hoodini-viz 0.2.11 → 0.2.13

package/dist/hoodini-viz.umd.js

@@ -76,7 +76,7 @@ ${ln}`,format:"a3m"}}}}],recycling_steps:1,sampling_steps:50,diffusion_samples:1
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Colors:"}),jsxRuntimeExports.jsxs(Select,{value:jo,onValueChange:qs,children:[jsxRuntimeExports.jsx(SelectTrigger,{id:"domain-colors",className:"w-full text-xs",style:{height:"20px",minHeight:"20px"},children:jsxRuntimeExports.jsx(SelectValue,{})}),jsxRuntimeExports.jsx(SelectContent,{children:$i.map(Gr=>jsxRuntimeExports.jsx(SelectItem,{value:Gr,children:Gr},Gr))})]})]}),jsxRuntimeExports.jsxs("div",{children:[jsxRuntimeExports.jsx(Label,{htmlFor:"domain-source",className:"text-xs mb-1 block",children:"Domain Source:"}),jsxRuntimeExports.jsxs(Select,{value:Ec||"all",onValueChange:Gr=>{try{typeof Sl=="function"?Sl(Gr):Va&&typeof Va.setDomainSource=="function"&&Va.setDomainSource(Gr)}catch{}},children:[jsxRuntimeExports.jsx(SelectTrigger,{id:"domain-source",className:"w-full text-xs",style:{height:"20px",minHeight:"20px"},children:jsxRuntimeExports.jsx(SelectValue,{})}),jsxRuntimeExports.jsxs(SelectContent,{children:[jsxRuntimeExports.jsx(SelectItem,{value:"all",children:"all"}),(()=>{try{const Gr=Wn&&Wn.current?Wn.current.genomeView:null;if(!Gr)return null;const Ti=Gr.getAllDomains?Gr.getAllDomains():[];return Array.from(new Set(Ti.map(es=>String(es&&(es.source||es.metadata&&es.metadata.source)||"unknown")))).sort().map(es=>jsxRuntimeExports.jsx(SelectItem,{value:String(es),children:String(es)},String(es)))}catch{return null}})()]})]})]})]})]}),jsxRuntimeExports.jsx(Separator,{className:"my-2"}),jsxRuntimeExports.jsx("div",{className:"mb-3",children:jsxRuntimeExports.jsx(UnifiedPaletteWidget,{genePalette:ya,setGenePalette:jl,phyloPalette:Bs,setPhyloPalette:Li,domainPalette:Pl,setDomainPalette:lc,ncRNAPalette:ss,setNcRNAPalette:Dl,regionPalette:xl,setRegionPalette:Jl,availableData:{parsedGFF:[1],parsedDomains:Xi?[1]:[],phyloData:[1],ncRNAFeatures:[1],regionFeatures:[1]}})}),jsxRuntimeExports.jsx(Separator,{className:"my-2"}),jsxRuntimeExports.jsxs("div",{className:"mb-3",children:[jsxRuntimeExports.jsx(Label,{className:"text-xs font-medium mb-1 block",children:"Links Color Selection:"}),jsxRuntimeExports.jsx("div",{className:"space-y-1",children:jsxRuntimeExports.jsx(LinkColorWidget,{proteinLinkConfig:Xa,nucleotideLinkConfig:dl,onProteinLinkConfigChange:rl,onNucleotideLinkConfigChange:Tl})})]})]}),lo==="legend"&&jsxRuntimeExports.jsxs("div",{className:"space-y-4",children:[jsxRuntimeExports.jsx("div",{className:"flex items-center gap-2 mb-3",children:jsxRuntimeExports.jsxs(Badge,{variant:"soft",className:"text-xs font-medium",children:[jsxRuntimeExports.jsx(BookOpen,{className:"h-3 w-3 mr-1"}),"Legend"]})}),jsxRuntimeExports.jsxs("div",{className:"bg-muted/30 p-3 rounded-lg border border-border/30",children:[jsxRuntimeExports.jsx("div",{className:"flex items-center gap-2 mb-2",children:jsxRuntimeExports.jsx(Badge,{variant:"muted",className:"text-xs",children:"Visualization Legend"})}),jsxRuntimeExports.jsx("div",{className:"space-y-2",children:bo?jsxRuntimeExports.jsx(LegendWidget,{legend:bo,genePalette:ya,phyloPalette:Bs,regionPalette:xl,proteinLinkConfig:Xa,nucleotideLinkConfig:dl,styleConfig:dc,className:"",style:{}}):jsxRuntimeExports.jsxs("div",{className:"p-3 bg-accent/30 rounded-lg text-center",children:[jsxRuntimeExports.jsx("p",{className:"text-xs text-muted-foreground mb-1",children:"No legend data available yet"}),jsxRuntimeExports.jsx("p",{className:"text-xs text-muted-foreground",children:"Legend will appear once data is loaded"})]})})]}),jsxRuntimeExports.jsxs("div",{className:"bg-muted/30 p-3 rounded-lg border border-border/30",children:[jsxRuntimeExports.jsx("div",{className:"flex items-center gap-2 mb-2",children:jsxRuntimeExports.jsx(Badge,{variant:"muted",className:"text-xs",children:"Guide"})}),jsxRuntimeExports.jsxs("div",{className:"text-xs space-y-2 text-muted-foreground",children:[jsxRuntimeExports.jsxs("div",{className:"p-2 bg-accent/20 rounded-md",children:[jsxRuntimeExports.jsx("p",{className:"font-medium mb-1 text-foreground/80",children:"Gene Tracks:"}),jsxRuntimeExports.jsx("p",{children:"• Arrows indicate gene direction and boundaries"}),jsxRuntimeExports.jsx("p",{children:"• Colors represent different metadata categories"})]}),jsxRuntimeExports.jsxs("div",{className:"p-2 bg-accent/20 rounded-md",children:[jsxRuntimeExports.jsx("p",{className:"font-medium mb-1 text-foreground/80",children:"Phylogenetic Tree:"}),jsxRuntimeExports.jsx("p",{children:"• Branch lengths show evolutionary distance"}),jsxRuntimeExports.jsx("p",{children:"• Node colors represent tree metadata"})]}),jsxRuntimeExports.jsxs("div",{className:"p-2 bg-accent/20 rounded-md",children:[jsxRuntimeExports.jsx("p",{className:"font-medium mb-1 text-foreground/80",children:"Protein Domains:"}),jsxRuntimeExports.jsx("p",{children:"• Colored regions within genes"}),jsxRuntimeExports.jsx("p",{children:"• Represent functional protein domains"})]}),jsxRuntimeExports.jsxs("div",{className:"p-2 bg-muted/50 rounded",children:[jsxRuntimeExports.jsx("p",{className:"font-medium mb-1",children:"Links:"}),jsxRuntimeExports.jsx("p",{children:"• Connect related elements across tracks"}),jsxRuntimeExports.jsx("p",{children:"• Show protein or nucleotide relationships"})]})]})]})]}),lo==="guides"&&jsxRuntimeExports.jsxs("div",{className:"space-y-4",children:[jsxRuntimeExports.jsx("div",{className:"flex items-center gap-2 mb-3",children:jsxRuntimeExports.jsxs(Badge,{variant:"soft",className:"text-xs font-medium",children:[jsxRuntimeExports.jsx(Crop,{className:"h-3 w-3 mr-1"}),"Format Guides"]})}),jsxRuntimeExports.jsx("div",{className:"bg-muted/30 p-3 rounded-lg border border-border/30",children:jsxRuntimeExports.jsx(GuideControlsWidget,{guidesVisible:Bl,selectedFormat:Hl,onGuidesVisibleChange:sl,onFormatChange:ko,scaleToFormat:kn,onScaleToFormatChange:Vn,cropToGuides:On,onCropToGuidesChange:Pn,scaleRulerWithCrop:fr,onScaleRulerWithCropChange:mr})})]})]})]})}function SVGExportButton({phyloTreeViewerRef:yt}){const Et=()=>{try{console.log("🖼️ SVGExportButton clicked, ref:",yt.current),console.log("🖼️ exportToSVG method:",yt.current?.exportToSVG),yt.current?.exportToSVG?.()}catch(xt){console.error("🖼️ SVGExportButton error:",xt)}};return jsxRuntimeExports.jsxs(Button,{variant:"ghost",size:"icon",className:"size-7 sm:size-7 min-w-[44px] min-h-[44px] sm:min-w-0 sm:min-h-0 flex items-center justify-center border touch-manipulation",onClick:Et,title:"Export current view to SVG",children:[jsxRuntimeExports.jsx(Camera,{size:16}),jsxRuntimeExports.jsx("span",{className:"sr-only",children:"Export SVG"})]})}function ThemeToggle(){const{theme:yt,resolvedTheme:Et,toggleTheme:xt}=useTheme(),vt=Et||yt||"light";return jsxRuntimeExports.jsxs(Button,{variant:"ghost",size:"icon",className:"size-7 sm:size-7 min-w-[44px] min-h-[44px] sm:min-w-0 sm:min-h-0 flex items-center justify-center border touch-manipulation",onClick:xt,title:`Switch to ${vt==="light"?"dark":"light"} theme`,children:[vt==="light"?jsxRuntimeExports.jsx(Moon,{size:16}):jsxRuntimeExports.jsx(Sun,{size:16}),jsxRuntimeExports.jsx("span",{className:"sr-only",children:"Toggle theme"})]})}class PhyloNode{constructor(){this.id=null,this.name=null,this.branchLength=0,this.parent=null,this.branchset=[],this.x=0,this.y=0,this.rootDist=0}getLeaves(){return this.branchset.length===0?[this]:this.branchset.flatMap(Et=>Et.getLeaves())}}class PhyloTree{constructor(Et,xt=DEFAULT_CONFIG$1,vt=!1,bt=null){if(this.config=xt,this.themeColors=bt,this.allNodes=[],this.leafNodes=[],Array.isArray(Et))this.hasTree=!1,this.root=this._createFlatRoot(Et);else if(!Et||Et.trim()==="")this.hasTree=!1,this.root=new PhyloNode,this.root.id=0;else try{this.root=this.parseNewick(Et),this.hasTree=!0}catch(At){console.warn("[PhyloTree] failed to parse Newick; using empty tree",At?.message||At),this.hasTree=!1,this.root=new PhyloNode,this.root.id=0}this.collectAll(),this.hasTree&&this.ladderize(!1),vt&&this.hasTree&&this.makeUltrametric()}_createFlatRoot(Et){const xt=new PhyloNode;return xt.id=0,xt.branchLength=0,xt.name="_root",Et.forEach((vt,bt)=>{const At=new PhyloNode;At.id=bt+1,At.name=String(vt),At.branchLength=1,xt.branchset.push(At)}),xt}parseNewick(Et){for(var xt=[],vt=new PhyloNode,bt=Et.split(/\s*(;|\(|\)|,|:)\s*/),At=0,Ft=0;Ft<bt.length;Ft++){var Ct=bt[Ft];switch(Ct){case"(":{var wt=new PhyloNode;wt.id=At++,vt.branchset=[wt],xt.push(vt),vt=wt;break}case",":{var wt=new PhyloNode;wt.id=At++,xt[xt.length-1].branchset.push(wt),vt=wt;break}case")":vt=xt.pop();break;case":":break;default:{var St=bt[Ft-1];St==")"||St=="("||St==","?vt.name=Ct:St==":"&&(vt.branchLength=parseFloat(Ct)),vt.id=vt.id!==null?vt.id:At++}}}return vt}ladderize(Et=!0){const xt=[],vt=[this.root];let bt=0;for(;vt.length>0;){const Ft=vt.pop();if(xt.push(Ft),Ft._sortIndex=bt++,Ft.branchset)for(const Ct of Ft.branchset)vt.push(Ct)}for(let Ft=xt.length-1;Ft>=0;Ft--){const Ct=xt[Ft];if(!Ct.branchset||Ct.branchset.length===0)Ct.num_tips=1;else{Ct.num_tips=0;for(const wt of Ct.branchset)Ct.num_tips+=wt.num_tips||1}}const At=[this.root];for(;At.length>0;){const Ft=At.pop();if(Ft.branchset&&Ft.branchset.length>0){Ft.branchset.sort((Ct,wt)=>{const St=Ct.num_tips||1,Tt=wt.num_tips||1;return St!==Tt?Et?St-Tt:Tt-St:(Ct._sortIndex||0)-(wt._sortIndex||0)});for(const Ct of Ft.branchset)At.push(Ct)}}this.collectAll()}collectAll(){this.allNodes=[];const Et=xt=>{this.allNodes.push(xt);for(let vt of xt.branchset)Et(vt)};Et(this.root)}setParents(){const Et=(xt,vt=null)=>{xt.parent=vt;for(let bt of xt.branchset)Et(bt,xt)};Et(this.root,null)}computeDistances(){const Et=xt=>{xt.rootDist=(xt.parent?xt.parent.rootDist:0)+(xt.branchLength||0);for(let vt of xt.branchset)Et(vt)};Et(this.root)}getLeafNodes(){return this.root.getLeaves()}assignX(Et){const xt=this.config.tree.ySpacing;for(let vt=0;vt<Et.length;vt++)Et[vt].x=vt*xt}assignInternalX(Et){if(Et.branchset.length===0)return Et.x;const xt=Et.branchset.map(vt=>this.assignInternalX(vt));return Et.x=xt.reduce((vt,bt)=>vt+bt,0)/xt.length,Et.x}scaleY(){const Et=this.allNodes.map(At=>At.rootDist),xt=Math.max(...Et),vt=this.config.tree.fixedCoordinateWidth||2e3,bt=xt>0?vt/xt:1;this.maxEvolutionaryDistance=xt;for(let At of this.allNodes)At.y=At.rootDist*bt}layout(Et){this.setParents(),Et?(this.leafNodes=this.getLeafNodes(),this.leafNodes.sort((xt,vt)=>Et.indexOf(xt.name)-Et.indexOf(vt.name)),this.assignX(this.leafNodes)):(this.leafNodes=this.getLeafNodes(),this.assignX(this.leafNodes)),this.assignInternalX(this.root),this.computeDistances(),this.scaleY()}buildEdges(){const Et=[],xt=this.themeColors?.treeEdges||this.config.tree.edgeColor||[85,85,85,255],vt=bt=>{for(let At of bt.branchset){const Ft=[[bt.y,bt.x],[bt.y,At.x],[At.y,At.x]];Et.push({path:Ft,color:xt,source:bt,target:At}),vt(At)}};return vt(this.root),Et}makeUltrametric(){(!this.allNodes||this.allNodes.length===0)&&this.collectAll(),this.setParents(),this.computeDistances();const Et=this.getLeafNodes(),xt=Math.max(...Et.map(At=>At.rootDist)),vt=At=>{if(At.branchset.length===0){At.rootDist=xt;return}for(let wt of At.branchset)vt(wt);const Ft=At.branchset.map(wt=>wt.rootDist),Ct=Math.min(...Ft);At.rootDist=Ct-Math.max(...At.branchset.map(wt=>wt.branchLength||0)),At.rootDist<0&&(At.rootDist=0)};vt(this.root);const bt=At=>{for(let Ft of At.branchset)Ft.branchLength=Ft.rootDist-At.rootDist,bt(Ft)};this.root.rootDist=0,bt(this.root),this.computeDistances()}}class GFFFeature{constructor(Et,xt,vt,bt,At,Ft){this.seqid=Et,this.start=xt,this.end=vt,this.strand=bt,this.type=At,this.attributes=Ft}}class Gene extends GFFFeature{constructor(Et,xt,vt,bt,At,Ft=DEFAULT_CONFIG$1){super(Et,xt,vt,bt,"gene",At),this.origStart=xt,this.origEnd=vt,this.origStrand=bt,this.domains=[],this.config=Ft||DEFAULT_CONFIG$1,this.fillColor=this.config.gene.fillColor,this.polygon=null,this.trackY=null,this.geneHeight=this.config.gene.height||this.config.gene.defaultHeight,this.centerLine=[],this.metadata={seqid:Et,start:xt,end:vt,strand:bt,attributes:At}}setTrackY(Et){this.trackY=Et,this.updatePolygon()}updatePolygon(){this.polygon=this._buildPolygon(this.trackY,this.geneHeight),this.centerLine=this.computeCenterLine();for(let Et of this.domains)Et.updatePolygon()}_buildPolygon(Et,xt){let vt=this.start,bt=this.end;if(vt>bt){const Rt=vt;vt=bt,bt=Rt}const At=Math.abs(bt-vt),Ft=calculateTipWidth(At,this.config),Ct=xt/2,wt=this.strand==="+",St=this.config.gene.arrowheadHeight||0;if(Ft<1)return[[vt,Et-Ct],[bt,Et-Ct],[bt,Et+Ct],[vt,Et+Ct]];if(St<.1)return wt?[[vt,Et-Ct],[bt-Ft,Et-Ct],[bt,Et],[bt-Ft,Et+Ct],[vt,Et+Ct]]:[[bt,Et-Ct],[vt+Ft,Et-Ct],[vt,Et],[vt+Ft,Et+Ct],[bt,Et+Ct]];const Tt=Ct+St/2;return wt?[[vt,Et-Ct],[bt-Ft,Et-Ct],[bt-Ft,Et-Tt],[bt,Et],[bt-Ft,Et+Tt],[bt-Ft,Et+Ct],[vt,Et+Ct]]:[[bt,Et-Ct],[vt+Ft,Et-Ct],[vt+Ft,Et-Tt],[vt,Et],[vt+Ft,Et+Tt],[vt+Ft,Et+Ct],[bt,Et+Ct]]}computeCenterLine(){const Et=this.polygon;if(!Et||Et.length===0)return[];if(Et.length===5){const xt=[(Et[0][0]+Et[4][0])/2,(Et[0][1]+Et[4][1])/2],vt=Et[2];return[xt,vt]}else if(Et.length===7){const xt=[(Et[0][0]+Et[6][0])/2,(Et[0][1]+Et[6][1])/2],vt=Et[3];return[xt,vt]}else if(Et.length===4){const xt=this.strand==="+",vt=[(Et[0][0]+Et[3][0])/2,(Et[0][1]+Et[3][1])/2],bt=[(Et[1][0]+Et[2][0])/2,(Et[1][1]+Et[2][1])/2];return xt?[vt,bt]:[bt,vt]}else{const xt=[(Et[0][0]+Et[Et.length-1][0])/2,(Et[0][1]+Et[Et.length-1][1])/2],vt=Et[Math.floor(Et.length/2)];return[xt,vt]}}addDomain(Et){Et.setParentGene(this),this.domains.push(Et)}}function clipPolygon(yt,Et){if(!yt||yt.length<3)return null;if(!Et||Et.length<3)return yt;let xt=yt.slice();for(let vt=0;vt<Et.length;vt++){if(xt.length===0)return null;const bt=xt;xt=[];const At=Et[vt],Ft=Et[(vt+1)%Et.length];for(let Ct=0;Ct<bt.length;Ct++){const wt=bt[Ct],St=bt[(Ct+bt.length-1)%bt.length],Tt=isInside(wt,At,Ft),Rt=isInside(St,At,Ft);if(Tt){if(!Rt){const Pt=lineIntersection(St,wt,At,Ft);Pt&&xt.push(Pt)}xt.push(wt)}else if(Rt){const Pt=lineIntersection(St,wt,At,Ft);Pt&&xt.push(Pt)}}}return xt.length>=3?xt:null}function isInside(yt,Et,xt){return(xt[0]-Et[0])*(yt[1]-Et[1])-(xt[1]-Et[1])*(yt[0]-Et[0])>=0}function lineIntersection(yt,Et,xt,vt){const bt=Et[0]-yt[0],At=Et[1]-yt[1],Ft=vt[0]-xt[0],Ct=vt[1]-xt[1],wt=bt*Ct-At*Ft;if(Math.abs(wt)<1e-10)return null;const St=xt[0]-yt[0],Tt=xt[1]-yt[1],Rt=(St*Ct-Tt*Ft)/wt;return[yt[0]+Rt*bt,yt[1]+Rt*At]}class Domain{constructor(Et,xt,vt,bt,At,Ft,Ct,wt=DEFAULT_CONFIG$1){this.geneId=Et,this.domainName=xt,this.origStart=vt,this.origEnd=bt,this.start=vt,this.end=bt,this.source=At,this.evalue=Ft,this.coverage=Ct,this.parentGene=null,this.polygon=null;const St=Ft&&Ft>0?Ft<.001?Ft.toExponential(2):Ft.toFixed(6):Ft,Tt=Ct&&`${(Ct*100).toFixed(1)}%`;this.metadata={geneId:Et,domainName:xt,start:vt,end:bt,source:At,evalue:St,coverage:Tt},this.config=wt||DEFAULT_CONFIG$1}setParentGene(Et){this.parentGene=Et,this.updatePolygon()}updatePolygon(){if(!this.parentGene||!this.parentGene.polygon)return;const Et=this.parentGene,xt=this.createDomainPolygon(Et,this.origStart,this.origEnd);if(xt&&Et.polygon){const vt=this.getConvexGenePolygon(Et);this.polygon=clipPolygon(xt,vt)}else this.polygon=xt}getConvexGenePolygon(Et){const xt=Et.geneHeight||Et.config?.gene?.height||60,vt=Et.config?.gene?.arrowheadHeight||0,bt=xt/2,At=bt+vt/2,Ft=Et.trackY;let Ct=Math.min(Et.start,Et.end),wt=Math.max(Et.start,Et.end);const St=wt-Ct,Tt=calculateTipWidth(St,Et.config?.gene),Rt=Et.strand==="+";return Tt<1?[[Ct,Ft-bt],[wt,Ft-bt],[wt,Ft+bt],[Ct,Ft+bt]]:Rt?[[Ct,Ft-bt],[wt-Tt,Ft-At],[wt,Ft],[wt-Tt,Ft+At],[Ct,Ft+bt]]:[[wt,Ft-bt],[Ct+Tt,Ft-At],[Ct,Ft],[Ct+Tt,Ft+At],[wt,Ft+bt]]}createDomainPolygon(Et,xt,vt){const bt=Et.start,At=Et.end,Ft=Math.min(bt,At),wt=Math.max(bt,At)-Ft;if(!Et.centerLine||!Array.isArray(Et.centerLine)||Et.centerLine.length<2||!isFinite(wt)||wt<=0)return null;const Tt=Math.abs(Et.origEnd-Et.origStart)/3;let Rt=xt/Tt,Pt=vt/Tt;Rt=Math.max(0,Math.min(1,Rt)),Pt=Math.max(0,Math.min(1,Pt));const Lt=this.interpolateOnLine(Et.centerLine,Rt),kt=this.interpolateOnLine(Et.centerLine,Pt),Ot=this.perpVector(Et.centerLine[0],Et.centerLine[1]),Mt=this.normalize(Ot),It=(typeof Et.geneHeight=="number"?Et.geneHeight:Et.config&&Et.config.gene&&Et.config.gene.height?Et.config.gene.height:10)/2,Nt=Et.config&&Et.config.domain&&typeof Et.config.domain.heightFactor=="number"?Et.config.domain.heightFactor:this.config&&this.config.domain&&this.config.domain.heightFactor||.6,Ut=It*Nt,jt=[Lt[0]-Mt[0]*Ut,Lt[1]-Mt[1]*Ut],Vt=[kt[0]-Mt[0]*Ut,kt[1]-Mt[1]*Ut],zt=[kt[0]+Mt[0]*Ut,kt[1]+Mt[1]*Ut],Ht=[Lt[0]+Mt[0]*Ut,Lt[1]+Mt[1]*Ut];return[jt,Vt,zt,Ht]}interpolateOnLine(Et,xt){const[vt,bt]=Et;return[vt[0]+(bt[0]-vt[0])*xt,vt[1]+(bt[1]-vt[1])*xt]}perpVector(Et,xt){const vt=xt[0]-Et[0];return[-(xt[1]-Et[1]),vt]}normalize(Et){const xt=Math.sqrt(Et[0]*Et[0]+Et[1]*Et[1]);return xt===0?[0,1]:[Et[0]/xt,Et[1]/xt]}}class Link{constructor(){}}class ProteinLink extends Link{constructor(Et,xt,vt,bt=[50,100,220]){super(),this.gAId=Et,this.gBId=xt,this.similarity=vt,this.baseColor=Array.isArray(bt)&&bt.length>=3?bt.slice(0,3):[50,100,220];const At=Math.round(255*(vt/100));this.fillColor=[...this.baseColor,At],this.metadata={gAId:Et,gBId:xt,similarity:vt}}updateColor(Et,xt=null,vt=null,bt=null,At=null){if(!Et){const St=Math.round(255*(this.similarity/100));this.fillColor=[...this.baseColor,St];return}let Ft=this.baseColor,Ct=255;const wt=At?At.slice(0,3):this.baseColor;switch(Et.colorBy){case"source_gene":Ft=xt?xt.slice(0,3):wt;break;case"target_gene":Ft=vt?vt.slice(0,3):wt;break;case"identity_solid":Ft=Et.solidColor?Et.solidColor.slice(0,3):this.baseColor;break;case"identity_gradient":bt&&(Ft=bt.slice(0,3));break;default:Ft=this.baseColor}if(Et.useAlpha){const St=this.similarity/100,Tt=Et.maxAlpha-Et.minAlpha,Rt=Et.minAlpha+St*Tt;Ct=Math.round(Rt*255)}else Ct=Et.colorBy==="identity_solid"?255:Math.round(255*(this.similarity/100));this.fillColor=[...Ft,Ct]}bezierCurve(Et,xt,vt,bt,At=120){const Ft=[];for(let Ct=0;Ct<=1;Ct+=1/At){const wt=Math.pow(1-Ct,3)*Et[0]+3*Math.pow(1-Ct,2)*Ct*xt[0]+3*(1-Ct)*Ct*Ct*vt[0]+Ct*Ct*Ct*bt[0],St=Math.pow(1-Ct,3)*Et[1]+3*Math.pow(1-Ct,2)*Ct*xt[1]+3*(1-Ct)*Ct*Ct*vt[1]+Ct*Ct*Ct*bt[1];Ft.push([wt,St])}return Ft}buildPolygon(Et,xt){if(!Et||!xt)return null;const vt=Math.min(Et.start,Et.end),bt=Math.max(Et.start,Et.end),At=Math.min(xt.start,xt.end),Ft=Math.max(xt.start,xt.end),Ct=Et.trackY,wt=xt.trackY;let St,Tt;Ct<=wt?(St={left:[vt,Ct],right:[bt,Ct]},Tt={left:[At,wt],right:[Ft,wt]}):(St={left:[At,wt],right:[Ft,wt]},Tt={left:[vt,Ct],right:[bt,Ct]});const Rt=(St.left[1]+Tt.right[1])/2,Pt=(Ot,Mt)=>this.bezierCurve(Ot,[Ot[0],Rt],[Mt[0],Rt],Mt,20),Lt=Pt(St.right,Tt.right),kt=Pt(Tt.left,St.left);return[St.left,St.right,...Lt,Tt.right,Tt.left,...kt]}}class NucleotideLink extends Link{constructor(Et,xt,vt,bt,At,Ft,Ct,wt=[220,50,50]){super(),this.seqidA=Et,this.seqidB=bt,this.strandA=xt<=vt?"+":"-",this.strandB=At<=Ft?"+":"-",xt>vt&&([xt,vt]=[vt,xt]),At>Ft&&([At,Ft]=[Ft,At]),this.origStartA=xt,this.origEndA=vt,this.origStartB=At,this.origEndB=Ft,this.startA=xt,this.endA=vt,this.startB=At,this.endB=Ft,this.similarity=Ct,this.baseColor=Array.isArray(wt)&&wt.length>=3?wt.slice(0,3):[220,50,50];const St=Math.round(255*(Ct/100));this.fillColor=[...this.baseColor,St]}updateColor(Et,xt=null){if(!Et){const At=Math.round(255*(this.similarity/100));this.fillColor=[...this.baseColor,At];return}let vt=this.baseColor,bt=255;switch(Et.colorBy){case"solid":vt=Et.solidColor?Et.solidColor.slice(0,3):this.baseColor,Et.useAlpha||(bt=Et.solidColor&&Et.solidColor.length>3?Et.solidColor[3]:255);break;case"identity_gradient":xt&&(vt=xt.slice(0,3)),bt=255;break;default:vt=this.baseColor,bt=Math.round(255*(this.similarity/100))}if(Et.useAlpha){const At=this.similarity/100,Ft=Et.maxAlpha-Et.minAlpha,Ct=Et.minAlpha+At*Ft;bt=Math.round(Ct*255)}this.fillColor=[...vt,bt]}buildPolygon(Et,xt){const vt=[this.startA,this.endA,this.startB,this.endB],bt=[Et,Et,xt,xt],At=Math.min(...vt),Ft=Math.max(...vt),Ct=Math.min(...bt),wt=Math.max(...bt);return[[At,wt],[Ft,wt],[Ft,Ct],[At,Ct]]}buildPolygonFromCoords(Et,xt,vt,bt,At,Ft){const Ct=[[Et,At],[xt,At]],wt=[[vt,Ft],[bt,Ft]];return Ct.sort((St,Tt)=>St[0]-Tt[0]),wt.sort((St,Tt)=>St[0]-Tt[0]),[Ct[0],Ct[1],wt[1],wt[0]]}}class Hood{constructor(Et,xt,vt){this.seqid=Et,this.start=xt,this.end=vt,this.origStart=xt,this.origEnd=vt}set(Et,xt){this.start=Et,this.end=xt,this.origStart=Et,this.origEnd=xt}update(Et,xt){this.start=Et,this.end=xt}get(){return{seqid:this.seqid,start:this.start,end:this.end,origStart:this.origStart,origEnd:this.origEnd}}}class Nucleotide{constructor(Et,xt,vt,bt="+"){this.seqid=Et,this.start=xt,this.end=vt,this.strand=bt,this.genes=[],this.metadata={seqid:Et,start:xt,end:vt,strand:bt},this.hood=null}addGene(Et){this.genes.push(Et)}flip(){const Et=this.start,xt=this.end;this.start=-xt,this.end=-Et,this.strand=this.strand==="+"?"-":"+";for(const vt of this.genes)vt.start=-vt.end,vt.end=-vt.start,vt.strand=vt.strand==="+"?"-":"+",typeof vt.updatePolygon=="function"&&vt.updatePolygon()}shift(Et){this.start+=Et,this.end+=Et;for(const xt of this.genes)xt.start+=Et,xt.end+=Et,typeof xt.updatePolygon=="function"&&xt.updatePolygon()}getGenePolygons(){return this.genes.map(Et=>Et.polygon).filter(Boolean)}setHood(Et,xt){this.hood?this.hood.set(Et,xt):this.hood=new Hood(this.seqid,Et,xt)}getHood(){return this.hood?this.hood.get():null}updateHood(Et,xt){this.hood?this.hood.update(Et,xt):this.setHood(Et,xt)}}class NonCodingFeature extends GFFFeature{constructor(Et,xt,vt,bt,At,Ft,Ct){super(Et,xt,vt,bt,At,Ft),this.config=Ct||DEFAULT_CONFIG$1,this.polygon=null,this.trackY=null,this.featureHeight=this.config?.gene?.height||60,this.metadata={seqid:Et,start:xt,end:vt,strand:bt,type:At,attributes:Ft}}setTrackY(Et){this.trackY=Et,this.updatePolygon()}updatePolygon(){this.polygon=this._buildHalfArrowPolygon(this.trackY,this.featureHeight)}_buildHalfArrowPolygon(Et,xt){let vt=this.start,bt=this.end;if(vt>bt){const Rt=vt;vt=bt,bt=Rt}const At=Math.abs(bt-vt),Ft=calculateTipWidth(At,this.config),Ct=xt/4,wt=this.strand==="+",St=this.config?.gene?.arrowheadHeight||0,Tt=Ct+St/2;return Ft<1?wt?[[vt,Et],[vt,Et+Ct],[bt,Et+Ct],[bt,Et]]:[[bt,Et],[bt,Et-Ct],[vt,Et-Ct],[vt,Et]]:wt?[[vt,Et],[vt,Et+Ct],[bt-Ft,Et+Ct],[bt-Ft,Et+Tt],[bt,Et]]:[[bt,Et],[bt,Et-Ct],[vt+Ft,Et-Ct],[vt+Ft,Et-Tt],[vt,Et]]}}class RegionFeature extends GFFFeature{constructor(Et,xt,vt,bt,At,Ft,Ct){super(Et,xt,vt,bt,At,Ft),this.config=Ct,this.polygon=null,this.trackY=null,this.padding=Ct?.region?.padding||10,this.fillColor=[0,0,0,0],this.strokeColor=[100,100,100,255],this.strokeWidth=Ct?.region?.strokeWidth||2,this.metadata={seqid:Et,start:xt,end:vt,type:At,length:Math.abs(vt-xt)},Ft&&(typeof Ft=="string"||Ft instanceof String?this.metadata.attributes=Ft.toString():typeof Ft=="object"&&Object.assign(this.metadata,Ft))}setTrackY(Et){this.trackY=Et}updatePolygon(Et=[],xt=null){xt!==null&&(this.trackY=xt),this.config||(console.warn("RegionFeature: No config provided, using defaults"),this.config={gene:{height:20,arrowheadHeight:30},region:{padding:10,strokeWidth:2}});const vt=Math.min(this.start,this.end),bt=Math.max(this.start,this.end),At=this.config.gene?.height||20,Ft=this.config.gene?.arrowheadHeight||30,Ct=this.config.region?.padding||this.padding,St=Math.max(At,Ft)/2,Tt=this.trackY-St-Ct,Rt=this.trackY+St+Ct;this.polygon=[[vt,Tt],[bt,Tt],[bt,Rt],[vt,Rt],[vt,Tt]]}containsGene(Et){const xt=Math.min(this.start,this.end),vt=Math.max(this.start,this.end),bt=Math.min(Et.start,Et.end);return!(Math.max(Et.start,Et.end)<xt||bt>vt)}getFillColor(){return[0,0,0,0]}getStrokeColor(){if(this.strokeColor&&this.strokeColor[3]!==0)return this.strokeColor;const Et=(this.type||"").toLowerCase(),xt=this.config?.region?.colors||{};return xt[Et]?xt[Et]:xt.default||[128,128,128,255]}getColorKey(){const Et=this.metadata?.region_id||this.metadata?.ID||this.originalId||"";if(Et){const xt=Et.match(/^([a-zA-Z]+)/);if(xt)return xt[1].toLowerCase()}return this.metadata?.region_type?this.metadata.region_type.toLowerCase():(this.type||"region").toLowerCase()}}const _paletteCache=new Map;function memoGetPalette(yt,Et,xt=!1,vt="qualitative"){const bt=`${yt}::${Et}::${xt}::${vt}`;if(_paletteCache.has(bt))return _paletteCache.get(bt);let At=[];try{At=getPaletteColors(yt,Et,xt,vt)}catch{At=[]}return _paletteCache.set(bt,At),At}class GenomeView{constructor(Et,xt,vt=DEFAULT_CONFIG$1){this.leaves=Et,this.tree=xt,this.config=vt||DEFAULT_CONFIG$1,this.featuresBySeqid={},this.genesById={},this.ncRNAsById={},this.regionsById={},this.nucleotidesBySeqid={},this.globalMin=1/0,this.globalMax=-1/0,this.geneHeight=this.config?.gene?.height||DEFAULT_CONFIG$1.gene.height,this.trackFlipped={},this.trackOffset={},this.hoodRanges={},this.hoodToSeqidMap={},this.seqidToHoodsMap={},this.proteinLinks=[],this.nucleotideLinks=[],this.domainsByGene={},this._genesByOriginalId=new Map,this._genesIndexReady=!1,this._leafIndex=null,this._hoodIndex=null,this._regionsByHood=null,this._rightmostByHood=new Map,this._paletteVersion=0}_ensureLeafIndex(){if(!this._leafIndex){if(!this.tree?.leafNodes){this._leafIndex=new Map;return}this._leafIndex=new Map(this.tree.leafNodes.map((Et,xt)=>[Et.name,xt]))}}_buildGeneIndex(){this._genesByOriginalId=new Map;for(const[Et,xt]of Object.entries(this.genesById)){const vt=xt.originalGeneId;vt&&(this._genesByOriginalId.has(vt)||this._genesByOriginalId.set(vt,[]),this._genesByOriginalId.get(vt).push(Et))}this._genesIndexReady=!0}_addOrUpdateGeneIndex(Et,xt){xt?.originalGeneId&&(this._genesByOriginalId.has(xt.originalGeneId)||this._genesByOriginalId.set(xt.originalGeneId,[]),this._genesByOriginalId.get(xt.originalGeneId).push(Et),this._genesIndexReady=!0)}_invalidateGeneIndex(){this._genesIndexReady=!1}_rebuildRegionsByHood(){this._regionsByHood=new Map;for(const Et of Object.values(this.regionsById))this._regionsByHood.has(Et.hood_id)||this._regionsByHood.set(Et.hood_id,[]),this._regionsByHood.get(Et.hood_id).push(Et)}_buildHoodIntervalIndex(){this._hoodIndex=new Map;for(const[Et,xt]of Object.entries(this.hoodRanges||{})){const vt=this._hoodIndex.get(xt.seqid)||[];vt.push({start:xt.origStart,end:xt.origEnd,hood_id:Et}),this._hoodIndex.set(xt.seqid,vt)}for(const Et of this._hoodIndex.values())Et.sort((xt,vt)=>xt.start-vt.start)}_queryHoodsCovering(Et,xt,vt){const bt=this._hoodIndex?.get(Et)||[];let At=0,Ft=bt.length;for(;At<Ft;){const wt=At+Ft>>1;bt[wt].start<=xt?At=wt+1:Ft=wt}const Ct=[];for(let wt=At-1;wt>=0&&bt[wt].start<=xt;--wt)bt[wt].end>=vt&&Ct.push(bt[wt].hood_id);for(let wt=At;wt<bt.length&&bt[wt].start<=xt;++wt)bt[wt].end>=vt&&Ct.push(bt[wt].hood_id);return Ct}static flipCoordinate(Et,xt){return 2*xt-Et}static getTransformedXUnified(Et,xt,vt,bt){let At=Et+(vt||0);return bt?GenomeView.flipCoordinate(At,xt):At}static getGeneVisualX(Et,xt){const vt=Et.hood_id,bt=xt.hoodRanges[vt];if(!bt)return null;const At=xt.trackOffset[vt]||0,Ft=!!xt.trackFlipped[vt],Ct=(bt.length||0)/2,St=(xt.config.genome&&typeof xt.config.genome.xScalePercent=="number"?xt.config.genome.xScalePercent:100)/100,Tt=Et.origStart||0,Rt=Et.origEnd||0,Pt=Et.origStrand==="+"?Math.min(Tt,Rt):Math.max(Tt,Rt),Lt=GenomeView.getTransformedXUnified(Pt,Ct,At,Ft);return Ct+(Lt-Ct)*St}addFeatures(Et){for(let xt of Et)if(!(!xt.seqid||typeof xt.start!="number"||isNaN(xt.start)||typeof xt.end!="number"||isNaN(xt.end))&&(this.featuresBySeqid[xt.seqid]?(xt.start<this.featuresBySeqid[xt.seqid].origMinStart&&(this.featuresBySeqid[xt.seqid].origMinStart=xt.start),xt.end>this.featuresBySeqid[xt.seqid].origMaxEnd&&(this.featuresBySeqid[xt.seqid].origMaxEnd=xt.end)):(this.featuresBySeqid[xt.seqid]=[],this.featuresBySeqid[xt.seqid].origMinStart=xt.start,this.featuresBySeqid[xt.seqid].origMaxEnd=xt.end),this.featuresBySeqid[xt.seqid].push(xt),!this.nucleotidesBySeqid[xt.seqid])){const vt=this.featuresBySeqid[xt.seqid],bt=Math.min(...vt.map(wt=>typeof wt.start=="bigint"?Number(wt.start):wt.start)),At=Math.max(...vt.map(wt=>typeof wt.end=="bigint"?Number(wt.end):wt.end)),Ft=vt.find(wt=>wt.type==="gene"||wt.type==="CDS"),Ct=Ft&&Ft.strand?Ft.strand:"+";this.nucleotidesBySeqid[xt.seqid]=new Nucleotide(xt.seqid,bt,At,Ct)}}initGenes(){this._invalidateGeneIndex();for(let Et of this.leaves){const xt=this.hoodToSeqidMap[Et];if(!xt)continue;const vt=this.hoodRanges[Et];if(!vt)continue;const bt=vt.origStart||0,At=vt.origEnd||0,Ft=this.featuresBySeqid[xt]||[];for(let Ct of Ft)if(Ct.type==="gene"||Ct.type==="CDS"){const wt=Ct.start||0,St=Ct.end||0;if(!(wt>=bt&&St<=At))continue;const Rt=wt-bt,Pt=St-bt;let Lt=Ct.gene_id||Ct.id||Ct.protein_id||Ct.originalGeneId;!Lt&&Ct.attributes&&(Lt=this.getGeneIdFromAttributes(Ct.attributes));const kt=`${Et}_${Lt}`;let Ot=new Gene(Ct.seqid,Rt,Pt,Ct.strand,Ct.attributes,this.config);Ot.hood_id=Et,Ot.originalGeneId=Lt,this.genesById[kt]=Ot,this._addOrUpdateGeneIndex(kt,Ot),this.nucleotidesBySeqid[xt]&&this.nucleotidesBySeqid[xt].addGene(Ot)}else if(typeof Ct.type=="string"&&Ct.type.toLowerCase().includes("ncrna")){const wt=Ct.start||0,St=Ct.end||0;if(!(wt>=bt&&St<=At))continue;const Rt=wt-bt,Pt=St-bt,Lt=this.getGeneIdFromAttributes(Ct.attributes),kt=`${Et}_${Lt}_${wt}_${St}`;let Ot=new NonCodingFeature(Ct.seqid,Rt,Pt,Ct.strand,Ct.type,Ct.attributes,this.config);Ot.hood_id=Et,Ot.id=kt,Ot.originalId=Lt,Ot.origStart=Rt,Ot.origEnd=Pt,Ot.genomicStart=wt,Ot.genomicEnd=St,Ot.origStrand=Ct.strand;let Mt=null;try{const Nt=Ct.attributes||{};Nt&&typeof Nt=="object"&&(Mt=Nt.ncrna_type||Nt.ncrnaType||Nt.ID||Nt.id||Nt.Name||null),typeof Mt=="object"&&(Mt=String(Mt)),Mt&&(Mt=String(Mt).replace(/^ID=/,"").replace(/;$/,"").trim()),Mt&&(Mt.toLowerCase()==="null"||Mt.toLowerCase()==="none"||Mt==="")&&(Mt=null)}catch{Mt=null}const It=Mt||Lt||Ct.type||"ncRNA";Ot.name=It,(!Ot.metadata||typeof Ot.metadata!="object")&&(Ot.metadata={}),Ot.metadata.type=It,Ot.metadata.attributes=Ct.attributes,this.ncRNAsById[kt]=Ot}else if(Ct.type==="region"){const wt=Ct.start||0,St=Ct.end||0;if(!(wt>=bt&&St<=At))continue;const Rt=wt-bt,Pt=St-bt,Lt=this.getGeneIdFromAttributes(Ct.attributes),kt=`${Et}_${Lt}`;let Ot=new RegionFeature(Ct.seqid,Rt,Pt,Ct.strand,Ct.type,Ct.attributes,this.config);Ot.id=kt,Ot.hood_id=Et,Ot.originalId=Lt,Ot.origStart=Rt,Ot.origEnd=Pt,Ot.origStrand=Ct.strand,this.regionsById[kt]=Ot}}}getGeneIdFromAttributes(Et){if(typeof Et=="string"){const xt=Et.match(/ID=([^;]+)/);return xt?xt[1]:null}else if(typeof Et=="object"&&Et!==null)return Et.ID||null;return null}computeTrackPositions(){const Et={},xt={};for(const At of Object.values(this.genesById))(Et[At.hood_id]||=[]).push(At);for(const At of Object.values(this.ncRNAsById))(xt[At.hood_id]||=[]).push(At);this._rebuildRegionsByHood();const bt=(this.config.genome&&typeof this.config.genome.xScalePercent=="number"?this.config.genome.xScalePercent:100)/100;this._rightmostByHood.clear();for(let At of this.leaves){const Ft=this.tree.leafNodes.find(jt=>jt.name===At);if(!Ft)continue;const wt=(typeof Ft?.x=="number"?Ft.x:Ft?.y||0)+(this.config?.layout?.geneOffset||0),St=this.hoodToSeqidMap[At];if(!St)continue;const Tt=this.nucleotidesBySeqid[St],Rt=this.trackOffset[At]||0,Pt=this.hoodRanges[At],kt=(Pt?.length||0)/2,Ot=!!this.trackFlipped[At];let Mt=-1/0;const It=Et[At]||[];for(const jt of It){jt.trackY=wt,jt.geneHeight=this.geneHeight;const Vt=jt.origStart||0,zt=jt.origEnd||0;let Ht=GenomeView.getTransformedXUnified(Vt,kt,Rt,Ot),Wt=GenomeView.getTransformedXUnified(zt,kt,Rt,Ot);Ht=kt+(Ht-kt)*bt,Wt=kt+(Wt-kt)*bt,jt.start=Ht,jt.end=Wt,jt.strand=Ot?jt.origStrand==="+"?"-":"+":jt.origStrand,["gene_1","gene_2"].includes(jt.id)||jt.originalGeneId?.includes("gene_1")||jt.originalGeneId?.includes("gene_2"),Mt=Math.max(Mt,Ht,Wt);for(let Gt of jt.domains)Gt.updatePolygon();jt.updatePolygon()}const Nt=xt[At]||[];for(const jt of Nt){jt.trackY=wt,jt.featureHeight=this.geneHeight;const Vt=jt.origStart||0,zt=jt.origEnd||0;let Ht=GenomeView.getTransformedXUnified(Vt,kt,Rt,Ot),Wt=GenomeView.getTransformedXUnified(zt,kt,Rt,Ot);Ht=kt+(Ht-kt)*bt,Wt=kt+(Wt-kt)*bt,jt.start=Ht,jt.end=Wt,jt.strand=Ot?jt.origStrand==="+"?"-":"+":jt.origStrand,jt.updatePolygon(),Mt=Math.max(Mt,Ht,Wt)}const Ut=this._regionsByHood?.get(At)||[];for(const jt of Ut){jt.trackY=wt;const Vt=jt.origStart||0,zt=jt.origEnd||0;let Ht=GenomeView.getTransformedXUnified(Vt,kt,Rt,Ot),Wt=GenomeView.getTransformedXUnified(zt,kt,Rt,Ot);Ht=kt+(Ht-kt)*bt,Wt=kt+(Wt-kt)*bt,jt.start=Ht,jt.end=Wt,jt.strand=Ot?jt.origStrand==="+"?"-":"+":jt.origStrand;const Gt=It.filter(qt=>jt.containsGene(qt));jt.updatePolygon(Gt,wt),Mt=Math.max(Mt,Ht,Wt)}if(Tt&&Tt.hood){const Vt=Pt?Pt.length||0:(Tt.hood.origEnd||0)-(Tt.hood.origStart||0);let zt=GenomeView.getTransformedXUnified(0,kt,Rt,Ot),Ht=GenomeView.getTransformedXUnified(Vt,kt,Rt,Ot);zt=kt+(zt-kt)*bt,Ht=kt+(Ht-kt)*bt,Tt.hood.start=zt,Tt.hood.end=Ht,Mt=Math.max(Mt,zt,Ht)}if(Tt){let jt=GenomeView.getTransformedXUnified(0,kt,Rt,Ot),Vt=GenomeView.getTransformedXUnified(Pt&&Pt.length||0,kt,Rt,Ot);jt=kt+(jt-kt)*bt,Vt=kt+(Vt-kt)*bt,Tt.start=jt,Tt.end=Vt,Mt=Math.max(Mt,jt,Vt)}isFinite(Mt)&&this._rightmostByHood.set(At,Mt)}this.updateLinkPositions(),this.updateGlobalBounds()}updateGlobalBounds(){let Et=1/0,xt=-1/0;const vt=this.leaves&&this.leaves.length>0,bt=vt?new Set(this.leaves.map(Ft=>String(Ft))):null,At=vt?new Set:null;if(vt)for(const Ft of bt){const Ct=this.hoodToSeqidMap[Ft];Ct&&At.add(Ct)}for(const Ft of Object.values(this.genesById))if(!(bt&&Ft.hood_id&&!bt.has(String(Ft.hood_id))))if(Ft.polygon)for(const[Ct]of Ft.polygon)Ct<Et&&(Et=Ct),Ct>xt&&(xt=Ct);else Ft.start!==void 0&&Ft.end!==void 0&&(Ft.start<Et&&(Et=Ft.start),Ft.end<Et&&(Et=Ft.end),Ft.start>xt&&(xt=Ft.start),Ft.end>xt&&(xt=Ft.end));for(const Ft of Object.values(this.ncRNAsById))if(!(bt&&Ft.hood_id&&!bt.has(String(Ft.hood_id))))if(Ft.polygon)for(const[Ct]of Ft.polygon)Et=Math.min(Et,Ct),xt=Math.max(xt,Ct);else Ft.start!==void 0&&Ft.end!==void 0&&(Et=Math.min(Et,Ft.start,Ft.end),xt=Math.max(xt,Ft.start,Ft.end));for(const Ft of this.getAllDomains()){const Ct=Ft.parentGene;if(bt&&Ct?.hood_id&&!bt.has(String(Ct.hood_id)))continue;const wt=Ft.polygon;if(wt)for(const[St]of wt)Et=Math.min(Et,St),xt=Math.max(xt,St)}isFinite(Et)&&isFinite(xt)&&(this.globalMin=Et,this.globalMax=xt)}updateLinkPositions(){for(let Et of this.nucleotideLinks)Et.startA=Et.origStartA,Et.endA=Et.origEndA,Et.startB=Et.origStartB,Et.endB=Et.origEndB}addDomains(Et){this.domainsByGene=Et,this._cachedAllDomains=void 0,this._genesIndexReady||this._buildGeneIndex();for(const xt in Et){const vt=this._genesByOriginalId.get(xt)||[];for(const bt of vt){const At=this.genesById[bt];if(At){for(let Ft of Et[xt]){this.hoodRanges[At.hood_id];let Ct=new Domain(bt,Ft.domainName,Ft.start,Ft.end,Ft.source,Ft.evalue,Ft.coverage);At.addDomain(Ct)}At.metadata||(At.metadata={}),At.metadata.domainsSummary=At.domains&&At.domains.length>0?At.domains.map(Ft=>`${Ft.domainName}(${Ft.start}-${Ft.end})`).join(";"):""}}}}addDomainMetadata(Et){if(!Et)return;this._cachedAllDomains=void 0;let xt=Et;if(Array.isArray(Et)){xt={};for(const vt of Et){const bt=vt.domain_id||vt.domain||vt.domainName||vt.domain_name||vt.id;bt&&(xt[bt]=vt)}}for(const vt in this.genesById){const bt=this.genesById[vt];if(!(!bt.domains||bt.domains.length===0))for(const At of bt.domains){const Ft=At.domainName,Ct=xt[Ft];Ct&&(At.metadata={...At.metadata,...Ct})}}}addProteinLinks(Et,xt=[50,100,220],vt=1/0){this._genesIndexReady||this._buildGeneIndex(),this._ensureLeafIndex(),this.proteinLinks.length=0;const bt=new Set;for(let At of Et){let Ft,Ct,wt;Array.isArray(At)?(Ft=At[0],Ct=At[1],wt=At[2]):At&&typeof At=="object"&&(Ft=At.geneA??At.gAId,Ct=At.geneB??At.gBId,wt=At.score??At.similarity);const St=this._genesByOriginalId.get(Ft)||[],Tt=this._genesByOriginalId.get(Ct)||[];for(const Rt of St)for(const Pt of Tt){const Lt=this.genesById[Rt],kt=this.genesById[Pt];if(!Lt||!kt)continue;const Ot=this._leafIndex.get(Lt.hood_id),Mt=this._leafIndex.get(kt.hood_id);if(Ot==null||Mt==null||Math.abs(Ot-Mt)<=vt){const It=Rt<Pt?`${Rt}|${Pt}`:`${Pt}|${Rt}`;if(bt.has(It))continue;bt.add(It),this.proteinLinks.push(new ProteinLink(Rt,Pt,wt,xt))}}}}addNucleotideLinks(Et,xt=[220,50,50],vt=1/0){this._hoodIndex||this._buildHoodIntervalIndex(),this._ensureLeafIndex(),this.nucleotideLinks.length=0;for(let bt of Et){const{seqidA:At,seqidB:Ft,startA:Ct,endA:wt,startB:St,endB:Tt,similarity:Rt}=bt,Pt=this._queryHoodsCovering(At,Ct,wt),Lt=this._queryHoodsCovering(Ft,St,Tt);for(const kt of Pt){const Ot=this.hoodRanges[kt];if(Ot)for(const Mt of Lt){const It=this.hoodRanges[Mt];if(!It)continue;const Nt=this._leafIndex.get(kt),Ut=this._leafIndex.get(Mt);if(Nt==null||Ut==null||Math.abs(Nt-Ut)<=vt){const jt=new NucleotideLink(At,Ct,wt,Ft,St,Tt,Rt,xt);jt.hoodA=kt,jt.hoodB=Mt,jt.hoodStartA=Ct-Ot.origStart,jt.hoodEndA=wt-Ot.origStart,jt.hoodStartB=St-It.origStart,jt.hoodEndB=Tt-It.origStart,this.nucleotideLinks.push(jt)}}}}}applyProteinLinkColors(Et,xt=null){if(!this.proteinLinks?.length)return;let vt=null;if(Et?.colorBy==="identity_gradient"&&Et?.palette?.enabled)try{vt=memoGetPalette(Et.palette.name,Et.palette.numColors,Et.palette.reverse)}catch{vt=null}for(const bt of this.proteinLinks){const At=this.genesById[bt.gAId],Ft=this.genesById[bt.gBId],Ct=Et?.colorBy==="source_gene"?At?.fillColor||xt:null,wt=Et?.colorBy==="target_gene"?Ft?.fillColor||xt:null;let St=null;if(Et?.colorBy==="identity_gradient"&&vt){const Tt=Math.max(0,Math.min(1,bt.similarity/100)),Rt=Math.floor(Tt*(vt.length-1));St=vt[Rt]}bt.updateColor(Et,Ct,wt,St,xt)}}applyNucleotideLinkColors(Et){if(!this.nucleotideLinks?.length)return;let xt=null;if(Et?.colorBy==="identity_gradient"&&Et?.palette?.enabled)try{xt=memoGetPalette(Et.palette.name,Et.palette.numColors,Et.palette.reverse)}catch{xt=null}for(const vt of this.nucleotideLinks){let bt=null;if(Et?.colorBy==="identity_gradient"&&xt){const At=Math.max(0,Math.min(1,vt.similarity/100)),Ft=Math.floor(At*(xt.length-1));bt=xt[Ft]}vt.updateColor(Et,bt)}}getTrackY(Et){const xt=this.getHoodIdsFromSeqid(Et);if(xt.length>0){const vt=xt[0],bt=this.tree.leafNodes.find(At=>At.name===vt);return bt?bt.x:null}return null}getTrackYByHoodId(Et){const xt=this.tree.leafNodes.find(vt=>vt.name===Et);return xt?xt.x:null}filterBySelectedNode(Et){if(!Et)return{genes:Object.values(this.genesById),proteinPolygons:this.getProteinPolygons(),nucleotidePolygons:this.getNucleotidePolygons(),domains:this.getAllDomains(),ncRNAs:Object.values(this.ncRNAsById)};const xt=new Set(this.getNodeDescendantLeaves(Et)),vt=Object.values(this.genesById).filter(wt=>xt.has(wt.hood_id||this.getHoodIdFromSeqid(wt.seqid))),bt=this.getProteinPolygons().filter(wt=>wt.seqids?wt.seqids.every(St=>xt.has(this.getHoodIdFromSeqid(St))):!0),At=this.getNucleotidePolygons().filter(wt=>wt.seqids.every(St=>xt.has(this.getHoodIdFromSeqid(St)))),Ft=this.getAllDomains().filter(wt=>{const St=wt.geneId?this.genesById[wt.geneId]:null,Tt=St?.hood_id||this.getHoodIdFromSeqid(St?.seqid);return Tt?xt.has(Tt):!0}),Ct=Object.values(this.ncRNAsById).filter(wt=>xt.has(wt.hood_id||this.getHoodIdFromSeqid(wt.seqid)));return{genes:vt,proteinPolygons:bt,nucleotidePolygons:At,domains:Ft,ncRNAs:Ct}}getProteinPolygons(){const Et=[];for(let xt of this.proteinLinks){const vt=this.genesById[xt.gAId],bt=this.genesById[xt.gBId];if(!vt||!bt)continue;const At=xt.buildPolygon(vt,bt);At&&Et.push({polygon:At,fillColor:xt.fillColor,metadata:xt.metadata})}return Et}getNucleotidePolygons(){const Et=[],vt=(this.config.genome&&typeof this.config.genome.xScalePercent=="number"?this.config.genome.xScalePercent:100)/100,bt={};for(let At of this.leaves){if(!this.hoodToSeqidMap[At])continue;const Ct=this.hoodRanges[At],wt=this.trackOffset[At]||0,St=!!this.trackFlipped[At],Tt=Ct?(Ct.length||0)/2:0;bt[At]={anchor:Tt,flipped:St,offset:wt,xScale:vt}}for(let At of this.nucleotideLinks){const Ft=At.hoodA,Ct=At.hoodB;if(!Ft||!Ct)continue;const wt=this.getTrackYByHoodId(Ft),St=this.getTrackYByHoodId(Ct);if(wt==null||St==null)continue;const Tt=bt[Ft],Rt=bt[Ct];if(!Tt||!Rt)continue;let Pt=GenomeView.getTransformedXUnified(At.hoodStartA||0,Tt.anchor,Tt.offset,Tt.flipped),Lt=GenomeView.getTransformedXUnified(At.hoodEndA||0,Tt.anchor,Tt.offset,Tt.flipped),kt=GenomeView.getTransformedXUnified(At.hoodStartB||0,Rt.anchor,Rt.offset,Rt.flipped),Ot=GenomeView.getTransformedXUnified(At.hoodEndB||0,Rt.anchor,Rt.offset,Rt.flipped);Pt=Tt.anchor+(Pt-Tt.anchor)*Tt.xScale,Lt=Tt.anchor+(Lt-Tt.anchor)*Tt.xScale,kt=Rt.anchor+(kt-Rt.anchor)*Rt.xScale,Ot=Rt.anchor+(Ot-Rt.anchor)*Rt.xScale;const Mt=At.buildPolygonFromCoords(Pt,Lt,kt,Ot,wt,St);Et.push({polygon:Mt,fillColor:At.fillColor,metadata:At.metadata,seqids:[At.seqidA,At.seqidB]})}return Et}getAllDomains(){if(this._cachedAllDomains!==void 0)return this._cachedAllDomains;const Et=[];let xt=0,vt=0;for(const bt in this.genesById){const At=this.genesById[bt];for(let Ft of At.domains){xt++;let Ct=Ft.polygon;Array.isArray(Ct)&&Ct.length===1&&Array.isArray(Ct[0])&&(Ct=Ct[0]),isValidPolygon(Ct)&&(vt++,Et.push({polygon:Ct,fillColor:Ft.fillColor,domainName:Ft.domainName,metadata:Ft.metadata,geneId:Ft.geneId}))}}try{typeof window<"u"&&window.__hoodini_debug&&console.debug(`GenomeView.getAllDomains: total=${xt}, valid=${vt}`)}catch{}return this._cachedAllDomains=Et,Et}getAllNcRNAs(){return Object.values(this.ncRNAsById)}getAllRegions(){return Object.values(this.regionsById)}getAllNonCodingFeatures(){return this.getAllNcRNAs()}getRegionPolygons(){const Et=[];for(const xt of Object.values(this.regionsById))xt.polygon&&Array.isArray(xt.polygon)&&xt.polygon.length>0&&Et.push({polygon:xt.polygon,fillColor:xt.getFillColor(),strokeColor:xt.getStrokeColor(),strokeWidth:xt.strokeWidth,metadata:xt.metadata});return Et}getNodeDescendantLeaves(Et){if(!Et)return[];function xt(vt){return vt.branchset.length===0&&vt.name?[vt.name]:vt.branchset.flatMap(xt)}return xt(Et)}buildScaleBar(){const Et=this.config?.layout?.scaleBarOffset??this.config?.layout?.padding??150,xt=this.tree.leafNodes[this.tree.leafNodes.length-1].x+Et;return[[{path:[[this.globalMin,xt],[this.globalMax,xt]],color:this.config?.colors?.black||[0,0,0,255]}],xt]}buildPhyloLabels(Et="after-tree"){const xt=this.config?.tree?.labelOffset||10,vt=this.config?.colors?.black||[10,10,10,255],bt=this.config?.text?.phyloLabelSize||14;return this.tree.leafNodes.map(At=>{let Ft;if(Et==="after-tracks"){const Ct=At.name;let wt=this._rightmostByHood.get(Ct);isFinite(wt)?wt+=xt:wt=At.y+xt,Ft=[wt,At.x]}else Ft=[At.y+xt,At.x];return{position:Ft,text:At.name,color:vt,size:bt,textAnchor:"start",leafNode:At}})}buildNodePoints(Et,xt){const vt=Et?new Set(this.getNodeDescendantLeaves(Et)):null,bt=this.config?.tree?.nodeRadius||DEFAULT_CONFIG$1.tree.nodeRadius;return this.tree.allNodes.map(At=>{const Ft=this.getNodeDescendantLeaves(At),Ct=!Et||Ft.some(St=>vt.has(St));let wt;if(At.branchset.length>0)wt=[0,0,0,255];else{const St=At.metadata||{};if(St[xt]){const Tt=String(St[xt]);let Rt=0;for(let Ot=0;Ot<Tt.length;++Ot)Rt=Tt.charCodeAt(Ot)+((Rt<<5)-Rt);const Pt=Rt>>0&255,Lt=Rt>>8&255,kt=Rt>>16&255;wt=[Math.abs(Pt),Math.abs(Lt),Math.abs(kt),255]}else wt=[100,100,100,255]}return Et&&!Ct&&(wt=this.fadeColor(wt,.1)),{id:At.id,node:At,position:[At.y,At.x],color:wt,radius:At.branchset.length>0?bt.internal:bt.leaf,metadata:At.metadata||{name:At.name,id:At.id}}})}buildEdgesWithMetadata(){return this.tree.buildEdges().map(Et=>({...Et,metadata:{source:Et.source?.name,target:Et.target?.name,branchLength:Et.source?.branchLength,id:Et.source?.id}}))}fadeColor(Et,xt){return[Et[0],Et[1],Et[2],Math.floor(Et[3]*xt)]}setProteinClusters(Et){if(!Et||Object.keys(Et).length===0){this.proteinClusters={},this._clusterSummary=null;return}this.proteinClusters={},this._genesIndexReady||this._buildGeneIndex();for(const bt of Object.keys(Et)){const At=Et[bt],Ft=At==null?null:String(At).trim(),Ct=this._genesByOriginalId.get(bt)||[];for(const wt of Ct)this.proteinClusters[wt]=Ft}if(this._clusterSummary=null,!this.clusterColors)return;const xt=this.genesById,vt=this.clusterColors;for(const bt in xt){const At=xt[bt],Ft=this.proteinClusters[bt];At.fillColor=Ft&&vt[Ft]?vt[Ft]:null,At.metadata||(At.metadata={}),At.metadata.clusterId=Ft||null}}setProteinClustersWithPalette(Et,xt=null){this.proteinClusters={},this._genesIndexReady||this._buildGeneIndex();for(const At in Et){const Ft=Et[At],Ct=Ft==null?null:String(Ft).trim(),wt=this._genesByOriginalId.get(At)||[];for(const St of wt)this.proteinClusters[St]=Ct}if(this._clusterSummary=null,!xt||!xt.enabled){for(const At in this.genesById){const Ft=this.genesById[At];Ft&&Ft.fillColor&&(Ft.fillColor=null)}this._paletteVersion++;return}this.clusterColors={};const vt=Array.from(new Set(Object.values(this.proteinClusters))).filter(At=>At!=null).sort((At,Ft)=>{const Ct=Number(At),wt=Number(Ft);return!isNaN(Ct)&&!isNaN(wt)?Ct-wt:String(At).localeCompare(String(Ft))});let bt=[];if(xt.name)try{bt=memoGetPalette(xt.name,Math.max(vt.length,xt.numColors||vt.length),xt.reverse||!1)}catch{bt=[]}if(bt.length===0&&(bt=vt.map((At,Ft)=>hslToRgb(Ft/vt.length,.6,.5).concat(255))),vt.forEach((At,Ft)=>{this.clusterColors[At]=bt[Ft%bt.length]}),xt.desaturateByPrevalence){const At=this.computeGenePrevalence("cluster");for(const Ft in this.clusterColors){const Ct=At.get(Ft)||0;this.clusterColors[Ft]=this._desaturateColorByPrevalence(this.clusterColors[Ft],Ct)}}this._clusterSummary=null;for(const At in this.genesById){const Ft=this.genesById[At],Ct=this.proteinClusters[At];Ft.fillColor=Ct&&this.clusterColors[Ct]?this.clusterColors[Ct]:null,Ft.metadata||(Ft.metadata={}),Ft.metadata.clusterId=Ct||null}this._paletteVersion++}computeGenePrevalence(Et="cluster"){const xt=Object.keys(this.hoodRanges).length;if(xt===0)return new Map;const vt=new Map;for(const At of Object.values(this.genesById)){if(!At.hood_id)continue;let Ft=null;if(Et==="cluster"?Ft=At.metadata?.cluster??At.metadata?.clusterId??At.cluster:Ft=At.metadata?.[Et],Ft==null||Ft==="")continue;const Ct=String(Ft);vt.has(Ct)||vt.set(Ct,new Set),vt.get(Ct).add(At.hood_id)}const bt=new Map;for(const[At,Ft]of vt){const Ct=Ft.size/xt;bt.set(At,Ct)}return bt}_desaturateColorByPrevalence(Et,xt){if(!Et||!Array.isArray(Et)||xt>=1)return Et;const[vt,bt,At,Ft=255]=Et,Ct=vt/255,wt=bt/255,St=At/255,Tt=Math.max(Ct,wt,St),Rt=Math.min(Ct,wt,St),Pt=Tt-Rt,Lt=(Tt+Rt)/2;let kt=0;Pt!==0&&(kt=Lt>.5?Pt/(2-Tt-Rt):Pt/(Tt+Rt));let Ot=0;Pt!==0&&(Tt===Ct?Ot=((wt-St)/Pt+(wt<St?6:0))/6:Tt===wt?Ot=((St-Ct)/Pt+2)/6:Ot=((Ct-wt)/Pt+4)/6);const Mt=1-xt,It=kt*(1-Mt*.8),Nt=(1-Math.abs(2*Lt-1))*It,Ut=Nt*(1-Math.abs(Ot*6%2-1)),jt=Lt-Nt/2;let Vt=0,zt=0,Ht=0;const Wt=Math.floor(Ot*6);return Wt===0?(Vt=Nt,zt=Ut,Ht=0):Wt===1?(Vt=Ut,zt=Nt,Ht=0):Wt===2?(Vt=0,zt=Nt,Ht=Ut):Wt===3?(Vt=0,zt=Ut,Ht=Nt):Wt===4?(Vt=Ut,zt=0,Ht=Nt):(Vt=Nt,zt=0,Ht=Ut),[Math.round((Vt+jt)*255),Math.round((zt+jt)*255),Math.round((Ht+jt)*255),Ft]}_transparentByPrevalence(Et,xt,vt=.1){if(!Et||!Array.isArray(Et))return Et;const[bt,At,Ft]=Et,Ct=Math.round(vt*255+xt*(255-vt*255));return[bt,At,Ft,Ct]}_computeClusterSummary(){const Et=this.proteinClusters||{},xt=Object.values(Et).reduce((bt,At)=>{const Ft=String(At);return bt[Ft]=(bt[Ft]||0)+1,bt},{}),vt=Object.entries(xt).map(([bt,At])=>({id:bt,size:Number(At),label:`Cluster ${bt} (${At} genes)`})).sort((bt,At)=>At.size-bt.size);return{items:vt,ids:vt.map(bt=>bt.id)}}getClusterSummary(){return this._clusterSummary?this._clusterSummary:(this._clusterSummary=this._computeClusterSummary(),this._clusterSummary)}setNcRNAColorsWithPalette(Et=null){const xt=Object.values(this.ncRNAsById);if(!Et||!Et.enabled){for(const Ct of xt)Ct.fillColor=this.config?.gene?.fillColor||[200,200,200,255];return}const vt=xt.filter(Ct=>{const wt=Ct.metadata&&Ct.metadata.type;return!isEmptyValue(wt)});if(vt.length===0)return;const bt=Array.from(new Set(vt.map(Ct=>normalizeKey(Ct.metadata.type))));let At=[];if(Et.name)try{At=memoGetPalette(Et.name,Math.max(bt.length,Et.numColors||bt.length),Et.reverse||!1)}catch{At=[]}At.length===0&&(At=bt.map((Ct,wt)=>{const St=wt/bt.length;return hslToRgb(St,.6,.5).concat(255)}));const Ft={};bt.forEach((Ct,wt)=>{Ft[Ct]=At[wt%At.length]});for(const Ct in this.ncRNAsById){const wt=this.ncRNAsById[Ct],St=wt.metadata&&wt.metadata.type;isEmptyValue(St)||(wt.fillColor=Ft[normalizeKey(St)])}}setRegionColorsWithPalette(Et=null){const xt=Object.values(this.regionsById);if(xt.length===0)return;if(!Et||!Et.enabled){for(const Ct of xt)Ct.fillColor=[0,0,0,0],Ct.strokeColor=[100,100,100,255];return}const vt=xt.map(Ct=>Ct.getColorKey()).map(Ct=>normalizeKey(Ct)).filter(Ct=>!isEmptyValue(Ct)),bt=[...new Set(vt)];if(bt.length===0)return;let At=[];if(Et.name)try{At=memoGetPalette(Et.name,Math.max(bt.length,Et.numColors||bt.length),Et.reverse||!1)}catch{At=[]}At.length===0&&(At=bt.map((Ct,wt)=>{const St=wt/bt.length;return hslToRgb(St,.6,.5).concat(255)}));const Ft={};bt.forEach((Ct,wt)=>{Ft[Ct]=At[wt%At.length]});for(const Ct in this.regionsById){const wt=this.regionsById[Ct],St=wt.getColorKey();isEmptyValue(St)||(wt.fillColor=Ft[normalizeKey(St)])}}toggleTrackFlip(Et){this.trackFlipped[Et]=!this.trackFlipped[Et]}flipTrack(Et){const xt=this.trackOffset[Et]||0,vt=this.getTrackAnchor(Et),At=!!this.trackFlipped[Et]?GenomeView.flipCoordinate(vt+xt,vt):vt+xt;this.trackFlipped[Et]=!this.trackFlipped[Et];const Ft=!!this.trackFlipped[Et];let Ct;Ft?Ct=vt-At:Ct=At-vt,this.trackOffset[Et]=Ct,this.computeTrackPositions()}flipTrackState(Et){this.trackFlipped[Et]=!this.trackFlipped[Et]}flipTrackStateWithCentering(Et){const xt=this.trackOffset[Et]||0,vt=this.getTrackAnchor(Et),At=!!this.trackFlipped[Et]?GenomeView.flipCoordinate(vt+xt,vt):vt+xt;this.trackFlipped[Et]=!this.trackFlipped[Et];const Ft=!!this.trackFlipped[Et];let Ct;Ft?Ct=vt-At:Ct=At-vt,this.trackOffset[Et]=Ct}shiftTrack(Et,xt){this.trackOffset[Et]||(this.trackOffset[Et]=0),this.trackFlipped[Et]&&(xt=-xt),this.trackOffset[Et]+=xt,this.computeTrackPositions()}shiftTrackPlus1kb(Et){this.shiftTrack(Et,1e3)}shiftTrackMinus1kb(Et){this.shiftTrack(Et,-1e3)}flipTrackToggle(Et){this.flipTrack(Et)}getTrackAnchor(Et){const xt=this.hoodToSeqidMap[Et];if(!xt)return 0;const vt=this.nucleotidesBySeqid[xt],bt=this.hoodRanges[Et];return bt?bt.length/2:vt&&vt.hood?(vt.hood.origEnd-vt.hood.origStart)/2:this.featuresBySeqid[xt]?(this.featuresBySeqid[xt].origMaxEnd-this.featuresBySeqid[xt].origMinStart)/2:0}alignCluster(Et){const xt=Et==null?null:String(Et).trim(),bt=(this.config.genome&&typeof this.config.genome.xScalePercent=="number"?this.config.genome.xScalePercent:100)/100,At=Object.entries(this.genesById).filter(([Tt,Rt])=>this.proteinClusters&&this.proteinClusters[Tt]===xt).map(([Tt,Rt])=>Rt);if(At.length===0)return;const Ft={};for(const Tt of At)(Ft[Tt.hood_id]||=[]).push(Tt);const Ct=[];for(const Tt in Ft){const Rt=Ft[Tt];Rt.sort((Pt,Lt)=>Pt.originalGeneId.localeCompare(Lt.originalGeneId)),Ct.push(Rt[0])}if(!Ct.length)return;Ct.sort((Tt,Rt)=>Tt.hood_id.localeCompare(Rt.hood_id)),Ct[0];for(const Tt of Ct){const Rt=Tt.hood_id;(!!this.trackFlipped[Rt]?Tt.origStrand==="+"?"-":"+":Tt.origStrand)==="-"&&this.flipTrackStateWithCentering(Rt)}this.computeTrackPositions();const wt=0;for(const Tt of Ct){const Rt=Tt.hood_id,Pt=GenomeView.getGeneVisualX(Tt,this);if(Pt===null)continue;let Lt=(wt-Pt)/bt;this.trackFlipped[Rt]&&(Lt=-Lt);const Ot=this.trackOffset[Rt]||0;this.trackOffset[Rt]=Ot+Lt}const St=new Set(Ct.map(Tt=>Tt.hood_id));for(const Tt of this.leaves){if(St.has(Tt))continue;const Rt=this.hoodRanges[Tt],Pt=this.hoodToSeqidMap[Tt],Lt=this.nucleotidesBySeqid[Pt];if(!Rt&&!Lt?.hood)continue;const kt=Rt?Rt.length/2:(Lt.hood.origEnd-Lt.hood.origStart)/2,Mt=!!this.trackFlipped[Tt]?-1:1,It=(wt-kt)/(Mt*bt);this.trackOffset[Tt]=It}this.computeTrackPositions()}alignAllToStart(){const Et=this.config.genome&&typeof this.config.genome.xScalePercent=="number"?this.config.genome.xScalePercent:100,xt=Et/100;for(const vt of this.leaves){this.trackFlipped[vt]=!1;const bt=this.hoodToSeqidMap[vt];if(!bt)continue;const At=this.nucleotidesBySeqid[bt];if(At?.hood){const wt=(this.hoodRanges[vt]?.length||At.hood.origEnd-At.hood.origStart||0)/2;this.trackOffset[vt]=wt*(1-1/xt)}}this.computeTrackPositions();try{if(this.config?.debug?.alignment){const bt=[],At=[];console.debug(`[GenomeView] alignAllToStart xScale=${Et}`);for(const Tt of this.leaves){const Rt=this.hoodToSeqidMap[Tt],Pt=Rt?this.nucleotidesBySeqid[Rt]:null,Lt=!!this.trackFlipped[Tt],kt=this.trackOffset[Tt]||0,Mt=this.hoodRanges[Tt]?.length||(Pt?.hood?Pt.hood.origEnd-Pt.hood.origStart:0)||0,It=Pt?.hood?.start,Nt=Pt?.hood?.end;typeof It=="number"&&isFinite(It)&&bt.push([Tt,It]),typeof Nt=="number"&&isFinite(Nt)&&At.push([Tt,Nt]),console.debug(`[start] hood=${Tt} flipped=${Lt} len=${Mt} offset=${kt} baseline=(${It??"n/a"}, ${Nt??"n/a"})`)}bt.sort((Tt,Rt)=>Tt[1]-Rt[1]),At.sort((Tt,Rt)=>Tt[1]-Rt[1]);const Ft=bt[0]?.[1],Ct=bt[0]?.[0],wt=At[At.length-1]?.[1],St=At[At.length-1]?.[0];console.debug(`[start] baselineMinStart=${Ft} (hood=${Ct}) baselineMaxEnd=${wt} (hood=${St})`),console.debug(`[start] global bounds: minX=${this.globalMin} maxX=${this.globalMax}`)}}catch{}}alignAllToEnd(){const xt=(this.config.genome&&typeof this.config.genome.xScalePercent=="number"?this.config.genome.xScalePercent:100)/100;for(const vt of this.leaves){this.trackFlipped[vt]=!1;const bt=this.hoodToSeqidMap[vt];if(!bt)continue;const At=this.nucleotidesBySeqid[bt];if(At?.hood){const wt=(this.hoodRanges[vt]?.length||At.hood.origEnd-At.hood.origStart||0)/2;this.trackOffset[vt]=-wt*(1+1/xt)}}this.computeTrackPositions()}alignAllToCenter(){const Et=this.config.genome&&typeof this.config.genome.xScalePercent=="number"?this.config.genome.xScalePercent:100,xt=Et/100;for(const vt of this.leaves){this.trackFlipped[vt]=!1;const bt=this.hoodToSeqidMap[vt];if(!bt)continue;const At=this.nucleotidesBySeqid[bt];if(At?.hood){const wt=(this.hoodRanges[vt]?.length||At.hood.origEnd-At.hood.origStart||0)/2;this.trackOffset[vt]=-wt/xt}}this.computeTrackPositions();try{if(this.config?.debug?.alignment){const bt=[],At=[];console.debug(`[GenomeView] alignAllToCenter xScale=${Et}`);for(const Tt of this.leaves){const Rt=this.hoodToSeqidMap[Tt],Pt=Rt?this.nucleotidesBySeqid[Rt]:null,Lt=!!this.trackFlipped[Tt],kt=this.trackOffset[Tt]||0,Mt=this.hoodRanges[Tt]?.length||(Pt?.hood?Pt.hood.origEnd-Pt.hood.origStart:0)||0,It=Pt?.hood?.start,Nt=Pt?.hood?.end;typeof It=="number"&&isFinite(It)&&bt.push([Tt,It]),typeof Nt=="number"&&isFinite(Nt)&&At.push([Tt,Nt]),console.debug(`[center] hood=${Tt} flipped=${Lt} len=${Mt} offset=${kt} baseline=(${It??"n/a"}, ${Nt??"n/a"})`)}bt.sort((Tt,Rt)=>Tt[1]-Rt[1]),At.sort((Tt,Rt)=>Tt[1]-Rt[1]);const Ft=bt[0]?.[1],Ct=bt[0]?.[0],wt=At[At.length-1]?.[1],St=At[At.length-1]?.[0];console.debug(`[center] baselineMinStart=${Ft} (hood=${Ct}) baselineMaxEnd=${wt} (hood=${St})`),console.debug(`[center] global bounds: minX=${this.globalMin} maxX=${this.globalMax}`)}}catch{}}applyHoods(Et){const xt=new Set(this.leaves.map(bt=>String(bt))),vt=[];for(const bt of Et){const At=bt.hood_id!=null?String(bt.hood_id).trim():null,Ft=bt.seqid!=null?String(bt.seqid).trim():null;let Ct=null;At&&xt.has(At)?Ct=At:Ft&&xt.has(Ft)&&(Ct=Ft),Ct&&(bt.hood_id=Ct,vt.push(bt))}for(const bt of vt)bt.hood_id&&bt.seqid&&(this.hoodToSeqidMap[bt.hood_id]=bt.seqid,(this.seqidToHoodsMap[bt.seqid]||=[]).push(bt.hood_id),this.hoodRanges[bt.hood_id]={seqid:bt.seqid,origStart:bt.start,origEnd:bt.end,start:bt.start,end:bt.end,length:bt.end-bt.start,align_gene:bt.align_gene}),this.nucleotidesBySeqid[bt.seqid]&&this.nucleotidesBySeqid[bt.seqid].setHood(bt.start,bt.end);this._buildHoodIntervalIndex()}getHoodIdsFromSeqid(Et){return this.seqidToHoodsMap[Et]||[Et]}getHoodIdFromSeqid(Et){return this.getHoodIdsFromSeqid(Et)[0]}getSeqidFromHoodId(Et){return this.hoodToSeqidMap[Et]||Et}alignByDefaultGenes(){const xt=(this.config.genome&&typeof this.config.genome.xScalePercent=="number"?this.config.genome.xScalePercent:100)/100,vt=[];for(const Ft of this.leaves){const Ct=this.hoodRanges[Ft];if(!Ct?.align_gene)continue;const wt=`${Ft}_${Ct.align_gene}`,St=this.genesById[wt];St&&vt.push(St)}if(!vt.length)return;vt.sort((Ft,Ct)=>Ft.hood_id.localeCompare(Ct.hood_id));const bt=0;for(const Ft of vt){const Ct=Ft.hood_id;(!!this.trackFlipped[Ct]?Ft.origStrand==="+"?"-":"+":Ft.origStrand)==="-"&&this.flipTrackStateWithCentering(Ct)}this.computeTrackPositions();for(const Ft of vt){const Ct=Ft.hood_id,wt=GenomeView.getGeneVisualX(Ft,this);if(wt===null)continue;const St=bt-wt,Rt=(!!this.trackFlipped[Ct]?-1:1)*(St/xt),Pt=this.trackOffset[Ct]||0;this.trackOffset[Ct]=Pt+Rt}const At=new Set(vt.map(Ft=>Ft.hood_id));for(const Ft of this.leaves){if(At.has(Ft))continue;const Ct=this.hoodToSeqidMap[Ft];if(!Ct)continue;const wt=this.nucleotidesBySeqid[Ct];if(wt?.hood){const St=this.hoodRanges[Ft],Tt=St?St.length/2:(wt.hood.origEnd-wt.hood.origStart)/2,Pt=!!this.trackFlipped[Ft]?-1:1,Lt=(bt-Tt)/(Pt*xt);this.trackOffset[Ft]=Lt}}this.computeTrackPositions()}applyDomainPalette(Et=null){if(this._cachedAllDomains=void 0,!Et||!Et.enabled){for(const Ft of Object.values(this.genesById))for(const Ct of Ft.domains)Ct&&Ct.fillColor&&(Ct.fillColor=null);this._paletteVersion++;return}const xt=new Set;for(const Ft of Object.values(this.genesById))for(const Ct of Ft.domains)xt.add(Ct.domainName);const vt=Array.from(xt).sort();let bt=[];if(Et.name)try{bt=memoGetPalette(Et.name,Math.max(vt.length,Et.numColors||vt.length),Et.reverse||!1)}catch{bt=[]}const At={};vt.forEach((Ft,Ct)=>{At[Ft]=bt[Ct%bt.length]});for(const Ft of Object.values(this.genesById))for(const Ct of Ft.domains)Ct.fillColor=At[Ct.domainName]||[128,128,128,255]}}function hslToRgb(yt,Et,xt){let vt,bt,At;{const Ft=(St,Tt,Rt)=>(Rt<0&&(Rt+=1),Rt>1&&(Rt-=1),Rt<.16666666666666666?St+(Tt-St)*6*Rt:Rt<.5?Tt:Rt<.6666666666666666?St+(Tt-St)*(.6666666666666666-Rt)*6:St),Ct=xt+Et-xt*Et,wt=2*xt-Ct;vt=Ft(wt,Ct,yt+1/3),bt=Ft(wt,Ct,yt),At=Ft(wt,Ct,yt-1/3)}return[Math.round(vt*255),Math.round(bt*255),Math.round(At*255)]}function isValidPolygon(yt){if(!Array.isArray(yt)||yt.length<3)return!1;const[Et,xt]=yt[0];return!yt.every(([vt,bt])=>vt===Et&&bt===xt)}function assert$7(yt,Et){if(!yt)throw new Error(Et||"loader assertion failed.")}const isBrowser$2=!!(typeof process!="object"||String(process)!=="[object process]"||process.browser),matches$1=typeof process<"u"&&process.version&&/v([0-9]*)/.exec(process.version);matches$1&&parseFloat(matches$1[1]);const window_=globalThis,process_=globalThis.process||{},navigator_=globalThis.navigator||{};function isElectron(yt){if(typeof window<"u"&&window.process?.type==="renderer"||typeof process<"u"&&process.versions?.electron)return!0;const xt=typeof navigator<"u"&&navigator.userAgent;return!!(xt&&xt.indexOf("Electron")>=0)}function isBrowser$1(){return!(typeof process=="object"&&String(process)==="[object process]"&&!process?.browser)||isElectron()}function getBrowser(yt){return isBrowser$1()?isElectron()?"Electron":(navigator_.userAgent||"").indexOf("Edge")>-1?"Edge":globalThis.chrome?"Chrome":globalThis.safari?"Safari":globalThis.mozInnerScreenX?"Firefox":"Unknown":"Node"}const VERSION$4="4.1.0";function getStorage(yt){try{const Et=window[yt],xt="__storage_test__";return Et.setItem(xt,xt),Et.removeItem(xt),Et}catch{return null}}class LocalStorage{constructor(Et,xt,vt="sessionStorage"){this.storage=getStorage(vt),this.id=Et,this.config=xt,this._loadConfiguration()}getConfiguration(){return this.config}setConfiguration(Et){if(Object.assign(this.config,Et),this.storage){const xt=JSON.stringify(this.config);this.storage.setItem(this.id,xt)}}_loadConfiguration(){let Et={};if(this.storage){const xt=this.storage.getItem(this.id);Et=xt?JSON.parse(xt):{}}return Object.assign(this.config,Et),this}}function formatTime(yt){let Et;return yt<10?Et=`${yt.toFixed(2)}ms`:yt<100?Et=`${yt.toFixed(1)}ms`:yt<1e3?Et=`${yt.toFixed(0)}ms`:Et=`${(yt/1e3).toFixed(2)}s`,Et}function leftPad(yt,Et=8){const xt=Math.max(Et-yt.length,0);return`${" ".repeat(xt)}${yt}`}var COLOR;(function(yt){yt[yt.BLACK=30]="BLACK",yt[yt.RED=31]="RED",yt[yt.GREEN=32]="GREEN",yt[yt.YELLOW=33]="YELLOW",yt[yt.BLUE=34]="BLUE",yt[yt.MAGENTA=35]="MAGENTA",yt[yt.CYAN=36]="CYAN",yt[yt.WHITE=37]="WHITE",yt[yt.BRIGHT_BLACK=90]="BRIGHT_BLACK",yt[yt.BRIGHT_RED=91]="BRIGHT_RED",yt[yt.BRIGHT_GREEN=92]="BRIGHT_GREEN",yt[yt.BRIGHT_YELLOW=93]="BRIGHT_YELLOW",yt[yt.BRIGHT_BLUE=94]="BRIGHT_BLUE",yt[yt.BRIGHT_MAGENTA=95]="BRIGHT_MAGENTA",yt[yt.BRIGHT_CYAN=96]="BRIGHT_CYAN",yt[yt.BRIGHT_WHITE=97]="BRIGHT_WHITE"})(COLOR||(COLOR={}));const BACKGROUND_INCREMENT=10;function getColor(yt){return typeof yt!="string"?yt:(yt=yt.toUpperCase(),COLOR[yt]||COLOR.WHITE)}function addColor(yt,Et,xt){return!isBrowser$1&&typeof yt=="string"&&(Et&&(yt=`\x1B[${getColor(Et)}m${yt}\x1B[39m`),xt&&(yt=`\x1B[${getColor(xt)+BACKGROUND_INCREMENT}m${yt}\x1B[49m`)),yt}function autobind(yt,Et=["constructor"]){const xt=Object.getPrototypeOf(yt),vt=Object.getOwnPropertyNames(xt),bt=yt;for(const At of vt){const Ft=bt[At];typeof Ft=="function"&&(Et.find(Ct=>At===Ct)||(bt[At]=Ft.bind(yt)))}}function assert$6(yt,Et){if(!yt)throw new Error("Assertion failed")}function getHiResTimestamp$1(){let yt;if(isBrowser$1()&&window_.performance)yt=window_?.performance?.now?.();else if("hrtime"in process_){const Et=process_?.hrtime?.();yt=Et[0]*1e3+Et[1]/1e6}else yt=Date.now();return yt}const originalConsole={debug:isBrowser$1()&&console.debug||console.log,log:console.log,info:console.info,warn:console.warn,error:console.error},DEFAULT_LOG_CONFIGURATION={enabled:!0,level:0};function noop$4(){}const cache$2={},ONCE={once:!0};class Log{constructor({id:Et}={id:""}){this.VERSION=VERSION$4,this._startTs=getHiResTimestamp$1(),this._deltaTs=getHiResTimestamp$1(),this.userData={},this.LOG_THROTTLE_TIMEOUT=0,this.id=Et,this.userData={},this._storage=new LocalStorage(`__probe-${this.id}__`,DEFAULT_LOG_CONFIGURATION),this.timeStamp(`${this.id} started`),autobind(this),Object.seal(this)}set level(Et){this.setLevel(Et)}get level(){return this.getLevel()}isEnabled(){return this._storage.config.enabled}getLevel(){return this._storage.config.level}getTotal(){return Number((getHiResTimestamp$1()-this._startTs).toPrecision(10))}getDelta(){return Number((getHiResTimestamp$1()-this._deltaTs).toPrecision(10))}set priority(Et){this.level=Et}get priority(){return this.level}getPriority(){return this.level}enable(Et=!0){return this._storage.setConfiguration({enabled:Et}),this}setLevel(Et){return this._storage.setConfiguration({level:Et}),this}get(Et){return this._storage.config[Et]}set(Et,xt){this._storage.setConfiguration({[Et]:xt})}settings(){console.table?console.table(this._storage.config):console.log(this._storage.config)}assert(Et,xt){if(!Et)throw new Error(xt||"Assertion failed")}warn(Et){return this._getLogFunction(0,Et,originalConsole.warn,arguments,ONCE)}error(Et){return this._getLogFunction(0,Et,originalConsole.error,arguments)}deprecated(Et,xt){return this.warn(`\`${Et}\` is deprecated and will be removed in a later version. Use \`${xt}\` instead`)}removed(Et,xt){return this.error(`\`${Et}\` has been removed. Use \`${xt}\` instead`)}probe(Et,xt){return this._getLogFunction(Et,xt,originalConsole.log,arguments,{time:!0,once:!0})}log(Et,xt){return this._getLogFunction(Et,xt,originalConsole.debug,arguments)}info(Et,xt){return this._getLogFunction(Et,xt,console.info,arguments)}once(Et,xt){return this._getLogFunction(Et,xt,originalConsole.debug||originalConsole.info,arguments,ONCE)}table(Et,xt,vt){return xt?this._getLogFunction(Et,xt,console.table||noop$4,vt&&[vt],{tag:getTableHeader(xt)}):noop$4}time(Et,xt){return this._getLogFunction(Et,xt,console.time?console.time:console.info)}timeEnd(Et,xt){return this._getLogFunction(Et,xt,console.timeEnd?console.timeEnd:console.info)}timeStamp(Et,xt){return this._getLogFunction(Et,xt,console.timeStamp||noop$4)}group(Et,xt,vt={collapsed:!1}){const bt=normalizeArguments({logLevel:Et,message:xt,opts:vt}),{collapsed:At}=vt;return bt.method=(At?console.groupCollapsed:console.group)||console.info,this._getLogFunction(bt)}groupCollapsed(Et,xt,vt={}){return this.group(Et,xt,Object.assign({},vt,{collapsed:!0}))}groupEnd(Et){return this._getLogFunction(Et,"",console.groupEnd||noop$4)}withGroup(Et,xt,vt){this.group(Et,xt)();try{vt()}finally{this.groupEnd(Et)()}}trace(){console.trace&&console.trace()}_shouldLog(Et){return this.isEnabled()&&this.getLevel()>=normalizeLogLevel(Et)}_getLogFunction(Et,xt,vt,bt,At){if(this._shouldLog(Et)){At=normalizeArguments({logLevel:Et,message:xt,args:bt,opts:At}),vt=vt||At.method,assert$6(vt),At.total=this.getTotal(),At.delta=this.getDelta(),this._deltaTs=getHiResTimestamp$1();const Ft=At.tag||At.message;if(At.once&&Ft)if(!cache$2[Ft])cache$2[Ft]=getHiResTimestamp$1();else return noop$4;return xt=decorateMessage(this.id,At.message,At),vt.bind(console,xt,...At.args)}return noop$4}}Log.VERSION=VERSION$4;function normalizeLogLevel(yt){if(!yt)return 0;let Et;switch(typeof yt){case"number":Et=yt;break;case"object":Et=yt.logLevel||yt.priority||0;break;default:return 0}return assert$6(Number.isFinite(Et)&&Et>=0),Et}function normalizeArguments(yt){const{logLevel:Et,message:xt}=yt;yt.logLevel=normalizeLogLevel(Et);const vt=yt.args?Array.from(yt.args):[];for(;vt.length&&vt.shift()!==xt;);switch(typeof Et){case"string":case"function":xt!==void 0&&vt.unshift(xt),yt.message=Et;break;case"object":Object.assign(yt,Et);break}typeof yt.message=="function"&&(yt.message=yt.message());const bt=typeof yt.message;return assert$6(bt==="string"||bt==="object"),Object.assign(yt,{args:vt},yt.opts)}function decorateMessage(yt,Et,xt){if(typeof Et=="string"){const vt=xt.time?leftPad(formatTime(xt.total)):"";Et=xt.time?`${yt}: ${vt}  ${Et}`:`${yt}: ${Et}`,Et=addColor(Et,xt.color,xt.background)}return Et}function getTableHeader(yt){for(const Et in yt)for(const xt in yt[Et])return xt||"untitled";return"empty"}const VERSION$3="4.3.3",version=VERSION$3[0]>="0"&&VERSION$3[0]<="9"?`v${VERSION$3}`:"";function createLog(){const yt=new Log({id:"loaders.gl"});return globalThis.loaders=globalThis.loaders||{},globalThis.loaders.log=yt,globalThis.loaders.version=version,globalThis.probe=globalThis.probe||{},globalThis.probe.loaders=yt,yt}const log$1=createLog();function mergeLoaderOptions(yt,Et){return mergeOptionsRecursively(yt||{},Et)}function mergeOptionsRecursively(yt,Et,xt=0){if(xt>3)return Et;const vt={...yt};for(const[bt,At]of Object.entries(Et))At&&typeof At=="object"&&!Array.isArray(At)?vt[bt]=mergeOptionsRecursively(vt[bt]||{},Et[bt],xt+1):vt[bt]=Et[bt];return vt}const NPM_TAG="latest";function getVersion(){return globalThis._loadersgl_?.version||(globalThis._loadersgl_=globalThis._loadersgl_||{},globalThis._loadersgl_.version="4.3.3"),globalThis._loadersgl_.version}const VERSION$2=getVersion();function assert$5(yt,Et){if(!yt)throw new Error(Et||"loaders.gl assertion failed.")}const isBrowser=typeof process!="object"||String(process)!=="[object process]"||process.browser,isMobile=typeof window<"u"&&typeof window.orientation<"u",matches=typeof process<"u"&&process.version&&/v([0-9]*)/.exec(process.version);matches&&parseFloat(matches[1]);class WorkerJob{name;workerThread;isRunning=!0;result;_resolve=()=>{};_reject=()=>{};constructor(Et,xt){this.name=Et,this.workerThread=xt,this.result=new Promise((vt,bt)=>{this._resolve=vt,this._reject=bt})}postMessage(Et,xt){this.workerThread.postMessage({source:"loaders.gl",type:Et,payload:xt})}done(Et){assert$5(this.isRunning),this.isRunning=!1,this._resolve(Et)}error(Et){assert$5(this.isRunning),this.isRunning=!1,this._reject(Et)}}class NodeWorker{terminate(){}}const workerURLCache=new Map;function getLoadableWorkerURL(yt){assert$5(yt.source&&!yt.url||!yt.source&&yt.url);let Et=workerURLCache.get(yt.source||yt.url);return Et||(yt.url&&(Et=getLoadableWorkerURLFromURL(yt.url),workerURLCache.set(yt.url,Et)),yt.source&&(Et=getLoadableWorkerURLFromSource(yt.source),workerURLCache.set(yt.source,Et))),assert$5(Et),Et}function getLoadableWorkerURLFromURL(yt){if(!yt.startsWith("http"))return yt;const Et=buildScriptSource(yt);return getLoadableWorkerURLFromSource(Et)}function getLoadableWorkerURLFromSource(yt){const Et=new Blob([yt],{type:"application/javascript"});return URL.createObjectURL(Et)}function buildScriptSource(yt){return`try {
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Colors:"}),jsxRuntimeExports.jsxs(Select,{value:jo,onValueChange:qs,children:[jsxRuntimeExports.jsx(SelectTrigger,{id:"domain-colors",className:"w-full text-xs",style:{height:"20px",minHeight:"20px"},children:jsxRuntimeExports.jsx(SelectValue,{})}),jsxRuntimeExports.jsx(SelectContent,{children:$i.map(Gr=>jsxRuntimeExports.jsx(SelectItem,{value:Gr,children:Gr},Gr))})]})]}),jsxRuntimeExports.jsxs("div",{children:[jsxRuntimeExports.jsx(Label,{htmlFor:"domain-source",className:"text-xs mb-1 block",children:"Domain Source:"}),jsxRuntimeExports.jsxs(Select,{value:Ec||"all",onValueChange:Gr=>{try{typeof Sl=="function"?Sl(Gr):Va&&typeof Va.setDomainSource=="function"&&Va.setDomainSource(Gr)}catch{}},children:[jsxRuntimeExports.jsx(SelectTrigger,{id:"domain-source",className:"w-full text-xs",style:{height:"20px",minHeight:"20px"},children:jsxRuntimeExports.jsx(SelectValue,{})}),jsxRuntimeExports.jsxs(SelectContent,{children:[jsxRuntimeExports.jsx(SelectItem,{value:"all",children:"all"}),(()=>{try{const Gr=Wn&&Wn.current?Wn.current.genomeView:null;if(!Gr)return null;const Ti=Gr.getAllDomains?Gr.getAllDomains():[];return Array.from(new Set(Ti.map(es=>String(es&&(es.source||es.metadata&&es.metadata.source)||"unknown")))).sort().map(es=>jsxRuntimeExports.jsx(SelectItem,{value:String(es),children:String(es)},String(es)))}catch{return null}})()]})]})]})]})]}),jsxRuntimeExports.jsx(Separator,{className:"my-2"}),jsxRuntimeExports.jsx("div",{className:"mb-3",children:jsxRuntimeExports.jsx(UnifiedPaletteWidget,{genePalette:ya,setGenePalette:jl,phyloPalette:Bs,setPhyloPalette:Li,domainPalette:Pl,setDomainPalette:lc,ncRNAPalette:ss,setNcRNAPalette:Dl,regionPalette:xl,setRegionPalette:Jl,availableData:{parsedGFF:[1],parsedDomains:Xi?[1]:[],phyloData:[1],ncRNAFeatures:[1],regionFeatures:[1]}})}),jsxRuntimeExports.jsx(Separator,{className:"my-2"}),jsxRuntimeExports.jsxs("div",{className:"mb-3",children:[jsxRuntimeExports.jsx(Label,{className:"text-xs font-medium mb-1 block",children:"Links Color Selection:"}),jsxRuntimeExports.jsx("div",{className:"space-y-1",children:jsxRuntimeExports.jsx(LinkColorWidget,{proteinLinkConfig:Xa,nucleotideLinkConfig:dl,onProteinLinkConfigChange:rl,onNucleotideLinkConfigChange:Tl})})]})]}),lo==="legend"&&jsxRuntimeExports.jsxs("div",{className:"space-y-4",children:[jsxRuntimeExports.jsx("div",{className:"flex items-center gap-2 mb-3",children:jsxRuntimeExports.jsxs(Badge,{variant:"soft",className:"text-xs font-medium",children:[jsxRuntimeExports.jsx(BookOpen,{className:"h-3 w-3 mr-1"}),"Legend"]})}),jsxRuntimeExports.jsxs("div",{className:"bg-muted/30 p-3 rounded-lg border border-border/30",children:[jsxRuntimeExports.jsx("div",{className:"flex items-center gap-2 mb-2",children:jsxRuntimeExports.jsx(Badge,{variant:"muted",className:"text-xs",children:"Visualization Legend"})}),jsxRuntimeExports.jsx("div",{className:"space-y-2",children:bo?jsxRuntimeExports.jsx(LegendWidget,{legend:bo,genePalette:ya,phyloPalette:Bs,regionPalette:xl,proteinLinkConfig:Xa,nucleotideLinkConfig:dl,styleConfig:dc,className:"",style:{}}):jsxRuntimeExports.jsxs("div",{className:"p-3 bg-accent/30 rounded-lg text-center",children:[jsxRuntimeExports.jsx("p",{className:"text-xs text-muted-foreground mb-1",children:"No legend data available yet"}),jsxRuntimeExports.jsx("p",{className:"text-xs text-muted-foreground",children:"Legend will appear once data is loaded"})]})})]}),jsxRuntimeExports.jsxs("div",{className:"bg-muted/30 p-3 rounded-lg border border-border/30",children:[jsxRuntimeExports.jsx("div",{className:"flex items-center gap-2 mb-2",children:jsxRuntimeExports.jsx(Badge,{variant:"muted",className:"text-xs",children:"Guide"})}),jsxRuntimeExports.jsxs("div",{className:"text-xs space-y-2 text-muted-foreground",children:[jsxRuntimeExports.jsxs("div",{className:"p-2 bg-accent/20 rounded-md",children:[jsxRuntimeExports.jsx("p",{className:"font-medium mb-1 text-foreground/80",children:"Gene Tracks:"}),jsxRuntimeExports.jsx("p",{children:"• Arrows indicate gene direction and boundaries"}),jsxRuntimeExports.jsx("p",{children:"• Colors represent different metadata categories"})]}),jsxRuntimeExports.jsxs("div",{className:"p-2 bg-accent/20 rounded-md",children:[jsxRuntimeExports.jsx("p",{className:"font-medium mb-1 text-foreground/80",children:"Phylogenetic Tree:"}),jsxRuntimeExports.jsx("p",{children:"• Branch lengths show evolutionary distance"}),jsxRuntimeExports.jsx("p",{children:"• Node colors represent tree metadata"})]}),jsxRuntimeExports.jsxs("div",{className:"p-2 bg-accent/20 rounded-md",children:[jsxRuntimeExports.jsx("p",{className:"font-medium mb-1 text-foreground/80",children:"Protein Domains:"}),jsxRuntimeExports.jsx("p",{children:"• Colored regions within genes"}),jsxRuntimeExports.jsx("p",{children:"• Represent functional protein domains"})]}),jsxRuntimeExports.jsxs("div",{className:"p-2 bg-muted/50 rounded",children:[jsxRuntimeExports.jsx("p",{className:"font-medium mb-1",children:"Links:"}),jsxRuntimeExports.jsx("p",{children:"• Connect related elements across tracks"}),jsxRuntimeExports.jsx("p",{children:"• Show protein or nucleotide relationships"})]})]})]})]}),lo==="guides"&&jsxRuntimeExports.jsxs("div",{className:"space-y-4",children:[jsxRuntimeExports.jsx("div",{className:"flex items-center gap-2 mb-3",children:jsxRuntimeExports.jsxs(Badge,{variant:"soft",className:"text-xs font-medium",children:[jsxRuntimeExports.jsx(Crop,{className:"h-3 w-3 mr-1"}),"Format Guides"]})}),jsxRuntimeExports.jsx("div",{className:"bg-muted/30 p-3 rounded-lg border border-border/30",children:jsxRuntimeExports.jsx(GuideControlsWidget,{guidesVisible:Bl,selectedFormat:Hl,onGuidesVisibleChange:sl,onFormatChange:ko,scaleToFormat:kn,onScaleToFormatChange:Vn,cropToGuides:On,onCropToGuidesChange:Pn,scaleRulerWithCrop:fr,onScaleRulerWithCropChange:mr})})]})]})]})}function SVGExportButton({phyloTreeViewerRef:yt}){const Et=()=>{try{console.log("🖼️ SVGExportButton clicked, ref:",yt.current),console.log("🖼️ exportToSVG method:",yt.current?.exportToSVG),yt.current?.exportToSVG?.()}catch(xt){console.error("🖼️ SVGExportButton error:",xt)}};return jsxRuntimeExports.jsxs(Button,{variant:"ghost",size:"icon",className:"size-7 sm:size-7 min-w-[44px] min-h-[44px] sm:min-w-0 sm:min-h-0 flex items-center justify-center border touch-manipulation",onClick:Et,title:"Export current view to SVG",children:[jsxRuntimeExports.jsx(Camera,{size:16}),jsxRuntimeExports.jsx("span",{className:"sr-only",children:"Export SVG"})]})}function ThemeToggle(){const{theme:yt,resolvedTheme:Et,toggleTheme:xt}=useTheme(),vt=Et||yt||"light";return jsxRuntimeExports.jsxs(Button,{variant:"ghost",size:"icon",className:"size-7 sm:size-7 min-w-[44px] min-h-[44px] sm:min-w-0 sm:min-h-0 flex items-center justify-center border touch-manipulation",onClick:xt,title:`Switch to ${vt==="light"?"dark":"light"} theme`,children:[vt==="light"?jsxRuntimeExports.jsx(Moon,{size:16}):jsxRuntimeExports.jsx(Sun,{size:16}),jsxRuntimeExports.jsx("span",{className:"sr-only",children:"Toggle theme"})]})}class PhyloNode{constructor(){this.id=null,this.name=null,this.branchLength=0,this.parent=null,this.branchset=[],this.x=0,this.y=0,this.rootDist=0}getLeaves(){return this.branchset.length===0?[this]:this.branchset.flatMap(Et=>Et.getLeaves())}}class PhyloTree{constructor(Et,xt=DEFAULT_CONFIG$1,vt=!1,bt=null){if(this.config=xt,this.themeColors=bt,this.allNodes=[],this.leafNodes=[],Array.isArray(Et))this.hasTree=!1,this.root=this._createFlatRoot(Et);else if(!Et||Et.trim()==="")this.hasTree=!1,this.root=new PhyloNode,this.root.id=0;else try{this.root=this.parseNewick(Et),this.hasTree=!0}catch(At){console.warn("[PhyloTree] failed to parse Newick; using empty tree",At?.message||At),this.hasTree=!1,this.root=new PhyloNode,this.root.id=0}this.collectAll(),this.hasTree&&this.ladderize(!1),vt&&this.hasTree&&this.makeUltrametric()}_createFlatRoot(Et){const xt=new PhyloNode;return xt.id=0,xt.branchLength=0,xt.name="_root",Et.forEach((vt,bt)=>{const At=new PhyloNode;At.id=bt+1,At.name=String(vt),At.branchLength=1,xt.branchset.push(At)}),xt}parseNewick(Et){for(var xt=[],vt=new PhyloNode,bt=Et.split(/\s*(;|\(|\)|,|:)\s*/),At=0,Ft=0;Ft<bt.length;Ft++){var Ct=bt[Ft];switch(Ct){case"(":{var wt=new PhyloNode;wt.id=At++,vt.branchset=[wt],xt.push(vt),vt=wt;break}case",":{var wt=new PhyloNode;wt.id=At++,xt[xt.length-1].branchset.push(wt),vt=wt;break}case")":vt=xt.pop();break;case":":break;default:{var St=bt[Ft-1];St==")"||St=="("||St==","?vt.name=Ct:St==":"&&(vt.branchLength=parseFloat(Ct)),vt.id=vt.id!==null?vt.id:At++}}}return vt}ladderize(Et=!0){const xt=[],vt=[this.root];let bt=0;for(;vt.length>0;){const Ft=vt.pop();if(xt.push(Ft),Ft._sortIndex=bt++,Ft.branchset)for(const Ct of Ft.branchset)vt.push(Ct)}for(let Ft=xt.length-1;Ft>=0;Ft--){const Ct=xt[Ft];if(!Ct.branchset||Ct.branchset.length===0)Ct.num_tips=1;else{Ct.num_tips=0;for(const wt of Ct.branchset)Ct.num_tips+=wt.num_tips||1}}const At=[this.root];for(;At.length>0;){const Ft=At.pop();if(Ft.branchset&&Ft.branchset.length>0){Ft.branchset.sort((Ct,wt)=>{const St=Ct.num_tips||1,Tt=wt.num_tips||1;return St!==Tt?Et?St-Tt:Tt-St:(Ct._sortIndex||0)-(wt._sortIndex||0)});for(const Ct of Ft.branchset)At.push(Ct)}}this.collectAll()}collectAll(){this.allNodes=[];const Et=xt=>{this.allNodes.push(xt);for(let vt of xt.branchset)Et(vt)};Et(this.root)}setParents(){const Et=(xt,vt=null)=>{xt.parent=vt;for(let bt of xt.branchset)Et(bt,xt)};Et(this.root,null)}computeDistances(){const Et=xt=>{xt.rootDist=(xt.parent?xt.parent.rootDist:0)+(xt.branchLength||0);for(let vt of xt.branchset)Et(vt)};Et(this.root)}getLeafNodes(){return this.root.getLeaves()}assignX(Et){const xt=this.config.tree.ySpacing;for(let vt=0;vt<Et.length;vt++)Et[vt].x=vt*xt}assignInternalX(Et){if(Et.branchset.length===0)return Et.x;const xt=Et.branchset.map(vt=>this.assignInternalX(vt));return Et.x=xt.reduce((vt,bt)=>vt+bt,0)/xt.length,Et.x}scaleY(){const Et=this.allNodes.map(At=>At.rootDist),xt=Math.max(...Et),vt=this.config.tree.fixedCoordinateWidth||2e3,bt=xt>0?vt/xt:1;this.maxEvolutionaryDistance=xt;for(let At of this.allNodes)At.y=At.rootDist*bt}layout(Et){this.setParents(),Et?(this.leafNodes=this.getLeafNodes(),this.leafNodes.sort((xt,vt)=>Et.indexOf(xt.name)-Et.indexOf(vt.name)),this.assignX(this.leafNodes)):(this.leafNodes=this.getLeafNodes(),this.assignX(this.leafNodes)),this.assignInternalX(this.root),this.computeDistances(),this.scaleY()}buildEdges(){const Et=[],xt=this.themeColors?.treeEdges||this.config.tree.edgeColor||[85,85,85,255],vt=bt=>{for(let At of bt.branchset){const Ft=[[bt.y,bt.x],[bt.y,At.x],[At.y,At.x]];Et.push({path:Ft,color:xt,source:bt,target:At}),vt(At)}};return vt(this.root),Et}makeUltrametric(){(!this.allNodes||this.allNodes.length===0)&&this.collectAll(),this.setParents(),this.computeDistances();const Et=this.getLeafNodes(),xt=Math.max(...Et.map(At=>At.rootDist)),vt=At=>{if(At.branchset.length===0){At.rootDist=xt;return}for(let wt of At.branchset)vt(wt);const Ft=At.branchset.map(wt=>wt.rootDist),Ct=Math.min(...Ft);At.rootDist=Ct-Math.max(...At.branchset.map(wt=>wt.branchLength||0)),At.rootDist<0&&(At.rootDist=0)};vt(this.root);const bt=At=>{for(let Ft of At.branchset)Ft.branchLength=Ft.rootDist-At.rootDist,bt(Ft)};this.root.rootDist=0,bt(this.root),this.computeDistances()}}class GFFFeature{constructor(Et,xt,vt,bt,At,Ft){this.seqid=Et,this.start=xt,this.end=vt,this.strand=bt,this.type=At,this.attributes=Ft}}class Gene extends GFFFeature{constructor(Et,xt,vt,bt,At,Ft=DEFAULT_CONFIG$1){super(Et,xt,vt,bt,"gene",At),this.origStart=xt,this.origEnd=vt,this.origStrand=bt,this.domains=[],this.config=Ft||DEFAULT_CONFIG$1,this.fillColor=this.config.gene.fillColor,this.polygon=null,this.trackY=null,this.geneHeight=this.config.gene.height||this.config.gene.defaultHeight,this.centerLine=[],this.metadata={seqid:Et,start:xt,end:vt,strand:bt,attributes:At}}setTrackY(Et){this.trackY=Et,this.updatePolygon()}updatePolygon(){this.polygon=this._buildPolygon(this.trackY,this.geneHeight),this.centerLine=this.computeCenterLine();for(let Et of this.domains)Et.updatePolygon()}_buildPolygon(Et,xt){let vt=this.start,bt=this.end;if(vt>bt){const Rt=vt;vt=bt,bt=Rt}const At=Math.abs(bt-vt),Ft=calculateTipWidth(At,this.config),Ct=xt/2,wt=this.strand==="+",St=this.config.gene.arrowheadHeight||0;if(Ft<1)return[[vt,Et-Ct],[bt,Et-Ct],[bt,Et+Ct],[vt,Et+Ct]];if(St<.1)return wt?[[vt,Et-Ct],[bt-Ft,Et-Ct],[bt,Et],[bt-Ft,Et+Ct],[vt,Et+Ct]]:[[bt,Et-Ct],[vt+Ft,Et-Ct],[vt,Et],[vt+Ft,Et+Ct],[bt,Et+Ct]];const Tt=Ct+St/2;return wt?[[vt,Et-Ct],[bt-Ft,Et-Ct],[bt-Ft,Et-Tt],[bt,Et],[bt-Ft,Et+Tt],[bt-Ft,Et+Ct],[vt,Et+Ct]]:[[bt,Et-Ct],[vt+Ft,Et-Ct],[vt+Ft,Et-Tt],[vt,Et],[vt+Ft,Et+Tt],[vt+Ft,Et+Ct],[bt,Et+Ct]]}computeCenterLine(){const Et=this.polygon;if(!Et||Et.length===0)return[];if(Et.length===5){const xt=[(Et[0][0]+Et[4][0])/2,(Et[0][1]+Et[4][1])/2],vt=Et[2];return[xt,vt]}else if(Et.length===7){const xt=[(Et[0][0]+Et[6][0])/2,(Et[0][1]+Et[6][1])/2],vt=Et[3];return[xt,vt]}else if(Et.length===4){const xt=this.strand==="+",vt=[(Et[0][0]+Et[3][0])/2,(Et[0][1]+Et[3][1])/2],bt=[(Et[1][0]+Et[2][0])/2,(Et[1][1]+Et[2][1])/2];return xt?[vt,bt]:[bt,vt]}else{const xt=[(Et[0][0]+Et[Et.length-1][0])/2,(Et[0][1]+Et[Et.length-1][1])/2],vt=Et[Math.floor(Et.length/2)];return[xt,vt]}}addDomain(Et){Et.setParentGene(this),this.domains.push(Et)}}function clipPolygon(yt,Et){if(!yt||yt.length<3)return null;if(!Et||Et.length<3)return yt;let xt=yt.slice();for(let vt=0;vt<Et.length;vt++){if(xt.length===0)return null;const bt=xt;xt=[];const At=Et[vt],Ft=Et[(vt+1)%Et.length];for(let Ct=0;Ct<bt.length;Ct++){const wt=bt[Ct],St=bt[(Ct+bt.length-1)%bt.length],Tt=isInside(wt,At,Ft),Rt=isInside(St,At,Ft);if(Tt){if(!Rt){const Pt=lineIntersection(St,wt,At,Ft);Pt&&xt.push(Pt)}xt.push(wt)}else if(Rt){const Pt=lineIntersection(St,wt,At,Ft);Pt&&xt.push(Pt)}}}return xt.length>=3?xt:null}function isInside(yt,Et,xt){return(xt[0]-Et[0])*(yt[1]-Et[1])-(xt[1]-Et[1])*(yt[0]-Et[0])>=0}function lineIntersection(yt,Et,xt,vt){const bt=Et[0]-yt[0],At=Et[1]-yt[1],Ft=vt[0]-xt[0],Ct=vt[1]-xt[1],wt=bt*Ct-At*Ft;if(Math.abs(wt)<1e-10)return null;const St=xt[0]-yt[0],Tt=xt[1]-yt[1],Rt=(St*Ct-Tt*Ft)/wt;return[yt[0]+Rt*bt,yt[1]+Rt*At]}class Domain{constructor(Et,xt,vt,bt,At,Ft,Ct,wt=DEFAULT_CONFIG$1){this.geneId=Et,this.domainName=xt,this.origStart=vt,this.origEnd=bt,this.start=vt,this.end=bt,this.source=At,this.evalue=Ft,this.coverage=Ct,this.parentGene=null,this.polygon=null;const St=Ft&&Ft>0?Ft<.001?Ft.toExponential(2):Ft.toFixed(6):Ft,Tt=Ct&&`${(Ct*100).toFixed(1)}%`;this.metadata={geneId:Et,domainName:xt,start:vt,end:bt,source:At,evalue:St,coverage:Tt},this.config=wt||DEFAULT_CONFIG$1}setParentGene(Et){this.parentGene=Et,this.updatePolygon()}updatePolygon(){if(!this.parentGene||!this.parentGene.polygon)return;const Et=this.parentGene,xt=this.createDomainPolygon(Et,this.origStart,this.origEnd);if(xt&&Et.polygon){const vt=this.getGeneClipRect(Et);this.polygon=clipPolygon(xt,vt)}else this.polygon=xt}getGeneClipRect(Et){const vt=(Et.geneHeight||Et.config?.gene?.height||60)/2,bt=Et.trackY,At=Math.min(Et.start,Et.end),Ft=Math.max(Et.start,Et.end);return[[At,bt-vt],[Ft,bt-vt],[Ft,bt+vt],[At,bt+vt]]}getConvexGenePolygon(Et){const xt=Et.geneHeight||Et.config?.gene?.height||60,vt=Et.config?.gene?.arrowheadHeight||0,bt=xt/2,At=bt+vt/2,Ft=Et.trackY;let Ct=Math.min(Et.start,Et.end),wt=Math.max(Et.start,Et.end);const St=wt-Ct,Tt=calculateTipWidth(St,Et.config?.gene),Rt=Et.strand==="+";return Tt<1?[[Ct,Ft-bt],[wt,Ft-bt],[wt,Ft+bt],[Ct,Ft+bt]]:Rt?[[Ct,Ft-bt],[wt-Tt,Ft-At],[wt,Ft],[wt-Tt,Ft+At],[Ct,Ft+bt]]:[[wt,Ft-bt],[Ct+Tt,Ft-At],[Ct,Ft],[Ct+Tt,Ft+At],[wt,Ft+bt]]}createDomainPolygon(Et,xt,vt){const bt=Et.start,At=Et.end,Ft=Math.min(bt,At),wt=Math.max(bt,At)-Ft;if(!Et.centerLine||!Array.isArray(Et.centerLine)||Et.centerLine.length<2||!isFinite(wt)||wt<=0)return null;const Tt=Math.abs(Et.origEnd-Et.origStart)/3;let Rt=xt/Tt,Pt=vt/Tt;if(Rt=Math.max(0,Math.min(1,Rt)),Pt=Math.max(0,Math.min(1,Pt)),Et.strand==="-"){const Wt=1-Pt,Gt=1-Rt;Rt=Wt,Pt=Gt}const Lt=this.interpolateOnLine(Et.centerLine,Rt),kt=this.interpolateOnLine(Et.centerLine,Pt),Ot=this.perpVector(Et.centerLine[0],Et.centerLine[1]),Mt=this.normalize(Ot),It=(typeof Et.geneHeight=="number"?Et.geneHeight:Et.config&&Et.config.gene&&Et.config.gene.height?Et.config.gene.height:10)/2,Nt=Et.config&&Et.config.domain&&typeof Et.config.domain.heightFactor=="number"?Et.config.domain.heightFactor:this.config&&this.config.domain&&this.config.domain.heightFactor||.6,Ut=It*Nt,jt=[Lt[0]-Mt[0]*Ut,Lt[1]-Mt[1]*Ut],Vt=[kt[0]-Mt[0]*Ut,kt[1]-Mt[1]*Ut],zt=[kt[0]+Mt[0]*Ut,kt[1]+Mt[1]*Ut],Ht=[Lt[0]+Mt[0]*Ut,Lt[1]+Mt[1]*Ut];return[jt,Vt,zt,Ht]}interpolateOnLine(Et,xt){const[vt,bt]=Et;return[vt[0]+(bt[0]-vt[0])*xt,vt[1]+(bt[1]-vt[1])*xt]}perpVector(Et,xt){const vt=xt[0]-Et[0];return[-(xt[1]-Et[1]),vt]}normalize(Et){const xt=Math.sqrt(Et[0]*Et[0]+Et[1]*Et[1]);return xt===0?[0,1]:[Et[0]/xt,Et[1]/xt]}}class Link{constructor(){}}class ProteinLink extends Link{constructor(Et,xt,vt,bt=[50,100,220]){super(),this.gAId=Et,this.gBId=xt,this.similarity=vt,this.baseColor=Array.isArray(bt)&&bt.length>=3?bt.slice(0,3):[50,100,220];const At=Math.round(255*(vt/100));this.fillColor=[...this.baseColor,At],this.metadata={gAId:Et,gBId:xt,similarity:vt}}updateColor(Et,xt=null,vt=null,bt=null,At=null){if(!Et){const St=Math.round(255*(this.similarity/100));this.fillColor=[...this.baseColor,St];return}let Ft=this.baseColor,Ct=255;const wt=At?At.slice(0,3):this.baseColor;switch(Et.colorBy){case"source_gene":Ft=xt?xt.slice(0,3):wt;break;case"target_gene":Ft=vt?vt.slice(0,3):wt;break;case"identity_solid":Ft=Et.solidColor?Et.solidColor.slice(0,3):this.baseColor;break;case"identity_gradient":bt&&(Ft=bt.slice(0,3));break;default:Ft=this.baseColor}if(Et.useAlpha){const St=this.similarity/100,Tt=Et.maxAlpha-Et.minAlpha,Rt=Et.minAlpha+St*Tt;Ct=Math.round(Rt*255)}else Ct=Et.colorBy==="identity_solid"?255:Math.round(255*(this.similarity/100));this.fillColor=[...Ft,Ct]}bezierCurve(Et,xt,vt,bt,At=120){const Ft=[];for(let Ct=0;Ct<=1;Ct+=1/At){const wt=Math.pow(1-Ct,3)*Et[0]+3*Math.pow(1-Ct,2)*Ct*xt[0]+3*(1-Ct)*Ct*Ct*vt[0]+Ct*Ct*Ct*bt[0],St=Math.pow(1-Ct,3)*Et[1]+3*Math.pow(1-Ct,2)*Ct*xt[1]+3*(1-Ct)*Ct*Ct*vt[1]+Ct*Ct*Ct*bt[1];Ft.push([wt,St])}return Ft}buildPolygon(Et,xt){if(!Et||!xt)return null;const vt=Math.min(Et.start,Et.end),bt=Math.max(Et.start,Et.end),At=Math.min(xt.start,xt.end),Ft=Math.max(xt.start,xt.end),Ct=Et.trackY,wt=xt.trackY;let St,Tt;Ct<=wt?(St={left:[vt,Ct],right:[bt,Ct]},Tt={left:[At,wt],right:[Ft,wt]}):(St={left:[At,wt],right:[Ft,wt]},Tt={left:[vt,Ct],right:[bt,Ct]});const Rt=(St.left[1]+Tt.right[1])/2,Pt=(Ot,Mt)=>this.bezierCurve(Ot,[Ot[0],Rt],[Mt[0],Rt],Mt,20),Lt=Pt(St.right,Tt.right),kt=Pt(Tt.left,St.left);return[St.left,St.right,...Lt,Tt.right,Tt.left,...kt]}}class NucleotideLink extends Link{constructor(Et,xt,vt,bt,At,Ft,Ct,wt=[220,50,50]){super(),this.seqidA=Et,this.seqidB=bt,this.strandA=xt<=vt?"+":"-",this.strandB=At<=Ft?"+":"-",xt>vt&&([xt,vt]=[vt,xt]),At>Ft&&([At,Ft]=[Ft,At]),this.origStartA=xt,this.origEndA=vt,this.origStartB=At,this.origEndB=Ft,this.startA=xt,this.endA=vt,this.startB=At,this.endB=Ft,this.similarity=Ct,this.baseColor=Array.isArray(wt)&&wt.length>=3?wt.slice(0,3):[220,50,50];const St=Math.round(255*(Ct/100));this.fillColor=[...this.baseColor,St]}updateColor(Et,xt=null){if(!Et){const At=Math.round(255*(this.similarity/100));this.fillColor=[...this.baseColor,At];return}let vt=this.baseColor,bt=255;switch(Et.colorBy){case"solid":vt=Et.solidColor?Et.solidColor.slice(0,3):this.baseColor,Et.useAlpha||(bt=Et.solidColor&&Et.solidColor.length>3?Et.solidColor[3]:255);break;case"identity_gradient":xt&&(vt=xt.slice(0,3)),bt=255;break;default:vt=this.baseColor,bt=Math.round(255*(this.similarity/100))}if(Et.useAlpha){const At=this.similarity/100,Ft=Et.maxAlpha-Et.minAlpha,Ct=Et.minAlpha+At*Ft;bt=Math.round(Ct*255)}this.fillColor=[...vt,bt]}buildPolygon(Et,xt){const vt=[this.startA,this.endA,this.startB,this.endB],bt=[Et,Et,xt,xt],At=Math.min(...vt),Ft=Math.max(...vt),Ct=Math.min(...bt),wt=Math.max(...bt);return[[At,wt],[Ft,wt],[Ft,Ct],[At,Ct]]}buildPolygonFromCoords(Et,xt,vt,bt,At,Ft){const Ct=[[Et,At],[xt,At]],wt=[[vt,Ft],[bt,Ft]];return Ct.sort((St,Tt)=>St[0]-Tt[0]),wt.sort((St,Tt)=>St[0]-Tt[0]),[Ct[0],Ct[1],wt[1],wt[0]]}}class Hood{constructor(Et,xt,vt){this.seqid=Et,this.start=xt,this.end=vt,this.origStart=xt,this.origEnd=vt}set(Et,xt){this.start=Et,this.end=xt,this.origStart=Et,this.origEnd=xt}update(Et,xt){this.start=Et,this.end=xt}get(){return{seqid:this.seqid,start:this.start,end:this.end,origStart:this.origStart,origEnd:this.origEnd}}}class Nucleotide{constructor(Et,xt,vt,bt="+"){this.seqid=Et,this.start=xt,this.end=vt,this.strand=bt,this.genes=[],this.metadata={seqid:Et,start:xt,end:vt,strand:bt},this.hood=null}addGene(Et){this.genes.push(Et)}flip(){const Et=this.start,xt=this.end;this.start=-xt,this.end=-Et,this.strand=this.strand==="+"?"-":"+";for(const vt of this.genes)vt.start=-vt.end,vt.end=-vt.start,vt.strand=vt.strand==="+"?"-":"+",typeof vt.updatePolygon=="function"&&vt.updatePolygon()}shift(Et){this.start+=Et,this.end+=Et;for(const xt of this.genes)xt.start+=Et,xt.end+=Et,typeof xt.updatePolygon=="function"&&xt.updatePolygon()}getGenePolygons(){return this.genes.map(Et=>Et.polygon).filter(Boolean)}setHood(Et,xt){this.hood?this.hood.set(Et,xt):this.hood=new Hood(this.seqid,Et,xt)}getHood(){return this.hood?this.hood.get():null}updateHood(Et,xt){this.hood?this.hood.update(Et,xt):this.setHood(Et,xt)}}class NonCodingFeature extends GFFFeature{constructor(Et,xt,vt,bt,At,Ft,Ct){super(Et,xt,vt,bt,At,Ft),this.config=Ct||DEFAULT_CONFIG$1,this.polygon=null,this.trackY=null,this.featureHeight=this.config?.gene?.height||60,this.metadata={seqid:Et,start:xt,end:vt,strand:bt,type:At,attributes:Ft}}setTrackY(Et){this.trackY=Et,this.updatePolygon()}updatePolygon(){this.polygon=this._buildHalfArrowPolygon(this.trackY,this.featureHeight)}_buildHalfArrowPolygon(Et,xt){let vt=this.start,bt=this.end;if(vt>bt){const Rt=vt;vt=bt,bt=Rt}const At=Math.abs(bt-vt),Ft=calculateTipWidth(At,this.config),Ct=xt/4,wt=this.strand==="+",St=this.config?.gene?.arrowheadHeight||0,Tt=Ct+St/2;return Ft<1?wt?[[vt,Et],[vt,Et+Ct],[bt,Et+Ct],[bt,Et]]:[[bt,Et],[bt,Et-Ct],[vt,Et-Ct],[vt,Et]]:wt?[[vt,Et],[vt,Et+Ct],[bt-Ft,Et+Ct],[bt-Ft,Et+Tt],[bt,Et]]:[[bt,Et],[bt,Et-Ct],[vt+Ft,Et-Ct],[vt+Ft,Et-Tt],[vt,Et]]}}class RegionFeature extends GFFFeature{constructor(Et,xt,vt,bt,At,Ft,Ct){super(Et,xt,vt,bt,At,Ft),this.config=Ct,this.polygon=null,this.trackY=null,this.padding=Ct?.region?.padding||10,this.fillColor=[0,0,0,0],this.strokeColor=[100,100,100,255],this.strokeWidth=Ct?.region?.strokeWidth||2,this.metadata={seqid:Et,start:xt,end:vt,type:At,length:Math.abs(vt-xt)},Ft&&(typeof Ft=="string"||Ft instanceof String?this.metadata.attributes=Ft.toString():typeof Ft=="object"&&Object.assign(this.metadata,Ft))}setTrackY(Et){this.trackY=Et}updatePolygon(Et=[],xt=null){xt!==null&&(this.trackY=xt),this.config||(console.warn("RegionFeature: No config provided, using defaults"),this.config={gene:{height:20,arrowheadHeight:30},region:{padding:10,strokeWidth:2}});const vt=Math.min(this.start,this.end),bt=Math.max(this.start,this.end),At=this.config.gene?.height||20,Ft=this.config.gene?.arrowheadHeight||30,Ct=this.config.region?.padding||this.padding,St=Math.max(At,Ft)/2,Tt=this.trackY-St-Ct,Rt=this.trackY+St+Ct;this.polygon=[[vt,Tt],[bt,Tt],[bt,Rt],[vt,Rt],[vt,Tt]]}containsGene(Et){const xt=Math.min(this.start,this.end),vt=Math.max(this.start,this.end),bt=Math.min(Et.start,Et.end);return!(Math.max(Et.start,Et.end)<xt||bt>vt)}getFillColor(){return[0,0,0,0]}getStrokeColor(){if(this.strokeColor&&this.strokeColor[3]!==0)return this.strokeColor;const Et=(this.type||"").toLowerCase(),xt=this.config?.region?.colors||{};return xt[Et]?xt[Et]:xt.default||[128,128,128,255]}getColorKey(){const Et=this.metadata?.region_id||this.metadata?.ID||this.originalId||"";if(Et){const xt=Et.match(/^([a-zA-Z]+)/);if(xt)return xt[1].toLowerCase()}return this.metadata?.region_type?this.metadata.region_type.toLowerCase():(this.type||"region").toLowerCase()}}const _paletteCache=new Map;function memoGetPalette(yt,Et,xt=!1,vt="qualitative"){const bt=`${yt}::${Et}::${xt}::${vt}`;if(_paletteCache.has(bt))return _paletteCache.get(bt);let At=[];try{At=getPaletteColors(yt,Et,xt,vt)}catch{At=[]}return _paletteCache.set(bt,At),At}class GenomeView{constructor(Et,xt,vt=DEFAULT_CONFIG$1){this.leaves=Et,this.tree=xt,this.config=vt||DEFAULT_CONFIG$1,this.featuresBySeqid={},this.genesById={},this.ncRNAsById={},this.regionsById={},this.nucleotidesBySeqid={},this.globalMin=1/0,this.globalMax=-1/0,this.geneHeight=this.config?.gene?.height||DEFAULT_CONFIG$1.gene.height,this.trackFlipped={},this.trackOffset={},this.hoodRanges={},this.hoodToSeqidMap={},this.seqidToHoodsMap={},this.proteinLinks=[],this.nucleotideLinks=[],this.domainsByGene={},this._genesByOriginalId=new Map,this._genesIndexReady=!1,this._leafIndex=null,this._hoodIndex=null,this._regionsByHood=null,this._rightmostByHood=new Map,this._paletteVersion=0}_ensureLeafIndex(){if(!this._leafIndex){if(!this.tree?.leafNodes){this._leafIndex=new Map;return}this._leafIndex=new Map(this.tree.leafNodes.map((Et,xt)=>[Et.name,xt]))}}_buildGeneIndex(){this._genesByOriginalId=new Map;for(const[Et,xt]of Object.entries(this.genesById)){const vt=xt.originalGeneId;vt&&(this._genesByOriginalId.has(vt)||this._genesByOriginalId.set(vt,[]),this._genesByOriginalId.get(vt).push(Et))}this._genesIndexReady=!0}_addOrUpdateGeneIndex(Et,xt){xt?.originalGeneId&&(this._genesByOriginalId.has(xt.originalGeneId)||this._genesByOriginalId.set(xt.originalGeneId,[]),this._genesByOriginalId.get(xt.originalGeneId).push(Et),this._genesIndexReady=!0)}_invalidateGeneIndex(){this._genesIndexReady=!1}_rebuildRegionsByHood(){this._regionsByHood=new Map;for(const Et of Object.values(this.regionsById))this._regionsByHood.has(Et.hood_id)||this._regionsByHood.set(Et.hood_id,[]),this._regionsByHood.get(Et.hood_id).push(Et)}_buildHoodIntervalIndex(){this._hoodIndex=new Map;for(const[Et,xt]of Object.entries(this.hoodRanges||{})){const vt=this._hoodIndex.get(xt.seqid)||[];vt.push({start:xt.origStart,end:xt.origEnd,hood_id:Et}),this._hoodIndex.set(xt.seqid,vt)}for(const Et of this._hoodIndex.values())Et.sort((xt,vt)=>xt.start-vt.start)}_queryHoodsCovering(Et,xt,vt){const bt=this._hoodIndex?.get(Et)||[];let At=0,Ft=bt.length;for(;At<Ft;){const wt=At+Ft>>1;bt[wt].start<=xt?At=wt+1:Ft=wt}const Ct=[];for(let wt=At-1;wt>=0&&bt[wt].start<=xt;--wt)bt[wt].end>=vt&&Ct.push(bt[wt].hood_id);for(let wt=At;wt<bt.length&&bt[wt].start<=xt;++wt)bt[wt].end>=vt&&Ct.push(bt[wt].hood_id);return Ct}static flipCoordinate(Et,xt){return 2*xt-Et}static getTransformedXUnified(Et,xt,vt,bt){let At=Et+(vt||0);return bt?GenomeView.flipCoordinate(At,xt):At}static getGeneVisualX(Et,xt){const vt=Et.hood_id,bt=xt.hoodRanges[vt];if(!bt)return null;const At=xt.trackOffset[vt]||0,Ft=!!xt.trackFlipped[vt],Ct=(bt.length||0)/2,St=(xt.config.genome&&typeof xt.config.genome.xScalePercent=="number"?xt.config.genome.xScalePercent:100)/100,Tt=Et.origStart||0,Rt=Et.origEnd||0,Pt=Et.origStrand==="+"?Math.min(Tt,Rt):Math.max(Tt,Rt),Lt=GenomeView.getTransformedXUnified(Pt,Ct,At,Ft);return Ct+(Lt-Ct)*St}addFeatures(Et){for(let xt of Et)if(!(!xt.seqid||typeof xt.start!="number"||isNaN(xt.start)||typeof xt.end!="number"||isNaN(xt.end))&&(this.featuresBySeqid[xt.seqid]?(xt.start<this.featuresBySeqid[xt.seqid].origMinStart&&(this.featuresBySeqid[xt.seqid].origMinStart=xt.start),xt.end>this.featuresBySeqid[xt.seqid].origMaxEnd&&(this.featuresBySeqid[xt.seqid].origMaxEnd=xt.end)):(this.featuresBySeqid[xt.seqid]=[],this.featuresBySeqid[xt.seqid].origMinStart=xt.start,this.featuresBySeqid[xt.seqid].origMaxEnd=xt.end),this.featuresBySeqid[xt.seqid].push(xt),!this.nucleotidesBySeqid[xt.seqid])){const vt=this.featuresBySeqid[xt.seqid],bt=Math.min(...vt.map(wt=>typeof wt.start=="bigint"?Number(wt.start):wt.start)),At=Math.max(...vt.map(wt=>typeof wt.end=="bigint"?Number(wt.end):wt.end)),Ft=vt.find(wt=>wt.type==="gene"||wt.type==="CDS"),Ct=Ft&&Ft.strand?Ft.strand:"+";this.nucleotidesBySeqid[xt.seqid]=new Nucleotide(xt.seqid,bt,At,Ct)}}initGenes(){this._invalidateGeneIndex();for(let Et of this.leaves){const xt=this.hoodToSeqidMap[Et];if(!xt)continue;const vt=this.hoodRanges[Et];if(!vt)continue;const bt=vt.origStart||0,At=vt.origEnd||0,Ft=this.featuresBySeqid[xt]||[];for(let Ct of Ft)if(Ct.type==="gene"||Ct.type==="CDS"){const wt=Ct.start||0,St=Ct.end||0;if(!(wt>=bt&&St<=At))continue;const Rt=wt-bt,Pt=St-bt;let Lt=Ct.gene_id||Ct.id||Ct.protein_id||Ct.originalGeneId;!Lt&&Ct.attributes&&(Lt=this.getGeneIdFromAttributes(Ct.attributes));const kt=`${Et}_${Lt}`;let Ot=new Gene(Ct.seqid,Rt,Pt,Ct.strand,Ct.attributes,this.config);Ot.hood_id=Et,Ot.originalGeneId=Lt,this.genesById[kt]=Ot,this._addOrUpdateGeneIndex(kt,Ot),this.nucleotidesBySeqid[xt]&&this.nucleotidesBySeqid[xt].addGene(Ot)}else if(typeof Ct.type=="string"&&Ct.type.toLowerCase().includes("ncrna")){const wt=Ct.start||0,St=Ct.end||0;if(!(wt>=bt&&St<=At))continue;const Rt=wt-bt,Pt=St-bt,Lt=this.getGeneIdFromAttributes(Ct.attributes),kt=`${Et}_${Lt}_${wt}_${St}`;let Ot=new NonCodingFeature(Ct.seqid,Rt,Pt,Ct.strand,Ct.type,Ct.attributes,this.config);Ot.hood_id=Et,Ot.id=kt,Ot.originalId=Lt,Ot.origStart=Rt,Ot.origEnd=Pt,Ot.genomicStart=wt,Ot.genomicEnd=St,Ot.origStrand=Ct.strand;let Mt=null;try{const Nt=Ct.attributes||{};Nt&&typeof Nt=="object"&&(Mt=Nt.ncrna_type||Nt.ncrnaType||Nt.ID||Nt.id||Nt.Name||null),typeof Mt=="object"&&(Mt=String(Mt)),Mt&&(Mt=String(Mt).replace(/^ID=/,"").replace(/;$/,"").trim()),Mt&&(Mt.toLowerCase()==="null"||Mt.toLowerCase()==="none"||Mt==="")&&(Mt=null)}catch{Mt=null}const It=Mt||Lt||Ct.type||"ncRNA";Ot.name=It,(!Ot.metadata||typeof Ot.metadata!="object")&&(Ot.metadata={}),Ot.metadata.type=It,Ot.metadata.attributes=Ct.attributes,this.ncRNAsById[kt]=Ot}else if(Ct.type==="region"){const wt=Ct.start||0,St=Ct.end||0;if(!(wt>=bt&&St<=At))continue;const Rt=wt-bt,Pt=St-bt,Lt=this.getGeneIdFromAttributes(Ct.attributes),kt=`${Et}_${Lt}`;let Ot=new RegionFeature(Ct.seqid,Rt,Pt,Ct.strand,Ct.type,Ct.attributes,this.config);Ot.id=kt,Ot.hood_id=Et,Ot.originalId=Lt,Ot.origStart=Rt,Ot.origEnd=Pt,Ot.origStrand=Ct.strand,this.regionsById[kt]=Ot}}}getGeneIdFromAttributes(Et){if(typeof Et=="string"){const xt=Et.match(/ID=([^;]+)/);return xt?xt[1]:null}else if(typeof Et=="object"&&Et!==null)return Et.ID||null;return null}computeTrackPositions(){const Et={},xt={};for(const At of Object.values(this.genesById))(Et[At.hood_id]||=[]).push(At);for(const At of Object.values(this.ncRNAsById))(xt[At.hood_id]||=[]).push(At);this._rebuildRegionsByHood();const bt=(this.config.genome&&typeof this.config.genome.xScalePercent=="number"?this.config.genome.xScalePercent:100)/100;this._rightmostByHood.clear();for(let At of this.leaves){const Ft=this.tree.leafNodes.find(jt=>jt.name===At);if(!Ft)continue;const wt=(typeof Ft?.x=="number"?Ft.x:Ft?.y||0)+(this.config?.layout?.geneOffset||0),St=this.hoodToSeqidMap[At];if(!St)continue;const Tt=this.nucleotidesBySeqid[St],Rt=this.trackOffset[At]||0,Pt=this.hoodRanges[At],kt=(Pt?.length||0)/2,Ot=!!this.trackFlipped[At];let Mt=-1/0;const It=Et[At]||[];for(const jt of It){jt.trackY=wt,jt.geneHeight=this.geneHeight;const Vt=jt.origStart||0,zt=jt.origEnd||0;let Ht=GenomeView.getTransformedXUnified(Vt,kt,Rt,Ot),Wt=GenomeView.getTransformedXUnified(zt,kt,Rt,Ot);Ht=kt+(Ht-kt)*bt,Wt=kt+(Wt-kt)*bt,jt.start=Ht,jt.end=Wt,jt.strand=Ot?jt.origStrand==="+"?"-":"+":jt.origStrand,["gene_1","gene_2"].includes(jt.id)||jt.originalGeneId?.includes("gene_1")||jt.originalGeneId?.includes("gene_2"),Mt=Math.max(Mt,Ht,Wt);for(let Gt of jt.domains)Gt.updatePolygon();jt.updatePolygon()}const Nt=xt[At]||[];for(const jt of Nt){jt.trackY=wt,jt.featureHeight=this.geneHeight;const Vt=jt.origStart||0,zt=jt.origEnd||0;let Ht=GenomeView.getTransformedXUnified(Vt,kt,Rt,Ot),Wt=GenomeView.getTransformedXUnified(zt,kt,Rt,Ot);Ht=kt+(Ht-kt)*bt,Wt=kt+(Wt-kt)*bt,jt.start=Ht,jt.end=Wt,jt.strand=Ot?jt.origStrand==="+"?"-":"+":jt.origStrand,jt.updatePolygon(),Mt=Math.max(Mt,Ht,Wt)}const Ut=this._regionsByHood?.get(At)||[];for(const jt of Ut){jt.trackY=wt;const Vt=jt.origStart||0,zt=jt.origEnd||0;let Ht=GenomeView.getTransformedXUnified(Vt,kt,Rt,Ot),Wt=GenomeView.getTransformedXUnified(zt,kt,Rt,Ot);Ht=kt+(Ht-kt)*bt,Wt=kt+(Wt-kt)*bt,jt.start=Ht,jt.end=Wt,jt.strand=Ot?jt.origStrand==="+"?"-":"+":jt.origStrand;const Gt=It.filter(qt=>jt.containsGene(qt));jt.updatePolygon(Gt,wt),Mt=Math.max(Mt,Ht,Wt)}if(Tt&&Tt.hood){const Vt=Pt?Pt.length||0:(Tt.hood.origEnd||0)-(Tt.hood.origStart||0);let zt=GenomeView.getTransformedXUnified(0,kt,Rt,Ot),Ht=GenomeView.getTransformedXUnified(Vt,kt,Rt,Ot);zt=kt+(zt-kt)*bt,Ht=kt+(Ht-kt)*bt,Tt.hood.start=zt,Tt.hood.end=Ht,Mt=Math.max(Mt,zt,Ht)}if(Tt){let jt=GenomeView.getTransformedXUnified(0,kt,Rt,Ot),Vt=GenomeView.getTransformedXUnified(Pt&&Pt.length||0,kt,Rt,Ot);jt=kt+(jt-kt)*bt,Vt=kt+(Vt-kt)*bt,Tt.start=jt,Tt.end=Vt,Mt=Math.max(Mt,jt,Vt)}isFinite(Mt)&&this._rightmostByHood.set(At,Mt)}this.updateLinkPositions(),this.updateGlobalBounds()}updateGlobalBounds(){let Et=1/0,xt=-1/0;const vt=this.leaves&&this.leaves.length>0,bt=vt?new Set(this.leaves.map(Ft=>String(Ft))):null,At=vt?new Set:null;if(vt)for(const Ft of bt){const Ct=this.hoodToSeqidMap[Ft];Ct&&At.add(Ct)}for(const Ft of Object.values(this.genesById))if(!(bt&&Ft.hood_id&&!bt.has(String(Ft.hood_id))))if(Ft.polygon)for(const[Ct]of Ft.polygon)Ct<Et&&(Et=Ct),Ct>xt&&(xt=Ct);else Ft.start!==void 0&&Ft.end!==void 0&&(Ft.start<Et&&(Et=Ft.start),Ft.end<Et&&(Et=Ft.end),Ft.start>xt&&(xt=Ft.start),Ft.end>xt&&(xt=Ft.end));for(const Ft of Object.values(this.ncRNAsById))if(!(bt&&Ft.hood_id&&!bt.has(String(Ft.hood_id))))if(Ft.polygon)for(const[Ct]of Ft.polygon)Et=Math.min(Et,Ct),xt=Math.max(xt,Ct);else Ft.start!==void 0&&Ft.end!==void 0&&(Et=Math.min(Et,Ft.start,Ft.end),xt=Math.max(xt,Ft.start,Ft.end));for(const Ft of this.getAllDomains()){const Ct=Ft.parentGene;if(bt&&Ct?.hood_id&&!bt.has(String(Ct.hood_id)))continue;const wt=Ft.polygon;if(wt)for(const[St]of wt)Et=Math.min(Et,St),xt=Math.max(xt,St)}isFinite(Et)&&isFinite(xt)&&(this.globalMin=Et,this.globalMax=xt)}updateLinkPositions(){for(let Et of this.nucleotideLinks)Et.startA=Et.origStartA,Et.endA=Et.origEndA,Et.startB=Et.origStartB,Et.endB=Et.origEndB}addDomains(Et){this.domainsByGene=Et,this._cachedAllDomains=void 0,this._genesIndexReady||this._buildGeneIndex();for(const xt in Et){const vt=this._genesByOriginalId.get(xt)||[];for(const bt of vt){const At=this.genesById[bt];if(At){for(let Ft of Et[xt]){this.hoodRanges[At.hood_id];let Ct=new Domain(bt,Ft.domainName,Ft.start,Ft.end,Ft.source,Ft.evalue,Ft.coverage);At.addDomain(Ct)}At.metadata||(At.metadata={}),At.metadata.domainsSummary=At.domains&&At.domains.length>0?At.domains.map(Ft=>`${Ft.domainName}(${Ft.start}-${Ft.end})`).join(";"):""}}}}addDomainMetadata(Et){if(!Et)return;this._cachedAllDomains=void 0;let xt=Et;if(Array.isArray(Et)){xt={};for(const vt of Et){const bt=vt.domain_id||vt.domain||vt.domainName||vt.domain_name||vt.id;bt&&(xt[bt]=vt)}}for(const vt in this.genesById){const bt=this.genesById[vt];if(!(!bt.domains||bt.domains.length===0))for(const At of bt.domains){const Ft=At.domainName,Ct=xt[Ft];Ct&&(At.metadata={...At.metadata,...Ct})}}}addProteinLinks(Et,xt=[50,100,220],vt=1/0){this._genesIndexReady||this._buildGeneIndex(),this._ensureLeafIndex(),this.proteinLinks.length=0;const bt=new Set;for(let At of Et){let Ft,Ct,wt;Array.isArray(At)?(Ft=At[0],Ct=At[1],wt=At[2]):At&&typeof At=="object"&&(Ft=At.geneA??At.gAId,Ct=At.geneB??At.gBId,wt=At.score??At.similarity);const St=this._genesByOriginalId.get(Ft)||[],Tt=this._genesByOriginalId.get(Ct)||[];for(const Rt of St)for(const Pt of Tt){const Lt=this.genesById[Rt],kt=this.genesById[Pt];if(!Lt||!kt)continue;const Ot=this._leafIndex.get(Lt.hood_id),Mt=this._leafIndex.get(kt.hood_id);if(Ot==null||Mt==null||Math.abs(Ot-Mt)<=vt){const It=Rt<Pt?`${Rt}|${Pt}`:`${Pt}|${Rt}`;if(bt.has(It))continue;bt.add(It),this.proteinLinks.push(new ProteinLink(Rt,Pt,wt,xt))}}}}addNucleotideLinks(Et,xt=[220,50,50],vt=1/0){this._hoodIndex||this._buildHoodIntervalIndex(),this._ensureLeafIndex(),this.nucleotideLinks.length=0;for(let bt of Et){const{seqidA:At,seqidB:Ft,startA:Ct,endA:wt,startB:St,endB:Tt,similarity:Rt}=bt,Pt=this._queryHoodsCovering(At,Ct,wt),Lt=this._queryHoodsCovering(Ft,St,Tt);for(const kt of Pt){const Ot=this.hoodRanges[kt];if(Ot)for(const Mt of Lt){const It=this.hoodRanges[Mt];if(!It)continue;const Nt=this._leafIndex.get(kt),Ut=this._leafIndex.get(Mt);if(Nt==null||Ut==null||Math.abs(Nt-Ut)<=vt){const jt=new NucleotideLink(At,Ct,wt,Ft,St,Tt,Rt,xt);jt.hoodA=kt,jt.hoodB=Mt,jt.hoodStartA=Ct-Ot.origStart,jt.hoodEndA=wt-Ot.origStart,jt.hoodStartB=St-It.origStart,jt.hoodEndB=Tt-It.origStart,this.nucleotideLinks.push(jt)}}}}}applyProteinLinkColors(Et,xt=null){if(!this.proteinLinks?.length)return;let vt=null;if(Et?.colorBy==="identity_gradient"&&Et?.palette?.enabled)try{vt=memoGetPalette(Et.palette.name,Et.palette.numColors,Et.palette.reverse)}catch{vt=null}for(const bt of this.proteinLinks){const At=this.genesById[bt.gAId],Ft=this.genesById[bt.gBId],Ct=Et?.colorBy==="source_gene"?At?.fillColor||xt:null,wt=Et?.colorBy==="target_gene"?Ft?.fillColor||xt:null;let St=null;if(Et?.colorBy==="identity_gradient"&&vt){const Tt=Math.max(0,Math.min(1,bt.similarity/100)),Rt=Math.floor(Tt*(vt.length-1));St=vt[Rt]}bt.updateColor(Et,Ct,wt,St,xt)}}applyNucleotideLinkColors(Et){if(!this.nucleotideLinks?.length)return;let xt=null;if(Et?.colorBy==="identity_gradient"&&Et?.palette?.enabled)try{xt=memoGetPalette(Et.palette.name,Et.palette.numColors,Et.palette.reverse)}catch{xt=null}for(const vt of this.nucleotideLinks){let bt=null;if(Et?.colorBy==="identity_gradient"&&xt){const At=Math.max(0,Math.min(1,vt.similarity/100)),Ft=Math.floor(At*(xt.length-1));bt=xt[Ft]}vt.updateColor(Et,bt)}}getTrackY(Et){const xt=this.getHoodIdsFromSeqid(Et);if(xt.length>0){const vt=xt[0],bt=this.tree.leafNodes.find(At=>At.name===vt);return bt?bt.x:null}return null}getTrackYByHoodId(Et){const xt=this.tree.leafNodes.find(vt=>vt.name===Et);return xt?xt.x:null}filterBySelectedNode(Et){if(!Et)return{genes:Object.values(this.genesById),proteinPolygons:this.getProteinPolygons(),nucleotidePolygons:this.getNucleotidePolygons(),domains:this.getAllDomains(),ncRNAs:Object.values(this.ncRNAsById)};const xt=new Set(this.getNodeDescendantLeaves(Et)),vt=Object.values(this.genesById).filter(wt=>xt.has(wt.hood_id||this.getHoodIdFromSeqid(wt.seqid))),bt=this.getProteinPolygons().filter(wt=>wt.seqids?wt.seqids.every(St=>xt.has(this.getHoodIdFromSeqid(St))):!0),At=this.getNucleotidePolygons().filter(wt=>wt.seqids.every(St=>xt.has(this.getHoodIdFromSeqid(St)))),Ft=this.getAllDomains().filter(wt=>{const St=wt.geneId?this.genesById[wt.geneId]:null,Tt=St?.hood_id||this.getHoodIdFromSeqid(St?.seqid);return Tt?xt.has(Tt):!0}),Ct=Object.values(this.ncRNAsById).filter(wt=>xt.has(wt.hood_id||this.getHoodIdFromSeqid(wt.seqid)));return{genes:vt,proteinPolygons:bt,nucleotidePolygons:At,domains:Ft,ncRNAs:Ct}}getProteinPolygons(){const Et=[];for(let xt of this.proteinLinks){const vt=this.genesById[xt.gAId],bt=this.genesById[xt.gBId];if(!vt||!bt)continue;const At=xt.buildPolygon(vt,bt);At&&Et.push({polygon:At,fillColor:xt.fillColor,metadata:xt.metadata})}return Et}getNucleotidePolygons(){const Et=[],vt=(this.config.genome&&typeof this.config.genome.xScalePercent=="number"?this.config.genome.xScalePercent:100)/100,bt={};for(let At of this.leaves){if(!this.hoodToSeqidMap[At])continue;const Ct=this.hoodRanges[At],wt=this.trackOffset[At]||0,St=!!this.trackFlipped[At],Tt=Ct?(Ct.length||0)/2:0;bt[At]={anchor:Tt,flipped:St,offset:wt,xScale:vt}}for(let At of this.nucleotideLinks){const Ft=At.hoodA,Ct=At.hoodB;if(!Ft||!Ct)continue;const wt=this.getTrackYByHoodId(Ft),St=this.getTrackYByHoodId(Ct);if(wt==null||St==null)continue;const Tt=bt[Ft],Rt=bt[Ct];if(!Tt||!Rt)continue;let Pt=GenomeView.getTransformedXUnified(At.hoodStartA||0,Tt.anchor,Tt.offset,Tt.flipped),Lt=GenomeView.getTransformedXUnified(At.hoodEndA||0,Tt.anchor,Tt.offset,Tt.flipped),kt=GenomeView.getTransformedXUnified(At.hoodStartB||0,Rt.anchor,Rt.offset,Rt.flipped),Ot=GenomeView.getTransformedXUnified(At.hoodEndB||0,Rt.anchor,Rt.offset,Rt.flipped);Pt=Tt.anchor+(Pt-Tt.anchor)*Tt.xScale,Lt=Tt.anchor+(Lt-Tt.anchor)*Tt.xScale,kt=Rt.anchor+(kt-Rt.anchor)*Rt.xScale,Ot=Rt.anchor+(Ot-Rt.anchor)*Rt.xScale;const Mt=At.buildPolygonFromCoords(Pt,Lt,kt,Ot,wt,St);Et.push({polygon:Mt,fillColor:At.fillColor,metadata:At.metadata,seqids:[At.seqidA,At.seqidB]})}return Et}getAllDomains(){if(this._cachedAllDomains!==void 0)return this._cachedAllDomains;const Et=[];let xt=0,vt=0;for(const bt in this.genesById){const At=this.genesById[bt];for(let Ft of At.domains){xt++;let Ct=Ft.polygon;Array.isArray(Ct)&&Ct.length===1&&Array.isArray(Ct[0])&&(Ct=Ct[0]),isValidPolygon(Ct)&&(vt++,Et.push({polygon:Ct,fillColor:Ft.fillColor,domainName:Ft.domainName,metadata:Ft.metadata,geneId:Ft.geneId}))}}try{typeof window<"u"&&window.__hoodini_debug&&console.debug(`GenomeView.getAllDomains: total=${xt}, valid=${vt}`)}catch{}return this._cachedAllDomains=Et,Et}getAllNcRNAs(){return Object.values(this.ncRNAsById)}getAllRegions(){return Object.values(this.regionsById)}getAllNonCodingFeatures(){return this.getAllNcRNAs()}getRegionPolygons(){const Et=[];for(const xt of Object.values(this.regionsById))xt.polygon&&Array.isArray(xt.polygon)&&xt.polygon.length>0&&Et.push({polygon:xt.polygon,fillColor:xt.getFillColor(),strokeColor:xt.getStrokeColor(),strokeWidth:xt.strokeWidth,metadata:xt.metadata});return Et}getNodeDescendantLeaves(Et){if(!Et)return[];function xt(vt){return vt.branchset.length===0&&vt.name?[vt.name]:vt.branchset.flatMap(xt)}return xt(Et)}buildScaleBar(){const Et=this.config?.layout?.scaleBarOffset??this.config?.layout?.padding??150,xt=this.tree.leafNodes[this.tree.leafNodes.length-1].x+Et;return[[{path:[[this.globalMin,xt],[this.globalMax,xt]],color:this.config?.colors?.black||[0,0,0,255]}],xt]}buildPhyloLabels(Et="after-tree"){const xt=this.config?.tree?.labelOffset||10,vt=this.config?.colors?.black||[10,10,10,255],bt=this.config?.text?.phyloLabelSize||14;return this.tree.leafNodes.map(At=>{let Ft;if(Et==="after-tracks"){const Ct=At.name;let wt=this._rightmostByHood.get(Ct);isFinite(wt)?wt+=xt:wt=At.y+xt,Ft=[wt,At.x]}else Ft=[At.y+xt,At.x];return{position:Ft,text:At.name,color:vt,size:bt,textAnchor:"start",leafNode:At}})}buildNodePoints(Et,xt){const vt=Et?new Set(this.getNodeDescendantLeaves(Et)):null,bt=this.config?.tree?.nodeRadius||DEFAULT_CONFIG$1.tree.nodeRadius;return this.tree.allNodes.map(At=>{const Ft=this.getNodeDescendantLeaves(At),Ct=!Et||Ft.some(St=>vt.has(St));let wt;if(At.branchset.length>0)wt=[0,0,0,255];else{const St=At.metadata||{};if(St[xt]){const Tt=String(St[xt]);let Rt=0;for(let Ot=0;Ot<Tt.length;++Ot)Rt=Tt.charCodeAt(Ot)+((Rt<<5)-Rt);const Pt=Rt>>0&255,Lt=Rt>>8&255,kt=Rt>>16&255;wt=[Math.abs(Pt),Math.abs(Lt),Math.abs(kt),255]}else wt=[100,100,100,255]}return Et&&!Ct&&(wt=this.fadeColor(wt,.1)),{id:At.id,node:At,position:[At.y,At.x],color:wt,radius:At.branchset.length>0?bt.internal:bt.leaf,metadata:At.metadata||{name:At.name,id:At.id}}})}buildEdgesWithMetadata(){return this.tree.buildEdges().map(Et=>({...Et,metadata:{source:Et.source?.name,target:Et.target?.name,branchLength:Et.source?.branchLength,id:Et.source?.id}}))}fadeColor(Et,xt){return[Et[0],Et[1],Et[2],Math.floor(Et[3]*xt)]}setProteinClusters(Et){if(!Et||Object.keys(Et).length===0){this.proteinClusters={},this._clusterSummary=null;return}this.proteinClusters={},this._genesIndexReady||this._buildGeneIndex();for(const bt of Object.keys(Et)){const At=Et[bt],Ft=At==null?null:String(At).trim(),Ct=this._genesByOriginalId.get(bt)||[];for(const wt of Ct)this.proteinClusters[wt]=Ft}if(this._clusterSummary=null,!this.clusterColors)return;const xt=this.genesById,vt=this.clusterColors;for(const bt in xt){const At=xt[bt],Ft=this.proteinClusters[bt];At.fillColor=Ft&&vt[Ft]?vt[Ft]:null,At.metadata||(At.metadata={}),At.metadata.clusterId=Ft||null}}setProteinClustersWithPalette(Et,xt=null){this.proteinClusters={},this._genesIndexReady||this._buildGeneIndex();for(const At in Et){const Ft=Et[At],Ct=Ft==null?null:String(Ft).trim(),wt=this._genesByOriginalId.get(At)||[];for(const St of wt)this.proteinClusters[St]=Ct}if(this._clusterSummary=null,!xt||!xt.enabled){for(const At in this.genesById){const Ft=this.genesById[At];Ft&&Ft.fillColor&&(Ft.fillColor=null)}this._paletteVersion++;return}this.clusterColors={};const vt=Array.from(new Set(Object.values(this.proteinClusters))).filter(At=>At!=null).sort((At,Ft)=>{const Ct=Number(At),wt=Number(Ft);return!isNaN(Ct)&&!isNaN(wt)?Ct-wt:String(At).localeCompare(String(Ft))});let bt=[];if(xt.name)try{bt=memoGetPalette(xt.name,Math.max(vt.length,xt.numColors||vt.length),xt.reverse||!1)}catch{bt=[]}if(bt.length===0&&(bt=vt.map((At,Ft)=>hslToRgb(Ft/vt.length,.6,.5).concat(255))),vt.forEach((At,Ft)=>{this.clusterColors[At]=bt[Ft%bt.length]}),xt.desaturateByPrevalence){const At=this.computeGenePrevalence("cluster");for(const Ft in this.clusterColors){const Ct=At.get(Ft)||0;this.clusterColors[Ft]=this._desaturateColorByPrevalence(this.clusterColors[Ft],Ct)}}this._clusterSummary=null;for(const At in this.genesById){const Ft=this.genesById[At],Ct=this.proteinClusters[At];Ft.fillColor=Ct&&this.clusterColors[Ct]?this.clusterColors[Ct]:null,Ft.metadata||(Ft.metadata={}),Ft.metadata.clusterId=Ct||null}this._paletteVersion++}computeGenePrevalence(Et="cluster"){const xt=Object.keys(this.hoodRanges).length;if(xt===0)return new Map;const vt=new Map;for(const At of Object.values(this.genesById)){if(!At.hood_id)continue;let Ft=null;if(Et==="cluster"?Ft=At.metadata?.cluster??At.metadata?.clusterId??At.cluster:Ft=At.metadata?.[Et],Ft==null||Ft==="")continue;const Ct=String(Ft);vt.has(Ct)||vt.set(Ct,new Set),vt.get(Ct).add(At.hood_id)}const bt=new Map;for(const[At,Ft]of vt){const Ct=Ft.size/xt;bt.set(At,Ct)}return bt}_desaturateColorByPrevalence(Et,xt){if(!Et||!Array.isArray(Et)||xt>=1)return Et;const[vt,bt,At,Ft=255]=Et,Ct=vt/255,wt=bt/255,St=At/255,Tt=Math.max(Ct,wt,St),Rt=Math.min(Ct,wt,St),Pt=Tt-Rt,Lt=(Tt+Rt)/2;let kt=0;Pt!==0&&(kt=Lt>.5?Pt/(2-Tt-Rt):Pt/(Tt+Rt));let Ot=0;Pt!==0&&(Tt===Ct?Ot=((wt-St)/Pt+(wt<St?6:0))/6:Tt===wt?Ot=((St-Ct)/Pt+2)/6:Ot=((Ct-wt)/Pt+4)/6);const Mt=1-xt,It=kt*(1-Mt*.8),Nt=(1-Math.abs(2*Lt-1))*It,Ut=Nt*(1-Math.abs(Ot*6%2-1)),jt=Lt-Nt/2;let Vt=0,zt=0,Ht=0;const Wt=Math.floor(Ot*6);return Wt===0?(Vt=Nt,zt=Ut,Ht=0):Wt===1?(Vt=Ut,zt=Nt,Ht=0):Wt===2?(Vt=0,zt=Nt,Ht=Ut):Wt===3?(Vt=0,zt=Ut,Ht=Nt):Wt===4?(Vt=Ut,zt=0,Ht=Nt):(Vt=Nt,zt=0,Ht=Ut),[Math.round((Vt+jt)*255),Math.round((zt+jt)*255),Math.round((Ht+jt)*255),Ft]}_transparentByPrevalence(Et,xt,vt=.1){if(!Et||!Array.isArray(Et))return Et;const[bt,At,Ft]=Et,Ct=Math.round(vt*255+xt*(255-vt*255));return[bt,At,Ft,Ct]}_computeClusterSummary(){const Et=this.proteinClusters||{},xt=Object.values(Et).reduce((bt,At)=>{const Ft=String(At);return bt[Ft]=(bt[Ft]||0)+1,bt},{}),vt=Object.entries(xt).map(([bt,At])=>({id:bt,size:Number(At),label:`Cluster ${bt} (${At} genes)`})).sort((bt,At)=>At.size-bt.size);return{items:vt,ids:vt.map(bt=>bt.id)}}getClusterSummary(){return this._clusterSummary?this._clusterSummary:(this._clusterSummary=this._computeClusterSummary(),this._clusterSummary)}setNcRNAColorsWithPalette(Et=null){const xt=Object.values(this.ncRNAsById);if(!Et||!Et.enabled){for(const Ct of xt)Ct.fillColor=this.config?.gene?.fillColor||[200,200,200,255];return}const vt=xt.filter(Ct=>{const wt=Ct.metadata&&Ct.metadata.type;return!isEmptyValue(wt)});if(vt.length===0)return;const bt=Array.from(new Set(vt.map(Ct=>normalizeKey(Ct.metadata.type))));let At=[];if(Et.name)try{At=memoGetPalette(Et.name,Math.max(bt.length,Et.numColors||bt.length),Et.reverse||!1)}catch{At=[]}At.length===0&&(At=bt.map((Ct,wt)=>{const St=wt/bt.length;return hslToRgb(St,.6,.5).concat(255)}));const Ft={};bt.forEach((Ct,wt)=>{Ft[Ct]=At[wt%At.length]});for(const Ct in this.ncRNAsById){const wt=this.ncRNAsById[Ct],St=wt.metadata&&wt.metadata.type;isEmptyValue(St)||(wt.fillColor=Ft[normalizeKey(St)])}}setRegionColorsWithPalette(Et=null){const xt=Object.values(this.regionsById);if(xt.length===0)return;if(!Et||!Et.enabled){for(const Ct of xt)Ct.fillColor=[0,0,0,0],Ct.strokeColor=[100,100,100,255];return}const vt=xt.map(Ct=>Ct.getColorKey()).map(Ct=>normalizeKey(Ct)).filter(Ct=>!isEmptyValue(Ct)),bt=[...new Set(vt)];if(bt.length===0)return;let At=[];if(Et.name)try{At=memoGetPalette(Et.name,Math.max(bt.length,Et.numColors||bt.length),Et.reverse||!1)}catch{At=[]}At.length===0&&(At=bt.map((Ct,wt)=>{const St=wt/bt.length;return hslToRgb(St,.6,.5).concat(255)}));const Ft={};bt.forEach((Ct,wt)=>{Ft[Ct]=At[wt%At.length]});for(const Ct in this.regionsById){const wt=this.regionsById[Ct],St=wt.getColorKey();isEmptyValue(St)||(wt.fillColor=Ft[normalizeKey(St)])}}toggleTrackFlip(Et){this.trackFlipped[Et]=!this.trackFlipped[Et]}flipTrack(Et){const xt=this.trackOffset[Et]||0,vt=this.getTrackAnchor(Et),At=!!this.trackFlipped[Et]?GenomeView.flipCoordinate(vt+xt,vt):vt+xt;this.trackFlipped[Et]=!this.trackFlipped[Et];const Ft=!!this.trackFlipped[Et];let Ct;Ft?Ct=vt-At:Ct=At-vt,this.trackOffset[Et]=Ct,this.computeTrackPositions()}flipTrackState(Et){this.trackFlipped[Et]=!this.trackFlipped[Et]}flipTrackStateWithCentering(Et){const xt=this.trackOffset[Et]||0,vt=this.getTrackAnchor(Et),At=!!this.trackFlipped[Et]?GenomeView.flipCoordinate(vt+xt,vt):vt+xt;this.trackFlipped[Et]=!this.trackFlipped[Et];const Ft=!!this.trackFlipped[Et];let Ct;Ft?Ct=vt-At:Ct=At-vt,this.trackOffset[Et]=Ct}shiftTrack(Et,xt){this.trackOffset[Et]||(this.trackOffset[Et]=0),this.trackFlipped[Et]&&(xt=-xt),this.trackOffset[Et]+=xt,this.computeTrackPositions()}shiftTrackPlus1kb(Et){this.shiftTrack(Et,1e3)}shiftTrackMinus1kb(Et){this.shiftTrack(Et,-1e3)}flipTrackToggle(Et){this.flipTrack(Et)}getTrackAnchor(Et){const xt=this.hoodToSeqidMap[Et];if(!xt)return 0;const vt=this.nucleotidesBySeqid[xt],bt=this.hoodRanges[Et];return bt?bt.length/2:vt&&vt.hood?(vt.hood.origEnd-vt.hood.origStart)/2:this.featuresBySeqid[xt]?(this.featuresBySeqid[xt].origMaxEnd-this.featuresBySeqid[xt].origMinStart)/2:0}alignCluster(Et){const xt=Et==null?null:String(Et).trim(),bt=(this.config.genome&&typeof this.config.genome.xScalePercent=="number"?this.config.genome.xScalePercent:100)/100,At=Object.entries(this.genesById).filter(([Tt,Rt])=>this.proteinClusters&&this.proteinClusters[Tt]===xt).map(([Tt,Rt])=>Rt);if(At.length===0)return;const Ft={};for(const Tt of At)(Ft[Tt.hood_id]||=[]).push(Tt);const Ct=[];for(const Tt in Ft){const Rt=Ft[Tt];Rt.sort((Pt,Lt)=>Pt.originalGeneId.localeCompare(Lt.originalGeneId)),Ct.push(Rt[0])}if(!Ct.length)return;Ct.sort((Tt,Rt)=>Tt.hood_id.localeCompare(Rt.hood_id)),Ct[0];for(const Tt of Ct){const Rt=Tt.hood_id;(!!this.trackFlipped[Rt]?Tt.origStrand==="+"?"-":"+":Tt.origStrand)==="-"&&this.flipTrackStateWithCentering(Rt)}this.computeTrackPositions();const wt=0;for(const Tt of Ct){const Rt=Tt.hood_id,Pt=GenomeView.getGeneVisualX(Tt,this);if(Pt===null)continue;let Lt=(wt-Pt)/bt;this.trackFlipped[Rt]&&(Lt=-Lt);const Ot=this.trackOffset[Rt]||0;this.trackOffset[Rt]=Ot+Lt}const St=new Set(Ct.map(Tt=>Tt.hood_id));for(const Tt of this.leaves){if(St.has(Tt))continue;const Rt=this.hoodRanges[Tt],Pt=this.hoodToSeqidMap[Tt],Lt=this.nucleotidesBySeqid[Pt];if(!Rt&&!Lt?.hood)continue;const kt=Rt?Rt.length/2:(Lt.hood.origEnd-Lt.hood.origStart)/2,Mt=!!this.trackFlipped[Tt]?-1:1,It=(wt-kt)/(Mt*bt);this.trackOffset[Tt]=It}this.computeTrackPositions()}alignAllToStart(){const Et=this.config.genome&&typeof this.config.genome.xScalePercent=="number"?this.config.genome.xScalePercent:100,xt=Et/100;for(const vt of this.leaves){this.trackFlipped[vt]=!1;const bt=this.hoodToSeqidMap[vt];if(!bt)continue;const At=this.nucleotidesBySeqid[bt];if(At?.hood){const wt=(this.hoodRanges[vt]?.length||At.hood.origEnd-At.hood.origStart||0)/2;this.trackOffset[vt]=wt*(1-1/xt)}}this.computeTrackPositions();try{if(this.config?.debug?.alignment){const bt=[],At=[];console.debug(`[GenomeView] alignAllToStart xScale=${Et}`);for(const Tt of this.leaves){const Rt=this.hoodToSeqidMap[Tt],Pt=Rt?this.nucleotidesBySeqid[Rt]:null,Lt=!!this.trackFlipped[Tt],kt=this.trackOffset[Tt]||0,Mt=this.hoodRanges[Tt]?.length||(Pt?.hood?Pt.hood.origEnd-Pt.hood.origStart:0)||0,It=Pt?.hood?.start,Nt=Pt?.hood?.end;typeof It=="number"&&isFinite(It)&&bt.push([Tt,It]),typeof Nt=="number"&&isFinite(Nt)&&At.push([Tt,Nt]),console.debug(`[start] hood=${Tt} flipped=${Lt} len=${Mt} offset=${kt} baseline=(${It??"n/a"}, ${Nt??"n/a"})`)}bt.sort((Tt,Rt)=>Tt[1]-Rt[1]),At.sort((Tt,Rt)=>Tt[1]-Rt[1]);const Ft=bt[0]?.[1],Ct=bt[0]?.[0],wt=At[At.length-1]?.[1],St=At[At.length-1]?.[0];console.debug(`[start] baselineMinStart=${Ft} (hood=${Ct}) baselineMaxEnd=${wt} (hood=${St})`),console.debug(`[start] global bounds: minX=${this.globalMin} maxX=${this.globalMax}`)}}catch{}}alignAllToEnd(){const xt=(this.config.genome&&typeof this.config.genome.xScalePercent=="number"?this.config.genome.xScalePercent:100)/100;for(const vt of this.leaves){this.trackFlipped[vt]=!1;const bt=this.hoodToSeqidMap[vt];if(!bt)continue;const At=this.nucleotidesBySeqid[bt];if(At?.hood){const wt=(this.hoodRanges[vt]?.length||At.hood.origEnd-At.hood.origStart||0)/2;this.trackOffset[vt]=-wt*(1+1/xt)}}this.computeTrackPositions()}alignAllToCenter(){const Et=this.config.genome&&typeof this.config.genome.xScalePercent=="number"?this.config.genome.xScalePercent:100,xt=Et/100;for(const vt of this.leaves){this.trackFlipped[vt]=!1;const bt=this.hoodToSeqidMap[vt];if(!bt)continue;const At=this.nucleotidesBySeqid[bt];if(At?.hood){const wt=(this.hoodRanges[vt]?.length||At.hood.origEnd-At.hood.origStart||0)/2;this.trackOffset[vt]=-wt/xt}}this.computeTrackPositions();try{if(this.config?.debug?.alignment){const bt=[],At=[];console.debug(`[GenomeView] alignAllToCenter xScale=${Et}`);for(const Tt of this.leaves){const Rt=this.hoodToSeqidMap[Tt],Pt=Rt?this.nucleotidesBySeqid[Rt]:null,Lt=!!this.trackFlipped[Tt],kt=this.trackOffset[Tt]||0,Mt=this.hoodRanges[Tt]?.length||(Pt?.hood?Pt.hood.origEnd-Pt.hood.origStart:0)||0,It=Pt?.hood?.start,Nt=Pt?.hood?.end;typeof It=="number"&&isFinite(It)&&bt.push([Tt,It]),typeof Nt=="number"&&isFinite(Nt)&&At.push([Tt,Nt]),console.debug(`[center] hood=${Tt} flipped=${Lt} len=${Mt} offset=${kt} baseline=(${It??"n/a"}, ${Nt??"n/a"})`)}bt.sort((Tt,Rt)=>Tt[1]-Rt[1]),At.sort((Tt,Rt)=>Tt[1]-Rt[1]);const Ft=bt[0]?.[1],Ct=bt[0]?.[0],wt=At[At.length-1]?.[1],St=At[At.length-1]?.[0];console.debug(`[center] baselineMinStart=${Ft} (hood=${Ct}) baselineMaxEnd=${wt} (hood=${St})`),console.debug(`[center] global bounds: minX=${this.globalMin} maxX=${this.globalMax}`)}}catch{}}applyHoods(Et){const xt=new Set(this.leaves.map(bt=>String(bt))),vt=[];for(const bt of Et){const At=bt.hood_id!=null?String(bt.hood_id).trim():null,Ft=bt.seqid!=null?String(bt.seqid).trim():null;let Ct=null;At&&xt.has(At)?Ct=At:Ft&&xt.has(Ft)&&(Ct=Ft),Ct&&(bt.hood_id=Ct,vt.push(bt))}for(const bt of vt)bt.hood_id&&bt.seqid&&(this.hoodToSeqidMap[bt.hood_id]=bt.seqid,(this.seqidToHoodsMap[bt.seqid]||=[]).push(bt.hood_id),this.hoodRanges[bt.hood_id]={seqid:bt.seqid,origStart:bt.start,origEnd:bt.end,start:bt.start,end:bt.end,length:bt.end-bt.start,align_gene:bt.align_gene}),this.nucleotidesBySeqid[bt.seqid]&&this.nucleotidesBySeqid[bt.seqid].setHood(bt.start,bt.end);this._buildHoodIntervalIndex()}getHoodIdsFromSeqid(Et){return this.seqidToHoodsMap[Et]||[Et]}getHoodIdFromSeqid(Et){return this.getHoodIdsFromSeqid(Et)[0]}getSeqidFromHoodId(Et){return this.hoodToSeqidMap[Et]||Et}alignByDefaultGenes(){const xt=(this.config.genome&&typeof this.config.genome.xScalePercent=="number"?this.config.genome.xScalePercent:100)/100,vt=[];for(const Ft of this.leaves){const Ct=this.hoodRanges[Ft];if(!Ct?.align_gene)continue;const wt=`${Ft}_${Ct.align_gene}`,St=this.genesById[wt];St&&vt.push(St)}if(!vt.length)return;vt.sort((Ft,Ct)=>Ft.hood_id.localeCompare(Ct.hood_id));const bt=0;for(const Ft of vt){const Ct=Ft.hood_id;(!!this.trackFlipped[Ct]?Ft.origStrand==="+"?"-":"+":Ft.origStrand)==="-"&&this.flipTrackStateWithCentering(Ct)}this.computeTrackPositions();for(const Ft of vt){const Ct=Ft.hood_id,wt=GenomeView.getGeneVisualX(Ft,this);if(wt===null)continue;const St=bt-wt,Rt=(!!this.trackFlipped[Ct]?-1:1)*(St/xt),Pt=this.trackOffset[Ct]||0;this.trackOffset[Ct]=Pt+Rt}const At=new Set(vt.map(Ft=>Ft.hood_id));for(const Ft of this.leaves){if(At.has(Ft))continue;const Ct=this.hoodToSeqidMap[Ft];if(!Ct)continue;const wt=this.nucleotidesBySeqid[Ct];if(wt?.hood){const St=this.hoodRanges[Ft],Tt=St?St.length/2:(wt.hood.origEnd-wt.hood.origStart)/2,Pt=!!this.trackFlipped[Ft]?-1:1,Lt=(bt-Tt)/(Pt*xt);this.trackOffset[Ft]=Lt}}this.computeTrackPositions()}applyDomainPalette(Et=null){if(this._cachedAllDomains=void 0,!Et||!Et.enabled){for(const Ft of Object.values(this.genesById))for(const Ct of Ft.domains)Ct&&Ct.fillColor&&(Ct.fillColor=null);this._paletteVersion++;return}const xt=new Set;for(const Ft of Object.values(this.genesById))for(const Ct of Ft.domains)xt.add(Ct.domainName);const vt=Array.from(xt).sort();let bt=[];if(Et.name)try{bt=memoGetPalette(Et.name,Math.max(vt.length,Et.numColors||vt.length),Et.reverse||!1)}catch{bt=[]}const At={};vt.forEach((Ft,Ct)=>{At[Ft]=bt[Ct%bt.length]});for(const Ft of Object.values(this.genesById))for(const Ct of Ft.domains)Ct.fillColor=At[Ct.domainName]||[128,128,128,255]}}function hslToRgb(yt,Et,xt){let vt,bt,At;{const Ft=(St,Tt,Rt)=>(Rt<0&&(Rt+=1),Rt>1&&(Rt-=1),Rt<.16666666666666666?St+(Tt-St)*6*Rt:Rt<.5?Tt:Rt<.6666666666666666?St+(Tt-St)*(.6666666666666666-Rt)*6:St),Ct=xt+Et-xt*Et,wt=2*xt-Ct;vt=Ft(wt,Ct,yt+1/3),bt=Ft(wt,Ct,yt),At=Ft(wt,Ct,yt-1/3)}return[Math.round(vt*255),Math.round(bt*255),Math.round(At*255)]}function isValidPolygon(yt){if(!Array.isArray(yt)||yt.length<3)return!1;const[Et,xt]=yt[0];return!yt.every(([vt,bt])=>vt===Et&&bt===xt)}function assert$7(yt,Et){if(!yt)throw new Error(Et||"loader assertion failed.")}const isBrowser$2=!!(typeof process!="object"||String(process)!=="[object process]"||process.browser),matches$1=typeof process<"u"&&process.version&&/v([0-9]*)/.exec(process.version);matches$1&&parseFloat(matches$1[1]);const window_=globalThis,process_=globalThis.process||{},navigator_=globalThis.navigator||{};function isElectron(yt){if(typeof window<"u"&&window.process?.type==="renderer"||typeof process<"u"&&process.versions?.electron)return!0;const xt=typeof navigator<"u"&&navigator.userAgent;return!!(xt&&xt.indexOf("Electron")>=0)}function isBrowser$1(){return!(typeof process=="object"&&String(process)==="[object process]"&&!process?.browser)||isElectron()}function getBrowser(yt){return isBrowser$1()?isElectron()?"Electron":(navigator_.userAgent||"").indexOf("Edge")>-1?"Edge":globalThis.chrome?"Chrome":globalThis.safari?"Safari":globalThis.mozInnerScreenX?"Firefox":"Unknown":"Node"}const VERSION$4="4.1.0";function getStorage(yt){try{const Et=window[yt],xt="__storage_test__";return Et.setItem(xt,xt),Et.removeItem(xt),Et}catch{return null}}class LocalStorage{constructor(Et,xt,vt="sessionStorage"){this.storage=getStorage(vt),this.id=Et,this.config=xt,this._loadConfiguration()}getConfiguration(){return this.config}setConfiguration(Et){if(Object.assign(this.config,Et),this.storage){const xt=JSON.stringify(this.config);this.storage.setItem(this.id,xt)}}_loadConfiguration(){let Et={};if(this.storage){const xt=this.storage.getItem(this.id);Et=xt?JSON.parse(xt):{}}return Object.assign(this.config,Et),this}}function formatTime(yt){let Et;return yt<10?Et=`${yt.toFixed(2)}ms`:yt<100?Et=`${yt.toFixed(1)}ms`:yt<1e3?Et=`${yt.toFixed(0)}ms`:Et=`${(yt/1e3).toFixed(2)}s`,Et}function leftPad(yt,Et=8){const xt=Math.max(Et-yt.length,0);return`${" ".repeat(xt)}${yt}`}var COLOR;(function(yt){yt[yt.BLACK=30]="BLACK",yt[yt.RED=31]="RED",yt[yt.GREEN=32]="GREEN",yt[yt.YELLOW=33]="YELLOW",yt[yt.BLUE=34]="BLUE",yt[yt.MAGENTA=35]="MAGENTA",yt[yt.CYAN=36]="CYAN",yt[yt.WHITE=37]="WHITE",yt[yt.BRIGHT_BLACK=90]="BRIGHT_BLACK",yt[yt.BRIGHT_RED=91]="BRIGHT_RED",yt[yt.BRIGHT_GREEN=92]="BRIGHT_GREEN",yt[yt.BRIGHT_YELLOW=93]="BRIGHT_YELLOW",yt[yt.BRIGHT_BLUE=94]="BRIGHT_BLUE",yt[yt.BRIGHT_MAGENTA=95]="BRIGHT_MAGENTA",yt[yt.BRIGHT_CYAN=96]="BRIGHT_CYAN",yt[yt.BRIGHT_WHITE=97]="BRIGHT_WHITE"})(COLOR||(COLOR={}));const BACKGROUND_INCREMENT=10;function getColor(yt){return typeof yt!="string"?yt:(yt=yt.toUpperCase(),COLOR[yt]||COLOR.WHITE)}function addColor(yt,Et,xt){return!isBrowser$1&&typeof yt=="string"&&(Et&&(yt=`\x1B[${getColor(Et)}m${yt}\x1B[39m`),xt&&(yt=`\x1B[${getColor(xt)+BACKGROUND_INCREMENT}m${yt}\x1B[49m`)),yt}function autobind(yt,Et=["constructor"]){const xt=Object.getPrototypeOf(yt),vt=Object.getOwnPropertyNames(xt),bt=yt;for(const At of vt){const Ft=bt[At];typeof Ft=="function"&&(Et.find(Ct=>At===Ct)||(bt[At]=Ft.bind(yt)))}}function assert$6(yt,Et){if(!yt)throw new Error("Assertion failed")}function getHiResTimestamp$1(){let yt;if(isBrowser$1()&&window_.performance)yt=window_?.performance?.now?.();else if("hrtime"in process_){const Et=process_?.hrtime?.();yt=Et[0]*1e3+Et[1]/1e6}else yt=Date.now();return yt}const originalConsole={debug:isBrowser$1()&&console.debug||console.log,log:console.log,info:console.info,warn:console.warn,error:console.error},DEFAULT_LOG_CONFIGURATION={enabled:!0,level:0};function noop$4(){}const cache$2={},ONCE={once:!0};class Log{constructor({id:Et}={id:""}){this.VERSION=VERSION$4,this._startTs=getHiResTimestamp$1(),this._deltaTs=getHiResTimestamp$1(),this.userData={},this.LOG_THROTTLE_TIMEOUT=0,this.id=Et,this.userData={},this._storage=new LocalStorage(`__probe-${this.id}__`,DEFAULT_LOG_CONFIGURATION),this.timeStamp(`${this.id} started`),autobind(this),Object.seal(this)}set level(Et){this.setLevel(Et)}get level(){return this.getLevel()}isEnabled(){return this._storage.config.enabled}getLevel(){return this._storage.config.level}getTotal(){return Number((getHiResTimestamp$1()-this._startTs).toPrecision(10))}getDelta(){return Number((getHiResTimestamp$1()-this._deltaTs).toPrecision(10))}set priority(Et){this.level=Et}get priority(){return this.level}getPriority(){return this.level}enable(Et=!0){return this._storage.setConfiguration({enabled:Et}),this}setLevel(Et){return this._storage.setConfiguration({level:Et}),this}get(Et){return this._storage.config[Et]}set(Et,xt){this._storage.setConfiguration({[Et]:xt})}settings(){console.table?console.table(this._storage.config):console.log(this._storage.config)}assert(Et,xt){if(!Et)throw new Error(xt||"Assertion failed")}warn(Et){return this._getLogFunction(0,Et,originalConsole.warn,arguments,ONCE)}error(Et){return this._getLogFunction(0,Et,originalConsole.error,arguments)}deprecated(Et,xt){return this.warn(`\`${Et}\` is deprecated and will be removed in a later version. Use \`${xt}\` instead`)}removed(Et,xt){return this.error(`\`${Et}\` has been removed. Use \`${xt}\` instead`)}probe(Et,xt){return this._getLogFunction(Et,xt,originalConsole.log,arguments,{time:!0,once:!0})}log(Et,xt){return this._getLogFunction(Et,xt,originalConsole.debug,arguments)}info(Et,xt){return this._getLogFunction(Et,xt,console.info,arguments)}once(Et,xt){return this._getLogFunction(Et,xt,originalConsole.debug||originalConsole.info,arguments,ONCE)}table(Et,xt,vt){return xt?this._getLogFunction(Et,xt,console.table||noop$4,vt&&[vt],{tag:getTableHeader(xt)}):noop$4}time(Et,xt){return this._getLogFunction(Et,xt,console.time?console.time:console.info)}timeEnd(Et,xt){return this._getLogFunction(Et,xt,console.timeEnd?console.timeEnd:console.info)}timeStamp(Et,xt){return this._getLogFunction(Et,xt,console.timeStamp||noop$4)}group(Et,xt,vt={collapsed:!1}){const bt=normalizeArguments({logLevel:Et,message:xt,opts:vt}),{collapsed:At}=vt;return bt.method=(At?console.groupCollapsed:console.group)||console.info,this._getLogFunction(bt)}groupCollapsed(Et,xt,vt={}){return this.group(Et,xt,Object.assign({},vt,{collapsed:!0}))}groupEnd(Et){return this._getLogFunction(Et,"",console.groupEnd||noop$4)}withGroup(Et,xt,vt){this.group(Et,xt)();try{vt()}finally{this.groupEnd(Et)()}}trace(){console.trace&&console.trace()}_shouldLog(Et){return this.isEnabled()&&this.getLevel()>=normalizeLogLevel(Et)}_getLogFunction(Et,xt,vt,bt,At){if(this._shouldLog(Et)){At=normalizeArguments({logLevel:Et,message:xt,args:bt,opts:At}),vt=vt||At.method,assert$6(vt),At.total=this.getTotal(),At.delta=this.getDelta(),this._deltaTs=getHiResTimestamp$1();const Ft=At.tag||At.message;if(At.once&&Ft)if(!cache$2[Ft])cache$2[Ft]=getHiResTimestamp$1();else return noop$4;return xt=decorateMessage(this.id,At.message,At),vt.bind(console,xt,...At.args)}return noop$4}}Log.VERSION=VERSION$4;function normalizeLogLevel(yt){if(!yt)return 0;let Et;switch(typeof yt){case"number":Et=yt;break;case"object":Et=yt.logLevel||yt.priority||0;break;default:return 0}return assert$6(Number.isFinite(Et)&&Et>=0),Et}function normalizeArguments(yt){const{logLevel:Et,message:xt}=yt;yt.logLevel=normalizeLogLevel(Et);const vt=yt.args?Array.from(yt.args):[];for(;vt.length&&vt.shift()!==xt;);switch(typeof Et){case"string":case"function":xt!==void 0&&vt.unshift(xt),yt.message=Et;break;case"object":Object.assign(yt,Et);break}typeof yt.message=="function"&&(yt.message=yt.message());const bt=typeof yt.message;return assert$6(bt==="string"||bt==="object"),Object.assign(yt,{args:vt},yt.opts)}function decorateMessage(yt,Et,xt){if(typeof Et=="string"){const vt=xt.time?leftPad(formatTime(xt.total)):"";Et=xt.time?`${yt}: ${vt}  ${Et}`:`${yt}: ${Et}`,Et=addColor(Et,xt.color,xt.background)}return Et}function getTableHeader(yt){for(const Et in yt)for(const xt in yt[Et])return xt||"untitled";return"empty"}const VERSION$3="4.3.3",version=VERSION$3[0]>="0"&&VERSION$3[0]<="9"?`v${VERSION$3}`:"";function createLog(){const yt=new Log({id:"loaders.gl"});return globalThis.loaders=globalThis.loaders||{},globalThis.loaders.log=yt,globalThis.loaders.version=version,globalThis.probe=globalThis.probe||{},globalThis.probe.loaders=yt,yt}const log$1=createLog();function mergeLoaderOptions(yt,Et){return mergeOptionsRecursively(yt||{},Et)}function mergeOptionsRecursively(yt,Et,xt=0){if(xt>3)return Et;const vt={...yt};for(const[bt,At]of Object.entries(Et))At&&typeof At=="object"&&!Array.isArray(At)?vt[bt]=mergeOptionsRecursively(vt[bt]||{},Et[bt],xt+1):vt[bt]=Et[bt];return vt}const NPM_TAG="latest";function getVersion(){return globalThis._loadersgl_?.version||(globalThis._loadersgl_=globalThis._loadersgl_||{},globalThis._loadersgl_.version="4.3.3"),globalThis._loadersgl_.version}const VERSION$2=getVersion();function assert$5(yt,Et){if(!yt)throw new Error(Et||"loaders.gl assertion failed.")}const isBrowser=typeof process!="object"||String(process)!=="[object process]"||process.browser,isMobile=typeof window<"u"&&typeof window.orientation<"u",matches=typeof process<"u"&&process.version&&/v([0-9]*)/.exec(process.version);matches&&parseFloat(matches[1]);class WorkerJob{name;workerThread;isRunning=!0;result;_resolve=()=>{};_reject=()=>{};constructor(Et,xt){this.name=Et,this.workerThread=xt,this.result=new Promise((vt,bt)=>{this._resolve=vt,this._reject=bt})}postMessage(Et,xt){this.workerThread.postMessage({source:"loaders.gl",type:Et,payload:xt})}done(Et){assert$5(this.isRunning),this.isRunning=!1,this._resolve(Et)}error(Et){assert$5(this.isRunning),this.isRunning=!1,this._reject(Et)}}class NodeWorker{terminate(){}}const workerURLCache=new Map;function getLoadableWorkerURL(yt){assert$5(yt.source&&!yt.url||!yt.source&&yt.url);let Et=workerURLCache.get(yt.source||yt.url);return Et||(yt.url&&(Et=getLoadableWorkerURLFromURL(yt.url),workerURLCache.set(yt.url,Et)),yt.source&&(Et=getLoadableWorkerURLFromSource(yt.source),workerURLCache.set(yt.source,Et))),assert$5(Et),Et}function getLoadableWorkerURLFromURL(yt){if(!yt.startsWith("http"))return yt;const Et=buildScriptSource(yt);return getLoadableWorkerURLFromSource(Et)}function getLoadableWorkerURLFromSource(yt){const Et=new Blob([yt],{type:"application/javascript"});return URL.createObjectURL(Et)}function buildScriptSource(yt){return`try {
   importScripts('${yt}');
 } catch (error) {
   console.error(error);