geneviewer-js 0.3.0 → 0.3.1

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
Files changed (10) hide show
  1. package/README.md +1 -1
  2. package/dist/SHA256SUMS +7 -7
  3. package/dist/geneviewer.core.js +10 -4
  4. package/dist/geneviewer.d.ts +1 -0
  5. package/dist/geneviewer.min.js +23 -23
  6. package/dist/geneviewer.min.js.map +3 -3
  7. package/dist/geneviewer.mjs +10 -4
  8. package/dist/geneviewer.standalone.mjs +23 -23
  9. package/dist/geneviewer.standalone.mjs.map +3 -3
  10. package/package.json +1 -1
package/dist/geneviewer.min.js CHANGED
@@ -1,30 +1,30 @@
1
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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 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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}},n8=2*Math.PI,Ai=Math.pow;function r8(t){return t[0]}function i8(t){return t[1]}function o8(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 a8(t,e,n){return[t+Math.sin(t+e)*n,e+Math.cos(t-e)*n]}var Bu=class t{static from(e,n=r8,r=i8,i){return new t("length"in e?s8(e,n,r,i):Float64Array.from(l8(e,n,r,i)))}constructor(e){this._delaunator=new Ds(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&&o8(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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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 mE(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 yE(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 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$},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===$.findIndex(M=>M.value===E.value)),A.sort((E,D)=>E.value-D.value),this.separateStrands)A.forEach(E=>{E.strand==="forward"?_.push(E):S.push(E)});else{let E=r.overlapThreshold;for(let 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n=R.select(t),r=t.textContent;t.textContent="",n.append("tspan").attr("class","label-name").text(r);let i=n.append("tspan").attr("class","label-measure").text(e.textContent);for(let o of e.style)o!=="text-anchor"&&i.style(o,e.style.getPropertyValue(o));if(e.remove(),r){i.attr("x",n.attr("x")).attr("dy","1.1em");let o=1.1*parseFloat(getComputedStyle(i.node()).fontSize);n.attr("y",parseFloat(n.attr("y"))-o)}}function bE(t){let e=R.select(t),n=e.select(".label-measure");n.empty()||n.attr("x",null).attr("dy",null).attr("dx",e.select(".label-name").text()?"0.3em":null)}function vE(t,e,n,r,i){let o=t.map((l,u)=>u).sort((l,u)=>t[l]-t[u]),a=[],s=l=>{l.start=Math.max(r,Math.min(l.total/l.members.length,i-l.width))};for(let l of o){let u={members:[{i:l,offset:0}],width:e[l],total:t[l]-e[l]/2};s(u);let h=a[a.length-1];for(;h&&h.start+h.width+n>u.start;){let 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Map(this.svg.selectAll(".link-text").nodes().map(j=>[j.getAttribute("rowID"),j]));A.selectAll("text.label").data(this.data).enter().append("text").attr("id",(j,H)=>`cluster-${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}, ${J})`}).style("font-size",v).style("font-style",_).style("font-family",S).style("cursor",C).text((j,H)=>D.get(H)?.text??j[t]).each(function(j){let H=q.get(String(j.rowID));H&&yE(this,H)}).each(function(j,H){let W=N[H];B(this,j,W),W.below&&(W.labelAdjustmentOptions.rotation=Math.abs(W.labelAdjustmentOptions.rotation))});let U=(j,H)=>{let 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i=this.width-this.margin.left-this.margin.right,o=k=>{let[C,F]=[this.xScale(k.start),this.xScale(k.end)].sort((D,$)=>D-$),A=Math.max(0,C),E=Math.min(i,F);return A<=E?[A,E]:null},a=[];if(t.selectAll("text.label").each(function(k,C){if(!e[C].spread||this.textContent.trim()==="")return;let F=o(k);if(!F){this.style.display="none";return}let{xPos:A}=e[C];a.push({node:this,d:k,geneX:(F[0]+F[1])/2,wanted:Math.min(F[1],Math.max(F[0],A))})}),!a.length)return this;let s=t.node().getCTM(),c=new Set(a.map(({d:k})=>String(k.rowID))),l=new Map,u=new Map,h=1/0,f=-1/0;this.svg.selectAll(".gene, .exon, .intron, .utr").each(function(){let k=this.getCTM();if(!k||!s)return;let C=s.inverse().multiply(k),F=this.getBBox(),A=1/0,E=-1/0;for(let[$,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($,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 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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},Gy(k),new MutationObserver(()=>Gy(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. 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6
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7
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8
+ V ${p-_}
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+ A ${_},${_} 0 0 1 ${e-_},${p}
10
+ H ${_}
11
+ A ${_},${_} 0 0 1 0,${p-_}
12
+ V ${_}
13
+ A ${_},${_} 0 0 1 ${_},0
14
+ Z`;break;case"cbox":_=Math.min(p/2,e/2),v=p,b=`M ${_} 0
15
+ L ${e-_} 0
16
+ Q ${e} ${p/2} ${e-_} ${p}
17
+ L ${_} ${p}
18
+ Q 0 ${p/2} ${_} 0
19
19
  Z`;break;case"intron":let k=e/2;v=p/2,b=`M0 ${v}
20
20
  L${k} 0
21
- L${e} ${v}`;break;default:Le(`Marker type '${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 zh(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)=>`${e.cluster}`)}function Nh(t,e,{xPos:n,yPos:r,height:i}){return`rotate(${t?e.direction==="forward"?180:0:e.direction==="forward"?0:180}, ${n}, ${r}) translate(${n}, ${r-i/2})`}function Rh(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),x={marker:l,markerSize:u,...p,y:c};return{xPos:v,yPos:b,path:h,arrowheadWidth:f,arrowheadHeight:d,height:m,drawn:x}}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=st(i.styleExons,r.styleExons),g=st(i.styleIntrons,r.styleIntrons),y=st(i.styleUTRs,r.styleUTRs),w=[...new Set(this.dataAll.map(A=>A[t]))],b=Wi(s,c,w);this.genesColorScale=b;let v=ji(this.svg,l,w,b,"exon"),x=this.svg.append("g").attr("data-component","transcript").attr("transform",`translate(${this.margin.left}, ${this.margin.top})`);this.data.sort((A,E)=>Math.min(A.start,A.end)-Math.min(E.start,E.end));let S=(A,E,D,$)=>Rh(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=Yi(L,m,D,$);return x.selectAll(`.${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)=>`${vr(U.cluster)}-${A}-${Z}`).call(zh).style("stroke-width",E.strokeWidth).style("stroke",N).style("cursor",E.cursor).each(function(U,Z){let Q=R.select(this);rt(Q,M),Ui(Q,q,Z)}),x.selectAll(`.${A}`)},C=(A,E)=>Nh(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;x.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'"),x.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 wE(t,e){return e.map(r=>{let 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Zi=X.append("rect").attr("class","legend-marker").attr("data-part","marker").attr("id",`legend-marker-${K}`).style("cursor",p.cursor).attr("x",B).attr("y",N).attr("width",M).attr("height",M).attr("rx",m).style("fill",A.fill(J)).style("stroke",A.outline??(Iy(A.fill(J))?"#bdbdbd":null)).each(()=>A.align(J,B,N)).each(function(){let At=R.select(this);rt(At,v),rt(At,tt),rt(At,ge)});De(ne,Dt),De(Zi,ge),L.push({node:ht[K],row:N,start:B,end:B+M+T+Gn}),u==="horizontal"?B+=Gn+M+2*T:N+=M+T}).on("mouseover",(J,K)=>{R.select(J.currentTarget).classed("hovered",!0)}).on("mouseout",(J,K)=>{R.select(J.currentTarget).classed("hovered",!1)}).on("click",(J,K)=>{if(J.detail>1||b&&J.bubbles)return;let ht=R.select(J.currentTarget);ht.classed("unselected")?ht.classed("unselected",!1):ht.classed("unselected",!0);let X=q.selectAll(".unselected").data(),tt=this.data.filter(it=>X.includes(it[t])).map(it=>it.rowID);n&&typeof n=="string"?R.select("#"+n).selectAll("[rowID]").each(function(){let it=+R.select(this).attr("rowID");tt.includes(it)?R.select(this).style("display","none"):R.select(this).style("display","")}):R.selectAll("[rowID]").each(function(){let it=+R.select(this).attr("rowID");tt.includes(it)?R.select(this).style("display","none"):R.select(this).style("display","")})}),i&&U==="right"&&Z();let Q={center:.5,right:1}[h]??0;if(Q>0){let J=this.width-this.margin.left-this.margin.right,K=X=>u==="horizontal"?X.row:0,ht=R.rollup(L,X=>R.max(X,tt=>tt.end)-R.min(X,tt=>tt.start),K);L.forEach(X=>{let tt=Math.max(0,J-ht.get(K(X)))*Q;R.select(X.node).attr("transform",`translate(${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}, ${this.margin.top+j/2})`)}return this};ft.prototype.links=function(t,e,n={}){let r={y:50,showLinks:!0,label:!0,measure:"identity",linkWidth:1,labelStyle:{cursor:"pointer",fontSize:"12px",fontStyle:"italic",fontFamily:"sans-serif",textAnchor:"middle"},labelAdjustmentOptions:{rotation:-65,offsetX:0,offsetY:0,dx:"0em",dy:"0em"}};if(!t||t.length===0)return this;let i=ut.call(this,r,"linkOptions",n),{x:o,y:a,cursor:s,fontSize:c,fontStyle:l,fontFamily:u,textAnchor:h,showLinks:f,label:d,measure:m,labelStyle:p,labelAdjustmentOptions:g,linkWidth:y}=i,w=st(n,r),b=st(p,r.labelStyle);var v=this.svg.append("g").attr("data-component","links").attr("transform",`translate(${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",$).attr("r",1)}}),d&&i.labelPosition!=="link"){let k=Ql(this,".link-text"),C=this.svg.selectAll(".link-text").nodes(),F=new Set(C.map(E=>E.getAttribute("rowID"))),A=this.data.filter(E=>!F.has(`${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-${vr(E.cluster)}-link-label-${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),ya(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: ${l(d).toFixed(1)}`).style("visibility","visible").style("left",R.pointer(h,a)[0]+10+"px").style("top",R.pointer(h,a)[1]-10+"px")}),this.svg.on("mouseout",()=>{s.style("visibility","hidden")}),this};var SE=["sequence","genes","transcript","links","coordinates","labels","annotations"];ft.prototype.clipZoom=function(){if(!this.zoom)return this;let t=this.svg.node(),e=Array.from(t.children).filter(i=>SE.includes(i.getAttribute("data-component")));if(!e.length)return this;let n=this.width-this.margin.left-this.margin.right,r=document.createElementNS("http://www.w3.org/2000/svg","svg");return r.setAttribute("class","geneviewer-zoom-clip"),r.setAttribute("x",this.margin.left),r.setAttribute("y",0),r.setAttribute("width",n),r.setAttribute("height",this.height),r.setAttribute("viewBox",`${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}, ${this.margin.top})`);return t.forEach(n=>{this.createAnnotation(e,n)}),this};ft.prototype.createAnnotation=function(t,e){switch(e.type){case"text":this.createTextAnnotation(t,e);break;case"line":this.createLineAnnotation(t,e);break;case"textMarker":this.createTextMarkerAnnotation(t,e);break;case"arrow":this.createArrowAnnotation(t,e);break;case"promoter":this.createPromoterAnnotation(t,e);break;case"terminator":this.createTerminatorAnnotation(t,e);break;case"rectangle":this.createRectangleAnnotation(t,e);break;case"symbol":this.createSymbolAnnotation(t,e);break;case"arc":this.createCurveAnnotation(t,e);break;default:Le("Unsupported annotation type: "+e.type)}};ft.prototype.createTextAnnotation=function(l,e){let n={x:0,y:60,text:"",style:{fontSize:"10px",fontStyle:"normal",fontWeight:"normal",textDecoration:"none",fontFamily:"sans-serif",cursor:"default"}},r=ut.call(this,n,"textAnnotationOptions",e),{x:i,y:o,text:a,style:s}=r;Array.isArray(i)||(i=[i]),Array.isArray(o)||(o=[o]),Array.isArray(a)||(a=[a]);let c=st(s,n.style);var l=this.svg.append("g").attr("data-component","annotations").attr("transform",`translate(${this.margin.left}, ${this.margin.top})`);for(let u=0;u<Math.max(i.length,o.length,a.length);u++){let h=i[Math.min(u,i.length-1)],f=o[Math.min(u,o.length-1)],d=a[Math.min(u,a.length-1)];l.append("text").attr("x",this.xScale(h)).attr("y",this.yScale(f)).style("font-size",s.fontSize).style("font-style",s.fontStyle).style("font-weight",s.fontWeight).style("text-decoration",s.textDecoration).style("font-family",s.fontFamily).style("cursor",s.cursor).each(function(){let m=R.select(this);wr(d,m,s),rt(m,c)})}};ft.prototype.createLineAnnotation=function(u,e){let n={x1:0,y1:70,x2:0,y2:50,style:{stroke:"black",strokeWidth:1}},r=ut.call(this,n,"lineAnnotationOptions",e),{x1:i,y1:o,x2:a,y2:s,style:c}=r;Array.isArray(i)||(i=[i]),Array.isArray(o)||(o=[o]),Array.isArray(a)||(a=[a]),Array.isArray(s)||(s=[s]);let l=st(c,n.style);var u=this.svg.append("g").attr("data-component","annotations").attr("transform",`translate(${this.margin.left}, ${this.margin.top})`);for(let h=0;h<Math.max(i.length,o.length,a.length,s.length);h++){let f=i[Math.min(h,i.length-1)],d=o[Math.min(h,o.length-1)],m=a[Math.min(h,a.length-1)],p=s[Math.min(h,s.length-1)];u.append("line").attr("x1",this.xScale(f)).attr("y1",this.yScale(d)).attr("x2",this.xScale(m)).attr("y2",this.yScale(p)).style("stroke",c.stroke).style("stroke-width",c.strokeWidth).each(function(){let g=R.select(this);rt(g,l)})}};ft.prototype.createArrowAnnotation=function(d,e){let n={x1:1,y1:70,x2:1,y2:50,arrowSize:8,arrowStyle:{fill:"black"},lineStyle:{stroke:"black",strokeWidth:1}},r=ut.call(this,n,"arrowAnnotationOptions",e),{x1:i,y1:o,x2:a,y2:s,arrowSize:c,arrowStyle:l,lineStyle:u}=r;Array.isArray(i)||(i=[i]),Array.isArray(o)||(o=[o]),Array.isArray(a)||(a=[a]),Array.isArray(s)||(s=[s]),Array.isArray(c)||(c=[c]);let h=st(u,n.lineStyle),f=st(l,n.arrowStyle);var d=this.svg.append("g").attr("data-component","annotations").attr("transform",`translate(${this.margin.left}, ${this.margin.top})`);for(let m=0;m<Math.max(i.length,o.length,a.length,s.length,c.length);m++){let p=i[Math.min(m,i.length-1)],g=o[Math.min(m,o.length-1)],y=a[Math.min(m,a.length-1)],w=s[Math.min(m,s.length-1)],b=c[Math.min(m,c.length-1)],v=jr("arrowhead");this.svg.append("defs").append("marker").attr("id",v).attr("viewBox","-0 -5 10 10").attr("refX",5).attr("refY",0).attr("orient","auto").attr("markerWidth",b).attr("markerHeight",b).attr("xoverflow","visible").append("path").attr("d","M 0,-5 L 10 ,0 L 0,5").attr("fill",l.fill).each(function(){let x=R.select(this);rt(x,f)}),d.append("line").attr("x1",this.xScale(p)).attr("y1",this.yScale(g)).attr("x2",this.xScale(y)).attr("y2",this.yScale(w+b/2)).attr("marker-end",`url(#${v})`).style("stroke",u.stroke).style("stroke-width",u.strokeWidth).each(function(){let x=R.select(this);rt(x,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=st(a,n.lineStyle),l=st(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}, ${this.margin.top})`);let p=Math.round(this.xScale(f.x1!==null?f.x1:f.position)),g=Math.round(this.xScale(f.x2!==null?f.x2:f.position)),y=t.append("line").attr("x1",p).attr("y1",this.yScale(f.y1)).attr("x2",g).attr("y2",this.yScale(f.y2+d)).style("stroke",a.stroke).style("stroke-width",a.strokeWidth).each(function(){let b=R.select(this);rt(b,c)}),w=jr("arrowhead-marker");this.svg.append("defs").append("marker").attr("id",w).attr("viewBox","-0 -5 10 10").attr("refX",5).attr("refY",0).attr("orient","auto").attr("markerWidth",f.arrowSize).attr("markerHeight",f.arrowSize).attr("xoverflow","visible").append("path").attr("d","M 0,-5 L 10 ,0 L 0,5").attr("fill",o.fill).each(function(){let b=R.select(this);rt(b,l)}),f.showArrow&&y.attr("marker-end",`url(#${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);wr(f.text,b,i),rt(b,st(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=st(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=st(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)}, ${this.yScale(p+w/2)})`).style("fill",o.fill).style("stroke",o.stroke).style("stroke-width",o.strokeWidth).each(function(){let b=R.select(this);rt(b,s)})}};ft.prototype.createPromoterAnnotation=function(d,e){let n={x:0,y:50,direction:"forward",rotation:0,scale:1,style:{fill:"none",stroke:"black",strokeWidth:1}},r=ut.call(this,n,"promoterAnnotationOptions",e),{x:i,y:o,direction:a,rotation:s,scale:c,style:l}=r,u=st(l,n.style);Array.isArray(i)||(i=[i]),Array.isArray(o)||(o=[o]),Array.isArray(a)||(a=[a]),Array.isArray(s)||(s=[s]),Array.isArray(c)||(c=[c]);let h="M -8 -17.5 L -13 -14 l 5 3.5 M -13 -14 L 0 -14 v 14",f="M 8 -17.5 L 13 -14 l -5 3.5 M 13 -14 H 0 v 14";var d=this.svg.append("g").attr("data-component","annotations").attr("transform",`translate(${this.margin.left}, ${this.margin.top})`);for(let m=0;m<Math.max(i.length,o.length,a.length,s.length,c.length);m++){let p=i[Math.min(m,i.length-1)],g=o[Math.min(m,o.length-1)],y=a[Math.min(m,a.length-1)],w=s[Math.min(m,s.length-1)],b=c[Math.min(m,c.length-1)],v=y==="forward"?f:h,x=this.xScale(p);d.append("path").attr("d",v).attr("transform",`translate(${x}, ${this.yScale(g)}) scale(${b}) rotate(${w})`).style("fill",l.fill).style("stroke",l.stroke).style("stroke-width",l.strokeWidth).each(function(){let S=R.select(this);rt(S,u)})}};ft.prototype.createTerminatorAnnotation=function(d,e){let n={x:0,y:50,direction:"forward",rotation:0,scale:1,style:{fill:"none",stroke:"black",strokeWidth:1}},r=ut.call(this,n,"terminatorAnnotationOptions",e),{x:i,y:o,direction:a,rotation:s,scale:c,style:l}=r,u=st(l,n.style);Array.isArray(i)||(i=[i]),Array.isArray(o)||(o=[o]),Array.isArray(a)||(a=[a]),Array.isArray(s)||(s=[s]),Array.isArray(c)||(c=[c]);let h="M -8 17.5 L -13 14 l 5 -3.5 M -13 14 H 0 v -14",f="M 8 17.5 L 13 14 l -5 -3.5 M 13 14 L 0 14 v -14";var d=this.svg.append("g").attr("data-component","annotations").attr("transform",`translate(${this.margin.left}, ${this.margin.top})`);for(let m=0;m<Math.max(i.length,o.length,a.length,s.length,c.length);m++){let p=i[Math.min(m,i.length-1)],g=o[Math.min(m,o.length-1)],y=a[Math.min(m,a.length-1)],w=s[Math.min(m,s.length-1)],b=c[Math.min(m,c.length-1)],v=y==="forward"?h:f,x=this.xScale(p);d.append("path").attr("d",v).attr("transform",`translate(${x}, ${this.yScale(g)}) scale(${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}, ${this.margin.top})`);for(let w=0;w<Math.max(o.length,a.length,s.length,c.length,d.length,m.length,p.length);w++){let b=o[w%o.length],v=a[w%a.length],x=s[w%s.length],S=c[w%c.length],k=l[w%l.length],C=u[w%u.length],F=h[w%h.length],A=d[w%d.length],E=m[w%m.length],D=p[w%p.length],$=(b+x)/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:$,y:k},{x,y:S}],B=y.append("path").attr("d",M(T)).style("stroke",C).style("stroke-width",F).style("fill","none");rt(B,st(f,n.lineStyle));let N=y.append("text").attr("x",this.xScale($)+E).attr("y",this.yScale(k)-D).text(A);rt(N,g)}};var Ze=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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o=="string"&&/%$/.test(o);if(n(t)&&n(e))return e;let r=t;if(typeof r=="string"&&/px$/.test(r)&&(r=Xi(r.replace("px",""))),n(e)){let o=Xi(String(e).replace("%",""))/100;return typeof r=="number"?r*o:null}let i=e;return typeof i=="string"&&/px$/.test(i)&&(i=Xi(String(i).replace("px",""))),Xi(i)}function pe(t){if(t===null||typeof t!="object")return t;if(typeof t.copy=="function")return t.copy();if(Array.isArray(t))return t.map(pe);let e={};for(let[n,r]of Object.entries(t))e[n]=pe(r);return e}var kE="<b>Start:</b> {start}<br><b>End:</b> {end}",AE=`<b>{protein_id}</b><br>
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+ L${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 Rh(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)=>`${e.cluster}`)}function Ph(t,e,{xPos:n,yPos:r,height:i}){return`rotate(${t?e.direction==="forward"?180:0:e.direction==="forward"?0:180}, ${n}, ${r}) translate(${n}, ${r-i/2})`}function Ih(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}=Vy(l,s,u,{arrowheadWidth:a.arrowheadWidth??i.arrowheadWidth,arrowheadHeight:a.arrowheadHeight??i.arrowheadHeight,markerHeight:a.markerHeight??i.markerHeight,cornerRadius:a.cornerRadius??i.cornerRadius}),g=Vy(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}, ${this.margin.top})`);this.data.sort((A,E)=>Math.min(A.start,A.end)-Math.min(E.start,E.end));let S=(A,E,D,$)=>Ih(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}-${Z}`).call(Rh).style("stroke-width",E.strokeWidth).style("stroke",N).style("cursor",E.cursor).each(function(U,Z){let Q=R.select(this);rt(Q,M),Hi(Q,q,Z)}),_.selectAll(`.${A}`)},C=(A,E)=>Ph(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 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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 Zy={normalColor:"#969696",invertedColor:"#d62728",lowColor:"#FFFFFF",vmin:0,vmax:100};function Ky(t,e,n,r){let i=R.interpolateRgb(t,e)(.1);return R.scaleLinear().domain([n,r]).range([i,e]).interpolate(R.interpolateRgb).clamp(!0)}function Qy(t,e,n={}){if(!e||e.length===0)return;let r={curve:!0,...Zy,useGroupColors:!1,color:"lightgrey",measure:"identity",label:!0,labelPosition:"gene",linkStyle:{stroke:"none",fillOpacity:.8},labelStyle:{fontSize:"10px",fontStyle:"normal",fontFamily:"sans-serif",cursor:"default",textAnchor:"middle",alignmentBaseline:"middle"}},i=t.node().getBoundingClientRect();var a=t.insert("div",":first-child").style("position","relative").style("width","100%").style("height","100%").insert("svg",":first-child").attr("width",i.width).attr("height",i.height).classed("GeneLink",!0).style("position","absolute").style("z-index",1);let s=[];e.forEach(function(u){let 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);_E(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=Ky(p,E,g,y);let $=h.measure==="none"?100:u.data?.[_]?.[A]??100,M=w?F[0].groupColor:D($);a.append("path").attr("data-component","links").datum(k[A]).attr("d",SE(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 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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}, ${this.margin.top})`);let S=this.data.some(k=>k.strand==="reverse")?this.geneStrandSpacing*1:0;if(f&&t.forEach(k=>{let C=(1-y)/2,F=k.start1+(k.end1-k.start1)*C,A=k.end1-(k.end1-k.start1)*C,E=k.start2+(k.end2-k.start2)*C,D=k.end2-(k.end2-k.start2)*C;if(k.cluster1===e){let 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$=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=Jl(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),ba(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: ${l(d).toFixed(1)}`).style("visibility","visible").style("left",R.pointer(h,a)[0]+10+"px").style("top",R.pointer(h,a)[1]-10+"px")}),this.svg.on("mouseout",()=>{s.style("visibility","hidden")}),this};var AE=["sequence","genes","transcript","links","coordinates","labels","annotations"];ft.prototype.clipZoom=function(){if(!this.zoom)return this;let t=this.svg.node(),e=Array.from(t.children).filter(i=>AE.includes(i.getAttribute("data-component")));if(!e.length)return this;let n=this.width-this.margin.left-this.margin.right,r=document.createElementNS("http://www.w3.org/2000/svg","svg");return r.setAttribute("class","geneviewer-zoom-clip"),r.setAttribute("x",this.margin.left),r.setAttribute("y",0),r.setAttribute("width",n),r.setAttribute("height",this.height),r.setAttribute("viewBox",`${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 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)$/.test(e)?null:Number(e.replace("Inf","Infinity"))}function gt(t,e){if(t!=null){if(Array.isArray(t)){if(!t.length)return;let n=t[e%t.length];return n!==null&&typeof n=="object"?[n]:n}if(Ht(t)){let n=Object.keys(t);if(!n.length)return;let r=n[e%n.length];return{[r]:t[r]}}return t}}function _a(t,e,n){return Object.prototype.hasOwnProperty.call(t,e)?t[e]:n}function Ht(t){return t!==null&&typeof t=="object"&&!Array.isArray(t)}function eb(t){return t==null?!0:Array.isArray(t)?t.length===0:Ht(t)?Object.keys(t).length===0:!1}function Ce(t){let e={};for(let[n,r]of Object.entries(t))r!=null&&(Array.isArray(r)&&r.length===0||Ht(r)&&Object.keys(r).length===0||(e[n]=r));return e}function Sa(t){let e={};for(let[n,r]of Object.entries(t))r!=null&&(e[n]=r);return e}function Gr(t,e){let n=Ht(t)?{...t}:{};for(let[r,i]of Object.entries(e||{}))i==null?delete n[r]:Ht(n[r])&&Ht(i)?n[r]=Gr(n[r],i):n[r]=i;return n}function Qe(t,e){return t==null?e:Gr(t,e)}function tc(t,e=2){if(typeof t=="number")return t/e;if(/px$/.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 EE="<b>Start:</b> {start}<br><b>End:</b> {end}",ME=`<b>{protein_id}</b><br>
22
22
  <b>Query gene</b><br>
23
- <b>Location:</b> {start} - {end}<br>`,EE=`<b>{protein_id}</b><br>
23
+ <b>Location:</b> {start} - {end}<br>`,CE=`<b>{protein_id}</b><br>
24
24
  <b>Best hit:</b> {BlastP}<br>
25
25
  <b>Identity:</b> {identity}%<br>
26
26
  <b>Similarity:</b> {similarity}%<br>
27
- <b>Location:</b> {start} - {end}<br>`,tb=["1","forward","+","sense"],ME=["-1","0","reverse","-","antisense","complement"];function CE(t,e=null){if(!t||t.nrow===0)return null;if(e===null&&t.has("strand")&&(e="strand"),!t.has("start"))throw new Error("start column not found in data");if(!t.has("end"))throw new Error("end column not found in data");let n=t.get("start"),r=t.get("end");if(e===null)return t.set("strand",n.map((c,l)=>c===null||r[l]===null?null:c<r[l]?"forward":"reverse")),t;if(!t.has(e))throw new Error("strand column not found in data");let i=t.get(e).map(de);if(!i.every(c=>tb.includes(c)||ME.includes(c)))throw new Error("Invalid strand values found. 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 Zt(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=>de(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 tc(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=pe(l)),f.params.save_button=h;let d=Ze.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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n={click:e.click??!0,highlight:e.highlight??!1};e.dblclick&&(n.dblclick=!0),e.select&&(n.select=!0),e.drag&&(n.drag=!0),e.legendClick===!1&&(n.legendClick=!1),e.zoom&&(n.zoom=!0),e.rendered&&(n.rendered=!0),e.renderId!=null&&(n.renderId=e.renderId),t.x.events=n}var cM=["show","position","buttons","size","color","hoverColor","tooltipBackground","tooltipColor","tooltipBorder","tooltipRadius","tooltipShadow","fontFamily","icons"];function $b(t,e){let n=_a(Object.fromEntries(cM.map(r=>[r,pe(e[r])])));n.buttons!==void 0&&!Array.isArray(n.buttons)&&(n.buttons=[n.buttons]),t.x.toolbar=Xr(t.x.toolbar||{},n)}var uM=["show","range","mode","min","update","height","overview","color","style","windowStyle","handleStyle"];function zb(t,e){let n=_a(Object.fromEntries(uM.map(i=>[i,pe(e[i])])));n.show===void 0&&(n.show=!0);let r={...t.x.zoom||{}};n.mode!==void 0&&n.mode!==r.mode&&(delete r.range,delete r.min),n.range!==void 0&&(n.range=[n.range].flat().map(Number).sort((i,o)=>i-o)),t.x.zoom=Xr(r,n)}var fM={cluster:eb,labels:rb,genes:ib,color:ob,pattern:ab,legend:sb,sequence:lb,coordinates:cb,tooltip:ub,title:mb,clusterTitle:yb,clusterLabel:bb,clusterFooter:vb,grid:Aa,scale:xb,scaleBar:_b,align:Sb,links:Ab,transcript:Eb,annotation:Tb,elementStyle:Ob,theme:db,zoom:zb,toolbar:$b,events:Db,trackMouse:Bb},Nb=1,hM=new Set(["version","data","fields","width","height","style"]);function dM(t){return t==null?[]:Array.isArray(t)?t:[t]}function Ea(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=pe(t);let e=tc(t);for(let[n,r]of Object.entries(t)){if(hM.has(n))continue;let i=fM[n];if(i)for(let o of dM(r))i(e,ec(o,fb[n]))}return oc(gb(e))}function oc(t){if(t instanceof Ze)return t.toJSON();if(t instanceof Map){let e={};for(let[n,r]of t)e[n]=oc(r);return e}if(Array.isArray(t))return t.map(oc);if(t!==null&&typeof 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27
+ <b>Location:</b> {start} - {end}<br>`,nb=["1","forward","+","sense"],FE=["-1","0","reverse","-","antisense","complement"];function TE(t,e=null){if(!t||t.nrow===0)return null;if(e===null&&t.has("strand")&&(e="strand"),!t.has("start"))throw new Error("start column not found in data");if(!t.has("end"))throw new Error("end column not found in data");let n=t.get("start"),r=t.get("end");if(e===null)return t.set("strand",n.map((c,l)=>c===null||r[l]===null?null:c<r[l]?"forward":"reverse")),t;if(!t.has(e))throw new Error("strand column not found in data");let i=t.get(e).map(pe);if(!i.every(c=>nb.includes(c)||FE.includes(c)))throw new Error("Invalid strand values found. 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Qh={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"},pb={text:"textAnnotationOptions",line:"lineAnnotationOptions",arrow:"arrowAnnotationOptions",textMarker:"textMarkerAnnotationOptions",symbol:"symbolAnnotationOptions",rectangle:"rectangleAnnotationOptions",promoter:"promoterAnnotationOptions",terminator:"terminatorAnnotationOptions",arc:"curveAnnotationOptions"},Aa=Yh.themes,Vi=Yh.palettes,qE=t=>t.replace(/_([a-z])/g,(e,n)=>n.toUpperCase());function rc(t){return Ht(t)?Object.fromEntries(Object.entries(t).map(([e,n])=>[qE(e),n])):t}function 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t;for(let[e,n]of Object.entries(t))e==="colorScheme"&&typeof n=="string"&&Vi[n]?t[e]=Vi[n].slice():n!==null&&typeof n=="object"&&(t[e]=ed(n));return t}function yb(t){let e=t.x;e.size={width:t.width};let n=mb(e.theme);return n===void 0?delete e.theme:e.theme=n,ed(e),WE(e),e}var jE=["title","subtitle","style","subtitleFont","titleFont","show","height","align","spacing"];function bb(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,jE)});t.x.title=Qe(t.x.title,r)}var XE=["title","subtitle","subtitleFont","titleFont","show","height","clusters","align","spacing"];function vb(t,e){let n=e.show??!0,r=Ft(e,XE);Vt(t,e.clusters).forEach((i,o)=>{let 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n=e.show??!0,r=Ft(e,VE);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 ZE(t,e){let n=10**e;return Math.round(t*n)/n}function Ea(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=`${pe(ZE(100/i.length,3))}%`;for(let h of i){let f=n.series.get(h).container;f.style={...f.style||{},width:u},f.width=u}}if(s!==null&&!a){let u=s.top!=null?Vn(o,s.top):0,h=s.bottom!=null?Vn(o,s.bottom):0;if(typeof u!="number"||typeof h!="number")throw new Error("Use pixel values for the top and bottom margins when the chart height is a percentage.");if(delete s.top,delete s.bottom,n.legend.margin=Qe(n.legend.margin,s),n.title.margin=Qe(n.title.margin,s),Array.isArray(n.style)&&(n.style={}),u>0&&(n.style.paddingTop=`${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)):tc(l,r.length))})}function _b(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 KE(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=ka(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=_b(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 QE(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 nd(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]));return t.position!==null&&t.position!==void 0&&(t.type==="rectangle"?t.position=[t.position].flat(0).map(i=>Array.isArray(i)?i.map(o=>Array.isArray(o)?[n(o[0]),...o.slice(1)]:n(o)):[n(i)]):t.position=r(t.position)),t}var JE=["clusters","start","end","padding","hidden","breaks","tickValues","reverse","axisPosition","axisType","y","autoBreaks","autoBreakThreshold","breakPadding","ticksCount","ticksFormat","tickStyle","textStyle","lineStyle"];function Sb(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"&&_b(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=Zh(m.sequence,y),m.annotations.length>0&&(m.annotations=m.annotations.map(_=>nd(_,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?KE(p.data,a,s):QE(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)}),Eb(t)}var tM=["show","clusters","lineStyle","tickStyle","labelStyle"];function kb(t,e){let n=e.show??!0,r=Ft(e,tM);Vr(t,e.clusters,"scaleBar",i=>En({show:gt(n,i),scaleBarLineStyle:e.lineStyle??{},scaleBarTickStyle:e.tickStyle??{},labelStyle:e.labelStyle??{}},r,i))}function eM(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 Ab(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},Eb(t)}function Eb(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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28
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