@datagrok/peptides 1.27.5 → 1.27.7

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 (14) hide show
  1. package/CLAUDE.md +12 -1
  2. package/dist/705.js +1 -1
  3. package/dist/705.js.map +1 -1
  4. package/dist/package-test.js +1 -1
  5. package/dist/package-test.js.map +1 -1
  6. package/dist/package.js +1 -1
  7. package/dist/package.js.map +1 -1
  8. package/package.json +6 -6
  9. package/src/package.g.ts +4 -4
  10. package/src/package.ts +5 -5
  11. package/src/viewers/sar-viewer.ts +151 -0
  12. package/src/widgets/peptides.ts +11 -10
  13. package/test-console-output-1.log +75 -143
  14. 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={}))},4971:(t,e,n)=>{"use strict";n.d(e,{pj:()=>o});var i=n(6082);async function o(){const t=i.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()}},439:(t,e,n)=>{"use strict";n.d(e,{B5:()=>a,Hi:()=>i,YI:()=>o,_S:()=>c,b9:()=>h,gp:()=>r,ot:()=>d,q7:()=>u});var i,o,r,s=n(2738);!function(t){t.FASTA="fasta",t.SEPARATOR="separator",t.HELM="helm",t.CUSTOM="custom",t.BILN="biln"}(i||(i={})),function(t){t.DNA="DNA",t.RNA="RNA",t.PT="PT",t.UN="UN"}(o||(o={})),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",t.positionShift=".positionShift",t.selectedPosition=".selectedPosition",t.polymerTypeColumnName=".polymerTypeColumnName"}(r||(r={}));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(o.PT,l.fasta.peptide,.5),new s.a(o.DNA,l.fasta.dna,.55),new s.a(o.RNA,l.fasta.rna,.55)],c="",h={[i.FASTA]:"-",[i.SEPARATOR]:"",[i.HELM]:"*",[i.BILN]:""},d=" , "},2003:(t,e,n)=>{"use strict";n.d(e,{Hi:()=>i.Hi,SM:()=>o.SM,YI:()=>i.YI,gp:()=>i.gp,ot:()=>i.ot,zS:()=>o.zS});var i=n(439),o=n(7194)},4025:(t,e,n)=>{"use strict";n.d(e,{j:()=>o});var i=n(6082);n(439),n(7194);const o=new class{constructor(){this.seqHandler="seq-handler",this.notationProvider="seq-handler.notation-provider"}};i.SemanticValue},2738:(t,e,n)=>{"use strict";n.d(e,{X:()=>o,a:()=>i});class i{constructor(t,e,n){this.name=t,this.alphabet=e,this.cutoff=n}}class o extends i{constructor(t,e,n){super(t.name,t.alphabet,t.cutoff),this.freq=e,this.similarity=n}}},7194:(t,e,n)=>{"use strict";n.d(e,{Mu:()=>A,zS:()=>N,SM:()=>M,qp:()=>E});var i=n(6082),o=n(144),r=n.n(o);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],o=t[1];n.forEach(((t,n)=>{i[t]=this.colourPalette[o][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 h 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,h)),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,h)),this.grokGroups}static get RasMol(){return void 0===this.rasMol&&(this.rasMol=new h({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 h.aaSynonyms?h.aaSynonyms[t]:t;return super.get(e)}}h.aaSynonyms={MeNle:"L",MeA:"A",MeG:"G",MeF:"F"};class d{static getPalette(t="grok"){switch(t){case"grok":return h.GrokGroups;case"lesk":return h.Lesk;default:throw new Error(`ChemPalette: scheme \`${t}\` does not exist`)}}static getInnerOuter(t){let e=0,n="",i="";for(const o of t)"("==o?e++:")"==o?e--:e?n+=o:i+=o;return isNaN(parseInt(n))?[i,n]:[i,""]}static getColorAAPivot(t="",e="grok"){const n=this.getPalette(e);let[i,o]=this.getInnerOuter(t);if(i=i.length>6?`${i.slice(0,3)}...`:i,o=o.length>6?`${o.slice(0,3)}...`:o,1==t.length||"("==t[1]){const e=t[0]?.toUpperCase();return e in n?[n.get(e),e,o,1]:[this.undefinedColor,i,o,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,o,2]:[this.undefinedColor,i,o,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,o,3]:[this.undefinedColor,i,o,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,o,4]:[this.undefinedColor,i,o,4]}return[this.undefinedColor,i,o,0]}}d.SemType="Aminoacids",d.SemTypeMultipleAlignment="AminoacidsMultipleAlignment",d.undefinedColor="rgb(100,100,100)",d.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"},d.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"},d.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(*)*"},d.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 f extends c{static get Chromatogram(){return void 0===this.chromatogram&&(this.chromatogram=new f({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 p=n(4971);function g(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),o=i.Color.b(n),r=Math.sqrt(Math.pow(0-e,2)+Math.pow(0-t,2)+Math.pow(0-o,2));if(r>210)return`rgb(${e/r*210},${t/r*210},${o/r*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 C{}class y extends C{get(t,e){return"#666666"}}class w extends C{static get palette(){return w._pallete||(w._pallete=w.buildPalette()),w._pallete}static buildPalette(){return(0,p.pj)().then((t=>{t.awaitLoaded(1/0).then((()=>{const e=t.getMonomerLib();e.onChanged.subscribe((()=>{w.customMonomerColors={},w.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]=g(n.meta.colors.default.background))}}}))}))})),[].concat(...Object.values(c.colourPalette))}get(t,e){const n=w.palette.length,i=w.customMonomerColors[t],o=e??"PEPTIDE";if(i&&i[o])return i[o];const r=v.hashCode(t)%n;return g(w.palette[r])}}w._pallete=null,w.customMonomerColors={},w.polymerTypes=[];class b extends c{static get Gray(){return void 0===this.gray&&(this.gray=new y),this.gray}static get Color(){return void 0===this.color&&(this.color=new w),this.color}}n(3981);class A{get length(){return this.mList.length}get graphInfo(){}isGap(t){return this.getOriginal(t)===this.gapOriginalMonomer}getCanonical(t){if(this.length<=t)throw new Error("Index out of bounds");const e=this.mList[t];return e!==this.gapOriginalMonomer?e:u._S}getOriginal(t){if(this.length<=t)throw new Error("Index out of bounds");return this.mList[t]}getCanonicalRegion(t,e){const n=Math.min(Math.max(0,t),this.length),i=Math.max(Math.min(this.length,e),0)-n,o=this.gapOriginalMonomer;return new Array(i).fill(null).map(((t,e)=>{const i=this.mList[e+n];return i===o?u._S:i}))}getOriginalRegion(t,e){const n=Math.min(Math.max(0,t),this.length),i=Math.max(Math.min(this.length,e),0);return new Array(i-n).fill(null).map(((t,e)=>this.mList[e+n]))}get gapOriginal(){return this.gapOriginalMonomer}constructor(t,e){this.mList=t,this.gapOriginalMonomer=e}}class S extends A{constructor(t,e,n,i){super(t.flat(),i),this.mListSeparated=t,this.connections=e,this._graphInfo=void 0,this.polymerTypes=t.map(((t,e)=>new Array(t.length).fill(n[e]))).flat()}get graphInfo(){return this._graphInfo??(this._graphInfo=this.parseConnections()),this._graphInfo}parseConnections(){const t={connections:[],disjointSeqStarts:[],polymerTypes:this.polymerTypes};if((this.connections?.length??0)>0){let e=0;for(let n=0;n<this.mListSeparated.length;++n)t.disjointSeqStarts.push(e),e+=this.mListSeparated[n].length;const n=(this.connections??"").split("|").filter((t=>(t?.length??0)>0)),i=/^(PEPTIDE|RNA|BLOB|CHEM)\d{1,2}$/,o=/^\d{1,2}:R\d{1}-\d{1,2}:R\d{1}$/;for(const e of n){const n=e.split(",");if(3!==n.length||!o.test(n[2])||!i.test(n[0])||!i.test(n[1]))continue;const r=parseInt(n[0].replace(/^(PEPTIDE|RNA|BLOB|CHEM)/,""))-1,s=parseInt(n[1].replace(/^(PEPTIDE|RNA|BLOB|CHEM)/,""))-1,a=n[0].replace(/\d{1,2}$/,""),l=n[1].replace(/\d{1,2}$/,"");if(r<0||r>=this.mListSeparated.length||s<0||s>=this.mListSeparated.length)continue;const u=n[2].split("-");if(2!==u.length)continue;const c=u[0].split(":"),h=u[1].split(":");if(2!==c.length||2!==h.length)continue;const 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analysisView(){var t,e,n;return void 0===this._analysisView&&(this._analysisView=this.id?S()(h.shell.tableViews).find((({dataFrame:t})=>(null==t?void 0:t.getTag(d.TAGS.ID))===this.id)):void 0,!this._analysisView&&(null===(t=h.shell.v)||void 0===t?void 0:t.preview)instanceof d.TableView&&(null===(n=null===(e=h.shell.v)||void 0===e?void 0:e.preview)||void 0===n?void 0:n.dataFrame)===this.df&&(this._analysisView=h.shell.v.preview),this._analysisView||(this._analysisView=h.shell.addTableView(this.df))),"1"===this.df.getTag(_.gp.MULTIPLE_VIEWS)||this._layoutEventInitialized||(0,x.Lv)()||(h.shell.v=this._analysisView),this._analysisView.grid.invalidate(),this._analysisView}get settings(){var t,e;const n=this.df.getTag(_.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 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e=this.findViewer($.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,e;return null!==(t=this._webLogoSelection)&&void 0!==t||(this._webLogoSelection=(0,x.ZR)(null!==(e=this.positionColumns)&&void 0!==e?e:[])),this._webLogoSelection}set webLogoSelection(t){this._webLogoSelection=t,this.fireBitsetChanged(null),this.analysisView.grid.invalidate()}get positionColumns(){const t=S()(this.df.columns.byTags({[_.gp.POSITION_COL]:"true"})).toArray();return 0===t.length?null:t}get id(){return this.df.getTag(d.TAGS.ID)}get alphabet(){return this.df.getCol(this.settings.sequenceColumnName).getTag(f.gp.alphabet)}static getInstance(t){if(t.columns.contains(_.$2.ACTIVITY_SCALED)&&!t.columns.contains(_.$2.ACTIVITY)&&(t.getCol(_.$2.ACTIVITY_SCALED).name=_.$2.ACTIVITY),!t.temp[Z.modelName]){const e=t.temp[Z.modelName]=new Z(t),n=e.settings;n&&e.init(n);let i=!0;e.subs.push(d.debounce(t.onSelectionChanged,10).subscribe((n=>{var o,r,s;if(i||t.selection.anyTrue||!e._analysisView||!document.contains(e._analysisView.root)||e._analysisView.dataFrame!==t)return void(i=!(null===(o=null==t?void 0:t.selection)||void 0===o?void 0:o.anyTrue));e.positionColumns&&(e.webLogoSelection=(0,x.ZR)(e.positionColumns));const a=e.findViewer($.SEQUENCE_VARIABILITY_MAP);if(null!=a){const t=null!==(r=e.positionColumns)&&void 0!==r?r:a.positionColumns;t&&(a.invariantMapSelection=(0,x.ZR)(t),a.mutationCliffsSelection=(0,x.ZR)(t))}const l=e.findViewer($.MOST_POTENT_RESIDUES);if(null!=l){const t=null!==(s=e.positionColumns)&&void 0!==s?s:l.positionColumns;t&&(l.mutationCliffsSelection=(0,x.ZR)(t),l.invariantMapSelection=(0,x.ZR)(t))}const u=e.findViewer($.LOGO_SUMMARY_TABLE);null!=u&&(u.initClusterSelection({notify:!0}),u.render()),i=!0})))}return t.temp[Z.modelName]}modifyWebLogoSelection(t,e={shiftPressed:!1,ctrlPressed:!1},n=!0){n?this.webLogoSelection=(0,x.vW)(this.webLogoSelection,t,e):this._webLogoSelection=(0,x.vW)(this.webLogoSelection,t,e)}getVisibleSelection(){return this.df.selection.clone().and(this.df.filter)}createAccordion(){var t,e,n,i,o,r,s,a,l;const u=null===(t=this.df)||void 0===t?void 0:t.temp[Z.modelName];if(!u)return null;const h=c.accordion("Peptides analysis panel");h.root.style.width="100%";const m=u.getVisibleSelection(),p=u.df.filter.anyFalse?` among ${u.df.filter.trueCount} filtered`:"",g=t=>{const e=[];for(const[n,i]of Object.entries(t))for(const t of i)e.push(`${n}:${t}`);return e.join(", ")},v=u.findViewer($.LOGO_SUMMARY_TABLE),C=[],y=(null===v?[]:(null!==(n=null===(e=v.clusterSelection)||void 0===e?void 0:e[P.W.ORIGINAL])&&void 0!==n?n:[]).concat(null!==(o=null===(i=v.clusterSelection)||void 0===i?void 0:i[P.W.CUSTOM])&&void 0!==o?o:[])).join(", "),w=t=>{const e=c.divText(t);return e.innerHTML=t,e};0!==y.length&&C.push(w(`<b>Logo Summary Table</b> clusters: ${y}`));const b=u.findViewer($.SEQUENCE_VARIABILITY_MAP),A=g(null!==(r=null==b?void 0:b.invariantMapSelection)&&void 0!==r?r:{}),S=g(null!==(s=null==b?void 0:b.mutationCliffsSelection)&&void 0!==s?s:{});0!==A.length&&C.push(w(`<b>Invariant map</b>: ${A}`)),0!==S.length&&C.push(w(`<b>Mutation cliffs</b>: ${S}`));const T=u.findViewer($.MOST_POTENT_RESIDUES),E=g(null!==(a=null==T?void 0:T.invariantMapSelection)&&void 0!==a?a:{});0!==E.length&&C.push(w(`<b>Most potent residues</b>: ${E}`));const _=g(u.webLogoSelection);0!==_.length&&C.push(w(`<b>WebLogo</b>: ${_}`)),0!==C.length&&C.unshift(c.h1("Selection Sources"));const N=c.div(c.divV(C));h.addTitle(c.divV([c.h1(`${m.trueCount} selected rows${p}`),N],"css-gap-small"));let R=u.settings;const k=[b,T,v].filter((t=>null!==t&&(t.type!==this.accordionSource||(R=t,!1))));if(null===R)throw new Error("PeptidesError: Model is the source of accordion but is not initialized");R!==u.settings&&k.push(u.settings),k.filter((t=>null!==t&&(0,x.$s)(R,t)&&(t!==u.settings||u.isInitialized))).push(R);const D=R;R===u.settings||D instanceof P.s||null==D.mutationCliffs||h.addPane("Mutation Cliffs pairs",(()=>(0,O.F)(u.df,{mutationCliffs:D.mutationCliffs,mutationCliffsSelection:D.mutationCliffsSelection,gridColumns:u.analysisView.grid.columns,sequenceColumnName:D.sequenceColumnName,positionColumns:D.positionColumns,activityCol:D.getScaledActivityColumn(),mutationCliffStats:D.cliffStats}).root),!0);const G=R===u.settings,U=G?this.webLogoSelection:R instanceof M.J?R.invariantMapSelection:{},q=R instanceof P.s?R.clusterSelection:null!==(l=null==v?void 0:v.clusterSelection)&&void 0!==l?l:{};h.addPane("Distribution",(()=>{var t;try{return(0,L.HV)(u.df,{columns:G?null!==(t=u.settings.columns)&&void 0!==t?t:{}:R.getAggregationColumns(),activityCol:G?u.getScaledActivityColumn():R.getScaledActivityColumn(),monomerPositionSelection:U,clusterSelection:q,clusterColName:null==v?void 0:v.clustersColumnName})}catch(t){const e=c.divText("Error in Distribution");return c.tooltip.bind(e,String(t)),e}}),!0);const B=(t,e)=>{if(null==t||null==e)return!1;for(const[n,i]of Object.entries(t))if(i!==e[n])return!1;return!0};return h.addPane("Selection",(()=>{var t;try{return function(t,e){var n,i,o;if(0===e.tableSelection.trueCount)return c.divText("No compounds selected");const r=d.DataFrame.create(t.rowCount);r.name="Selected compounds",r.filter.copyFrom(e.tableSelection);let s=null;for(let t=1;t<e.gridColumns.length;t++){const o=e.gridColumns.byIndex(t);if(!o.visible)continue;const a=o.column;if(a.type===d.COLUMN_TYPE.BOOL)continue;null===s&&o.grid&&(null===(n=o.grid.sortByColumns)||void 0===n?void 0:n.length)>0&&(null===(i=o.grid.sortTypes)||void 0===i?void 0:i.length)===o.grid.sortByColumns.length&&(s={cols:o.grid.sortByColumns,types:o.grid.sortTypes});let l=null,u=null;try{l=a.getRawData(),u=a.categories}catch(t){}const c=l&&u?a.isNumerical?t=>l[t]:t=>u[l[t]]:t=>a.get(t),h=t=>a.isNone(t)?null:c(t),f=a.name===e.activityColumn.name?r.columns.addNewFloat(o.name).init((t=>h(t))):r.columns.addNewVirtual(o.name,(t=>h(t)),a.type);for(const[t,e]of a.tags)f.setTag(t,e)}const a=r.plot.grid();a.props.showRowHeader=!1,a.root.style.maxWidth="100%",d.debounce(c.onSizeChanged(a.root),50).subscribe((t=>{var e;const n=a.root.parentElement;(null===(e=null==n?void 0:n.parentElement)||void 0===e?void 0:e.classList.contains("panel-content"))&&(a.root.style.height="calc(100% - 20px)",a.root.style.width="calc(100% - 20px)",a.root.style.position="absolute",a.root.style.right="10px",a.root.style.top="10px")})),(0,x.zz)(a);const l=c.box(a.root);l.style.marginLeft="0px",setTimeout((()=>{null!==s&&a.sort(s.cols,s.types);for(let t=1;t<e.gridColumns.length;t++){const n=e.gridColumns.byIndex(t);n.visible&&a.col(n.name)&&(a.col(n.name).width=n.width)}}),500);const u=(0,V.Ej)(e.activityColumn,r.filter,e.positionColumns,{isFiltered:!0}),h={isSelectionTable:!0,cachedWebLogoTooltip:()=>({bar:"",tooltip:null}),webLogoBounds:()=>({}),colorPalette:()=>e.colorPalette},f={x:0,y:0,monomerPosition:{},mpStats:u};return e.isAnalysis&&(0,I.FZ)(a,u,e.positionColumns,e.activityColumn,h,f),(null!==(o=t.columns.bySemTypeAll(d.SEMTYPE.MACROMOLECULE))&&void 0!==o?o:[]).forEach((t=>{r.col(t.name)&&(r.col(t.name).temp[F.j.notationProvider]=t.temp[F.j.notationProvider])})),l}(u.df,{positionColumns:G?u.positionColumns:R.positionColumns,columns:G?null!==(t=u.settings.columns)&&void 0!==t?t:{}:R.getAggregationColumns(),activityColumn:G?u.getScaledActivityColumn():R.getScaledActivityColumn(),gridColumns:u.analysisView.grid.columns,colorPalette:(0,f.SM)(u.df.getCol(G?u.settings.sequenceColumnName:R.sequenceColumnName),z.Z.getSeqHelper()),tableSelection:u.getCombinedSelection(),isAnalysis:null!==u.settings&&(G||B(u.settings.columns,R.getAggregationColumns()))})}catch(t){const e=c.divText("Error in Selection");return c.tooltip.bind(e,String(t)),e}}),!0),h}getScaledActivityColumn(t=!1){const e=this.df.col(_.$2.ACTIVITY);return t&&null!==e?d.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,f.SM)(this.df.getCol(this.settings.sequenceColumnName),z.Z.getSeqHelper()),webLogoBounds:()=>this.webLogoBounds,cachedWebLogoTooltip:()=>this.cachedWebLogoTooltip,highlightCallback:(t,e,n)=>{(0,x.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");I.FZ(this.analysisView.grid,this.monomerPositionStats,this.positionColumns,this.getScaledActivityColumn(),t),this._layoutEventInitialized||(h.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,v.R)(this.df.getCol(this.settings.sequenceColumnName),z.Z.getSeqHelper()),i=n.columns.names();if(i.every((t=>e.contains(t))))i.forEach((t=>{this.df.col(t).setTag(_.gp.ANALYSIS_COL,"true"),this.df.col(t).setTag(_.gp.POSITION_COL,"true"),I.rI(this.df.col(t),this.alphabet)}));else for(const t of i){let i=this.df.col(t);const o=n.getCol(t);null!==i&&e.remove(t);const r=o.categories,s=o.getRawData();i=e.addNew(o.name,o.type).init((t=>r[s[t]])),i.setTag(_.gp.ANALYSIS_COL,"true"),i.setTag(_.gp.POSITION_COL,"true"),I.rI(i,this.alphabet)}this.df.name=t}createScaledCol(){const t=this.analysisView.grid,e=(0,x.Y1)(this.df.getCol(this.settings.activityColumnName),this.settings.activityScaling);this.df.columns.replace(_.$2.ACTIVITY,e),t.columns.setOrder([e.name])}unhighlight(){this.isHighlighting&&(this.df.rows.highlight(null),this.isHighlighting=!1)}setTooltips(){this.analysisView.grid.onCellTooltip(((t,e,n)=>{var i,o;return!(!t.isColHeader||(null===(i=t.tableColumn)||void 0===i?void 0:i.semType)!==_.uF.MONOMER)||!(!t.isTableCell||(null===(o=t.tableColumn)||void 0===o?void 0:o.semType)!==_.uF.MONOMER)}))}getCombinedSelection(){var t,e,n,i,o,r,s,a;const l=new m.A(this.df.rowCount,!1),u=(t,e)=>{for(const[n,i]of Object.entries(t))for(const t of i){const i=null==e?void 0:e[n];if(void 0===i)continue;const o=i[t];void 0!==o&&l.or(o.mask)}};u(this.webLogoSelection,this.monomerPositionStats);const c=this.findViewer($.SEQUENCE_VARIABILITY_MAP);u(null!==(t=null==c?void 0:c.invariantMapSelection)&&void 0!==t?t:{},null!==(e=null==c?void 0:c.monomerPositionStats)&&void 0!==e?e:null),((t,e)=>{var n,i;for(const[o,r]of Object.entries(t))for(const t of r){const r=null!==(i=null===(n=null==e?void 0:e.get(t))||void 0===n?void 0:n.get(o))&&void 0!==i?i:null;if(null!==r)for(const[t,e]of r.entries()){l.setTrue(t);for(const t of e)l.setTrue(t)}}})(null!==(n=null==c?void 0:c.mutationCliffsSelection)&&void 0!==n?n:{},null!==(i=null==c?void 0:c.mutationCliffs)&&void 0!==i?i:null);const h=this.findViewer($.MOST_POTENT_RESIDUES);u(null!==(o=null==h?void 0:h.invariantMapSelection)&&void 0!==o?o:{},null!==(r=null==h?void 0:h.monomerPositionStats)&&void 0!==r?r:null);const f=this.findViewer($.LOGO_SUMMARY_TABLE);for(const t of Object.keys(null!==(s=null==f?void 0:f.clusterSelection)&&void 0!==s?s:{}))for(const e of null!==(a=f.clusterSelection[t])&&void 0!==a?a:[]){const n=f.clusterStats[t][e];l.or(n.mask)}const p=d.BitSet.fromBytes(l.buffer.buffer,l.length);return this.df.filter.anyFalse?p.and(this.df.filter):p}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;h.shell.o=t.root,n=setTimeout((()=>{h.shell.o!=t.root&&(h.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){k._package.logger.debug("Peptides: Error on selection changed"),k._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($.LOGO_SUMMARY_TABLE);null!==n&&void 0!==n.model&&(n._logoSummaryTable=null!==(t=n.createLogoSummaryTable())&&void 0!==t?t:n._logoSummaryTable,n._viewerGrid=null!==(e=n.createLogoSummaryTableGrid())&&void 0!==e?e:n._viewerGrid,n.render())}catch(t){k._package.logger.debug("Peptides: Error on filter changed"),k._package.logger.debug(t)}finally{i()}})),this.isBitsetChangedInitialized=!0}fireBitsetChanged(t,e=!1){this.accordionSource=t,this.isBitsetChangedInitialized||this.setBitsetCallback(),this.isUserChangedSelection=!1,this.df.selection.fireChanged(),e&&this.df.filter.fireChanged(),this.controlFire=!0,this.df.selection.fireChanged(),e&&this.df.filter.fireChanged(),this.isUserChangedSelection=!0,this.webLogoSelectedMonomers=(0,x.qx)(this.df)}setGridProperties(t){var e,n,i,o;const r=this.analysisView.grid,s=r.props;s.allowColSelection=null!==(e=null==t?void 0:t.allowColSelection)&&void 0!==e&&e,s.allowEdit=null!==(n=null==t?void 0:t.allowEdit)&&void 0!==n&&n,s.showReadOnlyNotifications=null!==(i=null==t?void 0:t.showReadOnlyNotifications)&&void 0!==i&&i,s.showCurrentRowIndicator=null!==(o=null==t?void 0:t.showCurrentRowIndicator)&&void 0!==o&&o;const a=this.positionColumns;if(null===a)throw new Error("PeptidesError: Could not set grid properties: positionColumns are null");let l=10;const u=r.canvas.getContext("2d");if(null===u)throw new Error("PeptidesError: Could not set grid properties: canvas context is null");for(const t of a){const e=(0,f.zS)(t.categories.reduce(((t,e)=>t.length>e.length?t:e)),6),n=Math.ceil(u.measureText(e).width);l=Math.max(l,n)}const c=a.map((t=>t.name));for(let t=1;t<this.analysisView.grid.columns.length;++t){const e=this.analysisView.grid.columns.byIndex(t);if(null===e)throw new Error(`PeptidesError: Could not get analysis view: grid column with index '${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=c.includes(e.column.name)||e.column.name===_.$2.ACTIVITY}setTimeout((()=>{for(const t of a){const e=r.col(t.name);if(null===e)throw new Error(`PeptidesError: Could not set column width: grid column '${t.name}' is null`);e.width=l+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 K(this,void 0,void 0,(function*(){const t=d.TaskBarProgressIndicator.create("Calculating distance matrix...");try{const t=d.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){k._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(_.gp.MULTIPLE_VIEWS)){const t=c.iconFA("wrench",(()=>(0,R.OH)(this)),"Peptides analysis settings");this.analysisView.setRibbonPanels([[t]],!1),this.isRibbonSet=!0,this.updateGrid()}this.subs.push(h.events.onAccordionConstructed.subscribe((t=>{if(!(h.shell.o instanceof d.SemanticValue||h.shell.o instanceof d.Column&&this.df.columns.toList().includes(h.shell.o)))return;const e=t.getPane("Actions"),n=E()(e.root).find(".d4-flex-col"),i=c.label("Calculate identity");i.classList.add("d4-link-action"),c.tooltip.bind(i,"Adds a column with fractions of matching monomers against sequence in the current row"),i.onclick=()=>{const t=this.df.getCol(this.settings.sequenceColumnName);w(this.df,t,t.get(this.df.currentRowIdx),g.IDENTITY,z.Z.getSeqHelper()).then((e=>e.setTag(_.gp.IDENTITY_TEMPLATE,t.get(this.df.currentRowIdx)))).catch((t=>k._package.logger.debug(t)))},n.append(c.span([i],"d4-markdown-row"));const o=c.label("Calculate similarity");o.classList.add("d4-link-action"),c.tooltip.bind(o,"Adds a column with sequence similarity scores against sequence in the current row"),o.onclick=()=>{const t=this.df.getCol(this.settings.sequenceColumnName);w(this.df,t,t.get(this.df.currentRowIdx),g.SIMILARITY,z.Z.getSeqHelper()).then((e=>e.setTag(_.gp.SIMILARITY_TEMPLATE,t.get(this.df.currentRowIdx)))).catch((t=>k._package.logger.debug(t)))},n.append(c.span([o],"d4-markdown-row"))}))),this.subs.push(h.events.onViewRemoved.subscribe((t=>{t.id===this.analysisView.id&&this.subs.forEach((t=>t.unsubscribe())),h.log.debug(`Peptides: view ${t.name} removed`)}))),this.subs.push(h.events.onTableRemoved.subscribe((t=>{t.id===this.df.id&&this.subs.forEach((t=>t.unsubscribe())),h.log.debug(`Peptides: table ${t.name} removed`)}))),this.subs.push(h.events.onProjectClosed.subscribe((t=>{t.id===h.shell.project.id&&this.subs.forEach((t=>t.unsubscribe())),h.log.debug(`Peptides: project ${t.name} closed`)}))),this.fireBitsetChanged(null,!0),this.analysisView.grid.invalidate()}}findViewer(t){return S()(this.analysisView.viewers).find((e=>e.type===t))||null}addLogoSummaryTable(t){return K(this,void 0,void 0,(function*(){null!=t||(t={sequenceColumnName:this.settings.sequenceColumnName,clustersColumnName:S()(this.df.columns.categorical).next().value,activityColumnName:this.settings.activityColumnName,activityScaling:this.settings.activityScaling});const e=yield this.df.plot.fromType($.LOGO_SUMMARY_TABLE,t);(0,x.Lv)()&&this.analysisView.addViewer(e),this.analysisView.dockManager.dock(e,d.DOCK_TYPE.RIGHT,null,$.LOGO_SUMMARY_TABLE),e.viewerGrid.invalidate()}))}addClusterMaxActivityViewer(t){return K(this,void 0,void 0,(function*(){var e,n,i,o,r,s,a,l,u;const c=null!==(o=null!==(n=null===(e=this._mclCols)||void 0===e?void 0:e.find((t=>t.toLowerCase().startsWith("cluster (mcl)"))))&&void 0!==n?n:null===(i=this.findViewer($.LOGO_SUMMARY_TABLE))||void 0===i?void 0:i.clustersColumnName)&&void 0!==o?o:null===(r=this._sequenceSpaceCols)||void 0===r?void 0:r.find((t=>t.toLowerCase().startsWith("cluster")));null!=t||(t={activityColumnName:this.settings.activityColumnName,clusterColumnName:null!=c?c:null===(s=S()(this.df.columns.categorical).next().value)||void 0===s?void 0:s.name,activityTarget:_.wf.HIGH,connectivityColumnName:null!==(l=null!==(a=this._mclCols.find((t=>t.toLowerCase().startsWith("connectivity"))))&&void 0!==a?a: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!==l?l:"",clusterSizeThreshold:20,activityThreshold:1e3});const h=yield this.df.plot.fromType($.CLUSTER_MAX_ACTIVITY,t),f=null!==(u=this.findViewerNode($.LOGO_SUMMARY_TABLE))&&void 0!==u?u:null;this.analysisView.dockManager.dock(h,f?d.DOCK_TYPE.DOWN:d.DOCK_TYPE.RIGHT,f,$.CLUSTER_MAX_ACTIVITY)}))}addMonomerPosition(t){return K(this,void 0,void 0,(function*(){null!=t||(t={maxMutations:1,activityScaling:this.settings.activityScaling,activityColumnName:this.settings.activityColumnName,sequenceColumnName:this.settings.sequenceColumnName,minActivityDelta:0,activityTarget:_.wf.HIGH});const e=yield this.df.plot.fromType($.SEQUENCE_VARIABILITY_MAP,t);(0,x.Lv)()&&this.analysisView.addViewer(e);const n=this.findViewer($.MOST_POTENT_RESIDUES),i=this.analysisView.dockManager,[o,r,s]=null===n?[d.DOCK_TYPE.DOWN,null,void 0]:[d.DOCK_TYPE.LEFT,this.findViewerNode($.MOST_POTENT_RESIDUES),.7];i.dock(e,o,r,$.SEQUENCE_VARIABILITY_MAP,s)}))}addMostPotentResidues(t){return K(this,void 0,void 0,(function*(){null!=t||(t={activityScaling:this.settings.activityScaling,activityColumnName:this.settings.activityColumnName,sequenceColumnName:this.settings.sequenceColumnName,minActivityDelta:0,maxMutations:1,activityTarget:_.wf.HIGH});const e=yield this.df.plot.fromType($.MOST_POTENT_RESIDUES,t);(0,x.Lv)()&&this.analysisView.addViewer(e);const n=this.findViewer($.SEQUENCE_VARIABILITY_MAP),i=this.analysisView.dockManager,[o,r,s]=null===n?[d.DOCK_TYPE.DOWN,null,void 0]:[d.DOCK_TYPE.RIGHT,this.findViewerNode($.SEQUENCE_VARIABILITY_MAP),.3];i.dock(e,o,r,$.MOST_POTENT_RESIDUES,s)}))}createNewView(){const t=this.getVisibleSelection(),e=this.df.clone(t);for(const[t,n]of e.tags)e.setTag(t,t===_.gp.SETTINGS?n:"");e.name="Peptides Multiple Views",e.setTag(_.gp.MULTIPLE_VIEWS,"1");const n=h.shell.addTableView(e),i=this.findViewer($.LOGO_SUMMARY_TABLE);return null!=i&&n.addViewer($.LOGO_SUMMARY_TABLE,{[`sequence${_.To}`]:i.sequenceColumnName,[`activity${_.To}`]:i.activityColumnName,activityScaling:i.activityScaling,webLogoMode:i.webLogoMode,membersRatioThreshold:i.membersRatioThreshold,[`clusters${_.To}`]:i.clustersColumnName}),e.getTag(d.TAGS.ID)}clusterEmbeddings(){return K(this,void 0,void 0,(function*(){var t,e;if(!this._sequenceSpaceCols||0===this._sequenceSpaceCols.length)return void h.shell.warning("Embeddings columns are not initialized");const i=this._sequenceSpaceCols.filter((t=>t.toLowerCase().startsWith("embed_")));if(2!==i.length)return void h.shell.warning(`Found ${i.length} embeddings columns, expected 2`);const o=this._sequenceSpaceCols.filter((t=>t.toLowerCase().startsWith("cluster")));o.length>0&&this.df.columns.remove(o[0]);const r=this.df.getCol(i[0]).getRawData(),s=this.df.getCol(i[1]).getRawData(),a=null!==(t=this.settings.sequenceSpaceParams.epsilon)&&void 0!==t?t:.01,l=null!==(e=this.settings.sequenceSpaceParams.minPts)&&void 0!==e?e:4,u=yield function(t,e,i,o){return r=this,s=void 0,l=function*(){return new Promise((function(r,s){const a=new Worker(new URL(n.p+n.u(682),n.b));a.postMessage({embedX:t,embedY:e,minPts:o,epsilon:i}),a.onmessage=({data:{error:t,clusters:e}})=>{a.terminate(),t?s(t):r(e)}}))},new((a=void 0)||(a=Promise))((function(t,e){function n(t){try{o(l.next(t))}catch(t){e(t)}}function i(t){try{o(l.throw(t))}catch(t){e(t)}}function o(e){var o;e.done?t(e.value):(o=e.value,o instanceof a?o:new a((function(t){t(o)}))).then(n,i)}o((l=l.apply(r,s||[])).next())}));var r,s,a,l}(r,s,a,l),c=this.df.columns.getUnusedName("Cluster (DBSCAN)"),d=this.df.columns.addNewString(c);d.init((t=>u[t].toString())),null!==this._sequenceSpaceViewer&&(this._sequenceSpaceViewer.props.colorColumnName=d.name),this._sequenceSpaceCols=[i[0],i[1],d.name];const f=this.analysisView.grid.col(d.name);f&&(f.visible=!1)}))}addMCLClusters(){return K(this,void 0,void 0,(function*(){var t,e,n,i,o;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 r=this.df.getCol(this.settings.sequenceColumnName);null!==(n=(o=this.settings).mclSettings)&&void 0!==n||(o.mclSettings=new N.av);const s=this.settings.mclSettings;let a=0;const l=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),a++}5===a&&l.unsubscribe()})),u=h.events.onViewerAdded.subscribe((t=>{try{const e=t.args.viewer;if(e.type===d.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,d.DOCK_TYPE.FILL,t)}))}u.unsubscribe()}}catch(t){console.error(t)}})),c=JSON.stringify({cols:[r].map((t=>t.name)),metrics:[s.distanceF],weights:[1],aggregationMethod:j.MANHATTAN,preprocessingFuncs:["macromoleculePreprocessingFunction"],preprocessingFuncArgs:[{gapOpen:s.gapOpen,gapExtend:s.gapExtend,fingerprintType:s.fingerprintType}],threshold:s.threshold,maxIterations:s.maxIterations,useWebGPU:s.useWebGPU,inflate:s.inflation,minClusterSize:s.minClusterSize}),f=null!==(i=this.analysisView)&&void 0!==i?i:h.shell.getTableView(this.df.name);if(f){const t=d.Func.find({package:"EDA",name:"markovClusteringViewer"})[0];if(!t)throw new Error("Markov clustering function is not found");if(yield t.apply(),f.addViewer($.MCL,{mclProps:c}),yield d.delay(500),this._mclViewer=this.findViewer($.MCL),yield this._mclViewer.initPromise,this._mclViewer=this.findViewer($.MCL),!this._mclViewer||!this._mclViewer.isDetached)return null==u||u.unsubscribe(),void(null==l||l.unsubscribe());const e=this.findViewer($.LOGO_SUMMARY_TABLE);e&&(e._clusterStats=null,e._clusterSelection=null,e._viewerGrid=null,e._logoSummaryTable=null,e.render())}}))}addSequenceSpace(){return K(this,arguments,void 0,(function*(t={}){var e,n,i,o;if(null!==this._sequenceSpaceViewer)try{null===(e=this._sequenceSpaceViewer)||void 0===e||e.detach(),null===(n=this._sequenceSpaceViewer)||void 0===n||n.close()}catch(t){}0!==this._sequenceSpaceCols.length&&this._sequenceSpaceCols.forEach((t=>this.df.columns.remove(t))),this._sequenceSpaceCols=[];let r=this.df.getCol(this.settings.sequenceColumnName);const s=z.Z.getSeqHelper().getSeqHandler(r);if(s.isHelm())try{h.shell.warning("Column is in HELM notation. Sequences space will linearize sequences from position 0 prior to analysis");const t=s.convert(f.Hi.SEPARATOR,"/"),e=this.df.columns.getUnusedName(`Separator(${r.name})`);t.name=e,this.df.columns.add(t,!0),this.analysisView.grid.col(e).visible=!1,r=t}catch(t){return h.shell.error("Error on converting HELM notation to linear notation"),void h.shell.error(t)}const a=!t.clusterCol&&!!t.clusterEmbeddings,l=null!==(o=null===(i=this.settings)||void 0===i?void 0:i.sequenceSpaceParams)&&void 0!==o?o:new N.GI(a);l.clusterEmbeddings=a;const u={table:this.df,molecules:r,methodName:b.UMAP,similarityMetric:l.distanceF,plotEmbeddings:!0,options:{bypassLargeDataWarning:!0,dbScanEpsilon:l.epsilon,dbScanMinPts:l.minPts,randomSeed:"1",preprocessingFuncArgs:{gapOpen:l.gapOpen,gapExtend:l.gapExtend,fingerprintType:l.fingerprintType}},clusterEmbeddings:l.clusterEmbeddings};let c=0;const m=l.clusterEmbeddings?3:2,p=this.df.onColumnsAdded.subscribe((t=>{for(const e of t.columns)if(e.name.toLowerCase().startsWith("embed_")||l.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),c++}c===m&&p.unsubscribe()})),g=h.events.onViewerAdded.subscribe((t=>{try{const e=t.args.viewer;if(e.type===d.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,d.DOCK_TYPE.FILL,t)}))}g.unsubscribe()}}catch(t){console.error(t)}})),v=yield h.functions.call("Bio:sequenceSpaceTopMenu",u);g.unsubscribe(),v instanceof d.ScatterPlotViewer&&(l.clusterEmbeddings||t.clusterCol||(v.props.colorColumnName=this.getScaledActivityColumn().name),v.props.showXSelector=!1,v.props.showYSelector=!1,t.clusterCol&&(v.props.colorColumnName=t.clusterCol.name),this._sequenceSpaceViewer=v,v.onContextMenu.subscribe((t=>{try{t.item("Modify Sequence space parameters",(()=>{(0,R.OH)(this)}))}catch(t){}})))}))}}Z.modelName="peptidesModel"},3262:(t,e,n)=>{"use strict";n.r(e),n.d(e,{PackageFunctions:()=>mt,Peptides:()=>j,_package:()=>ct,clusterMaxActivity:()=>tt,getMonomerWorksInstance:()=>ht,getTreeHelperInstance:()=>dt,initPeptides:()=>Y,logoSummaryTable:()=>X,lstPiechartCellRenderer:()=>it,macromoleculeSarFastaDemo:()=>nt,manualAlignment:()=>et,monomerPosition:()=>K,mostPotentResidues:()=>Z,mutationCliffs:()=>Q,peptidesDialog:()=>W,peptidesPanel:()=>z,sequencePositionStatistics:()=>J,testInitFunctionPeptides:()=>$});var i=n(4328),o=n(7389),r=n(6082),s=n(5082),a=n(7233),l=n.n(a),u=(n(4788),n(9499)),c=n(726),h=n(3541),d=n(5480);n(3981);class f{constructor(t){this.monomerLib=t}getCappedRotatedMonomer(t,e){const n=this.monomerLib.getMonomer(t,e);return n?n.molfile:null}}var m=n(4139),p=n(8608),g=n(2003),v=n(115),C=n(5072),y=n.n(C),w=n(7825),b=n.n(w),A=n(7659),S=n.n(A),T=n(5056),E=n.n(T),_=n(540),N=n.n(_),x=n(1113),M=n.n(x),I=n(6677),O={};O.styleTagTransform=M(),O.setAttributes=E(),O.insert=S().bind(null,"head"),O.domAPI=b(),O.insertStyleElement=N(),y()(I.A,O),I.A&&I.A.locals&&I.A.locals;var L;!function(t){let e,n;!function(t){t.vert=function(t){return o.divV(t.map((t=>o.render(t))),{classes:"u2-panel"})},t.horz=function(t){return o.divH(t.map((t=>o.render(t))),{classes:"u2-panel"})}}(e=t.panels||(t.panels={})),t.appHeader=function(t){const n=o.iconImage("",t.iconPath);l()(n).addClass("ui-app-header-icon").css("margin-right","20px");const i=e.horz([]);if(t.appTitle){i.classList.add("u2-app-header-with-name");const e=o.divV([o.divText(t.appTitle,"u2-app-header-app-name-div")],"u2-app-header-app-name-and-slogan-div");t.appSubTitle&&e.append(o.divText(t.appSubTitle));const r=o.div(n);i.append(o.divH([r,e]))}else i.append(n);const r=e.vert([o.markdown(t.description),t.learnMoreUrl?o.link("Learn more",t.learnMoreUrl,void 0,{style:{marginLeft:"15px"}}):null]);return r.classList.add("u2-app-header-description"),i.append(r),t.bottomLine&&i.classList.add("u2-app-header-bottom-line"),i},function(t){t.runAsync=function(t,e){return n=this,r=void 0,a=function*(){o.setUpdateIndicator(t,!0);try{return yield e()}catch(t){i.log.error(t)}finally{o.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 o(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,o)}l((a=a.apply(n,r||[])).next())}));var n,r,s,a}}(n=t.tools||(t.tools={}))}(L||(L={}));var P=n(144),R=n.n(P);const k=rxjs.operators;class V extends r.JsViewer{get scViewer(){return this._scViewer||(this._scViewer=this.createSCViewer()),this._scViewer}constructor(){super(),this._titleHost=o.divText(u.q.CLUSTER_MAX_ACTIVITY,{id:"pep-viewer-title",style:{marginRight:"auto"}}),this._selsectIcon=o.div(),this.activityTarget=m.wf.HIGH,this.viewerError="",this.renderTimeout=null,this.renderDebounceTime=500,this.scFilterQuery=`\${${V.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",m.wf.HIGH,{choices:[m.wf.HIGH,m.wf.LOW]}),this.clusterSizeThreshold=this.int("clusterSizeThreshold",20),this.activityThreshold=this.float("activityThreshold",1e3,{step:.1}),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:r.AxisType.logarithmic,yAxisType:r.AxisType.logarithmic,invertYAxis:this.activityTarget===m.wf.LOW,xColumnName:V.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(![r.COLUMN_TYPE.FLOAT,r.COLUMN_TYPE.INT,r.COLUMN_TYPE.BIG_INT,r.COLUMN_TYPE.QNUM].includes(n.type))return this.viewerError="Activity column should be numeric",null;const a=this.dataFrame.columns.getOrCreate(V.clusterSizeColName,r.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=r.AxisType.linear);const u={},c={};for(let t=0;t<this.dataFrame.rowCount;t++){const e=i.get(t);if(null==e||i.isNone(t)||n.isNone(t))continue;const o=n.get(t),r=u[e];if((null==r||null==r||o>n.get(r)&&this.activityTarget===m.wf.HIGH||o<n.get(r)&&this.activityTarget===m.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 h=this.dataFrame.columns.getOrCreate(V.maxActivityInClusterColName,r.COLUMN_TYPE.INT);h.init((t=>i.isNone(t)?0:t===u[i.get(t)]?1:0)),this.dataFrame.columns.getOrCreate(V.maxConnectivityInClusterColName,r.COLUMN_TYPE.INT).init((t=>i.isNone(t)?0:t===c[i.get(t)]?1:0)),this.dataFrame.columns.getOrCreate(V.synSelectionColName,r.TYPE.STRING).init((t=>{if(i.isNone(t))return null;let e=null;return t===u[i.get(t)]&&(e=V.maxActivityLabel),s&&t===c[i.get(t)]&&(e=e?`${e}, ${V.maxConnectivityLabel}`:V.maxConnectivityLabel),e})),e.xColumnName=V.clusterSizeColName,e.yColumnName=this.activityColumnName,e.filter=this.scFilterQuery,this.viewerError="";const d=r.Viewer.scatterPlot(this.dataFrame,e);this.selectionSubscription&&this.selectionSubscription.unsubscribe(),this.selectionSubscription=d.onDataEvent.pipe((0,k.filter)((t=>"d4-select"==t.type))).subscribe((t=>{var e,n;const o=null!==(n=null===(e=t.bitset)||void 0===e?void 0:e.getSelectedIndexes())&&void 0!==n?n:[],s=this.dataFrame.selection,a=r.BitSet.create(this.dataFrame.rowCount,(t=>1==h.get(t)));a.and(s);for(let t=0;t<o.length;t++){const e=o[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 f=()=>{const t=r.BitSet.create(this.dataFrame.rowCount);Object.entries(u).forEach((([e,i])=>{var o;if(null==e||null==i)return;const r=parseInt(e),s=n.get(i),a=null!==(o=l[r])&&void 0!==o?o:l[e];s<this.activityThreshold&&a<this.clusterSizeThreshold||(t.set(i,!0,!1),null!=c[r]&&t.set(c[r],!0,!1))})),t.fireChanged(),this.dataFrame.selection.copyFrom(t,!0)};return this._selsectIcon=o.iconSvg("select-all",(()=>{f()}),"Select 3 Active quadrants"),this._selsectIcon.style.cursor="pointer",this._selsectIcon.style.marginRight="5px",f(),this.linesDrawSubscription&&this.linesDrawSubscription.unsubscribe(),this.linesDrawSubscription=d.onBeforeDrawScene.subscribe((()=>{const t=d.getInfo().canvas.getContext("2d"),e=d.viewport,n=d.worldToScreen(e.x,this.activityThreshold),i=d.worldToScreen(this.clusterSizeThreshold,e.y),o=d.worldToScreen(e.x+e.width,this.activityThreshold),r=d.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(o.x,o.y),t.moveTo(i.x,i.y),t.lineTo(r.x,r.y),t.stroke(),t.closePath()})),d}onTableAttached(){var t,e,n,i,o,r,s,a,l,u,c,h;super.onTableAttached();const d=null!==(e=null===(t=this.dataFrame)||void 0===t?void 0:t.col(m.$2.ACTIVITY))&&void 0!==e?e:null===(i=R()(null===(n=this.dataFrame)||void 0===n?void 0:n.columns.numerical).next())||void 0===i?void 0:i.value;null!=d&&(null===(o=this.getProperty(`activity${m.To}`))||void 0===o||o.set(this,d.name));const f=null===(s=R()(null===(r=this.dataFrame)||void 0===r?void 0:r.columns.categorical).next())||void 0===s?void 0:s.value;null!=f&&(null===(a=this.getProperty(`cluster${m.To}`))||void 0===a||a.set(this,f.name));const p=null===(u=R()(null===(l=this.dataFrame)||void 0===l?void 0:l.columns.numerical).next())||void 0===u?void 0:u.value;null!=p&&(null===(c=this.getProperty(`connectivity${m.To}`))||void 0===c||c.set(this,p.name)),this.render(),null===(h=this.dataFrame)||void 0===h||h.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(o.divText(null!==(t=this.viewerError)&&void 0!==t?t:"Error creating scatter plot"));const i=o.div("Cluster Size",{style:{alignSelf:"center",color:"var(--grey-6)",marginBottom:"5px"}}),r=o.div(this.activityTarget===m.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(o.divH([r,o.divV([o.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${m.To}`&&(this._scViewer=null),this.render()}}V.clusterSizeColName="~cluster.size",V.maxActivityInClusterColName="~max.activity.for.cluster",V.maxConnectivityInClusterColName="~max.connectivity.for.cluster",V.synSelectionColName="Syn Selection",V.maxActivityLabel="Max Activity",V.maxConnectivityLabel="Max Connectivity";var F=n(3163);class D extends r.JsViewer{constructor(){super(),this.showPositionInfo=!0,this.positions=this.string("positions","1",{description:"Comma-separated sequence positions (1-based) to analyze"}),this.sequenceColumnName=this.column("sequence",{semType:r.SEMTYPE.MACROMOLECULE,nullable:!1}),this.valueColumnName=this.column("value",{columnTypeFilter:"numerical",nullable:!1}),this.showPositionInfo=this.bool("showPositionInfo",!0,{nullable:!1,defaultValue:!0,description:"Show position selector in the viewer header"}),this.subs.push(i.events.onContextMenu.subscribe((t=>{var e;t.causedBy&&t.causedBy.target&&(null===(e=this._boxPlotViewer)||void 0===e?void 0:e.root.contains(t.causedBy.target))&&(t.causedBy.preventDefault(),t.causedBy.stopPropagation(),t.causedBy.stopImmediatePropagation())})))}getPositionFromColumn(){var t;const e=this.dataFrame.col(this.sequenceColumnName);if(null==e)return 1;const n=null!==(t=e.getTag(g.gp.selectedPosition))&&void 0!==t?t:"1",i=parseInt(n);return Number.isNaN(i)?1:Math.max(1,i)}parsePositions(){if(!this.positions)return[1];const t=this.positions.split(",").map((t=>parseInt(t.trim()))).filter((t=>!Number.isNaN(t)&&t>=1));return[...new Set(t)].sort(((t,e)=>t-e))}_setPositions(t){const e=[...new Set(t)].sort(((t,e)=>t-e));this.getProperty("positions").set(this,e.join(", "))}onTableAttached(){if(super.onTableAttached(),null==this.dataFrame.columns.bySemType(r.SEMTYPE.MACROMOLECULE))throw i.shell.error("No sequence column found"),new Error("No sequence column found");const t=this.dataFrame.columns.getUnusedName("~sequence_position_monomers");this._positionColumn=this.dataFrame.columns.addNewString(t),this._positionColumn.semType="Monomer",this._positionColumn.setTag("cell.renderer","Monomer"),this.getProperty("sequenceColumnName").set(this,this.dataFrame.columns.bySemType(r.SEMTYPE.MACROMOLECULE).name),this.getProperty("valueColumnName").set(this,R()(this.dataFrame.columns.numerical).next().value.name),this.getProperty("positions").set(this,String(this.getPositionFromColumn())),this.subs.push(r.debounce(this.dataFrame.onMetadataChanged,200).subscribe((t=>{const e=this.getPositionFromColumn();this.parsePositions().includes(e)||this._setPositions([e])})))}render(){var t;const e=this.parsePositions();if(!(null!=this.dataFrame&&this.sequenceColumnName&&e.length&&this._positionColumn&&this.valueColumnName))return;l()(this.root).empty(),null===(t=this._boxPlotViewer)||void 0===t||t.detach();const n=c.Z.getSeqHelper(),i=this.dataFrame.col(this.sequenceColumnName),o=n.getSeqHandler(i),s=o.maxLength,a=e.map((t=>o.getMonomersAtPosition(t-1,!0)));if(this._positionColumn.init((t=>a.map((e=>e[t])).join(g.ot))),this._boxPlotViewer=this.dataFrame.plot.box({categoryColumnNames:[this._positionColumn.name],plotStyle:"violin",valueColumnName:this.valueColumnName,colorColumnName:this._positionColumn.name,showColorSelector:!1,showSizeSelector:!1,showCategorySelector:!1,legendVisibility:r.VisibilityMode.Never,markerColorColumnName:this._positionColumn.name,title:"Sequence Position Statistics",autoLayout:!1,labelOrientation:"Vert"}),this.showPositionInfo){const t=this._renderPositionSelector(e,s);this.root.appendChild(t)}this._boxPlotViewer.props.statistics=["min","max","avg","med","count"],this._boxPlotViewer.root.style.width="100%",this._boxPlotViewer.root.style.height="100%",this.root.appendChild(this._boxPlotViewer.root),this._boxPlotViewer.sub(this._boxPlotViewer.onPropertyValueChanged.subscribe((t=>{var e,n,i,o;if((null===(n=null===(e=this._boxPlotViewer)||void 0===e?void 0:e.props)||void 0===n?void 0:n.valueColumnName)&&(null===(o=null===(i=this._boxPlotViewer)||void 0===i?void 0:i.props)||void 0===o?void 0:o.valueColumnName)!==this.valueColumnName){const t=this._boxPlotViewer.props.valueColumnName;setTimeout((()=>this.getProperty("valueColumnName").set(this,t)),10)}})))}_renderPositionSelector(t,e){const n=o.divH([],{style:{alignItems:"center",justifyContent:"center",gap:"4px",flexWrap:"wrap",padding:"4px 8px",width:"100%"}}),i=o.label(`${this.sequenceColumnName}:`);i.style.fontWeight="bold",i.style.marginRight="4px",n.appendChild(i);for(const i of t)n.appendChild(this._createChip(i,t,e));return n.appendChild(this._createAddButton(n,t,e)),n}_createChip(t,e,n){const i=1===e.length,r=document.createElement("span");r.textContent=String(t),r.style.marginRight="3px";const s=i?o.iconFA("pencil",(()=>this._showInlineEdit(a,t,n)),"Edit position"):o.iconFA("times",(()=>this._setPositions(e.filter((e=>e!==t)))),"Remove position");s.style.cursor="pointer",s.style.fontSize="10px",s.style.opacity="0.6";const a=o.divH([r,s],{style:{display:"inline-flex",alignItems:"center",background:"#f0f0f0",borderRadius:"12px",padding:"2px 8px",fontSize:"12px",cursor:"default",border:"1px solid #d0d0d0"}});return a}_showInlineEdit(t,e,n){var i;const o=document.createElement("input");o.type="number",o.min="1",o.max=String(n),o.value=String(e),o.style.cssText="width:45px;height:22px;font-size:12px;text-align:center;border-radius:12px;border:1px solid #aaa;outline:none;padding:0 4px;";let r=!1;const s=()=>{if(r)return;r=!0;const i=parseInt(o.value),s=this.parsePositions();!Number.isNaN(i)&&i>=1&&i<=n&&i!==e?this._setPositions(s.map((t=>t===e?i:t))):o.replaceWith(t)};o.addEventListener("keydown",(e=>{var n;"Enter"===e.key&&s(),"Escape"===e.key&&(r=!0,null===(n=t.parentElement)||void 0===n||n.replaceChild(t,o))})),o.addEventListener("blur",s),null===(i=t.parentElement)||void 0===i||i.replaceChild(o,t),o.focus(),o.select()}_createAddButton(t,e,n){const i=o.iconFA("plus-circle",(()=>{if(t.querySelector(".position-add-input"))return;const o=document.createElement("input");o.type="number",o.min="1",o.max=String(n),o.className="position-add-input",o.style.cssText="width:45px;height:22px;font-size:12px;text-align:center;border-radius:12px;border:1px solid #aaa;outline:none;padding:0 4px;";let r=!1;const s=()=>{if(r)return;r=!0;const t=parseInt(o.value);!Number.isNaN(t)&&t>=1&&t<=n&&!e.includes(t)?this._setPositions([...e,t]):o.remove()};o.addEventListener("keydown",(t=>{"Enter"===t.key&&s(),"Escape"===t.key&&(r=!0,o.remove())})),o.addEventListener("blur",s),t.insertBefore(o,i),o.focus()}),"Add position");return i.style.cursor="pointer",i.style.fontSize="14px",i.style.color="#2083d5",i}onPropertyChanged(t){null!=this.dataFrame&&this.sequenceColumnName&&this.render()}}var G=n(7471),U=function(t,e,n,i){return new(n||(n=Promise))((function(o,r){function s(t){try{l(i.next(t))}catch(t){r(t)}}function a(t){try{l(i.throw(t))}catch(t){r(t)}}function l(t){var e;t.done?o(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())}))};class q extends r.JsViewer{constructor(){super(),this.position=1,this.currentRowMutationsOnly=!1,this.yAxisType="Linear",this._mutationCliffsData=null,this._dfSubs=[],this._positionColumns=null,this._innerDf=null,this._lineChart=null,this._debounceTimer=null,this.sequenceColumnName=this.column("sequence",{semType:r.SEMTYPE.MACROMOLECULE,nullable:!1}),this.seriesColumnName=this.column("series",{columnTypeFilter:"categorical",nullable:!1}),this.activityColumnName=this.column("activity",{columnTypeFilter:"numerical",nullable:!1}),this.position=this.int("position",1,{nullable:!1,showSlider:!1,min:1,max:100,showPlusMinus:!0,description:"Position in the sequence to analyze (1 Based).",category:"Data"}),this.yAxisType=this.string("yAxisType","Linear",{choices:["Linear","Logarithmic"],description:"Y-Axis scale type.",nullable:!1,category:"Data"}),this.currentRowMutationsOnly=this.bool("currentRowMutationsOnly",!1,{nullable:!1,defaultValue:!1,description:"When enabled, the viewer will show mutations related to the peptide in current row in the dataframe and selected position.",category:"Data"}),this.root.classList.add("peptides-viewer-show-title")}onTableAttached(){var t,e;super.onTableAttached();const n=this.dataFrame.columns.bySemType(r.SEMTYPE.MACROMOLECULE);n&&this.getProperty("sequenceColumnName").set(this,n.name),this.getProperty("activityColumnName").set(this,R()(this.dataFrame.columns.numerical).next().value.name);const o=null===(e=null===(t=R()(this.dataFrame.columns.categorical))||void 0===t?void 0:t.filter((t=>{var e;return t.name!==this.sequenceColumnName&&(null===(e=t.name)||void 0===e?void 0:e.toLowerCase().includes("series"))})).next())||void 0===e?void 0:e.value;o&&this.getProperty("seriesColumnName").set(this,o.name),this.subs.push(r.debounce(this.dataFrame.onFilterChanged,200).subscribe((()=>{this.clearCache(),this.debouncedRender()}))),this.debouncedRender(),this.subs.push(i.events.onContextMenu.subscribe((t=>{var e;t.causedBy&&t.causedBy.target&&(null===(e=this._lineChart)||void 0===e?void 0:e.root.contains(t.causedBy.target))&&(t.causedBy.preventDefault(),t.causedBy.stopPropagation(),t.causedBy.stopImmediatePropagation())})))}get mutationCliffsData(){if(this._mutationCliffsData)return this._mutationCliffsData;if(!this.activityColumnName||!this.sequenceColumnName||!this.position)throw new Error("Activity column or Sequence column is not set, or position is invalid");return this._mutationCliffsData=new Promise(((t,e)=>U(this,void 0,void 0,(function*(){try{const e=this.dataFrame.col(this.activityColumnName).getRawData(),n=this.positionColumns,i=n[this.position-1].toList(),o=n.map(p.eY),r=yield(new G.a).calc(e,o,{maxMutations:1,minActivityDelta:0,filter:this.dataFrame.filter.anyFalse?new Uint32Array(this.dataFrame.filter.getBuffer().buffer):void 0,singlePosition:{position:this.position-1}});t({cliffs:r,monomers:i})}catch(t){e(t)}})))),this._mutationCliffsData}calculateDf(){return U(this,void 0,void 0,(function*(){if(!(this.dataFrame&&this.activityColumnName&&this.sequenceColumnName&&this.position))throw new Error("Activity column or Sequence column is not set, or position is invalid");const t=yield this.mutationCliffsData,e=new Set;t.cliffs.forEach((t=>{t.forEach((t=>{Array.from(t.entries()).forEach((([t,n])=>{const i=Number(t);this.currentRowMutationsOnly&&this.dataFrame.currentRowIdx!==i||(e.add(i),n.forEach((t=>e.add(Number(t)))))}))}))}));const n=Array.from(e.values()).sort(((t,e)=>t-e)),i=new Map;n.forEach(((t,e)=>{i.set(t,e)}));const o=n.map((e=>t.monomers[e])),s=this.dataFrame.col(this.activityColumnName).getRawData(),a=n.map((t=>s[t])),l=[r.Column.fromList("string",`Position ${this.position}`,o),r.Column.fromList("double",this.activityColumnName,a)];if(this.seriesColumnName){const t=this.dataFrame.col(this.seriesColumnName).getRawData(),e=this.dataFrame.col(this.seriesColumnName).categories,i=n.map((n=>e[t[n]])),o=r.Column.fromList("string",this.seriesColumnName,i);l.push(o)}const u=r.DataFrame.fromColumns(l);Array.from(this.dataFrame.columns.numerical).filter((t=>t.name!==this.activityColumnName&&t.name!==this.seriesColumnName)).forEach((t=>{u.columns.addNew(t.name,t.type)})),this._dfSubs.push(u.onMouseOverRowChanged.subscribe((t=>{if(u.mouseOverRowIdx>=0){const t=n[u.mouseOverRowIdx];this.dataFrame.mouseOverRowIdx=t}}))),this._dfSubs.push(this.dataFrame.onMouseOverRowChanged.subscribe((t=>{if(this.dataFrame.mouseOverRowIdx>=0){const t=i.get(this.dataFrame.mouseOverRowIdx);u.mouseOverRowIdx=null!=t?t:-1}})));let c=!1;this._dfSubs.push(u.onCurrentRowChanged.subscribe((t=>{if(u.currentRowIdx>=0){c=!0;const t=n[u.currentRowIdx];this.dataFrame.currentRowIdx=t}}))),this.currentRowMutationsOnly&&this._dfSubs.push(this.dataFrame.onCurrentRowChanged.subscribe((t=>{c?c=!1:(this.clearCache(!1),this.debouncedRender())})));let h=!1,d=!1;return this._dfSubs.push(r.debounce(u.onSelectionChanged,100).subscribe((t=>{const e=u.selection;if(h)h=!1;else if(d=!0,this.dataFrame.selection.setAll(!1,!1),e.anyTrue){for(let t=-1;-1!==(t=e.findNext(t,!0));){const e=n[t];this.dataFrame.selection.set(e,!0,!1)}this.dataFrame.selection.fireChanged()}else this.dataFrame.selection.fireChanged()}))),this._dfSubs.push(r.debounce(this.dataFrame.onSelectionChanged,100).subscribe((t=>{const e=this.dataFrame.selection;if(d)d=!1;else if(h=!0,u.selection.setAll(!1,!1),e.anyTrue){for(let t=-1;-1!==(t=e.findNext(t,!0));){const e=i.get(t);null!=e&&u.selection.set(e,!0,!1)}u.selection.fireChanged()}else u.selection.fireChanged()}))),u}))}get positionColumns(){if(this._positionColumns)return this._positionColumns;if(!this.dataFrame)return[];const t=u.i.getInstance(this.dataFrame),e=null==t?void 0:t.positionColumns;if(e&&e.length>0)return this._positionColumns=e,this._positionColumns;const n=this.dataFrame.col(this.sequenceColumnName),i=c.Z.getSeqHelper().getSeqHandler(n),o=i.maxLength,s=[];for(let t=0;t<o;t++){const e=i.getMonomersAtPosition(t,!0),n=r.Column.fromList("string",`Position ${t+1}`,e);s.push(n)}return this._positionColumns=s,this._positionColumns}get innerDf(){return this._innerDf?Promise.resolve(this._innerDf):(this._innerDf=this.calculateDf(),this._innerDf)}render(){return U(this,void 0,void 0,(function*(){if(l()(this.root).empty(),!(this.dataFrame&&this.activityColumnName&&this.sequenceColumnName&&this.position))return o.setUpdateIndicator(this.root,!1),void this.root.appendChild(B("Please set Activity column, Sequence column and Position properties."));if(this._lineChart){try{this._lineChart.detach()}catch(t){console.error("Error detaching previous line chart:",t)}this._lineChart=null}o.setUpdateIndicator(this.root,!0),this.root.style.display="flex",this.root.style.flexDirection="column";const t=yield this.innerDf;o.setUpdateIndicator(this.root,!1),0===t.rowCount?this.currentRowMutationsOnly?this.dataFrame.currentRowIdx>=0?this.root.appendChild(B("No mutations cliffs found for the current peptide at the selected position.")):this.root.appendChild(B("Please select a row in the main table to see mutation cliffs for the corresponding peptide at the selected position.")):this.root.appendChild(B("No mutation cliffs found for the selected position.")):(this._lineChart=t.plot.line({xColumnName:`Position ${this.position}`,yColumnNames:[this.activityColumnName],splitColumnNames:this.seriesColumnName?[this.seriesColumnName]:[],legendVisibility:this.seriesColumnName?"Always":"Never",legendPosition:"Right",showXSelector:!1,showYSelector:!0,showSplitSelector:!1,packCategories:!1,xAxisLabelOrientation:"Auto",axisFont:'normal normal 14px "Roboto"',controlsFont:'normal normal 14px "Roboto"'}),this._lineChart.sub(this._lineChart.onPropertyValueChanged.subscribe((t=>{var e,n,i,o,r,s,a,l;if((null===(n=null===(e=this._lineChart)||void 0===e?void 0:e.props)||void 0===n?void 0:n.yColumnNames)&&(null===(r=null===(o=null===(i=this._lineChart)||void 0===i?void 0:i.props)||void 0===o?void 0:o.yColumnNames)||void 0===r?void 0:r[0])!==this.activityColumnName){const t=null===(l=null===(a=null===(s=this._lineChart)||void 0===s?void 0:s.props)||void 0===a?void 0:a.yColumnNames)||void 0===l?void 0:l[0];setTimeout((()=>this.getProperty("activityColumnName").set(this,t)),1)}}))),this.root.appendChild(this._lineChart.root));const e=this.positionColumns.length+1,n=new Array(e-1).fill(0).map(((t,e)=>e+1)).map((t=>t.toString())),i=o.input.choice("Position",{value:this.position.toString(),items:n,nullable:!1,onValueChanged:t=>{if(!t)return;const e=parseInt(t);this.getProperty("position").set(this,e)}});if(i.input.style.width="40px",this.root.appendChild(o.divH([i.root],{style:{justifyContent:"center",marginTop:"4px",width:"100%",font:'normal normal 14px "Roboto"'}})),t.rowCount>0){const t=o.input.column("Series",{table:this.dataFrame,filter:t=>t.isCategorical&&t.name!==this.sequenceColumnName,tooltipText:"Select column for series splitting.",onValueChanged:t=>{const e=t?t.name:void 0;this.getProperty("seriesColumnName").set(this,e)},value:this.seriesColumnName?this.dataFrame.col(this.seriesColumnName):void 0});this.root.prepend(o.divH([t.root],{style:{justifyContent:"flex-end",paddingBottom:"4px",padding:"8px",width:"100%",font:'normal normal 14px "Roboto"'}}))}}))}debouncedRender(){o.setUpdateIndicator(this.root,!0),this._debounceTimer&&clearTimeout(this._debounceTimer),this._debounceTimer=setTimeout((()=>this.render()),300)}clearCache(t=!0){t&&(this._mutationCliffsData=null),this._innerDf=null,this._dfSubs.forEach((t=>t.unsubscribe())),this._dfSubs=[]}detach(){super.detach(),this._dfSubs.forEach((t=>t.unsubscribe())),this._dfSubs=[],clearTimeout(this._debounceTimer)}onPropertyChanged(t){if(super.onPropertyChanged(t),"activityColumnName"===(null==t?void 0:t.name)||"sequenceColumnName"===(null==t?void 0:t.name)||"position"===(null==t?void 0:t.name)||"seriesColumnName"===(null==t?void 0:t.name)){const e="seriesColumnName"===(null==t?void 0:t.name)||"activityColumnName"===(null==t?void 0:t.name);this.clearCache(!e),"sequenceColumnName"===(null==t?void 0:t.name)&&(this._positionColumns=null),this.debouncedRender()}else"yAxisType"===(null==t?void 0:t.name)?this._lineChart&&(this._lineChart.props.yAxisType=this.yAxisType.toLowerCase()):"currentRowMutationsOnly"===(null==t?void 0:t.name)&&(this.clearCache(!1),this.debouncedRender())}}function B(t){const e=o.divText(t);return e.style.fontSize="14px",e.style.marginTop="10px",e.style.textAlign="center",e}var H=function(t,e,n,i){return new(n||(n=Promise))((function(o,r){function s(t){try{l(i.next(t))}catch(t){r(t)}}function a(t){try{l(i.throw(t))}catch(t){r(t)}}function l(t){var e;t.done?o(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 Y(){return H(this,void 0,void 0,(function*(){yield mt.initPeptides()}))}function j(){return mt.Peptides()}function W(){return mt.peptidesDialog()}function $(t){return H(this,void 0,void 0,(function*(){yield mt.testInitFunctionPeptides(t)}))}function z(t){return mt.peptidesPanel(t)}function K(){return mt.monomerPosition()}function Z(){return mt.mostPotentResidues()}function Q(){return mt.mutationCliffs()}function X(){return mt.logoSummaryTable()}function J(){return mt.sequencePositionStatistics()}function tt(){return mt.clusterMaxActivity()}function et(t){return mt.manualAlignment(t)}function nt(){return H(this,void 0,void 0,(function*(){yield mt.macromoleculeSarFastaDemo()}))}function it(){return mt.lstPiechartCellRenderer()}var ot=function(t,e,n,i){var o,r=arguments.length,s=r<3?e:null===i?i=Object.getOwnPropertyDescriptor(e,n):i;if("object"==typeof Reflect&&"function"==typeof Reflect.decorate)s=Reflect.decorate(t,e,n,i);else for(var a=t.length-1;a>=0;a--)(o=t[a])&&(s=(r<3?o(s):r>3?o(e,n,s):o(e,n))||s);return r>3&&s&&Object.defineProperty(e,n,s),s},rt=function(t,e){if("object"==typeof Reflect&&"function"==typeof Reflect.metadata)return Reflect.metadata(t,e)},st=function(t,e){return function(n,i){e(n,i,t)}},at=function(t,e,n,i){return new(n||(n=Promise))((function(o,r){function s(t){try{l(i.next(t))}catch(t){r(t)}}function a(t){try{l(i.throw(t))}catch(t){r(t)}}function l(t){var e;t.done?o(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 lt,ut=null;const ct=new r.Package;function ht(){return ut}function dt(){return lt}function ft(t){return at(this,void 0,void 0,(function*(){const e=r.TaskBarProgressIndicator.create("Loading Peptides"),n=ct.webRoot+"files/"+t,o=yield i.data.loadTable(n);o.name="Peptides",i.shell.addTableView(o).name="PeptidesView",i.shell.windows.showProperties=!0,e.close()}))}i.decorators||(i.decorators={}),["func","init","param","panel","editor","demo","app","appTreeBrowser","fileHandler","fileExporter","model","viewer","filter","cellRenderer","autostart","dashboard","folderViewer","semTypeDetector","packageSettingsEditor","functionAnalysis","converter","fileViewer","model","treeBrowser","polyfill"].forEach((t=>{i.decorators[t]||(i.decorators[t]=function(t){return function(t,e,n){}})}));class mt{static initPeptides(){return at(this,void 0,void 0,(function*(){try{null!=ut||(ut=new f(yield i.functions.call("Bio:getBioLib"))),null!=lt||(lt=yield async function(){const t="Dendrogram",e=r.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)}}))}static Peptides(){const t=L.appHeader({iconPath:ct.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=r.View.create();return n.name="Peptides",o.appendAll(n.root,[t,o.divH([o.button("Simple demo",(()=>ft("aligned.csv")),""),o.button("Complex demo",(()=>ft("aligned_2.csv")),""),o.button("HELM demo",(()=>ft("aligned_3.csv")),"")])]),n}static peptidesDialog(){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(!r.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=o.dialog("Analyze Peptides").add(e.host).onOK((()=>at(this,void 0,void 0,(function*(){e.callback()||n.show()}))));return n.show()}static testInitFunctionPeptides(t){return at(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)))}))}static peptidesPanel(t){if(!t.dataFrame||!r.Utils.firstOrNull(t.dataFrame.columns.numerical))return new r.Widget(o.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 r.Widget(e.host)}static monomerPosition(){return new h.J}static mostPotentResidues(){return new h.UJ}static mutationCliffs(){return new q}static logoSummaryTable(){return new d.s}static sequencePositionStatistics(){return new D}static clusterMaxActivity(){return new V}static manualAlignment(t){const e=i.shell.t,n=null==e?void 0:e.temp[u.i.modelName];return n?function(t,e){const n=o.input.textArea("",{value:t.get(e.currentRowIdx)});l()(n.root).addClass("pep-textinput");const s=o.button("Apply",(()=>{return o=this,r=void 0,a=function*(){const o=c.Z.getSeqHelper().getSeqHandler(t),r=n.value,s=o.splitter(r),a=e.currentRowIdx;t.set(a,r);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)},new((s=void 0)||(s=Promise))((function(t,e){function n(t){try{l(a.next(t))}catch(t){e(t)}}function i(t){try{l(a.throw(t))}catch(t){e(t)}}function l(e){var o;e.done?t(e.value):(o=e.value,o instanceof s?o:new s((function(t){t(o)}))).then(n,i)}l((a=a.apply(o,r||[])).next())}));var o,r,s,a}),"Apply changes"),a=o.button(o.iconFA("redo"),(()=>n.value=t.get(e.currentRowIdx)),"Reset");return l()(a).addClass("pep-snippet-editor-icon pep-reset-icon"),new r.Widget(o.divV([a,n.root,s],"pep-textarea-box"))}(e.getCol(n.settings.sequenceColumnName),e):new r.Widget(o.divText("Manual alignment works with peptides analysis"))}static macromoleculeSarFastaDemo(){return at(this,void 0,void 0,(function*(){return yield function(){return t=this,e=void 0,o=function*(){i.shell.windows.showContextPanel=!0;const t=r.DataFrame.fromCsv(yield ct.files.readAsText("aligned.csv"));t.name="Simple peptides",t.id||(t.id=`Simple-peptides-analysis-table-id-${Math.random()}-${Date.now()}`);const e=i.shell.addTableView(t);yield r.delay(50);const n=e.grid;yield new Promise((t=>{var e;let i=null;const o=null===(e=null==n?void 0:n.onAfterDrawContent)||void 0===e?void 0:e.subscribe((()=>{i&&clearTimeout(i),o.unsubscribe(),t(void 0)}));i=setTimeout((()=>{o.unsubscribe(),t(void 0)}),3e3)}));const 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A(t,e,n,c,h,d={x:0,y:0,mpStats:{},monomerPosition:{}}){var f;if(null!==(f=h.isSelectionTable)&&void 0!==f||(h.isSelectionTable=!1),0==Object.keys(d.mpStats).length&&(d.mpStats=e),h.isSelectionTable&&(!h.webLogoBounds||!h.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,l,u,d;if(!(null===(i=t.cell)||void 0===i?void 0:i.isColHeader))return;const f=t.g,v=t.bounds,C=t.cell.tableColumn;f.save();try{if(f.beginPath(),f.clearRect(v.x,v.y,v.width,v.height),f.rect(v.x,v.y,v.width,v.height),f.clip(),(null==C?void 0:C.semType)===r.uF.MONOMER){let i;if(m.filter.anyFalse){null!==(l=(d=m).jsOnlyTemp)&&void 0!==l||(d.jsOnlyTemp={});const t=null!==(u=m.jsOnlyTemp[r.gp.M_P_STATS_CACHE])&&void 0!==u?u:{},e=null==t?void 0:t[C.name];if(t&&e&&e.filterLength===m.filter.length&&e.filterVersion===m.filter.version)i=e.stats[C.name];else{const e=(0,a.Ej)(c,m.filter,n,{isFiltered:!0,columns:[C.name]});i=e[C.name],t[C.name]={filterVersion:m.filter.version,stats:e,filterLength:m.selection.length}}m.jsOnlyTemp[r.gp.M_P_STATS_CACHE]=t}else i=h.isSelectionTable?(0,a.Ej)(c,m.filter,n,{isFiltered:!0,columns:[C.name]})[C.name]:e[C.name];if(!i)return;const y=Object.keys(i).sort(((t,e)=>""===t||"-"===t?1:""===e||"-"===e?-1:0)).filter((t=>"general"!==t));h.webLogoBounds()[C.name]=function(t,e,n,i,r,a,l,u={},c={}){var h,d,f,m,v,C,y,w,b;const A=window.devicePixelRatio;null!==(h=c.symbolStyle)&&void 0!==h||(c.symbolStyle="16px Roboto, Roboto Local, sans-serif"),null!==(d=c.upperLetterHeight)&&void 0!==d||(c.upperLetterHeight=12.2),null!==(f=c.upperLetterAscent)&&void 0!==f||(c.upperLetterAscent=.25),null!==(m=c.marginVertical)&&void 0!==m||(c.marginVertical=1),null!==(v=c.marginHorizontal)&&void 0!==v||(c.marginHorizontal=1),null!==(C=c.selectionWidth)&&void 0!==C||(c.selectionWidth=2),null!==(y=c.textHeight)&&void 0!==y||(c.textHeight=13),null!==(w=c.headerStyle)&&void 0!==w||(c.headerStyle=`bold ${c.textHeight*A}px Roboto, Roboto Local, sans-serif`);const S=(r.length-1)*c.upperLetterAscent;let T=(e.y+c.marginVertical)*A;const E=(e.height-2*c.marginVertical-S-1.25*c.textHeight)*A,_=(e.x+c.marginHorizontal)*A,N=Math.max(c.selectionWidth*A,.05*e.width*A),x=2*c.marginHorizontal+c.selectionWidth,M=(e.width-(x+c.marginHorizontal))*A,I=(e.x+x)*A,O=p.Z.getMonomerLib(),L={};for(const e of r){const i=E*(n[e].count/a),r=E*((null!==(b=u[e])&&void 0!==b?b:0)/a);if(L[e]=new o.Rect(I/A,T/A,M/A,i/A),t.resetTransform(),"-"!==e&&""!==e){const n=(0,s.zS)(e,5),a=t.measureText(n);r>0&&(t.lineWidth=N,t.line(_,T,_,T+r,o.Color.rowSelection));const l=O.getMonomerTextColor(g.o.AA,e);t.fillStyle=l,t.textAlign="left",t.textBaseline="top",t.font=c.symbolStyle;const u=M/a.width,h=i/c.upperLetterHeight;t.setTransform(u,0,0,h,I,T),t.fillText(n,0,0,a.width)}T+=i+c.upperLetterAscent*A}return t.resetTransform(),t.fillStyle=o.Color.toHtml(o.Color.black),t.textAlign="center",t.textBaseline="top",t.font=c.headerStyle,t.fillText(i,(e.x+e.width/2)*A,(e.y+e.height-c.textHeight)*A),L}(f,v,i,C.name,y,m.filter.trueCount,h.colorPalette(),h.headerSelectedMonomers?h.headerSelectedMonomers()[C.name]:{}),t.preventDefault()}}catch(t){console.warn(`PeptidesHeaderLogoError: couldn't render WebLogo for column \`${C.name}\`. See original error below.`),console.warn(t)}finally{f.restore()}})(t)));const v=n=>{var o;const s=t.hitTest(n.offsetX,n.offsetY);if((null==s?void 0:s.isColHeader)&&(null===(o=s.tableColumn)||void 0===o?void 0:o.semType)===r.uF.MONOMER){const t=function(t,e,n){const i=n[t.tableColumn.name];if(!i)return null;for(const[n,o]of Object.entries(i)){const i=e.offsetX>=o.x&&e.offsetX<=o.x+o.width,r=e.offsetY>=o.y&&e.offsetY<=o.y+o.height;if(i&&r)return{monomerOrCluster:n,positionOrClusterType:t.tableColumn.name}}return null}(s,n,h.webLogoBounds());if(null===t)return void(h.isSelectionTable||null==h.unhighlightCallback||h.unhighlightCallback());d.monomerPosition=t;const o=m.filter.anyFalse?m.clone(m.filter):m,r=o.getCol(c.name);!function(t,e,n,o,r,s){if("click"!==t.type||r.isSelectionTable||null==r.selectionCallback){const a=`${e.positionOrClusterType} = ${e.monomerOrCluster}`;r.cachedWebLogoTooltip().bar===a?i.tooltip.show(r.cachedWebLogoTooltip().tooltip,t.clientX,t.clientY):(r.cachedWebLogoTooltip().bar=a,s.x=t.clientX,s.y=t.clientY,s.monomerPosition=e,r.cachedWebLogoTooltip().tooltip=(0,u.Y)(n,o,[],s))}else r.selectionCallback(e,{shiftPressed:t.shiftKey,ctrlPressed:t.ctrlKey})}(n,t,o,r,h,d),h.isSelectionTable||null==h.highlightCallback||h.highlightCallback(t,m,e)}else null!=h.unhighlightCallback&&h.unhighlightCallback()};l.fromEvent(t.overlay,"mousemove").subscribe((t=>v(t))),l.fromEvent(t.overlay,"click").subscribe((t=>v(t))),l.fromEvent(t.overlay,"mouseleave").subscribe((()=>{null!=h.unhighlightCallback&&h.unhighlightCallback()}))}class S extends o.GridCellRenderer{constructor(){super(...arguments),this.colorCacheKey="lst-pie-chart-color-cache",this.HoverTempKey="lst-pie-chart-hovered-sector",this.hoverSeparator=",,,,,"}get name(){return"LST Pie Chart"}get cellType(){return"lst-pie-chart"}get defaultWidth(){return 80}get defaultHeight(){return 80}categoryNumberCache(t){return t.temp[this.colorCacheKey]||(t.temp[this.colorCacheKey]={}),t.temp[this.colorCacheKey]}getPrevHoveredSector(t){return t.temp[this.HoverTempKey]}onMouseMove(t,e){const n=this.getPrevHoveredSector(t.cell.column),o=()=>{t.cell.column.temp[this.HoverTempKey]=null,i.tooltip.hide(),null!==n&&t.grid.invalidate()},r=t.cell.value;if(!r)return void o();const s=e.offsetX-t.bounds.midX,a=e.offsetY-t.bounds.midY,l=Math.sqrt(s*s+a*a),u=Math.atan2(a,s),c=u<0?u+2*Math.PI:u;if(l>Math.min(t.bounds.width,t.bounds.height)/2-2)return void o();let h;try{h=JSON.parse(r)}catch(e){return void o()}const d=new Float64Array(Object.keys(h).length+1),f=Object.values(h).reduce(((t,e)=>t+e),0);d[Object.keys(h).length]=2*Math.PI;let m=0,p=0;for(const t of Object.values(h))d[p++]=m,m+=2*Math.PI*t/f;let g=-1;for(let t=0;t<d.length-1;t++)if(c>=d[t]&&c<d[t+1]){g=t;break}if(-1===g)return void o();const v=Object.keys(h)[g],C=h[v],y=(C/f*100).toFixed(2);i.tooltip.show(i.h1(`${v}: ${C} (${y}%)`),e.x+16,e.y+16);const w=t.cell.rowIndex.toString()+this.hoverSeparator+v;t.cell.column.temp[this.HoverTempKey]=w,n!==w&&t.grid.invalidate()}render(t,e,n,i,r,s,a){const l=s.cell.dataFrame,u=new o.Rect(e,n,i,r).fitSquare().inflate(-2,-2);if(i<5||r<5||!l)return;const c=s.cell.value;if(t.clearRect(e,n,i,r),!c)return;let h;try{h=JSON.parse(c)}catch(t){return}const d=Object.values(h).reduce(((t,e)=>t+e),0);let f=0;const m=Object.fromEntries(Object.keys(h).map((t=>[t,255]))),p=s.cell.column.temp[this.HoverTempKey];if(p&&2===p.split(this.hoverSeparator).length){const[t,e]=p.split(this.hoverSeparator);if(t===s.cell.rowIndex.toString()){for(const[t,e]of Object.entries(h))m[t]=100;m[e]=255}}const g=Math.min(i,r)/2.2;for(const[e,n]of Object.entries(h)){const i=2*Math.PI*n/d;t.beginPath(),t.moveTo(u.midX,u.midY),t.arc(u.midX,u.midY,g,f,f+i),f+=i;const r=this.categoryNumberCache(s.cell.column);r[e]||(r[e]=Object.keys(r).length,s.cell.column.temp[this.colorCacheKey]=r),t.fillStyle=o.Color.toHtml(o.Color.setAlpha(o.Color.getCategoricalColor(r[e]),m[e])),t.fill(),t.strokeStyle=o.Color.toRgb(o.Color.lightGray),t.stroke();const a=e;t.fillStyle=o.Color.toRgb(o.Color.white),t.font="9px Arial";const l=t.measureText(a).width,c=f-i/2;for(let e=.8;e>=.4;e-=.05){const n=g*e,o=u.midX+Math.cos(c)*n,r=u.midY+Math.sin(c)*n;if([[o-l/2-2,r],[o+l/2+2,r]].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),o=n<0?n+2*Math.PI:n;return e<g-2&&o>f-i&&o<f}))){t.fillText(a,o,r);break}}}}}},4139:(t,e,n)=>{"use strict";n.d(e,{$2:()=>i,To:()=>l,V5:()=>d,gp:()=>r,i6:()=>o,rg:()=>u,uF:()=>s,wf:()=>c,zW:()=>f});var i,o,r,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",t.TOTAL_COUNT="∑"}(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"}(o||(o={})),function(t){t.MONOMER="monomer",t.POSITION="pos",t.SEPARATOR="separator",t.ALPHABET="alphabet",t.FILTER="filter",t.SAR_MODE="sarMode",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"}(r||(r={})),function(t){t.MONOMER="Monomer",t.MACROMOLECULE_DIFFERENCE="MacromoleculeDifference"}(s||(s={}));const l="ColumnName";var u,c,h;!function(t){t.NONE="none",t.LG="lg",t.MINUS_LG="-lg"}(u||(u={})),function(t){t.HIGH="High",t.LOW="Low"}(c||(c={})),function(t){t.LST="lst-",t.MP="mp-",t.MPR="mpr-",t.WL="wl-"}(h||(h={}));const d=Object.values(a.AGG).filter((t=>![a.AGG.FIRST,a.AGG.KEY,a.AGG.PIVOT,a.AGG.SELECTED_ROWS_COUNT].includes(t))),f={[a.AGG.TOTAL_COUNT]:"totalCount",[a.AGG.VALUE_COUNT]:"valueCount",[a.AGG.UNIQUE_COUNT]:"uniqueCount",[a.AGG.MISSING_VALUE_COUNT]:"missingValueCount",[a.AGG.MIN]:"min",[a.AGG.MAX]:"max",[a.AGG.SUM]:"sum",[a.AGG.MED]:"med",[a.AGG.AVG]:"avg",[a.AGG.STDEV]:"stdev",[a.AGG.VARIANCE]:"variance",[a.AGG.SKEW]:"skew",[a.AGG.KURT]:"kurt",[a.AGG.Q1]:"q1",[a.AGG.Q2]:"q2",[a.AGG.Q3]:"q3"}},8608:(t,e,n)=>{"use strict";n.d(e,{$s:()=>_,AN:()=>i,AY:()=>d,B2:()=>x,BE:()=>w,BX:()=>O,CD:()=>A,F2:()=>g,FZ:()=>v,Lv:()=>I,Y1:()=>f,Z7:()=>C,ZR:()=>E,dl:()=>T,eY:()=>p,qx:()=>m,sg:()=>M,vW:()=>S,vY:()=>b,zm:()=>N,zz:()=>y});var i,o=n(7389),r=n(6082),s=n(4328),a=n(4139),l=n(8774),u=n(144),c=n.n(u),h=function(t,e,n,i){return new(n||(n=Promise))((function(o,r){function s(t){try{l(i.next(t))}catch(t){r(t)}}function a(t){try{l(i.throw(t))}catch(t){r(t)}}function l(t){var e;t.done?o(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 d(t){var e;return null!==(e=t.getTag(a.gp.SEPARATOR))&&void 0!==e?e:""}function f(t,e=a.rg.NONE){let n=t=>t;switch(e){case a.rg.NONE:break;case a.rg.LG:n=t=>Math.log10(t);break;case a.rg.MINUS_LG:n=t=>-Math.log10(t);break;default:throw new Error(`ScalingError: method \`${e}\` is not available.`)}const i=t.getRawData(),o=r.Column.float(a.$2.ACTIVITY,t.length).init((t=>{const e=i[t];return e===r.FLOAT_NULL||e===r.INT_NULL?e:n(e)}));return o.setTag(a.gp.ANALYSIS_COL,"true"),o.setTag(r.TAGS.FORMULA,e),o}function m(t){var e,n,i,o;const r=t.columns.bySemTypeAll(a.uF.MONOMER),s={},l=t.filter.clone().and(t.selection).getSelectedIndexes();for(const t of l)for(const a of r){const r=a.get(t);r&&(null!==(e=s[i=a.name])&&void 0!==e||(s[i]={}),null!==(n=(o=s[a.name])[r])&&void 0!==n||(o[r]=0),s[a.name][r]+=1)}return s}function p(t){return{name:t.name,cat:t.categories,rawData:t.getRawData()}}function g(t,e,n={}){var i;const s=[],l=t.dataFrame.getCol(a.$2.SPLIT_COL).categories;for(let t=0;t<l.length;++t){if(!l[t])continue;const e=r.Color.toHtml(r.Color.categoricalPalette[t%r.Color.categoricalPalette.length]),a=o.label(null!==(i=n[l[t]])&&void 0!==i?i:l[t],{style:{color:e}});s.push(a)}const u=o.divV([o.divV(s),t.root,o.tableFromMap(e)]);return t.root.style.maxHeight="75px",u}function v(t,e,n){const o=n.filter,s=e.clone().and(o),l=t.length,u=t.getRawData(),c=o.trueCount,h=new Float32Array(c+s.trueCount),d=new Array(h.length);for(let t=0,e=0,n=0;t<l;++t){if(!o.get(t))continue;const r=s.get(t);h[e]=u[t],d[e]=r?i.SELECTION:i.ALL,e++,r&&(h[c+n]=u[t],d[c+n]=i.ALL,++n)}const f=r.Column.fromStrings(a.$2.SPLIT_COL,d),m=[i.ALL,i.SELECTION];return f.setCategoryOrder(m),f.meta.colors.setCategorical(),r.DataFrame.fromColumns([r.Column.fromFloat32Array(a.$2.ACTIVITY,h),f])}function C(t,e,n){t.dataFrame||r.DataFrame.fromColumns([t]);const i=t.dataFrame.filter,o=t.getRawData(),s=Array.from(new Set(e.keys())).map((t=>Number(t))).filter((t=>i.get(t))),l=new Set;for(const t of e.values())for(const e of t)l.add(e);const u=Array.from(l).filter((t=>i.get(t))),c=s.length+u.length,h=new Array(c),d=new Float32Array(c);for(let t=0;t<s.length;++t){const e=s[t];d[t]=o[e],h[t]=n}for(let t=0;t<u.length;++t){const e=u[t];d[s.length+t]=o[e],h[s.length+t]="Mutated"}const f=r.Column.fromStrings(a.$2.SPLIT_COL,h),m=[n,"Mutated"];return f.setCategoryOrder(m),f.meta.colors.setCategorical(),r.DataFrame.fromColumns([r.Column.fromFloat32Array(a.$2.ACTIVITY,d),f])}function y(t){const e=o.iconFA("expand-alt",(()=>{const e=t.dataFrame.plot.grid();b(e,!1),e.root.style.height="100%";const n=o.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 w(t,e,n,i){const r=o.iconFA("expand-alt",(()=>{const e=i(),n=o.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");r.style.marginLeft="auto",r.style.marginRight="15px",n.addEventListener("mouseenter",(()=>{r.style.visibility="visible"})),n.addEventListener("mouseleave",(()=>{r.style.visibility="hidden"})),e.appendChild(r)}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 A(t){for(const e of Object.values(t))if(0!==e.length)return!1;return!0}function S(t,e,n){const i=t[e.positionOrClusterType],o=i.indexOf(e.monomerOrCluster);if(n.shiftPressed&&n.ctrlPressed)-1!==o&&i.splice(o,1);else if(n.ctrlPressed)-1===o?i.push(e.monomerOrCluster):i.splice(o,1);else if(n.shiftPressed)-1===o&&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 T(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,e){return t.sequenceColumnName===e.sequenceColumnName&&t.activityColumnName===e.activityColumnName&&t.activityScaling===e.activityScaling}function N(t,e,n,i){const o=Object.entries(n),r=i?Object.entries(i).filter((t=>!e.includes(t[0])||n[t[0]]!==t[1])):[];return o.concat(r).filter((e=>t.columns.contains(e[0])&&t.col(e[0]).matches("numerical")))}function x(t,e=2){return t.columns.bySemTypeAll(r.SEMTYPE.MACROMOLECULE).length>0&&c()(t.columns.numerical).toArray().length>0&&t.rowCount>=e}function M(t,e=500){let n;return(...i)=>h(this,void 0,void 0,(function*(){return new Promise((o=>{clearTimeout(n),n=setTimeout((()=>o(t(...i))),e)}))}))}function I(){return"isInDemo"in s.shell&&!!s.shell.isInDemo}function O(t){return{set:function(e,n){return t[e]=n,this}}}!function(t){t.SELECTION="Selection",t.ALL="All",t.PEPTIDES_SELECTION="Peptides selection"}(i||(i={}))},7471:(t,e,n)=>{"use strict";n.d(e,{a:()=>i});class i{constructor(){const t=navigator.hardwareConcurrency;this._workerCount=Math.max(t-2,1),this._workers=new Array(this._workerCount).fill(null).map((()=>new Worker(new URL(n.p+n.u(216),n.b))))}calc(t,e){return n=this,i=arguments,r=function*(t,e,n={}){const i=new Map;try{const o=t.length,r=new Array(this._workerCount),s=o*(o-1)/2;this._workerCount=Math.min(this._workerCount,s);const a=s/this._workerCount;e.forEach((t=>{var e;t.cat=null===(e=t.cat)||void 0===e?void 0:e.slice()}));for(let i=0;i<this._workerCount;i++)r[i]=new Promise(((o,r)=>{const l=Math.floor(i*a),u=i===this._workerCount-1?s:Math.floor((i+1)*a);this._workers[i].postMessage({startIdx:l,endIdx:u,activityArray:t,monomerInfoArray:e,settings:n}),this._workers[i].onmessage=({data:{pos:t,seq1Idxs:e,seq2Idxs:n,error:s}})=>{var a;s?(null===(a=this._workers[i])||void 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0!==c||(r.isMutationCliffs=!1),null!==(h=r.isMostPotentResidues)&&void 0!==h||(r.isMostPotentResidues=!1),null!==(d=r.additionalStats)&&void 0!==d||(r.additionalStats={}),r.cliffStats&&r.isMutationCliffs&&r.cliffIndexes){const u=null===(g=null===(p=r.cliffStats)||void 0===p?void 0:p.get(r.monomerPosition.monomerOrCluster))||void 0===g?void 0:g.get(r.monomerPosition.positionOrClusterType);if(!u)return null;const c=o.BitSet.fromBytes(u.mask.buffer.buffer,e.length);c.and(t.filter);const h=(0,s.M1)((0,a.Z7)(e,r.cliffIndexes,r.monomerPosition.monomerOrCluster),!0),d="MP in cliffs count",f=(0,s.QD)(u,{countName:d});r.fromViewer&&(f["Mean difference"]=`${f["Mean difference"]} (Color)`,f[d]&&(f[d]=`${f[d]} (Size)`),r.additionalStats["Unique count"]=c.trueCount.toString());const m=null!==(v=r.aggrColValues)&&void 0!==v?v:(0,l.I_)(t,n,{mask:c}),C=Object.assign(Object.assign(Object.assign({},r.additionalStats),f),m),y=(0,a.F2)(h,C);return i.tooltip.show(y,r.x,r.y),y}{const 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(size)":""}`,d["p-value"]&&(d["p-value"]=`${d["p-value"]}${r.isMostPotentResidues?" 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a{constructor(t){this.distanceF=i.Z.NEEDLEMANN_WUNSCH,this.gapOpen=1.5,this.gapExtend=.2,this.clusterEmbeddings=!0,this.epsilon=.01,this.minPts=4,this.fingerprintType="Morgan",this.clusterEmbeddings=!!t}}},5480:(t,e,n)=>{"use strict";n.d(e,{W:()=>S,s:()=>E});var i=n(7389),o=n(4328),r=n(6082),s=n(7233),a=n.n(s),l=n(9499),u=n(4139),c=n(3163),h=n(4326),d=n(5070),f=n(144),m=n.n(f),p=n(7654),g=n(8608),v=n(8774),C=n(3262),y=n(1458),w=n(3077),b=n(726);const A=(t,e)=>`${t}(${e})`;var S,T;!function(t){t.ORIGINAL="original",t.CUSTOM="custom"}(S||(S={})),function(t){t.GENERAL="General",t.STYLE="WebLogo",t.AGGREGATION="Aggregation"}(T||(T={}));class E extends r.JsViewer{constructor(){super(),this.bitsets=[],this.keyPress=!1,this.currentRowIndex=null,this._scaledActivityColumn=null,this._webLogoCacheGeneration=0,this._viewerGrid=null,this._clusterStats=null,this._clusterSelection=null,this._logoSummaryTable=null,this._positionColumns=null,this.root.classList.add("peptides-viewer-show-title"),this.sequenceColumnName=this.column("sequence",{category:T.GENERAL,nullable:!1}),this.clustersColumnName=this.column("clusters",{category:T.GENERAL,nullable:!1,columnTypeFilter:r.TYPE.CATEGORICAL}),this.activityColumnName=this.column("activity",{category:T.GENERAL,nullable:!1,columnTypeFilter:r.TYPE.NUMERICAL}),this.activityScaling=this.string("activityScaling",u.rg.NONE,{category:T.GENERAL,choices:Object.values(u.rg)}),this.webLogoMode=this.string("webLogoMode",h.fH.Entropy,{choices:[h.fH.full,h.fH.Entropy],category:T.STYLE}),this.membersRatioThreshold=this.float("membersRatioThreshold",.1,{min:0,max:1,category:T.STYLE});const t=[r.AGG.KEY,r.AGG.PIVOT,r.AGG.MISSING_VALUE_COUNT,r.AGG.SKEW,r.AGG.KURT,r.AGG.SELECTED_ROWS_COUNT],e=Object.values(r.AGG).filter((e=>!t.includes(e)));this.webLogoAggregationType=this.string("webLogoAggregationType",r.AGG.TOTAL_COUNT,{category:T.STYLE,choices:e,description:"Aggregation method for WebLogo position heights"}),this.webLogoAggregationColumnName=this.column("webLogoAggregationColumnName",{defaultValue:null,category:T.STYLE,nullable:!0,columnTypeFilter:r.TYPE.NUMERICAL,description:`Column with values to aggregate for WebLogo position heights.\n Used if aggregation type is not '${r.AGG.TOTAL_COUNT}'.`}),this.columns=this.columnList("columns",[],{category:T.AGGREGATION}),this.aggregation=this.string("aggregation",r.AGG.AVG,{category:T.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,y.eW)(this.dataFrame,this.clustersColumnName,this.customClusters.toArray(),this.getScaledActivityColumn())),this._clusterStats}get clusterSelection(){var t;return null!==(t=this._clusterSelection)&&void 0!==t||(this._clusterSelection=this.initClusterSelection({notify:!1})),this._clusterSelection}set clusterSelection(t){this._clusterSelection=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 o=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=o(l.q.SEQUENCE_VARIABILITY_MAP))&&void 0!==n?n:o(l.q.MOST_POTENT_RESIDUES))&&void 0!==i?i:(0,w.R)(this.dataFrame.getCol(this.sequenceColumnName),b.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,g.Y1)(this.dataFrame.getCol(this.activityColumnName),this.activityScaling)),t?r.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,i,s,a,l,c,h,d,f,p,v;if(super.onTableAttached(),(0,g.B2)(this.dataFrame)){const o=null===(t=m()(this.dataFrame.columns.numerical).filter((t=>{var e;return null===(e=t.name)||void 0===e?void 0:e.includes("activ")})).take(1).toArray()[0])||void 0===t?void 0:t.name,g=null!=o?o:null===(n=null===(e=m()(this.dataFrame.columns.numerical).take(1).toArray())||void 0===e?void 0:e[0])||void 0===n?void 0:n.name,C=this.dataFrame.columns.bySemType(r.SEMTYPE.MACROMOLECULE);C&&(null===(i=this.getProperty(`sequence${u.To}`))||void 0===i||i.set(this,C.name)),g&&(null===(s=this.getProperty(`activity${u.To}`))||void 0===s||s.set(this,g),null===(a=this.getProperty("webLogoAggregationColumnName"))||void 0===a||a.set(this,g));const y=null===(h=null===(c=null===(l=m()(this.dataFrame.columns).filter((t=>{var e;return t.isCategorical&&(null===(e=t.name)||void 0===e?void 0:e.toLowerCase().includes("cluster"))&&t.name!=(null==C?void 0:C.name)&&t.type!==r.COLUMN_TYPE.BOOL})))||void 0===l?void 0:l.take(1))||void 0===c?void 0:c.toArray())||void 0===h?void 0:h[0],w=null!=y?y:null===(p=null===(f=null===(d=m()(this.dataFrame.columns.categorical).filter((t=>t.name!=(null==C?void 0:C.name)&&t.categories.length<=50&&t.type!==r.COLUMN_TYPE.BOOL)))||void 0===d?void 0:d.take(1))||void 0===f?void 0:f.toArray())||void 0===p?void 0:p[0];w&&(null===(v=this.getProperty(`clusters${u.To}`))||void 0===v||v.set(this,w.name))}else{const t="PeptidesError: dataframe is missing Macromolecule or numeric columns";o.log.error(t),o.shell.warning(t)}this.render()}detach(){this.subs.forEach((t=>t.unsubscribe()))}render(){if(a()(this.root).empty(),null==this.clustersColumnName||null==this.sequenceColumnName||null==this.activityColumnName)return void this.root.appendChild(i.divText("Please, select a sequence, cluster and activity columns in the viewer properties"));if(!this.logoSummaryTable.filter.anyTrue){const t=i.divText("No clusters to satisfy the threshold. Please, lower the threshold in viewer proeperties to include clusters");return void this.root.appendChild(i.divV([t]))}const t=i.iconFA("expand-alt",(()=>{const t=i.dialog("Logo Summary Table");t.add(this.viewerGrid.root),t.onCancel((()=>this.render())),t.showModal(!0),this.viewerGrid.invalidate()}),"Show Logo Summary Table in full screen");a()(t).addClass("pep-help-icon"),this.viewerGrid.root.style.width="auto",this.viewerGrid.root.style.height="auto",this.viewerGrid.root.style.overflow="hidden",this.root.appendChild(i.divV([i.divH([t],{style:{alignSelf:"center",lineHeight:"normal"}}),this.viewerGrid.root])),this.viewerGrid.invalidate()}onPropertyChanged(t){super.onPropertyChanged(t);let e=!1;switch(t.name){case"membersRatioThreshold":this.logoSummaryTable.filter.anyTrue||(e=!0),this.updateFilter();break;case`sequence${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}`:this.webLogoAggregationColumnName=this.activityColumnName;case"activityScaling":case`webLogoAggregationColumnName${u.To}`:case"webLogoAggregationType":this._webLogoCacheGeneration++,this._scaledActivityColumn=null,this._viewerGrid=null,this._clusterStats=null,this._logoSummaryTable=null,e=!0;break;case"columns":case"aggregation":this._viewerGrid=null,this._logoSummaryTable=null,e=!0;break;case"webLogoMode":this.viewerGrid.invalidate()}e&&this.render()}initClusterSelection(t={}){var e;null!==(e=t.notify)&&void 0!==e||(t.notify=!0);const n={};return n[S.ORIGINAL]=[],n[S.CUSTOM]=[],t.notify?this.clusterSelection=n:this._clusterSelection=n,this.clusterSelection}getTotalViewerAggColumns(){var t,e;const n=this.getAggregationColumns();return(0,g.zm)(this.model.df,this.columns,n,null===(e=null===(t=this.model)||void 0===t?void 0:t.settings)||void 0===e?void 0:e.columns)}getStringAggregatedColumns(){return this.columns.filter((t=>this.model.df.columns.contains(t)&&this.model.df.col(t).matches("categorical"))).map((t=>`dist(${t})`))}getNeededDfClone(){var t,e;const n=[this.clustersColumnName,this.sequenceColumnName,this.activityColumnName,...(null!==(t=this.getTotalViewerAggColumns())&&void 0!==t?t:[]).map((([t,e])=>t)),...(null!==(e=this.getStringAggregatedColumns())&&void 0!==e?e:[]).map((t=>t.substring(5,t.length-1)))];this.webLogoAggregationColumnName&&n.push(this.webLogoAggregationColumnName);const i=Array.from(new Set(n)).filter((t=>this.dataFrame.columns.contains(t)));return this.dataFrame.clone(this.dataFrame.filter,i)}createLogoSummaryTable(){var t,e,n;const i=this.clustersColumnName,o=this.dataFrame.filter.anyFalse,s=o?this.getNeededDfClone():this.dataFrame,a=s.columns,l=s.rowCount,c=this.getScaledActivityColumn(o).getRawData(),h=s.getCol(i),f=h.getRawData(),p=h.categories,g={};g[u.gp.CUSTOM_CLUSTER]="1";const C=m()(a.byTags(g)).filter((t=>t.max>0)).toArray(),y=r.DataFrame.create(C.length),w=y.columns,b=w.addNewString(u.i6.CLUSTER),T=w.addNewInt(u.i6.MEMBERS).getRawData(),E=w.addNewString(u.i6.WEB_LOGO),_=w.addNewString(u.i6.DISTRIBUTION),N=w.addNewFloat(u.i6.MEAN_DIFFERENCE).getRawData(),x=w.addNewFloat(u.i6.P_VALUE).getRawData(),M=w.addNewFloat(u.i6.RATIO).getRawData();let I=s.groupBy([i]);const O=this.getTotalViewerAggColumns(),L=this.getStringAggregatedColumns(),P=L.map((t=>w.addNewString(t))),R=O.map((([t,e])=>A(e,t))),k=new Array(R.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,R[t]);const i=w.addNewFloat(R[t]);k[t]=i.getRawData()}const F=new Array(C.length);for(let e=0;e<C.length;++e){const n=C[e];b.set(e,n.name);const i=v.A.fromUint32Array(l,n.getRawData());if(i.allFalse)continue;const a=r.BitSet.fromBytes(i.buffer.buffer,l),u=o?(0,d.GT)(c,i):this.clusterStats[S.CUSTOM][n.name];T[e]=u.count,F[e]=a,N[e]=u.meanDifference,x[e]=null!==(t=u.pValue)&&void 0!==t?t:r.FLOAT_NULL,M[e]=u.ratio;for(let t=0;t<R.length;++t){const[n,i]=V[t];k[t][e]=(0,d.lh)(n,i,a)}for(let t=R.length;t<k.length;++t){const n=L[t-R.length];P[t-R.length].set(e,(0,d.J1)(s,n,a))}}E.setTag(r.TAGS.CELL_RENDERER,"html"),_.setTag(r.TAGS.CELL_RENDERER,"html");const D=I.aggregate(),G=D.rowCount,U=D.columns;let q=D.getCol(i);q.name=u.i6.CLUSTER,q.type!==r.COLUMN_TYPE.STRING&&(D.columns.replace(q,q.convertTo(r.COLUMN_TYPE.STRING)),q=D.getCol(q.name));const B=q.categories,H=U.addNewInt(u.i6.MEMBERS).getRawData(),Y=U.addNewString(u.i6.WEB_LOGO),j=U.addNewString(u.i6.DISTRIBUTION),W=U.addNewFloat(u.i6.MEAN_DIFFERENCE).getRawData(),$=U.addNewFloat(u.i6.P_VALUE).getRawData(),z=U.addNewFloat(u.i6.RATIO).getRawData(),K=L.map((t=>U.addNewString(t))),Z=new Array(G),Q=Array.from({length:G},(()=>new v.A(l,!1)));for(let t=0;t<l;++t){const n=p[f[t]];null===(e=Q[B.indexOf(n)])||void 0===e||e.setTrue(t)}for(let t=0;t<G;++t){const e=Q[t];if(e.allFalse)continue;const i=r.BitSet.fromBytes(e.buffer.buffer,l),a=o?(0,d.GT)(c,e):this.clusterStats[S.ORIGINAL][B[t]];for(let e=0;e<L.length;++e){const n=L[e];K[e].set(t,(0,d.J1)(s,n,i))}H[t]=a.count,Z[t]=i,W[t]=a.meanDifference,$[t]=null!==(n=a.pValue)&&void 0!==n?n:r.FLOAT_NULL,z[t]=a.ratio}Y.setTag(r.TAGS.CELL_RENDERER,"html"),j.setTag(r.TAGS.CELL_RENDERER,"html");const X=D.append(y);return this.bitsets=Z.concat(F),L.forEach((t=>X.col(t).semType="lst-pie-chart")),X}createLogoSummaryTableGrid(){const t=this.dataFrame.filter.anyFalse,e=t?this.getNeededDfClone():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 o=new r.LruCache,s=new Map;let d=null;const f=new r.LruCache,m=this.positionColumns.length,p=i.columns.byName(u.i6.WEB_LOGO);p.cellType="html",p.width=350;const v=this.getScaledActivityColumn(t),C=e.getCol(this.sequenceColumnName);i.onCellRender.subscribe((t=>{var e,n,l;const p=t.cell,y=p.tableRowIndex;if(!p.isTableCell||null==y||-1===y)return;const w=t.g,b=t.bounds;w.save(),w.beginPath(),w.rect(b.x,b.y,b.width,b.height),w.clip();try{const A=Math.max(p.bounds.height-2,0),S=this.bitsets[y];if((null===(e=p.tableColumn)||void 0===e?void 0:e.name)===u.i6.CLUSTER)c.k8(w,p.cell.value,this.clusterSelection,b),t.preventDefault();else if((null===(n=p.tableColumn)||void 0===n?void 0:n.name)===u.i6.WEB_LOGO){const e=`${y}_${this.webLogoAggregationColumnName||"count"}_${this.webLogoAggregationType}_${this._webLogoCacheGeneration}`,n=o.get(e);if(!0===s.get(e))return void t.preventDefault();const l=Math.floor((p.bounds.width-2-4*(m-1))/m);if(void 0!==n){const e=n.getProperties();for(const t of e)"positionHeight"===t.name&&t.get(n)!==this.webLogoMode?t.set(n,this.webLogoMode):"positionWidth"===t.name&&t.get(n)!==l?t.set(n,l):"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`,p.element=n.root,t.preventDefault()}else{const n=[C];if(this.webLogoAggregationType!==r.AGG.TOTAL_COUNT&&this.webLogoAggregationColumnName){const t=this.dataFrame.columns.byName(this.webLogoAggregationColumnName);t&&n.push(t)}const a=r.DataFrame.fromColumns(n);a.filter.copyFrom(S),s.set(e,!0),a.plot.fromType("WebLogo",{valueColumnName:this.webLogoAggregationColumnName,valueAggrType:this.webLogoAggregationType,positionHeight:this.webLogoMode,horizontalAlignment:h.P4.LEFT,maxHeight:1e3,minHeight:A,positionWidth:l,showPositionLabels:!1}).then((t=>{o.set(e,t),s.delete(e),d&&clearTimeout(d),d=setTimeout((()=>i.invalidate()),200)})),t.preventDefault()}}else if((null===(l=p.tableColumn)||void 0===l?void 0:l.name)===u.i6.DISTRIBUTION){let e=f.get(y);void 0===e&&(v.dataFrame||r.DataFrame.fromColumns([v]),e=(0,g.FZ)(v,S,v.dataFrame).plot.histogram({filteringEnabled:!1,valueColumnName:v.name,splitColumnName:u.$2.SPLIT_COL,legendVisibility:"Never",showXAxis:!1,showColumnSelector:!1,showRangeSlider:!1,showBinSelector:!1,backColor:r.Color.toHtml(r.Color.white),xAxisHeight:1,showSplitSelector:!1}),e.root.style.width="auto",f.set(y,e)),e.root.style.height=`${A}px`,p.element=e.root,t.preventDefault()}}finally{w.restore()}})),i.root.addEventListener("mouseleave",(t=>this.model.unhighlight())),r.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 o=this.getCluster(n);this.modifyClusterSelection(o,{shiftPressed:t.shiftKey,ctrlPressed:t.ctrlKey}),i.invalidate()})),i.onCellTooltip(((t,e,n)=>{var i;if(!t.isTableCell)return this.model.unhighlight(),!0;const o=this.getCluster(t);return this.highlightCluster(o),(null===(i=t.tableColumn)||void 0===i?void 0:i.name)===u.i6.CLUSTER&&this.showTooltip(o,e,n),!0}));const y=i.props;return y.allowEdit=!1,y.allowRowSelection=!1,y.allowBlockSelection=!1,y.allowColSelection=!1,y.showCurrentRowIndicator=!1,y.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,o=i.indexOf("-1"),r=t.getRawData();let s=0;r.forEach(((t,e)=>{"-1"!==i[n[e]]&&(s=Math.max(s,r[e]))}));const a=Math.ceil(s*this.membersRatioThreshold);this.logoSummaryTable.filter.init((t=>r[t]>a&&(-1===o||"-1"!==i[n[t]])))}clusterFromSelection(){const t=this.model.getVisibleSelection(),e=this.logoSummaryTable.columns,n=e.length,i=new Array(e.length),o=this.getScaledActivityColumn(),r=(0,d.pY)(t),s=(0,d.GT)(o.getRawData(),r,(0,d.pY)(this.dataFrame.filter));this.bitsets.push(t.clone());const a=this.dataFrame.columns.getUnusedName("New Cluster"),l={},c={},h=this.getTotalViewerAggColumns(),f=this.getStringAggregatedColumns();for(const[e,n]of h){const i=A(n,e),o=this.dataFrame.getCol(e);l[i]=(0,d.lh)(o,n,t)}for(const e of f)c[e]=(0,d.J1)(this.dataFrame,e,t);for(let o=0;o<n;++o){const n=e.byIndex(o);i[o]=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[o]&&C._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 o.shell.warning("No custom clusters selected to be removed");const e=this.logoSummaryTable.rows,n=this.logoSummaryTable.getCol(u.i6.CLUSTER),i=n.categories,r=this.dataFrame.columns;for(const n of t){t.splice(t.indexOf(n),1),r.remove(n),delete this.clusterStats[S.CUSTOM][n];const o=i.indexOf(n);e.removeAt(o),this.bitsets.splice(o,1)}n.compact(),this.clusterSelection[S.CUSTOM]=t,this.render()}addNewCluster(t){const e=r.Column.fromBitSet(t,this.model.getVisibleSelection());e.setTag(u.gp.CUSTOM_CLUSTER,"1"),e.setTag(u.gp.ANALYSIS_COL,"true"),this.dataFrame.columns.add(e),this.model.analysisView.grid.col(e.name).visible=!1}modifyClusterSelection(t,e={shiftPressed:!1,ctrlPressed:!1},n=!0){n?this.clusterSelection=(0,g.vW)(this.clusterSelection,t,e):this._clusterSelection=(0,g.vW)(this.clusterSelection,t,e)}showTooltip(t,e,n){const o=this.dataFrame.filter,s=o.anyFalse?this.getNeededDfClone():this.dataFrame,a=s.rowCount,l=new v.A(a,!1),u=this.getScaledActivityColumn(o.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 h=o.anyFalse?(0,d.GT)(c,l):this.clusterStats[t.positionOrClusterType][t.monomerOrCluster];if(!h.count)return null;const f=r.BitSet.fromBytes(l.buffer.buffer,a);u.dataFrame||r.DataFrame.fromColumns([u]);const m=(0,g.FZ)(u,f,u.dataFrame),C=(0,p.M1)(m,!0),y=(0,p.QD)(h),w=(0,d.I_)(this.dataFrame,this.getTotalViewerAggColumns(),{filterDf:!0,mask:f}),b=Object.assign(Object.assign({},y),w),A=(0,g.F2)(C,b);return i.tooltip.show(A,e,n),A}createWebLogoDf(t,e){const n=r.DataFrame.fromColumns([t]);return n.filter.copyFrom(e),n}}},3541:(t,e,n)=>{"use strict";n.d(e,{J:()=>x,UJ:()=>M});var i,o,r,s,a=n(4328),l=n(7389),u=n(6082),c=n(7233),h=n.n(c),d=n(4139),f=n(3163),m=n(9499),p=n(144),g=n.n(p),v=n(5070),C=n(912),y=n(1458),w=n(8608),b=n(3077),A=n(439),S=n(2003),T=n(4971),E=n(726),_=function(t,e,n,i){return new(n||(n=Promise))((function(o,r){function s(t){try{l(i.next(t))}catch(t){r(t)}}function a(t){try{l(i.throw(t))}catch(t){r(t)}}function l(t){var e;t.done?o(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",t.DATA_SOURCE="dataSource"}(o||(o={})),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",t.SHOW_FILTER_CONTROLS="showFilterControls",t.SHOW_TOTAL_COUNT_COLUMN="showTotalCountColumn"}(r||(r={})),function(t){t.GENERAL="General",t.INVARIANT_MAP="Invariant Map",t.MUTATION_CLIFFS="Mutation Cliffs",t.AGGREGATION="Aggregation"}(s||(s={}));class N extends u.JsViewer{constructor(){super(),this.keyPressed=!1,this._scaledActivityColumn=null,this.doRender=!0,this.dataSource="Filtered",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(o.SEQUENCE,{category:s.GENERAL,semType:u.SEMTYPE.MACROMOLECULE,nullable:!1}),this.dataSource=this.string(o.DATA_SOURCE,"Filtered",{category:s.GENERAL,choices:["All","Filtered"],nullable:!1,description:"Data source for calculations and rendering. Can be set to whole data set or filtered data only."}),this.activityColumnName=this.column(o.ACTIVITY,{category:s.GENERAL,nullable:!1,columnTypeFilter:"numerical"}),this.activityScaling=this.string(o.ACTIVITY_SCALING,d.rg.NONE,{category:s.GENERAL,choices:Object.values(d.rg),nullable:!1}),this.activityTarget=this.string(o.ACTIVITY_TARGET,d.wf.HIGH,{category:s.GENERAL,choices:Object.values(d.wf),nullable:!1}),this.targetColumnName=this.column(o.TARGET,{category:s.GENERAL,nullable:!0,columnTypeFilter:"categorical",userEditable:!1}),this.minActivityDelta=this.float(o.MIN_ACTIVITY_DELTA,0,{category:s.MUTATION_CLIFFS,min:0,max:100}),this.maxMutations=this.int(o.MAX_MUTATIONS,1,{category:s.MUTATION_CLIFFS,min:1,max:20}),this.columns=this.columnList(o.COLUMNS,[],{category:s.AGGREGATION}),this.aggregation=this.string(o.AGGREGATION,u.AGG.AVG,{category:s.AGGREGATION,choices:d.V5}),this.valueColumnName=this.column(o.VALUE_INVARIANT_MAP,{category:s.INVARIANT_MAP,userEditable:!0,nullable:!1,columnTypeFilter:"numerical"}),this.valueAggregation=this.string(o.AGGREGATION_INVARIANT_MAP_VALUE,u.AGG.TOTAL_COUNT,{category:s.INVARIANT_MAP,choices:d.V5,userEditable:!0,nullable:!1}),this.mutationCliffsDebouncer=(0,w.sg)(((t,e,n)=>_(this,void 0,void 0,(function*(){return yield(0,y.uz)(t,e,n)})))),this.root.classList.add("peptides-viewer-show-title")}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 x?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,b.R)(this.dataFrame.getCol(this.sequenceColumnName),E.Z.getSeqHelper()).columns.toList()),this._positionColumns}get monomerPositionStats(){var t;if(null!=this._monomerPositionStats)return this._monomerPositionStats;const e=t=>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 N&&t.dataSource===this.dataSource&&(t instanceof N&&this.valueColumnName==(null==t?void 0:t.valueColumnName)&&this.valueAggregation==(null==t?void 0:t.valueAggregation)||!(t instanceof N)&&(!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 x?this._monomerPositionStats=n(m.q.MOST_POTENT_RESIDUES):this instanceof M&&(this._monomerPositionStats=n(m.q.SEQUENCE_VARIABILITY_MAP));const i=this.dataFrame.col(this.valueColumnName),o=this.valueAggregation;return null!==(t=this._monomerPositionStats)&&void 0!==t||(this._monomerPositionStats=(0,y.Ej)(this.getScaledActivityColumn(),this.dataFrame.filter,this.positionColumns,{isFiltered:"Filtered"===this.dataSource&&this.dataFrame.filter.anyFalse,aggValue:o&&i?{col:i,type:o}: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===(null==i?void 0:i.activityColumnName)&&n.activityScaling===(null==i?void 0:i.activityScaling)&&n.minActivityDelta===(null==i?void 0:i.minActivityDelta)&&n.maxMutations===(null==i?void 0:i.maxMutations)&&(null==n?void 0:n.dataSource)===(null==i?void 0:i.dataSource)?e._mutationCliffs:null;var n,i};return this instanceof x?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,y.Lw)(this.mutationCliffs,t)}return this._mutationCliffStats}set cliffStats(t){this._mutationCliffStats=t,this.viewerGrid.invalidate()}get mutationCliffsSelection(){var t;return null!==(t=this._mutationCliffsSelection)&&void 0!==t||(this._mutationCliffsSelection=(0,w.ZR)(this.positionColumns)),this._mutationCliffsSelection}set mutationCliffsSelection(t){var e,n;this._mutationCliffsSelection=t,this.model.fireBitsetChanged(this instanceof x?m.q.SEQUENCE_VARIABILITY_MAP:m.q.MOST_POTENT_RESIDUES);const i=this.model.findViewer(m.q.SEQUENCE_VARIABILITY_MAP);null===(e=null==i?void 0:i.viewerGrid)||void 0===e||e.invalidate();const o=this.model.findViewer(m.q.MOST_POTENT_RESIDUES);null===(n=null==o?void 0:o.viewerGrid)||void 0===n||n.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,w.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,w.vW)(this.mutationCliffsSelection,t,e):this._mutationCliffsSelection=(0,w.vW)(this.mutationCliffsSelection,t,e)}modifyInvariantMapSelection(t,e={shiftPressed:!1,ctrlPressed:!1},n=!0){n?this.invariantMapSelection=(0,w.vW)(this.invariantMapSelection,t,e):this._invariantMapSelection=(0,w.vW)(this.invariantMapSelection,t,e)}get invariantMapSelection(){var t;return null!==(t=this._invariantMapSelection)&&void 0!==t||(this._invariantMapSelection=(0,w.ZR)(this.positionColumns)),this._invariantMapSelection}set invariantMapSelection(t){this._invariantMapSelection=t,this.model.fireBitsetChanged(m.q.SEQUENCE_VARIABILITY_MAP),this.model.analysisView.grid.invalidate()}onPropertyChanged(t){switch(super.onPropertyChanged(t),this.doRender=!0,t.name){case`${o.SEQUENCE}${d.To}`:this._positionColumns=null,this._monomerPositionStats=null,this._mutationCliffs=null,this._mutationCliffStats=null,this._mutationCliffsSelection=null,this._viewerGrid=null;break;case`${o.ACTIVITY}${d.To}`:case o.ACTIVITY_SCALING:this._monomerPositionStats=null,this._mutationCliffs=null,this._mutationCliffStats=null,this._mutationCliffsSelection=null,this._viewerGrid=null,this._scaledActivityColumn=null;break;case`${o.VALUE_INVARIANT_MAP}${d.To}`:case o.AGGREGATION_INVARIANT_MAP_VALUE:this._monomerPositionStats=null,this._viewerGrid=null,this._invariantMapSelection=null;break;case o.MIN_ACTIVITY_DELTA:case o.MAX_MUTATIONS:this._mutationCliffs=null,this._mutationCliffStats=null,this._mutationCliffsSelection=null,this.doRender=!1;break;case o.COLUMNS:case o.AGGREGATION:this instanceof M&&(this._viewerGrid=null);break;case o.ACTIVITY_TARGET:(this instanceof M||this instanceof x)&&(this._viewerGrid=null);break;case o.DATA_SOURCE:this.onFilterChanged(!1,!1),this.doRender=!0}null===this._mutationCliffs&&this.sequenceColumnName&&this.activityColumnName&&this.dataFrame&&this.calculateMutationCliffs().then((t=>{this.mutationCliffs=t.cliffs,this.cliffStats=t.cliffStats}))}getAggregationColumns(){return Object.fromEntries(this.columns.map((t=>[t,this.aggregation])).filter((([t,e])=>this.model.df.columns.contains(t)&&this.model.df.col(t).matches("numerical"))))}getTotalViewerAggColumns(){var t,e;const n=this.getAggregationColumns();return(0,w.zm)(this.model.df,this.columns,n,null===(e=null===(t=this.model)||void 0===t?void 0:t.settings)||void 0===e?void 0:e.columns)}createViewerGrid(){throw new Error("Not implemented")}detach(){this.subs.forEach((t=>t.unsubscribe()))}onTableAttached(){var t,e,n,i;if(super.onTableAttached(),(0,w.B2)(this.dataFrame)){null===(t=this.getProperty(`${o.SEQUENCE}${d.To}`))||void 0===t||t.set(this,this.dataFrame.columns.bySemType(u.SEMTYPE.MACROMOLECULE).name);const r=null===(e=g()(this.dataFrame.columns.numerical).find((t=>t.name.toLowerCase().includes("activity"))))||void 0===e?void 0:e.name;null===(n=this.getProperty(`${o.ACTIVITY}${d.To}`))||void 0===n||n.set(this,null!=r?r:g()(this.dataFrame.columns.numerical).next().value.name),null===(i=this.getProperty(`${o.VALUE_INVARIANT_MAP}${d.To}`))||void 0===i||i.set(this,null!=r?r:g()(this.dataFrame.columns.numerical).next().value.name),null===this.mutationCliffs&&this.sequenceColumnName&&this.activityColumnName&&this.calculateMutationCliffs().then((t=>{this.mutationCliffs=t.cliffs,this.cliffStats=t.cliffStats})),this.subs.push(a.events.onContextMenu.subscribe((t=>{if(!(t&&t.causedBy&&t.args&&t.args.menu&&t.causedBy.target&&t.causedBy.target instanceof HTMLElement&&this.root.contains(t.causedBy.target)))return;const e=t.args.menu;(0,T.pj)().then((t=>{const n=t.getMonomerLib(),i=n.getMonomerSymbolsByType("PEPTIDE").map((t=>n.getMonomer("PEPTIDE",t))).filter(Boolean).map((t=>{var e;return null!==(e=t.meta)&&void 0!==e?e:{}})),o=new Set;i.forEach((t=>Object.keys(t).forEach((t=>o.add(t))))),o.delete("colors"),e.group("Monomer Meta").items(Array.from(o),(t=>{this._monomerMetaColumns.has(t)?this._monomerMetaColumns.delete(t):this._monomerMetaColumns.add(t),this._viewerGrid=null,this.render()}),{isChecked:t=>this._monomerMetaColumns.has(t)})}))}))),this.subs.push(u.debounce(this.dataFrame.onFilterChanged,300).subscribe((()=>{"Filtered"===this.dataSource&&this.onFilterChanged(!0,!1)})))}else{const t="PeptidesError: dataframe is missing Macromolecule or numeric columns";a.log.error(t),a.shell.warning(t)}}onFilterChanged(t,e=!1){if(this._monomerPositionStats=null,this._invariantMapSelection=null,this._mutationCliffStats=null,this._mutationCliffsSelection=null,this._mutationCliffs=null,e)return;this._viewerGrid=null;const n=this.model.findViewer(m.q.MOST_POTENT_RESIDUES);!n||this instanceof M||"Filtered"!==n.dataSource||n.onFilterChanged(!1,!0),t&&this.render(),this.sequenceColumnName&&this.activityColumnName&&this.calculateMutationCliffs().then((t=>{this.mutationCliffs=t.cliffs,this.cliffStats=t.cliffStats}))}calculateMutationCliffs(){return _(this,void 0,void 0,(function*(){var t;const e=this.dataFrame.getCol(this.activityColumnName),n=this.positionColumns.map(w.eY),i="Filtered"===this.dataSource&&this.dataFrame.filter.anyFalse?this.dataFrame.filter:null,o={maxMutations:this.maxMutations,minActivityDelta:this.minActivityDelta,filter:null!==(t=null==i?void 0:i.getBuffer())&&void 0!==t?t:void 0},r=e.getRawData(),s=yield this.mutationCliffsDebouncer(r,n,o);return{cliffs:s,cliffStats:(0,y.Lw)(s,r)}}))}}class x extends N{constructor(){super(),this.currentGridCell=null,this.customColorRange=!1,this.minColorValue=0,this.maxColorValue=0,this.logScaleColor=!1,this.showFilterControls=!0,this.showTotalCountColumn=!1,this._showSearchInput=!1,this.colorColumnName=this.column(r.COLOR,{category:s.INVARIANT_MAP,nullable:!1,columnTypeFilter:"numerical"}),this.colorAggregation=this.string(r.COLOR_AGGREGATION,u.AGG.AVG,{category:s.INVARIANT_MAP,choices:d.V5}),this.lowerBoundColor=this.int(r.LOWER_BOUND_COLOR,4278190335,{category:s.INVARIANT_MAP,editor:"color"}),this.middleColor=this.int(r.MIDDLE_COLOR,4294967295,{category:s.INVARIANT_MAP,editor:"color"}),this.upperBoundColor=this.int(r.UPPER_BOUND_COLOR,4294901760,{category:s.INVARIANT_MAP,editor:"color"}),this.showTotalCountColumn=this.bool(r.SHOW_TOTAL_COUNT_COLUMN,!1,{category:s.GENERAL,description:"Show total monomer count column"}),this.logScaleColor=this.bool(r.LOG_SCALE_COLOR,!1,{category:s.INVARIANT_MAP}),this.customColorRange=this.bool(r.CUSTOM_COLOR_RANGE,!1,{category:s.INVARIANT_MAP}),this.minColorValue=this.float(r.MIN_COLOR_VALUE,0,{category:s.INVARIANT_MAP}),this.maxColorValue=this.float(r.MAX_COLOR_VALUE,0,{category:s.INVARIANT_MAP}),this.showFilterControls=this.bool(r.SHOW_FILTER_CONTROLS,!0,{category:s.GENERAL,description:"Show monomer search and target controls",userEditable:!1}),this.monomerSearchInput=l.input.string("Search",{value:"",nullable:!0,placeholder:"Search monomer",tooltipText:"Search for monomer by symbol. For multiple monomers use comma as a separator.",onValueChanged:()=>{var t,e,n;const i=()=>{var t,e,n;return null===(n=null===(e=null===(t=this._viewerGrid)||void 0===t?void 0:t.dataFrame)||void 0===e?void 0:e.filter)||void 0===n?void 0:n.setAll(!0)},o=null!==(n=null===(e=null===(t=this.monomerSearchInput.value)||void 0===t?void 0:t.trim())||void 0===e?void 0:e.toLowerCase())&&void 0!==n?n:"";if(!o||null==this._viewerGrid||null==this._viewerGrid.dataFrame)return void i();const r=this._viewerGrid.dataFrame.col(d.$2.MONOMER);if(null==r)return void i();const s=o.split(",").map((t=>t.trim())).filter((t=>!!t)),a=r.toList();this._viewerGrid.dataFrame.filter.init((t=>s.some((e=>a[t].toLowerCase().includes(e)))))}})}get name(){return m.q.SEQUENCE_VARIABILITY_MAP}get mode(){var t;return null!==(t=this.dataFrame.getTag(d.gp.MONOMER_POSITION_MODE))&&void 0!==t?t:i.MUTATION_CLIFFS}set mode(t){this.dataFrame.setTag(d.gp.MONOMER_POSITION_MODE,t),this.viewerGrid.invalidate()}onTableAttached(){var t;if(super.onTableAttached(),(0,w.B2)(this.dataFrame))null===(t=this.getProperty(`${r.COLOR}${d.To}`))||void 0===t||t.set(this,this.activityColumnName);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;switch(super.onPropertyChanged(t),t.name){case o.SEQUENCE:this._invariantMapSelection=null;break;case r.SHOW_TOTAL_COUNT_COLUMN:this._viewerGrid&&this._viewerGrid.columns.byName(d.$2.TOTAL_COUNT)&&(this._viewerGrid.columns.byName(d.$2.TOTAL_COUNT).visible=this.showTotalCountColumn,this.doRender=!1)}null===(e=this.positionColumns)||void 0===e||e.forEach((t=>{t.temp[d.gp.INVARIANT_MAP_COLOR_CACHE]=null})),this.doRender?this.render():this.viewerGrid.invalidate()}createMonomerPositionDf(){const t=new Set,e=this.positionColumns;for(const e of Object.keys(this.monomerPositionStats)){if("general"===e)continue;const n=this.monomerPositionStats[e];for(const e of Object.keys(n))"general"!==e&&t.add(e)}const n=Array.from(t),i=u.Column.fromStrings(d.$2.MONOMER,n),o=u.DataFrame.fromColumns([i]),r=(0,T.pj)().then((t=>{const e=t.getMonomerLib();return e?n.map((t=>{var n,i;return null!==(i=null===(n=e.getMonomer("PEPTIDE",t))||void 0===n?void 0:n.meta)&&void 0!==i?i:{}})):n.map((t=>({})))})),s=o.columns.addNewInt(d.$2.TOTAL_COUNT),a={},l=this.monomerPositionStats;for(const t of Object.keys(l)){if("general"===t)continue;const e=l[t];for(const t of Object.keys(e))"general"!==t&&(a[t]||(a[t]=0),a[t]+=e[t].count)}s.init((t=>{var e;return null!==(e=a[i.get(t)])&&void 0!==e?e:0})),this._monomerMetaColumns.forEach((t=>{const e=o.columns.addNewString(t);r.then((n=>{e.init((e=>{var i,o;return null!==(o=null===(i=n[e][t])||void 0===i?void 0:i.toString())&&void 0!==o?o:""}))}))})),o.name="SAR";for(const t of e)o.columns.addNewBool(t.name);return o}cacheInvariantMapColors(){if(this.colorColumnName&&this.dataFrame.col(this.colorColumnName)){const t=this.dataFrame.getCol(this.colorColumnName).getRawData();let e=9999999,n=-9999999;const i="Filtered"===this.dataSource&&this.dataFrame.filter.anyFalse?this.dataFrame.filter:null,o=null==i?t=>!0:t=>i.get(t);for(const i of this.positionColumns){i.temp[d.gp.INVARIANT_MAP_COLOR_CACHE]={};const r=i.temp[d.gp.INVARIANT_MAP_COLOR_CACHE],s=i.name,a=i.getRawData(),l=i.categories;if(!this.monomerPositionStats[s])continue;const c=this.monomerPositionStats[s];for(const s of Object.keys(c)){if("general"===s)continue;const c=[];for(let t=0;t<i.length;++t)l[a[t]]===s&&o(t)&&c.push(t);const h=u.Column.float("color",c.length).init((e=>t[c[e]])).aggregate(this.colorAggregation);r[s]=h,e=Math.min(e,h),n=Math.max(n,h)}i.temp[d.gp.INVARIANT_MAP_COLOR_CACHE]=r}const r=this.customColorRange&&null!=this.minColorValue&&null!=this.maxColorValue;let s=r?this.minColorValue:e,a=r?this.maxColorValue:n;const l=this.logScaleColor&&s>1e-30&&a>1e-30&&e>1e-30&&n>1e-30;l&&(s=Math.log(s),a=Math.log(a));for(const t of this.positionColumns){const i=t.temp[d.gp.INVARIANT_MAP_COLOR_CACHE];if(i){for(const t of Object.keys(i))this.activityTarget===d.wf.LOW&&(i[t]=a-i[t]+s),i[t]=u.Color.scaleColor(l?Math.log(i[t]):i[t],s,a,void 0,[this.lowerBoundColor,this.middleColor,this.upperBoundColor]);t.temp[d.gp.INVARIANT_MAP_COLOR_CACHE]=i,t.temp[d.gp.INVARIANT_MAP_COLOR_MIN_CACHE]=e,t.temp[d.gp.INVARIANT_MAP_COLOR_MAX_CACHE]=n}}}}createViewerGrid(){const t=this.createMonomerPositionDf(),e=t.plot.grid();e.sort([d.$2.MONOMER]);const n=this.positionColumns.map((t=>t.name));e.columns.setOrder([d.$2.TOTAL_COUNT,d.$2.MONOMER,...this._monomerMetaColumns,...n]);const o=e.columns.byName(d.$2.TOTAL_COUNT);this.showTotalCountColumn&&null!=o?o.visible=!0:null!=o&&(o.visible=!1);const r=t.getCol(d.$2.MONOMER);f.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 o,r,s,a,l,c,h;if(!t.isTableCell||!(null===(o=null==t?void 0:t.cell.column)||void 0===o?void 0:o.name)||this._monomerMetaColumns.has(t.cell.column.name)||t.cell.column.name===d.$2.TOTAL_COUNT)return this.model.unhighlight(),!0;const f=this.getMonomerPosition(t);(0,w.dl)(f,this.dataFrame,this.monomerPositionStats),this.model.isHighlighting=!0;const m=this.getTotalViewerAggColumns(),p={},g={};if(this.mode===i.INVARIANT_MAP)this.colorColumnName&&this.colorAggregation&&this.colorColumnName!==this.valueColumnName?(m.unshift([this.colorColumnName,this.colorAggregation]),p[`${this.colorAggregation}(${this.colorColumnName})`]=" (color)"):this.colorColumnName&&this.colorAggregation&&this.colorColumnName===this.valueColumnName&&(p["Mean activity"]=" (color)"),this.valueColumnName&&this.valueAggregation&&this.valueAggregation!==u.AGG.VALUE_COUNT&&this.valueAggregation!==u.AGG.TOTAL_COUNT&&m.unshift([this.valueColumnName,this.valueAggregation]);else{const t=null===(s=null===(r=this.mutationCliffs)||void 0===r?void 0:r.get(f.monomerOrCluster))||void 0===s?void 0:s.get(f.positionOrClusterType);if(t){let e=0;for(const n of t.values())e+=n.length;g["Pairs count"]=e.toString()}}return(0,C.D)(this.model.df,this.getScaledActivityColumn(),m,{fromViewer:!0,isMutationCliffs:this.mode===i.MUTATION_CLIFFS,monomerPosition:f,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:p,additionalStats:g,cliffIndexes:null===(h=null===(c=this.mutationCliffs)||void 0===c?void 0:c.get(f.monomerOrCluster))||void 0===h?void 0:h.get(f.positionOrClusterType)})})),e.root.addEventListener("mouseleave",(t=>this.model.unhighlight())),u.debounce(e.onCurrentCellChanged,500).subscribe((t=>{var n,o,r,s,a,l,c,h,f,p,g,v,C;try{if(!t||!t.dart||!(null===(o=null===(n=null==t?void 0:t.cell)||void 0===n?void 0:n.column)||void 0===o?void 0:o.name)||this._monomerMetaColumns.has(t.cell.column.name)||t.cell.column.name==d.$2.TOTAL_COUNT||!t.isTableCell)return;if(-1===t.gridRow&&(this.mode===i.INVARIANT_MAP?this._invariantMapSelection=(0,w.ZR)(this.positionColumns):this._mutationCliffsSelection=(0,w.ZR)(this.positionColumns),this.model.fireBitsetChanged(m.q.SEQUENCE_VARIABILITY_MAP),e.invalidate()),!this.keyPressed||t.cell.column.name===d.$2.MONOMER)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===(r=this.mutationCliffs)||void 0===r?void 0:r.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===(h=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===h?void 0:h.size)&&this.modifyMutationCliffsSelection(u,{shiftPressed:!0,ctrlPressed:!1},!0),e.invalidate(),setTimeout((()=>null==e?void 0:e.invalidate()),300)}catch(t){console.error(t)}finally{this.keyPressed=!1,(null===(f=t.tableColumn)||void 0===f?void 0:f.name)&&t.grid&&t.isTableCell&&(null===(p=null==t?void 0:t.cell)||void 0===p?void 0:p.column.name)!=d.$2.MONOMER&&!this._monomerMetaColumns.has(null===(v=null===(g=t.cell)||void 0===g?void 0:g.column)||void 0===v?void 0:v.name)&&(null===(C=t.cell)||void 0===C?void 0:C.column.name)!==d.$2.TOTAL_COUNT?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,w.ZR)(this.positionColumns):this._mutationCliffsSelection=(0,w.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 o,r,s,a,l,u;const c=e.hitTest(n.offsetX,n.offsetY);if(!(null==c?void 0:c.isTableCell)||(null===(o=null==c?void 0:c.tableColumn)||void 0===o?void 0:o.name)===d.$2.MONOMER||(null===(r=null==c?void 0:c.tableColumn)||void 0===r?void 0:r.name)&&this._monomerMetaColumns.has(c.tableColumn.name)||(null===(s=null==c?void 0:c.tableColumn)||void 0===s?void 0:s.name)===d.$2.TOTAL_COUNT)return;const h=this.getMonomerPosition(c);this.mode===i.INVARIANT_MAP?(this.modifyInvariantMapSelection(h,{shiftPressed:n.shiftKey,ctrlPressed:n.ctrlKey}),(0,w.CD)(this.invariantMapSelection)&&(t.currentRowIdx=-1)):(null===(u=null===(l=null===(a=this.mutationCliffs)||void 0===a?void 0:a.get(h.monomerOrCluster))||void 0===l?void 0:l.get(h.positionOrClusterType))||void 0===u?void 0:u.size)&&this.modifyMutationCliffsSelection(h,{shiftPressed:n.shiftKey,ctrlPressed:n.ctrlKey}),e.invalidate()})),O(e),e.props.showRowHeader=!0;const s=e.onAfterDrawContent.subscribe((()=>{const t=e.col(d.$2.MONOMER);if(40!==t.width){t.width=40;for(const t of n)e.col(t).width=40}else s.unsubscribe()}));return e}getMonomerPosition(t){return{monomerOrCluster:t.cell.dataFrame.get(d.$2.MONOMER,t.tableRowIndex),positionOrClusterType:t.tableColumn.name}}render(){var t;if(h()(this.root).empty(),!this.activityColumnName||!this.sequenceColumnName)return void this.root.appendChild(l.divText("Please, select a sequence and activity columns in the viewer properties"));const e=this.getProperty(r.COLOR);e&&(e.choices=g()(a.shell.t.columns.numerical).toArray().map((t=>t.name)),e.get(this)===d.$2.ACTIVITY_SCALED&&e.set(this,d.$2.ACTIVITY)),h()(this.root).empty();let n=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 o=t=>{h()(t.root).find(".ui-input-editor").css("margin","0px").attr("type","radio"),h()(t.root).find(".ui-input-description").css("padding","0px").css("padding-right","16px"),h()(t.captionLabel).addClass("ui-label-right")};o(t),o(e),n=l.divH([t.root,e.root],{id:"pep-viewer-title"}),h()(n).css("width","auto").css("align-self","center")}const o=this.viewerGrid.root;o.style.width="auto";const s=l.icons.search((()=>{this._showSearchInput=!this._showSearchInput,this.monomerSearchInput.input.style.display=this._showSearchInput?"block":"none"}),"Toggle monomer search input visibility");this.monomerSearchInput.input.style.display=this._showSearchInput?"block":"none",h()(s).addClass("pep-help-icon"),(0,w.BX)(s.style).set("top","3px").set("fontSize","14px");const u=l.divH([this.monomerSearchInput.input],{style:{alignSelf:"center",justifyContent:"center",width:"100%",flexWrap:"wrap"}}),c=l.divH([s,n,u],{style:{alignSelf:"center",lineHeight:"normal",flexDirection:"column",width:"100%"}});this.root.appendChild(l.divV([c,o])),null===(t=this.viewerGrid)||void 0===t||t.invalidate(),this.monomerSearchInput.fireChanged()}}class M extends N{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()}onFilterChanged(t,e=!1){if(this._monomerPositionStats=null,this._invariantMapSelection=null,this._mutationCliffStats=null,this._mutationCliffsSelection=null,this._mutationCliffs=null,e)return;this._viewerGrid=null;const n=this.model.findViewer(m.q.SEQUENCE_VARIABILITY_MAP);"Filtered"===(null==n?void 0:n.dataSource)&&n.onFilterChanged(!1,!0),t&&this.render()}createMostPotentResiduesDf(){var t;const e=Object.entries(this.monomerPositionStats),n=new Array(e.length-1),i=new Array(n.length),o=new Array(n.length),r=new Array(n.length),s=new Array(n.length),a=new Array(n.length),l=new Array(n.length),c=this.getTotalViewerAggColumns(),h=c.map((([t,e])=>(0,v.hX)(e,t))),f=new Array(h.length);h.forEach(((t,e)=>f[e]=new Array(n.length)));let m=0;for(const[p,g]of e){const e=g.general;if(!e)continue;if(1===Object.entries(g).length)continue;const C=[];for(const[n,i]of Object.entries(g))"general"!==n&&(i.count>1&&(null==i.pValue||(null!==(t=i.pValue)&&void 0!==t?t:1)<=.05)&&C.push([n,i]),i.pValue===e.minPValue&&C.push([n,i]));let y=null;0===C.length&&(y=Object.entries(g).find((([t,e])=>"general"!=t)));for(const[t,e]of C)(null===y||this.activityTarget===d.wf.HIGH&&y[1].meanDifference<e.meanDifference||this.activityTarget===d.wf.LOW&&y[1].meanDifference>e.meanDifference)&&(y=[t,e]);if(null===y)continue;n[m]=parseInt(p),i[m]=y[0],o[m]=y[1].meanDifference,r[m]=y[1].pValue,s[m]=y[1].count,a[m]=y[1].ratio,l[m]=y[1].mean;const w=this.monomerPositionStats[p][y[0]],b=u.BitSet.fromBytes(w.mask.buffer.buffer,this.model.df.col(this.activityColumnName).length);for(let t=0;t<h.length;t++){const[e,n]=c[t];f[t][m]=(0,v.lh)(this.model.df.getCol(e),n,b)}++m}n.length=m,i.length=m,o.length=m,r.length=m,s.length=m,a.length=m,l.length=m;const p=u.DataFrame.create(m),g=p.columns;return g.add(u.Column.fromList(u.TYPE.INT,d.$2.POSITION,n)),g.add(u.Column.fromList(u.TYPE.STRING,d.$2.MONOMER,i)),g.add(u.Column.fromList(u.TYPE.FLOAT,d.$2.MEAN_DIFFERENCE,o)),g.add(u.Column.fromList(u.TYPE.FLOAT,d.$2.MEAN,l)),g.add(u.Column.fromList(u.TYPE.FLOAT,d.$2.P_VALUE,r)),g.add(u.Column.fromList(u.TYPE.INT,d.$2.COUNT,s)),g.add(u.Column.fromList(u.TYPE.FLOAT,d.$2.RATIO,a)),h.forEach(((t,e)=>g.add(u.Column.fromList(u.TYPE.FLOAT,t,f[e])))),p}createViewerGrid(){const t=this.createMostPotentResiduesDf(),e=t.plot.grid();e.sort([d.$2.POSITION]);const n=e.col(d.$2.P_VALUE);n.format="#.000",n.name="P-value";const i=t.getCol(d.$2.MONOMER);f.rI(i,this.alphabet,!0),e.onCellRender.subscribe((t=>I(t,this,!1))),e.onCellTooltip(((t,e,n)=>{var i,o;if(!t.isTableCell)return this.model.unhighlight(),!0;const r=this.getMonomerPosition(t);if((0,w.dl)(r,this.dataFrame,this.monomerPositionStats),this.model.isHighlighting=!0,(null===(i=t.tableColumn)||void 0===i?void 0:i.name)===d.$2.MONOMER)r.positionOrClusterType=d.$2.MONOMER;else if((null===(o=t.tableColumn)||void 0===o?void 0:o.name)!==d.$2.MEAN_DIFFERENCE)return!1;const s=this.getTotalViewerAggColumns(),a=null==t.tableRowIndex?void 0:(0,v.m2)(t.grid.dataFrame,t.tableRowIndex,s,{});return(0,C.D)(this.model.df,this.getScaledActivityColumn(),s,{fromViewer:!0,isMostPotentResidues:!0,monomerPosition:r,x:e,y:n,mpStats:this.monomerPositionStats,aggrColValues:a})})),u.debounce(e.onCurrentCellChanged,500).subscribe((n=>{var i,o,r;try{if(-1===n.gridRow)return this._mutationCliffsSelection=(0,w.ZR)(this.positionColumns),this._invariantMapSelection=(0,w.ZR)(this.positionColumns),this.model.fireBitsetChanged(m.q.MOST_POTENT_RESIDUES),void e.invalidate();if(this.keyPressed&&t.currentCol.name!==d.$2.MEAN_DIFFERENCE||!this.keyPressed)return;const s=this.getMonomerPosition(n);if(null!==this.currentGridRowIdx){const t=this.getMonomerPosition(e.cell("Diff",this.currentGridRowIdx));this.modifyInvariantMapSelection(t,{shiftPressed:!0,ctrlPressed:!0},!1)}(null===(r=null===(o=null===(i=this.mutationCliffs)||void 0===i?void 0:i.get(s.monomerOrCluster))||void 0===o?void 0:o.get(s.positionOrClusterType))||void 0===r?void 0:r.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,w.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,o;const r=e.hitTest(t.offsetX,t.offsetY);if(!(null==r?void 0:r.isTableCell)||r.tableColumn.name!==d.$2.MEAN_DIFFERENCE)return;const s=this.getMonomerPosition(r);(null===(o=null===(i=null===(n=this.monomerPositionStats)||void 0===n?void 0:n[s.positionOrClusterType])||void 0===i?void 0:i[s.monomerOrCluster])||void 0===o?void 0:o.count)&&(this.modifyInvariantMapSelection(s,{shiftPressed:t.shiftKey,ctrlPressed:t.ctrlKey}),e.invalidate())})),O(e);const o=e.col(d.$2.MEAN_DIFFERENCE);o.name="Diff";const r=e.onAfterDrawContent.subscribe((()=>{const t=e.col(d.$2.MONOMER);if(40===t.width)return o.width=40,void r.unsubscribe();t.width=40,o.width=40}));return e}getMonomerPosition(t){return{monomerOrCluster:t.cell.dataFrame.get(d.$2.MONOMER,t.tableRowIndex),positionOrClusterType:`${t.cell.dataFrame.get(d.$2.POSITION,t.tableRowIndex)}`}}render(){var t;if(h()(this.root).empty(),!this.activityColumnName||!this.sequenceColumnName)return void this.root.appendChild(l.divText("Please, select a sequence and activity columns in the viewer properties"));const e=this.viewerGrid.root;e.style.width="auto",this.root.appendChild(l.divV([e])),null===(t=this.viewerGrid)||void 0===t||t.invalidate()}}function I(t,e,n,i,o){var r,s,a,l,c;const h=[...e.positionColumns.map((t=>t.name)),d.$2.MEAN_DIFFERENCE],m=t.g,p=t.bounds;m.save(),m.beginPath(),m.rect(p.x,p.y,p.width,p.height),m.clip();const g=t.cell,v=null===(r=g.tableColumn)||void 0===r?void 0:r.name,C=g.tableRowIndex;if(!g.isTableCell||-1===h.indexOf(v))return void m.restore();const y=g.grid.table,w=y.get(d.$2.MONOMER,C),b=v!==d.$2.MEAN_DIFFERENCE?v:y.get(d.$2.POSITION,C).toFixed(),A=e.monomerPositionStats[b];if(!A[w])return t.preventDefault(),void m.restore();if(n){const t=null!==(s=A[w].aggValue)&&void 0!==s?s:A[w].count,n=e.positionColumns.find((t=>t.name===b)),i=null!==(a=n.temp[d.gp.INVARIANT_MAP_COLOR_CACHE])&&void 0!==a?a:{};let o=u.Color.white;null!=i[w]?o=i[w]:e instanceof x&&(e.cacheInvariantMapColors(),o=null!==(c=(null!==(l=n.temp[d.gp.INVARIANT_MAP_COLOR_CACHE])&&void 0!==l?l:{})[w])&&void 0!==c?c:u.Color.white),f.rW(m,w,b,e.invariantMapSelection,t,p,o)}else f.Yd(m,w,b,e,p);t.preventDefault(),m.restore()}function O(t){const e=t.props;e.allowEdit=!1,e.allowRowSelection=!1,e.allowBlockSelection=!1,e.allowColSelection=!1,e.showRowHeader=!1,e.showCurrentRowIndicator=!1,e.showReadOnlyNotifications=!1,e.rowHeight=20}},7654:(t,e,n)=>{"use strict";n.d(e,{HV:()=>p,M1:()=>g,QD:()=>v});var i,o=n(7389),r=n(6082),s=n(7233),a=n.n(s),l=n(4139),u=n(5070),c=n(8608),h=n(5480),d=n(8774);!function(t){t.SEPARATE_MONOMERS="separateMonomers",t.SEPARATE_POSITIONS="separatePositions",t.SEPARATE_CLUSTERS="separateClusters"}(i||(i={}));const f="general",m=t=>t===f?"General":t.substring(8);function p(t,e){if(!t.selection.anyTrue)return o.divText("No distribution");const n=()=>{const n=[y(f,t,e)];for(const o of Object.values(i))"true"!==t.getTag(o)||o===i.SEPARATE_CLUSTERS&&!e.clusterColName||n.push(y(o,t,e));return 1===n.length?n[0]:o.div(n)},r=o.div(n()),s=Object.values(i),l=new Array(s.length);for(let u=0;u<s.length;u++){const c=s[u].substring(8);l[u]=o.input.bool(c,{value:"true"===t.getTag(s[u]),onValueChanged:e=>{t.setTag(s[u],`${e}`),a()(r).empty(),r.append(n())}}),a()(l[u].captionLabel).addClass("ui-label-right").css("text-align","left"),a()(l[u].root).find(".ui-input-editor").css("margin","0px"),a()(l[u].root).find(".ui-input-description").css("margin","0px"),l[u].setTooltip(`Show distribution for each ${c}`),c===i.SEPARATE_CLUSTERS?l[u].enabled=!(!e.clusterColName||!e.clusterSelection[h.W.ORIGINAL]):c!==i.SEPARATE_MONOMERS&&c!==i.SEPARATE_POSITIONS||(l[u].enabled=0!==Object.entries(e.monomerPositionSelection).length)}const u=o.form(l,{style:{flexDirection:"row"}});return o.divV([u,r])}function g(t,e=!1){const n=t.plot.histogram({filteringEnabled:!1,valueColumnName:l.$2.ACTIVITY,splitColumnName:l.$2.SPLIT_COL,legendVisibility:"Never",showXAxis:!0,showColumnSelector:!1,showRangeSlider:!1,showBinSelector:!1,backColor:e?"#fdffe5":"#fffff"});return n.root.style.width="auto",n}function v(t,e={}){var n,i;null!==(n=e.fractionDigits)&&void 0!==n||(e.fractionDigits=3);const o={[null!==(i=null==e?void 0:e.countName)&&void 0!==i?i:"Count"]:`${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&&(o["p-value"]=t.pValue<.01?"<0.01":t.pValue.toFixed(e.fractionDigits)),o}function C(t,e,n,i={}){const o=g((0,c.FZ)(n.activityCol,t.selection,t)),s=(0,u.I_)(t,Object.entries(n.columns),{filterDf:!0,mask:r.BitSet.fromBytes(e.mask.buffer.buffer,e.mask.length)}),l=v(e),h=Object.assign(Object.assign({},l),s),d=(0,c.F2)(o,h,i);return a()(d).addClass("d4-flex-col"),d}function y(t,e,n){let r=o.divText("No distribution");const s=e.selection.clone().and(e.filter),a=d.A.fromUint32Array(s.length,new Uint32Array(s.getBuffer().buffer));switch(t){case f:r=C(e,e.selection.anyTrue&&e.selection.anyFalse?(0,u.GT)(n.activityCol.getRawData(),a,(0,u.pY)(e.filter)):{count:n.activityCol.length,pValue:null,meanDifference:0,ratio:1,mask:a,mean:n.activityCol.stats.avg},n);break;case i.SEPARATE_CLUSTERS:r=function(t,e,n){const i=t.rowCount,r=[],s=e.activityCol.getRawData(),a=t.getCol(e.clusterColName),l=a.categories,f=a.getRawData(),m=(0,u.pY)(t.filter),p=n[h.W.ORIGINAL].map((t=>l.indexOf(t))),g=new Array(p.length).fill(new d.A(i));for(let t=0;t<i;t++){const e=f[t],n=p.indexOf(e);-1!==n&&g[n].setTrue(t)}for(let n=0;n<p.length;n++){const i=p[n],o=(0,u.GT)(s,g[n],m);r.push(C(t,o,e,{[c.AN.SELECTION]:l[i]}))}const v=n[h.W.CUSTOM];for(const n of v){const o=t.getCol(n),a=d.A.fromUint32Array(i,o.getRawData()),l=(0,u.GT)(s,a,m);r.push(C(t,l,e,{[c.AN.SELECTION]:n}))}return o.div(r,"d4-flex-wrap")}(e,n,n.clusterSelection);break;case i.SEPARATE_MONOMERS:r=function(t,e,n){var i,r,s;const a=Object.keys(n),l=t.rowCount,h=[],f=[],m=[],p=[],g=e.activityCol.getRawData(),v=(0,u.pY)(t.filter);for(const o of a){const a=n[o],y=new d.A(l);for(let e=0;e<a.length;e++){const n=a[e];null!==(i=f[e])&&void 0!==i||(f[e]=t.getCol(n)),null!==(r=m[e])&&void 0!==r||(m[e]=f[e].categories),null!==(s=p[e])&&void 0!==s||(p[e]=f[e].getRawData());const u=m[e].indexOf(o);for(let t=0;t<l;t++)p[e][t]===u&&y.setTrue(t)}const w=(0,u.GT)(g,y,v);h.push(C(t,w,e,{[c.AN.SELECTION]:o}))}return o.div(h,"d4-flex-wrap")}(e,n,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));break;case i.SEPARATE_POSITIONS:r=function(t,e,n){var i,r,s;const a=Object.keys(n),l=t.rowCount,h=[],f=e.activityCol.getRawData(),m=[],p=[],g=[],v=(0,u.pY)(t.filter);for(let o=0;o<a.length;o++){const y=a[o],w=n[y];if(0===w.length)continue;null!==(i=m[o])&&void 0!==i||(m[o]=t.getCol(y)),null!==(r=p[o])&&void 0!==r||(p[o]=m[o].categories),null!==(s=g[o])&&void 0!==s||(g[o]=m[o].getRawData());const b=new d.A(t.rowCount);for(let t=0;t<w.length;t++){const e=w[t],n=p[o].indexOf(e);for(let t=0;t<l;t++)g[o][t]===n&&b.setTrue(t)}const A=(0,u.GT)(f,b,v);h.push(C(t,A,e,{[c.AN.SELECTION]:y}))}return o.div(h,"d4-flex-wrap")}(e,n,n.monomerPositionSelection)}return o.divV([o.h1(m(t)),r])}},7923:(t,e,n)=>{"use strict";n.d(e,{F:()=>c});var i=n(7389),o=n(6082),r=n(4139),s=n(8608),a=n(3163),l=n(4025),u=n(7654);function c(t,e,n=!0){var r,a,l,c,d;const f=h(t,e);if(!f)return new o.Widget(i.label("No mutations table generated"));const{pairsGrid:m,uniqueSequencesGrid:p,aminoToInput:g}=f,v=[m,p],C=i.divV([g.root,...v.map((t=>t.root))],{style:{width:"100%"}});if(1===Object.values(e.mutationCliffsSelection).filter((t=>t.length>0)).length){const t=Object.keys(e.mutationCliffsSelection).find((t=>e.mutationCliffsSelection[t].length>0)),n=e.mutationCliffsSelection[t];if(1===n.length){const i=n[0],o=null===(a=null===(r=e.mutationCliffs)||void 0===r?void 0:r.get(i))||void 0===a?void 0:a.get(t);if(o&&o.size>0){const n=(0,s.Z7)(e.activityCol,o,i),r=(0,u.M1)(n,!1),a=null===(d=null===(c=null===(l=e.mutationCliffStats)||void 0===l?void 0:l.stats)||void 0===c?void 0:c.get(i))||void 0===d?void 0:d.get(t),h={};let f=0;for(const t of o.values())f+=t.length;h["Pairs count"]=f.toString(),a&&(h["Unique Count"]=a.mask.trueCount().toString(),Object.assign(h,(0,u.QD)(a,{countName:"MP in cliffs count"})));const m=(0,s.F2)(r,h);r.root.style.maxHeight="100px",m.style.marginTop="10px",C.appendChild(m)}}}return n&&(0,s.BE)("Mutation Cliffs pairs",g.root,C,(()=>{const n=h(t,e),o=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(o)){const r=o.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="calc(100% - 20px)",a.style.marginTop="20px",r>400)){const t=Math.max(.33*r,200),i=n.pairsGrid.columns.byName("Mutation");i&&(i.width=t);const o=n.uniqueSequencesGrid.columns.byName(e.sequenceColumnName);o&&(o.width=t)}}}),500),o})),new o.Widget(C)}function h(t,e){var n,u;const c=t.filter.getSelectedIndexes(),h=Object.keys(e.mutationCliffsSelection);if(!h.length||null===e.mutationCliffs)return null;const d=[],f=[],m=[],p=[],g=[],v=[],C=t.getCol(e.sequenceColumnName),y=C.categories,w=C.getRawData(),b=e.activityCol.getRawData(),A=new Map,S=o.BitSet.create(t.rowCount),T={},E=Object.fromEntries(e.positionColumns.map((t=>[t.name,t])));for(const t of h){const i=E[t],o=i.categories,r=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,n]of s.entries()){if(!c.includes(t))continue;T[t]||(T[t]=Object.keys(T).length+1);const i=T[t],s=null!==(u=A.get(t))&&void 0!==u?u:[],a=y[w[t]],l=b[t],h=e.activityCol.isNone(t)?null:l;for(const l of n){if(s.includes(l)||!c.includes(l))continue;A.has(l)||A.set(l,[]);const n=y[w[l]],u=e.activityCol.isNone(l)?null:b[l],C=null==h||null==u?null:h-u;A.get(l).push(t),d.push(`${a}#${n}`),p.push(`${i}`),f.push(C),m.push(o[r[l]]),g.push(t),v.push(l),S.set(t,!0),S.set(l,!0)}}}}if(0===d.length)return null;const _=o.Column.fromStrings("Mutation",d),N=o.Column.fromList("double","Delta",f),x=o.Column.fromStrings("Group",p),M=o.Column.fromStrings("~to",m),I=o.Column.fromList(o.COLUMN_TYPE.INT,"~toIdx",v),O=o.Column.fromList(o.COLUMN_TYPE.INT,"~fromIdx",g),L=o.DataFrame.fromColumns([_,N,x,M,I,O]);L.name="Mutation Cliff pairs";const P=i.input.string("Mutated to:",{value:"",onValueChanged:t=>{const e=t;""!==e?L.filter.init((t=>M.get(t)===e)):L.filter.setAll(!0)}});P.setTooltip("Filter the rows by the monomer that the mutation was substituted to");const R=L.plot.grid();(0,s.vY)(R,!0),_.semType=r.uF.MACROMOLECULE_DIFFERENCE,_.tags[r.gp.SEPARATOR]=(0,s.AY)(C),_.tags[o.TAGS.UNITS]=C.tags[o.TAGS.UNITS],_.tags[o.TAGS.CELL_RENDERER]="MacromoleculeDifference",_.temp[l.j.notationProvider]=C.temp[l.j.notationProvider];let k=!1,V=null;const F=[];R.onCurrentCellChanged.subscribe((t=>{try{if(!t||!t.dart)return F.length=0,void j();const e=t.tableRowIndex;if(!k)return;if(null===e)return F.length=0,void j();null!==V&&F.splice(F.indexOf(V),1),F.includes(e)||(F.push(e),R.invalidate()),j()}finally{k=!1,V=t&&t.dart?t.tableRowIndex:null}})),R.root.addEventListener("keydown",(t=>{k=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=F.indexOf(n);-1===t?F.push(n):F.splice(t,1)}else F.length=0,F.push(n);j(),R.invalidate(),Y.invalidate()})),R.onCellPrepare((t=>{var e,n,i,r;if((null==t?void 0:t.isTableCell)&&"delta"==(null===(n=null===(e=null==t?void 0:t.gridColumn)||void 0===e?void 0:e.name)||void 0===n?void 0:n.toLowerCase())&&(null==(null===(i=null==t?void 0:t.cell)||void 0===i?void 0:i.value)||(null===(r=null==t?void 0:t.cell)||void 0===r?void 0:r.value)==o.FLOAT_NULL))try{t.customText="N/A"}catch(t){}})),R.onCellRender.subscribe((t=>{var e;(null===(e=t.cell.tableColumn)||void 0===e?void 0:e.name)===_.name&&F.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 U=t.clone(S,G);U.name="Unique sequences that form Mutation Cliffs pairs";const q=U.columns.addNewInt("~seqIdx"),B=q.getRawData();U.col(e.sequenceColumnName)&&(U.col(e.sequenceColumnName).temp[l.j.notationProvider]=C.temp[l.j.notationProvider]);const H=S.getSelectedIndexes();q.init((t=>H[t]));const Y=U.plot.grid();function j(){const t=[];for(const e of F)t.push(O.get(e)),t.push(I.get(e));U.filter.init((e=>0===F.length||t.includes(B[e])),!0),R.invalidate(),Y.invalidate()}return(0,s.vY)(Y,!0),Y.props.rowHeight=20,R.root.style.width="100% !important",Y.root.style.width="100% !important",setTimeout((()=>{R.autoSize(window.innerWidth,250,void 0,void 0,!1),Y.autoSize(window.innerWidth,250,void 0,void 0,!1),R.root.style.removeProperty("width"),R.root.style.setProperty("width","100%"),Y.root.style.removeProperty("width"),Y.root.style.setProperty("width","100%"),R.root.style.minHeight="70px",Y.root.style.minHeight="100px",R.root.style.height="unset",Y.root.style.height="unset"}),200),{pairsGrid:R,uniqueSequencesGrid:Y,aminoToInput:P}}},5082:(t,e,n)=>{"use strict";n.d(e,{n:()=>g,v:()=>p});var i=n(4328),o=n(7389),r=n(6082),s=n(4139),a=n(115),l=n(9499),u=n(7233),c=n.n(u),h=n(8608),d=n(1199),f=n(5429),m=(n(4788),function(t,e,n,i){return new(n||(n=Promise))((function(o,r){function s(t){try{l(i.next(t))}catch(t){r(t)}}function a(t){try{l(i.throw(t))}catch(t){r(t)}}function l(t){var e;t.done?o(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=o.div();let u=null;if(void 0===e){const e=r.Utils.firstOrNull(t.columns.toList().filter((t=>t.semType===r.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=o.input.column("Sequence",{table:t,value:e,onValueChanged:e=>{c()(l).empty().append(o.wait((()=>m(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===r.SEMTYPE.MACROMOLECULE,nullable:!1}),u.setTooltip("Macromolecule column in FASTA, HELM or separated format")}let p,v=r.Func.find({package:"Bio",name:"webLogoViewer"});if(0===v.length)return{host:o.label("Bio package is missing or out of date. Please install the latest version."),callback:()=>m(this,void 0,void 0,(function*(){return!1}))};if(v=r.Func.find({package:"Bio",name:"getBioLib"}),0===v.length)return{host:o.label("Bio package is missing or out of date. Please install the latest version."),callback:()=>m(this,void 0,void 0,(function*(){return!1}))};const C=t.col("activity")||t.col("IC50")||r.Utils.firstOrNull(t.columns.numerical),y=o.div([],{id:"pep-hist-host"}),w=o.input.choice("Scaling",{value:s.rg.NONE,items:Object.values(s.rg),onValueChanged:t=>m(this,void 0,void 0,(function*(){var e;p=(0,h.Y1)(A.value,t);const n=r.DataFrame.fromColumns([p]).plot.histogram({filteringEnabled:!1,valueColumnName:s.$2.ACTIVITY,legendVisibility:"Never",showXAxis:!0,showColumnSelector:!1,showRangeSlider:!1,showBinSelector:!1});null===(e=y.lastChild)||void 0===e||e.remove(),y.appendChild(n.root)}))});w.setTooltip("Activity column transformation method");const b=()=>{var t;w.enabled=null!==(t=A.value)&&void 0!==t&&t&&A.value.stats.min>0,w.value=s.rg.NONE,0!==A.value.stats.missingValueCount&&i.shell.info("Activity column contains missing values. They will be ignored during analysis")},A=o.input.column("Activity",{table:t,value:C,nullable:!1,onValueChanged:b,filter:t=>t.type===r.TYPE.INT||t.type===r.TYPE.FLOAT||t.type===r.TYPE.QNUM});A.setTooltip("Numerical activity column");const S=o.input.column("Clusters",{table:t,onValueChanged:t=>{t&&(T.value=!1,T.fireChanged())}});S.setTooltip("Optional. Clusters column is used to create Logo Summary Table"),S.nullable=!0;const T=o.input.bool("Generate clusters",{value:!0,onValueChanged:t=>{t&&(S.value=null,S.fireChanged())}});T.setTooltip("Generate clusters column based on MCL embeddings for Logo Summary Table"),A.fireChanged(),w.fireChanged(),T.fireChanged();const E=[A,w,S,T];null!==u&&E.splice(0,0,u);const _=o.input.float(f.t_.THRESHOLD,{value:n.threshold,nullable:!1,onValueChanged:t=>n.threshold=null!=t?t:n.threshold});_.setTooltip("Threshold for similarity between two sequences to create edges");const N=o.input.float(f.t_.INFLATION,{value:n.inflation,nullable:!1,onValueChanged:t=>n.inflation=null!=t?t:n.inflation});N.setTooltip("Inflation value for MCL algorithm");const x=o.input.int(f.t_.MAX_ITERATIONS,{value:n.maxIterations,nullable:!1,onValueChanged:t=>n.maxIterations=null!=t?t:n.maxIterations});x.setTooltip("Maximum iterations for MCL algorithm");const M=o.input.bool(f.t_.USE_WEBGPU,{value:n.useWebGPU,onValueChanged:t=>n.useWebGPU=t});M.enabled=!1,n.webGPUDescriptionPromise.then((()=>{n.webGPUDescription!==a.Ku?(M.setTooltip(`Use WebGPU for MCL algorithm (${n.webGPUDescription})`),M.enabled=!0):(M.setTooltip(a.Ku),M.enabled=!1,M.value=!1)}));const I=o.input.int(f.t_.MIN_CLUSTER_SIZE,{value:n.minClusterSize,nullable:!1,onValueChanged:t=>n.minClusterSize=null!=t?t:n.minClusterSize});I.setTooltip("Minimum cluster size for MCL algorithm");const O=o.input.choice(f.t_.DISTANCE_FUNCTION,{value:n.distanceF,items:[d.Z.NEEDLEMANN_WUNSCH,d.Z.MONOMER_CHEMICAL_DISTANCE,d.Z.HAMMING,d.Z.LEVENSHTEIN],nullable:!1,onValueChanged:t=>n.distanceF=t}),L=o.input.float(f.t_.GAP_OPEN,{value:n.gapOpen,onValueChanged:t=>n.gapOpen=null!=t?t:n.gapOpen}),P=o.input.float(f.t_.GAP_EXTEND,{value:n.gapExtend,onValueChanged:t=>n.gapExtend=null!=t?t:n.gapExtend}),R=[_,N,x,I,O,o.input.choice(f.t_.FINGERPRINT_TYPE,{value:n.fingerprintType,items:["Morgan","RDKit","Pattern","AtomPair","MACCS","TopologicalTorsion"],nullable:!1,onValueChanged:t=>n.fingerprintType=t}),L,P,M],k=o.form(R);k.style.display="none";const V=o.icons.settings((()=>{k.style.display="none"===k.style.display?"flex":"none",k.classList.remove("ui-form-condensed")}),"Adjust clustering parameters");V.style.fontSize="16px",T.root.appendChild(V);const F=t.filter.onChanged.subscribe((()=>b())),D=()=>m(this,void 0,void 0,(function*(){var i,o;const r=null!=e?e:u.value;return F.unsubscribe(),!!r&&null!==(yield g(A.value,r,S.value,t,p,null!==(i=w.value)&&void 0!==i?i:s.rg.NONE,{addSequenceSpace:!1,addMCL:T.value,useEmbeddingsClusters:null!==(o=T.value)&&void 0!==o&&o,mclSettings:n}))}));let G="auto";const U=[o.divV(E)];if(c()(U[0]).find("label").css("width","unset"),void 0!==e){const t=o.button("Launch SAR",D,"");t.style.alignSelf="center",U.push(t),G="215px"}return c()(l).empty().append(o.wait((()=>m(this,void 0,void 0,(function*(){var n;const i=yield t.plot.fromType("WebLogo",{sequenceColumnName:null!==(n=null==e?void 0:e.name)&&void 0!==n?n:u.value.name});return i.root.style.setProperty("height","130px"),i.root}))))),{host:o.divV([l,o.splitH([o.splitV(U),y],{style:{height:G,minWidth:"500px",maxWidth:"600px"}}),k]),callback:D}}function g(t,e,n,o,u,c){return m(this,arguments,void 0,(function*(t,e,n,o,u,c,h={}){var d,f,m,p,g;let v=null;if(t.type!==r.COLUMN_TYPE.FLOAT&&t.type!==r.COLUMN_TYPE.INT&&t.type!==r.COLUMN_TYPE.QNUM)return i.shell.error("The activity column must be of numeric type!"),v;const C=r.TaskBarProgressIndicator.create("Loading SAR...");o.tags.delete&&o.tags.delete(".script");const y=o.columns,w=o.col(u.name);w&&(w.name=y.getUnusedName(w.name));const b=u.getRawData();o.columns.addNew(u.name,u.type).init((t=>b[t])),y.setOrder([u.name,e.name,...y.names().filter((t=>t!==e.name&&t!==u.name))]);const A={sequenceColumnName:e.name,activityColumnName:t.name,activityScaling:c,columns:{},showDendrogram:!1,showSequenceSpace:!1,sequenceSpaceParams:new a.GI(!!h.useEmbeddingsClusters&&!n),mclSettings:null!==(d=h.mclSettings)&&void 0!==d?d:new a.av};if(n){const t=o.getCol(n.name);t.type!==r.COLUMN_TYPE.STRING&&y.replace(t,t.convertTo(r.COLUMN_TYPE.STRING))}if(o.setTag(s.gp.SETTINGS,JSON.stringify(A)),v=l.i.getInstance(o),v.init(A),n){const i={clustersColumnName:n.name,sequenceColumnName:e.name,activityScaling:c,activityColumnName:t.name};yield v.addLogoSummaryTable(i)}if(yield v.addMonomerPosition(),yield v.addMostPotentResidues(),null!==(f=h.addSequenceSpace)&&void 0!==f&&f){if(yield v.addSequenceSpace({clusterCol:n,clusterEmbeddings:h.useEmbeddingsClusters}),!n&&null!==(m=h.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)===r.COLUMN_TYPE.STRING}));if(n){const i={clustersColumnName:n,sequenceColumnName:e.name,activityScaling:c,activityColumnName:t.name};yield v.addLogoSummaryTable(i),setTimeout((()=>{var t,e;v&&(null===(t=null==v?void 0:v.findViewer(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!==(p=h.addMCL)&&void 0!==p&&p&&(yield v.addMCLClusters(),!n&&null!==(g=h.useEmbeddingsClusters)&&void 0!==g&&g)){const n=v._mclCols.find((t=>(null==v?void 0:v.df.col(t))&&t.toLowerCase().startsWith("cluster")&&!t.toLowerCase().includes("size")));if(n){const i={clustersColumnName:n,sequenceColumnName:e.name,activityScaling:c,activityColumnName:t.name};yield v.addLogoSummaryTable(i),setTimeout((()=>{var t,e;v&&(null===(t=null==v?void 0:v.findViewer(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)}}const S=v.df.plot.grid({rowSource:r.RowSet.Selected,selectedRowsColor:r.Color.fromHtml("#ffffff"),title:"Selection"}),T=null==v?void 0:v.findViewerNode(l.q.LOGO_SUMMARY_TABLE);return T&&v.analysisView.dockManager.dock(S,r.DOCK_TYPE.DOWN,T,"Selection",.4),C.close(),v}))}},5429:(t,e,n)=>{"use strict";n.d(e,{OH:()=>b,t_:()=>l});var i,o,r,s,a,l,u=n(7389),c=n(4328),h=n(6082),d=n(115),f=n(4139),m=n(9499),p=n(7233),g=n.n(p),v=n(144),C=n.n(v),y=n(3262),w=n(1199);function b(t){var e,n,r,p,v,b,A,S,T,E;null==t.settings&&c.log.error("PeptidesError: Settings are not initialized");const _=u.accordion(),N=t.settings,x=null!==(e=null==N?void 0:N.activityScaling)&&void 0!==e?e:f.rg.NONE,M=null!==(n=null==N?void 0:N.columns)&&void 0!==n?n:{},I={},O={},L=null!==(r=null==N?void 0:N.sequenceSpaceParams)&&void 0!==r?r:new d.GI,P=null!==(p=null==N?void 0:N.mclSettings)&&void 0!==p?p:new d.av,R=u.input.column(o.ACTIVITY,{table:t.df,value:t.df.getCol(t.settings.activityColumnName),onValueChanged:t=>{I.activityColumnName=t.name},filter:t=>(t.type===h.TYPE.FLOAT||t.type===h.TYPE.INT)&&t.name!==f.$2.ACTIVITY&&0===t.stats.missingValueCount});R.setTooltip("Numeric activity column");const k=u.input.choice(o.ACTIVITY_SCALING,{value:x,items:Object.values(f.rg),onValueChanged:t=>I.activityScaling=t});k.setTooltip("Activity column transformation method"),_.addPane(i.GENERAL,(()=>u.inputs([R,k])),!0),O[i.GENERAL]=[R,k];const V=C()(t.analysisView.viewers).some((t=>t.type===m.q.DENDROGRAM)),F=u.input.bool(m.q.DENDROGRAM,{value:null!=V&&V,onValueChanged:t=>I.showDendrogram=t}),D=u.input.bool(m.q.CLUSTER_MAX_ACTIVITY,{value:!!(null==N?void 0:N.showClusterMaxActivity),onValueChanged:t=>{I.showClusterMaxActivity=null!=t?t:void 0}}),G=u.input.bool("Sequence space",{value:!!(null==N?void 0:N.showSequenceSpace),onValueChanged:t=>{I.showSequenceSpace=null!=t?t:void 0,t?(ft.root.style.display="flex",(null==N?void 0:N.showSequenceSpace)||(I.sequenceSpaceParams=L)):(ft.root.style.display="none",delete I.sequenceSpaceParams),I.showSequenceSpace===(null==N?void 0:N.showSequenceSpace)&&delete I.showSequenceSpace}});D.setTooltip("Show cluster max activity viewer"),F.setTooltip("Show dendrogram viewer"),F.enabled=null!==(0,y.getTreeHelperInstance)(),_.addPane(i.VIEWERS,(()=>u.inputs([F,G,D])),!0),O[i.VIEWERS]=[F,G,D];const U=[],q=[];for(const e of t.df.columns.numerical){const t=e.name;if(t===N.activityColumnName||t===f.$2.ACTIVITY)continue;const n=u.input.bool(s.IS_INCLUDED,{value:void 0!==M[t],onValueChanged:e=>{var n;null!==(n=I.columns)&&void 0!==n||(I.columns={}),e?I.columns[t]=i.value:(delete I.columns[t],Object.keys(I.columns).length===Object.keys(M).length&&delete I.columns)}});n.setTooltip("Include aggregated column value in tooltips, Logo Summary Table and Distribution panel");const i=u.input.choice(s.AGGREGATION,{value:null!==(v=M[t])&&void 0!==v?v:h.AGG.AVG,items:Object.values(h.STATS),onValueChanged:i=>{var o;null!==(o=I.columns)&&void 0!==o||(I.columns={}),n.value?I.columns[t]=i:(delete I.columns[e.name],Object.keys(I.columns).length===Object.keys(M).length&&delete I.columns)}});i.setTooltip("Aggregation method"),g()(i.root).find("label").css("width","auto");const o=u.inputsRow(e.name,[n,i]);q.push(n,i),g()(o).find("div.ui-div").css("display","inline-flex"),U.push(o)}0!==U.length&&(_.addPane(i.COLUMNS,(()=>u.divV(U)),!1),O[i.COLUMNS]=q);const B={};function H(t,e){if(X(),null==e||""===e)return;B[t]=e;let n=!0;for(const[t,e]of Object.entries(B))if(e!==L[t]){n=!1;break}n?delete I.sequenceSpaceParams:I.sequenceSpaceParams=Object.assign(Object.assign({},L),B)}function 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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,h)),this.grokGroups}static get RasMol(){return void 0===this.rasMol&&(this.rasMol=new h({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 h.aaSynonyms?h.aaSynonyms[t]:t;return super.get(e)}}h.aaSynonyms={MeNle:"L",MeA:"A",MeG:"G",MeF:"F"};class d{static getPalette(t="grok"){switch(t){case"grok":return h.GrokGroups;case"lesk":return h.Lesk;default:throw new Error(`ChemPalette: scheme \`${t}\` does not exist`)}}static getInnerOuter(t){let e=0,n="",i="";for(const o of t)"("==o?e++:")"==o?e--:e?n+=o:i+=o;return 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n?[n.get(e),e,o,4]:[this.undefinedColor,i,o,4]}return[this.undefinedColor,i,o,0]}}d.SemType="Aminoacids",d.SemTypeMultipleAlignment="AminoacidsMultipleAlignment",d.undefinedColor="rgb(100,100,100)",d.Names={G:"Glycine",L:"Leucine",Y:"Tyrosine",S:"Serine",E:"Glutamic acid",Q:"Glutamine",D:"Aspartic 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f extends c{static get Chromatogram(){return void 0===this.chromatogram&&(this.chromatogram=new f({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 p=n(4971);function g(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),o=i.Color.b(n),r=Math.sqrt(Math.pow(0-e,2)+Math.pow(0-t,2)+Math.pow(0-o,2));if(r>210)return`rgb(${e/r*210},${t/r*210},${o/r*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 C{}class y extends C{get(t,e){return"#666666"}}class w extends C{static get palette(){return w._pallete||(w._pallete=w.buildPalette()),w._pallete}static buildPalette(){return(0,p.pj)().then((t=>{t.awaitLoaded(1/0).then((()=>{const 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Set([U.TANIMOTO,U.COSINE,U.SOKAL,U.ASYMMETRIC]),function(t){t.ADD="ADD",t.SUB="SUB",t.MULT="MULT"}(B||(B={})),function(t){t.SQUARE="SQUARE",t.INVERSE="INVERSE",t.TRANSPOSE="TRANSPOSE",t.NORM="NORM",t.COLUMN_NORM="COLUMN_NORM"}(H||(H={})),function(t){t.SCALARMULT="SCALARMULT",t.SCALARADD="SCALARADD",t.SCALARPOW="SCALARPOW"}(Y||(Y={})),Object.prototype.toString,function(t){t.EUCLIDEAN="EUCLIDEAN",t.MANHATTAN="MANHATTAN"}(j||(j={}));var $,z=n(726),K=function(t,e,n,i){return new(n||(n=Promise))((function(o,r){function s(t){try{l(i.next(t))}catch(t){r(t)}}function a(t){try{l(i.throw(t))}catch(t){r(t)}}function l(t){var e;t.done?o(t.value):(e=t.value,e instanceof n?e:new n((function(t){t(e)}))).then(s,a)}l((i=i.apply(t,e||[])).next())}))};!function(t){t.SEQUENCE_VARIABILITY_MAP="Sequence Variability Map",t.MOST_POTENT_RESIDUES="Most Potent Residues",t.LOGO_SUMMARY_TABLE="Logo Summary Table",t.DENDROGRAM="Dendrogram",t.CLUSTER_MAX_ACTIVITY="Active peptide selection",t.MCL="MCL",t.SEQUENCE_MUTATION_CLIFFS="Sequence Mutation Cliffs"}($||($={}));class Z{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,V.Ej)(e,this.df.filter,this.positionColumns)),this._monomerPositionStats)}get analysisView(){var t,e,n;return void 0===this._analysisView&&(this._analysisView=this.id?S()(h.shell.tableViews).find((({dataFrame:t})=>(null==t?void 0:t.getTag(d.TAGS.ID))===this.id)):void 0,!this._analysisView&&(null===(t=h.shell.v)||void 0===t?void 0:t.preview)instanceof d.TableView&&(null===(n=null===(e=h.shell.v)||void 0===e?void 0:e.preview)||void 0===n?void 0:n.dataFrame)===this.df&&(this._analysisView=h.shell.v.preview),this._analysisView||(this._analysisView=h.shell.addTableView(this.df))),"1"===this.df.getTag(_.gp.MULTIPLE_VIEWS)||this._layoutEventInitialized||(0,x.Lv)()||(h.shell.v=this._analysisView),this._analysisView.grid.invalidate(),this._analysisView}get settings(){var t,e;const n=this.df.getTag(_.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,W._)()),this._settings):null}set settings(t){var e,n,i;const o=Object.entries(t),r=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 o)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])=>r[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,x.ZR)(this.positionColumns),this.webLogoBounds={},this.cachedWebLogoTooltip={bar:"",tooltip:null},this._monomerPositionStats=null;break;case"dendrogram":this.settings.showDendrogram?this.addDendrogram():this.closeViewer($.DENDROGRAM);break;case"clusterMaxActivity":this.settings.showClusterMaxActivity?this.addClusterMaxActivityViewer():this.closeViewer($.CLUSTER_MAX_ACTIVITY);break;case"logoSummaryTable":this.settings.showLogoSummaryTable?this.addLogoSummaryTable():this.closeViewer($.LOGO_SUMMARY_TABLE);break;case"monomerPosition":this.settings.showMonomerPosition?this.addMonomerPosition():this.closeViewer($.SEQUENCE_VARIABILITY_MAP);break;case"mostPotentResidues":this.settings.showMostPotentResidues?this.addMostPotentResidues():this.closeViewer($.MOST_POTENT_RESIDUES);break;case"columns":const t=this.findViewer($.LOGO_SUMMARY_TABLE);t._viewerGrid=null,t._logoSummaryTable=null,t.render();const e=this.findViewer($.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,e;return null!==(t=this._webLogoSelection)&&void 0!==t||(this._webLogoSelection=(0,x.ZR)(null!==(e=this.positionColumns)&&void 0!==e?e:[])),this._webLogoSelection}set webLogoSelection(t){this._webLogoSelection=t,this.fireBitsetChanged(null),this.analysisView.grid.invalidate()}get positionColumns(){const t=S()(this.df.columns.byTags({[_.gp.POSITION_COL]:"true"})).toArray();return 0===t.length?null:t}get id(){return this.df.getTag(d.TAGS.ID)}get alphabet(){return this.df.getCol(this.settings.sequenceColumnName).getTag(f.gp.alphabet)}static getInstance(t){if(t.columns.contains(_.$2.ACTIVITY_SCALED)&&!t.columns.contains(_.$2.ACTIVITY)&&(t.getCol(_.$2.ACTIVITY_SCALED).name=_.$2.ACTIVITY),!t.temp[Z.modelName]){const e=t.temp[Z.modelName]=new Z(t),n=e.settings;n&&e.init(n);let i=!0;e.subs.push(d.debounce(t.onSelectionChanged,10).subscribe((n=>{var o,r,s;if(i||t.selection.anyTrue||!e._analysisView||!document.contains(e._analysisView.root)||e._analysisView.dataFrame!==t)return void(i=!(null===(o=null==t?void 0:t.selection)||void 0===o?void 0:o.anyTrue));e.positionColumns&&(e.webLogoSelection=(0,x.ZR)(e.positionColumns));const a=e.findViewer($.SEQUENCE_VARIABILITY_MAP);if(null!=a){const t=null!==(r=e.positionColumns)&&void 0!==r?r:a.positionColumns;t&&(a.invariantMapSelection=(0,x.ZR)(t),a.mutationCliffsSelection=(0,x.ZR)(t))}const l=e.findViewer($.MOST_POTENT_RESIDUES);if(null!=l){const t=null!==(s=e.positionColumns)&&void 0!==s?s:l.positionColumns;t&&(l.mutationCliffsSelection=(0,x.ZR)(t),l.invariantMapSelection=(0,x.ZR)(t))}const u=e.findViewer($.LOGO_SUMMARY_TABLE);null!=u&&(u.initClusterSelection({notify:!0}),u.render()),i=!0})))}return t.temp[Z.modelName]}modifyWebLogoSelection(t,e={shiftPressed:!1,ctrlPressed:!1},n=!0){n?this.webLogoSelection=(0,x.vW)(this.webLogoSelection,t,e):this._webLogoSelection=(0,x.vW)(this.webLogoSelection,t,e)}getVisibleSelection(){return this.df.selection.clone().and(this.df.filter)}createAccordion(){var t,e,n,i,o,r,s,a,l;const u=null===(t=this.df)||void 0===t?void 0:t.temp[Z.modelName];if(!u)return null;const h=c.accordion("Peptides analysis panel");h.root.style.width="100%";const m=u.getVisibleSelection(),p=u.df.filter.anyFalse?` among ${u.df.filter.trueCount} filtered`:"",g=t=>{const e=[];for(const[n,i]of Object.entries(t))for(const t of i)e.push(`${n}:${t}`);return e.join(", ")},v=u.findViewer($.LOGO_SUMMARY_TABLE),C=[],y=(null===v?[]:(null!==(n=null===(e=v.clusterSelection)||void 0===e?void 0:e[P.W.ORIGINAL])&&void 0!==n?n:[]).concat(null!==(o=null===(i=v.clusterSelection)||void 0===i?void 0:i[P.W.CUSTOM])&&void 0!==o?o:[])).join(", "),w=t=>{const e=c.divText(t);return e.innerHTML=t,e};0!==y.length&&C.push(w(`<b>Logo Summary Table</b> clusters: ${y}`));const A=u.findViewer($.SEQUENCE_VARIABILITY_MAP),b=g(null!==(r=null==A?void 0:A.invariantMapSelection)&&void 0!==r?r:{}),S=g(null!==(s=null==A?void 0:A.mutationCliffsSelection)&&void 0!==s?s:{});0!==b.length&&C.push(w(`<b>Invariant map</b>: ${b}`)),0!==S.length&&C.push(w(`<b>Mutation cliffs</b>: ${S}`));const T=u.findViewer($.MOST_POTENT_RESIDUES),E=g(null!==(a=null==T?void 0:T.invariantMapSelection)&&void 0!==a?a:{});0!==E.length&&C.push(w(`<b>Most potent residues</b>: ${E}`));const _=g(u.webLogoSelection);0!==_.length&&C.push(w(`<b>WebLogo</b>: ${_}`)),0!==C.length&&C.unshift(c.h1("Selection Sources"));const N=c.div(c.divV(C));h.addTitle(c.divV([c.h1(`${m.trueCount} selected rows${p}`),N],"css-gap-small"));let R=u.settings;const k=[A,T,v].filter((t=>null!==t&&(t.type!==this.accordionSource||(R=t,!1))));if(null===R)throw new Error("PeptidesError: Model is the source of accordion but is not initialized");R!==u.settings&&k.push(u.settings),k.filter((t=>null!==t&&(0,x.$s)(R,t)&&(t!==u.settings||u.isInitialized))).push(R);const D=R;R===u.settings||D instanceof P.s||null==D.mutationCliffs||h.addPane("Mutation Cliffs pairs",(()=>(0,O.F)(u.df,{mutationCliffs:D.mutationCliffs,mutationCliffsSelection:D.mutationCliffsSelection,gridColumns:u.analysisView.grid.columns,sequenceColumnName:D.sequenceColumnName,positionColumns:D.positionColumns,activityCol:D.getScaledActivityColumn(),mutationCliffStats:D.cliffStats}).root),!0);const G=R===u.settings,U=G?this.webLogoSelection:R instanceof M.J?R.invariantMapSelection:{},q=R instanceof P.s?R.clusterSelection:null!==(l=null==v?void 0:v.clusterSelection)&&void 0!==l?l:{};h.addPane("Distribution",(()=>{var t;try{return(0,L.HV)(u.df,{columns:G?null!==(t=u.settings.columns)&&void 0!==t?t:{}:R.getAggregationColumns(),activityCol:G?u.getScaledActivityColumn():R.getScaledActivityColumn(),monomerPositionSelection:U,clusterSelection:q,clusterColName:null==v?void 0:v.clustersColumnName})}catch(t){const e=c.divText("Error in Distribution");return c.tooltip.bind(e,String(t)),e}}),!0);const B=(t,e)=>{if(null==t||null==e)return!1;for(const[n,i]of Object.entries(t))if(i!==e[n])return!1;return!0};return h.addPane("Selection",(()=>{var t;try{return function(t,e){var n,i,o;if(0===e.tableSelection.trueCount)return c.divText("No compounds selected");const r=d.DataFrame.create(t.rowCount);r.name="Selected compounds",r.filter.copyFrom(e.tableSelection);let s=null;for(let t=1;t<e.gridColumns.length;t++){const o=e.gridColumns.byIndex(t);if(!o.visible)continue;const a=o.column;if(a.type===d.COLUMN_TYPE.BOOL)continue;null===s&&o.grid&&(null===(n=o.grid.sortByColumns)||void 0===n?void 0:n.length)>0&&(null===(i=o.grid.sortTypes)||void 0===i?void 0:i.length)===o.grid.sortByColumns.length&&(s={cols:o.grid.sortByColumns,types:o.grid.sortTypes});let l=null,u=null;try{l=a.getRawData(),u=a.categories}catch(t){}const c=l&&u?a.isNumerical?t=>l[t]:t=>u[l[t]]:t=>a.get(t),h=t=>a.isNone(t)?null:c(t),f=a.name===e.activityColumn.name?r.columns.addNewFloat(o.name).init((t=>h(t))):r.columns.addNewVirtual(o.name,(t=>h(t)),a.type);for(const[t,e]of a.tags)f.setTag(t,e)}const a=r.plot.grid();a.props.showRowHeader=!1,a.root.style.maxWidth="100%",d.debounce(c.onSizeChanged(a.root),50).subscribe((t=>{var e;const n=a.root.parentElement;(null===(e=null==n?void 0:n.parentElement)||void 0===e?void 0:e.classList.contains("panel-content"))&&(a.root.style.height="calc(100% - 20px)",a.root.style.width="calc(100% - 20px)",a.root.style.position="absolute",a.root.style.right="10px",a.root.style.top="10px")})),(0,x.zz)(a);const l=c.box(a.root);l.style.marginLeft="0px",setTimeout((()=>{null!==s&&a.sort(s.cols,s.types);for(let t=1;t<e.gridColumns.length;t++){const n=e.gridColumns.byIndex(t);n.visible&&a.col(n.name)&&(a.col(n.name).width=n.width)}}),500);const u=(0,V.Ej)(e.activityColumn,r.filter,e.positionColumns,{isFiltered:!0}),h={isSelectionTable:!0,cachedWebLogoTooltip:()=>({bar:"",tooltip:null}),webLogoBounds:()=>({}),colorPalette:()=>e.colorPalette},f={x:0,y:0,monomerPosition:{},mpStats:u};return e.isAnalysis&&(0,I.FZ)(a,u,e.positionColumns,e.activityColumn,h,f),(null!==(o=t.columns.bySemTypeAll(d.SEMTYPE.MACROMOLECULE))&&void 0!==o?o:[]).forEach((t=>{r.col(t.name)&&(r.col(t.name).temp[F.j.notationProvider]=t.temp[F.j.notationProvider])})),l}(u.df,{positionColumns:G?u.positionColumns:R.positionColumns,columns:G?null!==(t=u.settings.columns)&&void 0!==t?t:{}:R.getAggregationColumns(),activityColumn:G?u.getScaledActivityColumn():R.getScaledActivityColumn(),gridColumns:u.analysisView.grid.columns,colorPalette:(0,f.SM)(u.df.getCol(G?u.settings.sequenceColumnName:R.sequenceColumnName),z.Z.getSeqHelper()),tableSelection:u.getCombinedSelection(),isAnalysis:null!==u.settings&&(G||B(u.settings.columns,R.getAggregationColumns()))})}catch(t){const e=c.divText("Error in Selection");return c.tooltip.bind(e,String(t)),e}}),!0),h}getScaledActivityColumn(t=!1){const e=this.df.col(_.$2.ACTIVITY);return t&&null!==e?d.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,f.SM)(this.df.getCol(this.settings.sequenceColumnName),z.Z.getSeqHelper()),webLogoBounds:()=>this.webLogoBounds,cachedWebLogoTooltip:()=>this.cachedWebLogoTooltip,highlightCallback:(t,e,n)=>{(0,x.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");I.FZ(this.analysisView.grid,this.monomerPositionStats,this.positionColumns,this.getScaledActivityColumn(),t),this._layoutEventInitialized||(h.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,v.R)(this.df.getCol(this.settings.sequenceColumnName),z.Z.getSeqHelper()),i=n.columns.names();if(i.every((t=>e.contains(t))))i.forEach((t=>{this.df.col(t).setTag(_.gp.ANALYSIS_COL,"true"),this.df.col(t).setTag(_.gp.POSITION_COL,"true"),I.rI(this.df.col(t),this.alphabet)}));else for(const t of i){let i=this.df.col(t);const o=n.getCol(t);null!==i&&e.remove(t);const r=o.categories,s=o.getRawData();i=e.addNew(o.name,o.type).init((t=>r[s[t]])),i.setTag(_.gp.ANALYSIS_COL,"true"),i.setTag(_.gp.POSITION_COL,"true"),I.rI(i,this.alphabet)}this.df.name=t}createScaledCol(){const t=this.analysisView.grid,e=(0,x.Y1)(this.df.getCol(this.settings.activityColumnName),this.settings.activityScaling);this.df.columns.replace(_.$2.ACTIVITY,e),t.columns.setOrder([e.name])}unhighlight(){this.isHighlighting&&(this.df.rows.highlight(null),this.isHighlighting=!1)}setTooltips(){this.analysisView.grid.onCellTooltip(((t,e,n)=>{var i,o;return!(!t.isColHeader||(null===(i=t.tableColumn)||void 0===i?void 0:i.semType)!==_.uF.MONOMER)||!(!t.isTableCell||(null===(o=t.tableColumn)||void 0===o?void 0:o.semType)!==_.uF.MONOMER)}))}getCombinedSelection(){var t,e,n,i,o,r,s,a;const l=new m.A(this.df.rowCount,!1),u=(t,e)=>{for(const[n,i]of Object.entries(t))for(const t of i){const i=null==e?void 0:e[n];if(void 0===i)continue;const o=i[t];void 0!==o&&l.or(o.mask)}};u(this.webLogoSelection,this.monomerPositionStats);const c=this.findViewer($.SEQUENCE_VARIABILITY_MAP);u(null!==(t=null==c?void 0:c.invariantMapSelection)&&void 0!==t?t:{},null!==(e=null==c?void 0:c.monomerPositionStats)&&void 0!==e?e:null),((t,e)=>{var n,i;for(const[o,r]of Object.entries(t))for(const t of r){const r=null!==(i=null===(n=null==e?void 0:e.get(t))||void 0===n?void 0:n.get(o))&&void 0!==i?i:null;if(null!==r)for(const[t,e]of r.entries()){l.setTrue(t);for(const t of e)l.setTrue(t)}}})(null!==(n=null==c?void 0:c.mutationCliffsSelection)&&void 0!==n?n:{},null!==(i=null==c?void 0:c.mutationCliffs)&&void 0!==i?i:null);const h=this.findViewer($.MOST_POTENT_RESIDUES);u(null!==(o=null==h?void 0:h.invariantMapSelection)&&void 0!==o?o:{},null!==(r=null==h?void 0:h.monomerPositionStats)&&void 0!==r?r:null);const f=this.findViewer($.LOGO_SUMMARY_TABLE);for(const t of Object.keys(null!==(s=null==f?void 0:f.clusterSelection)&&void 0!==s?s:{}))for(const e of null!==(a=f.clusterSelection[t])&&void 0!==a?a:[]){const n=f.clusterStats[t][e];l.or(n.mask)}const p=d.BitSet.fromBytes(l.buffer.buffer,l.length);return this.df.filter.anyFalse?p.and(this.df.filter):p}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;h.shell.o=t.root,n=setTimeout((()=>{h.shell.o!=t.root&&(h.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){k._package.logger.debug("Peptides: Error on selection changed"),k._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($.LOGO_SUMMARY_TABLE);null!==n&&void 0!==n.model&&(n._logoSummaryTable=null!==(t=n.createLogoSummaryTable())&&void 0!==t?t:n._logoSummaryTable,n._viewerGrid=null!==(e=n.createLogoSummaryTableGrid())&&void 0!==e?e:n._viewerGrid,n.render())}catch(t){k._package.logger.debug("Peptides: Error on filter changed"),k._package.logger.debug(t)}finally{i()}})),this.isBitsetChangedInitialized=!0}fireBitsetChanged(t,e=!1){this.accordionSource=t,this.isBitsetChangedInitialized||this.setBitsetCallback(),this.isUserChangedSelection=!1,this.df.selection.fireChanged(),e&&this.df.filter.fireChanged(),this.controlFire=!0,this.df.selection.fireChanged(),e&&this.df.filter.fireChanged(),this.isUserChangedSelection=!0,this.webLogoSelectedMonomers=(0,x.qx)(this.df)}setGridProperties(t){var e,n,i,o;const r=this.analysisView.grid,s=r.props;s.allowColSelection=null!==(e=null==t?void 0:t.allowColSelection)&&void 0!==e&&e,s.allowEdit=null!==(n=null==t?void 0:t.allowEdit)&&void 0!==n&&n,s.showReadOnlyNotifications=null!==(i=null==t?void 0:t.showReadOnlyNotifications)&&void 0!==i&&i,s.showCurrentRowIndicator=null!==(o=null==t?void 0:t.showCurrentRowIndicator)&&void 0!==o&&o;const a=this.positionColumns;if(null===a)throw new Error("PeptidesError: Could not set grid properties: positionColumns are null");let l=10;const u=r.canvas.getContext("2d");if(null===u)throw new Error("PeptidesError: Could not set grid properties: canvas context is null");for(const t of a){const e=(0,f.zS)(t.categories.reduce(((t,e)=>t.length>e.length?t:e)),6),n=Math.ceil(u.measureText(e).width);l=Math.max(l,n)}const c=a.map((t=>t.name));for(let t=1;t<this.analysisView.grid.columns.length;++t){const e=this.analysisView.grid.columns.byIndex(t);if(null===e)throw new Error(`PeptidesError: Could not get analysis view: grid column with index '${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=c.includes(e.column.name)||e.column.name===_.$2.ACTIVITY}setTimeout((()=>{for(const t of a){const e=r.col(t.name);if(null===e)throw new Error(`PeptidesError: Could not set column width: grid column '${t.name}' is null`);e.width=l+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 K(this,void 0,void 0,(function*(){const t=d.TaskBarProgressIndicator.create("Calculating distance matrix...");try{const t=d.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){k._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(_.gp.MULTIPLE_VIEWS)){const t=c.iconFA("wrench",(()=>(0,R.OH)(this)),"Peptides analysis settings");this.analysisView.setRibbonPanels([[t]],!1),this.isRibbonSet=!0,this.updateGrid()}this.subs.push(h.events.onAccordionConstructed.subscribe((t=>{if(!(h.shell.o instanceof d.SemanticValue||h.shell.o instanceof d.Column&&this.df.columns.toList().includes(h.shell.o)))return;const e=t.getPane("Actions"),n=E()(e.root).find(".d4-flex-col"),i=c.label("Calculate identity");i.classList.add("d4-link-action"),c.tooltip.bind(i,"Adds a column with fractions of matching monomers against sequence in the current row"),i.onclick=()=>{const t=this.df.getCol(this.settings.sequenceColumnName);w(this.df,t,t.get(this.df.currentRowIdx),g.IDENTITY,z.Z.getSeqHelper()).then((e=>e.setTag(_.gp.IDENTITY_TEMPLATE,t.get(this.df.currentRowIdx)))).catch((t=>k._package.logger.debug(t)))},n.append(c.span([i],"d4-markdown-row"));const o=c.label("Calculate similarity");o.classList.add("d4-link-action"),c.tooltip.bind(o,"Adds a column with sequence similarity scores against sequence in the current row"),o.onclick=()=>{const t=this.df.getCol(this.settings.sequenceColumnName);w(this.df,t,t.get(this.df.currentRowIdx),g.SIMILARITY,z.Z.getSeqHelper()).then((e=>e.setTag(_.gp.SIMILARITY_TEMPLATE,t.get(this.df.currentRowIdx)))).catch((t=>k._package.logger.debug(t)))},n.append(c.span([o],"d4-markdown-row"))}))),this.subs.push(h.events.onViewRemoved.subscribe((t=>{t.id===this.analysisView.id&&this.subs.forEach((t=>t.unsubscribe())),h.log.debug(`Peptides: view ${t.name} removed`)}))),this.subs.push(h.events.onTableRemoved.subscribe((t=>{t.id===this.df.id&&this.subs.forEach((t=>t.unsubscribe())),h.log.debug(`Peptides: table ${t.name} removed`)}))),this.subs.push(h.events.onProjectClosed.subscribe((t=>{t.id===h.shell.project.id&&this.subs.forEach((t=>t.unsubscribe())),h.log.debug(`Peptides: project ${t.name} closed`)}))),this.fireBitsetChanged(null,!0),this.analysisView.grid.invalidate()}}findViewer(t){return S()(this.analysisView.viewers).find((e=>e.type===t))||null}addLogoSummaryTable(t){return K(this,void 0,void 0,(function*(){null!=t||(t={sequenceColumnName:this.settings.sequenceColumnName,clustersColumnName:S()(this.df.columns.categorical).next().value,activityColumnName:this.settings.activityColumnName,activityScaling:this.settings.activityScaling});const e=yield this.df.plot.fromType($.LOGO_SUMMARY_TABLE,t);(0,x.Lv)()&&this.analysisView.addViewer(e),this.analysisView.dockManager.dock(e,d.DOCK_TYPE.RIGHT,null,$.LOGO_SUMMARY_TABLE),e.viewerGrid.invalidate()}))}addClusterMaxActivityViewer(t){return K(this,void 0,void 0,(function*(){var e,n,i,o,r,s,a,l,u;const c=null!==(o=null!==(n=null===(e=this._mclCols)||void 0===e?void 0:e.find((t=>t.toLowerCase().startsWith("cluster (mcl)"))))&&void 0!==n?n:null===(i=this.findViewer($.LOGO_SUMMARY_TABLE))||void 0===i?void 0:i.clustersColumnName)&&void 0!==o?o:null===(r=this._sequenceSpaceCols)||void 0===r?void 0:r.find((t=>t.toLowerCase().startsWith("cluster")));null!=t||(t={activityColumnName:this.settings.activityColumnName,clusterColumnName:null!=c?c:null===(s=S()(this.df.columns.categorical).next().value)||void 0===s?void 0:s.name,activityTarget:_.wf.HIGH,connectivityColumnName:null!==(l=null!==(a=this._mclCols.find((t=>t.toLowerCase().startsWith("connectivity"))))&&void 0!==a?a: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!==l?l:"",clusterSizeThreshold:20,activityThreshold:1e3});const h=yield this.df.plot.fromType($.CLUSTER_MAX_ACTIVITY,t),f=null!==(u=this.findViewerNode($.LOGO_SUMMARY_TABLE))&&void 0!==u?u:null;this.analysisView.dockManager.dock(h,f?d.DOCK_TYPE.DOWN:d.DOCK_TYPE.RIGHT,f,$.CLUSTER_MAX_ACTIVITY)}))}addMonomerPosition(t){return K(this,void 0,void 0,(function*(){null!=t||(t={maxMutations:1,activityScaling:this.settings.activityScaling,activityColumnName:this.settings.activityColumnName,sequenceColumnName:this.settings.sequenceColumnName,minActivityDelta:0,activityTarget:_.wf.HIGH});const e=yield this.df.plot.fromType($.SEQUENCE_VARIABILITY_MAP,t);(0,x.Lv)()&&this.analysisView.addViewer(e);const n=this.findViewer($.MOST_POTENT_RESIDUES),i=this.analysisView.dockManager,[o,r,s]=null===n?[d.DOCK_TYPE.DOWN,null,void 0]:[d.DOCK_TYPE.LEFT,this.findViewerNode($.MOST_POTENT_RESIDUES),.7];i.dock(e,o,r,$.SEQUENCE_VARIABILITY_MAP,s)}))}addMostPotentResidues(t){return K(this,void 0,void 0,(function*(){null!=t||(t={activityScaling:this.settings.activityScaling,activityColumnName:this.settings.activityColumnName,sequenceColumnName:this.settings.sequenceColumnName,minActivityDelta:0,maxMutations:1,activityTarget:_.wf.HIGH});const e=yield this.df.plot.fromType($.MOST_POTENT_RESIDUES,t);(0,x.Lv)()&&this.analysisView.addViewer(e);const n=this.findViewer($.SEQUENCE_VARIABILITY_MAP),i=this.analysisView.dockManager,[o,r,s]=null===n?[d.DOCK_TYPE.DOWN,null,void 0]:[d.DOCK_TYPE.RIGHT,this.findViewerNode($.SEQUENCE_VARIABILITY_MAP),.3];i.dock(e,o,r,$.MOST_POTENT_RESIDUES,s)}))}createNewView(){const t=this.getVisibleSelection(),e=this.df.clone(t);for(const[t,n]of e.tags)e.setTag(t,t===_.gp.SETTINGS?n:"");e.name="Peptides Multiple Views",e.setTag(_.gp.MULTIPLE_VIEWS,"1");const n=h.shell.addTableView(e),i=this.findViewer($.LOGO_SUMMARY_TABLE);return null!=i&&n.addViewer($.LOGO_SUMMARY_TABLE,{[`sequence${_.To}`]:i.sequenceColumnName,[`activity${_.To}`]:i.activityColumnName,activityScaling:i.activityScaling,webLogoMode:i.webLogoMode,membersRatioThreshold:i.membersRatioThreshold,[`clusters${_.To}`]:i.clustersColumnName}),e.getTag(d.TAGS.ID)}clusterEmbeddings(){return K(this,void 0,void 0,(function*(){var t,e;if(!this._sequenceSpaceCols||0===this._sequenceSpaceCols.length)return void h.shell.warning("Embeddings columns are not initialized");const i=this._sequenceSpaceCols.filter((t=>t.toLowerCase().startsWith("embed_")));if(2!==i.length)return void h.shell.warning(`Found ${i.length} embeddings columns, expected 2`);const o=this._sequenceSpaceCols.filter((t=>t.toLowerCase().startsWith("cluster")));o.length>0&&this.df.columns.remove(o[0]);const r=this.df.getCol(i[0]).getRawData(),s=this.df.getCol(i[1]).getRawData(),a=null!==(t=this.settings.sequenceSpaceParams.epsilon)&&void 0!==t?t:.01,l=null!==(e=this.settings.sequenceSpaceParams.minPts)&&void 0!==e?e:4,u=yield function(t,e,i,o){return r=this,s=void 0,l=function*(){return new Promise((function(r,s){const a=new Worker(new URL(n.p+n.u(682),n.b));a.postMessage({embedX:t,embedY:e,minPts:o,epsilon:i}),a.onmessage=({data:{error:t,clusters:e}})=>{a.terminate(),t?s(t):r(e)}}))},new((a=void 0)||(a=Promise))((function(t,e){function n(t){try{o(l.next(t))}catch(t){e(t)}}function i(t){try{o(l.throw(t))}catch(t){e(t)}}function o(e){var o;e.done?t(e.value):(o=e.value,o instanceof a?o:new a((function(t){t(o)}))).then(n,i)}o((l=l.apply(r,s||[])).next())}));var r,s,a,l}(r,s,a,l),c=this.df.columns.getUnusedName("Cluster (DBSCAN)"),d=this.df.columns.addNewString(c);d.init((t=>u[t].toString())),null!==this._sequenceSpaceViewer&&(this._sequenceSpaceViewer.props.colorColumnName=d.name),this._sequenceSpaceCols=[i[0],i[1],d.name];const f=this.analysisView.grid.col(d.name);f&&(f.visible=!1)}))}addMCLClusters(){return K(this,void 0,void 0,(function*(){var t,e,n,i,o;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 r=this.df.getCol(this.settings.sequenceColumnName);null!==(n=(o=this.settings).mclSettings)&&void 0!==n||(o.mclSettings=new N.av);const s=this.settings.mclSettings;let a=0;const l=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),a++}5===a&&l.unsubscribe()})),u=h.events.onViewerAdded.subscribe((t=>{try{const e=t.args.viewer;if(e.type===d.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,d.DOCK_TYPE.FILL,t)}))}u.unsubscribe()}}catch(t){console.error(t)}})),c=JSON.stringify({cols:[r].map((t=>t.name)),metrics:[s.distanceF],weights:[1],aggregationMethod:j.MANHATTAN,preprocessingFuncs:["macromoleculePreprocessingFunction"],preprocessingFuncArgs:[{gapOpen:s.gapOpen,gapExtend:s.gapExtend,fingerprintType:s.fingerprintType}],threshold:s.threshold,maxIterations:s.maxIterations,useWebGPU:s.useWebGPU,inflate:s.inflation,minClusterSize:s.minClusterSize}),f=null!==(i=this.analysisView)&&void 0!==i?i:h.shell.getTableView(this.df.name);if(f){const t=d.Func.find({package:"EDA",name:"markovClusteringViewer"})[0];if(!t)throw new Error("Markov clustering function is not found");if(yield t.apply(),f.addViewer($.MCL,{mclProps:c}),yield d.delay(500),this._mclViewer=this.findViewer($.MCL),yield this._mclViewer.initPromise,this._mclViewer=this.findViewer($.MCL),!this._mclViewer||!this._mclViewer.isDetached)return null==u||u.unsubscribe(),void(null==l||l.unsubscribe());const e=this.findViewer($.LOGO_SUMMARY_TABLE);e&&(e._clusterStats=null,e._clusterSelection=null,e._viewerGrid=null,e._logoSummaryTable=null,e.render())}}))}addSequenceSpace(){return K(this,arguments,void 0,(function*(t={}){var e,n,i,o;if(null!==this._sequenceSpaceViewer)try{null===(e=this._sequenceSpaceViewer)||void 0===e||e.detach(),null===(n=this._sequenceSpaceViewer)||void 0===n||n.close()}catch(t){}0!==this._sequenceSpaceCols.length&&this._sequenceSpaceCols.forEach((t=>this.df.columns.remove(t))),this._sequenceSpaceCols=[];let r=this.df.getCol(this.settings.sequenceColumnName);const s=z.Z.getSeqHelper().getSeqHandler(r);if(s.isHelm())try{h.shell.warning("Column is in HELM notation. Sequences space will linearize sequences from position 0 prior to analysis");const t=s.convert(f.Hi.SEPARATOR,"/"),e=this.df.columns.getUnusedName(`Separator(${r.name})`);t.name=e,this.df.columns.add(t,!0),this.analysisView.grid.col(e).visible=!1,r=t}catch(t){return h.shell.error("Error on converting HELM notation to linear notation"),void h.shell.error(t)}const a=!t.clusterCol&&!!t.clusterEmbeddings,l=null!==(o=null===(i=this.settings)||void 0===i?void 0:i.sequenceSpaceParams)&&void 0!==o?o:new N.GI(a);l.clusterEmbeddings=a;const u={table:this.df,molecules:r,methodName:A.UMAP,similarityMetric:l.distanceF,plotEmbeddings:!0,options:{bypassLargeDataWarning:!0,dbScanEpsilon:l.epsilon,dbScanMinPts:l.minPts,randomSeed:"1",preprocessingFuncArgs:{gapOpen:l.gapOpen,gapExtend:l.gapExtend,fingerprintType:l.fingerprintType}},clusterEmbeddings:l.clusterEmbeddings};let c=0;const m=l.clusterEmbeddings?3:2,p=this.df.onColumnsAdded.subscribe((t=>{for(const e of t.columns)if(e.name.toLowerCase().startsWith("embed_")||l.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),c++}c===m&&p.unsubscribe()})),g=h.events.onViewerAdded.subscribe((t=>{try{const e=t.args.viewer;if(e.type===d.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,d.DOCK_TYPE.FILL,t)}))}g.unsubscribe()}}catch(t){console.error(t)}})),v=yield h.functions.call("Bio:sequenceSpaceTopMenu",u);g.unsubscribe(),v instanceof d.ScatterPlotViewer&&(l.clusterEmbeddings||t.clusterCol||(v.props.colorColumnName=this.getScaledActivityColumn().name),v.props.showXSelector=!1,v.props.showYSelector=!1,t.clusterCol&&(v.props.colorColumnName=t.clusterCol.name),this._sequenceSpaceViewer=v,v.onContextMenu.subscribe((t=>{try{t.item("Modify Sequence space parameters",(()=>{(0,R.OH)(this)}))}catch(t){}})))}))}}Z.modelName="peptidesModel"},3262:(t,e,n)=>{"use strict";n.r(e),n.d(e,{PackageFunctions:()=>mt,Peptides:()=>j,_package:()=>ct,clusterMaxActivity:()=>tt,getMonomerWorksInstance:()=>ht,getTreeHelperInstance:()=>dt,initPeptides:()=>Y,logoSummaryTable:()=>X,lstPiechartCellRenderer:()=>it,macromoleculeSarFastaDemo:()=>nt,manualAlignment:()=>et,monomerPosition:()=>K,mostPotentResidues:()=>Z,mutationCliffs:()=>Q,peptidesDialog:()=>W,peptidesPanel:()=>z,sequencePositionStatistics:()=>J,testInitFunctionPeptides:()=>$});var i=n(4328),o=n(7389),r=n(6082),s=n(440),a=n(7233),l=n.n(a),u=(n(4788),n(9499)),c=n(726),h=n(3541),d=n(5480);n(3981);class f{constructor(t){this.monomerLib=t}getCappedRotatedMonomer(t,e){const n=this.monomerLib.getMonomer(t,e);return n?n.molfile:null}}var m=n(4139),p=n(8608),g=n(2003),v=n(115),C=n(5072),y=n.n(C),w=n(7825),A=n.n(w),b=n(7659),S=n.n(b),T=n(5056),E=n.n(T),_=n(540),N=n.n(_),x=n(1113),M=n.n(x),I=n(6677),O={};O.styleTagTransform=M(),O.setAttributes=E(),O.insert=S().bind(null,"head"),O.domAPI=A(),O.insertStyleElement=N(),y()(I.A,O),I.A&&I.A.locals&&I.A.locals;var L;!function(t){let e,n;!function(t){t.vert=function(t){return o.divV(t.map((t=>o.render(t))),{classes:"u2-panel"})},t.horz=function(t){return o.divH(t.map((t=>o.render(t))),{classes:"u2-panel"})}}(e=t.panels||(t.panels={})),t.appHeader=function(t){const n=o.iconImage("",t.iconPath);l()(n).addClass("ui-app-header-icon").css("margin-right","20px"),t.iconSize&&(n.style.width=`${t.iconSize}px`,n.style.height=`${t.iconSize}px`);const i=e.horz([]);if(t.appTitle){i.classList.add("u2-app-header-with-name");const e=o.divV([o.divText(t.appTitle,"u2-app-header-app-name-div")],"u2-app-header-app-name-and-slogan-div");t.appSubTitle&&e.append(o.divText(t.appSubTitle));const r=o.div(n);i.append(o.divH([r,e]))}else i.append(n);const r=e.vert([o.markdown(t.description),t.learnMoreUrl?o.link("Learn more",t.learnMoreUrl,void 0,{style:{marginLeft:"15px"}}):null]);return r.classList.add("u2-app-header-description"),i.append(r),t.bottomLine&&i.classList.add("u2-app-header-bottom-line"),i},function(t){t.runAsync=function(t,e){return n=this,r=void 0,a=function*(){o.setUpdateIndicator(t,!0);try{return yield e()}catch(t){i.log.error(t)}finally{o.setUpdateIndicator(t,!1)}},new((s=void 0)||(s=Promise))((function(t,e){function i(t){try{l(a.next(t))}catch(t){e(t)}}function o(t){try{l(a.throw(t))}catch(t){e(t)}}function l(e){var n;e.done?t(e.value):(n=e.value,n instanceof s?n:new s((function(t){t(n)}))).then(i,o)}l((a=a.apply(n,r||[])).next())}));var n,r,s,a}}(n=t.tools||(t.tools={}))}(L||(L={}));var P=n(144),R=n.n(P);const k=rxjs.operators;class V extends r.JsViewer{get scViewer(){return this._scViewer||(this._scViewer=this.createSCViewer()),this._scViewer}constructor(){super(),this._titleHost=o.divText(u.q.CLUSTER_MAX_ACTIVITY,{id:"pep-viewer-title",style:{marginRight:"auto"}}),this._selsectIcon=o.div(),this.activityTarget=m.wf.HIGH,this.viewerError="",this.renderTimeout=null,this.renderDebounceTime=500,this.scFilterQuery=`\${${V.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",m.wf.HIGH,{choices:[m.wf.HIGH,m.wf.LOW]}),this.clusterSizeThreshold=this.int("clusterSizeThreshold",20),this.activityThreshold=this.float("activityThreshold",1e3,{step:.1}),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:r.AxisType.logarithmic,yAxisType:r.AxisType.logarithmic,invertYAxis:this.activityTarget===m.wf.LOW,xColumnName:V.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(![r.COLUMN_TYPE.FLOAT,r.COLUMN_TYPE.INT,r.COLUMN_TYPE.BIG_INT,r.COLUMN_TYPE.QNUM].includes(n.type))return this.viewerError="Activity column should be numeric",null;const a=this.dataFrame.columns.getOrCreate(V.clusterSizeColName,r.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=r.AxisType.linear);const u={},c={};for(let t=0;t<this.dataFrame.rowCount;t++){const e=i.get(t);if(null==e||i.isNone(t)||n.isNone(t))continue;const o=n.get(t),r=u[e];if((null==r||null==r||o>n.get(r)&&this.activityTarget===m.wf.HIGH||o<n.get(r)&&this.activityTarget===m.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 h=this.dataFrame.columns.getOrCreate(V.maxActivityInClusterColName,r.COLUMN_TYPE.INT);h.init((t=>i.isNone(t)?0:t===u[i.get(t)]?1:0)),this.dataFrame.columns.getOrCreate(V.maxConnectivityInClusterColName,r.COLUMN_TYPE.INT).init((t=>i.isNone(t)?0:t===c[i.get(t)]?1:0)),this.dataFrame.columns.getOrCreate(V.synSelectionColName,r.TYPE.STRING).init((t=>{if(i.isNone(t))return null;let e=null;return t===u[i.get(t)]&&(e=V.maxActivityLabel),s&&t===c[i.get(t)]&&(e=e?`${e}, ${V.maxConnectivityLabel}`:V.maxConnectivityLabel),e})),e.xColumnName=V.clusterSizeColName,e.yColumnName=this.activityColumnName,e.filter=this.scFilterQuery,this.viewerError="";const d=r.Viewer.scatterPlot(this.dataFrame,e);this.selectionSubscription&&this.selectionSubscription.unsubscribe(),this.selectionSubscription=d.onDataEvent.pipe((0,k.filter)((t=>"d4-select"==t.type))).subscribe((t=>{var e,n;const o=null!==(n=null===(e=t.bitset)||void 0===e?void 0:e.getSelectedIndexes())&&void 0!==n?n:[],s=this.dataFrame.selection,a=r.BitSet.create(this.dataFrame.rowCount,(t=>1==h.get(t)));a.and(s);for(let t=0;t<o.length;t++){const e=o[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 f=()=>{const t=r.BitSet.create(this.dataFrame.rowCount);Object.entries(u).forEach((([e,i])=>{var o;if(null==e||null==i)return;const r=parseInt(e),s=n.get(i),a=null!==(o=l[r])&&void 0!==o?o:l[e];s<this.activityThreshold&&a<this.clusterSizeThreshold||(t.set(i,!0,!1),null!=c[r]&&t.set(c[r],!0,!1))})),t.fireChanged(),this.dataFrame.selection.copyFrom(t,!0)};return this._selsectIcon=o.iconSvg("select-all",(()=>{f()}),"Select 3 Active quadrants"),this._selsectIcon.style.cursor="pointer",this._selsectIcon.style.marginRight="5px",f(),this.linesDrawSubscription&&this.linesDrawSubscription.unsubscribe(),this.linesDrawSubscription=d.onBeforeDrawScene.subscribe((()=>{const t=d.getInfo().canvas.getContext("2d"),e=d.viewport,n=d.worldToScreen(e.x,this.activityThreshold),i=d.worldToScreen(this.clusterSizeThreshold,e.y),o=d.worldToScreen(e.x+e.width,this.activityThreshold),r=d.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(o.x,o.y),t.moveTo(i.x,i.y),t.lineTo(r.x,r.y),t.stroke(),t.closePath()})),d}onTableAttached(){var t,e,n,i,o,r,s,a,l,u,c,h;super.onTableAttached();const d=null!==(e=null===(t=this.dataFrame)||void 0===t?void 0:t.col(m.$2.ACTIVITY))&&void 0!==e?e:null===(i=R()(null===(n=this.dataFrame)||void 0===n?void 0:n.columns.numerical).next())||void 0===i?void 0:i.value;null!=d&&(null===(o=this.getProperty(`activity${m.To}`))||void 0===o||o.set(this,d.name));const f=null===(s=R()(null===(r=this.dataFrame)||void 0===r?void 0:r.columns.categorical).next())||void 0===s?void 0:s.value;null!=f&&(null===(a=this.getProperty(`cluster${m.To}`))||void 0===a||a.set(this,f.name));const p=null===(u=R()(null===(l=this.dataFrame)||void 0===l?void 0:l.columns.numerical).next())||void 0===u?void 0:u.value;null!=p&&(null===(c=this.getProperty(`connectivity${m.To}`))||void 0===c||c.set(this,p.name)),this.render(),null===(h=this.dataFrame)||void 0===h||h.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(o.divText(null!==(t=this.viewerError)&&void 0!==t?t:"Error creating scatter plot"));const i=o.div("Cluster Size",{style:{alignSelf:"center",color:"var(--grey-6)",marginBottom:"5px"}}),r=o.div(this.activityTarget===m.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(o.divH([r,o.divV([o.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${m.To}`&&(this._scViewer=null),this.render()}}V.clusterSizeColName="~cluster.size",V.maxActivityInClusterColName="~max.activity.for.cluster",V.maxConnectivityInClusterColName="~max.connectivity.for.cluster",V.synSelectionColName="Syn Selection",V.maxActivityLabel="Max Activity",V.maxConnectivityLabel="Max Connectivity";var F=n(3163);class D extends r.JsViewer{constructor(){super(),this.showPositionInfo=!0,this.positions=this.string("positions","1",{description:"Comma-separated sequence positions (1-based) to analyze"}),this.sequenceColumnName=this.column("sequence",{semType:r.SEMTYPE.MACROMOLECULE,nullable:!1}),this.valueColumnName=this.column("value",{columnTypeFilter:"numerical",nullable:!1}),this.showPositionInfo=this.bool("showPositionInfo",!0,{nullable:!1,defaultValue:!0,description:"Show position selector in the viewer header"}),this.subs.push(i.events.onContextMenu.subscribe((t=>{var e;t.causedBy&&t.causedBy.target&&(null===(e=this._boxPlotViewer)||void 0===e?void 0:e.root.contains(t.causedBy.target))&&(t.causedBy.preventDefault(),t.causedBy.stopPropagation(),t.causedBy.stopImmediatePropagation())})))}getPositionFromColumn(){var t;const e=this.dataFrame.col(this.sequenceColumnName);if(null==e)return 1;const n=null!==(t=e.getTag(g.gp.selectedPosition))&&void 0!==t?t:"1",i=parseInt(n);return Number.isNaN(i)?1:Math.max(1,i)}parsePositions(){if(!this.positions)return[1];const t=this.positions.split(",").map((t=>parseInt(t.trim()))).filter((t=>!Number.isNaN(t)&&t>=1));return[...new Set(t)].sort(((t,e)=>t-e))}_setPositions(t){const e=[...new Set(t)].sort(((t,e)=>t-e));this.getProperty("positions").set(this,e.join(", "))}onTableAttached(){if(super.onTableAttached(),null==this.dataFrame.columns.bySemType(r.SEMTYPE.MACROMOLECULE))throw i.shell.error("No sequence column found"),new Error("No sequence column found");const t=this.dataFrame.columns.getUnusedName("~sequence_position_monomers");this._positionColumn=this.dataFrame.columns.addNewString(t),this._positionColumn.semType="Monomer",this._positionColumn.setTag("cell.renderer","Monomer"),this.getProperty("sequenceColumnName").set(this,this.dataFrame.columns.bySemType(r.SEMTYPE.MACROMOLECULE).name),this.getProperty("valueColumnName").set(this,R()(this.dataFrame.columns.numerical).next().value.name),this.getProperty("positions").set(this,String(this.getPositionFromColumn())),this.subs.push(r.debounce(this.dataFrame.onMetadataChanged,200).subscribe((t=>{const e=this.getPositionFromColumn();this.parsePositions().includes(e)||this._setPositions([e])})))}render(){var t;const e=this.parsePositions();if(!(null!=this.dataFrame&&this.sequenceColumnName&&e.length&&this._positionColumn&&this.valueColumnName))return;l()(this.root).empty(),null===(t=this._boxPlotViewer)||void 0===t||t.detach();const n=c.Z.getSeqHelper(),i=this.dataFrame.col(this.sequenceColumnName),o=n.getSeqHandler(i),s=o.maxLength,a=e.map((t=>o.getMonomersAtPosition(t-1,!0)));if(this._positionColumn.init((t=>a.map((e=>e[t])).join(g.ot))),this._boxPlotViewer=this.dataFrame.plot.box({categoryColumnNames:[this._positionColumn.name],plotStyle:"violin",valueColumnName:this.valueColumnName,colorColumnName:this._positionColumn.name,showColorSelector:!1,showSizeSelector:!1,showCategorySelector:!1,legendVisibility:r.VisibilityMode.Never,markerColorColumnName:this._positionColumn.name,title:"Sequence Position Statistics",autoLayout:!1,labelOrientation:"Vert"}),this.showPositionInfo){const t=this._renderPositionSelector(e,s);this.root.appendChild(t)}this._boxPlotViewer.props.statistics=["min","max","avg","med","count"],this._boxPlotViewer.root.style.width="100%",this._boxPlotViewer.root.style.height="100%",this.root.appendChild(this._boxPlotViewer.root),this._boxPlotViewer.sub(this._boxPlotViewer.onPropertyValueChanged.subscribe((t=>{var e,n,i,o;if((null===(n=null===(e=this._boxPlotViewer)||void 0===e?void 0:e.props)||void 0===n?void 0:n.valueColumnName)&&(null===(o=null===(i=this._boxPlotViewer)||void 0===i?void 0:i.props)||void 0===o?void 0:o.valueColumnName)!==this.valueColumnName){const t=this._boxPlotViewer.props.valueColumnName;setTimeout((()=>this.getProperty("valueColumnName").set(this,t)),10)}})))}_renderPositionSelector(t,e){const n=o.divH([],{style:{alignItems:"center",justifyContent:"center",gap:"4px",flexWrap:"wrap",padding:"4px 8px",width:"100%"}}),i=o.label(`${this.sequenceColumnName}:`);i.style.fontWeight="bold",i.style.marginRight="4px",n.appendChild(i);for(const i of t)n.appendChild(this._createChip(i,t,e));return n.appendChild(this._createAddButton(n,t,e)),n}_createChip(t,e,n){const i=1===e.length,r=document.createElement("span");r.textContent=String(t),r.style.marginRight="3px";const s=i?o.iconFA("pencil",(()=>this._showInlineEdit(a,t,n)),"Edit position"):o.iconFA("times",(()=>this._setPositions(e.filter((e=>e!==t)))),"Remove position");s.style.cursor="pointer",s.style.fontSize="10px",s.style.opacity="0.6";const a=o.divH([r,s],{style:{display:"inline-flex",alignItems:"center",background:"#f0f0f0",borderRadius:"12px",padding:"2px 8px",fontSize:"12px",cursor:"default",border:"1px solid #d0d0d0"}});return a}_showInlineEdit(t,e,n){var i;const o=document.createElement("input");o.type="number",o.min="1",o.max=String(n),o.value=String(e),o.style.cssText="width:45px;height:22px;font-size:12px;text-align:center;border-radius:12px;border:1px solid #aaa;outline:none;padding:0 4px;";let r=!1;const s=()=>{if(r)return;r=!0;const i=parseInt(o.value),s=this.parsePositions();!Number.isNaN(i)&&i>=1&&i<=n&&i!==e?this._setPositions(s.map((t=>t===e?i:t))):o.replaceWith(t)};o.addEventListener("keydown",(e=>{var n;"Enter"===e.key&&s(),"Escape"===e.key&&(r=!0,null===(n=t.parentElement)||void 0===n||n.replaceChild(t,o))})),o.addEventListener("blur",s),null===(i=t.parentElement)||void 0===i||i.replaceChild(o,t),o.focus(),o.select()}_createAddButton(t,e,n){const i=o.iconFA("plus-circle",(()=>{if(t.querySelector(".position-add-input"))return;const o=document.createElement("input");o.type="number",o.min="1",o.max=String(n),o.className="position-add-input",o.style.cssText="width:45px;height:22px;font-size:12px;text-align:center;border-radius:12px;border:1px solid #aaa;outline:none;padding:0 4px;";let r=!1;const s=()=>{if(r)return;r=!0;const t=parseInt(o.value);!Number.isNaN(t)&&t>=1&&t<=n&&!e.includes(t)?this._setPositions([...e,t]):o.remove()};o.addEventListener("keydown",(t=>{"Enter"===t.key&&s(),"Escape"===t.key&&(r=!0,o.remove())})),o.addEventListener("blur",s),t.insertBefore(o,i),o.focus()}),"Add position");return i.style.cursor="pointer",i.style.fontSize="14px",i.style.color="#2083d5",i}onPropertyChanged(t){null!=this.dataFrame&&this.sequenceColumnName&&this.render()}}var G=n(7471),U=function(t,e,n,i){return new(n||(n=Promise))((function(o,r){function s(t){try{l(i.next(t))}catch(t){r(t)}}function a(t){try{l(i.throw(t))}catch(t){r(t)}}function l(t){var e;t.done?o(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())}))};class q extends r.JsViewer{constructor(){super(),this.position=1,this.currentRowMutationsOnly=!1,this.yAxisType="Linear",this._mutationCliffsData=null,this._dfSubs=[],this._positionColumns=null,this._innerDf=null,this._lineChart=null,this._debounceTimer=null,this.sequenceColumnName=this.column("sequence",{semType:r.SEMTYPE.MACROMOLECULE,nullable:!1}),this.seriesColumnName=this.column("series",{columnTypeFilter:"categorical",nullable:!1}),this.activityColumnName=this.column("activity",{columnTypeFilter:"numerical",nullable:!1}),this.position=this.int("position",1,{nullable:!1,showSlider:!1,min:1,max:100,showPlusMinus:!0,description:"Position in the sequence to analyze (1 Based).",category:"Data"}),this.yAxisType=this.string("yAxisType","Linear",{choices:["Linear","Logarithmic"],description:"Y-Axis scale type.",nullable:!1,category:"Data"}),this.currentRowMutationsOnly=this.bool("currentRowMutationsOnly",!1,{nullable:!1,defaultValue:!1,description:"When enabled, the viewer will show mutations related to the peptide in current row in the dataframe and selected position.",category:"Data"}),this.root.classList.add("peptides-viewer-show-title")}onTableAttached(){var t,e;super.onTableAttached();const n=this.dataFrame.columns.bySemType(r.SEMTYPE.MACROMOLECULE);n&&this.getProperty("sequenceColumnName").set(this,n.name),this.getProperty("activityColumnName").set(this,R()(this.dataFrame.columns.numerical).next().value.name);const o=null===(e=null===(t=R()(this.dataFrame.columns.categorical))||void 0===t?void 0:t.filter((t=>{var e;return t.name!==this.sequenceColumnName&&(null===(e=t.name)||void 0===e?void 0:e.toLowerCase().includes("series"))})).next())||void 0===e?void 0:e.value;o&&this.getProperty("seriesColumnName").set(this,o.name),this.subs.push(r.debounce(this.dataFrame.onFilterChanged,200).subscribe((()=>{this.clearCache(),this.debouncedRender()}))),this.debouncedRender(),this.subs.push(i.events.onContextMenu.subscribe((t=>{var e;t.causedBy&&t.causedBy.target&&(null===(e=this._lineChart)||void 0===e?void 0:e.root.contains(t.causedBy.target))&&(t.causedBy.preventDefault(),t.causedBy.stopPropagation(),t.causedBy.stopImmediatePropagation())})))}get mutationCliffsData(){if(this._mutationCliffsData)return this._mutationCliffsData;if(!this.activityColumnName||!this.sequenceColumnName||!this.position)throw new Error("Activity column or Sequence column is not set, or position is invalid");return this._mutationCliffsData=new Promise(((t,e)=>U(this,void 0,void 0,(function*(){try{const e=this.dataFrame.col(this.activityColumnName).getRawData(),n=this.positionColumns,i=n[this.position-1].toList(),o=n.map(p.eY),r=yield(new G.a).calc(e,o,{maxMutations:1,minActivityDelta:0,filter:this.dataFrame.filter.anyFalse?new Uint32Array(this.dataFrame.filter.getBuffer().buffer):void 0,singlePosition:{position:this.position-1}});t({cliffs:r,monomers:i})}catch(t){e(t)}})))),this._mutationCliffsData}calculateDf(){return U(this,void 0,void 0,(function*(){if(!(this.dataFrame&&this.activityColumnName&&this.sequenceColumnName&&this.position))throw new Error("Activity column or Sequence column is not set, or position is invalid");const t=yield this.mutationCliffsData,e=new Set;t.cliffs.forEach((t=>{t.forEach((t=>{Array.from(t.entries()).forEach((([t,n])=>{const i=Number(t);this.currentRowMutationsOnly&&this.dataFrame.currentRowIdx!==i||(e.add(i),n.forEach((t=>e.add(Number(t)))))}))}))}));const n=Array.from(e.values()).sort(((t,e)=>t-e)),i=new Map;n.forEach(((t,e)=>{i.set(t,e)}));const o=n.map((e=>t.monomers[e])),s=this.dataFrame.col(this.activityColumnName).getRawData(),a=n.map((t=>s[t])),l=[r.Column.fromList("string",`Position ${this.position}`,o),r.Column.fromList("double",this.activityColumnName,a)];if(this.seriesColumnName){const t=this.dataFrame.col(this.seriesColumnName).getRawData(),e=this.dataFrame.col(this.seriesColumnName).categories,i=n.map((n=>e[t[n]])),o=r.Column.fromList("string",this.seriesColumnName,i);l.push(o)}const u=r.DataFrame.fromColumns(l);Array.from(this.dataFrame.columns.numerical).filter((t=>t.name!==this.activityColumnName&&t.name!==this.seriesColumnName)).forEach((t=>{u.columns.addNew(t.name,t.type)})),this._dfSubs.push(u.onMouseOverRowChanged.subscribe((t=>{if(u.mouseOverRowIdx>=0){const t=n[u.mouseOverRowIdx];this.dataFrame.mouseOverRowIdx=t}}))),this._dfSubs.push(this.dataFrame.onMouseOverRowChanged.subscribe((t=>{if(this.dataFrame.mouseOverRowIdx>=0){const t=i.get(this.dataFrame.mouseOverRowIdx);u.mouseOverRowIdx=null!=t?t:-1}})));let c=!1;this._dfSubs.push(u.onCurrentRowChanged.subscribe((t=>{if(u.currentRowIdx>=0){c=!0;const t=n[u.currentRowIdx];this.dataFrame.currentRowIdx=t}}))),this.currentRowMutationsOnly&&this._dfSubs.push(this.dataFrame.onCurrentRowChanged.subscribe((t=>{c?c=!1:(this.clearCache(!1),this.debouncedRender())})));let h=!1,d=!1;return this._dfSubs.push(r.debounce(u.onSelectionChanged,100).subscribe((t=>{const e=u.selection;if(h)h=!1;else if(d=!0,this.dataFrame.selection.setAll(!1,!1),e.anyTrue){for(let t=-1;-1!==(t=e.findNext(t,!0));){const e=n[t];this.dataFrame.selection.set(e,!0,!1)}this.dataFrame.selection.fireChanged()}else this.dataFrame.selection.fireChanged()}))),this._dfSubs.push(r.debounce(this.dataFrame.onSelectionChanged,100).subscribe((t=>{const e=this.dataFrame.selection;if(d)d=!1;else if(h=!0,u.selection.setAll(!1,!1),e.anyTrue){for(let t=-1;-1!==(t=e.findNext(t,!0));){const e=i.get(t);null!=e&&u.selection.set(e,!0,!1)}u.selection.fireChanged()}else u.selection.fireChanged()}))),u}))}get positionColumns(){if(this._positionColumns)return this._positionColumns;if(!this.dataFrame)return[];const t=u.i.getInstance(this.dataFrame),e=null==t?void 0:t.positionColumns;if(e&&e.length>0)return this._positionColumns=e,this._positionColumns;const n=this.dataFrame.col(this.sequenceColumnName),i=c.Z.getSeqHelper().getSeqHandler(n),o=i.maxLength,s=[];for(let t=0;t<o;t++){const e=i.getMonomersAtPosition(t,!0),n=r.Column.fromList("string",`Position ${t+1}`,e);s.push(n)}return this._positionColumns=s,this._positionColumns}get innerDf(){return this._innerDf?Promise.resolve(this._innerDf):(this._innerDf=this.calculateDf(),this._innerDf)}render(){return U(this,void 0,void 0,(function*(){if(l()(this.root).empty(),!(this.dataFrame&&this.activityColumnName&&this.sequenceColumnName&&this.position))return o.setUpdateIndicator(this.root,!1),void this.root.appendChild(B("Please set Activity column, Sequence column and Position properties."));if(this._lineChart){try{this._lineChart.detach()}catch(t){console.error("Error detaching previous line chart:",t)}this._lineChart=null}o.setUpdateIndicator(this.root,!0),this.root.style.display="flex",this.root.style.flexDirection="column";const t=yield this.innerDf;o.setUpdateIndicator(this.root,!1),0===t.rowCount?this.currentRowMutationsOnly?this.dataFrame.currentRowIdx>=0?this.root.appendChild(B("No mutations cliffs found for the current peptide at the selected position.")):this.root.appendChild(B("Please select a row in the main table to see mutation cliffs for the corresponding peptide at the selected position.")):this.root.appendChild(B("No mutation cliffs found for the selected position.")):(this._lineChart=t.plot.line({xColumnName:`Position ${this.position}`,yColumnNames:[this.activityColumnName],splitColumnNames:this.seriesColumnName?[this.seriesColumnName]:[],legendVisibility:this.seriesColumnName?"Always":"Never",legendPosition:"Right",showXSelector:!1,showYSelector:!0,showSplitSelector:!1,packCategories:!1,xAxisLabelOrientation:"Auto",axisFont:'normal normal 14px "Roboto"',controlsFont:'normal normal 14px "Roboto"'}),this._lineChart.sub(this._lineChart.onPropertyValueChanged.subscribe((t=>{var e,n,i,o,r,s,a,l;if((null===(n=null===(e=this._lineChart)||void 0===e?void 0:e.props)||void 0===n?void 0:n.yColumnNames)&&(null===(r=null===(o=null===(i=this._lineChart)||void 0===i?void 0:i.props)||void 0===o?void 0:o.yColumnNames)||void 0===r?void 0:r[0])!==this.activityColumnName){const t=null===(l=null===(a=null===(s=this._lineChart)||void 0===s?void 0:s.props)||void 0===a?void 0:a.yColumnNames)||void 0===l?void 0:l[0];setTimeout((()=>this.getProperty("activityColumnName").set(this,t)),1)}}))),this.root.appendChild(this._lineChart.root));const e=this.positionColumns.length+1,n=new Array(e-1).fill(0).map(((t,e)=>e+1)).map((t=>t.toString())),i=o.input.choice("Position",{value:this.position.toString(),items:n,nullable:!1,onValueChanged:t=>{if(!t)return;const e=parseInt(t);this.getProperty("position").set(this,e)}});if(i.input.style.width="40px",this.root.appendChild(o.divH([i.root],{style:{justifyContent:"center",marginTop:"4px",width:"100%",font:'normal normal 14px "Roboto"'}})),t.rowCount>0){const t=o.input.column("Series",{table:this.dataFrame,filter:t=>t.isCategorical&&t.name!==this.sequenceColumnName,tooltipText:"Select column for series splitting.",onValueChanged:t=>{const e=t?t.name:void 0;this.getProperty("seriesColumnName").set(this,e)},value:this.seriesColumnName?this.dataFrame.col(this.seriesColumnName):void 0});this.root.prepend(o.divH([t.root],{style:{justifyContent:"flex-end",paddingBottom:"4px",padding:"8px",width:"100%",font:'normal normal 14px "Roboto"'}}))}}))}debouncedRender(){o.setUpdateIndicator(this.root,!0),this._debounceTimer&&clearTimeout(this._debounceTimer),this._debounceTimer=setTimeout((()=>this.render()),300)}clearCache(t=!0){t&&(this._mutationCliffsData=null),this._innerDf=null,this._dfSubs.forEach((t=>t.unsubscribe())),this._dfSubs=[]}detach(){super.detach(),this._dfSubs.forEach((t=>t.unsubscribe())),this._dfSubs=[],clearTimeout(this._debounceTimer)}onPropertyChanged(t){if(super.onPropertyChanged(t),"activityColumnName"===(null==t?void 0:t.name)||"sequenceColumnName"===(null==t?void 0:t.name)||"position"===(null==t?void 0:t.name)||"seriesColumnName"===(null==t?void 0:t.name)){const e="seriesColumnName"===(null==t?void 0:t.name)||"activityColumnName"===(null==t?void 0:t.name);this.clearCache(!e),"sequenceColumnName"===(null==t?void 0:t.name)&&(this._positionColumns=null),this.debouncedRender()}else"yAxisType"===(null==t?void 0:t.name)?this._lineChart&&(this._lineChart.props.yAxisType=this.yAxisType.toLowerCase()):"currentRowMutationsOnly"===(null==t?void 0:t.name)&&(this.clearCache(!1),this.debouncedRender())}}function B(t){const e=o.divText(t);return e.style.fontSize="14px",e.style.marginTop="10px",e.style.textAlign="center",e}var H=function(t,e,n,i){return new(n||(n=Promise))((function(o,r){function s(t){try{l(i.next(t))}catch(t){r(t)}}function a(t){try{l(i.throw(t))}catch(t){r(t)}}function l(t){var e;t.done?o(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 Y(){return H(this,void 0,void 0,(function*(){yield mt.initPeptides()}))}function j(){return mt.Peptides()}function W(){return H(this,void 0,void 0,(function*(){return yield mt.peptidesDialog()}))}function $(t){return H(this,void 0,void 0,(function*(){yield mt.testInitFunctionPeptides(t)}))}function z(t){return H(this,void 0,void 0,(function*(){return yield mt.peptidesPanel(t)}))}function K(){return mt.monomerPosition()}function Z(){return mt.mostPotentResidues()}function Q(){return mt.mutationCliffs()}function X(){return mt.logoSummaryTable()}function J(){return mt.sequencePositionStatistics()}function tt(){return mt.clusterMaxActivity()}function et(t){return mt.manualAlignment(t)}function nt(){return H(this,void 0,void 0,(function*(){yield mt.macromoleculeSarFastaDemo()}))}function it(){return mt.lstPiechartCellRenderer()}var ot=function(t,e,n,i){var o,r=arguments.length,s=r<3?e:null===i?i=Object.getOwnPropertyDescriptor(e,n):i;if("object"==typeof Reflect&&"function"==typeof Reflect.decorate)s=Reflect.decorate(t,e,n,i);else for(var a=t.length-1;a>=0;a--)(o=t[a])&&(s=(r<3?o(s):r>3?o(e,n,s):o(e,n))||s);return r>3&&s&&Object.defineProperty(e,n,s),s},rt=function(t,e){if("object"==typeof Reflect&&"function"==typeof Reflect.metadata)return Reflect.metadata(t,e)},st=function(t,e){return function(n,i){e(n,i,t)}},at=function(t,e,n,i){return new(n||(n=Promise))((function(o,r){function s(t){try{l(i.next(t))}catch(t){r(t)}}function a(t){try{l(i.throw(t))}catch(t){r(t)}}function l(t){var e;t.done?o(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 lt,ut=null;const ct=new r.Package;function ht(){return ut}function dt(){return lt}function ft(t){return at(this,void 0,void 0,(function*(){const e=r.TaskBarProgressIndicator.create("Loading Peptides"),n=ct.webRoot+"files/"+t,o=yield i.data.loadTable(n);o.name="Peptides",i.shell.addTableView(o).name="PeptidesView",i.shell.windows.showProperties=!0,e.close()}))}i.decorators||(i.decorators={}),["func","init","param","panel","editor","demo","app","appTreeBrowser","fileHandler","fileExporter","model","viewer","filter","cellRenderer","autostart","dashboard","folderViewer","semTypeDetector","packageSettingsEditor","functionAnalysis","converter","fileViewer","model","treeBrowser","polyfill"].forEach((t=>{i.decorators[t]||(i.decorators[t]=function(t){return function(t,e,n){}})}));class mt{static initPeptides(){return at(this,void 0,void 0,(function*(){try{null!=ut||(ut=new f(yield i.functions.call("Bio:getBioLib"))),null!=lt||(lt=yield async function(){const t="Dendrogram",e=r.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)}}))}static Peptides(){const t=L.appHeader({iconPath:ct.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=r.View.create();return n.name="Peptides",o.appendAll(n.root,[t,o.divH([o.button("Simple demo",(()=>ft("aligned.csv")),""),o.button("Complex demo",(()=>ft("aligned_2.csv")),""),o.button("HELM demo",(()=>ft("aligned_3.csv")),"")])]),n}static peptidesDialog(){return at(this,void 0,void 0,(function*(){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(!r.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=yield(0,s.v)(i.shell.t),n=o.dialog("Analyze Peptides").add(e.host).onOK((()=>at(this,void 0,void 0,(function*(){e.callback()||n.show()}))));return n.show()}))}static testInitFunctionPeptides(t){return at(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)))}))}static peptidesPanel(t){return at(this,void 0,void 0,(function*(){if(!t.dataFrame||!r.Utils.firstOrNull(t.dataFrame.columns.numerical))return new r.Widget(o.divText("SAR Analysis requires an active table with at least one numerical column for activity"));const e=yield(0,s.v)(t.dataFrame,t);return new r.Widget(e.host)}))}static monomerPosition(){return new h.J}static mostPotentResidues(){return new h.UJ}static mutationCliffs(){return new q}static logoSummaryTable(){return new d.s}static sequencePositionStatistics(){return new D}static clusterMaxActivity(){return new V}static manualAlignment(t){const e=i.shell.t,n=null==e?void 0:e.temp[u.i.modelName];return n?function(t,e){const n=o.input.textArea("",{value:t.get(e.currentRowIdx)});l()(n.root).addClass("pep-textinput");const s=o.button("Apply",(()=>{return o=this,r=void 0,a=function*(){const o=c.Z.getSeqHelper().getSeqHandler(t),r=n.value,s=o.splitter(r),a=e.currentRowIdx;t.set(a,r);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)},new((s=void 0)||(s=Promise))((function(t,e){function n(t){try{l(a.next(t))}catch(t){e(t)}}function i(t){try{l(a.throw(t))}catch(t){e(t)}}function l(e){var o;e.done?t(e.value):(o=e.value,o instanceof s?o:new s((function(t){t(o)}))).then(n,i)}l((a=a.apply(o,r||[])).next())}));var o,r,s,a}),"Apply changes"),a=o.button(o.iconFA("redo"),(()=>n.value=t.get(e.currentRowIdx)),"Reset");return l()(a).addClass("pep-snippet-editor-icon pep-reset-icon"),new r.Widget(o.divV([a,n.root,s],"pep-textarea-box"))}(e.getCol(n.settings.sequenceColumnName),e):new r.Widget(o.divText("Manual alignment works with peptides analysis"))}static macromoleculeSarFastaDemo(){return at(this,void 0,void 0,(function*(){return yield function(){return t=this,e=void 0,o=function*(){i.shell.windows.showContextPanel=!0;const t=r.DataFrame.fromCsv(yield ct.files.readAsText("aligned.csv"));t.name="Simple peptides",t.id||(t.id=`Simple-peptides-analysis-table-id-${Math.random()}-${Date.now()}`);const e=i.shell.addTableView(t);yield r.delay(50);const n=e.grid;yield new Promise((t=>{var e;let i=null;const o=null===(e=null==n?void 0:n.onAfterDrawContent)||void 0===e?void 0:e.subscribe((()=>{i&&clearTimeout(i),o.unsubscribe(),t(void 0)}));i=setTimeout((()=>{o.unsubscribe(),t(void 0)}),3e3)}));const o=t.getCol("IC50"),a=t.getCol("AlignedSequence");a.semType=r.SEMTYPE.MACROMOLECULE,a.setTag(m.gp.ALPHABET,g.YI.PT),a.meta.units=g.Hi.FASTA,a.setTag(g.gp.aligned,"SEQ.MSA");const l=(0,p.Y1)(o,m.rg.MINUS_LG),u=new v.av;u.threshold=94,yield(0,s.n)(o,a,null,t,l,m.rg.MINUS_LG,{addMCL:!0,useEmbeddingsClusters:!0,mclSettings:u})},new((n=void 0)||(n=Promise))((function(i,r){function s(t){try{l(o.next(t))}catch(t){r(t)}}function a(t){try{l(o.throw(t))}catch(t){r(t)}}function l(t){var e;t.done?i(t.value):(e=t.value,e instanceof n?e:new n((function(t){t(e)}))).then(s,a)}l((o=o.apply(t,e||[])).next())}));var t,e,n,o}()}))}static lstPiechartCellRenderer(){return new F.DX}}ot([i.decorators.init({tags:["init"]}),rt("design:type",Function),rt("design:paramtypes",[]),rt("design:returntype",Promise)],mt,"initPeptides",null),ot([i.decorators.func(),rt("design:type",Function),rt("design:paramtypes",[]),rt("design:returntype",r.View)],mt,"Peptides",null),ot([i.decorators.func({"top-menu":"Bio | Analyze | SAR...",name:"Bio 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b(t,e,n,c,h,d={x:0,y:0,mpStats:{},monomerPosition:{}}){var f;if(null!==(f=h.isSelectionTable)&&void 0!==f||(h.isSelectionTable=!1),0==Object.keys(d.mpStats).length&&(d.mpStats=e),h.isSelectionTable&&(!h.webLogoBounds||!h.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,l,u,d;if(!(null===(i=t.cell)||void 0===i?void 0:i.isColHeader))return;const f=t.g,v=t.bounds,C=t.cell.tableColumn;f.save();try{if(f.beginPath(),f.clearRect(v.x,v.y,v.width,v.height),f.rect(v.x,v.y,v.width,v.height),f.clip(),(null==C?void 0:C.semType)===r.uF.MONOMER){let i;if(m.filter.anyFalse){null!==(l=(d=m).jsOnlyTemp)&&void 0!==l||(d.jsOnlyTemp={});const t=null!==(u=m.jsOnlyTemp[r.gp.M_P_STATS_CACHE])&&void 0!==u?u:{},e=null==t?void 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0!==v||(c.marginHorizontal=1),null!==(C=c.selectionWidth)&&void 0!==C||(c.selectionWidth=2),null!==(y=c.textHeight)&&void 0!==y||(c.textHeight=13),null!==(w=c.headerStyle)&&void 0!==w||(c.headerStyle=`bold ${c.textHeight*b}px Roboto, Roboto Local, sans-serif`);const S=(r.length-1)*c.upperLetterAscent;let T=(e.y+c.marginVertical)*b;const E=(e.height-2*c.marginVertical-S-1.25*c.textHeight)*b,_=(e.x+c.marginHorizontal)*b,N=Math.max(c.selectionWidth*b,.05*e.width*b),x=2*c.marginHorizontal+c.selectionWidth,M=(e.width-(x+c.marginHorizontal))*b,I=(e.x+x)*b,O=p.Z.getMonomerLib(),L={};for(const e of r){const i=E*(n[e].count/a),r=E*((null!==(A=u[e])&&void 0!==A?A:0)/a);if(L[e]=new o.Rect(I/b,T/b,M/b,i/b),t.resetTransform(),"-"!==e&&""!==e){const n=(0,s.zS)(e,5),a=t.measureText(n);r>0&&(t.lineWidth=N,t.line(_,T,_,T+r,o.Color.rowSelection));const l=O.getMonomerTextColor(g.o.AA,e);t.fillStyle=l,t.textAlign="left",t.textBaseline="top",t.font=c.symbolStyle;const u=M/a.width,h=i/c.upperLetterHeight;t.setTransform(u,0,0,h,I,T),t.fillText(n,0,0,a.width)}T+=i+c.upperLetterAscent*b}return t.resetTransform(),t.fillStyle=o.Color.toHtml(o.Color.black),t.textAlign="center",t.textBaseline="top",t.font=c.headerStyle,t.fillText(i,(e.x+e.width/2)*b,(e.y+e.height-c.textHeight)*b),L}(f,v,i,C.name,y,m.filter.trueCount,h.colorPalette(),h.headerSelectedMonomers?h.headerSelectedMonomers()[C.name]:{}),t.preventDefault()}}catch(t){console.warn(`PeptidesHeaderLogoError: couldn't render WebLogo for column \`${C.name}\`. See original error below.`),console.warn(t)}finally{f.restore()}})(t)));const v=n=>{var o;const s=t.hitTest(n.offsetX,n.offsetY);if((null==s?void 0:s.isColHeader)&&(null===(o=s.tableColumn)||void 0===o?void 0:o.semType)===r.uF.MONOMER){const t=function(t,e,n){const i=n[t.tableColumn.name];if(!i)return null;for(const[n,o]of Object.entries(i)){const i=e.offsetX>=o.x&&e.offsetX<=o.x+o.width,r=e.offsetY>=o.y&&e.offsetY<=o.y+o.height;if(i&&r)return{monomerOrCluster:n,positionOrClusterType:t.tableColumn.name}}return null}(s,n,h.webLogoBounds());if(null===t)return void(h.isSelectionTable||null==h.unhighlightCallback||h.unhighlightCallback());d.monomerPosition=t;const o=m.filter.anyFalse?m.clone(m.filter):m,r=o.getCol(c.name);!function(t,e,n,o,r,s){if("click"!==t.type||r.isSelectionTable||null==r.selectionCallback){const a=`${e.positionOrClusterType} = 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difference",t.COUNT="Count",t.RATIO="Ratio",t.MEAN="Mean",t.TOTAL_COUNT="∑"}(i||(i={})),function(t){t.MEMBERS="Members",t.WEB_LOGO="WebLogo",t.DISTRIBUTION="Distribution",t.MEAN_DIFFERENCE="Mean difference",t.P_VALUE="P-Value",t.RATIO="Ratio",t.CLUSTER="Cluster"}(o||(o={})),function(t){t.MONOMER="monomer",t.POSITION="pos",t.SEPARATOR="separator",t.ALPHABET="alphabet",t.FILTER="filter",t.SAR_MODE="sarMode",t.VISIBLE="visible",t.SETTINGS="settings",t.CUSTOM_CLUSTER="customCluster",t.MONOMER_POSITION_MODE="monomerPositionMode",t.MULTIPLE_VIEWS="isMultipleViews",t.IDENTITY_TEMPLATE="Identity template",t.SIMILARITY_TEMPLATE="Similarity template",t.ANALYSIS_COL="isAnalysisCol",t.POSITION_COL="isPositionCol",t.M_P_STATS_CACHE=".MPStatsCache",t.INVARIANT_MAP_COLOR_CACHE=".InvariantMapColorCache",t.INVARIANT_MAP_COLOR_MAX_CACHE=".InvariantMapColorMaxCache",t.INVARIANT_MAP_COLOR_MIN_CACHE=".InvariantMapColorMinCache"}(r||(r={})),function(t){t.MONOMER="Monomer",t.MACROMOLECULE_DIFFERENCE="MacromoleculeDifference"}(s||(s={}));const l="ColumnName";var u,c,h;!function(t){t.NONE="none",t.LG="lg",t.MINUS_LG="-lg"}(u||(u={})),function(t){t.HIGH="High",t.LOW="Low"}(c||(c={})),function(t){t.LST="lst-",t.MP="mp-",t.MPR="mpr-",t.WL="wl-"}(h||(h={}));const d=Object.values(a.AGG).filter((t=>![a.AGG.FIRST,a.AGG.KEY,a.AGG.PIVOT,a.AGG.SELECTED_ROWS_COUNT].includes(t))),f={[a.AGG.TOTAL_COUNT]:"totalCount",[a.AGG.VALUE_COUNT]:"valueCount",[a.AGG.UNIQUE_COUNT]:"uniqueCount",[a.AGG.MISSING_VALUE_COUNT]:"missingValueCount",[a.AGG.MIN]:"min",[a.AGG.MAX]:"max",[a.AGG.SUM]:"sum",[a.AGG.MED]:"med",[a.AGG.AVG]:"avg",[a.AGG.STDEV]:"stdev",[a.AGG.VARIANCE]:"variance",[a.AGG.SKEW]:"skew",[a.AGG.KURT]:"kurt",[a.AGG.Q1]:"q1",[a.AGG.Q2]:"q2",[a.AGG.Q3]:"q3"}},8608:(t,e,n)=>{"use strict";n.d(e,{$s:()=>_,AN:()=>i,AY:()=>d,B2:()=>x,BE:()=>w,BX:()=>O,CD:()=>b,F2:()=>g,FZ:()=>v,Lv:()=>I,Y1:()=>f,Z7:()=>C,ZR:()=>E,dl:()=>T,eY:()=>p,qx:()=>m,sg:()=>M,vW:()=>S,vY:()=>A,zm:()=>N,zz:()=>y});var i,o=n(7389),r=n(6082),s=n(4328),a=n(4139),l=n(8774),u=n(144),c=n.n(u),h=function(t,e,n,i){return new(n||(n=Promise))((function(o,r){function s(t){try{l(i.next(t))}catch(t){r(t)}}function a(t){try{l(i.throw(t))}catch(t){r(t)}}function l(t){var e;t.done?o(t.value):(e=t.value,e 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g(t,e,n={}){var i;const s=[],l=t.dataFrame.getCol(a.$2.SPLIT_COL).categories;for(let t=0;t<l.length;++t){if(!l[t])continue;const e=r.Color.toHtml(r.Color.categoricalPalette[t%r.Color.categoricalPalette.length]),a=o.label(null!==(i=n[l[t]])&&void 0!==i?i:l[t],{style:{color:e}});s.push(a)}const u=o.divV([o.divV(s),t.root,o.tableFromMap(e)]);return t.root.style.maxHeight="75px",u}function v(t,e,n){const o=n.filter,s=e.clone().and(o),l=t.length,u=t.getRawData(),c=o.trueCount,h=new Float32Array(c+s.trueCount),d=new Array(h.length);for(let t=0,e=0,n=0;t<l;++t){if(!o.get(t))continue;const r=s.get(t);h[e]=u[t],d[e]=r?i.SELECTION:i.ALL,e++,r&&(h[c+n]=u[t],d[c+n]=i.ALL,++n)}const f=r.Column.fromStrings(a.$2.SPLIT_COL,d),m=[i.ALL,i.SELECTION];return f.setCategoryOrder(m),f.meta.colors.setCategorical(),r.DataFrame.fromColumns([r.Column.fromFloat32Array(a.$2.ACTIVITY,h),f])}function C(t,e,n){t.dataFrame||r.DataFrame.fromColumns([t]);const i=t.dataFrame.filter,o=t.getRawData(),s=Array.from(new 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A(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 b(t){for(const e of Object.values(t))if(0!==e.length)return!1;return!0}function S(t,e,n){const i=t[e.positionOrClusterType],o=i.indexOf(e.monomerOrCluster);if(n.shiftPressed&&n.ctrlPressed)-1!==o&&i.splice(o,1);else if(n.ctrlPressed)-1===o?i.push(e.monomerOrCluster):i.splice(o,1);else if(n.shiftPressed)-1===o&&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 T(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 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t=a/u,e=l/c,n=(r-s)/Math.sqrt(t+e),i=Math.pow(t+e,2)/(Math.pow(t,2)/(u-1)+Math.pow(e,2)/(c-1));d=o.studentt.cdf(n,i),h=1-d,f=2*(d<h?d:h)}return{"p-value":f,"Mean difference":r-s,"p-value more":h,"p-value less":d}}(l,u),g=p["Mean difference"];return{count:l.length,pValue:p[g>=0?"p-value more":"p-value less"],mean:m,meanDifference:g,ratio:l.length/f,mask:a,aggValue:c}}function c(t,e,n){const o=s.zW[e],r=i.Stats.fromColumn(t,n);if(!(o in r))throw new Error(`Aggregation type ${o} is not supported`);return r[o]}function h(t,e,n={}){var i,o;null!==(i=n.filterDf)&&void 0!==i||(n.filterDf=!1),null!==(o=n.fractionDigits)&&void 0!==o||(n.fractionDigits=3);const r=!n.filterDf||!t.filter.anyFalse||n.mask&&n.mask.length!==t.filter.trueCount?t:t.clone(t.filter),s={};for(const[t,i]of e){const e=a(i,t),o=c(r.getCol(t),i,n.mask);s[e]=o.toFixed(n.fractionDigits)}return s}function d(t,e,n,i){var o;null!==(o=i.fractionDigits)&&void 0!==o||(i.fractionDigits=3);const r={};for(const[o,s]of n){const n=a(s,o),l=t.get(n,e);r[n]=l.toFixed(i.fractionDigits)}return r}function f(t,e,n){var o;const r=t.col(e.substring(5,e.length-1));if(!r||!r.matches("categorical"))return"{}";null!=n||(n=i.BitSet.create(t.rowCount,(()=>!0)));const s=r.getRawData(),a=new Map;for(let t=-1;-1!==(t=n.findNext(t,!0));)a.set(s[t],(null!==(o=a.get(s[t]))&&void 0!==o?o:0)+1);const l={};for(const[t,e]of a)l[r.categories[t]]=e;return JSON.stringify(l)}},912:(t,e,n)=>{"use strict";n.d(e,{D:()=>u,Y:()=>c});var i=n(7389),o=n(6082),r=n(4139),s=n(7654),a=n(8608),l=n(5070);function u(t,e,n,i){var o,s,a;return null!==(o=i.fromViewer)&&void 0!==o||(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!==r.$2.MONOMER&&c(t,e,n,i),!0}function c(t,e,n,r){var u,c,h,d,f,m,p,g,v;if(null!==(u=r.fromViewer)&&void 0!==u||(r.fromViewer=!1),null!==(c=r.isMutationCliffs)&&void 0!==c||(r.isMutationCliffs=!1),null!==(h=r.isMostPotentResidues)&&void 0!==h||(r.isMostPotentResidues=!1),null!==(d=r.additionalStats)&&void 0!==d||(r.additionalStats={}),r.cliffStats&&r.isMutationCliffs&&r.cliffIndexes){const u=null===(g=null===(p=r.cliffStats)||void 0===p?void 0:p.get(r.monomerPosition.monomerOrCluster))||void 0===g?void 0:g.get(r.monomerPosition.positionOrClusterType);if(!u)return null;const c=o.BitSet.fromBytes(u.mask.buffer.buffer,e.length);c.and(t.filter);const h=(0,s.M1)((0,a.Z7)(e,r.cliffIndexes,r.monomerPosition.monomerOrCluster),!0),d="MP in cliffs count",f=(0,s.QD)(u,{countName:d});r.fromViewer&&(f["Mean difference"]=`${f["Mean difference"]} (Color)`,f[d]&&(f[d]=`${f[d]} (Size)`),r.additionalStats["Unique count"]=c.trueCount.toString());const m=null!==(v=r.aggrColValues)&&void 0!==v?v:(0,l.I_)(t,n,{mask:c}),C=Object.assign(Object.assign(Object.assign({},r.additionalStats),f),m),y=(0,a.F2)(h,C);return i.tooltip.show(y,r.x,r.y),y}{const u=r.mpStats[r.monomerPosition.positionOrClusterType][r.monomerPosition.monomerOrCluster];if(!(null==u?void 0:u.count))return null;const c=o.BitSet.fromBytes(u.mask.buffer.buffer,e.length);c.and(t.filter);const h=(0,s.M1)((0,a.FZ)(e,c,t),!0),d=(0,s.QD)(u);r.fromViewer&&(d["Mean difference"]=`${d["Mean difference"]}${r.isMostPotentResidues?" (size)":""}`,d["p-value"]&&(d["p-value"]=`${d["p-value"]}${r.isMostPotentResidues?" (color)":""}`));const p=null!==(f=r.aggrColValues)&&void 0!==f?f:(0,l.I_)(t,n,{mask:c}),g=Object.assign(Object.assign(Object.assign({},r.additionalStats),d),p);for(const[t,e]of Object.entries(null!==(m=r.postfixes)&&void 0!==m?m:{}))g[t]&&(g[t]=`${g[t]}${e}`);const v=(0,a.F2)(h,g);return i.tooltip.show(v,r.x,r.y),r.fromViewer||setTimeout((()=>h.props.legendVisibility="Never"),100),v}}},115:(t,e,n)=>{"use strict";n.d(e,{GI:()=>a,Ku:()=>r,av:()=>s});var i=n(1199),o=n(4329);const r="WebGPU is not supported on this device";class s{constructor(){this.maxIterations=16,this.inflation=1.4,this.threshold=70,this.distanceF=i.Z.NEEDLEMANN_WUNSCH,this.gapOpen=1.5,this.gapExtend=.2,this.fingerprintType="Morgan",this.useWebGPU=!1,this.minClusterSize=5,this.webGPUDescription=r,this.webGPUDescriptionPromise=(0,o._)().then((t=>{t&&(this.webGPUDescription=t)}))}}class a{constructor(t){this.distanceF=i.Z.NEEDLEMANN_WUNSCH,this.gapOpen=1.5,this.gapExtend=.2,this.clusterEmbeddings=!0,this.epsilon=.01,this.minPts=4,this.fingerprintType="Morgan",this.clusterEmbeddings=!!t}}},5480:(t,e,n)=>{"use strict";n.d(e,{W:()=>S,s:()=>E});var i=n(7389),o=n(4328),r=n(6082),s=n(7233),a=n.n(s),l=n(9499),u=n(4139),c=n(3163),h=n(4326),d=n(5070),f=n(144),m=n.n(f),p=n(7654),g=n(8608),v=n(8774),C=n(3262),y=n(1458),w=n(3077),A=n(726);const b=(t,e)=>`${t}(${e})`;var S,T;!function(t){t.ORIGINAL="original",t.CUSTOM="custom"}(S||(S={})),function(t){t.GENERAL="General",t.STYLE="WebLogo",t.AGGREGATION="Aggregation"}(T||(T={}));class E extends r.JsViewer{constructor(){super(),this.bitsets=[],this.keyPress=!1,this.currentRowIndex=null,this._scaledActivityColumn=null,this._webLogoCacheGeneration=0,this._viewerGrid=null,this._clusterStats=null,this._clusterSelection=null,this._logoSummaryTable=null,this._positionColumns=null,this.root.classList.add("peptides-viewer-show-title"),this.sequenceColumnName=this.column("sequence",{category:T.GENERAL,nullable:!1}),this.clustersColumnName=this.column("clusters",{category:T.GENERAL,nullable:!1,columnTypeFilter:r.TYPE.CATEGORICAL}),this.activityColumnName=this.column("activity",{category:T.GENERAL,nullable:!1,columnTypeFilter:r.TYPE.NUMERICAL}),this.activityScaling=this.string("activityScaling",u.rg.NONE,{category:T.GENERAL,choices:Object.values(u.rg)}),this.webLogoMode=this.string("webLogoMode",h.fH.Entropy,{choices:[h.fH.full,h.fH.Entropy],category:T.STYLE}),this.membersRatioThreshold=this.float("membersRatioThreshold",.1,{min:0,max:1,category:T.STYLE});const t=[r.AGG.KEY,r.AGG.PIVOT,r.AGG.MISSING_VALUE_COUNT,r.AGG.SKEW,r.AGG.KURT,r.AGG.SELECTED_ROWS_COUNT],e=Object.values(r.AGG).filter((e=>!t.includes(e)));this.webLogoAggregationType=this.string("webLogoAggregationType",r.AGG.TOTAL_COUNT,{category:T.STYLE,choices:e,description:"Aggregation method for WebLogo position heights"}),this.webLogoAggregationColumnName=this.column("webLogoAggregationColumnName",{defaultValue:null,category:T.STYLE,nullable:!0,columnTypeFilter:r.TYPE.NUMERICAL,description:`Column with values to aggregate for WebLogo position heights.\n Used if aggregation type is not '${r.AGG.TOTAL_COUNT}'.`}),this.columns=this.columnList("columns",[],{category:T.AGGREGATION}),this.aggregation=this.string("aggregation",r.AGG.AVG,{category:T.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,y.eW)(this.dataFrame,this.clustersColumnName,this.customClusters.toArray(),this.getScaledActivityColumn())),this._clusterStats}get clusterSelection(){var t;return null!==(t=this._clusterSelection)&&void 0!==t||(this._clusterSelection=this.initClusterSelection({notify:!1})),this._clusterSelection}set clusterSelection(t){this._clusterSelection=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 o=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=o(l.q.SEQUENCE_VARIABILITY_MAP))&&void 0!==n?n:o(l.q.MOST_POTENT_RESIDUES))&&void 0!==i?i:(0,w.R)(this.dataFrame.getCol(this.sequenceColumnName),A.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,g.Y1)(this.dataFrame.getCol(this.activityColumnName),this.activityScaling)),t?r.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,i,s,a,l,c,h,d,f,p,v;if(super.onTableAttached(),(0,g.B2)(this.dataFrame)){const o=null===(t=m()(this.dataFrame.columns.numerical).filter((t=>{var e;return null===(e=t.name)||void 0===e?void 0:e.includes("activ")})).take(1).toArray()[0])||void 0===t?void 0:t.name,g=null!=o?o:null===(n=null===(e=m()(this.dataFrame.columns.numerical).take(1).toArray())||void 0===e?void 0:e[0])||void 0===n?void 0:n.name,C=this.dataFrame.columns.bySemType(r.SEMTYPE.MACROMOLECULE);C&&(null===(i=this.getProperty(`sequence${u.To}`))||void 0===i||i.set(this,C.name)),g&&(null===(s=this.getProperty(`activity${u.To}`))||void 0===s||s.set(this,g),null===(a=this.getProperty("webLogoAggregationColumnName"))||void 0===a||a.set(this,g));const y=null===(h=null===(c=null===(l=m()(this.dataFrame.columns).filter((t=>{var e;return t.isCategorical&&(null===(e=t.name)||void 0===e?void 0:e.toLowerCase().includes("cluster"))&&t.name!=(null==C?void 0:C.name)&&t.type!==r.COLUMN_TYPE.BOOL})))||void 0===l?void 0:l.take(1))||void 0===c?void 0:c.toArray())||void 0===h?void 0:h[0],w=null!=y?y:null===(p=null===(f=null===(d=m()(this.dataFrame.columns.categorical).filter((t=>t.name!=(null==C?void 0:C.name)&&t.categories.length<=50&&t.type!==r.COLUMN_TYPE.BOOL)))||void 0===d?void 0:d.take(1))||void 0===f?void 0:f.toArray())||void 0===p?void 0:p[0];w&&(null===(v=this.getProperty(`clusters${u.To}`))||void 0===v||v.set(this,w.name))}else{const t="PeptidesError: dataframe is missing Macromolecule or numeric columns";o.log.error(t),o.shell.warning(t)}this.render()}detach(){this.subs.forEach((t=>t.unsubscribe()))}render(){if(a()(this.root).empty(),null==this.clustersColumnName||null==this.sequenceColumnName||null==this.activityColumnName)return void this.root.appendChild(i.divText("Please, select a sequence, cluster and activity columns in the viewer properties"));if(!this.logoSummaryTable.filter.anyTrue){const t=i.divText("No clusters to satisfy the threshold. Please, lower the threshold in viewer proeperties to include clusters");return void this.root.appendChild(i.divV([t]))}const t=i.iconFA("expand-alt",(()=>{const t=i.dialog("Logo Summary Table");t.add(this.viewerGrid.root),t.onCancel((()=>this.render())),t.showModal(!0),this.viewerGrid.invalidate()}),"Show Logo Summary Table in full screen");a()(t).addClass("pep-help-icon"),this.viewerGrid.root.style.width="auto",this.viewerGrid.root.style.height="auto",this.viewerGrid.root.style.overflow="hidden",this.root.appendChild(i.divV([i.divH([t],{style:{alignSelf:"center",lineHeight:"normal"}}),this.viewerGrid.root])),this.viewerGrid.invalidate()}onPropertyChanged(t){super.onPropertyChanged(t);let e=!1;switch(t.name){case"membersRatioThreshold":this.logoSummaryTable.filter.anyTrue||(e=!0),this.updateFilter();break;case`sequence${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}`:this.webLogoAggregationColumnName=this.activityColumnName;case"activityScaling":case`webLogoAggregationColumnName${u.To}`:case"webLogoAggregationType":this._webLogoCacheGeneration++,this._scaledActivityColumn=null,this._viewerGrid=null,this._clusterStats=null,this._logoSummaryTable=null,e=!0;break;case"columns":case"aggregation":this._viewerGrid=null,this._logoSummaryTable=null,e=!0;break;case"webLogoMode":this.viewerGrid.invalidate()}e&&this.render()}initClusterSelection(t={}){var e;null!==(e=t.notify)&&void 0!==e||(t.notify=!0);const n={};return n[S.ORIGINAL]=[],n[S.CUSTOM]=[],t.notify?this.clusterSelection=n:this._clusterSelection=n,this.clusterSelection}getTotalViewerAggColumns(){var t,e;const n=this.getAggregationColumns();return(0,g.zm)(this.model.df,this.columns,n,null===(e=null===(t=this.model)||void 0===t?void 0:t.settings)||void 0===e?void 0:e.columns)}getStringAggregatedColumns(){return this.columns.filter((t=>this.model.df.columns.contains(t)&&this.model.df.col(t).matches("categorical"))).map((t=>`dist(${t})`))}getNeededDfClone(){var t,e;const n=[this.clustersColumnName,this.sequenceColumnName,this.activityColumnName,...(null!==(t=this.getTotalViewerAggColumns())&&void 0!==t?t:[]).map((([t,e])=>t)),...(null!==(e=this.getStringAggregatedColumns())&&void 0!==e?e:[]).map((t=>t.substring(5,t.length-1)))];this.webLogoAggregationColumnName&&n.push(this.webLogoAggregationColumnName);const i=Array.from(new Set(n)).filter((t=>this.dataFrame.columns.contains(t)));return this.dataFrame.clone(this.dataFrame.filter,i)}createLogoSummaryTable(){var t,e,n;const i=this.clustersColumnName,o=this.dataFrame.filter.anyFalse,s=o?this.getNeededDfClone():this.dataFrame,a=s.columns,l=s.rowCount,c=this.getScaledActivityColumn(o).getRawData(),h=s.getCol(i),f=h.getRawData(),p=h.categories,g={};g[u.gp.CUSTOM_CLUSTER]="1";const C=m()(a.byTags(g)).filter((t=>t.max>0)).toArray(),y=r.DataFrame.create(C.length),w=y.columns,A=w.addNewString(u.i6.CLUSTER),T=w.addNewInt(u.i6.MEMBERS).getRawData(),E=w.addNewString(u.i6.WEB_LOGO),_=w.addNewString(u.i6.DISTRIBUTION),N=w.addNewFloat(u.i6.MEAN_DIFFERENCE).getRawData(),x=w.addNewFloat(u.i6.P_VALUE).getRawData(),M=w.addNewFloat(u.i6.RATIO).getRawData();let I=s.groupBy([i]);const O=this.getTotalViewerAggColumns(),L=this.getStringAggregatedColumns(),P=L.map((t=>w.addNewString(t))),R=O.map((([t,e])=>b(e,t))),k=new Array(R.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,R[t]);const i=w.addNewFloat(R[t]);k[t]=i.getRawData()}const F=new Array(C.length);for(let e=0;e<C.length;++e){const n=C[e];A.set(e,n.name);const i=v.A.fromUint32Array(l,n.getRawData());if(i.allFalse)continue;const a=r.BitSet.fromBytes(i.buffer.buffer,l),u=o?(0,d.GT)(c,i):this.clusterStats[S.CUSTOM][n.name];T[e]=u.count,F[e]=a,N[e]=u.meanDifference,x[e]=null!==(t=u.pValue)&&void 0!==t?t:r.FLOAT_NULL,M[e]=u.ratio;for(let t=0;t<R.length;++t){const[n,i]=V[t];k[t][e]=(0,d.lh)(n,i,a)}for(let t=R.length;t<k.length;++t){const n=L[t-R.length];P[t-R.length].set(e,(0,d.J1)(s,n,a))}}E.setTag(r.TAGS.CELL_RENDERER,"html"),_.setTag(r.TAGS.CELL_RENDERER,"html");const D=I.aggregate(),G=D.rowCount,U=D.columns;let q=D.getCol(i);q.name=u.i6.CLUSTER,q.type!==r.COLUMN_TYPE.STRING&&(D.columns.replace(q,q.convertTo(r.COLUMN_TYPE.STRING)),q=D.getCol(q.name));const B=q.categories,H=U.addNewInt(u.i6.MEMBERS).getRawData(),Y=U.addNewString(u.i6.WEB_LOGO),j=U.addNewString(u.i6.DISTRIBUTION),W=U.addNewFloat(u.i6.MEAN_DIFFERENCE).getRawData(),$=U.addNewFloat(u.i6.P_VALUE).getRawData(),z=U.addNewFloat(u.i6.RATIO).getRawData(),K=L.map((t=>U.addNewString(t))),Z=new Array(G),Q=Array.from({length:G},(()=>new v.A(l,!1)));for(let t=0;t<l;++t){const n=p[f[t]];null===(e=Q[B.indexOf(n)])||void 0===e||e.setTrue(t)}for(let t=0;t<G;++t){const e=Q[t];if(e.allFalse)continue;const i=r.BitSet.fromBytes(e.buffer.buffer,l),a=o?(0,d.GT)(c,e):this.clusterStats[S.ORIGINAL][B[t]];for(let e=0;e<L.length;++e){const n=L[e];K[e].set(t,(0,d.J1)(s,n,i))}H[t]=a.count,Z[t]=i,W[t]=a.meanDifference,$[t]=null!==(n=a.pValue)&&void 0!==n?n:r.FLOAT_NULL,z[t]=a.ratio}Y.setTag(r.TAGS.CELL_RENDERER,"html"),j.setTag(r.TAGS.CELL_RENDERER,"html");const X=D.append(y);return this.bitsets=Z.concat(F),L.forEach((t=>X.col(t).semType="lst-pie-chart")),X}createLogoSummaryTableGrid(){const t=this.dataFrame.filter.anyFalse,e=t?this.getNeededDfClone():this.dataFrame,n=this.getTotalViewerAggColumns().map((([t,e])=>b(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 o=new r.LruCache,s=new Map;let d=null;const f=new r.LruCache,m=this.positionColumns.length,p=i.columns.byName(u.i6.WEB_LOGO);p.cellType="html",p.width=350;const v=this.getScaledActivityColumn(t),C=e.getCol(this.sequenceColumnName);i.onCellRender.subscribe((t=>{var e,n,l;const p=t.cell,y=p.tableRowIndex;if(!p.isTableCell||null==y||-1===y)return;const w=t.g,A=t.bounds;w.save(),w.beginPath(),w.rect(A.x,A.y,A.width,A.height),w.clip();try{const b=Math.max(p.bounds.height-2,0),S=this.bitsets[y];if((null===(e=p.tableColumn)||void 0===e?void 0:e.name)===u.i6.CLUSTER)c.k8(w,p.cell.value,this.clusterSelection,A),t.preventDefault();else if((null===(n=p.tableColumn)||void 0===n?void 0:n.name)===u.i6.WEB_LOGO){const e=`${y}_${this.webLogoAggregationColumnName||"count"}_${this.webLogoAggregationType}_${this._webLogoCacheGeneration}`,n=o.get(e);if(!0===s.get(e))return void t.preventDefault();const l=Math.floor((p.bounds.width-2-4*(m-1))/m);if(void 0!==n){const e=n.getProperties();for(const t of e)"positionHeight"===t.name&&t.get(n)!==this.webLogoMode?t.set(n,this.webLogoMode):"positionWidth"===t.name&&t.get(n)!==l?t.set(n,l):"minHeight"===t.name&&t.get(n)!==b&&t.set(n,b);a()(n.root).css("height",`${b}px`).children().first().css("overflow-y","hidden !important"),n.root.style.height=`${b}px`,p.element=n.root,t.preventDefault()}else{const n=[C];if(this.webLogoAggregationType!==r.AGG.TOTAL_COUNT&&this.webLogoAggregationColumnName){const t=this.dataFrame.columns.byName(this.webLogoAggregationColumnName);t&&n.push(t)}const a=r.DataFrame.fromColumns(n);a.filter.copyFrom(S),s.set(e,!0),a.plot.fromType("WebLogo",{valueColumnName:this.webLogoAggregationColumnName,valueAggrType:this.webLogoAggregationType,positionHeight:this.webLogoMode,horizontalAlignment:h.P4.LEFT,maxHeight:1e3,minHeight:b,positionWidth:l,showPositionLabels:!1}).then((t=>{o.set(e,t),s.delete(e),d&&clearTimeout(d),d=setTimeout((()=>i.invalidate()),200)})),t.preventDefault()}}else if((null===(l=p.tableColumn)||void 0===l?void 0:l.name)===u.i6.DISTRIBUTION){let e=f.get(y);void 0===e&&(v.dataFrame||r.DataFrame.fromColumns([v]),e=(0,g.FZ)(v,S,v.dataFrame).plot.histogram({filteringEnabled:!1,valueColumnName:v.name,splitColumnName:u.$2.SPLIT_COL,legendVisibility:"Never",showXAxis:!1,showColumnSelector:!1,showRangeSlider:!1,showBinSelector:!1,backColor:r.Color.toHtml(r.Color.white),xAxisHeight:1,showSplitSelector:!1}),e.root.style.width="auto",f.set(y,e)),e.root.style.height=`${b}px`,p.element=e.root,t.preventDefault()}}finally{w.restore()}})),i.root.addEventListener("mouseleave",(t=>this.model.unhighlight())),r.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 o=this.getCluster(n);this.modifyClusterSelection(o,{shiftPressed:t.shiftKey,ctrlPressed:t.ctrlKey}),i.invalidate()})),i.onCellTooltip(((t,e,n)=>{var i;if(!t.isTableCell)return this.model.unhighlight(),!0;const o=this.getCluster(t);return this.highlightCluster(o),(null===(i=t.tableColumn)||void 0===i?void 0:i.name)===u.i6.CLUSTER&&this.showTooltip(o,e,n),!0}));const y=i.props;return y.allowEdit=!1,y.allowRowSelection=!1,y.allowBlockSelection=!1,y.allowColSelection=!1,y.showCurrentRowIndicator=!1,y.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,o=i.indexOf("-1"),r=t.getRawData();let s=0;r.forEach(((t,e)=>{"-1"!==i[n[e]]&&(s=Math.max(s,r[e]))}));const a=Math.ceil(s*this.membersRatioThreshold);this.logoSummaryTable.filter.init((t=>r[t]>a&&(-1===o||"-1"!==i[n[t]])))}clusterFromSelection(){const t=this.model.getVisibleSelection(),e=this.logoSummaryTable.columns,n=e.length,i=new Array(e.length),o=this.getScaledActivityColumn(),r=(0,d.pY)(t),s=(0,d.GT)(o.getRawData(),r,(0,d.pY)(this.dataFrame.filter));this.bitsets.push(t.clone());const a=this.dataFrame.columns.getUnusedName("New Cluster"),l={},c={},h=this.getTotalViewerAggColumns(),f=this.getStringAggregatedColumns();for(const[e,n]of h){const i=b(n,e),o=this.dataFrame.getCol(e);l[i]=(0,d.lh)(o,n,t)}for(const e of f)c[e]=(0,d.J1)(this.dataFrame,e,t);for(let o=0;o<n;++o){const n=e.byIndex(o);i[o]=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[o]&&C._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 o.shell.warning("No custom clusters selected to be removed");const e=this.logoSummaryTable.rows,n=this.logoSummaryTable.getCol(u.i6.CLUSTER),i=n.categories,r=this.dataFrame.columns;for(const n of t){t.splice(t.indexOf(n),1),r.remove(n),delete this.clusterStats[S.CUSTOM][n];const o=i.indexOf(n);e.removeAt(o),this.bitsets.splice(o,1)}n.compact(),this.clusterSelection[S.CUSTOM]=t,this.render()}addNewCluster(t){const e=r.Column.fromBitSet(t,this.model.getVisibleSelection());e.setTag(u.gp.CUSTOM_CLUSTER,"1"),e.setTag(u.gp.ANALYSIS_COL,"true"),this.dataFrame.columns.add(e),this.model.analysisView.grid.col(e.name).visible=!1}modifyClusterSelection(t,e={shiftPressed:!1,ctrlPressed:!1},n=!0){n?this.clusterSelection=(0,g.vW)(this.clusterSelection,t,e):this._clusterSelection=(0,g.vW)(this.clusterSelection,t,e)}showTooltip(t,e,n){const o=this.dataFrame.filter,s=o.anyFalse?this.getNeededDfClone():this.dataFrame,a=s.rowCount,l=new v.A(a,!1),u=this.getScaledActivityColumn(o.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 h=o.anyFalse?(0,d.GT)(c,l):this.clusterStats[t.positionOrClusterType][t.monomerOrCluster];if(!h.count)return null;const f=r.BitSet.fromBytes(l.buffer.buffer,a);u.dataFrame||r.DataFrame.fromColumns([u]);const m=(0,g.FZ)(u,f,u.dataFrame),C=(0,p.M1)(m,!0),y=(0,p.QD)(h),w=(0,d.I_)(this.dataFrame,this.getTotalViewerAggColumns(),{filterDf:!0,mask:f}),A=Object.assign(Object.assign({},y),w),b=(0,g.F2)(C,A);return i.tooltip.show(b,e,n),b}createWebLogoDf(t,e){const n=r.DataFrame.fromColumns([t]);return n.filter.copyFrom(e),n}}},3541:(t,e,n)=>{"use strict";n.d(e,{J:()=>M,UJ:()=>I});var i,o,r,s,a=n(4328),l=n(7389),u=n(6082),c=n(7233),h=n.n(c),d=n(4139),f=n(3163),m=n(9499),p=n(144),g=n.n(p),v=n(5070),C=n(912),y=n(1458),w=n(8608),A=n(3077),b=n(439),S=n(2003),T=n(4971),E=n(726),_=n(4025),N=function(t,e,n,i){return new(n||(n=Promise))((function(o,r){function s(t){try{l(i.next(t))}catch(t){r(t)}}function a(t){try{l(i.throw(t))}catch(t){r(t)}}function l(t){var e;t.done?o(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",t.DATA_SOURCE="dataSource"}(o||(o={})),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",t.SHOW_FILTER_CONTROLS="showFilterControls",t.SHOW_TOTAL_COUNT_COLUMN="showTotalCountColumn"}(r||(r={})),function(t){t.GENERAL="General",t.INVARIANT_MAP="Invariant Map",t.MUTATION_CLIFFS="Mutation Cliffs",t.AGGREGATION="Aggregation"}(s||(s={}));class x extends u.JsViewer{constructor(){super(),this.keyPressed=!1,this._scaledActivityColumn=null,this.doRender=!0,this.dataSource="Filtered",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(o.SEQUENCE,{category:s.GENERAL,semType:u.SEMTYPE.MACROMOLECULE,nullable:!1}),this.dataSource=this.string(o.DATA_SOURCE,"Filtered",{category:s.GENERAL,choices:["All","Filtered"],nullable:!1,description:"Data source for calculations and rendering. Can be set to whole data set or filtered data only."}),this.activityColumnName=this.column(o.ACTIVITY,{category:s.GENERAL,nullable:!1,columnTypeFilter:"numerical"}),this.activityScaling=this.string(o.ACTIVITY_SCALING,d.rg.NONE,{category:s.GENERAL,choices:Object.values(d.rg),nullable:!1}),this.activityTarget=this.string(o.ACTIVITY_TARGET,d.wf.HIGH,{category:s.GENERAL,choices:Object.values(d.wf),nullable:!1}),this.targetColumnName=this.column(o.TARGET,{category:s.GENERAL,nullable:!0,columnTypeFilter:"categorical",userEditable:!1}),this.minActivityDelta=this.float(o.MIN_ACTIVITY_DELTA,0,{category:s.MUTATION_CLIFFS,min:0,max:100}),this.maxMutations=this.int(o.MAX_MUTATIONS,1,{category:s.MUTATION_CLIFFS,min:1,max:20}),this.columns=this.columnList(o.COLUMNS,[],{category:s.AGGREGATION}),this.aggregation=this.string(o.AGGREGATION,u.AGG.AVG,{category:s.AGGREGATION,choices:d.V5}),this.valueColumnName=this.column(o.VALUE_INVARIANT_MAP,{category:s.INVARIANT_MAP,userEditable:!0,nullable:!1,columnTypeFilter:"numerical"}),this.valueAggregation=this.string(o.AGGREGATION_INVARIANT_MAP_VALUE,u.AGG.TOTAL_COUNT,{category:s.INVARIANT_MAP,choices:d.V5,userEditable:!0,nullable:!1}),this.mutationCliffsDebouncer=(0,w.sg)(((t,e,n)=>N(this,void 0,void 0,(function*(){return yield(0,y.uz)(t,e,n)})))),this.root.classList.add("peptides-viewer-show-title")}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(b.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 M?this._positionColumns=i(m.q.MOST_POTENT_RESIDUES):this instanceof I&&(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,A.R)(this.dataFrame.getCol(this.sequenceColumnName),E.Z.getSeqHelper()).columns.toList()),this._positionColumns}get monomerPositionStats(){var t;if(null!=this._monomerPositionStats)return this._monomerPositionStats;const e=t=>this.sequenceColumnName===(null==t?void 0:t.sequenceColumnName)&&this.activityColumnName===(null==t?void 0:t.activityColumnName)&&this.activityScaling===(null==t?void 0:t.activityScaling)&&t instanceof x&&t.dataSource===this.dataSource&&(t instanceof x&&this.valueColumnName==(null==t?void 0:t.valueColumnName)&&this.valueAggregation==(null==t?void 0:t.valueAggregation)||!(t instanceof x)&&(!this.valueColumnName||!this.valueAggregation||this.valueAggregation==u.AGG.VALUE_COUNT||this.valueAggregation==u.AGG.TOTAL_COUNT)),n=t=>{const n=this.model.findViewer(t);return e(n)?n._monomerPositionStats:null};null!==this.model.monomerPositionStats&&e(this.model.settings)?this._monomerPositionStats=this.model.monomerPositionStats:this instanceof M?this._monomerPositionStats=n(m.q.MOST_POTENT_RESIDUES):this instanceof I&&(this._monomerPositionStats=n(m.q.SEQUENCE_VARIABILITY_MAP));const i=this.dataFrame.col(this.valueColumnName),o=this.valueAggregation;return null!==(t=this._monomerPositionStats)&&void 0!==t||(this._monomerPositionStats=(0,y.Ej)(this.getScaledActivityColumn(),this.dataFrame.filter,this.positionColumns,{isFiltered:"Filtered"===this.dataSource&&this.dataFrame.filter.anyFalse,aggValue:o&&i?{col:i,type:o}: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===(null==i?void 0:i.activityColumnName)&&n.activityScaling===(null==i?void 0:i.activityScaling)&&n.minActivityDelta===(null==i?void 0:i.minActivityDelta)&&n.maxMutations===(null==i?void 0:i.maxMutations)&&(null==n?void 0:n.dataSource)===(null==i?void 0:i.dataSource)?e._mutationCliffs:null;var n,i};return this instanceof M?this._mutationCliffs=t(m.q.MOST_POTENT_RESIDUES):this instanceof I&&(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,y.Lw)(this.mutationCliffs,t)}return this._mutationCliffStats}set cliffStats(t){this._mutationCliffStats=t,this.viewerGrid.invalidate()}get mutationCliffsSelection(){var t;return null!==(t=this._mutationCliffsSelection)&&void 0!==t||(this._mutationCliffsSelection=(0,w.ZR)(this.positionColumns)),this._mutationCliffsSelection}set mutationCliffsSelection(t){var e,n;this._mutationCliffsSelection=t,this.model.fireBitsetChanged(this instanceof M?m.q.SEQUENCE_VARIABILITY_MAP:m.q.MOST_POTENT_RESIDUES);const i=this.model.findViewer(m.q.SEQUENCE_VARIABILITY_MAP);null===(e=null==i?void 0:i.viewerGrid)||void 0===e||e.invalidate();const o=this.model.findViewer(m.q.MOST_POTENT_RESIDUES);null===(n=null==o?void 0:o.viewerGrid)||void 0===n||n.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,w.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,w.vW)(this.mutationCliffsSelection,t,e):this._mutationCliffsSelection=(0,w.vW)(this.mutationCliffsSelection,t,e)}modifyInvariantMapSelection(t,e={shiftPressed:!1,ctrlPressed:!1},n=!0){n?this.invariantMapSelection=(0,w.vW)(this.invariantMapSelection,t,e):this._invariantMapSelection=(0,w.vW)(this.invariantMapSelection,t,e)}get invariantMapSelection(){var t;return null!==(t=this._invariantMapSelection)&&void 0!==t||(this._invariantMapSelection=(0,w.ZR)(this.positionColumns)),this._invariantMapSelection}set invariantMapSelection(t){this._invariantMapSelection=t,this.model.fireBitsetChanged(m.q.SEQUENCE_VARIABILITY_MAP),this.model.analysisView.grid.invalidate()}onPropertyChanged(t){switch(super.onPropertyChanged(t),this.doRender=!0,t.name){case`${o.SEQUENCE}${d.To}`:this._positionColumns=null,this._monomerPositionStats=null,this._mutationCliffs=null,this._mutationCliffStats=null,this._mutationCliffsSelection=null,this._viewerGrid=null;break;case`${o.ACTIVITY}${d.To}`:case o.ACTIVITY_SCALING:this._monomerPositionStats=null,this._mutationCliffs=null,this._mutationCliffStats=null,this._mutationCliffsSelection=null,this._viewerGrid=null,this._scaledActivityColumn=null;break;case`${o.VALUE_INVARIANT_MAP}${d.To}`:case o.AGGREGATION_INVARIANT_MAP_VALUE:this._monomerPositionStats=null,this._viewerGrid=null,this._invariantMapSelection=null;break;case o.MIN_ACTIVITY_DELTA:case o.MAX_MUTATIONS:this._mutationCliffs=null,this._mutationCliffStats=null,this._mutationCliffsSelection=null,this.doRender=!1;break;case o.COLUMNS:case o.AGGREGATION:this instanceof I&&(this._viewerGrid=null);break;case o.ACTIVITY_TARGET:(this instanceof I||this instanceof M)&&(this._viewerGrid=null);break;case o.DATA_SOURCE:this.onFilterChanged(!1,!1),this.doRender=!0}null===this._mutationCliffs&&this.sequenceColumnName&&this.activityColumnName&&this.dataFrame&&this.calculateMutationCliffs().then((t=>{this.mutationCliffs=t.cliffs,this.cliffStats=t.cliffStats}))}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,w.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")}exportMutationCliffs(){if(!this.mutationCliffs)return void a.shell.warning("Mutation cliffs have not been calculated yet.");const t=this.dataFrame.columns.toList().filter((t=>t.name!==this.activityColumnName&&t.name!==this.sequenceColumnName&&!this.positionColumns.some((e=>e.name===t.name)))).map((t=>t.name)),e=l.input.columns("Extra columns",{table:this.dataFrame,value:[],available:t,nullable:!0});l.dialog("Export Mutation Cliffs").add(e.root).onOK((()=>{var t;return this._doExportMutationCliffs(null!==(t=e.value)&&void 0!==t?t:[])})).show()}_doExportMutationCliffs(t){var e;const n=this.mutationCliffs,i=this.dataFrame.getCol(this.sequenceColumnName),o=i.categories,r=i.getRawData(),s=this.dataFrame.getCol(this.activityColumnName),l=s.getRawData(),c=[],h=[],f=[],m=[],p=[],g=[],v=t.map((()=>[])),C=t.map((()=>[])),y=new Set;for(const[e,i]of n.entries())for(const[e,n]of i.entries())for(const[e,i]of n.entries())for(const n of i){const i=e<n?`${e}-${n}`:`${n}-${e}`;if(y.has(i))continue;y.add(i);const a=o[r[e]],u=o[r[n]];c.push(a),h.push(u),f.push(`${a}#${u}`);const d=s.isNone(e)?null:l[e],w=s.isNone(n)?null:l[n];m.push(d),p.push(w),g.push(null==d||null==w?null:d-w);for(let i=0;i<t.length;i++){const o=t[i];v[i].push(o.isNone(e)?null:o.get(e)),C[i].push(o.isNone(n)?null:o.get(n))}}if(0===c.length)return void a.shell.warning("No mutation cliffs found to export.");const A=u.Column.fromStrings("Seq 1",c),b=u.Column.fromStrings("Seq 2",h),S=u.Column.fromStrings("Mutation",f);for(const t of[A,b]){for(const e of i.tags.keys())".notationProvider"!==e&&t.setTag(e,i.getTag(e));t.semType=i.semType}S.semType=d.uF.MACROMOLECULE_DIFFERENCE,S.setTag(d.gp.SEPARATOR,(0,w.AY)(i)),S.setTag(u.TAGS.UNITS,null!==(e=i.getTag(u.TAGS.UNITS))&&void 0!==e?e:""),S.setTag(u.TAGS.CELL_RENDERER,"MacromoleculeDifference"),S.temp[_.j.notationProvider]=i.temp[_.j.notationProvider];const T=[A,b,S,u.Column.fromList(u.COLUMN_TYPE.FLOAT,`Seq 1 ${this.activityColumnName}`,m),u.Column.fromList(u.COLUMN_TYPE.FLOAT,`Seq 2 ${this.activityColumnName}`,p),u.Column.fromList(u.COLUMN_TYPE.FLOAT,"Delta",g)];for(let e=0;e<t.length;e++){const n=t[e].name,i=t[e].type;T.push(u.Column.fromList(i,`Seq 1 ${n}`,v[e])),T.push(u.Column.fromList(i,`Seq 2 ${n}`,C[e]))}const E=u.DataFrame.fromColumns(T);E.name="Mutation Cliffs",a.shell.addTableView(E)}exportInvariantMap(){const t=this.monomerPositionStats,e=new Set,n=[];for(const i of Object.keys(t)){if("general"===i)continue;n.push(i);const o=t[i];for(const t of Object.keys(o))"general"!==t&&e.add(t)}const i=Array.from(e).sort(),o=[u.Column.fromStrings(d.$2.MONOMER,i)];for(const e of n){const n=t[e],r=i.map((t=>{var e,i;return null!==(i=null===(e=n[t])||void 0===e?void 0:e.count)&&void 0!==i?i:0}));o.push(u.Column.fromList(u.COLUMN_TYPE.INT,e,r))}const r=u.DataFrame.fromColumns(o);r.name="Invariant Map",a.shell.addTableView(r)}detach(){this.subs.forEach((t=>t.unsubscribe()))}onTableAttached(){var t,e,n,i;if(super.onTableAttached(),(0,w.B2)(this.dataFrame)){null===(t=this.getProperty(`${o.SEQUENCE}${d.To}`))||void 0===t||t.set(this,this.dataFrame.columns.bySemType(u.SEMTYPE.MACROMOLECULE).name);const r=null===(e=g()(this.dataFrame.columns.numerical).find((t=>t.name.toLowerCase().includes("activity"))))||void 0===e?void 0:e.name;null===(n=this.getProperty(`${o.ACTIVITY}${d.To}`))||void 0===n||n.set(this,null!=r?r:g()(this.dataFrame.columns.numerical).next().value.name),null===(i=this.getProperty(`${o.VALUE_INVARIANT_MAP}${d.To}`))||void 0===i||i.set(this,null!=r?r:g()(this.dataFrame.columns.numerical).next().value.name),null===this.mutationCliffs&&this.sequenceColumnName&&this.activityColumnName&&this.calculateMutationCliffs().then((t=>{this.mutationCliffs=t.cliffs,this.cliffStats=t.cliffStats})),this.subs.push(a.events.onContextMenu.subscribe((t=>{if(!(t&&t.causedBy&&t.args&&t.args.menu&&t.causedBy.target&&t.causedBy.target instanceof HTMLElement&&this.root.contains(t.causedBy.target)))return;const e=t.args.menu,n=e.group("Export");n.item("Export Mutation Cliffs...",(()=>this.exportMutationCliffs())),n.item("Export Invariant Map",(()=>this.exportInvariantMap())),(0,T.pj)().then((t=>{const n=t.getMonomerLib(),i=n.getMonomerSymbolsByType("PEPTIDE").map((t=>n.getMonomer("PEPTIDE",t))).filter(Boolean).map((t=>{var e;return null!==(e=t.meta)&&void 0!==e?e:{}})),o=new Set;i.forEach((t=>Object.keys(t).forEach((t=>o.add(t))))),o.delete("colors"),e.group("Monomer Meta").items(Array.from(o),(t=>{this._monomerMetaColumns.has(t)?this._monomerMetaColumns.delete(t):this._monomerMetaColumns.add(t),this._viewerGrid=null,this.render()}),{isChecked:t=>this._monomerMetaColumns.has(t)})}))}))),this.subs.push(u.debounce(this.dataFrame.onFilterChanged,300).subscribe((()=>{"Filtered"===this.dataSource&&this.onFilterChanged(!0,!1)})))}else{const t="PeptidesError: dataframe is missing Macromolecule or numeric columns";a.log.error(t),a.shell.warning(t)}}onFilterChanged(t,e=!1){if(this._monomerPositionStats=null,this._invariantMapSelection=null,this._mutationCliffStats=null,this._mutationCliffsSelection=null,this._mutationCliffs=null,e)return;this._viewerGrid=null;const n=this.model.findViewer(m.q.MOST_POTENT_RESIDUES);!n||this instanceof I||"Filtered"!==n.dataSource||n.onFilterChanged(!1,!0),t&&this.render(),this.sequenceColumnName&&this.activityColumnName&&this.calculateMutationCliffs().then((t=>{this.mutationCliffs=t.cliffs,this.cliffStats=t.cliffStats}))}calculateMutationCliffs(){return N(this,void 0,void 0,(function*(){var t;const e=this.dataFrame.getCol(this.activityColumnName),n=this.positionColumns.map(w.eY),i="Filtered"===this.dataSource&&this.dataFrame.filter.anyFalse?this.dataFrame.filter:null,o={maxMutations:this.maxMutations,minActivityDelta:this.minActivityDelta,filter:null!==(t=null==i?void 0:i.getBuffer())&&void 0!==t?t:void 0},r=e.getRawData(),s=yield this.mutationCliffsDebouncer(r,n,o);return{cliffs:s,cliffStats:(0,y.Lw)(s,r)}}))}}class M extends x{constructor(){super(),this.currentGridCell=null,this.customColorRange=!1,this.minColorValue=0,this.maxColorValue=0,this.logScaleColor=!1,this.showFilterControls=!0,this.showTotalCountColumn=!1,this._showSearchInput=!1,this.colorColumnName=this.column(r.COLOR,{category:s.INVARIANT_MAP,nullable:!1,columnTypeFilter:"numerical"}),this.colorAggregation=this.string(r.COLOR_AGGREGATION,u.AGG.AVG,{category:s.INVARIANT_MAP,choices:d.V5}),this.lowerBoundColor=this.int(r.LOWER_BOUND_COLOR,4278190335,{category:s.INVARIANT_MAP,editor:"color"}),this.middleColor=this.int(r.MIDDLE_COLOR,4294967295,{category:s.INVARIANT_MAP,editor:"color"}),this.upperBoundColor=this.int(r.UPPER_BOUND_COLOR,4294901760,{category:s.INVARIANT_MAP,editor:"color"}),this.showTotalCountColumn=this.bool(r.SHOW_TOTAL_COUNT_COLUMN,!1,{category:s.GENERAL,description:"Show total monomer count column"}),this.logScaleColor=this.bool(r.LOG_SCALE_COLOR,!1,{category:s.INVARIANT_MAP}),this.customColorRange=this.bool(r.CUSTOM_COLOR_RANGE,!1,{category:s.INVARIANT_MAP}),this.minColorValue=this.float(r.MIN_COLOR_VALUE,0,{category:s.INVARIANT_MAP}),this.maxColorValue=this.float(r.MAX_COLOR_VALUE,0,{category:s.INVARIANT_MAP}),this.showFilterControls=this.bool(r.SHOW_FILTER_CONTROLS,!0,{category:s.GENERAL,description:"Show monomer search and target controls",userEditable:!1}),this.monomerSearchInput=l.input.string("Search",{value:"",nullable:!0,placeholder:"Search monomer",tooltipText:"Search for monomer by symbol. For multiple monomers use comma as a separator.",onValueChanged:()=>{var t,e,n;const i=()=>{var t,e,n;return null===(n=null===(e=null===(t=this._viewerGrid)||void 0===t?void 0:t.dataFrame)||void 0===e?void 0:e.filter)||void 0===n?void 0:n.setAll(!0)},o=null!==(n=null===(e=null===(t=this.monomerSearchInput.value)||void 0===t?void 0:t.trim())||void 0===e?void 0:e.toLowerCase())&&void 0!==n?n:"";if(!o||null==this._viewerGrid||null==this._viewerGrid.dataFrame)return void i();const r=this._viewerGrid.dataFrame.col(d.$2.MONOMER);if(null==r)return void i();const s=o.split(",").map((t=>t.trim())).filter((t=>!!t)),a=r.toList();this._viewerGrid.dataFrame.filter.init((t=>s.some((e=>a[t].toLowerCase().includes(e)))))}})}get name(){return m.q.SEQUENCE_VARIABILITY_MAP}get mode(){var t;return null!==(t=this.dataFrame.getTag(d.gp.MONOMER_POSITION_MODE))&&void 0!==t?t:i.MUTATION_CLIFFS}set mode(t){this.dataFrame.setTag(d.gp.MONOMER_POSITION_MODE,t),this.viewerGrid.invalidate()}onTableAttached(){var t;if(super.onTableAttached(),(0,w.B2)(this.dataFrame))null===(t=this.getProperty(`${r.COLOR}${d.To}`))||void 0===t||t.set(this,this.activityColumnName);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;switch(super.onPropertyChanged(t),t.name){case o.SEQUENCE:this._invariantMapSelection=null;break;case r.SHOW_TOTAL_COUNT_COLUMN:this._viewerGrid&&this._viewerGrid.columns.byName(d.$2.TOTAL_COUNT)&&(this._viewerGrid.columns.byName(d.$2.TOTAL_COUNT).visible=this.showTotalCountColumn,this.doRender=!1)}null===(e=this.positionColumns)||void 0===e||e.forEach((t=>{t.temp[d.gp.INVARIANT_MAP_COLOR_CACHE]=null})),this.doRender?this.render():this.viewerGrid.invalidate()}createMonomerPositionDf(){const t=new Set,e=this.positionColumns;for(const e of Object.keys(this.monomerPositionStats)){if("general"===e)continue;const n=this.monomerPositionStats[e];for(const e of Object.keys(n))"general"!==e&&t.add(e)}const n=Array.from(t),i=u.Column.fromStrings(d.$2.MONOMER,n),o=u.DataFrame.fromColumns([i]),r=(0,T.pj)().then((t=>{const e=t.getMonomerLib();return e?n.map((t=>{var n,i;return null!==(i=null===(n=e.getMonomer("PEPTIDE",t))||void 0===n?void 0:n.meta)&&void 0!==i?i:{}})):n.map((t=>({})))})),s=o.columns.addNewInt(d.$2.TOTAL_COUNT),a={},l=this.monomerPositionStats;for(const t of Object.keys(l)){if("general"===t)continue;const e=l[t];for(const t of Object.keys(e))"general"!==t&&(a[t]||(a[t]=0),a[t]+=e[t].count)}s.init((t=>{var e;return null!==(e=a[i.get(t)])&&void 0!==e?e:0})),this._monomerMetaColumns.forEach((t=>{const e=o.columns.addNewString(t);r.then((n=>{e.init((e=>{var i,o;return null!==(o=null===(i=n[e][t])||void 0===i?void 0:i.toString())&&void 0!==o?o:""}))}))})),o.name="SAR";for(const t of e)o.columns.addNewBool(t.name);return o}cacheInvariantMapColors(){if(this.colorColumnName&&this.dataFrame.col(this.colorColumnName)){const t=this.dataFrame.getCol(this.colorColumnName).getRawData();let e=9999999,n=-9999999;const i="Filtered"===this.dataSource&&this.dataFrame.filter.anyFalse?this.dataFrame.filter:null,o=null==i?t=>!0:t=>i.get(t);for(const i of this.positionColumns){i.temp[d.gp.INVARIANT_MAP_COLOR_CACHE]={};const r=i.temp[d.gp.INVARIANT_MAP_COLOR_CACHE],s=i.name,a=i.getRawData(),l=i.categories;if(!this.monomerPositionStats[s])continue;const c=this.monomerPositionStats[s];for(const s of Object.keys(c)){if("general"===s)continue;const c=[];for(let t=0;t<i.length;++t)l[a[t]]===s&&o(t)&&c.push(t);const h=u.Column.float("color",c.length).init((e=>t[c[e]])).aggregate(this.colorAggregation);r[s]=h,e=Math.min(e,h),n=Math.max(n,h)}i.temp[d.gp.INVARIANT_MAP_COLOR_CACHE]=r}const r=this.customColorRange&&null!=this.minColorValue&&null!=this.maxColorValue;let s=r?this.minColorValue:e,a=r?this.maxColorValue:n;const l=this.logScaleColor&&s>1e-30&&a>1e-30&&e>1e-30&&n>1e-30;l&&(s=Math.log(s),a=Math.log(a));for(const t of this.positionColumns){const i=t.temp[d.gp.INVARIANT_MAP_COLOR_CACHE];if(i){for(const t of Object.keys(i))this.activityTarget===d.wf.LOW&&(i[t]=a-i[t]+s),i[t]=u.Color.scaleColor(l?Math.log(i[t]):i[t],s,a,void 0,[this.lowerBoundColor,this.middleColor,this.upperBoundColor]);t.temp[d.gp.INVARIANT_MAP_COLOR_CACHE]=i,t.temp[d.gp.INVARIANT_MAP_COLOR_MIN_CACHE]=e,t.temp[d.gp.INVARIANT_MAP_COLOR_MAX_CACHE]=n}}}}createViewerGrid(){const t=this.createMonomerPositionDf(),e=t.plot.grid();e.sort([d.$2.MONOMER]);const n=this.positionColumns.map((t=>t.name));e.columns.setOrder([d.$2.TOTAL_COUNT,d.$2.MONOMER,...this._monomerMetaColumns,...n]);const o=e.columns.byName(d.$2.TOTAL_COUNT);this.showTotalCountColumn&&null!=o?o.visible=!0:null!=o&&(o.visible=!1);const r=t.getCol(d.$2.MONOMER);f.rI(r,this.alphabet,!0),this.cacheInvariantMapColors(),e.onCellRender.subscribe((t=>O(t,this,this.mode===i.INVARIANT_MAP,this.dataFrame.getCol(this.colorColumnName),this.colorAggregation))),e.onCellTooltip(((t,e,n)=>{var o,r,s,a,l,c,h;if(!t.isTableCell||!(null===(o=null==t?void 0:t.cell.column)||void 0===o?void 0:o.name)||this._monomerMetaColumns.has(t.cell.column.name)||t.cell.column.name===d.$2.TOTAL_COUNT)return this.model.unhighlight(),!0;const f=this.getMonomerPosition(t);(0,w.dl)(f,this.dataFrame,this.monomerPositionStats),this.model.isHighlighting=!0;const m=this.getTotalViewerAggColumns(),p={},g={};if(this.mode===i.INVARIANT_MAP)this.colorColumnName&&this.colorAggregation&&this.colorColumnName!==this.valueColumnName?(m.unshift([this.colorColumnName,this.colorAggregation]),p[`${this.colorAggregation}(${this.colorColumnName})`]=" (color)"):this.colorColumnName&&this.colorAggregation&&this.colorColumnName===this.valueColumnName&&(p["Mean activity"]=" (color)"),this.valueColumnName&&this.valueAggregation&&this.valueAggregation!==u.AGG.VALUE_COUNT&&this.valueAggregation!==u.AGG.TOTAL_COUNT&&m.unshift([this.valueColumnName,this.valueAggregation]);else{const t=null===(s=null===(r=this.mutationCliffs)||void 0===r?void 0:r.get(f.monomerOrCluster))||void 0===s?void 0:s.get(f.positionOrClusterType);if(t){let e=0;for(const n of t.values())e+=n.length;g["Pairs count"]=e.toString()}}return(0,C.D)(this.model.df,this.getScaledActivityColumn(),m,{fromViewer:!0,isMutationCliffs:this.mode===i.MUTATION_CLIFFS,monomerPosition:f,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:p,additionalStats:g,cliffIndexes:null===(h=null===(c=this.mutationCliffs)||void 0===c?void 0:c.get(f.monomerOrCluster))||void 0===h?void 0:h.get(f.positionOrClusterType)})})),e.root.addEventListener("mouseleave",(t=>this.model.unhighlight())),u.debounce(e.onCurrentCellChanged,500).subscribe((t=>{var n,o,r,s,a,l,c,h,f,p,g,v,C;try{if(!t||!t.dart||!(null===(o=null===(n=null==t?void 0:t.cell)||void 0===n?void 0:n.column)||void 0===o?void 0:o.name)||this._monomerMetaColumns.has(t.cell.column.name)||t.cell.column.name==d.$2.TOTAL_COUNT||!t.isTableCell)return;if(-1===t.gridRow&&(this.mode===i.INVARIANT_MAP?this._invariantMapSelection=(0,w.ZR)(this.positionColumns):this._mutationCliffsSelection=(0,w.ZR)(this.positionColumns),this.model.fireBitsetChanged(m.q.SEQUENCE_VARIABILITY_MAP),e.invalidate()),!this.keyPressed||t.cell.column.name===d.$2.MONOMER)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===(r=this.mutationCliffs)||void 0===r?void 0:r.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===(h=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===h?void 0:h.size)&&this.modifyMutationCliffsSelection(u,{shiftPressed:!0,ctrlPressed:!1},!0),e.invalidate(),setTimeout((()=>null==e?void 0:e.invalidate()),300)}catch(t){console.error(t)}finally{this.keyPressed=!1,(null===(f=t.tableColumn)||void 0===f?void 0:f.name)&&t.grid&&t.isTableCell&&(null===(p=null==t?void 0:t.cell)||void 0===p?void 0:p.column.name)!=d.$2.MONOMER&&!this._monomerMetaColumns.has(null===(v=null===(g=t.cell)||void 0===g?void 0:g.column)||void 0===v?void 0:v.name)&&(null===(C=t.cell)||void 0===C?void 0:C.column.name)!==d.$2.TOTAL_COUNT?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,w.ZR)(this.positionColumns):this._mutationCliffsSelection=(0,w.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 o,r,s,a,l,u;const c=e.hitTest(n.offsetX,n.offsetY);if(!(null==c?void 0:c.isTableCell)||(null===(o=null==c?void 0:c.tableColumn)||void 0===o?void 0:o.name)===d.$2.MONOMER||(null===(r=null==c?void 0:c.tableColumn)||void 0===r?void 0:r.name)&&this._monomerMetaColumns.has(c.tableColumn.name)||(null===(s=null==c?void 0:c.tableColumn)||void 0===s?void 0:s.name)===d.$2.TOTAL_COUNT)return;const h=this.getMonomerPosition(c);this.mode===i.INVARIANT_MAP?(this.modifyInvariantMapSelection(h,{shiftPressed:n.shiftKey,ctrlPressed:n.ctrlKey}),(0,w.CD)(this.invariantMapSelection)&&(t.currentRowIdx=-1)):(null===(u=null===(l=null===(a=this.mutationCliffs)||void 0===a?void 0:a.get(h.monomerOrCluster))||void 0===l?void 0:l.get(h.positionOrClusterType))||void 0===u?void 0:u.size)&&this.modifyMutationCliffsSelection(h,{shiftPressed:n.shiftKey,ctrlPressed:n.ctrlKey}),e.invalidate()})),L(e),e.props.showRowHeader=!0;const s=e.onAfterDrawContent.subscribe((()=>{const t=e.col(d.$2.MONOMER);if(40!==t.width){t.width=40;for(const t of n)e.col(t).width=40}else s.unsubscribe()}));return e}getMonomerPosition(t){return{monomerOrCluster:t.cell.dataFrame.get(d.$2.MONOMER,t.tableRowIndex),positionOrClusterType:t.tableColumn.name}}render(){var t;if(h()(this.root).empty(),!this.activityColumnName||!this.sequenceColumnName)return void this.root.appendChild(l.divText("Please, select a sequence and activity columns in the viewer properties"));const e=this.getProperty(r.COLOR);e&&(e.choices=g()(a.shell.t.columns.numerical).toArray().map((t=>t.name)),e.get(this)===d.$2.ACTIVITY_SCALED&&e.set(this,d.$2.ACTIVITY)),h()(this.root).empty();let n=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 o=t=>{h()(t.root).find(".ui-input-editor").css("margin","0px").attr("type","radio"),h()(t.root).find(".ui-input-description").css("padding","0px").css("padding-right","16px"),h()(t.captionLabel).addClass("ui-label-right")};o(t),o(e),n=l.divH([t.root,e.root],{id:"pep-viewer-title"}),h()(n).css("width","auto").css("align-self","center")}const o=this.viewerGrid.root;o.style.width="auto";const s=l.icons.search((()=>{this._showSearchInput=!this._showSearchInput,this.monomerSearchInput.input.style.display=this._showSearchInput?"block":"none"}),"Toggle monomer search input visibility");this.monomerSearchInput.input.style.display=this._showSearchInput?"block":"none",h()(s).addClass("pep-help-icon"),(0,w.BX)(s.style).set("top","3px").set("fontSize","14px");const u=l.divH([this.monomerSearchInput.input],{style:{alignSelf:"center",justifyContent:"center",width:"100%",flexWrap:"wrap"}}),c=l.divH([s,n,u],{style:{alignSelf:"center",lineHeight:"normal",flexDirection:"column",width:"100%"}});this.root.appendChild(l.divV([c,o])),null===(t=this.viewerGrid)||void 0===t||t.invalidate(),this.monomerSearchInput.fireChanged()}}class I extends x{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()}onFilterChanged(t,e=!1){if(this._monomerPositionStats=null,this._invariantMapSelection=null,this._mutationCliffStats=null,this._mutationCliffsSelection=null,this._mutationCliffs=null,e)return;this._viewerGrid=null;const n=this.model.findViewer(m.q.SEQUENCE_VARIABILITY_MAP);"Filtered"===(null==n?void 0:n.dataSource)&&n.onFilterChanged(!1,!0),t&&this.render()}createMostPotentResiduesDf(){var t;const e=Object.entries(this.monomerPositionStats),n=new Array(e.length-1),i=new Array(n.length),o=new Array(n.length),r=new Array(n.length),s=new Array(n.length),a=new Array(n.length),l=new Array(n.length),c=this.getTotalViewerAggColumns(),h=c.map((([t,e])=>(0,v.hX)(e,t))),f=new Array(h.length);h.forEach(((t,e)=>f[e]=new Array(n.length)));let m=0;for(const[p,g]of e){const e=g.general;if(!e)continue;if(1===Object.entries(g).length)continue;const C=[];for(const[n,i]of Object.entries(g))"general"!==n&&(i.count>1&&(null==i.pValue||(null!==(t=i.pValue)&&void 0!==t?t:1)<=.05)&&C.push([n,i]),i.pValue===e.minPValue&&C.push([n,i]));let y=null;0===C.length&&(y=Object.entries(g).find((([t,e])=>"general"!=t)));for(const[t,e]of C)(null===y||this.activityTarget===d.wf.HIGH&&y[1].meanDifference<e.meanDifference||this.activityTarget===d.wf.LOW&&y[1].meanDifference>e.meanDifference)&&(y=[t,e]);if(null===y)continue;n[m]=parseInt(p),i[m]=y[0],o[m]=y[1].meanDifference,r[m]=y[1].pValue,s[m]=y[1].count,a[m]=y[1].ratio,l[m]=y[1].mean;const w=this.monomerPositionStats[p][y[0]],A=u.BitSet.fromBytes(w.mask.buffer.buffer,this.model.df.col(this.activityColumnName).length);for(let t=0;t<h.length;t++){const[e,n]=c[t];f[t][m]=(0,v.lh)(this.model.df.getCol(e),n,A)}++m}n.length=m,i.length=m,o.length=m,r.length=m,s.length=m,a.length=m,l.length=m;const p=u.DataFrame.create(m),g=p.columns;return g.add(u.Column.fromList(u.TYPE.INT,d.$2.POSITION,n)),g.add(u.Column.fromList(u.TYPE.STRING,d.$2.MONOMER,i)),g.add(u.Column.fromList(u.TYPE.FLOAT,d.$2.MEAN_DIFFERENCE,o)),g.add(u.Column.fromList(u.TYPE.FLOAT,d.$2.MEAN,l)),g.add(u.Column.fromList(u.TYPE.FLOAT,d.$2.P_VALUE,r)),g.add(u.Column.fromList(u.TYPE.INT,d.$2.COUNT,s)),g.add(u.Column.fromList(u.TYPE.FLOAT,d.$2.RATIO,a)),h.forEach(((t,e)=>g.add(u.Column.fromList(u.TYPE.FLOAT,t,f[e])))),p}createViewerGrid(){const t=this.createMostPotentResiduesDf(),e=t.plot.grid();e.sort([d.$2.POSITION]);const n=e.col(d.$2.P_VALUE);n.format="#.000",n.name="P-value";const i=t.getCol(d.$2.MONOMER);f.rI(i,this.alphabet,!0),e.onCellRender.subscribe((t=>O(t,this,!1))),e.onCellTooltip(((t,e,n)=>{var i,o;if(!t.isTableCell)return this.model.unhighlight(),!0;const r=this.getMonomerPosition(t);if((0,w.dl)(r,this.dataFrame,this.monomerPositionStats),this.model.isHighlighting=!0,(null===(i=t.tableColumn)||void 0===i?void 0:i.name)===d.$2.MONOMER)r.positionOrClusterType=d.$2.MONOMER;else if((null===(o=t.tableColumn)||void 0===o?void 0:o.name)!==d.$2.MEAN_DIFFERENCE)return!1;const s=this.getTotalViewerAggColumns(),a=null==t.tableRowIndex?void 0:(0,v.m2)(t.grid.dataFrame,t.tableRowIndex,s,{});return(0,C.D)(this.model.df,this.getScaledActivityColumn(),s,{fromViewer:!0,isMostPotentResidues:!0,monomerPosition:r,x:e,y:n,mpStats:this.monomerPositionStats,aggrColValues:a})})),u.debounce(e.onCurrentCellChanged,500).subscribe((n=>{var i,o,r;try{if(-1===n.gridRow)return this._mutationCliffsSelection=(0,w.ZR)(this.positionColumns),this._invariantMapSelection=(0,w.ZR)(this.positionColumns),this.model.fireBitsetChanged(m.q.MOST_POTENT_RESIDUES),void e.invalidate();if(this.keyPressed&&t.currentCol.name!==d.$2.MEAN_DIFFERENCE||!this.keyPressed)return;const s=this.getMonomerPosition(n);if(null!==this.currentGridRowIdx){const t=this.getMonomerPosition(e.cell("Diff",this.currentGridRowIdx));this.modifyInvariantMapSelection(t,{shiftPressed:!0,ctrlPressed:!0},!1)}(null===(r=null===(o=null===(i=this.mutationCliffs)||void 0===i?void 0:i.get(s.monomerOrCluster))||void 0===o?void 0:o.get(s.positionOrClusterType))||void 0===r?void 0:r.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,w.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,o;const r=e.hitTest(t.offsetX,t.offsetY);if(!(null==r?void 0:r.isTableCell)||r.tableColumn.name!==d.$2.MEAN_DIFFERENCE)return;const s=this.getMonomerPosition(r);(null===(o=null===(i=null===(n=this.monomerPositionStats)||void 0===n?void 0:n[s.positionOrClusterType])||void 0===i?void 0:i[s.monomerOrCluster])||void 0===o?void 0:o.count)&&(this.modifyInvariantMapSelection(s,{shiftPressed:t.shiftKey,ctrlPressed:t.ctrlKey}),e.invalidate())})),L(e);const o=e.col(d.$2.MEAN_DIFFERENCE);o.name="Diff";const r=e.onAfterDrawContent.subscribe((()=>{const t=e.col(d.$2.MONOMER);if(40===t.width)return o.width=40,void r.unsubscribe();t.width=40,o.width=40}));return e}getMonomerPosition(t){return{monomerOrCluster:t.cell.dataFrame.get(d.$2.MONOMER,t.tableRowIndex),positionOrClusterType:`${t.cell.dataFrame.get(d.$2.POSITION,t.tableRowIndex)}`}}render(){var t;if(h()(this.root).empty(),!this.activityColumnName||!this.sequenceColumnName)return void this.root.appendChild(l.divText("Please, select a sequence and activity columns in the viewer properties"));const e=this.viewerGrid.root;e.style.width="auto",this.root.appendChild(l.divV([e])),null===(t=this.viewerGrid)||void 0===t||t.invalidate()}}function O(t,e,n,i,o){var r,s,a,l,c;const h=[...e.positionColumns.map((t=>t.name)),d.$2.MEAN_DIFFERENCE],m=t.g,p=t.bounds;m.save(),m.beginPath(),m.rect(p.x,p.y,p.width,p.height),m.clip();const g=t.cell,v=null===(r=g.tableColumn)||void 0===r?void 0:r.name,C=g.tableRowIndex;if(!g.isTableCell||-1===h.indexOf(v))return void m.restore();const y=g.grid.table,w=y.get(d.$2.MONOMER,C),A=v!==d.$2.MEAN_DIFFERENCE?v:y.get(d.$2.POSITION,C).toFixed(),b=e.monomerPositionStats[A];if(!b[w])return t.preventDefault(),void m.restore();if(n){const t=null!==(s=b[w].aggValue)&&void 0!==s?s:b[w].count,n=e.positionColumns.find((t=>t.name===A)),i=null!==(a=n.temp[d.gp.INVARIANT_MAP_COLOR_CACHE])&&void 0!==a?a:{};let o=u.Color.white;null!=i[w]?o=i[w]:e instanceof M&&(e.cacheInvariantMapColors(),o=null!==(c=(null!==(l=n.temp[d.gp.INVARIANT_MAP_COLOR_CACHE])&&void 0!==l?l:{})[w])&&void 0!==c?c:u.Color.white),f.rW(m,w,A,e.invariantMapSelection,t,p,o)}else f.Yd(m,w,A,e,p);t.preventDefault(),m.restore()}function L(t){const e=t.props;e.allowEdit=!1,e.allowRowSelection=!1,e.allowBlockSelection=!1,e.allowColSelection=!1,e.showRowHeader=!1,e.showCurrentRowIndicator=!1,e.showReadOnlyNotifications=!1,e.rowHeight=20}},7654:(t,e,n)=>{"use strict";n.d(e,{HV:()=>p,M1:()=>g,QD:()=>v});var i,o=n(7389),r=n(6082),s=n(7233),a=n.n(s),l=n(4139),u=n(5070),c=n(8608),h=n(5480),d=n(8774);!function(t){t.SEPARATE_MONOMERS="separateMonomers",t.SEPARATE_POSITIONS="separatePositions",t.SEPARATE_CLUSTERS="separateClusters"}(i||(i={}));const f="general",m=t=>t===f?"General":t.substring(8);function p(t,e){if(!t.selection.anyTrue)return o.divText("No distribution");const n=()=>{const n=[y(f,t,e)];for(const o of Object.values(i))"true"!==t.getTag(o)||o===i.SEPARATE_CLUSTERS&&!e.clusterColName||n.push(y(o,t,e));return 1===n.length?n[0]:o.div(n)},r=o.div(n()),s=Object.values(i),l=new Array(s.length);for(let u=0;u<s.length;u++){const c=s[u].substring(8);l[u]=o.input.bool(c,{value:"true"===t.getTag(s[u]),onValueChanged:e=>{t.setTag(s[u],`${e}`),a()(r).empty(),r.append(n())}}),a()(l[u].captionLabel).addClass("ui-label-right").css("text-align","left"),a()(l[u].root).find(".ui-input-editor").css("margin","0px"),a()(l[u].root).find(".ui-input-description").css("margin","0px"),l[u].setTooltip(`Show distribution for each ${c}`),c===i.SEPARATE_CLUSTERS?l[u].enabled=!(!e.clusterColName||!e.clusterSelection[h.W.ORIGINAL]):c!==i.SEPARATE_MONOMERS&&c!==i.SEPARATE_POSITIONS||(l[u].enabled=0!==Object.entries(e.monomerPositionSelection).length)}const u=o.form(l,{style:{flexDirection:"row"}});return o.divV([u,r])}function g(t,e=!1){const n=t.plot.histogram({filteringEnabled:!1,valueColumnName:l.$2.ACTIVITY,splitColumnName:l.$2.SPLIT_COL,legendVisibility:"Never",showXAxis:!0,showColumnSelector:!1,showRangeSlider:!1,showBinSelector:!1,backColor:e?"#fdffe5":"#fffff"});return n.root.style.width="auto",n}function v(t,e={}){var n,i;null!==(n=e.fractionDigits)&&void 0!==n||(e.fractionDigits=3);const o={[null!==(i=null==e?void 0:e.countName)&&void 0!==i?i:"Count"]:`${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&&(o["p-value"]=t.pValue<.01?"<0.01":t.pValue.toFixed(e.fractionDigits)),o}function C(t,e,n,i={}){const o=g((0,c.FZ)(n.activityCol,t.selection,t)),s=(0,u.I_)(t,Object.entries(n.columns),{filterDf:!0,mask:r.BitSet.fromBytes(e.mask.buffer.buffer,e.mask.length)}),l=v(e),h=Object.assign(Object.assign({},l),s),d=(0,c.F2)(o,h,i);return a()(d).addClass("d4-flex-col"),d}function y(t,e,n){let r=o.divText("No distribution");const s=e.selection.clone().and(e.filter),a=d.A.fromUint32Array(s.length,new Uint32Array(s.getBuffer().buffer));switch(t){case f:r=C(e,e.selection.anyTrue&&e.selection.anyFalse?(0,u.GT)(n.activityCol.getRawData(),a,(0,u.pY)(e.filter)):{count:n.activityCol.length,pValue:null,meanDifference:0,ratio:1,mask:a,mean:n.activityCol.stats.avg},n);break;case i.SEPARATE_CLUSTERS:r=function(t,e,n){const i=t.rowCount,r=[],s=e.activityCol.getRawData(),a=t.getCol(e.clusterColName),l=a.categories,f=a.getRawData(),m=(0,u.pY)(t.filter),p=n[h.W.ORIGINAL].map((t=>l.indexOf(t))),g=new Array(p.length).fill(new d.A(i));for(let t=0;t<i;t++){const e=f[t],n=p.indexOf(e);-1!==n&&g[n].setTrue(t)}for(let n=0;n<p.length;n++){const i=p[n],o=(0,u.GT)(s,g[n],m);r.push(C(t,o,e,{[c.AN.SELECTION]:l[i]}))}const v=n[h.W.CUSTOM];for(const n of v){const o=t.getCol(n),a=d.A.fromUint32Array(i,o.getRawData()),l=(0,u.GT)(s,a,m);r.push(C(t,l,e,{[c.AN.SELECTION]:n}))}return o.div(r,"d4-flex-wrap")}(e,n,n.clusterSelection);break;case i.SEPARATE_MONOMERS:r=function(t,e,n){var i,r,s;const a=Object.keys(n),l=t.rowCount,h=[],f=[],m=[],p=[],g=e.activityCol.getRawData(),v=(0,u.pY)(t.filter);for(const o of a){const a=n[o],y=new d.A(l);for(let e=0;e<a.length;e++){const n=a[e];null!==(i=f[e])&&void 0!==i||(f[e]=t.getCol(n)),null!==(r=m[e])&&void 0!==r||(m[e]=f[e].categories),null!==(s=p[e])&&void 0!==s||(p[e]=f[e].getRawData());const u=m[e].indexOf(o);for(let t=0;t<l;t++)p[e][t]===u&&y.setTrue(t)}const w=(0,u.GT)(g,y,v);h.push(C(t,w,e,{[c.AN.SELECTION]:o}))}return o.div(h,"d4-flex-wrap")}(e,n,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));break;case i.SEPARATE_POSITIONS:r=function(t,e,n){var i,r,s;const a=Object.keys(n),l=t.rowCount,h=[],f=e.activityCol.getRawData(),m=[],p=[],g=[],v=(0,u.pY)(t.filter);for(let o=0;o<a.length;o++){const y=a[o],w=n[y];if(0===w.length)continue;null!==(i=m[o])&&void 0!==i||(m[o]=t.getCol(y)),null!==(r=p[o])&&void 0!==r||(p[o]=m[o].categories),null!==(s=g[o])&&void 0!==s||(g[o]=m[o].getRawData());const A=new d.A(t.rowCount);for(let t=0;t<w.length;t++){const e=w[t],n=p[o].indexOf(e);for(let t=0;t<l;t++)g[o][t]===n&&A.setTrue(t)}const b=(0,u.GT)(f,A,v);h.push(C(t,b,e,{[c.AN.SELECTION]:y}))}return o.div(h,"d4-flex-wrap")}(e,n,n.monomerPositionSelection)}return o.divV([o.h1(m(t)),r])}},7923:(t,e,n)=>{"use strict";n.d(e,{F:()=>c});var i=n(7389),o=n(6082),r=n(4139),s=n(8608),a=n(3163),l=n(4025),u=n(7654);function c(t,e,n=!0){var r,a,l,c,d;const f=h(t,e);if(!f)return new o.Widget(i.label("No mutations table generated"));const{pairsGrid:m,uniqueSequencesGrid:p,aminoToInput:g}=f,v=[m,p],C=i.divV([g.root,...v.map((t=>t.root))],{style:{width:"100%"}});if(1===Object.values(e.mutationCliffsSelection).filter((t=>t.length>0)).length){const t=Object.keys(e.mutationCliffsSelection).find((t=>e.mutationCliffsSelection[t].length>0)),n=e.mutationCliffsSelection[t];if(1===n.length){const i=n[0],o=null===(a=null===(r=e.mutationCliffs)||void 0===r?void 0:r.get(i))||void 0===a?void 0:a.get(t);if(o&&o.size>0){const n=(0,s.Z7)(e.activityCol,o,i),r=(0,u.M1)(n,!1),a=null===(d=null===(c=null===(l=e.mutationCliffStats)||void 0===l?void 0:l.stats)||void 0===c?void 0:c.get(i))||void 0===d?void 0:d.get(t),h={};let f=0;for(const t of o.values())f+=t.length;h["Pairs count"]=f.toString(),a&&(h["Unique Count"]=a.mask.trueCount().toString(),Object.assign(h,(0,u.QD)(a,{countName:"MP in cliffs count"})));const m=(0,s.F2)(r,h);r.root.style.maxHeight="100px",m.style.marginTop="10px",C.appendChild(m)}}}return n&&(0,s.BE)("Mutation Cliffs pairs",g.root,C,(()=>{const n=h(t,e),o=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(o)){const r=o.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="calc(100% - 20px)",a.style.marginTop="20px",r>400)){const t=Math.max(.33*r,200),i=n.pairsGrid.columns.byName("Mutation");i&&(i.width=t);const o=n.uniqueSequencesGrid.columns.byName(e.sequenceColumnName);o&&(o.width=t)}}}),500),o})),new o.Widget(C)}function h(t,e){var n,u;const c=t.filter.getSelectedIndexes(),h=Object.keys(e.mutationCliffsSelection);if(!h.length||null===e.mutationCliffs)return null;const d=[],f=[],m=[],p=[],g=[],v=[],C=t.getCol(e.sequenceColumnName),y=C.categories,w=C.getRawData(),A=e.activityCol.getRawData(),b=new Map,S=o.BitSet.create(t.rowCount),T={},E=Object.fromEntries(e.positionColumns.map((t=>[t.name,t])));for(const t of h){const i=E[t],o=i.categories,r=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,n]of s.entries()){if(!c.includes(t))continue;T[t]||(T[t]=Object.keys(T).length+1);const i=T[t],s=null!==(u=b.get(t))&&void 0!==u?u:[],a=y[w[t]],l=A[t],h=e.activityCol.isNone(t)?null:l;for(const l of n){if(s.includes(l)||!c.includes(l))continue;b.has(l)||b.set(l,[]);const n=y[w[l]],u=e.activityCol.isNone(l)?null:A[l],C=null==h||null==u?null:h-u;b.get(l).push(t),d.push(`${a}#${n}`),p.push(`${i}`),f.push(C),m.push(o[r[l]]),g.push(t),v.push(l),S.set(t,!0),S.set(l,!0)}}}}if(0===d.length)return null;const _=o.Column.fromStrings("Mutation",d),N=o.Column.fromList("double","Delta",f),x=o.Column.fromStrings("Group",p),M=o.Column.fromStrings("~to",m),I=o.Column.fromList(o.COLUMN_TYPE.INT,"~toIdx",v),O=o.Column.fromList(o.COLUMN_TYPE.INT,"~fromIdx",g),L=o.DataFrame.fromColumns([_,N,x,M,I,O]);L.name="Mutation Cliff pairs";const P=i.input.string("Mutated to:",{value:"",onValueChanged:t=>{const e=t;""!==e?L.filter.init((t=>M.get(t)===e)):L.filter.setAll(!0)}});P.setTooltip("Filter the rows by the monomer that the mutation was substituted to");const R=L.plot.grid();(0,s.vY)(R,!0),_.semType=r.uF.MACROMOLECULE_DIFFERENCE,_.tags[r.gp.SEPARATOR]=(0,s.AY)(C),_.tags[o.TAGS.UNITS]=C.tags[o.TAGS.UNITS],_.tags[o.TAGS.CELL_RENDERER]="MacromoleculeDifference",_.temp[l.j.notationProvider]=C.temp[l.j.notationProvider];let k=!1,V=null;const F=[];R.onCurrentCellChanged.subscribe((t=>{try{if(!t||!t.dart)return F.length=0,void j();const e=t.tableRowIndex;if(!k)return;if(null===e)return F.length=0,void j();null!==V&&F.splice(F.indexOf(V),1),F.includes(e)||(F.push(e),R.invalidate()),j()}finally{k=!1,V=t&&t.dart?t.tableRowIndex:null}})),R.root.addEventListener("keydown",(t=>{k=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=F.indexOf(n);-1===t?F.push(n):F.splice(t,1)}else F.length=0,F.push(n);j(),R.invalidate(),Y.invalidate()})),R.onCellPrepare((t=>{var e,n,i,r;if((null==t?void 0:t.isTableCell)&&"delta"==(null===(n=null===(e=null==t?void 0:t.gridColumn)||void 0===e?void 0:e.name)||void 0===n?void 0:n.toLowerCase())&&(null==(null===(i=null==t?void 0:t.cell)||void 0===i?void 0:i.value)||(null===(r=null==t?void 0:t.cell)||void 0===r?void 0:r.value)==o.FLOAT_NULL))try{t.customText="N/A"}catch(t){}})),R.onCellRender.subscribe((t=>{var e;(null===(e=t.cell.tableColumn)||void 0===e?void 0:e.name)===_.name&&F.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 U=t.clone(S,G);U.name="Unique sequences that form Mutation Cliffs pairs";const q=U.columns.addNewInt("~seqIdx"),B=q.getRawData();U.col(e.sequenceColumnName)&&(U.col(e.sequenceColumnName).temp[l.j.notationProvider]=C.temp[l.j.notationProvider]);const H=S.getSelectedIndexes();q.init((t=>H[t]));const Y=U.plot.grid();function j(){const t=[];for(const e of F)t.push(O.get(e)),t.push(I.get(e));U.filter.init((e=>0===F.length||t.includes(B[e])),!0),R.invalidate(),Y.invalidate()}return(0,s.vY)(Y,!0),Y.props.rowHeight=20,R.root.style.width="100% !important",Y.root.style.width="100% !important",setTimeout((()=>{R.autoSize(window.innerWidth,250,void 0,void 0,!1),Y.autoSize(window.innerWidth,250,void 0,void 0,!1),R.root.style.removeProperty("width"),R.root.style.setProperty("width","100%"),Y.root.style.removeProperty("width"),Y.root.style.setProperty("width","100%"),R.root.style.minHeight="70px",Y.root.style.minHeight="100px",R.root.style.height="unset",Y.root.style.height="unset"}),200),{pairsGrid:R,uniqueSequencesGrid:Y,aminoToInput:P}}},440:(t,e,n)=>{"use strict";n.d(e,{v:()=>g,n:()=>v});var i=n(4328),o=n(7389),r=n(6082),s=n(4139),a=n(115),l=n(9499),u=n(7233),c=n.n(u),h=n(8608),d=n(1199),f=n(5429);class m{constructor(t){this._inputBase=t}get root(){return this._inputBase.root}get value(){return this._inputBase.value}set value(t){this._inputBase.value=t}get inputBase(){return this._inputBase}}n(4788);var p=function(t,e,n,i){return new(n||(n=Promise))((function(o,r){function s(t){try{l(i.next(t))}catch(t){r(t)}}function a(t){try{l(i.throw(t))}catch(t){r(t)}}function l(t){var e;t.done?o(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 g(t,e){return p(this,void 0,void 0,(function*(){const n=new a.av,l=o.div();let u=null;if(void 0===e){const e=r.Utils.firstOrNull(t.columns.toList().filter((t=>t.semType===r.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=yield async function(t,e){const n=r.Func.find({package:"Bio",name:"sequenceColumnInput"})[0];return n?await n.apply({name:t,options:e}):new m(o.input.column(t,e))}("Sequence",{table:t,value:e,onValueChanged:e=>{c()(l).empty().append(o.wait((()=>p(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===r.SEMTYPE.MACROMOLECULE,nullable:!1}),u.inputBase.setTooltip("Macromolecule column in FASTA, HELM or separated format")}let g,C=r.Func.find({package:"Bio",name:"webLogoViewer"});if(0===C.length)return{host:o.label("Bio package is missing or out of date. Please install the latest version."),callback:()=>p(this,void 0,void 0,(function*(){return!1}))};if(C=r.Func.find({package:"Bio",name:"getBioLib"}),0===C.length)return{host:o.label("Bio package is missing or out of date. Please install the latest version."),callback:()=>p(this,void 0,void 0,(function*(){return!1}))};const y=t.col("activity")||t.col("IC50")||r.Utils.firstOrNull(t.columns.numerical),w=o.div([],{id:"pep-hist-host"}),A=o.input.choice("Scaling",{value:s.rg.NONE,items:Object.values(s.rg),onValueChanged:t=>p(this,void 0,void 0,(function*(){var e;g=(0,h.Y1)(S.value,t);const n=r.DataFrame.fromColumns([g]).plot.histogram({filteringEnabled:!1,valueColumnName:s.$2.ACTIVITY,legendVisibility:"Never",showXAxis:!0,showColumnSelector:!1,showRangeSlider:!1,showBinSelector:!1});null===(e=w.lastChild)||void 0===e||e.remove(),w.appendChild(n.root)}))});A.setTooltip("Activity column transformation method");const b=()=>{var t;A.enabled=null!==(t=S.value)&&void 0!==t&&t&&S.value.stats.min>0,A.value=s.rg.NONE,0!==S.value.stats.missingValueCount&&i.shell.info("Activity column contains missing values. They will be ignored during analysis")},S=o.input.column("Activity",{table:t,value:y,nullable:!1,onValueChanged:b,filter:t=>t.type===r.TYPE.INT||t.type===r.TYPE.FLOAT||t.type===r.TYPE.QNUM});S.setTooltip("Numerical activity column");const T=o.input.column("Clusters",{table:t,onValueChanged:t=>{t&&(E.value=!1,E.fireChanged())}});T.setTooltip("Optional. Clusters column is used to create Logo Summary Table"),T.nullable=!0;const E=o.input.bool("Generate clusters",{value:!0,onValueChanged:t=>{t&&(T.value=null,T.fireChanged())}});E.setTooltip("Generate clusters column based on MCL embeddings for Logo Summary Table"),S.fireChanged(),A.fireChanged(),E.fireChanged();const _=[S,A,T,E];null!==u&&_.splice(0,0,u.inputBase);const N=o.input.float(f.t_.THRESHOLD,{value:n.threshold,nullable:!1,onValueChanged:t=>n.threshold=null!=t?t:n.threshold});N.setTooltip("Threshold for similarity between two sequences to create edges");const x=o.input.float(f.t_.INFLATION,{value:n.inflation,nullable:!1,onValueChanged:t=>n.inflation=null!=t?t:n.inflation});x.setTooltip("Inflation value for MCL algorithm");const M=o.input.int(f.t_.MAX_ITERATIONS,{value:n.maxIterations,nullable:!1,onValueChanged:t=>n.maxIterations=null!=t?t:n.maxIterations});M.setTooltip("Maximum iterations for MCL algorithm");const I=o.input.bool(f.t_.USE_WEBGPU,{value:n.useWebGPU,onValueChanged:t=>n.useWebGPU=t});I.enabled=!1,n.webGPUDescriptionPromise.then((()=>{n.webGPUDescription!==a.Ku?(I.setTooltip(`Use WebGPU for MCL algorithm (${n.webGPUDescription})`),I.enabled=!0):(I.setTooltip(a.Ku),I.enabled=!1,I.value=!1)}));const O=o.input.int(f.t_.MIN_CLUSTER_SIZE,{value:n.minClusterSize,nullable:!1,onValueChanged:t=>n.minClusterSize=null!=t?t:n.minClusterSize});O.setTooltip("Minimum cluster size for MCL algorithm");const L=o.input.choice(f.t_.DISTANCE_FUNCTION,{value:n.distanceF,items:[d.Z.NEEDLEMANN_WUNSCH,d.Z.MONOMER_CHEMICAL_DISTANCE,d.Z.HAMMING,d.Z.LEVENSHTEIN],nullable:!1,onValueChanged:t=>n.distanceF=t}),P=o.input.float(f.t_.GAP_OPEN,{value:n.gapOpen,onValueChanged:t=>n.gapOpen=null!=t?t:n.gapOpen}),R=o.input.float(f.t_.GAP_EXTEND,{value:n.gapExtend,onValueChanged:t=>n.gapExtend=null!=t?t:n.gapExtend}),k=[N,x,M,O,L,o.input.choice(f.t_.FINGERPRINT_TYPE,{value:n.fingerprintType,items:["Morgan","RDKit","Pattern","AtomPair","MACCS","TopologicalTorsion"],nullable:!1,onValueChanged:t=>n.fingerprintType=t}),P,R,I],V=o.form(k);V.style.display="none";const F=o.icons.settings((()=>{V.style.display="none"===V.style.display?"flex":"none",V.classList.remove("ui-form-condensed")}),"Adjust clustering parameters");F.style.fontSize="16px",E.root.appendChild(F);const D=t.filter.onChanged.subscribe((()=>b())),G=()=>p(this,void 0,void 0,(function*(){var i,o;const r=null!=e?e:u.value;return D.unsubscribe(),!!r&&null!==(yield v(S.value,r,T.value,t,g,null!==(i=A.value)&&void 0!==i?i:s.rg.NONE,{addSequenceSpace:!1,addMCL:E.value,useEmbeddingsClusters:null!==(o=E.value)&&void 0!==o&&o,mclSettings:n}))}));let U="auto";const q=[o.divV(_)];if(c()(q[0]).find("label").css("width","unset"),void 0!==e){const t=o.button("Launch SAR",G,"");t.style.alignSelf="center",q.push(t),U="215px"}return c()(l).empty().append(o.wait((()=>p(this,void 0,void 0,(function*(){var n;const i=yield t.plot.fromType("WebLogo",{sequenceColumnName:null!==(n=null==e?void 0:e.name)&&void 0!==n?n:u.value.name});return i.root.style.setProperty("height","130px"),i.root}))))),{host:o.divV([l,o.splitH([o.splitV(q,{style:{flex:"0 1 auto"}}),w],{style:{height:U,minWidth:"600px",maxWidth:"750px"}}),V]),callback:G}}))}function v(t,e,n,o,u,c){return p(this,arguments,void 0,(function*(t,e,n,o,u,c,h={}){var d,f,m,p,g;let v=null;if(t.type!==r.COLUMN_TYPE.FLOAT&&t.type!==r.COLUMN_TYPE.INT&&t.type!==r.COLUMN_TYPE.QNUM)return i.shell.error("The activity column must be of numeric type!"),v;const C=r.TaskBarProgressIndicator.create("Loading SAR...");o.tags.delete&&o.tags.delete(".script");const y=o.columns,w=o.col(u.name);w&&(w.name=y.getUnusedName(w.name));const A=u.getRawData();o.columns.addNew(u.name,u.type).init((t=>A[t])),y.setOrder([u.name,e.name,...y.names().filter((t=>t!==e.name&&t!==u.name))]);const b={sequenceColumnName:e.name,activityColumnName:t.name,activityScaling:c,columns:{},showDendrogram:!1,showSequenceSpace:!1,sequenceSpaceParams:new a.GI(!!h.useEmbeddingsClusters&&!n),mclSettings:null!==(d=h.mclSettings)&&void 0!==d?d:new a.av};if(n){const t=o.getCol(n.name);t.type!==r.COLUMN_TYPE.STRING&&y.replace(t,t.convertTo(r.COLUMN_TYPE.STRING))}if(o.setTag(s.gp.SETTINGS,JSON.stringify(b)),v=l.i.getInstance(o),v.init(b),n){const i={clustersColumnName:n.name,sequenceColumnName:e.name,activityScaling:c,activityColumnName:t.name};yield v.addLogoSummaryTable(i)}if(yield v.addMonomerPosition(),yield v.addMostPotentResidues(),null!==(f=h.addSequenceSpace)&&void 0!==f&&f){if(yield v.addSequenceSpace({clusterCol:n,clusterEmbeddings:h.useEmbeddingsClusters}),!n&&null!==(m=h.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)===r.COLUMN_TYPE.STRING}));if(n){const i={clustersColumnName:n,sequenceColumnName:e.name,activityScaling:c,activityColumnName:t.name};yield v.addLogoSummaryTable(i),setTimeout((()=>{var t,e;v&&(null===(t=null==v?void 0:v.findViewer(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!==(p=h.addMCL)&&void 0!==p&&p&&(yield v.addMCLClusters(),!n&&null!==(g=h.useEmbeddingsClusters)&&void 0!==g&&g)){const n=v._mclCols.find((t=>(null==v?void 0:v.df.col(t))&&t.toLowerCase().startsWith("cluster")&&!t.toLowerCase().includes("size")));if(n){const i={clustersColumnName:n,sequenceColumnName:e.name,activityScaling:c,activityColumnName:t.name};yield v.addLogoSummaryTable(i),setTimeout((()=>{var t,e;v&&(null===(t=null==v?void 0:v.findViewer(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)}}const S=v.df.plot.grid({rowSource:r.RowSet.Selected,selectedRowsColor:r.Color.fromHtml("#ffffff"),title:"Selection"}),T=null==v?void 0:v.findViewerNode(l.q.LOGO_SUMMARY_TABLE);return T&&v.analysisView.dockManager.dock(S,r.DOCK_TYPE.DOWN,T,"Selection",.4),C.close(),v}))}},5429:(t,e,n)=>{"use strict";n.d(e,{OH:()=>A,t_:()=>l});var i,o,r,s,a,l,u=n(7389),c=n(4328),h=n(6082),d=n(115),f=n(4139),m=n(9499),p=n(7233),g=n.n(p),v=n(144),C=n.n(v),y=n(3262),w=n(1199);function A(t){var e,n,r,p,v,A,b,S,T,E;null==t.settings&&c.log.error("PeptidesError: Settings are not initialized");const _=u.accordion(),N=t.settings,x=null!==(e=null==N?void 0:N.activityScaling)&&void 0!==e?e:f.rg.NONE,M=null!==(n=null==N?void 0:N.columns)&&void 0!==n?n:{},I={},O={},L=null!==(r=null==N?void 0:N.sequenceSpaceParams)&&void 0!==r?r:new d.GI,P=null!==(p=null==N?void 0:N.mclSettings)&&void 0!==p?p:new d.av,R=u.input.column(o.ACTIVITY,{table:t.df,value:t.df.getCol(t.settings.activityColumnName),onValueChanged:t=>{I.activityColumnName=t.name},filter:t=>(t.type===h.TYPE.FLOAT||t.type===h.TYPE.INT)&&t.name!==f.$2.ACTIVITY&&0===t.stats.missingValueCount});R.setTooltip("Numeric activity column");const k=u.input.choice(o.ACTIVITY_SCALING,{value:x,items:Object.values(f.rg),onValueChanged:t=>I.activityScaling=t});k.setTooltip("Activity column transformation method"),_.addPane(i.GENERAL,(()=>u.inputs([R,k])),!0),O[i.GENERAL]=[R,k];const V=C()(t.analysisView.viewers).some((t=>t.type===m.q.DENDROGRAM)),F=u.input.bool(m.q.DENDROGRAM,{value:null!=V&&V,onValueChanged:t=>I.showDendrogram=t}),D=u.input.bool(m.q.CLUSTER_MAX_ACTIVITY,{value:!!(null==N?void 0:N.showClusterMaxActivity),onValueChanged:t=>{I.showClusterMaxActivity=null!=t?t:void 0}}),G=u.input.bool("Sequence space",{value:!!(null==N?void 0:N.showSequenceSpace),onValueChanged:t=>{I.showSequenceSpace=null!=t?t:void 0,t?(ft.root.style.display="flex",(null==N?void 0:N.showSequenceSpace)||(I.sequenceSpaceParams=L)):(ft.root.style.display="none",delete I.sequenceSpaceParams),I.showSequenceSpace===(null==N?void 0:N.showSequenceSpace)&&delete I.showSequenceSpace}});D.setTooltip("Show cluster max activity viewer"),F.setTooltip("Show dendrogram viewer"),F.enabled=null!==(0,y.getTreeHelperInstance)(),_.addPane(i.VIEWERS,(()=>u.inputs([F,G,D])),!0),O[i.VIEWERS]=[F,G,D];const U=[],q=[];for(const e of t.df.columns.numerical){const t=e.name;if(t===N.activityColumnName||t===f.$2.ACTIVITY)continue;const n=u.input.bool(s.IS_INCLUDED,{value:void 0!==M[t],onValueChanged:e=>{var n;null!==(n=I.columns)&&void 0!==n||(I.columns={}),e?I.columns[t]=i.value:(delete I.columns[t],Object.keys(I.columns).length===Object.keys(M).length&&delete I.columns)}});n.setTooltip("Include aggregated column value in tooltips, Logo Summary Table and Distribution panel");const i=u.input.choice(s.AGGREGATION,{value:null!==(v=M[t])&&void 0!==v?v:h.AGG.AVG,items:Object.values(h.STATS),onValueChanged:i=>{var o;null!==(o=I.columns)&&void 0!==o||(I.columns={}),n.value?I.columns[t]=i:(delete I.columns[e.name],Object.keys(I.columns).length===Object.keys(M).length&&delete I.columns)}});i.setTooltip("Aggregation method"),g()(i.root).find("label").css("width","auto");const o=u.inputsRow(e.name,[n,i]);q.push(n,i),g()(o).find("div.ui-div").css("display","inline-flex"),U.push(o)}0!==U.length&&(_.addPane(i.COLUMNS,(()=>u.divV(U)),!1),O[i.COLUMNS]=q);const B={};function H(t,e){if(X(),null==e||""===e)return;B[t]=e;let n=!0;for(const[t,e]of Object.entries(B))if(e!==L[t]){n=!1;break}n?delete I.sequenceSpaceParams:I.sequenceSpaceParams=Object.assign(Object.assign({},L),B)}function 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