npm - jbrowse-plugin-msaview - Versions diffs - 5.2.0 → 5.3.0 - Mend

jbrowse-plugin-msaview 5.2.0 → 5.3.0

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Files changed (84) hide show

package/dist/chunks/chunk-CSCUNTGJ.js ADDED Viewed

@@ -0,0 +1,18 @@
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e.features.length>0?[...e.annotations,...Rl(e.features)]:e.annotations},get actuallyShowDomains(){return e.showDomains&&this.allAnnotations.length>0},get hostRestoresData(){return e.hostCarriesData},get viewInitialized(){return e.volatileWidth!==void 0},get width(){if(e.volatileWidth===void 0)throw new Error("not initialized");return e.volatileWidth}})).views(e=>({get colorScheme(){let{customColorScheme:t,colorSchemeName:r}=e;return t?Ai(t):Je[r]??Je[ut]},get dynamicColorSchemeName(){let{customColorScheme:t,colorSchemeName:r}=e;return!t&&r.includes("dynamic")?r:void 0},get header(){return this.MSA?.getHeader()??{}},get alignmentNames(){return this.MSA?.alignmentNames??[]},get noTree(){return!!this.tree.noTree},get noDomains(){return e.allAnnotations.length===0},get 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r=this.treeOverviewLayout;if(!r)return;let{root:o,numTips:i}=r,s=i/e.overviewHeight,a=(0,R.clamp)(Math.floor(t*s),0,i-1),l=(0,R.clamp)(Math.ceil((t+1)*s)-1,a,i-1),c=Ro(o,a+.5,l+.5);for(;!c.children&&c.parent;)c=c.parent;return c===o?void 0:{id:c.data.id,rows:xc(c)}},get rowPanelsWidth(){return(0,R.sum)(e.rowPanels.map(t=>hc(t,e)))},get rowPanelsHeaderHeight(){return e.rowPanels.length>0?Jr:0},get msaAreaWidth(){return e.width-this.effectiveTreeAreaWidth-this.rowPanelsWidth-e.resizeHandleWidth},get treeAreaWidthMinusMargin(){return this.effectiveTreeAreaWidth-e.marginLeft-this.cladeGutterWidth},get blanks(){let{hideGapsEffective:t,allowedGappyness:r}=e;if(!t)return[];let o=this.leaves.map(u=>this.MSA?.getRow(u.data.name)).filter(R.notEmpty);if(o.length===0)return[];let i=this.MSA?.getWidth()??0,s=o.length,a=Math.ceil(r/100*s),l=new Uint32Array(i);for(let u=0;u<s;u++){let d=o[u],m=d.length;for(let f=0;f<i;f++)(f>=m||d.charCodeAt(f)-45>>>0<=1)&&l[f]++}let c=[];for(let u=0;u<i;u++)l[u]>=a&&c.push(u);return c},get insertionPositions(){let{blanks:t,rows:r}=this;if(t.length===0)return new Map;let o=new Map;for(let[i,s]of r){let a=io(t,s);a.length>0&&o.set(i,a)}return o},get rows(){let t=this.MSA;return this.leaves.map(r=>[r.data.name,t?.getRow(r.data.name)]).filter(r=>!!r[1])},get numRows(){return this.leaves.length},seqPosIndex(t){let r=this.MSA;if(!r)return;let o=Tc.get(r);o||(o=new Map,Tc.set(r,o));let i=o.get(t);if(!i){let s=r.getRow(t);if(!s)return;i=nc(s),o.set(t,i)}return i},rowSequence(t){return this.MSA?.getRow(t)||void 0},get rowMap(){let t=this.MSA;return new Map(t?.getNames().map(r=>[r,t.getRow(r)]).filter(([,r])=>!!r))},get columns(){let t=this.columns2d;return new Map(this.rows.map((r,o)=>[r[0],t[o]]))},get columns2d(){let{hideGapsEffective:t}=e;return this.rows.map(([,r])=>(t?gt(this.blanks,r):r).toUpperCase())},get fontSize(){return Ir(e.rowHeight)},get colStats(){return So(this.columns2d,this.numColumns)},get sequenceType(){let t=this.colStats.lettersPresent,r=["N","R","Y","K","M","S","W"],o=new Set(["A","C","G","T",...r]),i=new Set(["A","C","G","U",...r]),s=t.size>0&&[...t].every(l=>o.has(l)),a=t.size>0&&[...t].every(l=>i.has(l));return s?"dna":a?"rna":"amino"},get colConsensus(){let{colStats:t}=this;return Array.from({length:t.numColumns},(r,o)=>{let i=t.total(o),s=0,a="";t.forEachResidue(o,(c,u)=>{u>s&&(s=u,a=wo(c))});let l=i?s/i:0;return{letter:a,color:l>.4?`hsl(240, 30%, ${100*Math.max(1-l/3,.3)}%)`:void 0}})},get colClustalX(){let{colStats:t}=this;return Array.from({length:t.numColumns},(r,o)=>yl(t,o))},get conservation(){let{colStats:t,alphabetMaxBits:r}=this;return Array.from({length:t.numColumns},(o,i)=>{let s=t.total(i),a=t.gapCount(i);return s>a?Math.max(0,1-t.entropy(i)/r)*(1-a/s):0})},get alphabetMaxBits(){return Mo(this.sequenceType)},get propertyConservation(){return this.sequenceType==="amino"?Xl(this.colStats):[]},get treeLayout(){let t=()=>this.effectiveTreeWidth;return pn(this.root,{get rowHeight(){return e.rowHeight},get treeWidth(){return t()}})},get hierarchy(){return this.treeLayout.root},get totalHeight(){return this.leaves.length*e.rowHeight},get leaves(){return this.treeLayout.leaves},get rootToTipLength(){return this.treeLayout.rootToTipLength},get pxPerBranchLength(){let t=this.rootToTipLength;return this.showBranchLenEffective&&t?this.effectiveTreeWidth/t:0},get maxDepthToLeaf(){return this.treeLayout.root.depthToLeaf},get allBranchesLength0(){return this.rootToTipLength===0},get showBranchLenEffective(){return this.allBranchesLength0?!1:e.showBranchLen}})).views(e=>({get totalWidth(){return e.numColumns*e.colWidth}})).views(e=>({get showMsaLetters(){return e.drawMsaLetters&&e.rowHeight>=dn&&e.colWidth>=Pr&&e.colWidth>e.rowHeight/2}})).views(e=>{let t=new WeakMap;return{get columnTrackContent(){let{MSA:r,blanks:o,hideGapsEffective:i}=e,s=r?.getWidth()??0,a=(u,d,m)=>{if(!u.row)return d;let f=Array.from({length:s},()=>m),g=e.seqPosIndex(u.row);return d.forEach((p,w)=>{let x=g?.[w];x!==void 0&&(f[x]=p)}),f},l=u=>i?oo(o,u):u,c=(u,d)=>{let m=u.row?e.seqPosIndex(u.row)?.[d-1]:d-1;if(!(m===void 0||m<0||m>=s))return i?$e(o,m):m};return new Map(e.columnTracks.map(u=>{if(u.kind==="arc"){let m=(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(R.notEmpty);return[u.id,{arcs:m}]}if(u.kind==="bar"){let m=u.max??1,f=l(a(u,u.values??[],0)).map(g=>Math.min(1,Math.max(0,g/m)));return[u.id,{values:f}]}let d=l(a(u,(u.data??"").split("")," "));return[u.id,{data:d.join("")}]}))},trackHeight(r,o=r,i){return e.trackHeights.get(o)??i??gh[r]??e.rowHeight},columnTrackModel(r){let o=t.get(r);return o||(o=(0,N.computed)(()=>{let i=dc.has(r.kind)?bh(r.id):void 0,s=this.columnTrackContent.get(r.id);return{model:{id:r.id,name:r.name,kind:r.kind,heightKey:i,height:this.trackHeight(r.kind,i,r.height),barColor:r.color,arcColor:r.color,customColorScheme:r.colors,data:s?.data,arcs:s?.arcs}}}),t.set(r,o)),o.get()},get columnTrackModels(){return e.columnTracks.map(r=>this.columnTrackModel(r))}}}).views(e=>({get secondaryStructureConsensus(){return e.MSA?.secondaryStructureConsensus},get secondaryStructureArcs(){let{blanks:t,hideGapsEffective:r}=e,o=this.secondaryStructureConsensus;if(o)return lc(r?gt(t,o):o).map(({start:i,end:s,pseudoknot:a})=>({start:i,end:s,color:a?Sh:vh}))},get adapterTrackModels(){let{MSA:t,hideGapsEffective:r,blanks:o}=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:r?gt(o,a.data):a.data,height:s}}))},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}}]:[]},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:dc.has(t.kind)?t.kind:void 0,height:e.trackHeight(t.kind)}}))},get tracks(){return[...this.adapterTrackModels,...this.basePairTrackModels,...e.columnTrackModels,...e.numColumns>0?this.computedTrackModels:[]]},get turnedOnTracks(){return this.tracks.filter(t=>!bc(e.turnedOffTracks,t.model.id,t.model.defaultOff))},get showHorizontalScrollbar(){return Ac(e.totalWidth,e.msaAreaWidth)},visibleColToRowLetter(t,r){return e.rowSequence(t)?.[this.visibleColToGlobalCol(r)]},visibleColToSeqPos(t,r){return tc(e.seqPosIndex(t),this.visibleColToGlobalCol(r))},visibleColToSeqPosOneBased(t,r){let o=this.visibleColToSeqPos(t,r);return o!==void 0?o+1:void 0},globalColToVisibleCol(t){let{blanks:r,hideGapsEffective:o}=e;return o?Jl(r,t):t},visibleColToGlobalCol(t){let{blanks:r,hideGapsEffective:o}=e;return o?Ql(r,t):t},seqPosToGlobalCol(t,r){let o=e.rowSequence(t);return o===void 0?void 0:e.seqPosIndex(t)?.[r]??(r===0?0:o.length)},seqEndToGlobalCol(t,r){let o=e.seqPosIndex(t);return o&&o.length>0?o[Math.min(r,o.length-1)]:void 0},seqPosToVisibleCol(t,r){let o=this.seqPosToGlobalCol(t,r);return o===void 0?void 0:this.globalColToVisibleCol(o)},visibleSpan({row:t,start:r,end:o}){let{blanks:i}=e,s=Math.max(1,Math.floor(r)),a=Math.ceil(o),l=s-1,c=Math.min(a,e.MSA?.getWidth()??a)-1;if(t!==void 0){let m=this.seqPosToGlobalCol(t,s-1),f=this.seqEndToGlobalCol(t,a-1);if(m===void 0||f===void 0)return;l=m,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 r of e.residueMappings){let o={row:r.row,structureId:r.structure.id},i=e.seqPosIndex(r.row)?.length;if(i===void 0){t.push({...o,scope:"mapping",reason:"no such row in the alignment"});continue}if(r.rowLength!==void 0&&r.rowLength!==i){t.push({...o,scope:"mapping",reason:`computed against a ${r.rowLength}-residue row; this one has ${i}`});continue}let s=r.segments.find(a=>a.rowEnd>i||a.rowStart<1);if(s){t.push({...o,scope:"mapping",reason:`segment ${s.rowStart}-${s.rowEnd} does not fit a ${i}-residue row`});continue}for(let a of r.segments)Ec(a)||t.push({...o,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(r=>r.scope==="mapping").map(r=>`${r.row}\0${r.structureId}`));return e.residueMappings.filter(r=>!t.has(`${r.row}\0${r.structure.id}`)).map(r=>({...r,segments:r.segments.filter(Ec)}))},get mappedStructures(){return this.usableResidueMappings.map(t=>({row:t.row,structure:t.structure}))},structureResidue(t,r,o){let i=[];for(let s of this.usableResidueMappings){if(s.row!==t||o!==void 0&&s.structure.id!==o)continue;let a=s.segments.find(l=>r>=l.rowStart&&r<=l.rowEnd);if(a){let l=a.structStart+(r-a.rowStart);i.push({structure:s.structure,position:l,observed:!Ih(s.unobserved,l)})}}return i.length===1?i[0]:void 0},rowResidue(t,r,o){let i=[];for(let s of this.usableResidueMappings){if(s.structure.id!==t||o!==void 0&&s.structure.asymId!==o)continue;let a=s.segments.find(l=>r>=l.structStart&&r<=l.structEnd);a&&i.push({rowName:s.row,seqPos:a.rowStart+(r-a.structStart)})}return i.length===1?i[0]:void 0}})).views(e=>({get treeScaleBar(){return El(e.pxPerBranchLength,e.effectiveTreeAreaWidth-e.marginLeft*2)},get topBandHeight(){return Math.max(e.showHorizontalScrollbar?e.minimapHeight:0,e.rowPanelsHeaderHeight,e.treeOverviewHeight+(this.treeScaleBar?Ue:0))},get msaAreaHeight(){return e.height-this.topBandHeight-e.headerHeight-this.totalTrackAreaHeight},get totalTrackAreaHeight(){return(0,R.sum)(e.turnedOnTracks.map(t=>t.model.height))},get annotationTypes(){let t=new Map;for(let r of e.allAnnotations)t.has(r.accession)||t.set(r.accession,r);return t},get filteredAnnotations(){return e.allAnnotations.filter(t=>!e.turnedOffFeatures.get(t.accession))},get annotationsByRow(){let{rowNamesSet:t}=e;return(0,R.groupBy)(this.filteredAnnotations,r=>yc(r.id,t))}})).views(e=>({get showVerticalScrollbar(){return Ac(e.totalHeight,e.msaAreaHeight)}})).views(e=>({get dataInitialized(){return!!(e.data.msa||e.data.tree)&&!e.error},get blocksX(){return Xn({viewportSize:e.msaAreaWidth,viewportPos:-e.scrollX,blockSize:e.blockSize,mapSize:e.totalWidth})},get blocksY(){return Xn({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(r=>[r,t]))},get isLoading(){return e.loadingMSA||e.loadingTree},get dataWarnings(){let{annotations:t,rowNamesSet:r}=e;return e.dataInitialized&&t.length>0&&!t.some(o=>r.has(yc(o.id,r)))?[`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 r=De(e.hierarchy,o=>o.data.id===t);e.hoveredTreeNode=r?{nodeId:t,descendantNames:Ie(r).map(o=>o.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>Ee)throw new Error(`Neighbor joining here is capped at ${Ee} sequences and this alignment has ${t.length}. Build the tree with FastTree or IQ-TREE and open it alongside the alignment: https://gmod.org/JBrowseMSA/tutorials/protein_family`);this.replaceTree($l(t))},rerootAt(t){let r=De(Ae(e.tree,i=>i.children),i=>i.data.id===t);if(!r?.parent)return;let o=Fc(Ae(e.inputTree,i=>i.children),Ie(r).map(i=>i.data.name));if(o){let i=Ie(o);e.setTreeRoot({outgroup:[...new Set([i[0].data.name,i.at(-1).data.name])]})}},replaceTree(t){(0,N.transaction)(()=>{e.setTreeFilehandle(void 0),e.collapsed.clear(),e.rotated.clear(),e.setShowOnly(void 0),e.setTree(t)})},resetZoom(){e.setColWidth(12),e.setRowHeight(16)},zoomAtCenter(t,r="both"){this.zoomToPos(t,e.msaCanvasWidth/2,e.msaAreaHeight/2,r)},zoomIn(){this.zoomAtCenter(1.5)},zoomOut(){this.zoomAtCenter(.75)},zoomToPos(t,r,o,i="both"){(0,N.transaction)(()=>{let s=(-e.scrollX+r)/e.colWidth,a=(-e.scrollY+o)/e.rowHeight;i!=="vertical"&&(e.colWidth=(0,R.clamp)(e.colWidth*t,lt,Te)),i!=="horizontal"&&(e.rowHeight=(0,R.clamp)(e.rowHeight*t,ct,Te)),e.scrollX=(0,R.clamp)(r-s*e.colWidth,e.maxScrollX,0);let l=o-a*e.rowHeight,c=Math.max(0,-e.maxScrollY),u=e.totalHeight-c,d=u>0?(0,R.clamp)(1-c/u,0,1):1;e.scrollY=(0,R.clamp)(l*(1-d),e.maxScrollY,0)})},doScrollY(t){this.setScrollY(e.scrollY+t)},setScrollY(t){e.scrollY=(0,R.clamp)(t,e.maxScrollY,0)},setAnnotations(t){e.annotations=t},applyGFFText(t){this.setAnnotations(zo(Wo(t)))},doScrollX(t){this.setScrollX(e.scrollX+t)},setScrollX(t){e.scrollX=(0,R.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 r=e.MSA?.tracks.find(o=>o.id===t)?.defaultOff;e.turnedOffTracks.set(t,!bc(e.turnedOffTracks,t,r))},setStatus(t){e.status=t}})).views(e=>({cellAt(t,r){let o=e.visibleColToGlobalCol(t),i=r===void 0?void 0:e.leaves[r]?.data.name;return i===void 0?{column:o+1}:{column:o+1,row:i,residue:e.visibleColToSeqPosOneBased(i,t),letter:e.rowSequence(i)?.[o]}},get hoveredCell(){let{mouseCol:t,mouseRow:r}=e;return t===void 0?void 0:this.cellAt(t,r)},get clickedCell(){let{mouseClickCol:t,mouseClickRow:r}=e;return t===void 0?void 0:this.cellAt(t,r)},get viewport(){let{scrollX:t,colWidth:r,numColumns:o,viewInitialized:i}=e;if(o===0||!i)return;let{xStart:s,xEnd:a}=mo({offsetX:-t,blockWidth:e.msaCanvasWidth,colWidth:r}),l=Math.max(0,Math.min(a,o)-1);return{startColumn:e.visibleColToGlobalCol(Math.min(s,l))+1,endColumn:e.visibleColToGlobalCol(l)+1}},get segmentDomainTypes(){return[...e.annotationTypes.values()].filter(t=>cn.has(t.featureType??"")).toSorted((t,r)=>t.start-r.start)},get categoricalDomainTypes(){return[...e.annotationTypes.values()].filter(t=>!cn.has(t.featureType??""))},get fillPalette(){let t=Object.fromEntries(this.segmentDomainTypes.map((o,i)=>[o.accession,un[i%un.length]])),r=Zt(this.categoricalDomainTypes.map(o=>o.accession));return{...t,...r}},get featureFillEncoding(){return this.resolvedEncodings.find(t=>t.channel==="featureFill")},get featureColors(){return mc(e.filteredAnnotations,this.featureFillEncoding,this.fillPalette)},get featureLabels(){let t=this.resolvedEncodings.find(r=>r.channel==="featureLabel");return t?fc(e.filteredAnnotations,t.field):void 0},get segmentLabels(){return new Map(this.segmentDomainTypes.map((t,r)=>{let o=/(\d+)\s*$/.exec(t.name);return[t.accession,o?o[1]:`${r+1}`]}))},get visibleDomainTypes(){return this.categoricalDomainTypes.filter(t=>!e.turnedOffFeatures.get(t.accession)).toSorted((t,r)=>t.start-r.start)},get legends(){let{featureFillEncoding:t,fillPalette:r,visibleDomainTypes:o}=this,i=new Map,s=(a,l,c)=>{if(l.length===0)return;let u=a===void 0?"domains":`field:${a}`,d=i.get(u);if(d){let m=new Set(d.entries.map(f=>f.id));d.entries.push(...l.filter(f=>!m.has(f.id)))}else i.set(u,{id:c??(a===void 0?"domains":`rowData-${a}`),title:a??"Domains",entries:[...l]})};e.actuallyShowDomains&&e.numColumns>0&&s(t?.field,t?t.legend:o.map(a=>({id:a.accession,label:a.name,color:a.color??r[a.accession]})),"domains");for(let{channel:a,field:l,legend:c}of this.resolvedEncodings)Cc.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,r=new Map;for(let[o,i]of Object.entries(e.annotationsByRow)){let s=i.toSorted((a,l)=>mn(l)-mn(a)).map(a=>{let l=e.seqPosToGlobalCol(o,a.start-1),c=e.seqEndToGlobalCol(o,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(R.notEmpty).map((a,l)=>({...a,stackIndex:l}));s.length>0&&r.set(o,st(s))}return r},get domainBandsByStart(){return new Map([...this.domainBands].map(([t,r])=>[t,r.toSorted((o,i)=>o.startCol-i.startCol)]))},get mouseOverDomains(){let{mouseCol:t}=e,r=e.mouseOverRowName;if(r===void 0||t===void 0)return vc;let o=(this.domainBands.get(r)??[]).filter(i=>t>=i.startCol&&t<i.endCol).map(i=>i.annotation);return o.length>0?o:vc},get referenceRowIndex(){let{relativeTo:t}=e;return t===void 0?void 0:e.rowNamesSet.get(t)},get hoveredRowIndices(){let{hoveredTreeNode:t,rowNamesSet:r}=e;return t?t.descendantNames.map(o=>r.get(o)).filter(R.notEmpty):[]},get highlightedColumnRuns(){return Lc([...e.highlightedColumns??[]].sort((t,r)=>t-r)).map(([t,r])=>({start:t,end:r}))},fillHighlightLabel(t,r,o){if(!t.includes("{"))return t;let i=r&&o!==void 0?e.seqPosIndex(r)?.[o-1]:void 0,s=r&&i!==void 0?e.MSA?.getRow(r)[i]??"":"";return t.replaceAll("{residue}",s).replaceAll("{position}",o===void 0?"":String(o))},get resolvedHighlights(){let{rowNamesSet:t,transientHighlights:r}=e;return[...e.highlights,...Object.values(r).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(R.notEmpty);return f.length?[{...d,rowIndices:f}]:[]}if(a===void 0||l===void 0)return[];let m=e.visibleSpan({row:i,start:a,end:l});return m?[{...d,...m,rowIndices:[]}]:[]})},get resolvedSelection(){let{selection:t,rowNamesSet:r,numRows:o}=e,i=t&&e.visibleSpan({start:t.start,end:t.end});if(!t||!i)return;let s=t.rows?Lc(t.rows.map(a=>r.get(a)).filter(R.notEmpty).sort((a,l)=>a-l)):o>0?[[0,o-1]]:[];return s.length>0?{...i,rowRuns:s}:void 0},get selectionSize(){let t=this.resolvedSelection,r=this.selectionFileSpan;return t&&r?{columns:r.end-r.start+1,rows:(0,R.sum)(t.rowRuns.map(([o,i])=>i-o+1))}:void 0},get selectionFileSpan(){let{selection:t}=e,r=e.MSA?.getWidth()??0,o=Math.max(1,Math.floor(t?.start??0)),i=Math.min(r,Math.ceil(t?.end??0));return t&&o<=i?{start:o,end:i}:void 0},get selectionFasta(){let{rowNames:t}=e,r=this.resolvedSelection,o=this.selectionFileSpan;if(!r||!o)return"";let i=r.rowRuns.flatMap(([s,a])=>t.slice(s,a+1)).flatMap(s=>{let a=e.rowSequence(s);return a===void 0?[]:[[s,a]]});return vl(i,o.start,o.end)},columnStatsAt(t){let{colStats:r,conservation:o,propertyConservation:i}=e;return Tl({col:t,colStats:r,conservation:o,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(r=>({...r,...Cc.has(r.channel)?gc(r.field,r.scale,e.allAnnotations,e.filteredAnnotations):en(r.scale,t.map(o=>o?.[r.field]).filter(R.notEmpty))}))},get rowPanelScales(){let{rowData:t}=e,{fillPalette:r,featureFillEncoding:o,featureLabels:i}=this,s=e.filteredAnnotations;return 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