npm - jbrowse-plugin-msaview - Versions diffs - 2.3.3 → 2.3.8 - Mend

jbrowse-plugin-msaview 2.3.3 → 2.3.8

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Files changed (76) hide show

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

@@ -1,13 +1,13 @@
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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],h=g.source===null?null:A.at(g.source);h!==null&&(h=D.computeSourceURL(a,h,u)),c({source:h,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=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,Lu.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};ic.SourceMapConsumer=he;function ot(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=ei.fromArray(i.map(String),!0),this._sources=ei.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}ot.prototype=Object.create(he.prototype);ot.prototype.consumer=he;ot.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};ot.fromSourceMap=function(t,r){var n=Object.create(ot.prototype),o=n._names=ei.fromArray(t._names.toArray(),!0),i=n._sources=ei.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 rE;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 ji(n.__originalMappings,D.compareByOriginalPositions),n};ot.prototype._version=3;Object.defineProperty(ot.prototype,"sources",{get:function(){return this._absoluteSources.slice()}});function rE(){this.generatedLine=0,this.generatedColumn=0,this.source=null,this.originalLine=null,this.originalColumn=null,this.name=null}var Nu=D.compareByGeneratedPositionsDeflatedNoLine;function tE(e,t){let r=e.length,n=e.length-t;if(!(n<=1))if(n==2){let o=e[t],i=e[t+1];Nu(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(Nu(s,a)<=0)break;e[i-1]=a,e[i]=s}else ji(e,Nu,t)}ot.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=[],h,I,C,x,y;let b=0;for(;A<l;)if(t.charAt(A)===";")n++,A++,o=0,tE(g,b),b=g.length;else if(t.charAt(A)===",")A++;else{for(h=new rE,h.generatedLine=n,x=A;x<l&&!this._charIsMappingSeparator(t,x);x++);for(I=t.slice(A,x),C=[];A<x;)ev.decode(t,A,d),y=d.value,A=d.rest,C.push(y);if(C.length===2)throw new Error("Found a source, but no line and column");if(C.length===3)throw new Error("Found a source and line, but no column");if(h.generatedColumn=o+C[0],o=h.generatedColumn,C.length>1&&(h.source=a+C[1],a+=C[1],h.originalLine=i+C[2],i=h.originalLine,h.originalLine+=1,h.originalColumn=s+C[3],s=h.originalColumn,C.length>4&&(h.name=c+C[4],c+=C[4])),g.push(h),typeof h.originalLine=="number"){let v=h.source;for(;m.length<=v;)m.push(null);m[v]===null&&(m[v]=[]),m[v].push(h)}}tE(g,b),this.__generatedMappings=g;for(var S=0;S<m.length;S++)m[S]!=null&&ji(m[S],D.compareByOriginalPositionsNoSource);this.__originalMappings=[].concat(...m)};ot.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 Lu.search(t,r,i,s)};ot.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}};ot.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}};ot.prototype.hasContentsOfAllSources=function(){return this.sourcesContent?this.sourcesContent.length>=this._sources.size()&&!this.sourcesContent.some(function(t){return t==null}):!1};ot.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.')};ot.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}};ic.BasicSourceMapConsumer=ot;function hr(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 ei,this._names=new ei;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)}})}hr.prototype=Object.create(he.prototype);hr.prototype.constructor=he;hr.prototype._version=3;Object.defineProperty(hr.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}});hr.prototype.originalPositionFor=function(t){var r={generatedLine:D.getArg(t,"line"),generatedColumn:D.getArg(t,"column")},n=Lu.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}};hr.prototype.hasContentsOfAllSources=function(){return this._sections.every(function(t){return t.consumer.hasContentsOfAllSources()})};hr.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.')};hr.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 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}};hr.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=D.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)}ji(this.__generatedMappings,D.compareByGeneratedPositionsDeflated),ji(this.__originalMappings,D.compareByOriginalPositions)};ic.IndexedSourceMapConsumer=hr});var iE=H(oE=>{var tv=Du().SourceMapGenerator,sc=Zo(),rv=/(\r?\n)/,nv=10,ti="$$$isSourceNode$$$";function Rt(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[ti]=!0,n!=null&&this.add(n)}Rt.fromStringWithSourceMap=function(t,r,n){var o=new Rt,i=t.split(rv),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=sc.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?sc.join(n,d.source):d.source;o.add(new Rt(d.originalLine,d.originalColumn,g,m,d.name))}}};Rt.prototype.add=function(t){if(Array.isArray(t))t.forEach(function(r){this.add(r)},this);else if(t[ti]||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};Rt.prototype.prepend=function(t){if(Array.isArray(t))for(var r=t.length-1;r>=0;r--)this.prepend(t[r]);else if(t[ti]||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};Rt.prototype.walk=function(t){for(var r,n=0,o=this.children.length;n<o;n++)r=this.children[n],r[ti]?r.walk(t):r!==""&&t(r,{source:this.source,line:this.line,column:this.column,name:this.name})};Rt.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};Rt.prototype.replaceRight=function(t,r){var n=this.children[this.children.length-1];return n[ti]?n.replaceRight(t,r):typeof n=="string"?this.children[this.children.length-1]=n.replace(t,r):this.children.push("".replace(t,r)),this};Rt.prototype.setSourceContent=function(t,r){this.sourceContents[sc.toSetString(t)]=r};Rt.prototype.walkSourceContents=function(t){for(var r=0,n=this.children.length;r<n;r++)this.children[r][ti]&&this.children[r].walkSourceContents(t);for(var o=Object.keys(this.sourceContents),r=0,n=o.length;r<n;r++)t(sc.fromSetString(o[r]),this.sourceContents[o[r]])};Rt.prototype.toString=function(){var t="";return this.walk(function(r){t+=r}),t};Rt.prototype.toStringWithSourceMap=function(t){var r={code:"",line:1,column:0},n=new tv(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)===nv?(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}};oE.SourceNode=Rt});var sE=H(ac=>{ac.SourceMapGenerator=Du().SourceMapGenerator;ac.SourceMapConsumer=nE().SourceMapConsumer;ac.SourceNode=iE().SourceNode});function lc(e){let{children:t,...r}=e;return(0,cc.jsxs)(aE.Link,{...r,target:"_blank",rel:"noopener noreferrer",children:[t," ",(0,cc.jsx)(pa,{fontSize:"small"})]})}var cc,aE,cE=p(()=>{cc=f(L(),1);CA();aE=f(k(),1)});function Fu({text:e,extra:t}){let{classes:r}=ov(),n=t?`supporting data: ${JSON.stringify(t,null,2)}`:"",o=[e,n].filter(Boolean).join(`
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Hu.call(this._set,r)};on.prototype.indexOf=function(t){if(zn){var r=this._set.get(t);if(r>=0)return r}else{var n=Gu.toSetString(t);if(Hu.call(this._set,n))return this._set[n]}throw new Error('"'+t+'" is not in the set.')};on.prototype.at=function(t){if(t>=0&&t<this._array.length)return this._array[t];throw new Error("No element indexed by "+t)};on.prototype.toArray=function(){return this._array.slice()};sE.ArraySet=on});var lE=U(cE=>{var aE=ti();function xv(e,t){var r=e.generatedLine,n=t.generatedLine,o=e.generatedColumn,i=t.generatedColumn;return n>r||n==r&&i>=o||aE.compareByGeneratedPositionsInflated(e,t)<=0}function lc(){this._array=[],this._sorted=!0,this._last={generatedLine:-1,generatedColumn:0}}lc.prototype.unsortedForEach=function(t,r){this._array.forEach(t,r)};lc.prototype.add=function(t){xv(this._last,t)?(this._last=t,this._array.push(t)):(this._sorted=!1,this._array.push(t))};lc.prototype.toArray=function(){return this._sorted||(this._array.sort(aE.compareByGeneratedPositionsInflated),this._sorted=!0),this._array};cE.MappingList=lc});var qu=U(AE=>{var zi=Pu(),Ne=ti(),Ac=Uu().ArraySet,wv=lE().MappingList;function sr(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 Ac,this._names=new Ac,this._mappings=new wv,this._sourcesContents=null}sr.prototype._version=3;sr.fromSourceMap=function(t,r){var n=t.sourceRoot,o=new sr(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};sr.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}))};sr.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))};sr.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 Ac,a=new Ac;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)};sr.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)}};sr.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,g=d.length;m<g;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+=zi.encode(l.generatedColumn-t),t=l.generatedColumn,l.source!=null&&(u=this._sources.indexOf(l.source),c+=zi.encode(u-s),s=u,c+=zi.encode(l.originalLine-1-o),o=l.originalLine-1,c+=zi.encode(l.originalColumn-n),n=l.originalColumn,l.name!=null&&(A=this._names.indexOf(l.name),c+=zi.encode(A-i),i=A)),a+=c}return a};sr.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)};sr.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};sr.prototype.toString=function(){return JSON.stringify(this.toJSON())};AE.SourceMapGenerator=sr});var uE=U($n=>{$n.GREATEST_LOWER_BOUND=1;$n.LEAST_UPPER_BOUND=2;function ju(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?ju(s,t,r,n,o,i):i==$n.LEAST_UPPER_BOUND?t<n.length?t:-1:s:s-e>1?ju(e,s,r,n,o,i):i==$n.LEAST_UPPER_BOUND?s:e<0?-1:e}$n.search=function(t,r,n,o){if(r.length===0)return-1;var i=ju(-1,r.length,t,r,n,o||$n.GREATEST_LOWER_BOUND);if(i<0)return-1;for(;i-1>=0&&n(r[i],r[i-1],!0)===0;)--i;return i}});var mE=U(dE=>{function bv(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 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 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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-------------------------------------
-`,qB=`CLUSTAL O(1.2.4) multiple sequence alignment
+`,cB=`CLUSTAL O(1.2.4) multiple sequence alignment
 sp|P69905|HBA_HUMAN       MVLSPADKTNVKAAWGKVGAHAGEYGAEALERMFLSFPTTKTYFPHFDLSHGSAQVKGHG	60
@@ -57,23 +57,23 @@ 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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pl="https://www.ebi.ac.uk/Tools/services/rest",zk={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 $k({onProgress:e,jobId:t,algorithm:r}){for(;;){for(let o=0;o<10;o++)await oa(1e3),e(`Re-checking MSA status in... ${10-o}`);let n=await Cr(`${pl}/${r}/status/${t}`);if(n==="FINISHED")break;if(n.includes("FAILURE"))throw new Error(`Failed to run: jobId ${t}`)}}async function ZS({algorithm:e,sequence:t,onProgress:r}){let n=zk[e];if(!n)throw new Error(`unknown algorithm: ${e}`);r(`Launching ${e} MSA...`);let o=await Cr(`${pl}/${e}/run`,{method:"POST",body:new URLSearchParams({...n.params,sequence:t})});return await 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C=/<GenbankCommonName>(.*?)<\/GenbankCommonName>/.exec(g),x=/<CommonName>(.*?)<\/CommonName>/.exec(g),I=/<ScientificName>(.*?)<\/ScientificName>/.exec(g),h=C?.[1]??x?.[1],y=I?.[1]??"";t.set(m,{sciname:y,commonName:h}),o.push({taxid:m,sciname:y,commonName:h})}else o.push({taxid:m,sciname:"",commonName:void 0})}}catch(c){console.error("Failed to fetch taxonomy data:",c)}}return o.length>0&&await rN(o),t}async function nQ({self:e}){let{baseUrl:t,blastDatabase:r,blastProgram:n,msaAlgorithm:o,proteinSequence:i,selectedTranscript:s,rid:a}=e.blastParams,c=aa(i),l,A;if(a){e.setRid(a);let I=await Gd({rid:a,baseUrl:t,onProgress:h=>{e.setProgress(h)}});l=I.hits,A=I.rid}else{let I=await eQ({query:c,blastDatabase:r,blastProgram:n,baseUrl:t,onProgress:h=>{e.setProgress(h)},onRid:h=>{e.setRid(h)}});l=I.hits,A=I.rid}e.setProgress("Fetching species taxonomy info...");let u=l.map(I=>I.description[0]?.taxid).filter(I=>I!==void 0),d=await rQ(u),m={},g=l.map(I=>{let 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0){if(o){let c=o.start+a;return c>=o.end?void 0:{refName:o.refName,start:c,end:c+1}}if(n){let{refName:c,p2g:l}=n,A=l[a],u=l[a+1];return A!==void 0&&u!==void 0?{refName:c,start:Math.min(A,u),end:Math.max(A,u)}:void 0}}}Di();var vk="jbrowse-msaview-data",Tk=1,ys="msa-data";async function Dd(){return Rn(vk,Tk,{upgrade(e){e.objectStoreNames.contains(ys)||e.createObjectStore(ys,{keyPath:"id"}).createIndex("timestamp","timestamp",{unique:!1})}})}function JS(){return`msa-${Date.now()}-${Math.random().toString(36).slice(2,11)}`}async function HS(e,t){try{let r=await Dd(),n={id:e,msa:t.msa,tree:t.tree,treeMetadata:t.treeMetadata,timestamp:Date.now()};return await r.put(ys,n),!0}catch(r){return console.warn("Failed to store MSA data:",r),!1}}async function US(e){try{let r=await(await Dd()).get(ys,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 qS(e=10080*60*1e3){try{let t=await Dd(),r=Date.now()-e,i=await t.transaction(ys,"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}}function YS(e){return typeof e=="object"&&e!==null&&"hoverFeature"in e&&"hoverPosition"in e}function jS(e){return/AF-([A-Z0-9]+)-F\d+/.exec(e)?.[1]}function VS(e){let{dataStoreId:t,rows:r}=e;t&&r.length===0&&(async()=>{try{e.setLoadingStoredData(!0);let n=await US(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 WS(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=JS();await HS(s,{msa:o,tree:i,treeMetadata:e.data.treeMetadata})&&e.setDataStoreId(s)}catch(s){console.error("Failed to store MSA data to 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0:xs({model:e,coord:r});e.setConnectedHighlights([n,o].filter(i=>!!i))}function XS(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=ul(i,t);if(s===void 0){o.clearHighlightFromExternal?.();continue}let a=n.msaToStructure[s];a===void 0?o.clearHighlightFromExternal?.():o.highlightFromExternal?.(a)}}function ZS(e){let{views:t}=(0,kd.getSession)(e),{connectedViewId:r,uniprotId:n,rows:o,connectedStructures:i}=e;if(!(!n||o.length===0))for(let s of t){let a=s;if(!(a.type!=="ProteinView"||!a.structures))for(let c=0;c<a.structures.length;c++){let l=a.structures[c];if(!(l.connectedViewId!==r||l.uniprotId!==n||i.some(u=>u.proteinViewId===a.id&&u.structureIdx===c))&&l.structureSequences?.[0])try{e.connectToStructure(a.id,c)}catch(u){console.error("Failed to auto-connect to 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iQ(e,t){let r=e.toUpperCase(),n=t.toUpperCase();return oQ[r]?.[n]??-4}var Dk=-10,kk=-.5;function Nk(e,t,r=Dk,n=kk){let o=e.length,i=t.length,s=[],a=[],c=[];for(let I=0;I<=o;I++){s[I]=[],a[I]=[],c[I]=[];for(let C=0;C<=i;C++)s[I][C]=-1/0,a[I][C]=-1/0,c[I][C]=-1/0}s[0][0]=0;for(let I=1;I<=o;I++)a[I][0]=r+(I-1)*n;for(let I=1;I<=i;I++)c[0][I]=r+(I-1)*n;for(let I=1;I<=o;I++)for(let C=1;C<=i;C++){let x=iQ(e[I-1],t[C-1]);s[I][C]=Math.max(s[I-1][C-1],a[I-1][C-1],c[I-1][C-1])+x,a[I][C]=Math.max(s[I-1][C]+r,a[I-1][C]+n),c[I][C]=Math.max(s[I][C-1]+r,c[I][C-1]+n)}let l="",A="",u=o,d=i,m=[s[o][i],a[o][i],c[o][i]],g=Math.max(...m),h=g===s[o][i]?"M":g===a[o][i]?"Ix":"Iy";for(;u>0||d>0;)if(h==="M"&&u>0&&d>0){l=e[u-1]+l,A=t[d-1]+A;let I=iQ(e[u-1],t[d-1]),C=s[u-1][d-1],x=a[u-1][d-1];s[u][d]===C+I?h="M":s[u][d]===x+I?h="Ix":h="Iy",u--,d--}else if(h==="Ix"&&u>0)l=e[u-1]+l,A="-"+A,h=a[u][d]===s[u-1][d]+r?"M":"Ix",u--;else if(d>0)l="-"+l,A=t[d-1]+A,h=c[u][d]===s[u][d-1]+r?"M":"Iy",d--;else break;return{alignedSeq1:l,alignedSeq2:A,score:g}}function Lk(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 sQ(e,t){let{alignedSeq1:r,alignedSeq2:n}=Nk(e,t);return{consensus:Lk(r,n),alns:[{id:"msa",seq:r},{id:"structure",seq:n}]}}function aQ(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}}var Pk=(0,dQ.lazy)(()=>Promise.resolve().then(()=>(fQ(),uQ)));function Nd(){return Ie.types.compose(mQ.BaseViewModel,ll(),Ie.types.model("MsaView",{connectedViewId:Ie.types.maybe(Ie.types.string),connectedFeature:Ie.types.frozen(),connectedHighlights:Ie.types.array(Ie.types.model({refName:Ie.types.string,start:Ie.types.number,end:Ie.types.number})),blastParams:Ie.types.frozen(),querySeqName:"QUERY",uniprotId:Ie.types.maybe(Ie.types.string),zoomToBaseLevel:!1,init:Ie.types.frozen(),connectedStructures:Ie.types.array(Ie.types.frozen()),dataStoreId:Ie.types.maybe(Ie.types.string),mafRegion:Ie.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?Fh(e.connectedFeature):void 0},get processing(){return!!e.progress},get connectedView(){let{views:t}=(0,Ii.getSession)(e);return t.find(r=>r.id===e.connectedViewId)},get connectedProteinViews(){let{views:t}=(0,Ii.getSession)(e);return e.connectedStructures.map(r=>{let n=t.find(o=>o.id===r.proteinViewId);return n?{...r,proteinView:n}:void 0}).filter(r=>!!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=GS(i,o);if(s!==void 0)return e.globalColToVisibleCol(s)}}}}}})).views(e=>({get mouseCol2(){let t=e.structureHoverCol;return t!==void 0?t:nQ({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,Ie.cast)(t)},addToConnectedHighlights(t){e.connectedHighlights.push(t)},clearConnectedHighlights(){e.connectedHighlights=(0,Ie.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,Ii.getSession)(e),i=xs({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,Ii.getSession)(e),c=a.find(h=>h.id===t);if(!c)throw new Error(`ProteinView "${t}" not found`);let l=c.structures?.[r];if(!l)throw new Error(`Structure at index ${r} not found`);let A=l.structureSequences?.[0];if(!A)throw new Error("Structure sequence not available");let u=sQ(s,A),{seq1ToSeq2:d,seq2ToSeq1:m}=aQ(u),g={proteinViewId:t,structureIdx:r,msaRowName:o,msaToStructure:_d(d),structureToMsa:_d(m)};e.connectedStructures.push(g)},disconnectFromStructure(t,r){let n=e.connectedStructures.findIndex(o=>o.proteinViewId===t&&o.structureIdx===r);n!==-1&&e.connectedStructures.splice(n,1)},disconnectAllStructures(){e.connectedStructures.clear()}})).actions(e=>{let t=e.setMouseClickPos.bind(e);return{setMouseClickPos(r,n){t(r,n),r!==void 0&&e.handleMsaClick(r)}}}).views(e=>({extraViewMenuItems(){return[{label:"Zoom to base level on click?",checked:e.zoomToBaseLevel,type:"checkbox",onClick:()=>{e.setZoomToBaseLevel(!e.zoomToBaseLevel)}},{label:"Connect to protein structure...",onClick:()=>{(0,Ii.getSession)(e).queueDialog(t=>[Pk,{model:e,handleClose:t}])}},...e.connectedStructures.length>0?[{label:"Disconnect from protein structures",onClick:()=>{e.disconnectAllStructures()}}]:[]]}})).actions(e=>({afterCreate(){tQ();for(let t of[VS,WS,zS,$S,KS,XS,ZS,eQ])(0,Ie.addDisposer)(e,(0,gQ.autorun)(()=>{t(e)}))}}))}var Yk=(0,QQ.lazy)(()=>Promise.resolve().then(()=>(SQ(),bQ)));function Pd(e){e.addViewType(()=>new MQ.default({name:"MsaView",stateModel:Nd(),ReactComponent:Yk}))}var vQ="2.3.3";var dl=class extends TQ.default{constructor(){super(...arguments);this.name="MsaViewPlugin";this.version=vQ;this.rootConfigurationSchema=r=>({msa:(0,Od.ConfigurationSchema)("MSA",{datasets:Gd.types.maybe(Gd.types.array((0,Od.ConfigurationSchema)("MSAEntry",{datasetId:{type:"string",defaultValue:""},description:{type:"string",defaultValue:""},name:{type:"string",defaultValue:""},adapter:r.pluggableConfigSchemaType("adapter")})))})})}install(r){Pd(r),qA(r),YA(r),wl(r),Hl(r)}configure(r){(0,_Q.isAbstractMenuManager)(r.rootModel)&&r.rootModel.appendToSubMenu(["Add"],{label:"Multiple sequence alignment view",icon:lm,onClick:n=>{n.addView("MsaView",{})}})}};return qQ(jk);})();
+`),onProgress:I=>{e.setProgress(I)}}),x=JSON.stringify(m);return await Cp({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 nN(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}Ss();function Qs({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=hl(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}}}Fi();var 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 break;return{alignedSeq1:l,alignedSeq2:A,score:x}}function AN(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 bQ(e,t){let{alignedSeq1:r,alignedSeq2:n}=lN(e,t);return{consensus:AN(r,n),alns:[{id:"msa",seq:r},{id:"structure",seq:n}]}}function BQ(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}}Ss();var mN=(0,_Q.lazy)(()=>Promise.resolve().then(()=>(TQ(),vQ)));function jd(){return 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);})();
 /*! Bundled license information:
 use-sync-external-store/cjs/use-sync-external-store-shim.production.js:
@@ -107,6 +107,6 @@ escape-html/index.js:
    *)
 dompurify/dist/purify.es.mjs:
-  (*! @license DOMPurify 3.3.3 | (c) Cure53 and other contributors | Released under the Apache license 2.0 and Mozilla Public License 2.0 | github.com/cure53/DOMPurify/blob/3.3.3/LICENSE *)
+  (*! @license DOMPurify 3.4.2 | (c) Cure53 and other contributors | Released under the Apache license 2.0 and Mozilla Public License 2.0 | github.com/cure53/DOMPurify/blob/3.4.2/LICENSE *)
 */
 //# sourceMappingURL=jbrowse-plugin-msaview.umd.production.min.js.map