react-msaview 9.3.0 → 9.4.0
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- package/bundle/index.js +2 -2
- package/bundle/index.js.map +3 -3
- package/dist/model.d.ts +4 -1
- package/dist/model.js +7 -2
- package/dist/model.js.map +1 -1
- package/dist/version.d.ts +1 -1
- package/dist/version.js +1 -1
- package/package.json +3 -3
- package/src/model.ts +10 -2
- package/src/version.ts +1 -1
package/bundle/index.js
CHANGED
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@@ -620,7 +620,7 @@ In order to be iterable, non-array objects must have a [Symbol.iterator]() metho
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`).trimStart();if(UGe.test(r))throw new Error("Received an HTML page, not an alignment. Check that the URL points at the file itself");if(o==="stockholm")return new Vp(r,t);if(o==="a3m")return new ef(r);if(o==="fasta")return new Gp(r);if(o==="emf")return new zp(r);if(o==="clustal")return new Hp(r);if(HE(r))return new Vp(r,t);if(tR(r)){let i=G3(r);return ef.sniff(i)?new ef(i):new Gp(i)}if(r.startsWith("SEQ"))return new zp(r);if(HGe.test(r))return new Hp(r);let n=r.split(`
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`,1)[0].slice(0,80);throw new Error(n?`Unrecognized alignment format: expected FASTA, A3M, Stockholm, Clustal or EMF, but the first line reads "${n}"`:"The alignment file is empty")}function r4(e){return e.replaceAll(/[.-]/g,"")}var UGe,HGe,Bme=A(()=>{"use strict";V3();$3();W3();q3();t4();oR();Y3();Z3();V3();$3();W3();q3();t4();UGe=/^<(!doctype\s+html|html[\s>])/i,HGe=/^(CLUSTAL|MUSCLE|PROBCONS|MSAPROBS|Kalign)/i});function n4(e){return Object.fromEntries(e.map(t=>[t.xref[0]?.id,t]).filter(t=>t[0]!==void 0))}function i4(e){return Object.entries(e).flatMap(([t,{matches:o}])=>o.flatMap(({signature:r,locations:n})=>{let{entry:i}=r,s=i?.accession??r.accession;if(!s)return[];let a=i?.name??r.name??s;return n.map(({start:l,end:c,strand:u})=>({id:t,accession:s,name:a,description:i?.description??r.description??a,start:l,end:c,strand:u}))}))}function s4(e){return i4(n4(e.results))}var aR=A(()=>{"use strict"});function _me(e){try{return decodeURIComponent(e)}catch{return e}}function zGe(e){return e.replace(/^"(.*)"$/,"$1")}function GGe(e){if(!e)return{};let t={};for(let o of e.split(";")){let r=o.indexOf("="),n=o.slice(0,r).trim(),i=o.slice(r+1);r!==-1&&n&&i&&(t[n]=i.split(",").map(s=>zGe(_me(s).trim())).join(" "))}return t}function lR(e){if(!e)return[];let t=[];for(let o of e.split(`
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`)){let r=o.trim();if(r.startsWith("##FASTA"))break;r&&!r.startsWith("#")&&r.split(" ").length>=8&&t.push(r)}return t.map(o=>{let r=o.split(" "),[n,i,s,a,l,c,u,p]=r,f=r[8];return{...GGe(f),seq_id:_me(n??""),source:i??"",type:s??"",start:Number(a)||0,end:Number(l)||0,score:Number(c)||0,strand:u??".",phase:p??"."}})}var Rme=A(()=>{"use strict"});function jGe({type:e,strand:t}){let o=t==="+"?1:t==="-"?-1:void 0;return VGe.has(e)?o:void 0}function YGe(e){let t=Object.entries(e).filter(([o,r])=>!$Ge.has(o)&&typeof r=="string");return t.length>0?Object.fromEntries(t):void 0}function qGe(e){let t=e.color??e.colour??e.Color??e.Colour;if(!t)return;let o=WGe.exec(t.trim());return o?`rgb(${o[1]},${o[2]},${o[3]})`:t.trim()}function cR(e){return e.filter(t=>!JGe.has(t.type)).map(t=>{let o=t.Name||t.ID||`${t.source}_${t.start}_${t.end}`,r=t.signature_desc||t.Name||o;return{id:t.seq_id,accession:o,name:r,description:t.description||t.Note||t.signature_desc||r,featureType:t.type,start:t.start,end:t.end,strand:jGe(t),color:qGe(t),attributes:YGe(t)}})}var VGe,$Ge,WGe,JGe,Mme=A(()=>{"use strict";VGe=new Set(["gene","CDS","pseudogene","mRNA","transcript","primary_transcript","ncRNA","tRNA","rRNA","snRNA","snoRNA","miRNA","lnc_RNA"]);$Ge=new Set(["seq_id","source","type","start","end","score","strand","phase"]);WGe=/^(\d{1,3})[\s,]+(\d{1,3})[\s,]+(\d{1,3})$/;JGe=new Set(["polypeptide","nucleic_acid"])});function zE(e,t=[]){return["##gff-version 3",...t.map(o=>`# ${o}`),...e.map(o=>{let{accession:r,name:n,description:i,featureType:s}=o,{id:a,start:l,end:c,strand:u}=o;return[a.replaceAll(/[%\t\n\r]/g,encodeURIComponent),"InterProScan",s??"protein_match",l,c,".",u===void 0?".":u>0?"+":"-",".",[`Name=${encodeURIComponent(r)}`,`signature_desc=${encodeURIComponent(n)}`,`description=${encodeURIComponent(i)}`].join(";")].join(" ")})].join(`
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@@ -647,7 +647,7 @@ UniProt/Swiss-Prot|Q7JFM4|IL2_AOTVO MLKPPLPLRSLLFLQLPLLGVGLNPKFLTPSGNEDIG
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t.width-this.effectiveTreeAreaWidth-this.rowPanelsWidth-t.resizeHandleWidth},get treeAreaWidthMinusMargin(){return this.effectiveTreeAreaWidth-t.marginLeft-this.cladeGutterWidth},get blanks(){let{hideGapsEffective:o,allowedGappyness:r}=t;if(!o)return[];let n=this.leaves.map(u=>this.MSA?.getRow(u.data.name)).filter(Oa);if(n.length===0)return[];let i=this.MSA?.getWidth()??0,s=n.length,a=Math.ceil(r/100*s),l=new Uint32Array(i);for(let u=0;u<s;u++){let p=n[u],f=p.length;for(let d=0;d<i;d++)(d>=f||p.charCodeAt(d)-45>>>0<=1)&&l[d]++}let c=[];for(let u=0;u<i;u++)l[u]>=a&&c.push(u);return c},get insertionPositions(){let{blanks:o,rows:r}=this;if(o.length===0)return new Map;let n=new Map;for(let[i,s]of r){let a=Xde(o,s);a.length>0&&n.set(i,a)}return n},get rows(){let o=this.MSA;return this.leaves.map(r=>[r.data.name,o?.getRow(r.data.name)]).filter(r=>!!r[1])},get numRows(){return this.leaves.length},seqPosIndex(o){let r=this.MSA;if(!r)return;let n=Dve.get(r);n||(n=new Map,Dve.set(r,n));let i=n.get(o);if(!i){let s=r.getRow(o);if(!s)return;i=tve(s),n.set(o,i)}return i},rowSequence(o){return this.MSA?.getRow(o)||void 0},get rowMap(){let o=this.MSA;return new Map(o?.getNames().map(r=>[r,o.getRow(r)]).filter(([,r])=>!!r))},get columns(){let o=this.columns2d;return new Map(this.rows.map((r,n)=>[r[0],o[n]]))},get columns2d(){let{hideGapsEffective:o}=t;return this.rows.map(([,r])=>(o?L_(this.blanks,r):r).toUpperCase())},get fontSize(){return k3(t.rowHeight)},get colStats(){return Mde(this.columns2d,this.numColumns)},get sequenceType(){let o=this.colStats.lettersPresent,r=["N","R","Y","K","M","S","W"],n=new Set(["A","C","G","T",...r]),i=new Set(["A","C","G","U",...r]),s=o.size>0&&[...o].every(l=>n.has(l)),a=o.size>0&&[...o].every(l=>i.has(l));return s?"dna":a?"rna":"amino"},get colConsensus(){let{colStats:o}=this;return Array.from({length:o.numColumns},(r,n)=>{let i=o.total(n),s=0,a="";o.forEachResidue(n,(c,u)=>{u>s&&(s=u,a=gm(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:o}=this;return Array.from({length:o.numColumns},(r,n)=>yEe(o,n))},get colSimilarity(){let{colStats:o,sequenceType:r}=this,n=r==="amino"?sve:ave;return Array.from({length:o.numColumns},(i,s)=>n(o,s))},get conservation(){let{colStats:o,alphabetMaxBits:r}=this;return Array.from({length:o.numColumns},(n,i)=>{let s=o.total(i),a=o.gapCount(i);return s>a?Math.max(0,1-o.entropy(i)/r)*(1-a/s):0})},get alphabetMaxBits(){return Qde(this.sequenceType)},get propertyConservation(){return this.sequenceType==="amino"?GEe(this.colStats):[]},get treeLayout(){let o=()=>this.effectiveTreeWidth;return K4(this.root,{get rowHeight(){return t.rowHeight},get treeWidth(){return o()}})},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 o=this.rootToTipLength;return this.showBranchLenEffective&&o?this.effectiveTreeWidth/o: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>=O3&&t.colWidth>=MAe&&t.colWidth>t.rowHeight/2}})).views(t=>{let o=new WeakMap;return{get columnTrackContent(){let{MSA:r,blanks:n,hideGapsEffective:i}=t,s=r?.getWidth()??0,a=(u,p,f)=>{if(!u.row)return p;let d=Array.from({length:s},()=>f),m=t.seqPosIndex(u.row);return p.forEach((y,b)=>{let h=m?.[b];h!==void 0&&(d[h]=y)}),d},l=u=>i?Kde(n,u):u,c=(u,p)=>{let f=u.row?t.seqPosIndex(u.row)?.[p-1]:p-1;if(!(f===void 0||f<0||f>=s))return i?dC(n,f):f};return new Map(t.columnTracks.map(u=>{if(u.kind==="arc"){let f=(u.arcs??[]).map(d=>{let m=c(u,Math.min(d.start,d.end)),y=c(u,Math.max(d.start,d.end));return m!==void 0&&y!==void 0&&m<y?{start:m,end:y,color:d.color}:void 0}).filter(Oa);return[u.id,{arcs:f}]}if(u.kind==="bar"){let f=u.scales?.y?.domainMax??1,d=l(a(u,u.values??[],0)).map(m=>Math.min(1,Math.max(0,m/f)));return[u.id,{values:d}]}let p=l(a(u,(u.data??"").split("")," "));return[u.id,{data:p.join("")}]}))},trackHeight(r,n=r,i){return t.trackHeights.get(n)??i??LYe[r]??t.rowHeight},columnTrackModel(r){let n=o.get(r);return n||(n=kf(()=>{let i=Bve.has(r.kind)?FYe(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.encoding?.color?bV(r.encoding.color,[...r.encoding.color.domain??[],...new Set(r.data)]):void 0,data:s?.data,arcs:s?.arcs}}}),o.set(r,n)),n.get()},get columnTrackModels(){return t.columnTracks.map(r=>this.columnTrackModel(r))}}}).views(t=>({get secondaryStructureConsensus(){return t.MSA?.secondaryStructureConsensus},get secondaryStructureArcs(){let{blanks:o,hideGapsEffective:r}=t,n=this.secondaryStructureConsensus;if(n)return hve(r?L_(o,n):n).map(({start:i,end:s,pseudoknot:a})=>({start:i,end:s,color:a?HYe:UYe}))},get adapterTrackModels(){let{MSA:o,hideGapsEffective:r,blanks:n}=t,i=(o?.tracks??[]).filter(a=>!!a.data);if(i.length===0)return[];let{rowHeight:s}=t;return i.map(a=>({model:{...a,kind:"text",data:r?L_(n,a.data):a.data,height:s}}))},get basePairTrackModels(){let o=this.secondaryStructureArcs;return o?.length?[{model:{id:"base-pairs",name:"Base pairs",kind:"arc",heightKey:"arc",height:t.trackHeight("arc"),arcs:o}}]:[]},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(o=>({model:{...o,heightKey:Bve.has(o.kind)?o.kind:void 0,height:t.trackHeight(o.kind)}}))},get referenceTrackModels(){let{relativeTo:o}=t,r=o===void 0?void 0:t.columns.get(o);return o===void 0||r===void 0?[]:[{model:{id:"reference-row",name:o,kind:"reference",data:r,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(o=>!Rve(t.turnedOffTracks,o.model.id))},get showHorizontalScrollbar(){return Nve(t.totalWidth,t.msaAreaWidth)},visibleColToRowLetter(o,r){return t.rowSequence(o)?.[this.visibleColToGlobalCol(r)]},visibleColToSeqPos(o,r){return qEe(t.seqPosIndex(o),this.visibleColToGlobalCol(r))},visibleColToSeqPosOneBased(o,r){let n=this.visibleColToSeqPos(o,r);return n!==void 0?n+1:void 0},globalColToVisibleCol(o){let{blanks:r,hideGapsEffective:n}=t;return n?YEe(r,o):o},visibleColToGlobalCol(o){let{blanks:r,hideGapsEffective:n}=t;return n?$Ee(r,o):o},seqPosToGlobalCol(o,r){let n=t.rowSequence(o);return n===void 0?void 0:t.seqPosIndex(o)?.[r]??(r===0?0:n.length)},seqEndToGlobalCol(o,r){let n=t.seqPosIndex(o);return n&&n.length>0?n[Math.min(r,n.length-1)]:void 0},seqPosToVisibleCol(o,r){let n=this.seqPosToGlobalCol(o,r);return n===void 0?void 0:this.globalColToVisibleCol(n)},visibleSpan({row:o,start:r,end:n}){let{blanks:i}=t,s=Math.max(1,Math.floor(r)),a=Math.ceil(n),l=s-1,c=Math.min(a,t.MSA?.getWidth()??a)-1;if(o!==void 0){let f=this.seqPosToGlobalCol(o,s-1),d=this.seqEndToGlobalCol(o,a-1);if(f===void 0||d===void 0)return;l=f,c=d}let u=this.globalColToVisibleCol(l)??dC(i,l),p=this.globalColToVisibleCol(c)??dC(i,c)-1;return u<=p?{startCol:u,endCol:p}:void 0},get residueMappingProblems(){let o=[];for(let r of t.residueMappings){let n={row:r.row,structureId:r.structure.id},i=t.seqPosIndex(r.row)?.length;if(i===void 0){o.push({...n,scope:"mapping",reason:"no such row in the alignment"});continue}if(r.rowLength!==void 0&&r.rowLength!==i){o.push({...n,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){o.push({...n,scope:"mapping",reason:`segment ${s.rowStart}-${s.rowEnd} does not fit a ${i}-residue row`});continue}for(let a of r.segments)Ove(a)||o.push({...n,scope:"segment",reason:`segment ${a.rowStart}-${a.rowEnd} maps to ${a.structStart}-${a.structEnd}, which is a different length`})}return o},get usableResidueMappings(){let o=new Set(this.residueMappingProblems.filter(r=>r.scope==="mapping").map(r=>`${r.row}\0${r.structureId}`));return t.residueMappings.filter(r=>!o.has(`${r.row}\0${r.structure.id}`)).map(r=>({...r,segments:r.segments.filter(Ove)}))},get mappedStructures(){return this.usableResidueMappings.map(o=>({row:o.row,structure:o.structure}))},structureResidue(o,r,n){let i=[];for(let s of this.usableResidueMappings){if(s.row!==o||n!==void 0&&s.structure.id!==n)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:!$Ye(s.unobserved,l)})}}return i.length===1?i[0]:void 0},rowResidue(o,r,n){let i=[];for(let s of this.usableResidueMappings){if(s.structure.id!==o||n!==void 0&&s.structure.asymId!==void 0&&s.structure.asymId!==n)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(t=>({get treeScaleBar(){if(t.showTreeScaleBar)return vEe(t.pxPerBranchLength,t.effectiveTreeAreaWidth-t.marginLeft*2)},get topBandHeight(){return Math.max(t.showHorizontalScrollbar?t.minimapHeight:0,t.rowPanelsHeaderHeight,t.treeOverviewHeight+(this.treeScaleBar?Zu:0))},get msaAreaHeight(){return t.height-this.topBandHeight-t.headerHeight-this.totalTrackAreaHeight},get totalTrackAreaHeight(){return w0(t.turnedOnTracks.map(o=>o.model.height))},get annotationTypes(){let o=new Map;for(let r of t.allAnnotations)o.has(r.accession)||o.set(r.accession,r);return o},get defaultOffAccessions(){return new Set(t.allAnnotations.filter(o=>o.defaultOff).map(o=>o.accession))},featureOff(o){return t.turnedOffFeatures.get(o)??this.defaultOffAccessions.has(o)},get filteredAnnotations(){return t.allAnnotations.filter(o=>!this.featureOff(o.accession))},get cellFill(){return t.bgColor?t.actuallyShowDomains&&t.domainFill&&this.filteredAnnotations.length>0?"domain":"residue":"none"},get annotationsByRow(){let{rowNamesSet:o}=t;return Gae(this.filteredAnnotations,r=>Pve(r.id,o))}})).views(t=>({get showVerticalScrollbar(){return Nve(t.totalHeight,t.msaAreaHeight)}})).views(t=>({get dataInitialized(){return!!(t.data.msa||t.data.tree)&&!t.error},get blocksX(){return qE({viewportSize:t.msaAreaWidth,viewportPos:-t.scrollX,blockSize:t.blockSize,mapSize:t.totalWidth})},get blocksY(){return qE({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(o=>t.blocksX.map(r=>[r,o]))},get wheelZooming(){return t.zoomSnapshot!==void 0},get isLoading(){return t.loadingMSA||t.loadingTree},get dataWarnings(){let{annotations:o,rowNamesSet:r}=t;return t.dataInitialized&&o.length>0&&!o.some(n=>r.has(Pve(n.id,r)))?[`0 of ${o.length} annotations name a row in this alignment`]:[]},get warnings(){return[...t.loadWarnings,...this.dataWarnings.filter(o=>!t.dismissedWarnings.includes(o))]},get maxScrollY(){return Math.min(-t.totalHeight+t.msaAreaHeight,0)},get wheelZoomAxis(){return t.scrollZoom?t.scrollZoomAxis:"both"}})).actions(t=>({setDrawMsaLetters(o){t.drawMsaLetters=o},clearWarnings(){t.loadWarnings=[],t.dismissedWarnings=t.dataWarnings},setScrollZoom(o){t.scrollZoom=o},setScrollZoomAxis(o){t.scrollZoomAxis=o},setHoveredTreeNode(o){if(o===t.hoveredTreeNode?.nodeId)return;if(!o){t.hoveredTreeNode=void 0;return}let r=tf(t.hierarchy,n=>n.data.id===o);t.hoveredTreeNode=r?{nodeId:o,descendantNames:Qc(r).map(n=>n.data.name)}:void 0},calculateNeighborJoiningTreeFromMSA(){let o=[...t.rowMap];if(o.length<2)throw new Error("Need at least 2 sequences to build a tree");if(o.length>ib)throw new Error(`Neighbor joining here is capped at ${ib} sequences and this alignment has ${o.length}. Build the tree with FastTree or IQ-TREE and open it alongside the alignment: https://gmod.org/JBrowseMSA/tutorials/protein_family`);this.replaceTree(UEe(o))},rerootAt(o){let r=tf(Jp(t.tree,i=>i.children),i=>i.data.id===o);if(!r?.parent)return;let n=vV(Jp(t.inputTree,i=>i.children),Qc(r).map(i=>i.data.name));if(n){let i=Qc(n);t.setTreeRoot({outgroup:[...new Set([i[0].data.name,i.at(-1).data.name])]})}},replaceTree(o){_r(()=>{t.setTreeFilehandle(void 0),t.collapsed.clear(),t.rotated.clear(),t.setShowOnly(void 0),t.setTree(o)})},resetZoom(){t.setColWidth(12),t.setRowHeight(16)},zoomAtCenter(o,r="both"){this.zoomToPos(o,t.msaCanvasWidth/2,t.msaAreaHeight/2,r)},zoomIn(){this.zoomAtCenter(1.5)},zoomOut(){this.zoomAtCenter(.75)},zoomToPos(o,r,n,i="both"){_r(()=>{let s=(-t.scrollX+r)/t.colWidth,a=(-t.scrollY+n)/t.rowHeight,l=i!=="both"||t.colWidth===12&&t.rowHeight===16;if(i!=="vertical"){let{value:d,held:m}=kve(t.colWidth,o,12,t.zoomHeld.col,$_,l);t.colWidth=d,t.zoomHeld={...t.zoomHeld,col:m}}if(i!=="horizontal"){let{value:d,held:m}=kve(t.rowHeight,o,16,t.zoomHeld.row,Y_,l);t.rowHeight=d,t.zoomHeld={...t.zoomHeld,row:m}}t.scrollX=dr(r-s*t.colWidth,t.maxScrollX,0);let c=n-a*t.rowHeight,u=Math.max(0,-t.maxScrollY),p=t.totalHeight-u,f=p>0?dr(1-u/p,0,1):1;t.scrollY=dr(c*(1-f),t.maxScrollY,0)})},wheelZoomToPos(o,r,n){t.zoomSnapshot??=P4(t,!1),this.zoomToPos(o,r,n,t.wheelZoomAxis),ohe(t,t.zoomSnapshot)||(t.zoomSnapshot=P4(t,!0))},endWheelZoom(){t.zoomSnapshot=void 0},doScrollY(o){this.setScrollY(t.scrollY+o)},setScrollY(o){t.scrollY=dr(o,t.maxScrollY,0)},setAnnotations(o){t.annotations=o},applyGFFText(o){this.setAnnotations(cR(lR(o)))},doScrollX(o){this.setScrollX(t.scrollX+o)},setScrollX(o){t.scrollX=dr(o,t.maxScrollX,0)},setColumnTracks(o){t.columnTracks.replace(o.map(yV))},setRowData(o){t.data.setTreeMetadata(JSON.stringify(o))},setEncodings(o){t.encodings.replace(o.map(gV))},setRowPanels(o){t.rowPanels.replace(o.map(hV))},setResidueMappings(o){t.residueMappings.replace(o)},toggleTrack(o){t.turnedOffTracks.set(o,!Rve(t.turnedOffTracks,o))},setTracksShown(o,r){for(let n of o)Fve.has(n)===!r?t.turnedOffTracks.delete(n):t.turnedOffTracks.set(n,!r)},setStatus(o){t.status=o}})).views(t=>({cellAt(o,r){let n=t.visibleColToGlobalCol(o),i=r===void 0?void 0:t.leaves[r]?.data.name;return i===void 0?{column:n+1}:{column:n+1,row:i,residue:t.visibleColToSeqPosOneBased(i,o),letter:t.rowSequence(i)?.[n]}},get hoveredCell(){let{mouseCol:o,mouseRow:r}=t;return o===void 0?void 0:this.cellAt(o,r)},get clickedCell(){let{mouseClickCol:o,mouseClickRow:r}=t;return o===void 0?void 0:this.cellAt(o,r)},get viewport(){let{scrollX:o,colWidth:r,numColumns:n,viewInitialized:i}=t;if(n===0||!i)return;let{xStart:s,xEnd:a}=Fa({offsetX:-o,blockWidth:t.msaCanvasWidth,colWidth:r}),l=Math.max(0,Math.min(a,n)-1);return{startColumn:t.visibleColToGlobalCol(Math.min(s,l))+1,endColumn:t.visibleColToGlobalCol(l)+1}},get segmentDomainTypes(){return[...t.annotationTypes.values()].filter(o=>P3.has(o.featureType??"")).toSorted((o,r)=>o.start-r.start)},get categoricalDomainTypes(){return[...t.annotationTypes.values()].filter(o=>!P3.has(o.featureType??""))},get fillPalette(){let o=Object.fromEntries(this.segmentDomainTypes.map((n,i)=>[n.accession,D3[i%D3.length]])),r=zQ(this.categoricalDomainTypes.map(n=>n.accession));return{...o,...r}},get featureFillEncoding(){return this.resolvedEncodings.find(o=>o.channel==="featureFill")},get featureColors(){return cV(t.filteredAnnotations,this.featureFillEncoding,this.fillPalette)},get featureLabels(){let o=this.resolvedEncodings.find(r=>r.channel==="featureLabel");return o?uV(t.filteredAnnotations,o.field):void 0},get segmentLabels(){return new Map(this.segmentDomainTypes.map((o,r)=>{let n=/(\d+)\s*$/.exec(o.name);return[o.accession,n?n[1]:`${r+1}`]}))},get visibleDomainTypes(){return this.categoricalDomainTypes.filter(o=>!t.featureOff(o.accession)).toSorted((o,r)=>o.start-r.start)},get legends(){let{featureFillEncoding:o,fillPalette:r,visibleDomainTypes:n}=this,i=new Map,s=new Set,a=(l,c,u,p=!1)=>{let f=l??"domains";if(u.length===0||i.has(f))return;let d=p||l===void 0?"domains":`rowData-${c}`,m=d;for(let y=2;s.has(m);y++)m=`${d}-${y}`;s.add(m),i.set(f,{id:m,title:c??"Domains",entries:u})};t.actuallyShowDomains&&t.numColumns>0&&a(o?.key,o?.title,o?o.legend:n.map(l=>({id:l.accession,label:l.name,color:l.color??r[l.accession]})),!0);for(let{channel:l,key:c,title:u,legend:p}of this.resolvedEncodings)BV.has(l)||a(c,u,p);for(let{legendKey:l,legendTitle:c,legend:u}of this.rowPanelScales)a(l,c,u);return[...i.values()]},get domainUnderline(){return t.actuallyShowDomains&&t.cellFill!=="domain"&&!t.subFeatureRows&&t.showMsaLetters},get domainBands(){let{blanks:o}=t,r=new Map;for(let[n,i]of Object.entries(t.annotationsByRow)){let s=i.toSorted((a,l)=>v3(l)-v3(a)).map(a=>{let l=t.seqPosToGlobalCol(n,a.start-1),c=t.seqEndToGlobalCol(n,a.end-1);if(l===void 0||c===void 0)return;let u=dC(o,l),p=dC(o,c+1);return p>u?{annotation:a,startCol:u,endCol:p}:void 0}).filter(Oa).map((a,l)=>({...a,stackIndex:l}));s.length>0&&r.set(n,uC(s))}return r},get domainBandsByStart(){return new Map([...this.domainBands].map(([o,r])=>[o,r.toSorted((n,i)=>n.startCol-i.startCol)]))},get mouseOverDomains(){let{mouseCol:o}=t,r=t.mouseOverRowName;if(r===void 0||o===void 0)return Mve;let n=(this.domainBands.get(r)??[]).filter(i=>o>=i.startCol&&o<i.endCol).map(i=>i.annotation);return n.length>0?n:Mve},get referenceRowIndex(){let{relativeTo:o}=t;return o===void 0?void 0:t.rowNamesSet.get(o)},get hoveredRowIndices(){let{hoveredTreeNode:o,rowNamesSet:r}=t;return o?o.descendantNames.map(n=>r.get(n)).filter(Oa):[]},get highlightedColumnRuns(){return Lve([...t.highlightedColumns??[]].sort((o,r)=>o-r)).map(([o,r])=>({start:o,end:r}))},fillHighlightLabel(o,r,n){if(!o.includes("{"))return o;let i=r&&n!==void 0?t.seqPosIndex(r)?.[n-1]:void 0,s=r&&i!==void 0?t.MSA?.getRow(r)[i]??"":"";return o.replaceAll("{residue}",s).replaceAll("{position}",n===void 0?"":String(n))},get resolvedHighlights(){let{rowNamesSet:o,transientHighlights:r}=t;return[...t.highlights,...Object.values(r).flat()].flatMap(({row:i,rows:s,start:a,end:l,label:c,color:u})=>{let p={label:c&&this.fillHighlightLabel(c,i,a),color:u};if(s){let d=s.map(m=>o.get(m)).filter(Oa);return d.length?[{...p,rowIndices:d}]:[]}if(a===void 0||l===void 0)return[];let f=t.visibleSpan({row:i,start:a,end:l});return f?[{...p,...f,rowIndices:[]}]:[]})},get resolvedSelection(){let{selection:o,rowNamesSet:r,numRows:n}=t,i=o&&t.visibleSpan({start:o.start,end:o.end});if(!o||!i)return;let s=o.rows?Lve(o.rows.map(a=>r.get(a)).filter(Oa).sort((a,l)=>a-l)):n>0?[[0,n-1]]:[];return s.length>0?{...i,rowRuns:s}:void 0},get selectionSize(){let o=this.resolvedSelection,r=this.selectionFileSpan;return o&&r?{columns:r.end-r.start+1,rows:w0(o.rowRuns.map(([n,i])=>i-n+1))}:void 0},get selectionFileSpan(){let{selection:o}=t,r=t.MSA?.getWidth()??0,n=Math.max(1,Math.floor(o?.start??0)),i=Math.min(r,Math.ceil(o?.end??0));return o&&n<=i?{start:n,end:i}:void 0},get selectionFasta(){let{rowNames:o}=t,r=this.resolvedSelection,n=this.selectionFileSpan;if(!r||!n)return"";let i=r.rowRuns.flatMap(([s,a])=>o.slice(s,a+1)).flatMap(s=>{let a=t.rowSequence(s);return a===void 0?[]:[[s,a]]});return dEe(i,n.start,n.end)},columnStatsAt(o){let{colStats:r,conservation:n,propertyConservation:i}=t;return EEe({col:o,colStats:r,conservation:n,propertyConservation:i})},getRowData(o){return{data:t.MSA?.getRowData(o),rowData:t.rowDataOf(o)}},get resolvedEncodings(){return t.encodings.map(o=>({...o,...this.scaleOf(o,BV.has(o.channel)?"features":"rows")}))},get resolvedScales(){let o=Object.values(t.rowData),r=(i,s)=>i.map(a=>af(a,s)).filter(Oa),n=(i,s)=>({spec:i,field:i.field,table:s,...s==="rows"?{values:o.map(a=>a?.[i.field]).filter(Oa)}:{values:r(t.allAnnotations,i.field),shown:r(t.filteredAnnotations,i.field)}});return eve([...t.encodings.map(i=>n(i,BV.has(i.channel)?"features":"rows")),...t.rowPanels.flatMap(i=>i.kind==="strip"?[n(i,"rows")]:i.encoding?.color?[n(i.encoding.color,"features")]:[])])},scaleOf(o,r){return this.resolvedScales.get(mV({spec:o,field:o.field,table:r}))},get rowPanelScales(){let{rowData:o}=t,{fillPalette:r,featureFillEncoding:n,featureLabels:i}=this,s=t.filteredAnnotations;return t.rowPanels.map(a=>{if(a.kind==="features"){let f=a.encoding?.color,d=f?{field:f.field,...this.scaleOf(f,"features")}:n,m=a.encoding?.label;return{kind:a.kind,x:a.x,header:a.header??"",field:d?.field,legendKey:d?.key,legendTitle:d?.title,colors:f?cV(s,d,r):this.featureColors,labels:m?uV(s,m):i,legend:d?.legend??this.visibleDomainTypes.map(y=>({id:y.accession,label:y.name,color:y.color??r[y.accession]}))}}let{colorOf:l,legend:c,key:u,title:p}=this.scaleOf(a,"rows");return{kind:a.kind,field:a.field,header:a.header??a.field,legendKey:u,legendTitle:p,colors:GQ(o,a.field,l),legend:c}})},get resolvedRowPanels(){let o=this.rowPanelScales,r=0;return t.rowPanels.map((n,i)=>{let s=lV(n,t),a={id:`rowpanel-${i}`,width:s,offsetX:r};if(r+=s,n.kind==="features"){let l=n.transform?.find(c=>c.type==="align");return{...a,...o[i],spans:BEe({panel:n,width:s,colWidth:t.colWidth,domainBands:this.domainBands,annotationsByRow:t.annotationsByRow,shifts:l?this.featureAlignShifts.get(l.on):void 0})}}return{...a,...o[i]}})},get featureAlignShifts(){let o=new 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t.width-this.effectiveTreeAreaWidth-this.rowPanelsWidth-t.resizeHandleWidth},get treeAreaWidthMinusMargin(){return this.effectiveTreeAreaWidth-t.marginLeft-this.cladeGutterWidth},get blanks(){let{hideGapsEffective:o,allowedGappyness:r}=t;if(!o)return[];let n=this.leaves.map(u=>this.MSA?.getRow(u.data.name)).filter(Oa);if(n.length===0)return[];let i=this.MSA?.getWidth()??0,s=n.length,a=Math.ceil(r/100*s),l=new Uint32Array(i);for(let u=0;u<s;u++){let p=n[u],f=p.length;for(let d=0;d<i;d++)(d>=f||p.charCodeAt(d)-45>>>0<=1)&&l[d]++}let c=[];for(let u=0;u<i;u++)l[u]>=a&&c.push(u);return c},get insertionPositions(){let{blanks:o,rows:r}=this;if(o.length===0)return new Map;let n=new Map;for(let[i,s]of r){let a=Xde(o,s);a.length>0&&n.set(i,a)}return n},get rows(){let o=this.MSA;return this.leaves.map(r=>[r.data.name,o?.getRow(r.data.name)]).filter(r=>!!r[1])},get numRows(){return this.leaves.length},seqPosIndex(o){let r=this.MSA;if(!r)return;let n=Dve.get(r);n||(n=new Map,Dve.set(r,n));let i=n.get(o);if(!i){let s=r.getRow(o);if(!s)return;i=tve(s),n.set(o,i)}return i},rowSequence(o){return this.MSA?.getRow(o)||void 0},get rowMap(){let o=this.MSA;return new Map(o?.getNames().map(r=>[r,o.getRow(r)]).filter(([,r])=>!!r))},get columns(){let o=this.columns2d;return new Map(this.rows.map((r,n)=>[r[0],o[n]]))},get columns2d(){let{hideGapsEffective:o}=t;return this.rows.map(([,r])=>(o?L_(this.blanks,r):r).toUpperCase())},get fontSize(){return k3(t.rowHeight)},get colStats(){return Mde(this.columns2d,this.numColumns)},get sequenceType(){let o=this.colStats.lettersPresent,r=["N","R","Y","K","M","S","W"],n=new Set(["A","C","G","T",...r]),i=new Set(["A","C","G","U",...r]),s=o.size>0&&[...o].every(l=>n.has(l)),a=o.size>0&&[...o].every(l=>i.has(l));return s?"dna":a?"rna":"amino"},get colConsensus(){let{colStats:o}=this;return Array.from({length:o.numColumns},(r,n)=>{let i=o.total(n),s=0,a="";o.forEachResidue(n,(c,u)=>{u>s&&(s=u,a=gm(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:o}=this;return Array.from({length:o.numColumns},(r,n)=>yEe(o,n))},get colSimilarity(){let{colStats:o,sequenceType:r}=this,n=r==="amino"?sve:ave;return Array.from({length:o.numColumns},(i,s)=>n(o,s))},get conservation(){let{colStats:o,alphabetMaxBits:r}=this;return Array.from({length:o.numColumns},(n,i)=>{let s=o.total(i),a=o.gapCount(i);return s>a?Math.max(0,1-o.entropy(i)/r)*(1-a/s):0})},get alphabetMaxBits(){return Qde(this.sequenceType)},get propertyConservation(){return this.sequenceType==="amino"?GEe(this.colStats):[]},get treeLayout(){let o=()=>this.effectiveTreeWidth;return K4(this.root,{get rowHeight(){return t.rowHeight},get treeWidth(){return o()}})},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 o=this.rootToTipLength;return this.showBranchLenEffective&&o?this.effectiveTreeWidth/o: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>=O3&&t.colWidth>=MAe&&t.colWidth>t.rowHeight/2}})).views(t=>{let o=new WeakMap;return{get columnTrackContent(){let{MSA:r,blanks:n,hideGapsEffective:i}=t,s=r?.getWidth()??0,a=(u,p,f)=>{if(!u.row)return p;let d=Array.from({length:s},()=>f),m=t.seqPosIndex(u.row);return p.forEach((y,b)=>{let h=m?.[b];h!==void 0&&(d[h]=y)}),d},l=u=>i?Kde(n,u):u,c=(u,p)=>{let f=u.row?t.seqPosIndex(u.row)?.[p-1]:p-1;if(!(f===void 0||f<0||f>=s))return i?dC(n,f):f};return new Map(t.columnTracks.map(u=>{if(u.kind==="arc"){let f=(u.arcs??[]).map(d=>{let m=c(u,Math.min(d.start,d.end)),y=c(u,Math.max(d.start,d.end));return m!==void 0&&y!==void 0&&m<y?{start:m,end:y,color:d.color}:void 0}).filter(Oa);return[u.id,{arcs:f}]}if(u.kind==="bar"){let f=u.scales?.y?.domainMax??1,d=l(a(u,u.values??[],0)).map(m=>Math.min(1,Math.max(0,m/f)));return[u.id,{values:d}]}let p=l(a(u,(u.data??"").split("")," "));return[u.id,{data:p.join("")}]}))},trackHeight(r,n=r,i){return t.trackHeights.get(n)??i??LYe[r]??t.rowHeight},columnTrackModel(r){let n=o.get(r);return n||(n=kf(()=>{let i=Bve.has(r.kind)?FYe(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.encoding?.color?bV(r.encoding.color,[...r.encoding.color.domain??[],...new Set(r.data)]):void 0,data:s?.data,arcs:s?.arcs}}}),o.set(r,n)),n.get()},get columnTrackModels(){return t.columnTracks.map(r=>this.columnTrackModel(r))}}}).views(t=>({get secondaryStructureConsensus(){return t.MSA?.secondaryStructureConsensus},get secondaryStructureArcs(){let{blanks:o,hideGapsEffective:r}=t,n=this.secondaryStructureConsensus;if(n)return hve(r?L_(o,n):n).map(({start:i,end:s,pseudoknot:a})=>({start:i,end:s,color:a?HYe:UYe}))},get adapterTrackModels(){let{MSA:o,hideGapsEffective:r,blanks:n}=t,i=(o?.tracks??[]).filter(a=>!!a.data);if(i.length===0)return[];let{rowHeight:s}=t;return i.map(a=>({model:{...a,kind:"text",data:r?L_(n,a.data):a.data,height:s}}))},get basePairTrackModels(){let o=this.secondaryStructureArcs;return o?.length?[{model:{id:"base-pairs",name:"Base pairs",kind:"arc",heightKey:"arc",height:t.trackHeight("arc"),arcs:o}}]:[]},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(o=>({model:{...o,heightKey:Bve.has(o.kind)?o.kind:void 0,height:t.trackHeight(o.kind)}}))},get referenceTrackModels(){let{relativeTo:o}=t,r=o===void 0?void 0:t.columns.get(o);return o===void 0||r===void 0?[]:[{model:{id:"reference-row",name:o,kind:"reference",data:r,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(o=>!Rve(t.turnedOffTracks,o.model.id))},get showHorizontalScrollbar(){return Nve(t.totalWidth,t.msaAreaWidth)},visibleColToRowLetter(o,r){return t.rowSequence(o)?.[this.visibleColToGlobalCol(r)]},visibleColToSeqPos(o,r){return qEe(t.seqPosIndex(o),this.visibleColToGlobalCol(r))},visibleColToSeqPosOneBased(o,r){let n=this.visibleColToSeqPos(o,r);return n!==void 0?n+1:void 0},globalColToVisibleCol(o){let{blanks:r,hideGapsEffective:n}=t;return n?YEe(r,o):o},visibleColToGlobalCol(o){let{blanks:r,hideGapsEffective:n}=t;return n?$Ee(r,o):o},seqPosToGlobalCol(o,r){let n=t.rowSequence(o);return n===void 0?void 0:t.seqPosIndex(o)?.[r]??(r===0?0:n.length)},seqEndToGlobalCol(o,r){let n=t.seqPosIndex(o);return n&&n.length>0?n[Math.min(r,n.length-1)]:void 0},seqPosToVisibleCol(o,r){let n=this.seqPosToGlobalCol(o,r);return n===void 0?void 0:this.globalColToVisibleCol(n)},visibleSpan({row:o,start:r,end:n}){let{blanks:i}=t,s=Math.max(1,Math.floor(r)),a=Math.ceil(n),l=s-1,c=Math.min(a,t.MSA?.getWidth()??a)-1;if(o!==void 0){let f=this.seqPosToGlobalCol(o,s-1),d=this.seqEndToGlobalCol(o,a-1);if(f===void 0||d===void 0)return;l=f,c=d}let u=this.globalColToVisibleCol(l)??dC(i,l),p=this.globalColToVisibleCol(c)??dC(i,c)-1;return u<=p?{startCol:u,endCol:p}:void 0},get residueMappingProblems(){let o=[];for(let r of t.residueMappings){let n={row:r.row,structureId:r.structure.id},i=t.seqPosIndex(r.row)?.length;if(i===void 0){o.push({...n,scope:"mapping",reason:"no such row in the alignment"});continue}if(r.rowLength!==void 0&&r.rowLength!==i){o.push({...n,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){o.push({...n,scope:"mapping",reason:`segment ${s.rowStart}-${s.rowEnd} does not fit a ${i}-residue row`});continue}for(let a of r.segments)Ove(a)||o.push({...n,scope:"segment",reason:`segment ${a.rowStart}-${a.rowEnd} maps to ${a.structStart}-${a.structEnd}, which is a different length`})}return o},get usableResidueMappings(){let o=new Set(this.residueMappingProblems.filter(r=>r.scope==="mapping").map(r=>`${r.row}\0${r.structureId}`));return t.residueMappings.filter(r=>!o.has(`${r.row}\0${r.structure.id}`)).map(r=>({...r,segments:r.segments.filter(Ove)}))},get mappedStructures(){return this.usableResidueMappings.map(o=>({row:o.row,structure:o.structure}))},structureResidue(o,r,n){let i=[];for(let s of this.usableResidueMappings){if(s.row!==o||n!==void 0&&s.structure.id!==n)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:!$Ye(s.unobserved,l)})}}return i.length===1?i[0]:void 0},rowResidue(o,r,n){let i=[];for(let s of this.usableResidueMappings){if(s.structure.id!==o||n!==void 0&&s.structure.asymId!==void 0&&s.structure.asymId!==n)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(t=>({get treeScaleBar(){if(t.showTreeScaleBar)return vEe(t.pxPerBranchLength,t.effectiveTreeAreaWidth-t.marginLeft*2)},get topBandHeight(){return Math.max(t.showHorizontalScrollbar?t.minimapHeight:0,t.rowPanelsHeaderHeight,t.treeOverviewHeight+(this.treeScaleBar?Zu:0))},get msaAreaHeight(){return t.height-this.topBandHeight-t.headerHeight-this.totalTrackAreaHeight},get totalTrackAreaHeight(){return w0(t.turnedOnTracks.map(o=>o.model.height))},get annotationTypes(){let o=new Map;for(let r of t.allAnnotations)o.has(r.accession)||o.set(r.accession,r);return o},get defaultOffAccessions(){return new Set(t.allAnnotations.filter(o=>o.defaultOff).map(o=>o.accession))},featureOff(o){return t.turnedOffFeatures.get(o)??this.defaultOffAccessions.has(o)},get filteredAnnotations(){return t.allAnnotations.filter(o=>!this.featureOff(o.accession))},get cellFill(){return t.bgColor?t.actuallyShowDomains&&t.domainFill&&this.filteredAnnotations.length>0?"domain":"residue":"none"},get annotationsByRow(){let{rowNamesSet:o}=t;return Gae(this.filteredAnnotations,r=>Pve(r.id,o))}})).views(t=>({get showVerticalScrollbar(){return Nve(t.totalHeight,t.msaAreaHeight)}})).views(t=>({get dataInitialized(){return!!(t.data.msa||t.data.tree)&&!t.error},get blocksX(){return qE({viewportSize:t.msaAreaWidth,viewportPos:-t.scrollX,blockSize:t.blockSize,mapSize:t.totalWidth})},get blocksY(){return qE({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(o=>t.blocksX.map(r=>[r,o]))},get wheelZooming(){return t.zoomSnapshot!==void 0},get isLoading(){return t.loadingMSA||t.loadingTree},get dataWarnings(){let{annotations:o,rowNamesSet:r}=t;return t.dataInitialized&&o.length>0&&!o.some(n=>r.has(Pve(n.id,r)))?[`0 of ${o.length} annotations name a row in this alignment`]:[]},get warnings(){return[...t.loadWarnings,...this.dataWarnings.filter(o=>!t.dismissedWarnings.includes(o))]},get maxScrollY(){return Math.min(-t.totalHeight+t.msaAreaHeight,0)},get wheelZoomAxis(){return t.scrollZoom?t.scrollZoomAxis:"both"}})).actions(t=>({setDrawMsaLetters(o){t.drawMsaLetters=o},clearWarnings(){t.loadWarnings=[],t.dismissedWarnings=t.dataWarnings},setScrollZoom(o){t.scrollZoom=o},setScrollZoomAxis(o){t.scrollZoomAxis=o},setHoveredTreeNode(o){if(o===t.hoveredTreeNode?.nodeId)return;if(!o){t.hoveredTreeNode=void 0;return}let r=tf(t.hierarchy,n=>n.data.id===o);t.hoveredTreeNode=r?{nodeId:o,descendantNames:Qc(r).map(n=>n.data.name)}:void 0},calculateNeighborJoiningTreeFromMSA(){let o=[...t.rowMap];if(o.length<2)throw new Error("Need at least 2 sequences to build a tree");if(o.length>ib)throw new Error(`Neighbor joining here is capped at ${ib} sequences and this alignment has ${o.length}. Build the tree with FastTree or IQ-TREE and open it alongside the alignment: https://gmod.org/JBrowseMSA/tutorials/protein_family`);this.replaceTree(UEe(o))},rerootAt(o){let r=tf(Jp(t.tree,i=>i.children),i=>i.data.id===o);if(!r?.parent)return;let n=vV(Jp(t.inputTree,i=>i.children),Qc(r).map(i=>i.data.name));if(n){let i=Qc(n);t.setTreeRoot({outgroup:[...new Set([i[0].data.name,i.at(-1).data.name])]})}},replaceTree(o){_r(()=>{t.setTreeFilehandle(void 0),t.collapsed.clear(),t.rotated.clear(),t.setShowOnly(void 0),t.setTree(o)})},resetZoom(){t.setColWidth(12),t.setRowHeight(16)},zoomAtCenter(o,r="both"){this.zoomToPos(o,t.msaCanvasWidth/2,t.msaAreaHeight/2,r)},zoomIn(){this.zoomAtCenter(1.5)},zoomOut(){this.zoomAtCenter(.75)},zoomToPos(o,r,n,i="both"){_r(()=>{let s=(-t.scrollX+r)/t.colWidth,a=(-t.scrollY+n)/t.rowHeight,l=i!=="both"||t.colWidth===12&&t.rowHeight===16;if(i!=="vertical"){let{value:d,held:m}=kve(t.colWidth,o,12,t.zoomHeld.col,$_,l);t.colWidth=d,t.zoomHeld={...t.zoomHeld,col:m}}if(i!=="horizontal"){let{value:d,held:m}=kve(t.rowHeight,o,16,t.zoomHeld.row,Y_,l);t.rowHeight=d,t.zoomHeld={...t.zoomHeld,row:m}}t.scrollX=dr(r-s*t.colWidth,t.maxScrollX,0);let c=n-a*t.rowHeight,u=Math.max(0,-t.maxScrollY),p=t.totalHeight-u,f=p>0?dr(1-u/p,0,1):1;t.scrollY=dr(c*(1-f),t.maxScrollY,0)})},wheelZoomToPos(o,r,n){t.zoomSnapshot??=P4(t,!1),this.zoomToPos(o,r,n,t.wheelZoomAxis),ohe(t,t.zoomSnapshot)||(t.zoomSnapshot=P4(t,!0))},endWheelZoom(){t.zoomSnapshot=void 0},doScrollY(o){this.setScrollY(t.scrollY+o)},setScrollY(o){t.scrollY=dr(o,t.maxScrollY,0)},setAnnotations(o){t.annotations=o},applyGFFText(o){this.setAnnotations(cR(lR(o)))},doScrollX(o){this.setScrollX(t.scrollX+o)},setScrollX(o){t.scrollX=dr(o,t.maxScrollX,0)},setColumnTracks(o){t.columnTracks.replace(o.map(yV))},setRowData(o){t.data.setTreeMetadata(JSON.stringify(o))},setEncodings(o){t.encodings.replace(o.map(gV))},setRowPanels(o){t.rowPanels.replace(o.map(hV))},setResidueMappings(o){t.residueMappings.replace(o)},toggleTrack(o){t.turnedOffTracks.set(o,!Rve(t.turnedOffTracks,o))},setTracksShown(o,r){for(let n of o)Fve.has(n)===!r?t.turnedOffTracks.delete(n):t.turnedOffTracks.set(n,!r)},setStatus(o){t.status=o}})).views(t=>({cellAt(o,r){let n=t.visibleColToGlobalCol(o),i=r===void 0?void 0:t.leaves[r]?.data.name;return i===void 0?{column:n+1}:{column:n+1,row:i,residue:t.visibleColToSeqPosOneBased(i,o),letter:t.rowSequence(i)?.[n]}},get hoveredCell(){let{mouseCol:o,mouseRow:r}=t;return o===void 0?void 0:this.cellAt(o,r)},get clickedCell(){let{mouseClickCol:o,mouseClickRow:r}=t;return o===void 0?void 0:this.cellAt(o,r)},get viewport(){let{scrollX:o,colWidth:r,numColumns:n,viewInitialized:i}=t;if(n===0||!i)return;let{xStart:s,xEnd:a}=Fa({offsetX:-o,blockWidth:t.msaCanvasWidth,colWidth:r}),l=Math.max(0,Math.min(a,n)-1);return{startColumn:t.visibleColToGlobalCol(Math.min(s,l))+1,endColumn:t.visibleColToGlobalCol(l)+1}},get segmentDomainTypes(){return[...t.annotationTypes.values()].filter(o=>P3.has(o.featureType??"")).toSorted((o,r)=>o.start-r.start)},get categoricalDomainTypes(){let o=[...t.annotationTypes.values()].filter(n=>!P3.has(n.featureType??"")),r=[...new Set(o.map(n=>n.featureType))];return o.toSorted((n,i)=>r.indexOf(n.featureType)-r.indexOf(i.featureType))},get fillPalette(){let o=Object.fromEntries(this.segmentDomainTypes.map((n,i)=>[n.accession,D3[i%D3.length]])),r=zQ(this.categoricalDomainTypes.map(n=>n.accession));return{...o,...r}},get featureFillEncoding(){return this.resolvedEncodings.find(o=>o.channel==="featureFill")},get featureColors(){return cV(t.filteredAnnotations,this.featureFillEncoding,this.fillPalette)},get featureLabels(){let o=this.resolvedEncodings.find(r=>r.channel==="featureLabel");return o?uV(t.filteredAnnotations,o.field):void 0},get segmentLabels(){return new Map(this.segmentDomainTypes.map((o,r)=>{let n=/(\d+)\s*$/.exec(o.name);return[o.accession,n?n[1]:`${r+1}`]}))},get visibleDomainTypes(){return this.categoricalDomainTypes.filter(o=>!t.featureOff(o.accession)).toSorted((o,r)=>o.start-r.start)},get legends(){let{featureFillEncoding:o,fillPalette:r,visibleDomainTypes:n}=this,i=new Map,s=new Set,a=(l,c,u,p=!1)=>{let f=l??"domains";if(u.length===0||i.has(f))return;let d=p||l===void 0?"domains":`rowData-${c}`,m=d;for(let y=2;s.has(m);y++)m=`${d}-${y}`;s.add(m),i.set(f,{id:m,title:c??"Domains",entries:u})};t.actuallyShowDomains&&t.numColumns>0&&a(o?.key,o?.title,o?o.legend:n.map(l=>({id:l.accession,label:l.name,color:l.color??r[l.accession]})),!0);for(let{channel:l,key:c,title:u,legend:p}of this.resolvedEncodings)BV.has(l)||a(c,u,p);for(let{legendKey:l,legendTitle:c,legend:u}of this.rowPanelScales)a(l,c,u);return[...i.values()]},get domainUnderline(){return t.actuallyShowDomains&&t.cellFill!=="domain"&&!t.subFeatureRows&&t.showMsaLetters},get domainBands(){let{blanks:o}=t,r=new Map;for(let[n,i]of Object.entries(t.annotationsByRow)){let s=i.toSorted((a,l)=>v3(l)-v3(a)).map(a=>{let l=t.seqPosToGlobalCol(n,a.start-1),c=t.seqEndToGlobalCol(n,a.end-1);if(l===void 0||c===void 0)return;let u=dC(o,l),p=dC(o,c+1);return p>u?{annotation:a,startCol:u,endCol:p}:void 0}).filter(Oa).map((a,l)=>({...a,stackIndex:l}));s.length>0&&r.set(n,uC(s))}return r},get domainBandsByStart(){return new Map([...this.domainBands].map(([o,r])=>[o,r.toSorted((n,i)=>n.startCol-i.startCol)]))},get mouseOverDomains(){let{mouseCol:o}=t,r=t.mouseOverRowName;if(r===void 0||o===void 0)return Mve;let n=(this.domainBands.get(r)??[]).filter(i=>o>=i.startCol&&o<i.endCol).map(i=>i.annotation);return n.length>0?n:Mve},get referenceRowIndex(){let{relativeTo:o}=t;return o===void 0?void 0:t.rowNamesSet.get(o)},get hoveredRowIndices(){let{hoveredTreeNode:o,rowNamesSet:r}=t;return o?o.descendantNames.map(n=>r.get(n)).filter(Oa):[]},get highlightedColumnRuns(){return Lve([...t.highlightedColumns??[]].sort((o,r)=>o-r)).map(([o,r])=>({start:o,end:r}))},fillHighlightLabel(o,r,n){if(!o.includes("{"))return o;let i=r&&n!==void 0?t.seqPosIndex(r)?.[n-1]:void 0,s=r&&i!==void 0?t.MSA?.getRow(r)[i]??"":"";return o.replaceAll("{residue}",s).replaceAll("{position}",n===void 0?"":String(n))},get resolvedHighlights(){let{rowNamesSet:o,transientHighlights:r}=t;return[...t.highlights,...Object.values(r).flat()].flatMap(({row:i,rows:s,start:a,end:l,label:c,color:u})=>{let p={label:c&&this.fillHighlightLabel(c,i,a),color:u};if(s){let d=s.map(m=>o.get(m)).filter(Oa);return d.length?[{...p,rowIndices:d}]:[]}if(a===void 0||l===void 0)return[];let f=t.visibleSpan({row:i,start:a,end:l});return f?[{...p,...f,rowIndices:[]}]:[]})},get resolvedSelection(){let{selection:o,rowNamesSet:r,numRows:n}=t,i=o&&t.visibleSpan({start:o.start,end:o.end});if(!o||!i)return;let s=o.rows?Lve(o.rows.map(a=>r.get(a)).filter(Oa).sort((a,l)=>a-l)):n>0?[[0,n-1]]:[];return s.length>0?{...i,rowRuns:s}:void 0},get selectionSize(){let o=this.resolvedSelection,r=this.selectionFileSpan;return o&&r?{columns:r.end-r.start+1,rows:w0(o.rowRuns.map(([n,i])=>i-n+1))}:void 0},get selectionFileSpan(){let{selection:o}=t,r=t.MSA?.getWidth()??0,n=Math.max(1,Math.floor(o?.start??0)),i=Math.min(r,Math.ceil(o?.end??0));return o&&n<=i?{start:n,end:i}:void 0},get selectionFasta(){let{rowNames:o}=t,r=this.resolvedSelection,n=this.selectionFileSpan;if(!r||!n)return"";let i=r.rowRuns.flatMap(([s,a])=>o.slice(s,a+1)).flatMap(s=>{let a=t.rowSequence(s);return a===void 0?[]:[[s,a]]});return dEe(i,n.start,n.end)},columnStatsAt(o){let{colStats:r,conservation:n,propertyConservation:i}=t;return EEe({col:o,colStats:r,conservation:n,propertyConservation:i})},getRowData(o){return{data:t.MSA?.getRowData(o),rowData:t.rowDataOf(o)}},get resolvedEncodings(){return t.encodings.map(o=>({...o,...this.scaleOf(o,BV.has(o.channel)?"features":"rows")}))},get resolvedScales(){let o=Object.values(t.rowData),r=(i,s)=>i.map(a=>af(a,s)).filter(Oa),n=(i,s)=>({spec:i,field:i.field,table:s,...s==="rows"?{values:o.map(a=>a?.[i.field]).filter(Oa)}:{values:r(t.allAnnotations,i.field),shown:r(t.filteredAnnotations,i.field)}});return eve([...t.encodings.map(i=>n(i,BV.has(i.channel)?"features":"rows")),...t.rowPanels.flatMap(i=>i.kind==="strip"?[n(i,"rows")]:i.encoding?.color?[n(i.encoding.color,"features")]:[])])},scaleOf(o,r){return this.resolvedScales.get(mV({spec:o,field:o.field,table:r}))},get rowPanelScales(){let{rowData:o}=t,{fillPalette:r,featureFillEncoding:n,featureLabels:i}=this,s=t.filteredAnnotations;return t.rowPanels.map(a=>{if(a.kind==="features"){let f=a.encoding?.color,d=f?{field:f.field,...this.scaleOf(f,"features")}:n,m=a.encoding?.label;return{kind:a.kind,x:a.x,header:a.header??"",field:d?.field,legendKey:d?.key,legendTitle:d?.title,colors:f?cV(s,d,r):this.featureColors,labels:m?uV(s,m):i,legend:d?.legend??this.visibleDomainTypes.map(y=>({id:y.accession,label:y.name,color:y.color??r[y.accession]}))}}let{colorOf:l,legend:c,key:u,title:p}=this.scaleOf(a,"rows");return{kind:a.kind,field:a.field,header:a.header??a.field,legendKey:u,legendTitle:p,colors:GQ(o,a.field,l),legend:c}})},get 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react/cjs/react.production.js:
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