@datagrok/peptides 1.22.1 → 1.22.2

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 (9) hide show
  1. package/dist/package-test.js +1 -1
  2. package/dist/package-test.js.map +1 -1
  3. package/dist/package.js +1 -1
  4. package/dist/package.js.map +1 -1
  5. package/package.json +2 -2
  6. package/src/demo/fasta.ts +2 -6
  7. package/src/widgets/distribution.ts +1 -1
  8. package/test-console-output-1.log +91 -82
  9. package/test-record-1.mp4 +0 -0
package/dist/package.js CHANGED
@@ -1,2 +1,2 @@
1
- var peptides;(()=>{var t={3981:(t,e,n)=>{"use strict";var i;n.d(e,{o:()=>i}),function(t){t.BASE="HELM_BASE",t.SUGAR="HELM_SUGAR",t.LINKER="HELM_LINKER",t.AA="HELM_AA",t.CHEM="HELM_CHEM",t.BLOB="HELM_BLOB",t.NUCLEOTIDE="HELM_NUCLETIDE"}(i||(i={}))},8223:(t,e,n)=>{"use strict";n.d(e,{pj:()=>g,uL:()=>p});var i,r,o,s,a,l,u,c=n(6082),f=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 h=n(1199);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,h.Z.HAMMING,h.Z.LEVENSHTEIN,h.Z.MONOMER_CHEMICAL_DISTANCE,h.Z.NEEDLEMANN_WUNSCH,new RegExp("[rd]\\((\\w)\\)p?","g");var d=n(3077),m=n(439);async function g(){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 p(t,e,n){t instanceof c.Column&&(t=(0,d.R)(t,n).columns.toList());const i=(await g()).getMonomerLib(),r=new Array(t.length),o=t[0].length,s=new Float32Array(o);for(let n=0;n<t.length;++n){const a=n<e.length?e.getCanonical(n):m._S,l=i.getMonomer("PEPTIDE",a)?.smiles??"",u=t[n],h=u.getRawData(),d=u.categories,g=d.indexOf("");if(r[n]={categories:d,data:h,emptyIndex:g},void 0===a)continue;const p=c.Column.fromStrings("smiles",d.map((t=>i.getMonomer("PEPTIDE",t)?.smiles??""))),v=(c.DataFrame.fromColumns([p]),await f.chem.getSimilarities(p,l)),y=v?v.getRawData():null;for(let t=0;t<o;++t){const e=h[t];a!==m._S&&e!==g?s[t]+=y[e]:a===m._S&&e===g&&(s[t]+=1)}}for(let n=0;n<s.length;++n){let i=s[n]/e.length;for(let o=0;o<t.length;++o){const t=r[o];if(o>=e.length&&t.data[n]!==t.emptyIndex||t.data[n]===t.emptyIndex&&o<e.length){i=c.FLOAT_NULL;break}}s[n]=i}return c.Column.fromFloat32Array("Similarity",s)}},439:(t,e,n)=>{"use strict";n.d(e,{B5:()=>a,Hi:()=>i,YI:()=>r,_S:()=>c,b9:()=>f,gp:()=>o,q7:()=>u});var i,r,o,s=n(2738);!function(t){t.FASTA="fasta",t.SEPARATOR="separator",t.HELM="helm",t.CUSTOM="custom"}(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=/(?:\[([A-Za-z0-9_\-,()]+)\])|([A-Za-z\-])/g,l=new class{constructor(){this.fasta={peptide:new Set(["G","L","Y","S","E","Q","D","N","F","A","K","R","H","C","V","P","W","I","M","T"]),dna:new Set(["A","C","G","T"]),rna:new Set(["A","C","G","U"])}}},u=[new s.a(r.PT,l.fasta.peptide,.5),new s.a(r.DNA,l.fasta.dna,.55),new s.a(r.RNA,l.fasta.rna,.55)],c="",f={[i.FASTA]:"-",[i.SEPARATOR]:"",[i.HELM]:"*"}},2003:(t,e,n)=>{"use strict";n.d(e,{Hi:()=>i.Hi,SM:()=>r.SM,YI:()=>i.YI,gp:()=>i.gp,zS:()=>r.zS});var i=n(439),r=n(9634)},2738:(t,e,n)=>{"use strict";n.d(e,{X:()=>r,a:()=>i});class i{constructor(t,e,n){this.name=t,this.alphabet=e,this.cutoff=n}}class r extends i{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,{zS:()=>T,SM:()=>x});var i=n(6082),r=n(144),o=n.n(r);class s extends Float32Array{}function a(t){let e=0;for(let n=0;n<t.length;n++)e+=t[n]*t[n];return Math.sqrt(e)}var l=n(2738),u=n(439);class c{static makePalette(t,e=!1,n=c){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]}}c.undefinedColor="rgb(100,100,100)",c.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 f extends c{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,f)),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,f)),this.grokGroups}static get RasMol(){return void 0===this.rasMol&&(this.rasMol=new f({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 f.aaSynonyms?f.aaSynonyms[t]:t;return super.get(e)}}f.aaSynonyms={MeNle:"L",MeA:"A",MeG:"G",MeF:"F"};class h{static getPalette(t="grok"){switch(t){case"grok":return f.GrokGroups;case"lesk":return f.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]}}h.SemType="Aminoacids",h.SemTypeMultipleAlignment="AminoacidsMultipleAlignment",h.undefinedColor="rgb(100,100,100)",h.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"},h.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"},h.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(*)*"},h.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 d extends c{static get Chromatogram(){return void 0===this.chromatogram&&(this.chromatogram=new d({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(8223);function p(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 v{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 y{}class C extends y{get(t,e){return"#666666"}}class b extends y{static get palette(){return b._pallete||(b._pallete=b.buildPalette()),b._pallete}static buildPalette(){return(0,g.pj)().then((t=>{t.awaitLoaded(1/0).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]=p(n.meta.colors.default.background))}}}))}))})),[].concat(...Object.values(c.colourPalette))}get(t,e){const n=b.palette.length,i=b.customMonomerColors[t],r=e??"PEPTIDE";if(i&&i[r])return i[r];const o=v.hashCode(t)%n;return p(b.palette[o])}}b._pallete=null,b.customMonomerColors={},b.polymerTypes=[];class w extends c{static get Gray(){return void 0===this.gray&&(this.gray=new C),this.gray}static get Color(){return void 0===this.color&&(this.color=new b),this.color}}class A{get length(){return this.mList.length}isGap(t){return this.getOriginal(t)===this.gapOriginalMonomer}getCanonical(t){if(this.length<=t)throw new Error("Index out of 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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",t.MCL="MCL"}(G||(G={}));class H{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,N.Ej)(e,this.df.filter,this.positionColumns)),this._monomerPositionStats)}get analysisView(){var t,e,n;return void 0===this._analysisView&&(this._analysisView=this.id?g()(o.shell.tableViews).find((({dataFrame:t})=>(null==t?void 0:t.getTag(s.TAGS.ID))===this.id)):void 0,!this._analysisView&&(null===(t=o.shell.v)||void 0===t?void 0:t.preview)instanceof s.TableView&&(null===(n=null===(e=o.shell.v)||void 0===e?void 0:e.preview)||void 0===n?void 0:n.dataFrame)===this.df&&(this._analysisView=o.shell.v.preview),this._analysisView||(this._analysisView=o.shell.addTableView(this.df))),"1"===this.df.getTag(y.gp.MULTIPLE_VIEWS)||this._layoutEventInitialized||(0,b.Lv)()||(o.shell.v=this._analysisView),this._analysisView.grid.invalidate(),this._analysisView}get settings(){var t,e;const n=this.df.getTag(y.gp.SETTINGS);return n?(null!==(t=this._settings)&&void 0!==t||(this._settings=JSON.parse(n)),!(null===(e=this._settings)||void 0===e?void 0:e.mclSettings)||this._settings.mclSettings.webGPUDescriptionPromise instanceof Promise||(this._settings.mclSettings.webGPUDescriptionPromise=(0,D._)()),this._settings):null}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(G.DENDROGRAM);break;case"clusterMaxActivity":this.settings.showClusterMaxActivity?this.addClusterMaxActivityViewer():this.closeViewer(G.CLUSTER_MAX_ACTIVITY);break;case"logoSummaryTable":this.settings.showLogoSummaryTable?this.addLogoSummaryTable():this.closeViewer(G.LOGO_SUMMARY_TABLE);break;case"monomerPosition":this.settings.showMonomerPosition?this.addMonomerPosition():this.closeViewer(G.SEQUENCE_VARIABILITY_MAP);break;case"mostPotentResidues":this.settings.showMostPotentResidues?this.addMostPotentResidues():this.closeViewer(G.MOST_POTENT_RESIDUES);break;case"columns":const t=this.findViewer(G.LOGO_SUMMARY_TABLE);t._viewerGrid=null,t._logoSummaryTable=null,t.render();const e=this.findViewer(G.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(`${y.YX.WL}${y.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(`${y.YX.WL}${y.gp.INVARIANT_MAP_SELECTION}`,JSON.stringify(t)),this.fireBitsetChanged(null),this.analysisView.grid.invalidate()}get positionColumns(){const t=g()(this.df.columns.byTags({[y.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){if(t.columns.contains(y.$2.ACTIVITY_SCALED)&&!t.columns.contains(y.$2.ACTIVITY)&&(t.getCol(y.$2.ACTIVITY_SCALED).name=y.$2.ACTIVITY),!t.temp[H.modelName]){const e=t.temp[H.modelName]=new H(t),n=e.settings;n&&e.init(n);let i=!0;e.subs.push(s.debounce(t.onSelectionChanged,10).subscribe((n=>{var r;if(i||t.selection.anyTrue||!e._analysisView||!document.contains(e._analysisView.root)||e._analysisView.dataFrame!==t||!e.positionColumns)return void(i=!(null===(r=null==t?void 0:t.selection)||void 0===r?void 0:r.anyTrue));e.webLogoSelection=(0,b.ZR)(e.positionColumns);const o=e.findViewer(G.SEQUENCE_VARIABILITY_MAP);null!=o&&(o.invariantMapSelection=(0,b.ZR)(e.positionColumns),o.mutationCliffsSelection=(0,b.ZR)(e.positionColumns));const s=e.findViewer(G.MOST_POTENT_RESIDUES);null!=s&&(s.mutationCliffsSelection=(0,b.ZR)(e.positionColumns),s.invariantMapSelection=(0,b.ZR)(e.positionColumns));const a=e.findViewer(G.LOGO_SUMMARY_TABLE);null!=a&&(a.initClusterSelection({notify:!0}),a.render()),i=!0})))}return t.temp[H.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,o,l;const u=null===(t=this.df)||void 0===t?void 0:t.temp[H.modelName];if(!u)return null;const c=r.accordion("Peptides analysis panel");c.root.style.width="100%";const f=u.getVisibleSelection(),h=u.df.filter.anyFalse?` among ${u.df.filter.trueCount} filtered`:"",d=t=>{const e=[];for(const[n,i]of Object.entries(t))for(const t of i)e.push(`${n}:${t}`);return e.join(", ")},m=u.findViewer(G.LOGO_SUMMARY_TABLE),p=[],y=(null===m?[]:m.clusterSelection[T.W.ORIGINAL].concat(m.clusterSelection[T.W.CUSTOM])).join(", "),C=t=>{const e=r.divText(t);return e.innerHTML=t,e};0!==y.length&&p.push(C(`<b>Logo Summary Table</b> clusters: ${y}`));const x=u.findViewer(G.SEQUENCE_VARIABILITY_MAP),_=d(null!==(e=null==x?void 0:x.invariantMapSelection)&&void 0!==e?e:{}),M=d(null!==(n=null==x?void 0:x.mutationCliffsSelection)&&void 0!==n?n:{});0!==_.length&&p.push(C(`<b>Invariant map</b>: ${_}`)),0!==M.length&&p.push(C(`<b>Mutation cliffs</b>: ${M}`));const I=u.findViewer(G.MOST_POTENT_RESIDUES),O=d(null!==(i=null==I?void 0:I.invariantMapSelection)&&void 0!==i?i:{});0!==O.length&&p.push(C(`<b>Most potent residues</b>: ${O}`));const L=d(u.webLogoSelection);0!==L.length&&p.push(C(`<b>WebLogo</b>: ${L}`)),0!==p.length&&p.unshift(r.h1("Selection Sources"));const R=r.div(r.divV(p));c.addTitle(r.divV([r.h1(`${f.trueCount} selected rows${h}`),R],"css-gap-small")),f.anyTrue&&c.addPane("Actions",(()=>{try{const t=r.label("New view");if(v()(t).addClass("d4-link-action"),t.onclick=()=>u.createNewView(),t.onmouseover=t=>r.tooltip.show("Creates a new view from current selection",t.clientX+5,t.clientY+5),null===m)return r.divV([t]);const e=r.label("New cluster");v()(e).addClass("d4-link-action"),e.onclick=()=>{if(null===m)throw new Error("Logo summary table viewer is not found");m.clusterFromSelection()},e.onmouseover=t=>r.tooltip.show("Creates a new cluster from selection",t.clientX+5,t.clientY+5);const n=r.label("Remove cluster");return v()(n).addClass("d4-link-action"),n.onclick=()=>{const t=u.findViewer(G.LOGO_SUMMARY_TABLE);if(null===t)throw new Error("Logo summary table viewer is not found");t.removeCluster()},n.onmouseover=t=>r.tooltip.show("Removes currently selected custom cluster",t.clientX+5,t.clientY+5),n.style.visibility=0===m.clusterSelection[T.W.CUSTOM].length?"hidden":"visible",r.divV([t,e,n])}catch(t){const e=r.divText("Error in Actions");return r.tooltip.bind(e,String(t)),e}}),!0);let P=u.settings;const k=[x,I,m].filter((t=>null!==t&&(t.type!==this.accordionSource||(P=t,!1))));if(null===P)throw new Error("PeptidesError: Model is the source of accordion but is not initialized");P!==u.settings&&k.push(u.settings);const V=k.filter((t=>null!==t&&(0,b.$s)(P,t)&&(t!==u.settings||u.isInitialized)));V.push(P);const D=s.BitSet.create(u.df.rowCount);for(const t of V){const e=t===this.settings?(0,b.KT)(this.webLogoSelection,this.monomerPositionStats):t instanceof T.s?(0,b.KT)(t.clusterSelection,t.clusterStats):t instanceof w.xN?(0,b.KT)(t.mutationCliffsSelection,(0,b.qI)(null!==(o=t.mutationCliffs)&&void 0!==o?o:new Map,u.df.rowCount)):null;if(null!==e&&D.or(e),t instanceof w.J){const e=(0,b.KT)(t.invariantMapSelection,t.monomerPositionStats);null!==e&&D.or(e)}}const U=P;P===u.settings||U instanceof T.s||null==U.mutationCliffs||c.addPane("Mutation Cliffs pairs",(()=>(0,S.F)(u.df,{mutationCliffs:U.mutationCliffs,mutationCliffsSelection:U.mutationCliffsSelection,gridColumns:u.analysisView.grid.columns,sequenceColumnName:U.sequenceColumnName,positionColumns:U.positionColumns,activityCol:U.getScaledActivityColumn()}).root),!0);const q=P===u.settings,B=q?this.webLogoSelection:P instanceof w.J?P.invariantMapSelection:{},Y=P instanceof T.s?P.clusterSelection:null!==(l=null==m?void 0:m.clusterSelection)&&void 0!==l?l:{};c.addPane("Distribution",(()=>{var t;try{return(0,E.HV)(u.df,{peptideSelection:D,columns:q?null!==(t=u.settings.columns)&&void 0!==t?t:{}:P.getAggregationColumns(),activityCol:q?u.getScaledActivityColumn():P.getScaledActivityColumn(),monomerPositionSelection:B,clusterSelection:Y,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 W=(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 c.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,f=null;try{c=u.getRawData(),f=u.categories}catch(t){}const h=c&&f?a.some((t=>t.name===u.name))?t=>c[t]:t=>f[c[t]]:t=>u.get(t),d=u.name===e.activityColumn.name?o.columns.addNewFloat(r.name).init((t=>h(t))):o.columns.addNewVirtual(r.name,(t=>h(t)),u.type);for(const[t,e]of u.tags)d.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 f=(0,N.Ej)(e.activityColumn,o.filter,e.positionColumns,{isFiltered:o.filter.anyTrue||o.filter.anyFalse}),h={isSelectionTable:!0,cachedWebLogoTooltip:()=>({bar:"",tooltip:null}),webLogoBounds:()=>({}),colorPalette:()=>e.colorPalette},d={x:0,y:0,monomerPosition:{},mpStats:f};return e.isAnalysis&&(0,A.FZ)(u,f,e.positionColumns,e.activityColumn,h,d),c}(u.df,{positionColumns:q?u.positionColumns:P.positionColumns,columns:q?null!==(t=u.settings.columns)&&void 0!==t?t:{}:P.getAggregationColumns(),activityColumn:q?u.getScaledActivityColumn():P.getScaledActivityColumn(),gridColumns:u.analysisView.grid.columns,colorPalette:(0,a.SM)(u.df.getCol(q?u.settings.sequenceColumnName:P.sequenceColumnName),F.Z.getSeqHelper()),tableSelection:u.getCombinedSelection(),isAnalysis:null!==u.settings&&(q||W(u.settings.columns,P.getAggregationColumns()))})}catch(t){const e=r.divText("Error in Selection");return r.tooltip.bind(e,String(t)),e}}),!0),c}getScaledActivityColumn(t=!1){const e=this.df.col(y.$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),F.Z.getSeqHelper()),webLogoBounds:()=>this.webLogoBounds,cachedWebLogoTooltip:()=>this.cachedWebLogoTooltip,highlightCallback:(t,e,n)=>{(0,b.dl)(t,e,n),this.isHighlighting=!0},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");A.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,u.R)(this.df.getCol(this.settings.sequenceColumnName),F.Z.getSeqHelper()),i=n.columns.names();if(i.every((t=>e.contains(t))))i.forEach((t=>A.rI(this.df.col(t),this.alphabet)));else 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(y.gp.ANALYSIS_COL,"true"),i.setTag(y.gp.POSITION_COL,"true"),A.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(y.$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)!==y.uF.MONOMER)||!(!t.isTableCell||(null===(r=t.tableColumn)||void 0===r?void 0:r.semType)!==y.uF.MONOMER)}))}getCombinedSelection(){var t,e,n,i,r,o,a,l;const u=new d.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 f=this.findViewer(G.SEQUENCE_VARIABILITY_MAP);c(null!==(t=null==f?void 0:f.invariantMapSelection)&&void 0!==t?t:{},null!==(e=null==f?void 0:f.monomerPositionStats)&&void 0!==e?e:null),((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)}}})(null!==(n=null==f?void 0:f.mutationCliffsSelection)&&void 0!==n?n:{},null!==(i=null==f?void 0:f.mutationCliffs)&&void 0!==i?i:null);const h=this.findViewer(G.MOST_POTENT_RESIDUES);c(null!==(r=null==h?void 0:h.invariantMapSelection)&&void 0!==r?r:{},null!==(o=null==h?void 0:h.monomerPositionStats)&&void 0!==o?o:null);const m=this.findViewer(G.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;let n=null;const i=()=>{try{null!=n&&(clearTimeout(n),n=null);const t=this.createAccordion();if(null===t)return;o.shell.o=t.root,n=setTimeout((()=>{o.shell.o!=t.root&&(o.shell.o=t.root)}),1500)}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){_._package.logger.debug("Peptides: Error on selection changed"),_._package.logger.debug(t)}finally{i()}})),e.onChanged.subscribe((()=>{var t,e;try{if(this.controlFire)return void(this.controlFire=!1);const n=this.findViewer(G.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){_._package.logger.debug("Peptides: Error on filter changed"),_._package.logger.debug(t)}finally{i()}})),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 f=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=f.includes(e.column.name)||e.column.name===y.$2.ACTIVITY}setTimeout((()=>{for(const t of l){const e=o.col(t.name);if(null===e)throw new Error(`PeptidesError: Could not set column width: grid column '${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 U(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){_._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(y.gp.MULTIPLE_VIEWS)){const t=r.iconFA("wrench",(()=>(0,x.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=v()(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);f(this.df,t,t.get(this.df.currentRowIdx),i.IDENTITY,F.Z.getSeqHelper()).then((e=>e.setTag(y.gp.IDENTITY_TEMPLATE,t.get(this.df.currentRowIdx)))).catch((t=>_._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);f(this.df,t,t.get(this.df.currentRowIdx),i.SIMILARITY,F.Z.getSeqHelper()).then((e=>e.setTag(y.gp.SIMILARITY_TEMPLATE,t.get(this.df.currentRowIdx)))).catch((t=>_._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 U(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(G.LOGO_SUMMARY_TABLE,t);(0,b.Lv)()&&this.analysisView.addViewer(e),this.analysisView.dockManager.dock(e,s.DOCK_TYPE.RIGHT,null,G.LOGO_SUMMARY_TABLE),e.viewerGrid.invalidate()}))}addClusterMaxActivityViewer(t){return U(this,void 0,void 0,(function*(){var e,n,i,r,o,a,l,u,c;const f=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(G.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!=f?f:null===(a=g()(this.df.columns.categorical).next().value)||void 0===a?void 0:a.name,activityTarget:y.wf.HIGH,connectivityColumnName:null!==(u=null!==(l=this._mclCols.find((t=>t.toLowerCase().startsWith("connectivity"))))&&void 0!==l?l:this.df.columns.names().find((t=>{var e;return t.toLowerCase().includes("connectivity")&&(null===(e=this.df.col(t))||void 0===e?void 0:e.isNumerical)})))&&void 0!==u?u:"",clusterSizeThreshold:20,activityThreshold:1e3});const h=yield this.df.plot.fromType(G.CLUSTER_MAX_ACTIVITY,t),d=null!==(c=this.findViewerNode(G.LOGO_SUMMARY_TABLE))&&void 0!==c?c:null;this.analysisView.dockManager.dock(h,d?s.DOCK_TYPE.DOWN:s.DOCK_TYPE.RIGHT,d,G.CLUSTER_MAX_ACTIVITY)}))}addMonomerPosition(t){return U(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:y.wf.HIGH});const e=yield this.df.plot.fromType(G.SEQUENCE_VARIABILITY_MAP,t);(0,b.Lv)()&&this.analysisView.addViewer(e);const n=this.findViewer(G.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(G.MOST_POTENT_RESIDUES),.7];i.dock(e,r,o,G.SEQUENCE_VARIABILITY_MAP,a)}))}addMostPotentResidues(t){return U(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:y.wf.HIGH});const e=yield this.df.plot.fromType(G.MOST_POTENT_RESIDUES,t);(0,b.Lv)()&&this.analysisView.addViewer(e);const n=this.findViewer(G.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(G.SEQUENCE_VARIABILITY_MAP),.3];i.dock(e,r,o,G.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===y.gp.SETTINGS?n:"");e.name="Peptides Multiple Views",e.setTag(y.gp.MULTIPLE_VIEWS,"1");const n=o.shell.addTableView(e),i=this.findViewer(G.LOGO_SUMMARY_TABLE);return null!=i&&n.addViewer(G.LOGO_SUMMARY_TABLE,{[`sequence${y.To}`]:i.sequenceColumnName,[`activity${y.To}`]:i.activityColumnName,activityScaling:i.activityScaling,webLogoMode:i.webLogoMode,membersRatioThreshold:i.membersRatioThreshold,[`clusters${y.To}`]:i.clustersColumnName}),e.getTag(s.TAGS.ID)}clusterEmbeddings(){return U(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),f=this.df.columns.getUnusedName("Cluster (DBSCAN)"),h=this.df.columns.addNewString(f);h.init((t=>c[t].toString())),null!==this._sequenceSpaceViewer&&(this._sequenceSpaceViewer.props.colorColumnName=h.name),this._sequenceSpaceCols=[i[0],i[1],h.name];const d=this.analysisView.grid.col(h.name);d&&(d.visible=!1)}))}addMCLClusters(){return U(this,void 0,void 0,(function*(){var t,e,n,i,r;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 a=this.df.getCol(this.settings.sequenceColumnName);null!==(n=(r=this.settings).mclSettings)&&void 0!==n||(r.mclSettings=new C.av);const l=this.settings.mclSettings;let u=0;const c=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),u++}5===u&&c.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)}})),h=JSON.stringify({cols:[a].map((t=>t.name)),metrics:[l.distanceF],weights:[1],aggregationMethod:V.MANHATTAN,preprocessingFuncs:["macromoleculePreprocessingFunction"],preprocessingFuncArgs:[{gapOpen:l.gapOpen,gapExtend:l.gapExtend,fingerprintType:l.fingerprintType}],threshold:l.threshold,maxIterations:l.maxIterations,useWebGPU:l.useWebGPU,inflate:l.inflation,minClusterSize:l.minClusterSize}),d=null!==(i=this.analysisView)&&void 0!==i?i:o.shell.getTableView(this.df.name);if(d){const t=s.Func.find({package:"EDA",name:"markovClusteringViewer"})[0];if(!t)throw new Error("Markov clustering function is not found");yield t.apply(),d.addViewer(G.MCL,{mclProps:h}),yield s.delay(500),this._mclViewer=this.findViewer(G.MCL),yield this._mclViewer.initPromise;const e=this.findViewer(G.LOGO_SUMMARY_TABLE);e&&(e._clusterStats=null,e._clusterSelection=null,e._viewerGrid=null,e._logoSummaryTable=null,e.render())}}))}addSequenceSpace(){return U(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=F.Z.getSeqHelper().getSeqHandler(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,f=null!==(r=null===(i=this.settings)||void 0===i?void 0:i.sequenceSpaceParams)&&void 0!==r?r:new C.GI(c);f.clusterEmbeddings=c;const d={table:this.df,molecules:l,methodName:h.UMAP,similarityMetric:f.distanceF,plotEmbeddings:!0,options:{bypassLargeDataWarning:!0,dbScanEpsilon:f.epsilon,dbScanMinPts:f.minPts,randomSeed:"1",preprocessingFuncArgs:{gapOpen:f.gapOpen,gapExtend:f.gapExtend,fingerprintType:f.fingerprintType}},clusterEmbeddings:f.clusterEmbeddings};let m=0;const g=f.clusterEmbeddings?3:2,p=this.df.onColumnsAdded.subscribe((t=>{for(const e of t.columns)if(e.name.toLowerCase().startsWith("embed_")||f.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&&p.unsubscribe()})),v=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)}))}v.unsubscribe()}}catch(t){console.error(t)}})),y=yield o.functions.call("Bio:sequenceSpaceTopMenu",d);v.unsubscribe(),y instanceof s.ScatterPlotViewer&&(f.clusterEmbeddings||t.clusterCol||(y.props.colorColumnName=this.getScaledActivityColumn().name),y.props.showXSelector=!1,y.props.showYSelector=!1,t.clusterCol&&(y.props.colorColumnName=t.clusterCol.name),this._sequenceSpaceViewer=y,y.onContextMenu.subscribe((t=>{try{t.item("Modify Sequence space parameters",(()=>{(0,x.OH)(this)}))}catch(t){}})))}))}}H.modelName="peptidesModel"},6920:(t,e,n)=>{"use strict";n.r(e),n.d(e,{Peptides:()=>K,_package:()=>Y,clusterMaxActivity:()=>nt,getMonomerWorksInstance:()=>W,getTreeHelperInstance:()=>j,initPeptides:()=>$,logoSummaryTable:()=>et,lstPiechartCellRenderer:()=>ot,macromoleculeSarFastaDemo:()=>rt,manualAlignment:()=>it,monomerPosition:()=>J,mostPotentResidues:()=>tt,peptidesDialog:()=>Q,peptidesPanel:()=>X,testInitFunctionPeptides:()=>Z});var i=n(4328),r=n(7389),o=n(6082),s=n(5082),a=n(7233),l=n.n(a),u=(n(4788),n(768)),c=n(726),f=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())}))},h=n(3541),d=n(5480);n(3981);class m{constructor(t){this.monomerLib=t}getCappedRotatedMonomer(t,e){const n=this.monomerLib.getMonomer(t,e);return n?n.molfile:null}}var g=n(4139),p=n(8608),v=n(2003),y=n(8070),C=n(115),b=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())}))},w=n(5072),A=n.n(w),S=n(7825),E=n.n(S),T=n(7659),x=n.n(T),_=n(5056),N=n.n(_),M=n(540),I=n.n(M),O=n(1113),L=n.n(O),R=n(6677),P={};P.styleTagTransform=L(),P.setAttributes=N(),P.insert=x().bind(null,"head"),P.domAPI=E(),P.insertStyleElement=I(),A()(R.A,P),R.A&&R.A.locals&&R.A.locals;var k;!function(t){let e,n;!function(t){t.vert=function(t){return r.divV(t.map((t=>r.render(t))),{classes:"u2-panel"})},t.horz=function(t){return r.divH(t.map((t=>r.render(t))),{classes:"u2-panel"})}}(e=t.panels||(t.panels={})),t.appHeader=function(t){const n=r.iconImage("",t.iconPath);return l()(n).addClass("ui-app-header-icon").css("margin-right","20px"),e.horz([n,e.vert([r.markdown(t.description),t.learnMoreUrl?r.link("Learn more",t.learnMoreUrl):null])])},function(t){t.runAsync=function(t,e){return n=this,o=void 0,a=function*(){r.setUpdateIndicator(t,!0);try{return yield 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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",g.wf.HIGH,{choices:[g.wf.HIGH,g.wf.LOW]}),this.clusterSizeThreshold=this.int("clusterSizeThreshold",20),this.activityThreshold=this.int("activityThreshold",1e3),this.connectivityColumnName=this.column("connectivity",{nullable:!0})}get model(){return u.i.getInstance(this.dataFrame)}createSCViewer(){var t;const e={showXAxis:!0,showYAxis:!0,showXSelector:!1,showYSelector:!1,showColorSelector:!1,xAxisType:o.AxisType.logarithmic,yAxisType:o.AxisType.logarithmic,invertYAxis:this.activityTarget===g.wf.LOW,xColumnName:F.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),s=null!=this.connectivityColumnName?this.dataFrame.columns.byName(this.connectivityColumnName):null;if(![o.COLUMN_TYPE.FLOAT,o.COLUMN_TYPE.INT,o.COLUMN_TYPE.BIG_INT,o.COLUMN_TYPE.QNUM].includes(n.type))return this.viewerError="Activity column should be numeric",null;const a=this.dataFrame.columns.getOrCreate(F.clusterSizeColName,o.TYPE.INT),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)}a.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=o.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 r=n.get(t),o=u[e];if((null==o||null==o||r>n.get(o)&&this.activityTarget===g.wf.HIGH||r<n.get(o)&&this.activityTarget===g.wf.LOW)&&(u[e]=t),s){const n=s.get(t),i=c[e];(null==i||null==i||n>s.get(i))&&(c[e]=t)}}const f=this.dataFrame.columns.getOrCreate(F.maxActivityInClusterColName,o.COLUMN_TYPE.INT);f.init((t=>i.isNone(t)?0:t===u[i.get(t)]?1:0)),this.dataFrame.columns.getOrCreate(F.maxConnectivityInClusterColName,o.COLUMN_TYPE.INT).init((t=>i.isNone(t)?0:t===c[i.get(t)]?1:0)),this.dataFrame.columns.getOrCreate(F.synSelectionColName,o.TYPE.STRING).init((t=>{if(i.isNone(t))return null;let e=null;return t===u[i.get(t)]&&(e=F.maxActivityLabel),s&&t===c[i.get(t)]&&(e=e?`${e}, ${F.maxConnectivityLabel}`:F.maxConnectivityLabel),e})),e.xColumnName=F.clusterSizeColName,e.yColumnName=this.activityColumnName,e.filter=this.scFilterQuery,this.viewerError="";const h=o.Viewer.scatterPlot(this.dataFrame,e);this.selectionSubscription&&this.selectionSubscription.unsubscribe(),this.selectionSubscription=h.onDataEvent.pipe((0,G.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:[],s=this.dataFrame.selection,a=o.BitSet.create(this.dataFrame.rowCount,(t=>1==f.get(t)));a.and(s);for(let t=0;t<r.length;t++){const e=r[t],n=i.get(e);i.isNone(e)||(a.set(e,!0),null!=c[n]&&a.set(c[n],!0))}a.fireChanged();const l=a.getSelectedIndexes();for(const t of l){const e=i.get(t);null!=e&&null!=c[e]&&a.set(c[e],!0)}setTimeout((()=>{this.dataFrame.selection.copyFrom(a,!0),setTimeout((()=>{this.model&&this.model.createAccordion()}),200)}),200)}));const d=()=>{const t=o.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=r.iconSvg("select-all",(()=>{d()}),"Select 3 Active quadrants"),this._selsectIcon.style.cursor="pointer",this._selsectIcon.style.marginRight="5px",d(),this.linesDrawSubscription&&this.linesDrawSubscription.unsubscribe(),this.linesDrawSubscription=h.onBeforeDrawScene.subscribe((()=>{const t=h.getInfo().canvas.getContext("2d"),e=h.viewport,n=h.worldToScreen(e.x,this.activityThreshold),i=h.worldToScreen(this.clusterSizeThreshold,e.y),r=h.worldToScreen(e.x+e.width,this.activityThreshold),o=h.worldToScreen(this.clusterSizeThreshold,e.y+e.height);t.beginPath(),t.strokeStyle="rgb(0,0,0)",t.lineWidth=1,t.moveTo(n.x,n.y),t.lineTo(r.x,r.y),t.moveTo(i.x,i.y),t.lineTo(o.x,o.y),t.stroke(),t.closePath()})),h}onTableAttached(){var t,e,n,i,r,o,s,a,l,u,c,f;super.onTableAttached();const h=null!==(e=null===(t=this.dataFrame)||void 0===t?void 0:t.col(g.$2.ACTIVITY))&&void 0!==e?e:null===(i=D()(null===(n=this.dataFrame)||void 0===n?void 0:n.columns.numerical).next())||void 0===i?void 0:i.value;null!=h&&(null===(r=this.getProperty(`activity${g.To}`))||void 0===r||r.set(this,h.name));const d=null===(s=D()(null===(o=this.dataFrame)||void 0===o?void 0:o.columns.categorical).next())||void 0===s?void 0:s.value;null!=d&&(null===(a=this.getProperty(`cluster${g.To}`))||void 0===a||a.set(this,d.name));const m=null===(u=D()(null===(l=this.dataFrame)||void 0===l?void 0:l.columns.numerical).next())||void 0===u?void 0:u.value;null!=m&&(null===(c=this.getProperty(`connectivity${g.To}`))||void 0===c||c.set(this,m.name)),this.render(),null===(f=this.dataFrame)||void 0===f||f.onDataChanged.subscribe((()=>{this.render()}))}render(){this.renderTimeout&&clearTimeout(this.renderTimeout),this.renderTimeout=setTimeout((()=>{var t,e;if(!this.dataFrame)return;l()(this.root).empty();const n=this.scViewer;if(null==n)return void this.root.appendChild(r.divText(null!==(t=this.viewerError)&&void 0!==t?t:"Error creating scatter plot"));const i=r.div("Cluster Size",{style:{alignSelf:"center",color:"var(--grey-6)",marginBottom:"5px"}}),o=r.div(this.activityTarget===g.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(r.divH([o,r.divV([r.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${g.To}`&&(this._scViewer=null),this.render()}}F.clusterSizeColName="~cluster.size",F.maxActivityInClusterColName="~max.activity.for.cluster",F.maxConnectivityInClusterColName="~max.connectivity.for.cluster",F.synSelectionColName="Syn Selection",F.maxActivityLabel="Max Activity",F.maxConnectivityLabel="Max Connectivity";var U=n(3163),H=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())}))};let q,B=null;const Y=new o.Package;function W(){return B}function j(){return q}function $(){return H(this,void 0,void 0,(function*(){try{null!=B||(B=new m(yield i.functions.call("Bio:getBioLib"))),null!=q||(q=yield async function(){const t="Dendrogram",e=o.Func.find({package:t,name:"getTreeHelper"});if(0===e.length)throw new Error(`Package "${t}" must be installed for TreeHelper.`);return(await e[0].prepare().call()).getOutputParamValue()}()),yield c.Z.loadComponents()}catch(t){i.log.error(t)}}))}function z(t){return H(this,void 0,void 0,(function*(){const e=o.TaskBarProgressIndicator.create("Loading Peptides"),n=Y.webRoot+"files/"+t,r=yield i.data.loadTable(n);r.name="Peptides",i.shell.addTableView(r).name="PeptidesView",i.shell.windows.showProperties=!0,e.close()}))}function K(){const t=k.appHeader({iconPath:Y.getIconUrl(),learnMoreUrl:"https://github.com/datagrok-ai/public/blob/master/help/domains/bio/peptides.md",description:"- Automatically recognizes peptides in your data\n- Invariant map and mutation cliffs\n- Logo plots to explore sequence composition\n- Hierarchical clustering\n- Sequence space to analyze clustering and activity cliffs\n- Finds statistically significant changes in activity for monomer/positions\n"}),e=i.shell.windows;e.showToolbox=!1,e.showHelp=!1,e.showProperties=!1;const n=o.View.create();return n.name="Peptides",r.appendAll(n.root,[t,r.divH([r.button("Simple demo",(()=>z("aligned.csv")),""),r.button("Complex demo",(()=>z("aligned_2.csv")),""),r.button("HELM demo",(()=>z("aligned_3.csv")),"")])]),n}function Q(){var t;if(!i.shell.t||!(null===(t=i.shell.t.columns.bySemType("Macromolecule"))||void 0===t?void 0:t.length))return i.shell.warning("SAR Analysis requires an active table with Macromolecule column"),null;if(!o.Utils.firstOrNull(i.shell.t.columns.numerical))return i.shell.warning("SAR Analysis requires an active table with at least one numerical column for activity"),null;const e=(0,s.v)(i.shell.t),n=r.dialog("Analyze Peptides").add(e.host).onOK((()=>H(this,void 0,void 0,(function*(){e.callback()||n.show()}))));return n.show()}function Z(t){return H(this,void 0,void 0,(function*(){i.shell.info("Test init function for Peptides package"),i.shell.info("Viewer name: "+t.dataFrame.name),yield new Promise((t=>setTimeout(t,1e3)))}))}function X(t){if(!t.dataFrame||!o.Utils.firstOrNull(t.dataFrame.columns.numerical))return new o.Widget(r.divText("SAR Analysis requires an active table with at least one numerical column for activity"));const e=(0,s.v)(t.dataFrame,t);return new o.Widget(e.host)}function J(){return new h.J}function tt(){return new h.UJ}function et(){return new d.s}function nt(){return new F}function it(t){const e=i.shell.t,n=null==e?void 0:e.temp[u.i.modelName];return n?function(t,e){const n=r.input.textArea("",{value:t.get(e.currentRowIdx)});l()(n.root).addClass("pep-textinput");const s=r.button("Apply",(()=>f(this,void 0,void 0,(function*(){const r=c.Z.getSeqHelper().getSeqHandler(t),o=n.value,s=r.splitter(o),a=e.currentRowIdx;t.set(a,o);for(let t=0;t<s.length;t++){const n=s.getCanonical(t);null!==e.col(t.toString())&&e.set(t.toString(),a,n)}const l=i.shell.o;i.shell.o=null,u.i.getInstance(e).updateGrid(),setTimeout((()=>{i.shell.o=l}),100)}))),"Apply changes"),a=r.button(r.iconFA("redo"),(()=>n.value=t.get(e.currentRowIdx)),"Reset");return l()(a).addClass("pep-snippet-editor-icon pep-reset-icon"),new o.Widget(r.divV([a,n.root,s],"pep-textarea-box"))}(e.getCol(n.settings.sequenceColumnName),e):new o.Widget(r.divText("Manual alignment works 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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[d.W.CUSTOM].includes(e)||n[d.W.ORIGINAL].includes(e))&&v(t,i)}function A(t,e,n,u,c,f={x:0,y:0,mpStats:{},monomerPosition:{}}){var d;if(null!==(d=c.isSelectionTable)&&void 0!==d||(c.isSelectionTable=!1),0==Object.keys(f.mpStats).length&&(f.mpStats=e),c.isSelectionTable&&(!c.webLogoBounds||!c.cachedWebLogoTooltip))throw new Error("Peptides: Cannot set WebLogo renderer for selection table without `headerSelectedMonomers`, `webLogoBounds` and `cachedWebLogoTooltip` options.");const m=t.dataFrame;t.setOptions({colHeaderHeight:130});t.onCellRender.subscribe((t=>(t=>{var i;const l=t.g,f=t.bounds,h=t.cell.tableColumn;l.save();try{if(l.beginPath(),l.clearRect(f.x,f.y,f.width,f.height),l.rect(f.x,f.y,f.width,f.height),l.clip(),t.cell.isColHeader&&(null==h?void 0:h.semType)===o.uF.MONOMER){let d;if(m.filter.anyFalse){const t=null!==(i=m.temp[o.gp.M_P_STATS_CACHE])&&void 0!==i?i:{},e=null==t?void 0:t[h.name],r=m.filter.getBuffer();if(t&&e&&e.filter.length===r.length&&e.filter.every(((t,e)=>t===r[e])))d=e.stats[h.name];else{const e=(0,a.Ej)(u,m.filter,n,{isFiltered:!0,columns:[h.name]});d=e[h.name],t[h.name]={filter:m.filter.getBuffer(),stats:e,selection:m.selection.getBuffer()}}m.temp[o.gp.M_P_STATS_CACHE]=t}else d=c.isSelectionTable?(0,a.Ej)(u,m.filter,n,{isFiltered:!0,columns:[h.name]})[h.name]:e[h.name];if(!d)return;const v=Object.keys(d).sort(((t,e)=>""===t||"-"===t?1:""===e||"-"===e?-1:0)).filter((t=>"general"!==t));c.webLogoBounds()[h.name]=function(t,e,n,i,o,a,l,u={},c={}){var f,h,d,m,v,y,C,b,w;const A=window.devicePixelRatio;null!==(f=c.symbolStyle)&&void 0!==f||(c.symbolStyle="16px Roboto, Roboto Local, sans-serif"),null!==(h=c.upperLetterHeight)&&void 0!==h||(c.upperLetterHeight=12.2),null!==(d=c.upperLetterAscent)&&void 0!==d||(c.upperLetterAscent=.25),null!==(m=c.marginVertical)&&void 0!==m||(c.marginVertical=1),null!==(v=c.marginHorizontal)&&void 0!==v||(c.marginHorizontal=1),null!==(y=c.selectionWidth)&&void 0!==y||(c.selectionWidth=2),null!==(C=c.textHeight)&&void 0!==C||(c.textHeight=13),null!==(b=c.headerStyle)&&void 0!==b||(c.headerStyle=`bold ${c.textHeight*A}px Roboto, Roboto Local, sans-serif`);const S=(o.length-1)*c.upperLetterAscent;let E=(e.y+c.marginVertical)*A;const T=(e.height-2*c.marginVertical-S-1.25*c.textHeight)*A,x=(e.x+c.marginHorizontal)*A,_=Math.max(c.selectionWidth*A,.05*e.width*A),N=2*c.marginHorizontal+c.selectionWidth,M=(e.width-(N+c.marginHorizontal))*A,I=(e.x+N)*A,O=g.Z.getMonomerLib(),L={};for(const e of o){const i=T*(n[e].count/a),o=T*((null!==(w=u[e])&&void 0!==w?w:0)/a);if(L[e]=new r.Rect(I/A,E/A,M/A,i/A),t.resetTransform(),"-"!==e&&""!==e){const n=(0,s.zS)(e,5),a=t.measureText(n);o>0&&(t.lineWidth=_,t.line(x,E,x,E+o,r.Color.rowSelection));const l=O.getMonomerTextColor(p.o.AA,e);t.fillStyle=l,t.textAlign="left",t.textBaseline="top",t.font=c.symbolStyle;const u=M/a.width,f=i/c.upperLetterHeight;t.setTransform(u,0,0,f,I,E),t.fillText(n,0,0,a.width)}E+=i+c.upperLetterAscent*A}return t.resetTransform(),t.fillStyle=r.Color.toHtml(r.Color.black),t.textAlign="center",t.textBaseline="top",t.font=c.headerStyle,t.fillText(i,(e.x+e.width/2)*A,(e.y+e.height-c.textHeight)*A),L}(l,f,d,h.name,v,m.filter.trueCount,c.colorPalette(),c.headerSelectedMonomers?c.headerSelectedMonomers()[h.name]:{}),t.preventDefault()}}catch(t){console.warn(`PeptidesHeaderLogoError: couldn't render WebLogo for column \`${h.name}\`. See original error below.`),console.warn(t)}finally{l.restore()}})(t)));const v=n=>{var r;const s=t.hitTest(n.offsetX,n.offsetY);if((null==s?void 0:s.isColHeader)&&(null===(r=s.tableColumn)||void 0===r?void 0:r.semType)===o.uF.MONOMER){const t=function(t,e,n){const i=n[t.tableColumn.name];if(!i)return null;for(const[n,r]of Object.entries(i)){const i=e.offsetX>=r.x&&e.offsetX<=r.x+r.width,o=e.offsetY>=r.y&&e.offsetY<=r.y+r.height;if(i&&o)return{monomerOrCluster:n,positionOrClusterType:t.tableColumn.name}}return null}(s,n,c.webLogoBounds());if(null===t)return void(c.isSelectionTable||null==c.unhighlightCallback||c.unhighlightCallback());f.monomerPosition=t,function(t,e,n,r,o,s){if("click"!==t.type||o.isSelectionTable||null==o.selectionCallback){const a=`${e.positionOrClusterType} = ${e.monomerOrCluster}`;o.cachedWebLogoTooltip().bar===a?i.tooltip.show(o.cachedWebLogoTooltip().tooltip,t.clientX,t.clientY):(o.cachedWebLogoTooltip().bar=a,s.x=t.clientX,s.y=t.clientY,s.monomerPosition=e,o.cachedWebLogoTooltip().tooltip=(0,h.Y)(n,r,[],s))}else o.selectionCallback(e,{shiftPressed:t.shiftKey,ctrlPressed:t.ctrlKey})}(n,t,m,u,c,f),c.isSelectionTable||null==c.highlightCallback||c.highlightCallback(t,m,e)}else null!=c.unhighlightCallback&&c.unhighlightCallback()};l.fromEvent(t.overlay,"mousemove").subscribe((t=>v(t))),l.fromEvent(t.overlay,"click").subscribe((t=>v(t))),l.fromEvent(t.overlay,"mouseleave").subscribe((()=>{null!=c.unhighlightCallback&&c.unhighlightCallback()}))}class S extends r.GridCellRenderer{constructor(){super(...arguments),this.colorCacheKey="lst-pie-chart-color-cache",this.HoverTempKey="lst-pie-chart-hovered-sector",this.hoverSeparator=",,,,,"}get name(){return"LST Pie Chart"}get cellType(){return"lst-pie-chart"}get defaultWidth(){return 80}get defaultHeight(){return 80}categoryNumberCache(t){return t.temp[this.colorCacheKey]||(t.temp[this.colorCacheKey]={}),t.temp[this.colorCacheKey]}getPrevHoveredSector(t){return t.temp[this.HoverTempKey]}onMouseMove(t,e){const n=this.getPrevHoveredSector(t.cell.column),r=()=>{t.cell.column.temp[this.HoverTempKey]=null,i.tooltip.hide(),null!==n&&t.grid.invalidate()},o=t.cell.value;if(!o)return void r();const s=e.offsetX-t.bounds.midX,a=e.offsetY-t.bounds.midY,l=Math.sqrt(s*s+a*a),u=Math.atan2(a,s),c=u<0?u+2*Math.PI:u;if(l>Math.min(t.bounds.width,t.bounds.height)/2-2)return void r();let f;try{f=JSON.parse(o)}catch(e){return void r()}const h=new Float64Array(Object.keys(f).length+1),d=Object.values(f).reduce(((t,e)=>t+e),0);h[Object.keys(f).length]=2*Math.PI;let m=0,g=0;for(const t of Object.values(f))h[g++]=m,m+=2*Math.PI*t/d;let p=-1;for(let t=0;t<h.length-1;t++)if(c>=h[t]&&c<h[t+1]){p=t;break}if(-1===p)return void r();const v=Object.keys(f)[p],y=f[v],C=(y/d*100).toFixed(2);i.tooltip.show(i.h1(`${v}: ${y} (${C}%)`),e.x+16,e.y+16);const b=t.cell.rowIndex.toString()+this.hoverSeparator+v;t.cell.column.temp[this.HoverTempKey]=b,n!==b&&t.grid.invalidate()}render(t,e,n,i,o,s,a){const l=s.cell.dataFrame,u=new r.Rect(e,n,i,o).fitSquare().inflate(-2,-2);if(i<5||o<5||!l)return;const c=s.cell.value;if(t.clearRect(e,n,i,o),!c)return;let f;try{f=JSON.parse(c)}catch(t){return}const h=Object.values(f).reduce(((t,e)=>t+e),0);let d=0;const m=Object.fromEntries(Object.keys(f).map((t=>[t,255]))),g=s.cell.column.temp[this.HoverTempKey];if(g&&2===g.split(this.hoverSeparator).length){const[t,e]=g.split(this.hoverSeparator);if(t===s.cell.rowIndex.toString()){for(const[t,e]of Object.entries(f))m[t]=100;m[e]=255}}const p=Math.min(i,o)/2.2;for(const[e,n]of Object.entries(f)){const i=2*Math.PI*n/h;t.beginPath(),t.moveTo(u.midX,u.midY),t.arc(u.midX,u.midY,p,d,d+i),d+=i;const o=this.categoryNumberCache(s.cell.column);o[e]||(o[e]=Object.keys(o).length,s.cell.column.temp[this.colorCacheKey]=o),t.fillStyle=r.Color.toHtml(r.Color.setAlpha(r.Color.getCategoricalColor(o[e]),m[e])),t.fill(),t.strokeStyle=r.Color.toRgb(r.Color.lightGray),t.stroke();const a=e;t.fillStyle=r.Color.toRgb(r.Color.white),t.font="9px Arial";const l=t.measureText(a).width,c=d-i/2;for(let e=.8;e>=.4;e-=.05){const n=p*e,r=u.midX+Math.cos(c)*n,o=u.midY+Math.sin(c)*n;if([[r-l/2-2,o],[r+l/2+2,o]].every((t=>{const e=Math.sqrt(Math.pow(t[0]-u.midX,2)+Math.pow(t[1]-u.midY,2)),n=Math.atan2(t[1]-u.midY,t[0]-u.midX),r=n<0?n+2*Math.PI:n;return e<p-2&&r>d-i&&r<d}))){t.fillText(a,r,o);break}}}}}},4139:(t,e,n)=>{"use strict";n.d(e,{$2:()=>i,To:()=>l,V5:()=>h,YX:()=>f,gp:()=>o,i6:()=>r,rg:()=>u,uF:()=>s,wf:()=>c,zW:()=>d});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,f;!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-"}(f||(f={}));const h=Object.values(a.AGG).filter((t=>![a.AGG.FIRST,a.AGG.KEY,a.AGG.PIVOT,a.AGG.SELECTED_ROWS_COUNT].includes(t))),d={[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:()=>x,AN:()=>i,AY:()=>h,B2:()=>M,BE:()=>C,CD:()=>w,F2:()=>p,FZ:()=>v,KT:()=>T,Lv:()=>O,Y1:()=>d,ZR:()=>E,dl:()=>S,eY:()=>g,qI:()=>_,qx:()=>m,sg:()=>I,vW:()=>A,vY:()=>b,zm:()=>N,zz:()=>y});var i,r=n(7389),o=n(6082),s=n(4328),a=n(4139),l=n(8774),u=n(144),c=n.n(u),f=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 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p(t,e,n={}){var s;const l=t.dataFrame.getCol(a.$2.SPLIT_COL),u=[],c=l.categories,f=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(f.indexOf(t))),a=r.label(null!==(s=n[c[t]])&&void 0!==s?s:c[t],{style:{color:e}});u.push(a)}const h=r.divV([r.divV(u),t.root,r.tableFromMap(e)]);return t.root.style.maxHeight="75px",h}function v(t,e,n){var r,s;const l=null!==(r=null==n?void 0:n.clone().xor(e).anyTrue)&&void 0!==r&&r,u=t.length,c=t.getRawData(),f=new Float32Array(u+e.trueCount+(l&&null!==(s=null==n?void 0:n.trueCount)&&void 0!==s?s:0)),h=new Array(f.length);for(let t=0,r=0,o=0;t<u;++t){const s=e.get(t);f[t]=c[t],h[t]=s?i.SELECTION:i.ALL,s&&(f[u+r]=c[t],h[u+r]=i.ALL,++r),l&&(null==n?void 0:n.get(t))&&(f[u+e.trueCount+o]=c[t],h[u+e.trueCount+o]=i.PEPTIDES_SELECTION,++o)}const d=o.Column.fromStrings(a.$2.SPLIT_COL,h),m=[i.ALL,i.SELECTION];return l&&m.push(i.PEPTIDES_SELECTION),d.setCategoryOrder(m),d.meta.colors.setCategorical(),o.DataFrame.fromColumns([o.Column.fromFloat32Array(a.$2.ACTIVITY,f),d])}function y(t){const e=r.iconFA("expand-alt",(()=>{const e=t.dataFrame.plot.grid();b(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 C(t,e,n,i){const o=r.iconFA("expand-alt",(()=>{const e=i(),n=r.dialog(t);n.add(e),n.show({resizable:!0,modal:!0,width:window.innerWidth-60,x:30,y:30,height:window.innerHeight-60})}),"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 b(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 A(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 S(t,e,n){if(!e)return;const i=new l.A(e.rowCount);if(t.positionOrClusterType===a.$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 e=n[t.positionOrClusterType];if(void 0!==e){const n=e[t.monomerOrCluster];void 0!==n&&i.or(n.mask)}}e.rows.highlight((t=>i.getBit(t)))}function E(t){const e={};for(const n of t)e[n.name]=[];return e}function T(t,e){let n=null;const i=Object.entries(t);for(const[t,r]of i){const i=e[t];for(const t of r){const e=i[t];e&&(null!=n||(n=new l.A(e.mask.length,!1)),n.or(e.mask))}}return null!=n?o.BitSet.fromBytes(n.buffer.buffer,n.length):null}function x(t,e){return t.sequenceColumnName===e.sequenceColumnName&&t.activityColumnName===e.activityColumnName&&t.activityScaling===e.activityScaling}function _(t,e){var n;const i={};for(const[r,o]of t)for(const[t,s]of o){null!==(n=i[t])&&void 0!==n||(i[t]={});const o=new l.A(e,!1);for(const[t,e]of s){o.setTrue(t);for(const t of 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t=u+c-2,e=(a*(u-1)+l*(c-1))/t,n=Math.sqrt(u*c/(u+c))*(o-s)/e;f=1-r.studentt.cdf(n,t),h=r.studentt.cdf(n,t),d=2*(h<f?h:f)}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));h=r.studentt.cdf(n,i),f=1-h,d=2*(h<f?h:f)}return{"p-value":d,"Mean difference":o-s,"p-value more":f,"p-value less":h}}(s,a),d=h["Mean difference"];return{count:s.length,pValue:h[d>=0?"p-value more":"p-value less"],mean:f,meanDifference:d,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 f(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,{D:()=>u,Y:()=>c});var i=n(7389),r=n(6082),o=n(4139),s=n(7654),a=n(8608),l=n(5070);function u(t,e,n,i){var r,s,a;return null!==(r=i.fromViewer)&&void 0!==r||(i.fromViewer=!1),null!==(s=i.isMutationCliffs)&&void 0!==s||(i.isMutationCliffs=!1),null!==(a=i.isMostPotentResidues)&&void 0!==a||(i.isMostPotentResidues=!1),i.monomerPosition.positionOrClusterType!==o.$2.MONOMER&&c(t,e,n,i),!0}function c(t,e,n,o){var u,c,f,h,d,m,g,p,v;if(null!==(u=o.fromViewer)&&void 0!==u||(o.fromViewer=!1),null!==(c=o.isMutationCliffs)&&void 0!==c||(o.isMutationCliffs=!1),null!==(f=o.isMostPotentResidues)&&void 0!==f||(o.isMostPotentResidues=!1),null!==(h=o.additionalStats)&&void 0!==h||(o.additionalStats={}),o.cliffStats&&o.isMutationCliffs){const u=null===(p=null===(g=o.cliffStats)||void 0===g?void 0:g.get(o.monomerPosition.monomerOrCluster))||void 0===p?void 0:p.get(o.monomerPosition.positionOrClusterType);if(!u)return null;const c=r.BitSet.fromBytes(u.mask.buffer.buffer,e.length),f=(0,s.M1)((0,a.FZ)(e,c),!0),h=(0,s.QD)(u,{countName:"Unique count"});o.fromViewer&&(h["Mean difference"]=`${h["Mean difference"]} (Color)`,h["Unique count"]&&(h["Unique count"]=`${h["Unique count"]} (Size)`));const d=null!==(v=o.aggrColValues)&&void 0!==v?v:(0,l.I_)(t,n,{mask:c}),m=Object.assign(Object.assign(Object.assign({},o.additionalStats),h),d),y=(0,a.F2)(f,m);return i.tooltip.show(y,o.x,o.y),y}{const u=o.mpStats[o.monomerPosition.positionOrClusterType][o.monomerPosition.monomerOrCluster];if(!(null==u?void 0:u.count))return null;const c=r.BitSet.fromBytes(u.mask.buffer.buffer,e.length),f=(0,s.M1)((0,a.FZ)(e,c),!0),h=(0,s.QD)(u);o.fromViewer&&(h["Mean difference"]=`${h["Mean difference"]}${o.isMostPotentResidues?" (size)":""}`,h["p-value"]&&(h["p-value"]=`${h["p-value"]}${o.isMostPotentResidues?" (color)":""}`));const g=null!==(d=o.aggrColValues)&&void 0!==d?d:(0,l.I_)(t,n,{mask:c}),p=Object.assign(Object.assign(Object.assign({},o.additionalStats),h),g);for(const[t,e]of Object.entries(null!==(m=o.postfixes)&&void 0!==m?m:{}))p[t]&&(p[t]=`${p[t]}${e}`);const v=(0,a.F2)(f,p);return i.tooltip.show(v,o.x,o.y),v}}},115:(t,e,n)=>{"use strict";n.d(e,{GI:()=>a,Ku:()=>o,av:()=>s});var i=n(1199),r=n(4329);const o="WebGPU is not supported on this device";class s{constructor(){this.maxIterations=16,this.inflation=1.4,this.threshold=70,this.distanceF=i.Z.NEEDLEMANN_WUNSCH,this.gapOpen=1.5,this.gapExtend=.2,this.fingerprintType="Morgan",this.useWebGPU=!1,this.minClusterSize=5,this.webGPUDescription=o,this.webGPUDescriptionPromise=(0,r._)().then((t=>{t&&(this.webGPUDescription=t)}))}}class a{constructor(t){this.distanceF=i.Z.NEEDLEMANN_WUNSCH,this.gapOpen=1.5,this.gapExtend=.2,this.clusterEmbeddings=!0,this.epsilon=.01,this.minPts=4,this.fingerprintType="Morgan",this.clusterEmbeddings=!!t}}},5480:(t,e,n)=>{"use strict";n.d(e,{W:()=>S,s:()=>T});var i=n(7389),r=n(4328),o=n(6082),s=n(7233),a=n.n(s),l=n(768),u=n(4139),c=n(3163),f=n(4326),h=n(5070),d=n(144),m=n.n(d),g=n(7654),p=n(8608),v=n(8774),y=n(6920),C=n(3657),b=n(3077),w=n(726);const A=(t,e)=>`${t}(${e})`;var S,E;!function(t){t.ORIGINAL="original",t.CUSTOM="custom"}(S||(S={})),function(t){t.GENERAL="General",t.STYLE="WebLogo",t.AGGREGATION="Aggregation"}(E||(E={}));class T 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",f.fH.Entropy,{choices:[f.fH.full,f.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,b.R)(this.dataFrame.getCol(this.sequenceColumnName),w.Z.getSeqHelper()).columns.toList()),this._positionColumns}get isClusterSelectionEmpty(){return 0===this.clusterSelection[S.ORIGINAL].length+this.clusterSelection[S.CUSTOM].length}get customClusters(){const t={};return t[u.gp.CUSTOM_CLUSTER]="1",m()(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,p.Y1)(this.dataFrame.getCol(this.activityColumnName),this.activityScaling)),t?o.DataFrame.fromColumns([this._scaledActivityColumn]).clone(this.dataFrame.rowCount===this._scaledActivityColumn.length?this.dataFrame.filter:null).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,p.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${u.To}`))||void 0===e||e.set(this,m()(this.dataFrame.columns.numerical).next().value.name),null===(n=this.getProperty(`clusters${u.To}`))||void 0===n||n.set(this,m()(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${u.To}`:case"activityScaling":this._scaledActivityColumn=null,this._viewerGrid=null,this._clusterStats=null,this._logoSummaryTable=null,e=!0;break;case"columns":case"aggregation":this._viewerGrid=null,this._logoSummaryTable=null,e=!0;break;case"webLogoMode":this.viewerGrid.invalidate()}e&&this.render()}initClusterSelection(t={}){var e;null!==(e=t.notify)&&void 0!==e||(t.notify=!0);const n={};return n[S.ORIGINAL]=[],n[S.CUSTOM]=[],t.notify?this.clusterSelection=n:this._clusterSelection=n,this.clusterSelection}getTotalViewerAggColumns(){var t,e;const n=this.getAggregationColumns();return(0,p.zm)(this.model.df,this.columns,n,null===(e=null===(t=this.model)||void 0===t?void 0:t.settings)||void 0===e?void 0:e.columns)}getStringAggregatedColumns(){return this.columns.filter((t=>this.model.df.columns.contains(t)&&this.model.df.col(t).matches("categorical"))).map((t=>`dist(${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(),f=s.getCol(i),d=f.getRawData(),g=f.categories,p={};p[u.gp.CUSTOM_CLUSTER]="1";const y=m()(a.byTags(p)).filter((t=>t.max>0)).toArray(),C=o.DataFrame.create(y.length),b=C.columns,w=b.addNewString(u.i6.CLUSTER),E=b.addNewInt(u.i6.MEMBERS).getRawData(),T=b.addNewString(u.i6.WEB_LOGO),x=b.addNewString(u.i6.DISTRIBUTION),_=b.addNewFloat(u.i6.MEAN_DIFFERENCE).getRawData(),N=b.addNewFloat(u.i6.P_VALUE).getRawData(),M=b.addNewFloat(u.i6.RATIO).getRawData();let I=s.groupBy([i]);const O=this.getTotalViewerAggColumns(),L=this.getStringAggregatedColumns(),R=L.map((t=>b.addNewString(t))),P=O.map((([t,e])=>A(e,t))),k=new Array(P.length+L.length),V=O.map((([t,e])=>[s.getCol(t),e]));for(let t=0;t<O.length;++t){const[e,n]=O[t];I=I.add(n,e,P[t]);const i=b.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];w.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,h.GT)(c,i):this.clusterStats[S.CUSTOM][n.name];E[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]=V[t];k[t][e]=(0,h.lh)(n,i,a)}for(let t=P.length;t<k.length;++t){const n=L[t-P.length];R[t-P.length].set(e,(0,h.J1)(s,n,a))}}T.setTag(o.TAGS.CELL_RENDERER,"html"),x.setTag(o.TAGS.CELL_RENDERER,"html");const G=I.aggregate(),F=G.rowCount,U=G.columns;let H=G.getCol(i);H.name=u.i6.CLUSTER,H.type!==o.COLUMN_TYPE.STRING&&(G.columns.replace(H,H.convertTo(o.COLUMN_TYPE.STRING)),H=G.getCol(H.name));const q=H.categories,B=U.addNewInt(u.i6.MEMBERS).getRawData(),Y=U.addNewString(u.i6.WEB_LOGO),W=U.addNewString(u.i6.DISTRIBUTION),j=U.addNewFloat(u.i6.MEAN_DIFFERENCE).getRawData(),$=U.addNewFloat(u.i6.P_VALUE).getRawData(),z=U.addNewFloat(u.i6.RATIO).getRawData(),K=L.map((t=>U.addNewString(t))),Q=new Array(F),Z=Array.from({length:F},(()=>new v.A(l,!1)));for(let t=0;t<l;++t){const n=g[d[t]];null===(e=Z[q.indexOf(n)])||void 0===e||e.setTrue(t)}for(let t=0;t<F;++t){const e=Z[t];if(e.allFalse)continue;const i=o.BitSet.fromBytes(e.buffer.buffer,l),a=r?(0,h.GT)(c,e):this.clusterStats[S.ORIGINAL][q[t]];for(let e=0;e<L.length;++e){const n=L[e];K[e].set(t,(0,h.J1)(s,n,i))}B[t]=a.count,Q[t]=i,j[t]=a.meanDifference,$[t]=null!==(n=a.pValue)&&void 0!==n?n:o.FLOAT_NULL,z[t]=a.ratio}Y.setTag(o.TAGS.CELL_RENDERER,"html"),W.setTag(o.TAGS.CELL_RENDERER,"html");const X=G.append(C);return this.bitsets=Q.concat(D),L.forEach((t=>X.col(t).semType="lst-pie-chart")),X}createLogoSummaryTableGrid(){const t=this.dataFrame.filter.anyFalse,e=t?this.dataFrame.clone(this.dataFrame.filter):this.dataFrame,n=this.getTotalViewerAggColumns().map((([t,e])=>A(e,t))),i=this.logoSummaryTable.plot.grid();i.sort([u.i6.MEMBERS],[!1]),this.updateFilter(),i.col(u.i6.CLUSTER).visible=!0,i.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]),i.columns.rowHeader.visible=!1,i.props.rowHeight=55;const r=new o.LruCache,s=new Map;let h=null;const d=new o.LruCache,m=this.positionColumns.length,g=i.columns.byName(u.i6.WEB_LOGO);g.cellType="html",g.width=350;const v=this.getScaledActivityColumn(t),y=e.getCol(this.sequenceColumnName);i.onCellRender.subscribe((t=>{var e,n,l;const g=t.cell,C=g.tableRowIndex;if(!g.isTableCell||null==C||-1===C)return;const b=t.g,w=t.bounds;b.save(),b.beginPath(),b.rect(w.x,w.y,w.width,w.height),b.clip();try{const A=Math.max(g.bounds.height-2,0),S=this.bitsets[C];if((null===(e=g.tableColumn)||void 0===e?void 0:e.name)===u.i6.CLUSTER)c.k8(b,g.cell.value,this.clusterSelection,w),t.preventDefault();else if((null===(n=g.tableColumn)||void 0===n?void 0:n.name)===u.i6.WEB_LOGO){if(!0===s.get(C))return void t.preventDefault();const e=Math.floor((g.bounds.width-2-4*(m-1))/m),n=r.get(C);if(void 0!==n){const i=n.getProperties();for(const t of i)"positionHeight"===t.name&&t.get(n)!==this.webLogoMode?t.set(n,this.webLogoMode):"positionWidth"===t.name&&t.get(n)!==e?t.set(n,e):"minHeight"===t.name&&t.get(n)!==A&&t.set(n,A);a()(n.root).css("height",`${A}px`).children().first().css("overflow-y","hidden !important"),n.root.style.height=`${A}px`,g.element=n.root,t.preventDefault()}else{const n=this.createWebLogoDf(y,S);s.set(C,!0),n.plot.fromType("WebLogo",{positionHeight:this.webLogoMode,horizontalAlignment:f.P4.LEFT,maxHeight:1e3,minHeight:A,positionWidth:e,showPositionLabels:!1}).then((t=>{r.set(C,t),s.delete(C),h&&clearTimeout(h),h=setTimeout((()=>i.invalidate()),200)})),t.preventDefault()}}else if((null===(l=g.tableColumn)||void 0===l?void 0:l.name)===u.i6.DISTRIBUTION){let e=d.get(C);void 0===e&&(e=(0,p.FZ)(v,S).plot.histogram({filteringEnabled:!1,valueColumnName:v.name,splitColumnName:u.$2.SPLIT_COL,legendVisibility:"Never",showXAxis:!1,showColumnSelector:!1,showRangeSlider:!1,showBinSelector:!1,backColor:o.Color.toHtml(o.Color.white),xAxisHeight:1,showSplitSelector:!1}),e.root.style.width="auto",d.set(C,e)),e.root.style.height=`${A}px`,g.element=e.root,t.preventDefault()}}finally{b.restore()}})),i.root.addEventListener("mouseleave",(t=>this.model.unhighlight())),o.debounce(i.onCurrentCellChanged,500).subscribe((t=>{var e;if(!t.isTableCell||-1===t.gridRow)return this.initClusterSelection({notify:!1}),this.model.fireBitsetChanged(l.q.LOGO_SUMMARY_TABLE),void i.invalidate();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(i.cell(u.i6.CLUSTER,this.currentRowIndex)),{shiftPressed:!0,ctrlPressed:!0},!1),this.modifyClusterSelection(this.getCluster(t),{shiftPressed:!0,ctrlPressed:!1}),i.invalidate()}finally{this.keyPress=!1,this.currentRowIndex=t.gridRow}})),i.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(i.cell(u.i6.CLUSTER,t)),{shiftPressed:!0,ctrlPressed:!1},!1);this.model.fireBitsetChanged(l.q.LOGO_SUMMARY_TABLE),i.invalidate()}})),i.root.addEventListener("click",(t=>{var e;const n=i.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 r=this.getCluster(n);this.modifyClusterSelection(r,{shiftPressed:t.shiftKey,ctrlPressed:t.ctrlKey}),i.invalidate()})),i.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 C=i.props;return C.allowEdit=!1,C.allowRowSelection=!1,C.allowBlockSelection=!1,C.allowColSelection=!1,C.showCurrentRowIndicator=!1,C.showReadOnlyNotifications=!1,i}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)?S.ORIGINAL:S.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,h.GT)(r.getRawData(),o);this.bitsets.push(t.clone());const a=this.dataFrame.columns.getUnusedName("New Cluster"),l={},c={},f=this.getTotalViewerAggColumns(),d=this.getStringAggregatedColumns();for(const[e,n]of f){const i=A(n,e),r=this.dataFrame.getCol(e);l[i]=(0,h.lh)(r,n,t)}for(const e of d)c[e]=(0,h.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[S.CUSTOM][a]=s,this.addNewCluster(a)}removeCluster(){const t=this.clusterSelection[S.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[S.CUSTOM][n];const r=i.indexOf(n);e.removeAt(r),this.bitsets.splice(r,1)}n.compact(),this.clusterSelection[S.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,p.vW)(this.clusterSelection,t,e):this._clusterSelection=(0,p.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===S.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 f=r.anyFalse?(0,h.GT)(c,l):this.clusterStats[t.positionOrClusterType][t.monomerOrCluster];if(!f.count)return null;const d=o.BitSet.fromBytes(l.buffer.buffer,a),m=(0,p.FZ)(u,d),y=(0,g.M1)(m,!0),C=(0,g.QD)(f),b=(0,h.I_)(this.dataFrame,this.getTotalViewerAggColumns(),{filterDf:!0,mask:d}),w=Object.assign(Object.assign({},C),b),A=(0,p.F2)(y,w);return i.tooltip.show(A,e,n),A}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,xN:()=>_});var i,r,o,s,a=n(4328),l=n(7389),u=n(6082),c=n(7233),f=n.n(c),h=n(4139),d=n(3163),m=n(768),g=n(144),p=n.n(g),v=n(5070),y=n(912),C=n(3657),b=n(8608),w=n(3077),A=n(439),S=n(2003),E=n(8223),T=n(726),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,h.rg.NONE,{category:s.GENERAL,choices:Object.values(h.rg),nullable:!1}),this.activityTarget=this.string(r.ACTIVITY_TARGET,h.wf.HIGH,{category:s.GENERAL,choices:Object.values(h.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:h.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:h.V5,userEditable:!0,nullable:!1}),this.mutationCliffsDebouncer=(0,b.sg)(((t,e,n)=>x(this,void 0,void 0,(function*(){return yield(0,C.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[h.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(A.gp.alphabet))&&void 0!==t?t:S.YI.UN}get model(){return m.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(m.q.MOST_POTENT_RESIDUES):this instanceof M&&(this._positionColumns=i(m.q.SEQUENCE_VARIABILITY_MAP)),null!==(e=this._positionColumns)&&void 0!==e||(this._positionColumns=null!==(n=i(m.q.LOGO_SUMMARY_TABLE))&&void 0!==n?n:(0,w.R)(this.dataFrame.getCol(this.sequenceColumnName),T.Z.getSeqHelper()).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(m.q.MOST_POTENT_RESIDUES):this instanceof M&&(this._monomerPositionStats=n(m.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,C.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(m.q.MOST_POTENT_RESIDUES):this instanceof M&&(this._mutationCliffs=t(m.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,C.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?h.YX.MP:h.YX.MPR,n=this.dataFrame.getTag(`${e}${h.gp.MUTATION_CLIFFS_SELECTION}`);return null!==(t=this._mutationCliffsSelection)&&void 0!==t||(this._mutationCliffsSelection=null===n?(0,b.ZR)(this.positionColumns):JSON.parse(n)),this._mutationCliffsSelection}set mutationCliffsSelection(t){this._mutationCliffsSelection=t;const e=this instanceof N?h.YX.MP:h.YX.MPR;this.dataFrame.setTag(`${e}${h.gp.MUTATION_CLIFFS_SELECTION}`,JSON.stringify(t)),this.model.fireBitsetChanged(this instanceof N?m.q.SEQUENCE_VARIABILITY_MAP:m.q.MOST_POTENT_RESIDUES);const n=this.model.findViewer(m.q.SEQUENCE_VARIABILITY_MAP);null==n||n.viewerGrid.invalidate();const i=this.model.findViewer(m.q.MOST_POTENT_RESIDUES);null==i||i.viewerGrid.invalidate(),this.model.analysisView.grid.invalidate()}getScaledActivityColumn(t=!1){var e,n,i;return(null===(e=this.model.settings)||void 0===e?void 0:e.activityColumnName)===this.activityColumnName&&(null===(n=this.model.settings)||void 0===n?void 0:n.activityScaling)===this.activityScaling&&(this._scaledActivityColumn=this.model.getScaledActivityColumn(t)),null!==(i=this._scaledActivityColumn)&&void 0!==i||(this._scaledActivityColumn=(0,b.Y1)(this.dataFrame.getCol(this.activityColumnName),this.activityScaling)),t?u.DataFrame.fromColumns([this._scaledActivityColumn]).clone(this.dataFrame.filter).getCol(this._scaledActivityColumn.name):this._scaledActivityColumn}modifyMutationCliffsSelection(t,e={shiftPressed:!1,ctrlPressed:!1},n=!0){n?this.mutationCliffsSelection=(0,b.vW)(this.mutationCliffsSelection,t,e):this._mutationCliffsSelection=(0,b.vW)(this.mutationCliffsSelection,t,e)}modifyInvariantMapSelection(t,e={shiftPressed:!1,ctrlPressed:!1},n=!0){n?this.invariantMapSelection=(0,b.vW)(this.invariantMapSelection,t,e):this._invariantMapSelection=(0,b.vW)(this.invariantMapSelection,t,e)}get invariantMapSelection(){var t;const e=this.dataFrame.getTag(`${h.YX.MP}${h.gp.INVARIANT_MAP_SELECTION}`);return null!==(t=this._invariantMapSelection)&&void 0!==t||(this._invariantMapSelection=null===e?(0,b.ZR)(this.positionColumns):JSON.parse(e)),this._invariantMapSelection}set invariantMapSelection(t){this._invariantMapSelection=t,this.dataFrame.setTag(`${h.YX.MP}${h.gp.INVARIANT_MAP_SELECTION}`,JSON.stringify(t)),this.model.fireBitsetChanged(m.q.SEQUENCE_VARIABILITY_MAP),this.model.analysisView.grid.invalidate()}resetTargetCategoryValue(){var t;const e=this.targetColumnName,n=e?this.dataFrame.col(e):null;this.targetCategoryInput.items=null!==(t=null==n?void 0:n.categories)&&void 0!==t?t:[],this.targetCategoryInput.value=null,this.targetCategoryInput.root.style.display=e?"flex":"none"}onPropertyChanged(t){switch(super.onPropertyChanged(t),this.doRender=!0,t.name){case`${r.SEQUENCE}${h.To}`:this._positionColumns=null,this._monomerPositionStats=null,this._mutationCliffs=null,this._mutationCliffStats=null,this._mutationCliffsSelection=null,this._viewerGrid=null;break;case`${r.ACTIVITY}${h.To}`:case r.ACTIVITY_SCALING:this._monomerPositionStats=null,this._mutationCliffs=null,this._mutationCliffStats=null,this._mutationCliffsSelection=null,this._viewerGrid=null,this._scaledActivityColumn=null;break;case`${r.VALUE_INVARIANT_MAP}${h.To}`:case r.AGGREGATION_INVARIANT_MAP_VALUE:this._monomerPositionStats=null,this._viewerGrid=null,this._invariantMapSelection=null;break;case r.MIN_ACTIVITY_DELTA:case r.MAX_MUTATIONS:this._mutationCliffs=null,this._mutationCliffStats=null,this._mutationCliffsSelection=null,this.doRender=!1;break;case r.COLUMNS:case r.AGGREGATION:this instanceof M&&(this._viewerGrid=null);break;case r.ACTIVITY_TARGET:(this instanceof M||this instanceof N)&&(this._viewerGrid=null)}null===this._mutationCliffs&&this.sequenceColumnName&&this.activityColumnName&&this.calculateMutationCliffs().then((t=>{this.mutationCliffs=t.cliffs,this.cliffStats=t.cliffStats})),t.name===`${r.TARGET}${h.To}`&&this.targetColumnInput&&(this.targetColumnInput.value=this.targetColumnName?this.dataFrame.col(this.targetColumnName):null,this.resetTargetCategoryValue())}getAggregationColumns(){return Object.fromEntries(this.columns.map((t=>[t,this.aggregation])).filter((([t,e])=>this.model.df.columns.contains(t)&&this.model.df.col(t).matches("numerical"))))}getTotalViewerAggColumns(){var t,e;const n=this.getAggregationColumns();return(0,b.zm)(this.model.df,this.columns,n,null===(e=null===(t=this.model)||void 0===t?void 0:t.settings)||void 0===e?void 0:e.columns)}createViewerGrid(){throw new Error("Not implemented")}detach(){this.subs.forEach((t=>t.unsubscribe()))}onTableAttached(){var t,e,n;if(super.onTableAttached(),(0,b.B2)(this.dataFrame))null===(t=this.getProperty(`${r.SEQUENCE}${h.To}`))||void 0===t||t.set(this,this.dataFrame.columns.bySemType(u.SEMTYPE.MACROMOLECULE).name),null===(e=this.getProperty(`${r.ACTIVITY}${h.To}`))||void 0===e||e.set(this,p()(this.dataFrame.columns.numerical).next().value.name),null===(n=this.getProperty(`${r.VALUE_INVARIANT_MAP}${h.To}`))||void 0===n||n.set(this,p()(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,E.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,C.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:h.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 m.q.SEQUENCE_VARIABILITY_MAP}get mode(){var t;return null!==(t=this.dataFrame.getTag(h.gp.MONOMER_POSITION_MODE))&&void 0!==t?t:i.MUTATION_CLIFFS}set mode(t){this.dataFrame.setTag(h.gp.MONOMER_POSITION_MODE,t),this.viewerGrid.invalidate()}onTableAttached(){var t;if(super.onTableAttached(),(0,b.B2)(this.dataFrame))null===(t=this.getProperty(`${o.COLOR}${h.To}`))||void 0===t||t.set(this,this.activityColumnName),this.targetColumnInput=l.input.column("Target",{value:void 0,nullable:!0,table:this.dataFrame,filter:t=>t.isCategorical,onValueChanged:t=>{var e,n;const i=this.getProperty(`${r.TARGET}${h.To}`);i&&i.get(this)!=(null!==(e=null==t?void 0:t.name)&&void 0!==e?e:null)&&(null==i||i.set(this,null!==(n=null==t?void 0:t.name)&&void 0!==n?n:null))}});else{const t="PeptidesError: dataframe is missing Macromolecule or numeric columns";a.log.error(t),a.shell.warning(t)}this.render()}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[h.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(h.$2.MONOMER,n),r=u.DataFrame.fromColumns([i]),o=(0,E.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[h.gp.INVARIANT_MAP_COLOR_CACHE]={};const o=i.temp[h.gp.INVARIANT_MAP_COLOR_CACHE],a=i.name,l=i.getRawData(),c=i.categories;if(!this.monomerPositionStats[a])continue;const f=this.monomerPositionStats[a];for(const a of Object.keys(f)){if("general"===a)continue;const f=[];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&&f.push(t)}const h=u.Column.float("color",f.length).init((e=>t[f[e]])).aggregate(this.colorAggregation);o[a]=h,e=Math.min(e,h),n=Math.max(n,h)}i.temp[h.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 f=this.logScaleColor&&l>1e-30&&c>1e-30&&e>1e-30&&n>1e-30;f&&(l=Math.log(l),c=Math.log(c));for(const t of this.positionColumns){const i=t.temp[h.gp.INVARIANT_MAP_COLOR_CACHE];if(i){for(const t of Object.keys(i))this.activityTarget===h.wf.LOW&&(i[t]=c-i[t]+l),i[t]=u.Color.scaleColor(f?Math.log(i[t]):i[t],l,c,void 0,[this.lowerBoundColor,this.middleColor,this.upperBoundColor]);t.temp[h.gp.INVARIANT_MAP_COLOR_CACHE]=i,t.temp[h.gp.INVARIANT_MAP_COLOR_MIN_CACHE]=e,t.temp[h.gp.INVARIANT_MAP_COLOR_MAX_CACHE]=n}}}}createViewerGrid(){const t=this.createMonomerPositionDf(),e=t.plot.grid();e.sort([h.$2.MONOMER]);const n=this.positionColumns.map((t=>t.name));e.columns.setOrder([h.$2.MONOMER,...this._monomerMetaColumns,...n]);const r=t.getCol(h.$2.MONOMER);d.rI(r,this.alphabet,!0),this.cacheInvariantMapColors(),e.onCellRender.subscribe((t=>I(t,this,this.mode===i.INVARIANT_MAP,this.dataFrame.getCol(this.colorColumnName),this.colorAggregation))),e.onCellTooltip(((t,e,n)=>{var r,o,s,a,l;if(!t.isTableCell||!(null===(r=null==t?void 0:t.cell.column)||void 0===r?void 0:r.name)||this._monomerMetaColumns.has(t.cell.column.name))return this.model.unhighlight(),!0;const c=this.getMonomerPosition(t);(0,b.dl)(c,this.dataFrame,this.monomerPositionStats),this.model.isHighlighting=!0;const f=this.getTotalViewerAggColumns(),h={},d={};if(this.mode===i.INVARIANT_MAP)this.colorColumnName&&this.colorAggregation&&this.colorColumnName!==this.valueColumnName?(f.unshift([this.colorColumnName,this.colorAggregation]),h[`${this.colorAggregation}(${this.colorColumnName})`]=" (color)"):this.colorColumnName&&this.colorAggregation&&this.colorColumnName===this.valueColumnName&&(h["Mean activity"]=" (color)"),this.valueColumnName&&this.valueAggregation&&this.valueAggregation!==u.AGG.VALUE_COUNT&&this.valueAggregation!==u.AGG.TOTAL_COUNT&&f.unshift([this.valueColumnName,this.valueAggregation]);else{const t=null===(s=null===(o=this.mutationCliffs)||void 0===o?void 0:o.get(c.monomerOrCluster))||void 0===s?void 0:s.get(c.positionOrClusterType);if(t){let e=0;for(const n of t.values())e+=n.length;d["Pairs count"]=e.toString()}}return(0,y.D)(this.model.df,this.getScaledActivityColumn(),f,{fromViewer:!0,isMutationCliffs:this.mode===i.MUTATION_CLIFFS,monomerPosition:c,x:e,y:n,mpStats:this.monomerPositionStats,cliffStats:null!==(l=null===(a=this.cliffStats)||void 0===a?void 0:a.stats)&&void 0!==l?l:void 0,postfixes:h,additionalStats:d})})),e.root.addEventListener("mouseleave",(t=>this.model.unhighlight())),u.debounce(e.onCurrentCellChanged,500).subscribe((t=>{var n,r,o,s,a,l,c,f,h;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(-1===t.gridRow&&(this.mode===i.INVARIANT_MAP?this._invariantMapSelection=(0,b.ZR)(this.positionColumns):this._mutationCliffsSelection=(0,b.ZR)(this.positionColumns),this.model.fireBitsetChanged(m.q.SEQUENCE_VARIABILITY_MAP),e.invalidate()),!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 u=this.getMonomerPosition(t);this.mode===i.INVARIANT_MAP?this.modifyInvariantMapSelection(u,{shiftPressed:!0,ctrlPressed:!1},!0):(null===(f=null===(c=null===(l=this.mutationCliffs)||void 0===l?void 0:l.get(u.monomerOrCluster))||void 0===c?void 0:c.get(u.positionOrClusterType))||void 0===f?void 0:f.size)&&this.modifyMutationCliffsSelection(u,{shiftPressed:!0,ctrlPressed:!1},!0),e.invalidate(),setTimeout((()=>null==e?void 0:e.invalidate()),300)}finally{this.keyPressed=!1,(null===(h=t.tableColumn)||void 0===h?void 0:h.name)&&t.grid?this.currentGridCell=u.GridCell.fromColumnRow(t.grid,t.tableColumn.name,t.gridRow):this.currentGridCell=null}})),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(m.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)===h.$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()})),O(e);const o=e.onAfterDrawContent.subscribe((()=>{const t=e.col(h.$2.MONOMER);if(40!==t.width){t.width=40;for(const t of n)e.col(t).width=40}else o.unsubscribe()}));return e}getMonomerPosition(t){return{monomerOrCluster:t.cell.dataFrame.get(h.$2.MONOMER,t.tableRowIndex),positionOrClusterType:t.tableColumn.name}}render(){var t,e,n;if(f()(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=p()(a.shell.t.columns.numerical).toArray().map((t=>t.name)),r.get(this)===h.$2.ACTIVITY_SCALED&&r.set(this,h.$2.ACTIVITY)),f()(this.root).empty();let s=l.divText(m.q.MOST_POTENT_RESIDUES,{id:"pep-viewer-title"});if(this.name===m.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})),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})),e.setTooltip("Number of sequences having monomer-position");const n=t=>{f()(t.root).find(".ui-input-editor").css("margin","0px").attr("type","radio"),f()(t.root).find(".ui-input-description").css("padding","0px").css("padding-right","16px"),f()(t.captionLabel).addClass("ui-label-right")};n(t),n(e),s=l.divH([t.root,e.root],{id:"pep-viewer-title"}),f()(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");f()(c).addClass("pep-help-icon"),this.targetColumnInput&&(this.targetColumnInput.root.style.width="50%");const d=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"}}),g=l.divH([c,s,d],{style:{alignSelf:"center",lineHeight:"normal",flexDirection:"column"}});this.root.appendChild(l.divV([g,u])),null===(n=this.viewerGrid)||void 0===n||n.invalidate()}}class M extends _{constructor(){super(),this.currentGridRowIdx=null}get name(){return m.q.MOST_POTENT_RESIDUES}onTableAttached(){super.onTableAttached(),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(),f=c.map((([t,e])=>(0,v.hX)(e,t))),d=new Array(f.length);f.forEach(((t,e)=>d[e]=new Array(n.length)));let m=0;for(const[g,p]of e){const e=p.general;if(!e)continue;if(1===Object.entries(p).length)continue;const y=[];for(const[n,i]of Object.entries(p))"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===h.wf.HIGH&&C[1].meanDifference<e.meanDifference||this.activityTarget===h.wf.LOW&&C[1].meanDifference>e.meanDifference)&&(C=[t,e]);if(null===C)continue;n[m]=parseInt(g),i[m]=C[0],r[m]=C[1].meanDifference,o[m]=C[1].pValue,s[m]=C[1].count,a[m]=C[1].ratio,l[m]=C[1].mean;const b=this.monomerPositionStats[g][C[0]],w=u.BitSet.fromBytes(b.mask.buffer.buffer,this.model.df.col(this.activityColumnName).length);for(let t=0;t<f.length;t++){const[e,n]=c[t];d[t][m]=(0,v.lh)(this.model.df.getCol(e),n,w)}++m}n.length=m,i.length=m,r.length=m,o.length=m,s.length=m,a.length=m,l.length=m;const g=u.DataFrame.create(m),p=g.columns;return p.add(u.Column.fromList(u.TYPE.INT,h.$2.POSITION,n)),p.add(u.Column.fromList(u.TYPE.STRING,h.$2.MONOMER,i)),p.add(u.Column.fromList(u.TYPE.FLOAT,h.$2.MEAN_DIFFERENCE,r)),p.add(u.Column.fromList(u.TYPE.FLOAT,h.$2.MEAN,l)),p.add(u.Column.fromList(u.TYPE.FLOAT,h.$2.P_VALUE,o)),p.add(u.Column.fromList(u.TYPE.INT,h.$2.COUNT,s)),p.add(u.Column.fromList(u.TYPE.FLOAT,h.$2.RATIO,a)),f.forEach(((t,e)=>p.add(u.Column.fromList(u.TYPE.FLOAT,t,d[e])))),g}createViewerGrid(){const t=this.createMostPotentResiduesDf(),e=t.plot.grid();e.sort([h.$2.POSITION]);const n=e.col(h.$2.P_VALUE);n.format="#.000",n.name="P-value";const i=t.getCol(h.$2.MONOMER);d.rI(i,this.alphabet,!0),e.onCellRender.subscribe((t=>I(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)===h.$2.MONOMER)o.positionOrClusterType=h.$2.MONOMER;else if((null===(r=t.tableColumn)||void 0===r?void 0:r.name)!==h.$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,y.D)(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(-1===n.gridRow)return this._mutationCliffsSelection=(0,b.ZR)(this.positionColumns),this._invariantMapSelection=(0,b.ZR)(this.positionColumns),this.model.fireBitsetChanged(m.q.MOST_POTENT_RESIDUES),void e.invalidate();if(this.keyPressed&&t.currentCol.name!==h.$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.modifyInvariantMapSelection(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.modifyInvariantMapSelection(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.modifyInvariantMapSelection(t,{shiftPressed:!0,ctrlPressed:!1},!1)}}this.model.fireBitsetChanged(m.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!==h.$2.MEAN_DIFFERENCE)return;const s=this.getMonomerPosition(o);(null===(r=null===(i=null===(n=this.monomerPositionStats)||void 0===n?void 0:n[s.positionOrClusterType])||void 0===i?void 0:i[s.monomerOrCluster])||void 0===r?void 0:r.count)&&(this.modifyInvariantMapSelection(s,{shiftPressed:t.shiftKey,ctrlPressed:t.ctrlKey}),e.invalidate())})),O(e);const r=e.col(h.$2.MEAN_DIFFERENCE);r.name="Diff";const o=e.onAfterDrawContent.subscribe((()=>{const t=e.col(h.$2.MONOMER);if(40===t.width)return r.width=40,void o.unsubscribe();t.width=40,r.width=40}));return e}getMonomerPosition(t){return{monomerOrCluster:t.cell.dataFrame.get(h.$2.MONOMER,t.tableRowIndex),positionOrClusterType:`${t.cell.dataFrame.get(h.$2.POSITION,t.tableRowIndex)}`}}render(){var t;if(f()(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(m.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 I(t,e,n,i,r){var o,s,a,l,c;const f=[...e.positionColumns.map((t=>t.name)),h.$2.MEAN_DIFFERENCE],m=t.g,g=t.bounds;m.save(),m.beginPath(),m.rect(g.x,g.y,g.width,g.height),m.clip();const p=t.cell;if(p.isRowHeader&&p.gridColumn.visible)return p.gridColumn.visible=!1,t.preventDefault(),void m.restore();const v=null===(o=p.tableColumn)||void 0===o?void 0:o.name,y=p.tableRowIndex;if(!p.isTableCell||-1===f.indexOf(v))return void m.restore();const C=p.grid.table,b=C.get(h.$2.MONOMER,y),w=v!==h.$2.MEAN_DIFFERENCE?v:C.get(h.$2.POSITION,y).toFixed(),A=e.monomerPositionStats[w];if(!A[b])return t.preventDefault(),void m.restore();if(n){const t=null!==(s=A[b].aggValue)&&void 0!==s?s:A[b].count,n=e.positionColumns.find((t=>t.name===w)),i=null!==(a=n.temp[h.gp.INVARIANT_MAP_COLOR_CACHE])&&void 0!==a?a:{};let r=u.Color.white;null!=i[b]?r=i[b]:e instanceof N&&(e.cacheInvariantMapColors(),r=null!==(c=(null!==(l=n.temp[h.gp.INVARIANT_MAP_COLOR_CACHE])&&void 0!==l?l:{})[b])&&void 0!==c?c:u.Color.white),d.rW(m,b,w,e.invariantMapSelection,t,g,r)}else d.Yd(m,b,w,e,g);t.preventDefault(),m.restore()}function O(t){const e=t.props;e.allowEdit=!1,e.allowRowSelection=!1,e.allowBlockSelection=!1,e.allowColSelection=!1,e.showRowHeader=!1,e.showCurrentRowIndicator=!1,e.showReadOnlyNotifications=!1,e.rowHeight=20}},7654:(t,e,n)=>{"use strict";n.d(e,{HV:()=>g,M1:()=>p,QD:()=>v});var i,r=n(7389),o=n(6082),s=n(7233),a=n.n(s),l=n(4139),u=n(5070),c=n(8608),f=n(5480),h=n(8774);!function(t){t.SEPARATE_MONOMERS="separateMonomers",t.SEPARATE_POSITIONS="separatePositions",t.SEPARATE_CLUSTERS="separateClusters"}(i||(i={}));const d="general",m=t=>t===d?"General":t.substring(8);function g(t,e){if(!t.selection.anyTrue)return r.divText("No distribution");const n=()=>{const n=[C(d,t,e)];for(const r of Object.values(i))"true"!==t.getTag(r)||r===i.SEPARATE_CLUSTERS&&!e.clusterColName||n.push(C(r,t,e));return 1===n.length?n[0]:r.div(n)},o=r.div(n()),s=Object.values(i),l=new Array(s.length);for(let u=0;u<s.length;u++){const c=s[u].substring(8);l[u]=r.input.bool(c,{value:"true"===t.getTag(s[u]),onValueChanged:e=>{t.setTag(s[u],`${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[f.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 p(t,e=!1){const n=t.plot.histogram({filteringEnabled:!1,valueColumnName:l.$2.ACTIVITY,splitColumnName:l.$2.SPLIT_COL,legendVisibility:"Never",showXAxis:!0,showColumnSelector:!1,showRangeSlider:!1,showBinSelector:!1,backColor:e?"#fdffe5":"#fffff"});return n.root.style.width="auto",n}function v(t,e={}){var n,i;null!==(n=e.fractionDigits)&&void 0!==n||(e.fractionDigits=3);const r={[null!==(i=null==e?void 0:e.countName)&&void 0!==i?i:"Count"]:`${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&&(r["p-value"]=t.pValue<.01?"<0.01":t.pValue.toFixed(e.fractionDigits)),r}function y(t,e,n,i={}){const r=p((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),f=Object.assign(Object.assign({},l),s),h=(0,c.F2)(r,f,i);return a()(h).addClass("d4-flex-col"),h}function C(t,e,n){let o=r.divText("No distribution");switch(t){case d:const t=h.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,d=a.getRawData(),m=n[f.W.ORIGINAL].map((t=>l.indexOf(t))),g=new Array(m.length).fill(new h.A(i));for(let t=0;t<i;t++){const e=d[t],n=m.indexOf(e);-1!==n&&g[n].setTrue(t)}for(let n=0;n<m.length;n++){const i=m[n],r=(0,u.GT)(s,g[n]);o.push(y(t,r,e,{[c.AN.SELECTION]:l[i]}))}const p=n[f.W.CUSTOM];for(const n of p){const r=t.getCol(n),a=h.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,f=[],d=[],m=[],g=[],p=e.activityCol.getRawData();for(const r of a){const a=n[r],v=new h.A(l);for(let e=0;e<a.length;e++){const n=a[e];null!==(i=d[e])&&void 0!==i||(d[e]=t.getCol(n)),null!==(o=m[e])&&void 0!==o||(m[e]=d[e].categories),null!==(s=g[e])&&void 0!==s||(g[e]=d[e].getRawData());const u=m[e].indexOf(r);for(let t=0;t<l;t++)g[e][t]===u&&v.setTrue(t)}const C=(0,u.GT)(p,v);f.push(y(t,C,e,{[c.AN.SELECTION]:r}))}return r.div(f,"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,f=[],d=e.activityCol.getRawData(),m=[],g=[],p=[];for(let r=0;r<a.length;r++){const v=a[r],C=n[v];if(0===C.length)continue;null!==(i=m[r])&&void 0!==i||(m[r]=t.getCol(v)),null!==(o=g[r])&&void 0!==o||(g[r]=m[r].categories),null!==(s=p[r])&&void 0!==s||(p[r]=m[r].getRawData());const b=new h.A(t.rowCount);for(let t=0;t<C.length;t++){const e=C[t],n=g[r].indexOf(e);for(let t=0;t<l;t++)p[r][t]===n&&b.setTrue(t)}const w=(0,u.GT)(d,b);f.push(y(t,w,e,{[c.AN.SELECTION]:v}))}return r.div(f,"d4-flex-wrap")}(e,n,n.monomerPositionSelection)}return r.divV([r.h1(m(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(3163);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,f=[a,l],h=i.divV([c.root,...f.map((t=>t.root))],{style:{width:"100%"}});return n&&(0,s.BE)("Mutation Cliffs pairs",c.root,h,(()=>{const n=u(t,e),r=i.splitH([i.divV([n.aminoToInput.root,n.pairsGrid.root],{style:{marginRight:"10px"}}),i.divV([n.uniqueSequencesGrid.root],{style:{marginLeft:"10px"}})],{style:{width:"100%",height:"100%"}},!0);return setTimeout((()=>{var t,i;if(document.contains(r)){const o=r.offsetWidth,s=null===(t=n.pairsGrid.canvas)||void 0===t?void 0:t.parentElement;n.pairsGrid.props.showRowHeader=!0,n.uniqueSequencesGrid.props.showRowHeader=!0;const a=null===(i=n.uniqueSequencesGrid.canvas)||void 0===i?void 0:i.parentElement;if(s&&a&&(s.style.height="100%",a.style.height="100%",a.style.marginTop="20px",o>400)){const t=Math.max(.33*o,200),i=n.pairsGrid.columns.byName("Mutation");i&&(i.width=t);const r=n.uniqueSequencesGrid.columns.byName(e.sequenceColumnName);r&&(r.width=t)}}}),500),r})),new r.Widget(h)}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 f=[],h=[],d=[],m=[],g=[],p=[],v=t.getCol(e.sequenceColumnName),y=v.categories,C=v.getRawData(),b=e.activityCol.getRawData(),w=new Map,A=r.BitSet.create(t.rowCount),S={},E=Object.fromEntries(e.positionColumns.map((t=>[t.name,t])));for(const t of c){const i=E[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;S[t]||(S[t]=Object.keys(S).length+1);const n=S[t],i=null!==(l=w.get(t))&&void 0!==l?l:[],s=y[C[t]],a=b[t];for(const l of e){if(i.includes(l)||!u.includes(l))continue;w.has(l)||w.set(l,[]);const e=y[C[l]];w.get(l).push(t),f.push(`${s}#${e}`),m.push(`${n}`),h.push(a-b[l]),d.push(r[o[l]]),g.push(t),p.push(l),A.set(t,!0),A.set(l,!0)}}}}if(0===f.length)return null;const T=r.Column.fromStrings("Mutation",f),x=r.Column.fromList("double","Delta",h),_=r.Column.fromStrings("Group",m),N=r.Column.fromStrings("~to",d),M=r.Column.fromList(r.COLUMN_TYPE.INT,"~toIdx",p),I=r.Column.fromList(r.COLUMN_TYPE.INT,"~fromIdx",g),O=r.DataFrame.fromColumns([T,x,_,N,M,I]);O.name="Mutation Cliff pairs";const L=i.input.string("Mutated to:",{value:"",onValueChanged:t=>{const e=t;""!==e?O.filter.init((t=>N.get(t)===e)):O.filter.setAll(!0)}});L.setTooltip("Filter the rows by the monomer that the mutation was substituted to");const R=O.plot.grid();(0,s.vY)(R,!0),T.semType=o.uF.MACROMOLECULE_DIFFERENCE,T.tags[o.gp.SEPARATOR]=(0,s.AY)(v),T.tags[r.TAGS.UNITS]=v.tags[r.TAGS.UNITS],T.tags[r.TAGS.CELL_RENDERER]="MacromoleculeDifference";let P=!1,k=null;const V=[];R.onCurrentCellChanged.subscribe((t=>{try{if(!t||!t.dart)return V.length=0,void Y();const e=t.tableRowIndex;if(!P)return;if(null===e)return V.length=0,void Y();null!==k&&V.splice(V.indexOf(k),1),V.includes(e)||(V.push(e),R.invalidate()),Y()}finally{P=!1,k=t&&t.dart?t.tableRowIndex:null}})),R.root.addEventListener("keydown",(t=>{P=t.key.startsWith("Arrow")})),R.root.addEventListener("click",(t=>{const e=R.hitTest(t.offsetX,t.offsetY);if(!e||null===e.tableRowIndex)return;const n=e.tableRowIndex;if(t.shiftKey){const t=V.indexOf(n);-1===t?V.push(n):V.splice(t,1)}else V.length=0,V.push(n);Y(),R.invalidate(),B.invalidate()})),R.onCellRender.subscribe((t=>{var e;(null===(e=t.cell.tableColumn)||void 0===e?void 0:e.name)===T.name&&V.includes(t.cell.tableRowIndex)&&(0,a.X5)(t.g,t.bounds)}));const D=e.gridColumns.length,G=[];for(let t=1;t<D;t++){const n=e.gridColumns.byIndex(t);((null==n?void 0:n.name)===e.sequenceColumnName||!0===(null==n?void 0:n.visible)&&!Object.hasOwn(E,n.name))&&G.push(n.name)}const F=t.clone(A,G);F.name="Unique sequences that form Mutation Cliffs pairs";const U=F.columns.addNewInt("~seqIdx"),H=U.getRawData(),q=A.getSelectedIndexes();U.init((t=>q[t]));const B=F.plot.grid();function Y(){const t=[];for(const e of V)t.push(I.get(e)),t.push(M.get(e));F.filter.init((e=>0===V.length||t.includes(H[e])),!0),R.invalidate(),B.invalidate()}return(0,s.vY)(B,!0),B.props.rowHeight=20,R.root.style.width="100% !important",B.root.style.width="100% !important",setTimeout((()=>{R.autoSize(window.innerWidth,250,void 0,void 0,!1),B.autoSize(window.innerWidth,250,void 0,void 0,!1),R.root.style.removeProperty("width"),R.root.style.setProperty("width","100%"),B.root.style.removeProperty("width"),B.root.style.setProperty("width","100%"),R.root.style.minHeight="70px",B.root.style.minHeight="100px",R.root.style.height="unset",B.root.style.height="unset"}),200),{pairsGrid:R,uniqueSequencesGrid:B,aminoToInput:L}}},5082:(t,e,n)=>{"use strict";n.d(e,{n:()=>v,v:()=>p});var i=n(4328),r=n(7389),o=n(6082),s=(n(4788),n(4139)),a=n(115),l=n(768),u=n(7233),c=n.n(u),f=n(8608),h=n(2003),d=n(1199),m=n(5429),g=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 p(t,e){const n=new a.av,l=r.div();let u=null;if(void 0===e){const e=o.Utils.firstOrNull(t.columns.toList().filter((t=>t.semType===o.SEMTYPE.MACROMOLECULE)));if(null===e)throw new Error("Peptides Error: table doesn't contain sequence columns");0!==e.stats.missingValueCount&&i.shell.info("Sequences column contains missing values. They will be ignored during analysis"),u=r.input.column("Sequence",{table:t,value:e,onValueChanged:e=>{c()(l).empty().append(r.wait((()=>g(this,void 0,void 0,(function*(){const n=yield t.plot.fromType("WebLogo",{sequenceColumnName:e.name});return n.root.style.setProperty("height","130px"),n.root}))))),0!==e.stats.missingValueCount&&i.shell.info("Sequences column contains missing values. They will be ignored during analysis")},filter:t=>t.semType===o.SEMTYPE.MACROMOLECULE}),u.setTooltip("Macromolecule column in FASTA, HELM or separated format")}else if("SEQ.MSA"!==e.getTag(h.gp.aligned)&&e.getTag(o.TAGS.UNITS)!==h.Hi.HELM)return{host:r.label("Peptides analysis only works with aligned sequences"),callback:()=>g(this,void 0,void 0,(function*(){return!1}))};let p,y=o.Func.find({package:"Bio",name:"webLogoViewer"});if(0===y.length)return{host:r.label("Bio package is missing or out of date. Please install the latest version."),callback:()=>g(this,void 0,void 0,(function*(){return!1}))};if(y=o.Func.find({package:"Bio",name:"getBioLib"}),0===y.length)return{host:r.label("Bio package is missing or out of date. Please install the latest version."),callback:()=>g(this,void 0,void 0,(function*(){return!1}))};const C=t.col("activity")||t.col("IC50")||o.Utils.firstOrNull(t.columns.numerical),b=r.div([],{id:"pep-hist-host"}),w=r.input.choice("Scaling",{value:s.rg.NONE,items:Object.values(s.rg),onValueChanged:t=>g(this,void 0,void 0,(function*(){var e;p=(0,f.Y1)(S.value,t);const n=o.DataFrame.fromColumns([p]).plot.histogram({filteringEnabled:!1,valueColumnName:s.$2.ACTIVITY,legendVisibility:"Never",showXAxis:!0,showColumnSelector:!1,showRangeSlider:!1,showBinSelector:!1});null===(e=b.lastChild)||void 0===e||e.remove(),b.appendChild(n.root)}))});w.setTooltip("Activity column transformation method");const A=()=>{var t;w.enabled=null!==(t=S.value)&&void 0!==t&&t&&S.value.stats.min>0,w.value=s.rg.NONE,0!==S.value.stats.missingValueCount&&i.shell.info("Activity column contains missing values. They will be ignored during analysis")},S=r.input.column("Activity",{table:t,value:C,onValueChanged:A,filter:t=>t.type===o.TYPE.INT||t.type===o.TYPE.FLOAT||t.type===o.TYPE.QNUM});S.setTooltip("Numerical activity column");const E=r.input.column("Clusters",{table:t,onValueChanged:t=>{t&&(T.value=!1,T.fireChanged())}});E.setTooltip("Optional. Clusters column is used to create Logo Summary Table"),E.nullable=!0;const T=r.input.bool("Generate clusters",{value:!0,onValueChanged:t=>{t&&(E.value=null,E.fireChanged())}});T.setTooltip("Generate clusters column based on MCL embeddings for Logo Summary Table"),S.fireChanged(),w.fireChanged(),T.fireChanged();const x=[S,w,E,T];null!==u&&x.splice(0,0,u);const _=r.input.float(m.t_.THRESHOLD,{value:n.threshold,nullable:!1,onValueChanged:t=>n.threshold=null!=t?t:n.threshold});_.setTooltip("Threshold for similarity between two sequences to create edges");const N=r.input.float(m.t_.INFLATION,{value:n.inflation,nullable:!1,onValueChanged:t=>n.inflation=null!=t?t:n.inflation});N.setTooltip("Inflation value for MCL algorithm");const M=r.input.int(m.t_.MAX_ITERATIONS,{value:n.maxIterations,nullable:!1,onValueChanged:t=>n.maxIterations=null!=t?t:n.maxIterations});M.setTooltip("Maximum iterations for MCL algorithm");const 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v.addMostPotentResidues(),null!==(d=f.addSequenceSpace)&&void 0!==d&&d){if(yield v.addSequenceSpace({clusterCol:n,clusterEmbeddings:f.useEmbeddingsClusters}),!n&&null!==(m=f.useEmbeddingsClusters)&&void 0!==m&&m){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)===o.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(l.q.LOGO_SUMMARY_TABLE))||void 0===t?void 0:t.render)&&(null===(e=null==v?void 0:v.findViewer(l.q.LOGO_SUMMARY_TABLE))||void 0===e||e.render())}),100)}}}else if(null!==(g=f.addMCL)&&void 0!==g&&g&&(yield v.addMCLClusters(),!n&&null!==(p=f.useEmbeddingsClusters)&&void 0!==p&&p)){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(l.q.LOGO_SUMMARY_TABLE))||void 0===t?void 0:t.render)&&(null===(e=null==v?void 0:v.findViewer(l.q.LOGO_SUMMARY_TABLE))||void 0===e||e.render())}),100)}}return y.close(),v}))}},5429:(t,e,n)=>{"use strict";n.d(e,{OH:()=>w,t_:()=>l});var i,r,o,s,a,l,u=n(7389),c=n(4328),f=n(6082),h=n(115),d=n(4139),m=n(768),g=n(7233),p=n.n(g),v=n(144),y=n.n(v),C=n(6920),b=n(1199);function w(t){var e,n,o,g,v,w,A,S,E,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:d.rg.NONE,M=null!==(n=null==_?void 0:_.columns)&&void 0!==n?n:{},I={},O={},L=null!==(o=null==_?void 0:_.sequenceSpaceParams)&&void 0!==o?o:new h.GI,R=null!==(g=null==_?void 0:_.mclSettings)&&void 0!==g?g:new h.av,P=u.input.column(r.ACTIVITY,{table:t.df,value:t.df.getCol(t.settings.activityColumnName),onValueChanged:t=>{I.activityColumnName=t.name},filter:t=>(t.type===f.TYPE.FLOAT||t.type===f.TYPE.INT)&&t.name!==d.$2.ACTIVITY&&0===t.stats.missingValueCount});P.setTooltip("Numeric activity column");const k=u.input.choice(r.ACTIVITY_SCALING,{value:N,items:Object.values(d.rg),onValueChanged:t=>I.activityScaling=t});k.setTooltip("Activity column transformation method"),x.addPane(i.GENERAL,(()=>u.inputs([P,k])),!0),O[i.GENERAL]=[P,k];const V=y()(t.analysisView.viewers).some((t=>t.type===m.q.DENDROGRAM)),D=u.input.bool(m.q.DENDROGRAM,{value:null!=V&&V,onValueChanged:t=>I.showDendrogram=t}),G=u.input.bool(m.q.CLUSTER_MAX_ACTIVITY,{value:!!(null==_?void 0:_.showClusterMaxActivity),onValueChanged:t=>{I.showClusterMaxActivity=null!=t?t:void 0}}),F=u.input.bool("Sequence space",{value:!!(null==_?void 0:_.showSequenceSpace),onValueChanged:t=>{I.showSequenceSpace=null!=t?t:void 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i,r,o,s,a,l,u,c=n(6082),f=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 h=n(1199);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,h.Z.HAMMING,h.Z.LEVENSHTEIN,h.Z.MONOMER_CHEMICAL_DISTANCE,h.Z.NEEDLEMANN_WUNSCH,new RegExp("[rd]\\((\\w)\\)p?","g");var d=n(3077),m=n(439);async function g(){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 p(t,e,n){t instanceof c.Column&&(t=(0,d.R)(t,n).columns.toList());const i=(await g()).getMonomerLib(),r=new Array(t.length),o=t[0].length,s=new Float32Array(o);for(let n=0;n<t.length;++n){const a=n<e.length?e.getCanonical(n):m._S,l=i.getMonomer("PEPTIDE",a)?.smiles??"",u=t[n],h=u.getRawData(),d=u.categories,g=d.indexOf("");if(r[n]={categories:d,data:h,emptyIndex:g},void 0===a)continue;const p=c.Column.fromStrings("smiles",d.map((t=>i.getMonomer("PEPTIDE",t)?.smiles??""))),v=(c.DataFrame.fromColumns([p]),await f.chem.getSimilarities(p,l)),y=v?v.getRawData():null;for(let t=0;t<o;++t){const e=h[t];a!==m._S&&e!==g?s[t]+=y[e]:a===m._S&&e===g&&(s[t]+=1)}}for(let n=0;n<s.length;++n){let i=s[n]/e.length;for(let o=0;o<t.length;++o){const t=r[o];if(o>=e.length&&t.data[n]!==t.emptyIndex||t.data[n]===t.emptyIndex&&o<e.length){i=c.FLOAT_NULL;break}}s[n]=i}return c.Column.fromFloat32Array("Similarity",s)}},439:(t,e,n)=>{"use strict";n.d(e,{B5:()=>a,Hi:()=>i,YI:()=>r,_S:()=>c,b9:()=>f,gp:()=>o,q7:()=>u});var i,r,o,s=n(2738);!function(t){t.FASTA="fasta",t.SEPARATOR="separator",t.HELM="helm",t.CUSTOM="custom"}(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=/(?:\[([A-Za-z0-9_\-,()]+)\])|([A-Za-z\-])/g,l=new class{constructor(){this.fasta={peptide:new Set(["G","L","Y","S","E","Q","D","N","F","A","K","R","H","C","V","P","W","I","M","T"]),dna:new Set(["A","C","G","T"]),rna:new Set(["A","C","G","U"])}}},u=[new s.a(r.PT,l.fasta.peptide,.5),new s.a(r.DNA,l.fasta.dna,.55),new s.a(r.RNA,l.fasta.rna,.55)],c="",f={[i.FASTA]:"-",[i.SEPARATOR]:"",[i.HELM]:"*"}},2003:(t,e,n)=>{"use strict";n.d(e,{Hi:()=>i.Hi,SM:()=>r.SM,YI:()=>i.YI,gp:()=>i.gp,zS:()=>r.zS});var i=n(439),r=n(9634)},2738:(t,e,n)=>{"use strict";n.d(e,{X:()=>r,a:()=>i});class i{constructor(t,e,n){this.name=t,this.alphabet=e,this.cutoff=n}}class r extends i{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,{zS:()=>T,SM:()=>x});var i=n(6082),r=n(144),o=n.n(r);class s extends Float32Array{}function a(t){let e=0;for(let n=0;n<t.length;n++)e+=t[n]*t[n];return Math.sqrt(e)}var l=n(2738),u=n(439);class c{static makePalette(t,e=!1,n=c){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]}}c.undefinedColor="rgb(100,100,100)",c.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 f extends c{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,f)),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,f)),this.grokGroups}static get RasMol(){return void 0===this.rasMol&&(this.rasMol=new f({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 f.aaSynonyms?f.aaSynonyms[t]:t;return super.get(e)}}f.aaSynonyms={MeNle:"L",MeA:"A",MeG:"G",MeF:"F"};class h{static getPalette(t="grok"){switch(t){case"grok":return f.GrokGroups;case"lesk":return f.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]}}h.SemType="Aminoacids",h.SemTypeMultipleAlignment="AminoacidsMultipleAlignment",h.undefinedColor="rgb(100,100,100)",h.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"},h.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"},h.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(*)*"},h.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 d extends c{static get Chromatogram(){return void 0===this.chromatogram&&(this.chromatogram=new d({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(8223);function p(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 v{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 y{}class C extends y{get(t,e){return"#666666"}}class b extends y{static get palette(){return b._pallete||(b._pallete=b.buildPalette()),b._pallete}static buildPalette(){return(0,g.pj)().then((t=>{t.awaitLoaded(1/0).then((()=>{const 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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",t.MCL="MCL"}(G||(G={}));class H{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,N.Ej)(e,this.df.filter,this.positionColumns)),this._monomerPositionStats)}get analysisView(){var t,e,n;return void 0===this._analysisView&&(this._analysisView=this.id?g()(o.shell.tableViews).find((({dataFrame:t})=>(null==t?void 0:t.getTag(s.TAGS.ID))===this.id)):void 0,!this._analysisView&&(null===(t=o.shell.v)||void 0===t?void 0:t.preview)instanceof s.TableView&&(null===(n=null===(e=o.shell.v)||void 0===e?void 0:e.preview)||void 0===n?void 0:n.dataFrame)===this.df&&(this._analysisView=o.shell.v.preview),this._analysisView||(this._analysisView=o.shell.addTableView(this.df))),"1"===this.df.getTag(y.gp.MULTIPLE_VIEWS)||this._layoutEventInitialized||(0,b.Lv)()||(o.shell.v=this._analysisView),this._analysisView.grid.invalidate(),this._analysisView}get settings(){var t,e;const n=this.df.getTag(y.gp.SETTINGS);return n?(null!==(t=this._settings)&&void 0!==t||(this._settings=JSON.parse(n)),!(null===(e=this._settings)||void 0===e?void 0:e.mclSettings)||this._settings.mclSettings.webGPUDescriptionPromise instanceof Promise||(this._settings.mclSettings.webGPUDescriptionPromise=(0,D._)()),this._settings):null}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(G.DENDROGRAM);break;case"clusterMaxActivity":this.settings.showClusterMaxActivity?this.addClusterMaxActivityViewer():this.closeViewer(G.CLUSTER_MAX_ACTIVITY);break;case"logoSummaryTable":this.settings.showLogoSummaryTable?this.addLogoSummaryTable():this.closeViewer(G.LOGO_SUMMARY_TABLE);break;case"monomerPosition":this.settings.showMonomerPosition?this.addMonomerPosition():this.closeViewer(G.SEQUENCE_VARIABILITY_MAP);break;case"mostPotentResidues":this.settings.showMostPotentResidues?this.addMostPotentResidues():this.closeViewer(G.MOST_POTENT_RESIDUES);break;case"columns":const t=this.findViewer(G.LOGO_SUMMARY_TABLE);t._viewerGrid=null,t._logoSummaryTable=null,t.render();const e=this.findViewer(G.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(`${y.YX.WL}${y.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(`${y.YX.WL}${y.gp.INVARIANT_MAP_SELECTION}`,JSON.stringify(t)),this.fireBitsetChanged(null),this.analysisView.grid.invalidate()}get positionColumns(){const t=g()(this.df.columns.byTags({[y.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){if(t.columns.contains(y.$2.ACTIVITY_SCALED)&&!t.columns.contains(y.$2.ACTIVITY)&&(t.getCol(y.$2.ACTIVITY_SCALED).name=y.$2.ACTIVITY),!t.temp[H.modelName]){const e=t.temp[H.modelName]=new H(t),n=e.settings;n&&e.init(n);let i=!0;e.subs.push(s.debounce(t.onSelectionChanged,10).subscribe((n=>{var r;if(i||t.selection.anyTrue||!e._analysisView||!document.contains(e._analysisView.root)||e._analysisView.dataFrame!==t||!e.positionColumns)return void(i=!(null===(r=null==t?void 0:t.selection)||void 0===r?void 0:r.anyTrue));e.webLogoSelection=(0,b.ZR)(e.positionColumns);const o=e.findViewer(G.SEQUENCE_VARIABILITY_MAP);null!=o&&(o.invariantMapSelection=(0,b.ZR)(e.positionColumns),o.mutationCliffsSelection=(0,b.ZR)(e.positionColumns));const s=e.findViewer(G.MOST_POTENT_RESIDUES);null!=s&&(s.mutationCliffsSelection=(0,b.ZR)(e.positionColumns),s.invariantMapSelection=(0,b.ZR)(e.positionColumns));const a=e.findViewer(G.LOGO_SUMMARY_TABLE);null!=a&&(a.initClusterSelection({notify:!0}),a.render()),i=!0})))}return t.temp[H.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,o,l;const u=null===(t=this.df)||void 0===t?void 0:t.temp[H.modelName];if(!u)return null;const c=r.accordion("Peptides analysis panel");c.root.style.width="100%";const f=u.getVisibleSelection(),h=u.df.filter.anyFalse?` among ${u.df.filter.trueCount} filtered`:"",d=t=>{const e=[];for(const[n,i]of Object.entries(t))for(const t of i)e.push(`${n}:${t}`);return e.join(", ")},m=u.findViewer(G.LOGO_SUMMARY_TABLE),p=[],y=(null===m?[]:m.clusterSelection[T.W.ORIGINAL].concat(m.clusterSelection[T.W.CUSTOM])).join(", "),C=t=>{const e=r.divText(t);return e.innerHTML=t,e};0!==y.length&&p.push(C(`<b>Logo Summary Table</b> clusters: ${y}`));const x=u.findViewer(G.SEQUENCE_VARIABILITY_MAP),_=d(null!==(e=null==x?void 0:x.invariantMapSelection)&&void 0!==e?e:{}),M=d(null!==(n=null==x?void 0:x.mutationCliffsSelection)&&void 0!==n?n:{});0!==_.length&&p.push(C(`<b>Invariant map</b>: ${_}`)),0!==M.length&&p.push(C(`<b>Mutation cliffs</b>: ${M}`));const I=u.findViewer(G.MOST_POTENT_RESIDUES),O=d(null!==(i=null==I?void 0:I.invariantMapSelection)&&void 0!==i?i:{});0!==O.length&&p.push(C(`<b>Most potent residues</b>: ${O}`));const L=d(u.webLogoSelection);0!==L.length&&p.push(C(`<b>WebLogo</b>: ${L}`)),0!==p.length&&p.unshift(r.h1("Selection Sources"));const R=r.div(r.divV(p));c.addTitle(r.divV([r.h1(`${f.trueCount} selected rows${h}`),R],"css-gap-small")),f.anyTrue&&c.addPane("Actions",(()=>{try{const t=r.label("New view");if(v()(t).addClass("d4-link-action"),t.onclick=()=>u.createNewView(),t.onmouseover=t=>r.tooltip.show("Creates a new view from current selection",t.clientX+5,t.clientY+5),null===m)return r.divV([t]);const e=r.label("New cluster");v()(e).addClass("d4-link-action"),e.onclick=()=>{if(null===m)throw new Error("Logo summary table viewer is not found");m.clusterFromSelection()},e.onmouseover=t=>r.tooltip.show("Creates a new cluster from selection",t.clientX+5,t.clientY+5);const n=r.label("Remove cluster");return v()(n).addClass("d4-link-action"),n.onclick=()=>{const t=u.findViewer(G.LOGO_SUMMARY_TABLE);if(null===t)throw new Error("Logo summary table viewer is not found");t.removeCluster()},n.onmouseover=t=>r.tooltip.show("Removes currently selected custom cluster",t.clientX+5,t.clientY+5),n.style.visibility=0===m.clusterSelection[T.W.CUSTOM].length?"hidden":"visible",r.divV([t,e,n])}catch(t){const e=r.divText("Error in Actions");return r.tooltip.bind(e,String(t)),e}}),!0);let P=u.settings;const k=[x,I,m].filter((t=>null!==t&&(t.type!==this.accordionSource||(P=t,!1))));if(null===P)throw new Error("PeptidesError: Model is the source of accordion but is not initialized");P!==u.settings&&k.push(u.settings);const V=k.filter((t=>null!==t&&(0,b.$s)(P,t)&&(t!==u.settings||u.isInitialized)));V.push(P);const D=s.BitSet.create(u.df.rowCount);for(const t of V){const e=t===this.settings?(0,b.KT)(this.webLogoSelection,this.monomerPositionStats):t instanceof T.s?(0,b.KT)(t.clusterSelection,t.clusterStats):t instanceof w.xN?(0,b.KT)(t.mutationCliffsSelection,(0,b.qI)(null!==(o=t.mutationCliffs)&&void 0!==o?o:new Map,u.df.rowCount)):null;if(null!==e&&D.or(e),t instanceof w.J){const e=(0,b.KT)(t.invariantMapSelection,t.monomerPositionStats);null!==e&&D.or(e)}}const U=P;P===u.settings||U instanceof T.s||null==U.mutationCliffs||c.addPane("Mutation Cliffs pairs",(()=>(0,S.F)(u.df,{mutationCliffs:U.mutationCliffs,mutationCliffsSelection:U.mutationCliffsSelection,gridColumns:u.analysisView.grid.columns,sequenceColumnName:U.sequenceColumnName,positionColumns:U.positionColumns,activityCol:U.getScaledActivityColumn()}).root),!0);const q=P===u.settings,B=q?this.webLogoSelection:P instanceof w.J?P.invariantMapSelection:{},Y=P instanceof T.s?P.clusterSelection:null!==(l=null==m?void 0:m.clusterSelection)&&void 0!==l?l:{};c.addPane("Distribution",(()=>{var t;try{return(0,E.HV)(u.df,{peptideSelection:D,columns:q?null!==(t=u.settings.columns)&&void 0!==t?t:{}:P.getAggregationColumns(),activityCol:q?u.getScaledActivityColumn():P.getScaledActivityColumn(),monomerPositionSelection:B,clusterSelection:Y,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 W=(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 c.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,f=null;try{c=u.getRawData(),f=u.categories}catch(t){}const h=c&&f?a.some((t=>t.name===u.name))?t=>c[t]:t=>f[c[t]]:t=>u.get(t),d=u.name===e.activityColumn.name?o.columns.addNewFloat(r.name).init((t=>h(t))):o.columns.addNewVirtual(r.name,(t=>h(t)),u.type);for(const[t,e]of u.tags)d.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 f=(0,N.Ej)(e.activityColumn,o.filter,e.positionColumns,{isFiltered:o.filter.anyTrue||o.filter.anyFalse}),h={isSelectionTable:!0,cachedWebLogoTooltip:()=>({bar:"",tooltip:null}),webLogoBounds:()=>({}),colorPalette:()=>e.colorPalette},d={x:0,y:0,monomerPosition:{},mpStats:f};return e.isAnalysis&&(0,A.FZ)(u,f,e.positionColumns,e.activityColumn,h,d),c}(u.df,{positionColumns:q?u.positionColumns:P.positionColumns,columns:q?null!==(t=u.settings.columns)&&void 0!==t?t:{}:P.getAggregationColumns(),activityColumn:q?u.getScaledActivityColumn():P.getScaledActivityColumn(),gridColumns:u.analysisView.grid.columns,colorPalette:(0,a.SM)(u.df.getCol(q?u.settings.sequenceColumnName:P.sequenceColumnName),F.Z.getSeqHelper()),tableSelection:u.getCombinedSelection(),isAnalysis:null!==u.settings&&(q||W(u.settings.columns,P.getAggregationColumns()))})}catch(t){const e=r.divText("Error in Selection");return r.tooltip.bind(e,String(t)),e}}),!0),c}getScaledActivityColumn(t=!1){const e=this.df.col(y.$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),F.Z.getSeqHelper()),webLogoBounds:()=>this.webLogoBounds,cachedWebLogoTooltip:()=>this.cachedWebLogoTooltip,highlightCallback:(t,e,n)=>{(0,b.dl)(t,e,n),this.isHighlighting=!0},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");A.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,u.R)(this.df.getCol(this.settings.sequenceColumnName),F.Z.getSeqHelper()),i=n.columns.names();if(i.every((t=>e.contains(t))))i.forEach((t=>A.rI(this.df.col(t),this.alphabet)));else 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(y.gp.ANALYSIS_COL,"true"),i.setTag(y.gp.POSITION_COL,"true"),A.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(y.$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)!==y.uF.MONOMER)||!(!t.isTableCell||(null===(r=t.tableColumn)||void 0===r?void 0:r.semType)!==y.uF.MONOMER)}))}getCombinedSelection(){var t,e,n,i,r,o,a,l;const u=new d.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 f=this.findViewer(G.SEQUENCE_VARIABILITY_MAP);c(null!==(t=null==f?void 0:f.invariantMapSelection)&&void 0!==t?t:{},null!==(e=null==f?void 0:f.monomerPositionStats)&&void 0!==e?e:null),((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)}}})(null!==(n=null==f?void 0:f.mutationCliffsSelection)&&void 0!==n?n:{},null!==(i=null==f?void 0:f.mutationCliffs)&&void 0!==i?i:null);const h=this.findViewer(G.MOST_POTENT_RESIDUES);c(null!==(r=null==h?void 0:h.invariantMapSelection)&&void 0!==r?r:{},null!==(o=null==h?void 0:h.monomerPositionStats)&&void 0!==o?o:null);const m=this.findViewer(G.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;let n=null;const i=()=>{try{null!=n&&(clearTimeout(n),n=null);const t=this.createAccordion();if(null===t)return;o.shell.o=t.root,n=setTimeout((()=>{o.shell.o!=t.root&&(o.shell.o=t.root)}),1500)}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){_._package.logger.debug("Peptides: Error on selection changed"),_._package.logger.debug(t)}finally{i()}})),e.onChanged.subscribe((()=>{var t,e;try{if(this.controlFire)return void(this.controlFire=!1);const n=this.findViewer(G.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){_._package.logger.debug("Peptides: Error on filter changed"),_._package.logger.debug(t)}finally{i()}})),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 f=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=f.includes(e.column.name)||e.column.name===y.$2.ACTIVITY}setTimeout((()=>{for(const t of l){const e=o.col(t.name);if(null===e)throw new Error(`PeptidesError: Could not set column width: grid column '${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 U(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){_._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(y.gp.MULTIPLE_VIEWS)){const t=r.iconFA("wrench",(()=>(0,x.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=v()(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);f(this.df,t,t.get(this.df.currentRowIdx),i.IDENTITY,F.Z.getSeqHelper()).then((e=>e.setTag(y.gp.IDENTITY_TEMPLATE,t.get(this.df.currentRowIdx)))).catch((t=>_._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);f(this.df,t,t.get(this.df.currentRowIdx),i.SIMILARITY,F.Z.getSeqHelper()).then((e=>e.setTag(y.gp.SIMILARITY_TEMPLATE,t.get(this.df.currentRowIdx)))).catch((t=>_._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 U(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(G.LOGO_SUMMARY_TABLE,t);(0,b.Lv)()&&this.analysisView.addViewer(e),this.analysisView.dockManager.dock(e,s.DOCK_TYPE.RIGHT,null,G.LOGO_SUMMARY_TABLE),e.viewerGrid.invalidate()}))}addClusterMaxActivityViewer(t){return U(this,void 0,void 0,(function*(){var e,n,i,r,o,a,l,u,c;const f=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(G.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!=f?f:null===(a=g()(this.df.columns.categorical).next().value)||void 0===a?void 0:a.name,activityTarget:y.wf.HIGH,connectivityColumnName:null!==(u=null!==(l=this._mclCols.find((t=>t.toLowerCase().startsWith("connectivity"))))&&void 0!==l?l:this.df.columns.names().find((t=>{var e;return t.toLowerCase().includes("connectivity")&&(null===(e=this.df.col(t))||void 0===e?void 0:e.isNumerical)})))&&void 0!==u?u:"",clusterSizeThreshold:20,activityThreshold:1e3});const h=yield this.df.plot.fromType(G.CLUSTER_MAX_ACTIVITY,t),d=null!==(c=this.findViewerNode(G.LOGO_SUMMARY_TABLE))&&void 0!==c?c:null;this.analysisView.dockManager.dock(h,d?s.DOCK_TYPE.DOWN:s.DOCK_TYPE.RIGHT,d,G.CLUSTER_MAX_ACTIVITY)}))}addMonomerPosition(t){return U(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:y.wf.HIGH});const e=yield this.df.plot.fromType(G.SEQUENCE_VARIABILITY_MAP,t);(0,b.Lv)()&&this.analysisView.addViewer(e);const n=this.findViewer(G.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(G.MOST_POTENT_RESIDUES),.7];i.dock(e,r,o,G.SEQUENCE_VARIABILITY_MAP,a)}))}addMostPotentResidues(t){return U(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:y.wf.HIGH});const e=yield this.df.plot.fromType(G.MOST_POTENT_RESIDUES,t);(0,b.Lv)()&&this.analysisView.addViewer(e);const n=this.findViewer(G.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(G.SEQUENCE_VARIABILITY_MAP),.3];i.dock(e,r,o,G.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===y.gp.SETTINGS?n:"");e.name="Peptides Multiple Views",e.setTag(y.gp.MULTIPLE_VIEWS,"1");const n=o.shell.addTableView(e),i=this.findViewer(G.LOGO_SUMMARY_TABLE);return null!=i&&n.addViewer(G.LOGO_SUMMARY_TABLE,{[`sequence${y.To}`]:i.sequenceColumnName,[`activity${y.To}`]:i.activityColumnName,activityScaling:i.activityScaling,webLogoMode:i.webLogoMode,membersRatioThreshold:i.membersRatioThreshold,[`clusters${y.To}`]:i.clustersColumnName}),e.getTag(s.TAGS.ID)}clusterEmbeddings(){return U(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),f=this.df.columns.getUnusedName("Cluster (DBSCAN)"),h=this.df.columns.addNewString(f);h.init((t=>c[t].toString())),null!==this._sequenceSpaceViewer&&(this._sequenceSpaceViewer.props.colorColumnName=h.name),this._sequenceSpaceCols=[i[0],i[1],h.name];const d=this.analysisView.grid.col(h.name);d&&(d.visible=!1)}))}addMCLClusters(){return U(this,void 0,void 0,(function*(){var t,e,n,i,r;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 a=this.df.getCol(this.settings.sequenceColumnName);null!==(n=(r=this.settings).mclSettings)&&void 0!==n||(r.mclSettings=new C.av);const l=this.settings.mclSettings;let u=0;const c=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),u++}5===u&&c.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)}})),h=JSON.stringify({cols:[a].map((t=>t.name)),metrics:[l.distanceF],weights:[1],aggregationMethod:V.MANHATTAN,preprocessingFuncs:["macromoleculePreprocessingFunction"],preprocessingFuncArgs:[{gapOpen:l.gapOpen,gapExtend:l.gapExtend,fingerprintType:l.fingerprintType}],threshold:l.threshold,maxIterations:l.maxIterations,useWebGPU:l.useWebGPU,inflate:l.inflation,minClusterSize:l.minClusterSize}),d=null!==(i=this.analysisView)&&void 0!==i?i:o.shell.getTableView(this.df.name);if(d){const t=s.Func.find({package:"EDA",name:"markovClusteringViewer"})[0];if(!t)throw new Error("Markov clustering function is not found");yield t.apply(),d.addViewer(G.MCL,{mclProps:h}),yield s.delay(500),this._mclViewer=this.findViewer(G.MCL),yield this._mclViewer.initPromise;const e=this.findViewer(G.LOGO_SUMMARY_TABLE);e&&(e._clusterStats=null,e._clusterSelection=null,e._viewerGrid=null,e._logoSummaryTable=null,e.render())}}))}addSequenceSpace(){return U(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=F.Z.getSeqHelper().getSeqHandler(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,f=null!==(r=null===(i=this.settings)||void 0===i?void 0:i.sequenceSpaceParams)&&void 0!==r?r:new C.GI(c);f.clusterEmbeddings=c;const d={table:this.df,molecules:l,methodName:h.UMAP,similarityMetric:f.distanceF,plotEmbeddings:!0,options:{bypassLargeDataWarning:!0,dbScanEpsilon:f.epsilon,dbScanMinPts:f.minPts,randomSeed:"1",preprocessingFuncArgs:{gapOpen:f.gapOpen,gapExtend:f.gapExtend,fingerprintType:f.fingerprintType}},clusterEmbeddings:f.clusterEmbeddings};let m=0;const g=f.clusterEmbeddings?3:2,p=this.df.onColumnsAdded.subscribe((t=>{for(const e of t.columns)if(e.name.toLowerCase().startsWith("embed_")||f.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&&p.unsubscribe()})),v=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)}))}v.unsubscribe()}}catch(t){console.error(t)}})),y=yield o.functions.call("Bio:sequenceSpaceTopMenu",d);v.unsubscribe(),y instanceof s.ScatterPlotViewer&&(f.clusterEmbeddings||t.clusterCol||(y.props.colorColumnName=this.getScaledActivityColumn().name),y.props.showXSelector=!1,y.props.showYSelector=!1,t.clusterCol&&(y.props.colorColumnName=t.clusterCol.name),this._sequenceSpaceViewer=y,y.onContextMenu.subscribe((t=>{try{t.item("Modify Sequence space parameters",(()=>{(0,x.OH)(this)}))}catch(t){}})))}))}}H.modelName="peptidesModel"},6920:(t,e,n)=>{"use strict";n.r(e),n.d(e,{Peptides:()=>K,_package:()=>Y,clusterMaxActivity:()=>nt,getMonomerWorksInstance:()=>W,getTreeHelperInstance:()=>j,initPeptides:()=>$,logoSummaryTable:()=>et,lstPiechartCellRenderer:()=>ot,macromoleculeSarFastaDemo:()=>rt,manualAlignment:()=>it,monomerPosition:()=>J,mostPotentResidues:()=>tt,peptidesDialog:()=>Q,peptidesPanel:()=>X,testInitFunctionPeptides:()=>Z});var i=n(4328),r=n(7389),o=n(6082),s=n(5082),a=n(7233),l=n.n(a),u=(n(4788),n(768)),c=n(726),f=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())}))},h=n(3541),d=n(5480);n(3981);class m{constructor(t){this.monomerLib=t}getCappedRotatedMonomer(t,e){const n=this.monomerLib.getMonomer(t,e);return n?n.molfile:null}}var g=n(4139),p=n(8608),v=n(2003),y=n(8070),C=n(115),b=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())}))},w=n(5072),A=n.n(w),S=n(7825),E=n.n(S),T=n(7659),x=n.n(T),_=n(5056),N=n.n(_),M=n(540),I=n.n(M),O=n(1113),L=n.n(O),R=n(6677),P={};P.styleTagTransform=L(),P.setAttributes=N(),P.insert=x().bind(null,"head"),P.domAPI=E(),P.insertStyleElement=I(),A()(R.A,P),R.A&&R.A.locals&&R.A.locals;var k;!function(t){let e,n;!function(t){t.vert=function(t){return r.divV(t.map((t=>r.render(t))),{classes:"u2-panel"})},t.horz=function(t){return r.divH(t.map((t=>r.render(t))),{classes:"u2-panel"})}}(e=t.panels||(t.panels={})),t.appHeader=function(t){const n=r.iconImage("",t.iconPath);return l()(n).addClass("ui-app-header-icon").css("margin-right","20px"),e.horz([n,e.vert([r.markdown(t.description),t.learnMoreUrl?r.link("Learn more",t.learnMoreUrl):null])])},function(t){t.runAsync=function(t,e){return n=this,o=void 0,a=function*(){r.setUpdateIndicator(t,!0);try{return yield e()}catch(t){i.log.error(t)}finally{r.setUpdateIndicator(t,!1)}},new((s=void 0)||(s=Promise))((function(t,e){function i(t){try{l(a.next(t))}catch(t){e(t)}}function r(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 s?n:new s((function(t){t(n)}))).then(i,r)}l((a=a.apply(n,o||[])).next())}));var n,o,s,a}}(n=t.tools||(t.tools={}))}(k||(k={}));var V=n(144),D=n.n(V);const G=rxjs.operators;class F extends o.JsViewer{get scViewer(){return this._scViewer||(this._scViewer=this.createSCViewer()),this._scViewer}constructor(){super(),this._titleHost=r.divText(u.q.CLUSTER_MAX_ACTIVITY,{id:"pep-viewer-title",style:{marginRight:"auto"}}),this._selsectIcon=r.div(),this.activityTarget=g.wf.HIGH,this.viewerError="",this.renderTimeout=null,this.renderDebounceTime=500,this.scFilterQuery=`\${${F.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",g.wf.HIGH,{choices:[g.wf.HIGH,g.wf.LOW]}),this.clusterSizeThreshold=this.int("clusterSizeThreshold",20),this.activityThreshold=this.int("activityThreshold",1e3),this.connectivityColumnName=this.column("connectivity",{nullable:!0})}get model(){return u.i.getInstance(this.dataFrame)}createSCViewer(){var t;const e={showXAxis:!0,showYAxis:!0,showXSelector:!1,showYSelector:!1,showColorSelector:!1,xAxisType:o.AxisType.logarithmic,yAxisType:o.AxisType.logarithmic,invertYAxis:this.activityTarget===g.wf.LOW,xColumnName:F.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),s=null!=this.connectivityColumnName?this.dataFrame.columns.byName(this.connectivityColumnName):null;if(![o.COLUMN_TYPE.FLOAT,o.COLUMN_TYPE.INT,o.COLUMN_TYPE.BIG_INT,o.COLUMN_TYPE.QNUM].includes(n.type))return this.viewerError="Activity column should be numeric",null;const a=this.dataFrame.columns.getOrCreate(F.clusterSizeColName,o.TYPE.INT),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)}a.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=o.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 r=n.get(t),o=u[e];if((null==o||null==o||r>n.get(o)&&this.activityTarget===g.wf.HIGH||r<n.get(o)&&this.activityTarget===g.wf.LOW)&&(u[e]=t),s){const n=s.get(t),i=c[e];(null==i||null==i||n>s.get(i))&&(c[e]=t)}}const f=this.dataFrame.columns.getOrCreate(F.maxActivityInClusterColName,o.COLUMN_TYPE.INT);f.init((t=>i.isNone(t)?0:t===u[i.get(t)]?1:0)),this.dataFrame.columns.getOrCreate(F.maxConnectivityInClusterColName,o.COLUMN_TYPE.INT).init((t=>i.isNone(t)?0:t===c[i.get(t)]?1:0)),this.dataFrame.columns.getOrCreate(F.synSelectionColName,o.TYPE.STRING).init((t=>{if(i.isNone(t))return null;let e=null;return t===u[i.get(t)]&&(e=F.maxActivityLabel),s&&t===c[i.get(t)]&&(e=e?`${e}, ${F.maxConnectivityLabel}`:F.maxConnectivityLabel),e})),e.xColumnName=F.clusterSizeColName,e.yColumnName=this.activityColumnName,e.filter=this.scFilterQuery,this.viewerError="";const h=o.Viewer.scatterPlot(this.dataFrame,e);this.selectionSubscription&&this.selectionSubscription.unsubscribe(),this.selectionSubscription=h.onDataEvent.pipe((0,G.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:[],s=this.dataFrame.selection,a=o.BitSet.create(this.dataFrame.rowCount,(t=>1==f.get(t)));a.and(s);for(let t=0;t<r.length;t++){const e=r[t],n=i.get(e);i.isNone(e)||(a.set(e,!0),null!=c[n]&&a.set(c[n],!0))}a.fireChanged();const l=a.getSelectedIndexes();for(const t of l){const e=i.get(t);null!=e&&null!=c[e]&&a.set(c[e],!0)}setTimeout((()=>{this.dataFrame.selection.copyFrom(a,!0),setTimeout((()=>{this.model&&this.model.createAccordion()}),200)}),200)}));const d=()=>{const t=o.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=r.iconSvg("select-all",(()=>{d()}),"Select 3 Active quadrants"),this._selsectIcon.style.cursor="pointer",this._selsectIcon.style.marginRight="5px",d(),this.linesDrawSubscription&&this.linesDrawSubscription.unsubscribe(),this.linesDrawSubscription=h.onBeforeDrawScene.subscribe((()=>{const t=h.getInfo().canvas.getContext("2d"),e=h.viewport,n=h.worldToScreen(e.x,this.activityThreshold),i=h.worldToScreen(this.clusterSizeThreshold,e.y),r=h.worldToScreen(e.x+e.width,this.activityThreshold),o=h.worldToScreen(this.clusterSizeThreshold,e.y+e.height);t.beginPath(),t.strokeStyle="rgb(0,0,0)",t.lineWidth=1,t.moveTo(n.x,n.y),t.lineTo(r.x,r.y),t.moveTo(i.x,i.y),t.lineTo(o.x,o.y),t.stroke(),t.closePath()})),h}onTableAttached(){var t,e,n,i,r,o,s,a,l,u,c,f;super.onTableAttached();const h=null!==(e=null===(t=this.dataFrame)||void 0===t?void 0:t.col(g.$2.ACTIVITY))&&void 0!==e?e:null===(i=D()(null===(n=this.dataFrame)||void 0===n?void 0:n.columns.numerical).next())||void 0===i?void 0:i.value;null!=h&&(null===(r=this.getProperty(`activity${g.To}`))||void 0===r||r.set(this,h.name));const d=null===(s=D()(null===(o=this.dataFrame)||void 0===o?void 0:o.columns.categorical).next())||void 0===s?void 0:s.value;null!=d&&(null===(a=this.getProperty(`cluster${g.To}`))||void 0===a||a.set(this,d.name));const m=null===(u=D()(null===(l=this.dataFrame)||void 0===l?void 0:l.columns.numerical).next())||void 0===u?void 0:u.value;null!=m&&(null===(c=this.getProperty(`connectivity${g.To}`))||void 0===c||c.set(this,m.name)),this.render(),null===(f=this.dataFrame)||void 0===f||f.onDataChanged.subscribe((()=>{this.render()}))}render(){this.renderTimeout&&clearTimeout(this.renderTimeout),this.renderTimeout=setTimeout((()=>{var t,e;if(!this.dataFrame)return;l()(this.root).empty();const n=this.scViewer;if(null==n)return void this.root.appendChild(r.divText(null!==(t=this.viewerError)&&void 0!==t?t:"Error creating scatter plot"));const i=r.div("Cluster Size",{style:{alignSelf:"center",color:"var(--grey-6)",marginBottom:"5px"}}),o=r.div(this.activityTarget===g.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(r.divH([o,r.divV([r.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${g.To}`&&(this._scViewer=null),this.render()}}F.clusterSizeColName="~cluster.size",F.maxActivityInClusterColName="~max.activity.for.cluster",F.maxConnectivityInClusterColName="~max.connectivity.for.cluster",F.synSelectionColName="Syn Selection",F.maxActivityLabel="Max Activity",F.maxConnectivityLabel="Max Connectivity";var U=n(3163),H=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())}))};let q,B=null;const Y=new o.Package;function W(){return B}function j(){return q}function $(){return H(this,void 0,void 0,(function*(){try{null!=B||(B=new m(yield i.functions.call("Bio:getBioLib"))),null!=q||(q=yield async function(){const t="Dendrogram",e=o.Func.find({package:t,name:"getTreeHelper"});if(0===e.length)throw new Error(`Package "${t}" must be installed for TreeHelper.`);return(await e[0].prepare().call()).getOutputParamValue()}()),yield c.Z.loadComponents()}catch(t){i.log.error(t)}}))}function z(t){return H(this,void 0,void 0,(function*(){const e=o.TaskBarProgressIndicator.create("Loading Peptides"),n=Y.webRoot+"files/"+t,r=yield i.data.loadTable(n);r.name="Peptides",i.shell.addTableView(r).name="PeptidesView",i.shell.windows.showProperties=!0,e.close()}))}function K(){const t=k.appHeader({iconPath:Y.getIconUrl(),learnMoreUrl:"https://github.com/datagrok-ai/public/blob/master/help/domains/bio/peptides.md",description:"- Automatically recognizes peptides in your data\n- Invariant map and mutation cliffs\n- Logo plots to explore sequence composition\n- Hierarchical clustering\n- Sequence space to analyze clustering and activity cliffs\n- Finds statistically significant changes in activity for monomer/positions\n"}),e=i.shell.windows;e.showToolbox=!1,e.showHelp=!1,e.showProperties=!1;const n=o.View.create();return n.name="Peptides",r.appendAll(n.root,[t,r.divH([r.button("Simple demo",(()=>z("aligned.csv")),""),r.button("Complex demo",(()=>z("aligned_2.csv")),""),r.button("HELM demo",(()=>z("aligned_3.csv")),"")])]),n}function Q(){var t;if(!i.shell.t||!(null===(t=i.shell.t.columns.bySemType("Macromolecule"))||void 0===t?void 0:t.length))return i.shell.warning("SAR Analysis requires an active table with Macromolecule column"),null;if(!o.Utils.firstOrNull(i.shell.t.columns.numerical))return i.shell.warning("SAR Analysis requires an active table with at least one numerical column for activity"),null;const e=(0,s.v)(i.shell.t),n=r.dialog("Analyze Peptides").add(e.host).onOK((()=>H(this,void 0,void 0,(function*(){e.callback()||n.show()}))));return n.show()}function Z(t){return H(this,void 0,void 0,(function*(){i.shell.info("Test init function for Peptides package"),i.shell.info("Viewer name: "+t.dataFrame.name),yield new Promise((t=>setTimeout(t,1e3)))}))}function X(t){if(!t.dataFrame||!o.Utils.firstOrNull(t.dataFrame.columns.numerical))return new o.Widget(r.divText("SAR Analysis requires an active table with at least one numerical column for activity"));const e=(0,s.v)(t.dataFrame,t);return new 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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[d.W.CUSTOM].includes(e)||n[d.W.ORIGINAL].includes(e))&&v(t,i)}function A(t,e,n,u,c,f={x:0,y:0,mpStats:{},monomerPosition:{}}){var d;if(null!==(d=c.isSelectionTable)&&void 0!==d||(c.isSelectionTable=!1),0==Object.keys(f.mpStats).length&&(f.mpStats=e),c.isSelectionTable&&(!c.webLogoBounds||!c.cachedWebLogoTooltip))throw new Error("Peptides: Cannot set WebLogo renderer for selection table without `headerSelectedMonomers`, `webLogoBounds` and `cachedWebLogoTooltip` options.");const m=t.dataFrame;t.setOptions({colHeaderHeight:130});t.onCellRender.subscribe((t=>(t=>{var i;const l=t.g,f=t.bounds,h=t.cell.tableColumn;l.save();try{if(l.beginPath(),l.clearRect(f.x,f.y,f.width,f.height),l.rect(f.x,f.y,f.width,f.height),l.clip(),t.cell.isColHeader&&(null==h?void 0:h.semType)===o.uF.MONOMER){let d;if(m.filter.anyFalse){const t=null!==(i=m.temp[o.gp.M_P_STATS_CACHE])&&void 0!==i?i:{},e=null==t?void 0:t[h.name],r=m.filter.getBuffer();if(t&&e&&e.filter.length===r.length&&e.filter.every(((t,e)=>t===r[e])))d=e.stats[h.name];else{const e=(0,a.Ej)(u,m.filter,n,{isFiltered:!0,columns:[h.name]});d=e[h.name],t[h.name]={filter:m.filter.getBuffer(),stats:e,selection:m.selection.getBuffer()}}m.temp[o.gp.M_P_STATS_CACHE]=t}else d=c.isSelectionTable?(0,a.Ej)(u,m.filter,n,{isFiltered:!0,columns:[h.name]})[h.name]:e[h.name];if(!d)return;const v=Object.keys(d).sort(((t,e)=>""===t||"-"===t?1:""===e||"-"===e?-1:0)).filter((t=>"general"!==t));c.webLogoBounds()[h.name]=function(t,e,n,i,o,a,l,u={},c={}){var f,h,d,m,v,y,C,b,w;const A=window.devicePixelRatio;null!==(f=c.symbolStyle)&&void 0!==f||(c.symbolStyle="16px Roboto, Roboto Local, sans-serif"),null!==(h=c.upperLetterHeight)&&void 0!==h||(c.upperLetterHeight=12.2),null!==(d=c.upperLetterAscent)&&void 0!==d||(c.upperLetterAscent=.25),null!==(m=c.marginVertical)&&void 0!==m||(c.marginVertical=1),null!==(v=c.marginHorizontal)&&void 0!==v||(c.marginHorizontal=1),null!==(y=c.selectionWidth)&&void 0!==y||(c.selectionWidth=2),null!==(C=c.textHeight)&&void 0!==C||(c.textHeight=13),null!==(b=c.headerStyle)&&void 0!==b||(c.headerStyle=`bold ${c.textHeight*A}px Roboto, Roboto Local, sans-serif`);const S=(o.length-1)*c.upperLetterAscent;let E=(e.y+c.marginVertical)*A;const T=(e.height-2*c.marginVertical-S-1.25*c.textHeight)*A,x=(e.x+c.marginHorizontal)*A,_=Math.max(c.selectionWidth*A,.05*e.width*A),N=2*c.marginHorizontal+c.selectionWidth,M=(e.width-(N+c.marginHorizontal))*A,I=(e.x+N)*A,O=g.Z.getMonomerLib(),L={};for(const e of o){const i=T*(n[e].count/a),o=T*((null!==(w=u[e])&&void 0!==w?w:0)/a);if(L[e]=new r.Rect(I/A,E/A,M/A,i/A),t.resetTransform(),"-"!==e&&""!==e){const n=(0,s.zS)(e,5),a=t.measureText(n);o>0&&(t.lineWidth=_,t.line(x,E,x,E+o,r.Color.rowSelection));const l=O.getMonomerTextColor(p.o.AA,e);t.fillStyle=l,t.textAlign="left",t.textBaseline="top",t.font=c.symbolStyle;const u=M/a.width,f=i/c.upperLetterHeight;t.setTransform(u,0,0,f,I,E),t.fillText(n,0,0,a.width)}E+=i+c.upperLetterAscent*A}return t.resetTransform(),t.fillStyle=r.Color.toHtml(r.Color.black),t.textAlign="center",t.textBaseline="top",t.font=c.headerStyle,t.fillText(i,(e.x+e.width/2)*A,(e.y+e.height-c.textHeight)*A),L}(l,f,d,h.name,v,m.filter.trueCount,c.colorPalette(),c.headerSelectedMonomers?c.headerSelectedMonomers()[h.name]:{}),t.preventDefault()}}catch(t){console.warn(`PeptidesHeaderLogoError: couldn't render WebLogo for column \`${h.name}\`. See original error below.`),console.warn(t)}finally{l.restore()}})(t)));const v=n=>{var r;const s=t.hitTest(n.offsetX,n.offsetY);if((null==s?void 0:s.isColHeader)&&(null===(r=s.tableColumn)||void 0===r?void 0:r.semType)===o.uF.MONOMER){const t=function(t,e,n){const i=n[t.tableColumn.name];if(!i)return null;for(const[n,r]of Object.entries(i)){const i=e.offsetX>=r.x&&e.offsetX<=r.x+r.width,o=e.offsetY>=r.y&&e.offsetY<=r.y+r.height;if(i&&o)return{monomerOrCluster:n,positionOrClusterType:t.tableColumn.name}}return null}(s,n,c.webLogoBounds());if(null===t)return void(c.isSelectionTable||null==c.unhighlightCallback||c.unhighlightCallback());f.monomerPosition=t,function(t,e,n,r,o,s){if("click"!==t.type||o.isSelectionTable||null==o.selectionCallback){const a=`${e.positionOrClusterType} = ${e.monomerOrCluster}`;o.cachedWebLogoTooltip().bar===a?i.tooltip.show(o.cachedWebLogoTooltip().tooltip,t.clientX,t.clientY):(o.cachedWebLogoTooltip().bar=a,s.x=t.clientX,s.y=t.clientY,s.monomerPosition=e,o.cachedWebLogoTooltip().tooltip=(0,h.Y)(n,r,[],s))}else o.selectionCallback(e,{shiftPressed:t.shiftKey,ctrlPressed:t.ctrlKey})}(n,t,m,u,c,f),c.isSelectionTable||null==c.highlightCallback||c.highlightCallback(t,m,e)}else null!=c.unhighlightCallback&&c.unhighlightCallback()};l.fromEvent(t.overlay,"mousemove").subscribe((t=>v(t))),l.fromEvent(t.overlay,"click").subscribe((t=>v(t))),l.fromEvent(t.overlay,"mouseleave").subscribe((()=>{null!=c.unhighlightCallback&&c.unhighlightCallback()}))}class S extends r.GridCellRenderer{constructor(){super(...arguments),this.colorCacheKey="lst-pie-chart-color-cache",this.HoverTempKey="lst-pie-chart-hovered-sector",this.hoverSeparator=",,,,,"}get name(){return"LST Pie Chart"}get cellType(){return"lst-pie-chart"}get defaultWidth(){return 80}get defaultHeight(){return 80}categoryNumberCache(t){return t.temp[this.colorCacheKey]||(t.temp[this.colorCacheKey]={}),t.temp[this.colorCacheKey]}getPrevHoveredSector(t){return t.temp[this.HoverTempKey]}onMouseMove(t,e){const n=this.getPrevHoveredSector(t.cell.column),r=()=>{t.cell.column.temp[this.HoverTempKey]=null,i.tooltip.hide(),null!==n&&t.grid.invalidate()},o=t.cell.value;if(!o)return void r();const s=e.offsetX-t.bounds.midX,a=e.offsetY-t.bounds.midY,l=Math.sqrt(s*s+a*a),u=Math.atan2(a,s),c=u<0?u+2*Math.PI:u;if(l>Math.min(t.bounds.width,t.bounds.height)/2-2)return void r();let f;try{f=JSON.parse(o)}catch(e){return void r()}const h=new Float64Array(Object.keys(f).length+1),d=Object.values(f).reduce(((t,e)=>t+e),0);h[Object.keys(f).length]=2*Math.PI;let m=0,g=0;for(const t of Object.values(f))h[g++]=m,m+=2*Math.PI*t/d;let p=-1;for(let t=0;t<h.length-1;t++)if(c>=h[t]&&c<h[t+1]){p=t;break}if(-1===p)return void r();const v=Object.keys(f)[p],y=f[v],C=(y/d*100).toFixed(2);i.tooltip.show(i.h1(`${v}: ${y} (${C}%)`),e.x+16,e.y+16);const b=t.cell.rowIndex.toString()+this.hoverSeparator+v;t.cell.column.temp[this.HoverTempKey]=b,n!==b&&t.grid.invalidate()}render(t,e,n,i,o,s,a){const l=s.cell.dataFrame,u=new r.Rect(e,n,i,o).fitSquare().inflate(-2,-2);if(i<5||o<5||!l)return;const c=s.cell.value;if(t.clearRect(e,n,i,o),!c)return;let f;try{f=JSON.parse(c)}catch(t){return}const h=Object.values(f).reduce(((t,e)=>t+e),0);let d=0;const m=Object.fromEntries(Object.keys(f).map((t=>[t,255]))),g=s.cell.column.temp[this.HoverTempKey];if(g&&2===g.split(this.hoverSeparator).length){const[t,e]=g.split(this.hoverSeparator);if(t===s.cell.rowIndex.toString()){for(const[t,e]of Object.entries(f))m[t]=100;m[e]=255}}const p=Math.min(i,o)/2.2;for(const[e,n]of Object.entries(f)){const i=2*Math.PI*n/h;t.beginPath(),t.moveTo(u.midX,u.midY),t.arc(u.midX,u.midY,p,d,d+i),d+=i;const o=this.categoryNumberCache(s.cell.column);o[e]||(o[e]=Object.keys(o).length,s.cell.column.temp[this.colorCacheKey]=o),t.fillStyle=r.Color.toHtml(r.Color.setAlpha(r.Color.getCategoricalColor(o[e]),m[e])),t.fill(),t.strokeStyle=r.Color.toRgb(r.Color.lightGray),t.stroke();const a=e;t.fillStyle=r.Color.toRgb(r.Color.white),t.font="9px Arial";const l=t.measureText(a).width,c=d-i/2;for(let e=.8;e>=.4;e-=.05){const n=p*e,r=u.midX+Math.cos(c)*n,o=u.midY+Math.sin(c)*n;if([[r-l/2-2,o],[r+l/2+2,o]].every((t=>{const e=Math.sqrt(Math.pow(t[0]-u.midX,2)+Math.pow(t[1]-u.midY,2)),n=Math.atan2(t[1]-u.midY,t[0]-u.midX),r=n<0?n+2*Math.PI:n;return e<p-2&&r>d-i&&r<d}))){t.fillText(a,r,o);break}}}}}},4139:(t,e,n)=>{"use strict";n.d(e,{$2:()=>i,To:()=>l,V5:()=>h,YX:()=>f,gp:()=>o,i6:()=>r,rg:()=>u,uF:()=>s,wf:()=>c,zW:()=>d});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,f;!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-"}(f||(f={}));const h=Object.values(a.AGG).filter((t=>![a.AGG.FIRST,a.AGG.KEY,a.AGG.PIVOT,a.AGG.SELECTED_ROWS_COUNT].includes(t))),d={[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:()=>x,AN:()=>i,AY:()=>h,B2:()=>M,BE:()=>C,CD:()=>w,F2:()=>p,FZ:()=>v,KT:()=>T,Lv:()=>O,Y1:()=>d,ZR:()=>E,dl:()=>S,eY:()=>g,qI:()=>_,qx:()=>m,sg:()=>I,vW:()=>A,vY:()=>b,zm:()=>N,zz:()=>y});var i,r=n(7389),o=n(6082),s=n(4328),a=n(4139),l=n(8774),u=n(144),c=n.n(u),f=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 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p(t,e,n={}){var s;const l=t.dataFrame.getCol(a.$2.SPLIT_COL),u=[],c=l.categories,f=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(f.indexOf(t))),a=r.label(null!==(s=n[c[t]])&&void 0!==s?s:c[t],{style:{color:e}});u.push(a)}const h=r.divV([r.divV(u),t.root,r.tableFromMap(e)]);return t.root.style.maxHeight="75px",h}function v(t,e,n){var r,s;const l=null!==(r=null==n?void 0:n.clone().xor(e).anyTrue)&&void 0!==r&&r,u=t.length,c=t.getRawData(),f=new Float32Array(u+e.trueCount+(l&&null!==(s=null==n?void 0:n.trueCount)&&void 0!==s?s:0)),h=new Array(f.length);for(let t=0,r=0,o=0;t<u;++t){const s=e.get(t);f[t]=c[t],h[t]=s?i.SELECTION:i.ALL,s&&(f[u+r]=c[t],h[u+r]=i.ALL,++r),l&&(null==n?void 0:n.get(t))&&(f[u+e.trueCount+o]=c[t],h[u+e.trueCount+o]=i.PEPTIDES_SELECTION,++o)}const d=o.Column.fromStrings(a.$2.SPLIT_COL,h),m=[i.ALL,i.SELECTION];return l&&m.push(i.PEPTIDES_SELECTION),d.setCategoryOrder(m),d.meta.colors.setCategorical(),o.DataFrame.fromColumns([o.Column.fromFloat32Array(a.$2.ACTIVITY,f),d])}function y(t){const e=r.iconFA("expand-alt",(()=>{const e=t.dataFrame.plot.grid();b(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 C(t,e,n,i){const o=r.iconFA("expand-alt",(()=>{const e=i(),n=r.dialog(t);n.add(e),n.show({resizable:!0,modal:!0,width:window.innerWidth-60,x:30,y:30,height:window.innerHeight-60})}),"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 b(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 A(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 S(t,e,n){if(!e)return;const i=new l.A(e.rowCount);if(t.positionOrClusterType===a.$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 e=n[t.positionOrClusterType];if(void 0!==e){const n=e[t.monomerOrCluster];void 0!==n&&i.or(n.mask)}}e.rows.highlight((t=>i.getBit(t)))}function E(t){const e={};for(const n of t)e[n.name]=[];return e}function T(t,e){let n=null;const i=Object.entries(t);for(const[t,r]of i){const i=e[t];for(const t of r){const e=i[t];e&&(null!=n||(n=new l.A(e.mask.length,!1)),n.or(e.mask))}}return null!=n?o.BitSet.fromBytes(n.buffer.buffer,n.length):null}function x(t,e){return t.sequenceColumnName===e.sequenceColumnName&&t.activityColumnName===e.activityColumnName&&t.activityScaling===e.activityScaling}function _(t,e){var n;const i={};for(const[r,o]of t)for(const[t,s]of o){null!==(n=i[t])&&void 0!==n||(i[t]={});const o=new l.A(e,!1);for(const[t,e]of s){o.setTrue(t);for(const t of 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t=u+c-2,e=(a*(u-1)+l*(c-1))/t,n=Math.sqrt(u*c/(u+c))*(o-s)/e;f=1-r.studentt.cdf(n,t),h=r.studentt.cdf(n,t),d=2*(h<f?h:f)}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));h=r.studentt.cdf(n,i),f=1-h,d=2*(h<f?h:f)}return{"p-value":d,"Mean difference":o-s,"p-value more":f,"p-value less":h}}(s,a),d=h["Mean difference"];return{count:s.length,pValue:h[d>=0?"p-value more":"p-value less"],mean:f,meanDifference:d,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 f(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,{D:()=>u,Y:()=>c});var i=n(7389),r=n(6082),o=n(4139),s=n(7654),a=n(8608),l=n(5070);function u(t,e,n,i){var r,s,a;return null!==(r=i.fromViewer)&&void 0!==r||(i.fromViewer=!1),null!==(s=i.isMutationCliffs)&&void 0!==s||(i.isMutationCliffs=!1),null!==(a=i.isMostPotentResidues)&&void 0!==a||(i.isMostPotentResidues=!1),i.monomerPosition.positionOrClusterType!==o.$2.MONOMER&&c(t,e,n,i),!0}function c(t,e,n,o){var u,c,f,h,d,m,g,p,v;if(null!==(u=o.fromViewer)&&void 0!==u||(o.fromViewer=!1),null!==(c=o.isMutationCliffs)&&void 0!==c||(o.isMutationCliffs=!1),null!==(f=o.isMostPotentResidues)&&void 0!==f||(o.isMostPotentResidues=!1),null!==(h=o.additionalStats)&&void 0!==h||(o.additionalStats={}),o.cliffStats&&o.isMutationCliffs){const u=null===(p=null===(g=o.cliffStats)||void 0===g?void 0:g.get(o.monomerPosition.monomerOrCluster))||void 0===p?void 0:p.get(o.monomerPosition.positionOrClusterType);if(!u)return null;const c=r.BitSet.fromBytes(u.mask.buffer.buffer,e.length),f=(0,s.M1)((0,a.FZ)(e,c),!0),h=(0,s.QD)(u,{countName:"Unique count"});o.fromViewer&&(h["Mean difference"]=`${h["Mean difference"]} (Color)`,h["Unique count"]&&(h["Unique count"]=`${h["Unique count"]} (Size)`));const d=null!==(v=o.aggrColValues)&&void 0!==v?v:(0,l.I_)(t,n,{mask:c}),m=Object.assign(Object.assign(Object.assign({},o.additionalStats),h),d),y=(0,a.F2)(f,m);return i.tooltip.show(y,o.x,o.y),y}{const u=o.mpStats[o.monomerPosition.positionOrClusterType][o.monomerPosition.monomerOrCluster];if(!(null==u?void 0:u.count))return null;const c=r.BitSet.fromBytes(u.mask.buffer.buffer,e.length),f=(0,s.M1)((0,a.FZ)(e,c),!0),h=(0,s.QD)(u);o.fromViewer&&(h["Mean difference"]=`${h["Mean difference"]}${o.isMostPotentResidues?" (size)":""}`,h["p-value"]&&(h["p-value"]=`${h["p-value"]}${o.isMostPotentResidues?" (color)":""}`));const g=null!==(d=o.aggrColValues)&&void 0!==d?d:(0,l.I_)(t,n,{mask:c}),p=Object.assign(Object.assign(Object.assign({},o.additionalStats),h),g);for(const[t,e]of Object.entries(null!==(m=o.postfixes)&&void 0!==m?m:{}))p[t]&&(p[t]=`${p[t]}${e}`);const v=(0,a.F2)(f,p);return i.tooltip.show(v,o.x,o.y),v}}},115:(t,e,n)=>{"use strict";n.d(e,{GI:()=>a,Ku:()=>o,av:()=>s});var i=n(1199),r=n(4329);const o="WebGPU is not supported on this device";class s{constructor(){this.maxIterations=16,this.inflation=1.4,this.threshold=70,this.distanceF=i.Z.NEEDLEMANN_WUNSCH,this.gapOpen=1.5,this.gapExtend=.2,this.fingerprintType="Morgan",this.useWebGPU=!1,this.minClusterSize=5,this.webGPUDescription=o,this.webGPUDescriptionPromise=(0,r._)().then((t=>{t&&(this.webGPUDescription=t)}))}}class a{constructor(t){this.distanceF=i.Z.NEEDLEMANN_WUNSCH,this.gapOpen=1.5,this.gapExtend=.2,this.clusterEmbeddings=!0,this.epsilon=.01,this.minPts=4,this.fingerprintType="Morgan",this.clusterEmbeddings=!!t}}},5480:(t,e,n)=>{"use strict";n.d(e,{W:()=>S,s:()=>T});var i=n(7389),r=n(4328),o=n(6082),s=n(7233),a=n.n(s),l=n(768),u=n(4139),c=n(3163),f=n(4326),h=n(5070),d=n(144),m=n.n(d),g=n(7654),p=n(8608),v=n(8774),y=n(6920),C=n(3657),b=n(3077),w=n(726);const A=(t,e)=>`${t}(${e})`;var S,E;!function(t){t.ORIGINAL="original",t.CUSTOM="custom"}(S||(S={})),function(t){t.GENERAL="General",t.STYLE="WebLogo",t.AGGREGATION="Aggregation"}(E||(E={}));class T 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",f.fH.Entropy,{choices:[f.fH.full,f.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,b.R)(this.dataFrame.getCol(this.sequenceColumnName),w.Z.getSeqHelper()).columns.toList()),this._positionColumns}get isClusterSelectionEmpty(){return 0===this.clusterSelection[S.ORIGINAL].length+this.clusterSelection[S.CUSTOM].length}get customClusters(){const t={};return t[u.gp.CUSTOM_CLUSTER]="1",m()(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,p.Y1)(this.dataFrame.getCol(this.activityColumnName),this.activityScaling)),t?o.DataFrame.fromColumns([this._scaledActivityColumn]).clone(this.dataFrame.rowCount===this._scaledActivityColumn.length?this.dataFrame.filter:null).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,p.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${u.To}`))||void 0===e||e.set(this,m()(this.dataFrame.columns.numerical).next().value.name),null===(n=this.getProperty(`clusters${u.To}`))||void 0===n||n.set(this,m()(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${u.To}`:case"activityScaling":this._scaledActivityColumn=null,this._viewerGrid=null,this._clusterStats=null,this._logoSummaryTable=null,e=!0;break;case"columns":case"aggregation":this._viewerGrid=null,this._logoSummaryTable=null,e=!0;break;case"webLogoMode":this.viewerGrid.invalidate()}e&&this.render()}initClusterSelection(t={}){var e;null!==(e=t.notify)&&void 0!==e||(t.notify=!0);const n={};return n[S.ORIGINAL]=[],n[S.CUSTOM]=[],t.notify?this.clusterSelection=n:this._clusterSelection=n,this.clusterSelection}getTotalViewerAggColumns(){var t,e;const n=this.getAggregationColumns();return(0,p.zm)(this.model.df,this.columns,n,null===(e=null===(t=this.model)||void 0===t?void 0:t.settings)||void 0===e?void 0:e.columns)}getStringAggregatedColumns(){return this.columns.filter((t=>this.model.df.columns.contains(t)&&this.model.df.col(t).matches("categorical"))).map((t=>`dist(${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(),f=s.getCol(i),d=f.getRawData(),g=f.categories,p={};p[u.gp.CUSTOM_CLUSTER]="1";const y=m()(a.byTags(p)).filter((t=>t.max>0)).toArray(),C=o.DataFrame.create(y.length),b=C.columns,w=b.addNewString(u.i6.CLUSTER),E=b.addNewInt(u.i6.MEMBERS).getRawData(),T=b.addNewString(u.i6.WEB_LOGO),x=b.addNewString(u.i6.DISTRIBUTION),_=b.addNewFloat(u.i6.MEAN_DIFFERENCE).getRawData(),N=b.addNewFloat(u.i6.P_VALUE).getRawData(),M=b.addNewFloat(u.i6.RATIO).getRawData();let I=s.groupBy([i]);const O=this.getTotalViewerAggColumns(),L=this.getStringAggregatedColumns(),R=L.map((t=>b.addNewString(t))),P=O.map((([t,e])=>A(e,t))),k=new Array(P.length+L.length),V=O.map((([t,e])=>[s.getCol(t),e]));for(let t=0;t<O.length;++t){const[e,n]=O[t];I=I.add(n,e,P[t]);const i=b.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];w.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,h.GT)(c,i):this.clusterStats[S.CUSTOM][n.name];E[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]=V[t];k[t][e]=(0,h.lh)(n,i,a)}for(let t=P.length;t<k.length;++t){const n=L[t-P.length];R[t-P.length].set(e,(0,h.J1)(s,n,a))}}T.setTag(o.TAGS.CELL_RENDERER,"html"),x.setTag(o.TAGS.CELL_RENDERER,"html");const G=I.aggregate(),F=G.rowCount,U=G.columns;let H=G.getCol(i);H.name=u.i6.CLUSTER,H.type!==o.COLUMN_TYPE.STRING&&(G.columns.replace(H,H.convertTo(o.COLUMN_TYPE.STRING)),H=G.getCol(H.name));const q=H.categories,B=U.addNewInt(u.i6.MEMBERS).getRawData(),Y=U.addNewString(u.i6.WEB_LOGO),W=U.addNewString(u.i6.DISTRIBUTION),j=U.addNewFloat(u.i6.MEAN_DIFFERENCE).getRawData(),$=U.addNewFloat(u.i6.P_VALUE).getRawData(),z=U.addNewFloat(u.i6.RATIO).getRawData(),K=L.map((t=>U.addNewString(t))),Q=new Array(F),Z=Array.from({length:F},(()=>new v.A(l,!1)));for(let t=0;t<l;++t){const n=g[d[t]];null===(e=Z[q.indexOf(n)])||void 0===e||e.setTrue(t)}for(let t=0;t<F;++t){const e=Z[t];if(e.allFalse)continue;const i=o.BitSet.fromBytes(e.buffer.buffer,l),a=r?(0,h.GT)(c,e):this.clusterStats[S.ORIGINAL][q[t]];for(let e=0;e<L.length;++e){const n=L[e];K[e].set(t,(0,h.J1)(s,n,i))}B[t]=a.count,Q[t]=i,j[t]=a.meanDifference,$[t]=null!==(n=a.pValue)&&void 0!==n?n:o.FLOAT_NULL,z[t]=a.ratio}Y.setTag(o.TAGS.CELL_RENDERER,"html"),W.setTag(o.TAGS.CELL_RENDERER,"html");const X=G.append(C);return this.bitsets=Q.concat(D),L.forEach((t=>X.col(t).semType="lst-pie-chart")),X}createLogoSummaryTableGrid(){const t=this.dataFrame.filter.anyFalse,e=t?this.dataFrame.clone(this.dataFrame.filter):this.dataFrame,n=this.getTotalViewerAggColumns().map((([t,e])=>A(e,t))),i=this.logoSummaryTable.plot.grid();i.sort([u.i6.MEMBERS],[!1]),this.updateFilter(),i.col(u.i6.CLUSTER).visible=!0,i.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]),i.columns.rowHeader.visible=!1,i.props.rowHeight=55;const r=new o.LruCache,s=new Map;let h=null;const d=new o.LruCache,m=this.positionColumns.length,g=i.columns.byName(u.i6.WEB_LOGO);g.cellType="html",g.width=350;const v=this.getScaledActivityColumn(t),y=e.getCol(this.sequenceColumnName);i.onCellRender.subscribe((t=>{var e,n,l;const g=t.cell,C=g.tableRowIndex;if(!g.isTableCell||null==C||-1===C)return;const b=t.g,w=t.bounds;b.save(),b.beginPath(),b.rect(w.x,w.y,w.width,w.height),b.clip();try{const A=Math.max(g.bounds.height-2,0),S=this.bitsets[C];if((null===(e=g.tableColumn)||void 0===e?void 0:e.name)===u.i6.CLUSTER)c.k8(b,g.cell.value,this.clusterSelection,w),t.preventDefault();else if((null===(n=g.tableColumn)||void 0===n?void 0:n.name)===u.i6.WEB_LOGO){if(!0===s.get(C))return void t.preventDefault();const e=Math.floor((g.bounds.width-2-4*(m-1))/m),n=r.get(C);if(void 0!==n){const i=n.getProperties();for(const t of i)"positionHeight"===t.name&&t.get(n)!==this.webLogoMode?t.set(n,this.webLogoMode):"positionWidth"===t.name&&t.get(n)!==e?t.set(n,e):"minHeight"===t.name&&t.get(n)!==A&&t.set(n,A);a()(n.root).css("height",`${A}px`).children().first().css("overflow-y","hidden !important"),n.root.style.height=`${A}px`,g.element=n.root,t.preventDefault()}else{const n=this.createWebLogoDf(y,S);s.set(C,!0),n.plot.fromType("WebLogo",{positionHeight:this.webLogoMode,horizontalAlignment:f.P4.LEFT,maxHeight:1e3,minHeight:A,positionWidth:e,showPositionLabels:!1}).then((t=>{r.set(C,t),s.delete(C),h&&clearTimeout(h),h=setTimeout((()=>i.invalidate()),200)})),t.preventDefault()}}else if((null===(l=g.tableColumn)||void 0===l?void 0:l.name)===u.i6.DISTRIBUTION){let e=d.get(C);void 0===e&&(e=(0,p.FZ)(v,S).plot.histogram({filteringEnabled:!1,valueColumnName:v.name,splitColumnName:u.$2.SPLIT_COL,legendVisibility:"Never",showXAxis:!1,showColumnSelector:!1,showRangeSlider:!1,showBinSelector:!1,backColor:o.Color.toHtml(o.Color.white),xAxisHeight:1,showSplitSelector:!1}),e.root.style.width="auto",d.set(C,e)),e.root.style.height=`${A}px`,g.element=e.root,t.preventDefault()}}finally{b.restore()}})),i.root.addEventListener("mouseleave",(t=>this.model.unhighlight())),o.debounce(i.onCurrentCellChanged,500).subscribe((t=>{var e;if(!t.isTableCell||-1===t.gridRow)return this.initClusterSelection({notify:!1}),this.model.fireBitsetChanged(l.q.LOGO_SUMMARY_TABLE),void i.invalidate();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(i.cell(u.i6.CLUSTER,this.currentRowIndex)),{shiftPressed:!0,ctrlPressed:!0},!1),this.modifyClusterSelection(this.getCluster(t),{shiftPressed:!0,ctrlPressed:!1}),i.invalidate()}finally{this.keyPress=!1,this.currentRowIndex=t.gridRow}})),i.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(i.cell(u.i6.CLUSTER,t)),{shiftPressed:!0,ctrlPressed:!1},!1);this.model.fireBitsetChanged(l.q.LOGO_SUMMARY_TABLE),i.invalidate()}})),i.root.addEventListener("click",(t=>{var e;const n=i.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 r=this.getCluster(n);this.modifyClusterSelection(r,{shiftPressed:t.shiftKey,ctrlPressed:t.ctrlKey}),i.invalidate()})),i.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 C=i.props;return C.allowEdit=!1,C.allowRowSelection=!1,C.allowBlockSelection=!1,C.allowColSelection=!1,C.showCurrentRowIndicator=!1,C.showReadOnlyNotifications=!1,i}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)?S.ORIGINAL:S.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,h.GT)(r.getRawData(),o);this.bitsets.push(t.clone());const a=this.dataFrame.columns.getUnusedName("New Cluster"),l={},c={},f=this.getTotalViewerAggColumns(),d=this.getStringAggregatedColumns();for(const[e,n]of f){const i=A(n,e),r=this.dataFrame.getCol(e);l[i]=(0,h.lh)(r,n,t)}for(const e of d)c[e]=(0,h.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[S.CUSTOM][a]=s,this.addNewCluster(a)}removeCluster(){const t=this.clusterSelection[S.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[S.CUSTOM][n];const r=i.indexOf(n);e.removeAt(r),this.bitsets.splice(r,1)}n.compact(),this.clusterSelection[S.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,p.vW)(this.clusterSelection,t,e):this._clusterSelection=(0,p.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===S.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 f=r.anyFalse?(0,h.GT)(c,l):this.clusterStats[t.positionOrClusterType][t.monomerOrCluster];if(!f.count)return null;const d=o.BitSet.fromBytes(l.buffer.buffer,a),m=(0,p.FZ)(u,d),y=(0,g.M1)(m,!0),C=(0,g.QD)(f),b=(0,h.I_)(this.dataFrame,this.getTotalViewerAggColumns(),{filterDf:!0,mask:d}),w=Object.assign(Object.assign({},C),b),A=(0,p.F2)(y,w);return i.tooltip.show(A,e,n),A}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,xN:()=>_});var i,r,o,s,a=n(4328),l=n(7389),u=n(6082),c=n(7233),f=n.n(c),h=n(4139),d=n(3163),m=n(768),g=n(144),p=n.n(g),v=n(5070),y=n(912),C=n(3657),b=n(8608),w=n(3077),A=n(439),S=n(2003),E=n(8223),T=n(726),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,h.rg.NONE,{category:s.GENERAL,choices:Object.values(h.rg),nullable:!1}),this.activityTarget=this.string(r.ACTIVITY_TARGET,h.wf.HIGH,{category:s.GENERAL,choices:Object.values(h.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:h.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:h.V5,userEditable:!0,nullable:!1}),this.mutationCliffsDebouncer=(0,b.sg)(((t,e,n)=>x(this,void 0,void 0,(function*(){return yield(0,C.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[h.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(A.gp.alphabet))&&void 0!==t?t:S.YI.UN}get model(){return m.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(m.q.MOST_POTENT_RESIDUES):this instanceof M&&(this._positionColumns=i(m.q.SEQUENCE_VARIABILITY_MAP)),null!==(e=this._positionColumns)&&void 0!==e||(this._positionColumns=null!==(n=i(m.q.LOGO_SUMMARY_TABLE))&&void 0!==n?n:(0,w.R)(this.dataFrame.getCol(this.sequenceColumnName),T.Z.getSeqHelper()).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(m.q.MOST_POTENT_RESIDUES):this instanceof M&&(this._monomerPositionStats=n(m.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,C.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(m.q.MOST_POTENT_RESIDUES):this instanceof M&&(this._mutationCliffs=t(m.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,C.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?h.YX.MP:h.YX.MPR,n=this.dataFrame.getTag(`${e}${h.gp.MUTATION_CLIFFS_SELECTION}`);return null!==(t=this._mutationCliffsSelection)&&void 0!==t||(this._mutationCliffsSelection=null===n?(0,b.ZR)(this.positionColumns):JSON.parse(n)),this._mutationCliffsSelection}set mutationCliffsSelection(t){this._mutationCliffsSelection=t;const e=this instanceof N?h.YX.MP:h.YX.MPR;this.dataFrame.setTag(`${e}${h.gp.MUTATION_CLIFFS_SELECTION}`,JSON.stringify(t)),this.model.fireBitsetChanged(this instanceof N?m.q.SEQUENCE_VARIABILITY_MAP:m.q.MOST_POTENT_RESIDUES);const n=this.model.findViewer(m.q.SEQUENCE_VARIABILITY_MAP);null==n||n.viewerGrid.invalidate();const i=this.model.findViewer(m.q.MOST_POTENT_RESIDUES);null==i||i.viewerGrid.invalidate(),this.model.analysisView.grid.invalidate()}getScaledActivityColumn(t=!1){var e,n,i;return(null===(e=this.model.settings)||void 0===e?void 0:e.activityColumnName)===this.activityColumnName&&(null===(n=this.model.settings)||void 0===n?void 0:n.activityScaling)===this.activityScaling&&(this._scaledActivityColumn=this.model.getScaledActivityColumn(t)),null!==(i=this._scaledActivityColumn)&&void 0!==i||(this._scaledActivityColumn=(0,b.Y1)(this.dataFrame.getCol(this.activityColumnName),this.activityScaling)),t?u.DataFrame.fromColumns([this._scaledActivityColumn]).clone(this.dataFrame.filter).getCol(this._scaledActivityColumn.name):this._scaledActivityColumn}modifyMutationCliffsSelection(t,e={shiftPressed:!1,ctrlPressed:!1},n=!0){n?this.mutationCliffsSelection=(0,b.vW)(this.mutationCliffsSelection,t,e):this._mutationCliffsSelection=(0,b.vW)(this.mutationCliffsSelection,t,e)}modifyInvariantMapSelection(t,e={shiftPressed:!1,ctrlPressed:!1},n=!0){n?this.invariantMapSelection=(0,b.vW)(this.invariantMapSelection,t,e):this._invariantMapSelection=(0,b.vW)(this.invariantMapSelection,t,e)}get invariantMapSelection(){var t;const e=this.dataFrame.getTag(`${h.YX.MP}${h.gp.INVARIANT_MAP_SELECTION}`);return null!==(t=this._invariantMapSelection)&&void 0!==t||(this._invariantMapSelection=null===e?(0,b.ZR)(this.positionColumns):JSON.parse(e)),this._invariantMapSelection}set invariantMapSelection(t){this._invariantMapSelection=t,this.dataFrame.setTag(`${h.YX.MP}${h.gp.INVARIANT_MAP_SELECTION}`,JSON.stringify(t)),this.model.fireBitsetChanged(m.q.SEQUENCE_VARIABILITY_MAP),this.model.analysisView.grid.invalidate()}resetTargetCategoryValue(){var t;const e=this.targetColumnName,n=e?this.dataFrame.col(e):null;this.targetCategoryInput.items=null!==(t=null==n?void 0:n.categories)&&void 0!==t?t:[],this.targetCategoryInput.value=null,this.targetCategoryInput.root.style.display=e?"flex":"none"}onPropertyChanged(t){switch(super.onPropertyChanged(t),this.doRender=!0,t.name){case`${r.SEQUENCE}${h.To}`:this._positionColumns=null,this._monomerPositionStats=null,this._mutationCliffs=null,this._mutationCliffStats=null,this._mutationCliffsSelection=null,this._viewerGrid=null;break;case`${r.ACTIVITY}${h.To}`:case r.ACTIVITY_SCALING:this._monomerPositionStats=null,this._mutationCliffs=null,this._mutationCliffStats=null,this._mutationCliffsSelection=null,this._viewerGrid=null,this._scaledActivityColumn=null;break;case`${r.VALUE_INVARIANT_MAP}${h.To}`:case r.AGGREGATION_INVARIANT_MAP_VALUE:this._monomerPositionStats=null,this._viewerGrid=null,this._invariantMapSelection=null;break;case r.MIN_ACTIVITY_DELTA:case r.MAX_MUTATIONS:this._mutationCliffs=null,this._mutationCliffStats=null,this._mutationCliffsSelection=null,this.doRender=!1;break;case r.COLUMNS:case r.AGGREGATION:this instanceof M&&(this._viewerGrid=null);break;case r.ACTIVITY_TARGET:(this instanceof M||this instanceof N)&&(this._viewerGrid=null)}null===this._mutationCliffs&&this.sequenceColumnName&&this.activityColumnName&&this.calculateMutationCliffs().then((t=>{this.mutationCliffs=t.cliffs,this.cliffStats=t.cliffStats})),t.name===`${r.TARGET}${h.To}`&&this.targetColumnInput&&(this.targetColumnInput.value=this.targetColumnName?this.dataFrame.col(this.targetColumnName):null,this.resetTargetCategoryValue())}getAggregationColumns(){return Object.fromEntries(this.columns.map((t=>[t,this.aggregation])).filter((([t,e])=>this.model.df.columns.contains(t)&&this.model.df.col(t).matches("numerical"))))}getTotalViewerAggColumns(){var t,e;const n=this.getAggregationColumns();return(0,b.zm)(this.model.df,this.columns,n,null===(e=null===(t=this.model)||void 0===t?void 0:t.settings)||void 0===e?void 0:e.columns)}createViewerGrid(){throw new Error("Not implemented")}detach(){this.subs.forEach((t=>t.unsubscribe()))}onTableAttached(){var t,e,n;if(super.onTableAttached(),(0,b.B2)(this.dataFrame))null===(t=this.getProperty(`${r.SEQUENCE}${h.To}`))||void 0===t||t.set(this,this.dataFrame.columns.bySemType(u.SEMTYPE.MACROMOLECULE).name),null===(e=this.getProperty(`${r.ACTIVITY}${h.To}`))||void 0===e||e.set(this,p()(this.dataFrame.columns.numerical).next().value.name),null===(n=this.getProperty(`${r.VALUE_INVARIANT_MAP}${h.To}`))||void 0===n||n.set(this,p()(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,E.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,C.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:h.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 m.q.SEQUENCE_VARIABILITY_MAP}get mode(){var t;return null!==(t=this.dataFrame.getTag(h.gp.MONOMER_POSITION_MODE))&&void 0!==t?t:i.MUTATION_CLIFFS}set mode(t){this.dataFrame.setTag(h.gp.MONOMER_POSITION_MODE,t),this.viewerGrid.invalidate()}onTableAttached(){var t;if(super.onTableAttached(),(0,b.B2)(this.dataFrame))null===(t=this.getProperty(`${o.COLOR}${h.To}`))||void 0===t||t.set(this,this.activityColumnName),this.targetColumnInput=l.input.column("Target",{value:void 0,nullable:!0,table:this.dataFrame,filter:t=>t.isCategorical,onValueChanged:t=>{var e,n;const i=this.getProperty(`${r.TARGET}${h.To}`);i&&i.get(this)!=(null!==(e=null==t?void 0:t.name)&&void 0!==e?e:null)&&(null==i||i.set(this,null!==(n=null==t?void 0:t.name)&&void 0!==n?n:null))}});else{const t="PeptidesError: dataframe is missing Macromolecule or numeric columns";a.log.error(t),a.shell.warning(t)}this.render()}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[h.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(h.$2.MONOMER,n),r=u.DataFrame.fromColumns([i]),o=(0,E.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[h.gp.INVARIANT_MAP_COLOR_CACHE]={};const o=i.temp[h.gp.INVARIANT_MAP_COLOR_CACHE],a=i.name,l=i.getRawData(),c=i.categories;if(!this.monomerPositionStats[a])continue;const f=this.monomerPositionStats[a];for(const a of Object.keys(f)){if("general"===a)continue;const f=[];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&&f.push(t)}const h=u.Column.float("color",f.length).init((e=>t[f[e]])).aggregate(this.colorAggregation);o[a]=h,e=Math.min(e,h),n=Math.max(n,h)}i.temp[h.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 f=this.logScaleColor&&l>1e-30&&c>1e-30&&e>1e-30&&n>1e-30;f&&(l=Math.log(l),c=Math.log(c));for(const t of this.positionColumns){const i=t.temp[h.gp.INVARIANT_MAP_COLOR_CACHE];if(i){for(const t of Object.keys(i))this.activityTarget===h.wf.LOW&&(i[t]=c-i[t]+l),i[t]=u.Color.scaleColor(f?Math.log(i[t]):i[t],l,c,void 0,[this.lowerBoundColor,this.middleColor,this.upperBoundColor]);t.temp[h.gp.INVARIANT_MAP_COLOR_CACHE]=i,t.temp[h.gp.INVARIANT_MAP_COLOR_MIN_CACHE]=e,t.temp[h.gp.INVARIANT_MAP_COLOR_MAX_CACHE]=n}}}}createViewerGrid(){const t=this.createMonomerPositionDf(),e=t.plot.grid();e.sort([h.$2.MONOMER]);const n=this.positionColumns.map((t=>t.name));e.columns.setOrder([h.$2.MONOMER,...this._monomerMetaColumns,...n]);const r=t.getCol(h.$2.MONOMER);d.rI(r,this.alphabet,!0),this.cacheInvariantMapColors(),e.onCellRender.subscribe((t=>I(t,this,this.mode===i.INVARIANT_MAP,this.dataFrame.getCol(this.colorColumnName),this.colorAggregation))),e.onCellTooltip(((t,e,n)=>{var r,o,s,a,l;if(!t.isTableCell||!(null===(r=null==t?void 0:t.cell.column)||void 0===r?void 0:r.name)||this._monomerMetaColumns.has(t.cell.column.name))return this.model.unhighlight(),!0;const c=this.getMonomerPosition(t);(0,b.dl)(c,this.dataFrame,this.monomerPositionStats),this.model.isHighlighting=!0;const f=this.getTotalViewerAggColumns(),h={},d={};if(this.mode===i.INVARIANT_MAP)this.colorColumnName&&this.colorAggregation&&this.colorColumnName!==this.valueColumnName?(f.unshift([this.colorColumnName,this.colorAggregation]),h[`${this.colorAggregation}(${this.colorColumnName})`]=" (color)"):this.colorColumnName&&this.colorAggregation&&this.colorColumnName===this.valueColumnName&&(h["Mean activity"]=" (color)"),this.valueColumnName&&this.valueAggregation&&this.valueAggregation!==u.AGG.VALUE_COUNT&&this.valueAggregation!==u.AGG.TOTAL_COUNT&&f.unshift([this.valueColumnName,this.valueAggregation]);else{const t=null===(s=null===(o=this.mutationCliffs)||void 0===o?void 0:o.get(c.monomerOrCluster))||void 0===s?void 0:s.get(c.positionOrClusterType);if(t){let e=0;for(const n of t.values())e+=n.length;d["Pairs count"]=e.toString()}}return(0,y.D)(this.model.df,this.getScaledActivityColumn(),f,{fromViewer:!0,isMutationCliffs:this.mode===i.MUTATION_CLIFFS,monomerPosition:c,x:e,y:n,mpStats:this.monomerPositionStats,cliffStats:null!==(l=null===(a=this.cliffStats)||void 0===a?void 0:a.stats)&&void 0!==l?l:void 0,postfixes:h,additionalStats:d})})),e.root.addEventListener("mouseleave",(t=>this.model.unhighlight())),u.debounce(e.onCurrentCellChanged,500).subscribe((t=>{var n,r,o,s,a,l,c,f,h;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(-1===t.gridRow&&(this.mode===i.INVARIANT_MAP?this._invariantMapSelection=(0,b.ZR)(this.positionColumns):this._mutationCliffsSelection=(0,b.ZR)(this.positionColumns),this.model.fireBitsetChanged(m.q.SEQUENCE_VARIABILITY_MAP),e.invalidate()),!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 u=this.getMonomerPosition(t);this.mode===i.INVARIANT_MAP?this.modifyInvariantMapSelection(u,{shiftPressed:!0,ctrlPressed:!1},!0):(null===(f=null===(c=null===(l=this.mutationCliffs)||void 0===l?void 0:l.get(u.monomerOrCluster))||void 0===c?void 0:c.get(u.positionOrClusterType))||void 0===f?void 0:f.size)&&this.modifyMutationCliffsSelection(u,{shiftPressed:!0,ctrlPressed:!1},!0),e.invalidate(),setTimeout((()=>null==e?void 0:e.invalidate()),300)}finally{this.keyPressed=!1,(null===(h=t.tableColumn)||void 0===h?void 0:h.name)&&t.grid?this.currentGridCell=u.GridCell.fromColumnRow(t.grid,t.tableColumn.name,t.gridRow):this.currentGridCell=null}})),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(m.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)===h.$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()})),O(e);const o=e.onAfterDrawContent.subscribe((()=>{const t=e.col(h.$2.MONOMER);if(40!==t.width){t.width=40;for(const t of n)e.col(t).width=40}else o.unsubscribe()}));return e}getMonomerPosition(t){return{monomerOrCluster:t.cell.dataFrame.get(h.$2.MONOMER,t.tableRowIndex),positionOrClusterType:t.tableColumn.name}}render(){var t,e,n;if(f()(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=p()(a.shell.t.columns.numerical).toArray().map((t=>t.name)),r.get(this)===h.$2.ACTIVITY_SCALED&&r.set(this,h.$2.ACTIVITY)),f()(this.root).empty();let s=l.divText(m.q.MOST_POTENT_RESIDUES,{id:"pep-viewer-title"});if(this.name===m.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})),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})),e.setTooltip("Number of sequences having monomer-position");const n=t=>{f()(t.root).find(".ui-input-editor").css("margin","0px").attr("type","radio"),f()(t.root).find(".ui-input-description").css("padding","0px").css("padding-right","16px"),f()(t.captionLabel).addClass("ui-label-right")};n(t),n(e),s=l.divH([t.root,e.root],{id:"pep-viewer-title"}),f()(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");f()(c).addClass("pep-help-icon"),this.targetColumnInput&&(this.targetColumnInput.root.style.width="50%");const d=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"}}),g=l.divH([c,s,d],{style:{alignSelf:"center",lineHeight:"normal",flexDirection:"column"}});this.root.appendChild(l.divV([g,u])),null===(n=this.viewerGrid)||void 0===n||n.invalidate()}}class M extends _{constructor(){super(),this.currentGridRowIdx=null}get name(){return m.q.MOST_POTENT_RESIDUES}onTableAttached(){super.onTableAttached(),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(),f=c.map((([t,e])=>(0,v.hX)(e,t))),d=new Array(f.length);f.forEach(((t,e)=>d[e]=new Array(n.length)));let m=0;for(const[g,p]of e){const e=p.general;if(!e)continue;if(1===Object.entries(p).length)continue;const y=[];for(const[n,i]of Object.entries(p))"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===h.wf.HIGH&&C[1].meanDifference<e.meanDifference||this.activityTarget===h.wf.LOW&&C[1].meanDifference>e.meanDifference)&&(C=[t,e]);if(null===C)continue;n[m]=parseInt(g),i[m]=C[0],r[m]=C[1].meanDifference,o[m]=C[1].pValue,s[m]=C[1].count,a[m]=C[1].ratio,l[m]=C[1].mean;const b=this.monomerPositionStats[g][C[0]],w=u.BitSet.fromBytes(b.mask.buffer.buffer,this.model.df.col(this.activityColumnName).length);for(let t=0;t<f.length;t++){const[e,n]=c[t];d[t][m]=(0,v.lh)(this.model.df.getCol(e),n,w)}++m}n.length=m,i.length=m,r.length=m,o.length=m,s.length=m,a.length=m,l.length=m;const g=u.DataFrame.create(m),p=g.columns;return p.add(u.Column.fromList(u.TYPE.INT,h.$2.POSITION,n)),p.add(u.Column.fromList(u.TYPE.STRING,h.$2.MONOMER,i)),p.add(u.Column.fromList(u.TYPE.FLOAT,h.$2.MEAN_DIFFERENCE,r)),p.add(u.Column.fromList(u.TYPE.FLOAT,h.$2.MEAN,l)),p.add(u.Column.fromList(u.TYPE.FLOAT,h.$2.P_VALUE,o)),p.add(u.Column.fromList(u.TYPE.INT,h.$2.COUNT,s)),p.add(u.Column.fromList(u.TYPE.FLOAT,h.$2.RATIO,a)),f.forEach(((t,e)=>p.add(u.Column.fromList(u.TYPE.FLOAT,t,d[e])))),g}createViewerGrid(){const t=this.createMostPotentResiduesDf(),e=t.plot.grid();e.sort([h.$2.POSITION]);const n=e.col(h.$2.P_VALUE);n.format="#.000",n.name="P-value";const i=t.getCol(h.$2.MONOMER);d.rI(i,this.alphabet,!0),e.onCellRender.subscribe((t=>I(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)===h.$2.MONOMER)o.positionOrClusterType=h.$2.MONOMER;else if((null===(r=t.tableColumn)||void 0===r?void 0:r.name)!==h.$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,y.D)(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(-1===n.gridRow)return this._mutationCliffsSelection=(0,b.ZR)(this.positionColumns),this._invariantMapSelection=(0,b.ZR)(this.positionColumns),this.model.fireBitsetChanged(m.q.MOST_POTENT_RESIDUES),void e.invalidate();if(this.keyPressed&&t.currentCol.name!==h.$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.modifyInvariantMapSelection(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.modifyInvariantMapSelection(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.modifyInvariantMapSelection(t,{shiftPressed:!0,ctrlPressed:!1},!1)}}this.model.fireBitsetChanged(m.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!==h.$2.MEAN_DIFFERENCE)return;const s=this.getMonomerPosition(o);(null===(r=null===(i=null===(n=this.monomerPositionStats)||void 0===n?void 0:n[s.positionOrClusterType])||void 0===i?void 0:i[s.monomerOrCluster])||void 0===r?void 0:r.count)&&(this.modifyInvariantMapSelection(s,{shiftPressed:t.shiftKey,ctrlPressed:t.ctrlKey}),e.invalidate())})),O(e);const r=e.col(h.$2.MEAN_DIFFERENCE);r.name="Diff";const o=e.onAfterDrawContent.subscribe((()=>{const t=e.col(h.$2.MONOMER);if(40===t.width)return r.width=40,void o.unsubscribe();t.width=40,r.width=40}));return e}getMonomerPosition(t){return{monomerOrCluster:t.cell.dataFrame.get(h.$2.MONOMER,t.tableRowIndex),positionOrClusterType:`${t.cell.dataFrame.get(h.$2.POSITION,t.tableRowIndex)}`}}render(){var t;if(f()(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(m.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 I(t,e,n,i,r){var o,s,a,l,c;const f=[...e.positionColumns.map((t=>t.name)),h.$2.MEAN_DIFFERENCE],m=t.g,g=t.bounds;m.save(),m.beginPath(),m.rect(g.x,g.y,g.width,g.height),m.clip();const p=t.cell;if(p.isRowHeader&&p.gridColumn.visible)return p.gridColumn.visible=!1,t.preventDefault(),void m.restore();const v=null===(o=p.tableColumn)||void 0===o?void 0:o.name,y=p.tableRowIndex;if(!p.isTableCell||-1===f.indexOf(v))return void m.restore();const C=p.grid.table,b=C.get(h.$2.MONOMER,y),w=v!==h.$2.MEAN_DIFFERENCE?v:C.get(h.$2.POSITION,y).toFixed(),A=e.monomerPositionStats[w];if(!A[b])return t.preventDefault(),void m.restore();if(n){const t=null!==(s=A[b].aggValue)&&void 0!==s?s:A[b].count,n=e.positionColumns.find((t=>t.name===w)),i=null!==(a=n.temp[h.gp.INVARIANT_MAP_COLOR_CACHE])&&void 0!==a?a:{};let r=u.Color.white;null!=i[b]?r=i[b]:e instanceof N&&(e.cacheInvariantMapColors(),r=null!==(c=(null!==(l=n.temp[h.gp.INVARIANT_MAP_COLOR_CACHE])&&void 0!==l?l:{})[b])&&void 0!==c?c:u.Color.white),d.rW(m,b,w,e.invariantMapSelection,t,g,r)}else d.Yd(m,b,w,e,g);t.preventDefault(),m.restore()}function O(t){const e=t.props;e.allowEdit=!1,e.allowRowSelection=!1,e.allowBlockSelection=!1,e.allowColSelection=!1,e.showRowHeader=!1,e.showCurrentRowIndicator=!1,e.showReadOnlyNotifications=!1,e.rowHeight=20}},7654:(t,e,n)=>{"use strict";n.d(e,{HV:()=>g,M1:()=>p,QD:()=>v});var i,r=n(7389),o=n(6082),s=n(7233),a=n.n(s),l=n(4139),u=n(5070),c=n(8608),f=n(5480),h=n(8774);!function(t){t.SEPARATE_MONOMERS="separateMonomers",t.SEPARATE_POSITIONS="separatePositions",t.SEPARATE_CLUSTERS="separateClusters"}(i||(i={}));const d="general",m=t=>t===d?"General":t.substring(8);function g(t,e){if(!t.selection.anyTrue)return r.divText("No distribution");const n=()=>{const n=[C(d,t,e)];for(const r of Object.values(i))"true"!==t.getTag(r)||r===i.SEPARATE_CLUSTERS&&!e.clusterColName||n.push(C(r,t,e));return 1===n.length?n[0]:r.div(n)},o=r.div(n()),s=Object.values(i),l=new Array(s.length);for(let u=0;u<s.length;u++){const c=s[u].substring(8);l[u]=r.input.bool(c,{value:"true"===t.getTag(s[u]),onValueChanged:e=>{t.setTag(s[u],`${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[f.W.ORIGINAL]):c!==i.SEPARATE_MONOMERS&&c!==i.SEPARATE_POSITIONS||(l[u].enabled=0!==Object.entries(e.monomerPositionSelection).length)}const u=r.form(l,{style:{flexDirection:"row"}});return r.divV([u,o])}function p(t,e=!1){const n=t.plot.histogram({filteringEnabled:!1,valueColumnName:l.$2.ACTIVITY,splitColumnName:l.$2.SPLIT_COL,legendVisibility:"Never",showXAxis:!0,showColumnSelector:!1,showRangeSlider:!1,showBinSelector:!1,backColor:e?"#fdffe5":"#fffff"});return n.root.style.width="auto",n}function v(t,e={}){var n,i;null!==(n=e.fractionDigits)&&void 0!==n||(e.fractionDigits=3);const r={[null!==(i=null==e?void 0:e.countName)&&void 0!==i?i:"Count"]:`${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&&(r["p-value"]=t.pValue<.01?"<0.01":t.pValue.toFixed(e.fractionDigits)),r}function y(t,e,n,i={}){const r=p((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),f=Object.assign(Object.assign({},l),s),h=(0,c.F2)(r,f,i);return a()(h).addClass("d4-flex-col"),h}function C(t,e,n){let o=r.divText("No distribution");switch(t){case d:const t=h.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,d=a.getRawData(),m=n[f.W.ORIGINAL].map((t=>l.indexOf(t))),g=new Array(m.length).fill(new h.A(i));for(let t=0;t<i;t++){const e=d[t],n=m.indexOf(e);-1!==n&&g[n].setTrue(t)}for(let n=0;n<m.length;n++){const i=m[n],r=(0,u.GT)(s,g[n]);o.push(y(t,r,e,{[c.AN.SELECTION]:l[i]}))}const p=n[f.W.CUSTOM];for(const n of p){const r=t.getCol(n),a=h.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,f=[],d=[],m=[],g=[],p=e.activityCol.getRawData();for(const r of a){const a=n[r],v=new h.A(l);for(let e=0;e<a.length;e++){const n=a[e];null!==(i=d[e])&&void 0!==i||(d[e]=t.getCol(n)),null!==(o=m[e])&&void 0!==o||(m[e]=d[e].categories),null!==(s=g[e])&&void 0!==s||(g[e]=d[e].getRawData());const u=m[e].indexOf(r);for(let t=0;t<l;t++)g[e][t]===u&&v.setTrue(t)}const C=(0,u.GT)(p,v);f.push(y(t,C,e,{[c.AN.SELECTION]:r}))}return r.div(f,"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,f=[],d=e.activityCol.getRawData(),m=[],g=[],p=[];for(let r=0;r<a.length;r++){const v=a[r],C=n[v];if(0===C.length)continue;null!==(i=m[r])&&void 0!==i||(m[r]=t.getCol(v)),null!==(o=g[r])&&void 0!==o||(g[r]=m[r].categories),null!==(s=p[r])&&void 0!==s||(p[r]=m[r].getRawData());const b=new h.A(t.rowCount);for(let t=0;t<C.length;t++){const e=C[t],n=g[r].indexOf(e);for(let t=0;t<l;t++)p[r][t]===n&&b.setTrue(t)}const w=(0,u.GT)(d,b);f.push(y(t,w,e,{[c.AN.SELECTION]:v}))}return r.div(f,"d4-flex-wrap")}(e,n,n.monomerPositionSelection)}return r.divV([r.h1(m(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(3163);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,f=[a,l],h=i.divV([c.root,...f.map((t=>t.root))],{style:{width:"100%"}});return n&&(0,s.BE)("Mutation Cliffs pairs",c.root,h,(()=>{const n=u(t,e),r=i.splitH([i.divV([n.aminoToInput.root,n.pairsGrid.root],{style:{marginRight:"10px"}}),i.divV([n.uniqueSequencesGrid.root],{style:{marginLeft:"10px"}})],{style:{width:"100%",height:"100%"}},!0);return setTimeout((()=>{var t,i;if(document.contains(r)){const o=r.offsetWidth,s=null===(t=n.pairsGrid.canvas)||void 0===t?void 0:t.parentElement;n.pairsGrid.props.showRowHeader=!0,n.uniqueSequencesGrid.props.showRowHeader=!0;const a=null===(i=n.uniqueSequencesGrid.canvas)||void 0===i?void 0:i.parentElement;if(s&&a&&(s.style.height="100%",a.style.height="100%",a.style.marginTop="20px",o>400)){const t=Math.max(.33*o,200),i=n.pairsGrid.columns.byName("Mutation");i&&(i.width=t);const r=n.uniqueSequencesGrid.columns.byName(e.sequenceColumnName);r&&(r.width=t)}}}),500),r})),new r.Widget(h)}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 f=[],h=[],d=[],m=[],g=[],p=[],v=t.getCol(e.sequenceColumnName),y=v.categories,C=v.getRawData(),b=e.activityCol.getRawData(),w=new Map,A=r.BitSet.create(t.rowCount),S={},E=Object.fromEntries(e.positionColumns.map((t=>[t.name,t])));for(const t of c){const i=E[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;S[t]||(S[t]=Object.keys(S).length+1);const n=S[t],i=null!==(l=w.get(t))&&void 0!==l?l:[],s=y[C[t]],a=b[t];for(const l of e){if(i.includes(l)||!u.includes(l))continue;w.has(l)||w.set(l,[]);const e=y[C[l]];w.get(l).push(t),f.push(`${s}#${e}`),m.push(`${n}`),h.push(a-b[l]),d.push(r[o[l]]),g.push(t),p.push(l),A.set(t,!0),A.set(l,!0)}}}}if(0===f.length)return null;const T=r.Column.fromStrings("Mutation",f),x=r.Column.fromList("double","Delta",h),_=r.Column.fromStrings("Group",m),N=r.Column.fromStrings("~to",d),M=r.Column.fromList(r.COLUMN_TYPE.INT,"~toIdx",p),I=r.Column.fromList(r.COLUMN_TYPE.INT,"~fromIdx",g),O=r.DataFrame.fromColumns([T,x,_,N,M,I]);O.name="Mutation Cliff pairs";const L=i.input.string("Mutated to:",{value:"",onValueChanged:t=>{const e=t;""!==e?O.filter.init((t=>N.get(t)===e)):O.filter.setAll(!0)}});L.setTooltip("Filter the rows by the monomer that the mutation was substituted to");const R=O.plot.grid();(0,s.vY)(R,!0),T.semType=o.uF.MACROMOLECULE_DIFFERENCE,T.tags[o.gp.SEPARATOR]=(0,s.AY)(v),T.tags[r.TAGS.UNITS]=v.tags[r.TAGS.UNITS],T.tags[r.TAGS.CELL_RENDERER]="MacromoleculeDifference";let P=!1,k=null;const V=[];R.onCurrentCellChanged.subscribe((t=>{try{if(!t||!t.dart)return V.length=0,void Y();const e=t.tableRowIndex;if(!P)return;if(null===e)return V.length=0,void Y();null!==k&&V.splice(V.indexOf(k),1),V.includes(e)||(V.push(e),R.invalidate()),Y()}finally{P=!1,k=t&&t.dart?t.tableRowIndex:null}})),R.root.addEventListener("keydown",(t=>{P=t.key.startsWith("Arrow")})),R.root.addEventListener("click",(t=>{const e=R.hitTest(t.offsetX,t.offsetY);if(!e||null===e.tableRowIndex)return;const n=e.tableRowIndex;if(t.shiftKey){const t=V.indexOf(n);-1===t?V.push(n):V.splice(t,1)}else V.length=0,V.push(n);Y(),R.invalidate(),B.invalidate()})),R.onCellRender.subscribe((t=>{var e;(null===(e=t.cell.tableColumn)||void 0===e?void 0:e.name)===T.name&&V.includes(t.cell.tableRowIndex)&&(0,a.X5)(t.g,t.bounds)}));const D=e.gridColumns.length,G=[];for(let t=1;t<D;t++){const n=e.gridColumns.byIndex(t);((null==n?void 0:n.name)===e.sequenceColumnName||!0===(null==n?void 0:n.visible)&&!Object.hasOwn(E,n.name))&&G.push(n.name)}const F=t.clone(A,G);F.name="Unique sequences that form Mutation Cliffs pairs";const U=F.columns.addNewInt("~seqIdx"),H=U.getRawData(),q=A.getSelectedIndexes();U.init((t=>q[t]));const B=F.plot.grid();function Y(){const t=[];for(const e of V)t.push(I.get(e)),t.push(M.get(e));F.filter.init((e=>0===V.length||t.includes(H[e])),!0),R.invalidate(),B.invalidate()}return(0,s.vY)(B,!0),B.props.rowHeight=20,R.root.style.width="100% !important",B.root.style.width="100% !important",setTimeout((()=>{R.autoSize(window.innerWidth,250,void 0,void 0,!1),B.autoSize(window.innerWidth,250,void 0,void 0,!1),R.root.style.removeProperty("width"),R.root.style.setProperty("width","100%"),B.root.style.removeProperty("width"),B.root.style.setProperty("width","100%"),R.root.style.minHeight="70px",B.root.style.minHeight="100px",R.root.style.height="unset",B.root.style.height="unset"}),200),{pairsGrid:R,uniqueSequencesGrid:B,aminoToInput:L}}},5082:(t,e,n)=>{"use strict";n.d(e,{n:()=>v,v:()=>p});var i=n(4328),r=n(7389),o=n(6082),s=(n(4788),n(4139)),a=n(115),l=n(768),u=n(7233),c=n.n(u),f=n(8608),h=n(2003),d=n(1199),m=n(5429),g=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 p(t,e){const n=new a.av,l=r.div();let u=null;if(void 0===e){const e=o.Utils.firstOrNull(t.columns.toList().filter((t=>t.semType===o.SEMTYPE.MACROMOLECULE)));if(null===e)throw new Error("Peptides Error: table doesn't contain sequence columns");0!==e.stats.missingValueCount&&i.shell.info("Sequences column contains missing values. They will be ignored during analysis"),u=r.input.column("Sequence",{table:t,value:e,onValueChanged:e=>{c()(l).empty().append(r.wait((()=>g(this,void 0,void 0,(function*(){const n=yield t.plot.fromType("WebLogo",{sequenceColumnName:e.name});return n.root.style.setProperty("height","130px"),n.root}))))),0!==e.stats.missingValueCount&&i.shell.info("Sequences column contains missing values. They will be ignored during analysis")},filter:t=>t.semType===o.SEMTYPE.MACROMOLECULE}),u.setTooltip("Macromolecule column in FASTA, HELM or separated format")}else if("SEQ.MSA"!==e.getTag(h.gp.aligned)&&e.getTag(o.TAGS.UNITS)!==h.Hi.HELM)return{host:r.label("Peptides analysis only works with aligned sequences"),callback:()=>g(this,void 0,void 0,(function*(){return!1}))};let p,y=o.Func.find({package:"Bio",name:"webLogoViewer"});if(0===y.length)return{host:r.label("Bio package is missing or out of date. Please install the latest version."),callback:()=>g(this,void 0,void 0,(function*(){return!1}))};if(y=o.Func.find({package:"Bio",name:"getBioLib"}),0===y.length)return{host:r.label("Bio package is missing or out of date. Please install the latest version."),callback:()=>g(this,void 0,void 0,(function*(){return!1}))};const C=t.col("activity")||t.col("IC50")||o.Utils.firstOrNull(t.columns.numerical),b=r.div([],{id:"pep-hist-host"}),w=r.input.choice("Scaling",{value:s.rg.NONE,items:Object.values(s.rg),onValueChanged:t=>g(this,void 0,void 0,(function*(){var e;p=(0,f.Y1)(S.value,t);const n=o.DataFrame.fromColumns([p]).plot.histogram({filteringEnabled:!1,valueColumnName:s.$2.ACTIVITY,legendVisibility:"Never",showXAxis:!0,showColumnSelector:!1,showRangeSlider:!1,showBinSelector:!1});null===(e=b.lastChild)||void 0===e||e.remove(),b.appendChild(n.root)}))});w.setTooltip("Activity column transformation method");const A=()=>{var t;w.enabled=null!==(t=S.value)&&void 0!==t&&t&&S.value.stats.min>0,w.value=s.rg.NONE,0!==S.value.stats.missingValueCount&&i.shell.info("Activity column contains missing values. They will be ignored during analysis")},S=r.input.column("Activity",{table:t,value:C,onValueChanged:A,filter:t=>t.type===o.TYPE.INT||t.type===o.TYPE.FLOAT||t.type===o.TYPE.QNUM});S.setTooltip("Numerical activity column");const E=r.input.column("Clusters",{table:t,onValueChanged:t=>{t&&(T.value=!1,T.fireChanged())}});E.setTooltip("Optional. Clusters column is used to create Logo Summary Table"),E.nullable=!0;const T=r.input.bool("Generate clusters",{value:!0,onValueChanged:t=>{t&&(E.value=null,E.fireChanged())}});T.setTooltip("Generate clusters column based on MCL embeddings for Logo Summary Table"),S.fireChanged(),w.fireChanged(),T.fireChanged();const x=[S,w,E,T];null!==u&&x.splice(0,0,u);const _=r.input.float(m.t_.THRESHOLD,{value:n.threshold,nullable:!1,onValueChanged:t=>n.threshold=null!=t?t:n.threshold});_.setTooltip("Threshold for similarity between two sequences to create edges");const N=r.input.float(m.t_.INFLATION,{value:n.inflation,nullable:!1,onValueChanged:t=>n.inflation=null!=t?t:n.inflation});N.setTooltip("Inflation value for MCL algorithm");const M=r.input.int(m.t_.MAX_ITERATIONS,{value:n.maxIterations,nullable:!1,onValueChanged:t=>n.maxIterations=null!=t?t:n.maxIterations});M.setTooltip("Maximum iterations for MCL algorithm");const 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v.addMostPotentResidues(),null!==(d=f.addSequenceSpace)&&void 0!==d&&d){if(yield v.addSequenceSpace({clusterCol:n,clusterEmbeddings:f.useEmbeddingsClusters}),!n&&null!==(m=f.useEmbeddingsClusters)&&void 0!==m&&m){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)===o.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(l.q.LOGO_SUMMARY_TABLE))||void 0===t?void 0:t.render)&&(null===(e=null==v?void 0:v.findViewer(l.q.LOGO_SUMMARY_TABLE))||void 0===e||e.render())}),100)}}}else if(null!==(g=f.addMCL)&&void 0!==g&&g&&(yield v.addMCLClusters(),!n&&null!==(p=f.useEmbeddingsClusters)&&void 0!==p&&p)){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(l.q.LOGO_SUMMARY_TABLE))||void 0===t?void 0:t.render)&&(null===(e=null==v?void 0:v.findViewer(l.q.LOGO_SUMMARY_TABLE))||void 0===e||e.render())}),100)}}return y.close(),v}))}},5429:(t,e,n)=>{"use strict";n.d(e,{OH:()=>w,t_:()=>l});var i,r,o,s,a,l,u=n(7389),c=n(4328),f=n(6082),h=n(115),d=n(4139),m=n(768),g=n(7233),p=n.n(g),v=n(144),y=n.n(v),C=n(6920),b=n(1199);function w(t){var e,n,o,g,v,w,A,S,E,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:d.rg.NONE,M=null!==(n=null==_?void 0:_.columns)&&void 0!==n?n:{},I={},O={},L=null!==(o=null==_?void 0:_.sequenceSpaceParams)&&void 0!==o?o:new h.GI,R=null!==(g=null==_?void 0:_.mclSettings)&&void 0!==g?g:new h.av,P=u.input.column(r.ACTIVITY,{table:t.df,value:t.df.getCol(t.settings.activityColumnName),onValueChanged:t=>{I.activityColumnName=t.name},filter:t=>(t.type===f.TYPE.FLOAT||t.type===f.TYPE.INT)&&t.name!==d.$2.ACTIVITY&&0===t.stats.missingValueCount});P.setTooltip("Numeric activity column");const k=u.input.choice(r.ACTIVITY_SCALING,{value:N,items:Object.values(d.rg),onValueChanged:t=>I.activityScaling=t});k.setTooltip("Activity column transformation method"),x.addPane(i.GENERAL,(()=>u.inputs([P,k])),!0),O[i.GENERAL]=[P,k];const V=y()(t.analysisView.viewers).some((t=>t.type===m.q.DENDROGRAM)),D=u.input.bool(m.q.DENDROGRAM,{value:null!=V&&V,onValueChanged:t=>I.showDendrogram=t}),G=u.input.bool(m.q.CLUSTER_MAX_ACTIVITY,{value:!!(null==_?void 0:_.showClusterMaxActivity),onValueChanged:t=>{I.showClusterMaxActivity=null!=t?t:void 0}}),F=u.input.bool("Sequence space",{value:!!(null==_?void 0:_.showSequenceSpace),onValueChanged:t=>{I.showSequenceSpace=null!=t?t:void 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