jbrowse-plugin-msaview 2.5.1 → 2.5.2

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

@@ -1,11 +1,11 @@
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Both were omitted.`);o=t.file}var i=this._sourceRoot;i!=null&&(o=Ne.relative(i,o));var s=new Ka,a=new Ka;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)};Wt.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. 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if(m>0){if(!Ne.compareByGeneratedPositionsInflated(l,d[m-1]))continue;c+=","}c+=ls.encode(l.generatedColumn-t),t=l.generatedColumn,l.source!=null&&(u=this._sources.indexOf(l.source),c+=ls.encode(u-s),s=u,c+=ls.encode(l.originalLine-1-o),o=l.originalLine-1,c+=ls.encode(l.originalColumn-n),n=l.originalColumn,l.name!=null&&(A=this._names.indexOf(l.name),c+=ls.encode(A-i),i=A)),a+=c}return a};Wt.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)};Wt.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};Wt.prototype.toString=function(){return JSON.stringify(this.toJSON())};x0.SourceMapGenerator=Wt});var y0=j(ro=>{ro.GREATEST_LOWER_BOUND=1;ro.LEAST_UPPER_BOUND=2;function xu(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?xu(s,t,r,n,o,i):i==ro.LEAST_UPPER_BOUND?t<n.length?t:-1:s:s-e>1?xu(e,s,r,n,o,i):i==ro.LEAST_UPPER_BOUND?s:e<0?-1:e}ro.search=function(t,r,n,o){if(r.length===0)return-1;var i=xu(-1,r.length,t,r,n,o||ro.GREATEST_LOWER_BOUND);if(i<0)return-1;for(;i-1>=0&&n(r[i],r[i-1],!0)===0;)--i;return i}});var B0=j(b0=>{function mv(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 pv(e){let t=mv.toString();return new Function(`return ${t}`)()(e)}var w0=new WeakMap;b0.quickSort=function(e,t,r=0){let n=w0.get(t);n===void 0&&(n=pv(t),w0.set(t,n)),n(e,t,r,e.length-1)}});var M0=j(Xa=>{var N=Xo(),wu=y0(),Zo=Eu().ArraySet,gv=pu(),As=B0().quickSort;function Ie(e,t){var r=e;return typeof e=="string"&&(r=N.parseSourceMapInput(e)),r.sections!=null?new fr(r,t):new at(r,t)}Ie.fromSourceMap=function(e,t){return at.fromSourceMap(e,t)};Ie.prototype._version=3;Ie.prototype.__generatedMappings=null;Object.defineProperty(Ie.prototype,"_generatedMappings",{configurable:!0,enumerable:!0,get:function(){return this.__generatedMappings||this._parseMappings(this._mappings,this.sourceRoot),this.__generatedMappings}});Ie.prototype.__originalMappings=null;Object.defineProperty(Ie.prototype,"_originalMappings",{configurable:!0,enumerable:!0,get:function(){return this.__originalMappings||this._parseMappings(this._mappings,this.sourceRoot),this.__originalMappings}});Ie.prototype._charIsMappingSeparator=function(t,r){var n=t.charAt(r);return n===";"||n===","};Ie.prototype._parseMappings=function(t,r){throw new Error("Subclasses must implement _parseMappings")};Ie.GENERATED_ORDER=1;Ie.ORIGINAL_ORDER=2;Ie.GREATEST_LOWER_BOUND=1;Ie.LEAST_UPPER_BOUND=2;Ie.prototype.eachMapping=function(t,r,n){var o=r||null,i=n||Ie.GENERATED_ORDER,s;switch(i){case Ie.GENERATED_ORDER:s=this._generatedMappings;break;case Ie.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 h=s[d],E=h.source===null?null:A.at(h.source);E!==null&&(E=N.computeSourceURL(a,E,u)),c({source:E,generatedLine:h.generatedLine,generatedColumn:h.generatedColumn,originalLine:h.originalLine,originalColumn:h.originalColumn,name:h.name===null?null:l.at(h.name)})}};Ie.prototype.allGeneratedPositionsFor=function(t){var r=N.getArg(t,"line"),n={source:N.getArg(t,"source"),originalLine:r,originalColumn:N.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",N.compareByOriginalPositions,wu.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:N.getArg(s,"generatedLine",null),column:N.getArg(s,"generatedColumn",null),lastColumn:N.getArg(s,"lastGeneratedColumn",null)}),s=this._originalMappings[++i];else for(var c=s.originalColumn;s&&s.originalLine===r&&s.originalColumn==c;)o.push({line:N.getArg(s,"generatedLine",null),column:N.getArg(s,"generatedColumn",null),lastColumn:N.getArg(s,"lastGeneratedColumn",null)}),s=this._originalMappings[++i]}return o};Xa.SourceMapConsumer=Ie;function at(e,t){var r=e;typeof e=="string"&&(r=N.parseSourceMapInput(e));var n=N.getArg(r,"version"),o=N.getArg(r,"sources"),i=N.getArg(r,"names",[]),s=N.getArg(r,"sourceRoot",null),a=N.getArg(r,"sourcesContent",null),c=N.getArg(r,"mappings"),l=N.getArg(r,"file",null);if(n!=this._version)throw new Error("Unsupported version: "+n);s&&(s=N.normalize(s)),o=o.map(String).map(N.normalize).map(function(A){return s&&N.isAbsolute(s)&&N.isAbsolute(A)?N.relative(s,A):A}),this._names=Zo.fromArray(i.map(String),!0),this._sources=Zo.fromArray(o,!0),this._absoluteSources=this._sources.toArray().map(function(A){return N.computeSourceURL(s,A,t)}),this.sourceRoot=s,this.sourcesContent=a,this._mappings=c,this._sourceMapURL=t,this.file=l}at.prototype=Object.create(Ie.prototype);at.prototype.consumer=Ie;at.prototype._findSourceIndex=function(e){var t=e;if(this.sourceRoot!=null&&(t=N.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=Zo.fromArray(t._names.toArray(),!0),i=n._sources=Zo.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 N.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 Q0;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 As(n.__originalMappings,N.compareByOriginalPositions),n};at.prototype._version=3;Object.defineProperty(at.prototype,"sources",{get:function(){return this._absoluteSources.slice()}});function Q0(){this.generatedLine=0,this.generatedColumn=0,this.source=null,this.originalLine=null,this.originalColumn=null,this.name=null}var yu=N.compareByGeneratedPositionsDeflatedNoLine;function S0(e,t){let r=e.length,n=e.length-t;if(!(n<=1))if(n==2){let o=e[t],i=e[t+1];yu(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(yu(s,a)<=0)break;e[i-1]=a,e[i]=s}else As(e,yu,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={},d={},m=[],h=[],E,x,I,p,y;let b=0;for(;A<l;)if(t.charAt(A)===";")n++,A++,o=0,S0(h,b),b=h.length;else if(t.charAt(A)===",")A++;else{for(E=new Q0,E.generatedLine=n,p=A;p<l&&!this._charIsMappingSeparator(t,p);p++);for(x=t.slice(A,p),I=[];A<p;)gv.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(E.generatedColumn=o+I[0],o=E.generatedColumn,I.length>1&&(E.source=a+I[1],a+=I[1],E.originalLine=i+I[2],i=E.originalLine,E.originalLine+=1,E.originalColumn=s+I[3],s=E.originalColumn,I.length>4&&(E.name=c+I[4],c+=I[4])),h.push(E),typeof E.originalLine=="number"){let S=E.source;for(;m.length<=S;)m.push(null);m[S]===null&&(m[S]=[]),m[S].push(E)}}S0(h,b),this.__generatedMappings=h;for(var w=0;w<m.length;w++)m[w]!=null&&As(m[w],N.compareByOriginalPositionsNoSource);this.__originalMappings=[].concat(...m)};at.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 wu.search(t,r,i,s)};at.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}};at.prototype.originalPositionFor=function(t){var r={generatedLine:N.getArg(t,"line"),generatedColumn:N.getArg(t,"column")},n=this._findMapping(r,this._generatedMappings,"generatedLine","generatedColumn",N.compareByGeneratedPositionsDeflated,N.getArg(t,"bias",Ie.GREATEST_LOWER_BOUND));if(n>=0){var o=this._generatedMappings[n];if(o.generatedLine===r.generatedLine){var i=N.getArg(o,"source",null);i!==null&&(i=this._sources.at(i),i=N.computeSourceURL(this.sourceRoot,i,this._sourceMapURL));var s=N.getArg(o,"name",null);return s!==null&&(s=this._names.at(s)),{source:i,line:N.getArg(o,"originalLine",null),column:N.getArg(o,"originalColumn",null),name:s}}}return{source:null,line:null,column:null,name:null}};at.prototype.hasContentsOfAllSources=function(){return this.sourcesContent?this.sourcesContent.length>=this._sources.size()&&!this.sourcesContent.some(function(t){return t==null}):!1};at.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=N.relative(this.sourceRoot,o));var i;if(this.sourceRoot!=null&&(i=N.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.')};at.prototype.generatedPositionFor=function(t){var r=N.getArg(t,"source");if(r=this._findSourceIndex(r),r<0)return{line:null,column:null,lastColumn:null};var n={source:r,originalLine:N.getArg(t,"line"),originalColumn:N.getArg(t,"column")},o=this._findMapping(n,this._originalMappings,"originalLine","originalColumn",N.compareByOriginalPositions,N.getArg(t,"bias",Ie.GREATEST_LOWER_BOUND));if(o>=0){var i=this._originalMappings[o];if(i.source===n.source)return{line:N.getArg(i,"generatedLine",null),column:N.getArg(i,"generatedColumn",null),lastColumn:N.getArg(i,"lastGeneratedColumn",null)}}return{line:null,column:null,lastColumn:null}};Xa.BasicSourceMapConsumer=at;function fr(e,t){var r=e;typeof e=="string"&&(r=N.parseSourceMapInput(e));var n=N.getArg(r,"version"),o=N.getArg(r,"sections");if(n!=this._version)throw new Error("Unsupported version: "+n);this._sources=new Zo,this._names=new Zo;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=N.getArg(s,"offset"),c=N.getArg(a,"line"),l=N.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 Ie(N.getArg(s,"map"),t)}})}fr.prototype=Object.create(Ie.prototype);fr.prototype.constructor=Ie;fr.prototype._version=3;Object.defineProperty(fr.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}});fr.prototype.originalPositionFor=function(t){var r={generatedLine:N.getArg(t,"line"),generatedColumn:N.getArg(t,"column")},n=wu.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}};fr.prototype.hasContentsOfAllSources=function(){return this._sections.every(function(t){return t.consumer.hasContentsOfAllSources()})};fr.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.')};fr.prototype.generatedPositionFor=function(t){for(var r=0;r<this._sections.length;r++){var n=this._sections[r];if(n.consumer._findSourceIndex(N.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}};fr.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=N.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)}As(this.__generatedMappings,N.compareByGeneratedPositionsDeflated),As(this.__originalMappings,N.compareByOriginalPositions)};Xa.IndexedSourceMapConsumer=fr});var T0=j(v0=>{var hv=Iu().SourceMapGenerator,Za=Xo(),Cv=/(\r?\n)/,Ev=10,ei="$$$isSourceNode$$$";function Lt(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[ei]=!0,n!=null&&this.add(n)}Lt.fromStringWithSourceMap=function(t,r,n){var o=new Lt,i=t.split(Cv),s=0,a=function(){var d=h(),m=h()||"";return d+m;function h(){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]||"",h=m.substr(0,d.generatedColumn-l);i[s]=m.substr(d.generatedColumn-l),l=d.generatedColumn,u(A,h),A=d;return}for(;c<d.generatedLine;)o.add(a()),c++;if(l<d.generatedColumn){var 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this._sourcesContents[Ne.toSetString(n)],Object.keys(this._sourcesContents).length===0&&(this._sourcesContents=null))};Xt.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. 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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)}};Xt.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,C=d.length;m<C;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+=fs.encode(l.generatedColumn-t),t=l.generatedColumn,l.source!=null&&(u=this._sources.indexOf(l.source),c+=fs.encode(u-s),s=u,c+=fs.encode(l.originalLine-1-o),o=l.originalLine-1,c+=fs.encode(l.originalColumn-n),n=l.originalColumn,l.name!=null&&(A=this._names.indexOf(l.name),c+=fs.encode(A-i),i=A)),a+=c}return a};Xt.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)};Xt.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};Xt.prototype.toString=function(){return JSON.stringify(this.toJSON())};L0.SourceMapGenerator=Xt});var R0=j(eo=>{eo.GREATEST_LOWER_BOUND=1;eo.LEAST_UPPER_BOUND=2;function Du(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?Du(s,t,r,n,o,i):i==eo.LEAST_UPPER_BOUND?t<n.length?t:-1:s:s-e>1?Du(e,s,r,n,o,i):i==eo.LEAST_UPPER_BOUND?s:e<0?-1:e}eo.search=function(t,r,n,o){if(r.length===0)return-1;var i=Du(-1,r.length,t,r,n,o||eo.GREATEST_LOWER_BOUND);if(i<0)return-1;for(;i-1>=0&&n(r[i],r[i-1],!0)===0;)--i;return i}});var O0=j(P0=>{function Fv(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 Pv(e){let t=Fv.toString();return new Function(`return ${t}`)()(e)}var F0=new WeakMap;P0.quickSort=function(e,t,r=0){let n=F0.get(t);n===void 0&&(n=Pv(t),F0.set(t,n)),n(e,t,r,e.length-1)}});var H0=j(tc=>{var L=ni(),Nu=R0(),oi=Tu().ArraySet,Ov=Su(),ds=O0().quickSort;function Ie(e,t){var r=e;return typeof e=="string"&&(r=L.parseSourceMapInput(e)),r.sections!=null?new ur(r,t):new it(r,t)}Ie.fromSourceMap=function(e,t){return it.fromSourceMap(e,t)};Ie.prototype._version=3;Ie.prototype.__generatedMappings=null;Object.defineProperty(Ie.prototype,"_generatedMappings",{configurable:!0,enumerable:!0,get:function(){return this.__generatedMappings||this._parseMappings(this._mappings,this.sourceRoot),this.__generatedMappings}});Ie.prototype.__originalMappings=null;Object.defineProperty(Ie.prototype,"_originalMappings",{configurable:!0,enumerable:!0,get:function(){return this.__originalMappings||this._parseMappings(this._mappings,this.sourceRoot),this.__originalMappings}});Ie.prototype._charIsMappingSeparator=function(t,r){var n=t.charAt(r);return n===";"||n===","};Ie.prototype._parseMappings=function(t,r){throw new Error("Subclasses must implement _parseMappings")};Ie.GENERATED_ORDER=1;Ie.ORIGINAL_ORDER=2;Ie.GREATEST_LOWER_BOUND=1;Ie.LEAST_UPPER_BOUND=2;Ie.prototype.eachMapping=function(t,r,n){var o=r||null,i=n||Ie.GENERATED_ORDER,s;switch(i){case Ie.GENERATED_ORDER:s=this._generatedMappings;break;case Ie.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 C=s[d],E=C.source===null?null:A.at(C.source);E!==null&&(E=L.computeSourceURL(a,E,u)),c({source:E,generatedLine:C.generatedLine,generatedColumn:C.generatedColumn,originalLine:C.originalLine,originalColumn:C.originalColumn,name:C.name===null?null:l.at(C.name)})}};Ie.prototype.allGeneratedPositionsFor=function(t){var r=L.getArg(t,"line"),n={source:L.getArg(t,"source"),originalLine:r,originalColumn:L.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",L.compareByOriginalPositions,Nu.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:L.getArg(s,"generatedLine",null),column:L.getArg(s,"generatedColumn",null),lastColumn:L.getArg(s,"lastGeneratedColumn",null)}),s=this._originalMappings[++i];else for(var c=s.originalColumn;s&&s.originalLine===r&&s.originalColumn==c;)o.push({line:L.getArg(s,"generatedLine",null),column:L.getArg(s,"generatedColumn",null),lastColumn:L.getArg(s,"lastGeneratedColumn",null)}),s=this._originalMappings[++i]}return o};tc.SourceMapConsumer=Ie;function it(e,t){var r=e;typeof e=="string"&&(r=L.parseSourceMapInput(e));var n=L.getArg(r,"version"),o=L.getArg(r,"sources"),i=L.getArg(r,"names",[]),s=L.getArg(r,"sourceRoot",null),a=L.getArg(r,"sourcesContent",null),c=L.getArg(r,"mappings"),l=L.getArg(r,"file",null);if(n!=this._version)throw new Error("Unsupported version: "+n);s&&(s=L.normalize(s)),o=o.map(String).map(L.normalize).map(function(A){return s&&L.isAbsolute(s)&&L.isAbsolute(A)?L.relative(s,A):A}),this._names=oi.fromArray(i.map(String),!0),this._sources=oi.fromArray(o,!0),this._absoluteSources=this._sources.toArray().map(function(A){return L.computeSourceURL(s,A,t)}),this.sourceRoot=s,this.sourcesContent=a,this._mappings=c,this._sourceMapURL=t,this.file=l}it.prototype=Object.create(Ie.prototype);it.prototype.consumer=Ie;it.prototype._findSourceIndex=function(e){var t=e;if(this.sourceRoot!=null&&(t=L.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=oi.fromArray(t._names.toArray(),!0),i=n._sources=oi.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 L.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 U0;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 ds(n.__originalMappings,L.compareByOriginalPositions),n};it.prototype._version=3;Object.defineProperty(it.prototype,"sources",{get:function(){return this._absoluteSources.slice()}});function U0(){this.generatedLine=0,this.generatedColumn=0,this.source=null,this.originalLine=null,this.originalColumn=null,this.name=null}var ku=L.compareByGeneratedPositionsDeflatedNoLine;function G0(e,t){let r=e.length,n=e.length-t;if(!(n<=1))if(n==2){let o=e[t],i=e[t+1];ku(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(ku(s,a)<=0)break;e[i-1]=a,e[i]=s}else ds(e,ku,t)}it.prototype._parseMappings=function(t,r){var n=1,o=0,i=0,s=0,a=0,c=0,l=t.length,A=0,u={},d={},m=[],C=[],E,x,I,p,y;let B=0;for(;A<l;)if(t.charAt(A)===";")n++,A++,o=0,G0(C,B),B=C.length;else if(t.charAt(A)===",")A++;else{for(E=new U0,E.generatedLine=n,p=A;p<l&&!this._charIsMappingSeparator(t,p);p++);for(x=t.slice(A,p),I=[];A<p;)Ov.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(E.generatedColumn=o+I[0],o=E.generatedColumn,I.length>1&&(E.source=a+I[1],a+=I[1],E.originalLine=i+I[2],i=E.originalLine,E.originalLine+=1,E.originalColumn=s+I[3],s=E.originalColumn,I.length>4&&(E.name=c+I[4],c+=I[4])),C.push(E),typeof E.originalLine=="number"){let S=E.source;for(;m.length<=S;)m.push(null);m[S]===null&&(m[S]=[]),m[S].push(E)}}G0(C,B),this.__generatedMappings=C;for(var b=0;b<m.length;b++)m[b]!=null&&ds(m[b],L.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 Nu.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:L.getArg(t,"line"),generatedColumn:L.getArg(t,"column")},n=this._findMapping(r,this._generatedMappings,"generatedLine","generatedColumn",L.compareByGeneratedPositionsDeflated,L.getArg(t,"bias",Ie.GREATEST_LOWER_BOUND));if(n>=0){var o=this._generatedMappings[n];if(o.generatedLine===r.generatedLine){var i=L.getArg(o,"source",null);i!==null&&(i=this._sources.at(i),i=L.computeSourceURL(this.sourceRoot,i,this._sourceMapURL));var s=L.getArg(o,"name",null);return s!==null&&(s=this._names.at(s)),{source:i,line:L.getArg(o,"originalLine",null),column:L.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=L.relative(this.sourceRoot,o));var i;if(this.sourceRoot!=null&&(i=L.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=L.getArg(t,"source");if(r=this._findSourceIndex(r),r<0)return{line:null,column:null,lastColumn:null};var n={source:r,originalLine:L.getArg(t,"line"),originalColumn:L.getArg(t,"column")},o=this._findMapping(n,this._originalMappings,"originalLine","originalColumn",L.compareByOriginalPositions,L.getArg(t,"bias",Ie.GREATEST_LOWER_BOUND));if(o>=0){var i=this._originalMappings[o];if(i.source===n.source)return{line:L.getArg(i,"generatedLine",null),column:L.getArg(i,"generatedColumn",null),lastColumn:L.getArg(i,"lastGeneratedColumn",null)}}return{line:null,column:null,lastColumn:null}};tc.BasicSourceMapConsumer=it;function ur(e,t){var r=e;typeof e=="string"&&(r=L.parseSourceMapInput(e));var n=L.getArg(r,"version"),o=L.getArg(r,"sections");if(n!=this._version)throw new Error("Unsupported version: "+n);this._sources=new oi,this._names=new oi;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=L.getArg(s,"offset"),c=L.getArg(a,"line"),l=L.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 Ie(L.getArg(s,"map"),t)}})}ur.prototype=Object.create(Ie.prototype);ur.prototype.constructor=Ie;ur.prototype._version=3;Object.defineProperty(ur.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}});ur.prototype.originalPositionFor=function(t){var r={generatedLine:L.getArg(t,"line"),generatedColumn:L.getArg(t,"column")},n=Nu.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}};ur.prototype.hasContentsOfAllSources=function(){return this._sections.every(function(t){return t.consumer.hasContentsOfAllSources()})};ur.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.')};ur.prototype.generatedPositionFor=function(t){for(var r=0;r<this._sections.length;r++){var n=this._sections[r];if(n.consumer._findSourceIndex(L.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}};ur.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=L.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)}ds(this.__generatedMappings,L.compareByGeneratedPositionsDeflated),ds(this.__originalMappings,L.compareByOriginalPositions)};tc.IndexedSourceMapConsumer=ur});var q0=j(j0=>{var Gv=_u().SourceMapGenerator,rc=ni(),Uv=/(\r?\n)/,Hv=10,ii="$$$isSourceNode$$$";function Ot(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[ii]=!0,n!=null&&this.add(n)}Ot.fromStringWithSourceMap=function(t,r,n){var o=new Ot,i=t.split(Uv),s=0,a=function(){var d=C(),m=C()||"";return d+m;function C(){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]||"",C=m.substr(0,d.generatedColumn-l);i[s]=m.substr(d.generatedColumn-l),l=d.generatedColumn,u(A,C),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=rc.join(n,d)),o.setSourceContent(d,m))}),o;function u(d,m){if(d===null||d.source===void 0)o.add(m);else{var C=n?rc.join(n,d.source):d.source;o.add(new Ot(d.originalLine,d.originalColumn,C,m,d.name))}}};Ot.prototype.add=function(t){if(Array.isArray(t))t.forEach(function(r){this.add(r)},this);else if(t[ii]||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};Ot.prototype.prepend=function(t){if(Array.isArray(t))for(var r=t.length-1;r>=0;r--)this.prepend(t[r]);else if(t[ii]||typeof t=="string")this.children.unshift(t);else throw new TypeError("Expected a SourceNode, string, or an array of SourceNodes and strings. 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 UniProt/Swiss-Prot|P36835|IL2_CAPHI        -----------LLGVGLNPKFLTP------------------------------------
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hideGapsEffective(){return e.hideGaps&&(e.collapsed.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 co[e.colorSchemeName]??co[Ps]},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?qf(t,e.currentAlignment,e.msaFormat):null},get numColumns(){return(this.MSA?.getWidth()??0)-this.blanks.length},get tree(){let t=e.data.tree;return t?Ci(fN(t)):this.MSA?.getTree()??{noTree:!0,children:[],id:"empty",name:"empty"}},get rowNames(){return this.leaves.map(t=>t.data.name)},get rowNamesSet(){return new Map(this.leaves.map((t,r)=>[t.data.name,r]))},get mouseOverRowName(){let{mouseRow:t}=e;return t===void 0?void 0:this.leaves[t]?.data.name},get hoveredInsertion(){let{mouseCol:t,mouseRow:r}=e;if(t!==void 0&&r!==void 0){let n=this.leaves[r]?.data.name;if(n){let o=this.insertionPositions.get(n)?.find(i=>i.pos===t);if(o)return{rowName:n,col:t,letters:o.letters}}}},get root(){let t=kp(this.tree,r=>r.children);if(Np(t,r=>r.children.length>0?0:1),Lp(t,(r,n)=>(r.data.length??1)-(n.data.length??1)),e.showOnly){let r=Ca(t,n=>n.data.id===e.showOnly);r&&(t=r)}for(let r of e.collapsed){let n=Ca(t,o=>o.data.id===r);n&&(n.children?Pp(n):n.parent?.children&&(n.parent.children=n.parent.children.filter(o=>o.data.id!==r)))}return t},get msaAreaWidth(){return e.width-e.treeAreaWidth-e.resizeHandleWidth},get treeAreaWidthMinusMargin(){return 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s=0;s<r.length;s+=o){let a=r.slice(s,s+o),c=a.join(",");try{let A=await(await fetch(xl({db:"taxonomy",id:c,retmode:"xml"}))).text(),u=new Map,d=/<Taxon>\s*<TaxId>(\d+)<\/TaxId>/g,m;for(;(m=d.exec(A))!==null;){let h=Number(m[1]),E=m.index,x=1,I=E+m[0].length;for(;x>0&&I<A.length;){let S=A.indexOf("<Taxon>",I),M=A.indexOf("</Taxon>",I);if(M===-1)break;S!==-1&&S<M?(x++,I=S+7):(x--,I=M+8)}let p=A.slice(E,I),y=u.get(h),b=p.includes("<LineageEx>"),w=y?.includes("<LineageEx>");(!y||b&&!w)&&u.set(h,p)}for(let h of a){let E=u.get(h);if(E){let x=/<GenbankCommonName>(.*?)<\/GenbankCommonName>/.exec(E),I=/<CommonName>(.*?)<\/CommonName>/.exec(E),p=/<ScientificName>(.*?)<\/ScientificName>/.exec(E),y=x?.[1]??I?.[1],b=p?.[1]??"";t.set(h,{sciname:b,commonName:y}),i.push({taxid:h,sciname:b,commonName:y})}}}catch(l){console.error("Failed to fetch taxonomy data:",l)}}return i.length>0&&await _N(i),t}async function 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i=o[1],s=Ln(i,"GBInterval_from"),a=Ln(i,"GBInterval_to"),c=Ln(i,"GBInterval_point");s&&a?(t.push(Number(s)),r.push(Number(a))):c&&(t.push(Number(c)),r.push(Number(c)))}return t.length>0?{start:Math.min(...t),end:Math.max(...r)}:void 0}var FN=2;function PN(e){let t=Ln(e,"GBFeature_key"),r=LN(e),n=r.db_xref,o=RN(e);if((t==="Region"||t==="Site")&&n?.startsWith("CDD:")&&o&&o.end-o.start+1>=FN){let i=n.replace("CDD:",""),s=t==="Region",a=r.note?.split(/[[(]/)[0]?.trim(),c=s?r.region_name??i:a||r.site_type||"site",l=s?i:`${i}:${c}`;return{signature:{entry:{name:c,description:r.note??c,accession:l}},locations:[o]}}}function ON(e){let t=new Map,r=/<GBSeq>([\s\S]*?)<\/GBSeq>/g,n;for(;(n=r.exec(e))!==null;){let o=n[1],i=[],s=/<GBFeature>([\s\S]*?)<\/GBFeature>/g,a;for(;(a=s.exec(o))!==null;){let c=PN(a[1]);c&&i.push(c)}for(let c of[Ln(o,"GBSeq_accession-version"),Ln(o,"GBSeq_primary-accession")])c&&t.set(c,i)}return t}async function NS(e){let t=[...new Set(e)].filter(Boolean),r=new Map,n=await DS(t),o=[];t.forEach((a,c)=>{let l=n[c];l?r.set(a,l.matches):o.push(a)});let i=[],s=100;for(let a=0;a<o.length;a+=s){let c=o.slice(a,a+s),l=await jr(xl({db:"protein",id:c.join(","),rettype:"gp",retmode:"xml"})),A=ON(l);for(let u of c){let d=A.get(u)??[];r.set(u,d),i.push({accession:u,matches:d})}}return i.length>0&&await kS(i),r}async function LS(e){let t=e.data.treeMetadata;if(!t)throw new Error("No sequence metadata available to look up domains");let r=JSON.parse(t),n=Object.entries(r).map(([s,a])=>({rowName:s,accession:a.Accession})).filter(s=>!!s.accession);if(n.length===0)throw new Error("No NCBI accessions found in alignment rows");e.setProgress(`Fetching protein domains from NCBI for ${n.length} sequences...`);let o=await NS(n.map(s=>s.accession)),i={};for(let{rowName:s,accession:a}of n){let c=o.get(a);c&&c.length>0&&(i[s]={matches:c,xref:[{id:s}]})}if(Object.keys(i).length===0)throw new Error("No CDD domain annotations found for these proteins");e.setDomains(i)}Ai();var GN="jbrowse-msaview-data",UN=1,Hs="msa-data";async function Ud(){return en(GN,UN,{upgrade(e){e.objectStoreNames.contains(Hs)||e.createObjectStore(Hs,{keyPath:"id"}).createIndex("timestamp","timestamp",{unique:!1})}})}function RS(){return`msa-${Date.now()}-${Math.random().toString(36).slice(2,11)}`}async function FS(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(Hs,n),!0}catch(r){return console.warn("Failed to store MSA data:",r),!1}}async function PS(e){try{let r=await(await Ud()).get(Hs,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 OS(e=10080*60*1e3){try{let t=await Ud(),r=Date.now()-e,i=await t.transaction(Hs,"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 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sS(e){if(e.length<2)throw new Error("Need at least 2 sequences to build a tree");let t=e.map(o=>o[0]),r=QN(e),n=MN(r,t);return vN(n)+";"}var fl,BN,iS,aS=g(()=>{fl="ARNDCQEGHILKMFPSTWYVBZX*",BN=[[4,-1,-2,-2,0,-1,-1,0,-2,-1,-1,-1,-1,-2,-1,1,0,-3,-2,0,-2,-1,0,-4],[-1,5,0,-2,-3,1,0,-2,0,-3,-2,2,-1,-3,-2,-1,-1,-3,-2,-3,-1,0,-1,-4],[-2,0,6,1,-3,0,0,0,1,-3,-3,0,-2,-3,-2,1,0,-4,-2,-3,3,0,-1,-4],[-2,-2,1,6,-3,0,2,-1,-1,-3,-4,-1,-3,-3,-1,0,-1,-4,-3,-3,4,1,-1,-4],[0,-3,-3,-3,9,-3,-4,-3,-3,-1,-1,-3,-1,-2,-3,-1,-1,-2,-2,-1,-3,-3,-2,-4],[-1,1,0,0,-3,5,2,-2,0,-3,-2,1,0,-3,-1,0,-1,-2,-1,-2,0,3,-1,-4],[-1,0,0,2,-4,2,5,-2,0,-3,-3,1,-2,-3,-1,0,-1,-3,-2,-2,1,4,-1,-4],[0,-2,0,-1,-3,-2,-2,6,-2,-4,-4,-2,-3,-3,-2,0,-2,-2,-3,-3,-1,-2,-1,-4],[-2,0,1,-1,-3,0,0,-2,8,-3,-3,-1,-2,-1,-2,-1,-2,-2,2,-3,0,0,-1,-4],[-1,-3,-3,-3,-1,-3,-3,-4,-3,4,2,-3,1,0,-3,-2,-1,-3,-1,3,-3,-3,-1,-4],[-1,-2,-3,-4,-1,-2,-3,-4,-3,2,4,-2,2,0,-3,-2,-1,-2,-1,1,-4,-3,-1,-4],[-1,2,0,-1,-3,1,1,-2,-1,-3,-2,5,-1,-3,-1,0,-1,-3,-2,-2,0,1,-1,-4],[-1,-1,-2,-3,-1,0,-2,-3,-2,1,2,-1,5,0,-2,-1,-1,-1,-1,1,-3,-1,-1,-4],[-2,-3,-3,-3,-2,-3,-3,-3,-1,0,0,-3,0,6,-4,-2,-2,1,3,-1,-3,-3,-1,-4],[-1,-2,-2,-1,-3,-1,-1,-2,-2,-3,-3,-1,-2,-4,7,-1,-1,-4,-3,-2,-2,-1,-2,-4],[1,-1,1,0,-1,0,0,0,-1,-2,-2,0,-1,-2,-1,4,1,-3,-2,-2,0,0,0,-4],[0,-1,0,-1,-1,-1,-1,-2,-2,-1,-1,-1,-1,-2,-1,1,5,-2,-2,0,-1,-1,0,-4],[-3,-3,-4,-4,-2,-2,-3,-2,-2,-3,-2,-3,-1,1,-4,-3,-2,11,2,-3,-4,-3,-2,-4],[-2,-2,-2,-3,-2,-1,-2,-3,2,-1,-1,-2,-1,3,-3,-2,-2,2,7,-1,-3,-2,-1,-4],[0,-3,-3,-3,-1,-2,-2,-3,-3,3,1,-2,1,-1,-2,-2,0,-3,-1,4,-3,-2,-1,-4],[-2,-1,3,4,-3,0,1,-1,0,-3,-4,0,-3,-3,-2,0,-1,-4,-3,-3,4,1,-1,-4],[-1,0,0,1,-3,3,4,-2,0,-3,-3,1,-1,-3,-1,0,-1,-3,-2,-2,1,4,-1,-4],[0,-1,-1,-1,-2,-1,-1,-1,-1,-1,-1,-1,-1,-1,-2,0,0,-2,-1,-1,-1,-1,-1,-4],[-4,-4,-4,-4,-4,-4,-4,-4,-4,-4,-4,-4,-4,-4,-4,-4,-4,-4,-4,-4,-4,-4,-4,1]],iS=new Map;for(let e=0;e<fl.length;e++){let t=new Map;for(let r=0;r<fl.length;r++)t.set(fl[r],BN[e][r]);iS.set(fl[e],t)}});function Hd(e){let t=[],r=0;for(;r<e.length&&(r=e.indexOf("{",r),r!==-1);){let n=1,o=r+1;for(r++;r<e.length&&n>0;)e[r]==="{"?n++:e[r]==="}"&&n--,r++;n===0&&t.push(e.slice(o,r-1).trim())}return t}function _N(e,t){let r=e.indexOf("{",t);if(r===-1)return;let n=1,o=r+1;for(;o<e.length&&n>0;)e[o]==="{"?n++:e[o]==="}"&&n--,o++;return n===0?e.slice(r+1,o-1).trim():void 0}function cS(e){let t=e.replace(/\s+/g," ").replace(/\s*{\s*/g,"{").replace(/\s*}\s*/g,"}").replace(/\s*,\s*/g,",").replace(/\s*::\s*=\s*/g,"::=").replace(/^.*?::=/,""),r=DN(t),{fdict:n,nodes:o}=r;if(n===void 0||o===void 0)throw new Error(`invalid BioTreeContainer ASN.1: missing '${n===void 0?"fdict":"nodes"}' section`);let i=Object.fromEntries(Hd(n).flatMap(s=>{let a=kN(s);return a?[[a.id,TN[a.name]||a.name]]:[]}));return Hd(o).flatMap(s=>{let a=NN(s);if(!a)return[];let{features:c=[],...l}=a;return[{...l,...Object.fromEntries(c.map(A=>[i[A.featureid],A.value]))}]})}function DN(e){let t={},r=e.trim();r.startsWith("{")&&r.endsWith("}")&&(r=r.slice(1,-1).trim());let n=0;for(;n<r.length;){for(;n<r.length&&/\s/.test(r[n]);)n++;if(n>=r.length)break;let o=n;for(;n<r.length&&/\w/.test(r[n]);)n++;if(n>=r.length||r[n]!==" "&&r[n]!=="{"){n=r.indexOf(",",n),n=n===-1?r.length:n+1;continue}let i=r.slice(o,n).trim();for(;n<r.length&&/\s/.test(r[n]);)n++;if(n>=r.length||r[n]!=="{"){n=r.indexOf(",",n),n=n===-1?r.length:n+1;continue}let s=1,a=n+1;for(n++;n<r.length&&s>0;)r[n]==="{"?s++:r[n]==="}"&&s--,n++;s===0&&(t[i]=r.slice(a,n-1).trim()),n=r.indexOf(",",n),n=n===-1?r.length:n+1}return t}function kN(e){let t=/id\s+(\d+)/.exec(e),r=/name\s+"((?:[^"\\]|\\.)*)"/s.exec(e);return!t||!r?null:{id:parseInt(t[1],10),name:r[1].replace(/\\"/g,'"').replace(/\\\\/g,"\\")}}function NN(e){let t=/id\s+(\d+)/.exec(e);if(!t)return null;let r=/parent\s+(\d+)/.exec(e),n=e.indexOf("features"),o=n!==-1?_N(e,n):void 0;return{id:parseInt(t[1],10),...r?{parent:parseInt(r[1],10)}:{},features:o?Hd(o).flatMap(i=>{let s=LN(i);return s?[s]:[]}):[]}}function LN(e){let t=/featureid\s+(\d+)/.exec(e),r=/value\s+"((?:[^"\\]|\\.)*)"/s.exec(e);return!t||!r?null:{featureid:parseInt(t[1],10),value:r[1].replace(/\\"/g,'"').replace(/\\\\/g,"\\")}}var TN,lS=g(()=>{TN={$NODE_COLLAPSED:"collapsed",$NODE_COLOR:"color",$LABEL_BG_COLOR:"color","seq-id":"seqId","seq-title":"seqTitle","align-index":"alignIndex","accession-nbr":"accessionNbr","blast-name":"blastName","common-name":"commonName","leaf-count":"leafCount"}});function jd(e,t){let r=0,n=0,o=0,i=e.length;for(;n<i&&e[n]===o;)n++,o++;for(;r<t;)for(r++,o++;n<i&&e[n]===o;)n++,o++;return o}function AS(e,t){let r=0,n=e.length-1;for(;r<=n;){let i=Math.floor((r+n)/2);if(e[i]===t)return;e[i]<t?r=i+1:n=i-1}return t-r}function RN({seq:e,blanks:t,visibleCol:r}){let n=jd(t,r),o=e.length;if(n<o&&zi(e[n]))return;let i=0;for(let s=0;s<n&&s<o;s++)zi(e[s])||i++;return n<o?i:void 0}function uS({rowName:e,visibleCol:t,rowMap:r,blanks:n}){let o=r.get(e);return o!==void 0?RN({seq:o,visibleCol:t,blanks:n}):void 0}var fS=g(()=>{mn()});function dS({row:e,seqPos:t}){let r=0,n=0;for(;n<e.length;){if(!zi(e[n])){if(r===t)return n;r++}n++}return t===0?0:n}var mS=g(()=>{mn()});function pS(e,t){let r=URL.createObjectURL(e),n=document.createElement("a");n.href=r,n.download=t,n.click(),setTimeout(()=>{URL.revokeObjectURL(r)},4e4)}var gS=g(()=>{});function PN(e){return e.startsWith("BioTreeContainer")?JB(cS(e)):co(e.startsWith("SEQ")?Rc(e).tree:e)}function ON(){return K.types.compose(XB(),rS(),eS(),K.types.model("MsaView",{id:mo.ElementId,showDomains:!1,hideGaps:!0,allowedGappyness:100,subFeatureRows:!1,type:K.types.literal("MsaView"),drawMsaLetters:!0,scrollZoom:!1,height:K.types.optional(K.types.number,550),rowHeight:16,scrollY:0,scrollX:0,colWidth:12,treeFilehandle:K.types.maybe(mo.FileLocation),msaFilehandle:K.types.maybe(mo.FileLocation),treeMetadataFilehandle:K.types.maybe(mo.FileLocation),gffFilehandle:K.types.maybe(mo.FileLocation),currentAlignment:0,collapsed:K.types.array(K.types.string),showOnly:K.types.maybe(K.types.string),turnedOffTracks:K.types.map(K.types.boolean),data:K.types.optional(zB(),{tree:"",msa:"",treeMetadata:""}),featureFilters:K.types.map(K.types.boolean),relativeTo:K.types.maybe(K.types.string),highlightColumns:K.types.frozen()})).volatile(()=>({headerHeight:0,status:void 0,highResScaleFactor:typeof window>"u"?1:window.devicePixelRatio,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,minimapHeight:56,conservationTrackHeight:40,marginLeft:20,error:void 0,interProAnnotations:void 0})).actions(e=>({drawRelativeTo(t){e.relativeTo=t},setHideGaps(t){e.hideGaps=t},setAllowedGappyness(t){e.allowedGappyness=t},setLoadingMSA(t){e.loadingMSA=t},setLoadingTree(t){e.loadingTree=t},setWidth(t){e.volatileWidth=t},setHighResScaleFactor(t){e.highResScaleFactor=t},setHeight(t){e.height=t},setError(t){e.error=t},setMousePos(t,r){e.mouseCol=t,e.mouseRow=r},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)},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.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 ao[e.colorSchemeName]??ao[Hs]},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?td(t,e.currentAlignment,e.msaFormat):null},get numColumns(){return(this.MSA?.getWidth()??0)-this.blanks.length},get tree(){let t=e.data.tree;return t?xi(PN(t)):this.MSA?.getTree()??{noTree:!0,children:[],id:"empty",name:"empty"}},get rowNames(){return this.leaves.map(t=>t.data.name)},get rowNamesSet(){return new Map(this.leaves.map((t,r)=>[t.data.name,r]))},get mouseOverRowName(){let{mouseRow:t}=e;return t===void 0?void 0:this.leaves[t]?.data.name},get hoveredInsertion(){let{mouseCol:t,mouseRow:r}=e;if(t!==void 0&&r!==void 0){let n=this.leaves[r]?.data.name;if(n){let o=this.insertionPositions.get(n)?.find(i=>i.pos===t);if(o)return{rowName:n,col:t,letters:o.letters}}}},get root(){let t=Yp(this.tree,r=>r.children);if(Wp(t,r=>r.children.length>0?0:1),zp(t,(r,n)=>(r.data.length??1)-(n.data.length??1)),e.showOnly){let r=xa(t,n=>n.data.id===e.showOnly);r&&(t=r)}for(let r of e.collapsed){let n=xa(t,o=>o.data.id===r);n&&(n.children?Xp(n):n.parent?.children&&(n.parent.children=n.parent.children.filter(o=>o.data.id!==r)))}return t},get msaAreaWidth(){return e.width-e.treeAreaWidth-e.resizeHandleWidth},get treeAreaWidthMinusMargin(){return e.treeAreaWidth-e.marginLeft},get blanks(){let{hideGapsEffective:t,realAllowedGappyness:r}=e;if(!t)return[];let n=this.leaves.map(l=>this.MSA?.getRow(l.data.name)).filter(je.notEmpty);if(n.length===0)return[];let o=n[0].length,i=n.length,s=Math.ceil(r/100*i),a=new Uint16Array(o);for(let l=0;l<i;l++){let A=n[l];for(let u=0;u<o;u++)A.charCodeAt(u)-45>>>0<=1&&a[u]++}let c=[];for(let l=0;l<o;l++)a[l]>=s&&c.push(l);return c},get blanksSet(){return new Set(this.blanks)},get insertionPositions(){let{blanks:t,rows:r}=this;if(t.length===0||!e.hideGapsEffective)return new Map;let n=new Map;for(let[o,i]of r){let s=qp(t,i);s.length>0&&n.set(o,s)}return n},get rows(){let t=this.MSA;return 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(){let t=this.columns2d;return new Map(this.rows.map((r,n)=>[r[0],t[n]]))},get columns2d(){let{hideGapsEffective:t}=e;return this.rows.map(([,r])=>(t?vA(this.blanks,r):r).toUpperCase())},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)+1}return t},get colStatsSums(){return this.colStats.map(t=>(0,je.sum)(Object.values(t)))},get sequenceType(){let t=new Set;for(let s of this.colStats)for(let a of Object.keys(s))a!=="-"&&a!=="."&&t.add(a);let r=new Set(["A","C","G","T","N"]),n=new Set(["A","C","G","U","N"]),o=t.size>0&&[...t].every(s=>r.has(s)),i=t.size>0&&[...t].every(s=>n.has(s));return o?"dna":i?"rna":"amino"},get colConsensus(){let{colStats:t,colStatsSums:r}=this;return t.map((n,o)=>{let i=r[o];if(!i)return{letter:"",color:void 0};let s=0,a="";for(let[l,A]of Object.entries(n))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 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Error("No hits found")}throw new Error(`BLAST ${e} returned unexpected status: ${o??"unknown"}`)}})}pi();var KN="jbrowse-plugin-msaview",XN="colin.diesh@gmail.com",ZN="https://eutils.ncbi.nlm.nih.gov/entrez/eutils";function bl(e){let t=new URLSearchParams({...e,tool:KN,email:XN});return`${ZN}/efetch.fcgi?${t.toString()}`}var eL="jbrowse-msaview-taxonomy-cache",Js="common-names",tL=2;async function US(){return en(eL,tL,{upgrade(e){e.objectStoreNames.contains(Js)&&e.deleteObjectStore(Js),e.createObjectStore(Js,{keyPath:"taxid"})}})}async function rL(e){let r=(await US()).transaction(Js,"readonly"),n=await Promise.all(e.map(o=>r.store.get(o)));return await r.done,n}async function nL(e){let r=(await US()).transaction(Js,"readwrite");for(let n of e)await r.store.put(n);await r.done}async function HS(e){let t=new Map,r=[],n=await rL(e);for(let s=0;s<e.length;s++){let a=e[s],c=n[s];c?t.set(a,{sciname:c.sciname,commonName:c.commonName}):r.push(a)}if(r.length===0)return t;let o=100,i=[];for(let s=0;s<r.length;s+=o){let a=r.slice(s,s+o),c=a.join(",");try{let A=await(await fetch(bl({db:"taxonomy",id:c,retmode:"xml"}))).text(),u=new Map,d=/<Taxon>\s*<TaxId>(\d+)<\/TaxId>/g,m;for(;(m=d.exec(A))!==null;){let C=Number(m[1]),E=m.index,x=1,I=E+m[0].length;for(;x>0&&I<A.length;){let S=A.indexOf("<Taxon>",I),M=A.indexOf("</Taxon>",I);if(M===-1)break;S!==-1&&S<M?(x++,I=S+7):(x--,I=M+8)}let p=A.slice(E,I),y=u.get(C),B=p.includes("<LineageEx>"),b=y?.includes("<LineageEx>");(!y||B&&!b)&&u.set(C,p)}for(let C of a){let E=u.get(C);if(E){let x=/<GenbankCommonName>(.*?)<\/GenbankCommonName>/.exec(E),I=/<CommonName>(.*?)<\/CommonName>/.exec(E),p=/<ScientificName>(.*?)<\/ScientificName>/.exec(E),y=x?.[1]??I?.[1],B=p?.[1]??"";t.set(C,{sciname:B,commonName:y}),i.push({taxid:C,sciname:B,commonName:y})}}}catch(l){console.error("Failed to fetch taxonomy data:",l)}}return i.length>0&&await nL(i),t}async function jS({self:e}){let{baseUrl:t,blastDatabase:r,blastProgram:n,msaAlgorithm:o,proteinSequence:i,selectedTranscript:s,rid:a}=e.blastParams,c=Cl(i),l,A;if(a){e.setRid(a);let I=await Kd({rid:a,baseUrl:t,onProgress:p=>{e.setProgress(p)}});l=I.hits,A=I.rid}else{let I=await GS({query:c,blastDatabase:r,blastProgram:n,baseUrl:t,onProgress:p=>{e.setProgress(p)},onRid:p=>{e.setRid(p)}});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 HS(u),m={},C=l.map(I=>{let p=I.description[0]??{accession:"unknown",id:"unknown",sciname:"unknown"},y=QS(p,d),B=MS(I.hsps[0]?.hseq??"");return m[y]=oL(p,d),`>${y}
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+`),onProgress:I=>{e.setProgress(I)}}),x=JSON.stringify(m);return await DS({proteinSequence:c,blastDatabase:r,blastProgram:n,msaAlgorithm:o,msa:E.msa,tree:E.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")}),{...E,treeMetadata:x}}function oL(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 qS=f(de());function JS({model:e}){let{hovered:t}=(0,qS.getSession)(e),{querySeqName:r,transcriptToMsaMap:n,connectedView:o,mafRegion:i}=e;if(!o?.initialized||!qn(t))return;let{coord:s,refName:a}=t.hoverPosition;if(i)return a!==i.refName||!o.assemblyNames.includes(i.assemblyName)||s<i.start||s>=i.end?void 0:e.seqPosToVisibleCol(r,s-i.start);if(n){let c=n.g2p[s];if(c!==void 0)return e.seqPosToVisibleCol(r,c)}}pi();var iL="jbrowse-msaview-domain-cache",Bl="domains",sL=1;async function VS(){return en(iL,sL,{upgrade(e){e.objectStoreNames.contains(Bl)||e.createObjectStore(Bl,{keyPath:"accession"})}})}async function YS(e){let r=(await VS()).transaction(Bl,"readonly"),n=await Promise.all(e.map(o=>r.store.get(o)));return await r.done,n}async function WS(e){let r=(await VS()).transaction(Bl,"readwrite");for(let n of e)await r.store.put(n);await r.done}function Fn(e,t){return new RegExp(`<${t}>(.*?)</${t}>`,"s").exec(e)?.[1]}function aL(e){let t={},r=/<GBQualifier>([\s\S]*?)<\/GBQualifier>/g,n;for(;(n=r.exec(e))!==null;){let o=Fn(n[1],"GBQualifier_name"),i=Fn(n[1],"GBQualifier_value");o&&i!==void 0&&t[o]===void 0&&(t[o]=i)}return t}function cL(e){let t=[],r=[],n=/<GBInterval>([\s\S]*?)<\/GBInterval>/g,o;for(;(o=n.exec(e))!==null;){let i=o[1],s=Fn(i,"GBInterval_from"),a=Fn(i,"GBInterval_to"),c=Fn(i,"GBInterval_point");s&&a?(t.push(Number(s)),r.push(Number(a))):c&&(t.push(Number(c)),r.push(Number(c)))}return t.length>0?{start:Math.min(...t),end:Math.max(...r)}:void 0}var lL=2;function AL(e){let t=Fn(e,"GBFeature_key"),r=aL(e),n=r.db_xref,o=cL(e);if((t==="Region"||t==="Site")&&n?.startsWith("CDD:")&&o&&o.end-o.start+1>=lL){let i=n.replace("CDD:",""),s=t==="Region",a=r.note?.split(/[[(]/)[0]?.trim(),c=s?r.region_name??i:a||r.site_type||"site",l=s?i:`${i}:${c}`;return{signature:{entry:{name:c,description:r.note??c,accession:l}},locations:[o]}}}function uL(e){let t=new Map,r=/<GBSeq>([\s\S]*?)<\/GBSeq>/g,n;for(;(n=r.exec(e))!==null;){let o=n[1],i=[],s=/<GBFeature>([\s\S]*?)<\/GBFeature>/g,a;for(;(a=s.exec(o))!==null;){let c=AL(a[1]);c&&i.push(c)}for(let c of[Fn(o,"GBSeq_accession-version"),Fn(o,"GBSeq_primary-accession")])c&&t.set(c,i)}return t}async function zS(e){let t=[...new Set(e)].filter(Boolean),r=new Map,n=await YS(t),o=[];t.forEach((a,c)=>{let l=n[c];l?r.set(a,l.matches):o.push(a)});let i=[],s=100;for(let a=0;a<o.length;a+=s){let c=o.slice(a,a+s),l=await Ur(bl({db:"protein",id:c.join(","),rettype:"gp",retmode:"xml"})),A=uL(l);for(let u of c){let d=A.get(u)??[];r.set(u,d),i.push({accession:u,matches:d})}}return i.length>0&&await WS(i),r}async function $S(e){let t=e.data.treeMetadata;if(!t)throw new Error("No sequence metadata available to look up domains");let r=JSON.parse(t),n=Object.entries(r).map(([s,a])=>({rowName:s,accession:a.Accession})).filter(s=>!!s.accession);if(n.length===0)throw new Error("No NCBI accessions found in alignment rows");e.setProgress(`Fetching protein domains from NCBI for ${n.length} sequences...`);let o=await zS(n.map(s=>s.accession)),i={};for(let{rowName:s,accession:a}of n){let c=o.get(a);c&&c.length>0&&(i[s]={matches:c,xref:[{id:s}]})}if(Object.keys(i).length===0)throw new Error("No CDD domain annotations found for these proteins");e.setDomains(i)}pi();var fL="jbrowse-msaview-data",dL=1,Vs="msa-data";async function Xd(){return en(fL,dL,{upgrade(e){e.objectStoreNames.contains(Vs)||e.createObjectStore(Vs,{keyPath:"id"}).createIndex("timestamp","timestamp",{unique:!1})}})}function KS(){return`msa-${Date.now()}-${Math.random().toString(36).slice(2,11)}`}async function XS(e,t){try{let r=await Xd(),n={id:e,msa:t.msa,tree:t.tree,treeMetadata:t.treeMetadata,timestamp:Date.now()};return await r.put(Vs,n),!0}catch(r){return console.warn("Failed to store MSA data:",r),!1}}async function ZS(e){try{let r=await(await Xd()).get(Vs,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 e1(e=10080*60*1e3){try{let t=await Xd(),r=Date.now()-e,i=await t.transaction(Vs,"readwrite").store.index("timestamp").openCursor(IDBKeyRange.upperBound(r)),s=0;for(;i;)await i.delete(),s++,i=await i.continue();return s}catch(t){return console.warn("Failed to cleanup old MSA data:",t),0}}Ys();function t1(e){let{dataStoreId:t,rows:r}=e;t&&r.length===0&&(async()=>{try{e.setLoadingStoredData(!0);let n=await ZS(t);n&&(n.msa&&e.setMSA(n.msa),n.tree&&e.setTree(n.tree),n.treeMetadata&&e.setTreeMetadata(n.treeMetadata))}catch(n){console.error("Failed to load MSA data from IndexedDB:",n)}finally{e.setLoadingStoredData(!1)}})()}function r1(e){let{rows:t,dataStoreId:r,isStoringData:n}=e;if(t.length>0&&!r&&!n){if(e.msaFilehandle||e.treeFilehandle)return;let o=e.data.msa,i=e.data.tree;(o||i)&&(e.setIsStoringData(!0),(async()=>{try{let s=KS();await XS(s,{msa:o,tree:i,treeMetadata:e.data.treeMetadata})&&e.setDataStoreId(s)}catch(s){console.error("Failed to store MSA data to IndexedDB:",s)}finally{e.setIsStoringData(!1)}})())}}function n1(e){e.blastParams&&(async()=>{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("")}})()}function 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Vl({newViewTitle:e,view:t,feature:r,blastParams:n}){(0,Mm.getSession)(t).addView("MsaView",{type:"MsaView",displayName:e,connectedViewId:t.id,connectedFeature:r.toJSON(),drawNodeBubbles:!0,colWidth:10,rowHeight:12,blastParams:n})}function bQ({newViewTitle:e,view:t,cached:r}){(0,Mm.getSession)(t).addView("MsaView",{type:"MsaView",displayName:e,connectedViewId:t.id,drawNodeBubbles:!0,colWidth:10,rowHeight:12,data:{msa:r.msa,tree:r.tree,treeMetadata:r.treeMetadata}})}function Yl(e){let{data:t,error:r,mutate:n}=ho(`cached-blast-${e.join(",")}`,async()=>(await kS()).filter(a=>a.geneId&&e.includes(a.geneId)),Co);return{results:t??[],error:r,isLoading:!t&&!r,handleDelete:async s=>{await NS(s),await n(a=>a?.filter(c=>c.id!==s)??[],!1)},handleClearAll:async()=>{await LS(),await n([],!1)}}}var dR=(0,MQ.makeStyles)()({header:{display:"flex",justifyContent:"space-between",alignItems:"center",marginBottom:8},resultList:{maxHeight:300,overflow:"auto"}});function BQ(e){let t=[e.geneName,e.transcriptName!==e.geneName?e.transcriptName:void 0].filter(r=>!!r);return t.length>0?t.join(" - "):e.geneId??e.transcriptId??"Unknown"}var mR=(0,QQ.observer)(function({model:e,handleClose:t,feature:r}){let{classes:n}=dR(),o=tr(e),[i,s]=(0,tt.useState)(),a=(0,tt.useMemo)(()=>El(r),[r]),{results:c,error:l,isLoading:A,handleDelete:u,handleClearAll:d}=Yl(a),m=E=>{bQ({view:o,cached:E,newViewTitle:`BLAST - ${BQ(E)}`}),t()},C=l??i;return C?tt.default.createElement(SQ.ErrorMessage,{error:C}):A?tt.default.createElement(gt.Typography,null,"Loading cached results..."):c.length===0?tt.default.createElement(gt.Typography,{color:"textSecondary"},"No cached BLAST results found for this gene. Run a BLAST query to cache results."):tt.default.createElement("div",null,tt.default.createElement("div",{className:n.header},tt.default.createElement(gt.Typography,{variant:"subtitle1"},"Cached BLAST Results (",c.length,")"),tt.default.createElement(gt.Button,{size:"small",color:"error",onClick:async()=>{try{s(void 0),await d()}catch(E){s(E)}}},"Clear All")),tt.default.createElement(gt.List,{dense:!0,className:n.resultList},c.map(E=>tt.default.createElement(gt.ListItem,{key:E.id,disablePadding:!0,secondaryAction:tt.default.createElement(gt.IconButton,{edge:"end",size:"small",onClick:async x=>{x.stopPropagation();try{s(void 0),await u(E.id)}catch(I){s(I)}}},tt.default.createElement(wQ,{fontSize:"small"}))},tt.default.createElement(gt.ListItemButton,{onClick:()=>{m(E)}},tt.default.createElement(gt.ListItemText,{primary:`${BQ(E)} - ${E.blastDatabase}/${E.blastProgram} (${E.msaAlgorithm})`,secondary:`${new Date(E.timestamp).toLocaleString()} - Seq: ${E.proteinSequence.slice(0,30)}...`}))))))}),vQ=mR;var vm=f(Q()),kQ=f(N());var Wl="https://blast.ncbi.nlm.nih.gov/Blast.cgi",TQ=["clustalo","muscle","kalign","mafft"],_Q=["nr","nr_cluster_seq"],DQ=["blastp","quick-blastp"];function Zs({value:e,onChange:t,className:r}){return vm.default.createElement(lt,{variant:"outlined",label:"MSA Algorithm",className:r,select:!0,value:e,onChange:n=>{t(n.target.value)}},TQ.map(n=>vm.default.createElement(kQ.MenuItem,{value:n,key:n},n)))}var pR=(0,LQ.makeStyles)()({selectField:{width:150},databaseFieldContainer:{display:"flex"},clusterSeqMessage:{marginLeft:4,alignContent:"center"},cachedResultsAccordion:{marginTop:20},infoText:{marginTop:20}}),gR=(0,NQ.observer)(function({handleClose:e,feature:t,model:r,children:n,baseUrl:o}){let{classes:i}=pR(),s=tr(r),[a,c]=(0,fe.useState)(),[l,A]=(0,fe.useState)("nr"),[u,d]=(0,fe.useState)("clustalo"),[m,C]=(0,fe.useState)("quick-blastp"),E=(0,fe.useMemo)(()=>El(t),[t]),{results:x,error:I}=Yl(E),p=Hr({feature:t,view:s}),{selectedTranscript:y,proteinSequence:B}=p,b=p.error??a??I;return fe.default.createElement(fe.default.Fragment,null,fe.default.createElement(hr,{error:b},n,fe.default.createElement(lt,{variant:"outlined",label:"BLAST database",className:i.selectField,select:!0,value:l,onChange:S=>{let M=S.target.value;A(M),M==="nr_cluster_seq"&&C("blastp")}},_Q.map(S=>fe.default.createElement(Vt.MenuItem,{value:S,key:S},S))),fe.default.createElement(Zs,{className:i.selectField,value:u,onChange:d}),fe.default.createElement("div",{className:i.databaseFieldContainer},fe.default.createElement(lt,{variant:"outlined",label:"BLAST program",disabled:l==="nr_cluster_seq",className:i.selectField,select:!0,value:m,onChange:S=>{C(S.target.value)}},DQ.map(S=>fe.default.createElement(Vt.MenuItem,{value:S,key:S},S))),l==="nr_cluster_seq"?fe.default.createElement(Vt.Typography,{variant:"subtitle2",className:i.clusterSeqMessage},"Can only use blastp on nr_cluster_seq"):null),fe.default.createElement(Er,{feature:t,...p}),fe.default.createElement(Vt.Typography,{className:i.infoText},"This panel will automatically submit a query to NCBI. Using blastp can take 10+ minutes to run, quick-blastp is generally a lot faster but is not available for the clustered database. After completion, all the hits will be run through a multiple sequence alignment. Note: we are not able to currently run NCBI COBALT automatically on the BLAST results, even though that is the method NCBI uses on their website. If you need a COBALT alignment, please use the manual approach of submitting BLAST yourself and downloading the resulting files"),x.length>0?fe.default.createElement(Vt.Accordion,{className:i.cachedResultsAccordion},fe.default.createElement(Vt.AccordionSummary,{expandIcon:fe.default.createElement(Jc,null)},fe.default.createElement(Vt.Typography,null,"Previous BLAST Results")),fe.default.createElement(Vt.AccordionDetails,null,fe.default.createElement(vQ,{model:r,handleClose:e,feature:t}))):null),fe.default.createElement(cn,{submitDisabled:!B,onSubmit:()=>{try{y&&(c(void 0),Vl({feature:y,view:s,newViewTitle:hl(t,y),blastParams:{baseUrl:o,blastProgram:m,blastDatabase:l,msaAlgorithm:u,selectedTranscript:y,proteinSequence:B}}),e())}catch(S){console.error(S),c(S)}},onCancel:e}))}),RQ=gR;var jr=f(Q()),PQ=f(de()),Gi=f(N()),OQ=f(U()),GQ=f(Qe());zl();var hR=(0,GQ.makeStyles)()({ncbiLink:{wordBreak:"break-all",margin:30,maxWidth:600},infoText:{marginTop:20}}),CR=(0,OQ.observer)(function({handleClose:e,feature:t,model:r,children:n,baseUrl:o}){let{classes:i}=hR(),s=tr(r),a=Hr({feature:t,view:s}),{proteinSequence:c,error:l}=a,A=Cl(c),u=`${o}?PAGE_TYPE=BlastSearch&PAGE=Proteins&PROGRAM=blastp&QUERY=${A}`,d=`${o}?PAGE_TYPE=BlastSearch&PAGE=Proteins&PROGRAM=blastp&QUERY=${(0,PQ.shorten2)(A,10)}`;return jr.default.createElement(jr.default.Fragment,null,jr.default.createElement(hr,{error:l},n,jr.default.createElement(Er,{feature:t,...a}),c?jr.default.createElement("div",{className:i.ncbiLink},"Link to NCBI BLAST: ",jr.default.createElement(Eo,{href:u},d)):null,jr.default.createElement(Gi.Typography,{className:i.infoText},`Click the link above and run your BLAST query, and once you have results, click "Multiple Alignment" at the top of the results page to be redirected to COBALT, NCBI's multiple sequence aligner. 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You can find the RID in the BLAST results page URL or at the top of the results page. RIDs are typically valid for 24-36 hours after submission."),ht.default.createElement(lt,{variant:"outlined",label:"BLAST RID",placeholder:"e.g., ABC12345",fullWidth:!0,className:i.marginBottom,value:l,onChange:p=>{A(p.target.value)}}),I?ht.default.createElement($l.Typography,{variant:"body2",className:i.marginBottom},ht.default.createElement(Eo,{href:`${o}?CMD=Get&RID=${I}`},"View BLAST results on NCBI")):null,ht.default.createElement(Zs,{className:i.ridField,value:u,onChange:d}),ht.default.createElement(Er,{feature:t,...m}),ht.default.createElement($l.Typography,{className:i.infoText},"This will fetch the BLAST results for the provided RID and run them through a multiple sequence alignment. 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br.default.createElement(br.default.Fragment,null,br.default.createElement(YQ.IconButton,{className:l.settingsButton,size:"small",onClick:()=>{c(!0)}},br.default.createElement(_c,null)),br.default.createElement(A,{model:t,feature:r,handleClose:e,baseUrl:i},br.default.createElement(_m,{lookupMethod:n,setLookupMethod:o})),a?br.default.createElement(Dm,{baseUrl:i,handleClose:u=>{u&&s(u),c(!1)}}):null)}var Ct=f(Q()),ea=f(Me()),Xl=f(de()),rM=f(N()),nM=f(U());var oM=f(Qe());Cn();function Nm(e,t="",r=5e3){let n=[e];for(;n.length;){let o=n.pop();for(let[i,s]of Object.entries(o)){if(t.length>r)return If(t);typeof s=="object"&&s!==null?n.push(s):i==="locationType"&&s==="FileHandleLocation"?t+=`${i}-BlobLocation`:i==="handleId"?t+=`blobId-fh-blob-${s}`:t+=`${i}-${s}`}}return`adp-${If(t)}`}function zQ(e={}){return e.type&&e.adapterId?`${e.type}-${e.adapterId}`:`${Nm(e)}`}var $Q={};async function bR(e,t,r){let n=r?.type;if(!n)throw new Error(`could not determine adapter type from adapter config 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Kl(e){return(0,tM.readConfObject)(e,["msa","datasets"])}var BR=(0,oM.makeStyles)()({selectedContainer:{marginTop:50}}),SR=(0,nM.observer)(function({model:e,feature:t,handleClose:r}){let n=(0,Xl.getSession)(e),o=tr(e),{classes:i}=BR(),{pluginManager:s}=(0,Xl.getEnv)(e),{assemblyNames:a}=o,[c,l]=(0,Ct.useState)(),A=Kl(n.jbrowse),[u,d]=(0,Ct.useState)(A?.[0]?.datasetId),m=A?.find(G=>G.datasetId===u),{data:C,isLoading:E,error:x}=ho(m?`${m.datasetId}-msa-list`:null,()=>XQ({config:m.adapter,pluginManager:s}),Co),I=Hr({feature:t,view:o,validIds:C}),{selectedId:p,selectedTranscript:y}=I,{data:B,isLoading:b,error:S}=ho(p&&m&&C?`${m.datasetId}-${p}-${C.length}-msa`:null,()=>ZQ({msaId:p,config:m.adapter,pluginManager:s}),Co),M=x??S??I.error??c;return Ct.default.createElement(Ct.default.Fragment,null,Ct.default.createElement(hr,{error:M},Ct.default.createElement(lt,{select:!0,label:"Select MSA dataset",value:u,onChange:G=>{d(G.target.value)}},A?.map(G=>Ct.default.createElement(rM.MenuItem,{key:G.datasetId,value:G.datasetId},G.name))),m?Ct.default.createElement("div",{className:i.selectedContainer},!E&&b?Ct.default.createElement(ea.LoadingEllipses,{variant:"h6",message:`Loading MSA for (${p})`}):null,E?Ct.default.createElement(ea.LoadingEllipses,{variant:"h6",message:`Loading available MSAs for (${m.name})`}):null,C?Ct.default.createElement("div",null,Ct.default.createElement(ea.SanitizedHTML,{html:m.description}),Ct.default.createElement(Er,{feature:t,...I})):null):null),Ct.default.createElement(cn,{submitDisabled:!y||!B?.length,onSubmit:()=>{try{if(y&&B){let G=`${p}_${a[0]}`;eM({session:n,newViewTitle:go(y),view:o,querySeqName:G,feature:y,data:{msa:B.map(R=>`>${R.get("refName")}
+${R.get("seq")}`).join(`
+`)}}),r()}}catch(G){l(G)}},onCancel:r}))}),iM=SR;var sM=f(Q());function ta({children:e,value:t,index:r,...n}){return sM.default.createElement("div",{role:"tabpanel",hidden:t!==r,...n},t===r?e:null)}function Rm({handleClose:e,feature:t,model:r}){let n=(0,cM.getSession)(r),i=!!Kl(n.jbrowse)?.length,[s,a]=(0,Nt.useState)("ncbi_blast");return Nt.default.createElement(aM.Dialog,{maxWidth:"xl",title:"Launch MSA view",open:!0,onClose:e},Nt.default.createElement(Ui.Tabs,{value:s,onChange:(c,l)=>{a(l)}},Nt.default.createElement(Ui.Tab,{label:"NCBI BLAST query",value:"ncbi_blast"}),i?Nt.default.createElement(Ui.Tab,{label:"Pre-loaded MSA datasets",value:"preloaded_msa"}):null,Nt.default.createElement(Ui.Tab,{label:"Manual upload",value:"manual_msa"})),Nt.default.createElement(ta,{value:s,index:"ncbi_blast"},Nt.default.createElement(km,{handleClose:e,feature:t,model:r})),i?Nt.default.createElement(ta,{value:s,index:"preloaded_msa"},Nt.default.createElement(iM,{model:r,feature:t,handleClose:e})):null,Nt.default.createElement(ta,{value:s,index:"manual_msa"},Nt.default.createElement(xQ,{model:r,feature:t,handleClose:e})))}function QR(e){return e.name==="LinearBasicDisplay"}function MR(e){return e.views(t=>{let r=t.contextMenuItems;return{contextMenuItems(){let n=t.contextMenuFeature,o=(0,Zl.getContainingTrack)(t),i=n?.get("type"),s=n&&["gene","mRNA","transcript"].includes(i);return[...r(),...s?[{label:"Launch MSA view",icon:P1,onClick:()=>{(0,Zl.getSession)(o).queueDialog(a=>[Rm,{model:o,handleClose:a,feature:n}])}}]:[]]}}})}function Fm(e){e.addToExtensionPoint("Core-extendPluggableElement",t=>(QR(t)&&(t.stateModel=MR(t.stateModel)),t))}function Pm(e){e.addToExtensionPoint("LaunchView-MsaView",({session:t,data:r,msaFileLocation:n,treeFileLocation:o,connectedViewId:i,connectedFeature:s,displayName:a,colorSchemeName:c,colWidth:l,rowHeight:A,treeAreaWidth:u,treeWidth:d,drawNodeBubbles:m,labelsAlignRight:C,showBranchLen:E,querySeqName:x,highlightColumns:I})=>{if(!r&&!n)throw new Error("No MSA data or file location provided when launching MSA view");t.addView("MsaView",{type:"MsaView",displayName:a,connectedViewId:i,connectedFeature:s,colorSchemeName:c,colWidth:l,rowHeight:A,treeAreaWidth:u,treeWidth:d,drawNodeBubbles:m,labelsAlignRight:C,showBranchLen:E,highlightColumns:I,init:{msaData:r?.msa,treeData:r?.tree,msaUrl:n?.uri,treeUrl:o?.uri,querySeqName:x}})})}var BM=f(Q()),SM=f(AM());var RR=(0,BM.lazy)(()=>Promise.resolve().then(()=>(bM(),wM)));function Hm(e){e.addViewType(()=>new SM.default({name:"MsaView",stateModel:em(),ReactComponent:RR}))}var QM="2.5.2";var rA=class extends MM.default{constructor(){super(...arguments);this.name="MsaViewPlugin";this.version=QM;this.rootConfigurationSchema=r=>({msa:(0,jm.ConfigurationSchema)("MSA",{datasets:qm.types.maybe(qm.types.array((0,jm.ConfigurationSchema)("MSAEntry",{datasetId:{type:"string",defaultValue:""},description:{type:"string",defaultValue:""},name:{type:"string",defaultValue:""},adapter:r.pluggableConfigSchemaType("adapter")})))})})}install(r){Hm(r),Fm(r),Pm(r),im(r),am(r)}configure(r){(0,vM.isAbstractMenuManager)(r.rootModel)&&r.rootModel.appendToSubMenu(["Add"],{label:"Multiple sequence alignment view",icon:Cp,onClick:n=>{n.addView("MsaView",{})}})}};return KM(FR);})();
 /*! Bundled license information:
 
 react-is/cjs/react-is.production.min.js:
@@ -95,7 +95,7 @@ escape-html/index.js:
    *)
 
 dompurify/dist/purify.es.mjs:
-  (*! @license DOMPurify 3.4.7 | (c) Cure53 and other contributors | Released under the Apache license 2.0 and Mozilla Public License 2.0 | github.com/cure53/DOMPurify/blob/3.4.7/LICENSE *)
+  (*! @license DOMPurify 3.4.11 | (c) Cure53 and other contributors | Released under the Apache license 2.0 and Mozilla Public License 2.0 | github.com/cure53/DOMPurify/blob/3.4.11/LICENSE *)
 
 use-sync-external-store/cjs/use-sync-external-store-shim.production.js:
   (**