jbrowse-plugin-msaview 5.7.0 → 5.9.0

package/dist/chunks/chunk-3IMKCK3L.js

@@ -0,0 +1,164 @@
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dw(e){return et(e)||typeof e>"u"||typeof e=="string"||typeof e=="boolean"||typeof e=="number"||Array.isArray(e)}function $i(e={}){let t={...e};function r(n){let o=Object.entries(n);for(let i=0;i<o.length;i++){let[a,s]=o[i];!dw(s)||a.startsWith("unstable_")||a.startsWith("internal_")?delete n[a]:et(s)&&(n[a]={...s},r(n[a]))}}return r(t),`import { unstable_createBreakpoints as createBreakpoints, createTransitions } from '@mui/material/styles';
+
+const theme = ${JSON.stringify(t,null,2)};
+
+theme.breakpoints = createBreakpoints(theme.breakpoints || {});
+theme.motion = { reducedMotion: 'never', ...theme.motion };
+theme.transitions = createTransitions(theme.transitions || {});
+
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+  position: absolute;
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+   * (pulsate) ripple keeps 'pulsateKeyframe' (no opacity animation) on exit, so
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+    height: 100%;
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Ta(this.tree,{collapsed:t.collapsed,rotated:t.rotated,order:t.treeOrder,showOnly:t.showOnly})},get treeNewick(){return s0(Ta(this.tree,{collapsed:[],rotated:t.rotated,order:t.treeOrder}))},get treeOverviewHeight(){return t.showTreeOverview?t.overviewHeight:0},get treeOverviewLayout(){if(!t.showTreeOverview)return;let r=Da(Ta(this.tree,{collapsed:t.collapsed,rotated:t.rotated,order:t.treeOrder}),{rowHeight:1,treeWidth:1});return{root:r.root,numTips:r.leaves.length,maxDepthToLeaf:r.root.depthToLeaf,showBranchLen:t.showBranchLen&&r.rootToTipLength>0}},get treeOverviewClades(){let r=this.treeOverviewLayout;return!r||t.clades.length===0?m0:zl(t.clades,Pt(this.tree,n=>n.children),r.root)},get treeOverviewFocusRows(){let r=this.treeOverviewLayout;if(!r||!t.showOnly)return;let n=or(r.root,o=>o.data.id===t.showOnly);return n?Vl(n):void 0},treeOverviewHit(r){let n=this.treeOverviewLayout;if(!n)return;let{root:o,numTips:i}=n,a=i/t.overviewHeight,s=(0,H.clamp)(Math.floor(r*a),0,i-1),l=(0,H.clamp)(Math.ceil((r+1)*a)-1,s,i-1),c=bu(o,s+.5,l+.5);for(;!c.children&&c.parent;)c=c.parent;return c===o?void 0:{id:c.data.id,rows:Vl(c)}},get rowPanelsWidth(){return(0,H.sum)(t.rowPanels.map(r=>Al(r,t)))},get rowPanelsHeaderHeight(){return t.rowPanels.length>0?qc:0},get msaAreaWidth(){return t.width-this.effectiveTreeAreaWidth-this.rowPanelsWidth-t.resizeHandleWidth},get treeAreaWidthMinusMargin(){return this.effectiveTreeAreaWidth-t.marginLeft-this.cladeGutterWidth},get blanks(){let{hideGapsEffective:r,allowedGappyness:n}=t;if(!r)return[];let o=this.leaves.map(u=>this.MSA?.getRow(u.data.name)).filter(H.notEmpty);if(o.length===0)return[];let i=this.MSA?.getWidth()??0,a=o.length,s=Math.ceil(n/100*a),l=new Uint32Array(i);for(let u=0;u<a;u++){let f=o[u],m=f.length;for(let p=0;p<i;p++)(p>=m||f.charCodeAt(p)-45>>>0<=1)&&l[p]++}let c=[];for(let u=0;u<i;u++)l[u]>=s&&c.push(u);return c},get insertionPositions(){let{blanks:r,rows:n}=this;if(r.length===0)return new Map;let o=new Map;for(let[i,a]of n){let s=ru(r,a);s.length>0&&o.set(i,s)}return o},get rows(){let r=this.MSA;return this.leaves.map(n=>[n.data.name,r?.getRow(n.data.name)]).filter(n=>!!n[1])},get numRows(){return this.leaves.length},seqPosIndex(r){let n=this.MSA;if(!n)return;let o=g0.get(n);o||(o=new Map,g0.set(n,o));let i=o.get(r);if(!i){let a=n.getRow(r);if(!a)return;i=Yg(a),o.set(r,i)}return i},rowSequence(r){return this.MSA?.getRow(r)||void 0},get rowMap(){let r=this.MSA;return new Map(r?.getNames().map(n=>[n,r.getRow(n)]).filter(([,n])=>!!n))},get columns(){let r=this.columns2d;return new Map(this.rows.map((n,o)=>[n[0],r[o]]))},get columns2d(){let{hideGapsEffective:r}=t;return this.rows.map(([,n])=>(r?Oo(this.blanks,n):n).toUpperCase())},get fontSize(){return Oc(t.rowHeight)},get colStats(){return lu(this.columns2d,this.numColumns)},get sequenceType(){let r=this.colStats.lettersPresent,n=["N","R","Y","K","M","S","W"],o=new Set(["A","C","G","T",...n]),i=new Set(["A","C","G","U",...n]),a=r.size>0&&[...r].every(l=>o.has(l)),s=r.size>0&&[...r].every(l=>i.has(l));return a?"dna":s?"rna":"amino"},get colConsensus(){let{colStats:r}=this;return Array.from({length:r.numColumns},(n,o)=>{let i=r.total(o),a=0,s="";r.forEachResidue(o,(c,u)=>{u>a&&(a=u,s=Tn(c))});let l=i?a/i:0;return{letter:s,color:l>.4?`hsl(240, 30%, ${100*Math.max(1-l/3,.3)}%)`:void 0}})},get colClustalX(){let{colStats:r}=this;return Array.from({length:r.numColumns},(n,o)=>sg(r,o))},get colSimilarity(){let{colStats:r,sequenceType:n}=this,o=n==="amino"?Qg:Jg;return Array.from({length:r.numColumns},(i,a)=>o(r,a))},get conservation(){let{colStats:r,alphabetMaxBits:n}=this;return Array.from({length:r.numColumns},(o,i)=>{let a=r.total(i),s=r.gapCount(i);return a>s?Math.max(0,1-r.entropy(i)/n)*(1-s/a):0})},get alphabetMaxBits(){return cu(this.sequenceType)},get propertyConservation(){return this.sequenceType==="amino"?Dg(this.colStats):[]},get treeLayout(){let r=()=>this.effectiveTreeWidth;return Da(this.root,{get rowHeight(){return t.rowHeight},get treeWidth(){return r()}})},get hierarchy(){return this.treeLayout.root},get totalHeight(){return this.leaves.length*t.rowHeight},get leaves(){return this.treeLayout.leaves},get rootToTipLength(){return this.treeLayout.rootToTipLength},get pxPerBranchLength(){let r=this.rootToTipLength;return this.showBranchLenEffective&&r?this.effectiveTreeWidth/r:0},get maxDepthToLeaf(){return this.treeLayout.root.depthToLeaf},get allBranchesLength0(){return this.rootToTipLength===0},get showBranchLenEffective(){return this.allBranchesLength0?!1:t.showBranchLen}})).views(t=>({get totalWidth(){return t.numColumns*t.colWidth}})).views(t=>({get showMsaLetters(){return t.drawMsaLetters&&t.rowHeight>=Fa&&t.colWidth>=Pc&&t.colWidth>t.rowHeight/2}})).views(t=>{let r=new WeakMap;return{get columnTrackContent(){let{MSA:n,blanks:o,hideGapsEffective:i}=t,a=n?.getWidth()??0,s=(u,f,m)=>{if(!u.row)return f;let p=Array.from({length:a},()=>m),h=t.seqPosIndex(u.row);return f.forEach((g,b)=>{let v=h?.[b];v!==void 0&&(p[v]=g)}),p},l=u=>i?tu(o,u):u,c=(u,f)=>{let m=u.row?t.seqPosIndex(u.row)?.[f-1]:f-1;if(!(m===void 0||m<0||m>=a))return i?xn(o,m):m};return new Map(t.columnTracks.map(u=>{if(u.kind==="arc"){let m=(u.arcs??[]).map(p=>{let h=c(u,Math.min(p.start,p.end)),g=c(u,Math.max(p.start,p.end));return h!==void 0&&g!==void 0&&h<g?{start:h,end:g,color:p.color}:void 0}).filter(H.notEmpty);return[u.id,{arcs:m}]}if(u.kind==="bar"){let m=u.scales?.y?.domainMax??1,p=l(s(u,u.values??[],0)).map(h=>Math.min(1,Math.max(0,h/m)));return[u.id,{values:p}]}let f=l(s(u,(u.data??"").split("")," "));return[u.id,{data:f.join("")}]}))},trackHeight(n,o=n,i){return t.trackHeights.get(o)??i??VS[n]??t.rowHeight},columnTrackModel(n){let o=r.get(n);return o||(o=(0,de.computed)(()=>{let i=u0.has(n.kind)?jS(n.id):void 0,a=this.columnTrackContent.get(n.id);return{model:{id:n.id,name:n.name,kind:n.kind,heightKey:i,height:this.trackHeight(n.kind,i,n.height),barColor:n.color,arcColor:n.color,customColorScheme:n.encoding?.color?_l(n.encoding.color,[...n.encoding.color.domain??[],...new Set(n.data)]):void 0,data:a?.data,arcs:a?.arcs}}}),r.set(n,o)),o.get()},get columnTrackModels(){return t.columnTracks.map(n=>this.columnTrackModel(n))}}}).views(t=>({get secondaryStructureConsensus(){return t.MSA?.secondaryStructureConsensus},get secondaryStructureArcs(){let{blanks:r,hideGapsEffective:n}=t,o=this.secondaryStructureConsensus;if(o)return c0(n?Oo(r,o):o).map(({start:i,end:a,pseudoknot:s})=>({start:i,end:a,color:s?US:GS}))},get adapterTrackModels(){let{MSA:r,hideGapsEffective:n,blanks:o}=t,i=(r?.tracks??[]).filter(s=>!!s.data);if(i.length===0)return[];let{rowHeight:a}=t;return i.map(s=>({model:{...s,kind:"text",data:n?Oo(o,s.data):s.data,height:a}}))},get basePairTrackModels(){let r=this.secondaryStructureArcs;return r?.length?[{model:{id:"base-pairs",name:"Base pairs",kind:"arc",heightKey:"arc",height:t.trackHeight("arc"),arcs:r}}]:[]},get computedTrackModels(){return[{id:"conservation",name:"Conservation",kind:"bar",barColor:"gray"},...t.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(r=>({model:{...r,heightKey:u0.has(r.kind)?r.kind:void 0,height:t.trackHeight(r.kind)}}))},get referenceTrackModels(){let{relativeTo:r}=t,n=r===void 0?void 0:t.columns.get(r);return r===void 0||n===void 0?[]:[{model:{id:"reference-row",name:r,kind:"reference",data:n,height:t.rowHeight}}]},get tracks(){return[...this.adapterTrackModels,...this.basePairTrackModels,...t.columnTrackModels,...t.numColumns>0?this.computedTrackModels:[],...this.referenceTrackModels]},get turnedOnTracks(){return this.tracks.filter(r=>!d0(t.turnedOffTracks,r.model.id))},get showHorizontalScrollbar(){return x0(t.totalWidth,t.msaAreaWidth)},visibleColToRowLetter(r,n){return t.rowSequence(r)?.[this.visibleColToGlobalCol(n)]},visibleColToSeqPos(r,n){return zg(t.seqPosIndex(r),this.visibleColToGlobalCol(n))},visibleColToSeqPosOneBased(r,n){let o=this.visibleColToSeqPos(r,n);return o!==void 0?o+1:void 0},globalColToVisibleCol(r){let{blanks:n,hideGapsEffective:o}=t;return o?$g(n,r):r},visibleColToGlobalCol(r){let{blanks:n,hideGapsEffective:o}=t;return o?_g(n,r):r},seqPosToGlobalCol(r,n){let o=t.rowSequence(r);return o===void 0?void 0:t.seqPosIndex(r)?.[n]??(n===0?0:o.length)},seqEndToGlobalCol(r,n){let o=t.seqPosIndex(r);return o&&o.length>0?o[Math.min(n,o.length-1)]:void 0},seqPosToVisibleCol(r,n){let o=this.seqPosToGlobalCol(r,n);return o===void 0?void 0:this.globalColToVisibleCol(o)},visibleSpan({row:r,start:n,end:o}){let{blanks:i}=t,a=Math.max(1,Math.floor(n)),s=Math.ceil(o),l=a-1,c=Math.min(s,t.MSA?.getWidth()??s)-1;if(r!==void 0){let m=this.seqPosToGlobalCol(r,a-1),p=this.seqEndToGlobalCol(r,s-1);if(m===void 0||p===void 0)return;l=m,c=p}let u=this.globalColToVisibleCol(l)??xn(i,l),f=this.globalColToVisibleCol(c)??xn(i,c)-1;return u<=f?{startCol:u,endCol:f}:void 0},get residueMappingProblems(){let r=[];for(let n of t.residueMappings){let o={row:n.row,structureId:n.structure.id},i=t.seqPosIndex(n.row)?.length;if(i===void 0){r.push({...o,scope:"mapping",reason:"no such row in the alignment"});continue}if(n.rowLength!==void 0&&n.rowLength!==i){r.push({...o,scope:"mapping",reason:`computed against a ${n.rowLength}-residue row; this one has ${i}`});continue}let a=n.segments.find(s=>s.rowEnd>i||s.rowStart<1);if(a){r.push({...o,scope:"mapping",reason:`segment ${a.rowStart}-${a.rowEnd} does not fit a ${i}-residue row`});continue}for(let s of n.segments)y0(s)||r.push({...o,scope:"segment",reason:`segment ${s.rowStart}-${s.rowEnd} maps to ${s.structStart}-${s.structEnd}, which is a different length`})}return r},get usableResidueMappings(){let r=new Set(this.residueMappingProblems.filter(n=>n.scope==="mapping").map(n=>`${n.row}\0${n.structureId}`));return t.residueMappings.filter(n=>!r.has(`${n.row}\0${n.structure.id}`)).map(n=>({...n,segments:n.segments.filter(y0)}))},get mappedStructures(){return this.usableResidueMappings.map(r=>({row:r.row,structure:r.structure}))},structureResidue(r,n,o){let i=[];for(let a of this.usableResidueMappings){if(a.row!==r||o!==void 0&&a.structure.id!==o)continue;let s=a.segments.find(l=>n>=l.rowStart&&n<=l.rowEnd);if(s){let l=s.structStart+(n-s.rowStart);i.push({structure:a.structure,position:l,observed:!ZS(a.unobserved,l)})}}return i.length===1?i[0]:void 0},rowResidue(r,n,o){let i=[];for(let a of this.usableResidueMappings){if(a.structure.id!==r||o!==void 0&&a.structure.asymId!==void 0&&a.structure.asymId!==o)continue;let s=a.segments.find(l=>n>=l.structStart&&n<=l.structEnd);s&&i.push({rowName:a.row,seqPos:s.rowStart+(n-s.structStart)})}return i.length===1?i[0]:void 0}})).views(t=>({get treeScaleBar(){return dg(t.pxPerBranchLength,t.effectiveTreeAreaWidth-t.marginLeft*2)},get topBandHeight(){return Math.max(t.showHorizontalScrollbar?t.minimapHeight:0,t.rowPanelsHeaderHeight,t.treeOverviewHeight+(this.treeScaleBar?Sn:0))},get msaAreaHeight(){return t.height-this.topBandHeight-t.headerHeight-this.totalTrackAreaHeight},get totalTrackAreaHeight(){return(0,H.sum)(t.turnedOnTracks.map(r=>r.model.height))},get annotationTypes(){let r=new Map;for(let n of t.allAnnotations)r.has(n.accession)||r.set(n.accession,n);return r},get defaultOffAccessions(){return new Set(t.allAnnotations.filter(r=>r.defaultOff).map(r=>r.accession))},featureOff(r){return t.turnedOffFeatures.get(r)??this.defaultOffAccessions.has(r)},get filteredAnnotations(){return t.allAnnotations.filter(r=>!this.featureOff(r.accession))},get cellFill(){return t.bgColor?t.actuallyShowDomains&&t.domainFill&&this.filteredAnnotations.length>0?"domain":"residue":"none"},get annotationsByRow(){let{rowNamesSet:r}=t;return(0,H.groupBy)(this.filteredAnnotations,n=>h0(n.id,r))}})).views(t=>({get showVerticalScrollbar(){return x0(t.totalHeight,t.msaAreaHeight)}})).views(t=>({get dataInitialized(){return!!(t.data.msa||t.data.tree)&&!t.error},get blocksX(){return no({viewportSize:t.msaAreaWidth,viewportPos:-t.scrollX,blockSize:t.blockSize,mapSize:t.totalWidth})},get blocksY(){return no({viewportSize:t.msaAreaHeight,viewportPos:-t.scrollY,blockSize:t.blockSize,mapSize:t.totalHeight})}})).views(t=>({get verticalScrollbarWidth(){return t.showVerticalScrollbar?20:0},get msaCanvasWidth(){return t.msaAreaWidth-this.verticalScrollbarWidth},get maxScrollX(){return Math.min(-t.totalWidth+this.msaCanvasWidth,0)},get blocks2d(){return t.blocksY.flatMap(r=>t.blocksX.map(n=>[n,r]))},get wheelZooming(){return t.zoomSnapshot!==void 0},get isLoading(){return t.loadingMSA||t.loadingTree},get dataWarnings(){let{annotations:r,rowNamesSet:n}=t;return t.dataInitialized&&r.length>0&&!r.some(o=>n.has(h0(o.id,n)))?[`0 of ${r.length} annotations name a row in this alignment`]:[]},get warnings(){return[...t.loadWarnings,...this.dataWarnings.filter(r=>!t.dismissedWarnings.includes(r))]},get maxScrollY(){return Math.min(-t.totalHeight+t.msaAreaHeight,0)},get wheelZoomAxis(){return t.scrollZoom?t.scrollZoomAxis:"both"}})).actions(t=>({setDrawMsaLetters(r){t.drawMsaLetters=r},clearWarnings(){t.loadWarnings=[],t.dismissedWarnings=t.dataWarnings},setScrollZoom(r){t.scrollZoom=r},setScrollZoomAxis(r){t.scrollZoomAxis=r},setHoveredTreeNode(r){if(r===t.hoveredTreeNode?.nodeId)return;if(!r){t.hoveredTreeNode=void 0;return}let n=or(t.hierarchy,o=>o.data.id===r);t.hoveredTreeNode=n?{nodeId:r,descendantNames:nr(n).map(o=>o.data.name)}:void 0},calculateNeighborJoiningTreeFromMSA(){let r=[...t.rowMap];if(r.length<2)throw new Error("Need at least 2 sequences to build a tree");if(r.length>ar)throw new Error(`Neighbor joining here is capped at ${ar} sequences and this alignment has ${r.length}. Build the tree with FastTree or IQ-TREE and open it alongside the alignment: https://gmod.org/JBrowseMSA/tutorials/protein_family`);this.replaceTree(Fg(r))},rerootAt(r){let n=or(Pt(t.tree,i=>i.children),i=>i.data.id===r);if(!n?.parent)return;let o=Wl(Pt(t.inputTree,i=>i.children),nr(n).map(i=>i.data.name));if(o){let i=nr(o);t.setTreeRoot({outgroup:[...new Set([i[0].data.name,i.at(-1).data.name])]})}},replaceTree(r){(0,de.transaction)(()=>{t.setTreeFilehandle(void 0),t.collapsed.clear(),t.rotated.clear(),t.setShowOnly(void 0),t.setTree(r)})},resetZoom(){t.setColWidth(12),t.setRowHeight(16)},zoomAtCenter(r,n="both"){this.zoomToPos(r,t.msaCanvasWidth/2,t.msaAreaHeight/2,n)},zoomIn(){this.zoomAtCenter(1.5)},zoomOut(){this.zoomAtCenter(.75)},zoomToPos(r,n,o,i="both"){(0,de.transaction)(()=>{let a=(-t.scrollX+n)/t.colWidth,s=(-t.scrollY+o)/t.rowHeight,l=i!=="both"||t.colWidth===12&&t.rowHeight===16;if(i!=="vertical"){let{value:p,held:h}=b0(t.colWidth,r,12,t.zoomHeld.col,So,l);t.colWidth=p,t.zoomHeld={...t.zoomHeld,col:h}}if(i!=="horizontal"){let{value:p,held:h}=b0(t.rowHeight,r,16,t.zoomHeld.row,To,l);t.rowHeight=p,t.zoomHeld={...t.zoomHeld,row:h}}t.scrollX=(0,H.clamp)(n-a*t.colWidth,t.maxScrollX,0);let c=o-s*t.rowHeight,u=Math.max(0,-t.maxScrollY),f=t.totalHeight-u,m=f>0?(0,H.clamp)(1-u/f,0,1):1;t.scrollY=(0,H.clamp)(c*(1-m),t.maxScrollY,0)})},wheelZoomToPos(r,n,o){t.zoomSnapshot??=qs(t,!1),this.zoomToPos(r,n,o,t.wheelZoomAxis),Om(t,t.zoomSnapshot)||(t.zoomSnapshot=qs(t,!0))},endWheelZoom(){t.zoomSnapshot=void 0},doScrollY(r){this.setScrollY(t.scrollY+r)},setScrollY(r){t.scrollY=(0,H.clamp)(r,t.maxScrollY,0)},setAnnotations(r){t.annotations=r},applyGFFText(r){this.setAnnotations(Au(Mu(r)))},doScrollX(r){this.setScrollX(t.scrollX+r)},setScrollX(r){t.scrollX=(0,H.clamp)(r,t.maxScrollX,0)},setColumnTracks(r){t.columnTracks.replace(r.map(Nl))},setRowData(r){t.data.setTreeMetadata(JSON.stringify(r))},setEncodings(r){t.encodings.replace(r.map(Dl))},setRowPanels(r){t.rowPanels.replace(r.map(Bl))},setResidueMappings(r){t.residueMappings.replace(r)},toggleTrack(r){t.turnedOffTracks.set(r,!d0(t.turnedOffTracks,r))},setTracksShown(r,n){for(let o of r)v0.has(o)===!n?t.turnedOffTracks.delete(o):t.turnedOffTracks.set(o,!n)},setStatus(r){t.status=r}})).views(t=>({cellAt(r,n){let o=t.visibleColToGlobalCol(r),i=n===void 0?void 0:t.leaves[n]?.data.name;return i===void 0?{column:o+1}:{column:o+1,row:i,residue:t.visibleColToSeqPosOneBased(i,r),letter:t.rowSequence(i)?.[o]}},get hoveredCell(){let{mouseCol:r,mouseRow:n}=t;return r===void 0?void 0:this.cellAt(r,n)},get clickedCell(){let{mouseClickCol:r,mouseClickRow:n}=t;return r===void 0?void 0:this.cellAt(r,n)},get viewport(){let{scrollX:r,colWidth:n,numColumns:o,viewInitialized:i}=t;if(o===0||!i)return;let{xStart:a,xEnd:s}=nu({offsetX:-r,blockWidth:t.msaCanvasWidth,colWidth:n}),l=Math.max(0,Math.min(s,o)-1);return{startColumn:t.visibleColToGlobalCol(Math.min(a,l))+1,endColumn:t.visibleColToGlobalCol(l)+1}},get segmentDomainTypes(){return[...t.annotationTypes.values()].filter(r=>Pa.has(r.featureType??"")).toSorted((r,n)=>r.start-n.start)},get categoricalDomainTypes(){let r=[...t.annotationTypes.values()].filter(o=>!Pa.has(o.featureType??"")),n=[...new Set(r.map(o=>o.featureType))];return r.toSorted((o,i)=>n.indexOf(o.featureType)-n.indexOf(i.featureType))},get fillPalette(){let r=Object.fromEntries(this.segmentDomainTypes.map((o,i)=>[o.accession,Oa[i%Oa.length]])),n=ha(this.categoricalDomainTypes.map(o=>o.accession));return{...r,...n}},get featureFillEncoding(){return this.resolvedEncodings.find(r=>r.channel==="featureFill")},get featureColors(){return kl(t.filteredAnnotations,this.featureFillEncoding,this.fillPalette)},get featureLabels(){let r=this.resolvedEncodings.find(n=>n.channel==="featureLabel");return r?Rl(t.filteredAnnotations,r.field):void 0},get segmentLabels(){return new Map(this.segmentDomainTypes.map((r,n)=>{let o=/(\d+)\s*$/.exec(r.name);return[r.accession,o?o[1]:`${n+1}`]}))},get visibleDomainTypes(){return this.categoricalDomainTypes.filter(r=>!t.featureOff(r.accession)).toSorted((r,n)=>r.start-n.start)},get legends(){let{featureFillEncoding:r,fillPalette:n,visibleDomainTypes:o}=this,i=new Map,a=new Set,s=(l,c,u,f=!1)=>{let m=l??"domains";if(u.length===0||i.has(m))return;let p=f||l===void 0?"domains":`rowData-${c}`,h=p;for(let g=2;a.has(h);g++)h=`${p}-${g}`;a.add(h),i.set(m,{id:h,title:c??"Domains",entries:u})};t.actuallyShowDomains&&t.numColumns>0&&s(r?.key,r?.title,r?r.legend:o.map(l=>({id:l.accession,label:l.name,color:l.color??n[l.accession]})),!0);for(let{channel:l,key:c,title:u,legend:f}of this.resolvedEncodings)jl.has(l)||s(c,u,f);for(let{legendKey:l,legendTitle:c,legend:u}of this.rowPanelScales)s(l,c,u);return[...i.values()]},get domainUnderline(){return t.actuallyShowDomains&&t.cellFill!=="domain"&&!t.subFeatureRows&&t.showMsaLetters},get domainBands(){let{blanks:r}=t,n=new Map;for(let[o,i]of Object.entries(t.annotationsByRow)){let a=i.toSorted((s,l)=>La(l)-La(s)).map(s=>{let l=t.seqPosToGlobalCol(o,s.start-1),c=t.seqEndToGlobalCol(o,s.end-1);if(l===void 0||c===void 0)return;let u=xn(r,l),f=xn(r,c+1);return f>u?{annotation:s,startCol:u,endCol:f}:void 0}).filter(H.notEmpty).map((s,l)=>({...s,stackIndex:l}));a.length>0&&n.set(o,hn(a))}return n},get domainBandsByStart(){return new Map([...this.domainBands].map(([r,n])=>[r,n.toSorted((o,i)=>o.startCol-i.startCol)]))},get mouseOverDomains(){let{mouseCol:r}=t,n=t.mouseOverRowName;if(n===void 0||r===void 0)return p0;let o=(this.domainBands.get(n)??[]).filter(i=>r>=i.startCol&&r<i.endCol).map(i=>i.annotation);return o.length>0?o:p0},get referenceRowIndex(){let{relativeTo:r}=t;return r===void 0?void 0:t.rowNamesSet.get(r)},get hoveredRowIndices(){let{hoveredTreeNode:r,rowNamesSet:n}=t;return r?r.descendantNames.map(o=>n.get(o)).filter(H.notEmpty):[]},get highlightedColumnRuns(){return w0([...t.highlightedColumns??[]].sort((r,n)=>r-n)).map(([r,n])=>({start:r,end:n}))},fillHighlightLabel(r,n,o){if(!r.includes("{"))return r;let i=n&&o!==void 0?t.seqPosIndex(n)?.[o-1]:void 0,a=n&&i!==void 0?t.MSA?.getRow(n)[i]??"":"";return r.replaceAll("{residue}",a).replaceAll("{position}",o===void 0?"":String(o))},get 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+/*! Bundled license information:
+
+react-is/cjs/react-is.production.js:
+  (**
+   * @license React
+   * react-is.production.js
+   *
+   * Copyright (c) Meta Platforms, Inc. and affiliates.
+   *
+   * This source code is licensed under the MIT license found in the
+   * LICENSE file in the root directory of this source tree.
+   *)
+
+react-is/cjs/react-is.production.min.js:
+  (** @license React v16.13.1
+   * react-is.production.min.js
+   *
+   * Copyright (c) Facebook, Inc. and its affiliates.
+   *
+   * This source code is licensed under the MIT license found in the
+   * LICENSE file in the root directory of this source tree.
+   *)
+
+@mui/styled-engine/index.mjs:
+  (**
+   * @mui/styled-engine v9.5.0
+   *
+   * @license MIT
+   * This source code is licensed under the MIT license found in the
+   * LICENSE file in the root directory of this source tree.
+   *)
+
+@mui/system/index.mjs:
+  (**
+   * @mui/system v9.5.0
+   *
+   * @license MIT
+   * This source code is licensed under the MIT license found in the
+   * LICENSE file in the root directory of this source tree.
+   *)
+*/
+//# sourceMappingURL=chunk-3IMKCK3L.js.map