npm - jbrowse-plugin-msaview - Versions diffs - 2.4.4 → 2.5.0 - Mend

jbrowse-plugin-msaview 2.4.4 → 2.5.0

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Files changed (180) hide show

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

@@ -1,13 +1,11 @@
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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,Ku.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};fc.SourceMapConsumer=pe;function st(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=Xo.fromArray(i.map(String),!0),this._sources=Xo.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}st.prototype=Object.create(pe.prototype);st.prototype.consumer=pe;st.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};st.fromSourceMap=function(t,r){var n=Object.create(st.prototype),o=n._names=Xo.fromArray(t._names.toArray(),!0),i=n._sources=Xo.fromArray(t._sources.toArray(),!0);n.sourceRoot=t._sourceRoot,n.sourcesContent=t._generateSourcesContent(n._sources.toArray(),n.sourceRoot),n.file=t._file,n._sourceMapURL=r,n._absoluteSources=n._sources.toArray().map(function(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 IE;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 Xi(n.__originalMappings,N.compareByOriginalPositions),n};st.prototype._version=3;Object.defineProperty(st.prototype,"sources",{get:function(){return this._absoluteSources.slice()}});function IE(){this.generatedLine=0,this.generatedColumn=0,this.source=null,this.originalLine=null,this.originalColumn=null,this.name=null}var $u=N.compareByGeneratedPositionsDeflatedNoLine;function EE(e,t){let r=e.length,n=e.length-t;if(!(n<=1))if(n==2){let o=e[t],i=e[t+1];$u(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($u(s,a)<=0)break;e[i-1]=a,e[i]=s}else Xi(e,$u,t)}st.prototype._parseMappings=function(t,r){var n=1,o=0,i=0,s=0,a=0,c=0,l=t.length,A=0,u={},m={},d=[],p=[],C,y,I,h,x;let S=0;for(;A<l;)if(t.charAt(A)===";")n++,A++,o=0,EE(p,S),S=p.length;else if(t.charAt(A)===",")A++;else{for(C=new IE,C.generatedLine=n,h=A;h<l&&!this._charIsMappingSeparator(t,h);h++);for(y=t.slice(A,h),I=[];A<h;)Bv.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)}}EE(p,S),this.__generatedMappings=p;for(var M=0;M<d.length;M++)d[M]!=null&&Xi(d[M],N.compareByOriginalPositionsNoSource);this.__originalMappings=[].concat(...d)};st.prototype._findMapping=function(t,r,n,o,i,s){if(t[n]<=0)throw new TypeError("Line must be greater than or equal to 1, got "+t[n]);if(t[o]<0)throw new TypeError("Column must be greater than or equal to 0, got "+t[o]);return Ku.search(t,r,i,s)};st.prototype.computeColumnSpans=function(){for(var t=0;t<this._generatedMappings.length;++t){var r=this._generatedMappings[t];if(t+1<this._generatedMappings.length){var n=this._generatedMappings[t+1];if(r.generatedLine===n.generatedLine){r.lastGeneratedColumn=n.generatedColumn-1;continue}}r.lastGeneratedColumn=1/0}};st.prototype.originalPositionFor=function(t){var r={generatedLine: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}};st.prototype.hasContentsOfAllSources=function(){return this.sourcesContent?this.sourcesContent.length>=this._sources.size()&&!this.sourcesContent.some(function(t){return t==null}):!1};st.prototype.sourceContentFor=function(t,r){if(!this.sourcesContent)return null;var n=this._findSourceIndex(t);if(n>=0)return this.sourcesContent[n];var o=t;this.sourceRoot!=null&&(o=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.')};st.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}};fc.BasicSourceMapConsumer=st;function dr(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 Xo,this._names=new Xo;var i={line:-1,column:0};this._sections=o.map(function(s){if(s.url)throw new Error("Support for url field in sections not implemented.");var a=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)}})}dr.prototype=Object.create(pe.prototype);dr.prototype.constructor=pe;dr.prototype._version=3;Object.defineProperty(dr.prototype,"sources",{get:function(){for(var e=[],t=0;t<this._sections.length;t++)for(var r=0;r<this._sections[t].consumer.sources.length;r++)e.push(this._sections[t].consumer.sources[r]);return e}});dr.prototype.originalPositionFor=function(t){var r={generatedLine:N.getArg(t,"line"),generatedColumn:N.getArg(t,"column")},n=Ku.search(r,this._sections,function(i,s){var a=i.generatedLine-s.generatedOffset.generatedLine;return a||i.generatedColumn-s.generatedOffset.generatedColumn}),o=this._sections[n];return o?o.consumer.originalPositionFor({line:r.generatedLine-(o.generatedOffset.generatedLine-1),column:r.generatedColumn-(o.generatedOffset.generatedLine===r.generatedLine?o.generatedOffset.generatedColumn-1:0),bias:t.bias}):{source:null,line:null,column:null,name:null}};dr.prototype.hasContentsOfAllSources=function(){return this._sections.every(function(t){return t.consumer.hasContentsOfAllSources()})};dr.prototype.sourceContentFor=function(t,r){for(var n=0;n<this._sections.length;n++){var o=this._sections[n],i=o.consumer.sourceContentFor(t,!0);if(i||i==="")return i}if(r)return null;throw new Error('"'+t+'" is not in the SourceMap.')};dr.prototype.generatedPositionFor=function(t){for(var r=0;r<this._sections.length;r++){var n=this._sections[r];if(n.consumer._findSourceIndex(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}};dr.prototype._parseMappings=function(t,r){this.__generatedMappings=[],this.__originalMappings=[];for(var n=0;n<this._sections.length;n++)for(var o=this._sections[n],i=o.consumer._generatedMappings,s=0;s<i.length;s++){var a=i[s],c=o.consumer._sources.at(a.source);c!==null&&(c=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)}Xi(this.__generatedMappings,N.compareByGeneratedPositionsDeflated),Xi(this.__originalMappings,N.compareByOriginalPositions)};fc.IndexedSourceMapConsumer=dr});var wE=G(yE=>{var Sv=Wu().SourceMapGenerator,mc=Ko(),Qv=/(\r?\n)/,Mv=10,Zo="$$$isSourceNode$$$";function Ft(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[Zo]=!0,n!=null&&this.add(n)}Ft.fromStringWithSourceMap=function(t,r,n){var o=new Ft,i=t.split(Qv),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 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Got "+t);return this};Ft.prototype.prepend=function(t){if(Array.isArray(t))for(var r=t.length-1;r>=0;r--)this.prepend(t[r]);else if(t[Zo]||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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this.__originalMappings||this._parseMappings(this._mappings,this.sourceRoot),this.__originalMappings}});Ee.prototype._charIsMappingSeparator=function(t,r){var n=t.charAt(r);return n===";"||n===","};Ee.prototype._parseMappings=function(t,r){throw new Error("Subclasses must implement _parseMappings")};Ee.GENERATED_ORDER=1;Ee.ORIGINAL_ORDER=2;Ee.GREATEST_LOWER_BOUND=1;Ee.LEAST_UPPER_BOUND=2;Ee.prototype.eachMapping=function(t,r,n){var o=r||null,i=n||Ee.GENERATED_ORDER,s;switch(i){case Ee.GENERATED_ORDER:s=this._generatedMappings;break;case Ee.ORIGINAL_ORDER:s=this._originalMappings;break;default:throw new Error("Unknown order of iteration.")}for(var a=this.sourceRoot,c=t.bind(o),l=this._names,A=this._sources,u=this._sourceMapURL,m=0,d=s.length;m<d;m++){var p=s[m],E=p.source===null?null:A.at(p.source);E!==null&&(E=D.computeSourceURL(a,E,u)),c({source:E,generatedLine:p.generatedLine,generatedColumn:p.generatedColumn,originalLine:p.originalLine,originalColumn:p.originalColumn,name:p.name===null?null:l.at(p.name)})}};Ee.prototype.allGeneratedPositionsFor=function(t){var r=D.getArg(t,"line"),n={source:D.getArg(t,"source"),originalLine:r,originalColumn:D.getArg(t,"column",0)};if(n.source=this._findSourceIndex(n.source),n.source<0)return[];var o=[],i=this._findMapping(n,this._originalMappings,"originalLine","originalColumn",D.compareByOriginalPositions,DA.LEAST_UPPER_BOUND);if(i>=0){var s=this._originalMappings[i];if(t.column===void 0)for(var a=s.originalLine;s&&s.originalLine===a;)o.push({line:D.getArg(s,"generatedLine",null),column:D.getArg(s,"generatedColumn",null),lastColumn:D.getArg(s,"lastGeneratedColumn",null)}),s=this._originalMappings[++i];else for(var c=s.originalColumn;s&&s.originalLine===r&&s.originalColumn==c;)o.push({line:D.getArg(s,"generatedLine",null),column:D.getArg(s,"generatedColumn",null),lastColumn:D.getArg(s,"lastGeneratedColumn",null)}),s=this._originalMappings[++i]}return o};Ba.SourceMapConsumer=Ee;function ot(e,t){var r=e;typeof e=="string"&&(r=D.parseSourceMapInput(e));var n=D.getArg(r,"version"),o=D.getArg(r,"sources"),i=D.getArg(r,"names",[]),s=D.getArg(r,"sourceRoot",null),a=D.getArg(r,"sourcesContent",null),c=D.getArg(r,"mappings"),l=D.getArg(r,"file",null);if(n!=this._version)throw new Error("Unsupported version: "+n);s&&(s=D.normalize(s)),o=o.map(String).map(D.normalize).map(function(A){return s&&D.isAbsolute(s)&&D.isAbsolute(A)?D.relative(s,A):A}),this._names=Go.fromArray(i.map(String),!0),this._sources=Go.fromArray(o,!0),this._absoluteSources=this._sources.toArray().map(function(A){return D.computeSourceURL(s,A,t)}),this.sourceRoot=s,this.sourcesContent=a,this._mappings=c,this._sourceMapURL=t,this.file=l}ot.prototype=Object.create(Ee.prototype);ot.prototype.consumer=Ee;ot.prototype._findSourceIndex=function(e){var t=e;if(this.sourceRoot!=null&&(t=D.relative(this.sourceRoot,t)),this._sources.has(t))return this._sources.indexOf(t);var r;for(r=0;r<this._absoluteSources.length;++r)if(this._absoluteSources[r]==e)return r;return-1};ot.fromSourceMap=function(t,r){var n=Object.create(ot.prototype),o=n._names=Go.fromArray(t._names.toArray(),!0),i=n._sources=Go.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 D.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 mh;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 ji(n.__originalMappings,D.compareByOriginalPositions),n};ot.prototype._version=3;Object.defineProperty(ot.prototype,"sources",{get:function(){return this._absoluteSources.slice()}});function mh(){this.generatedLine=0,this.generatedColumn=0,this.source=null,this.originalLine=null,this.originalColumn=null,this.name=null}var kA=D.compareByGeneratedPositionsDeflatedNoLine;function fh(e,t){let r=e.length,n=e.length-t;if(!(n<=1))if(n==2){let o=e[t],i=e[t+1];kA(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(kA(s,a)<=0)break;e[i-1]=a,e[i]=s}else ji(e,kA,t)}ot.prototype._parseMappings=function(t,r){var n=1,o=0,i=0,s=0,a=0,c=0,l=t.length,A=0,u={},m={},d=[],p=[],E,x,I,h,y;let Q=0;for(;A<l;)if(t.charAt(A)===";")n++,A++,o=0,fh(p,Q),Q=p.length;else if(t.charAt(A)===",")A++;else{for(E=new mh,E.generatedLine=n,h=A;h<l&&!this._charIsMappingSeparator(t,h);h++);for(x=t.slice(A,h),I=[];A<h;)VM.decode(t,A,m),y=m.value,A=m.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])),p.push(E),typeof E.originalLine=="number"){let B=E.source;for(;d.length<=B;)d.push(null);d[B]===null&&(d[B]=[]),d[B].push(E)}}fh(p,Q),this.__generatedMappings=p;for(var M=0;M<d.length;M++)d[M]!=null&&ji(d[M],D.compareByOriginalPositionsNoSource);this.__originalMappings=[].concat(...d)};ot.prototype._findMapping=function(t,r,n,o,i,s){if(t[n]<=0)throw new TypeError("Line must be greater than or equal to 1, got "+t[n]);if(t[o]<0)throw new TypeError("Column must be greater than or equal to 0, got "+t[o]);return DA.search(t,r,i,s)};ot.prototype.computeColumnSpans=function(){for(var t=0;t<this._generatedMappings.length;++t){var r=this._generatedMappings[t];if(t+1<this._generatedMappings.length){var n=this._generatedMappings[t+1];if(r.generatedLine===n.generatedLine){r.lastGeneratedColumn=n.generatedColumn-1;continue}}r.lastGeneratedColumn=1/0}};ot.prototype.originalPositionFor=function(t){var r={generatedLine:D.getArg(t,"line"),generatedColumn:D.getArg(t,"column")},n=this._findMapping(r,this._generatedMappings,"generatedLine","generatedColumn",D.compareByGeneratedPositionsDeflated,D.getArg(t,"bias",Ee.GREATEST_LOWER_BOUND));if(n>=0){var o=this._generatedMappings[n];if(o.generatedLine===r.generatedLine){var i=D.getArg(o,"source",null);i!==null&&(i=this._sources.at(i),i=D.computeSourceURL(this.sourceRoot,i,this._sourceMapURL));var s=D.getArg(o,"name",null);return s!==null&&(s=this._names.at(s)),{source:i,line:D.getArg(o,"originalLine",null),column:D.getArg(o,"originalColumn",null),name:s}}}return{source:null,line:null,column:null,name:null}};ot.prototype.hasContentsOfAllSources=function(){return this.sourcesContent?this.sourcesContent.length>=this._sources.size()&&!this.sourcesContent.some(function(t){return t==null}):!1};ot.prototype.sourceContentFor=function(t,r){if(!this.sourcesContent)return null;var n=this._findSourceIndex(t);if(n>=0)return this.sourcesContent[n];var o=t;this.sourceRoot!=null&&(o=D.relative(this.sourceRoot,o));var i;if(this.sourceRoot!=null&&(i=D.urlParse(this.sourceRoot))){var s=o.replace(/^file:\/\//,"");if(i.scheme=="file"&&this._sources.has(s))return this.sourcesContent[this._sources.indexOf(s)];if((!i.path||i.path=="/")&&this._sources.has("/"+o))return this.sourcesContent[this._sources.indexOf("/"+o)]}if(r)return null;throw new Error('"'+o+'" is not in the SourceMap.')};ot.prototype.generatedPositionFor=function(t){var r=D.getArg(t,"source");if(r=this._findSourceIndex(r),r<0)return{line:null,column:null,lastColumn:null};var n={source:r,originalLine:D.getArg(t,"line"),originalColumn:D.getArg(t,"column")},o=this._findMapping(n,this._originalMappings,"originalLine","originalColumn",D.compareByOriginalPositions,D.getArg(t,"bias",Ee.GREATEST_LOWER_BOUND));if(o>=0){var i=this._originalMappings[o];if(i.source===n.source)return{line:D.getArg(i,"generatedLine",null),column:D.getArg(i,"generatedColumn",null),lastColumn:D.getArg(i,"lastGeneratedColumn",null)}}return{line:null,column:null,lastColumn:null}};Ba.BasicSourceMapConsumer=ot;function sr(e,t){var r=e;typeof e=="string"&&(r=D.parseSourceMapInput(e));var n=D.getArg(r,"version"),o=D.getArg(r,"sections");if(n!=this._version)throw new Error("Unsupported version: "+n);this._sources=new Go,this._names=new Go;var i={line:-1,column:0};this._sections=o.map(function(s){if(s.url)throw new Error("Support for url field in sections not implemented.");var a=D.getArg(s,"offset"),c=D.getArg(a,"line"),l=D.getArg(a,"column");if(c<i.line||c===i.line&&l<i.column)throw new Error("Section offsets must be ordered and non-overlapping.");return i=a,{generatedOffset:{generatedLine:c+1,generatedColumn:l+1},consumer:new Ee(D.getArg(s,"map"),t)}})}sr.prototype=Object.create(Ee.prototype);sr.prototype.constructor=Ee;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:D.getArg(t,"line"),generatedColumn:D.getArg(t,"column")},n=DA.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(D.getArg(t,"source"))!==-1){var o=n.consumer.generatedPositionFor(t);if(o){var i={line:o.line+(n.generatedOffset.generatedLine-1),column:o.column+(n.generatedOffset.generatedLine===o.line?n.generatedOffset.generatedColumn-1:0)};return i}}}return{line:null,column:null}};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=D.computeSourceURL(o.consumer.sourceRoot,c,this._sourceMapURL)),this._sources.add(c),c=this._sources.indexOf(c);var l=null;a.name&&(l=o.consumer._names.at(a.name),this._names.add(l),l=this._names.indexOf(l));var A={source:c,generatedLine:a.generatedLine+(o.generatedOffset.generatedLine-1),generatedColumn:a.generatedColumn+(o.generatedOffset.generatedLine===a.generatedLine?o.generatedOffset.generatedColumn-1:0),originalLine:a.originalLine,originalColumn:a.originalColumn,name:l};this.__generatedMappings.push(A),typeof A.originalLine=="number"&&this.__originalMappings.push(A)}ji(this.__generatedMappings,D.compareByGeneratedPositionsDeflated),ji(this.__originalMappings,D.compareByOriginalPositions)};Ba.IndexedSourceMapConsumer=sr});var ph=U(gh=>{var YM=TA().SourceMapGenerator,Sa=Oo(),WM=/(\r?\n)/,zM=10,Uo="$$$isSourceNode$$$";function Dt(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[Uo]=!0,n!=null&&this.add(n)}Dt.fromStringWithSourceMap=function(t,r,n){var o=new Dt,i=t.split(WM),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 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Got "+t);return this};Dt.prototype.prepend=function(t){if(Array.isArray(t))for(var r=t.length-1;r>=0;r--)this.prepend(t[r]);else if(t[Uo]||typeof t=="string")this.children.unshift(t);else throw new TypeError("Expected a SourceNode, string, or an array of SourceNodes and strings. Got "+t);return this};Dt.prototype.walk=function(t){for(var r,n=0,o=this.children.length;n<o;n++)r=this.children[n],r[Uo]?r.walk(t):r!==""&&t(r,{source:this.source,line:this.line,column:this.column,name:this.name})};Dt.prototype.join=function(t){var r,n,o=this.children.length;if(o>0){for(r=[],n=0;n<o-1;n++)r.push(this.children[n]),r.push(t);r.push(this.children[n]),this.children=r}return this};Dt.prototype.replaceRight=function(t,r){var n=this.children[this.children.length-1];return n[Uo]?n.replaceRight(t,r):typeof n=="string"?this.children[this.children.length-1]=n.replace(t,r):this.children.push("".replace(t,r)),this};Dt.prototype.setSourceContent=function(t,r){this.sourceContents[Sa.toSetString(t)]=r};Dt.prototype.walkSourceContents=function(t){for(var r=0,n=this.children.length;r<n;r++)this.children[r][Uo]&&this.children[r].walkSourceContents(t);for(var o=Object.keys(this.sourceContents),r=0,n=o.length;r<n;r++)t(Sa.fromSetString(o[r]),this.sourceContents[o[r]])};Dt.prototype.toString=function(){var t="";return this.walk(function(r){t+=r}),t};Dt.prototype.toStringWithSourceMap=function(t){var r={code:"",line:1,column:0},n=new YM(t),o=!1,i=null,s=null,a=null,c=null;return this.walk(function(l,A){r.code+=l,A.source!==null&&A.line!==null&&A.column!==null?((i!==A.source||s!==A.line||a!==A.column||c!==A.name)&&n.addMapping({source:A.source,original:{line:A.line,column:A.column},generated:{line:r.line,column:r.column},name:A.name}),i=A.source,s=A.line,a=A.column,c=A.name,o=!0):o&&(n.addMapping({generated:{line:r.line,column:r.column}}),i=null,o=!1);for(var u=0,m=l.length;u<m;u++)l.charCodeAt(u)===zM?(r.line++,r.column=0,u+1===m?(i=null,o=!1):o&&n.addMapping({source:A.source,original:{line:A.line,column:A.column},generated:{line:r.line,column:r.column},name:A.name})):r.column++}),this.walkSourceContents(function(l,A){n.setSourceContent(l,A)}),{code:r.code,map:n}};gh.SourceNode=Dt});var hh=U(Qa=>{Qa.SourceMapGenerator=TA().SourceMapGenerator;Qa.SourceMapConsumer=dh().SourceMapConsumer;Qa.SourceNode=ph().SourceNode});var Ch,Ma,NA=g(()=>{"use client";W();Ch=f(R(),1),Ma=(0,_.createSvgIcon)((0,Ch.jsx)("path",{d:"M19 19H5V5h7V3H5c-1.11 0-2 .9-2 2v14c0 1.1.89 2 2 2h14c1.1 0 2-.9 2-2v-7h-2zM14 3v2h3.59l-9.83 9.83 1.41 1.41L19 6.41V10h2V3z"}),"OpenInNew")});function Ta(e){let{children:t,...r}=e;return(0,va.jsxs)(Eh.Link,{...r,target:"_blank",rel:"noopener noreferrer",children:[t," ",(0,va.jsx)(Ma,{fontSize:"small"})]})}var va,Eh,Ih=g(()=>{va=f(R(),1);NA();Eh=f(k(),1)});function LA({text:e,extra:t}){let{classes:r}=$M(),n=t?`supporting data: ${JSON.stringify(t,null,2)}`:"",o=[e,n].filter(Boolean).join(`
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 UniProt/Swiss-Prot|P36835|IL2_CAPHI        -----------LLGVGLNPKFLTP------------------------------------
 UniProt/Swiss-Prot|Q7JFM4|IL2_AOTVO        MLKPPLPLRSLLFLQLPLLGVGLNPKFLTPSGNEDIGGKPGTGGDFFLTSTPAGTLDVST
 UniProt/Swiss-Prot|Q29416|IL2_CANFA        --------------LFLQLSLLG-------------------------------------
-`,fB=`CLUSTAL O(1.2.4) multiple sequence alignment
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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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e.showVerticalScrollbar?20:0},get fillPalette(){return iS([...e.tidyInterProAnnotationTypes.keys()])},get strokePalette(){return Object.fromEntries(Object.entries(this.fillPalette).map(([t,r])=>[t,yt(r).darken(.1).toHex()]))},getRowData(t){return{data:e.MSA?.getRowData(t),treeMetadata:e.treeMetadata[t]}}})).actions(e=>({setHeaderHeight(t){e.headerHeight=t},setConservationTrackHeight(t){e.conservationTrackHeight=t},reset(){e.setData({tree:"",msa:""}),e.resetZoom(),e.setError(void 0),e.setScrollY(0),e.setScrollX(0),e.setCurrentAlignment(0),e.setTreeFilehandle(void 0),e.setMSAFilehandle(void 0),e.setGFFFilehandle(void 0),e.setInterProAnnotations({}),e.setShowDomains(!1)},async exportSVG(t){let{renderToSvg:r}=await Promise.resolve().then(()=>(qS(),jS)),n=await r(e,t),o=new Blob([n],{type:"image/svg+xml"});_S(o,"image.svg")},incrementRef(){e.nref++},initFilter(t){e.featureFilters.get(t)===void 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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 nN({rid:e,onProgress:t,baseUrl:r}){for(;;){for(let c=0;c<20;c++)await hl(1e3),t(`Re-checking BLAST status in... ${20-c}`);let o=await bn(`${r}?CMD=Get&FORMAT_OBJECT=SearchInfo&RID=${e}`),s=/\s+Status=(\S+)/m.exec(o)?.[1],a=/\s+ThereAreHits=yes/m.test(o);if(s!=="WAITING"){if(s==="FAILED")throw new Error(`BLAST ${e} failed`);if(s==="READY"){if(a)return!0;throw new Error("No hits found")}throw new Error(`BLAST ${e} returned unexpected status: ${s??"unknown"}`)}}}Li();var oN="jbrowse-msaview-taxonomy-cache",bs="common-names",iN=2;async function a1(){return Fn(oN,iN,{upgrade(e){e.objectStoreNames.contains(bs)&&e.deleteObjectStore(bs),e.createObjectStore(bs,{keyPath:"taxid"})}})}async function sN(e){let r=(await a1()).transaction(bs,"readonly"),n=await Promise.all(e.map(o=>r.store.get(o)));return await r.done,n}async function aN(e){let r=(await a1()).transaction(bs,"readwrite");for(let n of e)await r.store.put(n);await r.done}async function c1(e){let t=new Map,r=[],n=await sN(e);for(let s=0;s<e.length;s++){let a=e[s],c=n[s];c?t.set(a,{sciname:c.sciname,commonName:c.commonName}):r.push(a)}if(r.length===0)return t;let o=100,i=[];for(let s=0;s<r.length;s+=o){let a=r.slice(s,s+o),c=a.join(",");try{let A=await(await fetch(`https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=taxonomy&id=${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 aN(i),t}async function l1({self:e}){let{baseUrl:t,blastDatabase:r,blastProgram:n,msaAlgorithm:o,proteinSequence:i,selectedTranscript:s,rid:a}=e.blastParams,c=Zs(i),l,A;if(a){e.setRid(a);let I=await Jm({rid:a,baseUrl:t,onProgress:h=>{e.setProgress(h)}});l=I.hits,A=I.rid}else{let I=await s1({query:c,blastDatabase:r,blastProgram:n,baseUrl:t,onProgress:h=>{e.setProgress(h)},onRid:h=>{e.setRid(h)}});l=I.hits,A=I.rid}e.setProgress("Fetching species taxonomy info...");let u=l.map(I=>I.description[0]?.taxid).filter(I=>I!==void 0),m=await c1(u),d={},p=l.map(I=>{let h=I.description[0]??{accession:"unknown",id:"unknown",sciname:"unknown"},x=t1(h,m),S=r1(I.hsps[0]?.hseq??"");return d[x]=cN(h,m),`>${x}
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B=A.indexOf("<Taxon>",I),v=A.indexOf("</Taxon>",I);if(v===-1)break;B!==-1&&B<v?(x++,I=B+7):(x--,I=v+8)}let h=A.slice(E,I),y=u.get(p),Q=h.includes("<LineageEx>"),M=y?.includes("<LineageEx>");(!y||Q&&!M)&&u.set(p,h)}for(let p of a){let E=u.get(p);if(E){let x=/<GenbankCommonName>(.*?)<\/GenbankCommonName>/.exec(E),I=/<CommonName>(.*?)<\/CommonName>/.exec(E),h=/<ScientificName>(.*?)<\/ScientificName>/.exec(E),y=x?.[1]??I?.[1],Q=h?.[1]??"";t.set(p,{sciname:Q,commonName:y}),i.push({taxid:p,sciname:Q,commonName:y})}}}catch(l){console.error("Failed to fetch taxonomy data:",l)}}return i.length>0&&await BD(i),t}async function OB({self:e}){let{baseUrl:t,blastDatabase:r,blastProgram:n,msaAlgorithm:o,proteinSequence:i,selectedTranscript:s,rid:a}=e.blastParams,c=Zc(i),l,A;if(a){e.setRid(a);let I=await Cm({rid:a,baseUrl:t,onProgress:h=>{e.setProgress(h)}});l=I.hits,A=I.rid}else{let I=await 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Ie.types.compose(F1.BaseViewModel,pl(),Ie.types.model("MsaView",{connectedViewId:Ie.types.maybe(Ie.types.string),connectedFeature:Ie.types.frozen(),connectedHighlights:Ie.types.array(Ie.types.model({refName:Ie.types.string,start:Ie.types.number,end:Ie.types.number})),blastParams:Ie.types.frozen(),querySeqName:"QUERY",uniprotId:Ie.types.maybe(Ie.types.string),zoomToBaseLevel:!1,init:Ie.types.frozen(),connectedStructures:Ie.types.array(Ie.types.frozen()),dataStoreId:Ie.types.maybe(Ie.types.string),mafRegion:Ie.types.frozen()})).volatile(()=>({rid:void 0,progress:"",error:void 0,loadingStoredData:!1,isStoringData:!1})).views(e=>({getRowByName(t){return e.rows.find(r=>r[0]===t)},getSequenceByRowName(t){return e.rows.find(r=>r[0]===t)?.[1]}})).views(e=>({get transcriptToMsaMap(){return e.connectedFeature?e0(e.connectedFeature):void 0},get connectedView(){let{views:t}=(0,wi.getSession)(e);return t.find(r=>r.id===e.connectedViewId)},get connectedProteinViews(){let t=Bn((0,wi.getSession)(e).views),r=[];for(let n of e.connectedStructures){let o=t.find(i=>i.id===n.proteinViewId);o&&r.push({...n,proteinView:o})}return r}})).views(e=>({get structureHoverCol(){for(let t of e.connectedProteinViews){let n=t.proteinView.structures[t.structureIdx]?.hoverPosition?.structureSeqPos;if(n!==void 0){let o=t.structureToMsa[n];if(o!==void 0){let i=e.getSequenceByRowName(t.msaRowName);if(i){let s=A1(i,o);if(s!==void 0)return e.globalColToVisibleCol(s)}}}}}})).views(e=>({get mouseCol2(){let t=e.structureHoverCol;return t!==void 0?t:B1({model:e})}})).actions(e=>({setZoomToBaseLevel(t){e.zoomToBaseLevel=t},setError(t){e.error=t},setProgress(t){e.progress=t},setRid(t){e.rid=t},setConnectedHighlights(t){e.connectedHighlights=(0,Ie.cast)(t)},addToConnectedHighlights(t){e.connectedHighlights.push(t)},clearConnectedHighlights(){e.connectedHighlights=(0,Ie.cast)([])},setBlastParams(t){e.blastParams=t},setInit(t){e.init=t},setQuerySeqName(t){e.querySeqName=t},setUniprotId(t){e.uniprotId=t},setDataStoreId(t){e.dataStoreId=t},setMafRegion(t){e.mafRegion=t},setLoadingStoredData(t){e.loadingStoredData=t},setIsStoringData(t){e.isStoringData=t},handleMsaClick(t){let{connectedView:r,zoomToBaseLevel:n}=e,{assemblyManager:o}=(0,wi.getSession)(e),i=Ss({model:e,coord:t});if(!(!i||!r))if(n)r.navTo(i);else{let s=Gs({assemblyManager:o,assemblyNames:r.assemblyNames,refName:i.refName});r.centerAt(i.start,s)}},connectToStructure(t,r,n){let o=n??e.querySeqName,i=e.getSequenceByRowName(o);if(!i)throw new Error(`MSA row "${o}" not found`);let s=i.replaceAll("-",""),a=Bn((0,wi.getSession)(e).views).find(p=>p.id===t);if(!a)throw new Error(`ProteinView "${t}" not found`);let c=a.structures[r];if(!c)throw new Error(`Structure at index ${r} not found`);let l=c.structureSequences?.[0];if(!l)throw new Error("Structure sequence not available");let A=M1(s,l),{seq1ToSeq2:u,seq2ToSeq1:m}=v1(A),d={proteinViewId:t,structureIdx:r,msaRowName:o,msaToStructure:Object.fromEntries(u),structureToMsa:Object.fromEntries(m)};e.connectedStructures.push(d)},disconnectFromStructure(t,r){let n=e.connectedStructures.findIndex(o=>o.proteinViewId===t&&o.structureIdx===r);n!==-1&&e.connectedStructures.splice(n,1)},disconnectAllStructures(){e.connectedStructures.clear()}})).actions(e=>{let t=e.setMouseClickPos.bind(e);return{setMouseClickPos(r,n){t(r,n),r!==void 0&&e.handleMsaClick(r)}}}).views(e=>({extraViewMenuItems(){return[{label:"Zoom to base level on click?",checked:e.zoomToBaseLevel,type:"checkbox",onClick:()=>{e.setZoomToBaseLevel(!e.zoomToBaseLevel)}},{label:"Connect to protein structure...",onClick:()=>{(0,wi.getSession)(e).queueDialog(t=>[IN,{model:e,handleClose:t}])}},...e.connectedStructures.length>0?[{label:"Disconnect from protein structures",onClick:()=>{e.disconnectAllStructures()}}]:[]]}})).actions(e=>({afterCreate(){w1();for(let t of[g1,p1,h1,C1,E1,I1,x1,y1])(0,Ie.addDisposer)(e,(0,R1.autorun)(()=>{t(e)}))}}))}var MN=(0,X1.lazy)(()=>Promise.resolve().then(()=>(K1(),$1)));function Xm(e){e.addViewType(()=>new Z1.default({name:"MsaView",stateModel:Wm(),ReactComponent:MN}))}var eQ="2.4.4";var wl=class extends tQ.default{constructor(){super(...arguments);this.name="MsaViewPlugin";this.version=eQ;this.rootConfigurationSchema=r=>({msa:(0,Zm.ConfigurationSchema)("MSA",{datasets:ed.types.maybe(ed.types.array((0,Zm.ConfigurationSchema)("MSAEntry",{datasetId:{type:"string",defaultValue:""},description:{type:"string",defaultValue:""},name:{type:"string",defaultValue:""},adapter:r.pluggableConfigSchemaType("adapter")})))})})}install(r){Xm(r),su(r),au(r),Rl(r),rA(r)}configure(r){(0,rQ.isAbstractMenuManager)(r.rootModel)&&r.rootModel.appendToSubMenu(["Add"],{label:"Multiple sequence alignment view",icon:bd,onClick:n=>{n.addView("MsaView",{})}})}};return gQ(vN);})();
+`),onProgress:I=>{e.setProgress(I)}}),x=JSON.stringify(d);return await vB({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 SD(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 GB=f(Ce());function UB({model:e}){let{hovered:t}=(0,GB.getSession)(e),{querySeqName:r,transcriptToMsaMap:n,connectedView:o,mafRegion:i}=e;if(!o?.initialized||!Dn(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)}}Wi();var QD="jbrowse-msaview-data",MD=1,Ss="msa-data";async function Em(){return jn(QD,MD,{upgrade(e){e.objectStoreNames.contains(Ss)||e.createObjectStore(Ss,{keyPath:"id"}).createIndex("timestamp","timestamp",{unique:!1})}})}function HB(){return`msa-${Date.now()}-${Math.random().toString(36).slice(2,11)}`}async function jB(e,t){try{let r=await Em(),n={id:e,msa:t.msa,tree:t.tree,treeMetadata:t.treeMetadata,timestamp:Date.now()};return await r.put(Ss,n),!0}catch(r){return console.warn("Failed to store MSA data:",r),!1}}async function qB(e){try{let r=await(await Em()).get(Ss,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 JB(e=10080*60*1e3){try{let t=await Em(),r=Date.now()-e,i=await t.transaction(Ss,"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}}Qs();function VB(e){let{dataStoreId:t,rows:r}=e;t&&r.length===0&&(async()=>{try{e.setLoadingStoredData(!0);let n=await qB(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 YB(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=HB();await jB(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 WB(e){e.blastParams&&(async()=>{try{e.setProgress("Submitting query"),e.setError(void 0);let t=await OB({self:e});e.setData(t),e.setBlastParams(void 0)}catch(t){e.setError(t),console.error(t)}finally{e.setProgress("")}})()}function zB(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=Gd(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 $B(e){let t=!1;return()=>{let r=UB({model:e});r!==void 0?(e.setMousePos(r),t=!0):t&&(e.setMousePos(void 0),t=!1)}}function KB(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=il(i,t);if(s===void 0){o.clearHighlightFromExternal?.();continue}let a=n.msaToStructure[s];a===void 0?o.clearHighlightFromExternal?.():o.highlightFromExternal?.(a)}}function XB(e){let{connectedViewId:t,uniprotId:r,rows:n,connectedStructures:o}=e;if(!(!r||n.length===0))for(let i of bn((0,Im.getSession)(e).views))for(let s=0;s<i.structures.length;s++){let a=i.structures[s];if(!(!a||a.connectedViewId!==t||a.uniprotId!==r||o.some(l=>l.proteinViewId===i.id&&l.structureIdx===s))&&a.structureSequences?.[0])try{e.connectToStructure(i.id,s)}catch(l){console.error("Failed to auto-connect to ProteinView:",l)}}}function ZB(e){let{connectedViewId:t,transcriptToMsaMap:r,querySeqName:n}=e;if(!t||!r)return;let o=new Set;for(let s of bn((0,Im.getSession)(e).views))for(let a of s.structures){if(a.connectedViewId!==t)continue;let c=a.hoverGenomeHighlights;if(!c||c.length===0)continue;let{g2p:l}=r;for(let A of c)for(let u=A.start;u<A.end;u++){let m=l[u];if(m!==void 0){let d=e.seqPosToGlobalCol(n,m);o.add(d)}}}let i=Array.from(o).map(s=>e.globalColToVisibleCol(s)).filter(s=>s!==void 0);e.setHighlightedColumns(i.length>0?i:void 0)}function eS(){JB().catch(e=>{console.error("Failed to cleanup old MSA data:",e)})}Qs();function sl({model:e,coord:t}){let{querySeqName:r,transcriptToMsaMap:n,mafRegion:o}=e,i=e.rows.find(a=>a[0]===r)?.[1];if(!i)return;let s=il(i,t);if(s!==void 0){if(o){let a=o.start+s;return a<o.end?{refName:o.refName,start:a,end:a+1}:void 0}if(n){let{refName:a,p2g:c}=n,l=c[s],A=c[s+1];return l!==void 0&&A!==void 0?{refName:a,start:Math.min(l,A),end:Math.max(l,A)}:void 0}}}var 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rS(e,t){return tS[e.toUpperCase()]?.[t.toUpperCase()]??-4}var _D=-10,kD=-.5;function DD(e,t,r=_D,n=kD){let o=e.length,i=t.length,s=[],a=[],c=[];for(let h=0;h<=o;h++){s[h]=[],a[h]=[],c[h]=[];for(let y=0;y<=i;y++)s[h][y]=-1/0,a[h][y]=-1/0,c[h][y]=-1/0}s[0][0]=0;for(let h=1;h<=o;h++)a[h][0]=r+(h-1)*n;for(let h=1;h<=i;h++)c[0][h]=r+(h-1)*n;for(let h=1;h<=o;h++)for(let y=1;y<=i;y++){let Q=rS(e[h-1],t[y-1]);s[h][y]=Math.max(s[h-1][y-1],a[h-1][y-1],c[h-1][y-1])+Q,a[h][y]=Math.max(s[h-1][y]+r,a[h-1][y]+n),c[h][y]=Math.max(s[h][y-1]+r,c[h][y-1]+n)}let l="",A="",u=o,m=i,d=s[o][i],p=a[o][i],E=c[o][i],x=Math.max(d,p,E),I=x===d?"M":x===p?"Ix":"Iy";for(;u>0||m>0;)if(I==="M"&&u>0&&m>0){l=e[u-1]+l,A=t[m-1]+A;let h=rS(e[u-1],t[m-1]),y=s[u-1][m-1],Q=a[u-1][m-1],M=s[u][m];M===y+h?I="M":M===Q+h?I="Ix":I="Iy",u--,m--}else if(I==="Ix"&&u>0){l=e[u-1]+l,A="-"+A;let h=a[u][m],y=s[u-1][m]+r;I=h===y?"M":"Ix",u--}else if(m>0){l="-"+l,A=t[m-1]+A;let h=c[u][m],y=s[u][m-1]+r;I=h===y?"M":"Iy",m--}else 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Ir.default.createElement(Ir.default.Fragment,null,Ir.default.createElement(P1.IconButton,{className:l.settingsButton,size:"small",onClick:()=>{c(!0)}},Ir.default.createElement(sc,null)),Ir.default.createElement(A,{model:t,feature:r,handleClose:e,baseUrl:i},Ir.default.createElement(Zm,{lookupMethod:n,setLookupMethod:o})),a?Ir.default.createElement(ed,{baseUrl:i,handleClose:u=>{u&&s(u),c(!1)}}):null)}var gt=f(w()),Ns=f(we()),vl=f(Ce()),Y1=f(k()),W1=f(G());var z1=f(Se());ln();function rd(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 Iu(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}-${s}`}}return`adp-${Iu(t)}`}function G1(e={}){return e.type&&e.adapterId?`${e.type}-${e.adapterId}`:`${rd(e)}`}var U1={};async function ON(e,t,r){let n=r?.type;if(!n)throw new Error(`could not determine adapter type from adapter config snapshot ${JSON.stringify(r)}`);let o=e.getAdapterType(n);if(!o)throw new Error(`unknown data adapter type ${n}`);let i=o.configSchema.create(r,{pluginManager:e}),s=nd.bind(null,e,t),a=await o.getAdapterClass();return{dataAdapter:new a(i,s,e),sessionIds:new Set([t])}}async function nd(e,t,r){let n=G1(r);U1[n]??=ON(e,t,r);let o=await U1[n];return o.sessionIds.add(t),o}async function H1(e,t){return(await nd(e,"msa",t)).dataAdapter}async function j1({config:e,pluginManager:t}){return(await H1(t,e)).getMSAList()}async function q1({config:e,pluginManager:t,msaId:r}){return(await H1(t,e)).getMSA(r)}function J1({session:e,newViewTitle:t,view:r,feature:n,data:o,querySeqName:i}){e.addView("MsaView",{type:"MsaView",displayName:t,treeAreaWidth:200,querySeqName:i,treeWidth:100,drawNodeBubbles:!1,labelsAlignRight:!0,showBranchLen:!1,colWidth:10,rowHeight:12,colorSchemeName:"percent_identity_dynamic",data:o,connectedViewId:r.id,connectedFeature:n.toJSON()})}var V1=f(Eo());function Ml(e){return(0,V1.readConfObject)(e,["msa","datasets"])}var GN=(0,z1.makeStyles)()({selectedContainer:{marginTop:50}}),UN=(0,W1.observer)(function({model:e,feature:t,handleClose:r}){let n=(0,vl.getSession)(e),o=$t(e),{classes:i}=GN(),{pluginManager:s}=(0,vl.getEnv)(e),{assemblyNames:a}=o,[c,l]=(0,gt.useState)(),A=Ml(n.jbrowse),[u,m]=(0,gt.useState)(A?.[0]?.datasetId),d=A?.find(P=>P.datasetId===u),{data:p,isLoading:E,error:x}=lo(d?`${d.datasetId}-msa-list`:null,()=>j1({config:d.adapter,pluginManager:s}),Ao),I=Fr({feature:t,view:o,validIds:p}),{selectedId:h,selectedTranscript:y}=I,{data:Q,isLoading:M,error:B}=lo(h&&d&&p?`${d.datasetId}-${h}-${p.length}-msa`:null,()=>q1({msaId:h,config:d.adapter,pluginManager:s}),Ao),v=x??B??I.error??c;return gt.default.createElement(gt.default.Fragment,null,gt.default.createElement(mr,{error:v},gt.default.createElement(at,{select:!0,label:"Select MSA dataset",value:u,onChange:P=>{m(P.target.value)}},A?.map(P=>gt.default.createElement(Y1.MenuItem,{key:P.datasetId,value:P.datasetId},P.name))),d?gt.default.createElement("div",{className:i.selectedContainer},!E&&M?gt.default.createElement(Ns.LoadingEllipses,{variant:"h6",message:`Loading MSA for (${h})`}):null,E?gt.default.createElement(Ns.LoadingEllipses,{variant:"h6",message:`Loading available MSAs for (${d.name})`}):null,p?gt.default.createElement("div",null,gt.default.createElement(Ns.SanitizedHTML,{html:d.description}),gt.default.createElement(gr,{feature:t,...I})):null):null),gt.default.createElement(Xr,{submitDisabled:!y||!Q?.length,onSubmit:()=>{try{if(y&&Q){let P=`${h}_${a[0]}`;J1({session:n,newViewTitle:co(y),view:o,querySeqName:P,feature:y,data:{msa:Q.map(N=>`>${N.get("refName")}
+${N.get("seq")}`).join(`
+`)}}),r()}}catch(P){l(P)}},onCancel:r}))}),$1=UN;var K1=f(w());function Ls({children:e,value:t,index:r,...n}){return K1.default.createElement("div",{role:"tabpanel",hidden:t!==r,...n},t===r?e:null)}function od({handleClose:e,feature:t,model:r}){let n=(0,Z1.getSession)(r),i=!!Ml(n.jbrowse)?.length,[s,a]=(0,vt.useState)("ncbi_blast");return vt.default.createElement(X1.Dialog,{maxWidth:"xl",title:"Launch MSA view",open:!0,onClose:e},vt.default.createElement(Qi.Tabs,{value:s,onChange:(c,l)=>{a(l)}},vt.default.createElement(Qi.Tab,{label:"NCBI BLAST query",value:"ncbi_blast"}),i?vt.default.createElement(Qi.Tab,{label:"Pre-loaded MSA datasets",value:"preloaded_msa"}):null,vt.default.createElement(Qi.Tab,{label:"Manual upload",value:"manual_msa"})),vt.default.createElement(Ls,{value:s,index:"ncbi_blast"},vt.default.createElement(td,{handleClose:e,feature:t,model:r})),i?vt.default.createElement(Ls,{value:s,index:"preloaded_msa"},vt.default.createElement($1,{model:r,feature:t,handleClose:e})):null,vt.default.createElement(Ls,{value:s,index:"manual_msa"},vt.default.createElement(f1,{model:r,feature:t,handleClose:e})))}function HN(e){return e.name==="LinearBasicDisplay"}function jN(e){return e.views(t=>{let r=t.contextMenuItems;return{contextMenuItems(){let n=t.contextMenuFeature,o=(0,Tl.getContainingTrack)(t),i=n?.get("type"),s=n&&["gene","mRNA","transcript"].includes(i);return[...r(),...s?[{label:"Launch MSA view",icon:MS,onClick:()=>{(0,Tl.getSession)(o).queueDialog(a=>[od,{model:o,handleClose:a,feature:n}])}}]:[]]}}})}function id(e){e.addToExtensionPoint("Core-extendPluggableElement",t=>(HN(t)&&(t.stateModel=jN(t.stateModel)),t))}function sd(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:m,drawNodeBubbles:d,labelsAlignRight:p,showBranchLen:E,querySeqName:x})=>{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:m,drawNodeBubbles:d,labelsAlignRight:p,showBranchLen:E,init:{msaData:r?.msa,treeData:r?.tree,msaUrl:n?.uri,treeUrl:o?.uri,querySeqName:x}})})}var pQ=f(w()),hQ=f(tQ());var KN=(0,pQ.lazy)(()=>Promise.resolve().then(()=>(gQ(),dQ)));function Ad(e){e.addViewType(()=>new hQ.default({name:"MsaView",stateModel:ym(),ReactComponent:KN}))}var CQ="2.5.0";var Dl=class extends EQ.default{constructor(){super(...arguments);this.name="MsaViewPlugin";this.version=CQ;this.rootConfigurationSchema=r=>({msa:(0,ud.ConfigurationSchema)("MSA",{datasets:fd.types.maybe(fd.types.array((0,ud.ConfigurationSchema)("MSAEntry",{datasetId:{type:"string",defaultValue:""},description:{type:"string",defaultValue:""},name:{type:"string",defaultValue:""},adapter:r.pluggableConfigSchemaType("adapter")})))})})}install(r){Ad(r),id(r),sd(r),Qm(r),vm(r)}configure(r){(0,IQ.isAbstractMenuManager)(r.rootModel)&&r.rootModel.appendToSubMenu(["Add"],{label:"Multiple sequence alignment view",icon:Fd,onClick:n=>{n.addView("MsaView",{})}})}};return DQ(XN);})();
 /*! Bundled license information:
-use-sync-external-store/cjs/use-sync-external-store-shim.production.js:
-  (**
-   * @license React
-   * use-sync-external-store-shim.production.js
-   *
-   * Copyright (c) Meta Platforms, Inc. and affiliates.
-   *
-   * This source code is licensed under the MIT license found in the
-   * LICENSE file in the root directory of this source tree.
-   *)
 react-is/cjs/react-is.production.min.js:
   (** @license React v16.13.1
    * react-is.production.min.js
@@ -106,6 +95,17 @@ 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:
+  (**
+   * @license React
+   * use-sync-external-store-shim.production.js
+   *
+   * Copyright (c) Meta Platforms, Inc. and affiliates.
+   *
+   * This source code is licensed under the MIT license found in the
+   * LICENSE file in the root directory of this source tree.
+   *)
 */
 //# sourceMappingURL=jbrowse-plugin-msaview.umd.production.min.js.map