geneviewer-js 0.3.1 → 0.3.3

package/dist/geneviewer.standalone.mjs

@@ -1,8 +1,8 @@
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this._triangles[s]=e,this._triangles[s+1]=n,this._triangles[s+2]=r,this._link(s,i),this._link(s+1,o),this._link(s+2,a),this.trianglesLen+=3,s}};function j_(t,e){let n=t/(Math.abs(t)+Math.abs(e));return(e>0?3-n:1+n)/4}function Bu(t,e,n,r){let i=t-n,o=e-r;return i*i+o*o}function X_(t,e,n,r,i,o,a,s){let c=t-a,l=e-s,u=n-a,h=r-s,f=i-a,d=o-s,m=c*c+l*l,p=u*u+h*h,g=f*f+d*d;return c*(h*g-p*d)-l*(u*g-p*f)+m*(u*d-h*f)<0}function G_(t,e,n,r,i,o){let a=n-t,s=r-e,c=i-t,l=o-e,u=a*a+s*s,h=c*c+l*l,f=.5/(a*l-s*c),d=(l*u-s*h)*f,m=(a*h-c*u)*f;return d*d+m*m}function V_(t,e,n,r,i,o){let a=n-t,s=r-e,c=i-t,l=o-e,u=a*a+s*s,h=c*c+l*l,f=.5/(a*l-s*c),d=t+(l*u-s*h)*f,m=e+(a*h-c*u)*f;return{x:d,y:m}}function Mi(t,e,n,r){if(r-n<=20)for(let i=n+1;i<=r;i++){let o=t[i],a=e[o],s=i-1;for(;s>=n&&e[t[s]]>a;)t[s+1]=t[s--];t[s+1]=o}else{let i=n+r>>1,o=n+1,a=r;Eo(t,i,o),e[t[n]]>e[t[r]]&&Eo(t,n,r),e[t[o]]>e[t[r]]&&Eo(t,o,r),e[t[n]]>e[t[o]]&&Eo(t,n,o);let s=t[o],c=e[s];for(;;){do o++;while(e[t[o]]<c);do a--;while(e[t[a]]>c);if(a<o)break;Eo(t,o,a)}t[n+1]=t[a],t[a]=s,r-o+1>=a-n?(Mi(t,e,o,r),Mi(t,e,n,a-1)):(Mi(t,e,n,a-1),Mi(t,e,o,r))}}function Eo(t,e,n){let r=t[e];t[e]=t[n],t[n]=r}function Z_(t){return t[0]}function K_(t){return t[1]}var Ap=1e-6,Rn=class{constructor(){this._x0=this._y0=this._x1=this._y1=null,this._=""}moveTo(e,n){this._+=`M${this._x0=this._x1=+e},${this._y0=this._y1=+n}`}closePath(){this._x1!==null&&(this._x1=this._x0,this._y1=this._y0,this._+="Z")}lineTo(e,n){this._+=`L${this._x1=+e},${this._y1=+n}`}arc(e,n,r){e=+e,n=+n,r=+r;let i=e+r,o=n;if(r<0)throw new Error("negative radius");this._x1===null?this._+=`M${i},${o}`:(Math.abs(this._x1-i)>Ap||Math.abs(this._y1-o)>Ap)&&(this._+="L"+i+","+o),r&&(this._+=`A${r},${r},0,1,1,${e-r},${n}A${r},${r},0,1,1,${this._x1=i},${this._y1=o}`)}rect(e,n,r,i){this._+=`M${this._x0=this._x1=+e},${this._y0=this._y1=+n}h${+r}v${+i}h${-r}Z`}value(){return this._||null}},Mo=class{constructor(){this._=[]}moveTo(e,n){this._.push([e,n])}closePath(){this._.push(this._[0].slice())}lineTo(e,n){this._.push([e,n])}value(){return this._.length?this._:null}},Bs=class{constructor(e,[n,r,i,o]=[0,0,960,500]){if(!((i=+i)>=(n=+n))||!((o=+o)>=(r=+r)))throw new Error("invalid bounds");this.delaunay=e,this._circumcenters=new Float64Array(e.points.length*2),this.vectors=new Float64Array(e.points.length*2),this.xmax=i,this.xmin=n,this.ymax=o,this.ymin=r,this._init()}update(){return this.delaunay.update(),this._init(),this}_init(){let{delaunay:{points:e,hull:n,triangles:r},vectors:i}=this,o,a,s=this.circumcenters=this._circumcenters.subarray(0,r.length/3*2);for(let p=0,g=0,y=r.length,w,b;p<y;p+=3,g+=2){let v=r[p]*2,_=r[p+1]*2,S=r[p+2]*2,k=e[v],C=e[v+1],F=e[_],A=e[_+1],E=e[S],D=e[S+1],z=F-k,M=A-C,T=E-k,B=D-C,N=(z*B-M*T)*2;if(Math.abs(N)<1e-9){if(o===void 0){o=a=0;for(let q of n)o+=e[q*2],a+=e[q*2+1];o/=n.length,a/=n.length}let L=1e9*Math.sign((o-k)*B-(a-C)*T);w=(k+E)/2-L*B,b=(C+D)/2+L*T}else{let L=1/N,q=z*z+M*M,U=T*T+B*B;w=k+(B*q-M*U)*L,b=C+(z*U-T*q)*L}s[g]=w,s[g+1]=b}let c=n[n.length-1],l,u=c*4,h,f=e[2*c],d,m=e[2*c+1];i.fill(0);for(let p=0;p<n.length;++p)c=n[p],l=u,h=f,d=m,u=c*4,f=e[2*c],m=e[2*c+1],i[l+2]=i[u]=d-m,i[l+3]=i[u+1]=f-h}render(e){let n=e==null?e=new Rn:void 0,{delaunay:{halfedges:r,inedges:i,hull:o},circumcenters:a,vectors:s}=this;if(o.length<=1)return null;for(let u=0,h=r.length;u<h;++u){let f=r[u];if(f<u)continue;let d=Math.floor(u/3)*2,m=Math.floor(f/3)*2,p=a[d],g=a[d+1],y=a[m],w=a[m+1];this._renderSegment(p,g,y,w,e)}let c,l=o[o.length-1];for(let u=0;u<o.length;++u){c=l,l=o[u];let h=Math.floor(i[l]/3)*2,f=a[h],d=a[h+1],m=c*4,p=this._project(f,d,s[m+2],s[m+3]);p&&this._renderSegment(f,d,p[0],p[1],e)}return n&&n.value()}renderBounds(e){let n=e==null?e=new Rn:void 0;return e.rect(this.xmin,this.ymin,this.xmax-this.xmin,this.ymax-this.ymin),n&&n.value()}renderCell(e,n){let r=n==null?n=new Rn:void 0,i=this._clip(e);if(i===null||!i.length)return;n.moveTo(i[0],i[1]);let o=i.length;for(;i[0]===i[o-2]&&i[1]===i[o-1]&&o>1;)o-=2;for(let a=2;a<o;a+=2)(i[a]!==i[a-2]||i[a+1]!==i[a-1])&&n.lineTo(i[a],i[a+1]);return n.closePath(),r&&r.value()}*cellPolygons(){let{delaunay:{points:e}}=this;for(let n=0,r=e.length/2;n<r;++n){let i=this.cellPolygon(n);i&&(i.index=n,yield i)}}cellPolygon(e){let n=new Mo;return this.renderCell(e,n),n.value()}_renderSegment(e,n,r,i,o){let a,s=this._regioncode(e,n),c=this._regioncode(r,i);s===0&&c===0?(o.moveTo(e,n),o.lineTo(r,i)):(a=this._clipSegment(e,n,r,i,s,c))&&(o.moveTo(a[0],a[1]),o.lineTo(a[2],a[3]))}contains(e,n,r){return n=+n,n!==n||(r=+r,r!==r)?!1:this.delaunay._step(e,n,r)===e}*neighbors(e){let n=this._clip(e);if(n)for(let r of this.delaunay.neighbors(e)){let i=this._clip(r);if(i){t:for(let o=0,a=n.length;o<a;o+=2)for(let s=0,c=i.length;s<c;s+=2)if(n[o]===i[s]&&n[o+1]===i[s+1]&&n[(o+2)%a]===i[(s+c-2)%c]&&n[(o+3)%a]===i[(s+c-1)%c]){yield r;break t}}}}_cell(e){let{circumcenters:n,delaunay:{inedges:r,halfedges:i,triangles:o}}=this,a=r[e];if(a===-1)return null;let s=[],c=a;do{let l=Math.floor(c/3);if(s.push(n[l*2],n[l*2+1]),c=c%3===2?c-2:c+1,o[c]!==e)break;c=i[c]}while(c!==a&&c!==-1);return s}_clip(e){if(e===0&&this.delaunay.hull.length===1)return[this.xmax,this.ymin,this.xmax,this.ymax,this.xmin,this.ymax,this.xmin,this.ymin];let n=this._cell(e);if(n===null)return null;let{vectors:r}=this,i=e*4;return this._simplify(r[i]||r[i+1]?this._clipInfinite(e,n,r[i],r[i+1],r[i+2],r[i+3]):this._clipFinite(e,n))}_clipFinite(e,n){let r=n.length,i=null,o,a,s=n[r-2],c=n[r-1],l,u=this._regioncode(s,c),h,f=0;for(let d=0;d<r;d+=2)if(o=s,a=c,s=n[d],c=n[d+1],l=u,u=this._regioncode(s,c),l===0&&u===0)h=f,f=0,i?i.push(s,c):i=[s,c];else{let m,p,g,y,w;if(l===0){if((m=this._clipSegment(o,a,s,c,l,u))===null)continue;[p,g,y,w]=m}else{if((m=this._clipSegment(s,c,o,a,u,l))===null)continue;[y,w,p,g]=m,h=f,f=this._edgecode(p,g),h&&f&&this._edge(e,h,f,i,i.length),i?i.push(p,g):i=[p,g]}h=f,f=this._edgecode(y,w),h&&f&&this._edge(e,h,f,i,i.length),i?i.push(y,w):i=[y,w]}if(i)h=f,f=this._edgecode(i[0],i[1]),h&&f&&this._edge(e,h,f,i,i.length);else if(this.contains(e,(this.xmin+this.xmax)/2,(this.ymin+this.ymax)/2))return[this.xmax,this.ymin,this.xmax,this.ymax,this.xmin,this.ymax,this.xmin,this.ymin];return i}_clipSegment(e,n,r,i,o,a){let s=o<a;for(s&&([e,n,r,i,o,a]=[r,i,e,n,a,o]);;){if(o===0&&a===0)return s?[r,i,e,n]:[e,n,r,i];if(o&a)return null;let c,l,u=o||a;u&8?(c=e+(r-e)*(this.ymax-n)/(i-n),l=this.ymax):u&4?(c=e+(r-e)*(this.ymin-n)/(i-n),l=this.ymin):u&2?(l=n+(i-n)*(this.xmax-e)/(r-e),c=this.xmax):(l=n+(i-n)*(this.xmin-e)/(r-e),c=this.xmin),o?(e=c,n=l,o=this._regioncode(e,n)):(r=c,i=l,a=this._regioncode(r,i))}}_clipInfinite(e,n,r,i,o,a){let s=Array.from(n),c;if((c=this._project(s[0],s[1],r,i))&&s.unshift(c[0],c[1]),(c=this._project(s[s.length-2],s[s.length-1],o,a))&&s.push(c[0],c[1]),s=this._clipFinite(e,s))for(let l=0,u=s.length,h,f=this._edgecode(s[u-2],s[u-1]);l<u;l+=2)h=f,f=this._edgecode(s[l],s[l+1]),h&&f&&(l=this._edge(e,h,f,s,l),u=s.length);else this.contains(e,(this.xmin+this.xmax)/2,(this.ymin+this.ymax)/2)&&(s=[this.xmin,this.ymin,this.xmax,this.ymin,this.xmax,this.ymax,this.xmin,this.ymax]);return s}_edge(e,n,r,i,o){for(;n!==r;){let a,s;switch(n){case 5:n=4;continue;case 4:n=6,a=this.xmax,s=this.ymin;break;case 6:n=2;continue;case 2:n=10,a=this.xmax,s=this.ymax;break;case 10:n=8;continue;case 8:n=9,a=this.xmin,s=this.ymax;break;case 9:n=1;continue;case 1:n=5,a=this.xmin,s=this.ymin;break}(i[o]!==a||i[o+1]!==s)&&this.contains(e,a,s)&&(i.splice(o,0,a,s),o+=2)}return o}_project(e,n,r,i){let o=1/0,a,s,c;if(i<0){if(n<=this.ymin)return null;(a=(this.ymin-n)/i)<o&&(c=this.ymin,s=e+(o=a)*r)}else if(i>0){if(n>=this.ymax)return null;(a=(this.ymax-n)/i)<o&&(c=this.ymax,s=e+(o=a)*r)}if(r>0){if(e>=this.xmax)return null;(a=(this.xmax-e)/r)<o&&(s=this.xmax,c=n+(o=a)*i)}else if(r<0){if(e<=this.xmin)return null;(a=(this.xmin-e)/r)<o&&(s=this.xmin,c=n+(o=a)*i)}return[s,c]}_edgecode(e,n){return(e===this.xmin?1:e===this.xmax?2:0)|(n===this.ymin?4:n===this.ymax?8:0)}_regioncode(e,n){return(e<this.xmin?1:e>this.xmax?2:0)|(n<this.ymin?4:n>this.ymax?8:0)}_simplify(e){if(e&&e.length>4){for(let n=0;n<e.length;n+=2){let r=(n+2)%e.length,i=(n+4)%e.length;(e[n]===e[r]&&e[r]===e[i]||e[n+1]===e[r+1]&&e[r+1]===e[i+1])&&(e.splice(r,2),n-=2)}e.length||(e=null)}return e}},Q_=2*Math.PI,Ei=Math.pow;function J_(t){return t[0]}function t8(t){return t[1]}function e8(t){let{triangles:e,coords:n}=t;for(let r=0;r<e.length;r+=3){let i=2*e[r],o=2*e[r+1],a=2*e[r+2];if((n[a]-n[i])*(n[o+1]-n[i+1])-(n[o]-n[i])*(n[a+1]-n[i+1])>1e-10)return!1}return!0}function n8(t,e,n){return[t+Math.sin(t+e)*n,e+Math.cos(t-e)*n]}var Du=class t{static from(e,n=J_,r=t8,i){return new t("length"in e?r8(e,n,r,i):Float64Array.from(i8(e,n,r,i)))}constructor(e){this._delaunator=new Os(e),this.inedges=new Int32Array(e.length/2),this._hullIndex=new Int32Array(e.length/2),this.points=this._delaunator.coords,this._init()}update(){return this._delaunator.update(),this._init(),this}_init(){let e=this._delaunator,n=this.points;if(e.hull&&e.hull.length>2&&e8(e)){this.collinear=Int32Array.from({length:n.length/2},(f,d)=>d).sort((f,d)=>n[2*f]-n[2*d]||n[2*f+1]-n[2*d+1]);let c=this.collinear[0],l=this.collinear[this.collinear.length-1],u=[n[2*c],n[2*c+1],n[2*l],n[2*l+1]],h=1e-8*Math.hypot(u[3]-u[1],u[2]-u[0]);for(let 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o=R.select(this);xr(e,o,n),rt(o,i)}),De(t,n)}ft.prototype.title=function(t,e,n=!0,r={},i="titleOptions"){if(!t&&!e)return this;if(!n)return this;let o=Gn(this.themeOptions),a={x:0,y:20*o,align:"center",spacing:20*o,titleFont:{fontSize:"16px",fontStyle:"normal",fontWeight:"bold",textDecoration:"normal",fontFamily:"sans-serif",cursor:"default"},subtitleFont:{fontSize:"14px",fontStyle:"normal",fontWeight:"normal",textDecoration:"none",fontFamily:"sans-serif",cursor:"default"}},s=ut.call(this,a,i,r),{x:c,y:l,align:u,spacing:h,itemStyle:f}=s,d=Xn(f,"title"),m=Xn(f,"subtitle"),p={...s.titleFont,...d.style},g={...s.subtitleFont,...m.style};t=d.text??t,e=m.text??e;let{xPos:y,textAnchor:w}=Dh(this,u,c);var b=this.svg.append("g").attr("data-component",i==="clusterTitleOptions"?"clusterTitle":"title").attr("transform",`translate(${this.margin.left}, ${this.margin.top})`);return t&&b.append("text").attr("data-part","title").property("__text__",t).attr("x",y).attr("y",l+this.margin.top/2).attr("text-anchor",w).call(ba,t,p,a.titleFont),e&&b.append("text").attr("data-part","subtitle").property("__text__",e).attr("x",y).attr("y",l+this.margin.top/2+h).attr("text-anchor",w).call(ba,e,g,a.subtitleFont),this};ft.prototype.footer=function(t,e,n=!0,r={}){if(!t&&!e)return this;if(!n)return this;let i={x:0,y:0,align:"left",spacing:12*Gn(this.themeOptions),titleFont:{fontSize:"12px",fontWeight:"bold",fontStyle:"normal",fontFamily:"sans-serif",cursor:"default"},subtitleFont:{fontSize:"10px",fontWeight:"normal",fontStyle:"normal",fontFamily:"sans-serif",cursor:"default"}},o=ut.call(this,i,"footerOptions",r),{x:a,y:s,align:c,spacing:l,itemStyle:u}=o,h=Xn(u,"title"),f=Xn(u,"subtitle"),d={...o.titleFont,...h.style},m={...o.subtitleFont,...f.style};t=h.text??t,e=f.text??e;let{xPos:p,textAnchor:g}=Dh(this,c,a,!0),y=this.height-this.margin.bottom+s-20,w=y+l;return t&&this.svg.append("text").attr("data-component","clusterFooter").attr("data-part","title").property("__text__",t).attr("x",p).attr("y",y).attr("text-anchor",g).call(ba,t,d,i.titleFont),e&&this.svg.append("text").attr("data-component","clusterFooter").attr("data-part","subtitle").property("__text__",e).attr("x",p).attr("y",w).attr("text-anchor",g).call(ba,e,m,i.subtitleFont),this};function Wy(t,e,n={}){let r=n?.clusterLabelOptions??{},i=e?.position??r.position??"left",o=e?.width??t?.margin?.[i]??r.width??n?.containerOptions?.margin?.[i]??`${100*Gn(n)}px`;return{[i]:o}}ft.prototype.clusterLabel=function(t,e=!0,n={}){if(!e)return this;let r={x:0,y:0,position:"left",align:"center",width:null,wrapLabel:!0,wrapOptions:{},fontSize:"12px",fontStyle:"normal",fontWeight:"bold",fontFamily:"sans-serif",cursor:"default",subtitle:null,spacing:null,subtitleFont:{fontSize:"11px",fontStyle:"normal",fontWeight:"normal",fontFamily:"sans-serif",cursor:"default"}},{itemStyle:i,...o}=ut.call(this,r,"clusterLabelOptions",n),a=Xn(i,"title"),s=Xn(i,"subtitle"),c={...o,...a.style,subtitle:s.text??o.subtitle,subtitleFont:{...o.subtitleFont,...s.style}};t=a.text??t;let{x:l,y:u,position:h,align:f,wrapLabel:d,wrapOptions:m,fontSize:p,fontStyle:g,fontWeight:y,fontFamily:w,cursor:b,subtitle:v,spacing:_,subtitleFont:S}=c,k=at(m,r.wrapOptions),C=at(c,r),F={size:p,style:g,weight:y,family:w,cursor:b},A=this.height-this.margin.top-this.margin.bottom,E=this.margin.top+A/2+u,D=h==="left"?this.margin.left-l:this.margin.right-l,$={left:0,right:1}[f]??.5,M={left:"start",right:"end"}[f]??"middle",T;h==="left"?T=this.margin.left*$+l:T=this.width-this.margin.right*(1-$)-l;let B=this.svg.append("text").attr("data-component","clusterLabel").attr("data-part","title").property("__text__",t).attr("x",T).attr("y",E).attr("text-anchor",M).attr("dominant-baseline","central").style("font-size",p).style("font-style",g).style("font-weight",y).style("font-family",w).style("cursor",b).each(function(){let N=R.select(this);d?(N.text(t),Bh(N,D,m)):xr(t,N,F),rt(N,C)});if(v){let N=at(S,r.subtitleFont),L={size:S.fontSize,style:S.fontStyle,weight:S.fontWeight,family:S.fontFamily,cursor:S.cursor},q=this.svg.append("text").attr("data-component","clusterLabel").attr("data-part","subtitle").property("__text__",v).attr("x",T).attr("y",E).attr("text-anchor",M).attr("dominant-baseline","central").style("font-size",S.fontSize).style("font-style",S.fontStyle).style("font-weight",S.fontWeight).style("font-family",S.fontFamily).style("cursor",S.cursor).each(function(){let H=R.select(this);d?(H.text(v),Bh(H,D,m)):xr(v,H,L),rt(H,N)}),U=Uy(B),Z=Uy(q),Q=_??1.2*(U.fontSize+Z.fontSize)/2,j=E-(U.first+U.last+Q-Z.first+Z.last)/2;Hy(B,j),Hy(q,j+U.last+Q-Z.first)}return De(B,a.style),this.svg.selectAll('text[data-component="clusterLabel"][data-part="subtitle"]').call(De,s.style),this};function Uy(t){let e=parseFloat(getComputedStyle(t.node()).fontSize),n=t.selectAll("tspan.wrap-line").nodes();if(!n.length)return{fontSize:e,first:0,last:0};let r=i=>(parseFloat(i.getAttribute("dy"))||0)*e;return{fontSize:e,first:r(n[0]),last:r(n[n.length-1])}}function Hy(t,e){t.attr("y",e),t.selectAll("tspan.wrap-line").attr("y",e)}ft.prototype.sequence=function(t=!0,e={}){if(!t)return this;if(!this.data)return console.error("No data has been added to this cluster container. 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g)b>w&&y.push([w,Math.min(b,p)]),w=Math.max(w,v);w<p&&y.push([w,p]),u.selectAll("line.baseline").data(y).enter().append("line").attr("class","baseline").attr("x1",b=>b[0]).attr("y1",this.yScale(i)).attr("x2",b=>b[1]).attr("y2",this.yScale(i)).style("stroke",c.stroke).style("stroke-width",c.strokeWidth).each(function(){let b=R.select(this);rt(b,l)});for(let{xStart:b,xEnd:v}of d){let _=this.yScale(i),S=_-s.markerHeight/2,k=_+s.markerHeight/2;u.append("line").attr("x1",b).attr("y1",S).attr("x2",b+s.tiltAmount).attr("y2",k).attr("stroke",s.stroke).attr("stroke-width",s.strokeWidth),u.append("line").attr("x1",v-s.tiltAmount).attr("y1",S).attr("x2",v).attr("y2",k).attr("stroke",s.stroke).attr("stroke-width",s.strokeWidth)}return this};ft.prototype.coordinates=function(t=!0,e={}){if(!t)return this;let n={rotate:-45,yPositionTop:53,yPositionBottom:48,tickValuesTop:null,tickValuesBottom:null,overlapThreshold:20,ticksFormat:",.0f",groupStyle:{},styleBy:null,itemStyle:[],tickStyle:{stroke:"black",strokeWidth:1,lineLength:6},textStyle:{fill:"black",fontSize:"10px",fontFamily:"Arial",cursor:"default",x:0,y:0}},r=ut.call(this,n,"coordinatesOptions",e),{rotate:i,yPositionTop:o,yPositionBottom:a,tickValuesBottom:s,tickValuesTop:c,ticksFormat:l,tickStyle:u,textStyle:h,groupStyle:f,styleBy:d,itemStyle:m}=r,p=A=>m.filter(E=>A?.rowID!=null&&E.rowID===A.rowID&&(E.end==null||E.end===A.end)).reduce((E,{rowID:D,end:$,...M})=>({...E,...M}),{}),g=A=>{let E=(d&&A?.gene?f[A.gene[d]]:void 0)??{},D=p(A);return{...E,...D,tick:{...E.tick,...D.tick}}},y=A=>{let{show:E,tick:D,...$}=g(A);return $},w=at(u,n.tickStyle),b=at(h,n.textStyle),v=this.svg.append("g").attr("data-component","coordinates").attr("transform","translate("+this.margin.left+","+this.margin.top+")"),_=Array.isArray(c)?c.map(A=>({value:A,rowID:null})):c!=null?[{value:c,rowID:null}]:[],S=Array.isArray(s)?s.map(A=>({value:A,rowID:null})):s!=null?[{value:s,rowID:null}]:[];if(!c&&!s){let A=this.data.reduce((E,D)=>{let $={value:D.start,rowID:D.rowID,end:"start",gene:D},M={value:D.end,rowID:D.rowID,end:"end",gene:D};return $.strand=D.strand,M.strand=D.strand,"geneTrack"in D&&($.geneTrack=D.geneTrack,M.geneTrack=D.geneTrack),E.push($),E.push(M),E},[]);if(A=A.filter(E=>g(E).show!==!1),A=A.filter((E,D,$)=>D===$.findIndex(M=>M.value===E.value)),A.sort((E,D)=>E.value-D.value),this.separateStrands)A.forEach(E=>{E.strand==="forward"?_.push(E):S.push(E)});else{let E=r.overlapThreshold;for(let D=0;D<A.length;D++){if(D===0){S.push(A[D]);continue}this.xScale(A[D].value)-this.xScale(A[D-1].value)<E?(_.push(A[D]),D+1<A.length&&(S.push(A[D+1]),D++)):S.push(A[D])}}}let k=this,C=v.append("g").attr("transform","translate(0,"+this.yScale(o)+")").call(R.axisTop(this.xScale).tickValues(_.map(A=>A.value)).tickFormat(R.format(l)));C.selectAll(".tick").data(_).attr("rowID",A=>A.rowID).attr("transform",function(A){let E=k.xScale(A.value);var D=A.geneTrack?(A.geneTrack-1)*k.geneOverlapSpacing:0;return"translate("+E+","+-D+")"}),C.select(".domain").attr("stroke","none"),C.selectAll("text").data(_).attr("class","coordinate").style("text-anchor","end").attr("dx",`${-.8+h.x}em`).attr("dy",`${.4+h.y}em`).attr("transform","rotate("+-i+")").style("fill",h.fill).style("font-size",h.fontSize).style("font-family",h.fontFamily).style("cursor",h.cursor).each(function(A){let E=R.select(this);rt(E,b),rt(E,y(A))}),C.selectAll(".tick line").style("stroke",u.stroke).style("stroke-width",u.strokeWidth).attr("y2",-u.lineLength).each(function(){let A=R.select(this);rt(A,w),rt(A,g(R.select(this.parentNode).datum()).tick??{})});let F=v.append("g").attr("transform","translate(0,"+this.yScale(a)+")").call(R.axisBottom(this.xScale).tickValues(S.map(A=>A.value)).tickFormat(R.format(l)));return F.selectAll(".tick").data(S).attr("rowID",A=>A.rowID).attr("transform",function(A){let E=k.xScale(A.value);var D=A.geneTrack?-(A.geneTrack-1)*k.geneOverlapSpacing:0;return"translate("+E+","+-D+")"}),F.select(".domain").attr("stroke","none"),F.selectAll("text").data(S).attr("class","coordinate").style("text-anchor","start").attr("dx",`${.8+h.x}em`).attr("dy",`${-.15+h.y}em`).attr("transform","rotate("+-i+")").style("fill",h.fill).style("font-size",h.fontSize).style("font-family",h.fontFamily).style("cursor",h.cursor).each(function(A){let E=R.select(this);rt(E,b),rt(E,y(A))}),F.selectAll(".tick 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n=R.select(t),r=t.textContent;t.textContent="",n.append("tspan").attr("class","label-name").text(r);let i=n.append("tspan").attr("class","label-measure").text(e.textContent);for(let o of e.style)o!=="text-anchor"&&i.style(o,e.style.getPropertyValue(o));if(e.remove(),r){i.attr("x",n.attr("x")).attr("dy","1.1em");let o=1.1*parseFloat(getComputedStyle(i.node()).fontSize);n.attr("y",parseFloat(n.attr("y"))-o)}}function fE(t){let e=R.select(t),n=e.select(".label-measure");n.empty()||n.attr("x",null).attr("dy",null).attr("dx",e.select(".label-name").text()?"0.3em":null)}function hE(t,e,n,r,i){let o=t.map((l,u)=>u).sort((l,u)=>t[l]-t[u]),a=[],s=l=>{l.start=Math.max(r,Math.min(l.total/l.members.length,i-l.width))};for(let l of o){let u={members:[{i:l,offset:0}],width:e[l],total:t[l]-e[l]/2};s(u);let h=a[a.length-1];for(;h&&h.start+h.width+n>u.start;){let f=h.width+n;u.members.forEach(d=>{d.offset+=f}),h.members.push(...u.members),h.total+=u.total-u.members.length*f,h.width+=n+u.width,u=a.pop(),s(u),h=a[a.length-1]}a.push(u)}let c=new Array(t.length);return a.forEach(l=>l.members.forEach(({i:u,offset:h})=>{c[u]=l.start+h+e[u]/2})),c}function jy(t){let e=t.__leader__;if(!e||!e.line.isConnected)return;let n=!t.isConnected||getComputedStyle(t).display==="none";if(e.line.style.display=n?"none":null,n)return;let r=t.getScreenCTM?.(),i=e.line.parentNode.getScreenCTM?.(),o=t.transform?.baseVal?.consolidate(),a=r&&i?i.inverse().multiply(r):o?o.matrix:new DOMMatrix,s=t.getBBox(),c=new DOMPoint(s.x+s.width/2,s.y).matrixTransform(a),l=new DOMPoint(s.x+s.width/2,s.y+s.height).matrixTransform(a),u=l.y<=(e.geneTop+e.geneBottom)/2,h=u?l:c;e.line.setAttribute("y1",u?e.geneTop-e.gap:e.geneBottom+e.gap),e.line.setAttribute("x2",h.x),e.line.setAttribute("y2",u?h.y+e.gap:h.y-e.gap)}ft.prototype.labels=function(t,e=!0,n={}){if(!e)return this;if(!t)return 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t&&this.svg.append("text").attr("data-component","clusterFooter").attr("data-part","title").property("__text__",t).attr("x",p).attr("y",y).attr("text-anchor",g).call(ba,t,d,i.titleFont),e&&this.svg.append("text").attr("data-component","clusterFooter").attr("data-part","subtitle").property("__text__",e).attr("x",p).attr("y",w).attr("text-anchor",g).call(ba,e,m,i.subtitleFont),this};function Wy(t,e,n={}){let r=n?.clusterLabelOptions??{},i=e?.position??r.position??"left",o=e?.width??t?.margin?.[i]??r.width??n?.containerOptions?.margin?.[i]??`${100*Gn(n)}px`;return{[i]:o}}ft.prototype.clusterLabel=function(t,e=!0,n={}){if(!e)return this;let 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B=this.svg.append("text").attr("data-component","clusterLabel").attr("data-part","title").property("__text__",t).attr("x",T).attr("y",E).attr("text-anchor",M).attr("dominant-baseline","central").style("font-size",p).style("font-style",g).style("font-weight",y).style("font-family",w).style("cursor",b).each(function(){let N=R.select(this);d?(N.text(t),Bh(N,D,m)):xr(t,N,F),rt(N,C)});if(v){let N=at(S,r.subtitleFont),L={size:S.fontSize,style:S.fontStyle,weight:S.fontWeight,family:S.fontFamily,cursor:S.cursor},q=this.svg.append("text").attr("data-component","clusterLabel").attr("data-part","subtitle").property("__text__",v).attr("x",T).attr("y",E).attr("text-anchor",M).attr("dominant-baseline","central").style("font-size",S.fontSize).style("font-style",S.fontStyle).style("font-weight",S.fontWeight).style("font-family",S.fontFamily).style("cursor",S.cursor).each(function(){let 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n=R.select(t),r=t.textContent;t.textContent="",n.append("tspan").attr("class","label-name").text(r);let i=n.append("tspan").attr("class","label-measure").text(e.textContent);for(let o of e.style)o!=="text-anchor"&&i.style(o,e.style.getPropertyValue(o));if(e.remove(),r){i.attr("x",n.attr("x")).attr("dy","1.1em");let o=1.1*parseFloat(getComputedStyle(i.node()).fontSize);n.attr("y",parseFloat(n.attr("y"))-o)}}function hE(t){let e=R.select(t),n=e.select(".label-measure");n.empty()||n.attr("x",null).attr("dy",null).attr("dx",e.select(".label-name").text()?"0.3em":null)}function dE(t,e,n,r,i){let o=t.map((l,u)=>u).sort((l,u)=>t[l]-t[u]),a=[],s=l=>{l.start=Math.max(r,Math.min(l.total/l.members.length,i-l.width))};for(let l of o){let u={members:[{i:l,offset:0}],width:e[l],total:t[l]-e[l]/2};s(u);let h=a[a.length-1];for(;h&&h.start+h.width+n>u.start;){let f=h.width+n;u.members.forEach(d=>{d.offset+=f}),h.members.push(...u.members),h.total+=u.total-u.members.length*f,h.width+=n+u.width,u=a.pop(),s(u),h=a[a.length-1]}a.push(u)}let c=new Array(t.length);return a.forEach(l=>l.members.forEach(({i:u,offset:h})=>{c[u]=l.start+h+e[u]/2})),c}function jy(t){let e=t.__leader__;if(!e||!e.line.isConnected)return;let n=!t.isConnected||getComputedStyle(t).display==="none";if(e.line.style.display=n?"none":null,n)return;let r=t.getScreenCTM?.(),i=e.line.parentNode.getScreenCTM?.(),o=t.transform?.baseVal?.consolidate(),a=r&&i?i.inverse().multiply(r):o?o.matrix:new DOMMatrix,s=t.getBBox(),c=new DOMPoint(s.x+s.width/2,s.y).matrixTransform(a),l=new DOMPoint(s.x+s.width/2,s.y+s.height).matrixTransform(a),u=l.y<=(e.geneTop+e.geneBottom)/2,h=u?l:c;e.line.setAttribute("y1",u?e.geneTop-e.gap:e.geneBottom+e.gap),e.line.setAttribute("x2",h.x),e.line.setAttribute("y2",u?h.y+e.gap:h.y-e.gap)}ft.prototype.labels=function(t,e=!0,n={}){if(!e)return this;if(!t)return this;if(!this.data)return console.error("No data has been added to this cluster container. Please use the addGeneData() function before attempting to draw genes."),this;let r={x:0,y:55,dy:"0em",dx:"0em",rotate:0,start:null,end:null,adjustLabels:!0,spreadPosition:"bottom",leaderLine:{length:20,stroke:"#999999",strokeWidth:.75},fontSize:"12px",fontStyle:"italic",fontFamily:"sans-serif",textAnchor:"middle",cursor:"default",labelAdjustmentOptions:{rotation:65,offsetX:0,offsetY:0,dx:"0em",dy:"0em"},itemStyle:[],groupStyle:{},styleBy:null,group:null},i=ut.call(this,r,"labelsOptions",n),{x:o,y:a,start:s,end:c,adjustLabels:l,labelAdjustmentOptions:u,spreadPosition:h,leaderLine:f,groupStyle:d,styleBy:m,group:p,dx:g,dy:y,anchor:w,rotate:b,fontSize:v,fontStyle:_,fontFamily:S,textAnchor:k,cursor:C}=i,F=at(i,r),A=this.svg.append("g").attr("data-component","labels").attr("transform",`translate(${this.margin.left},${this.margin.top})`);this.data.sort((j,H)=>Math.min(j.start,j.end)-Math.min(H.start,H.end));let E=Ui(this.data,m??p,d,i.itemStyle),D=new Map(E.map(j=>[j.index,j])),z=(j,H)=>{let W=D.get(H)||{},J=W.x??o,K=W.y??a,ht=W.dx??g,G=W.dy??y,tt=W.adjustLabels!==void 0?W.adjustLabels:l,ot=tt==="spread",X=ot?0:W.rotate??b,vt=!ot&&j.geneTrack>1,yt={...W.labelAdjustmentOptions??u};yt.rotation=-Math.abs(yt.rotation);let Tt=j.strand=="forward"&&this.geneStrandSpacing!==0?this.geneStrandSpacing:-this.geneStrandSpacing;var Mt=j.geneTrack?(j.geneTrack-1)*this.geneOverlapSpacing:0;let st=this.yScale(this.markerY??50),St=this.yScale(K)-this.markerHeight/2-Tt+Mt,ne=2*st-this.yScale(K)+this.markerHeight/2-Tt+Mt,Zt=vt?ne:St;return{xPos:this.xScale((j.start+j.end)/2)+J,yPos:Zt,dx:ht,dy:G,rotate:X,labelAdjustmentOptions:yt,adjustLabels:tt,spread:ot,below:vt,yAbove:St}},M=R.group(this.data,j=>j.geneTrack??1),T=(j,H,W)=>(M.get(j)||[]).some(J=>{let[K,ht]=[this.xScale(J.start),this.xScale(J.end)].sort((G,tt)=>G-tt);return K<W&&ht>H}),B=(j,H,W)=>{if(!W.below)return;let J=j.getBBox(),K=J.x,ht=J.x+J.width;T(H.geneTrack+1,K,ht)&&!T(H.geneTrack-1,K,ht)&&(W.below=!1,W.yPos=W.yAbove,R.select(j).attr("dominant-baseline",null).attr("y",W.yPos).attr("transform",`rotate(${W.rotate}, ${W.xPos}, ${W.yPos})`))},N=this.data.map((j,H)=>z(j,H)),L=Zl(this,"text.label",{left:0,right:this.width-this.margin.left-this.margin.right,top:-this.margin.top,bottom:this.height-this.margin.top}),q=new Map(this.svg.selectAll(".link-text").nodes().map(j=>[j.getAttribute("rowID"),j]));A.selectAll("text.label").data(this.data).enter().append("text").attr("id",(j,H)=>`cluster-${wr(j.cluster)}-label-${H}`).attr("rowID",(j,H)=>`${j.rowID}`).attr("class","label").each(function(j,H){let{dx:W,dy:J,rotate:K}=N[H];this.__drawn__={dx:W,dy:J,rotate:K}}).attr("x",(j,H)=>N[H].xPos).attr("y",(j,H)=>N[H].yPos).attr("dx",(j,H)=>N[H].dx).attr("dy",(j,H)=>N[H].dy).attr("text-anchor",k).attr("dominant-baseline",(j,H)=>N[H].below?"hanging":null).attr("transform",(j,H)=>{let{xPos:W,yPos:J,rotate:K}=N[H];return`rotate(${K}, ${W}, ${J})`}).style("font-size",v).style("font-style",_).style("font-family",S).style("cursor",C).text((j,H)=>D.get(H)?.text??j[t]).each(function(j){let H=q.get(String(j.rowID));H&&fE(this,H)}).each(function(j,H){let W=N[H];B(this,j,W),W.below&&(W.labelAdjustmentOptions.rotation=Math.abs(W.labelAdjustmentOptions.rotation))});let U=(j,H)=>{let W=R.select(j);rt(W,F),Hi(W,D.has(H)?[D.get(H)]:[],H),(j.childElementCount||ma(F)||ma(D.get(H)))&&L.refresh(j)};A.selectAll("text.label").each(function(j,H){N[H].spread&&U(this,H)});let{length:Z,...Q}={...r.leaderLine,...Wr(f)?f:{}};return this.spreadLabels(A,N,{length:Number.isFinite(Number(Z))?Number(Z):r.leaderLine.length,lineStyle:f===!1?null:Q,onTop:h==="top"}),A.selectAll("text.label").each(function(j,H){let W=N[H];W.spread||(W.adjustLabels&&L.adjust(this,{...W.labelAdjustmentOptions,hide:W.adjustLabels==="hide"})&&hE(this),U(this,H))}),A.selectAll("text.label").each(function(j,H){De(R.select(this),D.get(H)??{})}),this.labels=A.selectAll(".label"),this};ft.prototype.spreadLabels=function(t,e,n){let r=this.svg.node();if(!r.getClientRects().length){let k=new ResizeObserver(()=>{if(!r.isConnected)return k.disconnect();r.getClientRects().length&&(k.disconnect(),this.spreadLabels(t,e,n))});return k.observe(r),this}let i=this.width-this.margin.left-this.margin.right,o=k=>{let[C,F]=[this.xScale(k.start),this.xScale(k.end)].sort((D,z)=>D-z),A=Math.max(0,C),E=Math.min(i,F);return A<=E?[A,E]:null},a=[];if(t.selectAll("text.label").each(function(k,C){if(!e[C].spread||this.textContent.trim()==="")return;let F=o(k);if(!F){this.style.display="none";return}let{xPos:A}=e[C];a.push({node:this,d:k,geneX:(F[0]+F[1])/2,wanted:Math.min(F[1],Math.max(F[0],A))})}),!a.length)return this;let s=t.node().getCTM(),c=new Set(a.map(({d:k})=>String(k.rowID))),l=new Map,u=new Map,h=1/0,f=-1/0;this.svg.selectAll(".gene, .exon, .intron, .utr").each(function(){let k=this.getCTM();if(!k||!s)return;let C=s.inverse().multiply(k),F=this.getBBox(),A=1/0,E=-1/0;for(let[z,M]of[[F.x,F.y],[F.x+F.width,F.y],[F.x,F.y+F.height],[F.x+F.width,F.y+F.height]]){let T=new DOMPoint(z,M).matrixTransform(C).y;A=Math.min(A,T),E=Math.max(E,T)}h=Math.min(h,A),f=Math.max(f,E);let D=this.getAttribute("rowID");c.has(D)&&(l.set(D,Math.min(l.get(D)??1/0,A)),u.set(D,Math.max(u.get(D)??-1/0,E)))});let d=this.yScale(this.markerY??50),m=(this.markerHeight??0)/2;Number.isFinite(h)||(h=d-m),Number.isFinite(f)||(f=d+m);let p=6,g=2,y=a.map(({node:k})=>k.getBBox()),w=dE(a.map(({wanted:k})=>k),y.map(k=>k.width),p,0,i),b=y.reduce((k,C)=>Math.max(k,C.height),0),v=n.onTop?h-b+this.margin.top:this.height-this.margin.top-f-b,_=Math.max(2*g,Math.min(n.length,v));if(a.forEach(({node:k},C)=>{let F=y[C],A=w[C]-F.width/2;if(A<-.5||A+F.width>i+.5){k.style.display="none";return}let E=n.onTop?h-_-(F.y+F.height):f+_-F.y,{moveX:D=0,moveY:z=0}=k.__drawn__??{},M=D||z?`translate(${D}, ${z}) `:"";k.setAttribute("transform",`${M}translate(${w[C]-(F.x+F.width/2)}, ${E})`)}),!n.lineStyle)return this;let S=t.insert("g","text.label").attr("class","leader-lines").style("pointer-events","none");return a.forEach(({node:k,d:C,geneX:F})=>{if(k.style.display==="none")return;let A=S.append("line").attr("x1",F).attr("x2",F);rt(A,n.lineStyle),k.__leader__={line:A.node(),gap:g,geneTop:l.get(String(C.rowID))??h,geneBottom:u.get(String(C.rowID))??f},jy(k),new MutationObserver(()=>jy(k)).observe(k,{attributes:!0,attributeFilter:["transform","style"]})}),this};ft.prototype.tooltip=function(t=!0,e={}){if(!t)return this;let n={triggers:["markers","genes","labels","exons","introns","utrs"],formatter:"<b>Start:</b> {start}<br><b>End: {end}</b>",opacity:0,position:"absolute",backgroundColor:"rgba(255, 255, 255, 0.9)",padding:"8px",borderRadius:"4px",border:"1px solid rgba(0,0,0,0.1)",boxShadow:"0 4px 6px rgba(0, 0, 0, 0.1)",pointerEvents:"none",fontFamily:"Arial, sans-serif",fontSize:"12px",zIndex:1e3,color:"#333",lineHeight:"1.5"},r=ut.call(this,n,"tooltipOptions",e),i=at(r,n);typeof r.triggers=="string"&&(r.triggers=[r.triggers]);let o=this.svg.node().closest(".html-widget")||document.body,a=R.select(o).append("div").attr("class","cluster-tooltip").style("opacity",r.opacity).style("position",r.position).style("background-color",r.backgroundColor).style("--tooltip-bg",r.backgroundColor).style("padding",r.padding).style("border-radius",r.borderRadius).style("border",r.border).style("box-shadow",r.boxShadow).style("pointer-events",r.pointerEvents).style("font-family",r.fontFamily).style("font-size",r.fontSize).style("z-index",r.zIndex).style("color",r.color).style("line-height",r.lineHeight);rt(a,i);let s=h=>{let[f,d]=R.pointer(h,o);a.style("left",f-a.node().offsetWidth/2+"px").style("top",d-a.node().offsetHeight-15+"px")},c=R.format(","),l=h=>h==null||h===""||typeof h=="number"&&isNaN(h),u=h=>r.formatter.split(/<br\s*\/?>/i).filter(f=>{let d=[...f.matchAll(/\{(\w+)\}/g)].map(m=>m[1]);return d.length===0||!d.every(m=>l(h[m]))}).join("<br>").replace(/\{(\w+)\}/g,(f,d)=>typeof h[d]=="number"?c(h[d]):h[d]||"");return r.triggers.forEach(h=>{if(!this.hasOwnProperty(h))return;let f=this[h];!f||f.empty()||(f.on("mouseover",(d,m)=>{let p=this.data.find(y=>y===m);R.select(d.currentTarget).classed("hovered",!0),a.transition().duration(200).style("opacity",1),a.html(u(p)),s(d)}),f.on("mousemove",s),f.on("mouseout",d=>{R.select(d.currentTarget).classed("hovered",!1),a.transition().duration(500).style("opacity",0)}))}),this};function ji(t,e,n){let r=["#1f77b4","#ff7f0e","#2ca02c","#d62728","#9467bd","#8c564b","#e377c2","#7f7f7f","#bcbd22","#17becf","#393b79","#637939","#8c6d31","#843c39","#7b4173","#bd9e39","#ad494a","#d6616b","#31a354","#cedb9c","#9c9ede","#5254a3","#8ca252","#b5cf6b","#e7ba52","#ce6dbd","#e7cb94","#e7969c","#6b6ecf","#a55194"],i=n.filter(s=>s!==null),o=(s=()=>!0)=>{if(t&&(Array.isArray(t)||R[t])){let c=Array.isArray(t)?t:R[t];return i.some((l,u)=>u>=c.length&&s(l))&&qe("Warning: More unique groups than colors. Some colors will repeat."),i.map((l,u)=>c[u%c.length])}return t&&qe(`Warning: The color scheme "${t}" does not exist. Defaulting to schemeCategory30.`),i.map((c,l)=>c==="No Hit"?"#FFF":r[l%r.length])},a;if(e&&typeof e=="string")a=i.map(()=>e);else if(e&&Array.isArray(e))a=i.map((s,c)=>e[c%e.length]||"#FFF");else if(e&&typeof e=="object"){let s=o(c=>!e[c]);a=i.map((c,l)=>e[c]||s[l])}else a=o();return R.scaleOrdinal().domain([...i,null]).range([...a,"#FFF"])}var va={none:()=>{},solid:(t,e,n)=>t.append("rect").attr("width",e).attr("height",e).attr("fill",n),horizontal:(t,e,n,r)=>t.append("path").attr("d",`M0,${e/2}H${e}`).attr("stroke",n).attr("stroke-width",r),vertical:(t,e,n,r)=>t.append("path").attr("d",`M${e/2},0V${e}`).attr("stroke",n).attr("stroke-width",r),diagonal:(t,e,n,r)=>t.append("path").attr("d",`M0,${e}L${e},0M${-e/4},${e/4}L${e/4},${-e/4}M${e*3/4},${e*5/4}L${e*5/4},${e*3/4}`).attr("stroke",n).attr("stroke-width",r),antidiagonal:(t,e,n,r)=>t.append("path").attr("d",`M0,0L${e},${e}M${-e/4},${e*3/4}L${e/4},${e*5/4}M${e*3/4},${-e/4}L${e*5/4},${e/4}`).attr("stroke",n).attr("stroke-width",r),grid:(t,e,n,r)=>t.append("path").attr("d",`M0,${e/2}H${e}M${e/2},0V${e}`).attr("stroke",n).attr("stroke-width",r),crosshatch:(t,e,n,r)=>{va.diagonal(t,e,n,r),va.antidiagonal(t,e,n,r)},dots:(t,e,n)=>t.append("circle").attr("cx",e/2).attr("cy",e/2).attr("r",e/5).attr("fill",n),zigzag:(t,e,n,r)=>t.append("path").attr("d",`M0,${e*.7}L${e/2},${e*.3}L${e},${e*.7}`).attr("fill","none").attr("stroke",n).attr("stroke-width",r),checkerboard:(t,e,n)=>t.append("path").attr("d",`M0,0H${e/2}V${e/2}H0ZM${e/2},${e/2}H${e}V${e}H${e/2}Z`).attr("fill",n),rings:(t,e,n,r)=>t.append("circle").attr("cx",e/2).attr("cy",e/2).attr("r",e/3.2).attr("fill","none").attr("stroke",n).attr("stroke-width",r*.8),bricks:(t,e,n,r)=>t.append("path").attr("d",`M0,0H${e}M0,${e/2}H${e}M${e/4},0V${e/2}M${e*3/4},${e/2}V${e}`).attr("stroke",n).attr("stroke-width",r),plus:(t,e,n,r)=>t.append("path").attr("d",`M${e/2},${e*.2}V${e*.8}M${e*.2},${e/2}H${e*.8}`).attr("stroke",n).attr("stroke-width",r),wideStripes:(t,e,n)=>t.append("path").attr("d",`M0,${e}L${e},0H${e/2}L0,${e/2}ZM${e},${e/2}V${e}H${e/2}Z`).attr("fill",n),inverseDots:(t,e,n,r,i)=>{va.solid(t,e,n),t.append("circle").attr("cx",e/2).attr("cy",e/2).attr("r",e/4).attr("fill",i)}},pE={checkerboard:4/3,rings:7/6,bricks:5/3,plus:4/3,wideStripes:4/3},$h=["diagonal","dots","horizontal","crosshatch","vertical","zigzag","checkerboard","solid","rings","bricks","inverseDots","grid","wideStripes","plus","antidiagonal"];function zh(t,e,n){return t==null?e.map(()=>n):typeof t=="string"?e.map(()=>t):Array.isArray(t)?e.map((r,i)=>t[i%t.length]):e.map(r=>t[r]??n)}function Xi(t,e,n,r,i){if(!e)return{fill:r,stroke:r,outline:null,align:()=>{}};let{patterns:o=null,color:a="black",background:s=null,size:c=6,strokeWidth:l=1}=e,u=n.filter(b=>b!==null),h=zh(o,u,"none");o==null&&(u.forEach((b,v)=>{h[v]=$h[v%$h.length]}),u.length>$h.length&&qe("Warning: More unique groups than patterns. Some patterns will repeat."));let f=zh(s,u,null),d=zh(a,u,"black"),m=t.attr("id")||"geneviewer",p=t.append("defs"),g=new Map,y=new Map;u.forEach((b,v)=>{let _=h[v];va[_]||(qe(`Warning: The pattern "${_}" does not exist. Using "none".`),_="none"),b==="No Hit"&&o==null&&(_="none");let S=`${m}-${i}-pattern-${v}`,k=c*(pE[_]??1),C=f[v]??r(b),F=p.append("pattern").attr("id",S).attr("patternUnits","userSpaceOnUse").attr("width",k).attr("height",k);F.append("rect").attr("width",k).attr("height",k).attr("fill",C),va[_](F,k,d[v],l,C),g.set(b,`url(#${S})`),y.set(b,F)});let w=new Map(u.map((b,v)=>[b,d[v]]));return{fill:b=>g.get(b)??r(b),stroke:b=>s==null?r(b):w.get(b)??d[0],outline:typeof a=="string"?a:"black",align:(b,v,_)=>y.get(b)?.attr("x",v).attr("y",_)}}function gE(t,e){let n=t.filter((u,h)=>{let f=t[(h-1+t.length)%t.length];return Math.abs(u[0]-f[0])>1e-6||Math.abs(u[1]-f[1])>1e-6});if(!(e>0)||n.length<3)return`M${n.map(u=>`${u[0]} ${u[1]}`).join(" L")} Z`;let r=n.length,i=(u,h)=>Math.hypot(h[0]-u[0],h[1]-u[1]),o=(u,h,f)=>{let d=i(u,h);return[u[0]+(h[0]-u[0])*f/d,u[1]+(h[1]-u[1])*f/d]},a=(u,h,f)=>(h[0]-u[0])*(f[1]-h[1])-(h[1]-u[1])*(f[0]-h[0]),s=Math.sign(n.reduce((u,h,f)=>{let d=n[(f+1)%r];return u+h[0]*d[1]-d[0]*h[1]},0)),c=n.map((u,h)=>{let f=n[(h-1+r)%r],d=n[(h+1)%r],p=Math.sign(a(f,u,d))===s?Math.min(e,i(f,u)/2,i(u,d)/2):0;return{p:u,start:o(u,f,p),end:o(u,d,p)}}),l=`M${c[0].end[0]} ${c[0].end[1]}`;for(let u=1;u<=r;u++){let{p:h,start:f,end:d}=c[u%r];l+=` L${f[0]} ${f[1]} Q${h[0]} ${h[1]} ${d[0]} ${d[1]}`}return l+" Z"}function Xy(t,e,n,r={}){let i={small:{scale:.75},medium:{scale:1},large:{scale:1.25}},o={arrow:{arrowheadWidth:10,arrowheadHeight:30,markerHeight:15},boxarrow:{arrowheadWidth:10,arrowheadHeight:30,markerHeight:30},box:{arrowheadWidth:0,arrowheadHeight:30,markerHeight:30},rbox:{arrowheadWidth:0,arrowheadHeight:30,markerHeight:30,cornerRadius:5},cbox:{arrowheadWidth:10,arrowheadHeight:30,markerHeight:30},intron:{arrowheadWidth:0,arrowheadHeight:0,markerHeight:20}},a=i[n]||i.medium,s=o[t]||{},c=ya(s,r),{arrowheadWidth:l,arrowheadHeight:u,markerHeight:h,cornerRadius:f}=c,d=l*a.scale,m=u*a.scale,p=h*a.scale,g=e-d;g=Math.max(0,g);let y=(m-p)/2,w=y+p,b,v=Math.max(p,m),_;switch(t){case"arrow":case"boxarrow":case"box":b=gE([[0,y],[0,w],[g,w],[g,m],[e,m/2],[g,0],[g,y]],f||0);break;case"rbox":_=Math.min(f,p/2,e/2),v=p,b=`M ${_},0
                      H ${e-_}
                      A ${_},${_} 0 0 1 ${e},${_}
                      V ${p-_}
@@ -18,13 +18,13 @@ var v2=Object.defineProperty;var w2=(t,e)=>{for(var n in e)v2(t,n,{get:e[n],enum
                  Q 0 ${p/2} ${_} 0
                  Z`;break;case"intron":let k=e/2;v=p/2,b=`M0 ${v}
                     L${k} 0
-                    L${e} ${v}`;break;default:qe(`Marker type '${t}' not recognized.`),b=""}return{path:b,length:e,scaledArrowheadWidth:d,scaledArrowheadHeight:m,height:v,used:{arrowheadWidth:l,arrowheadHeight:u,markerHeight:h,cornerRadius:f??0}}}function Nh(t){t.attr("rowID",(e,n)=>`${e.rowID}`).attr("start",(e,n)=>`${e.start}`).attr("end",(e,n)=>`${e.end}`).attr("strand",(e,n)=>`${e.strand}`).attr("cluster",(e,n)=>`${e.cluster}`)}function Rh(t,e,{xPos:n,yPos:r,height:i}){return`rotate(${t?e.direction==="forward"?180:0:e.direction==="forward"?0:180}, ${n}, ${r}) translate(${n}, ${r-i/2})`}function Ph(t,e,n,r,i,o){let a=o.find(S=>S.index===n)||{},s=Math.abs(t.xScale(e.end)-t.xScale(e.start)),c=a.y??r,l=a.marker??i.marker,u=a.markerSize??i.markerSize,{path:h,arrowheadWidth:f,arrowheadHeight:d,height:m,used:p}=Xy(l,s,u,{arrowheadWidth:a.arrowheadWidth??i.arrowheadWidth,arrowheadHeight:a.arrowheadHeight??i.arrowheadHeight,markerHeight:a.markerHeight??i.markerHeight,cornerRadius:a.cornerRadius??i.cornerRadius}),g=Xy(i.marker,s,i.markerSize,{arrowheadWidth:i.arrowheadWidth,arrowheadHeight:i.arrowheadHeight,markerHeight:i.markerHeight,cornerRadius:i.cornerRadius}).height;t.markerHeight=g,t.markerY=r,t.geneStrandSpacing=t.separateStrands?g/2+t.strandSpacing:0,t.geneOverlapSpacing=g+t.overlapSpacing;let y=e.strand==="forward"&&t.geneStrandSpacing!==0?t.geneStrandSpacing:-t.geneStrandSpacing,w=e.geneTrack?(e.geneTrack-1)*t.geneOverlapSpacing:0,b=t.yScale(c)-y+w,v=t.xScale(e.start),_={marker:l,markerSize:u,...p,y:c};return{xPos:v,yPos:b,path:h,arrowheadWidth:f,arrowheadHeight:d,height:m,drawn:_}}ft.prototype.genes=function(t,e=!0,n={}){if(!e)return this;if(!this.data)return console.error("No data has been added to this cluster container. 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r={x:1,y:50,colorScheme:null,customColors:null,pattern:null,styleExons:{show:!0,strokeWidth:0,cursor:"default",marker:"box",markerSize:"medium",arrowheadWidth:null,arrowheadHeight:null,markerHeight:null,cornerRadius:null},styleIntrons:{show:!0,strokeWidth:1,fill:"none",cursor:"default",marker:"intron",markerSize:"medium",arrowheadWidth:null,arrowheadHeight:null,markerHeight:null,cornerRadius:null},styleUTRs:{show:!0,fontSize:"10px",fontStyle:"normal",fontFamily:"sans-serif",cursor:"default",color:"black",fill:"#FFF",strokeWidth:1,marker:"box",markerSize:"medium",arrowheadWidth:null,arrowheadHeight:null,markerHeight:null,cornerRadius:null},labelOptions:{show:!0,xOffset:2,yOffset:0,fontSize:"12px",fontStyle:"normal",fontWeight:"normal",fontFamily:"sans-serif",cursor:"default",color:"black"},itemStyleExons:[],itemStyleIntrons:[],itemStyleUTRs:[],groupStyleExons:{},groupStyleIntrons:{},groupStyleUTRs:{},styleBy:null},i=ut.call(this,r,"transcriptOptions",n),{x:o,y:a,colorScheme:s,customColors:c,pattern:l,styleExons:u,styleIntrons:h,styleUTRs:f,labelOptions:d}=i,m=i.styleBy??t,p=at(i.styleExons,r.styleExons),g=at(i.styleIntrons,r.styleIntrons),y=at(i.styleUTRs,r.styleUTRs),w=[...new Set(this.dataAll.map(A=>A[t]))],b=ji(s,c,w);this.genesColorScale=b;let v=Xi(this.svg,l,w,b,"exon"),_=this.svg.append("g").attr("data-component","transcript").attr("transform",`translate(${this.margin.left}, ${this.margin.top})`);this.data.sort((A,E)=>Math.min(A.start,A.end)-Math.min(E.start,E.end));let S=(A,E,D,$)=>Ph(this,A,E,a,D,$),k=(A,E,D,$,M,T,B,N)=>{let L=this.data.filter(U=>new RegExp(A,"i").test(U.type)),q=Ui(L,m,D,$);return _.selectAll(`.${A}`).data(L).enter().append("path").attr("d",(U,Z)=>S(U,Z,E,q).path).attr("transform",(U,Z)=>T(U,S(U,Z,E,q))).attr("fill",B).attr("class",A).attr("id",(U,Z)=>`${wr(U.cluster)}-${A}-${Z}`).call(Nh).style("stroke-width",E.strokeWidth).style("stroke",N).style("cursor",E.cursor).each(function(U,Z){let Q=R.select(this);rt(Q,M),Hi(Q,q,Z)}),_.selectAll(`.${A}`)},C=(A,E)=>Rh(this.reverse,A,E),F=A=>v.stroke(A[t]);if(u.show&&(this.exons=k("exon",u,i.groupStyleExons,i.itemStyleExons,p,C,A=>v.fill(A[t]),u.stroke)),h.show){let A=(E,{xPos:D,yPos:$,height:M})=>{let T=E.direction==="forward"?-M:+M;return`rotate(${this.reverse?E.direction==="reverse"?180:0:E.direction==="forward"?0:180}, ${D}, ${$+T}) translate(${D}, ${$+T})`};this.introns=k("intron",h,i.groupStyleIntrons,i.itemStyleIntrons,g,A,h.fill,F)}if(f.show&&(this.utrs=k("utr",f,i.groupStyleUTRs,i.itemStyleUTRs,y,C,f.fill,F),d.show)){let A=this.data[0].direction==="forward"?this.xScale(this.maxEnd)+d.xOffset:this.xScale(this.minStart)-d.xOffset,E=this.data[0].direction==="forward"?this.xScale(this.minStart)-d.xOffset:this.xScale(this.maxEnd)+d.xOffset;_.append("text").attr("x",A).attr("y",D=>this.yScale(a+d.yOffset)).attr("class","three-prime-label").attr("text-anchor","middle").attr("alignment-baseline","middle").style("font-size",d.fontSize).style("font-style",d.fontStyle).style("font-weight",d.fontWeight).style("font-family",d.fontFamily).style("cursor",d.cursor).style("fill",d.color).text("3'"),_.append("text").attr("x",E).attr("y",D=>this.yScale(a+d.yOffset)).attr("class","five-prime-label").attr("text-anchor","middle").attr("alignment-baseline","middle").style("font-size",d.fontSize).style("font-style",d.fontStyle).style("font-weight",d.fontWeight).style("font-family",d.fontFamily).style("cursor",d.cursor).style("fill",d.color).text("5'")}return this};function gE(t,e){return e.map(r=>{let 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Zr=G.append("rect").attr("class","legend-marker").attr("data-part","marker").attr("id",`legend-marker-${K}`).style("cursor",p.cursor).attr("x",B).attr("y",N).attr("width",M).attr("height",M).attr("rx",m).style("fill",A.fill(J)).style("stroke",A.outline??(Iy(A.fill(J))?"#bdbdbd":null)).each(()=>A.align(J,B,N)).each(function(){let ie=R.select(this);rt(ie,v),rt(ie,tt),rt(ie,ne)});De(Zt,Mt),De(Zr,ne),L.push({node:ht[K],row:N,start:B,end:B+M+T+Mn}),u==="horizontal"?B+=Mn+M+2*T:N+=M+T}).on("mouseover",(J,K)=>{R.select(J.currentTarget).classed("hovered",!0)}).on("mouseout",(J,K)=>{R.select(J.currentTarget).classed("hovered",!1)}).on("click",(J,K)=>{if(J.detail>1||b&&J.bubbles)return;let ht=R.select(J.currentTarget);ht.classed("unselected")?ht.classed("unselected",!1):ht.classed("unselected",!0);let G=q.selectAll(".unselected").data(),tt=this.data.filter(ot=>G.includes(ot[t])).map(ot=>ot.rowID);n&&typeof n=="string"?R.select("#"+n).selectAll("[rowID]").each(function(){let ot=+R.select(this).attr("rowID");tt.includes(ot)?R.select(this).style("display","none"):R.select(this).style("display","")}):R.selectAll("[rowID]").each(function(){let ot=+R.select(this).attr("rowID");tt.includes(ot)?R.select(this).style("display","none"):R.select(this).style("display","")})}),i&&U==="right"&&Z();let Q={center:.5,right:1}[h]??0;if(Q>0){let J=this.width-this.margin.left-this.margin.right,K=G=>u==="horizontal"?G.row:0,ht=R.rollup(L,G=>R.max(G,tt=>tt.end)-R.min(G,tt=>tt.start),K);L.forEach(G=>{let tt=Math.max(0,J-ht.get(K(G)))*Q;R.select(G.node).attr("transform",`translate(${tt}, 0)`)})}if(f&&this.height===0){var j=20,H=N+M+T+j;S.attr("height",H);var W=k;S.attr("viewBox",`0 0 ${W} ${H}`),q.attr("transform",`translate(${this.margin.left}, ${this.margin.top+j/2})`)}return this};ft.prototype.links=function(t,e,n={}){let r={y:50,showLinks:!0,label:!0,measure:"identity",linkWidth:1,labelStyle:{cursor:"pointer",fontSize:"12px",fontStyle:"italic",fontFamily:"sans-serif",textAnchor:"middle"},labelAdjustmentOptions:{rotation:-65,offsetX:0,offsetY:0,dx:"0em",dy:"0em"}};if(!t||t.length===0)return this;let i=ut.call(this,r,"linkOptions",n),{x:o,y:a,cursor:s,fontSize:c,fontStyle:l,fontFamily:u,textAnchor:h,showLinks:f,label:d,measure:m,labelStyle:p,labelAdjustmentOptions:g,linkWidth:y}=i,w=at(n,r),b=at(p,r.labelStyle);var v=this.svg.append("g").attr("data-component","links").attr("transform",`translate(${this.margin.left}, ${this.margin.top})`);let S=this.data.some(k=>k.strand==="reverse")?this.geneStrandSpacing*1:0;if(f&&t.forEach(k=>{let C=(1-y)/2,F=k.start1+(k.end1-k.start1)*C,A=k.end1-(k.end1-k.start1)*C,E=k.start2+(k.end2-k.start2)*C,D=k.end2-(k.end2-k.start2)*C;if(k.cluster1===e){let $=k.groupColor?this.genesColorScale(k.groupColor):this.genesColorScale(k.group1);v.append("circle").attr("cx",this.xScale(F)).attr("cy",this.yScale(a)+S).attr("position",k.start1).attr("r",1).attr("cluster",e).attr("visibility","hidden").attr("groupColor",$).attr("linkID",k.linkID).attr("class","link-marker"),v.append("circle").attr("cx",this.xScale(A)).attr("cy",this.yScale(a)+S).attr("position",k.end1).attr("class","link-marker").attr("groupColor",$).attr("visibility","hidden").attr("linkID",k.linkID).attr("cluster",e).attr("r",1)}if(k.cluster2===e){let $=k.groupColor?this.genesColorScale(k.groupColor):this.genesColorScale(k.group2);v.append("circle").attr("cx",this.xScale(E)).attr("cy",this.yScale(a)-S).attr("position",k.start2).attr("class","link-marker").attr("cluster",e).attr("visibility","hidden").attr("groupColor",$).attr("linkID",k.linkID).attr("r",1),v.append("circle").attr("cx",this.xScale(D)).attr("cy",this.yScale(a)-S).attr("position",k.end2).attr("class","link-marker").attr("linkID",k.linkID).attr("cluster",e).attr("visibility","hidden").attr("groupColor",$).attr("r",1)}}),d&&i.labelPosition!=="link"){let k=Zl(this,".link-text"),C=this.svg.selectAll(".link-text").nodes(),F=new Set(C.map(E=>E.getAttribute("rowID"))),A=this.data.filter(E=>!F.has(`${E.rowID}`)&&E[m]!=null&&E.BlastP!="No Hit"&&(E.BlastP===void 0||E.BlastP!=E.protein_id&&E.BlastP)&&(n.value1===void 0&&n.value2===void 0||n.value1&&n.value1.includes(E[n.group])||n.value2&&n.value2.includes(E[n.group])));v.selectAll(".link-text").data(A).enter().append("text").attr("id",(E,D)=>`cluster-${wr(E.cluster)}-link-label-${C.length+D}`).attr("rowID",(E,D)=>`${E.rowID}`).attr("class","link-text").attr("x",(E,D)=>this.xScale((E.start+E.end)/2)).attr("y",(E,D)=>this.yScale(a)-this.markerHeight/1.5-S).text(E=>`${parseFloat(E[m].toFixed(1))}%`).style("font-size",p.fontSize).style("font-style",p.fontStyle).style("font-family",p.fontFamily).style("cursor",p.cursor).attr("text-anchor",p.textAnchor).attr("cluster",e).each(function(E,D){let $=R.select(this);k.adjust(this,g),rt($,b),ma(b)&&k.refresh(this)})}return this};ft.prototype.trackMouse=function(t=!0,e={}){if(!t)return this;let n={cursor:"crosshair",backgroundColor:"rgba(255, 255, 255, 0.9)",padding:"8px",borderRadius:"4px",border:"1px solid rgba(0,0,0,0.1)",boxShadow:"0 4px 6px rgba(0, 0, 0, 0.1)",fontFamily:"Arial, sans-serif",fontSize:"12px",color:"#333",lineHeight:"1.5",zIndex:1e3},{cursor:r,show:i,...o}=ut.call(this,n,"trackMouseOptions",e);this.svg.style("cursor",r),this.svg.selectAll("*").each(function(){this.style.cssText+=`cursor: ${r} !important;`});let a=this.svg.node().closest(".html-widget")||document.body,s=R.select(a).append("div").attr("class","coordinate-tooltip").style("pointer-events","none").style("position","absolute").style("visibility","hidden");rt(s,o);let c=R.scaleLinear().domain([0+this.margin.left,this.width-this.margin.right]).range([0,100]),l=R.scaleLinear().domain([this.height-this.margin.bottom,0+this.margin.top]).range([0,100]),u=R.scaleLinear().domain([0-this.margin.left,this.width]).range([0,100]);return this.svg.on("mousemove",h=>{let[f,d]=R.pointer(h),m=f-this.margin.left,p=Math.round(this.xScale.invert(m)),g=R.format(",");s.html(`x: ${g(p)} <br>y: ${l(d).toFixed(1)}`).style("visibility","visible").style("left",R.pointer(h,a)[0]+10+"px").style("top",R.pointer(h,a)[1]-10+"px")}),this.svg.on("mouseout",()=>{s.style("visibility","hidden")}),this};var bE=["sequence","genes","transcript","links","coordinates","labels","annotations"];ft.prototype.clipZoom=function(){if(!this.zoom)return this;let t=this.svg.node(),e=Array.from(t.children).filter(i=>bE.includes(i.getAttribute("data-component")));if(!e.length)return this;let n=this.width-this.margin.left-this.margin.right,r=document.createElementNS("http://www.w3.org/2000/svg","svg");return r.setAttribute("class","geneviewer-zoom-clip"),r.setAttribute("x",this.margin.left),r.setAttribute("y",0),r.setAttribute("width",n),r.setAttribute("height",this.height),r.setAttribute("viewBox",`${this.margin.left} 0 ${n} ${this.height}`),r.setAttribute("preserveAspectRatio","none"),r.setAttribute("overflow","hidden"),t.insertBefore(r,e[0]),e.forEach(i=>r.appendChild(i)),this};ft.prototype.addAnnotations=function(t){if(!t||t.length===0)return this;var e=this.svg.append("g").attr("data-component","annotations").attr("transform",`translate(${this.margin.left}, ${this.margin.top})`);return t.forEach(n=>{this.createAnnotation(e,n)}),this};ft.prototype.createAnnotation=function(t,e){switch(e.type){case"text":this.createTextAnnotation(t,e);break;case"line":this.createLineAnnotation(t,e);break;case"textMarker":this.createTextMarkerAnnotation(t,e);break;case"arrow":this.createArrowAnnotation(t,e);break;case"promoter":this.createPromoterAnnotation(t,e);break;case"terminator":this.createTerminatorAnnotation(t,e);break;case"rectangle":this.createRectangleAnnotation(t,e);break;case"symbol":this.createSymbolAnnotation(t,e);break;case"arc":this.createCurveAnnotation(t,e);break;default:qe("Unsupported annotation type: "+e.type)}};ft.prototype.createTextAnnotation=function(l,e){let n={x:0,y:60,text:"",style:{fontSize:"10px",fontStyle:"normal",fontWeight:"normal",textDecoration:"none",fontFamily:"sans-serif",cursor:"default"}},r=ut.call(this,n,"textAnnotationOptions",e),{x:i,y:o,text:a,style:s}=r;Array.isArray(i)||(i=[i]),Array.isArray(o)||(o=[o]),Array.isArray(a)||(a=[a]);let c=at(s,n.style);var l=this.svg.append("g").attr("data-component","annotations").attr("transform",`translate(${this.margin.left}, ${this.margin.top})`);for(let u=0;u<Math.max(i.length,o.length,a.length);u++){let h=i[Math.min(u,i.length-1)],f=o[Math.min(u,o.length-1)],d=a[Math.min(u,a.length-1)];l.append("text").attr("x",this.xScale(h)).attr("y",this.yScale(f)).style("font-size",s.fontSize).style("font-style",s.fontStyle).style("font-weight",s.fontWeight).style("text-decoration",s.textDecoration).style("font-family",s.fontFamily).style("cursor",s.cursor).each(function(){let m=R.select(this);xr(d,m,s),rt(m,c)})}};ft.prototype.createLineAnnotation=function(u,e){let n={x1:0,y1:70,x2:0,y2:50,style:{stroke:"black",strokeWidth:1}},r=ut.call(this,n,"lineAnnotationOptions",e),{x1:i,y1:o,x2:a,y2:s,style:c}=r;Array.isArray(i)||(i=[i]),Array.isArray(o)||(o=[o]),Array.isArray(a)||(a=[a]),Array.isArray(s)||(s=[s]);let l=at(c,n.style);var u=this.svg.append("g").attr("data-component","annotations").attr("transform",`translate(${this.margin.left}, ${this.margin.top})`);for(let h=0;h<Math.max(i.length,o.length,a.length,s.length);h++){let f=i[Math.min(h,i.length-1)],d=o[Math.min(h,o.length-1)],m=a[Math.min(h,a.length-1)],p=s[Math.min(h,s.length-1)];u.append("line").attr("x1",this.xScale(f)).attr("y1",this.yScale(d)).attr("x2",this.xScale(m)).attr("y2",this.yScale(p)).style("stroke",c.stroke).style("stroke-width",c.strokeWidth).each(function(){let g=R.select(this);rt(g,l)})}};ft.prototype.createArrowAnnotation=function(d,e){let n={x1:1,y1:70,x2:1,y2:50,arrowSize:8,arrowStyle:{fill:"black"},lineStyle:{stroke:"black",strokeWidth:1}},r=ut.call(this,n,"arrowAnnotationOptions",e),{x1:i,y1:o,x2:a,y2:s,arrowSize:c,arrowStyle:l,lineStyle:u}=r;Array.isArray(i)||(i=[i]),Array.isArray(o)||(o=[o]),Array.isArray(a)||(a=[a]),Array.isArray(s)||(s=[s]),Array.isArray(c)||(c=[c]);let h=at(u,n.lineStyle),f=at(l,n.arrowStyle);var d=this.svg.append("g").attr("data-component","annotations").attr("transform",`translate(${this.margin.left}, ${this.margin.top})`);for(let m=0;m<Math.max(i.length,o.length,a.length,s.length,c.length);m++){let p=i[Math.min(m,i.length-1)],g=o[Math.min(m,o.length-1)],y=a[Math.min(m,a.length-1)],w=s[Math.min(m,s.length-1)],b=c[Math.min(m,c.length-1)],v=Xr("arrowhead");this.svg.append("defs").append("marker").attr("id",v).attr("viewBox","-0 -5 10 10").attr("refX",5).attr("refY",0).attr("orient","auto").attr("markerWidth",b).attr("markerHeight",b).attr("xoverflow","visible").append("path").attr("d","M 0,-5 L 10 ,0 L 0,5").attr("fill",l.fill).each(function(){let _=R.select(this);rt(_,f)}),d.append("line").attr("x1",this.xScale(p)).attr("y1",this.yScale(g)).attr("x2",this.xScale(y)).attr("y2",this.yScale(w+b/2)).attr("marker-end",`url(#${v})`).style("stroke",u.stroke).style("stroke-width",u.strokeWidth).each(function(){let _=R.select(this);rt(_,h)})}};ft.prototype.createTextMarkerAnnotation=function(t,e){let n={x1:null,y1:66,x2:null,y2:50,position:0,text:"",labelX:0,labelY:0,showArrow:!1,arrowSize:8,textStyle:{fontSize:"10px",fontFamily:"sans-serif",fill:"black",textAnchor:"middle"},arrowStyle:{fill:"black"},lineStyle:{stroke:"black",strokeWidth:1}},r=ut.call(this,n,"textMarkerAnnotationOptions",e),{textStyle:i,arrowStyle:o,lineStyle:a}=r,s=["x1","y1","x2","y2","position","text","labelX","labelY","showArrow","arrowSize"];s.forEach(h=>{Array.isArray(r[h])||(r[h]=[r[h]])});let c=at(a,n.lineStyle),l=at(o,n.arrowStyle),u=Math.max(...s.map(h=>r[h].length));for(let h=0;h<u;h++){let f={};s.forEach(b=>{f[b]=r[b][h%r[b].length]});let d=f.showArrow?f.arrowSize/2:0;var t=this.svg.insert("g",":first-child").attr("transform",`translate(${this.margin.left}, ${this.margin.top})`);let p=Math.round(this.xScale(f.x1!==null?f.x1:f.position)),g=Math.round(this.xScale(f.x2!==null?f.x2:f.position)),y=t.append("line").attr("x1",p).attr("y1",this.yScale(f.y1)).attr("x2",g).attr("y2",this.yScale(f.y2+d)).style("stroke",a.stroke).style("stroke-width",a.strokeWidth).each(function(){let b=R.select(this);rt(b,c)}),w=Xr("arrowhead-marker");this.svg.append("defs").append("marker").attr("id",w).attr("viewBox","-0 -5 10 10").attr("refX",5).attr("refY",0).attr("orient","auto").attr("markerWidth",f.arrowSize).attr("markerHeight",f.arrowSize).attr("xoverflow","visible").append("path").attr("d","M 0,-5 L 10 ,0 L 0,5").attr("fill",o.fill).each(function(){let b=R.select(this);rt(b,l)}),f.showArrow&&y.attr("marker-end",`url(#${w})`),f.text&&t.append("text").attr("x",this.xScale(f.x1!==null?f.x1:f.position)+f.labelX).attr("y",this.yScale(f.y1)-5-f.labelY).style("text-anchor",i.textAnchor).style("font-size",i.fontSize).style("font-family",i.fontFamily).style("fill",i.fill).each(function(){let b=R.select(this);xr(f.text,b,i),rt(b,at(i,n.textStyle))})}return t};ft.prototype.createSymbolAnnotation=function(u,e){let n={x:0,y:50,size:64,symbol:"circle",style:{fill:"black",stroke:"black",strokeWidth:2},rotation:0},r=ut.call(this,n,"symbolAnnotationOptions",e),{x:i,y:o,size:a,symbol:s,style:c,rotation:l}=r;Array.isArray(i)||(i=[i]),Array.isArray(o)||(o=[o]),Array.isArray(s)||(s=[s]),Array.isArray(l)||(l=[l]),Array.isArray(a)||(a=[a]);var u=this.svg.append("g").attr("data-component","annotations").attr("transform",`translate(${this.margin.left}, ${this.margin.top})`);let h=at(c,n.style),f={circle:R.symbolCircle,cross:R.symbolCross,diamond:R.symbolDiamond,square:R.symbolSquare,star:R.symbolStar,triangle:R.symbolTriangle,wye:R.symbolWye};for(let d=0;d<Math.max(i.length,o.length,s.length,l.length);d++){let m=i[Math.min(d,i.length-1)],p=o[Math.min(d,o.length-1)],g=s[Math.min(d,s.length-1)],y=l[Math.min(d,l.length-1)],w=a[Math.min(d,a.length-1)];if(!f[g]){console.error(`Unsupported symbol type: ${g}`);continue}let b=R.symbol().type(f[g]).size(w);u.append("path").attr("d",b).attr("transform",`translate(${this.xScale(m)}, ${this.yScale(p)}) rotate(${y})`).style("fill",c.fill).style("stroke",c.stroke).style("stroke-width",c.strokeWidth).each(function(){let v=R.select(this);rt(v,h)})}return u};ft.prototype.createRectangleAnnotation=function(c,e){let n={position:[[[9300,20],[9400,50]]],rotation:[0],style:{fill:"#0000",stroke:"black",strokeWidth:2}},r=ut.call(this,n,"rectangleAnnotationOptions",e),{position:i,style:o,rotation:a}=r;Array.isArray(i[0][0])||(i=[i]),Array.isArray(a)||(a=[a]);let s=at(o,n.style);var c=this.svg.append("g").attr("data-component","annotations").attr("transform",`translate(${this.margin.left}, ${this.margin.top})`);let l=Math.max(i.length,a.length);for(let u=0;u<l;u++){let h=i[Math.min(u,i.length-1)],f=a[Math.min(u,a.length-1)],d=Math.min(h[0][0],h[1][0]),m=Math.max(h[0][0],h[1][0]),p=Math.max(h[0][1],h[1][1]),g=Math.min(h[0][1],h[1][1]),y=Math.abs(d-m),w=Math.abs(g-p);c.append("rect").attr("x",this.xScale(d)).attr("y",this.yScale(p)).attr("width",this.xScale(m)-this.xScale(d)).attr("height",this.yScale(g)-this.yScale(p)).attr("transform",`rotate(${f}, ${this.xScale(d+y/2)}, ${this.yScale(p+w/2)})`).style("fill",o.fill).style("stroke",o.stroke).style("stroke-width",o.strokeWidth).each(function(){let b=R.select(this);rt(b,s)})}};ft.prototype.createPromoterAnnotation=function(d,e){let n={x:0,y:50,direction:"forward",rotation:0,scale:1,style:{fill:"none",stroke:"black",strokeWidth:1}},r=ut.call(this,n,"promoterAnnotationOptions",e),{x:i,y:o,direction:a,rotation:s,scale:c,style:l}=r,u=at(l,n.style);Array.isArray(i)||(i=[i]),Array.isArray(o)||(o=[o]),Array.isArray(a)||(a=[a]),Array.isArray(s)||(s=[s]),Array.isArray(c)||(c=[c]);let h="M -8 -17.5 L -13 -14 l 5 3.5 M -13 -14 L 0 -14 v 14",f="M 8 -17.5 L 13 -14 l -5 3.5 M 13 -14 H 0 v 14";var d=this.svg.append("g").attr("data-component","annotations").attr("transform",`translate(${this.margin.left}, ${this.margin.top})`);for(let m=0;m<Math.max(i.length,o.length,a.length,s.length,c.length);m++){let p=i[Math.min(m,i.length-1)],g=o[Math.min(m,o.length-1)],y=a[Math.min(m,a.length-1)],w=s[Math.min(m,s.length-1)],b=c[Math.min(m,c.length-1)],v=y==="forward"?f:h,_=this.xScale(p);d.append("path").attr("d",v).attr("transform",`translate(${_}, ${this.yScale(g)}) scale(${b}) rotate(${w})`).style("fill",l.fill).style("stroke",l.stroke).style("stroke-width",l.strokeWidth).each(function(){let S=R.select(this);rt(S,u)})}};ft.prototype.createTerminatorAnnotation=function(d,e){let n={x:0,y:50,direction:"forward",rotation:0,scale:1,style:{fill:"none",stroke:"black",strokeWidth:1}},r=ut.call(this,n,"terminatorAnnotationOptions",e),{x:i,y:o,direction:a,rotation:s,scale:c,style:l}=r,u=at(l,n.style);Array.isArray(i)||(i=[i]),Array.isArray(o)||(o=[o]),Array.isArray(a)||(a=[a]),Array.isArray(s)||(s=[s]),Array.isArray(c)||(c=[c]);let h="M -8 17.5 L -13 14 l 5 -3.5 M -13 14 H 0 v -14",f="M 8 17.5 L 13 14 l -5 -3.5 M 13 14 L 0 14 v -14";var d=this.svg.append("g").attr("data-component","annotations").attr("transform",`translate(${this.margin.left}, ${this.margin.top})`);for(let m=0;m<Math.max(i.length,o.length,a.length,s.length,c.length);m++){let p=i[Math.min(m,i.length-1)],g=o[Math.min(m,o.length-1)],y=a[Math.min(m,a.length-1)],w=s[Math.min(m,s.length-1)],b=c[Math.min(m,c.length-1)],v=y==="forward"?h:f,_=this.xScale(p);d.append("path").attr("d",v).attr("transform",`translate(${_}, ${this.yScale(g)}) scale(${b}) rotate(${w})`).style("fill",l.fill).style("stroke",l.stroke).style("stroke-width",l.strokeWidth).each(function(){let S=R.select(this);rt(S,u)})}};ft.prototype.createCurveAnnotation=function(y,e){let n={x1:[0],y1:[50],x2:[100],y2:[50],midY:[80],stroke:["black"],strokeWidth:[1],lineStyle:{},text:[""],labelX:[0],labelY:[0],textStyle:{fontSize:"10px",fontFamily:"sans-serif",fill:"black",textAnchor:"middle"}},r=ut.call(this,n,"curveAnnotationOptions",e);["x1","y1","x2","y2","midY","stroke","strokeWidth","text","labelX","labelY"].forEach(w=>{Array.isArray(r[w])||(r[w]=[r[w]])});let{x1:o,y1:a,x2:s,y2:c,midY:l,stroke:u,strokeWidth:h,lineStyle:f,text:d,labelX:m,labelY:p,textStyle:g}=r;var y=this.svg.append("g").attr("data-component","annotations").attr("transform",`translate(${this.margin.left}, ${this.margin.top})`);for(let w=0;w<Math.max(o.length,a.length,s.length,c.length,d.length,m.length,p.length);w++){let b=o[w%o.length],v=a[w%a.length],_=s[w%s.length],S=c[w%c.length],k=l[w%l.length],C=u[w%u.length],F=h[w%h.length],A=d[w%d.length],E=m[w%m.length],D=p[w%p.length],$=(b+_)/2,M=R.line().curve(R.curveBasis).x(L=>this.xScale(L.x)).y(L=>this.yScale(L.y)),T=[{x:b,y:v},{x:$,y:k},{x:_,y:S}],B=y.append("path").attr("d",M(T)).style("stroke",C).style("stroke-width",F).style("fill","none");rt(B,at(f,n.lineStyle));let N=y.append("text").attr("x",this.xScale($)+E).attr("y",this.yScale(k)-D).text(A);rt(N,g)}};var Ke=class t{constructor(e={}){this.columns=new Map(Object.entries(e))}static from(e){if(e instanceof t)return e.copy();if(Array.isArray(e)){let r=[];for(let o of e)for(let a of Object.keys(o))r.includes(a)||r.push(a);let i=new t;for(let o of 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n=Object.keys(t);if(!n.length)return;let r=n[e%n.length];return{[r]:t[r]}}return t}}function wa(t,e,n){return Object.prototype.hasOwnProperty.call(t,e)?t[e]:n}function Ht(t){return t!==null&&typeof t=="object"&&!Array.isArray(t)}function Jy(t){return t==null?!0:Array.isArray(t)?t.length===0:Ht(t)?Object.keys(t).length===0:!1}function Ce(t){let e={};for(let[n,r]of Object.entries(t))r!=null&&(Array.isArray(r)&&r.length===0||Ht(r)&&Object.keys(r).length===0||(e[n]=r));return e}function xa(t){let e={};for(let[n,r]of Object.entries(t))r!=null&&(e[n]=r);return e}function Gr(t,e){let n=Ht(t)?{...t}:{};for(let[r,i]of Object.entries(e||{}))i==null?delete n[r]:Ht(n[r])&&Ht(i)?n[r]=Gr(n[r],i):n[r]=i;return n}function Qe(t,e){return t==null?e:Gr(t,e)}function Kl(t,e=2){if(typeof t=="number")return t/e;if(/px$/.test(t))return`${pe(Gi(t.replace(/px$/,""))/e)}px`;if(/%$/.test(t))return`${pe(Gi(t.replace(/%$/,""))/e)}%`;throw new Error("Unsupported format")}function Vn(t,e){let n=o=>typeof 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r={x:1,y:50,colorScheme:null,customColors:null,pattern:null,styleExons:{show:!0,strokeWidth:0,cursor:"default",marker:"box",markerSize:"medium",arrowheadWidth:null,arrowheadHeight:null,markerHeight:null,cornerRadius:null},styleIntrons:{show:!0,strokeWidth:1,fill:"none",cursor:"default",marker:"intron",markerSize:"medium",arrowheadWidth:null,arrowheadHeight:null,markerHeight:null,cornerRadius:null},styleUTRs:{show:!0,fontSize:"10px",fontStyle:"normal",fontFamily:"sans-serif",cursor:"default",color:"black",fill:"#FFF",strokeWidth:1,marker:"box",markerSize:"medium",arrowheadWidth:null,arrowheadHeight:null,markerHeight:null,cornerRadius:null},labelOptions:{show:!0,xOffset:2,yOffset:0,fontSize:"12px",fontStyle:"normal",fontWeight:"normal",fontFamily:"sans-serif",cursor:"default",color:"black"},itemStyleExons:[],itemStyleIntrons:[],itemStyleUTRs:[],groupStyleExons:{},groupStyleIntrons:{},groupStyleUTRs:{},styleBy:null},i=ut.call(this,r,"transcriptOptions",n),{x:o,y:a,colorScheme:s,customColors:c,pattern:l,styleExons:u,styleIntrons:h,styleUTRs:f,labelOptions:d}=i,m=i.styleBy??t,p=at(i.styleExons,r.styleExons),g=at(i.styleIntrons,r.styleIntrons),y=at(i.styleUTRs,r.styleUTRs),w=[...new Set(this.dataAll.map(A=>A[t]))],b=ji(s,c,w);this.genesColorScale=b;let v=Xi(this.svg,l,w,b,"exon"),_=this.svg.append("g").attr("data-component","transcript").attr("transform",`translate(${this.margin.left}, ${this.margin.top})`);this.data.sort((A,E)=>Math.min(A.start,A.end)-Math.min(E.start,E.end));let S=(A,E,D,z)=>Ph(this,A,E,a,D,z),k=(A,E,D,z,M,T,B,N)=>{let L=this.data.filter(U=>new RegExp(A,"i").test(U.type)),q=Ui(L,m,D,z);return _.selectAll(`.${A}`).data(L).enter().append("path").attr("d",(U,Z)=>S(U,Z,E,q).path).attr("transform",(U,Z)=>T(U,S(U,Z,E,q))).attr("fill",B).attr("class",A).attr("id",(U,Z)=>`${wr(U.cluster)}-${A}-${Z}`).call(Nh).style("stroke-width",E.strokeWidth).style("stroke",N).style("cursor",E.cursor).each(function(U,Z){let Q=R.select(this);rt(Q,M),Hi(Q,q,Z)}),_.selectAll(`.${A}`)},C=(A,E)=>Rh(this.reverse,A,E),F=A=>v.stroke(A[t]);if(u.show&&(this.exons=k("exon",u,i.groupStyleExons,i.itemStyleExons,p,C,A=>v.fill(A[t]),u.stroke)),h.show){let A=(E,{xPos:D,yPos:z,height:M})=>{let T=E.direction==="forward"?-M:+M;return`rotate(${this.reverse?E.direction==="reverse"?180:0:E.direction==="forward"?0:180}, ${D}, ${z+T}) translate(${D}, ${z+T})`};this.introns=k("intron",h,i.groupStyleIntrons,i.itemStyleIntrons,g,A,h.fill,F)}if(f.show&&(this.utrs=k("utr",f,i.groupStyleUTRs,i.itemStyleUTRs,y,C,f.fill,F),d.show)){let A=this.data[0].direction==="forward"?this.xScale(this.maxEnd)+d.xOffset:this.xScale(this.minStart)-d.xOffset,E=this.data[0].direction==="forward"?this.xScale(this.minStart)-d.xOffset:this.xScale(this.maxEnd)+d.xOffset;_.append("text").attr("x",A).attr("y",D=>this.yScale(a+d.yOffset)).attr("class","three-prime-label").attr("text-anchor","middle").attr("alignment-baseline","middle").style("font-size",d.fontSize).style("font-style",d.fontStyle).style("font-weight",d.fontWeight).style("font-family",d.fontFamily).style("cursor",d.cursor).style("fill",d.color).text("3'"),_.append("text").attr("x",E).attr("y",D=>this.yScale(a+d.yOffset)).attr("class","five-prime-label").attr("text-anchor","middle").attr("alignment-baseline","middle").style("font-size",d.fontSize).style("font-style",d.fontStyle).style("font-weight",d.fontWeight).style("font-family",d.fontFamily).style("cursor",d.cursor).style("fill",d.color).text("5'")}return this};function mE(t,e){return e.map(r=>{let i=`.link-marker[cluster='${r.cluster1}'][linkID='${r.linkID}'][position='${r.start1}']`,o=`.link-marker[cluster='${r.cluster2}'][linkID='${r.linkID}'][position='${r.start2}']`,a=`.link-marker[cluster='${r.cluster1}'][linkID='${r.linkID}'][position='${r.end1}']`,s=`.link-marker[cluster='${r.cluster2}'][linkID='${r.linkID}'][position='${r.end2}']`,c=t.select(i).node(),l=t.select(o).node(),u=t.select(a).node(),h=t.select(s).node();if(!c||!l||!u||!h)return null;let f=c.getBoundingClientRect(),d=l.getBoundingClientRect(),m=u.getBoundingClientRect(),p=h.getBoundingClientRect(),g=t.node().getBoundingClientRect(),y=S=>({x:S.left-g.left,y:S.top-g.top}),w=r.start1<=r.end1?"forward":"reverse",b=r.start2<=r.end2?"forward":"reverse",v=c.getAttribute("groupColor"),_=l.getAttribute("groupColor");return[{startPoint:y(f),endPoint:y(d),strand:w,groupColor:v},{startPoint:y(m),endPoint:y(p),strand:b,groupColor:_}]})}var 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h=ut(r,"linkOptions",u.options,n),{curve:f,invertedColor:d,normalColor:m,lowColor:p,vmin:g,vmax:y,useGroupColors:w,color:b,linkStyle:v,measure:_}=h,S=at(v,r.linkStyle),k=jr(u.data);mE(t,k).forEach(function(F,A){if(!F)return;let E=F[0].strand==F[1].strand?R.rgb(m):R.rgb(d);var D=Vy(p,E,g,y);let z=h.measure==="none"?100:u.data?.[_]?.[A]??100,M=w?F[0].groupColor:D(z);a.append("path").attr("data-component","links").datum(k[A]).attr("d",yE(F[0],F[1],f)).style("fill",M).style("stroke",v.stroke).style("fill-opacity",v.fillOpacity).classed("GeneLink",!0).each(function(){let B=R.select(this);rt(B,S)});let T=u.data?.[_]?.[A];if(h.label&&h.labelPosition==="link"&&_!=="none"&&T!=null&&Number.isFinite(+T)){let B=(F[0].startPoint.x+F[0].endPoint.x)/2,N=(F[1].startPoint.x+F[1].endPoint.x)/2;s.push({x:(B+N)/2,y:(F[0].startPoint.y+F[0].endPoint.y)/2,width:Math.abs(N-B),text:`${parseFloat((+T).toFixed(1))}%`,fill:R.hsl(R.color(M)??"#ffffff").l<.55?"#ffffff":"#333333",datum:k[A],labelStyle:h.labelStyle,defaults:r.labelStyle})}})});let c=a.append("g").attr("class","link-measure-labels"),l=[];s.sort((u,h)=>h.width-u.width).forEach(u=>{let{labelStyle:h}=u,f=c.append("text").attr("class","link-measure").attr("data-component","links").datum(u.datum).attr("x",u.x).attr("y",u.y).attr("text-anchor","middle").attr("dominant-baseline","central").style("font-size",h.fontSize).style("font-style",h.fontStyle).style("font-family",h.fontFamily).style("fill",u.fill).style("pointer-events","none").text(u.text).each(function(){let p=at(h,u.defaults);delete 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Set(t)],this};ft.prototype.legend=function(t,e=!0,n=null,r={},i=null){if(!e)return this;let o={x:0,y:0,width:null,orientation:"horizontal",align:"left",adjustHeight:!0,order:[],cornerRadius:0,groupStyle:{},legendOptions:{cursor:"pointer",colorScheme:null,customColors:null,pattern:null},legendTextOptions:{cursor:"pointer",textAnchor:"start",dy:".35em",fontSize:"12px",fontFamily:"sans-serif"}},a=ut.call(this,o,"legendOptions",r),{x:s,y:c,width:l,orientation:u,align:h,adjustHeight:f,order:d,cornerRadius:m,legendOptions:p,legendTextOptions:g,groupStyle:y,itemStyle:w=[],editable:b=!1}=a,v=at(p,o.legendOptions),_=at(g,o.legendTextOptions),S=this.svg,k=Le(l,S.node().getBoundingClientRect().width)||S.node().getBoundingClientRect().width,C=[...new Set(this.data.map(J=>J[t]))];C=C.filter(J=>J!==null);let F=ji(p.colorScheme,p.customColors,C),A=Xi(this.svg,p.pattern,C,F,"legend"),E=["Other","No 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ot=+R.select(this).attr("rowID");tt.includes(ot)?R.select(this).style("display","none"):R.select(this).style("display","")}):R.selectAll("[rowID]").each(function(){let ot=+R.select(this).attr("rowID");tt.includes(ot)?R.select(this).style("display","none"):R.select(this).style("display","")})}),i&&U==="right"&&Z();let Q={center:.5,right:1}[h]??0;if(Q>0){let J=this.width-this.margin.left-this.margin.right,K=G=>u==="horizontal"?G.row:0,ht=R.rollup(L,G=>R.max(G,tt=>tt.end)-R.min(G,tt=>tt.start),K);L.forEach(G=>{let tt=Math.max(0,J-ht.get(K(G)))*Q;R.select(G.node).attr("transform",`translate(${tt}, 0)`)})}if(f&&this.height===0){var j=20,H=N+M+T+j;S.attr("height",H);var W=k;S.attr("viewBox",`0 0 ${W} ${H}`),q.attr("transform",`translate(${this.margin.left}, ${this.margin.top+j/2})`)}return this};ft.prototype.links=function(t,e,n={}){let r={y:50,showLinks:!0,label:!0,measure:"identity",linkWidth:1,labelStyle:{cursor:"pointer",fontSize:"12px",fontStyle:"italic",fontFamily:"sans-serif",textAnchor:"middle"},labelAdjustmentOptions:{rotation:-65,offsetX:0,offsetY:0,dx:"0em",dy:"0em"}};if(!t||t.length===0)return this;let i=ut.call(this,r,"linkOptions",n),{x:o,y:a,cursor:s,fontSize:c,fontStyle:l,fontFamily:u,textAnchor:h,showLinks:f,label:d,measure:m,labelStyle:p,labelAdjustmentOptions:g,linkWidth:y}=i,w=at(n,r),b=at(p,r.labelStyle);var v=this.svg.append("g").attr("data-component","links").attr("transform",`translate(${this.margin.left}, ${this.margin.top})`);let S=this.data.some(k=>k.strand==="reverse")?this.geneStrandSpacing*1:0;if(f&&t.forEach(k=>{let C=(1-y)/2,F=k.start1+(k.end1-k.start1)*C,A=k.end1-(k.end1-k.start1)*C,E=k.start2+(k.end2-k.start2)*C,D=k.end2-(k.end2-k.start2)*C;if(k.cluster1===e){let z=k.groupColor?this.genesColorScale(k.groupColor):this.genesColorScale(k.group1);v.append("circle").attr("cx",this.xScale(F)).attr("cy",this.yScale(a)+S).attr("position",k.start1).attr("r",1).attr("cluster",e).attr("visibility","hidden").attr("groupColor",z).attr("linkID",k.linkID).attr("class","link-marker"),v.append("circle").attr("cx",this.xScale(A)).attr("cy",this.yScale(a)+S).attr("position",k.end1).attr("class","link-marker").attr("groupColor",z).attr("visibility","hidden").attr("linkID",k.linkID).attr("cluster",e).attr("r",1)}if(k.cluster2===e){let z=k.groupColor?this.genesColorScale(k.groupColor):this.genesColorScale(k.group2);v.append("circle").attr("cx",this.xScale(E)).attr("cy",this.yScale(a)-S).attr("position",k.start2).attr("class","link-marker").attr("cluster",e).attr("visibility","hidden").attr("groupColor",z).attr("linkID",k.linkID).attr("r",1),v.append("circle").attr("cx",this.xScale(D)).attr("cy",this.yScale(a)-S).attr("position",k.end2).attr("class","link-marker").attr("linkID",k.linkID).attr("cluster",e).attr("visibility","hidden").attr("groupColor",z).attr("r",1)}}),d&&i.labelPosition!=="link"){let k=Zl(this,".link-text"),C=this.svg.selectAll(".link-text").nodes(),F=new Set(C.map(E=>E.getAttribute("rowID"))),A=this.data.filter(E=>!F.has(`${E.rowID}`)&&E[m]!=null&&E.BlastP!="No Hit"&&(E.BlastP===void 0||E.BlastP!=E.protein_id&&E.BlastP)&&(n.value1===void 0&&n.value2===void 0||n.value1&&n.value1.includes(E[n.group])||n.value2&&n.value2.includes(E[n.group])));v.selectAll(".link-text").data(A).enter().append("text").attr("id",(E,D)=>`cluster-${wr(E.cluster)}-link-label-${C.length+D}`).attr("rowID",(E,D)=>`${E.rowID}`).attr("class","link-text").attr("x",(E,D)=>this.xScale((E.start+E.end)/2)).attr("y",(E,D)=>this.yScale(a)-this.markerHeight/1.5-S).text(E=>`${parseFloat(E[m].toFixed(1))}%`).style("font-size",p.fontSize).style("font-style",p.fontStyle).style("font-family",p.fontFamily).style("cursor",p.cursor).attr("text-anchor",p.textAnchor).attr("cluster",e).each(function(E,D){let z=R.select(this);k.adjust(this,g),rt(z,b),ma(b)&&k.refresh(this)})}return this};ft.prototype.trackMouse=function(t=!0,e={}){if(!t)return this;let n={cursor:"crosshair",backgroundColor:"rgba(255, 255, 255, 0.9)",padding:"8px",borderRadius:"4px",border:"1px solid rgba(0,0,0,0.1)",boxShadow:"0 4px 6px rgba(0, 0, 0, 0.1)",fontFamily:"Arial, sans-serif",fontSize:"12px",color:"#333",lineHeight:"1.5",zIndex:1e3},{cursor:r,show:i,...o}=ut.call(this,n,"trackMouseOptions",e);this.svg.style("cursor",r),this.svg.selectAll("*").each(function(){this.style.cssText+=`cursor: ${r} !important;`});let a=this.svg.node().closest(".html-widget")||document.body,s=R.select(a).append("div").attr("class","coordinate-tooltip").style("pointer-events","none").style("position","absolute").style("visibility","hidden");rt(s,o);let c=R.scaleLinear().domain([0+this.margin.left,this.width-this.margin.right]).range([0,100]),l=R.scaleLinear().domain([this.height-this.margin.bottom,0+this.margin.top]).range([0,100]),u=R.scaleLinear().domain([0-this.margin.left,this.width]).range([0,100]);return this.svg.on("mousemove",h=>{let[f,d]=R.pointer(h),m=f-this.margin.left,p=Math.round(this.xScale.invert(m)),g=R.format(",");s.html(`x: ${g(p)} <br>y: ${l(d).toFixed(1)}`).style("visibility","visible").style("left",R.pointer(h,a)[0]+10+"px").style("top",R.pointer(h,a)[1]-10+"px")}),this.svg.on("mouseout",()=>{s.style("visibility","hidden")}),this};var vE=["sequence","genes","transcript","links","coordinates","labels","annotations"];ft.prototype.clipZoom=function(){if(!this.zoom)return this;let t=this.svg.node(),e=Array.from(t.children).filter(i=>vE.includes(i.getAttribute("data-component")));if(!e.length)return this;let n=this.width-this.margin.left-this.margin.right,r=document.createElementNS("http://www.w3.org/2000/svg","svg");return r.setAttribute("class","geneviewer-zoom-clip"),r.setAttribute("x",this.margin.left),r.setAttribute("y",0),r.setAttribute("width",n),r.setAttribute("height",this.height),r.setAttribute("viewBox",`${this.margin.left} 0 ${n} ${this.height}`),r.setAttribute("preserveAspectRatio","none"),r.setAttribute("overflow","hidden"),t.insertBefore(r,e[0]),e.forEach(i=>r.appendChild(i)),this};ft.prototype.addAnnotations=function(t){if(!t||t.length===0)return this;var e=this.svg.append("g").attr("data-component","annotations").attr("transform",`translate(${this.margin.left}, ${this.margin.top})`);return t.forEach(n=>{this.createAnnotation(e,n)}),this};ft.prototype.createAnnotation=function(t,e){switch(e.type){case"text":this.createTextAnnotation(t,e);break;case"line":this.createLineAnnotation(t,e);break;case"textMarker":this.createTextMarkerAnnotation(t,e);break;case"arrow":this.createArrowAnnotation(t,e);break;case"promoter":this.createPromoterAnnotation(t,e);break;case"terminator":this.createTerminatorAnnotation(t,e);break;case"rectangle":this.createRectangleAnnotation(t,e);break;case"symbol":this.createSymbolAnnotation(t,e);break;case"arc":this.createCurveAnnotation(t,e);break;default:qe("Unsupported annotation type: "+e.type)}};ft.prototype.createTextAnnotation=function(l,e){let n={x:0,y:60,text:"",style:{fontSize:"10px",fontStyle:"normal",fontWeight:"normal",textDecoration:"none",fontFamily:"sans-serif",cursor:"default"}},r=ut.call(this,n,"textAnnotationOptions",e),{x:i,y:o,text:a,style:s}=r;Array.isArray(i)||(i=[i]),Array.isArray(o)||(o=[o]),Array.isArray(a)||(a=[a]);let c=at(s,n.style);var l=this.svg.append("g").attr("data-component","annotations").attr("transform",`translate(${this.margin.left}, ${this.margin.top})`);for(let u=0;u<Math.max(i.length,o.length,a.length);u++){let h=i[Math.min(u,i.length-1)],f=o[Math.min(u,o.length-1)],d=a[Math.min(u,a.length-1)];l.append("text").attr("x",this.xScale(h)).attr("y",this.yScale(f)).style("font-size",s.fontSize).style("font-style",s.fontStyle).style("font-weight",s.fontWeight).style("text-decoration",s.textDecoration).style("font-family",s.fontFamily).style("cursor",s.cursor).each(function(){let m=R.select(this);xr(d,m,s),rt(m,c)})}};ft.prototype.createLineAnnotation=function(u,e){let n={x1:0,y1:70,x2:0,y2:50,style:{stroke:"black",strokeWidth:1}},r=ut.call(this,n,"lineAnnotationOptions",e),{x1:i,y1:o,x2:a,y2:s,style:c}=r;Array.isArray(i)||(i=[i]),Array.isArray(o)||(o=[o]),Array.isArray(a)||(a=[a]),Array.isArray(s)||(s=[s]);let l=at(c,n.style);var u=this.svg.append("g").attr("data-component","annotations").attr("transform",`translate(${this.margin.left}, ${this.margin.top})`);for(let h=0;h<Math.max(i.length,o.length,a.length,s.length);h++){let f=i[Math.min(h,i.length-1)],d=o[Math.min(h,o.length-1)],m=a[Math.min(h,a.length-1)],p=s[Math.min(h,s.length-1)];u.append("line").attr("x1",this.xScale(f)).attr("y1",this.yScale(d)).attr("x2",this.xScale(m)).attr("y2",this.yScale(p)).style("stroke",c.stroke).style("stroke-width",c.strokeWidth).each(function(){let g=R.select(this);rt(g,l)})}};ft.prototype.createArrowAnnotation=function(d,e){let n={x1:1,y1:70,x2:1,y2:50,arrowSize:8,arrowStyle:{fill:"black"},lineStyle:{stroke:"black",strokeWidth:1}},r=ut.call(this,n,"arrowAnnotationOptions",e),{x1:i,y1:o,x2:a,y2:s,arrowSize:c,arrowStyle:l,lineStyle:u}=r;Array.isArray(i)||(i=[i]),Array.isArray(o)||(o=[o]),Array.isArray(a)||(a=[a]),Array.isArray(s)||(s=[s]),Array.isArray(c)||(c=[c]);let h=at(u,n.lineStyle),f=at(l,n.arrowStyle);var d=this.svg.append("g").attr("data-component","annotations").attr("transform",`translate(${this.margin.left}, ${this.margin.top})`);for(let m=0;m<Math.max(i.length,o.length,a.length,s.length,c.length);m++){let p=i[Math.min(m,i.length-1)],g=o[Math.min(m,o.length-1)],y=a[Math.min(m,a.length-1)],w=s[Math.min(m,s.length-1)],b=c[Math.min(m,c.length-1)],v=Xr("arrowhead");this.svg.append("defs").append("marker").attr("id",v).attr("viewBox","-0 -5 10 10").attr("refX",5).attr("refY",0).attr("orient","auto").attr("markerWidth",b).attr("markerHeight",b).attr("xoverflow","visible").append("path").attr("d","M 0,-5 L 10 ,0 L 0,5").attr("fill",l.fill).each(function(){let _=R.select(this);rt(_,f)}),d.append("line").attr("x1",this.xScale(p)).attr("y1",this.yScale(g)).attr("x2",this.xScale(y)).attr("y2",this.yScale(w+b/2)).attr("marker-end",`url(#${v})`).style("stroke",u.stroke).style("stroke-width",u.strokeWidth).each(function(){let _=R.select(this);rt(_,h)})}};ft.prototype.createTextMarkerAnnotation=function(t,e){let n={x1:null,y1:66,x2:null,y2:50,position:0,text:"",labelX:0,labelY:0,showArrow:!1,arrowSize:8,textStyle:{fontSize:"10px",fontFamily:"sans-serif",fill:"black",textAnchor:"middle"},arrowStyle:{fill:"black"},lineStyle:{stroke:"black",strokeWidth:1}},r=ut.call(this,n,"textMarkerAnnotationOptions",e),{textStyle:i,arrowStyle:o,lineStyle:a}=r,s=["x1","y1","x2","y2","position","text","labelX","labelY","showArrow","arrowSize"];s.forEach(h=>{Array.isArray(r[h])||(r[h]=[r[h]])});let c=at(a,n.lineStyle),l=at(o,n.arrowStyle),u=Math.max(...s.map(h=>r[h].length));for(let h=0;h<u;h++){let f={};s.forEach(b=>{f[b]=r[b][h%r[b].length]});let d=f.showArrow?f.arrowSize/2:0;var t=this.svg.insert("g",":first-child").attr("transform",`translate(${this.margin.left}, ${this.margin.top})`);let p=Math.round(this.xScale(f.x1!==null?f.x1:f.position)),g=Math.round(this.xScale(f.x2!==null?f.x2:f.position)),y=t.append("line").attr("x1",p).attr("y1",this.yScale(f.y1)).attr("x2",g).attr("y2",this.yScale(f.y2+d)).style("stroke",a.stroke).style("stroke-width",a.strokeWidth).each(function(){let b=R.select(this);rt(b,c)}),w=Xr("arrowhead-marker");this.svg.append("defs").append("marker").attr("id",w).attr("viewBox","-0 -5 10 10").attr("refX",5).attr("refY",0).attr("orient","auto").attr("markerWidth",f.arrowSize).attr("markerHeight",f.arrowSize).attr("xoverflow","visible").append("path").attr("d","M 0,-5 L 10 ,0 L 0,5").attr("fill",o.fill).each(function(){let b=R.select(this);rt(b,l)}),f.showArrow&&y.attr("marker-end",`url(#${w})`),f.text&&t.append("text").attr("x",this.xScale(f.x1!==null?f.x1:f.position)+f.labelX).attr("y",this.yScale(f.y1)-5-f.labelY).style("text-anchor",i.textAnchor).style("font-size",i.fontSize).style("font-family",i.fontFamily).style("fill",i.fill).each(function(){let b=R.select(this);xr(f.text,b,i),rt(b,at(i,n.textStyle))})}return t};ft.prototype.createSymbolAnnotation=function(u,e){let n={x:0,y:50,size:64,symbol:"circle",style:{fill:"black",stroke:"black",strokeWidth:2},rotation:0},r=ut.call(this,n,"symbolAnnotationOptions",e),{x:i,y:o,size:a,symbol:s,style:c,rotation:l}=r;Array.isArray(i)||(i=[i]),Array.isArray(o)||(o=[o]),Array.isArray(s)||(s=[s]),Array.isArray(l)||(l=[l]),Array.isArray(a)||(a=[a]);var u=this.svg.append("g").attr("data-component","annotations").attr("transform",`translate(${this.margin.left}, ${this.margin.top})`);let h=at(c,n.style),f={circle:R.symbolCircle,cross:R.symbolCross,diamond:R.symbolDiamond,square:R.symbolSquare,star:R.symbolStar,triangle:R.symbolTriangle,wye:R.symbolWye};for(let d=0;d<Math.max(i.length,o.length,s.length,l.length);d++){let m=i[Math.min(d,i.length-1)],p=o[Math.min(d,o.length-1)],g=s[Math.min(d,s.length-1)],y=l[Math.min(d,l.length-1)],w=a[Math.min(d,a.length-1)];if(!f[g]){console.error(`Unsupported symbol type: ${g}`);continue}let b=R.symbol().type(f[g]).size(w);u.append("path").attr("d",b).attr("transform",`translate(${this.xScale(m)}, ${this.yScale(p)}) rotate(${y})`).style("fill",c.fill).style("stroke",c.stroke).style("stroke-width",c.strokeWidth).each(function(){let v=R.select(this);rt(v,h)})}return u};ft.prototype.createRectangleAnnotation=function(c,e){let n={position:[[[9300,20],[9400,50]]],rotation:[0],style:{fill:"#0000",stroke:"black",strokeWidth:2}},r=ut.call(this,n,"rectangleAnnotationOptions",e),{position:i,style:o,rotation:a}=r;Array.isArray(i[0][0])||(i=[i]),Array.isArray(a)||(a=[a]);let s=at(o,n.style);var c=this.svg.append("g").attr("data-component","annotations").attr("transform",`translate(${this.margin.left}, ${this.margin.top})`);let l=Math.max(i.length,a.length);for(let u=0;u<l;u++){let h=i[Math.min(u,i.length-1)],f=a[Math.min(u,a.length-1)],d=Math.min(h[0][0],h[1][0]),m=Math.max(h[0][0],h[1][0]),p=Math.max(h[0][1],h[1][1]),g=Math.min(h[0][1],h[1][1]),y=Math.abs(d-m),w=Math.abs(g-p);c.append("rect").attr("x",this.xScale(d)).attr("y",this.yScale(p)).attr("width",this.xScale(m)-this.xScale(d)).attr("height",this.yScale(g)-this.yScale(p)).attr("transform",`rotate(${f}, ${this.xScale(d+y/2)}, ${this.yScale(p+w/2)})`).style("fill",o.fill).style("stroke",o.stroke).style("stroke-width",o.strokeWidth).each(function(){let b=R.select(this);rt(b,s)})}};ft.prototype.createPromoterAnnotation=function(d,e){let n={x:0,y:50,direction:"forward",rotation:0,scale:1,style:{fill:"none",stroke:"black",strokeWidth:1}},r=ut.call(this,n,"promoterAnnotationOptions",e),{x:i,y:o,direction:a,rotation:s,scale:c,style:l}=r,u=at(l,n.style);Array.isArray(i)||(i=[i]),Array.isArray(o)||(o=[o]),Array.isArray(a)||(a=[a]),Array.isArray(s)||(s=[s]),Array.isArray(c)||(c=[c]);let h="M -8 -17.5 L -13 -14 l 5 3.5 M -13 -14 L 0 -14 v 14",f="M 8 -17.5 L 13 -14 l -5 3.5 M 13 -14 H 0 v 14";var d=this.svg.append("g").attr("data-component","annotations").attr("transform",`translate(${this.margin.left}, ${this.margin.top})`);for(let m=0;m<Math.max(i.length,o.length,a.length,s.length,c.length);m++){let p=i[Math.min(m,i.length-1)],g=o[Math.min(m,o.length-1)],y=a[Math.min(m,a.length-1)],w=s[Math.min(m,s.length-1)],b=c[Math.min(m,c.length-1)],v=y==="forward"?f:h,_=this.xScale(p);d.append("path").attr("d",v).attr("transform",`translate(${_}, 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p=i[Math.min(m,i.length-1)],g=o[Math.min(m,o.length-1)],y=a[Math.min(m,a.length-1)],w=s[Math.min(m,s.length-1)],b=c[Math.min(m,c.length-1)],v=y==="forward"?h:f,_=this.xScale(p);d.append("path").attr("d",v).attr("transform",`translate(${_}, ${this.yScale(g)}) scale(${b}) rotate(${w})`).style("fill",l.fill).style("stroke",l.stroke).style("stroke-width",l.strokeWidth).each(function(){let S=R.select(this);rt(S,u)})}};ft.prototype.createCurveAnnotation=function(y,e){let n={x1:[0],y1:[50],x2:[100],y2:[50],midY:[80],stroke:["black"],strokeWidth:[1],lineStyle:{},text:[""],labelX:[0],labelY:[0],textStyle:{fontSize:"10px",fontFamily:"sans-serif",fill:"black",textAnchor:"middle"}},r=ut.call(this,n,"curveAnnotationOptions",e);["x1","y1","x2","y2","midY","stroke","strokeWidth","text","labelX","labelY"].forEach(w=>{Array.isArray(r[w])||(r[w]=[r[w]])});let{x1:o,y1:a,x2:s,y2:c,midY:l,stroke:u,strokeWidth:h,lineStyle:f,text:d,labelX:m,labelY:p,textStyle:g}=r;var y=this.svg.append("g").attr("data-component","annotations").attr("transform",`translate(${this.margin.left}, ${this.margin.top})`);for(let w=0;w<Math.max(o.length,a.length,s.length,c.length,d.length,m.length,p.length);w++){let b=o[w%o.length],v=a[w%a.length],_=s[w%s.length],S=c[w%c.length],k=l[w%l.length],C=u[w%u.length],F=h[w%h.length],A=d[w%d.length],E=m[w%m.length],D=p[w%p.length],z=(b+_)/2,M=R.line().curve(R.curveBasis).x(L=>this.xScale(L.x)).y(L=>this.yScale(L.y)),T=[{x:b,y:v},{x:z,y:k},{x:_,y:S}],B=y.append("path").attr("d",M(T)).style("stroke",C).style("stroke-width",F).style("fill","none");rt(B,at(f,n.lineStyle));let N=y.append("text").attr("x",this.xScale(z)+E).attr("y",this.yScale(k)-D).text(A);rt(N,g)}};var Ke=class t{constructor(e={}){this.columns=new Map(Object.entries(e))}static from(e){if(e instanceof t)return e.copy();if(Array.isArray(e)){let r=[];for(let o of e)for(let a of Object.keys(o))r.includes(a)||r.push(a);let i=new t;for(let o of r)i.columns.set(o,e.map(a=>a[o]===void 0?null:a[o]));return i}let n=new t;for(let[r,i]of Object.entries(e||{}))n.columns.set(r,Array.isArray(i)?i.slice():[i]);return n}copy(){let e=new t;for(let[n,r]of this.columns)e.columns.set(n,r.slice());return e}get nrow(){let e=this.columns.values().next();return e.done?0:e.value.length}get names(){return[...this.columns.keys()]}has(e){return this.columns.has(e)}get(e){return this.columns.get(e)}set(e,n){let r=this.nrow;return this.columns.set(e,Array.isArray(n)?n:Array.from({length:r},()=>n)),this}drop(e){return this.columns.delete(e),this}rows(e){let n=new t;for(let[r,i]of this.columns)n.columns.set(r,e.map(o=>i[o]));return n}filter(e){let n=[];for(let r=0;r<this.nrow;r++)e(r)&&n.push(r);return this.rows(n)}select(e){let n=new t;for(let r of e)this.columns.has(r)&&n.columns.set(r,this.columns.get(r).slice());return n}row(e){let n={};for(let[r,i]of this.columns)n[r]=i[e];return n}toJSON(){return Object.fromEntries(this.columns)}};function pe(t){if(t==null)return null;if(typeof t=="boolean")return t?"TRUE":"FALSE";if(typeof t!="number")return String(t);if(Number.isNaN(t))return"NaN";if(!Number.isFinite(t))return t>0?"Inf":"-Inf";if(t===0)return"0";let e=Number(t.toPrecision(15)),n=e!==t&&Number.isInteger(t)?t:e,[r,i]=Math.abs(n).toExponential().split("e"),o=r.replace(".",""),a=Number(i),s=n<0?"-":"",c;a>=0?c=o.length>a+1?`${o.slice(0,a+1)}.${o.slice(a+1)}`:o+"0".repeat(a+1-o.length):c=`0.${"0".repeat(-a-1)}${o}`;let l=`${r}e${a<0?"-":"+"}${String(Math.abs(a)).padStart(2,"0")}`;return s+(c.length<=l.length?c:l)}function Gi(t){if(t==null)return null;if(typeof t=="number")return t;if(typeof t=="boolean")return t?1:0;let e=String(t).trim();return e===""||!/^[-+]?(\d+\.?\d*|\.\d+)([eE][-+]?\d+)?$|^[-+]?(Inf|NaN)$/.test(e)?null:Number(e.replace("Inf","Infinity"))}function gt(t,e){if(t!=null){if(Array.isArray(t)){if(!t.length)return;let n=t[e%t.length];return n!==null&&typeof n=="object"?[n]:n}if(Ht(t)){let n=Object.keys(t);if(!n.length)return;let r=n[e%n.length];return{[r]:t[r]}}return t}}function wa(t,e,n){return Object.prototype.hasOwnProperty.call(t,e)?t[e]:n}function Ht(t){return t!==null&&typeof t=="object"&&!Array.isArray(t)}function Jy(t){return t==null?!0:Array.isArray(t)?t.length===0:Ht(t)?Object.keys(t).length===0:!1}function Ce(t){let e={};for(let[n,r]of Object.entries(t))r!=null&&(Array.isArray(r)&&r.length===0||Ht(r)&&Object.keys(r).length===0||(e[n]=r));return e}function xa(t){let e={};for(let[n,r]of Object.entries(t))r!=null&&(e[n]=r);return e}function Gr(t,e){let n=Ht(t)?{...t}:{};for(let[r,i]of Object.entries(e||{}))i==null?delete n[r]:Ht(n[r])&&Ht(i)?n[r]=Gr(n[r],i):n[r]=i;return n}function Qe(t,e){return t==null?e:Gr(t,e)}function Kl(t,e=2){if(typeof t=="number")return t/e;if(/px$/.test(t))return`${pe(Gi(t.replace(/px$/,""))/e)}px`;if(/%$/.test(t))return`${pe(Gi(t.replace(/%$/,""))/e)}%`;throw new Error("Unsupported format")}function Vn(t,e){let n=o=>typeof o=="string"&&/%$/.test(o);if(n(t)&&n(e))return e;let r=t;if(typeof r=="string"&&/px$/.test(r)&&(r=Gi(r.replace("px",""))),n(e)){let o=Gi(String(e).replace("%",""))/100;return typeof r=="number"?r*o:null}let i=e;return typeof i=="string"&&/px$/.test(i)&&(i=Gi(String(i).replace("px",""))),Gi(i)}function ge(t){if(t===null||typeof t!="object")return t;if(typeof t.copy=="function")return t.copy();if(Array.isArray(t))return t.map(ge);let e={};for(let[n,r]of Object.entries(t))e[n]=ge(r);return e}var wE="<b>Start:</b> {start}<br><b>End:</b> {end}",xE=`<b>{protein_id}</b><br>
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         <b>Best hit:</b> {BlastP}<br>
         <b>Identity:</b> {identity}%<br>
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Valid values are 1/forward/+/sense or -1/0/reverse/-/antisense/complement.");let o=i.map(c=>tb.includes(c)?"forward":"reverse");t.set("strand",o);let a=n.slice(),s=r.slice();return o.forEach((c,l)=>{(c==="forward"&&n[l]>r[l]||c==="reverse"&&n[l]<r[l])&&(a[l]=r[l],s[l]=n[l])}),t.set("start",a),t.set("end",s),t}function Vt(t,e){let n=[...t.x.series.keys()];if(e==null)return n;let r=Array.isArray(e)?e:[e];if(r.length&&r.every(o=>typeof o=="number"))return r.some(o=>o>n.length||o<1)?(t.warnings.push("Some cluster numbers provided are out of range. Please check the cluster numbers."),[]):r.map(o=>n[Math.trunc(o)-1]);let i=r.map(o=>pe(o));return i.every(o=>n.includes(o))?i:(t.warnings.push("Some cluster names provided are not valid. Please check the cluster names."),[])}function Ql(t){let e=t.fields||{},n=e.start??"start",r=e.end??"end",i=e.cluster??null,o=e.group??null,a=e.strand??null,s=t.width??"100%",c=t.height??"400px",l=t.style??{},u=t.toolbar&&!Array.isArray(t.toolbar)?t.toolbar.buttons:void 0,h=!(Array.isArray(u)&&!u.includes("save")),f={};f.params={start:n,end:r},i!==null&&(f.params.cluster=i),o!==null&&(f.params.group=o),a!==null&&(f.params.strand=a),f.params.width=s,f.params.height=c,Object.keys(l).length&&(f.params.style=ge(l)),f.params.save_button=h;let d=Ke.from(t.data);for(let[k,C]of[[n,"start"],[r,"end"],[i,"cluster"],[o,"group"],[a,"strand"]])if(k!==null&&!d.has(k))throw new Error(`${C} column not found in data`);let m=d.names,p=d.get(n),g=d.get(r),y=d.filter(k=>p[k]!==null&&g[k]!==null),w=[];y.nrow<d.nrow&&w.push("Rows with NA values in 'start' or 'end' columns have been filtered out."),d=y,d.set("rowID",Array.from({length:d.nrow},(k,C)=>C+1));let 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Kh={chart:"chartOptions",grid:"containerOptions",cluster:"clusterOptions",title:"titleOptions",clusterTitle:"clusterTitleOptions",clusterFooter:"footerOptions",clusterLabel:"clusterLabelOptions",sequence:"sequenceOptions",genes:"geneOptions",transcript:"transcriptOptions",labels:"labelsOptions",coordinates:"coordinatesOptions",scale:"scaleOptions",scaleBar:"scaleBarOptions",legend:"legendOptions",links:"linkOptions",tooltip:"tooltipOptions",trackMouse:"trackMouseOptions",toolbar:"toolbarOptions"},hb={text:"textAnnotationOptions",line:"lineAnnotationOptions",arrow:"arrowAnnotationOptions",textMarker:"textMarkerAnnotationOptions",symbol:"symbolAnnotationOptions",rectangle:"rectangleAnnotationOptions",promoter:"promoterAnnotationOptions",terminator:"terminatorAnnotationOptions",arc:"curveAnnotationOptions"},tc=qh.themes,Sa=qh.palettes,$E=t=>t.replace(/_([a-z])/g,(e,n)=>n.toUpperCase());function ec(t){return Ht(t)?Object.fromEntries(Object.entries(t).map(([e,n])=>[$E(e),n])):t}function 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n=e.show??!0,r=Ft(e,YE);Vr(t,e.clusters,"footer",i=>{let o={title:gt(e.title,i)??null,subtitle:gt(e.subtitle,i)??null,show:gt(n,i),subtitleFont:e.subtitleFont??{},titleFont:e.titleFont??{}};return ee(o,["align"],gt(e.align,i)),ee(o,["spacing"],gt(e.spacing,i)),En(o,r,i)})}function UE(t,e){let n=10**e;return Math.round(t*n)/n}function ka(t,e){let n=t.x,r=[...n.series.keys()],i=Vt(t,e.clusters),o=t.height,a=e.clusters!=null,s=e.margin==null?null:{...e.margin},c=e.width??null,l=e.height??null;if(c!==null&&!a&&(t.width=Vn(t.width,c)),(e.direction??"column")==="row"&&(n.graphContainer.direction="row",i.length>0)){let u=`${pe(UE(100/i.length,3))}%`;for(let h of i){let f=n.series.get(h).container;f.style={...f.style||{},width:u},f.width=u}}if(s!==null&&!a){let u=s.top!=null?Vn(o,s.top):0,h=s.bottom!=null?Vn(o,s.bottom):0;if(typeof u!="number"||typeof h!="number")throw new Error("Use pixel values for the top and bottom margins when the chart height is a percentage.");if(delete s.top,delete 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o=Math.max(...i)-Math.min(...r)+1,a=o*e/100,s=_a(r.length,[f=>r[f]]);r=s.map(f=>r[f]),i=s.map(f=>i[f]);let c=[],l={start:r[0],end:i[0]};for(let f=1;f<r.length;f++)r[f]<=l.end?l.end=Math.max(l.end,i[f]):(c.push(l),l={start:r[f],end:i[f]});c.push(l);let u=[];for(let f=0;f<c.length-1;f++){let d=c[f].end+1,m=c[f+1].start-1;m-d+1>=a&&u.push({start:d,end:m})}let h;return typeof n=="string"?h=wb(n):h=(o-u.reduce((d,m)=>d+(m.end-m.start+1),0))*n/100,u=u.map(f=>({start:f.start+h,end:f.end-h})),u.filter(f=>f.start<f.end)}function WE(t,e,n){if(Ht(t)){if(!("start"in t)||!("end"in t))throw new Error("A data frame of breaks needs a start and an end column");let r=[t.start].flat(),i=[t.end].flat(),o=r.map((a,s)=>s);if("cluster"in t){let a=[t.cluster].flat();o=o.filter(s=>pe(a[s])===e)}t=o.map(a=>({start:r[a],end:i[a]}))}return n?(t||[]).map(r=>({...r,start:r.start-n,end:r.end-n})):t}function ed(t,e){if(!e)return t;let n=i=>typeof i=="number"?i-e:i,r=i=>Array.isArray(i)?i.map(n):n(i);for(let i 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y=g-1;m.sequence=Vh(m.sequence,y),m.annotations.length>0&&(m.annotations=m.annotations.map(_=>ed(_,y))),m.positionShift=m.positionShift==null?y:m.positionShift+y;let w=n.data.get("rowID"),b=n.data.get("start"),v=n.data.get("end");p.get("rowID").forEach((_,S)=>{let k=w.indexOf(_);b[k]=p.get("start")[S],v[k]=p.get("end")[S]})}l=1,u=Math.max(...h.flatMap(d=>{let m=n.series.get(d).data;return[...m.get("start"),...m.get("end")]}))}let f=Ft(e,jE);h.forEach((d,m)=>{let p=n.series.get(d),g=r==="range"&&!i&&m<h.length-1?!0:i,y=o?HE(p.data,a,s):WE(e.breaks??[],d,p.positionShift),w={start:gt(e.start,m)??null,end:gt(e.end,m)??null,xMin:l,xMax:u,padding:e.padding??null,hidden:g,breaks:y,tickValues:e.tickValues??null,reverse:gt(e.reverse??!1,m),axisPosition:e.axisPosition??null,axisType:r,scale_breaks:o,scale_break_threshold:a,scale_break_padding:s,ticksCount:e.ticksCount??null,ticksFormat:c,y:e.y??null,tickStyle:e.tickStyle??{},textStyle:e.textStyle??{},lineStyle:e.lineStyle??{}};p.scale=En(w,f,m)}),kb(t)}var XE=["show","clusters","lineStyle","tickStyle","labelStyle"];function _b(t,e){let n=e.show??!0,r=Ft(e,XE);Vr(t,e.clusters,"scaleBar",i=>En({show:gt(n,i),scaleBarLineStyle:e.lineStyle??{},scaleBarTickStyle:e.tickStyle??{},labelStyle:e.labelStyle??{}},r,i))}function GE(t,e,n,r){return t==="left"&&!r||t==="right"&&r?e:t==="right"&&!r||t==="left"&&r?n:t==="center"?(e+n)/2:e}function Sb(t,e){let n=t.x;if(n.cluster===void 0){t.warnings.push("Could not align selected gene. Please define cluster in the GC_chart function.");return}if(!n.data.has(e.idColumn)){t.warnings.push(`Column ${e.idColumn} not found in the data.`);return}let r=pe(e.id);if(!n.data.get(e.idColumn).some(i=>pe(i)===r)){t.warnings.push(`ID ${e.id} not found in the ${e.idColumn} column.`);return}t.align={idColumn:e.idColumn,id:e.id,align:e.align??"left"},n.align={id_column:e.idColumn,id:e.id,align:t.align.align},kb(t)}function kb(t){let e=t.align;if(!e)return;let n=t.x,r=n.data,i=n.cluster,o=r.get(i),a=[...new Set(o)],s=new Set(a.filter(w=>n.series.get(w)?.scale?.reverse===!0)),c=r.get("start").map((w,b)=>Math.min(w,r.get("end")[b])),l=r.get("start").map((w,b)=>Math.max(w,r.get("end")[b])),u=r.get(e.idColumn),h=pe(e.id),f=[];for(let w=0;w<r.nrow;w++)u[w]!==null&&pe(u[w])===h&&f.push(w);if(!f.length){t.warnings.push(`Selected gene coud not be aligned. Gene ${e.id} not found in the ${e.idColumn} column.`);return}if(new Set(f.map(w=>o[w])).size<f.length){t.warnings.push(`The selected gene ${e.id} appears multiple times in some clusters. 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aM={cluster:eb,labels:rb,genes:ib,color:ob,pattern:ab,legend:sb,sequence:lb,coordinates:cb,tooltip:ub,title:mb,clusterTitle:yb,clusterLabel:bb,clusterFooter:vb,grid:ka,scale:xb,scaleBar:_b,align:Sb,links:Ab,transcript:Eb,annotation:Tb,elementStyle:Ob,theme:db,zoom:zb,toolbar:$b,events:Db,trackMouse:Bb},Nb=1,sM=new Set(["version","data","fields","width","height","style"]);function lM(t){return t==null?[]:Array.isArray(t)?t:[t]}function oc(t){if(!t||typeof t!="object")throw new Error("compile() needs a spec object");typeof t.version=="number"&&t.version>Nb&&console.warn(`geneviewer: spec version ${t.version} is newer than this library's (${Nb}); drawing what it knows`),t=ge(t);let e=Ql(t);for(let[n,r]of Object.entries(t)){if(sM.has(n))continue;let i=aM[n];if(i)for(let o of lM(r))i(e,Jl(o,fb[n]))}return ic(gb(e))}function ic(t){if(t instanceof Ke)return t.toJSON();if(t instanceof Map){let e={};for(let[n,r]of t)e[n]=ic(r);return e}if(Array.isArray(t))return t.map(ic);if(t!==null&&typeof 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i={...e.style??{}};e.backgroundColor!=null&&i.backgroundColor==null&&(i.backgroundColor=e.backgroundColor);let o=Ce({group:n,show:r,order:e.order,position:e.position,align:e.align,cornerRadius:e.cornerRadius,style:i,legendOptions:e.markerStyle,legendTextOptions:e.textStyle,groupStyle:e.groupStyle,...Ft(e,OE)});t.x.legend=Qe(t.x.legend,o)}var BE=["show","clusters","y","lineStyle","markerStyle"];function Vh(t,e){if(!t||!e)return t;for(let n of["start","end"])typeof t[n]=="number"&&(t[n]-=e);return t}function lb(t,e){let n=e.show??!0,r=Ft(e,BE);Vr(t,e.clusters,"sequence",(i,o)=>{let a={show:gt(n,i),y:gt(e.y,i)??null,sequenceStyle:e.lineStyle??{},markerStyle:e.markerStyle??{}};return Vh(En(a,r,i),o.positionShift)})}var DE=["show","tickValuesTop","tickValuesBottom","ticksFormat","tickStyle","textStyle","clusters","groupStyle","styleBy"];function cb(t,e){let n=e.show??!0,r=e.styleBy??null;if(r===null&&t.x.group!==void 0&&(r=t.x.group),e.groupStyle!=null&&r===null)throw new Error("groupStyle 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fb={scaleBar:{unit:"scaleBarUnit"},labels:{labelAdjustment:"labelAdjustmentOptions"},links:{labelAdjustment:"labelAdjustmentOptions"}},Zh={legend:{markerStyle:"legendOptions",textStyle:"legendTextOptions"},sequence:{lineStyle:"sequenceStyle"},scaleBar:{lineStyle:"scaleBarLineStyle",tickStyle:"scaleBarTickStyle",unit:"scaleBarUnit"},links:{show:"showLinks",labelAdjustment:"labelAdjustmentOptions"},labels:{labelAdjustment:"labelAdjustmentOptions"},scale:{autoBreaks:"scaleBreaks",autoBreakThreshold:"scaleBreakThreshold",breakPadding:"scaleBreakPadding"}};function Jl(t,e){return!e||t===null||typeof t!="object"||Array.isArray(t)?t:Object.fromEntries(Object.entries(t).map(([n,r])=>[e[n]??n,r]))}var Kh={chart:"chartOptions",grid:"containerOptions",cluster:"clusterOptions",title:"titleOptions",clusterTitle:"clusterTitleOptions",clusterFooter:"footerOptions",clusterLabel:"clusterLabelOptions",sequence:"sequenceOptions",genes:"geneOptions",transcript:"transcriptOptions",labels:"labelsOptions",coordinates:"coordinatesOptions",scale:"scaleOptions",scaleBar:"scaleBarOptions",legend:"legendOptions",links:"linkOptions",tooltip:"tooltipOptions",trackMouse:"trackMouseOptions",toolbar:"toolbarOptions"},hb={text:"textAnnotationOptions",line:"lineAnnotationOptions",arrow:"arrowAnnotationOptions",textMarker:"textMarkerAnnotationOptions",symbol:"symbolAnnotationOptions",rectangle:"rectangleAnnotationOptions",promoter:"promoterAnnotationOptions",terminator:"terminatorAnnotationOptions",arc:"curveAnnotationOptions"},tc=qh.themes,Sa=qh.palettes,zE=t=>t.replace(/_([a-z])/g,(e,n)=>n.toUpperCase());function ec(t){return Ht(t)?Object.fromEntries(Object.entries(t).map(([e,n])=>[zE(e),n])):t}function 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Qh({chart:{style:c},title:{titleFont:n,subtitleFont:n},clusterTitle:{titleFont:n,subtitleFont:n},clusterFooter:{titleFont:n,subtitleFont:n},clusterLabel:{...n,subtitleFont:n},sequence:{sequenceStyle:i,markerStyle:i},genes:{...a,...s},transcript:{...a,...s,labelOptions:r,styleUTRs:t.background!=null?{fill:t.background}:{}},labels:{...n,leaderLine:i},coordinates:{textStyle:n,tickStyle:i},scale:{textStyle:n,tickStyle:i,lineStyle:i},scaleBar:{labelStyle:n,scaleBarLineStyle:i,scaleBarTickStyle:i},legend:{legendOptions:{...a,...s},legendTextOptions:n},links:{labelStyle:n,colorBarOptions:{labelOptions:n,titleOptions:n}},tooltip:r,trackMouse:r,toolbar:e,annotations:{text:{style:n},textMarker:{textStyle:n},arc:{textStyle:n}}})}function pb(t){if(!t||Object.keys(t).length===0)return;let e={};for(let i of Object.keys(t))i in Kh&&(e[i]=ec(t[i]));t.annotations!=null&&(e.annotations=Object.fromEntries(Object.entries(t.annotations).map(([i,o])=>[i,ec(o)])));let n=Jh(RE(t),e),r={};for(let[i,o]of 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t;for(let[e,n]of Object.entries(t))e==="colorScheme"&&typeof n=="string"&&Sa[n]?t[e]=Sa[n].slice():n!==null&&typeof n=="object"&&(t[e]=td(n));return t}function gb(t){let e=t.x;e.size={width:t.width};let n=pb(e.theme);return n===void 0?delete e.theme:e.theme=n,td(e),IE(e),e}var LE=["title","subtitle","style","subtitleFont","titleFont","show","height","align","spacing"];function mb(t,e){let n=e.show??!0;if(!n||e.title==null&&e.subtitle==null)return;let r=Ce({title:e.title,subtitle:e.subtitle,subtitleFont:e.subtitleFont,titleFont:e.titleFont,style:e.style,height:e.height,show:n,align:e.align,spacing:e.spacing,...Ft(e,LE)});t.x.title=Qe(t.x.title,r)}var qE=["title","subtitle","subtitleFont","titleFont","show","height","clusters","align","spacing"];function yb(t,e){let n=e.show??!0,r=Ft(e,qE);Vt(t,e.clusters).forEach((i,o)=>{let a=t.x.series.get(i),s={title:gt(e.title,o)??null,subtitle:gt(e.subtitle,o)??null,subtitleFont:e.subtitleFont??{},titleFont:e.titleFont??{},show:gt(n,o)};ee(s,["align"],gt(e.align,o)),ee(s,["spacing"],gt(e.spacing,o)),En(s,r,o),ee(a,["grid","margin","top"],gt(e.height,o)),a.clusterTitle=s})}var YE=["title","show","width","clusters","position","align","wrapLabel","wrapOptions","subtitle","subtitleFont","spacing"];function bb(t,e){let n=e.show??!0,r=Ft(e,YE),i=Vt(t,e.clusters),o=e.title??null;t.x.cluster!==void 0&&o===null&&(o=i),i.forEach((a,s)=>{let c=t.x.series.get(a),l=xa({title:gt(o,s),show:gt(n,s),width:gt(e.width,s),wrapLabel:e.wrapLabel,wrapOptions:e.wrapOptions??{},position:gt(e.position,s),align:gt(e.align,s),subtitle:gt(e.subtitle,s),spacing:gt(e.spacing,s)});Jy(e.subtitleFont)||(l.subtitleFont=e.subtitleFont),c.clusterLabel=En(l,r,s)})}var UE=["title","subtitle","show","clusters","subtitleFont","titleFont","align","spacing"];function vb(t,e){let n=e.show??!0,r=Ft(e,UE);Vr(t,e.clusters,"footer",i=>{let o={title:gt(e.title,i)??null,subtitle:gt(e.subtitle,i)??null,show:gt(n,i),subtitleFont:e.subtitleFont??{},titleFont:e.titleFont??{}};return ee(o,["align"],gt(e.align,i)),ee(o,["spacing"],gt(e.spacing,i)),En(o,r,i)})}function HE(t,e){let n=10**e;return Math.round(t*n)/n}function ka(t,e){let n=t.x,r=[...n.series.keys()],i=Vt(t,e.clusters),o=t.height,a=e.clusters!=null,s=e.margin==null?null:{...e.margin},c=e.width??null,l=e.height??null;if(c!==null&&!a&&(t.width=Vn(t.width,c)),(e.direction??"column")==="row"&&(n.graphContainer.direction="row",i.length>0)){let u=`${pe(HE(100/i.length,3))}%`;for(let h of i){let f=n.series.get(h).container;f.style={...f.style||{},width:u},f.width=u}}if(s!==null&&!a){let u=s.top!=null?Vn(o,s.top):0,h=s.bottom!=null?Vn(o,s.bottom):0;if(typeof u!="number"||typeof h!="number")throw new Error("Use pixel values for the top and bottom margins when the chart height is a percentage.");if(delete s.top,delete s.bottom,n.legend.margin=Qe(n.legend.margin,s),n.title.margin=Qe(n.title.margin,s),Array.isArray(n.style)&&(n.style={}),u>0&&(n.style.paddingTop=`${pe(u)}px`),h>0&&(n.style.paddingBottom=`${pe(h)}px`),u>0||h>0){t.height="100%";for(let f of r){let d=n.series.get(f).container;if(typeof d.height=="string"&&/%$/.test(d.height))continue;let m=Number(Vn(d.height,d.height));d.height=m-(u+h)/r.length}}}i.forEach((u,h)=>{let f=n.series.get(u).container;if(s!==null&&(f.margin=Qe(f.margin,s)),c!==null&&a){let d=Vn(t.width,gt(c,h));f.style={...f.style||{},width:d},f.width=d}l!==null&&(f.height=a?Vn(o,gt(l,h)):Kl(l,r.length))})}function wb(t){if(!/^\s*[0-9]*\.?[0-9]+\s*bp\s*$/.test(t))throw new Error('scale_break_padding must be a percentage, e.g. 1, or base pairs, e.g. "500bp"');return Number(t.replace(/\s*bp\s*$/,""))}function WE(t,e=0,n=0){let r=t.get("start").slice(),i=t.get("end").slice();r.forEach((f,d)=>{f>i[d]&&([r[d],i[d]]=[i[d],f])});let o=Math.max(...i)-Math.min(...r)+1,a=o*e/100,s=_a(r.length,[f=>r[f]]);r=s.map(f=>r[f]),i=s.map(f=>i[f]);let c=[],l={start:r[0],end:i[0]};for(let f=1;f<r.length;f++)r[f]<=l.end?l.end=Math.max(l.end,i[f]):(c.push(l),l={start:r[f],end:i[f]});c.push(l);let u=[];for(let f=0;f<c.length-1;f++){let d=c[f].end+1,m=c[f+1].start-1;m-d+1>=a&&u.push({start:d,end:m})}let h;return typeof n=="string"?h=wb(n):h=(o-u.reduce((d,m)=>d+(m.end-m.start+1),0))*n/100,u=u.map(f=>({start:f.start+h,end:f.end-h})),u.filter(f=>f.start<f.end)}function jE(t,e,n){if(Ht(t)){if(!("start"in t)||!("end"in t))throw new Error("A data frame of breaks needs a start and an end column");let r=[t.start].flat(),i=[t.end].flat(),o=r.map((a,s)=>s);if("cluster"in t){let a=[t.cluster].flat();o=o.filter(s=>pe(a[s])===e)}t=o.map(a=>({start:r[a],end:i[a]}))}return n?(t||[]).map(r=>({...r,start:r.start-n,end:r.end-n})):t}function ed(t,e){if(!e)return t;let n=i=>typeof i=="number"?i-e:i,r=i=>Array.isArray(i)?i.map(n):n(i);for(let i of["x","x1","x2"])i in t&&(t[i]=r(t[i]));if(t.position!==null&&t.position!==void 0)if(t.type==="rectangle"){let i=Array.isArray(t.position)?t.position:[t.position];t.position=i.map(o=>Array.isArray(o)?o.map(a=>Array.isArray(a)?[n(a[0]),...a.slice(1)]:n(a)):[n(o)])}else t.position=r(t.position);return t}var XE=["clusters","start","end","padding","hidden","breaks","tickValues","reverse","axisPosition","axisType","y","autoBreaks","autoBreakThreshold","breakPadding","ticksCount","ticksFormat","tickStyle","textStyle","lineStyle"];function xb(t,e){let n=t.x,r=e.axisType??"position",i=e.hidden??!1,o=e.autoBreaks??!1,a=e.autoBreakThreshold??20,s=e.breakPadding??1,c=e.ticksFormat??null;typeof s=="string"&&wb(s);let l=null,u=null,h=Vt(t,e.clusters);if(r==="range"){c===null&&(c=".2s");for(let d of h){let m=n.series.get(d),p=m.data,g=Math.min(...p.get("start"),...p.get("end"));p.set("start",p.get("start").map(_=>_-g+1)),p.set("end",p.get("end").map(_=>_-g+1));let y=g-1;m.sequence=Vh(m.sequence,y),m.annotations.length>0&&(m.annotations=m.annotations.map(_=>ed(_,y))),m.positionShift=m.positionShift==null?y:m.positionShift+y;let w=n.data.get("rowID"),b=n.data.get("start"),v=n.data.get("end");p.get("rowID").forEach((_,S)=>{let k=w.indexOf(_);b[k]=p.get("start")[S],v[k]=p.get("end")[S]})}l=1,u=Math.max(...h.flatMap(d=>{let m=n.series.get(d).data;return[...m.get("start"),...m.get("end")]}))}let f=Ft(e,XE);h.forEach((d,m)=>{let p=n.series.get(d),g=r==="range"&&!i&&m<h.length-1?!0:i,y=o?WE(p.data,a,s):jE(e.breaks??[],d,p.positionShift),w={start:gt(e.start,m)??null,end:gt(e.end,m)??null,xMin:l,xMax:u,padding:e.padding??null,hidden:g,breaks:y,tickValues:e.tickValues??null,reverse:gt(e.reverse??!1,m),axisPosition:e.axisPosition??null,axisType:r,scale_breaks:o,scale_break_threshold:a,scale_break_padding:s,ticksCount:e.ticksCount??null,ticksFormat:c,y:e.y??null,tickStyle:e.tickStyle??{},textStyle:e.textStyle??{},lineStyle:e.lineStyle??{}};p.scale=En(w,f,m)}),kb(t)}var GE=["show","clusters","lineStyle","tickStyle","labelStyle"];function _b(t,e){let n=e.show??!0,r=Ft(e,GE);Vr(t,e.clusters,"scaleBar",i=>En({show:gt(n,i),scaleBarLineStyle:e.lineStyle??{},scaleBarTickStyle:e.tickStyle??{},labelStyle:e.labelStyle??{}},r,i))}function VE(t,e,n,r){return t==="left"&&!r||t==="right"&&r?e:t==="right"&&!r||t==="left"&&r?n:t==="center"?(e+n)/2:e}function Sb(t,e){let n=t.x;if(n.cluster===void 0){t.warnings.push("Could not align selected gene. Please define cluster in the GC_chart function.");return}if(!n.data.has(e.idColumn)){t.warnings.push(`Column ${e.idColumn} not found in the data.`);return}let r=pe(e.id);if(!n.data.get(e.idColumn).some(i=>pe(i)===r)){t.warnings.push(`ID ${e.id} not found in the ${e.idColumn} column.`);return}t.align={idColumn:e.idColumn,id:e.id,align:e.align??"left"},n.align={id_column:e.idColumn,id:e.id,align:t.align.align},kb(t)}function kb(t){let e=t.align;if(!e)return;let n=t.x,r=n.data,i=n.cluster,o=r.get(i),a=[...new Set(o)],s=new Set(a.filter(w=>n.series.get(w)?.scale?.reverse===!0)),c=r.get("start").map((w,b)=>Math.min(w,r.get("end")[b])),l=r.get("start").map((w,b)=>Math.max(w,r.get("end")[b])),u=r.get(e.idColumn),h=pe(e.id),f=[];for(let w=0;w<r.nrow;w++)u[w]!==null&&pe(u[w])===h&&f.push(w);if(!f.length){t.warnings.push(`Selected gene coud not be aligned. 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sc(i,oe?oe.node():null)},destroy:function(){C||(C=!0,Zi=null,Zn(),Ta(!1),Rt&&Rt.stopListening(),Rt=null,clearTimeout(_r),clearTimeout(Ji),Qn&&cancelAnimationFrame(Qn),Ca===fd&&(Ca=null),k={},[["click",hd,!0],["click",Zr],["pointerdown",$a,!0],["focusin",$a],["click",Zt],["dblclick",Mn],["keydown",pc],["pointerdown",uc],["mousemove",hc],["mouseleave",dc]].forEach(function(x){i.removeEventListener(x[0],x[1],x[2])}),R.select(i).on("mouseleave",null).selectAll("*").remove(),F.forEach(function(x){i.style[x]=""}),i.classList.remove("geneviewer-draggable","geneviewer-selectable","geneviewer-highlight","geneviewer-dragging","geneviewer-hover-below"),o&&i.classList.remove("geneviewer"))}};return Object.keys(n.on||{}).forEach(function(x){eo.on(x,n.on[x])}),_c(e),eo}export{sc as chartToPNG,Aa as chartToSVG,oc as compile,xM as newChart,Sa as palettes,tc as themes,pM as version};
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