npm - jbrowse-plugin-msaview - Versions diffs - 2.2.7 → 2.2.11 - Mend

jbrowse-plugin-msaview 2.2.7 → 2.2.11

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Files changed (65) hide show

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

@@ -1,13 +1,13 @@
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f=l+1;n(o,i,s,f-1),n(o,i,f+1,a)}}return n}function kv(e){let t=Dv.toString();return new Function(`return ${t}`)()(e)}var JC=new WeakMap;UC.quickSort=function(e,t,r=0){let n=JC.get(t);n===void 0&&(n=kv(t),JC.set(t,n)),n(e,t,r,e.length-1)}});var VC=O(Wa=>{var k=qo(),xu=HC(),jo=hu().ArraySet,Nv=du(),Ji=YC().quickSort;function he(e,t){var r=e;return typeof e=="string"&&(r=k.parseSourceMapInput(e)),r.sections!=null?new dr(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,f=0,m=s.length;f<m;f++){var g=s[f],h=g.source===null?null:A.at(g.source);h!==null&&(h=k.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=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,xu.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};Wa.SourceMapConsumer=he;function it(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=jo.fromArray(i.map(String),!0),this._sources=jo.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}it.prototype=Object.create(he.prototype);it.prototype.consumer=he;it.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};it.fromSourceMap=function(t,r){var n=Object.create(it.prototype),o=n._names=jo.fromArray(t._names.toArray(),!0),i=n._sources=jo.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],f=new jC;f.generatedLine=u.generatedLine,f.generatedColumn=u.generatedColumn,u.source&&(f.source=i.indexOf(u.source),f.originalLine=u.originalLine,f.originalColumn=u.originalColumn,u.name&&(f.name=o.indexOf(u.name)),c.push(f)),a.push(f)}return Ji(n.__originalMappings,k.compareByOriginalPositions),n};it.prototype._version=3;Object.defineProperty(it.prototype,"sources",{get:function(){return this._absoluteSources.slice()}});function jC(){this.generatedLine=0,this.generatedColumn=0,this.source=null,this.originalLine=null,this.originalColumn=null,this.name=null}var Iu=k.compareByGeneratedPositionsDeflatedNoLine;function qC(e,t){let r=e.length,n=e.length-t;if(!(n<=1))if(n==2){let o=e[t],i=e[t+1];Iu(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(Iu(s,a)<=0)break;e[i-1]=a,e[i]=s}else Ji(e,Iu,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={},f={},m=[],g=[],h,C,E,x,y;let w=0;for(;A<l;)if(t.charAt(A)===";")n++,A++,o=0,qC(g,w),w=g.length;else if(t.charAt(A)===",")A++;else{for(h=new jC,h.generatedLine=n,x=A;x<l&&!this._charIsMappingSeparator(t,x);x++);for(C=t.slice(A,x),E=[];A<x;)Nv.decode(t,A,f),y=f.value,A=f.rest,E.push(y);if(E.length===2)throw new Error("Found a source, but no line and column");if(E.length===3)throw new Error("Found a source and line, but no column");if(h.generatedColumn=o+E[0],o=h.generatedColumn,E.length>1&&(h.source=a+E[1],a+=E[1],h.originalLine=i+E[2],i=h.originalLine,h.originalLine+=1,h.originalColumn=s+E[3],s=h.originalColumn,E.length>4&&(h.name=c+E[4],c+=E[4])),g.push(h),typeof h.originalLine=="number"){let M=h.source;for(;m.length<=M;)m.push(null);m[M]===null&&(m[M]=[]),m[M].push(h)}}qC(g,w),this.__generatedMappings=g;for(var b=0;b<m.length;b++)m[b]!=null&&Ji(m[b],k.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 xu.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: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}};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=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.')};it.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}};Wa.BasicSourceMapConsumer=it;function dr(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 jo,this._names=new jo;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)}})}dr.prototype=Object.create(he.prototype);dr.prototype.constructor=he;dr.prototype._version=3;Object.defineProperty(dr.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}});dr.prototype.originalPositionFor=function(t){var r={generatedLine:k.getArg(t,"line"),generatedColumn:k.getArg(t,"column")},n=xu.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}};dr.prototype.hasContentsOfAllSources=function(){return this._sections.every(function(t){return t.consumer.hasContentsOfAllSources()})};dr.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.')};dr.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}};dr.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)}Ji(this.__generatedMappings,k.compareByGeneratedPositionsDeflated),Ji(this.__originalMappings,k.compareByOriginalPositions)};Wa.IndexedSourceMapConsumer=dr});var KC=O(WC=>{var Lv=Cu().SourceMapGenerator,Ka=qo(),Fv=/(\r?\n)/,Rv=10,Vo="$$$isSourceNode$$$";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[Vo]=!0,n!=null&&this.add(n)}Rt.fromStringWithSourceMap=function(t,r,n){var o=new Rt,i=t.split(Fv),s=0,a=function(){var f=g(),m=g()||"";return f+m;function g(){return s<i.length?i[s++]:void 0}},c=1,l=0,A=null;return r.eachMapping(function(f){if(A!==null)if(c<f.generatedLine)u(A,a()),c++,l=0;else{var m=i[s]||"",g=m.substr(0,f.generatedColumn-l);i[s]=m.substr(f.generatedColumn-l),l=f.generatedColumn,u(A,g),A=f;return}for(;c<f.generatedLine;)o.add(a()),c++;if(l<f.generatedColumn){var m=i[s]||"";o.add(m.substr(0,f.generatedColumn)),i[s]=m.substr(f.generatedColumn),l=f.generatedColumn}A=f},this),s<i.length&&(A&&u(A,a()),o.add(i.splice(s).join(""))),r.sources.forEach(function(f){var m=r.sourceContentFor(f);m!=null&&(n!=null&&(f=Ka.join(n,f)),o.setSourceContent(f,m))}),o;function u(f,m){if(f===null||f.source===void 0)o.add(m);else{var g=n?Ka.join(n,f.source):f.source;o.add(new Rt(f.originalLine,f.originalColumn,g,m,f.name))}}};Rt.prototype.add=function(t){if(Array.isArray(t))t.forEach(function(r){this.add(r)},this);else if(t[Vo]||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[Vo]||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[Vo]?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[Vo]?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[Ka.toSetString(t)]=r};Rt.prototype.walkSourceContents=function(t){for(var r=0,n=this.children.length;r<n;r++)this.children[r][Vo]&&this.children[r].walkSourceContents(t);for(var o=Object.keys(this.sourceContents),r=0,n=o.length;r<n;r++)t(Ka.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 Lv(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,f=l.length;u<f;u++)l.charCodeAt(u)===Rv?(r.line++,r.column=0,u+1===f?(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}};WC.SourceNode=Rt});var zC=O(za=>{za.SourceMapGenerator=Cu().SourceMapGenerator;za.SourceMapConsumer=VC().SourceMapConsumer;za.SourceNode=KC().SourceNode});function Xa(e){let{children:t,...r}=e;return(0,$a.jsxs)($C.Link,{...r,target:"_blank",rel:"noopener noreferrer",children:[t," ",(0,$a.jsx)(oa,{fontSize:"small"})]})}var $a,$C,XC=p(()=>{$a=d(F(),1);oA();$C=d(N(),1)});function yu({text:e,extra:t}){let{classes:r}=Pv(),n=t?`supporting data: ${JSON.stringify(t,null,2)}`:"",o=[e,n].filter(Boolean).join(`
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Jv(e){return YC(e)?e.slice(1):e}$e.fromSetString=JC?UC:Jv;function YC(e){if(!e)return!1;var t=e.length;if(t<9||e.charCodeAt(t-1)!==95||e.charCodeAt(t-2)!==95||e.charCodeAt(t-3)!==111||e.charCodeAt(t-4)!==116||e.charCodeAt(t-5)!==111||e.charCodeAt(t-6)!==114||e.charCodeAt(t-7)!==112||e.charCodeAt(t-8)!==95||e.charCodeAt(t-9)!==95)return!1;for(var r=t-10;r>=0;r--)if(e.charCodeAt(r)!==36)return!1;return!0}function Uv(e,t,r){var n=Zr(e.source,t.source);return n!==0||(n=e.originalLine-t.originalLine,n!==0)||(n=e.originalColumn-t.originalColumn,n!==0||r)||(n=e.generatedColumn-t.generatedColumn,n!==0)||(n=e.generatedLine-t.generatedLine,n!==0)?n:Zr(e.name,t.name)}$e.compareByOriginalPositions=Uv;function Yv(e,t,r){var n;return n=e.originalLine-t.originalLine,n!==0||(n=e.originalColumn-t.originalColumn,n!==0||r)||(n=e.generatedColumn-t.generatedColumn,n!==0)||(n=e.generatedLine-t.generatedLine,n!==0)?n:Zr(e.name,t.name)}$e.compareByOriginalPositionsNoSource=Yv;function qv(e,t,r){var n=e.generatedLine-t.generatedLine;return n!==0||(n=e.generatedColumn-t.generatedColumn,n!==0||r)||(n=Zr(e.source,t.source),n!==0)||(n=e.originalLine-t.originalLine,n!==0)||(n=e.originalColumn-t.originalColumn,n!==0)?n:Zr(e.name,t.name)}$e.compareByGeneratedPositionsDeflated=qv;function jv(e,t,r){var n=e.generatedColumn-t.generatedColumn;return n!==0||r||(n=Zr(e.source,t.source),n!==0)||(n=e.originalLine-t.originalLine,n!==0)||(n=e.originalColumn-t.originalColumn,n!==0)?n:Zr(e.name,t.name)}$e.compareByGeneratedPositionsDeflatedNoLine=jv;function Zr(e,t){return e===t?0:e===null?1:t===null?-1:e>t?1:-1}function Vv(e,t){var r=e.generatedLine-t.generatedLine;return r!==0||(r=e.generatedColumn-t.generatedColumn,r!==0)||(r=Zr(e.source,t.source),r!==0)||(r=e.originalLine-t.originalLine,r!==0)||(r=e.originalColumn-t.originalColumn,r!==0)?r:Zr(e.name,t.name)}$e.compareByGeneratedPositionsInflated=Vv;function Wv(e){return JSON.parse(e.replace(/^\)]}'[^\n]*\n/,""))}$e.parseSourceMapInput=Wv;function Kv(e,t,r){if(t=t||"",e&&(e[e.length-1]!=="/"&&t[0]!=="/"&&(e+="/"),t=e+t),r){var n=Hi(r);if(!n)throw new Error("sourceMapURL could not be parsed");if(n.path){var o=n.path.lastIndexOf("/");o>=0&&(n.path=n.path.substring(0,o+1))}t=HC(Ko(n),t)}return Eu(t)}$e.computeSourceURL=Kv});var yu=J(qC=>{var Iu=zo(),xu=Object.prototype.hasOwnProperty,Xn=typeof Map<"u";function en(){this._array=[],this._set=Xn?new Map:Object.create(null)}en.fromArray=function(t,r){for(var n=new en,o=0,i=t.length;o<i;o++)n.add(t[o],r);return n};en.prototype.size=function(){return Xn?this._set.size:Object.getOwnPropertyNames(this._set).length};en.prototype.add=function(t,r){var n=Xn?t:Iu.toSetString(t),o=Xn?this.has(t):xu.call(this._set,n),i=this._array.length;(!o||r)&&this._array.push(t),o||(Xn?this._set.set(t,i):this._set[n]=i)};en.prototype.has=function(t){if(Xn)return this._set.has(t);var r=Iu.toSetString(t);return xu.call(this._set,r)};en.prototype.indexOf=function(t){if(Xn){var r=this._set.get(t);if(r>=0)return r}else{var n=Iu.toSetString(t);if(xu.call(this._set,n))return this._set[n]}throw new Error('"'+t+'" is not in the set.')};en.prototype.at=function(t){if(t>=0&&t<this._array.length)return this._array[t];throw new Error("No element indexed by "+t)};en.prototype.toArray=function(){return this._array.slice()};qC.ArraySet=en});var WC=J(VC=>{var jC=zo();function zv(e,t){var r=e.generatedLine,n=t.generatedLine,o=e.generatedColumn,i=t.generatedColumn;return n>r||n==r&&i>=o||jC.compareByGeneratedPositionsInflated(e,t)<=0}function $a(){this._array=[],this._sorted=!0,this._last={generatedLine:-1,generatedColumn:0}}$a.prototype.unsortedForEach=function(t,r){this._array.forEach(t,r)};$a.prototype.add=function(t){zv(this._last,t)?(this._last=t,this._array.push(t)):(this._sorted=!1,this._array.push(t))};$a.prototype.toArray=function(){return this._sorted||(this._array.sort(jC.compareByGeneratedPositionsInflated),this._sorted=!0),this._array};VC.MappingList=$a});var wu=J(KC=>{var Ji=Cu(),ke=zo(),Xa=yu().ArraySet,$v=WC().MappingList;function ar(e){e||(e={}),this._file=ke.getArg(e,"file",null),this._sourceRoot=ke.getArg(e,"sourceRoot",null),this._skipValidation=ke.getArg(e,"skipValidation",!1),this._ignoreInvalidMapping=ke.getArg(e,"ignoreInvalidMapping",!1),this._sources=new Xa,this._names=new Xa,this._mappings=new $v,this._sourcesContents=null}ar.prototype._version=3;ar.fromSourceMap=function(t,r){var n=t.sourceRoot,o=new ar(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=ke.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=ke.relative(n,i)),o._sources.has(s)||o._sources.add(s);var a=t.sourceContentFor(i);a!=null&&o.setSourceContent(i,a)}),o};ar.prototype.addMapping=function(t){var r=ke.getArg(t,"generated"),n=ke.getArg(t,"original",null),o=ke.getArg(t,"source",null),i=ke.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}))};ar.prototype.setSourceContent=function(t,r){var n=t;this._sourceRoot!=null&&(n=ke.relative(this._sourceRoot,n)),r!=null?(this._sourcesContents||(this._sourcesContents=Object.create(null)),this._sourcesContents[ke.toSetString(n)]=r):this._sourcesContents&&(delete this._sourcesContents[ke.toSetString(n)],Object.keys(this._sourcesContents).length===0&&(this._sourcesContents=null))};ar.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=ke.relative(i,o));var s=new Xa,a=new Xa;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=ke.join(n,c.source)),i!=null&&(c.source=ke.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=ke.join(n,c)),i!=null&&(c=ke.relative(i,c)),this.setSourceContent(c,l))},this)};ar.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)}};ar.prototype._serializeMappings=function(){for(var t=0,r=1,n=0,o=0,i=0,s=0,a="",c,l,A,u,f=this._mappings.toArray(),m=0,p=f.length;m<p;m++){if(l=f[m],c="",l.generatedLine!==r)for(t=0;l.generatedLine!==r;)c+=";",r++;else if(m>0){if(!ke.compareByGeneratedPositionsInflated(l,f[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};ar.prototype._generateSourcesContent=function(t,r){return t.map(function(n){if(!this._sourcesContents)return null;r!=null&&(n=ke.relative(r,n));var o=ke.toSetString(n);return Object.prototype.hasOwnProperty.call(this._sourcesContents,o)?this._sourcesContents[o]:null},this)};ar.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};ar.prototype.toString=function(){return JSON.stringify(this.toJSON())};KC.SourceMapGenerator=ar});var zC=J(Zn=>{Zn.GREATEST_LOWER_BOUND=1;Zn.LEAST_UPPER_BOUND=2;function Bu(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?Bu(s,t,r,n,o,i):i==Zn.LEAST_UPPER_BOUND?t<n.length?t:-1:s:s-e>1?Bu(e,s,r,n,o,i):i==Zn.LEAST_UPPER_BOUND?s:e<0?-1:e}Zn.search=function(t,r,n,o){if(r.length===0)return-1;var i=Bu(-1,r.length,t,r,n,o||Zn.GREATEST_LOWER_BOUND);if(i<0)return-1;for(;i-1>=0&&n(r[i],r[i-1],!0)===0;)--i;return i}});var ZC=J(XC=>{function Xv(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 f=l+1;n(o,i,s,f-1),n(o,i,f+1,a)}}return n}function Zv(e){let t=Xv.toString();return new Function(`return ${t}`)()(e)}var $C=new WeakMap;XC.quickSort=function(e,t,r=0){let n=$C.get(t);n===void 0&&(n=Zv(t),$C.set(t,n)),n(e,t,r,e.length-1)}});var rE=J(Za=>{var k=zo(),Su=zC(),$o=yu().ArraySet,e2=Cu(),Ui=ZC().quickSort;function Ee(e,t){var r=e;return typeof e=="string"&&(r=k.parseSourceMapInput(e)),r.sections!=null?new xr(r,t):new at(r,t)}Ee.fromSourceMap=function(e,t){return at.fromSourceMap(e,t)};Ee.prototype._version=3;Ee.prototype.__generatedMappings=null;Object.defineProperty(Ee.prototype,"_generatedMappings",{configurable:!0,enumerable:!0,get:function(){return this.__generatedMappings||this._parseMappings(this._mappings,this.sourceRoot),this.__generatedMappings}});Ee.prototype.__originalMappings=null;Object.defineProperty(Ee.prototype,"_originalMappings",{configurable:!0,enumerable:!0,get:function(){return this.__originalMappings||this._parseMappings(this._mappings,this.sourceRoot),this.__originalMappings}});Ee.prototype._charIsMappingSeparator=function(t,r){var n=t.charAt(r);return n===";"||n===","};Ee.prototype._parseMappings=function(t,r){throw new Error("Subclasses must implement _parseMappings")};Ee.GENERATED_ORDER=1;Ee.ORIGINAL_ORDER=2;Ee.GREATEST_LOWER_BOUND=1;Ee.LEAST_UPPER_BOUND=2;Ee.prototype.eachMapping=function(t,r,n){var o=r||null,i=n||Ee.GENERATED_ORDER,s;switch(i){case Ee.GENERATED_ORDER:s=this._generatedMappings;break;case Ee.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,f=0,m=s.length;f<m;f++){var p=s[f],h=p.source===null?null:A.at(p.source);h!==null&&(h=k.computeSourceURL(a,h,u)),c({source:h,generatedLine:p.generatedLine,generatedColumn:p.generatedColumn,originalLine:p.originalLine,originalColumn:p.originalColumn,name:p.name===null?null:l.at(p.name)})}};Ee.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,Su.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};Za.SourceMapConsumer=Ee;function at(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=$o.fromArray(i.map(String),!0),this._sources=$o.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}at.prototype=Object.create(Ee.prototype);at.prototype.consumer=Ee;at.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};at.fromSourceMap=function(t,r){var n=Object.create(at.prototype),o=n._names=$o.fromArray(t._names.toArray(),!0),i=n._sources=$o.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],f=new tE;f.generatedLine=u.generatedLine,f.generatedColumn=u.generatedColumn,u.source&&(f.source=i.indexOf(u.source),f.originalLine=u.originalLine,f.originalColumn=u.originalColumn,u.name&&(f.name=o.indexOf(u.name)),c.push(f)),a.push(f)}return Ui(n.__originalMappings,k.compareByOriginalPositions),n};at.prototype._version=3;Object.defineProperty(at.prototype,"sources",{get:function(){return this._absoluteSources.slice()}});function tE(){this.generatedLine=0,this.generatedColumn=0,this.source=null,this.originalLine=null,this.originalColumn=null,this.name=null}var bu=k.compareByGeneratedPositionsDeflatedNoLine;function eE(e,t){let r=e.length,n=e.length-t;if(!(n<=1))if(n==2){let o=e[t],i=e[t+1];bu(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(bu(s,a)<=0)break;e[i-1]=a,e[i]=s}else Ui(e,bu,t)}at.prototype._parseMappings=function(t,r){var n=1,o=0,i=0,s=0,a=0,c=0,l=t.length,A=0,u={},f={},m=[],p=[],h,E,C,x,y;let w=0;for(;A<l;)if(t.charAt(A)===";")n++,A++,o=0,eE(p,w),w=p.length;else if(t.charAt(A)===",")A++;else{for(h=new tE,h.generatedLine=n,x=A;x<l&&!this._charIsMappingSeparator(t,x);x++);for(E=t.slice(A,x),C=[];A<x;)e2.decode(t,A,f),y=f.value,A=f.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])),p.push(h),typeof h.originalLine=="number"){let S=h.source;for(;m.length<=S;)m.push(null);m[S]===null&&(m[S]=[]),m[S].push(h)}}eE(p,w),this.__generatedMappings=p;for(var B=0;B<m.length;B++)m[B]!=null&&Ui(m[B],k.compareByOriginalPositionsNoSource);this.__originalMappings=[].concat(...m)};at.prototype._findMapping=function(t,r,n,o,i,s){if(t[n]<=0)throw new TypeError("Line 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 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-------------------------------------
-`,aB=`CLUSTAL O(1.2.4) multiple sequence alignment
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-`)[Symbol.iterator]();return pD(t)}var ob=p(()=>{rb();Of()});var Bn,Hf=p(()=>{ob();Bn=class{MSA;constructor(t){this.MSA=nb(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}getRowData(){}getHeader(){return this.MSA.header}getNames(){return this.MSA.alns.map(t=>t.id)}getStructures(){return{}}get alignmentNames(){return[]}getTree(){return{id:"root",name:"root",noTree:!0,children:this.getNames().map(t=>({id:t,name:t,children:[]}))}}get seqConsensus(){return this.MSA.consensus}get secondaryStructureConsensus(){}get tracks(){return[]}}});function ib(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,f,m]=i.split(" ");return{species:s,protein:a,chr:c,start:+l,end:+A,strand:+u,geneId:f,unknown:m,seq:""}});for(let i of n)for(let s=0;s<r.length;s++)o[s].seq+=i[s];return o}function Jc(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,f,m]=i.split(" ");return{species:s,protein:a,chr:c,start:+l,end:+A,strand:+u,geneId:f,unknown:m}});return{tree:n,seqs:o}}var Jf=p(()=>{});var bn,Uf=p(()=>{Jf();bn=class{MSA;constructor(t){this.MSA=ib(t)}getMSA(){return this.MSA}getRow(t){return this.MSA.find(r=>r.protein===t)?.seq||""}getWidth(){return this.MSA[0].seq.length}getRowData(){}getHeader(){return""}getNames(){return this.MSA.map(t=>t.protein)}getStructures(){return{}}get alignmentNames(){return[]}getTree(){return{id:"root",name:"root",noTree:!0,children:this.getNames().map(t=>({id:t,name:t,children:[]}))}}get seqConsensus(){}get secondaryStructureConsensus(){}get tracks(){return[]}}});var Sn,Yf=p(()=>{Sn=class{MSA;constructor(t){let r={};for(let n of t.split(">")){if(!/\S/.test(n))continue;let o=n.indexOf(`
-`);if(o===-1)continue;let i=n.slice(0,o),s=i.indexOf(" "),a=s===-1?i:i.slice(0,s);a&&(r[a]=n.slice(o+1).replaceAll(/\s/g,""))}this.MSA={seqdata:r}}getMSA(){return this.MSA}getRowData(){}getNames(){return Object.keys(this.MSA.seqdata)}getRow(t){return this.MSA.seqdata[t]||""}getWidth(){let t=Object.keys(this.MSA.seqdata)[0];return this.getRow(t).length}getStructures(){return{}}get alignmentNames(){return[]}getHeader(){return{}}getTree(){return{id:"root",name:"root",noTree:!0,children:this.getNames().map(t=>({id:t,children:[],name:t}))}}get seqConsensus(){}get secondaryStructureConsensus(){}get tracks(){return[]}}});function eo(e){let t=[],r={},n=e.split(/\s*(;|\(|\)|,|:)\s*/);for(let o=0;o<n.length;o++){let i=n[o],s={};switch(i){case"(":r.children=[s],t.push(r),r=s;break;case",":t.at(-1)?.children.push(s),r=s;break;case")":r=t.pop();break;case":":break;default:{let a=n[o-1];a===")"||a==="("||a===","?r.name=i:a===":"&&(r.length=Number.parseFloat(i))}}}return r}var qf=p(()=>{});function Ai(){return{gf:{},gc:{},gs:{},gr:{},seqname:[],seqdata:{}}}function ui(e){return sb.test(e)}function ab(e,t){let r=t??{},n=[],o=null,i=e.split(`
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hb({model:e,ctx:f,offsetX:o,contrastScheme:A,blockSizeXOverride:u,highResScaleFactorOverride:1}),ce.default.createElement("g",{transform:`translate(${s} 0)`},ce.default.createElement("defs",null,ce.default.createElement("clipPath",{id:l},ce.default.createElement("rect",{x:0,y:0,width:u,height:n}))),ce.default.createElement("g",{clipPath:`url(#${l})`,dangerouslySetInnerHTML:{__html:f.getSvg().innerHTML}}))}function ek({model:e,children:t}){let{minimapHeight:r,treeAreaWidth:n}=e;return ce.default.createElement(ce.default.Fragment,null,ce.default.createElement("g",{transform:`translate(${n} 0)`},ce.default.createElement(tS,{model:e})),ce.default.createElement("g",{transform:`translate(0 ${r})`},t))}function tk({width:e,height:t,children:r}){return ce.default.createElement("svg",{width:e,height:t,xmlns:"http://www.w3.org/2000/svg",xmlnsXlink:"http://www.w3.org/1999/xlink",viewBox:[0,0,e,t].toString()},r)}function rk({children:e}){return e}var ce,cS,lS,uS=p(()=>{ce=d(S(),1),cS=d(se(),1),lS=d(Yr(),1);rS();Mf();vf();qc();Rc();yn()});function nk(){return K.types.compose(kb(),Pb(),Fb(),K.types.model("MsaView",{id:ro.ElementId,showDomains:!1,hideGaps:!0,allowedGappyness:100,contrastLettering:!0,subFeatureRows:!1,type:K.types.literal("MsaView"),drawMsaLetters:!0,height:K.types.optional(K.types.number,550),rowHeight:16,scrollY:0,scrollX:0,colWidth:12,treeFilehandle:K.types.maybe(ro.FileLocation),msaFilehandle:K.types.maybe(ro.FileLocation),treeMetadataFilehandle:K.types.maybe(ro.FileLocation),gffFilehandle:K.types.maybe(ro.FileLocation),currentAlignment:0,collapsed:K.types.array(K.types.string),collapsedLeaves:K.types.array(K.types.string),showOnly:K.types.maybe(K.types.string),turnedOffTracks:K.types.map(K.types.boolean),data:K.types.optional(Tb(),{tree:"",msa:"",treeMetadata:""}),featureFilters:K.types.map(K.types.boolean),relativeTo:K.types.maybe(K.types.string)})).volatile(()=>({headerHeight:0,status:void 0,highResScaleFactor:2,showZoomStar:(0,we.localStorageGetBoolean)(yS,!1),loadingMSA:!1,loadingTree:!1,volatileWidth:void 0,resizeHandleWidth:5,blockSize:500,mouseRow:void 0,mouseCol:void 0,mouseClickRow:void 0,mouseClickCol:void 0,hoveredTreeNode:void 0,highlightedColumns:void 0,nref:0,minimapHeight:56,conservationTrackHeight:40,marginLeft:20,error:void 0,annotPos:void 0,interProAnnotations:void 0})).actions(e=>({drawRelativeTo(t){e.relativeTo=t},setHideGaps(t){e.hideGaps=t},setAllowedGappyness(t){e.allowedGappyness=t},setContrastLettering(t){e.contrastLettering=t},setLoadingMSA(t){e.loadingMSA=t},setShowZoomStar(t){e.showZoomStar=t},setLoadingTree(t){e.loadingTree=t},setWidth(t){e.volatileWidth=t},setHeight(t){e.height=t},setError(t){e.error=t},setMousePos(t,r){e.mouseCol=t,e.mouseRow=r},setHoveredTreeNode(t){if(!t){e.hoveredTreeNode=void 0;return}let r=e.hierarchy.find(o=>o.data.id===t);if(!r){e.hoveredTreeNode=void 0;return}let n=r.leaves().map(o=>o.data.name);e.hoveredTreeNode={nodeId:t,descendantNames:n}},setHighlightedColumns(t){e.highlightedColumns=t},setShowDomains(t){e.showDomains=t},setSubFeatureRows(t){e.subFeatureRows=t},setMouseClickPos(t,r){e.mouseClickCol=t,e.mouseClickRow=r},setRowHeight(t){e.rowHeight=t},setColWidth(t){e.colWidth=t},setScrollY(t){e.scrollY=t},setCurrentAlignment(t){e.currentAlignment=t},toggleCollapsed(t){e.collapsed.includes(t)?e.collapsed.remove(t):e.collapsed.push(t)},toggleCollapsedLeaf(t){e.collapsedLeaves.includes(t)?e.collapsedLeaves.remove(t):e.collapsedLeaves.push(t)},setShowOnly(t){e.showOnly=t},setData(t){e.data=(0,K.cast)(t)},setMSAFilehandle(t){e.msaFilehandle=t},setTreeFilehandle(t){e.treeFilehandle=t},setGFFFilehandle(t){e.gffFilehandle=t},setMSA(t){e.data.setMSA(t)},setTree(t){e.data.setTree(t)},setTreeMetadata(t){e.data.setTreeMetadata(t)}})).views(e=>({get hideGapsEffective(){return e.hideGaps&&(e.collapsed.length>0||e.collapsedLeaves.length>0||e.allowedGappyness<100)},get realAllowedGappyness(){return this.hideGapsEffective?e.allowedGappyness:100},get actuallyShowDomains(){return e.showDomains&&!!e.interProAnnotations},get viewInitialized(){return e.volatileWidth!==void 0},get width(){if(e.volatileWidth===void 0)throw new Error("not initialized");return e.volatileWidth}})).views(e=>({extraViewMenuItems(){return[]},get colorScheme(){return ri[e.colorSchemeName]},get header(){return this.MSA?.getHeader()||{}},get alignmentNames(){return this.MSA?.alignmentNames||[]},get noTree(){return!!this.tree.noTree},get noDomains(){return!e.interProAnnotations},menuItems(){return[]},get treeMetadata(){return e.data.treeMetadata?JSON.parse(e.data.treeMetadata):{}},get MSA(){let t=e.data.msa;return t?ui(t)?new Qn(t,e.currentAlignment):tn.sniff(t)?new tn(t):t.startsWith(">")?new Sn(t):t.startsWith("SEQ")?new bn(t):new Bn(t):null},get numColumns(){return(this.MSA?.getWidth()||0)-this.blanks.length},get tree(){let t=e.data.tree;return Ad(t?ci(t.startsWith("BioTreeContainer")?Sb(Jb(t)):eo(t.startsWith("SEQ")?Jc(t).tree:t)):this.MSA?.getTree()||{noTree:!0,children:[],id:"empty",name:"empty"})},get rowNames(){return this.leaves.map(t=>t.data.name)},get mouseOverRowName(){let{mouseRow:t}=e;return t===void 0?void 0:this.rowNames[t]},get hoveredInsertion(){let{mouseCol:t,mouseRow:r}=e;if(t===void 0||r===void 0)return;let n=this.rowNames[r];if(!n)return;let o=this.insertionPositions.get(n);if(!o)return;let i=o.find(s=>s.pos===t);if(i)return{rowName:n,col:t,letters:i.letters}},get root(){let t=ai(this.tree,r=>r.children).sum(r=>r.children?0:1).sort((r,n)=>yc(r.data.length||1,n.data.length||1));if(e.showOnly){let r=t.find(n=>n.data.id===e.showOnly);r&&(t=r)}return[...e.collapsed,...e.collapsedLeaves].map(r=>t.find(n=>n.data.id===r)).filter(we.notEmpty).forEach(r=>{Ux(r)}),t},get msaAreaWidth(){return 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this.leaves.map(r=>[r.data.name,t?.getRow(r.data.name)]).filter(r=>!!r[1])},get numRows(){return this.rows.length},get rowMap(){return new Map(this.rows)},get columns(){return Object.fromEntries(this.rows.map((t,r)=>[t[0],this.columns2d[r]]))},get columns2d(){let{hideGapsEffective:t}=e;return this.rows.map(r=>r[1]).map(r=>t?uf(this.blanks,r):r)},get fontSize(){return Math.min(Math.max(6,e.rowHeight-3),18)},get colStats(){let t=[],r=this.columns2d;for(let n of r)for(let o=0;o<n.length;o++){let i=t[o]||{},s=n[o];i[s]||(i[s]=0),i[s]++,t[o]=i}return t},get colStatsSums(){return this.colStats.map(t=>(0,we.sum)(Object.values(t)))},get sequenceType(){let t=new Set;for(let s of this.colStats)for(let a of Object.keys(s)){let c=a.toUpperCase();c!=="-"&&c!=="."&&t.add(c)}let r=new Set(["A","C","G","T","N"]),n=new Set(["A","C","G","U","N"]),o=[...t].every(s=>r.has(s)),i=[...t].every(s=>n.has(s));return o&&!t.has("U")?"dna":i&&!t.has("T")?"rna":"amino"},get colConsensus(){let{colStats:t,colStatsSums:r}=this;return t.map((n,o)=>{let i=r[o],s=0,a="";for(let l in n){let A=n[l];A>s&&l!=="-"&&l!=="."&&(s=A,a=l)}let c=s/i;return{letter:a,color:c>.4?`hsl(240, 30%, ${100*Math.max(1-c/3,.3)}%)`:void 0}})},get colClustalX(){let{colStats:t,colStatsSums:r}=this;return t.map((n,o)=>{let i=r[o],s={},a=n.W??0,c=n.L??0,l=n.V??0,A=n.I??0,u=n.M??0,f=n.A??0,m=n.F??0,g=n.C??0,h=n.H??0,C=n.P??0,E=n.R??0,x=n.K??0,y=n.Q??0,w=n.E??0,b=n.D??0,M=n.T??0,v=n.S??0,T=n.G??0,_=n.Y??0,P=n.N??0,B=a+c+l+A+u+f+m+g+h+C+_,J=x+E,X=y+w,H=w+b,Be=M+v;return B/i>.6&&(s.W="rgb(128,179,230)",s.L="rgb(128,179,230)",s.V="rgb(128,179,230)",s.A="rgb(128,179,230)",s.I="rgb(128,179,230)",s.M="rgb(128,179,230)",s.F="rgb(128,179,230)",s.C="rgb(128,179,230)"),(J/i>.6||x/i>.8||E/i>.8||y/i>.8)&&(s.K="#d88",s.R="#d88"),(J/i>.6||X/i>.5||w/i>.8||y/i>.8||b/i>.8)&&(s.E="rgb(192, 72, 192)"),(J/i>.6||H/i>.5||x/i>.8||E/i>.8||y/i>.8)&&(s.D="rgb(204, 77, 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Rf().size([this.totalHeight,e.treeWidth]).separation(()=>1)(t),ff(t,t.data.length=0,e.treeWidth/df(t)),t},get totalHeight(){return this.root.leaves().length*e.rowHeight},get leaves(){return this.hierarchy.leaves()},get allBranchesLength0(){return this.hierarchy.links().every(t=>!t.source.data.length)},get showBranchLenEffective(){return this.allBranchesLength0?!1:e.showBranchLen}})).views(e=>({get totalWidth(){return e.numColumns*e.colWidth}})).views(e=>({get dataInitialized(){return(e.data.msa||e.data.tree)&&!e.error},get blocksX(){return gb({viewportWidth:e.msaAreaWidth,viewportX:-e.scrollX,blockSize:e.blockSize,mapWidth:e.totalWidth})},get blocksY(){return mb({viewportHeight:e.height,viewportY:-e.scrollY,blockSize:e.blockSize,mapHeight:e.totalHeight})}})).views(e=>({get blocks2d(){let t=[];for(let r of e.blocksY)for(let n of e.blocksX)t.push([n,r]);return t},get isLoading(){return e.loadingMSA||e.loadingTree},get maxScrollX(){return Math.min(-e.totalWidth+(e.msaAreaWidth-100),0)},get showMsaLetters(){return e.drawMsaLetters&&e.rowHeight>=5&&e.colWidth>e.rowHeight/2},get showTreeText(){return e.drawLabels&&e.rowHeight>=5}})).actions(e=>({setDrawMsaLetters(t){e.drawMsaLetters=t},calculateNeighborJoiningTreeFromMSA(){if(e.rows.length<2)throw new Error("Need at least 2 sequences to build a tree");let t=Ob(e.rows);e.setTree(t)},resetZoom(){e.setColWidth(12),e.setRowHeight(16)},zoomOutHorizontal(){e.colWidth=Math.max(1,Math.floor(e.colWidth*.75)),e.scrollX=(0,we.clamp)(e.scrollX,e.maxScrollX,0)},zoomInHorizontal(){e.colWidth=Math.ceil(e.colWidth*1.5),e.scrollX=(0,we.clamp)(e.scrollX,e.maxScrollX,0)},zoomInVertical(){e.rowHeight=Math.ceil(e.rowHeight*1.5)},zoomOutVertical(){e.rowHeight=Math.max(1.5,Math.floor(e.rowHeight*.75))},zoomIn(){(0,Ut.transaction)(()=>{e.colWidth=Math.ceil(e.colWidth*1.5),e.rowHeight=Math.ceil(e.rowHeight*1.5),e.scrollX=(0,we.clamp)(e.scrollX,e.maxScrollX,0)})},zoomOut(){(0,Ut.transaction)(()=>{e.colWidth=Math.max(1,Math.floor(e.colWidth*.75)),e.rowHeight=Math.max(1.5,Math.floor(e.rowHeight*.75)),e.scrollX=(0,we.clamp)(e.scrollX,e.maxScrollX,0)})},setInterProAnnotations(t){e.interProAnnotations=t},doScrollY(t){e.scrollY=(0,we.clamp)(e.scrollY+t,-e.totalHeight+10,0)},doScrollX(t){this.setScrollX(e.scrollX+t)},setScrollX(t){e.scrollX=(0,we.clamp)(t,e.maxScrollX,0)},toggleTrack(t){e.turnedOffTracks.has(t)?e.turnedOffTracks.delete(t):e.turnedOffTracks.set(t,!0)},setStatus(t){e.status=t}})).views(e=>({get labelsWidth(){let t=0,{rowHeight:r,leaves:n,treeMetadata:o,fontSize:i}=e;if(r>5)for(let s of n)t=Math.max(Mb(o[s.data.name]?.genome||s.data.name,i),t);return t},get secondaryStructureConsensus(){return e.MSA?.secondaryStructureConsensus},get seqConsensus(){return e.MSA?.seqConsensus},get adapterTrackModels(){let{rowHeight:t,MSA:r,hideGapsEffective:n,blanks:o}=e;return r?.tracks.filter(i=>i.data).map(i=>({model:{...i,data:n?uf(o,i.data):i.data,height:t},ReactComponent:yb}))||[]},get tracks(){let t={model:{id:"conservation",name:"Conservation",height:e.conservationTrackHeight},ReactComponent:Eb};return[...this.adapterTrackModels,t]},get turnedOnTracks(){return this.tracks.filter(t=>!e.turnedOffTracks.has(t.model.id))},get showHorizontalScrollbar(){return e.msaAreaWidth<e.totalWidth},get rowNamesSet(){return new Map(e.rowNames.map((t,r)=>[t,r]))},visibleColToRowLetter(t,r){let{rowMap:n,blanks:o}=e;return n.get(t)?.[ud(o,r)]},visibleColToSeqPos(t,r){return jb({rowName:t,visibleCol:r,rowMap:e.rowMap,blanks:e.blanks})},visibleColToSeqPosOneBased(t,r){let n=this.visibleColToSeqPos(t,r);return n!==void 0?n+1:void 0},globalColToVisibleCol(t){let{blanks:r,hideGapsEffective:n}=e;return n?qb(r,t):t},seqPosToGlobalCol(t,r){let{rows:n}=e,o=this.rowNamesSet.get(t);return o!==void 0&&n[o]?Wb({row:n[o][1],seqPos:r}):0},seqPosToVisibleCol(t,r){let n=this.seqPosToGlobalCol(t,r);return this.globalColToVisibleCol(n)}})).views(e=>({get msaAreaHeight(){return e.height-(e.showHorizontalScrollbar?e.minimapHeight:0)-e.headerHeight},get totalTrackAreaHeight(){return(0,we.sum)(e.turnedOnTracks.map(t=>t.model.height))},get tidyInterProAnnotationTypes(){let t=new Map;for(let r of this.tidyInterProAnnotations)t.set(r.accession,r);return t},get tidyInterProAnnotations(){let t=[],{interProAnnotations:r}=e;if(r)for(let[n,o]of Object.entries(r))for(let{signature:i,locations:s}of o.matches){let{entry:a}=i;if(a){let{name:c,accession:l,description:A}=a;for(let{start:u,end:f}of s)t.push({id:n,name:c,accession:l,description:A,start:u,end:f})}}return t.toSorted((n,o)=>mf(o)-mf(n))},get tidyFilteredInterProAnnotations(){return this.tidyInterProAnnotations.filter(t=>e.featureFilters.get(t.accession))},get tidyFilteredGatheredInterProAnnotations(){return(0,we.groupBy)(this.tidyFilteredInterProAnnotations,t=>t.id)}})).views(e=>({get showVerticalScrollbar(){return e.msaAreaHeight<e.totalHeight}})).views(e=>({get verticalScrollbarWidth(){return e.showVerticalScrollbar?20:0},get fillPalette(){return Bb([...e.tidyInterProAnnotationTypes.keys()])},get strokePalette(){return Object.fromEntries(Object.entries(this.fillPalette).map(([t,r])=>[t,Qt(r).darken(.1).toHex()]))},getRowData(t){return{data:e.MSA?.getRowData(t),treeMetadata:e.treeMetadata[t]}}})).actions(e=>({setHeaderHeight(t){e.headerHeight=t},setConservationTrackHeight(t){e.conservationTrackHeight=t},reset(){e.setData({tree:"",msa:""}),e.resetZoom(),e.setError(void 0),e.setScrollY(0),e.setScrollX(0),e.setCurrentAlignment(0),e.setTreeFilehandle(void 0),e.setMSAFilehandle(void 0)},async exportSVG(t){let{renderToSvg:r}=await Promise.resolve().then(()=>(uS(),AS)),n=await r(e,t),o=new Blob([n],{type:"image/svg+xml"});Xb(o,"image.svg")},incrementRef(){e.nref++},initFilter(t){e.featureFilters.get(t)===void 0&&e.featureFilters.set(t,!0)},setFilter(t,r){e.featureFilters.set(t,r)},fit(){e.rowHeight=e.msaAreaHeight/e.numRows,e.colWidth=e.msaAreaWidth/e.numColumns,e.scrollX=0,e.scrollY=0},fitVertically(){e.rowHeight=e.msaAreaHeight/e.numRows,e.scrollY=0},fitHorizontally(){e.colWidth=e.msaAreaWidth/e.numColumns,e.scrollX=0},afterCreate(){(0,K.addDisposer)(e,(0,Ut.autorun)(()=>{for(let t of e.tidyInterProAnnotationTypes.keys())this.initFilter(t)})),(0,K.addDisposer)(e,(0,Ut.autorun)(()=>{(0,we.localStorageSetBoolean)(yS,e.showZoomStar)})),(0,K.addDisposer)(e,(0,Ut.autorun)(async()=>{let{treeFilehandle:t}=e;if(t)try{e.setLoadingTree(!0),e.setTree(await(0,we.fetchAndMaybeUnzipText)((0,ms.openLocation)(t))),t.locationType==="BlobLocation"&&e.setTreeFilehandle(void 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URLSearchParams({email:"colin.diesh@gmail.com",sequence:e})});return await Wc({jobId:r,algorithm:"clustalo",onProgress:t}),{msa:await Le(`${Yt}/clustalo/result/${r}/aln-clustal_num`),tree:await Le(`${Yt}/clustalo/result/${r}/phylotree`)}}async function ik({sequence:e,onProgress:t}){let r=await Le(`${Yt}/muscle/run`,{method:"POST",body:new URLSearchParams({email:"colin.diesh@gmail.com",format:"clw",tree:"tree1",sequence:e})});return await Wc({jobId:r,algorithm:"muscle",onProgress:t}),{msa:await Le(`${Yt}/muscle/result/${r}/fa`),tree:await Le(`${Yt}/muscle/result/${r}/phylotree`)}}async function sk({sequence:e,onProgress:t}){let r=await Le(`${Yt}/kalign/run`,{method:"POST",body:new URLSearchParams({email:"colin.diesh@gmail.com",stype:"protein",sequence:e})});return await Wc({jobId:r,algorithm:"kalign",onProgress:t}),{msa:await Le(`${Yt}/kalign/result/${r}/fa`),tree:await Le(`${Yt}/kalign/result/${r}/phylotree`)}}async function ak({sequence:e,onProgress:t}){let r=await Le(`${Yt}/mafft/run`,{method:"POST",body:new URLSearchParams({email:"colin.diesh@gmail.com",stype:"protein",sequence:e})});return await Wc({jobId:r,algorithm:"mafft",onProgress:t}),{msa:await Le(`${Yt}/mafft/result/${r}/fa`),tree:await Le(`${Yt}/mafft/result/${r}/phylotree`)}}async function Wc({onProgress:e,jobId:t,algorithm:r}){for(;;){for(let o=0;o<10;o++)await Ys(1e3),e(`Re-checking MSA status in... ${10-o}`);let n=await Le(`${Yt}/${r}/status/${t}`);if(n==="FINISHED")break;if(n.includes("FAILURE"))throw new Error(`Failed to run: jobId ${t}`)}}async function SS({algorithm:e,sequence:t,onProgress:r}){switch(r(`Launching ${e} MSA...`),e){case"clustalo":return ok({sequence:t,onProgress:r});case"muscle":return ik({sequence:t,onProgress:r});case"kalign":return sk({sequence:t,onProgress:r});case"mafft":return ak({sequence:t,onProgress:r});default:throw new Error("unknown algorithm")}}async function QS({query:e,blastDatabase:t,blastProgram:r,baseUrl:n,onProgress:o,onRid:i}){o("Submitting to NCBI BLAST...");let{rid:s}=await ck({query:e,blastDatabase:t,blastProgram:r,baseUrl:n});i(s),await lk({rid:s,onProgress:o,baseUrl:n});let a=await Eo(`${n}?CMD=Get&RID=${s}&FORMAT_TYPE=JSON2_S&FORMAT_OBJECT=Alignment`);return{rid:s,hits:a.BlastOutput2[0]?.report.results.search.hits??[]}}async function ck({query:e,blastProgram:t,blastDatabase:r,baseUrl:n}){let o=await Le(n,{method:"POST",body:new URLSearchParams({CMD:"Put",PROGRAM:t==="quick-blastp"?"blastp":t,DATABASE:r,QUERY:e,...r==="nr_clustered_seq"?{CLUSTERED_DB:"on",DB_TYPE:"Experimental Databases"}:{},...t==="quick-blastp"?{BLAST_PROGRAMS:"kmerBlastp"}:{}})}),i=/^ {4}RID = (.*$)/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 lk({rid:e,onProgress:t,baseUrl:r}){for(;;){for(let l=0;l<20;l++)await Ys(1e3),t(`Re-checking BLAST status in... ${20-l}`);let o=await Le(`${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 ${e} failed`);if(a){if(c)return!0;throw new Error("No hits found")}}}}ta();var Ak="jbrowse-msaview-taxonomy-cache",gs="common-names",uk=2;async function MS(){return Qi(Ak,uk,{upgrade(e){e.objectStoreNames.contains(gs)&&e.deleteObjectStore(gs),e.createObjectStore(gs,{keyPath:"taxid"})}})}async function fk(e){return(await MS()).get(gs,e)}async function dk(e){let r=(await MS()).transaction(gs,"readwrite");for(let n of e)await r.store.put(n);await r.done}async function vS(e){let t=new Map,r=[];for(let i of e){let s=await fk(i);s?t.set(i,{sciname:s.sciname,commonName:s.commonName}):r.push(i)}if(r.length===0)return t;let n=100,o=[];for(let i=0;i<r.length;i+=n){let s=r.slice(i,i+n),a=s.join(",");try{let l=await(await fetch(`https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=taxonomy&id=${a}&retmode=xml`)).text(),A=new Map,u=/<Taxon>\s*<TaxId>(\d+)<\/TaxId>/g,f;for(;(f=u.exec(l))!==null;){let m=Number(f[1]),g=f.index,h=1,C=g+f[0].length;for(;h>0&&C<l.length;){let b=l.indexOf("<Taxon>",C),M=l.indexOf("</Taxon>",C);if(M===-1)break;b!==-1&&b<M?(h++,C=b+7):(h--,C=M+8)}let E=l.slice(g,C),x=A.get(m),y=E.includes("<LineageEx>"),w=x?.includes("<LineageEx>");(!x||y&&!w)&&A.set(m,E)}for(let m of s){let g=A.get(m);if(g){let h=/<GenbankCommonName>(.*?)<\/GenbankCommonName>/.exec(g),C=/<CommonName>(.*?)<\/CommonName>/.exec(g),E=/<ScientificName>(.*?)<\/ScientificName>/.exec(g),x=h?.[1]??C?.[1],y=E?.[1]??"";t.set(m,{sciname:y,commonName:x}),o.push({taxid:m,sciname:y,commonName:x})}else o.push({taxid:m,sciname:"",commonName:void 0})}}catch(c){console.error("Failed to fetch taxonomy data:",c)}}return o.length>0&&await dk(o),t}async function TS({self:e}){let{baseUrl:t,blastDatabase:r,blastProgram:n,msaAlgorithm:o,proteinSequence:i,selectedTranscript:s}=e.blastParams,a=js(i),{hits:c,rid:l}=await QS({query:a,blastDatabase:r,blastProgram:n,baseUrl:t,onProgress:C=>{e.setProgress(C)},onRid:C=>{e.setRid(C)}});e.setProgress("Fetching species taxonomy info...");let A=c.map(C=>C.description[0]?.taxid).filter(C=>C!==void 0),u=await vS(A),f={},m=c.map(C=>{let E=C.description[0]??{accession:"unknown",id:"unknown",sciname:"unknown"},x=BS(E,u),y=bS(C.hsps[0]?.hseq??"");return f[x]=mk(E,u),`>${x}
-${y}`}),g=await SS({algorithm:o,sequence:[`>QUERY
-${a}`,...m].join(`
-`),onProgress:C=>{e.setProgress(C)}}),h=JSON.stringify(f);return await Kg({proteinSequence:a,blastDatabase:r,blastProgram:n,msaAlgorithm:o,msa:g.msa,tree:g.tree,treeMetadata:h,rid:l,geneId:s?.get("parentId"),transcriptId:s?.get("id")}),{...g,treeMetadata:h}}function mk(e,t){let r={},n=e.taxid?t.get(e.taxid):void 0;return n?.sciname&&(r["Scientific name"]=n.sciname),n?.commonName&&(r["Common name"]=n.commonName),e.accession&&(r.Accession=e.accession),e.id&&(r.ID=e.id),e.title&&(r.Description=e.title),r}var kS=d(se());function _S(e){return typeof e=="object"&&e!==null&&"hoverFeature"in e&&"hoverPosition"in e}function DS(e){return/AF-([A-Z0-9]+)-F\d+/.exec(e)?.[1]}function NS({model:e}){let{hovered:t}=(0,kS.getSession)(e),{querySeqName:r,transcriptToMsaMap:n,connectedView:o,mafRegion:i}=e;if(!o?.initialized||!_S(t))return;let{coord:s,refName:a}=t.hoverPosition;if(i){if(a!==i.refName||!o.assemblyNames.includes(i.assemblyName)||s<i.start||s>=i.end)return;let l=s-i.start;return e.seqPosToVisibleCol(r,l)}if(n){let{g2p:c}=n,l=c[s];if(l!==void 0)return e.seqPosToVisibleCol(r,l)}}function Kc(e,t){if(t<0||t>=e.length)return;let r=0;for(let n=0;n<t;n++)e[n]!=="-"&&r++;if(e[t]!=="-")return r}function LS(e,t){let r=0;for(let n=0;n<e.length;n++)if(e[n]!=="-"){if(r===t)return n;r++}}function Ed(e){let t={};for(let[r,n]of e)t[r]=n;return t}function zc({model:e,coord:t}){let{querySeqName:r,transcriptToMsaMap:n,mafRegion:o}=e,s=e.rows.find(c=>c[0]===r)?.[1];if(!s)return;let a=Kc(s,t);if(a!==void 0){if(o){let c=o.start+a;return c>=o.end?void 0:{refName:o.refName,start:c,end:c+1}}if(n){let{refName:c,p2g:l}=n,A=l[a],u=l[a+1];return A!==void 0&&u!==void 0?{refName:c,start:Math.min(A,u),end:Math.max(A,u)}:void 0}}}var gk="jbrowse-msaview-data";var vn="msa-data",$c,no;function pk(){if(no!==void 0)return no;try{return typeof indexedDB>"u"?(no=!1,!1):(no=!0,!0)}catch{return no=!1,!1}}async function Id(){if(pk())return $c||($c=new Promise(e=>{try{let t=indexedDB.open(gk,1);t.addEventListener("error",()=>{console.warn("IndexedDB unavailable - MSA data will not persist across page refreshes"),no=!1,e(void 0)}),t.onsuccess=()=>{e(t.result)},t.onupgradeneeded=r=>{let n=r.target.result;n.objectStoreNames.contains(vn)||n.createObjectStore(vn,{keyPath:"id"}).createIndex("timestamp","timestamp",{unique:!1})}}catch(t){console.warn("Failed to open IndexedDB:",t),no=!1,e(void 0)}}),$c)}function FS(){return`msa-${Date.now()}-${Math.random().toString(36).slice(2,11)}`}async function RS(e,t){let r=await Id();return r?new Promise(n=>{try{let i=r.transaction(vn,"readwrite").objectStore(vn),s={id:e,msa:t.msa,tree:t.tree,treeMetadata:t.treeMetadata,timestamp:Date.now()},a=i.put(s);a.addEventListener("error",()=>{console.warn("Failed to store MSA data:",a.error),n(!1)}),a.onsuccess=()=>{n(!0)}}catch(o){console.warn("Failed to store MSA data:",o),n(!1)}}):!1}async function PS(e){let t=await Id();if(t)return new Promise(r=>{try{let 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OS(e,t){let r=e.toUpperCase(),n=t.toUpperCase();return hk[r]?.[n]??-4}var Ck=-10,Ek=-.5;function Ik(e,t,r=Ck,n=Ek){let o=e.length,i=t.length,s=[],a=[],c=[];for(let C=0;C<=o;C++){s[C]=[],a[C]=[],c[C]=[];for(let E=0;E<=i;E++)s[C][E]=-1/0,a[C][E]=-1/0,c[C][E]=-1/0}s[0][0]=0;for(let C=1;C<=o;C++)a[C][0]=r+(C-1)*n;for(let C=1;C<=i;C++)c[0][C]=r+(C-1)*n;for(let C=1;C<=o;C++)for(let E=1;E<=i;E++){let x=OS(e[C-1],t[E-1]);s[C][E]=Math.max(s[C-1][E-1],a[C-1][E-1],c[C-1][E-1])+x,a[C][E]=Math.max(s[C-1][E]+r,a[C-1][E]+n),c[C][E]=Math.max(s[C][E-1]+r,c[C][E-1]+n)}let l="",A="",u=o,f=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||f>0;)if(h==="M"&&u>0&&f>0){l=e[u-1]+l,A=t[f-1]+A;let C=OS(e[u-1],t[f-1]),E=s[u-1][f-1],x=a[u-1][f-1];s[u][f]===E+C?h="M":s[u][f]===x+C?h="Ix":h="Iy",u--,f--}else if(h==="Ix"&&u>0)l=e[u-1]+l,A="-"+A,h=a[u][f]===s[u-1][f]+r?"M":"Ix",u--;else if(f>0)l="-"+l,A=t[f-1]+A,h=c[u][f]===s[u][f-1]+r?"M":"Iy",f--;else break;return{alignedSeq1:l,alignedSeq2:A,score:g}}function xk(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 HS(e,t){let{alignedSeq1:r,alignedSeq2:n}=Ik(e,t);return{consensus:xk(r,n),alns:[{id:"msa",seq:r},{id:"structure",seq:n}]}}function JS(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 Bk=(0,WS.lazy)(()=>Promise.resolve().then(()=>(VS(),jS)));function bk(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=Kc(i,t);if(s===void 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Expected 1 or -1.`);if(!r)throw new Error("refName is required");let n=e.subfeatures?.filter(u=>u.type==="CDS")??[],o=new Set,i=n.filter(u=>{if(u.start>=u.end)return!1;let f=`${u.start}-${u.end}`;return o.has(f)?!1:(o.add(f),!0)}).sort((u,f)=>t*(u.start-f.start)),s={},a={};if(i.length===0)return{g2p:s,p2g:a,refName:r,strand:t};let l=(3-(i[0]?.phase??0))%3,A=-1;for(let u of i)for(let f of RM(u,t)){let m=Math.floor(l++/3);s[f]=m,m!==A&&(a[m]=f,A=m)}return{g2p:s,p2g:a,refName:r,strand:t}}var An=d(zr());xd();function NS(e,t){let r=e.sciname.replaceAll(" ","_");if(e.taxid&&t?.has(e.taxid)){let n=t.get(e.taxid);n.commonName&&(r=n.commonName.split(" ").map(o=>o.charAt(0).toUpperCase()+o.slice(1).toLowerCase()).join("_"))}return`${e.accession}-${r}`}function LS(e){return e.replace("-","")}var Kt="https://www.ebi.ac.uk/Tools/services/rest";async function Sk({sequence:e,onProgress:t}){let r=await Fe(`${Kt}/clustalo/run`,{method:"POST",body:new URLSearchParams({email:"colin.diesh@gmail.com",sequence:e})});return await el({jobId:r,algorithm:"clustalo",onProgress:t}),{msa:await Fe(`${Kt}/clustalo/result/${r}/aln-clustal_num`),tree:await Fe(`${Kt}/clustalo/result/${r}/phylotree`)}}async function Qk({sequence:e,onProgress:t}){let r=await Fe(`${Kt}/muscle/run`,{method:"POST",body:new URLSearchParams({email:"colin.diesh@gmail.com",format:"clw",tree:"tree1",sequence:e})});return await el({jobId:r,algorithm:"muscle",onProgress:t}),{msa:await Fe(`${Kt}/muscle/result/${r}/fa`),tree:await Fe(`${Kt}/muscle/result/${r}/phylotree`)}}async function Mk({sequence:e,onProgress:t}){let r=await Fe(`${Kt}/kalign/run`,{method:"POST",body:new URLSearchParams({email:"colin.diesh@gmail.com",stype:"protein",sequence:e})});return await el({jobId:r,algorithm:"kalign",onProgress:t}),{msa:await Fe(`${Kt}/kalign/result/${r}/fa`),tree:await Fe(`${Kt}/kalign/result/${r}/phylotree`)}}async function vk({sequence:e,onProgress:t}){let r=await Fe(`${Kt}/mafft/run`,{method:"POST",body:new URLSearchParams({email:"colin.diesh@gmail.com",stype:"protein",sequence:e})});return await el({jobId:r,algorithm:"mafft",onProgress:t}),{msa:await Fe(`${Kt}/mafft/result/${r}/fa`),tree:await Fe(`${Kt}/mafft/result/${r}/phylotree`)}}async function el({onProgress:e,jobId:t,algorithm:r}){for(;;){for(let o=0;o<10;o++)await Vs(1e3),e(`Re-checking MSA status in... ${10-o}`);let n=await Fe(`${Kt}/${r}/status/${t}`);if(n==="FINISHED")break;if(n.includes("FAILURE"))throw new Error(`Failed to run: jobId ${t}`)}}async function FS({algorithm:e,sequence:t,onProgress:r}){switch(r(`Launching ${e} MSA...`),e){case"clustalo":return Sk({sequence:t,onProgress:r});case"muscle":return Qk({sequence:t,onProgress:r});case"kalign":return Mk({sequence:t,onProgress:r});case"mafft":return vk({sequence:t,onProgress:r});default:throw new Error("unknown algorithm")}}async function RS({rid:e,baseUrl:t,onProgress:r}){r(`Checking BLAST status for RID: ${e}...`),await GS({rid:e,onProgress:r,baseUrl:t});let n=await Gn(`${t}?CMD=Get&RID=${e}&FORMAT_TYPE=JSON2_S&FORMAT_OBJECT=Alignment`);return{rid:e,hits:n.BlastOutput2[0]?.report.results.search.hits??[]}}async function PS({query:e,blastDatabase:t,blastProgram:r,baseUrl:n,onProgress:o,onRid:i}){o("Submitting to NCBI BLAST...");let{rid:s}=await Tk({query:e,blastDatabase:t,blastProgram:r,baseUrl:n});i(s),await GS({rid:s,onProgress:o,baseUrl:n});let a=await Gn(`${n}?CMD=Get&RID=${s}&FORMAT_TYPE=JSON2_S&FORMAT_OBJECT=Alignment`);return{rid:s,hits:a.BlastOutput2[0]?.report.results.search.hits??[]}}async function Tk({query:e,blastProgram:t,blastDatabase:r,baseUrl:n}){let o=await Fe(n,{method:"POST",body:new URLSearchParams({CMD:"Put",PROGRAM:t==="quick-blastp"?"blastp":t,DATABASE:r,QUERY:e,...r==="nr_clustered_seq"?{CLUSTERED_DB:"on",DB_TYPE:"Experimental Databases"}:{},...t==="quick-blastp"?{BLAST_PROGRAMS:"kmerBlastp"}:{}})}),i=/^ {4}RID = (.*$)/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 GS({rid:e,onProgress:t,baseUrl:r}){for(;;){for(let l=0;l<20;l++)await Vs(1e3),t(`Re-checking BLAST status in... ${20-l}`);let o=await Fe(`${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 ${e} failed`);if(a){if(c)return!0;throw new Error("No hits found")}}}}ia();var Dk="jbrowse-msaview-taxonomy-cache",ps="common-names",_k=2;async function OS(){return vi(Dk,_k,{upgrade(e){e.objectStoreNames.contains(ps)&&e.deleteObjectStore(ps),e.createObjectStore(ps,{keyPath:"taxid"})}})}async function kk(e){return(await OS()).get(ps,e)}async function Nk(e){let r=(await OS()).transaction(ps,"readwrite");for(let n of e)await r.store.put(n);await r.done}async function HS(e){let t=new Map,r=[];for(let i of e){let s=await kk(i);s?t.set(i,{sciname:s.sciname,commonName:s.commonName}):r.push(i)}if(r.length===0)return t;let n=100,o=[];for(let i=0;i<r.length;i+=n){let s=r.slice(i,i+n),a=s.join(",");try{let l=await(await fetch(`https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=taxonomy&id=${a}&retmode=xml`)).text(),A=new Map,u=/<Taxon>\s*<TaxId>(\d+)<\/TaxId>/g,f;for(;(f=u.exec(l))!==null;){let m=Number(f[1]),p=f.index,h=1,E=p+f[0].length;for(;h>0&&E<l.length;){let B=l.indexOf("<Taxon>",E),S=l.indexOf("</Taxon>",E);if(S===-1)break;B!==-1&&B<S?(h++,E=B+7):(h--,E=S+8)}let C=l.slice(p,E),x=A.get(m),y=C.includes("<LineageEx>"),w=x?.includes("<LineageEx>");(!x||y&&!w)&&A.set(m,C)}for(let m of s){let p=A.get(m);if(p){let h=/<GenbankCommonName>(.*?)<\/GenbankCommonName>/.exec(p),E=/<CommonName>(.*?)<\/CommonName>/.exec(p),C=/<ScientificName>(.*?)<\/ScientificName>/.exec(p),x=h?.[1]??E?.[1],y=C?.[1]??"";t.set(m,{sciname:y,commonName:x}),o.push({taxid:m,sciname:y,commonName:x})}else 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XS(e,t){let r=e.toUpperCase(),n=t.toUpperCase();return Pk[r]?.[n]??-4}var Gk=-10,Ok=-.5;function Hk(e,t,r=Gk,n=Ok){let o=e.length,i=t.length,s=[],a=[],c=[];for(let E=0;E<=o;E++){s[E]=[],a[E]=[],c[E]=[];for(let C=0;C<=i;C++)s[E][C]=-1/0,a[E][C]=-1/0,c[E][C]=-1/0}s[0][0]=0;for(let E=1;E<=o;E++)a[E][0]=r+(E-1)*n;for(let E=1;E<=i;E++)c[0][E]=r+(E-1)*n;for(let E=1;E<=o;E++)for(let C=1;C<=i;C++){let x=XS(e[E-1],t[C-1]);s[E][C]=Math.max(s[E-1][C-1],a[E-1][C-1],c[E-1][C-1])+x,a[E][C]=Math.max(s[E-1][C]+r,a[E-1][C]+n),c[E][C]=Math.max(s[E][C-1]+r,c[E][C-1]+n)}let l="",A="",u=o,f=i,m=[s[o][i],a[o][i],c[o][i]],p=Math.max(...m),h=p===s[o][i]?"M":p===a[o][i]?"Ix":"Iy";for(;u>0||f>0;)if(h==="M"&&u>0&&f>0){l=e[u-1]+l,A=t[f-1]+A;let E=XS(e[u-1],t[f-1]),C=s[u-1][f-1],x=a[u-1][f-1];s[u][f]===C+E?h="M":s[u][f]===x+E?h="Ix":h="Iy",u--,f--}else if(h==="Ix"&&u>0)l=e[u-1]+l,A="-"+A,h=a[u][f]===s[u-1][f]+r?"M":"Ix",u--;else if(f>0)l="-"+l,A=t[f-1]+A,h=c[u][f]===s[u][f-1]+r?"M":"Iy",f--;else break;return{alignedSeq1:l,alignedSeq2:A,score:p}}function Jk(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 ZS(e,t){let{alignedSeq1:r,alignedSeq2:n}=Hk(e,t);return{consensus:Jk(r,n),alns:[{id:"msa",seq:r},{id:"structure",seq:n}]}}function eQ(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 qk=(0,sQ.lazy)(()=>Promise.resolve().then(()=>(iQ(),oQ)));function jk(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=tl(i,t);if(s===void 0){o.clearHighlightFromExternal?.();continue}let a=n.msaToStructure[s];a===void 0?o.clearHighlightFromExternal?.():o.highlightFromExternal?.(a)}}function Bd(){return ee.types.compose(aQ.BaseViewModel,Id(),ee.types.model("MsaView",{connectedViewId:ee.types.maybe(ee.types.string),connectedFeature:ee.types.frozen(),connectedHighlights:ee.types.array(ee.types.model({refName:ee.types.string,start:ee.types.number,end:ee.types.number})),blastParams:ee.types.frozen(),querySeqName:"QUERY",uniprotId:ee.types.maybe(ee.types.string),zoomToBaseLevel:!1,init:ee.types.frozen(),connectedStructures:ee.types.array(ee.types.frozen()),dataStoreId:ee.types.maybe(ee.types.string),mafRegion:ee.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?bh(e.connectedFeature):void 0},get processing(){return!!e.progress},get connectedView(){let{views:t}=(0,kn.getSession)(e);return t.find(r=>r.id===e.connectedViewId)},get connectedProteinViews(){let{views:t}=(0,kn.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=VS(i,o);if(s!==void 0)return e.globalColToVisibleCol(s)}}}}}})).views(e=>({get mouseCol2(){let t=e.structureHoverCol;return t!==void 0?t:jS({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,ee.cast)(t)},addToConnectedHighlights(t){e.connectedHighlights.push(t)},clearConnectedHighlights(){e.connectedHighlights=(0,ee.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,kn.getSession)(e),i=rl({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 "${o}" not found`);let s=i.replaceAll("-",""),{views:a}=(0,kn.getSession)(e),c=a.find(h=>h.id===t);if(!c)throw new Error(`ProteinView "${t}" not found`);let l=c.structures?.[r];if(!l)throw new Error(`Structure at index ${r} not found`);let A=l.structureSequences?.[0];if(!A)throw new Error("Structure sequence not available");let u=ZS(s,A),{seq1ToSeq2:f,seq2ToSeq1:m}=eQ(u),p={proteinViewId:t,structureIdx:r,msaRowName:o,msaToStructure:yd(f),structureToMsa:yd(m)};e.connectedStructures.push(p)},disconnectFromStructure(t,r){let n=e.connectedStructures.findIndex(o=>o.proteinViewId===t&&o.structureIdx===r);n!==-1&&e.connectedStructures.splice(n,1)},disconnectAllStructures(){e.connectedStructures.clear()}})).actions(e=>{let t=e.setMouseClickPos.bind(e);return{setMouseClickPos(r,n){t(r,n),r!==void 0&&e.handleMsaClick(r)}}}).views(e=>({extraViewMenuItems(){return[{label:"Zoom to base level on click?",checked:e.zoomToBaseLevel,type:"checkbox",onClick:()=>{e.setZoomToBaseLevel(!e.zoomToBaseLevel)}},{label:"Connect to protein structure...",onClick:()=>{(0,kn.getSession)(e).queueDialog(t=>[qk,{model:e,handleClose:t}])}},...e.connectedStructures.length>0?[{label:"Disconnect from protein structures",onClick:()=>{e.disconnectAllStructures()}}]:[]]}})).actions(e=>({afterCreate(){$S().catch(t=>{console.error("Failed to cleanup old MSA data:",t)}),(0,ee.addDisposer)(e,(0,An.autorun)(async()=>{let{dataStoreId:t,rows:r}=e;if(t&&r.length===0)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)}})),(0,ee.addDisposer)(e,(0,An.autorun)(async()=>{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;if(o||i)try{let s=WS();await KS(s,{msa:o,tree:i,treeMetadata:e.data.treeMetadata})&&e.setDataStoreId(s)}catch(s){console.error("Failed to store MSA data to IndexedDB:",s)}}})),(0,ee.addDisposer)(e,(0,An.autorun)(async()=>{if(e.blastParams)try{e.setProgress("Submitting query"),e.setError(void 0);let t=await JS({self:e});e.setData(t),e.setBlastParams(void 0)}catch(t){e.setError(t),console.error(t)}finally{e.setProgress("")}})),(0,ee.addDisposer)(e,(0,An.autorun)(async()=>{let{init:t}=e;if(t)try{e.setError(void 0);let{msaData:r,msaUrl:n,treeData:o,treeUrl:i,querySeqName:s}=t;if(n){let a=YS(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)}})),(0,ee.addDisposer)(e,(0,An.autorun)(()=>{let{mouseCol:t,mouseClickCol:r}=e,n=t===void 0?void 0:rl({model:e,coord:t}),o=r===void 0?void 0:rl({model:e,coord:r});e.setConnectedHighlights([n,o].filter(i=>!!i))})),(0,ee.addDisposer)(e,(0,An.autorun)(()=>{jk(e)})),(0,ee.addDisposer)(e,(0,An.autorun)(()=>{let{views:t}=(0,kn.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 ProteinView:",u)}}}})),(0,ee.addDisposer)(e,(0,An.autorun)(()=>{let{views:t}=(0,kn.getSession)(e),{connectedViewId:r,transcriptToMsaMap:n,querySeqName:o}=e;if(!r||!n)return;let i=[];for(let a of t){let c=a;if(!(c.type!=="ProteinView"||!c.structures))for(let l of c.structures){if(l.connectedViewId!==r)continue;let A=l.hoverGenomeHighlights;if(!A||A.length===0)continue;let{g2p:u}=n;for(let f of A)for(let m=f.start;m<f.end;m++){let p=u[m];if(p!==void 0){let h=e.seqPosToGlobalCol(o,p);i.includes(h)||i.push(h)}}}}let s=i.map(a=>e.globalColToVisibleCol(a)).filter(a=>a!==void 0);e.setHighlightedColumns(s.length>0?s:void 0)}))}}))}var Zk=(0,EQ.lazy)(()=>Promise.resolve().then(()=>(CQ(),hQ)));function Md(e){e.addViewType(()=>new IQ.default({name:"MsaView",stateModel:Bd(),ReactComponent:Zk}))}var xQ="2.2.11";var il=class extends yQ.default{constructor(){super(...arguments);this.name="MsaViewPlugin";this.version=xQ;this.rootConfigurationSchema=r=>({msa:(0,vd.ConfigurationSchema)("MSA",{datasets:Td.types.maybe(Td.types.array((0,vd.ConfigurationSchema)("MSAEntry",{datasetId:{type:"string",defaultValue:""},description:{type:"string",defaultValue:""},name:{type:"string",defaultValue:""},adapter:r.pluggableConfigSchemaType("adapter")})))})})}install(r){Md(r),FA(r),RA(r),gl(r),Nl(r)}configure(r){(0,wQ.isAbstractMenuManager)(r.rootModel)&&r.rootModel.appendToSubMenu(["Add"],{label:"Multiple sequence alignment view",icon:Zd,onClick:n=>{n.addView("MsaView",{})}})}};return FQ(eN);})();
 /*! Bundled license information:
 use-sync-external-store/cjs/use-sync-external-store-shim.production.js:
@@ -98,7 +98,7 @@ react-is/cjs/react-is.production.min.js:
    *)
 dompurify/dist/purify.es.mjs:
-  (*! @license DOMPurify 3.3.1 | (c) Cure53 and other contributors | Released under the Apache license 2.0 and Mozilla Public License 2.0 | github.com/cure53/DOMPurify/blob/3.3.1/LICENSE *)
+  (*! @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 *)
 escape-html/index.js:
   (*!