npm - jbrowse-plugin-msaview - Versions diffs - 2.3.8 → 2.4.1 - Mend

jbrowse-plugin-msaview 2.3.8 → 2.4.1

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Files changed (128) hide show

package/dist/jbrowse-plugin-msaview.umd.production.min.js CHANGED Viewed

@@ -1,13 +1,13 @@
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d=l+1;n(o,i,s,d-1),n(o,i,d+1,a)}}return n}function Bv(e){let t=bv.toString();return new Function(`return ${t}`)()(e)}var fE=new WeakMap;dE.quickSort=function(e,t,r=0){let n=fE.get(t);n===void 0&&(n=Bv(t),fE.set(t,n)),n(e,t,r,e.length-1)}});var hE=U(uc=>{var k=ti(),Vu=uE(),ri=Uu().ArraySet,Sv=Pu(),$i=mE().quickSort;function he(e,t){var r=e;return typeof e=="string"&&(r=k.parseSourceMapInput(e)),r.sections!=null?new wr(r,t):new st(r,t)}he.fromSourceMap=function(e,t){return st.fromSourceMap(e,t)};he.prototype._version=3;he.prototype.__generatedMappings=null;Object.defineProperty(he.prototype,"_generatedMappings",{configurable:!0,enumerable:!0,get:function(){return this.__generatedMappings||this._parseMappings(this._mappings,this.sourceRoot),this.__generatedMappings}});he.prototype.__originalMappings=null;Object.defineProperty(he.prototype,"_originalMappings",{configurable:!0,enumerable:!0,get:function(){return this.__originalMappings||this._parseMappings(this._mappings,this.sourceRoot),this.__originalMappings}});he.prototype._charIsMappingSeparator=function(t,r){var n=t.charAt(r);return n===";"||n===","};he.prototype._parseMappings=function(t,r){throw new Error("Subclasses must implement _parseMappings")};he.GENERATED_ORDER=1;he.ORIGINAL_ORDER=2;he.GREATEST_LOWER_BOUND=1;he.LEAST_UPPER_BOUND=2;he.prototype.eachMapping=function(t,r,n){var o=r||null,i=n||he.GENERATED_ORDER,s;switch(i){case he.GENERATED_ORDER:s=this._generatedMappings;break;case he.ORIGINAL_ORDER:s=this._originalMappings;break;default:throw new Error("Unknown order of iteration.")}for(var a=this.sourceRoot,c=t.bind(o),l=this._names,A=this._sources,u=this._sourceMapURL,d=0,m=s.length;d<m;d++){var g=s[d],C=g.source===null?null:A.at(g.source);C!==null&&(C=k.computeSourceURL(a,C,u)),c({source:C,generatedLine:g.generatedLine,generatedColumn:g.generatedColumn,originalLine:g.originalLine,originalColumn:g.originalColumn,name:g.name===null?null:l.at(g.name)})}};he.prototype.allGeneratedPositionsFor=function(t){var r=k.getArg(t,"line"),n={source:k.getArg(t,"source"),originalLine:r,originalColumn:k.getArg(t,"column",0)};if(n.source=this._findSourceIndex(n.source),n.source<0)return[];var o=[],i=this._findMapping(n,this._originalMappings,"originalLine","originalColumn",k.compareByOriginalPositions,Vu.LEAST_UPPER_BOUND);if(i>=0){var s=this._originalMappings[i];if(t.column===void 0)for(var a=s.originalLine;s&&s.originalLine===a;)o.push({line:k.getArg(s,"generatedLine",null),column:k.getArg(s,"generatedColumn",null),lastColumn:k.getArg(s,"lastGeneratedColumn",null)}),s=this._originalMappings[++i];else for(var c=s.originalColumn;s&&s.originalLine===r&&s.originalColumn==c;)o.push({line:k.getArg(s,"generatedLine",null),column:k.getArg(s,"generatedColumn",null),lastColumn:k.getArg(s,"lastGeneratedColumn",null)}),s=this._originalMappings[++i]}return o};uc.SourceMapConsumer=he;function st(e,t){var r=e;typeof e=="string"&&(r=k.parseSourceMapInput(e));var n=k.getArg(r,"version"),o=k.getArg(r,"sources"),i=k.getArg(r,"names",[]),s=k.getArg(r,"sourceRoot",null),a=k.getArg(r,"sourcesContent",null),c=k.getArg(r,"mappings"),l=k.getArg(r,"file",null);if(n!=this._version)throw new Error("Unsupported version: "+n);s&&(s=k.normalize(s)),o=o.map(String).map(k.normalize).map(function(A){return s&&k.isAbsolute(s)&&k.isAbsolute(A)?k.relative(s,A):A}),this._names=ri.fromArray(i.map(String),!0),this._sources=ri.fromArray(o,!0),this._absoluteSources=this._sources.toArray().map(function(A){return k.computeSourceURL(s,A,t)}),this.sourceRoot=s,this.sourcesContent=a,this._mappings=c,this._sourceMapURL=t,this.file=l}st.prototype=Object.create(he.prototype);st.prototype.consumer=he;st.prototype._findSourceIndex=function(e){var t=e;if(this.sourceRoot!=null&&(t=k.relative(this.sourceRoot,t)),this._sources.has(t))return this._sources.indexOf(t);var r;for(r=0;r<this._absoluteSources.length;++r)if(this._absoluteSources[r]==e)return r;return-1};st.fromSourceMap=function(t,r){var n=Object.create(st.prototype),o=n._names=ri.fromArray(t._names.toArray(),!0),i=n._sources=ri.fromArray(t._sources.toArray(),!0);n.sourceRoot=t._sourceRoot,n.sourcesContent=t._generateSourcesContent(n._sources.toArray(),n.sourceRoot),n.file=t._file,n._sourceMapURL=r,n._absoluteSources=n._sources.toArray().map(function(m){return k.computeSourceURL(n.sourceRoot,m,r)});for(var s=t._mappings.toArray().slice(),a=n.__generatedMappings=[],c=n.__originalMappings=[],l=0,A=s.length;l<A;l++){var u=s[l],d=new pE;d.generatedLine=u.generatedLine,d.generatedColumn=u.generatedColumn,u.source&&(d.source=i.indexOf(u.source),d.originalLine=u.originalLine,d.originalColumn=u.originalColumn,u.name&&(d.name=o.indexOf(u.name)),c.push(d)),a.push(d)}return $i(n.__originalMappings,k.compareByOriginalPositions),n};st.prototype._version=3;Object.defineProperty(st.prototype,"sources",{get:function(){return this._absoluteSources.slice()}});function pE(){this.generatedLine=0,this.generatedColumn=0,this.source=null,this.originalLine=null,this.originalColumn=null,this.name=null}var Ju=k.compareByGeneratedPositionsDeflatedNoLine;function gE(e,t){let r=e.length,n=e.length-t;if(!(n<=1))if(n==2){let o=e[t],i=e[t+1];Ju(o,i)>0&&(e[t]=i,e[t+1]=o)}else if(n<20)for(let o=t;o<r;o++)for(let i=o;i>t;i--){let s=e[i-1],a=e[i];if(Ju(s,a)<=0)break;e[i-1]=a,e[i]=s}else $i(e,Ju,t)}st.prototype._parseMappings=function(t,r){var n=1,o=0,i=0,s=0,a=0,c=0,l=t.length,A=0,u={},d={},m=[],g=[],C,x,I,h,y;let b=0;for(;A<l;)if(t.charAt(A)===";")n++,A++,o=0,gE(g,b),b=g.length;else if(t.charAt(A)===",")A++;else{for(C=new pE,C.generatedLine=n,h=A;h<l&&!this._charIsMappingSeparator(t,h);h++);for(x=t.slice(A,h),I=[];A<h;)Sv.decode(t,A,d),y=d.value,A=d.rest,I.push(y);if(I.length===2)throw new Error("Found a source, but no line and column");if(I.length===3)throw new Error("Found a source and line, but no column");if(C.generatedColumn=o+I[0],o=C.generatedColumn,I.length>1&&(C.source=a+I[1],a+=I[1],C.originalLine=i+I[2],i=C.originalLine,C.originalLine+=1,C.originalColumn=s+I[3],s=C.originalColumn,I.length>4&&(C.name=c+I[4],c+=I[4])),g.push(C),typeof C.originalLine=="number"){let v=C.source;for(;m.length<=v;)m.push(null);m[v]===null&&(m[v]=[]),m[v].push(C)}}gE(g,b),this.__generatedMappings=g;for(var w=0;w<m.length;w++)m[w]!=null&&$i(m[w],k.compareByOriginalPositionsNoSource);this.__originalMappings=[].concat(...m)};st.prototype._findMapping=function(t,r,n,o,i,s){if(t[n]<=0)throw new TypeError("Line must be greater than or equal to 1, got "+t[n]);if(t[o]<0)throw new TypeError("Column must be greater than or equal to 0, got "+t[o]);return Vu.search(t,r,i,s)};st.prototype.computeColumnSpans=function(){for(var t=0;t<this._generatedMappings.length;++t){var r=this._generatedMappings[t];if(t+1<this._generatedMappings.length){var n=this._generatedMappings[t+1];if(r.generatedLine===n.generatedLine){r.lastGeneratedColumn=n.generatedColumn-1;continue}}r.lastGeneratedColumn=1/0}};st.prototype.originalPositionFor=function(t){var r={generatedLine:k.getArg(t,"line"),generatedColumn:k.getArg(t,"column")},n=this._findMapping(r,this._generatedMappings,"generatedLine","generatedColumn",k.compareByGeneratedPositionsDeflated,k.getArg(t,"bias",he.GREATEST_LOWER_BOUND));if(n>=0){var o=this._generatedMappings[n];if(o.generatedLine===r.generatedLine){var i=k.getArg(o,"source",null);i!==null&&(i=this._sources.at(i),i=k.computeSourceURL(this.sourceRoot,i,this._sourceMapURL));var s=k.getArg(o,"name",null);return s!==null&&(s=this._names.at(s)),{source:i,line:k.getArg(o,"originalLine",null),column:k.getArg(o,"originalColumn",null),name:s}}}return{source:null,line:null,column:null,name:null}};st.prototype.hasContentsOfAllSources=function(){return this.sourcesContent?this.sourcesContent.length>=this._sources.size()&&!this.sourcesContent.some(function(t){return t==null}):!1};st.prototype.sourceContentFor=function(t,r){if(!this.sourcesContent)return null;var n=this._findSourceIndex(t);if(n>=0)return this.sourcesContent[n];var o=t;this.sourceRoot!=null&&(o=k.relative(this.sourceRoot,o));var i;if(this.sourceRoot!=null&&(i=k.urlParse(this.sourceRoot))){var s=o.replace(/^file:\/\//,"");if(i.scheme=="file"&&this._sources.has(s))return this.sourcesContent[this._sources.indexOf(s)];if((!i.path||i.path=="/")&&this._sources.has("/"+o))return this.sourcesContent[this._sources.indexOf("/"+o)]}if(r)return null;throw new Error('"'+o+'" is not in the SourceMap.')};st.prototype.generatedPositionFor=function(t){var r=k.getArg(t,"source");if(r=this._findSourceIndex(r),r<0)return{line:null,column:null,lastColumn:null};var n={source:r,originalLine:k.getArg(t,"line"),originalColumn:k.getArg(t,"column")},o=this._findMapping(n,this._originalMappings,"originalLine","originalColumn",k.compareByOriginalPositions,k.getArg(t,"bias",he.GREATEST_LOWER_BOUND));if(o>=0){var i=this._originalMappings[o];if(i.source===n.source)return{line:k.getArg(i,"generatedLine",null),column:k.getArg(i,"generatedColumn",null),lastColumn:k.getArg(i,"lastGeneratedColumn",null)}}return{line:null,column:null,lastColumn:null}};uc.BasicSourceMapConsumer=st;function wr(e,t){var r=e;typeof e=="string"&&(r=k.parseSourceMapInput(e));var n=k.getArg(r,"version"),o=k.getArg(r,"sections");if(n!=this._version)throw new Error("Unsupported version: "+n);this._sources=new ri,this._names=new ri;var i={line:-1,column:0};this._sections=o.map(function(s){if(s.url)throw new Error("Support for url field in sections not implemented.");var a=k.getArg(s,"offset"),c=k.getArg(a,"line"),l=k.getArg(a,"column");if(c<i.line||c===i.line&&l<i.column)throw new Error("Section offsets must be ordered and non-overlapping.");return i=a,{generatedOffset:{generatedLine:c+1,generatedColumn:l+1},consumer:new he(k.getArg(s,"map"),t)}})}wr.prototype=Object.create(he.prototype);wr.prototype.constructor=he;wr.prototype._version=3;Object.defineProperty(wr.prototype,"sources",{get:function(){for(var e=[],t=0;t<this._sections.length;t++)for(var r=0;r<this._sections[t].consumer.sources.length;r++)e.push(this._sections[t].consumer.sources[r]);return e}});wr.prototype.originalPositionFor=function(t){var r={generatedLine:k.getArg(t,"line"),generatedColumn:k.getArg(t,"column")},n=Vu.search(r,this._sections,function(i,s){var a=i.generatedLine-s.generatedOffset.generatedLine;return a||i.generatedColumn-s.generatedOffset.generatedColumn}),o=this._sections[n];return o?o.consumer.originalPositionFor({line:r.generatedLine-(o.generatedOffset.generatedLine-1),column:r.generatedColumn-(o.generatedOffset.generatedLine===r.generatedLine?o.generatedOffset.generatedColumn-1:0),bias:t.bias}):{source:null,line:null,column:null,name:null}};wr.prototype.hasContentsOfAllSources=function(){return this._sections.every(function(t){return t.consumer.hasContentsOfAllSources()})};wr.prototype.sourceContentFor=function(t,r){for(var n=0;n<this._sections.length;n++){var o=this._sections[n],i=o.consumer.sourceContentFor(t,!0);if(i||i==="")return i}if(r)return null;throw new Error('"'+t+'" is not in the SourceMap.')};wr.prototype.generatedPositionFor=function(t){for(var r=0;r<this._sections.length;r++){var n=this._sections[r];if(n.consumer._findSourceIndex(k.getArg(t,"source"))!==-1){var o=n.consumer.generatedPositionFor(t);if(o){var i={line:o.line+(n.generatedOffset.generatedLine-1),column:o.column+(n.generatedOffset.generatedLine===o.line?n.generatedOffset.generatedColumn-1:0)};return i}}}return{line:null,column:null}};wr.prototype._parseMappings=function(t,r){this.__generatedMappings=[],this.__originalMappings=[];for(var n=0;n<this._sections.length;n++)for(var o=this._sections[n],i=o.consumer._generatedMappings,s=0;s<i.length;s++){var a=i[s],c=o.consumer._sources.at(a.source);c!==null&&(c=k.computeSourceURL(o.consumer.sourceRoot,c,this._sourceMapURL)),this._sources.add(c),c=this._sources.indexOf(c);var l=null;a.name&&(l=o.consumer._names.at(a.name),this._names.add(l),l=this._names.indexOf(l));var A={source:c,generatedLine:a.generatedLine+(o.generatedOffset.generatedLine-1),generatedColumn:a.generatedColumn+(o.generatedOffset.generatedLine===a.generatedLine?o.generatedOffset.generatedColumn-1:0),originalLine:a.originalLine,originalColumn:a.originalColumn,name:l};this.__generatedMappings.push(A),typeof A.originalLine=="number"&&this.__originalMappings.push(A)}$i(this.__generatedMappings,k.compareByGeneratedPositionsDeflated),$i(this.__originalMappings,k.compareByOriginalPositions)};uc.IndexedSourceMapConsumer=wr});var EE=U(CE=>{var Qv=qu().SourceMapGenerator,fc=ti(),Mv=/(\r?\n)/,vv=10,ni="$$$isSourceNode$$$";function Gt(e,t,r,n,o){this.children=[],this.sourceContents={},this.line=e??null,this.column=t??null,this.source=r??null,this.name=o??null,this[ni]=!0,n!=null&&this.add(n)}Gt.fromStringWithSourceMap=function(t,r,n){var o=new Gt,i=t.split(Mv),s=0,a=function(){var d=g(),m=g()||"";return d+m;function g(){return s<i.length?i[s++]:void 0}},c=1,l=0,A=null;return r.eachMapping(function(d){if(A!==null)if(c<d.generatedLine)u(A,a()),c++,l=0;else{var m=i[s]||"",g=m.substr(0,d.generatedColumn-l);i[s]=m.substr(d.generatedColumn-l),l=d.generatedColumn,u(A,g),A=d;return}for(;c<d.generatedLine;)o.add(a()),c++;if(l<d.generatedColumn){var m=i[s]||"";o.add(m.substr(0,d.generatedColumn)),i[s]=m.substr(d.generatedColumn),l=d.generatedColumn}A=d},this),s<i.length&&(A&&u(A,a()),o.add(i.splice(s).join(""))),r.sources.forEach(function(d){var m=r.sourceContentFor(d);m!=null&&(n!=null&&(d=fc.join(n,d)),o.setSourceContent(d,m))}),o;function u(d,m){if(d===null||d.source===void 0)o.add(m);else{var g=n?fc.join(n,d.source):d.source;o.add(new Gt(d.originalLine,d.originalColumn,g,m,d.name))}}};Gt.prototype.add=function(t){if(Array.isArray(t))t.forEach(function(r){this.add(r)},this);else if(t[ni]||typeof t=="string")t&&this.children.push(t);else throw new TypeError("Expected a SourceNode, string, or an array of SourceNodes and strings. Got "+t);return this};Gt.prototype.prepend=function(t){if(Array.isArray(t))for(var r=t.length-1;r>=0;r--)this.prepend(t[r]);else if(t[ni]||typeof t=="string")this.children.unshift(t);else throw new TypeError("Expected a SourceNode, string, or an array of SourceNodes and strings. Got "+t);return this};Gt.prototype.walk=function(t){for(var r,n=0,o=this.children.length;n<o;n++)r=this.children[n],r[ni]?r.walk(t):r!==""&&t(r,{source:this.source,line:this.line,column:this.column,name:this.name})};Gt.prototype.join=function(t){var r,n,o=this.children.length;if(o>0){for(r=[],n=0;n<o-1;n++)r.push(this.children[n]),r.push(t);r.push(this.children[n]),this.children=r}return this};Gt.prototype.replaceRight=function(t,r){var n=this.children[this.children.length-1];return n[ni]?n.replaceRight(t,r):typeof n=="string"?this.children[this.children.length-1]=n.replace(t,r):this.children.push("".replace(t,r)),this};Gt.prototype.setSourceContent=function(t,r){this.sourceContents[fc.toSetString(t)]=r};Gt.prototype.walkSourceContents=function(t){for(var r=0,n=this.children.length;r<n;r++)this.children[r][ni]&&this.children[r].walkSourceContents(t);for(var o=Object.keys(this.sourceContents),r=0,n=o.length;r<n;r++)t(fc.fromSetString(o[r]),this.sourceContents[o[r]])};Gt.prototype.toString=function(){var t="";return this.walk(function(r){t+=r}),t};Gt.prototype.toStringWithSourceMap=function(t){var r={code:"",line:1,column:0},n=new Qv(t),o=!1,i=null,s=null,a=null,c=null;return this.walk(function(l,A){r.code+=l,A.source!==null&&A.line!==null&&A.column!==null?((i!==A.source||s!==A.line||a!==A.column||c!==A.name)&&n.addMapping({source:A.source,original:{line:A.line,column:A.column},generated:{line:r.line,column:r.column},name:A.name}),i=A.source,s=A.line,a=A.column,c=A.name,o=!0):o&&(n.addMapping({generated:{line:r.line,column:r.column}}),i=null,o=!1);for(var u=0,d=l.length;u<d;u++)l.charCodeAt(u)===vv?(r.line++,r.column=0,u+1===d?(i=null,o=!1):o&&n.addMapping({source:A.source,original:{line:A.line,column:A.column},generated:{line:r.line,column:r.column},name:A.name})):r.column++}),this.walkSourceContents(function(l,A){n.setSourceContent(l,A)}),{code:r.code,map:n}};CE.SourceNode=Gt});var IE=U(dc=>{dc.SourceMapGenerator=qu().SourceMapGenerator;dc.SourceMapConsumer=hE().SourceMapConsumer;dc.SourceNode=EE().SourceNode});function gc(e){let{children:t,...r}=e;return(0,mc.jsxs)(yE.Link,{...r,target:"_blank",rel:"noopener noreferrer",children:[t," ",(0,mc.jsx)(xa,{fontSize:"small"})]})}var mc,yE,xE=p(()=>{mc=f(F(),1);vA();yE=f(L(),1)});function Yu({text:e,extra:t}){let{classes:r}=Tv(),n=t?`supporting data: ${JSON.stringify(t,null,2)}`:"",o=[e,n].filter(Boolean).join(`
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JSON.parse(e.replace(/^\)]}'[^\n]*\n/,""))}Ze.parseSourceMapInput=sv;function av(e,t,r){if(t=t||"",e&&(e[e.length-1]!=="/"&&t[0]!=="/"&&(e+="/"),t=e+t),r){var n=ji(r);if(!n)throw new Error("sourceMapURL could not be parsed");if(n.path){var o=n.path.lastIndexOf("/");o>=0&&(n.path=n.path.substring(0,o+1))}t=VC($o(n),t)}return Nu(t)}Ze.computeSourceURL=av});var Ru=H($C=>{var Lu=Ko(),Fu=Object.prototype.hasOwnProperty,Jn=typeof Map<"u";function Zr(){this._array=[],this._set=Jn?new Map:Object.create(null)}Zr.fromArray=function(t,r){for(var n=new Zr,o=0,i=t.length;o<i;o++)n.add(t[o],r);return n};Zr.prototype.size=function(){return Jn?this._set.size:Object.getOwnPropertyNames(this._set).length};Zr.prototype.add=function(t,r){var n=Jn?t:Lu.toSetString(t),o=Jn?this.has(t):Fu.call(this._set,n),i=this._array.length;(!o||r)&&this._array.push(t),o||(Jn?this._set.set(t,i):this._set[n]=i)};Zr.prototype.has=function(t){if(Jn)return this._set.has(t);var r=Lu.toSetString(t);return Fu.call(this._set,r)};Zr.prototype.indexOf=function(t){if(Jn){var r=this._set.get(t);if(r>=0)return r}else{var n=Lu.toSetString(t);if(Fu.call(this._set,n))return this._set[n]}throw new Error('"'+t+'" is not in the set.')};Zr.prototype.at=function(t){if(t>=0&&t<this._array.length)return this._array[t];throw new Error("No element indexed by "+t)};Zr.prototype.toArray=function(){return this._array.slice()};$C.ArraySet=Zr});var ZC=H(XC=>{var KC=Ko();function cv(e,t){var r=e.generatedLine,n=t.generatedLine,o=e.generatedColumn,i=t.generatedColumn;return n>r||n==r&&i>=o||KC.compareByGeneratedPositionsInflated(e,t)<=0}function oc(){this._array=[],this._sorted=!0,this._last={generatedLine:-1,generatedColumn:0}}oc.prototype.unsortedForEach=function(t,r){this._array.forEach(t,r)};oc.prototype.add=function(t){cv(this._last,t)?(this._last=t,this._array.push(t)):(this._sorted=!1,this._array.push(t))};oc.prototype.toArray=function(){return this._sorted||(this._array.sort(KC.compareByGeneratedPositionsInflated),this._sorted=!0),this._array};XC.MappingList=oc});var Pu=H(eE=>{var Ji=ku(),Ne=Ko(),ic=Ru().ArraySet,lv=ZC().MappingList;function tr(e){e||(e={}),this._file=Ne.getArg(e,"file",null),this._sourceRoot=Ne.getArg(e,"sourceRoot",null),this._skipValidation=Ne.getArg(e,"skipValidation",!1),this._ignoreInvalidMapping=Ne.getArg(e,"ignoreInvalidMapping",!1),this._sources=new ic,this._names=new ic,this._mappings=new lv,this._sourcesContents=null}tr.prototype._version=3;tr.fromSourceMap=function(t,r){var n=t.sourceRoot,o=new tr(Object.assign(r||{},{file:t.file,sourceRoot:n}));return t.eachMapping(function(i){var s={generated:{line:i.generatedLine,column:i.generatedColumn}};i.source!=null&&(s.source=i.source,n!=null&&(s.source=Ne.relative(n,s.source)),s.original={line:i.originalLine,column:i.originalColumn},i.name!=null&&(s.name=i.name)),o.addMapping(s)}),t.sources.forEach(function(i){var s=i;n!==null&&(s=Ne.relative(n,i)),o._sources.has(s)||o._sources.add(s);var a=t.sourceContentFor(i);a!=null&&o.setSourceContent(i,a)}),o};tr.prototype.addMapping=function(t){var r=Ne.getArg(t,"generated"),n=Ne.getArg(t,"original",null),o=Ne.getArg(t,"source",null),i=Ne.getArg(t,"name",null);!this._skipValidation&&this._validateMapping(r,n,o,i)===!1||(o!=null&&(o=String(o),this._sources.has(o)||this._sources.add(o)),i!=null&&(i=String(i),this._names.has(i)||this._names.add(i)),this._mappings.add({generatedLine:r.line,generatedColumn:r.column,originalLine:n!=null&&n.line,originalColumn:n!=null&&n.column,source:o,name:i}))};tr.prototype.setSourceContent=function(t,r){var n=t;this._sourceRoot!=null&&(n=Ne.relative(this._sourceRoot,n)),r!=null?(this._sourcesContents||(this._sourcesContents=Object.create(null)),this._sourcesContents[Ne.toSetString(n)]=r):this._sourcesContents&&(delete this._sourcesContents[Ne.toSetString(n)],Object.keys(this._sourcesContents).length===0&&(this._sourcesContents=null))};tr.prototype.applySourceMap=function(t,r,n){var o=r;if(r==null){if(t.file==null)throw new Error(`SourceMapGenerator.prototype.applySourceMap requires either an explicit source file, or the source map's "file" property. Both were omitted.`);o=t.file}var i=this._sourceRoot;i!=null&&(o=Ne.relative(i,o));var s=new ic,a=new ic;this._mappings.unsortedForEach(function(c){if(c.source===o&&c.originalLine!=null){var l=t.originalPositionFor({line:c.originalLine,column:c.originalColumn});l.source!=null&&(c.source=l.source,n!=null&&(c.source=Ne.join(n,c.source)),i!=null&&(c.source=Ne.relative(i,c.source)),c.originalLine=l.line,c.originalColumn=l.column,l.name!=null&&(c.name=l.name))}var A=c.source;A!=null&&!s.has(A)&&s.add(A);var u=c.name;u!=null&&!a.has(u)&&a.add(u)},this),this._sources=s,this._names=a,t.sources.forEach(function(c){var l=t.sourceContentFor(c);l!=null&&(n!=null&&(c=Ne.join(n,c)),i!=null&&(c=Ne.relative(i,c)),this.setSourceContent(c,l))},this)};tr.prototype._validateMapping=function(t,r,n,o){if(r&&typeof r.line!="number"&&typeof r.column!="number"){var i="original.line and original.column are not numbers -- you probably meant to omit the original mapping entirely and only map the generated position. If so, pass null for the original mapping instead of an object with empty or null values.";if(this._ignoreInvalidMapping)return typeof console<"u"&&console.warn&&console.warn(i),!1;throw new Error(i)}if(!(t&&"line"in t&&"column"in t&&t.line>0&&t.column>=0&&!r&&!n&&!o)){if(t&&"line"in t&&"column"in t&&r&&"line"in r&&"column"in r&&t.line>0&&t.column>=0&&r.line>0&&r.column>=0&&n)return;var i="Invalid mapping: "+JSON.stringify({generated:t,source:n,original:r,name:o});if(this._ignoreInvalidMapping)return typeof console<"u"&&console.warn&&console.warn(i),!1;throw new Error(i)}};tr.prototype._serializeMappings=function(){for(var t=0,r=1,n=0,o=0,i=0,s=0,a="",c,l,A,u,d=this._mappings.toArray(),m=0,p=d.length;m<p;m++){if(l=d[m],c="",l.generatedLine!==r)for(t=0;l.generatedLine!==r;)c+=";",r++;else if(m>0){if(!Ne.compareByGeneratedPositionsInflated(l,d[m-1]))continue;c+=","}c+=Ji.encode(l.generatedColumn-t),t=l.generatedColumn,l.source!=null&&(u=this._sources.indexOf(l.source),c+=Ji.encode(u-s),s=u,c+=Ji.encode(l.originalLine-1-o),o=l.originalLine-1,c+=Ji.encode(l.originalColumn-n),n=l.originalColumn,l.name!=null&&(A=this._names.indexOf(l.name),c+=Ji.encode(A-i),i=A)),a+=c}return a};tr.prototype._generateSourcesContent=function(t,r){return t.map(function(n){if(!this._sourcesContents)return null;r!=null&&(n=Ne.relative(r,n));var o=Ne.toSetString(n);return Object.prototype.hasOwnProperty.call(this._sourcesContents,o)?this._sourcesContents[o]:null},this)};tr.prototype.toJSON=function(){var t={version:this._version,sources:this._sources.toArray(),names:this._names.toArray(),mappings:this._serializeMappings()};return this._file!=null&&(t.file=this._file),this._sourceRoot!=null&&(t.sourceRoot=this._sourceRoot),this._sourcesContents&&(t.sourcesContent=this._generateSourcesContent(t.sources,t.sourceRoot)),t};tr.prototype.toString=function(){return JSON.stringify(this.toJSON())};eE.SourceMapGenerator=tr});var tE=H(Vn=>{Vn.GREATEST_LOWER_BOUND=1;Vn.LEAST_UPPER_BOUND=2;function Ou(e,t,r,n,o,i){var s=Math.floor((t-e)/2)+e,a=o(r,n[s],!0);return a===0?s:a>0?t-s>1?Ou(s,t,r,n,o,i):i==Vn.LEAST_UPPER_BOUND?t<n.length?t:-1:s:s-e>1?Ou(e,s,r,n,o,i):i==Vn.LEAST_UPPER_BOUND?s:e<0?-1:e}Vn.search=function(t,r,n,o){if(r.length===0)return-1;var i=Ou(-1,r.length,t,r,n,o||Vn.GREATEST_LOWER_BOUND);if(i<0)return-1;for(;i-1>=0&&n(r[i],r[i-1],!0)===0;)--i;return i}});var oE=H(nE=>{function Av(e){function t(o,i,s){var a=o[i];o[i]=o[s],o[s]=a}function r(o,i){return Math.round(o+Math.random()*(i-o))}function n(o,i,s,a){if(s<a){var c=r(s,a),l=s-1;t(o,c,a);for(var A=o[a],u=s;u<a;u++)i(o[u],A,!1)<=0&&(l+=1,t(o,l,u));t(o,l+1,u);var d=l+1;n(o,i,s,d-1),n(o,i,d+1,a)}}return n}function uv(e){let t=Av.toString();return new Function(`return ${t}`)()(e)}var rE=new WeakMap;nE.quickSort=function(e,t,r=0){let n=rE.get(t);n===void 0&&(n=uv(t),rE.set(t,n)),n(e,t,r,e.length-1)}});var aE=H(sc=>{var D=Ko(),Hu=tE(),Xo=Ru().ArraySet,fv=ku(),Vi=oE().quickSort;function he(e,t){var r=e;return typeof e=="string"&&(r=D.parseSourceMapInput(e)),r.sections!=null?new Er(r,t):new it(r,t)}he.fromSourceMap=function(e,t){return it.fromSourceMap(e,t)};he.prototype._version=3;he.prototype.__generatedMappings=null;Object.defineProperty(he.prototype,"_generatedMappings",{configurable:!0,enumerable:!0,get:function(){return this.__generatedMappings||this._parseMappings(this._mappings,this.sourceRoot),this.__generatedMappings}});he.prototype.__originalMappings=null;Object.defineProperty(he.prototype,"_originalMappings",{configurable:!0,enumerable:!0,get:function(){return this.__originalMappings||this._parseMappings(this._mappings,this.sourceRoot),this.__originalMappings}});he.prototype._charIsMappingSeparator=function(t,r){var n=t.charAt(r);return n===";"||n===","};he.prototype._parseMappings=function(t,r){throw new Error("Subclasses must implement _parseMappings")};he.GENERATED_ORDER=1;he.ORIGINAL_ORDER=2;he.GREATEST_LOWER_BOUND=1;he.LEAST_UPPER_BOUND=2;he.prototype.eachMapping=function(t,r,n){var o=r||null,i=n||he.GENERATED_ORDER,s;switch(i){case he.GENERATED_ORDER:s=this._generatedMappings;break;case he.ORIGINAL_ORDER:s=this._originalMappings;break;default:throw new Error("Unknown order of iteration.")}for(var a=this.sourceRoot,c=t.bind(o),l=this._names,A=this._sources,u=this._sourceMapURL,d=0,m=s.length;d<m;d++){var p=s[d],C=p.source===null?null:A.at(p.source);C!==null&&(C=D.computeSourceURL(a,C,u)),c({source:C,generatedLine:p.generatedLine,generatedColumn:p.generatedColumn,originalLine:p.originalLine,originalColumn:p.originalColumn,name:p.name===null?null:l.at(p.name)})}};he.prototype.allGeneratedPositionsFor=function(t){var r=D.getArg(t,"line"),n={source:D.getArg(t,"source"),originalLine:r,originalColumn:D.getArg(t,"column",0)};if(n.source=this._findSourceIndex(n.source),n.source<0)return[];var o=[],i=this._findMapping(n,this._originalMappings,"originalLine","originalColumn",D.compareByOriginalPositions,Hu.LEAST_UPPER_BOUND);if(i>=0){var s=this._originalMappings[i];if(t.column===void 0)for(var a=s.originalLine;s&&s.originalLine===a;)o.push({line:D.getArg(s,"generatedLine",null),column:D.getArg(s,"generatedColumn",null),lastColumn:D.getArg(s,"lastGeneratedColumn",null)}),s=this._originalMappings[++i];else for(var c=s.originalColumn;s&&s.originalLine===r&&s.originalColumn==c;)o.push({line:D.getArg(s,"generatedLine",null),column:D.getArg(s,"generatedColumn",null),lastColumn:D.getArg(s,"lastGeneratedColumn",null)}),s=this._originalMappings[++i]}return o};sc.SourceMapConsumer=he;function it(e,t){var r=e;typeof e=="string"&&(r=D.parseSourceMapInput(e));var n=D.getArg(r,"version"),o=D.getArg(r,"sources"),i=D.getArg(r,"names",[]),s=D.getArg(r,"sourceRoot",null),a=D.getArg(r,"sourcesContent",null),c=D.getArg(r,"mappings"),l=D.getArg(r,"file",null);if(n!=this._version)throw new Error("Unsupported version: "+n);s&&(s=D.normalize(s)),o=o.map(String).map(D.normalize).map(function(A){return s&&D.isAbsolute(s)&&D.isAbsolute(A)?D.relative(s,A):A}),this._names=Xo.fromArray(i.map(String),!0),this._sources=Xo.fromArray(o,!0),this._absoluteSources=this._sources.toArray().map(function(A){return D.computeSourceURL(s,A,t)}),this.sourceRoot=s,this.sourcesContent=a,this._mappings=c,this._sourceMapURL=t,this.file=l}it.prototype=Object.create(he.prototype);it.prototype.consumer=he;it.prototype._findSourceIndex=function(e){var t=e;if(this.sourceRoot!=null&&(t=D.relative(this.sourceRoot,t)),this._sources.has(t))return this._sources.indexOf(t);var r;for(r=0;r<this._absoluteSources.length;++r)if(this._absoluteSources[r]==e)return r;return-1};it.fromSourceMap=function(t,r){var n=Object.create(it.prototype),o=n._names=Xo.fromArray(t._names.toArray(),!0),i=n._sources=Xo.fromArray(t._sources.toArray(),!0);n.sourceRoot=t._sourceRoot,n.sourcesContent=t._generateSourcesContent(n._sources.toArray(),n.sourceRoot),n.file=t._file,n._sourceMapURL=r,n._absoluteSources=n._sources.toArray().map(function(m){return D.computeSourceURL(n.sourceRoot,m,r)});for(var s=t._mappings.toArray().slice(),a=n.__generatedMappings=[],c=n.__originalMappings=[],l=0,A=s.length;l<A;l++){var u=s[l],d=new sE;d.generatedLine=u.generatedLine,d.generatedColumn=u.generatedColumn,u.source&&(d.source=i.indexOf(u.source),d.originalLine=u.originalLine,d.originalColumn=u.originalColumn,u.name&&(d.name=o.indexOf(u.name)),c.push(d)),a.push(d)}return Vi(n.__originalMappings,D.compareByOriginalPositions),n};it.prototype._version=3;Object.defineProperty(it.prototype,"sources",{get:function(){return this._absoluteSources.slice()}});function sE(){this.generatedLine=0,this.generatedColumn=0,this.source=null,this.originalLine=null,this.originalColumn=null,this.name=null}var Gu=D.compareByGeneratedPositionsDeflatedNoLine;function iE(e,t){let r=e.length,n=e.length-t;if(!(n<=1))if(n==2){let o=e[t],i=e[t+1];Gu(o,i)>0&&(e[t]=i,e[t+1]=o)}else if(n<20)for(let o=t;o<r;o++)for(let i=o;i>t;i--){let s=e[i-1],a=e[i];if(Gu(s,a)<=0)break;e[i-1]=a,e[i]=s}else Vi(e,Gu,t)}it.prototype._parseMappings=function(t,r){var n=1,o=0,i=0,s=0,a=0,c=0,l=t.length,A=0,u={},d={},m=[],p=[],C,x,I,h,y;let w=0;for(;A<l;)if(t.charAt(A)===";")n++,A++,o=0,iE(p,w),w=p.length;else if(t.charAt(A)===",")A++;else{for(C=new sE,C.generatedLine=n,h=A;h<l&&!this._charIsMappingSeparator(t,h);h++);for(x=t.slice(A,h),I=[];A<h;)fv.decode(t,A,d),y=d.value,A=d.rest,I.push(y);if(I.length===2)throw new Error("Found a source, but no line and column");if(I.length===3)throw new Error("Found a source and line, but no column");if(C.generatedColumn=o+I[0],o=C.generatedColumn,I.length>1&&(C.source=a+I[1],a+=I[1],C.originalLine=i+I[2],i=C.originalLine,C.originalLine+=1,C.originalColumn=s+I[3],s=C.originalColumn,I.length>4&&(C.name=c+I[4],c+=I[4])),p.push(C),typeof C.originalLine=="number"){let v=C.source;for(;m.length<=v;)m.push(null);m[v]===null&&(m[v]=[]),m[v].push(C)}}iE(p,w),this.__generatedMappings=p;for(var S=0;S<m.length;S++)m[S]!=null&&Vi(m[S],D.compareByOriginalPositionsNoSource);this.__originalMappings=[].concat(...m)};it.prototype._findMapping=function(t,r,n,o,i,s){if(t[n]<=0)throw new TypeError("Line must be greater than or equal to 1, got "+t[n]);if(t[o]<0)throw new TypeError("Column must be greater than or equal to 0, got "+t[o]);return Hu.search(t,r,i,s)};it.prototype.computeColumnSpans=function(){for(var t=0;t<this._generatedMappings.length;++t){var r=this._generatedMappings[t];if(t+1<this._generatedMappings.length){var n=this._generatedMappings[t+1];if(r.generatedLine===n.generatedLine){r.lastGeneratedColumn=n.generatedColumn-1;continue}}r.lastGeneratedColumn=1/0}};it.prototype.originalPositionFor=function(t){var r={generatedLine:D.getArg(t,"line"),generatedColumn:D.getArg(t,"column")},n=this._findMapping(r,this._generatedMappings,"generatedLine","generatedColumn",D.compareByGeneratedPositionsDeflated,D.getArg(t,"bias",he.GREATEST_LOWER_BOUND));if(n>=0){var o=this._generatedMappings[n];if(o.generatedLine===r.generatedLine){var i=D.getArg(o,"source",null);i!==null&&(i=this._sources.at(i),i=D.computeSourceURL(this.sourceRoot,i,this._sourceMapURL));var s=D.getArg(o,"name",null);return s!==null&&(s=this._names.at(s)),{source:i,line:D.getArg(o,"originalLine",null),column:D.getArg(o,"originalColumn",null),name:s}}}return{source:null,line:null,column:null,name:null}};it.prototype.hasContentsOfAllSources=function(){return this.sourcesContent?this.sourcesContent.length>=this._sources.size()&&!this.sourcesContent.some(function(t){return t==null}):!1};it.prototype.sourceContentFor=function(t,r){if(!this.sourcesContent)return null;var n=this._findSourceIndex(t);if(n>=0)return this.sourcesContent[n];var o=t;this.sourceRoot!=null&&(o=D.relative(this.sourceRoot,o));var i;if(this.sourceRoot!=null&&(i=D.urlParse(this.sourceRoot))){var s=o.replace(/^file:\/\//,"");if(i.scheme=="file"&&this._sources.has(s))return this.sourcesContent[this._sources.indexOf(s)];if((!i.path||i.path=="/")&&this._sources.has("/"+o))return this.sourcesContent[this._sources.indexOf("/"+o)]}if(r)return null;throw new Error('"'+o+'" is not in the SourceMap.')};it.prototype.generatedPositionFor=function(t){var r=D.getArg(t,"source");if(r=this._findSourceIndex(r),r<0)return{line:null,column:null,lastColumn:null};var n={source:r,originalLine:D.getArg(t,"line"),originalColumn:D.getArg(t,"column")},o=this._findMapping(n,this._originalMappings,"originalLine","originalColumn",D.compareByOriginalPositions,D.getArg(t,"bias",he.GREATEST_LOWER_BOUND));if(o>=0){var i=this._originalMappings[o];if(i.source===n.source)return{line:D.getArg(i,"generatedLine",null),column:D.getArg(i,"generatedColumn",null),lastColumn:D.getArg(i,"lastGeneratedColumn",null)}}return{line:null,column:null,lastColumn:null}};sc.BasicSourceMapConsumer=it;function Er(e,t){var r=e;typeof e=="string"&&(r=D.parseSourceMapInput(e));var n=D.getArg(r,"version"),o=D.getArg(r,"sections");if(n!=this._version)throw new Error("Unsupported version: "+n);this._sources=new Xo,this._names=new Xo;var i={line:-1,column:0};this._sections=o.map(function(s){if(s.url)throw new Error("Support for url field in sections not implemented.");var a=D.getArg(s,"offset"),c=D.getArg(a,"line"),l=D.getArg(a,"column");if(c<i.line||c===i.line&&l<i.column)throw new Error("Section offsets must be ordered and non-overlapping.");return i=a,{generatedOffset:{generatedLine:c+1,generatedColumn:l+1},consumer:new he(D.getArg(s,"map"),t)}})}Er.prototype=Object.create(he.prototype);Er.prototype.constructor=he;Er.prototype._version=3;Object.defineProperty(Er.prototype,"sources",{get:function(){for(var e=[],t=0;t<this._sections.length;t++)for(var r=0;r<this._sections[t].consumer.sources.length;r++)e.push(this._sections[t].consumer.sources[r]);return e}});Er.prototype.originalPositionFor=function(t){var r={generatedLine:D.getArg(t,"line"),generatedColumn:D.getArg(t,"column")},n=Hu.search(r,this._sections,function(i,s){var a=i.generatedLine-s.generatedOffset.generatedLine;return a||i.generatedColumn-s.generatedOffset.generatedColumn}),o=this._sections[n];return o?o.consumer.originalPositionFor({line:r.generatedLine-(o.generatedOffset.generatedLine-1),column:r.generatedColumn-(o.generatedOffset.generatedLine===r.generatedLine?o.generatedOffset.generatedColumn-1:0),bias:t.bias}):{source:null,line:null,column:null,name:null}};Er.prototype.hasContentsOfAllSources=function(){return this._sections.every(function(t){return t.consumer.hasContentsOfAllSources()})};Er.prototype.sourceContentFor=function(t,r){for(var n=0;n<this._sections.length;n++){var o=this._sections[n],i=o.consumer.sourceContentFor(t,!0);if(i||i==="")return i}if(r)return null;throw new Error('"'+t+'" is not in the SourceMap.')};Er.prototype.generatedPositionFor=function(t){for(var r=0;r<this._sections.length;r++){var n=this._sections[r];if(n.consumer._findSourceIndex(D.getArg(t,"source"))!==-1){var o=n.consumer.generatedPositionFor(t);if(o){var 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 UniProt/Swiss-Prot|P26898|IL2RA_SHEEP      MEPSLLMWRFFVFIVVPGCVTEACHDDPPSLRNA----------MFKVLRYE----VGTM
 UniProt/Swiss-Prot|P01590|IL2RA_MOUSE      MEPRLLMLGFLSLTIVPSCRAELCLYDPPEVPNA----------TFKALSYK----NGTI
 UniProt/Swiss-Prot|P41690|IL2RA_FELCA      MEPSLLLWGILTFVVVHGHVTELCDENPPDIQHA----------TFKALTYK----TGTM
@@ -41,7 +41,7 @@ UniProt/Swiss-Prot|Q8BZM1|GLMN_MOUSE       PLPLRSLLFLQLPLLGVGLNP----------------
 UniProt/Swiss-Prot|P36835|IL2_CAPHI        -----------LLGVGLNPKFLTP------------------------------------
 UniProt/Swiss-Prot|Q7JFM4|IL2_AOTVO        MLKPPLPLRSLLFLQLPLLGVGLNPKFLTPSGNEDIGGKPGTGGDFFLTSTPAGTLDVST
 UniProt/Swiss-Prot|Q29416|IL2_CANFA        --------------LFLQLSLLG-------------------------------------
-`,cB=`CLUSTAL O(1.2.4) multiple sequence alignment
+`,Xb=`CLUSTAL O(1.2.4) multiple sequence alignment
 sp|P69905|HBA_HUMAN       MVLSPADKTNVKAAWGKVGAHAGEYGAEALERMFLSFPTTKTYFPHFDLSHGSAQVKGHG	60
@@ -57,23 +57,21 @@ sp|P13786|HBAZ_CAPHI      SKVVAAVGDAVKSIDNVTSALSKLSELHAYVLRVDPVNFKFLSHCLLVTLASHF
 sp|P69905|HBA_HUMAN       AVHASLDKFLASVSTVLTSKYR	142
 sp|P01942|HBA_MOUSE       AVHASLDKFLASVSTVLTSKYR	142
 sp|P13786|HBAZ_CAPHI      DAHAAWDKFLSIVSGVLTEKYR	142
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Databases"}:{},...t==="quick-blastp"?{BLAST_PROGRAMS:"kmerBlastp"}:{}})}),i=/^ {4}RID = (.*$)/m.exec(o)?.[1],s=/^ {4}RTOE = (.*$)/m.exec(o)?.[1];if(!i)throw new Error("Failed to get RID from BLAST request");return{rid:i,rtoe:s}}async function Xk({rid:e,onProgress:t,baseUrl:r}){for(;;){for(let l=0;l<20;l++)await oa(1e3),t(`Re-checking BLAST status in... ${20-l}`);let o=await Cr(`${r}?CMD=Get&FORMAT_OBJECT=SearchInfo&RID=${e}`),i=/\s+Status=WAITING/m.test(o),s=/\s+Status=FAILED/m.test(o),a=/\s+Status=READY/m.test(o),c=/\s+ThereAreHits=yes/m.test(o);if(!i){if(s)throw new Error(`BLAST ${e} failed`);if(a){if(c)return!0;throw new Error("No hits found")}}}}Fi();var Zk="jbrowse-msaview-taxonomy-cache",Bs="common-names",eN=2;async function tQ(){return Gn(Zk,eN,{upgrade(e){e.objectStoreNames.contains(Bs)&&e.deleteObjectStore(Bs),e.createObjectStore(Bs,{keyPath:"taxid"})}})}async function tN(e){return(await tQ()).get(Bs,e)}async function rN(e){let r=(await tQ()).transaction(Bs,"readwrite");for(let n of e)await r.store.put(n);await r.done}async function rQ(e){let t=new Map,r=[];for(let i of e){let s=await tN(i);s?t.set(i,{sciname:s.sciname,commonName:s.commonName}):r.push(i)}if(r.length===0)return t;let n=100,o=[];for(let i=0;i<r.length;i+=n){let s=r.slice(i,i+n),a=s.join(",");try{let l=await(await fetch(`https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=taxonomy&id=${a}&retmode=xml`)).text(),A=new Map,u=/<Taxon>\s*<TaxId>(\d+)<\/TaxId>/g,d;for(;(d=u.exec(l))!==null;){let m=Number(d[1]),g=d.index,C=1,x=g+d[0].length;for(;C>0&&x<l.length;){let w=l.indexOf("<Taxon>",x),v=l.indexOf("</Taxon>",x);if(v===-1)break;w!==-1&&w<v?(C++,x=w+7):(C--,x=v+8)}let I=l.slice(g,x),h=A.get(m),y=I.includes("<LineageEx>"),b=h?.includes("<LineageEx>");(!h||y&&!b)&&A.set(m,I)}for(let m of s){let g=A.get(m);if(g){let C=/<GenbankCommonName>(.*?)<\/GenbankCommonName>/.exec(g),x=/<CommonName>(.*?)<\/CommonName>/.exec(g),I=/<ScientificName>(.*?)<\/ScientificName>/.exec(g),h=C?.[1]??x?.[1],y=I?.[1]??"";t.set(m,{sciname:y,commonName:h}),o.push({taxid:m,sciname:y,commonName:h})}else o.push({taxid:m,sciname:"",commonName:void 0})}}catch(c){console.error("Failed to fetch taxonomy data:",c)}}return o.length>0&&await rN(o),t}async function nQ({self:e}){let{baseUrl:t,blastDatabase:r,blastProgram:n,msaAlgorithm:o,proteinSequence:i,selectedTranscript:s,rid:a}=e.blastParams,c=aa(i),l,A;if(a){e.setRid(a);let I=await Gd({rid:a,baseUrl:t,onProgress:h=>{e.setProgress(h)}});l=I.hits,A=I.rid}else{let I=await eQ({query:c,blastDatabase:r,blastProgram:n,baseUrl:t,onProgress:h=>{e.setProgress(h)},onRid:h=>{e.setRid(h)}});l=I.hits,A=I.rid}e.setProgress("Fetching species taxonomy info...");let u=l.map(I=>I.description[0]?.taxid).filter(I=>I!==void 0),d=await rQ(u),m={},g=l.map(I=>{let h=I.description[0]??{accession:"unknown",id:"unknown",sciname:"unknown"},y=KS(h,d),b=XS(I.hsps[0]?.hseq??"");return m[y]=nN(h,d),`>${y}
-${b}`}),C=await ZS({algorithm:o,sequence:[`>QUERY
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oN="jbrowse-msaview-data",iN=1,Ms="msa-data";async function Ud(){return Gn(oN,iN,{upgrade(e){e.objectStoreNames.contains(Ms)||e.createObjectStore(Ms,{keyPath:"id"}).createIndex("timestamp","timestamp",{unique:!1})}})}function iQ(){return`msa-${Date.now()}-${Math.random().toString(36).slice(2,11)}`}async function sQ(e,t){try{let r=await Ud(),n={id:e,msa:t.msa,tree:t.tree,treeMetadata:t.treeMetadata,timestamp:Date.now()};return await r.put(Ms,n),!0}catch(r){return console.warn("Failed to store MSA data:",r),!1}}async function aQ(e){try{let r=await(await Ud()).get(Ms,e);return r?{msa:r.msa,tree:r.tree,treeMetadata:r.treeMetadata}:void 0}catch(t){console.warn("Failed to retrieve MSA data:",t);return}}async function cQ(e=10080*60*1e3){try{let t=await Ud(),r=Date.now()-e,i=await t.transaction(Ms,"readwrite").store.index("timestamp").openCursor(IDBKeyRange.upperBound(r)),s=0;for(;i;)await i.delete(),s++,i=await i.continue();return s}catch(t){return console.warn("Failed to cleanup old MSA data:",t),0}}Ss();function lQ(e){return typeof e=="object"&&e!==null&&"hoverFeature"in e&&"hoverPosition"in e}function AQ(e){return/AF-([A-Z0-9]+)-F\d+/.exec(e)?.[1]}function uQ(e){let{dataStoreId:t,rows:r}=e;t&&r.length===0&&(async()=>{try{e.setLoadingStoredData(!0);let n=await aQ(t);n&&(n.msa&&e.setMSA(n.msa),n.tree&&e.setTree(n.tree))}catch(n){console.error("Failed to load MSA data from IndexedDB:",n)}finally{e.setLoadingStoredData(!1)}})()}function fQ(e){let{rows:t,dataStoreId:r}=e;if(t.length>0&&!r){if(!!(e.msaFilehandle??e.treeFilehandle))return;let o=e.data.msa,i=e.data.tree;(o||i)&&(async()=>{try{let s=iQ();await sQ(s,{msa:o,tree:i,treeMetadata:e.data.treeMetadata})&&e.setDataStoreId(s)}catch(s){console.error("Failed to store MSA data to IndexedDB:",s)}})()}}function dQ(e){e.blastParams&&(async()=>{try{e.setProgress("Submitting query"),e.setError(void 0);let t=await nQ({self:e});e.setData(t),e.setBlastParams(void 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wQ(e,t){return xQ[e.toUpperCase()]?.[t.toUpperCase()]??-4}var aN=-10,cN=-.5;function lN(e,t,r=aN,n=cN){let o=e.length,i=t.length,s=[],a=[],c=[];for(let h=0;h<=o;h++){s[h]=[],a[h]=[],c[h]=[];for(let y=0;y<=i;y++)s[h][y]=-1/0,a[h][y]=-1/0,c[h][y]=-1/0}s[0][0]=0;for(let h=1;h<=o;h++)a[h][0]=r+(h-1)*n;for(let h=1;h<=i;h++)c[0][h]=r+(h-1)*n;for(let h=1;h<=o;h++)for(let y=1;y<=i;y++){let b=wQ(e[h-1],t[y-1]);s[h][y]=Math.max(s[h-1][y-1],a[h-1][y-1],c[h-1][y-1])+b,a[h][y]=Math.max(s[h-1][y]+r,a[h-1][y]+n),c[h][y]=Math.max(s[h][y-1]+r,c[h][y-1]+n)}let l="",A="",u=o,d=i,m=s[o][i],g=a[o][i],C=c[o][i],x=Math.max(m,g,C),I=x===m?"M":x===g?"Ix":"Iy";for(;u>0||d>0;)if(I==="M"&&u>0&&d>0){l=e[u-1]+l,A=t[d-1]+A;let h=wQ(e[u-1],t[d-1]),y=s[u-1][d-1],b=a[u-1][d-1],w=s[u][d];w===y+h?I="M":w===b+h?I="Ix":I="Iy",u--,d--}else if(I==="Ix"&&u>0){l=e[u-1]+l,A="-"+A;let h=a[u][d],y=s[u-1][d]+r;I=h===y?"M":"Ix",u--}else if(d>0){l="-"+l,A=t[d-1]+A;let h=c[u][d],y=s[u][d-1]+r;I=h===y?"M":"Iy",d--}else 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ye.types.compose(DQ.BaseViewModel,gl(),ye.types.model("MsaView",{connectedViewId:ye.types.maybe(ye.types.string),connectedFeature:ye.types.frozen(),connectedHighlights:ye.types.array(ye.types.model({refName:ye.types.string,start:ye.types.number,end:ye.types.number})),blastParams:ye.types.frozen(),querySeqName:"QUERY",uniprotId:ye.types.maybe(ye.types.string),zoomToBaseLevel:!1,init:ye.types.frozen(),connectedStructures:ye.types.array(ye.types.frozen()),dataStoreId:ye.types.maybe(ye.types.string),mafRegion:ye.types.frozen()})).volatile(()=>({rid:void 0,progress:"",error:void 0,loadingStoredData:!1})).views(e=>({getRowByName(t){return e.rows.find(r=>r[0]===t)},getSequenceByRowName(t){return e.rows.find(r=>r[0]===t)?.[1]}})).views(e=>({get transcriptToMsaMap(){return e.connectedFeature?$h(e.connectedFeature):void 0},get processing(){return!!e.progress},get connectedView(){let{views:t}=(0,Bi.getSession)(e);return t.find(r=>r.id===e.connectedViewId)},get connectedProteinViews(){let{views:t}=(0,Bi.getSession)(e),r=t,n=[];for(let o of e.connectedStructures){let i=r.find(s=>Dn(s)&&s.id===o.proteinViewId);i&&n.push({...o,proteinView:i})}return n}})).views(e=>({get structureHoverCol(){for(let t of e.connectedProteinViews){let n=t.proteinView.structures[t.structureIdx]?.hoverPosition?.structureSeqPos;if(n!==void 0){let o=t.structureToMsa[n];if(o!==void 0){let i=e.getSequenceByRowName(t.msaRowName);if(i){let s=oQ(i,o);if(s!==void 0)return e.globalColToVisibleCol(s)}}}}}})).views(e=>({get mouseCol2(){let t=e.structureHoverCol;return t!==void 0?t:yQ({model:e})},get clickCol2(){}})).actions(e=>({setZoomToBaseLevel(t){e.zoomToBaseLevel=t},setError(t){e.error=t},setProgress(t){e.progress=t},setRid(t){e.rid=t},setConnectedHighlights(t){e.connectedHighlights=(0,ye.cast)(t)},addToConnectedHighlights(t){e.connectedHighlights.push(t)},clearConnectedHighlights(){e.connectedHighlights=(0,ye.cast)([])},setBlastParams(t){e.blastParams=t},setInit(t){e.init=t},setQuerySeqName(t){e.querySeqName=t},setUniprotId(t){e.uniprotId=t},setDataStoreId(t){e.dataStoreId=t},setMafRegion(t){e.mafRegion=t},setLoadingStoredData(t){e.loadingStoredData=t},handleMsaClick(t){let{connectedView:r,zoomToBaseLevel:n}=e,{assemblyManager:o}=(0,Bi.getSession)(e),i=Qs({model:e,coord:t});if(!(!i||!r))if(n)r.navTo(i);else{let s=o.get(r.assemblyNames[0])?.getCanonicalRefName(i.refName)??i.refName;r.centerAt(i.start,s)}},connectToStructure(t,r,n){let o=n??e.querySeqName,i=e.getSequenceByRowName(o);if(!i)throw new Error(`MSA row "${o}" not found`);let s=i.replaceAll("-",""),{views:a}=(0,Bi.getSession)(e),c=a.find(C=>Dn(C)&&C.id===t);if(!c)throw new Error(`ProteinView "${t}" not found`);let l=c.structures[r];if(!l)throw new Error(`Structure at index ${r} not found`);let A=l.structureSequences?.[0];if(!A)throw new Error("Structure sequence not available");let u=bQ(s,A),{seq1ToSeq2:d,seq2ToSeq1:m}=BQ(u),g={proteinViewId:t,structureIdx:r,msaRowName:o,msaToStructure:Hd(d),structureToMsa:Hd(m)};e.connectedStructures.push(g)},disconnectFromStructure(t,r){let n=e.connectedStructures.findIndex(o=>o.proteinViewId===t&&o.structureIdx===r);n!==-1&&e.connectedStructures.splice(n,1)},disconnectAllStructures(){e.connectedStructures.clear()}})).actions(e=>{let t=e.setMouseClickPos.bind(e);return{setMouseClickPos(r,n){t(r,n),r!==void 0&&e.handleMsaClick(r)}}}).views(e=>({extraViewMenuItems(){return[{label:"Zoom to base level on click?",checked:e.zoomToBaseLevel,type:"checkbox",onClick:()=>{e.setZoomToBaseLevel(!e.zoomToBaseLevel)}},{label:"Connect to protein structure...",onClick:()=>{(0,Bi.getSession)(e).queueDialog(t=>[mN,{model:e,handleClose:t}])}},...e.connectedStructures.length>0?[{label:"Disconnect from protein structures",onClick:()=>{e.disconnectAllStructures()}}]:[]]}})).actions(e=>({afterCreate(){EQ();for(let t of[uQ,fQ,dQ,mQ,gQ,pQ,hQ,CQ])(0,ye.addDisposer)(e,(0,kQ.autorun)(()=>{t(e)}))}}))}var xN=(0,WQ.lazy)(()=>Promise.resolve().then(()=>(YQ(),VQ)));function Wd(e){e.addViewType(()=>new zQ.default({name:"MsaView",stateModel:jd(),ReactComponent:xN}))}var $Q="2.3.8";var yl=class extends KQ.default{constructor(){super(...arguments);this.name="MsaViewPlugin";this.version=$Q;this.rootConfigurationSchema=r=>({msa:(0,zd.ConfigurationSchema)("MSA",{datasets:$d.types.maybe($d.types.array((0,zd.ConfigurationSchema)("MSAEntry",{datasetId:{type:"string",defaultValue:""},description:{type:"string",defaultValue:""},name:{type:"string",defaultValue:""},adapter:r.pluggableConfigSchemaType("adapter")})))})})}install(r){Wd(r),tu(r),ru(r),Nl(r),Zl(r)}configure(r){(0,XQ.isAbstractMenuManager)(r.rootModel)&&r.rootModel.appendToSubMenu(["Add"],{label:"Multiple sequence alignment view",icon:Em,onClick:n=>{n.addView("MsaView",{})}})}};return u1(wN);})();
+`);if(a===-1)continue;let c=s.slice(a+1).replaceAll(/\s/g,"");c&&r.push(c)}if(r.length<2)return!1;let n=!1,o=-1,i=!0;for(let s of r){let a=0;for(let c=0;c<s.length;c++){let l=s.charCodeAt(c);Ci(l)?n=!0:(l>=pB&&l<=hB||l===CB)&&a++}o===-1?o=a:a!==o&&(i=!1)}return n&&i}expandA3M(t,r){let n=r.length;if(n===0)return{};let o=[],i=[];for(let l=0;l<n;l++){let A=t[l],u=[],d=[],m=0;for(;m<A.length;){let p=A.charCodeAt(m);if(p>=pB&&p<=hB||p===CB){u.push(A[m]);let C="",x=m+1;for(;x<A.length;){let I=A.charCodeAt(x);if(Ci(I)||I===EB)C+=A[x],x++;else break}d.push(C),m=x}else if(p===EB)m++;else if(Ci(p)){let C="";for(;m<A.length&&Ci(A.charCodeAt(m));)C+=A[m],m++;u.push(""),d.push(C)}else m++}o.push(u),i.push(d)}let s=Math.max(...o.map(l=>l.length),0),a=new Array(s).fill(0);for(let l=0;l<n;l++){let A=i[l];for(let u=0;u<A.length;u++){let d=0;for(let m of A[u])Ci(m.charCodeAt(0))&&d++;d>a[u]&&(a[u]=d)}}let c={};for(let l=0;l<n;l++){let A=o[l],u=i[l],d=[];for(let m=0;m<s;m++){let p=a[m];if(m<A.length){let C=A[m],x=u[m]||"";d.push(C||"-");let I="";for(let y of x)Ci(y.charCodeAt(0))&&(I+=y.toUpperCase());d.push(I);let h=p-I.length;h>0&&d.push(".".repeat(h))}else d.push("-"),p>0&&d.push(".".repeat(p))}c[r[l]]=d.join("")}return c}getMSA(){return this.MSA}getNames(){return this.orderedNames}getRow(t){return this.MSA.seqdata[t]||""}getWidth(){let t=Object.keys(this.MSA.seqdata)[0];return t?this.getRow(t).length:0}}});function JD(e){let t=/\(?(\d+(\.\d+)+)\)?/.exec(e);return t&&t.length>1?t[1]:""}function xB(e){let t=["CLUSTAL","PROBCONS","MUSCLE","MSAPROBS","Kalign"];t.some(n=>e.startsWith(n))||console.warn(`${e} is not a known CLUSTAL header: ${t.join(",")}, proceeding but could indicate an issue`);let r=JD(e);return{info:e,version:r}}function rl(e){let t=e.next();for(;!t.done&&t.value.trim()==="";)t=e.next();return t.value}function VD(e){let t=e.split(/\s+/),r=e.slice(t[0].length),n=t[0].length+r.indexOf(t[1]),o=n+t[1].length;return[n,o]}function IB(e){let t=rl(e),r=[],n="";if(!t)return;for(;t;)t.startsWith(" ")?n=t:r.push(t),t=e.next().value;let[o,i]=VD(r[0]),a=r.map(u=>u.split(/\s+/)).map(u=>u[0]),c=r.map(u=>u.slice(o,i)),l=n.slice(o,i),A=c[0].length-l.length;return A&&(l+=" ".repeat(A)),{ids:a,seqs:c,consensus:l}}function yB(e){let t,r=IB(e);if(r!==void 0)for(;t=IB(e);){for(let n=0;n<t.seqs.length;n++)r.seqs[n]+=t.seqs[n];r.consensus+=t.consensus}return r}var td=g(()=>{});var wB=g(()=>{td()});function YD(e){let t=rl(e);if(!t)throw new Error("Empty file received");let r=xB(t),n=yB(e);if(n===void 0)throw new Error("No blocks parsed");let o=n.seqs.map((s,a)=>({id:n.ids[a],seq:s})),{consensus:i}=n;if(i.length!==o[0].seq.length)throw new Error(`Consensus length != sequence length. Con ${i.length} seq ${o[0].seq.length}`);return{consensus:i,alns:o,header:r}}function bB(e){let t=e.split(`
+`)[Symbol.iterator]();return YD(t)}var BB=g(()=>{wB();td()});var no,rd=g(()=>{BB();hi();no=class extends jt{MSA;constructor(t){super(),this.MSA=bB(t)}getMSA(){return this.MSA}getRow(t){return this.MSA.alns.find(r=>r.id===t)?.seq||""}getWidth(){return this.MSA.alns[0].seq.length}getHeader(){return this.MSA.header}getNames(){return this.MSA.alns.map(t=>t.id)}get seqConsensus(){return this.MSA.consensus}}});function SB(e){let t=e.split(`
+`).map(i=>i.trim()).filter(i=>!!i),r=[],n=[];for(let i of t)if(i.startsWith("SEQ"))r.push(i);else{if(i.startsWith("DATA"))continue;if(i.startsWith("//"))break;n.push(i)}let o=r.map(i=>{let[,s,a,c,l,A,u,d,m]=i.split(" ");return{species:s,protein:a,chr:c,start:+l,end:+A,strand:+u,geneId:d,unknown:m,seq:""}});for(let i of n)for(let s=0;s<r.length;s++)o[s].seq+=i[s];return o}function nl(e){let t=e.split(`
+`).map(i=>i.trim()).filter(i=>!!i),r=[],n="";for(let i of t)if(i.startsWith("SEQ"))r.push(i);else{if(i.startsWith("DATA"))continue;if(i.startsWith("//"))break;n=i}let o=r.map(i=>{let[,s,a,c,l,A,u,d,m]=i.split(" ");return{species:s,protein:a,chr:c,start:+l,end:+A,strand:+u,geneId:d,unknown:m}});return{tree:n,seqs:o}}var nd=g(()=>{});var oo,od=g(()=>{nd();hi();oo=class extends jt{MSA;constructor(t){super(),this.MSA=SB(t)}getMSA(){return this.MSA}getRow(t){return this.MSA.find(r=>r.protein===t)?.seq||""}getWidth(){return this.MSA[0].seq.length}getHeader(){return""}getNames(){return this.MSA.map(t=>t.protein)}}});var io,id=g(()=>{hi();io=class extends jt{MSA;constructor(t){super();let r={},n={};for(let o of t.split(">")){if(!/\S/.test(o))continue;let i=o.indexOf(`
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Expected 1 or -1.`);if(!r)throw new Error("refName is required");let n=e.subfeatures?.filter(c=>c.type==="CDS")??[],o=new Set,i=n.filter(c=>{if(c.start>=c.end)return!1;let l=`${c.start}-${c.end}`;return o.has(l)?!1:(o.add(l),!0)}).sort((c,l)=>t*(c.start-l.start)),s={},a={};if(i.length!==0){let l=(3-(i[0]?.phase??0))%3,A=-1;for(let u of i)for(let d of Z2(u,t)){let m=Math.floor(l++/3);s[d]=m,m!==A&&(a[m]=d,A=m)}}return{g2p:s,p2g:a,refName:r,strand:t}}var wQ=f(zr());Nd();var Rd=f(ie());function HS(e,t){let r=e.sciname.replaceAll(" ","_");if(e.taxid&&t?.has(e.taxid)){let n=t.get(e.taxid);n.commonName&&(r=n.commonName.split(" ").map(o=>o.charAt(0).toUpperCase()+o.slice(1).toLowerCase()).join("_"))}return`${e.accession}-${r}`}function US(e){return e.replaceAll("-","")}async function qS(e,t){let r=await fetch(e,t);if(!r.ok)throw new Error(`HTTP ${r.status} fetching ${e} ${await r.text()}`);return r}async function Mn(e,t){return(await qS(e,t)).text()}async function jS(e,t){return(await qS(e,t)).json()}function ul(e){return new Promise(t=>setTimeout(t,e))}var fl="https://www.ebi.ac.uk/Tools/services/rest",Lk={clustalo:{params:{email:"colin.diesh@gmail.com"},msaResult:"aln-clustal_num",treeResult:"phylotree"},muscle:{params:{email:"colin.diesh@gmail.com",format:"clw",tree:"tree1"},msaResult:"fa",treeResult:"phylotree"},kalign:{params:{email:"colin.diesh@gmail.com",stype:"protein"},msaResult:"fa",treeResult:"phylotree"},mafft:{params:{email:"colin.diesh@gmail.com",stype:"protein"},msaResult:"fa",treeResult:"phylotree"}};async function Fk({onProgress:e,jobId:t,algorithm:r}){for(;;){for(let o=0;o<10;o++)await ul(1e3),e(`Re-checking MSA status in... ${10-o}`);let n=await Mn(`${fl}/${r}/status/${t}`);if(n==="FINISHED")break;if(n.includes("FAILURE"))throw new Error(`Failed to run: jobId ${t}`)}}async function JS({algorithm:e,sequence:t,onProgress:r}){let n=Lk[e];r(`Launching ${e} MSA...`);let o=await Mn(`${fl}/${e}/run`,{method:"POST",body:new URLSearchParams({...n.params,sequence:t})});return await Fk({jobId:o,algorithm:e,onProgress:r}),{msa:await Mn(`${fl}/${e}/result/${o}/${n.msaResult}`),tree:await Mn(`${fl}/${e}/result/${o}/${n.treeResult}`)}}async function Ld({rid:e,baseUrl:t,onProgress:r}){r(`Checking BLAST status for RID: ${e}...`),await Pk({rid:e,onProgress:r,baseUrl:t});let n=await jS(`${t}?CMD=Get&RID=${e}&FORMAT_TYPE=JSON2_S&FORMAT_OBJECT=Alignment`);return{rid:e,hits:n.BlastOutput2[0]?.report.results.search.hits??[]}}async function VS({query:e,blastDatabase:t,blastProgram:r,baseUrl:n,onProgress:o,onRid:i}){o("Submitting to NCBI BLAST...");let{rid:s}=await Rk({query:e,blastDatabase:t,blastProgram:r,baseUrl:n});return i(s),Ld({rid:s,baseUrl:n,onProgress:o})}async function Rk({query:e,blastProgram:t,blastDatabase:r,baseUrl:n}){let o=await Mn(n,{method:"POST",body:new URLSearchParams({CMD:"Put",PROGRAM:t==="quick-blastp"?"blastp":t,DATABASE:r,QUERY:e,...r==="nr_cluster_seq"?{CLUSTERED_DB:"on",DB_TYPE:"Experimental Databases"}:{},...t==="quick-blastp"?{BLAST_PROGRAMS:"kmerBlastp"}:{}})}),i=/^ {4}RID = (.*$)/m.exec(o)?.[1],s=/^ {4}RTOE = (.*$)/m.exec(o)?.[1];if(!i)throw new Error("Failed to get RID from BLAST request");return{rid:i,rtoe:s}}async function Pk({rid:e,onProgress:t,baseUrl:r}){for(;;){for(let c=0;c<20;c++)await ul(1e3),t(`Re-checking BLAST status in... ${20-c}`);let o=await Mn(`${r}?CMD=Get&FORMAT_OBJECT=SearchInfo&RID=${e}`),s=/\s+Status=(\S+)/m.exec(o)?.[1],a=/\s+ThereAreHits=yes/m.test(o);if(s!=="WAITING"){if(s==="FAILED")throw new Error(`BLAST ${e} failed`);if(s==="READY"){if(a)return!0;throw new Error("No hits found")}throw new Error(`BLAST ${e} returned unexpected status: ${s??"unknown"}`)}}}_i();var Ok="jbrowse-msaview-taxonomy-cache",xs="common-names",Gk=2;async function YS(){return Rn(Ok,Gk,{upgrade(e){e.objectStoreNames.contains(xs)&&e.deleteObjectStore(xs),e.createObjectStore(xs,{keyPath:"taxid"})}})}async function Hk(e){let r=(await YS()).transaction(xs,"readonly"),n=await Promise.all(e.map(o=>r.store.get(o)));return await r.done,n}async function Uk(e){let r=(await YS()).transaction(xs,"readwrite");for(let n of e)await r.store.put(n);await r.done}async function WS(e){let t=new Map,r=[],n=await Hk(e);for(let s=0;s<e.length;s++){let a=e[s],c=n[s];c?t.set(a,{sciname:c.sciname,commonName:c.commonName}):r.push(a)}if(r.length===0)return t;let o=100,i=[];for(let s=0;s<r.length;s+=o){let a=r.slice(s,s+o),c=a.join(",");try{let A=await(await fetch(`https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=taxonomy&id=${c}&retmode=xml`)).text(),u=new Map,d=/<Taxon>\s*<TaxId>(\d+)<\/TaxId>/g,m;for(;(m=d.exec(A))!==null;){let p=Number(m[1]),C=m.index,x=1,I=C+m[0].length;for(;x>0&&I<A.length;){let v=A.indexOf("<Taxon>",I),M=A.indexOf("</Taxon>",I);if(M===-1)break;v!==-1&&v<M?(x++,I=v+7):(x--,I=M+8)}let h=A.slice(C,I),y=u.get(p),w=h.includes("<LineageEx>"),S=y?.includes("<LineageEx>");(!y||w&&!S)&&u.set(p,h)}for(let p of a){let C=u.get(p);if(C){let x=/<GenbankCommonName>(.*?)<\/GenbankCommonName>/.exec(C),I=/<CommonName>(.*?)<\/CommonName>/.exec(C),h=/<ScientificName>(.*?)<\/ScientificName>/.exec(C),y=x?.[1]??I?.[1],w=h?.[1]??"";t.set(p,{sciname:w,commonName:y}),i.push({taxid:p,sciname:w,commonName:y})}}}catch(l){console.error("Failed to fetch taxonomy data:",l)}}return i.length>0&&await Uk(i),t}async function zS({self:e}){let{baseUrl:t,blastDatabase:r,blastProgram:n,msaAlgorithm:o,proteinSequence:i,selectedTranscript:s,rid:a}=e.blastParams,c=Vs(i),l,A;if(a){e.setRid(a);let I=await Ld({rid:a,baseUrl:t,onProgress:h=>{e.setProgress(h)}});l=I.hits,A=I.rid}else{let I=await VS({query:c,blastDatabase:r,blastProgram:n,baseUrl:t,onProgress:h=>{e.setProgress(h)},onRid:h=>{e.setRid(h)}});l=I.hits,A=I.rid}e.setProgress("Fetching species taxonomy info...");let u=l.map(I=>I.description[0]?.taxid).filter(I=>I!==void 0),d=await WS(u),m={},p=l.map(I=>{let h=I.description[0]??{accession:"unknown",id:"unknown",sciname:"unknown"},y=HS(h,d),w=US(I.hsps[0]?.hseq??"");return m[y]=qk(h,d),`>${y}
+${w}`}),C=await JS({algorithm:o,sequence:[`>QUERY
+${c}`,...p].join(`
+`),onProgress:I=>{e.setProgress(I)}}),x=JSON.stringify(m);return await ap({proteinSequence:c,blastDatabase:r,blastProgram:n,msaAlgorithm:o,msa:C.msa,tree:C.tree,treeMetadata:x,rid:A,geneId:s?.get("parentId"),transcriptId:s?.id(),transcriptName:s?.get("name")??s?.get("id"),geneName:s?.get("gene_name")??s?.get("parentId")}),{...C,treeMetadata:x}}function qk(e,t){let r={},n=e.taxid?t.get(e.taxid):void 0;return n?.sciname&&(r["Scientific name"]=n.sciname),n?.commonName&&(r["Common name"]=n.commonName),e.accession&&(r.Accession=e.accession),e.id&&(r.ID=e.id),e.title&&(r.Description=e.title),r}ys();function ws({model:e,coord:t}){let{querySeqName:r,transcriptToMsaMap:n,mafRegion:o}=e,s=e.rows.find(c=>c[0]===r)?.[1];if(!s)return;let a=dl(s,t);if(a!==void 0){if(o){let c=o.start+a;return c>=o.end?void 0:{refName:o.refName,start:c,end:c+1}}if(n){let{refName:c,p2g:l}=n,A=l[a],u=l[a+1];return A!==void 0&&u!==void 0?{refName:c,start:Math.min(A,u),end:Math.max(A,u)}:void 0}}}_i();var Jk="jbrowse-msaview-data",Vk=1,bs="msa-data";async function Fd(){return Rn(Jk,Vk,{upgrade(e){e.objectStoreNames.contains(bs)||e.createObjectStore(bs,{keyPath:"id"}).createIndex("timestamp","timestamp",{unique:!1})}})}function KS(){return`msa-${Date.now()}-${Math.random().toString(36).slice(2,11)}`}async function XS(e,t){try{let r=await Fd(),n={id:e,msa:t.msa,tree:t.tree,treeMetadata:t.treeMetadata,timestamp:Date.now()};return await r.put(bs,n),!0}catch(r){return console.warn("Failed to store MSA data:",r),!1}}async function ZS(e){try{let r=await(await Fd()).get(bs,e);return r?{msa:r.msa,tree:r.tree,treeMetadata:r.treeMetadata}:void 0}catch(t){console.warn("Failed to retrieve MSA data:",t);return}}async function eQ(e=10080*60*1e3){try{let t=await Fd(),r=Date.now()-e,i=await t.transaction(bs,"readwrite").store.index("timestamp").openCursor(IDBKeyRange.upperBound(r)),s=0;for(;i;)await i.delete(),s++,i=await i.continue();return s}catch(t){return console.warn("Failed to cleanup old MSA data:",t),0}}ys();function tQ(e){let{dataStoreId:t,rows:r}=e;t&&r.length===0&&(async()=>{try{e.setLoadingStoredData(!0);let n=await ZS(t);n&&(n.msa&&e.setMSA(n.msa),n.tree&&e.setTree(n.tree))}catch(n){console.error("Failed to load MSA data from IndexedDB:",n)}finally{e.setLoadingStoredData(!1)}})()}function rQ(e){let{rows:t,dataStoreId:r,isStoringData:n}=e;if(t.length>0&&!r&&!n){if(e.msaFilehandle||e.treeFilehandle)return;let o=e.data.msa,i=e.data.tree;(o||i)&&(e.setIsStoringData(!0),(async()=>{try{let s=KS();await XS(s,{msa:o,tree:i,treeMetadata:e.data.treeMetadata})&&e.setDataStoreId(s)}catch(s){console.error("Failed to store MSA data to IndexedDB:",s)}finally{e.setIsStoringData(!1)}})())}}function nQ(e){e.blastParams&&(async()=>{try{e.setProgress("Submitting query"),e.setError(void 0);let t=await zS({self:e});e.setData(t),e.setBlastParams(void 0)}catch(t){e.setError(t),console.error(t)}finally{e.setProgress("")}})()}function oQ(e){let{init:t}=e;t&&(async()=>{try{e.setError(void 0);let{msaData:r,msaUrl:n,treeData:o,treeUrl:i,querySeqName:s}=t;if(n){let a=xm(n);a&&(e.setUniprotId(a),e.setQuerySeqName("query"))}if(s&&e.setQuerySeqName(s),r)e.setMSA(r);else if(n){let a=await fetch(n);if(!a.ok)throw new Error(`Failed to fetch MSA: ${a.status}`);let c=await a.text();e.setMSA(c)}if(o)e.setTree(o);else if(i){let a=await fetch(i);if(!a.ok)throw new Error(`Failed to fetch tree: ${a.status}`);let c=await a.text();e.setTree(c)}e.setInit(void 0)}catch(r){e.setError(r),console.error(r)}})()}function iQ(e){let{mouseCol:t,mouseClickCol:r}=e,n=t===void 0?void 0:ws({model:e,coord:t}),o=r===void 0?void 0:ws({model:e,coord:r});e.setConnectedHighlights([n,o].filter(i=>!!i))}function sQ(e){let{mouseCol:t,connectedProteinViews:r}=e;if(r.length!==0)for(let n of r){let o=n.proteinView.structures[n.structureIdx];if(!o)continue;if(t===void 0){o.clearHighlightFromExternal?.();continue}let i=e.getSequenceByRowName(n.msaRowName);if(!i)continue;let s=dl(i,t);if(s===void 0){o.clearHighlightFromExternal?.();continue}let a=n.msaToStructure[s];a===void 0?o.clearHighlightFromExternal?.():o.highlightFromExternal?.(a)}}function aQ(e){let{connectedViewId:t,uniprotId:r,rows:n,connectedStructures:o}=e;if(!(!r||n.length===0))for(let i of vn((0,Rd.getSession)(e).views))for(let s=0;s<i.structures.length;s++){let a=i.structures[s];if(!(!a||a.connectedViewId!==t||a.uniprotId!==r||o.some(l=>l.proteinViewId===i.id&&l.structureIdx===s))&&a.structureSequences?.[0])try{e.connectToStructure(i.id,s)}catch(l){console.error("Failed to auto-connect to ProteinView:",l)}}}function cQ(e){let{connectedViewId:t,transcriptToMsaMap:r,querySeqName:n}=e;if(!t||!r)return;let o=new Set;for(let s of vn((0,Rd.getSession)(e).views))for(let a of s.structures){if(a.connectedViewId!==t)continue;let c=a.hoverGenomeHighlights;if(!c||c.length===0)continue;let{g2p:l}=r;for(let A of c)for(let u=A.start;u<A.end;u++){let d=l[u];if(d!==void 0){let m=e.seqPosToGlobalCol(n,d);o.add(m)}}}let i=Array.from(o).map(s=>e.globalColToVisibleCol(s)).filter(s=>s!==void 0);e.setHighlightedColumns(i.length>0?i:void 0)}function lQ(){eQ().catch(e=>{console.error("Failed to cleanup old MSA data:",e)})}var AQ=f(ie());function uQ({model:e}){let{hovered:t}=(0,AQ.getSession)(e),{querySeqName:r,transcriptToMsaMap:n,connectedView:o,mafRegion:i}=e;if(!o?.initialized||!Im(t))return;let{coord:s,refName:a}=t.hoverPosition;if(i){if(a!==i.refName||!o.assemblyNames.includes(i.assemblyName)||s<i.start||s>=i.end)return;let l=s-i.start;return e.seqPosToVisibleCol(r,l)}if(n){let{g2p:c}=n,l=c[s];if(l!==void 0)return e.seqPosToVisibleCol(r,l)}}var 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dQ(e,t){return fQ[e.toUpperCase()]?.[t.toUpperCase()]??-4}var Wk=-10,zk=-.5;function $k(e,t,r=Wk,n=zk){let o=e.length,i=t.length,s=[],a=[],c=[];for(let h=0;h<=o;h++){s[h]=[],a[h]=[],c[h]=[];for(let y=0;y<=i;y++)s[h][y]=-1/0,a[h][y]=-1/0,c[h][y]=-1/0}s[0][0]=0;for(let h=1;h<=o;h++)a[h][0]=r+(h-1)*n;for(let h=1;h<=i;h++)c[0][h]=r+(h-1)*n;for(let h=1;h<=o;h++)for(let y=1;y<=i;y++){let w=dQ(e[h-1],t[y-1]);s[h][y]=Math.max(s[h-1][y-1],a[h-1][y-1],c[h-1][y-1])+w,a[h][y]=Math.max(s[h-1][y]+r,a[h-1][y]+n),c[h][y]=Math.max(s[h][y-1]+r,c[h][y-1]+n)}let l="",A="",u=o,d=i,m=s[o][i],p=a[o][i],C=c[o][i],x=Math.max(m,p,C),I=x===m?"M":x===p?"Ix":"Iy";for(;u>0||d>0;)if(I==="M"&&u>0&&d>0){l=e[u-1]+l,A=t[d-1]+A;let h=dQ(e[u-1],t[d-1]),y=s[u-1][d-1],w=a[u-1][d-1],S=s[u][d];S===y+h?I="M":S===w+h?I="Ix":I="Iy",u--,d--}else if(I==="Ix"&&u>0){l=e[u-1]+l,A="-"+A;let h=a[u][d],y=s[u-1][d]+r;I=h===y?"M":"Ix",u--}else if(d>0){l="-"+l,A=t[d-1]+A;let h=c[u][d],y=s[u][d-1]+r;I=h===y?"M":"Iy",d--}else break;return{alignedSeq1:l,alignedSeq2:A,score:x}}function Kk(e,t){let r="";for(let n=0;n<e.length;n++){let o=e[n],i=t[n];o==="-"||i==="-"?r+=" ":o.toUpperCase()===i.toUpperCase()?r+="|":r+=" "}return r}function mQ(e,t){let{alignedSeq1:r,alignedSeq2:n}=$k(e,t);return{consensus:Kk(r,n),alns:[{id:"msa",seq:r},{id:"structure",seq:n}]}}function gQ(e){let t=e.alns[0].seq,r=e.alns[1].seq;if(t.length!==r.length)throw new Error("Aligned sequences must have same length");let n=0,o=0,i=new Map,s=new Map;for(let a=0;a<t.length;a++){let c=t[a],l=r[a];c!=="-"&&l!=="-"?(i.set(n,o),s.set(o,n),n++,o++):c==="-"?o++:n++}return{seq1ToSeq2:i,seq2ToSeq1:s}}ys();var tN=(0,xQ.lazy)(()=>Promise.resolve().then(()=>(IQ(),EQ)));function Pd(){return xe.types.compose(yQ.BaseViewModel,Al(),xe.types.model("MsaView",{connectedViewId:xe.types.maybe(xe.types.string),connectedFeature:xe.types.frozen(),connectedHighlights:xe.types.array(xe.types.model({refName:xe.types.string,start:xe.types.number,end:xe.types.number})),blastParams:xe.types.frozen(),querySeqName:"QUERY",uniprotId:xe.types.maybe(xe.types.string),zoomToBaseLevel:!1,init:xe.types.frozen(),connectedStructures:xe.types.array(xe.types.frozen()),dataStoreId:xe.types.maybe(xe.types.string),mafRegion:xe.types.frozen()})).volatile(()=>({rid:void 0,progress:"",error:void 0,loadingStoredData:!1,isStoringData:!1})).views(e=>({getRowByName(t){return e.rows.find(r=>r[0]===t)},getSequenceByRowName(t){return e.rows.find(r=>r[0]===t)?.[1]}})).views(e=>({get transcriptToMsaMap(){return e.connectedFeature?Gh(e.connectedFeature):void 0},get connectedView(){let{views:t}=(0,xi.getSession)(e);return t.find(r=>r.id===e.connectedViewId)},get connectedProteinViews(){let t=vn((0,xi.getSession)(e).views),r=[];for(let n of e.connectedStructures){let o=t.find(i=>i.id===n.proteinViewId);o&&r.push({...n,proteinView:o})}return r}})).views(e=>({get structureHoverCol(){for(let t of e.connectedProteinViews){let n=t.proteinView.structures[t.structureIdx]?.hoverPosition?.structureSeqPos;if(n!==void 0){let o=t.structureToMsa[n];if(o!==void 0){let i=e.getSequenceByRowName(t.msaRowName);if(i){let s=$S(i,o);if(s!==void 0)return e.globalColToVisibleCol(s)}}}}}})).views(e=>({get mouseCol2(){let t=e.structureHoverCol;return t!==void 0?t:uQ({model:e})}})).actions(e=>({setZoomToBaseLevel(t){e.zoomToBaseLevel=t},setError(t){e.error=t},setProgress(t){e.progress=t},setRid(t){e.rid=t},setConnectedHighlights(t){e.connectedHighlights=(0,xe.cast)(t)},addToConnectedHighlights(t){e.connectedHighlights.push(t)},clearConnectedHighlights(){e.connectedHighlights=(0,xe.cast)([])},setBlastParams(t){e.blastParams=t},setInit(t){e.init=t},setQuerySeqName(t){e.querySeqName=t},setUniprotId(t){e.uniprotId=t},setDataStoreId(t){e.dataStoreId=t},setMafRegion(t){e.mafRegion=t},setLoadingStoredData(t){e.loadingStoredData=t},setIsStoringData(t){e.isStoringData=t},handleMsaClick(t){let{connectedView:r,zoomToBaseLevel:n}=e,{assemblyManager:o}=(0,xi.getSession)(e),i=ws({model:e,coord:t});if(!(!i||!r))if(n)r.navTo(i);else{let s=Ls({assemblyManager:o,assemblyNames:r.assemblyNames,refName:i.refName});r.centerAt(i.start,s)}},connectToStructure(t,r,n){let o=n??e.querySeqName,i=e.getSequenceByRowName(o);if(!i)throw new Error(`MSA row "${o}" not found`);let s=i.replaceAll("-",""),a=vn((0,xi.getSession)(e).views).find(p=>p.id===t);if(!a)throw new Error(`ProteinView "${t}" not found`);let c=a.structures[r];if(!c)throw new Error(`Structure at index ${r} not found`);let l=c.structureSequences?.[0];if(!l)throw new Error("Structure sequence not available");let A=mQ(s,l),{seq1ToSeq2:u,seq2ToSeq1:d}=gQ(A),m={proteinViewId:t,structureIdx:r,msaRowName:o,msaToStructure:Object.fromEntries(u),structureToMsa:Object.fromEntries(d)};e.connectedStructures.push(m)},disconnectFromStructure(t,r){let n=e.connectedStructures.findIndex(o=>o.proteinViewId===t&&o.structureIdx===r);n!==-1&&e.connectedStructures.splice(n,1)},disconnectAllStructures(){e.connectedStructures.clear()}})).actions(e=>{let t=e.setMouseClickPos.bind(e);return{setMouseClickPos(r,n){t(r,n),r!==void 0&&e.handleMsaClick(r)}}}).views(e=>({extraViewMenuItems(){return[{label:"Zoom to base level on click?",checked:e.zoomToBaseLevel,type:"checkbox",onClick:()=>{e.setZoomToBaseLevel(!e.zoomToBaseLevel)}},{label:"Connect to protein structure...",onClick:()=>{(0,xi.getSession)(e).queueDialog(t=>[tN,{model:e,handleClose:t}])}},...e.connectedStructures.length>0?[{label:"Disconnect from protein structures",onClick:()=>{e.disconnectAllStructures()}}]:[]]}})).actions(e=>({afterCreate(){lQ();for(let t of[tQ,rQ,nQ,oQ,iQ,sQ,aQ,cQ])(0,xe.addDisposer)(e,(0,wQ.autorun)(()=>{t(e)}))}}))}var lN=(0,PQ.lazy)(()=>Promise.resolve().then(()=>(RQ(),FQ)));function Ud(e){e.addViewType(()=>new OQ.default({name:"MsaView",stateModel:Pd(),ReactComponent:lN}))}var GQ="2.4.1";var hl=class extends HQ.default{constructor(){super(...arguments);this.name="MsaViewPlugin";this.version=GQ;this.rootConfigurationSchema=r=>({msa:(0,qd.ConfigurationSchema)("MSA",{datasets:jd.types.maybe(jd.types.array((0,qd.ConfigurationSchema)("MSAEntry",{datasetId:{type:"string",defaultValue:""},description:{type:"string",defaultValue:""},name:{type:"string",defaultValue:""},adapter:r.pluggableConfigSchemaType("adapter")})))})})}install(r){Ud(r),$A(r),KA(r),Tl(r),zl(r)}configure(r){(0,UQ.isAbstractMenuManager)(r.rootModel)&&r.rootModel.appendToSubMenu(["Add"],{label:"Multiple sequence alignment view",icon:dm,onClick:n=>{n.addView("MsaView",{})}})}};return t1(AN);})();
 /*! Bundled license information:
 use-sync-external-store/cjs/use-sync-external-store-shim.production.js: