jbrowse-plugin-msaview 5.1.0 → 5.2.0

package/dist/chunks/chunk-NMYD2GWF.js

@@ -0,0 +1,18 @@
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0,loadWarnings:[],dismissedWarnings:[],resetCount:0,hostCarriesData:!1,annotations:[]})).actions(e=>({drawRelativeTo(t){e.relativeTo=t},setHideGaps(t){e.hideGaps=t},setAllowedGappyness(t){e.allowedGappyness=t},setLoadingMSA(t){e.loadingMSA=t},setLoadingTree(t){e.loadingTree=t},setWidth(t){e.volatileWidth=t},setHighResScaleFactor(t){e.highResScaleFactor=t},setHeight(t){e.height=t},setError(t){e.error=t},addWarning(t){e.loadWarnings.includes(t)||(e.loadWarnings=[...e.loadWarnings,t])},setHostCarriesData(t){e.hostCarriesData=t},setMousePos(t,o){e.mouseCol=t,e.mouseRow=o},setHighlightedColumns(t){e.highlightedColumns=t},setRegion(t){e.region=t},setHighlights(t){e.highlights.replace(t)},setFeatures(t){e.features.replace(t)},setSelection(t){let o=t&&{start:Math.min(t.start,t.end),end:Math.max(t.start,t.end),...t.rows?{rows:t.rows}:{}};(0,G.compareStructural)(o,e.selection)||(e.selection=o)},clearSelection(){this.setSelection(void 0)},setClades(t){e.clades.replace(t)},applyHighlight(t,o){e.transientHighlights={...e.transientHighlights,[t]:o}},clearHighlight(t){if(t in e.transientHighlights){let{[t]:o,...r}=e.transientHighlights;e.transientHighlights=r}},setShowDomains(t){e.showDomains=t},setShowDomainLegend(t){e.showDomainLegend=t},setSubFeatureRows(t){e.subFeatureRows=t},setMouseClickPos(t,o){e.mouseClickCol=t,e.mouseClickRow=o},setRowHeight(t){e.rowHeight=t},setColWidth(t){e.colWidth=t},setCurrentAlignment(t){t!==e.currentAlignment&&(0,G.transaction)(()=>{e.currentAlignment=t,e.collapsed.clear(),e.rotated.clear(),this.setShowOnly(void 0),this.drawRelativeTo(void 0),e.scrollX=0,e.scrollY=0})},toggleCollapsed(t){e.collapsed.includes(t)?e.collapsed.remove(t):e.collapsed.push(t)},toggleRotated(t){e.rotated.includes(t)?e.rotated.remove(t):e.rotated.push(t)},clearRotated(){e.rotated.clear()},setTreeRoot(t){(0,G.compareStructural)(e.treeRoot,t)||(0,G.transaction)(()=>{e.treeRoot=t,e.collapsed.clear(),e.rotated.clear(),this.setShowOnly(void 0)})},setShowOnly(t){e.showOnly=t},setData(t){e.data=(0,b.cast)(t)},setMSAFilehandle(t){e.msaFilehandle=(0,b.cast)(t)},setTreeFilehandle(t){e.treeFilehandle=(0,b.cast)(t)},setTreeMetadataFilehandle(t){e.treeMetadataFilehandle=(0,b.cast)(t)},setGFFFilehandle(t){e.gffFilehandle=(0,b.cast)(t)},setMSA(t){e.data.setMSA(t)},setTree(t){e.data.setTree(t)},setTreeMetadata(t){e.data.setTreeMetadata(t)},setGFF(t){e.data.setGFF(t)}})).views(e=>({get hideGapsEffective(){return e.hideGaps&&(e.collapsed.length>0||e.allowedGappyness<100)},get realAllowedGappyness(){return this.hideGapsEffective?e.allowedGappyness:100},get allAnnotations(){return e.features.length>0?[...e.annotations,...sc(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:o}=e;return t?Xi(t):nt[o]??nt[ft]},get dynamicColorSchemeName(){let{customColorScheme:t,colorSchemeName:o}=e;return!t&&o.includes("dynamic")?o: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 unshareableData(){if(e.hostRestoresData)return[];let{data:t}=e,o=au(e.columnTracks).filter(r=>r>n).reduce((r,i)=>r+i,0);return[["alignment",t.msa,e.msaFilehandle],["tree",t.tree,e.treeFilehandle],["annotations",t.gff,e.gffFilehandle],["row metadata",t.treeMetadata,e.treeMetadataFilehandle]].flatMap(([r,i,s])=>!s&&i&&i.length>n?[{what:r,bytes:i.length}]:[]).concat(o?[{what:"data tracks",bytes:o}]:[]).sort((r,i)=>i.bytes-r.bytes)},menuItems(){return[]},get rowData(){let t=e.data.treeMetadata;if(!t)return{};try{let o=JSON.parse(t);return typeof o=="object"&&o!==null?Object.fromEntries(Object.entries(o).map(([r,i])=>[r,Qm(i)])):{}}catch(o){return console.error("failed to parse rowData",o),{}}},rowDataOf(t){return this.rowData[t]},get rowFields(){let t=new Set;for(let o of Object.values(this.rowData))for(let r of Object.keys(o??{}))t.add(r);return[...t].sort((o,r)=>o.localeCompare(r))},get MSA(){let t=e.data.msa;return t?zo(t,e.currentAlignment,e.msaFormat):null},get numColumns(){return(this.MSA?.getWidth()??0)-this.blanks.length},get inputTree(){let t=e.data.tree;return t?dt(Ym(t)):this.MSA?.getTree()??{noTree:!0,children:[],id:"empty",name:"empty"}},get tree(){let t=this.inputTree;return e.treeRoot&&!t.noTree?lh(t,e.treeRoot):t},get rowNames(){return this.leaves.map(t=>t.data.name)},get rowNamesSet(){return new Map(this.leaves.map((t,o)=>[t.data.name,o]))},get resolvedClades(){return e.clades.length===0?Zc:Jc(e.clades,Oe(this.tree,t=>t.children),this.rowNamesSet)},get cladeGutterWidth(){return Jr(e.clades)},get treeDrawn(){return e.drawTree&&!this.noTree},get treeTips(){return Ic(this.tree)},get maxTipLabelWidth(){return Oc(this.treeTips.names.map(t=>this.rowDataOf(t)?.genome||t),tr)},get labelColumnWidth(){return e.drawLabels?this.maxTipLabelWidth+(this.treeDrawn?10:6):0},get fittedTreeAreaWidth(){let t=e.marginLeft+this.cladeGutterWidth,o=this.treeDrawn?e.treeWidth??(0,H.clamp)(this.treeTips.depth*sr,pt,ar):0,r=t+o+this.labelColumnWidth,i=e.viewInitialized?this.numColumns>0?e.width*lr:e.width-this.rowPanelsWidth-e.resizeHandleWidth:1/0,s=Math.max(i,t+Math.min(o,pt));return Math.ceil(Math.min(r,s))},get effectiveTreeAreaWidth(){return e.treeAreaWidth??this.fittedTreeAreaWidth},get effectiveTreeWidth(){let t=this.showTreeText?this.labelColumnWidth:0;return e.treeWidth??Math.max(pt,Math.floor(this.effectiveTreeAreaWidth-e.marginLeft-this.cladeGutterWidth-t))},get showTreeText(){return e.drawLabels&&e.rowHeight>=gn},get mouseOverRowName(){let{mouseRow:t}=e;return t===void 0?void 0:this.leaves[t]?.data.name},get hoveredInsertion(){let{mouseCol:t,mouseRow:o}=e;if(t!==void 0&&o!==void 0){let r=this.leaves[o]?.data.name;if(r){let i=this.insertionPositions.get(r)?.find(s=>s.pos===t);if(i)return{rowName:r,col:t,letters:i.letters}}}},get root(){return so(this.tree,{collapsed:e.collapsed,rotated:e.rotated,order:e.treeOrder,showOnly:e.showOnly})},get treeNewick(){return Nc(so(this.tree,{collapsed:[],rotated:e.rotated,order:e.treeOrder}))},get treeOverviewHeight(){return e.showTreeOverview?e.overviewHeight:0},get treeOverviewLayout(){if(!e.showTreeOverview)return;let t=so(this.tree,{collapsed:e.collapsed,rotated:e.rotated,order:e.treeOrder}),o=fe(t).length;Qr(t,o,1);let r=Math.max(t.data.length||0,0),i=oi(t)-r;return ri(t,-r,i?1/i:0),{root:t,numTips:o,maxDepthToLeaf:ni(t),showBranchLen:e.showBranchLen&&i>0}},get treeOverviewClades(){let t=this.treeOverviewLayout;if(!t||e.clades.length===0)return Zc;let o=new Map(fe(t.root).map((r,i)=>[r.data.name,i]));return Jc(e.clades,t.root,o)},get treeOverviewFocusRows(){let t=this.treeOverviewLayout;if(!t||!e.showOnly)return;let o=Ie(t.root,r=>r.data.id===e.showOnly);return o?Qc(o):void 0},treeOverviewHit(t){let o=this.treeOverviewLayout;if(!o)return;let{root:r,numTips:i}=o,s=i/e.overviewHeight,a=(0,H.clamp)(Math.floor(t*s),0,i-1),l=(0,H.clamp)(Math.ceil((t+1)*s)-1,a,i-1),c=ii(r,a+.5,l+.5);for(;!c.children&&c.parent;)c=c.parent;return c===r?void 0:{id:c.data.id,rows:Qc(c)}},get rowPanelsWidth(){return(0,H.sum)(e.rowPanels.map(t=>Vc(t,e)))},get rowPanelsHeaderHeight(){return e.rowPanels.length>0?vr: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,realAllowedGappyness:o}=e;if(!t)return[];let r=this.leaves.map(u=>this.MSA?.getRow(u.data.name)).filter(H.notEmpty);if(r.length===0)return[];let i=this.MSA?.getWidth()??0,s=r.length,a=Math.ceil(o/100*s),l=new Uint32Array(i);for(let u=0;u<s;u++){let d=r[u],h=d.length;for(let f=0;f<i;f++)(f>=h||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:o}=this;if(t.length===0)return new Map;let r=new Map;for(let[i,s]of o){let a=Er(t,s);a.length>0&&r.set(i,a)}return r},get rows(){let t=this.MSA;return this.leaves.map(o=>[o.data.name,t?.getRow(o.data.name)]).filter(o=>!!o[1])},get numRows(){return this.leaves.length},seqPosIndex(t){let o=this.MSA;if(!o)return;let r=tu.get(o);r||(r=new Map,tu.set(o,r));let i=r.get(t);if(!i){let s=o.getRow(t);if(!s)return;i=Pc(s),r.set(t,i)}return i},get rowMap(){let t=this.MSA;return new Map(t?.getNames().map(o=>[o,t.getRow(o)]).filter(([,o])=>!!o))},get columns(){let t=this.columns2d;return new Map(this.rows.map((o,r)=>[o[0],t[r]]))},get columns2d(){let{hideGapsEffective:t}=e;return this.rows.map(([,o])=>(t?St(this.blanks,o):o).toUpperCase())},get fontSize(){return er(e.rowHeight)},get colStats(){return Wr(this.columns2d,this.numColumns)},get sequenceType(){let t=this.colStats.lettersPresent,o=new Set(["A","C","G","T","N"]),r=new 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=Nr(c))});let l=i?s/i:0;return{letter:a,color:l>.4?`hsl(240, 30%, ${100*Math.max(1-l/3,.3)}%)`:void 0}})},get colClustalX(){let{colStats:t}=this;return Array.from({length:t.numColumns},(o,r)=>ec(t,r))},get conservation(){let{colStats:t,alphabetMaxBits:o}=this;return Array.from({length:t.numColumns},(r,i)=>{let s=t.total(i),a=t.gapCount(i);return s>a?Math.max(0,1-t.entropy(i)/o)*(1-a/s):0})},get alphabetMaxBits(){return Gr(this.sequenceType)},get propertyConservation(){return this.sequenceType==="amino"?Ac(this.colStats):[]},get treeLayout(){let t=()=>this.effectiveTreeWidth;return ei(this.root,{get rowHeight(){return e.rowHeight},get treeWidth(){return t()}})},get hierarchy(){return this.treeLayout.root},get totalHeight(){return this.leaves.length*e.rowHeight},get leaves(){return this.treeLayout.leaves},get rootToTipLength(){return this.treeLayout.rootToTipLength},get maxBranchLength(){return this.rootToTipLength?this.effectiveTreeWidth:0},get pxPerBranchLength(){let t=this.rootToTipLength;return this.showBranchLenEffective&&t?this.effectiveTreeWidth/t:0},get maxDepthToLeaf(){return this.treeLayout.root.depthToLeaf},get allBranchesLength0(){return this.rootToTipLength===0},get showBranchLenEffective(){return this.allBranchesLength0?!1:e.showBranchLen}})).views(e=>({get totalWidth(){return e.numColumns*e.colWidth}})).views(e=>({get showMsaLetters(){return e.drawMsaLetters&&e.rowHeight>=gn&&e.colWidth>=Qo&&e.colWidth>e.rowHeight/2}})).views(e=>{let t=new WeakMap;return{get columnTrackContent(){let{MSA:o,blanks:r,hideGapsEffective:i}=e,s=o?.getWidth()??0,a=(u,d,h)=>{if(!u.row)return d;let f=Array.from({length:s},()=>h),g=e.seqPosIndex(u.row);return d.forEach((p,w)=>{let C=g?.[w];C!==void 0&&(f[C]=p)}),f},l=u=>i?Tr(r,u):u,c=(u,d)=>{let h=u.row?e.seqPosIndex(u.row)?.[d-1]:d-1;if(!(h===void 0||h<0||h>=s))return i?$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??jm[o]??e.rowHeight},columnTrackModel(o){let r=t.get(o);return r||(r=(0,G.computed)(()=>{let i=_c.has(o.kind)?Um(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 secondaryStructureConsensus(){return e.MSA?.secondaryStructureConsensus},get secondaryStructureArcs(){let{blanks:t,hideGapsEffective:o}=e,r=this.secondaryStructureConsensus;if(r)return Bc(o?St(t,r):r).map(({start:i,end:s,pseudoknot:a})=>({start:i,end:s,color:a?qm:Xm}))},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?St(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:_c.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=>!Xc(e.turnedOffTracks,t.model.id,t.model.defaultOff))},get showHorizontalScrollbar(){return ou(e.totalWidth,e.msaAreaWidth)},visibleColToRowLetter(t,o){return e.rowMap.get(t)?.[this.visibleColToGlobalCol(o)]},visibleColToSeqPos(t,o){return Hc(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?kc(o,t):t},visibleColToGlobalCol(t){let{blanks:o,hideGapsEffective:r}=e;return r?Rc(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)nu(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(nu)}))},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:!ch(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 oc(e.pxPerBranchLength,e.effectiveTreeAreaWidth-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 ou(e.totalHeight,e.msaAreaHeight)}})).views(e=>({get dataInitialized(){return!!(e.data.msa||e.data.tree)&&!e.error},get blocksX(){return Zn({viewportSize:e.msaAreaWidth,viewportPos:-e.scrollX,blockSize:e.blockSize,mapSize:e.totalWidth})},get blocksY(){return Zn({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>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(Mc(t))},rerootAt(t){let o=Ie(Oe(e.tree,i=>i.children),i=>i.data.id===t);if(!o?.parent)return;let r=su(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,G.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,G.transaction)(()=>{let s=(-e.scrollX+o)/e.colWidth,a=(-e.scrollY+r)/e.rowHeight;i!=="vertical"&&(e.colWidth=(0,H.clamp)(e.colWidth*t,mt,Te)),i!=="horizontal"&&(e.rowHeight=(0,H.clamp)(e.rowHeight*t,ht,Te)),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?Bo(t):[])},applyGFFText(t){this.setAnnotations(Go(Wo(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,!Xc(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}=Pr({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 $c(e.filteredAnnotations,this.featureFillEncoding,this.fillPalette)},get featureLabels(){let t=this.resolvedEncodings.find(o=>o.channel==="featureLabel");return t?Yc(e.filteredAnnotations,t.field):void 0},get segmentLabels(){return new Map(this.segmentDomainTypes.map((t,o)=>{let r=/(\d+)\s*$/.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-${a}`),title:a??"Domains",entries:[...l]})};e.actuallyShowDomains&&e.numColumns>0&&s(t?.field,t?t.legend:r.map(a=>({id:a.accession,label:a.name,color:o[a.accession]})),"domains");for(let{channel:a,field:l,legend:c}of this.resolvedEncodings)eu.has(a)||s(l,c);for(let{legendTitle:a,legend:l}of this.rowPanelScales)s(a,l);return[...i.values()]},get domainUnderline(){return e.actuallyShowDomains&&!e.bgColor&&!e.subFeatureRows&&e.showMsaLetters},get domainBands(){let{blanks:t}=e,o=new Map;for(let[r,i]of Object.entries(e.annotationsByRow)){let s=i.toSorted((a,l)=>bn(l)-bn(a)).map(a=>{let l=e.seqPosToGlobalCol(r,a.start-1),c=e.seqEndToGlobalCol(r,a.end-1);if(l===void 0||c===void 0)return;let u=$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 qc;let r=(this.domainBands.get(o)??[]).filter(i=>t>=i.startCol&&t<i.endCol).map(i=>i.annotation);return r.length>0?r:qc},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 ru([...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?ru(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 Xl(s,i.start,i.end)},columnStatsAt(t){let{colStats:o,conservation:r,propertyConservation:i}=e;return tc({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,...eu.has(o.channel)?Kc(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?Kc(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?$c(s,d,o):this.featureColors,labels:h?Yc(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:ao(t,a.field,l),legend:c}})},get resolvedRowPanels(){let t=this.rowPanelScales,o=0;return e.rowPanels.map((r,i)=>{let s=Vc(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:th({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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