jbrowse-plugin-msaview 3.9.0 → 4.0.0

package/dist/chunks/chunk-QMLPITS4.js

@@ -0,0 +1,18 @@
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Set(["A","C","G","U","N"]),i=t.size>0&&[...t].every(a=>o.has(a)),s=t.size>0&&[...t].every(a=>r.has(a));return i?"dna":s?"rna":"amino"},get colConsensus(){let{colStats:t}=this;return Array.from({length:t.numColumns},(o,r)=>{let i=t.total(r),s=0,a="";t.forEachResidue(r,(c,u)=>{u>s&&(s=u,a=Rr(c))});let l=i?s/i:0;return{letter:a,color:l>.4?`hsl(240, 30%, ${100*Math.max(1-l/3,.3)}%)`:void 0}})},get colClustalX(){let{colStats:t}=this;return Array.from({length:t.numColumns},(o,r)=>Zl(t,r))},get conservation(){let{colStats:t,alphabetMaxBits:o}=this;return Array.from({length:t.numColumns},(r,i)=>{let s=t.total(i),a=t.gapCount(i);return s>a?Math.max(0,1-t.entropy(i)/o)*(1-a/s):0})},get alphabetMaxBits(){return Pr(this.sequenceType)},get propertyConservation(){return this.sequenceType==="amino"?xc(this.colStats):[]},get treeLayout(){return jr(this.root,{get rowHeight(){return e.rowHeight},get treeWidth(){return e.treeWidth}})},get hierarchy(){return this.treeLayout.root},get totalHeight(){return this.leaves.length*e.rowHeight},get leaves(){return this.treeLayout.leaves},get rootToTipLength(){return this.treeLayout.rootToTipLength},get maxBranchLength(){return this.rootToTipLength?e.treeWidth:0},get pxPerBranchLength(){let t=this.rootToTipLength;return this.showBranchLenEffective&&t?e.treeWidth/t:0},get maxDepthToLeaf(){return this.treeLayout.root.depthToLeaf},get allBranchesLength0(){return this.rootToTipLength===0},get showBranchLenEffective(){return this.allBranchesLength0?!1:e.showBranchLen}})).views(e=>({get totalWidth(){return e.numColumns*e.colWidth}})).views(e=>({get showMsaLetters(){return e.drawMsaLetters&&e.rowHeight>=gn&&e.colWidth>=Xo&&e.colWidth>e.rowHeight/2},get showTreeText(){return e.drawLabels&&e.rowHeight>=gn}})).views(e=>{let t=new WeakMap;return{get columnTrackContent(){let{MSA:o,blanks:r,hideGapsEffective:i}=e,s=o?.getWidth()??0,a=(u,d,h)=>{if(!u.row)return d;let f=Array.from({length:s},()=>h),g=e.seqPosIndex(u.row);return d.forEach((p,w)=>{let x=g?.[w];x!==void 0&&(f[x]=p)}),f},l=u=>i?br(r,u):u,c=(u,d)=>{let h=u.row?e.seqPosIndex(u.row)?.[d-1]:d-1;if(!(h===void 0||h<0||h>=s))return i?$e(r,h):h};return new Map(e.columnTracks.map(u=>{if(u.kind==="arc"){let h=(u.arcs??[]).map(f=>{let g=c(u,Math.min(f.start,f.end)),p=c(u,Math.max(f.start,f.end));return g!==void 0&&p!==void 0&&g<p?{start:g,end:p,color:f.color}:void 0}).filter(H.notEmpty);return[u.id,{arcs:h}]}if(u.kind==="bar"){let h=u.max??1,f=l(a(u,u.values??[],0)).map(g=>Math.min(1,Math.max(0,g/h)));return[u.id,{values:f}]}let d=l(a(u,(u.data??"").split("")," "));return[u.id,{data:d.join("")}]}))},trackHeight(o,r=o,i){return e.trackHeights.get(r)??i??Gm[o]??e.rowHeight},columnTrackModel(o){let r=t.get(o);return r||(r=(0,W.computed)(()=>{let i=Oc.has(o.kind)?Vm(o.id):void 0,s=this.columnTrackContent.get(o.id);return{model:{id:o.id,name:o.name,kind:o.kind,heightKey:i,height:this.trackHeight(o.kind,i,o.height),barColor:o.color,arcColor:o.color,customColorScheme:o.colors,data:s?.data,arcs:s?.arcs},ReactComponent:ct}}),t.set(o,r)),r.get()},get columnTrackModels(){return e.columnTracks.map(o=>this.columnTrackModel(o))}}}).views(e=>({get labelWidthMap(){let{showTreeText:t,leaves:o}=e;return t?new Map(o.map(r=>{let{name:i}=r.data,s=e.rowDataOf(i)?.genome||i;return[i,zr(s,wn)]})):new Map},get labelWidthScale(){return e.fontSize/wn},get labelsWidth(){let t=0;for(let o of this.labelWidthMap.values())o>t&&(t=o);return t*this.labelWidthScale},get secondaryStructureConsensus(){return e.MSA?.secondaryStructureConsensus},get secondaryStructureArcs(){let{blanks:t,hideGapsEffective:o}=e,r=this.secondaryStructureConsensus;if(r)return Pc(o?vt(t,r):r).map(({start:i,end:s,pseudoknot:a})=>({start:i,end:s,color:a?Ym:$m}))},get adapterTrackModels(){let{MSA:t,hideGapsEffective:o,blanks:r}=e,i=(t?.tracks??[]).filter(a=>!!a.data);if(i.length===0)return[];let{rowHeight:s}=e;return i.map(a=>({model:{...a,kind:"text",data:o?vt(r,a.data):a.data,height:s},ReactComponent:ct}))},get basePairTrackModels(){let t=this.secondaryStructureArcs;return t?.length?[{model:{id:"base-pairs",name:"Base pairs",kind:"arc",heightKey:"arc",height:e.trackHeight("arc"),arcs:t},ReactComponent:ct}]:[]},get computedTrackModels(){return[{id:"conservation",name:"Conservation",kind:"bar",barColor:"gray"},...e.sequenceType==="amino"?[{id:"property-conservation",name:"Property conservation",kind:"bar",barColor:"#6a51a3"}]:[],{id:"sequence-logo",name:"Sequence logo",kind:"logo"},{id:"position-ruler",name:"Position",kind:"ruler"}].map(t=>({model:{...t,heightKey:Oc.has(t.kind)?t.kind:void 0,height:e.trackHeight(t.kind)},ReactComponent:ct}))},get tracks(){return[...this.adapterTrackModels,...this.basePairTrackModels,...e.columnTrackModels,...e.numColumns>0?this.computedTrackModels:[]]},get turnedOnTracks(){return this.tracks.filter(t=>!Vc(e.turnedOffTracks,t.model.id,t.model.defaultOff))},get showHorizontalScrollbar(){return Zc(e.totalWidth,e.msaAreaWidth)},visibleColToRowLetter(t,o){return e.rowMap.get(t)?.[this.visibleColToGlobalCol(o)]},visibleColToSeqPos(t,o){return Rc(e.seqPosIndex(t),this.visibleColToGlobalCol(o))},visibleColToSeqPosOneBased(t,o){let r=this.visibleColToSeqPos(t,o);return r!==void 0?r+1:void 0},globalColToVisibleCol(t){let{blanks:o,hideGapsEffective:r}=e;return r?Tc(o,t):t},visibleColToGlobalCol(t){let{blanks:o,hideGapsEffective:r}=e;return r?Ec(o,t):t},seqPosToGlobalCol(t,o){let r=e.rowMap.get(t);return r===void 0?void 0:e.seqPosIndex(t)?.[o]??(o===0?0:r.length)},seqEndToGlobalCol(t,o){let r=e.seqPosIndex(t);return r&&r.length>0?r[Math.min(o,r.length-1)]:void 0},seqPosToVisibleCol(t,o){let r=this.seqPosToGlobalCol(t,o);return r===void 0?void 0:this.globalColToVisibleCol(r)},visibleSpan({row:t,start:o,end:r}){let{blanks:i}=e,s=Math.max(1,Math.floor(o)),a=Math.ceil(r),l=s-1,c=Math.min(a,e.MSA?.getWidth()??a)-1;if(t!==void 0){let h=this.seqPosToGlobalCol(t,s-1),f=this.seqEndToGlobalCol(t,a-1);if(h===void 0||f===void 0)return;l=h,c=f}let u=this.globalColToVisibleCol(l)??$e(i,l),d=this.globalColToVisibleCol(c)??$e(i,c)-1;return u<=d?{startCol:u,endCol:d}:void 0},get residueMappingProblems(){let t=[];for(let o of e.residueMappings){let r={row:o.row,structureId:o.structure.id},i=e.seqPosIndex(o.row)?.length;if(i===void 0){t.push({...r,scope:"mapping",reason:"no such row in the alignment"});continue}if(o.rowLength!==void 0&&o.rowLength!==i){t.push({...r,scope:"mapping",reason:`computed against a ${o.rowLength}-residue row; this one has ${i}`});continue}let s=o.segments.find(a=>a.rowEnd>i||a.rowStart<1);if(s){t.push({...r,scope:"mapping",reason:`segment ${s.rowStart}-${s.rowEnd} does not fit a ${i}-residue row`});continue}for(let a of o.segments)qc(a)||t.push({...r,scope:"segment",reason:`segment ${a.rowStart}-${a.rowEnd} maps to ${a.structStart}-${a.structEnd}, which is a different length`})}return t},get usableResidueMappings(){let t=new Set(this.residueMappingProblems.filter(o=>o.scope==="mapping").map(o=>`${o.row}\0${o.structureId}`));return e.residueMappings.filter(o=>!t.has(`${o.row}\0${o.structure.id}`)).map(o=>({...o,segments:o.segments.filter(qc)}))},get mappedStructures(){return this.usableResidueMappings.map(t=>({row:t.row,structure:t.structure}))},structureResidue(t,o,r){let i=[];for(let s of this.usableResidueMappings){if(s.row!==t||r!==void 0&&s.structure.id!==r)continue;let a=s.segments.find(l=>o>=l.rowStart&&o<=l.rowEnd);if(a){let l=a.structStart+(o-a.rowStart);i.push({structure:s.structure,position:l,observed:!rh(s.unobserved,l)})}}return i.length===1?i[0]:void 0},rowResidue(t,o,r){let i=[];for(let s of this.usableResidueMappings){if(s.structure.id!==t||r!==void 0&&s.structure.asymId!==r)continue;let a=s.segments.find(l=>o>=l.structStart&&o<=l.structEnd);a&&i.push({rowName:s.row,seqPos:a.rowStart+(o-a.structStart)})}return i.length===1?i[0]:void 0}})).views(e=>({get treeScaleBar(){return ec(e.pxPerBranchLength,e.treeAreaWidth-e.marginLeft*2)},get topBandHeight(){return Math.max(e.showHorizontalScrollbar?e.minimapHeight:0,e.rowPanelsHeaderHeight,e.treeOverviewHeight+(this.treeScaleBar?qe:0))},get msaAreaHeight(){return e.height-this.topBandHeight-e.headerHeight-this.totalTrackAreaHeight},get totalTrackAreaHeight(){return(0,H.sum)(e.turnedOnTracks.map(t=>t.model.height))},get annotationTypes(){let t=new Map;for(let o of e.allAnnotations)t.has(o.accession)||t.set(o.accession,o);return t},get filteredAnnotations(){return e.allAnnotations.filter(t=>!e.turnedOffFeatures.get(t.accession))},get annotationsByRow(){return(0,H.groupBy)(this.filteredAnnotations,t=>t.id)}})).views(e=>({get showVerticalScrollbar(){return Zc(e.totalHeight,e.msaAreaHeight)}})).views(e=>({get dataInitialized(){return!!(e.data.msa||e.data.tree)&&!e.error},get blocksX(){return Jn({viewportSize:e.msaAreaWidth,viewportPos:-e.scrollX,blockSize:e.blockSize,mapSize:e.totalWidth})},get blocksY(){return Jn({viewportSize:e.msaAreaHeight,viewportPos:-e.scrollY,blockSize:e.blockSize,mapSize:e.totalHeight})}})).views(e=>({get verticalScrollbarWidth(){return e.showVerticalScrollbar?20:0},get msaCanvasWidth(){return e.msaAreaWidth-this.verticalScrollbarWidth},get maxScrollX(){return Math.min(-e.totalWidth+this.msaCanvasWidth,0)},get blocks2d(){return e.blocksY.flatMap(t=>e.blocksX.map(o=>[o,t]))},get isLoading(){return e.loadingMSA||e.loadingTree},get dataWarnings(){let{annotations:t,rowNamesSet:o}=e;return e.dataInitialized&&t.length>0&&!t.some(r=>o.has(r.id))?[`0 of ${t.length} annotations name a row in this alignment`]:[]},get warnings(){return[...e.loadWarnings,...this.dataWarnings.filter(t=>!e.dismissedWarnings.includes(t))]},get maxScrollY(){return Math.min(-e.totalHeight+e.msaAreaHeight,0)},get wheelZoomAxis(){return e.scrollZoom?e.scrollZoomAxis:"both"}})).actions(e=>({setDrawMsaLetters(t){e.drawMsaLetters=t},clearWarnings(){e.loadWarnings=[],e.dismissedWarnings=e.dataWarnings},setScrollZoom(t){e.scrollZoom=t},setScrollZoomAxis(t){e.scrollZoomAxis=t},setHoveredTreeNode(t){if(t===e.hoveredTreeNode?.nodeId)return;if(!t){e.hoveredTreeNode=void 0;return}let o=Ie(e.hierarchy,r=>r.data.id===t);e.hoveredTreeNode=o?{nodeId:t,descendantNames:fe(o).map(r=>r.data.name)}:void 0},calculateNeighborJoiningTreeFromMSA(){let t=[...e.rowMap];if(t.length<2)throw new Error("Need at least 2 sequences to build a tree");if(t.length>Te)throw new Error(`Neighbor joining here is capped at ${Te} sequences and this alignment has ${t.length}. Build the tree with FastTree or IQ-TREE and open it alongside the alignment: https://gmod.org/JBrowseMSA/tutorials/protein_family`);this.replaceTree(bc(t))},rerootAt(t){let o=Ie(Oe(e.tree,i=>i.children),i=>i.data.id===t);if(!o?.parent)return;let r=tu(Oe(e.inputTree,i=>i.children),fe(o).map(i=>i.data.name));if(r){let i=fe(r);e.setTreeRoot({outgroup:[...new Set([i[0].data.name,i.at(-1).data.name])]})}},replaceTree(t){(0,W.transaction)(()=>{e.collapsed.clear(),e.rotated.clear(),e.setShowOnly(void 0),e.setTree(t)})},resetZoom(){e.setColWidth(12),e.setRowHeight(16)},zoomAtCenter(t,o="both"){this.zoomToPos(t,e.msaCanvasWidth/2,e.msaAreaHeight/2,o)},zoomOutHorizontal(){this.zoomAtCenter(.75,"horizontal")},zoomInHorizontal(){this.zoomAtCenter(1.5,"horizontal")},zoomInVertical(){this.zoomAtCenter(1.5,"vertical")},zoomOutVertical(){this.zoomAtCenter(.75,"vertical")},zoomIn(){this.zoomAtCenter(1.5)},zoomOut(){this.zoomAtCenter(.75)},zoomToPos(t,o,r,i="both"){(0,W.transaction)(()=>{let s=(-e.scrollX+o)/e.colWidth,a=(-e.scrollY+r)/e.rowHeight;i!=="vertical"&&(e.colWidth=(0,H.clamp)(e.colWidth*t,dt,Ee)),i!=="horizontal"&&(e.rowHeight=(0,H.clamp)(e.rowHeight*t,mt,Ee)),e.scrollX=(0,H.clamp)(o-s*e.colWidth,e.maxScrollX,0);let l=r-a*e.rowHeight,c=Math.max(0,-e.maxScrollY),u=e.totalHeight-c,d=u>0?(0,H.clamp)(1-c/u,0,1):1;e.scrollY=(0,H.clamp)(l*(1-d),e.maxScrollY,0)})},doScrollY(t){this.setScrollY(e.scrollY+t)},setScrollY(t){e.scrollY=(0,H.clamp)(t,e.maxScrollY,0)},setAnnotations(t){e.annotations=t},setDomains(t){this.setAnnotations(t?ri(t):[])},applyGFFText(t){this.setAnnotations(ai(ii(t)))},doScrollX(t){this.setScrollX(e.scrollX+t)},setScrollX(t){e.scrollX=(0,H.clamp)(t,e.maxScrollX,0)},setColumnTracks(t){e.columnTracks.replace(t)},setRowData(t){e.data.setTreeMetadata(JSON.stringify(t))},setEncodings(t){e.encodings.replace(t)},setRowPanels(t){e.rowPanels.replace(t)},setResidueMappings(t){e.residueMappings.replace(t)},toggleTrack(t){let o=e.MSA?.tracks.find(r=>r.id===t)?.defaultOff;e.turnedOffTracks.set(t,!Vc(e.turnedOffTracks,t,o))},setStatus(t){e.status=t}})).views(e=>({cellAt(t,o){let r=e.visibleColToGlobalCol(t),i=o===void 0?void 0:e.leaves[o]?.data.name;return i===void 0?{column:r+1}:{column:r+1,row:i,residue:e.visibleColToSeqPosOneBased(i,t),letter:e.rowMap.get(i)?.[r]}},get hoveredCell(){let{mouseCol:t,mouseRow:o}=e;return t===void 0?void 0:this.cellAt(t,o)},get clickedCell(){let{mouseClickCol:t,mouseClickRow:o}=e;return t===void 0?void 0:this.cellAt(t,o)},get viewport(){let{scrollX:t,colWidth:o,numColumns:r,viewInitialized:i}=e;if(r===0||!i)return;let{xStart:s,xEnd:a}=Ar({offsetX:-t,blockWidth:e.msaCanvasWidth,colWidth:o}),l=Math.max(0,Math.min(a,r)-1);return{startColumn:e.visibleColToGlobalCol(Math.min(s,l))+1,endColumn:e.visibleColToGlobalCol(l)+1}},get segmentDomainTypes(){return[...e.annotationTypes.values()].filter(t=>fn.has(t.featureType??"")).toSorted((t,o)=>t.start-o.start)},get categoricalDomainTypes(){return[...e.annotationTypes.values()].filter(t=>!fn.has(t.featureType??""))},get fillPalette(){let t=Object.fromEntries(this.segmentDomainTypes.map((r,i)=>[r.accession,pn[i%pn.length]])),o=tn(this.categoricalDomainTypes.map(r=>r.accession));return{...t,...o}},get featureFillEncoding(){return this.resolvedEncodings.find(t=>t.channel==="featureFill")},get featureColors(){return zc(e.filteredAnnotations,this.featureFillEncoding,this.fillPalette)},get featureLabels(){let t=this.resolvedEncodings.find(o=>o.channel==="featureLabel");return t?Bc(e.filteredAnnotations,t.field):void 0},get segmentLabels(){return new Map(this.segmentDomainTypes.map((t,o)=>{let r=/(\d+)\s*$/.exec(t.name);return[t.accession,r?r[1]:`${o+1}`]}))},get visibleDomainTypes(){return this.categoricalDomainTypes.filter(t=>!e.turnedOffFeatures.get(t.accession)).toSorted((t,o)=>t.start-o.start)},get legends(){let{featureFillEncoding:t,fillPalette:o,visibleDomainTypes:r}=this,i=new Map,s=(a,l,c)=>{if(l.length===0)return;let u=a===void 0?"domains":`field:${a}`,d=i.get(u);if(d){let h=new Set(d.entries.map(f=>f.id));d.entries.push(...l.filter(f=>!h.has(f.id)))}else i.set(u,{id:c??(a===void 0?"domains":`rowData-${a}`),title:a??"Domains",entries:[...l]})};e.actuallyShowDomains&&e.numColumns>0&&s(t?.field,t?t.legend:r.map(a=>({id:a.accession,label:a.name,color:o[a.accession]})),"domains");for(let{channel:a,field:l,legend:c}of this.resolvedEncodings)Uc.has(a)||s(l,c);for(let{legendTitle:a,legend:l}of this.rowPanelScales)s(a,l);return[...i.values()]},get domainUnderline(){return e.actuallyShowDomains&&!e.bgColor&&!e.subFeatureRows&&e.showMsaLetters},get domainBands(){let{blanks:t}=e,o=new Map;for(let[r,i]of Object.entries(e.annotationsByRow)){let s=i.toSorted((a,l)=>vn(l)-vn(a)).map(a=>{let l=e.seqPosToGlobalCol(r,a.start-1),c=e.seqEndToGlobalCol(r,a.end-1);if(l===void 0||c===void 0)return;let u=$e(t,l),d=$e(t,c+1);return d>u?{annotation:a,startCol:u,endCol:d}:void 0}).filter(H.notEmpty).map((a,l)=>({...a,stackIndex:l}));s.length>0&&o.set(r,lt(s))}return o},get domainBandsByStart(){return new Map([...this.domainBands].map(([t,o])=>[t,o.toSorted((r,i)=>r.startCol-i.startCol)]))},get mouseOverDomains(){let{mouseCol:t}=e,o=e.mouseOverRowName;if(o===void 0||t===void 0)return $c;let r=(this.domainBands.get(o)??[]).filter(i=>t>=i.startCol&&t<i.endCol).map(i=>i.annotation);return r.length>0?r:$c},get referenceRowIndex(){let{relativeTo:t}=e;return t===void 0?void 0:e.rowNamesSet.get(t)},get hoveredRowIndices(){let{hoveredTreeNode:t,rowNamesSet:o}=e;return t?t.descendantNames.map(r=>o.get(r)).filter(H.notEmpty):[]},get highlightedColumnRuns(){return Jc([...e.highlightedColumns??[]].sort((t,o)=>t-o)).map(([t,o])=>({start:t,end:o}))},fillHighlightLabel(t,o,r){if(!t.includes("{"))return t;let i=o&&r!==void 0?e.seqPosIndex(o)?.[r-1]:void 0,s=o&&i!==void 0?e.MSA?.getRow(o)[i]??"":"";return t.replaceAll("{residue}",s).replaceAll("{position}",r===void 0?"":String(r))},get resolvedHighlights(){let{rowNamesSet:t,transientHighlights:o}=e;return[...e.highlights,...Object.values(o).flat()].flatMap(({row:i,rows:s,start:a,end:l,label:c,color:u})=>{let d={label:c&&this.fillHighlightLabel(c,i,a),color:u};if(s){let f=s.map(g=>t.get(g)).filter(H.notEmpty);return f.length?[{...d,rowIndices:f}]:[]}if(a===void 0||l===void 0)return[];let h=e.visibleSpan({row:i,start:a,end:l});return h?[{...d,...h,rowIndices:[]}]:[]})},get resolvedSelection(){let{selection:t,rowNamesSet:o,numRows:r}=e,i=t&&e.visibleSpan({start:t.start,end:t.end});if(!t||!i)return;let s=t.rows?Jc(t.rows.map(a=>o.get(a)).filter(H.notEmpty).sort((a,l)=>a-l)):r>0?[[0,r-1]]:[];return s.length>0?{...i,rowRuns:s}:void 0},get selectionSize(){let t=this.resolvedSelection,o=this.selectionFileSpan;return t&&o?{columns:o.end-o.start+1,rows:(0,H.sum)(t.rowRuns.map(([r,i])=>i-r+1))}:void 0},get selectionFileSpan(){let{selection:t}=e,o=e.MSA?.getWidth()??0,r=Math.max(1,Math.floor(t?.start??0)),i=Math.min(o,Math.ceil(t?.end??0));return t&&r<=i?{start:r,end:i}:void 0},get selectionFasta(){let{rowNames:t,rowMap:o}=e,r=this.resolvedSelection,i=this.selectionFileSpan;if(!r||!i)return"";let s=r.rowRuns.flatMap(([a,l])=>t.slice(a,l+1)).flatMap(a=>{let l=o.get(a);return l===void 0?[]:[[a,l]]});return jl(s,i.start,i.end)},columnStatsAt(t){let{colStats:o,conservation:r,propertyConservation:i}=e;return Jl({col:t,colStats:o,conservation:r,propertyConservation:i})},getRowData(t){return{data:e.MSA?.getRowData(t),rowData:e.rowDataOf(t)}},get resolvedEncodings(){let t=Object.values(e.rowData);return e.encodings.map(o=>({...o,...Uc.has(o.channel)?Gc(o.field,o.scale,e.allAnnotations,e.filteredAnnotations):an(o.scale,t.map(r=>r?.[o.field]).filter(H.notEmpty))}))},get rowPanelScales(){let{rowData:t}=e,{fillPalette:o,featureFillEncoding:r,featureLabels:i}=this,s=e.filteredAnnotations;return e.rowPanels.map(a=>{if(a.kind==="features"){let u=a.encoding?.color,d=u?Gc(u.field,u.scale,e.allAnnotations,s):r,h=a.encoding?.label;return{kind:a.kind,x:a.x,header:a.header??"",field:d?.field,legendTitle:d?.field,colors:u?zc(s,d,o):this.featureColors,labels:h?Bc(s,h):i,legend:d?.legend??this.visibleDomainTypes.map(f=>({id:f.accession,label:f.name,color:o[f.accession]}))}}let{colorOf:l,legend:c}=an(a.scale,Object.values(t).map(u=>u?.[a.field]).filter(H.notEmpty));return{kind:a.kind,field:a.field,header:a.header??a.field,legendTitle:a.legend??a.field,colors:so(t,a.field,l),legend:c}})},get resolvedRowPanels(){let t=this.rowPanelScales,o=0;return e.rowPanels.map((r,i)=>{let s=Nc(r,e),a={id:`rowpanel-${i}`,width:s,offsetX:o};if(o+=s,r.kind==="features"){let l=r.transform?.find(c=>c.type==="align");return{...a,...t[i],spans:qm({panel:r,width:s,colWidth:e.colWidth,domainBands:this.domainBands,annotationsByRow:e.annotationsByRow,shifts:l?this.featureAlignShifts.get(l.on):void 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