geneviewer-js 0.3.1 → 0.3.2

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Files changed (10) hide show
  1. package/README.md +7 -6
  2. package/dist/SHA256SUMS +7 -7
  3. package/dist/geneviewer.core.js +3 -2
  4. package/dist/geneviewer.min.js +2 -2
  5. package/dist/geneviewer.min.js.map +3 -3
  6. package/dist/geneviewer.mjs +3 -2
  7. package/dist/geneviewer.standalone.mjs +2 -2
  8. package/dist/geneviewer.standalone.mjs.map +3 -3
  9. package/dist/geneviewerwidget.js +13 -9
  10. package/package.json +1 -1
package/dist/geneviewer.mjs CHANGED
@@ -6047,7 +6047,8 @@ function shiftAnnotation(options, shift) {
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  }
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  if (options.position !== null && options.position !== void 0) {
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  if (options.type === "rectangle") {
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- options.position = [options.position].flat(0).map((corners) => {
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+ const rectangles = Array.isArray(options.position) ? options.position : [options.position];
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+ options.position = rectangles.map((corners) => {
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  if (!Array.isArray(corners)) return [move(corners)];
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  return corners.map((point) => Array.isArray(point) ? [move(point[0]), ...point.slice(1)] : move(point));
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  });
@@ -7297,7 +7298,7 @@ function createSaveIcon(widgetId, el, container2, iconClass = null, save = downl
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  }
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  // src/lib/chart.js
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- var version = "0.3.1";
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+ var version = "0.3.2";
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  var renderSequence = 0;
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  var chartCount = 0;
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  var activeShortcuts = null;
package/dist/geneviewer.standalone.mjs CHANGED
@@ -24,7 +24,7 @@ var v2=Object.defineProperty;var w2=(t,e)=>{for(var n in e)v2(t,n,{get:e[n],enum
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  <b>Best hit:</b> {BlastP}<br>
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  <b>Identity:</b> {identity}%<br>
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  <b>Similarity:</b> {similarity}%<br>
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- <b>Location:</b> {start} - {end}<br>`,tb=["1","forward","+","sense"],_E=["-1","0","reverse","-","antisense","complement"];function SE(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=>tb.includes(c)||_E.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 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(`${C} column not found in data`);let m=d.names,p=d.get(n),g=d.get(r),y=d.filter(k=>p[k]!==null&&g[k]!==null),w=[];y.nrow<d.nrow&&w.push("Rows with NA values in 'start' or 'end' columns have been filtered out."),d=y,d.set("rowID",Array.from({length:d.nrow},(k,C)=>C+1));let b=d.copy();d.set("start",b.get(n).slice()),d.set("end",b.get(r).slice()),i!==null&&d.set(i,d.get(i).map(pe)),d=SE(d,a),f.data=d,o!==null&&(f.group=o),i!==null&&(f.cluster=i),f.graphContainer={direction:"column"},f.style=l,f.title={style:{width:"100%"}},f.legend={group:o,show:o!==null,width:s},f.legend.style={width:"100%",backgroundColor:l.backgroundColor??null},f.saveButton=h;let v=i===null?["cluster"]:[...new Set(d.get(i))],_=m.includes("BlastP")&&m.includes("protein_id"),S=new Map;for(let k of v){let C=i===null?d.copy():d.filter(M=>d.get(i)[M]===k);C.set("cluster",k);let F=typeof c=="string"&&/%$/.test(c)?Kl(c,v.length):Number(Vn(c,c))/v.length,A=C.get("start"),E=C.get("end"),D=[...A,...E].filter(M=>M!==null),$=vE;if(_){let M=C.get("BlastP"),T=C.get("protein_id");$=M.some((N,L)=>N!==null&&T[L]!==null&&N===T[L])&&M.every(N=>N===null||N==="No Hit"||T.includes(N))?wE:xE}S.set(k,{clusterName:k,data:C,cluster:{},container:{height:F,width:s,style:{width:"100%",backgroundColor:l.backgroundColor??null}},genes:{group:o,show:!0},sequence:{show:!0},scale:{xMin:Math.min(...D),xMax:Math.max(...D)},transcript:{group:o,show:!1},labels:{group:o,show:!0},coordinates:{show:!1},scaleBar:{},footer:{},clusterLabel:{},clusterTitle:{},annotations:[],trackMouse:{show:!1},tooltip:{show:!0,formatter:$}})}return f.series=S,{x:f,width:s,height:c,spec:t,warnings:w}}var 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sans-serif",textColor:"black",lineColor:"black",palette:"okabeIto",title:{titleFont:{fontSize:"9.33px",fill:"black"},subtitleFont:{fontSize:"9.33px"}},clusterTitle:{titleFont:{fontSize:"9.33px"},subtitleFont:{fontSize:"9.33px"}},clusterFooter:{titleFont:{fontSize:"9.33px"},subtitleFont:{fontSize:"9.33px"}},clusterLabel:{fontSize:"9.33px",subtitleFont:{fontSize:"9.33px"}},genes:{stroke:"black",strokeWidth:.75,corner_radius:3},transcript:{styleExons:{strokeWidth:0,cornerRadius:3},styleUTRs:{cornerRadius:3,fontSize:"9.33px"},labelOptions:{fontSize:"9.33px"}},labels:{fontStyle:"italic",fontSize:"9.33px",leaderLine:{strokeWidth:.75}},coordinates:{textStyle:{fontSize:"9.33px"},tickStyle:{lineLength:4}},scale:{textStyle:{fontSize:"9.33px"},tickStyle:{lineLength:4}},scaleBar:{labelStyle:{fontSize:"9.33px"}},legend:{corner_radius:2,legendOptions:{stroke:"black",strokeWidth:.75},legendTextOptions:{fontSize:"9.33px"}},links:{normal_color:"#0072B2",inverted_color:"#D55E00",linkStyle:{fillOpacity:.6},labelStyle:{fontSize:"9.33px"},colorBarOptions:{barOptions:{stroke:"none"},labelOptions:{fontSize:9.33},titleOptions:{fontSize:9.33}}},annotations:{text:{style:{fontSize:"9.33px"}},textMarker:{textStyle:{fontSize:"9.33px"}},arc:{textStyle:{fontSize:"9.33px"}}},tooltip:{backgroundColor:"white",color:"black",border:"1px 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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 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 HE(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 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 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 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,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 ${e.idColumn} column.`);return}t.align={idColumn:e.idColumn,id:e.id,align:e.align??"left"},n.align={id_column:e.idColumn,id:e.id,align:t.align.align},kb(t)}function kb(t){let e=t.align;if(!e)return;let n=t.x,r=n.data,i=n.cluster,o=r.get(i),a=[...new Set(o)],s=new Set(a.filter(w=>n.series.get(w)?.scale?.reverse===!0)),c=r.get("start").map((w,b)=>Math.min(w,r.get("end")[b])),l=r.get("start").map((w,b)=>Math.max(w,r.get("end")[b])),u=r.get(e.idColumn),h=pe(e.id),f=[];for(let w=0;w<r.nrow;w++)u[w]!==null&&pe(u[w])===h&&f.push(w);if(!f.length){t.warnings.push(`Selected gene coud not be aligned. 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d=l.select(u.filter(y=>l.has(y))),m=d.get("start2")||[];d=d.rows(_a(d.nrow,[y=>m[y]]));let p=Ce({group:s,curve:e.curve,measure:n,showLinks:e.show??!0,label:c,labelPosition:r,normalColor:e.normalColor,invertedColor:e.invertedColor,lowColor:e.lowColor,vmin:o,vmax:a,useGroupColors:h,value1:e.value1,value2:e.value2,colorBar:f,colorBarOptions:i,linkWidth:e.linkWidth,linkStyle:e.linkStyle,labelStyle:e.labelStyle,...Ft(e,ZE)}),g=t.x.links||[];d.set("linkID",Array.from({length:d.nrow},(y,w)=>`${g.length}-${w+1}`)),t.x.links=[...g,{data:d,options:p}]}var QE=["transcript","type","strand","group","selection","show","colorScheme","customColors","styleExons","styleIntrons","styleUTRs","itemStyleExons","itemStyleIntrons","itemStyleUTRs","groupStyleExons","groupStyleIntrons","groupStyleUTRs","styleBy","labelOptions"];function JE(t,e){return JSON.stringify(t)===JSON.stringify(e)}function tM(t,e){for(let a of["title","legend","theme","events","toolbar","zoom"])e.x[a]===void 0?delete t.x[a]:t.x[a]=e.x[a];t.width=e.width;let n=[...e.x.series.values()].map(a=>a.container.margin),i=n.length>0&&n.every(a=>JE(a,n[0]))?n[0]:{},o=Array.isArray(e.x.style)?{}:e.x.style||{};o.paddingTop!=null&&(i={...i||{},top:o.paddingTop}),o.paddingBottom!=null&&(i={...i||{},bottom:o.paddingBottom}),i&&Object.keys(i).length>0&&ka(t,{margin:i}),e.x.graphContainer?.direction==="row"&&ka(t,{direction:"row"})}function Eb(t,e){if(!t.x.transcript_called){let o=t.x.params,a={...t,x:t.x},s={start:o.start,end:o.end,cluster:e.transcript??"transcript"};o.group!==void 0&&(s.group=o.group),e.strand!=null&&(s.strand=e.strand);let c=Ql({...t.spec,fields:s,width:o.width,height:o.height,style:o.style});c.x.saveButton=o.save_button,c.x.params.save_button=o.save_button,t.x=c.x,t.width=c.width,t.height=c.height,tM(t,a);let l=[...new Set(t.x.data.get("transcript").map(String))];for(let u of l){let h=t.x.series.get(u);h.genes={group:null,show:!1},h.sequence={show:!1},h.transcript={group:null,show:!0}}}let n=e.group??null,r=e.show??!0;if(n===null&&t.x.group!==void 0&&(n=t.x.group),n!==null&&![n].flat().every(o=>t.x.data.has(o)))throw new Error("group column not found in data");let i=Ft(e,QE);Vt(t,e.selection).forEach((o,a)=>{let s=t.x.series.get(o),c=Ce({group:gt(n,a),show:gt(r,a),colorScheme:e.colorScheme,customColors:e.customColors,styleExons:e.styleExons,styleIntrons:e.styleIntrons,styleUTRs:e.styleUTRs,itemStyleExons:e.itemStyleExons,itemStyleIntrons:e.itemStyleIntrons,itemStyleUTRs:e.itemStyleUTRs,groupStyleExons:e.groupStyleExons,groupStyleIntrons:e.groupStyleIntrons,groupStyleUTRs:e.groupStyleUTRs,styleBy:e.styleBy,labelOptions:e.labelOptions,...i});s.transcript=jh(c,s.transcript)}),e.selection==null&&Xh(t,e.colorScheme,e.customColors),t.x.transcript_called=!0}var Mb=["text","textMarker","line","arrow","symbol","rectangle","promoter","terminator","arc"];function Tb(t,e){let n=e.type??"text";if(typeof n!="string"||!Mb.includes(n))throw new Error(`'type' must be one of ${Mb.map(i=>`"${i}"`).join(", ")}.`);let r=Ft(e,["type","clusters"]);for(let i of Vt(t,e.clusters)){let o=t.x.series.get(i),a=ed(Ce({type:n,...ge(r)}),o.positionShift);o.annotations=[...o.annotations||[],a]}}var eM=["genes","labels","coordinates"],nM=["legend","title"],rM=["scaleBar","scale"],Cb=["genes","labels","coordinates","clusterTitle","clusterFooter","clusterLabel","legend","title","scaleBar","scale"];function Fb(t,e,n,r){let i=Array.isArray(t)?t:[],o=i.find(e)||{},a=i.filter(c=>!e(c)),s=Gr(o,r);for(let[c,l]of Object.entries(n))s[c]=l;return[...a,s]}function Ob(t,e){let n=e.component??"genes";if(!Cb.includes(n))throw new Error(`'component' must be one of ${Cb.join(", ")}`);let{rowID:r=null,cluster:i=null,part:o=null,end:a=null,group:s=null}=e,c=ge(Ft(e,["component","rowID","cluster","part","end","group"])),l=eM.includes(n),u=t.x;if(nM.includes(n)){if(n==="legend"){let y=u.legend?.group;if(s===null||y==null||!u.data.get(y)?.some(w=>String(w)===String(s)))throw new Error("'group' must identify one group in the legend.")}let p=n==="legend"?{group:s,part:o}:{part:o},g=y=>y.part===o&&(n==="title"||y.group===s);u[n].itemStyle=Fb(u[n].itemStyle,g,p,c);return}let h=n==="clusterFooter"?"footer":n,f,d,m;if(l){if(typeof r!="number"||!u.data.get("rowID").includes(r))throw new Error("'row_id' must identify one row in the chart's data.");f=a===null?{rowID:r}:{rowID:r,end:a},d=p=>Number(p.rowID)===Number(r)&&(p.end??null)===a,m=[...u.series.keys()]}else if(f=rM.includes(n)?{}:{part:o},d=p=>(p.part??null)===o,m=Vt(t,i),!m.length)throw new Error("'cluster' must be the name or number of a cluster of the chart.");for(let p of m){let g=u.series.get(p);l&&!g.data.get("rowID").includes(r)||((!g[h]||Array.isArray(g[h]))&&(g[h]={}),g[h].itemStyle=Fb(g[h].itemStyle,d,f,c))}}function Bb(t,e){let n=e.show??!0,r=Ft(e,["show","clusters"]);Vt(t,e.clusters).forEach((i,o)=>{t.x.series.get(i).trackMouse={show:gt(n,o),...ge(r)}})}function Db(t,e){let 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 iM=["show","position","buttons","size","color","hoverColor","tooltipBackground","tooltipColor","tooltipBorder","tooltipRadius","tooltipShadow","fontFamily","icons"];function $b(t,e){let n=xa(Object.fromEntries(iM.map(r=>[r,ge(e[r])])));n.buttons!==void 0&&!Array.isArray(n.buttons)&&(n.buttons=[n.buttons]),t.x.toolbar=Gr(t.x.toolbar||{},n)}var oM=["show","range","mode","min","update","height","overview","color","style","windowStyle","handleStyle"];function zb(t,e){let n=xa(Object.fromEntries(oM.map(i=>[i,ge(e[i])])));n.show===void 0&&(n.show=!0);let r={...t.x.zoom||{}};n.mode!==void 0&&n.mode!==r.mode&&(delete r.range,delete r.min),n.range!==void 0&&(n.range=[n.range].flat().map(Number).sort((i,o)=>i-o)),t.x.zoom=Gr(r,n)}var aM={cluster:eb,labels:rb,genes:ib,color:ob,pattern:ab,legend:sb,sequence:lb,coordinates:cb,tooltip:ub,title:mb,clusterTitle:yb,clusterLabel:bb,clusterFooter:vb,grid:ka,scale:xb,scaleBar:_b,align:Sb,links:Ab,transcript:Eb,annotation:Tb,elementStyle:Ob,theme:db,zoom:zb,toolbar:$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 t=="object"){let e={};for(let[n,r]of Object.entries(t))r!==void 0&&(e[n]=ic(r));return e}return t}var Rb=t=>t!==null&&typeof t=="object"&&!Array.isArray(t);function nd(t,e){let n={...t};for(let[r,i]of Object.entries(e||{}))i!==void 0&&(n[r]=r!=="data"&&Rb(n[r])&&Rb(i)?nd(n[r],i):structuredClone(i));return n}var Pb=`.geneviewer-container {
27
+ <b>Location:</b> {start} - {end}<br>`,tb=["1","forward","+","sense"],_E=["-1","0","reverse","-","antisense","complement"];function SE(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=>tb.includes(c)||_E.includes(c)))throw new Error("Invalid strand values found. 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b=d.copy();d.set("start",b.get(n).slice()),d.set("end",b.get(r).slice()),i!==null&&d.set(i,d.get(i).map(pe)),d=SE(d,a),f.data=d,o!==null&&(f.group=o),i!==null&&(f.cluster=i),f.graphContainer={direction:"column"},f.style=l,f.title={style:{width:"100%"}},f.legend={group:o,show:o!==null,width:s},f.legend.style={width:"100%",backgroundColor:l.backgroundColor??null},f.saveButton=h;let v=i===null?["cluster"]:[...new Set(d.get(i))],_=m.includes("BlastP")&&m.includes("protein_id"),S=new Map;for(let k of v){let C=i===null?d.copy():d.filter(M=>d.get(i)[M]===k);C.set("cluster",k);let F=typeof c=="string"&&/%$/.test(c)?Kl(c,v.length):Number(Vn(c,c))/v.length,A=C.get("start"),E=C.get("end"),D=[...A,...E].filter(M=>M!==null),$=vE;if(_){let M=C.get("BlastP"),T=C.get("protein_id");$=M.some((N,L)=>N!==null&&T[L]!==null&&N===T[L])&&M.every(N=>N===null||N==="No 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Kh={chart:"chartOptions",grid:"containerOptions",cluster:"clusterOptions",title:"titleOptions",clusterTitle:"clusterTitleOptions",clusterFooter:"footerOptions",clusterLabel:"clusterLabelOptions",sequence:"sequenceOptions",genes:"geneOptions",transcript:"transcriptOptions",labels:"labelsOptions",coordinates:"coordinatesOptions",scale:"scaleOptions",scaleBar:"scaleBarOptions",legend:"legendOptions",links:"linkOptions",tooltip:"tooltipOptions",trackMouse:"trackMouseOptions",toolbar:"toolbarOptions"},hb={text:"textAnnotationOptions",line:"lineAnnotationOptions",arrow:"arrowAnnotationOptions",textMarker:"textMarkerAnnotationOptions",symbol:"symbolAnnotationOptions",rectangle:"rectangleAnnotationOptions",promoter:"promoterAnnotationOptions",terminator:"terminatorAnnotationOptions",arc:"curveAnnotationOptions"},tc=qh.themes,Sa=qh.palettes,$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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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(NE(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),PE(e),e}var IE=["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,IE)});t.x.title=Qe(t.x.title,r)}var LE=["title","subtitle","subtitleFont","titleFont","show","height","clusters","align","spacing"];function yb(t,e){let n=e.show??!0,r=Ft(e,LE);Vt(t,e.clusters).forEach((i,o)=>{let 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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 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 jE=["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,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 ${e.idColumn} column.`);return}t.align={idColumn:e.idColumn,id:e.id,align:e.align??"left"},n.align={id_column:e.idColumn,id:e.id,align:t.align.align},kb(t)}function kb(t){let e=t.align;if(!e)return;let n=t.x,r=n.data,i=n.cluster,o=r.get(i),a=[...new Set(o)],s=new Set(a.filter(w=>n.series.get(w)?.scale?.reverse===!0)),c=r.get("start").map((w,b)=>Math.min(w,r.get("end")[b])),l=r.get("start").map((w,b)=>Math.max(w,r.get("end")[b])),u=r.get(e.idColumn),h=pe(e.id),f=[];for(let w=0;w<r.nrow;w++)u[w]!==null&&pe(u[w])===h&&f.push(w);if(!f.length){t.warnings.push(`Selected gene coud not be aligned. 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Ut={...f,width:i.clientWidth,height:Le(f.height,i.clientHeight),editable:y.select===!0||y.dblclick===!0||y.click===!0&&y.legendClick!==!1};Vl(`#geneviewer-legend-container-${S}`,"svg-container","legendOptions",Ut,d).legendData(c).legend(Ut.group??!1,Ut.show??!1,i.id,Ut,za);var hn=R.select(`#geneviewer-legend-container-${S}`).node(),Tn=hn.getBoundingClientRect();ae=Tn.height}R.select(i).append("div").attr("id",`geneviewer-graph-container-${S}`).style("flex-direction",a.direction).style("position","relative").classed("geneviewer-container",!0);var Sr=Object.keys(u),no=Nt?Nt.height??24:0,Sc=Nt?no+8:0,rn=Nt&&Yt?{from:Yt[0],to:Yt[1],mode:Ne()}:null,Jn=(Array.isArray(l)?l:[]).map(se=>({data:jr(se.data),options:se.options??{}}));Sr.forEach(function(se){var me=u[se],Ia=me.container,g2=me.cluster,m2=jr(u[se].data),_d=me.scale,La=me.clusterTitle,qa=me.footer,io=me.clusterLabel,kc=me.labels,Sd=me.sequence,Ya=me.genes,Ac=me.transcript,kd=me.coordinates,Ad=me.scaleBar,y2=me.annotations,Ed=me.trackMouse,Md=me.tooltip,on=JSON.parse(JSON.stringify(Ia));if(on.height=Le(on.height,i.clientHeight),on.height-=wt/Sr.length,on.height-=ae?ae/Sr.length:0,on.height-=Sc/Sr.length,typeof Ia.height=="string"&&Ia.height.endsWith("%")){var b2=(parseFloat(Y.paddingTop)||0)+(parseFloat(Y.paddingBottom)||0);on.height-=b2/Sr.length}on.width=Le(on.width,i.clientWidth),io?.show&&(on.margin={...on.margin,...Wy(Ia,io,d)});var Ua=Vl(`#geneviewer-graph-container-${S}`,"svg-container","containerOptions",on,d).cluster(g2).title(La?.title,La?.subtitle,La?.show??!1,La,"clusterTitleOptions").footer(qa?.title,qa?.subtitle,qa?.show??!1,qa).clusterLabel(io?.title,io?.show??!1,io).geneData(c,m2).scale(rn?Object.assign({},_d,{zoom:rn}):_d).sequence(Sd?.show??!1,Sd).genes(Ya?.group,Ya?.show??!1,Ya).transcript(Ac?.group,Ac?.show??!1,Ac);Ua.svg.attr("data-cluster",se),Jn.forEach(Cd=>{Ua.links(Ky(Cd.data,se),se,Cd.options)}),Ua.coordinates(kd?.show??!1,kd).labels(kc?.label,kc?.show??!1,kc).scaleBar(Ad?.show??!1,Ad).addAnnotations(y2).trackMouse(Ed?.show??!1,Ed).tooltip(Md?.show??!1,Md).clipZoom(),tn.push({key:se,chart:Ua,group:Ya?.group})}),u2(no);var ro=ut({position:"bottom"},"legendOptions",f,d).position;ro=="bottom"&&f?.show&&f?.group!==null&&i.appendChild(hn),n2(),i.querySelectorAll(".legend").forEach(function(se){x.includes(se.__data__)&&se.dispatchEvent(new MouseEvent("click",{bubbles:!1}))})},xd=function(){if(!l||l.length===0)return;let x=R.select(`#geneviewer-graph-container-${S}`);Zy(x,l,d),Qy(x,l,d,za!==null),f2()},d2=function(x){for(var O=[],z=i.parentElement;z;z=z.parentElement)(z.scrollTop||z.scrollLeft)&&O.push([z,z.scrollTop,z.scrollLeft]);var P=document.scrollingElement;P&&!O.some(function(I){return I[0]===P})&&O.push([P,P.scrollTop,P.scrollLeft]);try{x()}finally{O.forEach(function(I){I[0].scrollTop!==I[1]&&(I[0].scrollTop=I[1]),I[0].scrollLeft!==I[2]&&(I[0].scrollLeft=I[2])})}},xc=function(){var x=nn&&nn.contains(document.activeElement)?document.activeElement.getAttribute("data-zoom-part"):null;d2(function(){wd(),xd(),ie(),Jb(),pd(),ud()}),x&&nn&&nn.querySelector('[data-zoom-part="'+x+'"]')?.focus({preventScroll:!0})},p2=function(x){if(x.data)return jr(x.data);var O=x.dataColumns??[],z=[];return Object.values(x.series??{}).forEach(function(P){jr(P.data).forEach(function(I){var Y={};O.forEach(function(nt){Y[nt]=I[nt]}),z.push(Y)})}),z.sort(function(P,I){return P.rowID-I.rowID})},Pa=function(x){var O=p2(x),z=JSON.stringify([O,x.group,x.cluster,x.legend?.group]);if($e&&z===L&&x.events?.drag===!0){Zi=x;return}Zi=null,Zn(),Nt=x.zoom&&x.zoom.show!==!1?x.zoom:null;var P=Nt?JSON.stringify([Nt.range??null,Ne()]):null,I=x.events?.renderId??null,Y=I!==null&&I!==md;if(md=I,(z!==L||P!==gd||Y)&&(Yt=r2(),Na=null),Nt||(Na=null),gd=P,L!==null&&z!==L&&(q=!1,T.length&&(N([]),X()),ze.clear(),Kr={},Qr={}),Ba={},L=z,a=x.graphContainer,s=x.style,c=O,l=x.links,u=x.series,m=x.saveButton,p=x.toolbar??{},h=x.title,f=x.legend,d=x.theme??{},y=x.events??{},g=x.size??{},wd(),xd(),ie(),pd(),ud(),to("render"),y.rendered===!0){var nt={id:y.renderId??i.id+"-render-"+ ++pM,chartId:i.id,width:i.clientWidth,height:i.clientHeight};K("rendered",nt)}},Cn=null,_c=function(x){x&&x.version!==void 0?(Cn=structuredClone(x),Pa(oc(Cn))):(Cn=null,Pa(x))},eo={update:function(x){C||(Cn!==null?(Cn=nd(Cn,x),Pa(oc(Cn))):_c(x))},setSpec:function(x){if(!C){if(!x||x.version===void 0)throw new Error("setSpec() needs a spec with a version");_c(x)}},getSpec:function(){return Cn===null?null:structuredClone(Cn)},resize:function(){C||xc()},on:function(x,O){if(!bM.includes(x))throw new Error("Unknown event: "+x);return(k[x]=k[x]||[]).push(O),function(){eo.off(x,O)}},off:function(x,O){var z=k[x]||[],P=z.indexOf(O);P>=0&&z.splice(P,1)},zoomTo:h2,select:function(x){if(!C){if(y.select!==!0){qe("chart.select() needs events: { select: true }; nothing was selected.");return}Tt(St(x==null?[]:Array.isArray(x)?x:[x]),"replace")}},getSelection:function(){return ot()},undo:function(){C||Qi(!0)},redo:function(){C||Qi(!1)},download:function(x,O){if(x!=="svg"&&x!=="png")return Promise.reject(new Error('download() needs the format "svg" or "png"'));var z=O??"graph."+x,P=n.saveAs||rd;return Promise.resolve().then(function(){return x==="svg"?new Blob([eo.toSVG()],{type:"image/svg+xml;charset=utf-8"}):eo.toPNG()}).then(function(I){return P(I,z)}).then(function(){})},toSVG:function(){return Aa(i,oe?oe.node():null)},toPNG:function(){return 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,wM as newChart,Sa as palettes,tc as themes,dM as version};
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