(e,i,r,o,a,l,u){t[s++]=n(e,i,r,o,a,l,u)}))}else t=[],e.push((function(e,i,r,o,s,a,l){t.push(n(e,i,r,o,s,a,l))}));return this[o].apply(this,e),t};var a="filter"+n[0].toUpperCase()+n.slice(1);t.prototype[a]=function(){var t=Array.prototype.slice.call(arguments),e=t.pop(),n=[];return t.push((function(t,i,r,o,s,a,l){e(t,i,r,o,s,a,l)&&n.push(t)})),this[o].apply(this,t),n};var l="reduce"+n[0].toUpperCase()+n.slice(1);t.prototype[l]=function(){var t,e,n=Array.prototype.slice.call(arguments);if(n.length<2||n.length>4)throw new H("Graph.".concat(l,": invalid number of arguments (expecting 2, 3 or 4 and got ").concat(n.length,")."));if("function"==typeof n[n.length-1]&&"function"!=typeof n[n.length-2])throw new H("Graph.".concat(l,": missing initial value. 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O,L,I,R,P,k,D,G=n(912);n(5540),n(4329),(L=O||(O={})).EUCLIDEAN="EUCLIDEAN",L.MANHATTAN="MANHATTAN",O.EUCLIDEAN,O.MANHATTAN,(R=I||(I={})).HAMMING="Hamming",R.EUCLIDEAN="Euclidean",R.MANHATTAN="Manhattan",R.TANIMOTO="Tanimoto",R.LEVENSTEIN="Levenshtein",R.NEEDLEMAN_WUNSCH="Needlemann-Wunsch",R.MONOMER_CHEMICAL_DISTANCE="Monomer chemical distance",R.SOKAL="Sokal",R.COSINE="Cosine",R.ASYMMETRIC="Asymmetric",R.Difference="Difference",R.OneHot="One-Hot",I.HAMMING,I.EUCLIDEAN,I.MANHATTAN,I.TANIMOTO,I.LEVENSTEIN,I.NEEDLEMAN_WUNSCH,I.MONOMER_CHEMICAL_DISTANCE,I.SOKAL,I.COSINE,I.ASYMMETRIC,I.Difference,I.OneHot,I.HAMMING,I.EUCLIDEAN,I.MANHATTAN,I.TANIMOTO,I.SOKAL,I.COSINE,I.ASYMMETRIC,I.LEVENSTEIN,I.NEEDLEMAN_WUNSCH,I.MONOMER_CHEMICAL_DISTANCE,I.Difference,I.OneHot,new Set([I.HAMMING,I.LEVENSTEIN,I.NEEDLEMAN_WUNSCH,I.MONOMER_CHEMICAL_DISTANCE,I.OneHot]),new Set([I.HAMMING,I.EUCLIDEAN,I.MANHATTAN,I.MONOMER_CHEMICAL_DISTANCE,I.LEVENSTEIN,I.NEEDLEMAN_WUNSCH,I.TANIMOTO,I.COSINE,I.SOKAL,I.ASYMMETRIC,I.OneHot,I.Difference]),new Set([I.EUCLIDEAN,I.MANHATTAN,I.OneHot,I.Difference]),new Set([I.EUCLIDEAN,I.MANHATTAN,I.Difference]),new Set([I.EUCLIDEAN,I.MANHATTAN,I.Difference]),new Set([I.TANIMOTO,I.COSINE,I.SOKAL,I.ASYMMETRIC]),function(t){t.ADD="ADD",t.SUB="SUB",t.MULT="MULT"}(P||(P={})),function(t){t.SQUARE="SQUARE",t.INVERSE="INVERSE",t.TRANSPOSE="TRANSPOSE",t.NORM="NORM",t.COLUMN_NORM="COLUMN_NORM"}(k||(k={})),function(t){t.SCALARMULT="SCALARMULT",t.SCALARADD="SCALARADD",t.SCALARPOW="SCALARPOW"}(D||(D={})),Object.prototype.toString,Promise.resolve(),n(934),n(8903);var U,V,F=n(1858);!function(t){t.none="none",t.bold="bold",t.dashed="dashed"}(U||(U={}));class H{get currentLineId(){return this._currentLineIdx}set currentLineId(t){t!==this._currentLineIdx&&(this._currentLineIdx=t,this.sp.render(this.ctx))}set linesToRender(t){this.updateLines(t),this.sp.render(this.ctx)}set linesVisibility(t){this.visibility=t,this.sp.render(this.ctx)}constructor(t,e,n,i,r=U.none){var o;this._currentLineIdx=-1,this.lineClicked=new F.Subject,this.lineHover=new F.Subject,this.mouseOverLineId=-1,this.arrowWidth=15,this.sp=t,this.xAxisCol=this.sp.dataFrame.columns.byName(e),this.yAxisCol=this.sp.dataFrame.columns.byName(n),this.canvas=this.sp.getInfo().canvas,this.ctx=this.canvas.getContext("2d"),this.currentLineStyle=r,this.updateLines(i),this.visibility=null!==(o=i.visibility)&&void 0!==o?o:new p.A(this.lines.from.length),i.visibility||this.visibility.setAll(!0,!1),i.arrowSize&&(this.arrowWidth=i.arrowSize),this.canvas.onmousedown=t=>{var e;(null===(e=this.lines)||void 0===e?void 0:e.skipMouseOverDetection)&&(this.mouseOverLineId=this.checkCoordsOnLine(t.offsetX,t.offsetY)),-1!==this.mouseOverLineId&&this.lineClicked.next({x:t.clientX,y:t.clientY,id:this.mouseOverLineId,event:t})},this.canvas.onmousemove=t=>{var e;this.mouseOverLineId=(null===(e=this.lines)||void 0===e?void 0:e.skipMouseOverDetection)?-1:this.checkCoordsOnLine(t.offsetX,t.offsetY),-1!==this.mouseOverLineId&&this.lineHover.next({x:t.clientX,y:t.clientY,id:this.mouseOverLineId,event:t})},t.onEvent("d4-before-draw-scene").subscribe((t=>{this.renderLines()}))}updateLines(t){this.lines=t,this.multipleLinesCounts=new Uint8Array(this.lines.from.length),t.skipMultiLineCalculation?this.multipleLinesCounts.fill(0):this.createMultiLinesIndices()}renderLines(){var t,e,n,i,r,o,s,a,l,u,c,h,d,f,p,m,g;const v=this.sp.getOptions().look,y=this.lines.colors||this.lines.widths||this.lines.opacities||this.lines.drawArrowsArr;y||(this.ctx.lineWidth=null!==(t=this.lines.width)&&void 0!==t?t:1,this.ctx.strokeStyle=`rgba(${null!==(e=this.lines.color)&&void 0!==e?e:"0,128,0"},${null!==(n=this.lines.opacity)&&void 0!==n?n:1})`);const C=v.sizeColumnName?this.sp.dataFrame.col(v.sizeColumnName):null,w=this.sp.dataFrame.filter,b=Math.pow(null!==(i=this.lines.shortLineThreshold)&&void 0!==i?i:5,2);for(let t=0;t<this.lines.from.length;t++)if(w.get(this.lines.from[t])&&w.get(this.lines.to[t])&&this.visibility.getBit(t)){let e=0;const{sizeFrom:n,sizeTo:i}=this.getMarkersSizes(v,C,t),w=this.sp.worldToScreen(this.xAxisCol.get(this.lines.from[t]),this.yAxisCol.get(this.lines.from[t]));let A=null==w?void 0:w.x,E=null==w?void 0:w.y;const S=this.sp.worldToScreen(this.xAxisCol.get(this.lines.to[t]),this.yAxisCol.get(this.lines.to[t]));let T=null==S?void 0:S.x,x=null==S?void 0:S.y;const _=Math.min(this.sp.viewBox.width,this.sp.viewBox.height);if(this.ctx.beginPath(),A&&E&&T&&x&&Math.hypot(T-A,x-E)/_>.01){if(y){const e=(null===(r=this.lines.colors)||void 0===r?void 0:r[t])?null===(o=this.lines.colors)||void 0===o?void 0:o[t]:null!==(s=this.lines.color)&&void 0!==s?s:"0,128,0",n=(null===(a=this.lines.opacities)||void 0===a?void 0:a[t])?null===(l=this.lines.opacities)||void 0===l?void 0:l[t]:null!==(u=this.lines.opacity)&&void 0!==u?u:1;this.ctx.strokeStyle=`rgba(${e},${n})`,this.ctx.lineWidth=(null===(c=this.lines.widths)||void 0===c?void 0:c[t])?null===(h=this.lines.widths)||void 0===h?void 0:h[t]:null!==(d=this.lines.width)&&void 0!==d?d:1}t===this._currentLineIdx&&this.toggleCurrentLineStyle(!0);const v=this.multipleLinesCounts[t];let C=null;if(v){e=this.getLineLength(A,E,T,x);const r=this.getPointOnDistance(A,E,T,x,i,e),o=this.getPointOnDistance(T,x,A,E,n,e);A=r.x,E=r.y,T=o.x,x=o.y,C=this.lines.from[t]>this.lines.to[t]?this.findControlPoint(v,A,E,T,x,t):this.findControlPoint(v,T,x,A,E,t),this.ctx.moveTo(A,E),this.ctx.quadraticCurveTo(C.x,C.y,T,x)}else(!this.lines.skipShortLines||Math.pow(T-A,2)+Math.pow(x-E,2)>b)&&(this.ctx.moveTo(A,E),this.ctx.lineTo(T,x));if((null!==(f=this.lines.drawArrows)&&void 0!==f?f:null===(p=this.lines.drawArrowsArr)||void 0===p?void 0:p.getBit(t))&&(e||(e=this.getLineLength(A,E,T,x)),e>this.arrowWidth)){const t=v?null:this.getPointOnDistance(A,E,T,x,i,e),n=v?C.x:A,r=v?C.y:E;this.canvasArrow(this.ctx,null!==(m=null==t?void 0:t.x)&&void 0!==m?m:A,null!==(g=null==t?void 0:t.y)&&void 0!==g?g:E,n,r)}this.ctx.stroke(),this.ctx.closePath(),t===this._currentLineIdx&&this.toggleCurrentLineStyle(!1)}}this.fillLeftBottomRect()}toggleCurrentLineStyle(t){switch(this.currentLineStyle){case U.bold:t?this.ctx.lineWidth+=2:this.ctx.lineWidth-=2;break;case U.dashed:t?this.ctx.setLineDash([5,5]):this.ctx.setLineDash([]);break;default:return}}getMarkersSizes(t,e,n){let i=3,r=3;return e?(i=(t.markerMinSize+(t.markerMaxSize-t.markerMinSize)*e.scale(this.lines.from[n]))/2,r=(t.markerMinSize+(t.markerMaxSize-t.markerMinSize)*e.scale(this.lines.to[n]))/2):t.markerDefaultSize&&(i=t.markerDefaultSize/2,r=t.markerDefaultSize/2),{sizeFrom:i,sizeTo:r}}fillLeftBottomRect(){const t=new Path2D;t.rect(this.sp.yAxisBox.minX,this.sp.yAxisBox.maxY,this.sp.yAxisBox.width,this.sp.xAxisBox.height),this.ctx.fillStyle="white",this.ctx.beginPath(),this.ctx.fill(t),this.ctx.closePath()}createMultiLinesIndices(){const t={};for(let e=0;e<this.lines.from.length;e++){let n=0,i=0;this.lines.from[e]<this.lines.to[e]?(n=this.lines.from[e],i=this.lines.to[e]):(n=this.lines.to[e],i=this.lines.from[e]),t[`${n}|${i}`]?(1===t[`${n}|${i}`].length&&(this.multipleLinesCounts[t[`${n}|${i}`][0]]=1,t[`${n}|${i}`].push(1)),this.multipleLinesCounts[e]=++t[`${n}|${i}`][1]):t[`${n}|${i}`]=[e]}}checkCoordsOnLine(t,e){let n=-1,i=null,r=null;const o=this.sp.getOptions().look,s=o.sizeColumnName?this.sp.dataFrame.col(o.sizeColumnName):null,a=this.sp.dataFrame.filter;for(let l=0;l<this.lines.from.length;l++)if(a.get(this.lines.from[l])&&a.get(this.lines.to[l])&&this.visibility.getBit(l)){const{sizeFrom:a,sizeTo:u}=this.getMarkersSizes(o,s,l),c=this.sp.worldToScreen(this.xAxisCol.get(this.lines.from[l]),this.yAxisCol.get(this.lines.from[l])),h=this.sp.worldToScreen(this.xAxisCol.get(this.lines.to[l]),this.yAxisCol.get(this.lines.to[l]));if(this.multipleLinesCounts[l]){const n=this.getLineLength(c.x,c.y,h.x,h.y),i=this.getPointOnDistance(c.x,c.y,h.x,h.y,u,n),o=this.getPointOnDistance(h.x,h.y,null==c?void 0:c.x,null==c?void 0:c.y,a,n),s=this.lines.from[l]>this.lines.to[l]?this.findControlPoint(this.multipleLinesCounts[l],i.x,i.y,o.x,o.y,l):this.findControlPoint(this.multipleLinesCounts[l],o.x,o.y,i.x,i.y,l);r=this.calculateDistToCurveLine(l,t,e,i,o,s)}else r=this.calculateDistToStraightLine(t,e,c,h);(!i&&null!==r&&r<5||i&&null!==r&&r<i)&&(i=r,n=l)}return n}calculateDistToStraightLine(t,e,n,i){const r=Math.min(n.x,i.x),o=Math.max(n.x,i.x),s=Math.min(n.y,i.y),a=Math.max(n.y,i.y);return t>=r-2&&t<=o+2&&e>=s-2&&e<=a+2?this.distToStraightLineSegment(t,e,n,i):null}distToStraightLineSegment(t,e,n,i){const r=(t,e,n,i)=>Math.pow(t-n,2)+Math.pow(e-i,2),o=r(n.x,n.y,i.x,i.y);if(0==o)return r(t,e,n.x,n.y);let s=((t-n.x)*(i.x-n.x)+(e-n.y)*(i.y-n.y))/o;return s=Math.max(0,Math.min(1,s)),r(t,e,n.x+s*(i.x-n.x),n.y+s*(i.y-n.y))}calculateDistToCurveLine(t,e,n,i,r,o){const s=Math.min(i.x,r.x,o.x),a=Math.max(i.x,r.x,o.x),l=Math.min(i.y,r.y,o.y),u=Math.max(i.y,r.y,o.y);if(e>=s-2&&e<=a+2&&n>=l-2&&n<=u+2){const t=a-s,c=u-l;return this.calculateDistToCurveInRect(e,n,i,o,r,t,c)}return null}calculateDistToCurveInRect(t,e,n,i,r,o,s){const a=Math.floor((o+s)/3),l=1/a,u=new Uint32Array(a),c=new Uint32Array(a),h=new Uint32Array(a);let d=null;const f=new p.A(a);for(let o=0;o<u.length;o++){const s=o*l,a=Math.pow(1-s,2)*n.x+2*s*(1-s)*i.x+Math.pow(s,2)*r.x,f=Math.pow(1-s,2)*n.y+2*s*(1-s)*i.y+Math.pow(s,2)*r.y,p=Math.abs(t-a),m=Math.abs(e-f),g=p+m;(!d||d>g)&&(d=g),h[o]=Math.max(p,m),u[o]=a,c[o]=f}for(let t=0;t<u.length;t++)h[t]<d&&f.setBit(t,!0,!1);let m=null;for(let n=-1;-1!==(n=f.findNext(n));){const i=Math.hypot(u[n]-t,c[n]-e);(!m||m>i)&&(m=i)}return m}getLineLength(t,e,n,i){return Math.sqrt(Math.pow(n-t,2)+Math.pow(i-e,2))}getPointOnDistance(t,e,n,i,r,o){const a=n-r*((n-t)/o),l=i-r*((i-e)/o);return new s.Point(a,l)}findControlPoint(t,e,n,i,r,o){const a=e+(i-e)/2,l=n+(r-n)/2;let u=a-e,c=l-n;const h=Math.sqrt(u*u+c*c);u/=h,c/=h;const d=50*Math.ceil(t/2);return t%2==0?new s.Point(a+d/2*c,l-d/2*u):new s.Point(a-d/2*c,l+d/2*u)}canvasArrow(t,e,n,i,r){const o=Math.atan2(i-e,r-n)+Math.PI;t.moveTo(e-this.arrowWidth*Math.sin(o-Math.PI/10),n-this.arrowWidth*Math.cos(o-Math.PI/10)),t.lineTo(e,n),t.lineTo(e-this.arrowWidth*Math.sin(o+Math.PI/10),n-this.arrowWidth*Math.cos(o+Math.PI/10))}}!function(t){t.EUCLIDEAN="EUCLIDEAN",t.MANHATTAN="MANHATTAN"}(V||(V={}));var B,q=function(t,e,n,i){return new(n||(n=Promise))((function(r,o){function s(t){try{l(i.next(t))}catch(t){o(t)}}function a(t){try{l(i.throw(t))}catch(t){o(t)}}function l(t){var e;t.done?r(t.value):(e=t.value,e instanceof n?e:new n((function(t){t(e)}))).then(s,a)}l((i=i.apply(t,e||[])).next())}))};!function(t){t.SEQUENCE_VARIABILITY_MAP="Sequence Variability Map",t.MOST_POTENT_RESIDUES="Most Potent Residues",t.LOGO_SUMMARY_TABLE="Logo Summary Table",t.DENDROGRAM="Dendrogram",t.CLUSTER_MAX_ACTIVITY="Active peptide selection"}(B||(B={}));class Y{constructor(t){this.isBitsetChangedInitialized=!1,this.isUserChangedSelection=!0,this._dm=null,this.isInitialized=!1,this.isRibbonSet=!1,this.webLogoSelectedMonomers={},this.webLogoBounds={},this.cachedWebLogoTooltip={bar:"",tooltip:null},this._layoutEventInitialized=!1,this.subs=[],this.isHighlighting=!1,this.controlFire=!1,this.accordionSource=null,this._sequenceSpaceViewer=null,this._mclViewer=null,this._monomerPositionStats=null,this._settings=null,this._sequenceSpaceCols=[],this._mclCols=[],this._webLogoSelection=null,this.df=t}get monomerPositionStats(){var t;if(null!==this._monomerPositionStats)return this._monomerPositionStats;const e=this.getScaledActivityColumn();return null===this.positionColumns||null===e?null:(null!==(t=this._monomerPositionStats)&&void 0!==t||(this._monomerPositionStats=(0,M.Ej)(e,this.df.filter,this.positionColumns)),this._monomerPositionStats)}get analysisView(){return void 0===this._analysisView&&(this._analysisView=g()(o.shell.tableViews).find((({dataFrame:t})=>(null==t?void 0:t.getTag(s.TAGS.ID))===this.id)),void 0===this._analysisView&&(this._analysisView=o.shell.addTableView(this.df))),"1"===this.df.getTag(C.gp.MULTIPLE_VIEWS)||this._layoutEventInitialized||o.shell.isInDemo||(o.shell.v=this._analysisView),this._analysisView.grid.invalidate(),this._analysisView}get settings(){var t;const e=this.df.getTag(C.gp.SETTINGS);return null==e?null:(null!==(t=this._settings)&&void 0!==t||(this._settings=JSON.parse(e)),this._settings)}set settings(t){var e,n,i;const r=Object.entries(t),o=Object.assign({},null!==(n=null===(e=this.settings)||void 0===e?void 0:e.sequenceSpaceParams)&&void 0!==n?n:{}),s=new Set;for(const[t,e]of r)switch(this.settings[t]=e,t){case"activityColumnName":case"activityScaling":s.add("activity"),s.add("stats");break;case"showDendrogram":s.add("dendrogram");break;case"showClusterMaxActivity":s.add("clusterMaxActivity");break;case"showSequenceSpace":s.add("showSequenceSpace");break;case"showLogoSummaryTable":s.add("logoSummaryTable");break;case"showMonomerPosition":s.add("monomerPosition");break;case"showMostPotentResidues":s.add("mostPotentResidues");break;case"columns":s.add("columns");break;case"sequenceSpaceParams":s.add("sequenceSpaceParams");break;case"mclSettings":s.add("mclSettings")}if(this.df.setTag("settings",JSON.stringify(this._settings)),this.isInitialized){if(s.has("sequenceSpaceParams")){const t=this.settings.sequenceSpaceParams;Object.entries(t).some((([t,e])=>o[t]!==e&&"epsilon"!==t&&"minPts"!==t&&"clusterEmbeddings"!==t))||(s.delete("sequenceSpaceParams"),this.settings.sequenceSpaceParams.clusterEmbeddings&&s.add("clusterParams"))}s.has("sequenceSpaceParams")&&s.delete("clusterParams");for(const t of s)switch(t){case"activity":this.createScaledCol();break;case"stats":this.webLogoSelection=(0,b.ZR)(this.positionColumns),this.webLogoBounds={},this.cachedWebLogoTooltip={bar:"",tooltip:null},this._monomerPositionStats=null;break;case"dendrogram":this.settings.showDendrogram?this.addDendrogram():this.closeViewer(B.DENDROGRAM);break;case"clusterMaxActivity":this.settings.showClusterMaxActivity?this.addClusterMaxActivityViewer():this.closeViewer(B.CLUSTER_MAX_ACTIVITY);break;case"logoSummaryTable":this.settings.showLogoSummaryTable?this.addLogoSummaryTable():this.closeViewer(B.LOGO_SUMMARY_TABLE);break;case"monomerPosition":this.settings.showMonomerPosition?this.addMonomerPosition():this.closeViewer(B.SEQUENCE_VARIABILITY_MAP);break;case"mostPotentResidues":this.settings.showMostPotentResidues?this.addMostPotentResidues():this.closeViewer(B.MOST_POTENT_RESIDUES);break;case"columns":const t=this.findViewer(B.LOGO_SUMMARY_TABLE);t._viewerGrid=null,t._logoSummaryTable=null,t.render();const e=this.findViewer(B.MOST_POTENT_RESIDUES);e._viewerGrid=null,e.render();break;case"sequenceSpaceParams":case"showSequenceSpace":this.settings.showSequenceSpace&&this.addSequenceSpace({clusterEmbeddings:null===(i=this.settings.sequenceSpaceParams)||void 0===i?void 0:i.clusterEmbeddings});break;case"clusterParams":this.clusterEmbeddings();break;case"mclSettings":this.addMCLClusters()}}}get webLogoSelection(){var t;const e=this.df.getTag(`${C.YX.WL}${C.gp.INVARIANT_MAP_SELECTION}`);return null!==(t=this._webLogoSelection)&&void 0!==t||(this._webLogoSelection=null===e&&null!==this.positionColumns?(0,b.ZR)(this.positionColumns):JSON.parse(null!=e?e:"{}")),this._webLogoSelection}set webLogoSelection(t){this._webLogoSelection=t,this.df.setTag(`${C.YX.WL}${C.gp.INVARIANT_MAP_SELECTION}`,JSON.stringify(t)),this.fireBitsetChanged(null),this.analysisView.grid.invalidate()}get positionColumns(){const t=g()(this.df.columns.byTags({[C.gp.POSITION_COL]:"true"})).toArray();return 0===t.length?null:t}get id(){return this.df.getTag(s.TAGS.ID)}get alphabet(){return this.df.getCol(this.settings.sequenceColumnName).getTag(a.gp.alphabet)}static getInstance(t){var e,n,i;return t.columns.contains(C.$2.ACTIVITY_SCALED)&&!t.columns.contains(C.$2.ACTIVITY)&&(t.getCol(C.$2.ACTIVITY_SCALED).name=C.$2.ACTIVITY),null!==(e=(n=t.temp)[i=Y.modelName])&&void 0!==e||(n[i]=new Y(t)),t.temp[Y.modelName]}modifyWebLogoSelection(t,e={shiftPressed:!1,ctrlPressed:!1},n=!0){n?this.webLogoSelection=(0,b.vW)(this.webLogoSelection,t,e):this._webLogoSelection=(0,b.vW)(this.webLogoSelection,t,e)}getVisibleSelection(){return this.df.selection.clone().and(this.df.filter)}createAccordion(){var t,e,n,i,l,u;const c=null===(t=o.shell.t)||void 0===t?void 0:t.temp[Y.modelName];if(!c)return null;const h=r.accordion("Peptides analysis panel");h.root.style.width="100%";const d=c.getVisibleSelection(),f=c.df.filter.anyFalse?` among ${c.df.filter.trueCount} filtered`:"",p=t=>{const e=[];for(const[n,i]of Object.entries(t))for(const t of i)e.push(`${n}:${t}`);return e.join(", ")},m=c.findViewer(B.LOGO_SUMMARY_TABLE),v=[],C=(null===m?[]:m.clusterSelection[x.W.ORIGINAL].concat(m.clusterSelection[x.W.CUSTOM])).join(", ");0!==C.length&&(v.push(r.h1("Logo summary table selection")),v.push(r.divText(`Selected clusters: ${C}`)));const w=c.findViewer(B.SEQUENCE_VARIABILITY_MAP),_=p(null!==(e=null==w?void 0:w.invariantMapSelection)&&void 0!==e?e:{}),N=p(null!==(n=null==w?void 0:w.mutationCliffsSelection)&&void 0!==n?n:{});0===_.length&&0===N.length||v.push(r.h1("Sequence Variabily Map viewer selection")),0!==_.length&&v.push(r.divText(`Selected monomer-positions: ${_}`)),0!==N.length&&v.push(r.divText(`Selected mutation cliffs pairs: ${N}`));const O=c.findViewer(B.MOST_POTENT_RESIDUES),L=p(null!==(i=null==O?void 0:O.mutationCliffsSelection)&&void 0!==i?i:{});0!==L.length&&(v.push(r.h1("Most Potent Residues viewer selection")),v.push(r.divText(`Selected monomer-positions: ${L}`)));const I=p(c.webLogoSelection);0!==I.length&&(v.push(r.h1("WebLogo selection")),v.push(r.divText(`Selected monomers: ${I}`)));const R=r.div(r.divV(v));h.addTitle(r.divV([r.h1(`${d.trueCount} selected rows${f}`),R],"css-gap-small")),d.anyTrue&&h.addPane("Actions",(()=>{try{const t=r.label("New view");if(y()(t).addClass("d4-link-action"),t.onclick=()=>c.createNewView(),t.onmouseover=t=>r.tooltip.show("Creates a new view from current selection",t.clientX+5,t.clientY+5),null===m)return r.divV([t]);const e=r.label("New cluster");y()(e).addClass("d4-link-action"),e.onclick=()=>{if(null===m)throw new Error("Logo summary table viewer is not found");m.clusterFromSelection()},e.onmouseover=t=>r.tooltip.show("Creates a new cluster from selection",t.clientX+5,t.clientY+5);const n=r.label("Remove cluster");return y()(n).addClass("d4-link-action"),n.onclick=()=>{const t=c.findViewer(B.LOGO_SUMMARY_TABLE);if(null===t)throw new Error("Logo summary table viewer is not found");t.removeCluster()},n.onmouseover=t=>r.tooltip.show("Removes currently selected custom cluster",t.clientX+5,t.clientY+5),n.style.visibility=0===m.clusterSelection[x.W.CUSTOM].length?"hidden":"visible",r.divV([t,e,n])}catch(t){const e=r.divText("Error in Actions");return r.tooltip.bind(e,String(t)),e}}),!0);let P=c.settings;const k=[w,O,m].filter((t=>null!==t&&(t.type!==this.accordionSource||(P=t,!1))));if(null===P)throw new Error("PeptidesError: Model is the source of accordion but is not initialized");P!==c.settings&&k.push(c.settings);const D=k.filter((t=>null!==t&&(0,b.$s)(P,t)&&(t!==c.settings||c.isInitialized)));D.push(P);const G=s.BitSet.create(c.df.rowCount);for(const t of D){const e=t===this.settings?(0,b.KT)(this.webLogoSelection,this.monomerPositionStats):t instanceof x.s?(0,b.KT)(t.clusterSelection,t.clusterStats):t instanceof A.xN?(0,b.KT)(t.mutationCliffsSelection,(0,b.qI)(null!==(l=t.mutationCliffs)&&void 0!==l?l:new Map,c.df.rowCount)):null;if(null!==e&&G.or(e),t instanceof A.J){const e=(0,b.KT)(t.invariantMapSelection,t.monomerPositionStats);null!==e&&G.or(e)}}const U=P;P===c.settings||U instanceof x.s||null==U.mutationCliffs||h.addPane("Mutation Cliffs pairs",(()=>(0,S.F)(c.df,{mutationCliffs:U.mutationCliffs,mutationCliffsSelection:U.mutationCliffsSelection,gridColumns:c.analysisView.grid.columns,sequenceColumnName:U.sequenceColumnName,positionColumns:U.positionColumns,activityCol:U.getScaledActivityColumn()}).root),!0);const V=P===c.settings,F=V?this.webLogoSelection:P instanceof A.J?P.invariantMapSelection:{},H=P instanceof x.s?P.clusterSelection:null!==(u=null==m?void 0:m.clusterSelection)&&void 0!==u?u:{};h.addPane("Distribution",(()=>{var t;try{return(0,T.HV)(c.df,{peptideSelection:G,columns:V?null!==(t=c.settings.columns)&&void 0!==t?t:{}:P.getAggregationColumns(),activityCol:V?c.getScaledActivityColumn():P.getScaledActivityColumn(),monomerPositionSelection:F,clusterSelection:H,clusterColName:null==m?void 0:m.clustersColumnName})}catch(t){const e=r.divText("Error in Distribution");return r.tooltip.bind(e,String(t)),e}}),!0);const q=(t,e)=>{if(null==t||null==e)return!1;for(const[n,i]of Object.entries(t))if(i!==e[n])return!1;return!0};return h.addPane("Selection",(()=>{var t;try{return function(t,e){var n,i;if(0===e.tableSelection.trueCount)return r.divText("No compounds selected");const o=s.DataFrame.create(t.rowCount);o.name="Selected compounds",o.filter.copyFrom(e.tableSelection);const a=g()(t.columns.numerical);let l=null;for(let t=1;t<e.gridColumns.length;t++){const r=e.gridColumns.byIndex(t);if(!r.visible)continue;const u=r.column;if(u.type===s.COLUMN_TYPE.BOOL)continue;null===l&&r.grid&&(null===(n=r.grid.sortByColumns)||void 0===n?void 0:n.length)>0&&(null===(i=r.grid.sortTypes)||void 0===i?void 0:i.length)===r.grid.sortByColumns.length&&(l={cols:r.grid.sortByColumns,types:r.grid.sortTypes});let c=null,h=null;try{c=u.getRawData(),h=u.categories}catch(t){}const d=c&&h?a.some((t=>t.name===u.name))?t=>c[t]:t=>h[c[t]]:t=>u.get(t),f=u.name===e.activityColumn.name?o.columns.addNewFloat(r.name).init((t=>d(t))):o.columns.addNewVirtual(r.name,(t=>d(t)),u.type);for(const[t,e]of u.tags)f.setTag(t,e)}const u=o.plot.grid();u.props.showRowHeader=!1,u.root.style.maxWidth="100%",s.debounce(r.onSizeChanged(u.root),50).subscribe((t=>{var e;const n=u.root.parentElement;(null===(e=null==n?void 0:n.parentElement)||void 0===e?void 0:e.classList.contains("panel-content"))&&(u.root.style.height="calc(100% - 20px)",u.root.style.width="calc(100% - 20px)",u.root.style.position="absolute",u.root.style.right="10px",u.root.style.top="10px")})),(0,b.zz)(u);const c=r.box(u.root);c.style.marginLeft="0px",setTimeout((()=>{null!==l&&u.sort(l.cols,l.types);for(let t=1;t<e.gridColumns.length;t++){const n=e.gridColumns.byIndex(t);n.visible&&u.col(n.name)&&(u.col(n.name).width=n.width)}}),500);const h=(0,M.Ej)(e.activityColumn,o.filter,e.positionColumns,{isFiltered:o.filter.anyTrue||o.filter.anyFalse}),d={isSelectionTable:!0,cachedWebLogoTooltip:()=>({bar:"",tooltip:null}),webLogoBounds:()=>({}),colorPalette:()=>e.colorPalette},f={x:0,y:0,monomerPosition:{},mpStats:h};return e.isAnalysis&&(0,E.FZ)(u,h,e.positionColumns,e.activityColumn,d,f),c}(c.df,{positionColumns:V?c.positionColumns:P.positionColumns,columns:V?null!==(t=c.settings.columns)&&void 0!==t?t:{}:P.getAggregationColumns(),activityColumn:V?c.getScaledActivityColumn():P.getScaledActivityColumn(),gridColumns:c.analysisView.grid.columns,colorPalette:(0,a.SM)(c.df.getCol(V?c.settings.sequenceColumnName:P.sequenceColumnName)),tableSelection:c.getCombinedSelection(),isAnalysis:null!==c.settings&&(V||q(c.settings.columns,P.getAggregationColumns()))})}catch(t){const e=r.divText("Error in Selection");return r.tooltip.bind(e,String(t)),e}}),!0),h}getScaledActivityColumn(t=!1){const e=this.df.col(C.$2.ACTIVITY);return t&&null!==e?s.DataFrame.fromColumns([e]).clone(this.df.filter).getCol(e.name):e}updateGrid(){this.joinDataFrames(),this.createScaledCol(),this.webLogoBounds={};const t={selectionCallback:(t,e)=>this.modifyWebLogoSelection(t,e),unhighlightCallback:()=>this.unhighlight(),colorPalette:()=>(0,a.SM)(this.df.getCol(this.settings.sequenceColumnName)),webLogoBounds:()=>this.webLogoBounds,cachedWebLogoTooltip:()=>this.cachedWebLogoTooltip,highlightCallback:(t,e,n)=>(0,b.dl)(t,e,n),isSelectionTable:!1,headerSelectedMonomers:()=>this.webLogoSelectedMonomers};if(null===this.monomerPositionStats||null===this.positionColumns)throw new Error("PeptidesError: Could not updage grid: monomerPositionStats or positionColumns are null");E.FZ(this.analysisView.grid,this.monomerPositionStats,this.positionColumns,this.getScaledActivityColumn(),t),this._layoutEventInitialized||(o.events.onViewLayoutApplied.subscribe((t=>{t.view.id===this.analysisView.id&&this.updateGrid()})),this._layoutEventInitialized=!0),this.setTooltips(),this.setBitsetCallback(),this.setGridProperties()}joinDataFrames(){const t=this.df.name,e=this.df.columns,n=(0,c.R)(this.df.getCol(this.settings.sequenceColumnName)),i=n.columns.names();for(const t of i){let i=this.df.col(t);const r=n.getCol(t);null!==i&&e.remove(t);const o=r.categories,s=r.getRawData();i=e.addNew(r.name,r.type).init((t=>o[s[t]])),i.setTag(C.gp.ANALYSIS_COL,"true"),i.setTag(C.gp.POSITION_COL,"true"),E.rI(i,this.alphabet)}this.df.name=t}createScaledCol(){const t=this.analysisView.grid,e=(0,b.Y1)(this.df.getCol(this.settings.activityColumnName),this.settings.activityScaling);this.df.columns.replace(C.$2.ACTIVITY,e),t.columns.setOrder([e.name])}unhighlight(){this.isHighlighting&&(this.df.rows.highlight(null),this.isHighlighting=!1)}setTooltips(){this.analysisView.grid.onCellTooltip(((t,e,n)=>{var i,r;return!(!t.isColHeader||(null===(i=t.tableColumn)||void 0===i?void 0:i.semType)!==C.uF.MONOMER)||!(!t.isTableCell||(null===(r=t.tableColumn)||void 0===r?void 0:r.semType)!==C.uF.MONOMER)&&((0,G.cr)(t.cell.value,e,n),!0)}))}getCombinedSelection(){var t,e,n,i,r,o,a,l;const u=new p.A(this.df.rowCount,!1),c=(t,e)=>{for(const[n,i]of Object.entries(t))for(const t of i){const i=null==e?void 0:e[n];if(void 0===i)continue;const r=i[t];void 0!==r&&u.or(r.mask)}};c(this.webLogoSelection,this.monomerPositionStats);const h=this.findViewer(B.SEQUENCE_VARIABILITY_MAP);c(null!==(t=null==h?void 0:h.invariantMapSelection)&&void 0!==t?t:{},null!==(e=null==h?void 0:h.monomerPositionStats)&&void 0!==e?e:null);const d=(t,e)=>{var n,i;for(const[r,o]of Object.entries(t))for(const t of o){const o=null!==(i=null===(n=null==e?void 0:e.get(t))||void 0===n?void 0:n.get(r))&&void 0!==i?i:null;if(null!==o)for(const[t,e]of o.entries()){u.setTrue(t);for(const t of e)u.setTrue(t)}}};d(null!==(n=null==h?void 0:h.mutationCliffsSelection)&&void 0!==n?n:{},null!==(i=null==h?void 0:h.mutationCliffs)&&void 0!==i?i:null);const f=this.findViewer(B.MOST_POTENT_RESIDUES);d(null!==(r=null==f?void 0:f.mutationCliffsSelection)&&void 0!==r?r:{},null!==(o=null==f?void 0:f.mutationCliffs)&&void 0!==o?o:null);const m=this.findViewer(B.LOGO_SUMMARY_TABLE);for(const t of Object.keys(null!==(a=null==m?void 0:m.clusterSelection)&&void 0!==a?a:{}))for(const e of null!==(l=m.clusterSelection[t])&&void 0!==l?l:[]){const n=m.clusterStats[t][e];u.or(n.mask)}return s.BitSet.fromBytes(u.buffer.buffer,u.length)}setBitsetCallback(){if(this.isBitsetChangedInitialized)return;const t=this.df.selection,e=this.df.filter,n=()=>{try{const t=this.createAccordion();if(null===t)return;o.shell.o=t.root}catch(t){console.error(t)}};t.onChanged.subscribe((()=>{if(this.controlFire)this.controlFire=!1;else try{this.isUserChangedSelection||t.copyFrom(this.getCombinedSelection(),!1)}catch(t){N._package.logger.debug("Peptides: Error on selection changed"),N._package.logger.debug(t)}finally{n()}})),e.onChanged.subscribe((()=>{var t,e;try{if(this.controlFire)return void(this.controlFire=!1);const n=this.findViewer(B.LOGO_SUMMARY_TABLE);null!==n&&void 0!==n.model&&(n._logoSummaryTable=null!==(t=n.createLogoSummaryTable())&&void 0!==t?t:n._logoSummaryTable,n._viewerGrid=null!==(e=n.createLogoSummaryTableGrid())&&void 0!==e?e:n._viewerGrid,n.render())}catch(t){N._package.logger.debug("Peptides: Error on filter changed"),N._package.logger.debug(t)}finally{n()}})),this.isBitsetChangedInitialized=!0}fireBitsetChanged(t,e=!1){this.accordionSource=t,this.isBitsetChangedInitialized||this.setBitsetCallback(),this.isUserChangedSelection=!1,this.df.selection.fireChanged(),e&&this.df.filter.fireChanged(),this.controlFire=!0,this.df.selection.fireChanged(),e&&this.df.filter.fireChanged(),this.isUserChangedSelection=!0,this.webLogoSelectedMonomers=(0,b.qx)(this.df)}setGridProperties(t){var e,n,i,r;const o=this.analysisView.grid,s=o.props;s.allowColSelection=null!==(e=null==t?void 0:t.allowColSelection)&&void 0!==e&&e,s.allowEdit=null!==(n=null==t?void 0:t.allowEdit)&&void 0!==n&&n,s.showReadOnlyNotifications=null!==(i=null==t?void 0:t.showReadOnlyNotifications)&&void 0!==i&&i,s.showCurrentRowIndicator=null!==(r=null==t?void 0:t.showCurrentRowIndicator)&&void 0!==r&&r;const l=this.positionColumns;if(null===l)throw new Error("PeptidesError: Could not set grid properties: positionColumns are null");let u=10;const c=o.canvas.getContext("2d");if(null===c)throw new Error("PeptidesError: Could not set grid properties: canvas context is null");for(const t of l){const e=(0,a.zS)(t.categories.reduce(((t,e)=>t.length>e.length?t:e)),6),n=Math.ceil(c.measureText(e).width);u=Math.max(u,n)}const h=l.map((t=>t.name));for(let t=1;t<this.analysisView.grid.columns.length;++t){const e=this.analysisView.grid.columns.byIndex(t);if(null===e)throw new Error(`PeptidesError: Could not get analysis view: grid column with index '${t}' is null`);if(null===e.column)throw new Error(`PeptidesError: Could not get analysis view: grid column with index '${t}' has null column`);e.visible=h.includes(e.column.name)||e.column.name===C.$2.ACTIVITY}setTimeout((()=>{for(const t of l){const e=o.col(t.name);if(null===e)throw new Error(`PeptidesError: Could not set column width: grid column '${t.name}' is null`);e.width=u+15}}),100)}closeViewer(t){const e=this.findViewer(t);null==e||e.detach(),null==e||e.close()}findViewerNode(t){for(const e of this.analysisView.dockManager.rootNode.children)if(e.container.containerElement.innerHTML.includes(t))return e;return null}addDendrogram(){return q(this,void 0,void 0,(function*(){const t=s.TaskBarProgressIndicator.create("Calculating distance matrix...");try{const t=s.Func.find({package:"Dendrogram",name:"hierarchicalClustering"})[0];if(!t||4!==t.inputs.length)throw new Error("Correct dendrogram function is not found");yield t.apply({df:this.df,colNameList:[this.settings.sequenceColumnName],distance:"euclidean",linkage:"complete"})}catch(t){N._package.logger.error(t)}finally{t.close()}}))}init(t){if(!this.isInitialized){if(this.settings=t,this.isInitialized=!0,!this.isRibbonSet&&"1"!==this.df.getTag(C.gp.MULTIPLE_VIEWS)){const t=r.iconFA("wrench",(()=>(0,_.OH)(this)),"Peptides analysis settings");this.analysisView.setRibbonPanels([[t]],!1),this.isRibbonSet=!0,this.updateGrid()}this.subs.push(o.events.onAccordionConstructed.subscribe((t=>{if(!(o.shell.o instanceof s.SemanticValue||o.shell.o instanceof s.Column&&this.df.columns.toList().includes(o.shell.o)))return;const e=t.getPane("Actions"),n=y()(e.root).find(".d4-flex-col"),a=r.label("Calculate identity");a.classList.add("d4-link-action"),r.tooltip.bind(a,"Adds a column with fractions of matching monomers against sequence in the current row"),a.onclick=()=>{const t=this.df.getCol(this.settings.sequenceColumnName);d(this.df,t,t.get(this.df.currentRowIdx),i.IDENTITY).then((e=>e.setTag(C.gp.IDENTITY_TEMPLATE,t.get(this.df.currentRowIdx)))).catch((t=>N._package.logger.debug(t)))},n.append(r.span([a],"d4-markdown-row"));const l=r.label("Calculate similarity");l.classList.add("d4-link-action"),r.tooltip.bind(l,"Adds a column with sequence similarity scores against sequence in the current row"),l.onclick=()=>{const t=this.df.getCol(this.settings.sequenceColumnName);d(this.df,t,t.get(this.df.currentRowIdx),i.SIMILARITY).then((e=>e.setTag(C.gp.SIMILARITY_TEMPLATE,t.get(this.df.currentRowIdx)))).catch((t=>N._package.logger.debug(t)))},n.append(r.span([l],"d4-markdown-row"))}))),this.subs.push(o.events.onViewRemoved.subscribe((t=>{t.id===this.analysisView.id&&this.subs.forEach((t=>t.unsubscribe())),o.log.debug(`Peptides: view ${t.name} removed`)}))),this.subs.push(o.events.onTableRemoved.subscribe((t=>{t.id===this.df.id&&this.subs.forEach((t=>t.unsubscribe())),o.log.debug(`Peptides: table ${t.name} removed`)}))),this.subs.push(o.events.onProjectClosed.subscribe((t=>{t.id===o.shell.project.id&&this.subs.forEach((t=>t.unsubscribe())),o.log.debug(`Peptides: project ${t.name} closed`)}))),this.fireBitsetChanged(null,!0),this.analysisView.grid.invalidate()}}findViewer(t){return g()(this.analysisView.viewers).find((e=>e.type===t))||null}addLogoSummaryTable(t){return q(this,void 0,void 0,(function*(){null!=t||(t={sequenceColumnName:this.settings.sequenceColumnName,clustersColumnName:g()(this.df.columns.categorical).next().value,activityColumnName:this.settings.activityColumnName,activityScaling:this.settings.activityScaling});const e=yield this.df.plot.fromType(B.LOGO_SUMMARY_TABLE,t);this.analysisView.dockManager.dock(e,s.DOCK_TYPE.RIGHT,null,B.LOGO_SUMMARY_TABLE),e.viewerGrid.invalidate()}))}addClusterMaxActivityViewer(t){return q(this,void 0,void 0,(function*(){var e,n,i,r,o,a,l;const u=null!==(r=null!==(n=null===(e=this._mclCols)||void 0===e?void 0:e.find((t=>t.toLowerCase().startsWith("cluster (mcl)"))))&&void 0!==n?n:null===(i=this.findViewer(B.LOGO_SUMMARY_TABLE))||void 0===i?void 0:i.clustersColumnName)&&void 0!==r?r:null===(o=this._sequenceSpaceCols)||void 0===o?void 0:o.find((t=>t.toLowerCase().startsWith("cluster")));null!=t||(t={activityColumnName:this.settings.activityColumnName,clusterColumnName:null!=u?u:null===(a=g()(this.df.columns.categorical).next().value)||void 0===a?void 0:a.name,activityTarget:C.wf.HIGH,connectivityColumnName:this._mclCols.find((t=>t.toLowerCase().startsWith("connectivity"))),clusterSizeThreshold:20,activityThreshold:1e3});const c=yield this.df.plot.fromType(B.CLUSTER_MAX_ACTIVITY,t),h=null!==(l=this.findViewerNode(B.LOGO_SUMMARY_TABLE))&&void 0!==l?l:null;this.analysisView.dockManager.dock(c,h?s.DOCK_TYPE.DOWN:s.DOCK_TYPE.RIGHT,h,B.CLUSTER_MAX_ACTIVITY)}))}addMonomerPosition(t){return q(this,void 0,void 0,(function*(){null!=t||(t={maxMutations:1,activityScaling:this.settings.activityScaling,activityColumnName:this.settings.activityColumnName,sequenceColumnName:this.settings.sequenceColumnName,minActivityDelta:0,activityTarget:C.wf.HIGH});const e=yield this.df.plot.fromType(B.SEQUENCE_VARIABILITY_MAP,t),n=this.findViewer(B.MOST_POTENT_RESIDUES),i=this.analysisView.dockManager,[r,o,a]=null===n?[s.DOCK_TYPE.DOWN,null,void 0]:[s.DOCK_TYPE.LEFT,this.findViewerNode(B.MOST_POTENT_RESIDUES),.7];i.dock(e,r,o,B.SEQUENCE_VARIABILITY_MAP,a)}))}addMostPotentResidues(t){return q(this,void 0,void 0,(function*(){null!=t||(t={activityScaling:this.settings.activityScaling,activityColumnName:this.settings.activityColumnName,sequenceColumnName:this.settings.sequenceColumnName,minActivityDelta:0,maxMutations:1,activityTarget:C.wf.HIGH});const e=yield this.df.plot.fromType(B.MOST_POTENT_RESIDUES,t),n=this.findViewer(B.SEQUENCE_VARIABILITY_MAP),i=this.analysisView.dockManager,[r,o,a]=null===n?[s.DOCK_TYPE.DOWN,null,void 0]:[s.DOCK_TYPE.RIGHT,this.findViewerNode(B.SEQUENCE_VARIABILITY_MAP),.3];i.dock(e,r,o,B.MOST_POTENT_RESIDUES,a)}))}createNewView(){const t=this.getVisibleSelection(),e=this.df.clone(t);for(const[t,n]of e.tags)e.setTag(t,t===C.gp.SETTINGS?n:"");e.name="Peptides Multiple Views",e.setTag(C.gp.MULTIPLE_VIEWS,"1");const n=o.shell.addTableView(e),i=this.findViewer(B.LOGO_SUMMARY_TABLE);return null!=i&&n.addViewer(B.LOGO_SUMMARY_TABLE,{[`sequence${C.To}`]:i.sequenceColumnName,[`activity${C.To}`]:i.activityColumnName,activityScaling:i.activityScaling,webLogoMode:i.webLogoMode,membersRatioThreshold:i.membersRatioThreshold,[`clusters${C.To}`]:i.clustersColumnName}),e.getTag(s.TAGS.ID)}clusterEmbeddings(){return q(this,void 0,void 0,(function*(){var t,e;if(!this._sequenceSpaceCols||0===this._sequenceSpaceCols.length)return void o.shell.warning("Embeddings columns are not initialized");const i=this._sequenceSpaceCols.filter((t=>t.toLowerCase().startsWith("embed_")));if(2!==i.length)return void o.shell.warning(`Found ${i.length} embeddings columns, expected 2`);const r=this._sequenceSpaceCols.filter((t=>t.toLowerCase().startsWith("cluster")));r.length>0&&this.df.columns.remove(r[0]);const s=this.df.getCol(i[0]).getRawData(),a=this.df.getCol(i[1]).getRawData(),l=null!==(t=this.settings.sequenceSpaceParams.epsilon)&&void 0!==t?t:.01,u=null!==(e=this.settings.sequenceSpaceParams.minPts)&&void 0!==e?e:4,c=yield function(t,e,i,r){return o=this,s=void 0,l=function*(){return new Promise((function(o,s){const a=new Worker(new URL(n.p+n.u(682),n.b));a.postMessage({embedX:t,embedY:e,minPts:r,epsilon:i}),a.onmessage=({data:{error:t,clusters:e}})=>{a.terminate(),t?s(t):o(e)}}))},new((a=void 0)||(a=Promise))((function(t,e){function n(t){try{r(l.next(t))}catch(t){e(t)}}function i(t){try{r(l.throw(t))}catch(t){e(t)}}function r(e){var r;e.done?t(e.value):(r=e.value,r instanceof a?r:new a((function(t){t(r)}))).then(n,i)}r((l=l.apply(o,s||[])).next())}));var o,s,a,l}(s,a,l,u),h=this.df.columns.getUnusedName("Cluster (DBSCAN)"),d=this.df.columns.addNewString(h);d.init((t=>c[t].toString())),null!==this._sequenceSpaceViewer&&(this._sequenceSpaceViewer.props.colorColumnName=d.name),this._sequenceSpaceCols=[i[0],i[1],d.name];const f=this.analysisView.grid.col(d.name);f&&(f.visible=!1)}))}addMCLClusters(){return q(this,void 0,void 0,(function*(){var t,e,i,a,l;if(null!==this._mclViewer)try{null===(t=this._mclViewer)||void 0===t||t.detach(),null===(e=this._mclViewer)||void 0===e||e.close()}catch(t){}0!==this._mclCols.length&&this._mclCols.forEach((t=>this.df.columns.remove(t))),this._mclCols=[];const u=this.df.getCol(this.settings.sequenceColumnName);null!==(i=(l=this.settings).mclSettings)&&void 0!==i||(l.mclSettings=new w.av);const c=this.settings.mclSettings;let h=0;const d=this.df.onColumnsAdded.subscribe((t=>{for(const e of t.columns)if((e.name.toLowerCase().startsWith("embed")||e.name.toLowerCase().startsWith("cluster")||e.name.toLowerCase().startsWith("connectivity"))&&e.name.toLowerCase().includes("mcl")){const t=this.analysisView.grid.col(e.name);if(null==t||this._mclCols.includes(e.name))continue;t.visible=!1,this._mclCols.push(e.name),h++}5===h&&d.unsubscribe()})),f=o.events.onViewerAdded.subscribe((t=>{try{const e=t.args.viewer;if(e.type===s.VIEWER.SCATTER_PLOT){if(this._sequenceSpaceViewer&&this.analysisView.dockManager.findNode(this._sequenceSpaceViewer.root)){const t=this.analysisView.dockManager.findNode(this._sequenceSpaceViewer.root);setTimeout((()=>{this.analysisView.dockManager.dock(e,s.DOCK_TYPE.FILL,t)}))}f.unsubscribe()}}catch(t){console.error(t)}})),p=s.Func.find({package:"Bio",name:"macromoleculePreprocessingFunction"})[0],m=yield async function(t,e,i,a,l,u,c,h=80,d=10,f=!1,p=2,m=5,g){const v=o.shell.tableView(t.name)??o.shell.addTableView(t),y=g??v.scatterPlot({showXAxis:!1,showYAxis:!1,showXSelector:!1,showYSelector:!1,title:"MCL"});r.setUpdateIndicator(y.root,!0);const C=[],w=[];for(let t=0;t<u.length;++t){const n=u[t];if(n){const r=n.inputs[0].name,o=n.inputs[1].name,{entries:s,options:a}=await n.apply({[r]:e[t],[o]:i[t],...c[t]??{}});w.push({entries:s,options:a}),C.push(a??{})}else{const n=e[t].toList(),i={};w.push({entries:n,options:i}),C.push(i)}}const b=function(t,e,i,r,o,s,a=10,l=!1,u=2){const c=new Worker(new URL(n.p+n.u(51),n.b));let h;return c.postMessage({data:t,threshold:e,weights:i,aggregationMethod:r,distanceFns:o,distanceFnArgs:s,maxIterations:a,useWebGPU:l,inflate:u}),{promise:new Promise(((t,e)=>{h=t,c.onmessage=e=>{setTimeout((()=>c.terminate()),100),t(e.data.res)},c.onerror=t=>{setTimeout((()=>c.terminate()),100),e(t)}})),terminate:()=>{try{h(null),c.terminate()}catch(t){console.error(t)}}}}(w.map((t=>t.entries)),h,a,l,i,C,d,f,p),A=o.events.onViewerClosed.subscribe((t=>{t.args.viewer?.props?.title===y.props.title&&y.type===t.args?.viewer?.type&&(A.unsubscribe(),b.terminate())})),E=await b.promise;if(!E)return;const S=t.columns.getUnusedName("Cluster (MCL)"),T=t.columns.getUnusedName("EmbedX (MCL)"),x=t.columns.getUnusedName("EmbedY (MCL)"),_={};E.clusters.forEach((t=>{_[t]||(_[t]=0),_[t]++}));const N=new Uint32Array(E.embedX.length);for(let t=0;t<E.is.length;t++)N[E.is[t]]++,N[E.js[t]]++;const M=t.columns.getUnusedName("Cluster size (MCL)"),O=t.columns.getUnusedName("Connectivity (MCL)"),L=t.columns.addNewFloat(T);L.init((t=>E.embedX[t]));const I=t.columns.addNewFloat(x);I.init((t=>E.embedY[t]));const R=t.columns.addNewString(S);R.init((t=>_[E.clusters[t]]>=m?E.clusters[t].toString():"-1"));const P={"-1":s.Color.setAlpha(s.Color.lightBlue,100)};R.setTag(s.TAGS.COLOR_CODING_CATEGORICAL,JSON.stringify(P)),R.temp[s.TAGS.COLOR_CODING_CATEGORICAL]=P;const k=t.columns.addNewInt(M);k.init((t=>_[E.clusters[t]]));const D=t.columns.addNewInt(O);D.init((t=>N[t])),y.props.xColumnName=T,y.props.yColumnName=x,y.props.colorColumnName=S,y.props.markerDefaultSize=6,A.unsubscribe();const G=[],V=[],F=new Map;for(let t=0;t<E.is.length;t++){let e=E.clusters[E.is[t]],n=E.clusters[E.js[t]];if(e===n){G.push(E.is[t]),V.push(E.js[t]);continue}if(e>n){const t=e;e=n,n=t}let i=F.get(e);i||(i=new Map,F.set(e,i));let r=i.get(n);r||(r=0),r>=20||(r++,i.set(n,r),G.push(E.is[t]),V.push(E.js[t]))}return new H(y,T,x,{from:new Uint32Array(G),to:new Uint32Array(V),drawArrows:!1,opacity:.3,skipMultiLineCalculation:!0,skipShortLines:!0,skipMouseOverDetection:!0,shortLineThreshold:6,width:.75,color:"128,128,128"},U.none),r.setUpdateIndicator(y.root,!1),{sc:y,embedXCol:L,embedYCol:I,clusterCol:R,clusterCounterCol:k,connectivityCol:D}}(this.df,[u],[c.distanceF],[1],V.MANHATTAN,[p],[{gapOpen:c.gapOpen,gapExtend:c.gapExtend,fingerprintType:c.fingerprintType}],c.threshold,c.maxIterations,c.useWebGPU,c.inflation,c.minClusterSize);f.unsubscribe();const g=this.findViewer(B.LOGO_SUMMARY_TABLE);if(g&&(g._clusterStats=null,g._clusterSelection=null,g._viewerGrid=null,g._logoSummaryTable=null,g.render()),null==m?void 0:m.sc){const t=JSON.stringify({cols:[u].map((t=>t.name)),metrics:[c.distanceF],weights:[1],aggregationMethod:V.MANHATTAN,preprocessingFuncs:[p].map((t=>{var e;return null!==(e=null==t?void 0:t.name)&&void 0!==e?e:null})),preprocessingFuncArgs:[{gapOpen:c.gapOpen,gapExtend:c.gapExtend,fingerprintType:c.fingerprintType}],threshold:c.threshold,maxIterations:c.maxIterations,useWebGPU:c.useWebGPU,inflate:c.inflation,minClusterSize:c.minClusterSize});this.df.setTag("MCL_OPTIONS",t),m.sc.props.initializationFunction="EDA:MCLInitializationFunction",this._mclViewer=null!==(a=null==m?void 0:m.sc)&&void 0!==a?a:null}}))}addSequenceSpace(){return q(this,arguments,void 0,(function*(t={}){var e,n,i,r;if(null!==this._sequenceSpaceViewer)try{null===(e=this._sequenceSpaceViewer)||void 0===e||e.detach(),null===(n=this._sequenceSpaceViewer)||void 0===n||n.close()}catch(t){}0!==this._sequenceSpaceCols.length&&this._sequenceSpaceCols.forEach((t=>this.df.columns.remove(t))),this._sequenceSpaceCols=[];let l=this.df.getCol(this.settings.sequenceColumnName);const u=h.GO.forColumn(l);if(u.isHelm())try{o.shell.warning("Column is in HELM notation. Sequences space will linearize sequences from position 0 prior to analysis");const t=u.convert(a.Hi.SEPARATOR,"/"),e=this.df.columns.getUnusedName(`Separator(${l.name})`);t.name=e,this.df.columns.add(t,!0),this.analysisView.grid.col(e).visible=!1,l=t}catch(t){return o.shell.error("Error on converting HELM notation to linear notation"),void o.shell.error(t)}const c=!t.clusterCol&&!!t.clusterEmbeddings,d=null!==(r=null===(i=this.settings)||void 0===i?void 0:i.sequenceSpaceParams)&&void 0!==r?r:new w.GI(c);d.clusterEmbeddings=c;const p={table:this.df,molecules:l,methodName:f.UMAP,similarityMetric:d.distanceF,plotEmbeddings:!0,options:{bypassLargeDataWarning:!0,dbScanEpsilon:d.epsilon,dbScanMinPts:d.minPts,randomSeed:"1",preprocessingFuncArgs:{gapOpen:d.gapOpen,gapExtend:d.gapExtend,fingerprintType:d.fingerprintType}},clusterEmbeddings:d.clusterEmbeddings};let m=0;const g=d.clusterEmbeddings?3:2,v=this.df.onColumnsAdded.subscribe((t=>{for(const e of t.columns)if(e.name.toLowerCase().startsWith("embed_")||d.clusterEmbeddings&&e.name.toLowerCase().startsWith("cluster")){const t=this.analysisView.grid.col(e.name);if(null==t||this._sequenceSpaceCols.includes(e.name))continue;t.visible=!1,this._sequenceSpaceCols.push(e.name),m++}m===g&&v.unsubscribe()})),y=o.events.onViewerAdded.subscribe((t=>{try{const e=t.args.viewer;if(e.type===s.VIEWER.SCATTER_PLOT){if(this._mclViewer&&this.analysisView.dockManager.findNode(this._mclViewer.root)){const t=this.analysisView.dockManager.findNode(this._mclViewer.root);setTimeout((()=>{this.analysisView.dockManager.dock(e,s.DOCK_TYPE.FILL,t)}))}y.unsubscribe()}}catch(t){console.error(t)}})),C=yield o.functions.call("Bio:sequenceSpaceTopMenu",p);y.unsubscribe(),C instanceof s.ScatterPlotViewer&&(d.clusterEmbeddings||t.clusterCol||(C.props.colorColumnName=this.getScaledActivityColumn().name),C.props.showXSelector=!1,C.props.showYSelector=!1,t.clusterCol&&(C.props.colorColumnName=t.clusterCol.name),this._sequenceSpaceViewer=C,C.onContextMenu.subscribe((t=>{try{t.item("Modify Sequence space parameters",(()=>{(0,_.OH)(this)}))}catch(t){}})))}))}}Y.modelName="peptidesModel"},3273:(t,e,n)=>{"use strict";n.d(e,{_package:()=>R,getMonomerWorksInstance:()=>P,getTreeHelperInstance:()=>k});var i,r,o=n(4328),s=n(7389),a=n(6082),l=(n(5082),n(7233)),u=n.n(l),c=(n(4788),n(9484));n(826),n(3541),n(5480),(r=i||(i={})).BASE="HELM_BASE",r.SUGAR="HELM_SUGAR",r.LINKER="HELM_LINKER",r.AA="HELM_AA",r.CHEM="HELM_CHEM",r.BLOB="HELM_BLOB",r.NUCLEOTIDE="HELM_NUCLETIDE";var h=n(4139);n(8608),n(2003),n(8070);var d=n(5072),f=n.n(d),p=n(7825),m=n.n(p),g=n(7659),v=n.n(g),y=n(5056),C=n.n(y),w=n(540),b=n.n(w),A=n(1113),E=n.n(A),S=n(6677),T={};T.styleTagTransform=E(),T.setAttributes=C(),T.insert=v().bind(null,"head"),T.domAPI=m(),T.insertStyleElement=b(),f()(S.A,T),S.A&&S.A.locals&&S.A.locals;var x;!function(t){let e,n;!function(t){t.vert=function(t){return s.divV(t.map((t=>s.render(t))),{classes:"u2-panel"})},t.horz=function(t){return s.divH(t.map((t=>s.render(t))),{classes:"u2-panel"})}}(e=t.panels||(t.panels={})),t.appHeader=function(t){const n=s.iconImage("",t.iconPath);return u()(n).addClass("ui-app-header-icon").css("margin-right","20px"),e.horz([n,e.vert([s.markdown(t.description),t.learnMoreUrl?s.link("Learn more",t.learnMoreUrl):null])])},function(t){t.runAsync=function(t,e){return n=this,i=void 0,a=function*(){s.setUpdateIndicator(t,!0);try{return yield e()}catch(t){o.log.error(t)}finally{s.setUpdateIndicator(t,!1)}},new((r=void 0)||(r=Promise))((function(t,e){function o(t){try{l(a.next(t))}catch(t){e(t)}}function s(t){try{l(a.throw(t))}catch(t){e(t)}}function l(e){var n;e.done?t(e.value):(n=e.value,n instanceof r?n:new r((function(t){t(n)}))).then(o,s)}l((a=a.apply(n,i||[])).next())}));var n,i,r,a}}(n=t.tools||(t.tools={}))}(x||(x={}));var _=n(144),N=n.n(_);const M=rxjs.operators;class O extends a.JsViewer{get scViewer(){return this._scViewer||(this._scViewer=this.createSCViewer()),this._scViewer}constructor(){super(),this._titleHost=s.divText(c.q.CLUSTER_MAX_ACTIVITY,{id:"pep-viewer-title",style:{marginRight:"auto"}}),this._selsectIcon=s.div(),this.activityTarget=h.wf.HIGH,this.viewerError="",this.renderTimeout=null,this.renderDebounceTime=500,this.scFilterQuery=`\${${O.maxActivityInClusterColName}} == 1`,this.selectionSubscription=null,this.linesDrawSubscription=null,this.clusterColumnName=this.column("cluster",{nullable:!1}),this.activityColumnName=this.column("activity",{nullable:!1}),this.colorColumnName=this.column("color",{nullable:!0,defaultValue:null}),this.activityTarget=this.string("activityTarget",h.wf.HIGH,{choices:[h.wf.HIGH,h.wf.LOW]}),this.clusterSizeThreshold=this.int("clusterSizeThreshold",20),this.activityThreshold=this.int("activityThreshold",1e3),this.connectivityColumnName=this.column("connectivity",{nullable:!0})}get model(){return c.i.getInstance(this.dataFrame)}createSCViewer(){var t;const e={showXAxis:!0,showYAxis:!0,showXSelector:!1,showYSelector:!1,showColorSelector:!1,xAxisType:a.AxisType.logarithmic,yAxisType:a.AxisType.logarithmic,invertYAxis:this.activityTarget===h.wf.LOW,xColumnName:O.clusterSizeColName,markerType:"circle",markerDefaultSize:10,showSizeSelector:!1};if(null==this.clusterColumnName||null==this.activityColumnName||!this.dataFrame.columns.contains(this.clusterColumnName)||!this.dataFrame.columns.contains(this.activityColumnName))return this.viewerError="Please set valid cluster and activity columns",null;const n=this.dataFrame.columns.byName(this.activityColumnName),i=this.dataFrame.columns.byName(this.clusterColumnName),r=null!=this.connectivityColumnName?this.dataFrame.columns.byName(this.connectivityColumnName):null;if(![a.COLUMN_TYPE.FLOAT,a.COLUMN_TYPE.INT,a.COLUMN_TYPE.BIG_INT,a.COLUMN_TYPE.QNUM].includes(n.type))return this.viewerError="Activity column should be numeric",null;const o=this.dataFrame.columns.getOrCreate(O.clusterSizeColName,a.TYPE.INT,this.dataFrame.rowCount),l={};for(let e=0;e<this.dataFrame.rowCount;e++){const n=i.get(e);null!=n&&"-1"!=n&&(l[n]=(null!==(t=l[n])&&void 0!==t?t:0)+1)}o.init((t=>{var e;return i.isNone(t)?null:null!==(e=l[i.get(t)])&&void 0!==e?e:null})),n.stats.min<=0&&(e.yAxisType=a.AxisType.linear);const u={},c={};for(let t=0;t<this.dataFrame.rowCount;t++){const e=i.get(t);if(null==e||i.isNone(t)||n.isNone(t))continue;const o=n.get(t),s=u[e];if((null==s||null==s||o>n.get(s)&&this.activityTarget===h.wf.HIGH||o<n.get(s)&&this.activityTarget===h.wf.LOW)&&(u[e]=t),r){const n=r.get(t),i=c[e];(null==i||null==i||n>r.get(i))&&(c[e]=t)}}const d=this.dataFrame.columns.getOrCreate(O.maxActivityInClusterColName,a.COLUMN_TYPE.INT,this.dataFrame.rowCount);d.init((t=>i.isNone(t)?0:t===u[i.get(t)]?1:0)),this.dataFrame.columns.getOrCreate(O.maxConnectivityInClusterColName,a.COLUMN_TYPE.INT,this.dataFrame.rowCount).init((t=>i.isNone(t)?0:t===c[i.get(t)]?1:0)),this.dataFrame.columns.getOrCreate(O.synSelectionColName,a.TYPE.STRING,this.dataFrame.rowCount).init((t=>{if(i.isNone(t))return null;let e=null;return t===u[i.get(t)]&&(e=O.maxActivityLabel),r&&t===c[i.get(t)]&&(e=e?`${e}, ${O.maxConnectivityLabel}`:O.maxConnectivityLabel),e})),e.xColumnName=O.clusterSizeColName,e.yColumnName=this.activityColumnName,e.filter=this.scFilterQuery,this.viewerError="";const f=a.Viewer.scatterPlot(this.dataFrame,e);this.selectionSubscription&&this.selectionSubscription.unsubscribe(),this.selectionSubscription=f.onDataEvent.pipe((0,M.filter)((t=>"d4-select"==t.type))).subscribe((t=>{var e,n;const r=null!==(n=null===(e=t.bitset)||void 0===e?void 0:e.getSelectedIndexes())&&void 0!==n?n:[],o=this.dataFrame.selection,s=a.BitSet.create(this.dataFrame.rowCount,(t=>1==d.get(t)));s.and(o);for(let t=0;t<r.length;t++){const e=r[t],n=i.get(e);i.isNone(e)||(s.set(e,!0),null!=c[n]&&s.set(c[n],!0))}s.fireChanged();const l=s.getSelectedIndexes();for(const t of l){const e=i.get(t);null!=e&&null!=c[e]&&s.set(c[e],!0)}setTimeout((()=>{this.dataFrame.selection.copyFrom(s,!0),setTimeout((()=>{this.model&&this.model.createAccordion()}),200)}),200)}));const p=()=>{const t=a.BitSet.create(this.dataFrame.rowCount);Object.entries(u).forEach((([e,i])=>{var r;if(null==e||null==i)return;const o=parseInt(e),s=n.get(i),a=null!==(r=l[o])&&void 0!==r?r:l[e];s<this.activityThreshold&&a<this.clusterSizeThreshold||(t.set(i,!0,!1),null!=c[o]&&t.set(c[o],!0,!1))})),t.fireChanged(),this.dataFrame.selection.copyFrom(t,!0)};return this._selsectIcon=s.iconSvg("select-all",(()=>{p()}),"Select 3 Active 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Size",{style:{alignSelf:"center",color:"var(--grey-6)",marginBottom:"5px"}}),r=s.div(this.activityTarget===h.wf.HIGH?"Maximum Activity":"Minimum Activity",{style:{color:"var(--grey-6)",alignSelf:"center",textOrientation:"mixed",writingMode:"tb",transform:"rotate(180deg)",marginLeft:"5px"}});n.props.colorColumnName=null!==(e=this.colorColumnName)&&void 0!==e?e:null,this.root.appendChild(s.divH([r,s.divV([s.divH([this._titleHost,this._selsectIcon],{style:{alignSelf:"center",lineHeight:"normal",width:"100%"}}),n.root,i],{style:{flexGrow:"1"}})])),n.root.style.width="100%",setTimeout((()=>{n.props.filter=this.scFilterQuery,n.invalidateCanvas()}),100)}),this.renderDebounceTime)}onPropertyChanged(t){super.onPropertyChanged(t),(null==t?void 0:t.name)!==`color${h.To}`&&(this._scViewer=null),this.render()}}O.clusterSizeColName="~cluster.size",O.maxActivityInClusterColName="~max.activity.for.cluster",O.maxConnectivityInClusterColName="~max.connectivity.for.cluster",O.synSelectionColName="Syn 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i=0;i<this._workerCount;i++)u[i]=new Promise(((r,o)=>{const s=Math.floor(i*h),l=i===this._workerCount-1?c:Math.floor((i+1)*h);this._workers[i].postMessage({startIdx:s,endIdx:l,activityArray:t,monomerInfoArray:e,settings:n,currentTargetIdx:a}),this._workers[i].onmessage=({data:{pos:t,seq1Idxs:e,seq2Idxs:n,error:s}})=>{var a;s?(null===(a=this._workers[i])||void 0===a||a.terminate(),o(s)):(this._workers[i].terminate(),r({pos:t,seq1Idxs:e,seq2Idxs:n}))}}));const d=yield Promise.all(u),f=new Map;e.forEach(((t,e)=>{f.set(t.name,e)})),d.filter(Boolean).forEach((t=>{for(let n=0;n<t.pos.length;n++){const i=f.get(t.pos[n]),r=e[i].rawData[t.seq1Idxs[n]],o=e[i].cat[r],a=e[i].rawData[t.seq2Idxs[n]],l=e[i].cat[a];s.has(o)||s.set(o,new Map),s.has(l)||s.set(l,new Map);const u=s.get(o),c=s.get(l);u.has(t.pos[n])||u.set(t.pos[n],new Map),c.has(t.pos[n])||c.set(t.pos[n],new Map);const h=u.get(t.pos[n]),d=c.get(t.pos[n]);h.has(t.seq1Idxs[n])||h.set(t.seq1Idxs[n],[]),d.has(t.seq2Idxs[n])||d.set(t.seq2Idxs[n],[]);const p=h.get(t.seq1Idxs[n]),m=d.get(t.seq2Idxs[n]);p.push(t.seq2Idxs[n]),m.push(t.seq1Idxs[n])}}))}catch(t){this.terminate(),console.error(t)}return s},new((r=void 0)||(r=Promise))((function(t,e){function s(t){try{l(o.next(t))}catch(t){e(t)}}function a(t){try{l(o.throw(t))}catch(t){e(t)}}function l(e){var n;e.done?t(e.value):(n=e.value,n instanceof r?n:new r((function(t){t(n)}))).then(s,a)}l((o=o.apply(n,i||[])).next())}));var n,i,r,o}terminate(){var t;null===(t=this._workers)||void 0===t||t.forEach((t=>{try{null==t||t.terminate()}catch(t){console.error(t)}}))}}var s=n(5480),a=n(8774),l=n(5070),u=function(t,e,n,i){return new(n||(n=Promise))((function(r,o){function s(t){try{l(i.next(t))}catch(t){o(t)}}function a(t){try{l(i.throw(t))}catch(t){o(t)}}function l(t){var e;t.done?r(t.value):(e=t.value,e instanceof n?e:new n((function(t){t(e)}))).then(s,a)}l((i=i.apply(t,e||[])).next())}))};function c(t,e){return u(this,arguments,void 0,(function*(t,e,n={}){var i,s;if(0===e.length)throw new Error(`PepAlgorithmError: Couldn't find any column of semType '${r.uF.MONOMER}'`);null!==(i=n.minActivityDelta)&&void 0!==i||(n.minActivityDelta=0),null!==(s=n.maxMutations)&&void 0!==s||(n.maxMutations=1);const a=new o,l=yield a.calc(t,e,n);return a.terminate(),l}))}function h(t,e){const n=new Map;let i=999999,r=-999999,o=2,s=2;for(const u of t.keys()){const c=new Map;n.set(u,c);const h=t.get(u);for(const t of h.keys()){const n=h.get(t),u=new a.A(e.length,!1);if(0===n.size)continue;for(const t of n.keys())u.setFast(t,!0),n.get(t).forEach((t=>u.setFast(t,!0)));const d=(0,l.GT)(e,u);i=Math.min(i,d.meanDifference),r=Math.max(r,d.meanDifference),o=Math.min(o,d.count),s=Math.max(s,d.count),c.set(t,d)}}return{stats:n,minDiff:i,maxDiff:r,minCount:o,maxCount:s}}function d(t,e,n,r={}){var o,s,u,c,h,d;null!==(o=r.isFiltered)&&void 0!==o||(r.isFiltered=!1);const p={general:{}};let m=t.getRawData(),g=t.length;if(r.isFiltered){g=e.trueCount;const t=new Float64Array(g),o=e.getSelectedIndexes();for(let e=0;e<g;++e)t[e]=m[o[e]];m=t,n=i.DataFrame.fromColumns(n).clone(e).columns.toList(),r.target&&(r.target.col=r.target.col.clone(e)),r.aggValue&&(r.aggValue.col=r.aggValue.col.clone(e))}null!==(s=r.columns)&&void 0!==s||(r.columns=n.map((t=>t.name)));const v=null===(c=null===(u=r.target)||void 0===u?void 0:u.col)||void 0===c?void 0:c.getRawData(),y=null===(h=r.target)||void 0===h?void 0:h.col.categories,C=(null===(d=r.target)||void 0===d?void 0:d.cat)?null==y?void 0:y.indexOf(r.target.cat):-1;for(const t of n){if(!r.columns.includes(t.name))continue;const e=t.getRawData(),n=t.categories,i={general:{}};for(let t=0;t<n.length;++t){const o=n[t];if(""===o)continue;const s=new Array(g).fill(!1);for(let n=0;n<g;++n)e[n]!==t||v&&-1!==C&&v[n]!==C||(s[n]=!0);const u=a.A.fromValues(s);if(u.allFalse)continue;const c=(0,l.GT)(m,u,r.aggValue);i[o]=c,f(i.general,c)}p[t.name]=i,f(p.general,null,i.general)}return p}function f(t,e=null,n=null){var i,r,o,s,a,l,u,c,h,d,f,p,m,g,v,y,C;if(null===e&&null===n)throw new Error("MonomerPositionStatsError: either stats or summaryStats must be present");const w=null!==(i=null==e?void 0:e.count)&&void 0!==i?i:n.maxCount;null!==(r=t.maxCount)&&void 0!==r||(t.maxCount=w),t.maxCount<w&&(t.maxCount=w);const b=null!==(o=null==e?void 0:e.count)&&void 0!==o?o:n.minCount;null!==(s=t.minCount)&&void 0!==s||(t.minCount=b),t.minCount>b&&(t.minCount=b);const A=null!==(a=null==e?void 0:e.meanDifference)&&void 0!==a?a:n.maxMeanDifference;null!==(l=t.maxMeanDifference)&&void 0!==l||(t.maxMeanDifference=A),t.maxMeanDifference<A&&(t.maxMeanDifference=A);const E=null!==(u=null==e?void 0:e.meanDifference)&&void 0!==u?u:n.minMeanDifference;if(null!==(c=t.minMeanDifference)&&void 0!==c||(t.minMeanDifference=E),t.minMeanDifference>E&&(t.minMeanDifference=E),!isNaN(null!==(h=null==e?void 0:e.pValue)&&void 0!==h?h:NaN)){const i=null!==(d=null==e?void 0:e.pValue)&&void 0!==d?d:n.maxPValue;null!==(f=t.maxPValue)&&void 0!==f||(t.maxPValue=i),t.maxPValue<i&&(t.maxPValue=i);const r=null!==(p=null==e?void 0:e.pValue)&&void 0!==p?p:n.minPValue;null!==(m=t.minPValue)&&void 0!==m||(t.minPValue=r),t.minPValue>r&&(t.minPValue=r)}const S=null!==(g=null==e?void 0:e.ratio)&&void 0!==g?g:n.maxRatio;null!==(v=t.maxRatio)&&void 0!==v||(t.maxRatio=S),t.maxRatio<S&&(t.maxRatio=S);const T=null!==(y=null==e?void 0:e.ratio)&&void 0!==y?y:n.minRatio;null!==(C=t.minRatio)&&void 0!==C||(t.minRatio=T),t.minRatio>T&&(t.minRatio=T)}function p(t,e,n,i){const r=t.rowCount,o=t.getCol(e),u=o.getRawData(),c=o.categories,h=Array.from({length:c.length},(()=>new a.A(r,!1)));for(let t=0;t<r;++t)h[u[t]].setTrue(t);const d=n.map((t=>a.A.fromUint32Array(r,t.getRawData()))),f=n.map((t=>t.name)),p=i.getRawData(),m={},g={};for(const t of Object.values(s.W)){const e=t===s.W.ORIGINAL?h:d,n=t===s.W.ORIGINAL?c:f,r=t===s.W.ORIGINAL?m:g;for(let t=0;t<e.length;++t){const o=e[t];r[n[t]]=o.allTrue||o.allFalse?{count:o.length,meanDifference:0,ratio:1,pValue:null,mask:o,mean:i.stats.avg}:(0,l.GT)(p,o)}}const v={};return v[s.W.ORIGINAL]=m,v[s.W.CUSTOM]=g,v}},2935:(t,e,n)=>{"use strict";n.d(e,{X5:()=>m,rW:()=>y,k8:()=>C,Yd:()=>v,rI:()=>g,FZ:()=>w});var i,r,o,s=n(7389),a=n(6082),l=n(4139),u=n(2003),c=n(3657),h=n(1858),d=n(912),f=n(5480),p=n(3541);function m(t,e){t.strokeStyle=a.Color.toHtml(a.Color.selectedRows),t.lineWidth=3,t.strokeRect(e.x+1,e.y+1,e.width-1,e.height-1)}function g(t,e,n){t.semType=l.uF.MONOMER,t.setTag(a.TAGS.CELL_RENDERER,l.uF.MONOMER),t.setTag(l.gp.ALPHABET,e),n&&t.setTag(r.applyToBackground,"true")}function v(t,e,n,i,r){var o,s,l,u,c,h,d;const f=r.width/2,g=Math.ceil(r.x+1+f),v=Math.ceil(r.y+1+r.height/2),y=.9*f/2;if(i instanceof p.UJ){const r=i.monomerPositionStats[n],o=r[e].pValue,s=r[e].meanDifference,l=1-r.general.maxPValue,u=1-r.general.minPValue,c=Math.min(l,u),h=l-c,d=u-c,p=Math.max(h,d),m=null===o?0:1-o-c,C=s>=0?m:-m,w=a.Color.toHtml(null===o?a.Color.lightLightGray:a.Color.scaleColor(C,-p,p,255)),b=Math.max(Math.abs(i.monomerPositionStats.general.minMeanDifference),i.monomerPositionStats.general.maxMeanDifference),A=Math.abs(s)/b,E=Math.floor(y*A);t.beginPath(),t.fillStyle=w,t.arc(g-f/2,v,E<3||null===o?3:E,0,2*Math.PI,!0),t.closePath(),t.fill()}else if(i instanceof p.J&&i.mutationCliffs&&i.cliffStats){const r=i.cliffStats.maxCount,u=i.cliffStats.minDiff,c=i.cliffStats.maxDiff,h=null===(l=null===(s=null===(o=i.cliffStats)||void 0===o?void 0:o.stats)||void 0===s?void 0:s.get(e))||void 0===l?void 0:l.get(n);if(h){const e=h.count,n=h.meanDifference,i=Math.floor(Math.abs(e/Math.max(r,2))*y),o=Math.max(Math.abs(u),Math.abs(c)),s=a.Color.toHtml(null===n?a.Color.lightLightGray:a.Color.scaleColor(n,-o,o,255));t.beginPath(),t.fillStyle=s,t.arc(g-f/2,v,i<3||0==e?3:i,0,2*Math.PI,!0),t.closePath(),t.fill()}}t.textBaseline="middle",t.textAlign="end",t.fillStyle="#606060",t.font="13px Roboto, Roboto Local, sans-serif",t.shadowBlur=5,t.shadowColor=a.Color.toHtml(a.Color.white);const C=new Set,w=null!==(d=null===(h=null===(c=null===(u=i.mutationCliffs)||void 0===u?void 0:u.get(e))||void 0===c?void 0:c.get(n))||void 0===h?void 0:h.entries())&&void 0!==d?d:null;if(null!==w)for(const[t,e]of w){C.add(t);for(const t of e)C.add(t)}0!==C.size&&t.fillText(C.size.toString(),g+f-5,v,f-5);const b=i.mutationCliffsSelection[n];b&&b.includes(e)&&m(t,r)}function y(t,e,n,i,r,o,s){s=a.Color.fromHtml(a.Color.toHtml(function(t,e){return(16777215&t|255<<24)>>>0}(s)));let l=r.toFixed(2);l.endsWith(".00")&&(l=r.toFixed(0)),l.endsWith("0")&&l.includes(".")&&(l=r.toFixed(1));const u=Math.min(13,Math.floor(o.width/40/l.length*6*13));t.fillStyle=a.Color.toHtml(s),t.fillRect(o.x,o.y,o.width,o.height),t.font=`${u}px Roboto, Roboto Local, sans-serif`,t.textAlign="center",t.textBaseline="middle",t.fillStyle=a.Color.toHtml(a.Color.getContrastColor(s)),t.fillText(l,o.x+o.width/2,o.y+o.height/2,o.width);const c=i[n];c&&c.includes(e)&&m(t,o)}function C(t,e,n,i){t.font="13px Roboto, Roboto Local, sans-serif",t.textAlign="center",t.textBaseline="middle",t.fillStyle="#000",t.fillText(e.toString(),i.x+i.width/2,i.y+i.height/2,i.width),(n[f.W.CUSTOM].includes(e)||n[f.W.ORIGINAL].includes(e))&&m(t,i)}function w(t,e,n,i,r,o={x:0,y:0,mpStats:{},monomerPosition:{}}){var f;if(null!==(f=r.isSelectionTable)&&void 0!==f||(r.isSelectionTable=!1),0==Object.keys(o.mpStats).length&&(o.mpStats=e),r.isSelectionTable&&(!r.webLogoBounds||!r.cachedWebLogoTooltip))throw new Error("Peptides: Cannot set WebLogo renderer for selection table without `headerSelectedMonomers`, `webLogoBounds` and `cachedWebLogoTooltip` options.");const p=t.dataFrame;t.setOptions({colHeaderHeight:130});t.onCellRender.subscribe((t=>(t=>{var o;const s=t.g,h=t.bounds,d=t.cell.tableColumn;s.save();try{if(s.beginPath(),s.rect(h.x,h.y,h.width,h.height),s.clip(),t.cell.isColHeader&&(null==d?void 0:d.semType)===l.uF.MONOMER){let f;if(p.filter.anyFalse){const t=null!==(o=p.temp[l.gp.M_P_STATS_CACHE])&&void 0!==o?o:{},e=null==t?void 0:t[d.name],r=p.filter.getBuffer();if(t&&e&&e.filter.length===r.length&&e.filter.every(((t,e)=>t===r[e])))f=e.stats[d.name];else{const e=(0,c.Ej)(i,p.filter,n,{isFiltered:!0,columns:[d.name]});f=e[d.name],t[d.name]={filter:p.filter.getBuffer(),stats:e,selection:p.selection.getBuffer()}}p.temp[l.gp.M_P_STATS_CACHE]=t}else f=r.isSelectionTable?(0,c.Ej)(i,p.filter,n,{isFiltered:!0,columns:[d.name]})[d.name]:e[d.name];if(!f)return;const m=Object.keys(f).sort(((t,e)=>""===t||"-"===t?1:""===e||"-"===e?-1:0)).filter((t=>"general"!==t));r.webLogoBounds()[d.name]=function(t,e,n,i,r,o,s,l={},c={}){var h,d,f,p,m,g,v,y,C,w;const b=window.devicePixelRatio;null!==(h=c.symbolStyle)&&void 0!==h||(c.symbolStyle="16px Roboto, Roboto Local, sans-serif"),null!==(d=c.upperLetterHeight)&&void 0!==d||(c.upperLetterHeight=12.2),null!==(f=c.upperLetterAscent)&&void 0!==f||(c.upperLetterAscent=.25),null!==(p=c.marginVertical)&&void 0!==p||(c.marginVertical=1),null!==(m=c.marginHorizontal)&&void 0!==m||(c.marginHorizontal=1),null!==(g=c.selectionWidth)&&void 0!==g||(c.selectionWidth=2),null!==(v=c.textHeight)&&void 0!==v||(c.textHeight=13),null!==(y=c.headerStyle)&&void 0!==y||(c.headerStyle=`bold ${c.textHeight*b}px Roboto, Roboto Local, sans-serif`);const A=(r.length-1)*c.upperLetterAscent;let E=(e.y+c.marginVertical)*b;const S=(e.height-2*c.marginVertical-A-1.25*c.textHeight)*b,T=(e.x+c.marginHorizontal)*b,x=Math.max(c.selectionWidth*b,.05*e.width*b),_=2*c.marginHorizontal+c.selectionWidth,N=(e.width-(_+c.marginHorizontal))*b,M=(e.x+_)*b,O={};for(const e of r){const i=S*(n[e].count/o),r=S*((null!==(C=l[e])&&void 0!==C?C:0)/o);if(O[e]=new a.Rect(M/b,E/b,N/b,i/b),t.resetTransform(),"-"!==e&&""!==e){const n=(0,u.zS)(e,5),o=t.measureText(n);r>0&&(t.lineWidth=x,t.line(T,E,T,E+r,a.Color.rowSelection)),t.fillStyle=null!==(w=s.get(e))&&void 0!==w?w:s.get("other"),t.textAlign="left",t.textBaseline="top",t.font=c.symbolStyle;const l=N/o.width,h=i/c.upperLetterHeight;t.setTransform(l,0,0,h,M,E),t.fillText(n,0,0,o.width)}E+=i+c.upperLetterAscent*b}return t.resetTransform(),t.fillStyle=a.Color.toHtml(a.Color.black),t.textAlign="center",t.textBaseline="top",t.font=c.headerStyle,t.fillText(i,(e.x+e.width/2)*b,(e.y+e.height-c.textHeight)*b),O}(s,h,f,d.name,m,p.filter.trueCount,r.colorPalette(),r.headerSelectedMonomers?r.headerSelectedMonomers()[d.name]:{}),t.preventDefault()}}catch(t){console.warn(`PeptidesHeaderLogoError: couldn't render WebLogo for column \`${d.name}\`. 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class{constructor(){this.color="rgb(100,100,100)",this.pivot=0,this.left=!1,this.transparencyRate=1,this.separator="",this.last=!1,this.drawStyle=o.classic,this.maxWord=[],this.wordIdx=0,this.gridCell=null,this.referenceSequence=null,this.maxLengthOfMonomer=null,this.monomerTextSizeMap={},this.logger=void 0}},a.GridCellRenderer},4139:(t,e,n)=>{"use strict";n.d(e,{$2:()=>i,To:()=>l,V5:()=>d,YX:()=>h,gp:()=>o,i6:()=>r,rg:()=>u,uF:()=>s,wf:()=>c,zW:()=>f});var i,r,o,s,a=n(6082);!function(t){t.SPLIT_COL="~split",t.ACTIVITY="Activity",t.ACTIVITY_SCALED="Scaled activity",t.MONOMER="AAR",t.POSITION="Pos",t.P_VALUE="pValue",t.MEAN_DIFFERENCE="Mean difference",t.COUNT="Count",t.RATIO="Ratio",t.MEAN="Mean"}(i||(i={})),function(t){t.MEMBERS="Members",t.WEB_LOGO="WebLogo",t.DISTRIBUTION="Distribution",t.MEAN_DIFFERENCE="Mean difference",t.P_VALUE="P-Value",t.RATIO="Ratio",t.CLUSTER="Cluster"}(r||(r={})),function(t){t.MONOMER="monomer",t.POSITION="pos",t.SEPARATOR="separator",t.SELECTION="selection",t.MUTATION_CLIFFS_SELECTION="mutationCliffsSelection",t.ALPHABET="alphabet",t.FILTER="filter",t.INVARIANT_MAP_SELECTION="invariantMapSelection",t.SAR_MODE="sarMode",t.CLUSTER_SELECTION="clusterSelection",t.VISIBLE="visible",t.SETTINGS="settings",t.CUSTOM_CLUSTER="customCluster",t.MONOMER_POSITION_MODE="monomerPositionMode",t.MULTIPLE_VIEWS="isMultipleViews",t.IDENTITY_TEMPLATE="Identity template",t.SIMILARITY_TEMPLATE="Similarity template",t.ANALYSIS_COL="isAnalysisCol",t.POSITION_COL="isPositionCol",t.M_P_STATS_CACHE=".MPStatsCache",t.INVARIANT_MAP_COLOR_CACHE=".InvariantMapColorCache",t.INVARIANT_MAP_COLOR_MAX_CACHE=".InvariantMapColorMaxCache",t.INVARIANT_MAP_COLOR_MIN_CACHE=".InvariantMapColorMinCache"}(o||(o={})),function(t){t.MONOMER="Monomer",t.MACROMOLECULE_DIFFERENCE="MacromoleculeDifference"}(s||(s={}));const l="ColumnName";var u,c,h;!function(t){t.NONE="none",t.LG="lg",t.MINUS_LG="-lg"}(u||(u={})),function(t){t.HIGH="High",t.LOW="Low"}(c||(c={})),function(t){t.LST="lst-",t.MP="mp-",t.MPR="mpr-",t.WL="wl-"}(h||(h={}));const d=Object.values(a.AGG).filter((t=>![a.AGG.FIRST,a.AGG.KEY,a.AGG.PIVOT,a.AGG.SELECTED_ROWS_COUNT].includes(t))),f={[a.AGG.TOTAL_COUNT]:"totalCount",[a.AGG.VALUE_COUNT]:"valueCount",[a.AGG.UNIQUE_COUNT]:"uniqueCount",[a.AGG.MISSING_VALUE_COUNT]:"missingValueCount",[a.AGG.MIN]:"min",[a.AGG.MAX]:"max",[a.AGG.SUM]:"sum",[a.AGG.MED]:"med",[a.AGG.AVG]:"avg",[a.AGG.STDEV]:"stdev",[a.AGG.VARIANCE]:"variance",[a.AGG.SKEW]:"skew",[a.AGG.KURT]:"kurt",[a.AGG.Q1]:"q1",[a.AGG.Q2]:"q2",[a.AGG.Q3]:"q3"}},8608:(t,e,n)=>{"use strict";n.d(e,{$s:()=>T,AN:()=>i,AY:()=>h,B2:()=>N,BE:()=>y,CD:()=>w,F2:()=>m,FZ:()=>g,KT:()=>S,Y1:()=>d,ZR:()=>E,dl:()=>A,eY:()=>p,qI:()=>x,qx:()=>f,sg:()=>M,vW:()=>b,vY:()=>C,zm:()=>_,zz:()=>v});var i,r=n(7389),o=n(6082),s=n(4139),a=n(8774),l=n(144),u=n.n(l),c=function(t,e,n,i){return new(n||(n=Promise))((function(r,o){function s(t){try{l(i.next(t))}catch(t){o(t)}}function a(t){try{l(i.throw(t))}catch(t){o(t)}}function l(t){var e;t.done?r(t.value):(e=t.value,e instanceof n?e:new n((function(t){t(e)}))).then(s,a)}l((i=i.apply(t,e||[])).next())}))};function h(t){var e;return null!==(e=t.getTag(s.gp.SEPARATOR))&&void 0!==e?e:""}function d(t,e=s.rg.NONE){let n=t=>t;switch(e){case s.rg.NONE:break;case s.rg.LG:n=t=>Math.log10(t);break;case s.rg.MINUS_LG:n=t=>-Math.log10(t);break;default:throw new Error(`ScalingError: method \`${e}\` is not available.`)}const i=t.getRawData(),r=o.Column.float(s.$2.ACTIVITY,t.length).init((t=>{const e=i[t];return e===o.FLOAT_NULL||e===o.INT_NULL?e:n(e)}));return r.setTag(s.gp.ANALYSIS_COL,"true"),r.setTag(o.TAGS.FORMULA,e),r}function f(t){var e,n,i,r;const o=t.columns.bySemTypeAll(s.uF.MONOMER),a={},l=t.filter.clone().and(t.selection).getSelectedIndexes();for(const t of l)for(const s of o){const o=s.get(t);o&&(null!==(e=a[i=s.name])&&void 0!==e||(a[i]={}),null!==(n=(r=a[s.name])[o])&&void 0!==n||(r[o]=0),a[s.name][o]+=1)}return a}function p(t){return{name:t.name,cat:t.categories,rawData:t.getRawData()}}function m(t,e,n={}){var a;const l=t.dataFrame.getCol(s.$2.SPLIT_COL),u=[],c=l.categories,h=l.getRawData();for(let t=0;t<c.length;++t){if(!Object.values(i).includes(c[t]))continue;const e=o.Color.toHtml(l.meta.colors.getColor(h.indexOf(t))),s=r.label(null!==(a=n[c[t]])&&void 0!==a?a:c[t],{style:{color:e}});u.push(s)}const d=r.divV([r.divV(u),t.root,r.tableFromMap(e)]);return t.root.style.maxHeight="75px",d}function g(t,e,n){var r,a;const l=null!==(r=null==n?void 0:n.clone().xor(e).anyTrue)&&void 0!==r&&r,u=t.length,c=t.getRawData(),h=new Float32Array(u+e.trueCount+(l&&null!==(a=null==n?void 0:n.trueCount)&&void 0!==a?a:0)),d=new Array(h.length);for(let t=0,r=0,o=0;t<u;++t){const s=e.get(t);h[t]=c[t],d[t]=s?i.SELECTION:i.ALL,s&&(h[u+r]=c[t],d[u+r]=i.ALL,++r),l&&(null==n?void 0:n.get(t))&&(h[u+e.trueCount+o]=c[t],d[u+e.trueCount+o]=i.PEPTIDES_SELECTION,++o)}const f=o.Column.fromStrings(s.$2.SPLIT_COL,d),p=[i.ALL,i.SELECTION];return l&&p.push(i.PEPTIDES_SELECTION),f.setCategoryOrder(p),f.meta.colors.setCategorical(),o.DataFrame.fromColumns([o.Column.fromFloat32Array(s.$2.ACTIVITY,h),f])}function v(t){const e=r.iconFA("expand-alt",(()=>{const e=t.dataFrame.plot.grid();C(e,!1),e.root.style.height="100%";const n=r.dialog(t.dataFrame.name);n.add(e.root),n.showModal(!0),e.invalidate()}));t.root.appendChild(e),e.style.position="absolute",e.style.right="0px",e.style.top="0px",e.style.visibility="hidden",t.root.addEventListener("mouseenter",(t=>{e.style.visibility="visible"})),t.root.addEventListener("mouseleave",(t=>{e.style.visibility="hidden"}))}function y(t,e,n,i){const o=r.iconFA("expand-alt",(()=>{const e=i(),n=r.dialog(t);n.add(e),n.showModal(!0)}),"Expand to full screen");o.style.marginLeft="auto",o.style.marginRight="15px",n.addEventListener("mouseenter",(()=>{o.style.visibility="visible"})),n.addEventListener("mouseleave",(()=>{o.style.visibility="hidden"})),e.appendChild(o)}function C(t,e=!0){t.props.allowEdit=!1,t.props.showReadOnlyNotifications=!1,t.props.allowRowSelection=!1,t.props.allowBlockSelection=!1,t.props.allowColSelection=!1,t.props.showRowHeader=!1,t.props.showCurrentRowIndicator=!1,t.root.style.width="100%",t.root.style.maxWidth="100%",e&&t.autoSize(1e3,175,0,0,!0)}function w(t){for(const e of Object.values(t))if(0!==e.length)return!1;return!0}function b(t,e,n){const i=t[e.positionOrClusterType],r=i.indexOf(e.monomerOrCluster);if(n.shiftPressed&&n.ctrlPressed)-1!==r&&i.splice(r,1);else if(n.ctrlPressed)-1===r?i.push(e.monomerOrCluster):i.splice(r,1);else if(n.shiftPressed)-1===r&&i.push(e.monomerOrCluster);else{const n=Object.keys(t);t={};for(const i of n)t[i]=[],i===e.positionOrClusterType&&t[i].push(e.monomerOrCluster)}return t}function A(t,e,n){if(!e)return;const i=new a.A(e.rowCount);if(t.positionOrClusterType===s.$2.MONOMER){const e=Object.values(n);for(const n of e){const e=n[t.monomerOrCluster];void 0!==e&&i.or(e.mask)}}else{const 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r.concat(o).filter((e=>t.columns.contains(e[0])&&t.col(e[0]).matches("numerical")))}function N(t,e=2){return t.columns.bySemTypeAll(o.SEMTYPE.MACROMOLECULE).length>0&&u()(t.columns.numerical).toArray().length>0&&t.rowCount>=e}function M(t,e=500){let n;return(...i)=>c(this,void 0,void 0,(function*(){return new Promise((r=>{clearTimeout(n),n=setTimeout((()=>r(t(...i))),e)}))}))}!function(t){t.SELECTION="Selection",t.ALL="All",t.PEPTIDES_SELECTION="Peptides selection"}(i||(i={}))},5070:(t,e,n)=>{"use strict";n.d(e,{hX:()=>s,I_:()=>u,m2:()=>c,lh:()=>l,GT:()=>a,J1:()=>h});var i=n(6082),r=n(6572),o=n(4139);const s=(t,e)=>`${t}(${e})`;function a(t,e,n){var o;if(t.length!==e.length&&t.some(((t,n)=>n>=e.length&&0!==t)))throw new Error("PeptidesError: Data and bit array have different lengths");const s=new Float32Array(e.trueCount()),a=new Float32Array(e.falseCount());let l;if(n)try{l=null===(o=i.DataFrame.fromColumns([n.col]).clone(i.BitSet.fromBytes(e.buffer.buffer,e.length)).col(n.col.name))||void 0===o?void 0:o.aggregate(n.type)}catch(t){console.error(t)}let u=0,c=0;for(let n=0;n<e.length;++n)e.getBit(n)?s[u++]=t[n]:a[c++]=t[n];const h=s.reduce(((t,e)=>t+e),0)/Math.max(s.length,1);if(s.length<2||a.length<2){const t=a.reduce(((t,e)=>t+e),0)/Math.max(a.length,1);return{count:s.length,pValue:null,mean:h,meanDifference:h-t,ratio:s.length/e.length,mask:e,aggValue:l}}const d=function(t,e,n=!1,i=!1){if(t.length<=1||e.length<=1)throw new Error(`StatisticsError: Wrong sample size; expected at least 2, got ${Math.min(t.length,e.length)})`);const o=r.mean(t),s=r.mean(e),a=r.variance(t),l=r.variance(e),u=t.length,c=e.length;let h,d,f;if(n){const t=a/u,e=l/c,n=(o-s)/Math.sqrt(t+e);d=r.normal.pdf(n,0,1),h=1-d,f=2*(d<h?d:h)}else if(i){const t=u+c-2,e=(a*(u-1)+l*(c-1))/t,n=Math.sqrt(u*c/(u+c))*(o-s)/e;h=1-r.studentt.cdf(n,t),d=r.studentt.cdf(n,t),f=2*(d<h?d:h)}else{const t=a/u,e=l/c,n=(o-s)/Math.sqrt(t+e),i=Math.pow(t+e,2)/(Math.pow(t,2)/(u-1)+Math.pow(e,2)/(c-1));d=r.studentt.cdf(n,i),h=1-d,f=2*(d<h?d:h)}return{"p-value":f,"Mean difference":o-s,"p-value more":h,"p-value less":d}}(s,a),f=d["Mean difference"];return{count:s.length,pValue:d[f>=0?"p-value more":"p-value less"],mean:h,meanDifference:f,ratio:s.length/e.length,mask:e,aggValue:l}}function l(t,e,n){const r=o.zW[e],s=i.Stats.fromColumn(t,n);if(!(r in s))throw new Error(`Aggregation type ${r} is not supported`);return s[r]}function u(t,e,n={}){var i,r;null!==(i=n.filterDf)&&void 0!==i||(n.filterDf=!1),null!==(r=n.fractionDigits)&&void 0!==r||(n.fractionDigits=3);const o=n.filterDf&&t.filter.anyFalse?t.clone(t.filter):t,a={};for(const[t,i]of e){const e=s(i,t),r=l(o.getCol(t),i,n.mask);a[e]=r.toFixed(n.fractionDigits)}return a}function c(t,e,n,i){var r;null!==(r=i.fractionDigits)&&void 0!==r||(i.fractionDigits=3);const o={};for(const[r,a]of n){const n=s(a,r),l=t.get(n,e);o[n]=l.toFixed(i.fractionDigits)}return o}function h(t,e,n){var r;const o=t.col(e.substring(5,e.length-1));if(!o||!o.matches("categorical"))return"{}";null!=n||(n=i.BitSet.create(t.rowCount,(()=>!0)));const s=o.getRawData(),a=new Map;for(let t=-1;-1!==(t=n.findNext(t,!0));)a.set(s[t],(null!==(r=a.get(s[t]))&&void 0!==r?r:0)+1);const l={};for(const[t,e]of a)l[o.categories[t]]=e;return JSON.stringify(l)}},912:(t,e,n)=>{"use strict";n.d(e,{DK:()=>d,YE:()=>f,cr:()=>h});var i=n(7389),r=n(4328),o=n(6082),s=n(4139),a=n(7654),l=n(8608),u=n(3273),c=n(5070);function h(t,e,n){const o=[],s=t.toLowerCase(),a=(0,u.getMonomerWorksInstance)(),l=null==a?void 0:a.getCappedRotatedMonomer("PEPTIDE",t);if(l){o.push(i.div(s));const t={autoCrop:!0,autoCropMargin:0,suppressChiralText:!0};o.push(r.chem.svgMol(l,void 0,void 0,t))}else{if(""===t)return!0;o.push(i.div(t))}return i.tooltip.show(i.divV(o),e,n),!0}function d(t,e,n,i){var r,o,a;return null!==(r=i.fromViewer)&&void 0!==r||(i.fromViewer=!1),null!==(o=i.isMutationCliffs)&&void 0!==o||(i.isMutationCliffs=!1),null!==(a=i.isMostPotentResidues)&&void 0!==a||(i.isMostPotentResidues=!1),i.monomerPosition.positionOrClusterType===s.$2.MONOMER?h(i.monomerPosition.monomerOrCluster,i.x,i.y):f(t,e,n,i),!0}function f(t,e,n,r){var s,u,h,d,f,p,m;if(null!==(s=r.fromViewer)&&void 0!==s||(r.fromViewer=!1),null!==(u=r.isMutationCliffs)&&void 0!==u||(r.isMutationCliffs=!1),null!==(h=r.isMostPotentResidues)&&void 0!==h||(r.isMostPotentResidues=!1),r.cliffStats&&r.isMutationCliffs){const s=null===(p=null===(f=r.cliffStats)||void 0===f?void 0:f.get(r.monomerPosition.monomerOrCluster))||void 0===p?void 0:p.get(r.monomerPosition.positionOrClusterType);if(!s)return null;const u=o.BitSet.fromBytes(s.mask.buffer.buffer,e.length),h=(0,a.M1)((0,l.FZ)(e,u),!0),d=(0,a.QD)(s);r.fromViewer&&(d["Mean difference"]=`${d["Mean difference"]} (Color)`,d.Count&&(d.Count=`${d.Count} (Size)`));const g=null!==(m=r.aggrColValues)&&void 0!==m?m:(0,c.I_)(t,n,{mask:u}),v=Object.assign(Object.assign({},d),g),y=(0,l.F2)(h,v);return i.tooltip.show(y,r.x,r.y),y}{const s=r.mpStats[r.monomerPosition.positionOrClusterType][r.monomerPosition.monomerOrCluster];if(!(null==s?void 0:s.count))return null;const u=o.BitSet.fromBytes(s.mask.buffer.buffer,e.length),h=(0,a.M1)((0,l.FZ)(e,u),!0),f=(0,a.QD)(s);r.fromViewer&&(f["Mean difference"]=`${f["Mean difference"]}${r.isMostPotentResidues?" (size)":""}`,f["p-value"]&&(f["p-value"]=`${f["p-value"]}${r.isMostPotentResidues?" (color)":""}`));const p=null!==(d=r.aggrColValues)&&void 0!==d?d:(0,c.I_)(t,n,{mask:u}),m=Object.assign(Object.assign({},f),p),g=(0,l.F2)(h,m);return i.tooltip.show(g,r.x,r.y),g}}},115:(t,e,n)=>{"use strict";n.d(e,{GI:()=>a,Ku:()=>o,av:()=>s});var i=n(4572),r=n(4329);const o="WebGPU is not supported on this device";class s{constructor(){this.maxIterations=16,this.inflation=1.4,this.threshold=70,this.distanceF=i.Z.NEEDLEMANN_WUNSCH,this.gapOpen=1.5,this.gapExtend=.2,this.fingerprintType="Morgan",this.useWebGPU=!1,this.minClusterSize=5,this.webGPUDescription=o,this.webGPUDescriptionPromise=(0,r._)().then((t=>{t&&(this.webGPUDescription=t)}))}}class a{constructor(t){this.distanceF=i.Z.NEEDLEMANN_WUNSCH,this.gapOpen=1.5,this.gapExtend=.2,this.clusterEmbeddings=!0,this.epsilon=.01,this.minPts=4,this.fingerprintType="Morgan",this.clusterEmbeddings=!!t}}},5480:(t,e,n)=>{"use strict";n.d(e,{W:()=>A,s:()=>S});var i=n(7389),r=n(4328),o=n(6082),s=n(7233),a=n.n(s),l=n(9484),u=n(4139),c=n(2935),h=n(4326),d=n(5070),f=n(144),p=n.n(f),m=n(7654),g=n(8608),v=n(8774),y=n(3273),C=n(3657),w=n(3077);const b=(t,e)=>`${t}(${e})`;var A,E;!function(t){t.ORIGINAL="original",t.CUSTOM="custom"}(A||(A={})),function(t){t.GENERAL="General",t.STYLE="WebLogo",t.AGGREGATION="Aggregation"}(E||(E={}));class S extends o.JsViewer{constructor(){super(),this._titleHost=i.divText(l.q.LOGO_SUMMARY_TABLE,{id:"pep-viewer-title"}),this.bitsets=[],this.keyPress=!1,this.currentRowIndex=null,this._scaledActivityColumn=null,this._viewerGrid=null,this._clusterStats=null,this._clusterSelection=null,this._logoSummaryTable=null,this._positionColumns=null,this.sequenceColumnName=this.column("sequence",{category:E.GENERAL,nullable:!1}),this.clustersColumnName=this.column("clusters",{category:E.GENERAL,nullable:!1,columnTypeFilter:o.TYPE.CATEGORICAL}),this.activityColumnName=this.column("activity",{category:E.GENERAL,nullable:!1,columnTypeFilter:o.TYPE.NUMERICAL}),this.activityScaling=this.string("activityScaling",u.rg.NONE,{category:E.GENERAL,choices:Object.values(u.rg)}),this.webLogoMode=this.string("webLogoMode",h.fH.Entropy,{choices:[h.fH.full,h.fH.Entropy],category:E.STYLE}),this.membersRatioThreshold=this.float("membersRatioThreshold",.1,{min:0,max:1,category:E.STYLE}),this.columns=this.columnList("columns",[],{category:E.AGGREGATION}),this.aggregation=this.string("aggregation",o.AGG.AVG,{category:E.AGGREGATION,choices:u.V5})}get model(){return l.i.getInstance(this.dataFrame)}get viewerGrid(){var t;return null!==(t=this._viewerGrid)&&void 0!==t||(this._viewerGrid=this.createLogoSummaryTableGrid()),this._viewerGrid}get clusterStats(){var t;return null!==(t=this._clusterStats)&&void 0!==t||(this._clusterStats=(0,C.eW)(this.dataFrame,this.clustersColumnName,this.customClusters.toArray(),this.getScaledActivityColumn())),this._clusterStats}get clusterSelection(){var t;const e=this.dataFrame.getTag(u.gp.CLUSTER_SELECTION);return null!==(t=this._clusterSelection)&&void 0!==t||(this._clusterSelection=null===e?this.initClusterSelection({notify:!1}):JSON.parse(e)),this._clusterSelection}set clusterSelection(t){this._clusterSelection=t,this.dataFrame.setTag(u.gp.CLUSTER_SELECTION,JSON.stringify(t)),this.model.fireBitsetChanged(l.q.LOGO_SUMMARY_TABLE),this.model.analysisView.grid.invalidate()}get logoSummaryTable(){var t;return null!==(t=this._logoSummaryTable)&&void 0!==t||(this._logoSummaryTable=this.createLogoSummaryTable()),this._logoSummaryTable}set logoSummaryTable(t){this._logoSummaryTable=t}get positionColumns(){var t,e,n,i;if(null!=this._positionColumns)return this._positionColumns;const r=t=>{const e=this.model.findViewer(t);return this.sequenceColumnName===(null==e?void 0:e.sequenceColumnName)?e._positionColumns:null};return null!=this.model.positionColumns&&this.sequenceColumnName===(null===(t=this.model.settings)||void 0===t?void 0:t.sequenceColumnName)&&(this._positionColumns=this.model.positionColumns),null!==(e=this._positionColumns)&&void 0!==e||(this._positionColumns=null!==(i=null!==(n=r(l.q.SEQUENCE_VARIABILITY_MAP))&&void 0!==n?n:r(l.q.MOST_POTENT_RESIDUES))&&void 0!==i?i:(0,w.R)(this.dataFrame.getCol(this.sequenceColumnName)).columns.toList()),this._positionColumns}get isClusterSelectionEmpty(){return 0===this.clusterSelection[A.ORIGINAL].length+this.clusterSelection[A.CUSTOM].length}get customClusters(){const t={};return t[u.gp.CUSTOM_CLUSTER]="1",p()(this.dataFrame.columns.byTags(t))}getScaledActivityColumn(t=!1){var e,n,i;return(null===(e=this.model.settings)||void 0===e?void 0:e.activityColumnName)===this.activityColumnName&&(null===(n=this.model.settings)||void 0===n?void 0:n.activityScaling)===this.activityScaling&&(this._scaledActivityColumn=this.model.getScaledActivityColumn(t)),null!==(i=this._scaledActivityColumn)&&void 0!==i||(this._scaledActivityColumn=(0,g.Y1)(this.dataFrame.getCol(this.activityColumnName),this.activityScaling)),t?o.DataFrame.fromColumns([this._scaledActivityColumn]).clone(this.dataFrame.filter).getCol(this._scaledActivityColumn.name):this._scaledActivityColumn}getAggregationColumns(){return Object.fromEntries(this.columns.map((t=>[t,this.aggregation])).filter((([t,e])=>this.model.df.columns.contains(t)&&this.model.df.col(t).matches("numerical"))))}onTableAttached(){var t,e,n;if(super.onTableAttached(),(0,g.B2)(this.dataFrame))null===(t=this.getProperty(`sequence${u.To}`))||void 0===t||t.set(this,this.dataFrame.columns.bySemType(o.SEMTYPE.MACROMOLECULE).name),null===(e=this.getProperty(`activity${u.To}`))||void 0===e||e.set(this,p()(this.dataFrame.columns.numerical).next().value.name),null===(n=this.getProperty(`clusters${u.To}`))||void 0===n||n.set(this,p()(this.dataFrame.columns.categorical).next().value.name);else{const t="PeptidesError: dataframe is missing Macromolecule or numeric columns";r.log.error(t),r.shell.warning(t)}this.render()}detach(){this.subs.forEach((t=>t.unsubscribe()))}render(){if(a()(this.root).empty(),null==this.clustersColumnName||null==this.sequenceColumnName||null==this.activityColumnName)return void this.root.appendChild(i.divText("Please, select a sequence, cluster and activity columns in the viewer properties"));if(!this.logoSummaryTable.filter.anyTrue){const t=i.divText("No clusters to satisfy the threshold. Please, lower the threshold in viewer proeperties to include clusters");return void this.root.appendChild(i.divV([this._titleHost,t]))}const t=i.iconFA("expand-alt",(()=>{const t=i.dialog("Logo Summary Table");t.add(this.viewerGrid.root),t.onCancel((()=>this.render())),t.showModal(!0),this.viewerGrid.invalidate()}),"Show Logo Summary Table in full screen");a()(t).addClass("pep-help-icon"),this.viewerGrid.root.style.width="auto",this.root.appendChild(i.divV([i.divH([this._titleHost,t],{style:{alignSelf:"center",lineHeight:"normal"}}),this.viewerGrid.root])),this.viewerGrid.invalidate()}onPropertyChanged(t){super.onPropertyChanged(t);let e=!1;switch(t.name){case"membersRatioThreshold":this.logoSummaryTable.filter.anyTrue||(e=!0),this.updateFilter();break;case`sequence${u.To}`:this._viewerGrid=null,this._logoSummaryTable=null,e=!0;break;case`clusters${u.To}`:this._clusterStats=null,this._clusterSelection=null,this._viewerGrid=null,this._logoSummaryTable=null,e=!0;break;case`activity${u.To}`:case"activityScaling":this._scaledActivityColumn=null,this._viewerGrid=null,this._clusterStats=null,this._logoSummaryTable=null,e=!0;break;case"columns":case"aggregation":this._viewerGrid=null,this._logoSummaryTable=null,e=!0;break;case"webLogoMode":this.viewerGrid.invalidate()}e&&this.render()}initClusterSelection(t={}){var e;null!==(e=t.notify)&&void 0!==e||(t.notify=!0);const n={};return n[A.ORIGINAL]=[],n[A.CUSTOM]=[],t.notify?this.clusterSelection=n:this._clusterSelection=n,this.clusterSelection}getTotalViewerAggColumns(){var t,e;const n=this.getAggregationColumns();return(0,g.zm)(this.model.df,this.columns,n,null===(e=null===(t=this.model)||void 0===t?void 0:t.settings)||void 0===e?void 0:e.columns)}getStringAggregatedColumns(){return this.columns.filter((t=>this.model.df.columns.contains(t)&&this.model.df.col(t).matches("categorical"))).map((t=>`dist(${t})`))}createLogoSummaryTable(){var t,e,n;const i=this.clustersColumnName,r=this.dataFrame.filter.anyFalse,s=r?this.dataFrame.clone(this.dataFrame.filter):this.dataFrame,a=s.columns,l=s.rowCount,c=this.getScaledActivityColumn(r).getRawData(),h=s.getCol(i),f=h.getRawData(),m=h.categories,g={};g[u.gp.CUSTOM_CLUSTER]="1";const y=p()(a.byTags(g)).filter((t=>t.max>0)).toArray(),C=o.DataFrame.create(y.length),w=C.columns,E=w.addNewString(u.i6.CLUSTER),S=w.addNewInt(u.i6.MEMBERS).getRawData(),T=w.addNewString(u.i6.WEB_LOGO),x=w.addNewString(u.i6.DISTRIBUTION),_=w.addNewFloat(u.i6.MEAN_DIFFERENCE).getRawData(),N=w.addNewFloat(u.i6.P_VALUE).getRawData(),M=w.addNewFloat(u.i6.RATIO).getRawData();let O=s.groupBy([i]);const L=this.getTotalViewerAggColumns(),I=this.getStringAggregatedColumns(),R=I.map((t=>w.addNewString(t))),P=L.map((([t,e])=>b(e,t))),k=new Array(P.length+I.length),D=L.map((([t,e])=>[s.getCol(t),e]));for(let t=0;t<L.length;++t){const[e,n]=L[t];O=O.add(n,e,P[t]);const i=w.addNewFloat(P[t]);k[t]=i.getRawData()}const G=new Array(y.length);for(let e=0;e<y.length;++e){const n=y[e];E.set(e,n.name);const i=v.A.fromUint32Array(l,n.getRawData());if(i.allFalse)continue;const a=o.BitSet.fromBytes(i.buffer.buffer,l),u=r?(0,d.GT)(c,i):this.clusterStats[A.CUSTOM][n.name];S[e]=u.count,G[e]=a,_[e]=u.meanDifference,N[e]=null!==(t=u.pValue)&&void 0!==t?t:o.FLOAT_NULL,M[e]=u.ratio;for(let t=0;t<P.length;++t){const[n,i]=D[t];k[t][e]=(0,d.lh)(n,i,a)}for(let t=P.length;t<k.length;++t){const n=I[t-P.length];R[t-P.length].set(e,(0,d.J1)(s,n,a))}}T.setTag(o.TAGS.CELL_RENDERER,"html"),x.setTag(o.TAGS.CELL_RENDERER,"html");const U=O.aggregate(),V=U.rowCount,F=U.columns;let H=U.getCol(i);H.name=u.i6.CLUSTER,H.type!==o.COLUMN_TYPE.STRING&&(U.columns.replace(H,H.convertTo(o.COLUMN_TYPE.STRING)),H=U.getCol(H.name));const B=H.categories,q=F.addNewInt(u.i6.MEMBERS).getRawData(),Y=F.addNewString(u.i6.WEB_LOGO),$=F.addNewString(u.i6.DISTRIBUTION),j=F.addNewFloat(u.i6.MEAN_DIFFERENCE).getRawData(),W=F.addNewFloat(u.i6.P_VALUE).getRawData(),z=F.addNewFloat(u.i6.RATIO).getRawData(),K=I.map((t=>F.addNewString(t))),Q=new Array(V),X=Array.from({length:V},(()=>new v.A(l,!1)));for(let t=0;t<l;++t){const n=m[f[t]];null===(e=X[B.indexOf(n)])||void 0===e||e.setTrue(t)}for(let t=0;t<V;++t){const e=X[t];if(e.allFalse)continue;const i=o.BitSet.fromBytes(e.buffer.buffer,l),a=r?(0,d.GT)(c,e):this.clusterStats[A.ORIGINAL][B[t]];for(let e=0;e<I.length;++e){const n=I[e];K[e].set(t,(0,d.J1)(s,n,i))}q[t]=a.count,Q[t]=i,j[t]=a.meanDifference,W[t]=null!==(n=a.pValue)&&void 0!==n?n:o.FLOAT_NULL,z[t]=a.ratio}Y.setTag(o.TAGS.CELL_RENDERER,"html"),$.setTag(o.TAGS.CELL_RENDERER,"html");const J=U.append(C);return this.bitsets=Q.concat(G),I.forEach((t=>J.col(t).semType="lst-pie-chart")),J}createLogoSummaryTableGrid(){const t=this.dataFrame.filter.anyFalse,e=t?this.dataFrame.clone(this.dataFrame.filter):this.dataFrame,n=this.getTotalViewerAggColumns().map((([t,e])=>b(e,t))),s=this.logoSummaryTable.plot.grid();s.sort([u.i6.MEMBERS],[!1]),this.updateFilter(),s.col(u.i6.CLUSTER).visible=!0,s.columns.setOrder([u.i6.CLUSTER,u.i6.MEMBERS,u.i6.WEB_LOGO,...this.getStringAggregatedColumns(),u.i6.DISTRIBUTION,u.i6.MEAN_DIFFERENCE,u.i6.P_VALUE,u.i6.RATIO,...n]),s.columns.rowHeader.visible=!1,s.props.rowHeight=55;const d=new o.LruCache,f=new o.LruCache,p=this.positionColumns.length,m=s.columns.byName(u.i6.WEB_LOGO);m.cellType="html",m.width=350;const v=this.getScaledActivityColumn(t),C=e.getCol(this.sequenceColumnName);s.onCellRender.subscribe((t=>{return e=this,n=void 0,r=function*(){var e,n,i;const r=t.cell,s=r.tableRowIndex;if(!r.isTableCell||null==s||-1===s)return;const l=t.g,m=t.bounds;l.save(),l.beginPath(),l.rect(m.x,m.y,m.width,m.height),l.clip();try{const y=Math.max(r.bounds.height-2,0),w=this.bitsets[s];if((null===(e=r.tableColumn)||void 0===e?void 0:e.name)===u.i6.CLUSTER)c.k8(l,r.cell.value,this.clusterSelection,m),t.preventDefault();else if((null===(n=r.tableColumn)||void 0===n?void 0:n.name)===u.i6.WEB_LOGO){const e=Math.floor((r.bounds.width-2-4*(p-1))/p);let n=d.get(s);if(void 0!==n){const t=n.getProperties();for(const i of t)"positionHeight"===i.name&&i.get(n)!==this.webLogoMode?i.set(n,this.webLogoMode):"positionWidth"===i.name&&i.get(n)!==e?i.set(n,e):"minHeight"===i.name&&i.get(n)!==y&&i.set(n,y);a()(n.root).css("height",`${y}px`).children().first().css("overflow-y","hidden !important")}else{const t=this.createWebLogoDf(C,w);n=yield t.plot.fromType("WebLogo",{positionHeight:this.webLogoMode,horizontalAlignment:h.P4.LEFT,maxHeight:1e3,minHeight:y,positionWidth:e,showPositionLabels:!1}),d.set(s,n)}n.root.style.height=`${y}px`,r.element=n.root,t.preventDefault()}else if((null===(i=r.tableColumn)||void 0===i?void 0:i.name)===u.i6.DISTRIBUTION){let e=f.get(s);void 0===e&&(e=(0,g.FZ)(v,w).plot.histogram({filteringEnabled:!1,valueColumnName:v.name,splitColumnName:u.$2.SPLIT_COL,legendVisibility:"Never",showXAxis:!1,showColumnSelector:!1,showRangeSlider:!1,showBinSelector:!1,backColor:o.Color.toHtml(o.Color.white),xAxisHeight:1,showSplitSelector:!1}),e.root.style.width="auto",f.set(s,e)),e.root.style.height=`${y}px`,r.element=e.root,t.preventDefault()}}finally{l.restore()}},new((i=void 0)||(i=Promise))((function(t,o){function s(t){try{l(r.next(t))}catch(t){o(t)}}function a(t){try{l(r.throw(t))}catch(t){o(t)}}function l(e){var n;e.done?t(e.value):(n=e.value,n instanceof i?n:new i((function(t){t(n)}))).then(s,a)}l((r=r.apply(e,n||[])).next())}));var e,n,i,r})),s.root.addEventListener("mouseleave",(t=>this.model.unhighlight())),o.debounce(s.onCurrentCellChanged,500).subscribe((t=>{var e;if(t.isTableCell)try{if(!this.keyPress||(null===(e=t.tableColumn)||void 0===e?void 0:e.name)!==u.i6.CLUSTER)return;null!==this.currentRowIndex&&-1!==this.currentRowIndex&&this.modifyClusterSelection(this.getCluster(s.cell(u.i6.CLUSTER,this.currentRowIndex)),{shiftPressed:!0,ctrlPressed:!0},!1),this.modifyClusterSelection(this.getCluster(t),{shiftPressed:!0,ctrlPressed:!1}),s.invalidate()}finally{this.keyPress=!1,this.currentRowIndex=t.gridRow}})),s.root.addEventListener("keydown",(t=>{if(this.keyPress=t.key.startsWith("Arrow"),!this.keyPress){if("Escape"===t.key||"KeyA"===t.code&&t.shiftKey&&t.ctrlKey)this.initClusterSelection({notify:!1});else if("KeyA"===t.code&&t.ctrlKey)for(let t=0;t<this.logoSummaryTable.rowCount;++t)this.modifyClusterSelection(this.getCluster(s.cell(u.i6.CLUSTER,t)),{shiftPressed:!0,ctrlPressed:!1},!1);this.model.fireBitsetChanged(l.q.LOGO_SUMMARY_TABLE),s.invalidate()}})),s.root.addEventListener("click",(t=>{var e;const n=s.hitTest(t.offsetX,t.offsetY);if(!n||!n.isTableCell||(null===(e=n.tableColumn)||void 0===e?void 0:e.name)!==u.i6.CLUSTER)return;const o=this.getCluster(n);this.modifyClusterSelection(o,{shiftPressed:t.shiftKey,ctrlPressed:t.ctrlKey}),s.invalidate(),y._package.files.readAsText("help/logo-summary-table.md").then((t=>{r.shell.windows.help.showHelp(i.markdown(t))})).catch((t=>r.log.error(t)))})),s.onCellTooltip(((t,e,n)=>{var i;if(!t.isTableCell)return this.model.unhighlight(),!0;const r=this.getCluster(t);return this.highlightCluster(r),(null===(i=t.tableColumn)||void 0===i?void 0:i.name)===u.i6.CLUSTER&&this.showTooltip(r,e,n),!0}));const w=s.props;return w.allowEdit=!1,w.allowRowSelection=!1,w.allowBlockSelection=!1,w.allowColSelection=!1,w.showCurrentRowIndicator=!1,w.showReadOnlyNotifications=!1,s}highlightCluster(t){const e=this.clusterStats[t.positionOrClusterType][t.monomerOrCluster].mask;this.dataFrame.rows.highlight((t=>e.getBit(t))),this.model.isHighlighting=!0}getCluster(t){const e=this.logoSummaryTable.get(u.i6.CLUSTER,t.tableRowIndex);return{positionOrClusterType:this.dataFrame.getCol(this.clustersColumnName).categories.includes(e)?A.ORIGINAL:A.CUSTOM,monomerOrCluster:e}}updateFilter(){const t=this.logoSummaryTable.getCol(u.i6.MEMBERS),e=this.logoSummaryTable.getCol(u.i6.CLUSTER),n=e.getRawData(),i=e.categories,r=i.indexOf("-1"),o=t.getRawData();let s=0;o.forEach(((t,e)=>{"-1"!==i[n[e]]&&(s=Math.max(s,o[e]))}));const a=Math.ceil(s*this.membersRatioThreshold);this.logoSummaryTable.filter.init((t=>o[t]>a&&(-1===r||"-1"!==i[n[t]])))}clusterFromSelection(){const t=this.model.getVisibleSelection(),e=this.logoSummaryTable.columns,n=e.length,i=new Array(e.length),r=this.getScaledActivityColumn(),o=v.A.fromString(t.toBinaryString()),s=(0,d.GT)(r.getRawData(),o);this.bitsets.push(t.clone());const a=this.dataFrame.columns.getUnusedName("New Cluster"),l={},c={},h=this.getTotalViewerAggColumns(),f=this.getStringAggregatedColumns();for(const[e,n]of h){const i=b(n,e),r=this.dataFrame.getCol(e);l[i]=(0,d.lh)(r,n,t)}for(const e of f)c[e]=(0,d.J1)(this.dataFrame,e,t);for(let r=0;r<n;++r){const n=e.byIndex(r);i[r]=n.name===u.i6.CLUSTER?a:n.name===u.i6.MEMBERS?t.trueCount:n.name===u.i6.WEB_LOGO||n.name===u.i6.DISTRIBUTION?null:n.name===u.i6.MEAN_DIFFERENCE?s.meanDifference:n.name===u.i6.P_VALUE?s.pValue:n.name===u.i6.RATIO?s.ratio:n.name in l?l[n.name]:n.name in c?c[n.name]:void 0,void 0===i[r]&&y._package.logger.warning(`PeptidesLSTWarn: value for column ${n.name} is undefined`)}this.logoSummaryTable.rows.addNew(i),this.clusterStats[A.CUSTOM][a]=s,this.addNewCluster(a)}removeCluster(){const t=this.clusterSelection[A.CUSTOM];if(0===t.length)return void r.shell.warning("No custom clusters selected to be removed");const e=this.logoSummaryTable.rows,n=this.logoSummaryTable.getCol(u.i6.CLUSTER),i=n.categories,o=this.dataFrame.columns;for(const n of t){t.splice(t.indexOf(n),1),o.remove(n),delete this.clusterStats[A.CUSTOM][n];const r=i.indexOf(n);e.removeAt(r),this.bitsets.splice(r,1)}n.compact(),this.clusterSelection[A.CUSTOM]=t,this.render()}addNewCluster(t){const e=o.Column.fromBitSet(t,this.model.getVisibleSelection());e.setTag(u.gp.CUSTOM_CLUSTER,"1"),e.setTag(u.gp.ANALYSIS_COL,"true"),this.dataFrame.columns.add(e),this.model.analysisView.grid.col(e.name).visible=!1}modifyClusterSelection(t,e={shiftPressed:!1,ctrlPressed:!1},n=!0){n?this.clusterSelection=(0,g.vW)(this.clusterSelection,t,e):this._clusterSelection=(0,g.vW)(this.clusterSelection,t,e)}showTooltip(t,e,n){const r=this.dataFrame.filter,s=r.anyFalse?this.dataFrame.clone(r):this.dataFrame,a=s.rowCount,l=new v.A(a,!1),u=this.getScaledActivityColumn(r.anyFalse),c=u.getRawData();if(t.positionOrClusterType===A.ORIGINAL){const e=s.getCol(this.clustersColumnName),n=e.getRawData(),i=e.categories.indexOf(t.monomerOrCluster);for(let t=0;t<a;++t)n[t]===i&&l.setTrue(t);l.incrementVersion()}else{const e=s.getCol(t.monomerOrCluster);l.buffer=e.getRawData()}const h=r.anyFalse?(0,d.GT)(c,l):this.clusterStats[t.positionOrClusterType][t.monomerOrCluster];if(!h.count)return null;const f=o.BitSet.fromBytes(l.buffer.buffer,a),p=(0,g.FZ)(u,f),y=(0,m.M1)(p,!0),C=(0,m.QD)(h),w=(0,d.I_)(this.dataFrame,this.getTotalViewerAggColumns(),{filterDf:!0,mask:f}),b=Object.assign(Object.assign({},C),w),E=(0,g.F2)(y,b);return i.tooltip.show(E,e,n),E}createWebLogoDf(t,e){const n=o.DataFrame.fromColumns([t]);return n.filter.copyFrom(e),n}}},3541:(t,e,n)=>{"use strict";n.d(e,{J:()=>N,UJ:()=>M,ds:()=>i,xN:()=>_});var i,r,o,s,a=n(4328),l=n(7389),u=n(6082),c=n(7233),h=n.n(c),d=n(4139),f=n(2935),p=n(9484),m=n(144),g=n.n(m),v=n(5070),y=n(3273),C=n(912),w=n(3657),b=n(8608),A=n(3077),E=n(439),S=n(2003),T=n(9135),x=function(t,e,n,i){return new(n||(n=Promise))((function(r,o){function s(t){try{l(i.next(t))}catch(t){o(t)}}function a(t){try{l(i.throw(t))}catch(t){o(t)}}function l(t){var e;t.done?r(t.value):(e=t.value,e instanceof n?e:new n((function(t){t(e)}))).then(s,a)}l((i=i.apply(t,e||[])).next())}))};!function(t){t.MUTATION_CLIFFS="Mutation Cliffs",t.INVARIANT_MAP="Invariant Map"}(i||(i={})),function(t){t.SEQUENCE="sequence",t.ACTIVITY="activity",t.ACTIVITY_SCALING="activityScaling",t.TARGET="target",t.TARGET_CATEGORY="targetCategory",t.MIN_ACTIVITY_DELTA="minActivityDelta",t.MAX_MUTATIONS="maxMutations",t.COLUMNS="columns",t.AGGREGATION="aggregation",t.ACTIVITY_TARGET="activityTarget",t.VALUE_INVARIANT_MAP="value",t.AGGREGATION_INVARIANT_MAP_VALUE="valueAggregation"}(r||(r={})),function(t){t.COLOR="color",t.COLOR_AGGREGATION="colorAggregation",t.CUSTOM_COLOR_RANGE="customColorRange",t.MIN_COLOR_VALUE="minColorValue",t.MAX_COLOR_VALUE="maxColorValue",t.LOWER_BOUND_COLOR="lowerBoundColor",t.MIDDLE_COLOR="middleColor",t.UPPER_BOUND_COLOR="upperBoundColor",t.LOG_SCALE_COLOR="logScaleColor"}(o||(o={})),function(t){t.GENERAL="General",t.INVARIANT_MAP="Invariant Map",t.MUTATION_CLIFFS="Mutation Cliffs",t.AGGREGATION="Aggregation"}(s||(s={}));class _ extends u.JsViewer{constructor(){super(),this.keyPressed=!1,this._scaledActivityColumn=null,this.doRender=!0,this._viewerGrid=null,this._positionColumns=null,this._monomerPositionStats=null,this._mutationCliffs=null,this._mutationCliffStats=null,this._invariantMapSelection=null,this._mutationCliffsSelection=null,this._monomerMetaColumns=new Set,this.sequenceColumnName=this.column(r.SEQUENCE,{category:s.GENERAL,semType:u.SEMTYPE.MACROMOLECULE,nullable:!1}),this.activityColumnName=this.column(r.ACTIVITY,{category:s.GENERAL,nullable:!1}),this.activityScaling=this.string(r.ACTIVITY_SCALING,d.rg.NONE,{category:s.GENERAL,choices:Object.values(d.rg),nullable:!1}),this.activityTarget=this.string(r.ACTIVITY_TARGET,d.wf.HIGH,{category:s.GENERAL,choices:Object.values(d.wf),nullable:!1}),this.targetColumnName=this.column(r.TARGET,{category:s.GENERAL,nullable:!0,columnTypeFilter:"categorical",userEditable:!0}),this.minActivityDelta=this.float(r.MIN_ACTIVITY_DELTA,0,{category:s.MUTATION_CLIFFS,min:0,max:100}),this.maxMutations=this.int(r.MAX_MUTATIONS,1,{category:s.MUTATION_CLIFFS,min:1,max:20}),this.columns=this.columnList(r.COLUMNS,[],{category:s.AGGREGATION}),this.aggregation=this.string(r.AGGREGATION,u.AGG.AVG,{category:s.AGGREGATION,choices:d.V5}),this.valueColumnName=this.column(r.VALUE_INVARIANT_MAP,{category:s.INVARIANT_MAP,userEditable:!0,nullable:!1,columnTypeFilter:"numerical"}),this.valueAggregation=this.string(r.AGGREGATION_INVARIANT_MAP_VALUE,u.AGG.TOTAL_COUNT,{category:s.INVARIANT_MAP,choices:d.V5,userEditable:!0,nullable:!1}),this.mutationCliffsDebouncer=(0,b.sg)(((t,e,n)=>x(this,void 0,void 0,(function*(){return yield(0,w.uz)(t,e,n)})))),this.targetCategoryInput=l.input.choice("Category",{value:null,items:[],nullable:!0,onValueChanged:()=>{var t;this._mutationCliffs=null,this._mutationCliffStats=null,this._mutationCliffsSelection=null,this._invariantMapSelection=null,this.doRender=!1,this._monomerPositionStats=null,null===(t=this.positionColumns)||void 0===t||t.forEach((t=>{t.temp[d.gp.INVARIANT_MAP_COLOR_CACHE]=null})),this.sequenceColumnName&&this.activityColumnName&&this.calculateMutationCliffs().then((t=>{this.mutationCliffs=t.cliffs,this.cliffStats=t.cliffStats})),this.viewerGrid.invalidate()}}),this.targetCategoryInput.root.style.display="none",this.targetCategoryInput.root.style.width="50%",this.targetCategoryInput.root.style.marginLeft="8px"}get viewerGrid(){var t;return null!==(t=this._viewerGrid)&&void 0!==t||(this._viewerGrid=this.createViewerGrid()),this._viewerGrid}render(){}get alphabet(){var t;return null!==(t=this.dataFrame.getCol(this.sequenceColumnName).getTag(E.gp.alphabet))&&void 0!==t?t:S.YI.UN}get model(){return p.i.getInstance(this.dataFrame)}get positionColumns(){var t,e,n;if(null!=this._positionColumns)return this._positionColumns;const i=t=>{const e=this.model.findViewer(t);return this.sequenceColumnName===(null==e?void 0:e.sequenceColumnName)?e._positionColumns:null};return null!=this.model.positionColumns&&this.sequenceColumnName===(null===(t=this.model.settings)||void 0===t?void 0:t.sequenceColumnName)?this._positionColumns=this.model.positionColumns:this instanceof N?this._positionColumns=i(p.q.MOST_POTENT_RESIDUES):this instanceof M&&(this._positionColumns=i(p.q.SEQUENCE_VARIABILITY_MAP)),null!==(e=this._positionColumns)&&void 0!==e||(this._positionColumns=null!==(n=i(p.q.LOGO_SUMMARY_TABLE))&&void 0!==n?n:(0,A.R)(this.dataFrame.getCol(this.sequenceColumnName)).columns.toList()),this._positionColumns}get monomerPositionStats(){var t;if(null!=this._monomerPositionStats)return this._monomerPositionStats;const e=t=>{var e,n,i;return!(this.sequenceColumnName!==(null==t?void 0:t.sequenceColumnName)||this.activityColumnName!==(null==t?void 0:t.activityColumnName)||this.activityScaling!==(null==t?void 0:t.activityScaling)||!(t instanceof _&&this.targetColumnName==(null==t?void 0:t.targetColumnName)&&(null===(e=this.targetCategoryInput)||void 0===e?void 0:e.value)===(null===(n=null==t?void 0:t.targetCategoryInput)||void 0===n?void 0:n.value))&&(t instanceof _||null!=this.targetColumnName&&null!=(null===(i=this.targetCategoryInput)||void 0===i?void 0:i.value))||!(t instanceof _&&this.valueColumnName==(null==t?void 0:t.valueColumnName)&&this.valueAggregation==(null==t?void 0:t.valueAggregation))&&(t instanceof _||this.valueColumnName&&this.valueAggregation&&this.valueAggregation!=u.AGG.VALUE_COUNT&&this.valueAggregation!=u.AGG.TOTAL_COUNT))},n=t=>{const n=this.model.findViewer(t);return e(n)?n._monomerPositionStats:null};null!==this.model.monomerPositionStats&&e(this.model.settings)?this._monomerPositionStats=this.model.monomerPositionStats:this instanceof N?this._monomerPositionStats=n(p.q.MOST_POTENT_RESIDUES):this instanceof M&&(this._monomerPositionStats=n(p.q.SEQUENCE_VARIABILITY_MAP));const i=this.targetColumnName?this.dataFrame.col(this.targetColumnName):null,r=this.targetCategoryInput.value,o=this.dataFrame.col(this.valueColumnName),s=this.valueAggregation;return null!==(t=this._monomerPositionStats)&&void 0!==t||(this._monomerPositionStats=(0,w.Ej)(this.getScaledActivityColumn(),this.dataFrame.filter,this.positionColumns,{target:i&&r?{col:i,cat:r}:void 0,aggValue:s&&o?{col:o,type:s}:void 0})),this._monomerPositionStats}get mutationCliffs(){if(null!=this._mutationCliffs)return this._mutationCliffs;const t=t=>{const e=this.model.findViewer(t);return i=e,(n=this).sequenceColumnName===(null==i?void 0:i.sequenceColumnName)&&n.activityColumnName===i.activityColumnName&&n.activityScaling===i.activityScaling&&n.targetColumnName===(null==i?void 0:i.targetColumnName)&&(null===(r=n.targetCategoryInput)||void 0===r?void 0:r.value)===(null===(o=null==i?void 0:i.targetCategoryInput)||void 0===o?void 0:o.value)&&n.minActivityDelta===(null==i?void 0:i.minActivityDelta)&&n.maxMutations===(null==i?void 0:i.maxMutations)?e._mutationCliffs:null;var n,i,r,o};return this instanceof N?this._mutationCliffs=t(p.q.MOST_POTENT_RESIDUES):this instanceof M&&(this._mutationCliffs=t(p.q.SEQUENCE_VARIABILITY_MAP)),this._mutationCliffs}set mutationCliffs(t){this._mutationCliffs=t,this.viewerGrid.invalidate()}get cliffStats(){if(!this._mutationCliffStats&&this.mutationCliffs&&this.activityColumnName&&this.sequenceColumnName&&this.dataFrame.col(this.activityColumnName)){const t=this.dataFrame.col(this.activityColumnName).getRawData();this._mutationCliffStats=(0,w.Lw)(this.mutationCliffs,t)}return this._mutationCliffStats}set cliffStats(t){this._mutationCliffStats=t,this.viewerGrid.invalidate}get mutationCliffsSelection(){var t;const e=this instanceof N?d.YX.MP:d.YX.MPR,n=this.dataFrame.getTag(`${e}${d.gp.MUTATION_CLIFFS_SELECTION}`);return null!==(t=this._mutationCliffsSelection)&&void 0!==t||(this._mutationCliffsSelection=null===n?(0,b.ZR)(this.positionColumns):JSON.parse(n)),this._mutationCliffsSelection}set mutationCliffsSelection(t){this._mutationCliffsSelection=t;const e=this instanceof N?d.YX.MP:d.YX.MPR;this.dataFrame.setTag(`${e}${d.gp.MUTATION_CLIFFS_SELECTION}`,JSON.stringify(t)),this.model.fireBitsetChanged(this instanceof N?p.q.SEQUENCE_VARIABILITY_MAP:p.q.MOST_POTENT_RESIDUES);const n=this.model.findViewer(p.q.SEQUENCE_VARIABILITY_MAP);null==n||n.viewerGrid.invalidate();const i=this.model.findViewer(p.q.MOST_POTENT_RESIDUES);null==i||i.viewerGrid.invalidate(),this.model.analysisView.grid.invalidate()}getScaledActivityColumn(t=!1){var e,n,i;return(null===(e=this.model.settings)||void 0===e?void 0:e.activityColumnName)===this.activityColumnName&&(null===(n=this.model.settings)||void 0===n?void 0:n.activityScaling)===this.activityScaling&&(this._scaledActivityColumn=this.model.getScaledActivityColumn(t)),null!==(i=this._scaledActivityColumn)&&void 0!==i||(this._scaledActivityColumn=(0,b.Y1)(this.dataFrame.getCol(this.activityColumnName),this.activityScaling)),t?u.DataFrame.fromColumns([this._scaledActivityColumn]).clone(this.dataFrame.filter).getCol(this._scaledActivityColumn.name):this._scaledActivityColumn}modifyMutationCliffsSelection(t,e={shiftPressed:!1,ctrlPressed:!1},n=!0){n?this.mutationCliffsSelection=(0,b.vW)(this.mutationCliffsSelection,t,e):this._mutationCliffsSelection=(0,b.vW)(this.mutationCliffsSelection,t,e)}resetTargetCategoryValue(){var t;const e=this.targetColumnName,n=this.dataFrame.col(e);this.targetCategoryInput.items=null!==(t=null==n?void 0:n.categories)&&void 0!==t?t:[],this.targetCategoryInput.value=null,this.targetCategoryInput.root.style.display=e?"flex":"none"}onPropertyChanged(t){switch(super.onPropertyChanged(t),this.doRender=!0,t.name){case`${r.SEQUENCE}${d.To}`:this._positionColumns=null,this._monomerPositionStats=null,this._mutationCliffs=null,this._mutationCliffStats=null,this._mutationCliffsSelection=null,this._viewerGrid=null;break;case`${r.ACTIVITY}${d.To}`:case r.ACTIVITY_SCALING:this._monomerPositionStats=null,this._mutationCliffs=null,this._mutationCliffStats=null,this._mutationCliffsSelection=null,this._viewerGrid=null,this._scaledActivityColumn=null;break;case`${r.VALUE_INVARIANT_MAP}${d.To}`:case r.AGGREGATION_INVARIANT_MAP_VALUE:this._monomerPositionStats=null,this._viewerGrid=null,this._invariantMapSelection=null;break;case r.MIN_ACTIVITY_DELTA:case r.MAX_MUTATIONS:this._mutationCliffs=null,this._mutationCliffStats=null,this._mutationCliffsSelection=null,this.doRender=!1;break;case r.COLUMNS:case r.AGGREGATION:this instanceof M&&(this._viewerGrid=null);break;case r.ACTIVITY_TARGET:(this instanceof M||this instanceof N)&&(this._viewerGrid=null)}null===this._mutationCliffs&&this.sequenceColumnName&&this.activityColumnName&&this.calculateMutationCliffs().then((t=>{this.mutationCliffs=t.cliffs,this.cliffStats=t.cliffStats})),t.name===`${r.TARGET}${d.To}`&&this.targetColumnInput&&(this.targetColumnInput.value=this.targetColumnName?this.dataFrame.col(this.targetColumnName):null,this.resetTargetCategoryValue())}getAggregationColumns(){return Object.fromEntries(this.columns.map((t=>[t,this.aggregation])).filter((([t,e])=>this.model.df.columns.contains(t)&&this.model.df.col(t).matches("numerical"))))}getTotalViewerAggColumns(){var t,e;const n=this.getAggregationColumns();return(0,b.zm)(this.model.df,this.columns,n,null===(e=null===(t=this.model)||void 0===t?void 0:t.settings)||void 0===e?void 0:e.columns)}createViewerGrid(){throw new Error("Not implemented")}detach(){this.subs.forEach((t=>t.unsubscribe()))}onTableAttached(){var t,e,n;if(super.onTableAttached(),this.helpUrl="https://datagrok.ai/help/datagrok/solutions/domains/bio/peptides-sar",(0,b.B2)(this.dataFrame))null===(t=this.getProperty(`${r.SEQUENCE}${d.To}`))||void 0===t||t.set(this,this.dataFrame.columns.bySemType(u.SEMTYPE.MACROMOLECULE).name),null===(e=this.getProperty(`${r.ACTIVITY}${d.To}`))||void 0===e||e.set(this,g()(this.dataFrame.columns.numerical).next().value.name),null===(n=this.getProperty(`${r.VALUE_INVARIANT_MAP}${d.To}`))||void 0===n||n.set(this,g()(this.dataFrame.columns.numerical).next().value.name),null===this.mutationCliffs&&this.sequenceColumnName&&this.activityColumnName&&this.calculateMutationCliffs().then((t=>{this.mutationCliffs=t.cliffs,this.cliffStats=t.cliffStats})),this.subs.push(a.events.onContextMenu.subscribe((t=>{if(!(t&&t.causedBy&&t.args&&t.args.menu&&t.causedBy.target&&t.causedBy.target instanceof HTMLElement&&this.root.contains(t.causedBy.target)))return;const e=t.args.menu;(0,T.pj)().then((t=>{const n=t.getMonomerLib(),i=n.getMonomerSymbolsByType("PEPTIDE").map((t=>n.getMonomer("PEPTIDE",t))).filter(Boolean).map((t=>{var e;return null!==(e=t.meta)&&void 0!==e?e:{}})),r=new Set;i.forEach((t=>Object.keys(t).forEach((t=>r.add(t))))),r.delete("colors"),e.group("Monomer Meta").items(Array.from(r),(t=>{this._monomerMetaColumns.has(t)?this._monomerMetaColumns.delete(t):this._monomerMetaColumns.add(t),this._viewerGrid=null,this.render()}),{isChecked:t=>this._monomerMetaColumns.has(t)})}))})));else{const t="PeptidesError: dataframe is missing Macromolecule or numeric columns";a.log.error(t),a.shell.warning(t)}}calculateMutationCliffs(){return x(this,void 0,void 0,(function*(){const t=this.dataFrame.getCol(this.activityColumnName),e=this.positionColumns.map(b.eY),n=this.targetColumnName?(0,b.eY)(this.dataFrame.getCol(this.targetColumnName)):null,i={maxMutations:this.maxMutations,minActivityDelta:this.minActivityDelta,targetCol:n,currentTarget:this.targetCategoryInput.value},r=t.getRawData(),o=yield this.mutationCliffsDebouncer(r,e,i);return{cliffs:o,cliffStats:(0,w.Lw)(o,r)}}))}}class N extends _{constructor(){super(),this.currentGridCell=null,this.customColorRange=!1,this.minColorValue=0,this.maxColorValue=0,this.logScaleColor=!1,this.colorColumnName=this.column(o.COLOR,{category:s.INVARIANT_MAP,nullable:!1,columnTypeFilter:"numerical"}),this.colorAggregation=this.string(o.COLOR_AGGREGATION,u.AGG.AVG,{category:s.INVARIANT_MAP,choices:d.V5}),this.lowerBoundColor=this.int(o.LOWER_BOUND_COLOR,4278190335,{category:s.INVARIANT_MAP,editor:"color"}),this.middleColor=this.int(o.MIDDLE_COLOR,4294967295,{category:s.INVARIANT_MAP,editor:"color"}),this.upperBoundColor=this.int(o.UPPER_BOUND_COLOR,4294901760,{category:s.INVARIANT_MAP,editor:"color"}),this.logScaleColor=this.bool(o.LOG_SCALE_COLOR,!1,{category:s.INVARIANT_MAP}),this.customColorRange=this.bool(o.CUSTOM_COLOR_RANGE,!1,{category:s.INVARIANT_MAP}),this.minColorValue=this.float(o.MIN_COLOR_VALUE,0,{category:s.INVARIANT_MAP}),this.maxColorValue=this.float(o.MAX_COLOR_VALUE,0,{category:s.INVARIANT_MAP})}get name(){return p.q.SEQUENCE_VARIABILITY_MAP}get mode(){var t;return null!==(t=this.dataFrame.getTag(d.gp.MONOMER_POSITION_MODE))&&void 0!==t?t:i.MUTATION_CLIFFS}set mode(t){this.dataFrame.setTag(d.gp.MONOMER_POSITION_MODE,t),this.viewerGrid.invalidate()}get invariantMapSelection(){var t;const e=this.dataFrame.getTag(`${d.YX.MP}${d.gp.INVARIANT_MAP_SELECTION}`);return null!==(t=this._invariantMapSelection)&&void 0!==t||(this._invariantMapSelection=null===e?(0,b.ZR)(this.positionColumns):JSON.parse(e)),this._invariantMapSelection}set invariantMapSelection(t){this._invariantMapSelection=t,this.dataFrame.setTag(`${d.YX.MP}${d.gp.INVARIANT_MAP_SELECTION}`,JSON.stringify(t)),this.model.fireBitsetChanged(p.q.SEQUENCE_VARIABILITY_MAP),this.model.analysisView.grid.invalidate()}onTableAttached(){var t;if(super.onTableAttached(),(0,b.B2)(this.dataFrame))null===(t=this.getProperty(`${o.COLOR}${d.To}`))||void 0===t||t.set(this,this.activityColumnName),this.targetColumnInput=l.input.column("Target",{value:void 0,nullable:!0,table:this.dataFrame,onValueChanged:t=>{var e;const n=this.getProperty(`${r.TARGET}${d.To}`);n&&n.get(this)!==t.name&&(null==n||n.set(this,null!==(e=t.name)&&void 0!==e?e:null))}});else{const t="PeptidesError: dataframe is missing Macromolecule or numeric columns";a.log.error(t),a.shell.warning(t)}this.render()}modifyInvariantMapSelection(t,e={shiftPressed:!1,ctrlPressed:!1},n=!0){n?this.invariantMapSelection=(0,b.vW)(this.invariantMapSelection,t,e):this._invariantMapSelection=(0,b.vW)(this.invariantMapSelection,t,e)}onPropertyChanged(t){var e;super.onPropertyChanged(t),t.name===r.SEQUENCE&&(this._invariantMapSelection=null),null===(e=this.positionColumns)||void 0===e||e.forEach((t=>{t.temp[d.gp.INVARIANT_MAP_COLOR_CACHE]=null})),this.doRender?this.render():this.viewerGrid.invalidate()}createMonomerPositionDf(){const t=new Set,e=this.positionColumns;for(const n of e){const e=n.categories;for(const n of e)""!==n&&t.add(n)}const n=Array.from(t),i=u.Column.fromStrings(d.$2.MONOMER,n),r=u.DataFrame.fromColumns([i]),o=(0,T.pj)().then((t=>{const e=t.getMonomerLib();return e?n.map((t=>{var n,i;return null!==(i=null===(n=e.getMonomer("PEPTIDE",t))||void 0===n?void 0:n.meta)&&void 0!==i?i:{}})):n.map((t=>({})))}));this._monomerMetaColumns.forEach((t=>{const e=r.columns.addNewString(t);o.then((n=>{e.init((e=>{var i,r;return null!==(r=null===(i=n[e][t])||void 0===i?void 0:i.toString())&&void 0!==r?r:""}))}))})),r.name="SAR";for(const t of e)r.columns.addNewBool(t.name);return r}cacheInvariantMapColors(){if(this.colorColumnName&&this.dataFrame.col(this.colorColumnName)){const t=this.dataFrame.getCol(this.colorColumnName).getRawData();let e=9999999,n=-9999999;const i=this.targetColumnName?this.dataFrame.col(this.targetColumnName):null,r=null==i?void 0:i.getRawData(),o=this.targetCategoryInput.value,s=null==o?null:null==i?void 0:i.categories.indexOf(o);for(const i of this.positionColumns){i.temp[d.gp.INVARIANT_MAP_COLOR_CACHE]={};const o=i.temp[d.gp.INVARIANT_MAP_COLOR_CACHE],a=i.name,l=i.getRawData(),c=i.categories;if(!this.monomerPositionStats[a])continue;const h=this.monomerPositionStats[a];for(const a of Object.keys(h)){if("general"===a)continue;const h=[];for(let t=0;t<i.length;++t){const e=c[l[t]]===a,n=!r||null==s||-1==s||r[t]===s;e&&n&&h.push(t)}const d=u.Column.float("color",h.length).init((e=>t[h[e]])).aggregate(this.colorAggregation);o[a]=d,e=Math.min(e,d),n=Math.max(n,d)}i.temp[d.gp.INVARIANT_MAP_COLOR_CACHE]=o}const a=this.customColorRange&&null!=this.minColorValue&&null!=this.maxColorValue;let l=a?this.minColorValue:e,c=a?this.maxColorValue:n;const h=this.logScaleColor&&l>1e-30&&c>1e-30&&e>1e-30&&n>1e-30;h&&(l=Math.log(l),c=Math.log(c));for(const t of this.positionColumns){const i=t.temp[d.gp.INVARIANT_MAP_COLOR_CACHE];if(i){for(const t of Object.keys(i))this.activityTarget===d.wf.LOW&&(i[t]=c-i[t]+l),i[t]=u.Color.scaleColor(h?Math.log(i[t]):i[t],l,c,void 0,[this.lowerBoundColor,this.middleColor,this.upperBoundColor]);t.temp[d.gp.INVARIANT_MAP_COLOR_CACHE]=i,t.temp[d.gp.INVARIANT_MAP_COLOR_MIN_CACHE]=e,t.temp[d.gp.INVARIANT_MAP_COLOR_MAX_CACHE]=n}}}}createViewerGrid(){const t=this.createMonomerPositionDf(),e=t.plot.grid();e.sort([d.$2.MONOMER]);const n=this.positionColumns.map((t=>t.name));e.columns.setOrder([d.$2.MONOMER,...this._monomerMetaColumns,...n]);const r=t.getCol(d.$2.MONOMER);f.rI(r,this.alphabet,!0),this.cacheInvariantMapColors(),e.onCellRender.subscribe((t=>O(t,this,this.mode===i.INVARIANT_MAP,this.dataFrame.getCol(this.colorColumnName),this.colorAggregation))),e.onCellTooltip(((t,e,n)=>{var r,o,s;if(!t.isTableCell||!(null===(r=null==t?void 0:t.cell.column)||void 0===r?void 0:r.name)||this._monomerMetaColumns.has(t.cell.column.name))return this.model.unhighlight(),!0;const a=this.getMonomerPosition(t);(0,b.dl)(a,this.dataFrame,this.monomerPositionStats),this.model.isHighlighting=!0;const l=this.getTotalViewerAggColumns();return this.mode===i.INVARIANT_MAP&&(this.colorColumnName&&this.colorAggregation&&l.unshift([this.colorColumnName,this.colorAggregation]),this.valueColumnName&&this.valueAggregation&&this.valueAggregation!==u.AGG.VALUE_COUNT&&this.valueAggregation!==u.AGG.TOTAL_COUNT&&l.unshift([this.valueColumnName,this.valueAggregation])),(0,C.DK)(this.model.df,this.getScaledActivityColumn(),l,{fromViewer:!0,isMutationCliffs:this.mode===i.MUTATION_CLIFFS,monomerPosition:a,x:e,y:n,mpStats:this.monomerPositionStats,cliffStats:null!==(s=null===(o=this.cliffStats)||void 0===o?void 0:o.stats)&&void 0!==s?s:void 0})})),e.root.addEventListener("mouseleave",(t=>this.model.unhighlight())),u.debounce(e.onCurrentCellChanged,500).subscribe((t=>{var n,r,o,s,a,l,u,c;try{if(!t||!t.dart||!(null===(r=null===(n=null==t?void 0:t.cell)||void 0===n?void 0:n.column)||void 0===r?void 0:r.name)||this._monomerMetaColumns.has(t.cell.column.name))return;if(!this.keyPressed)return;if(null!==this.currentGridCell){const t=this.getMonomerPosition(this.currentGridCell);this.mode===i.INVARIANT_MAP?this.modifyInvariantMapSelection(t,{shiftPressed:!0,ctrlPressed:!0},!1):(null===(a=null===(s=null===(o=this.mutationCliffs)||void 0===o?void 0:o.get(t.monomerOrCluster))||void 0===s?void 0:s.get(t.positionOrClusterType))||void 0===a?void 0:a.size)&&this.modifyMutationCliffsSelection(t,{shiftPressed:!0,ctrlPressed:!0},!1)}const h=this.getMonomerPosition(t);this.mode===i.INVARIANT_MAP?this.modifyInvariantMapSelection(h,{shiftPressed:!0,ctrlPressed:!1},!0):(null===(c=null===(u=null===(l=this.mutationCliffs)||void 0===l?void 0:l.get(h.monomerOrCluster))||void 0===u?void 0:u.get(h.positionOrClusterType))||void 0===c?void 0:c.size)&&this.modifyMutationCliffsSelection(h,{shiftPressed:!0,ctrlPressed:!1},!0),e.invalidate(),setTimeout((()=>null==e?void 0:e.invalidate()),300)}finally{this.keyPressed=!1,this.currentGridCell=t}})),e.root.addEventListener("keydown",(t=>{if(this.keyPressed=t.key.startsWith("Arrow"),!this.keyPressed){if("Escape"===t.key||"KeyA"===t.code&&t.ctrlKey&&t.shiftKey)this.mode===i.INVARIANT_MAP?this._invariantMapSelection=(0,b.ZR)(this.positionColumns):this._mutationCliffsSelection=(0,b.ZR)(this.positionColumns);else{if("KeyA"!==t.code||!t.ctrlKey)return;{const t=Object.keys(this.monomerPositionStats).filter((t=>"general"!==t));for(const e of t){const t=Object.keys(this.monomerPositionStats[e]).filter((t=>"general"!==t));for(const n of t){const t={monomerOrCluster:n,positionOrClusterType:e};this.mode===i.INVARIANT_MAP?this.modifyInvariantMapSelection(t,{shiftPressed:!0,ctrlPressed:!1},!1):this.modifyMutationCliffsSelection(t,{shiftPressed:!0,ctrlPressed:!1},!1)}}}}this.model.fireBitsetChanged(p.q.SEQUENCE_VARIABILITY_MAP),e.invalidate()}})),e.root.addEventListener("click",(n=>{var r,o,s,a,l;const u=e.hitTest(n.offsetX,n.offsetY);if(!(null==u?void 0:u.isTableCell)||(null===(r=null==u?void 0:u.tableColumn)||void 0===r?void 0:r.name)===d.$2.MONOMER||(null===(o=null==u?void 0:u.tableColumn)||void 0===o?void 0:o.name)&&this._monomerMetaColumns.has(u.tableColumn.name))return;const c=this.getMonomerPosition(u);this.mode===i.INVARIANT_MAP?(this.modifyInvariantMapSelection(c,{shiftPressed:n.shiftKey,ctrlPressed:n.ctrlKey}),(0,b.CD)(this.invariantMapSelection)&&(t.currentRowIdx=-1)):(null===(l=null===(a=null===(s=this.mutationCliffs)||void 0===s?void 0:s.get(c.monomerOrCluster))||void 0===a?void 0:a.get(c.positionOrClusterType))||void 0===l?void 0:l.size)&&this.modifyMutationCliffsSelection(c,{shiftPressed:n.shiftKey,ctrlPressed:n.ctrlKey}),e.invalidate(),this.showHelp()})),L(e);const o=e.onAfterDrawContent.subscribe((()=>{const t=e.col(d.$2.MONOMER);if(40!==t.width){t.width=40;for(const t of n)e.col(t).width=40}else o.unsubscribe()}));return e}showHelp(){y._package.files.readAsText("help/monomer-position.md").then((t=>{a.shell.windows.help.showHelp(l.markdown(t))})).catch((t=>a.log.error(t)))}getMonomerPosition(t){return{monomerOrCluster:t.cell.dataFrame.get(d.$2.MONOMER,t.tableRowIndex),positionOrClusterType:t.tableColumn.name}}render(){var t,e,n;if(h()(this.root).empty(),!this.activityColumnName||!this.sequenceColumnName)return void this.root.appendChild(l.divText("Please, select a sequence and activity columns in the viewer properties"));const r=this.getProperty(o.COLOR);r&&(r.choices=g()(a.shell.t.columns.numerical).toArray().map((t=>t.name)),r.get(this)===d.$2.ACTIVITY_SCALED&&r.set(this,d.$2.ACTIVITY)),h()(this.root).empty();let s=l.divText(p.q.MOST_POTENT_RESIDUES,{id:"pep-viewer-title"});if(this.name===p.q.SEQUENCE_VARIABILITY_MAP){const t=l.input.bool(i.MUTATION_CLIFFS,{value:this.mode===i.MUTATION_CLIFFS});t.root.addEventListener("click",(()=>{e.value=!1,t.value=!0,this.mode=i.MUTATION_CLIFFS,this.showHelp()})),t.setTooltip("Statistically significant changes in activity");const e=l.input.bool(i.INVARIANT_MAP,{value:this.mode===i.INVARIANT_MAP});e.root.addEventListener("click",(()=>{t.value=!1,e.value=!0,this.mode=i.INVARIANT_MAP,this.showHelp()})),e.setTooltip("Number of sequences having monomer-position");const n=t=>{h()(t.root).find(".ui-input-editor").css("margin","0px").attr("type","radio"),h()(t.root).find(".ui-input-description").css("padding","0px").css("padding-right","16px"),h()(t.captionLabel).addClass("ui-label-right")};n(t),n(e),s=l.divH([t.root,e.root],{id:"pep-viewer-title"}),h()(s).css("width","auto").css("align-self","center")}const u=this.viewerGrid.root;u.style.width="auto";const c=l.iconFA("expand-alt",(()=>{const t=l.dialog();t.add(l.divV([s,u],{style:{height:"100%"}})),t.onCancel((()=>this.render())),t.showModal(!0),this.viewerGrid.invalidate()}),"Show Sequence Variability Map Table in full screen");h()(c).addClass("pep-help-icon"),this.targetColumnInput&&(this.targetColumnInput.root.style.width="50%");const f=l.divH([null!==(e=null===(t=this.targetColumnInput)||void 0===t?void 0:t.root)&&void 0!==e?e:l.div(),this.targetCategoryInput.root],{style:{alignSelf:"center",justifyContent:"center"}}),m=l.divH([c,s,f],{style:{alignSelf:"center",lineHeight:"normal",flexDirection:"column"}});this.root.appendChild(l.divV([m,u])),null===(n=this.viewerGrid)||void 0===n||n.invalidate()}}class M extends _{constructor(){super(),this.currentGridRowIdx=null}get name(){return p.q.MOST_POTENT_RESIDUES}onTableAttached(){super.onTableAttached(),this.helpUrl="https://datagrok.ai/help/datagrok/solutions/domains/bio/peptides-sar",this.render()}onPropertyChanged(t){super.onPropertyChanged(t),this.doRender&&this.render()}createMostPotentResiduesDf(){var t;const e=Object.entries(this.monomerPositionStats),n=new Array(e.length-1),i=new Array(n.length),r=new Array(n.length),o=new Array(n.length),s=new Array(n.length),a=new Array(n.length),l=new Array(n.length),c=this.getTotalViewerAggColumns(),h=c.map((([t,e])=>(0,v.hX)(e,t))),f=new Array(h.length);h.forEach(((t,e)=>f[e]=new Array(n.length)));let p=0;for(const[m,g]of e){const e=g.general;if(!e)continue;if(1===Object.entries(g).length)continue;const y=[];for(const[n,i]of Object.entries(g))"general"!==n&&(i.count>1&&(null==i.pValue||(null!==(t=i.pValue)&&void 0!==t?t:1)<=.05)&&y.push([n,i]),i.pValue===e.minPValue&&y.push([n,i]));if(0===y.length)continue;let C=null;for(const[t,e]of y)(null===C||this.activityTarget===d.wf.HIGH&&C[1].meanDifference<e.meanDifference||this.activityTarget===d.wf.LOW&&C[1].meanDifference>e.meanDifference)&&(C=[t,e]);if(null===C)continue;n[p]=parseInt(m),i[p]=C[0],r[p]=C[1].meanDifference,o[p]=C[1].pValue,s[p]=C[1].count,a[p]=C[1].ratio,l[p]=C[1].mean;const w=this.monomerPositionStats[m][C[0]],b=u.BitSet.fromBytes(w.mask.buffer.buffer,this.model.df.col(this.activityColumnName).length);for(let t=0;t<h.length;t++){const[e,n]=c[t];f[t][p]=(0,v.lh)(this.model.df.getCol(e),n,b)}++p}n.length=p,i.length=p,r.length=p,o.length=p,s.length=p,a.length=p,l.length=p;const m=u.DataFrame.create(p),g=m.columns;return g.add(u.Column.fromList(u.TYPE.INT,d.$2.POSITION,n)),g.add(u.Column.fromList(u.TYPE.STRING,d.$2.MONOMER,i)),g.add(u.Column.fromList(u.TYPE.FLOAT,d.$2.MEAN_DIFFERENCE,r)),g.add(u.Column.fromList(u.TYPE.FLOAT,d.$2.MEAN,l)),g.add(u.Column.fromList(u.TYPE.FLOAT,d.$2.P_VALUE,o)),g.add(u.Column.fromList(u.TYPE.INT,d.$2.COUNT,s)),g.add(u.Column.fromList(u.TYPE.FLOAT,d.$2.RATIO,a)),h.forEach(((t,e)=>g.add(u.Column.fromList(u.TYPE.FLOAT,t,f[e])))),m}createViewerGrid(){const t=this.createMostPotentResiduesDf(),e=t.plot.grid();e.sort([d.$2.POSITION]);const n=e.col(d.$2.P_VALUE);n.format="#.000",n.name="P-value";const i=t.getCol(d.$2.MONOMER);f.rI(i,this.alphabet,!0),e.onCellRender.subscribe((t=>O(t,this,!1))),e.onCellTooltip(((t,e,n)=>{var i,r;if(!t.isTableCell)return this.model.unhighlight(),!0;const o=this.getMonomerPosition(t);if((0,b.dl)(o,this.dataFrame,this.monomerPositionStats),this.model.isHighlighting=!0,(null===(i=t.tableColumn)||void 0===i?void 0:i.name)===d.$2.MONOMER)o.positionOrClusterType=d.$2.MONOMER;else if((null===(r=t.tableColumn)||void 0===r?void 0:r.name)!==d.$2.MEAN_DIFFERENCE)return!1;const s=this.getTotalViewerAggColumns(),a=null==t.tableRowIndex?void 0:(0,v.m2)(t.grid.dataFrame,t.tableRowIndex,s,{});return(0,C.DK)(this.model.df,this.getScaledActivityColumn(),s,{fromViewer:!0,isMostPotentResidues:!0,monomerPosition:o,x:e,y:n,mpStats:this.monomerPositionStats,aggrColValues:a})})),u.debounce(e.onCurrentCellChanged,500).subscribe((n=>{var i,r,o;try{if(this.keyPressed&&t.currentCol.name!==d.$2.MEAN_DIFFERENCE||!this.keyPressed)return;const s=this.getMonomerPosition(n);if(null!==this.currentGridRowIdx){const t=this.getMonomerPosition(e.cell("Diff",this.currentGridRowIdx));this.modifyMutationCliffsSelection(t,{shiftPressed:!0,ctrlPressed:!0},!1)}(null===(o=null===(r=null===(i=this.mutationCliffs)||void 0===i?void 0:i.get(s.monomerOrCluster))||void 0===r?void 0:r.get(s.positionOrClusterType))||void 0===o?void 0:o.size)&&this.modifyMutationCliffsSelection(s,{shiftPressed:!0,ctrlPressed:!1}),e.invalidate()}finally{this.keyPressed=!1,this.currentGridRowIdx=n.gridRow}})),e.root.addEventListener("keydown",(n=>{if(this.keyPressed=n.key.startsWith("Arrow"),!this.keyPressed){if("Escape"===n.key||"KeyA"===n.code&&n.ctrlKey&&n.shiftKey)this._mutationCliffsSelection=(0,b.ZR)(this.positionColumns);else{if("KeyA"!==n.code||!n.ctrlKey)return;for(let n=0;n<t.rowCount;++n){const t=this.getMonomerPosition(e.cell("Diff",n));this.modifyMutationCliffsSelection(t,{shiftPressed:!0,ctrlPressed:!1},!1)}}this.model.fireBitsetChanged(p.q.MOST_POTENT_RESIDUES),e.invalidate()}})),e.root.addEventListener("mouseleave",(t=>this.model.unhighlight())),e.root.addEventListener("click",(t=>{var n,i,r;const o=e.hitTest(t.offsetX,t.offsetY);if(!(null==o?void 0:o.isTableCell)||o.tableColumn.name!==d.$2.MEAN_DIFFERENCE)return;const s=this.getMonomerPosition(o);(null===(r=null===(i=null===(n=this.mutationCliffs)||void 0===n?void 0:n.get(s.monomerOrCluster))||void 0===i?void 0:i.get(s.positionOrClusterType))||void 0===r?void 0:r.size)&&(this.modifyMutationCliffsSelection(s,{shiftPressed:t.shiftKey,ctrlPressed:t.ctrlKey}),e.invalidate(),y._package.files.readAsText("help/most-potent-residues.md").then((t=>{a.shell.windows.help.showHelp(l.markdown(t))})).catch((t=>a.log.error(t))))})),L(e);const r=e.col(d.$2.MEAN_DIFFERENCE);r.name="Diff";const o=e.onAfterDrawContent.subscribe((()=>{const t=e.col(d.$2.MONOMER);40!==t.width?(t.width=40,r.width=40):o.unsubscribe()}));return e}getMonomerPosition(t){return{monomerOrCluster:t.cell.dataFrame.get(d.$2.MONOMER,t.tableRowIndex),positionOrClusterType:`${t.cell.dataFrame.get(d.$2.POSITION,t.tableRowIndex)}`}}render(){var t;if(h()(this.root).empty(),!this.activityColumnName||!this.sequenceColumnName)return void this.root.appendChild(l.divText("Please, select a sequence and activity columns in the viewer properties"));const e=l.divText(p.q.MOST_POTENT_RESIDUES,{id:"pep-viewer-title"}),n=this.viewerGrid.root;n.style.width="auto";const i=l.divH([e],{style:{alignSelf:"center",lineHeight:"normal"}});this.root.appendChild(l.divV([i,n])),null===(t=this.viewerGrid)||void 0===t||t.invalidate()}}function O(t,e,n,i,r){var o,s,a,l,c;const h=[...e.positionColumns.map((t=>t.name)),d.$2.MEAN_DIFFERENCE],p=t.g,m=t.bounds;p.save(),p.beginPath(),p.rect(m.x,m.y,m.width,m.height),p.clip();const g=t.cell;if(g.isRowHeader&&g.gridColumn.visible)return g.gridColumn.visible=!1,t.preventDefault(),void p.restore();const v=null===(o=g.tableColumn)||void 0===o?void 0:o.name,y=g.tableRowIndex;if(!g.isTableCell||-1===h.indexOf(v))return void p.restore();const C=g.grid.table,w=C.get(d.$2.MONOMER,y),b=v!==d.$2.MEAN_DIFFERENCE?v:C.get(d.$2.POSITION,y).toFixed(),A=e.monomerPositionStats[b];if(!A[w])return t.preventDefault(),void p.restore();if(n){const t=null!==(s=A[w].aggValue)&&void 0!==s?s:A[w].count,n=e.positionColumns.find((t=>t.name===b)),i=null!==(a=n.temp[d.gp.INVARIANT_MAP_COLOR_CACHE])&&void 0!==a?a:{};let r=u.Color.white;null!=i[w]?r=i[w]:e instanceof N&&(e.cacheInvariantMapColors(),r=null!==(c=(null!==(l=n.temp[d.gp.INVARIANT_MAP_COLOR_CACHE])&&void 0!==l?l:{})[w])&&void 0!==c?c:u.Color.white),f.rW(p,w,b,e.invariantMapSelection,t,m,r)}else f.Yd(p,w,b,e,m);t.preventDefault(),p.restore()}function L(t){const e=t.props;e.allowEdit=!1,e.allowRowSelection=!1,e.allowBlockSelection=!1,e.allowColSelection=!1,e.showRowHeader=!1,e.showCurrentRowIndicator=!1,e.showReadOnlyNotifications=!1,e.rowHeight=20}},7654:(t,e,n)=>{"use strict";n.d(e,{HV:()=>m,M1:()=>g,QD:()=>v});var i,r=n(7389),o=n(6082),s=n(7233),a=n.n(s),l=n(4139),u=n(5070),c=n(8608),h=n(5480),d=n(8774);!function(t){t.SEPARATE_MONOMERS="separateMonomers",t.SEPARATE_POSITIONS="separatePositions",t.SEPARATE_CLUSTERS="separateClusters"}(i||(i={}));const f="general",p=t=>t===f?"General":t.substring(8);function m(t,e){if(!t.selection.anyTrue)return r.divText("No distribution");const n=()=>{const n=[C(f,t,e)];for(const r of Object.values(i))"true"!==t.getTag(r)||r===i.SEPARATE_CLUSTERS&&!e.clusterColName||n.push(C(r,t,e));return 1===n.length?n[0]:r.div(n)},o=r.div(n()),s=Object.values(i),l=new Array(s.length);for(let u=0;u<s.length;u++){const c=s[u].substring(8);l[u]=r.input.bool(c,{value:"true"===t.getTag(s[u]),onValueChanged:e=>{t.setTag(s[u],`${e}`),a()(o).empty(),o.append(n())}}),a()(l[u].captionLabel).addClass("ui-label-right").css("text-align","left"),a()(l[u].root).find(".ui-input-editor").css("margin","0px"),a()(l[u].root).find(".ui-input-description").css("margin","0px"),l[u].setTooltip(`Show distribution for each ${c}`),c===i.SEPARATE_CLUSTERS?l[u].enabled=!(!e.clusterColName||!e.clusterSelection[h.W.ORIGINAL]):c!==i.SEPARATE_MONOMERS&&c!==i.SEPARATE_POSITIONS||(l[u].enabled=0!==Object.entries(e.monomerPositionSelection).length)}const u=r.form(l);return r.divV([u,o])}function g(t,e=!1){const n=t.plot.histogram({filteringEnabled:!1,valueColumnName:l.$2.ACTIVITY,splitColumnName:l.$2.SPLIT_COL,legendVisibility:"Never",showXAxis:!0,showColumnSelector:!1,showRangeSlider:!1,showBinSelector:!1,backColor:e?"#fdffe5":"#fffff"});return n.root.style.width="auto",n}function v(t,e={}){var n;null!==(n=e.fractionDigits)&&void 0!==n||(e.fractionDigits=3);const i={Count:`${t.count} (${(100*t.ratio).toFixed(e.fractionDigits)}%)`,"Mean difference":t.meanDifference.toFixed(e.fractionDigits),"Mean activity":t.mean.toFixed(e.fractionDigits)};return null!=t.pValue&&(i["p-value"]=t.pValue<.01?"<0.01":t.pValue.toFixed(e.fractionDigits)),i}function y(t,e,n,i={}){const r=g((0,c.FZ)(n.activityCol,t.selection,n.peptideSelection)),s=(0,u.I_)(t,Object.entries(n.columns),{filterDf:!0,mask:o.BitSet.fromBytes(e.mask.buffer.buffer,e.mask.length)}),l=v(e),h=Object.assign(Object.assign({},l),s),d=(0,c.F2)(r,h,i);return a()(d).addClass("d4-flex-col"),d}function C(t,e,n){let o=r.divText("No distribution");switch(t){case f:const t=d.A.fromSeq(e.selection.length,(t=>e.selection.get(t))),s=e.selection.anyTrue&&e.selection.anyFalse?(0,u.GT)(n.activityCol.getRawData(),t):{count:n.activityCol.length,pValue:null,meanDifference:0,ratio:1,mask:t,mean:n.activityCol.stats.avg};o=y(e,s,n);break;case i.SEPARATE_CLUSTERS:o=function(t,e,n){const i=t.rowCount,o=[],s=e.activityCol.getRawData(),a=t.getCol(e.clusterColName),l=a.categories,f=a.getRawData(),p=n[h.W.ORIGINAL].map((t=>l.indexOf(t))),m=new Array(p.length).fill(new d.A(i));for(let t=0;t<i;t++){const e=f[t],n=p.indexOf(e);-1!==n&&m[n].setTrue(t)}for(let n=0;n<p.length;n++){const i=p[n],r=(0,u.GT)(s,m[n]);o.push(y(t,r,e,{[c.AN.SELECTION]:l[i]}))}const g=n[h.W.CUSTOM];for(const n of g){const r=t.getCol(n),a=d.A.fromUint32Array(i,r.getRawData()),l=(0,u.GT)(s,a);o.push(y(t,l,e,{[c.AN.SELECTION]:n}))}return r.div(o,"d4-flex-wrap")}(e,n,n.clusterSelection);break;case i.SEPARATE_MONOMERS:const a=function(t){const e={},n=Object.keys(t);for(const i of n)for(const n of t[i])e.hasOwnProperty(n)?e[n].includes(i)||e[n].push(i):e[n]=[i];return e}(n.monomerPositionSelection);o=function(t,e,n){var i,o,s;const a=Object.keys(n),l=t.rowCount,h=[],f=[],p=[],m=[],g=e.activityCol.getRawData();for(const r of a){const a=n[r],v=new d.A(l);for(let e=0;e<a.length;e++){const n=a[e];null!==(i=f[e])&&void 0!==i||(f[e]=t.getCol(n)),null!==(o=p[e])&&void 0!==o||(p[e]=f[e].categories),null!==(s=m[e])&&void 0!==s||(m[e]=f[e].getRawData());const u=p[e].indexOf(r);for(let t=0;t<l;t++)m[e][t]===u&&v.setTrue(t)}const C=(0,u.GT)(g,v);h.push(y(t,C,e,{[c.AN.SELECTION]:r}))}return r.div(h,"d4-flex-wrap")}(e,n,a);break;case i.SEPARATE_POSITIONS:o=function(t,e,n){var i,o,s;const a=Object.keys(n),l=t.rowCount,h=[],f=e.activityCol.getRawData(),p=[],m=[],g=[];for(let r=0;r<a.length;r++){const v=a[r],C=n[v];if(0===C.length)continue;null!==(i=p[r])&&void 0!==i||(p[r]=t.getCol(v)),null!==(o=m[r])&&void 0!==o||(m[r]=p[r].categories),null!==(s=g[r])&&void 0!==s||(g[r]=p[r].getRawData());const w=new d.A(t.rowCount);for(let t=0;t<C.length;t++){const e=C[t],n=m[r].indexOf(e);for(let t=0;t<l;t++)g[r][t]===n&&w.setTrue(t)}const b=(0,u.GT)(f,w);h.push(y(t,b,e,{[c.AN.SELECTION]:v}))}return r.div(h,"d4-flex-wrap")}(e,n,n.monomerPositionSelection)}return r.divV([r.h1(p(t)),o])}},7923:(t,e,n)=>{"use strict";n.d(e,{F:()=>l});var i=n(7389),r=n(6082),o=n(4139),s=n(8608),a=n(2935);function l(t,e,n=!0){const o=u(t,e);if(!o)return new r.Widget(i.label("No mutations table generated"));const{pairsGrid:a,uniqueSequencesGrid:l,aminoToInput:c}=o,h=[a,l],d=i.divV([c.root,...h.map((t=>t.root))],{style:{width:"100%"}});return n&&(0,s.BE)("Mutation Cliffs pairs",c.root,d,(()=>{const n=u(t,e);return i.divV([n.aminoToInput.root,n.pairsGrid.root,n.uniqueSequencesGrid.root],{style:{width:"100%",height:"100%"}})})),new r.Widget(d)}function u(t,e){var n,l;const u=t.filter.getSelectedIndexes(),c=Object.keys(e.mutationCliffsSelection);if(!c.length||null===e.mutationCliffs)return null;const h=[],d=[],f=[],p=[],m=[],g=t.getCol(e.sequenceColumnName),v=g.categories,y=g.getRawData(),C=e.activityCol.getRawData(),w=new Map,b=r.BitSet.create(t.rowCount),A=Object.fromEntries(e.positionColumns.map((t=>[t.name,t])));for(const t of c){const i=A[t],r=i.categories,o=i.getRawData();for(const i of e.mutationCliffsSelection[t]){const s=null===(n=e.mutationCliffs.get(i))||void 0===n?void 0:n.get(t);if(void 0!==s)for(const[t,e]of s.entries()){if(!u.includes(t))continue;const n=null!==(l=w.get(t))&&void 0!==l?l:[],i=v[y[t]],s=C[t];for(const a of e){if(n.includes(a)||!u.includes(a))continue;w.has(a)||w.set(a,[]);const e=v[y[a]];w.get(a).push(t),h.push(`${i}#${e}`),d.push(s-C[a]),f.push(r[o[a]]),p.push(t),m.push(a),b.set(t,!0),b.set(a,!0)}}}}if(0===h.length)return null;const E=r.Column.fromStrings("Mutation",h),S=r.Column.fromList("double","Delta",d),T=r.Column.fromStrings("~to",f),x=r.Column.fromList(r.COLUMN_TYPE.INT,"~toIdx",m),_=r.Column.fromList(r.COLUMN_TYPE.INT,"~fromIdx",p),N=r.DataFrame.fromColumns([E,S,T,x,_]);N.name="Mutation Cliff pairs";const M=i.input.string("Mutated to:",{value:"",onValueChanged:t=>{const e=t;""!==e?N.filter.init((t=>T.get(t)===e)):N.filter.setAll(!0)}});M.setTooltip("Filter the rows by the monomer that the mutation was substituted to");const O=N.plot.grid();(0,s.vY)(O,!0),E.semType=o.uF.MACROMOLECULE_DIFFERENCE,E.tags[o.gp.SEPARATOR]=(0,s.AY)(g),E.tags[r.TAGS.UNITS]=g.tags[r.TAGS.UNITS],E.tags[r.TAGS.CELL_RENDERER]="MacromoleculeDifference";let L=!1,I=null;const R=[];O.onCurrentCellChanged.subscribe((t=>{try{if(!t||!t.dart)return R.length=0,void H();const e=t.tableRowIndex;if(!L)return;if(null===e)return R.length=0,void H();null!==I&&R.splice(R.indexOf(I),1),R.includes(e)||(R.push(e),O.invalidate()),H()}finally{L=!1,I=t&&t.dart?t.tableRowIndex:null}})),O.root.addEventListener("keydown",(t=>{L=t.key.startsWith("Arrow")})),O.root.addEventListener("click",(t=>{const e=O.hitTest(t.offsetX,t.offsetY);if(!e||null===e.tableRowIndex)return;const n=e.tableRowIndex;if(t.shiftKey){const t=R.indexOf(n);-1===t?R.push(n):R.splice(t,1)}else R.length=0,R.push(n);H(),O.invalidate(),F.invalidate()})),O.onCellRender.subscribe((t=>{var e;(null===(e=t.cell.tableColumn)||void 0===e?void 0:e.name)===E.name&&R.includes(t.cell.tableRowIndex)&&(0,a.X5)(t.g,t.bounds)}));const P=e.gridColumns.length,k=[];for(let t=1;t<P;t++){const n=e.gridColumns.byIndex(t);((null==n?void 0:n.name)===e.sequenceColumnName||!0===(null==n?void 0:n.visible)&&!Object.hasOwn(A,n.name))&&k.push(n.name)}const D=t.clone(b,k);D.name="Unique sequences that form Mutation Cliffs pairs";const G=D.columns.addNewInt("~seqIdx"),U=G.getRawData(),V=b.getSelectedIndexes();G.init((t=>V[t]));const F=D.plot.grid();function H(){const t=[];for(const e of R)t.push(_.get(e)),t.push(x.get(e));D.filter.init((e=>0===R.length||t.includes(U[e])),!0),O.invalidate(),F.invalidate()}return(0,s.vY)(F,!0),F.props.rowHeight=20,O.root.style.width="100% !important",F.root.style.width="100% !important",setTimeout((()=>{O.root.style.removeProperty("width"),O.root.style.setProperty("width","100%"),F.root.style.removeProperty("width"),F.root.style.setProperty("width","100%"),O.root.style.minHeight="250px",F.root.style.minHeight="250px"}),200),{pairsGrid:O,uniqueSequencesGrid:F,aminoToInput:M}}},5082:(t,e,n)=>{"use strict";n.d(e,{n:()=>u});var i=n(4328),r=(n(7389),n(6082)),o=(n(4788),n(4139)),s=n(115),a=n(9484),l=(n(7233),n(8608),n(2003),n(4572),n(5429),function(t,e,n,i){return new(n||(n=Promise))((function(r,o){function s(t){try{l(i.next(t))}catch(t){o(t)}}function a(t){try{l(i.throw(t))}catch(t){o(t)}}function l(t){var e;t.done?r(t.value):(e=t.value,e instanceof n?e:new n((function(t){t(e)}))).then(s,a)}l((i=i.apply(t,e||[])).next())}))});function u(t,e,n,u,c,h){return l(this,arguments,void 0,(function*(t,e,n,l,u,c,h={}){var d,f,p,m,g;let v=null;if(t.type!==r.COLUMN_TYPE.FLOAT&&t.type!==r.COLUMN_TYPE.INT&&t.type!==r.COLUMN_TYPE.QNUM)return i.shell.error("The activity column must be of numeric type!"),v;const y=r.TaskBarProgressIndicator.create("Loading SAR..."),C=r.DataFrame.create(l.rowCount);C.name="Peptides analysis";const w=C.columns;w.add(u);for(const t of l.columns)"true"!==t.getTag(o.gp.ANALYSIS_COL)&&(t.name.toLowerCase()===u.name.toLowerCase()&&(t.name=l.columns.getUnusedName(t.name)),w.add(t));const b={sequenceColumnName:e.name,activityColumnName:t.name,activityScaling:c,columns:{},showDendrogram:!1,showSequenceSpace:!1,sequenceSpaceParams:new s.GI(!!h.useEmbeddingsClusters&&!n),mclSettings:null!==(d=h.mclSettings)&&void 0!==d?d:new s.av};if(n){const t=C.getCol(n.name);t.type!==r.COLUMN_TYPE.STRING&&w.replace(t,t.convertTo(r.COLUMN_TYPE.STRING))}C.setTag(o.gp.SETTINGS,JSON.stringify(b));const A=r.BitSet.create(l.rowCount,(n=>!t.isNone(n)&&!e.isNone(n)&&l.filter.get(n)));if(v=a.i.getInstance(C.clone(A)),v.init(b),n){const i={clustersColumnName:n.name,sequenceColumnName:e.name,activityScaling:c,activityColumnName:t.name};yield v.addLogoSummaryTable(i)}if(yield v.addMonomerPosition(),yield v.addMostPotentResidues(),null!==(f=h.addSequenceSpace)&&void 0!==f&&f){if(yield v.addSequenceSpace({clusterCol:n,clusterEmbeddings:h.useEmbeddingsClusters}),!n&&null!==(p=h.useEmbeddingsClusters)&&void 0!==p&&p){const n=v._sequenceSpaceCols.find((t=>{var e;return v.df.col(t)&&(null===(e=v.df.col(t))||void 0===e?void 0:e.type)===r.COLUMN_TYPE.STRING}));if(n){const i={clustersColumnName:n,sequenceColumnName:e.name,activityScaling:c,activityColumnName:t.name};yield v.addLogoSummaryTable(i),setTimeout((()=>{var t,e;v&&(null===(t=null==v?void 0:v.findViewer(a.q.LOGO_SUMMARY_TABLE))||void 0===t?void 0:t.render)&&(null===(e=null==v?void 0:v.findViewer(a.q.LOGO_SUMMARY_TABLE))||void 0===e||e.render())}),100)}}}else if(null!==(m=h.addMCL)&&void 0!==m&&m&&(yield v.addMCLClusters(),!n&&null!==(g=h.useEmbeddingsClusters)&&void 0!==g&&g)){const n=v._mclCols.find((t=>(null==v?void 0:v.df.col(t))&&t.toLowerCase().startsWith("cluster")&&!t.toLowerCase().includes("size")));if(n){const i={clustersColumnName:n,sequenceColumnName:e.name,activityScaling:c,activityColumnName:t.name};yield v.addLogoSummaryTable(i),setTimeout((()=>{var t,e;v&&(null===(t=null==v?void 0:v.findViewer(a.q.LOGO_SUMMARY_TABLE))||void 0===t?void 0:t.render)&&(null===(e=null==v?void 0:v.findViewer(a.q.LOGO_SUMMARY_TABLE))||void 0===e||e.render())}),100)}}return y.close(),v}))}},5429:(t,e,n)=>{"use strict";n.d(e,{Av:()=>b,OH:()=>A,OO:()=>i});var i,r,o,s,a,l,u=n(7389),c=n(4328),h=n(6082),d=n(115),f=n(4139),p=n(9484),m=n(7233),g=n.n(m),v=n(144),y=n.n(v),C=n(3273),w=n(4572);!function(t){t.GENERAL="General",t.VIEWERS="Viewers",t.COLUMNS="Columns",t.SEQUENCE_SPACE="Sequence space",t.MCL="MCL"}(i||(i={})),function(t){t.ACTIVITY="Activity",t.ACTIVITY_SCALING="Activity scaling"}(r||(r={})),function(t){t.DENDROGRAM="Dendrogram"}(o||(o={})),function(t){t.IS_INCLUDED="",t.AGGREGATION="Aggregation"}(s||(s={})),function(t){t.DISTANCE_FUNCTION="Distance Function",t.GAP_OPEN="Gap Open Penalty",t.GAP_EXTEND="Gap Extend Penalty",t.CLUSTER_EMBEDDINGS="Cluster Embeddings",t.EPSILON="Epsilon",t.MIN_PTS="Minimum Points",t.FINGERPRINT_TYPE="Fingerprint Type"}(a||(a={})),function(t){t.DISTANCE_FUNCTION="Distance Function",t.GAP_OPEN="Gap Open Penalty",t.GAP_EXTEND="Gap Extend Penalty",t.FINGERPRINT_TYPE="Fingerprint Type",t.THRESHOLD="Similarity Threshold",t.INFLATION="Inflation Factor",t.MAX_ITERATIONS="Max Iterations",t.USE_WEBGPU="Use WebGPU",t.MIN_CLUSTER_SIZE="Min Cluster Size"}(l||(l={}));const b={[i.GENERAL]:r,[i.VIEWERS]:o,[i.COLUMNS]:s,[i.SEQUENCE_SPACE]:a,[i.MCL]:l};function A(t){var e,n,o,m,v,b,A,E,S,T;null==t.settings&&c.log.error("PeptidesError: Settings are not initialized");const x=u.accordion(),_=t.settings,N=null!==(e=null==_?void 0:_.activityScaling)&&void 0!==e?e:f.rg.NONE,M=null!==(n=null==_?void 0:_.columns)&&void 0!==n?n:{},O={},L={},I=null!==(o=null==_?void 0:_.sequenceSpaceParams)&&void 0!==o?o:new d.GI,R=null!==(m=null==_?void 0:_.mclSettings)&&void 0!==m?m:new d.av,P=u.input.column(r.ACTIVITY,{table:t.df,value:t.df.getCol(t.settings.activityColumnName),onValueChanged:t=>{O.activityColumnName=t.name},filter:t=>(t.type===h.TYPE.FLOAT||t.type===h.TYPE.INT)&&t.name!==f.$2.ACTIVITY&&0===t.stats.missingValueCount});P.setTooltip("Numeric activity column");const k=u.input.choice(r.ACTIVITY_SCALING,{value:N,items:Object.values(f.rg),onValueChanged:t=>O.activityScaling=t});k.setTooltip("Activity column 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F=[],H=[];for(const e of t.df.columns.numerical){const t=e.name;if(t===_.activityColumnName||t===f.$2.ACTIVITY)continue;const n=u.input.bool(s.IS_INCLUDED,{value:void 0!==M[t],onValueChanged:e=>{var n;null!==(n=O.columns)&&void 0!==n||(O.columns={}),e?O.columns[t]=i.value:(delete O.columns[t],Object.keys(O.columns).length===Object.keys(M).length&&delete O.columns)}});n.setTooltip("Include aggregated column value in tooltips, Logo Summary Table and Distribution panel");const i=u.input.choice(s.AGGREGATION,{value:null!==(v=M[t])&&void 0!==v?v:h.AGG.AVG,items:Object.values(h.STATS),onValueChanged:i=>{var r;null!==(r=O.columns)&&void 0!==r||(O.columns={}),n.value?O.columns[t]=i:(delete O.columns[e.name],Object.keys(O.columns).length===Object.keys(M).length&&delete O.columns)}});i.setTooltip("Aggregation method"),g()(i.root).find("label").css("width","auto");const 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m,g=n(3541),v=n(5480),y=n(4326);!function(t){t.SEQUENCE="sequence",t.ACTIVITY="activity",t.CLUSTER="cluster"}(m||(m={}));var C=n(912),w=function(t,e,n,i){return new(n||(n=Promise))((function(r,o){function s(t){try{l(i.next(t))}catch(t){o(t)}}function a(t){try{l(i.throw(t))}catch(t){o(t)}}function l(t){var e;t.done?r(t.value):(e=t.value,e instanceof n?e:new n((function(t){t(e)}))).then(s,a)}l((i=i.apply(t,e||[])).next())}))};(0,e.L1)("Viewers: Basic",(()=>{let n;(0,e.gM)((()=>w(void 0,void 0,void 0,(function*(){n=t.DataFrame.fromCsv(yield I.files.readAsText("tests/HELM_small.csv")),yield(0,e.cb)(500)}))));const i=t.Func.find({package:"Peptides",tags:["viewer"]}).map((t=>t.friendlyName));for(const t of i)(0,e.t6)(t,(()=>w(void 0,void 0,void 0,(function*(){yield(0,e.Bl)(t,n.clone(),{detectSemanticTypes:!0,arbitraryDfTest:!1,readOnly:!0}),yield(0,e.cb)(1e3)}))))})),(0,e.L1)("Viewers: Monomer-Position",(()=>{let n,i,r,c,h,d,f;(0,e.gM)((()=>w(void 0,void 0,void 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c=u.temp[s.i.modelName].findViewer(s.q.LOGO_SUMMARY_TABLE);(0,e.E3)(null!==c,!0,"New view is expected to have Logo Summary Table viewer attached")})))),(0,e.t6)("Custom clusters",(()=>x(void 0,void 0,void 0,(function*(){const t=i.df.filter;t.setAll(!1,!1),t.set(0,!0,!1),t.set(1,!0,!1),i.df.selection.set(0,!0,!1);const n=i.findViewer(s.q.LOGO_SUMMARY_TABLE);if(null===n)throw new Error("Logo summary table viewer is not found");(0,e.E3)(T()(n.customClusters).toArray().length,0,"Expected to have 0 custom clusters before creating one"),n.clusterFromSelection();const r=T()(n.customClusters).toArray();(0,e.E3)(r.length,1,"Expected to have 1 custom cluster");const o=r[0].name;(0,e.E3)(null!==i.df.col(o),!0,"Expected to have custom cluster column in the table"),(0,e.E3)(-1!==n.viewerGrid.table.getCol(a.i6.CLUSTER).categories.indexOf(o),!0,"Expected to have custom cluster in the Logo Summary 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f="none",p={monomerOrCluster:"Aze",positionOrClusterType:"10",mcCount:3,imCount:1},g={monomerOrCluster:"meI",positionOrClusterType:"1",mcCount:2,imCount:10},y={monomerOrCluster:"0",positionOrClusterType:v.W.ORIGINAL,count:3},w={monomerOrCluster:"1",positionOrClusterType:v.W.ORIGINAL,count:3};(0,e.gM)((()=>_(void 0,void 0,void 0,(function*(){n=t.DataFrame.fromCsv(yield I.files.readAsText("tests/HELM_small.csv")),r=n.getCol(m.ACTIVITY),c=n.getCol(m.SEQUENCE),c.semType=t.SEMTYPE.MACROMOLECULE,c.setTag(t.TAGS.UNITS,u.Hi.HELM),d=(0,l.Y1)(r,f),h=n.getCol(m.CLUSTER);const s=yield(0,o.n)(r,c,h,n,d,f);if(null===s)throw new Error("Model is null");i=s,yield(0,e.cb)(500)})))),(0,e.Pl)((()=>_(void 0,void 0,void 0,(function*(){return yield(0,e.cb)(3e3)})))),(0,e.t6)("Tooltip",(()=>_(void 0,void 0,void 0,(function*(){(0,e.E3)((0,C.cr)(p.monomerOrCluster,0,0),!0,`Couldn't structure for monomer ${p.monomerOrCluster}`)}))),{skipReason:"Need to find a way to replace _package variable to call for Bio 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${p.positionOrClusterType}`),n.mutationCliffsSelection=(0,l.ZR)(n.positionColumns);for(const[t,i]of Object.entries(n.mutationCliffsSelection))(0,e.E3)(i.length,0,`Selection is not empty for position ${t} after clearing monomer-position selection`);(0,e.E3)(t.trueCount,0,"Selection count is not equal to 0 after clearing monomer-position selection");const r=i.findViewer(s.q.LOGO_SUMMARY_TABLE);(0,e.E3)(null!==r,!0,"Couldn't find Logo Summary Table viewer"),r.modifyClusterSelection(y),(0,e.E3)(r.clusterSelection[y.positionOrClusterType].includes(y.monomerOrCluster),!0,`Cluster ${y.monomerOrCluster} is not selected`),(0,e.E3)(t.trueCount,y.count,`Selection count is not equal to ${y.count} for cluster ${y.monomerOrCluster}`),r.modifyClusterSelection(w,{shiftPressed:!0,ctrlPressed:!1}),(0,e.E3)(r.clusterSelection[w.positionOrClusterType].includes(w.monomerOrCluster),!0,`Cluster ${w.monomerOrCluster} is not selected`),(0,e.E3)(t.trueCount,y.count+w.count,`Selection count is not equal to ${y.count+w.count} for cluster ${y.monomerOrCluster} and cluster \n ${w.monomerOrCluster}`),r.modifyClusterSelection(y,{shiftPressed:!0,ctrlPressed:!0}),(0,e.E3)(r.clusterSelection[y.positionOrClusterType].includes(y.monomerOrCluster),!1,`Cluster ${y.monomerOrCluster} is still selected after deselection`),(0,e.E3)(t.trueCount,w.count,`Selection count is not equal to ${w.count} for cluster ${w.monomerOrCluster} after deselection of cluster ${y.monomerOrCluster}`),r.initClusterSelection(),(0,e.E3)(r.isClusterSelectionEmpty,!0,"Selection is not empty after clearing cluster selection"),(0,e.E3)(t.trueCount,0,"Selection count is not equal to 0 after clearing cluster selection")})))),(0,e.t6)("Invariant Map selection",(()=>_(void 0,void 0,void 0,(function*(){const t=i.df.selection;for(const[t,n]of Object.entries(i.webLogoSelection))(0,e.E3)(n.length,0,`Filter is not empty for position ${t} after initialization`);i.modifyWebLogoSelection(g),(0,e.E3)(i.webLogoSelection[g.positionOrClusterType].includes(g.monomerOrCluster),!0,`Monomer ${g.monomerOrCluster} is not filtered at position ${g.positionOrClusterType}`),(0,e.E3)(t.trueCount,g.imCount,`Filter count is not equal to ${g.imCount} for monomer ${g.monomerOrCluster} at position ${g.positionOrClusterType}`),i.modifyWebLogoSelection(p,{shiftPressed:!0,ctrlPressed:!1}),(0,e.E3)(i.webLogoSelection[p.positionOrClusterType].includes(p.monomerOrCluster),!0,`Monomer ${p.monomerOrCluster} is not filtered at position ${p.positionOrClusterType}`),(0,e.E3)(t.trueCount,g.imCount,`Filter count is not equal to ${g.imCount} for monomer ${p.monomerOrCluster} at position ${p.positionOrClusterType}`),i.modifyWebLogoSelection(g,{shiftPressed:!0,ctrlPressed:!0}),(0,e.E3)(i.webLogoSelection[g.positionOrClusterType].includes(g.monomerOrCluster),!1,`Monomer ${g.monomerOrCluster} is still filtered at position \n ${g.positionOrClusterType} after deselection`),(0,e.E3)(t.trueCount,p.imCount,`Filter count is not equal to ${p.imCount} for monomer ${p.monomerOrCluster} at position ${p.positionOrClusterType} after deselection of monomer ${g.monomerOrCluster} at position ${g.positionOrClusterType}`),(0,e.E3)(null!==i.positionColumns,!0,"Position columns are not initialized"),i.webLogoSelection=(0,l.ZR)(i.positionColumns),(0,e.E3)(t.trueCount,0,"Filter count is not equal to 0 after clearing monomer-position filter");for(const[t,n]of Object.entries(i.webLogoSelection))(0,e.E3)(n.length,0,`Filter is not empty for position ${t} after clearing monomer-position filter`)}))))}),{clear:!1});var N=n(5070),M=function(t,e,n,i){return new(n||(n=Promise))((function(r,o){function s(t){try{l(i.next(t))}catch(t){o(t)}}function a(t){try{l(i.throw(t))}catch(t){o(t)}}function l(t){var e;t.done?r(t.value):(e=t.value,e instanceof n?e:new n((function(t){t(e)}))).then(s,a)}l((i=i.apply(t,e||[])).next())}))};(0,e.L1)("Model: Settings",(()=>{let n,i,r,c,h,d;(0,e.gM)((()=>M(void 0,void 0,void 0,(function*(){n=t.DataFrame.fromCsv(yield I.files.readAsText("tests/HELM_small.csv")),r=n.getCol(m.ACTIVITY),c=n.getCol(m.SEQUENCE),c.semType=t.SEMTYPE.MACROMOLECULE,c.setTag(t.TAGS.UNITS,u.Hi.HELM),d=(0,l.Y1)(r,a.rg.NONE),h=n.getCol(m.CLUSTER);const s=yield(0,o.n)(r,c,h,n,d,a.rg.NONE);if(null===s)throw new Error("Model is null");i=s,yield(0,e.cb)(500)})))),(0,e.Pl)((()=>M(void 0,void 0,void 0,(function*(){return yield(0,e.cb)(3e3)})))),(0,e.t6)("Activity scaling",(()=>M(void 0,void 0,void 0,(function*(){var t;const n=(t,e)=>`Activity mismatch at row ${t} for scaling method '${e}'`,o=1e-4,s=i.df.getCol(null===(t=i.settings)||void 0===t?void 0:t.activityColumnName).getRawData(),u=i.df.getCol(a.$2.ACTIVITY),c=i.df.rowCount;let h=u.getRawData();for(let t=0;t<c;t++)(0,e.Wj)(h[t],s[t],o,n(t,a.rg.NONE));h=(0,l.Y1)(r,a.rg.LG).getRawData();for(let t=0;t<c;t++)(0,e.Wj)(h[t],Math.log10(s[t]),o,n(t,a.rg.LG));h=(0,l.Y1)(r,a.rg.MINUS_LG).getRawData();for(let t=0;t<c;t++)(0,e.Wj)(h[t],-Math.log10(s[t]),o,n(t,a.rg.MINUS_LG));h=d.getRawData();for(let t=0;t<c;t++)(0,e.Wj)(h[t],s[t],o,n(t,a.rg.NONE))})))),(0,e.t6)("Mutation Cliffs",(()=>M(void 0,void 0,void 0,(function*(){const t=i.findViewer(s.q.SEQUENCE_VARIABILITY_MAP);(0,e.E3)(t.maxMutations,1,`Max mutations mismatch: expected 1, actual ${t.maxMutations}`),(0,e.E3)(t.minActivityDelta,0,`Min activity delta mismatch: expected 0, actual ${t.minActivityDelta}`),t.maxMutations=2,t.minActivityDelta=.5,(0,e.E3)(t.maxMutations,2,`Max mutations mismatch: expected 2, actual ${t.maxMutations}`),(0,e.E3)(t.minActivityDelta,.5,`Min activity delta mismatch: expected 0.5, actual ${t.minActivityDelta}`)})))),(0,e.t6)("Include columns",(()=>M(void 0,void 0,void 0,(function*(){var n,r;const o="rank",a={[o]:t.AGG.AVG};i.settings={columns:a};const l=i.findViewer(s.q.LOGO_SUMMARY_TABLE),u=(0,N.hX)(t.AGG.AVG,o);(0,e.E3)(null!==l.viewerGrid.col(u),!0,`Expected to include column '${o}' in ${s.q.LOGO_SUMMARY_TABLE} but it is absent`),i.settings={columns:{}},(0,e.E3)(Object.keys(null===(n=i.settings)||void 0===n?void 0:n.columns).length,0,`Expected to remove all column aggregations but columns {${Object.keys(null===(r=i.settings)||void 0===r?void 0:r.columns).join(" & ")}} are still included`),(0,e.E3)(null===l.viewerGrid.col(u),!0,`Expected to remove column '${o}' from ${s.q.LOGO_SUMMARY_TABLE} but it is still present`)})))),(0,e.t6)("Dendrogram",(()=>M(void 0,void 0,void 0,(function*(){var t,n;i.settings={showDendrogram:!0},(0,e.E3)(null===(t=i.settings)||void 0===t?void 0:t.showDendrogram,!0,"Dendrogram is disabled after enabling"),yield(0,e.bk)((()=>null!==i.findViewer(s.q.DENDROGRAM)),"Dendrogram is not present in the view after 5s delay",5e3),i.settings={showDendrogram:!1},(0,e.E3)(null===(n=i.settings)||void 0===n?void 0:n.showDendrogram,!1,"Dendrogram is enabled after disabling"),(0,e.E3)(null===i.findViewer(s.q.DENDROGRAM),!0,"Dendrogram is present in the view after disabling")}))),{skipReason:"Need to find a way to replace _package variable to call for Bio function with tests"})}),{clear:!1});var O=function(t,e,n,i){return new(n||(n=Promise))((function(r,o){function s(t){try{l(i.next(t))}catch(t){o(t)}}function a(t){try{l(i.throw(t))}catch(t){o(t)}}function l(t){var e;t.done?r(t.value):(e=t.value,e instanceof n?e:new n((function(t){t(e)}))).then(s,a)}l((i=i.apply(t,e||[])).next())}))};(0,e.L1)("Algorithms",(()=>{let n,i,r,o;(0,e.gM)((()=>O(void 0,void 0,void 0,(function*(){n=t.Column.fromList("int","test",[1,2,5]).getRawData(),i=[t.Column.fromList("string","1","AAA".split("")),t.Column.fromList("string","2","BCC".split("")),t.Column.fromList("string","3","CCD".split(""))].map((t=>({name:t.name,rawData:t.getRawData(),cat:t.categories}))),o=(0,l.eY)(t.Column.fromList("string","target",["1","2","2"])),r={maxMutations:1,minActivityDelta:2}})))),(0,e.t6)("MutationCliffs",(()=>O(void 0,void 0,void 0,(function*(){let t=yield(0,h.uz)(n,i,r);(0,e.E3)(t.has("C"),!0,"MutationCliffsInfo should have key 'C'"),(0,e.E3)(t.has("D"),!0,"MutationCliffsInfo should have key 'D'"),(0,e.E3)(t.has("A"),!1,"MutationCliffsInfo should not have key 'A'");const s=t.get("C"),a=t.get("D");(0,e.E3)(s.has("3"),!0,"MutationCliffsInfo['C'] should have key '3'"),(0,e.E3)(a.has("3"),!0,"MutationCliffsInfo['D'] should have key '3'");const l=s.get("3"),u=a.get("3");(0,e.E3)(l.has(1),!0,"MutationCliffsInfo['C']['3'] should have key 1"),(0,e.E3)(u.has(2),!0,"MutationCliffsInfo['D']['3'] should have key 2");const c=l.get(1),d=u.get(2);(0,e.E3)(c[0],2,"MutationCliffsInfo['C']['3'][1] should have value 2"),(0,e.E3)(d[0],1,"MutationCliffsInfo['D']['3'][2] should have value 1"),r.targetCol=o,r.currentTarget="1",t=yield(0,h.uz)(n,i,r),(0,e.E3)(t.size,0,"MutationCliffsInfo should be empty for target '1'")}))))}));var L=function(t,e,n,i){return new(n||(n=Promise))((function(r,o){function s(t){try{l(i.next(t))}catch(t){o(t)}}function a(t){try{l(i.throw(t))}catch(t){o(t)}}function l(t){var e;t.done?r(t.value):(e=t.value,e instanceof n?e:new n((function(t){t(e)}))).then(s,a)}l((i=i.apply(t,e||[])).next())}))};const I=new t.Package;function R(n,i,r){return L(this,void 0,void 0,(function*(){r.catchUnhandled=!1;const o=yield(0,e.N$)({category:n,test:i,testContext:r});return t.DataFrame.fromObjects(o)}))}function P(){return L(this,void 0,void 0,(function*(){yield(0,e.Xb)(I,I.getModule("package-test.js"))}))}})(),peptides_test=i})();
2
2
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