jbrowse-plugin-msaview 2.4.5 → 2.5.1

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

@@ -1,11 +1,11 @@
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m=l+1;n(o,i,s,m-1),n(o,i,m+1,a)}}return n}function SM(e){let t=BM.toString();return new Function(`return ${t}`)()(e)}var Kp=new WeakMap;Xp.quickSort=function(e,t,r=0){let n=Kp.get(t);n===void 0&&(n=SM(t),Kp.set(t,n)),n(e,t,r,e.length-1)}});var rh=G(pa=>{var N=Fo(),BA=$p(),Ro=xA().ArraySet,QM=hA(),Gi=Zp().quickSort;function pe(e,t){var r=e;return typeof e=="string"&&(r=N.parseSourceMapInput(e)),r.sections!=null?new sr(r,t):new nt(r,t)}pe.fromSourceMap=function(e,t){return nt.fromSourceMap(e,t)};pe.prototype._version=3;pe.prototype.__generatedMappings=null;Object.defineProperty(pe.prototype,"_generatedMappings",{configurable:!0,enumerable:!0,get:function(){return this.__generatedMappings||this._parseMappings(this._mappings,this.sourceRoot),this.__generatedMappings}});pe.prototype.__originalMappings=null;Object.defineProperty(pe.prototype,"_originalMappings",{configurable:!0,enumerable:!0,get:function(){return this.__originalMappings||this._parseMappings(this._mappings,this.sourceRoot),this.__originalMappings}});pe.prototype._charIsMappingSeparator=function(t,r){var n=t.charAt(r);return n===";"||n===","};pe.prototype._parseMappings=function(t,r){throw new Error("Subclasses must implement _parseMappings")};pe.GENERATED_ORDER=1;pe.ORIGINAL_ORDER=2;pe.GREATEST_LOWER_BOUND=1;pe.LEAST_UPPER_BOUND=2;pe.prototype.eachMapping=function(t,r,n){var o=r||null,i=n||pe.GENERATED_ORDER,s;switch(i){case pe.GENERATED_ORDER:s=this._generatedMappings;break;case pe.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,m=0,d=s.length;m<d;m++){var p=s[m],C=p.source===null?null:A.at(p.source);C!==null&&(C=N.computeSourceURL(a,C,u)),c({source:C,generatedLine:p.generatedLine,generatedColumn:p.generatedColumn,originalLine:p.originalLine,originalColumn:p.originalColumn,name:p.name===null?null:l.at(p.name)})}};pe.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,BA.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};pa.SourceMapConsumer=pe;function nt(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=Ro.fromArray(i.map(String),!0),this._sources=Ro.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}nt.prototype=Object.create(pe.prototype);nt.prototype.consumer=pe;nt.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};nt.fromSourceMap=function(t,r){var n=Object.create(nt.prototype),o=n._names=Ro.fromArray(t._names.toArray(),!0),i=n._sources=Ro.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(d){return N.computeSourceURL(n.sourceRoot,d,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],m=new th;m.generatedLine=u.generatedLine,m.generatedColumn=u.generatedColumn,u.source&&(m.source=i.indexOf(u.source),m.originalLine=u.originalLine,m.originalColumn=u.originalColumn,u.name&&(m.name=o.indexOf(u.name)),c.push(m)),a.push(m)}return Gi(n.__originalMappings,N.compareByOriginalPositions),n};nt.prototype._version=3;Object.defineProperty(nt.prototype,"sources",{get:function(){return this._absoluteSources.slice()}});function th(){this.generatedLine=0,this.generatedColumn=0,this.source=null,this.originalLine=null,this.originalColumn=null,this.name=null}var bA=N.compareByGeneratedPositionsDeflatedNoLine;function eh(e,t){let r=e.length,n=e.length-t;if(!(n<=1))if(n==2){let o=e[t],i=e[t+1];bA(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(bA(s,a)<=0)break;e[i-1]=a,e[i]=s}else Gi(e,bA,t)}nt.prototype._parseMappings=function(t,r){var n=1,o=0,i=0,s=0,a=0,c=0,l=t.length,A=0,u={},m={},d=[],p=[],C,y,I,h,x;let S=0;for(;A<l;)if(t.charAt(A)===";")n++,A++,o=0,eh(p,S),S=p.length;else if(t.charAt(A)===",")A++;else{for(C=new th,C.generatedLine=n,h=A;h<l&&!this._charIsMappingSeparator(t,h);h++);for(y=t.slice(A,h),I=[];A<h;)QM.decode(t,A,m),x=m.value,A=m.rest,I.push(x);if(I.length===2)throw new Error("Found a source, but no line and column");if(I.length===3)throw new Error("Found a source and line, but no column");if(C.generatedColumn=o+I[0],o=C.generatedColumn,I.length>1&&(C.source=a+I[1],a+=I[1],C.originalLine=i+I[2],i=C.originalLine,C.originalLine+=1,C.originalColumn=s+I[3],s=C.originalColumn,I.length>4&&(C.name=c+I[4],c+=I[4])),p.push(C),typeof C.originalLine=="number"){let B=C.source;for(;d.length<=B;)d.push(null);d[B]===null&&(d[B]=[]),d[B].push(C)}}eh(p,S),this.__generatedMappings=p;for(var M=0;M<d.length;M++)d[M]!=null&&Gi(d[M],N.compareByOriginalPositionsNoSource);this.__originalMappings=[].concat(...d)};nt.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 BA.search(t,r,i,s)};nt.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}};nt.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",pe.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}};nt.prototype.hasContentsOfAllSources=function(){return this.sourcesContent?this.sourcesContent.length>=this._sources.size()&&!this.sourcesContent.some(function(t){return t==null}):!1};nt.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.')};nt.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",pe.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}};pa.BasicSourceMapConsumer=nt;function sr(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 Ro,this._names=new Ro;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 pe(N.getArg(s,"map"),t)}})}sr.prototype=Object.create(pe.prototype);sr.prototype.constructor=pe;sr.prototype._version=3;Object.defineProperty(sr.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}});sr.prototype.originalPositionFor=function(t){var r={generatedLine:N.getArg(t,"line"),generatedColumn:N.getArg(t,"column")},n=BA.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}};sr.prototype.hasContentsOfAllSources=function(){return this._sections.every(function(t){return t.consumer.hasContentsOfAllSources()})};sr.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.')};sr.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}};sr.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)}Gi(this.__generatedMappings,N.compareByGeneratedPositionsDeflated),Gi(this.__originalMappings,N.compareByOriginalPositions)};pa.IndexedSourceMapConsumer=sr});var oh=G(nh=>{var MM=yA().SourceMapGenerator,ha=Fo(),vM=/(\r?\n)/,TM=10,Po="$$$isSourceNode$$$";function Nt(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[Po]=!0,n!=null&&this.add(n)}Nt.fromStringWithSourceMap=function(t,r,n){var o=new Nt,i=t.split(vM),s=0,a=function(){var m=p(),d=p()||"";return m+d;function p(){return s<i.length?i[s++]:void 0}},c=1,l=0,A=null;return r.eachMapping(function(m){if(A!==null)if(c<m.generatedLine)u(A,a()),c++,l=0;else{var d=i[s]||"",p=d.substr(0,m.generatedColumn-l);i[s]=d.substr(m.generatedColumn-l),l=m.generatedColumn,u(A,p),A=m;return}for(;c<m.generatedLine;)o.add(a()),c++;if(l<m.generatedColumn){var d=i[s]||"";o.add(d.substr(0,m.generatedColumn)),i[s]=d.substr(m.generatedColumn),l=m.generatedColumn}A=m},this),s<i.length&&(A&&u(A,a()),o.add(i.splice(s).join(""))),r.sources.forEach(function(m){var d=r.sourceContentFor(m);d!=null&&(n!=null&&(m=ha.join(n,m)),o.setSourceContent(m,d))}),o;function u(m,d){if(m===null||m.source===void 0)o.add(d);else{var p=n?ha.join(n,m.source):m.source;o.add(new Nt(m.originalLine,m.originalColumn,p,d,m.name))}}};Nt.prototype.add=function(t){if(Array.isArray(t))t.forEach(function(r){this.add(r)},this);else if(t[Po]||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};Nt.prototype.prepend=function(t){if(Array.isArray(t))for(var r=t.length-1;r>=0;r--)this.prepend(t[r]);else if(t[Po]||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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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 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=Za.join(n,d)),o.setSourceContent(d,m))}),o;function u(d,m){if(d===null||d.source===void 0)o.add(m);else{var h=n?Za.join(n,d.source):d.source;o.add(new Lt(d.originalLine,d.originalColumn,h,m,d.name))}}};Lt.prototype.add=function(t){if(Array.isArray(t))t.forEach(function(r){this.add(r)},this);else if(t[ei]||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};Lt.prototype.prepend=function(t){if(Array.isArray(t))for(var r=t.length-1;r>=0;r--)this.prepend(t[r]);else if(t[ei]||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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i=r[o],s={},a=n.W??0,c=n.L??0,l=n.V??0,A=n.I??0,u=n.M??0,m=n.A??0,d=n.F??0,p=n.C??0,C=n.H??0,y=n.P??0,I=n.R??0,h=n.K??0,x=n.Q??0,S=n.E??0,M=n.D??0,B=n.T??0,Q=n.S??0,L=n.G??0,T=n.Y??0,re=n.N??0,k=a+c+l+A+u+m+d+p+C+y+T,j=h+I,J=x+S,R=S+M,ie=B+Q;return k/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||h/i>.8||I/i>.8||x/i>.8)&&(s.K="#d88",s.R="#d88"),(j/i>.6||J/i>.5||S/i>.8||x/i>.8||M/i>.8)&&(s.E="rgb(192, 72, 192)"),(j/i>.6||R/i>.5||h/i>.8||I/i>.8||x/i>.8)&&(s.D="rgb(204, 77, 204)"),(re/i>.5||T/i>.85)&&(s.N="#8f8"),(j/i>.6||J/i>.6||x/i>.85||S/i>.85||h/i>.85||I/i>.85)&&(s.Q="#8f8"),(k/i>.6||ie/i>.5||Q/i>.85||B/i>.85)&&(s.S="rgb(26,204,26)",s.T="rgb(26,204,26)"),p/i>.85&&(s.C="rgb(240, 128, 128)"),L/i>0&&(s.G="rgb(240, 144, 72)"),y/i>0&&(s.P="rgb(204, 204, 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${s??"unknown"}`)}}}Ji();var Xk="jbrowse-msaview-taxonomy-cache",Cs="common-names",Zk=2;async function hB(){return Gn(Xk,Zk,{upgrade(e){e.objectStoreNames.contains(Cs)&&e.deleteObjectStore(Cs),e.createObjectStore(Cs,{keyPath:"taxid"})}})}async function eD(e){let r=(await hB()).transaction(Cs,"readonly"),n=await Promise.all(e.map(o=>r.store.get(o)));return await r.done,n}async function tD(e){let r=(await hB()).transaction(Cs,"readwrite");for(let n of e)await r.store.put(n);await r.done}async function CB(e){let t=new Map,r=[],n=await eD(e);for(let s=0;s<e.length;s++){let a=e[s],c=n[s];c?t.set(a,{sciname:c.sciname,commonName:c.commonName}):r.push(a)}if(r.length===0)return t;let o=100,i=[];for(let s=0;s<r.length;s+=o){let a=r.slice(s,s+o),c=a.join(",");try{let A=await(await fetch(`https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=taxonomy&id=${c}&retmode=xml`)).text(),u=new Map,m=/<Taxon>\s*<TaxId>(\d+)<\/TaxId>/g,d;for(;(d=m.exec(A))!==null;){let p=Number(d[1]),C=d.index,y=1,I=C+d[0].length;for(;y>0&&I<A.length;){let B=A.indexOf("<Taxon>",I),Q=A.indexOf("</Taxon>",I);if(Q===-1)break;B!==-1&&B<Q?(y++,I=B+7):(y--,I=Q+8)}let h=A.slice(C,I),x=u.get(p),S=h.includes("<LineageEx>"),M=x?.includes("<LineageEx>");(!x||S&&!M)&&u.set(p,h)}for(let p of a){let C=u.get(p);if(C){let y=/<GenbankCommonName>(.*?)<\/GenbankCommonName>/.exec(C),I=/<CommonName>(.*?)<\/CommonName>/.exec(C),h=/<ScientificName>(.*?)<\/ScientificName>/.exec(C),x=y?.[1]??I?.[1],S=h?.[1]??"";t.set(p,{sciname:S,commonName:x}),i.push({taxid:p,sciname:S,commonName:x})}}}catch(l){console.error("Failed to fetch taxonomy data:",l)}}return i.length>0&&await tD(i),t}async function EB({self:e}){let{baseUrl:t,blastDatabase:r,blastProgram:n,msaAlgorithm:o,proteinSequence:i,selectedTranscript:s,rid:a}=e.blastParams,c=Jc(i),l,A;if(a){e.setRid(a);let I=await am({rid:a,baseUrl:t,onProgress:h=>{e.setProgress(h)}});l=I.hits,A=I.rid}else{let I=await 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cm(),n={id:e,msa:t.msa,tree:t.tree,treeMetadata:t.treeMetadata,timestamp:Date.now()};return await r.put(Es,n),!0}catch(r){return console.warn("Failed to store MSA data:",r),!1}}async function yB(e){try{let r=await(await cm()).get(Es,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 wB(e=10080*60*1e3){try{let t=await cm(),r=Date.now()-e,i=await t.transaction(Es,"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}}Is();function BB(e){let{dataStoreId:t,rows:r}=e;t&&r.length===0&&(async()=>{try{e.setLoadingStoredData(!0);let n=await yB(t);n&&(n.msa&&e.setMSA(n.msa),n.tree&&e.setTree(n.tree))}catch(n){console.error("Failed to load MSA data from IndexedDB:",n)}finally{e.setLoadingStoredData(!1)}})()}function SB(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=IB();await xB(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 QB(e){e.blastParams&&(async()=>{try{e.setProgress("Submitting query"),e.setError(void 0);let t=await EB({self:e});e.setData(t),e.setBlastParams(void 0)}catch(t){e.setError(t),console.error(t)}finally{e.setProgress("")}})()}function MB(e){let{init:t}=e;t&&(async()=>{try{e.setError(void 0);let{msaData:r,msaUrl:n,treeData:o,treeUrl:i,querySeqName:s}=t;if(n){let a=Md(n);a&&(e.setUniprotId(a),e.setQuerySeqName("query"))}if(s&&e.setQuerySeqName(s),r)e.setMSA(r);else if(n){let a=await fetch(n);if(!a.ok)throw new Error(`Failed to fetch MSA: ${a.status}`);let c=await a.text();e.setMSA(c)}if(o)e.setTree(o);else if(i){let a=await fetch(i);if(!a.ok)throw new Error(`Failed to fetch tree: ${a.status}`);let c=await a.text();e.setTree(c)}e.setInit(void 0)}catch(r){e.setError(r),console.error(r)}})()}function vB(e){let{mouseCol:t,connectedProteinViews:r}=e;if(r.length!==0)for(let n of r){let o=n.proteinView.structures[n.structureIdx];if(!o)continue;if(t===void 0){o.clearHighlightFromExternal?.();continue}let i=e.getSequenceByRowName(n.msaRowName);if(!i)continue;let s=$c(i,t);if(s===void 0){o.clearHighlightFromExternal?.();continue}let a=n.msaToStructure[s];a===void 0?o.clearHighlightFromExternal?.():o.highlightFromExternal?.(a)}}function TB(e){let{connectedViewId:t,uniprotId:r,rows:n,connectedStructures:o}=e;if(!(!r||n.length===0))for(let i of yn((0,lm.getSession)(e).views))for(let s=0;s<i.structures.length;s++){let 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mS([e.id(),e.get("id"),e.get("name"),e.get("gene_id"),e.get("gene_name")])}Ai();var CN="jbrowse-msaview-blast-cache",Nn="blast-results",EN=2;async function hl(){return en(CN,EN,{upgrade(e,t){t<2&&e.objectStoreNames.contains(Nn)&&e.deleteObjectStore(Nn),e.objectStoreNames.contains(Nn)||e.createObjectStore(Nn,{keyPath:"id"})}})}function IN(e,t,r,n){let o=n?`:${n}`:"";return`${t}:${r}${o}:${e}`}async function hS({proteinSequence:e,blastDatabase:t,blastProgram:r,msaAlgorithm:n,msa:o,tree:i,treeMetadata:s,rid:a,geneId:c,transcriptId:l,transcriptName:A,geneName:u}){let d=await hl(),h={id:IN(e,t,r,l),proteinSequence:e,blastDatabase:t,blastProgram:r,msaAlgorithm:n,msa:o,tree:i,treeMetadata:s,rid:a,timestamp:Date.now(),geneId:c,transcriptId:l,transcriptName:A,geneName:u};return await d.put(Nn,h),h}async function CS(){return(await(await hl()).getAll(Nn)).toSorted((r,n)=>n.timestamp-r.timestamp)}async function ES(e){await(await hl()).delete(Nn,e)}async function IS(){await(await 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${n}`)},check:async()=>{let n=await jr(`${Il}/${r}/status/${t}`);if(n.includes("FINISHED"))return!0;if(n.includes("FAILURE"))throw new Error(`Failed to run: jobId ${t}`);return!1}})}async function bS({algorithm:e,sequence:t,onProgress:r}){let n=xN[e];r(`Launching ${e} MSA...`);let o=await jr(`${Il}/${e}/run`,{method:"POST",body:new URLSearchParams({...n.params,sequence:t})});return await yN({jobId:o,algorithm:e,onProgress:r}),{msa:await jr(`${Il}/${e}/result/${o}/${n.msaResult}`),tree:await jr(`${Il}/${e}/result/${o}/${n.treeResult}`)}}async function Gd({rid:e,baseUrl:t,onProgress:r}){r(`Checking BLAST status for RID: ${e}...`),await bN({rid:e,onProgress:r,baseUrl:t});let n=await yS(`${t}?CMD=Get&RID=${e}&FORMAT_TYPE=JSON2_S&FORMAT_OBJECT=Alignment`);return{rid:e,hits:n.BlastOutput2[0]?.report.results.search.hits??[]}}async function BS({query:e,blastDatabase:t,blastProgram:r,baseUrl:n,onProgress:o,onRid:i}){o("Submitting to NCBI BLAST...");let{rid:s}=await wN({query:e,blastDatabase:t,blastProgram:r,baseUrl:n});return i(s),Gd({rid:s,baseUrl:n,onProgress:o})}async function wN({query:e,blastProgram:t,blastDatabase:r,baseUrl:n}){let o=await jr(n,{method:"POST",body:new URLSearchParams({CMD:"Put",PROGRAM:t==="quick-blastp"?"blastp":t,DATABASE:r,QUERY:e,...r==="nr_cluster_seq"?{CLUSTERED_DB:"on",DB_TYPE:"Experimental Databases"}:{},...t==="quick-blastp"?{BLAST_PROGRAMS:"kmerBlastp"}:{}})}),i=/^ {4}RID = (.*$)/m.exec(o)?.[1],s=/^ {4}RTOE = (.*$)/m.exec(o)?.[1];if(!i)throw new Error("Failed to get RID from BLAST request");return{rid:i,rtoe:s}}async function bN({rid:e,onProgress:t,baseUrl:r}){await Cl({intervalSeconds:20,onCountdown:n=>{t(`Re-checking BLAST status in... ${n}`)},check:async()=>{let n=await jr(`${r}?CMD=Get&FORMAT_OBJECT=SearchInfo&RID=${e}`),o=/\s+Status=(\S+)/m.exec(n)?.[1],i=/\s+ThereAreHits=yes/m.test(n);if(o==="WAITING")return!1;if(o==="FAILED")throw new Error(`BLAST ${e} failed`);if(o==="READY"){if(i)return!0;throw new Error("No hits found")}throw new Error(`BLAST ${e} returned unexpected status: ${o??"unknown"}`)}})}Ai();var BN="jbrowse-plugin-msaview",SN="colin.diesh@gmail.com",QN="https://eutils.ncbi.nlm.nih.gov/entrez/eutils";function xl(e){let t=new URLSearchParams({...e,tool:BN,email:SN});return`${QN}/efetch.fcgi?${t.toString()}`}var MN="jbrowse-msaview-taxonomy-cache",Us="common-names",vN=2;async function SS(){return en(MN,vN,{upgrade(e){e.objectStoreNames.contains(Us)&&e.deleteObjectStore(Us),e.createObjectStore(Us,{keyPath:"taxid"})}})}async function TN(e){let r=(await SS()).transaction(Us,"readonly"),n=await Promise.all(e.map(o=>r.store.get(o)));return await r.done,n}async function _N(e){let r=(await SS()).transaction(Us,"readwrite");for(let n of e)await r.store.put(n);await r.done}async function QS(e){let t=new Map,r=[],n=await TN(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(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 MS({self:e}){let{baseUrl:t,blastDatabase:r,blastProgram:n,msaAlgorithm:o,proteinSequence:i,selectedTranscript:s,rid:a}=e.blastParams,c=pl(i),l,A;if(a){e.setRid(a);let I=await Gd({rid:a,baseUrl:t,onProgress:p=>{e.setProgress(p)}});l=I.hits,A=I.rid}else{let I=await BS({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 QS(u),m={},h=l.map(I=>{let p=I.description[0]??{accession:"unknown",id:"unknown",sciname:"unknown"},y=fS(p,d),b=dS(I.hsps[0]?.hseq??"");return m[y]=DN(p,d),`>${y}
+${b}`}),E=await bS({algorithm:o,sequence:[`>QUERY
+${c}`,...h].join(`
+`),onProgress:I=>{e.setProgress(I)}}),x=JSON.stringify(m);return await hS({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 DN(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 vS=f(de());function TS({model:e}){let{hovered:t}=(0,vS.getSession)(e),{querySeqName:r,transcriptToMsaMap:n,connectedView:o,mafRegion:i}=e;if(!o?.initialized||!Vn(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)}}Ai();var kN="jbrowse-msaview-domain-cache",yl="domains",NN=1;async function _S(){return en(kN,NN,{upgrade(e){e.objectStoreNames.contains(yl)||e.createObjectStore(yl,{keyPath:"accession"})}})}async function DS(e){let r=(await _S()).transaction(yl,"readonly"),n=await Promise.all(e.map(o=>r.store.get(o)));return await r.done,n}async function kS(e){let r=(await _S()).transaction(yl,"readwrite");for(let n of e)await r.store.put(n);await r.done}function Ln(e,t){return new RegExp(`<${t}>(.*?)</${t}>`,"s").exec(e)?.[1]}function LN(e){let t={},r=/<GBQualifier>([\s\S]*?)<\/GBQualifier>/g,n;for(;(n=r.exec(e))!==null;){let o=Ln(n[1],"GBQualifier_name"),i=Ln(n[1],"GBQualifier_value");o&&i!==void 0&&t[o]===void 0&&(t[o]=i)}return t}function RN(e){let t=[],r=[],n=/<GBInterval>([\s\S]*?)<\/GBInterval>/g,o;for(;(o=n.exec(e))!==null;){let 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 data:",t),0}}js();function GS(e){let{dataStoreId:t,rows:r}=e;t&&r.length===0&&(async()=>{try{e.setLoadingStoredData(!0);let n=await PS(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 US(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=RS();await FS(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 HS(e){e.blastParams&&(async()=>{try{e.setProgress("Submitting query"),e.setError(void 0);let t=await MS({self:e});e.setData(t),e.setBlastParams(void 0)}catch(t){e.setError(t),console.error(t)}finally{e.setProgress("")}})()}function jS(e){let{rows:t,domainsRequested:r,interProAnnotations:n}=e,o=e.data.treeMetadata?.includes('"Accession"')??!1;t.length>0&&o&&!n&&!r&&(e.setDomainsRequested(!0),(async()=>{try{await LS(e)}catch(i){console.error("[msaview-domains] auto-load failed:",i)}finally{e.setProgress("")}})())}function qS(e){let{init:t}=e;t&&(async()=>{try{e.setError(void 0);let{msaData:r,msaUrl:n,treeData:o,treeUrl:i,querySeqName:s}=t;if(n){let a=cp(n);a&&(e.setUniprotId(a),e.setQuerySeqName("query"))}if(s&&e.setQuerySeqName(s),r)e.setMSA(r);else if(n){let a=await fetch(n);if(!a.ok)throw new Error(`Failed to fetch MSA: ${a.status}`);let c=await a.text();e.setMSA(c)}if(o)e.setTree(o);else if(i){let a=await fetch(i);if(!a.ok)throw new Error(`Failed to fetch tree: ${a.status}`);let c=await a.text();e.setTree(c)}e.setInit(void 0)}catch(r){e.setError(r),console.error(r)}})()}function JS(e){let t=!1;return()=>{let r=TS({model:e});r!==void 0?(e.setMousePos(r),t=!0):t&&(e.setMousePos(void 0),t=!1)}}function 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Ul({newViewTitle:e,view:t,feature:r,blastParams:n}){(0,Cm.getSession)(t).addView("MsaView",{type:"MsaView",displayName:e,connectedViewId:t.id,connectedFeature:r.toJSON(),drawNodeBubbles:!0,colWidth:10,rowHeight:12,blastParams:n})}function AQ({newViewTitle:e,view:t,cached:r}){(0,Cm.getSession)(t).addView("MsaView",{type:"MsaView",displayName:e,connectedViewId:t.id,drawNodeBubbles:!0,colWidth:10,rowHeight:12,data:{msa:r.msa,tree:r.tree,treeMetadata:r.treeMetadata}})}function Hl(e){let{data:t,error:r,mutate:n}=Co(`cached-blast-${e.join(",")}`,async()=>(await CS()).filter(a=>a.geneId&&e.includes(a.geneId)),Eo);return{results:t??[],error:r,isLoading:!t&&!r,handleDelete:async s=>{await ES(s),await n(a=>a?.filter(c=>c.id!==s)??[],!1)},handleClearAll:async()=>{await IS(),await n([],!1)}}}var UL=(0,mQ.makeStyles)()({header:{display:"flex",justifyContent:"space-between",alignItems:"center",marginBottom:8},resultList:{maxHeight:300,overflow:"auto"}});function uQ(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 HL=(0,dQ.observer)(function({model:e,handleClose:t,feature:r}){let{classes:n}=UL(),o=Xt(e),[i,s]=(0,tt.useState)(),a=(0,tt.useMemo)(()=>gl(r),[r]),{results:c,error:l,isLoading:A,handleDelete:u,handleClearAll:d}=Hl(a),m=E=>{AQ({view:o,cached:E,newViewTitle:`BLAST - ${uQ(E)}`}),t()},h=l??i;return h?tt.default.createElement(fQ.ErrorMessage,{error:h}):A?tt.default.createElement(pt.Typography,null,"Loading cached results..."):c.length===0?tt.default.createElement(pt.Typography,{color:"textSecondary"},"No cached BLAST results found for this gene. 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If you need a COBALT alignment, please use the manual approach of submitting BLAST yourself and downloading the resulting files"),x.length>0?Ae.default.createElement(Ht.Accordion,{className:i.cachedResultsAccordion},Ae.default.createElement(Ht.AccordionSummary,{expandIcon:Ae.default.createElement(Hc,null)},Ae.default.createElement(Ht.Typography,null,"Previous BLAST Results")),Ae.default.createElement(Ht.AccordionDetails,null,Ae.default.createElement(pQ,{model:r,handleClose:e,feature:t}))):null),Ae.default.createElement(cn,{submitDisabled:!b,onSubmit:()=>{try{y&&(c(void 0),Ul({feature:y,view:s,newViewTitle:ml(t,y),blastParams:{baseUrl:o,blastProgram:m,blastDatabase:l,msaAlgorithm:u,selectedTranscript:y,proteinSequence:b}}),e())}catch(S){console.error(S),c(S)}},onCancel:e}))}),yQ=qL;var Jr=f(Q()),bQ=f(de()),Fi=f(k()),BQ=f(G()),SQ=f(Se());ql();var JL=(0,SQ.makeStyles)()({ncbiLink:{wordBreak:"break-all",margin:30,maxWidth:600},infoText:{marginTop:20}}),VL=(0,BQ.observer)(function({handleClose:e,feature:t,model:r,children:n,baseUrl:o}){let{classes:i}=JL(),s=Xt(r),a=qr({feature:t,view:s}),{proteinSequence:c,error:l}=a,A=pl(c),u=`${o}?PAGE_TYPE=BlastSearch&PAGE=Proteins&PROGRAM=blastp&QUERY=${A}`,d=`${o}?PAGE_TYPE=BlastSearch&PAGE=Proteins&PROGRAM=blastp&QUERY=${(0,bQ.shorten2)(A,10)}`;return Jr.default.createElement(Jr.default.Fragment,null,Jr.default.createElement(Cr,{error:l},n,Jr.default.createElement(Ir,{feature:t,...a}),c?Jr.default.createElement("div",{className:i.ncbiLink},"Link to NCBI BLAST: ",Jr.default.createElement(Io,{href:u},d)):null,Jr.default.createElement(Fi.Typography,{className:i.infoText},`Click the link above and run your BLAST query, and once you have results, click "Multiple Alignment" at the top of the results page to be redirected to COBALT, NCBI's multiple sequence aligner. 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You can find the RID in the BLAST results page URL or at the top of the results page. RIDs are typically valid for 24-36 hours after submission."),gt.default.createElement(lt,{variant:"outlined",label:"BLAST RID",placeholder:"e.g., ABC12345",fullWidth:!0,className:i.marginBottom,value:l,onChange:p=>{A(p.target.value)}}),I?gt.default.createElement(Jl.Typography,{variant:"body2",className:i.marginBottom},gt.default.createElement(Io,{href:`${o}?CMD=Get&RID=${I}`},"View BLAST results on NCBI")):null,gt.default.createElement(zs,{className:i.ridField,value:u,onChange:d}),gt.default.createElement(Ir,{feature:t,...m}),gt.default.createElement(Jl.Typography,{className:i.infoText},"This will fetch the BLAST results for the provided RID and run them through a multiple sequence alignment. The protein sequence from the selected transcript will be added as the query sequence in the MSA.")),gt.default.createElement(cn,{submitDisabled:!E||!I,onSubmit:()=>{try{h&&I&&(c(void 0),Ul({feature:h,view:s,newViewTitle:ml(t,h),blastParams:{baseUrl:o,blastProgram:"blastp",blastDatabase:"nr",msaAlgorithm:u,selectedTranscript:h,proteinSequence:E,rid:I}}),e())}catch(p){console.error(p),c(p)}},onCancel:e}))}),TQ=WL;var br=f(Q()),tr=f(k()),_Q=f(Se());var zL=(0,_Q.makeStyles)()({urlField:{minWidth:300}});function ym({handleClose:e,baseUrl:t}){let{classes:r}=zL(),[n,o]=(0,br.useState)(t);return br.default.createElement(tr.Dialog,{open:!0,maxWidth:"lg",onClose:()=>{e()}},br.default.createElement(tr.DialogTitle,null,"BLAST Settings"),br.default.createElement(tr.DialogContent,null,br.default.createElement(lt,{autoFocus:!0,margin:"dense",label:"BLAST Base 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Br.default.createElement(Br.default.Fragment,null,Br.default.createElement(kQ.IconButton,{className:l.settingsButton,size:"small",onClick:()=>{c(!0)}},Br.default.createElement(Mc,null)),Br.default.createElement(A,{model:t,feature:r,handleClose:e,baseUrl:i},Br.default.createElement(xm,{lookupMethod:n,setLookupMethod:o})),a?Br.default.createElement(ym,{baseUrl:i,handleClose:u=>{u&&s(u),c(!1)}}):null)}var ht=f(Q()),$s=f(Qe()),Yl=f(de()),HQ=f(k()),jQ=f(G());var qQ=f(Se());Cn();function bm(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 lf(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-${lf(t)}`}function LQ(e={}){return e.type&&e.adapterId?`${e.type}-${e.adapterId}`:`${bm(e)}`}var RQ={};async function XL(e,t,r){let n=r?.type;if(!n)throw new Error(`could not determine adapter type from adapter config 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Vl(e){return(0,UQ.readConfObject)(e,["msa","datasets"])}var ZL=(0,qQ.makeStyles)()({selectedContainer:{marginTop:50}}),eR=(0,jQ.observer)(function({model:e,feature:t,handleClose:r}){let n=(0,Yl.getSession)(e),o=Xt(e),{classes:i}=ZL(),{pluginManager:s}=(0,Yl.getEnv)(e),{assemblyNames:a}=o,[c,l]=(0,ht.useState)(),A=Vl(n.jbrowse),[u,d]=(0,ht.useState)(A?.[0]?.datasetId),m=A?.find(F=>F.datasetId===u),{data:h,isLoading:E,error:x}=Co(m?`${m.datasetId}-msa-list`:null,()=>PQ({config:m.adapter,pluginManager:s}),Eo),I=qr({feature:t,view:o,validIds:h}),{selectedId:p,selectedTranscript:y}=I,{data:b,isLoading:w,error:S}=Co(p&&m&&h?`${m.datasetId}-${p}-${h.length}-msa`:null,()=>OQ({msaId:p,config:m.adapter,pluginManager:s}),Eo),M=x??S??I.error??c;return ht.default.createElement(ht.default.Fragment,null,ht.default.createElement(Cr,{error:M},ht.default.createElement(lt,{select:!0,label:"Select MSA dataset",value:u,onChange:F=>{d(F.target.value)}},A?.map(F=>ht.default.createElement(HQ.MenuItem,{key:F.datasetId,value:F.datasetId},F.name))),m?ht.default.createElement("div",{className:i.selectedContainer},!E&&w?ht.default.createElement($s.LoadingEllipses,{variant:"h6",message:`Loading MSA for (${p})`}):null,E?ht.default.createElement($s.LoadingEllipses,{variant:"h6",message:`Loading available MSAs for (${m.name})`}):null,h?ht.default.createElement("div",null,ht.default.createElement($s.SanitizedHTML,{html:m.description}),ht.default.createElement(Ir,{feature:t,...I})):null):null),ht.default.createElement(cn,{submitDisabled:!y||!b?.length,onSubmit:()=>{try{if(y&&b){let F=`${p}_${a[0]}`;GQ({session:n,newViewTitle:ho(y),view:o,querySeqName:F,feature:y,data:{msa:b.map(D=>`>${D.get("refName")}
+${D.get("seq")}`).join(`
+`)}}),r()}}catch(F){l(F)}},onCancel:r}))}),JQ=eR;var VQ=f(Q());function Ks({children:e,value:t,index:r,...n}){return VQ.default.createElement("div",{role:"tabpanel",hidden:t!==r,...n},t===r?e:null)}function Sm({handleClose:e,feature:t,model:r}){let n=(0,WQ.getSession)(r),i=!!Vl(n.jbrowse)?.length,[s,a]=(0,Dt.useState)("ncbi_blast");return Dt.default.createElement(YQ.Dialog,{maxWidth:"xl",title:"Launch MSA view",open:!0,onClose:e},Dt.default.createElement(Pi.Tabs,{value:s,onChange:(c,l)=>{a(l)}},Dt.default.createElement(Pi.Tab,{label:"NCBI BLAST query",value:"ncbi_blast"}),i?Dt.default.createElement(Pi.Tab,{label:"Pre-loaded MSA datasets",value:"preloaded_msa"}):null,Dt.default.createElement(Pi.Tab,{label:"Manual upload",value:"manual_msa"})),Dt.default.createElement(Ks,{value:s,index:"ncbi_blast"},Dt.default.createElement(wm,{handleClose:e,feature:t,model:r})),i?Dt.default.createElement(Ks,{value:s,index:"preloaded_msa"},Dt.default.createElement(JQ,{model:r,feature:t,handleClose:e})):null,Dt.default.createElement(Ks,{value:s,index:"manual_msa"},Dt.default.createElement(aQ,{model:r,feature:t,handleClose:e})))}function tR(e){return e.name==="LinearBasicDisplay"}function rR(e){return e.views(t=>{let r=t.contextMenuItems;return{contextMenuItems(){let n=t.contextMenuFeature,o=(0,Wl.getContainingTrack)(t),i=n?.get("type"),s=n&&["gene","mRNA","transcript"].includes(i);return[...r(),...s?[{label:"Launch MSA view",icon:w1,onClick:()=>{(0,Wl.getSession)(o).queueDialog(a=>[Sm,{model:o,handleClose:a,feature:n}])}}]:[]]}}})}function Qm(e){e.addToExtensionPoint("Core-extendPluggableElement",t=>(tR(t)&&(t.stateModel=rR(t.stateModel)),t))}function Mm(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:h,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:h,showBranchLen:E,highlightColumns:I,init:{msaData:r?.msa,treeData:r?.tree,msaUrl:n?.uri,treeUrl:o?.uri,querySeqName:x}})})}var uM=f(Q()),fM=f($Q());var AR=(0,uM.lazy)(()=>Promise.resolve().then(()=>(AM(),lM)));function Dm(e){e.addViewType(()=>new fM.default({name:"MsaView",stateModel:qd(),ReactComponent:AR}))}var dM="2.5.1";var Kl=class extends mM.default{constructor(){super(...arguments);this.name="MsaViewPlugin";this.version=dM;this.rootConfigurationSchema=r=>({msa:(0,km.ConfigurationSchema)("MSA",{datasets:Nm.types.maybe(Nm.types.array((0,km.ConfigurationSchema)("MSAEntry",{datasetId:{type:"string",defaultValue:""},description:{type:"string",defaultValue:""},name:{type:"string",defaultValue:""},adapter:r.pluggableConfigSchemaType("adapter")})))})})}install(r){Dm(r),Qm(r),Mm(r),zd(r),Kd(r)}configure(r){(0,pM.isAbstractMenuManager)(r.rootModel)&&r.rootModel.appendToSubMenu(["Add"],{label:"Multiple sequence alignment view",icon:op,onClick:n=>{n.addView("MsaView",{})}})}};return MM(uR);})();
 /*! 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 3.4.5 | (c) Cure53 and other contributors | Released under the Apache license 2.0 and Mozilla Public License 2.0 | github.com/cure53/DOMPurify/blob/3.4.5/LICENSE *)
+  (*! @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 *)
 
 use-sync-external-store/cjs/use-sync-external-store-shim.production.js:
   (**