jbrowse-plugin-msaview 2.2.4 → 2.2.5

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Files changed (4) hide show
  1. package/dist/MsaViewPanel/model.d.ts +2 -0
  2. package/dist/jbrowse-plugin-msaview.umd.production.min.js +22 -22
  3. package/dist/jbrowse-plugin-msaview.umd.production.min.js.map +3 -3
  4. package/package.json +3 -3
package/dist/jbrowse-plugin-msaview.umd.production.min.js CHANGED
@@ -1,13 +1,13 @@
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if(m>0){if(!_e.compareByGeneratedPositionsInflated(l,f[m-1]))continue;c+=","}c+=Hi.encode(l.generatedColumn-t),t=l.generatedColumn,l.source!=null&&(u=this._sources.indexOf(l.source),c+=Hi.encode(u-s),s=u,c+=Hi.encode(l.originalLine-1-o),o=l.originalLine-1,c+=Hi.encode(l.originalColumn-n),n=l.originalColumn,l.name!=null&&(A=this._names.indexOf(l.name),c+=Hi.encode(A-i),i=A)),a+=c}return a};Xt.prototype._generateSourcesContent=function(t,r){return t.map(function(n){if(!this._sourcesContents)return null;r!=null&&(n=_e.relative(r,n));var o=_e.toSetString(n);return Object.prototype.hasOwnProperty.call(this._sourcesContents,o)?this._sourcesContents[o]:null},this)};Xt.prototype.toJSON=function(){var t={version:this._version,sources:this._sources.toArray(),names:this._names.toArray(),mappings:this._serializeMappings()};return this._file!=null&&(t.file=this._file),this._sourceRoot!=null&&(t.sourceRoot=this._sourceRoot),this._sourcesContents&&(t.sourcesContent=this._generateSourcesContent(t.sources,t.sourceRoot)),t};Xt.prototype.toString=function(){return JSON.stringify(this.toJSON())};HC.SourceMapGenerator=Xt});var JC=O(jn=>{jn.GREATEST_LOWER_BOUND=1;jn.LEAST_UPPER_BOUND=2;function Eu(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?Eu(s,t,r,n,o,i):i==jn.LEAST_UPPER_BOUND?t<n.length?t:-1:s:s-e>1?Eu(e,s,r,n,o,i):i==jn.LEAST_UPPER_BOUND?s:e<0?-1:e}jn.search=function(t,r,n,o){if(r.length===0)return-1;var i=Eu(-1,r.length,t,r,n,o||jn.GREATEST_LOWER_BOUND);if(i<0)return-1;for(;i-1>=0&&n(r[i],r[i-1],!0)===0;)--i;return i}});var qC=O(YC=>{function Dv(e){function t(o,i,s){var a=o[i];o[i]=o[s],o[s]=a}function r(o,i){return Math.round(o+Math.random()*(i-o))}function n(o,i,s,a){if(s<a){var c=r(s,a),l=s-1;t(o,c,a);for(var A=o[a],u=s;u<a;u++)i(o[u],A,!1)<=0&&(l+=1,t(o,l,u));t(o,l+1,u);var f=l+1;n(o,i,s,f-1),n(o,i,f+1,a)}}return n}function kv(e){let t=Dv.toString();return new Function(`return ${t}`)()(e)}var UC=new WeakMap;YC.quickSort=function(e,t,r=0){let n=UC.get(t);n===void 0&&(n=kv(t),UC.set(t,n)),n(e,t,r,e.length-1)}});var WC=O(Va=>{var k=qo(),xu=JC(),jo=hu().ArraySet,Nv=du(),Ji=qC().quickSort;function he(e,t){var r=e;return typeof e=="string"&&(r=k.parseSourceMapInput(e)),r.sections!=null?new dr(r,t):new it(r,t)}he.fromSourceMap=function(e,t){return it.fromSourceMap(e,t)};he.prototype._version=3;he.prototype.__generatedMappings=null;Object.defineProperty(he.prototype,"_generatedMappings",{configurable:!0,enumerable:!0,get:function(){return this.__generatedMappings||this._parseMappings(this._mappings,this.sourceRoot),this.__generatedMappings}});he.prototype.__originalMappings=null;Object.defineProperty(he.prototype,"_originalMappings",{configurable:!0,enumerable:!0,get:function(){return this.__originalMappings||this._parseMappings(this._mappings,this.sourceRoot),this.__originalMappings}});he.prototype._charIsMappingSeparator=function(t,r){var n=t.charAt(r);return n===";"||n===","};he.prototype._parseMappings=function(t,r){throw new Error("Subclasses must implement _parseMappings")};he.GENERATED_ORDER=1;he.ORIGINAL_ORDER=2;he.GREATEST_LOWER_BOUND=1;he.LEAST_UPPER_BOUND=2;he.prototype.eachMapping=function(t,r,n){var o=r||null,i=n||he.GENERATED_ORDER,s;switch(i){case he.GENERATED_ORDER:s=this._generatedMappings;break;case he.ORIGINAL_ORDER:s=this._originalMappings;break;default:throw new Error("Unknown order of iteration.")}for(var a=this.sourceRoot,c=t.bind(o),l=this._names,A=this._sources,u=this._sourceMapURL,f=0,m=s.length;f<m;f++){var p=s[f],h=p.source===null?null:A.at(p.source);h!==null&&(h=k.computeSourceURL(a,h,u)),c({source:h,generatedLine:p.generatedLine,generatedColumn:p.generatedColumn,originalLine:p.originalLine,originalColumn:p.originalColumn,name:p.name===null?null:l.at(p.name)})}};he.prototype.allGeneratedPositionsFor=function(t){var r=k.getArg(t,"line"),n={source:k.getArg(t,"source"),originalLine:r,originalColumn:k.getArg(t,"column",0)};if(n.source=this._findSourceIndex(n.source),n.source<0)return[];var o=[],i=this._findMapping(n,this._originalMappings,"originalLine","originalColumn",k.compareByOriginalPositions,xu.LEAST_UPPER_BOUND);if(i>=0){var s=this._originalMappings[i];if(t.column===void 0)for(var a=s.originalLine;s&&s.originalLine===a;)o.push({line:k.getArg(s,"generatedLine",null),column:k.getArg(s,"generatedColumn",null),lastColumn:k.getArg(s,"lastGeneratedColumn",null)}),s=this._originalMappings[++i];else for(var c=s.originalColumn;s&&s.originalLine===r&&s.originalColumn==c;)o.push({line:k.getArg(s,"generatedLine",null),column:k.getArg(s,"generatedColumn",null),lastColumn:k.getArg(s,"lastGeneratedColumn",null)}),s=this._originalMappings[++i]}return o};Va.SourceMapConsumer=he;function it(e,t){var r=e;typeof e=="string"&&(r=k.parseSourceMapInput(e));var n=k.getArg(r,"version"),o=k.getArg(r,"sources"),i=k.getArg(r,"names",[]),s=k.getArg(r,"sourceRoot",null),a=k.getArg(r,"sourcesContent",null),c=k.getArg(r,"mappings"),l=k.getArg(r,"file",null);if(n!=this._version)throw new Error("Unsupported version: "+n);s&&(s=k.normalize(s)),o=o.map(String).map(k.normalize).map(function(A){return s&&k.isAbsolute(s)&&k.isAbsolute(A)?k.relative(s,A):A}),this._names=jo.fromArray(i.map(String),!0),this._sources=jo.fromArray(o,!0),this._absoluteSources=this._sources.toArray().map(function(A){return k.computeSourceURL(s,A,t)}),this.sourceRoot=s,this.sourcesContent=a,this._mappings=c,this._sourceMapURL=t,this.file=l}it.prototype=Object.create(he.prototype);it.prototype.consumer=he;it.prototype._findSourceIndex=function(e){var t=e;if(this.sourceRoot!=null&&(t=k.relative(this.sourceRoot,t)),this._sources.has(t))return this._sources.indexOf(t);var r;for(r=0;r<this._absoluteSources.length;++r)if(this._absoluteSources[r]==e)return r;return-1};it.fromSourceMap=function(t,r){var n=Object.create(it.prototype),o=n._names=jo.fromArray(t._names.toArray(),!0),i=n._sources=jo.fromArray(t._sources.toArray(),!0);n.sourceRoot=t._sourceRoot,n.sourcesContent=t._generateSourcesContent(n._sources.toArray(),n.sourceRoot),n.file=t._file,n._sourceMapURL=r,n._absoluteSources=n._sources.toArray().map(function(m){return k.computeSourceURL(n.sourceRoot,m,r)});for(var s=t._mappings.toArray().slice(),a=n.__generatedMappings=[],c=n.__originalMappings=[],l=0,A=s.length;l<A;l++){var u=s[l],f=new VC;f.generatedLine=u.generatedLine,f.generatedColumn=u.generatedColumn,u.source&&(f.source=i.indexOf(u.source),f.originalLine=u.originalLine,f.originalColumn=u.originalColumn,u.name&&(f.name=o.indexOf(u.name)),c.push(f)),a.push(f)}return Ji(n.__originalMappings,k.compareByOriginalPositions),n};it.prototype._version=3;Object.defineProperty(it.prototype,"sources",{get:function(){return this._absoluteSources.slice()}});function VC(){this.generatedLine=0,this.generatedColumn=0,this.source=null,this.originalLine=null,this.originalColumn=null,this.name=null}var Iu=k.compareByGeneratedPositionsDeflatedNoLine;function jC(e,t){let r=e.length,n=e.length-t;if(!(n<=1))if(n==2){let o=e[t],i=e[t+1];Iu(o,i)>0&&(e[t]=i,e[t+1]=o)}else if(n<20)for(let o=t;o<r;o++)for(let i=o;i>t;i--){let s=e[i-1],a=e[i];if(Iu(s,a)<=0)break;e[i-1]=a,e[i]=s}else Ji(e,Iu,t)}it.prototype._parseMappings=function(t,r){var n=1,o=0,i=0,s=0,a=0,c=0,l=t.length,A=0,u={},f={},m=[],p=[],h,C,E,x,y;let w=0;for(;A<l;)if(t.charAt(A)===";")n++,A++,o=0,jC(p,w),w=p.length;else if(t.charAt(A)===",")A++;else{for(h=new VC,h.generatedLine=n,x=A;x<l&&!this._charIsMappingSeparator(t,x);x++);for(C=t.slice(A,x),E=[];A<x;)Nv.decode(t,A,f),y=f.value,A=f.rest,E.push(y);if(E.length===2)throw new Error("Found a source, but no line and column");if(E.length===3)throw new Error("Found a source and line, but no column");if(h.generatedColumn=o+E[0],o=h.generatedColumn,E.length>1&&(h.source=a+E[1],a+=E[1],h.originalLine=i+E[2],i=h.originalLine,h.originalLine+=1,h.originalColumn=s+E[3],s=h.originalColumn,E.length>4&&(h.name=c+E[4],c+=E[4])),p.push(h),typeof h.originalLine=="number"){let v=h.source;for(;m.length<=v;)m.push(null);m[v]===null&&(m[v]=[]),m[v].push(h)}}jC(p,w),this.__generatedMappings=p;for(var S=0;S<m.length;S++)m[S]!=null&&Ji(m[S],k.compareByOriginalPositionsNoSource);this.__originalMappings=[].concat(...m)};it.prototype._findMapping=function(t,r,n,o,i,s){if(t[n]<=0)throw new TypeError("Line must be greater than or equal to 1, got "+t[n]);if(t[o]<0)throw new TypeError("Column must be greater than or equal to 0, got "+t[o]);return xu.search(t,r,i,s)};it.prototype.computeColumnSpans=function(){for(var t=0;t<this._generatedMappings.length;++t){var r=this._generatedMappings[t];if(t+1<this._generatedMappings.length){var n=this._generatedMappings[t+1];if(r.generatedLine===n.generatedLine){r.lastGeneratedColumn=n.generatedColumn-1;continue}}r.lastGeneratedColumn=1/0}};it.prototype.originalPositionFor=function(t){var r={generatedLine:k.getArg(t,"line"),generatedColumn:k.getArg(t,"column")},n=this._findMapping(r,this._generatedMappings,"generatedLine","generatedColumn",k.compareByGeneratedPositionsDeflated,k.getArg(t,"bias",he.GREATEST_LOWER_BOUND));if(n>=0){var o=this._generatedMappings[n];if(o.generatedLine===r.generatedLine){var i=k.getArg(o,"source",null);i!==null&&(i=this._sources.at(i),i=k.computeSourceURL(this.sourceRoot,i,this._sourceMapURL));var s=k.getArg(o,"name",null);return s!==null&&(s=this._names.at(s)),{source:i,line:k.getArg(o,"originalLine",null),column:k.getArg(o,"originalColumn",null),name:s}}}return{source:null,line:null,column:null,name:null}};it.prototype.hasContentsOfAllSources=function(){return this.sourcesContent?this.sourcesContent.length>=this._sources.size()&&!this.sourcesContent.some(function(t){return t==null}):!1};it.prototype.sourceContentFor=function(t,r){if(!this.sourcesContent)return null;var n=this._findSourceIndex(t);if(n>=0)return this.sourcesContent[n];var o=t;this.sourceRoot!=null&&(o=k.relative(this.sourceRoot,o));var i;if(this.sourceRoot!=null&&(i=k.urlParse(this.sourceRoot))){var s=o.replace(/^file:\/\//,"");if(i.scheme=="file"&&this._sources.has(s))return this.sourcesContent[this._sources.indexOf(s)];if((!i.path||i.path=="/")&&this._sources.has("/"+o))return this.sourcesContent[this._sources.indexOf("/"+o)]}if(r)return null;throw new Error('"'+o+'" is not in the SourceMap.')};it.prototype.generatedPositionFor=function(t){var r=k.getArg(t,"source");if(r=this._findSourceIndex(r),r<0)return{line:null,column:null,lastColumn:null};var n={source:r,originalLine:k.getArg(t,"line"),originalColumn:k.getArg(t,"column")},o=this._findMapping(n,this._originalMappings,"originalLine","originalColumn",k.compareByOriginalPositions,k.getArg(t,"bias",he.GREATEST_LOWER_BOUND));if(o>=0){var i=this._originalMappings[o];if(i.source===n.source)return{line:k.getArg(i,"generatedLine",null),column:k.getArg(i,"generatedColumn",null),lastColumn:k.getArg(i,"lastGeneratedColumn",null)}}return{line:null,column:null,lastColumn:null}};Va.BasicSourceMapConsumer=it;function dr(e,t){var r=e;typeof e=="string"&&(r=k.parseSourceMapInput(e));var n=k.getArg(r,"version"),o=k.getArg(r,"sections");if(n!=this._version)throw new Error("Unsupported version: "+n);this._sources=new jo,this._names=new jo;var i={line:-1,column:0};this._sections=o.map(function(s){if(s.url)throw new Error("Support for url field in sections not implemented.");var a=k.getArg(s,"offset"),c=k.getArg(a,"line"),l=k.getArg(a,"column");if(c<i.line||c===i.line&&l<i.column)throw new Error("Section offsets must be ordered and non-overlapping.");return i=a,{generatedOffset:{generatedLine:c+1,generatedColumn:l+1},consumer:new he(k.getArg(s,"map"),t)}})}dr.prototype=Object.create(he.prototype);dr.prototype.constructor=he;dr.prototype._version=3;Object.defineProperty(dr.prototype,"sources",{get:function(){for(var e=[],t=0;t<this._sections.length;t++)for(var r=0;r<this._sections[t].consumer.sources.length;r++)e.push(this._sections[t].consumer.sources[r]);return e}});dr.prototype.originalPositionFor=function(t){var r={generatedLine:k.getArg(t,"line"),generatedColumn:k.getArg(t,"column")},n=xu.search(r,this._sections,function(i,s){var a=i.generatedLine-s.generatedOffset.generatedLine;return a||i.generatedColumn-s.generatedOffset.generatedColumn}),o=this._sections[n];return o?o.consumer.originalPositionFor({line:r.generatedLine-(o.generatedOffset.generatedLine-1),column:r.generatedColumn-(o.generatedOffset.generatedLine===r.generatedLine?o.generatedOffset.generatedColumn-1:0),bias:t.bias}):{source:null,line:null,column:null,name:null}};dr.prototype.hasContentsOfAllSources=function(){return this._sections.every(function(t){return t.consumer.hasContentsOfAllSources()})};dr.prototype.sourceContentFor=function(t,r){for(var n=0;n<this._sections.length;n++){var o=this._sections[n],i=o.consumer.sourceContentFor(t,!0);if(i||i==="")return i}if(r)return null;throw new Error('"'+t+'" is not in the SourceMap.')};dr.prototype.generatedPositionFor=function(t){for(var r=0;r<this._sections.length;r++){var n=this._sections[r];if(n.consumer._findSourceIndex(k.getArg(t,"source"))!==-1){var o=n.consumer.generatedPositionFor(t);if(o){var i={line:o.line+(n.generatedOffset.generatedLine-1),column:o.column+(n.generatedOffset.generatedLine===o.line?n.generatedOffset.generatedColumn-1:0)};return i}}}return{line:null,column:null}};dr.prototype._parseMappings=function(t,r){this.__generatedMappings=[],this.__originalMappings=[];for(var n=0;n<this._sections.length;n++)for(var o=this._sections[n],i=o.consumer._generatedMappings,s=0;s<i.length;s++){var a=i[s],c=o.consumer._sources.at(a.source);c!==null&&(c=k.computeSourceURL(o.consumer.sourceRoot,c,this._sourceMapURL)),this._sources.add(c),c=this._sources.indexOf(c);var l=null;a.name&&(l=o.consumer._names.at(a.name),this._names.add(l),l=this._names.indexOf(l));var A={source:c,generatedLine:a.generatedLine+(o.generatedOffset.generatedLine-1),generatedColumn:a.generatedColumn+(o.generatedOffset.generatedLine===a.generatedLine?o.generatedOffset.generatedColumn-1:0),originalLine:a.originalLine,originalColumn:a.originalColumn,name:l};this.__generatedMappings.push(A),typeof A.originalLine=="number"&&this.__originalMappings.push(A)}Ji(this.__generatedMappings,k.compareByGeneratedPositionsDeflated),Ji(this.__originalMappings,k.compareByOriginalPositions)};Va.IndexedSourceMapConsumer=dr});var zC=O(KC=>{var Lv=Cu().SourceMapGenerator,Wa=qo(),Fv=/(\r?\n)/,Rv=10,Vo="$$$isSourceNode$$$";function Rt(e,t,r,n,o){this.children=[],this.sourceContents={},this.line=e??null,this.column=t??null,this.source=r??null,this.name=o??null,this[Vo]=!0,n!=null&&this.add(n)}Rt.fromStringWithSourceMap=function(t,r,n){var o=new Rt,i=t.split(Fv),s=0,a=function(){var f=p(),m=p()||"";return f+m;function p(){return s<i.length?i[s++]:void 0}},c=1,l=0,A=null;return r.eachMapping(function(f){if(A!==null)if(c<f.generatedLine)u(A,a()),c++,l=0;else{var m=i[s]||"",p=m.substr(0,f.generatedColumn-l);i[s]=m.substr(f.generatedColumn-l),l=f.generatedColumn,u(A,p),A=f;return}for(;c<f.generatedLine;)o.add(a()),c++;if(l<f.generatedColumn){var m=i[s]||"";o.add(m.substr(0,f.generatedColumn)),i[s]=m.substr(f.generatedColumn),l=f.generatedColumn}A=f},this),s<i.length&&(A&&u(A,a()),o.add(i.splice(s).join(""))),r.sources.forEach(function(f){var m=r.sourceContentFor(f);m!=null&&(n!=null&&(f=Wa.join(n,f)),o.setSourceContent(f,m))}),o;function u(f,m){if(f===null||f.source===void 0)o.add(m);else{var p=n?Wa.join(n,f.source):f.source;o.add(new Rt(f.originalLine,f.originalColumn,p,m,f.name))}}};Rt.prototype.add=function(t){if(Array.isArray(t))t.forEach(function(r){this.add(r)},this);else if(t[Vo]||typeof t=="string")t&&this.children.push(t);else throw new TypeError("Expected a SourceNode, string, or an array of SourceNodes and strings. Got "+t);return this};Rt.prototype.prepend=function(t){if(Array.isArray(t))for(var r=t.length-1;r>=0;r--)this.prepend(t[r]);else if(t[Vo]||typeof t=="string")this.children.unshift(t);else throw new TypeError("Expected a SourceNode, string, or an array of SourceNodes and strings. Got "+t);return this};Rt.prototype.walk=function(t){for(var r,n=0,o=this.children.length;n<o;n++)r=this.children[n],r[Vo]?r.walk(t):r!==""&&t(r,{source:this.source,line:this.line,column:this.column,name:this.name})};Rt.prototype.join=function(t){var r,n,o=this.children.length;if(o>0){for(r=[],n=0;n<o-1;n++)r.push(this.children[n]),r.push(t);r.push(this.children[n]),this.children=r}return this};Rt.prototype.replaceRight=function(t,r){var n=this.children[this.children.length-1];return n[Vo]?n.replaceRight(t,r):typeof n=="string"?this.children[this.children.length-1]=n.replace(t,r):this.children.push("".replace(t,r)),this};Rt.prototype.setSourceContent=function(t,r){this.sourceContents[Wa.toSetString(t)]=r};Rt.prototype.walkSourceContents=function(t){for(var r=0,n=this.children.length;r<n;r++)this.children[r][Vo]&&this.children[r].walkSourceContents(t);for(var o=Object.keys(this.sourceContents),r=0,n=o.length;r<n;r++)t(Wa.fromSetString(o[r]),this.sourceContents[o[r]])};Rt.prototype.toString=function(){var t="";return this.walk(function(r){t+=r}),t};Rt.prototype.toStringWithSourceMap=function(t){var r={code:"",line:1,column:0},n=new Lv(t),o=!1,i=null,s=null,a=null,c=null;return this.walk(function(l,A){r.code+=l,A.source!==null&&A.line!==null&&A.column!==null?((i!==A.source||s!==A.line||a!==A.column||c!==A.name)&&n.addMapping({source:A.source,original:{line:A.line,column:A.column},generated:{line:r.line,column:r.column},name:A.name}),i=A.source,s=A.line,a=A.column,c=A.name,o=!0):o&&(n.addMapping({generated:{line:r.line,column:r.column}}),i=null,o=!1);for(var u=0,f=l.length;u<f;u++)l.charCodeAt(u)===Rv?(r.line++,r.column=0,u+1===f?(i=null,o=!1):o&&n.addMapping({source:A.source,original:{line:A.line,column:A.column},generated:{line:r.line,column:r.column},name:A.name})):r.column++}),this.walkSourceContents(function(l,A){n.setSourceContent(l,A)}),{code:r.code,map:n}};KC.SourceNode=Rt});var $C=O(Ka=>{Ka.SourceMapGenerator=Cu().SourceMapGenerator;Ka.SourceMapConsumer=WC().SourceMapConsumer;Ka.SourceNode=zC().SourceNode});function $a(e){let{children:t,...r}=e;return(0,za.jsxs)(XC.Link,{...r,target:"_blank",rel:"noopener noreferrer",children:[t," ",(0,za.jsx)(na,{fontSize:"small"})]})}var za,XC,ZC=g(()=>{za=d(F(),1);oA();XC=d(N(),1)});function yu({text:e,extra:t}){let{classes:r}=Pv(),n=t?`supporting data: ${JSON.stringify(t,null,2)}`:"",o=[e,n].filter(Boolean).join(`
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n=e.generatedLine-t.generatedLine;return n!==0||(n=e.generatedColumn-t.generatedColumn,n!==0||r)||(n=Vr(e.source,t.source),n!==0)||(n=e.originalLine-t.originalLine,n!==0)||(n=e.originalColumn-t.originalColumn,n!==0)?n:Vr(e.name,t.name)}Ke.compareByGeneratedPositionsDeflated=Sv;function Qv(e,t,r){var n=e.generatedColumn-t.generatedColumn;return n!==0||r||(n=Vr(e.source,t.source),n!==0)||(n=e.originalLine-t.originalLine,n!==0)||(n=e.originalColumn-t.originalColumn,n!==0)?n:Vr(e.name,t.name)}Ke.compareByGeneratedPositionsDeflatedNoLine=Qv;function Vr(e,t){return e===t?0:e===null?1:t===null?-1:e>t?1:-1}function Mv(e,t){var r=e.generatedLine-t.generatedLine;return r!==0||(r=e.generatedColumn-t.generatedColumn,r!==0)||(r=Vr(e.source,t.source),r!==0)||(r=e.originalLine-t.originalLine,r!==0)||(r=e.originalColumn-t.originalColumn,r!==0)?r:Vr(e.name,t.name)}Ke.compareByGeneratedPositionsInflated=Mv;function vv(e){return JSON.parse(e.replace(/^\)]}'[^\n]*\n/,""))}Ke.parseSourceMapInput=vv;function Tv(e,t,r){if(t=t||"",e&&(e[e.length-1]!=="/"&&t[0]!=="/"&&(e+="/"),t=e+t),r){var n=Oi(r);if(!n)throw new Error("sourceMapURL could not be parsed");if(n.path){var o=n.path.lastIndexOf("/");o>=0&&(n.path=n.path.substring(0,o+1))}t=kC(Yo(n),t)}return mu(t)}Ke.computeSourceURL=Tv});var hu=O(RC=>{var gu=qo(),pu=Object.prototype.hasOwnProperty,qn=typeof Map<"u";function Wr(){this._array=[],this._set=qn?new Map:Object.create(null)}Wr.fromArray=function(t,r){for(var n=new Wr,o=0,i=t.length;o<i;o++)n.add(t[o],r);return n};Wr.prototype.size=function(){return qn?this._set.size:Object.getOwnPropertyNames(this._set).length};Wr.prototype.add=function(t,r){var n=qn?t:gu.toSetString(t),o=qn?this.has(t):pu.call(this._set,n),i=this._array.length;(!o||r)&&this._array.push(t),o||(qn?this._set.set(t,i):this._set[n]=i)};Wr.prototype.has=function(t){if(qn)return this._set.has(t);var r=gu.toSetString(t);return pu.call(this._set,r)};Wr.prototype.indexOf=function(t){if(qn){var r=this._set.get(t);if(r>=0)return r}else{var n=gu.toSetString(t);if(pu.call(this._set,n))return this._set[n]}throw new Error('"'+t+'" is not in the set.')};Wr.prototype.at=function(t){if(t>=0&&t<this._array.length)return this._array[t];throw new Error("No element indexed by "+t)};Wr.prototype.toArray=function(){return this._array.slice()};RC.ArraySet=Wr});var OC=O(GC=>{var PC=qo();function _v(e,t){var r=e.generatedLine,n=t.generatedLine,o=e.generatedColumn,i=t.generatedColumn;return n>r||n==r&&i>=o||PC.compareByGeneratedPositionsInflated(e,t)<=0}function qa(){this._array=[],this._sorted=!0,this._last={generatedLine:-1,generatedColumn:0}}qa.prototype.unsortedForEach=function(t,r){this._array.forEach(t,r)};qa.prototype.add=function(t){_v(this._last,t)?(this._last=t,this._array.push(t)):(this._sorted=!1,this._array.push(t))};qa.prototype.toArray=function(){return this._sorted||(this._array.sort(PC.compareByGeneratedPositionsInflated),this._sorted=!0),this._array};GC.MappingList=qa});var Cu=O(HC=>{var Hi=du(),_e=qo(),ja=hu().ArraySet,Dv=OC().MappingList;function Xt(e){e||(e={}),this._file=_e.getArg(e,"file",null),this._sourceRoot=_e.getArg(e,"sourceRoot",null),this._skipValidation=_e.getArg(e,"skipValidation",!1),this._ignoreInvalidMapping=_e.getArg(e,"ignoreInvalidMapping",!1),this._sources=new ja,this._names=new ja,this._mappings=new Dv,this._sourcesContents=null}Xt.prototype._version=3;Xt.fromSourceMap=function(t,r){var n=t.sourceRoot,o=new Xt(Object.assign(r||{},{file:t.file,sourceRoot:n}));return t.eachMapping(function(i){var s={generated:{line:i.generatedLine,column:i.generatedColumn}};i.source!=null&&(s.source=i.source,n!=null&&(s.source=_e.relative(n,s.source)),s.original={line:i.originalLine,column:i.originalColumn},i.name!=null&&(s.name=i.name)),o.addMapping(s)}),t.sources.forEach(function(i){var s=i;n!==null&&(s=_e.relative(n,i)),o._sources.has(s)||o._sources.add(s);var a=t.sourceContentFor(i);a!=null&&o.setSourceContent(i,a)}),o};Xt.prototype.addMapping=function(t){var r=_e.getArg(t,"generated"),n=_e.getArg(t,"original",null),o=_e.getArg(t,"source",null),i=_e.getArg(t,"name",null);!this._skipValidation&&this._validateMapping(r,n,o,i)===!1||(o!=null&&(o=String(o),this._sources.has(o)||this._sources.add(o)),i!=null&&(i=String(i),this._names.has(i)||this._names.add(i)),this._mappings.add({generatedLine:r.line,generatedColumn:r.column,originalLine:n!=null&&n.line,originalColumn:n!=null&&n.column,source:o,name:i}))};Xt.prototype.setSourceContent=function(t,r){var n=t;this._sourceRoot!=null&&(n=_e.relative(this._sourceRoot,n)),r!=null?(this._sourcesContents||(this._sourcesContents=Object.create(null)),this._sourcesContents[_e.toSetString(n)]=r):this._sourcesContents&&(delete this._sourcesContents[_e.toSetString(n)],Object.keys(this._sourcesContents).length===0&&(this._sourcesContents=null))};Xt.prototype.applySourceMap=function(t,r,n){var o=r;if(r==null){if(t.file==null)throw new Error(`SourceMapGenerator.prototype.applySourceMap requires either an explicit source file, or the source map's "file" property. Both were omitted.`);o=t.file}var i=this._sourceRoot;i!=null&&(o=_e.relative(i,o));var s=new ja,a=new ja;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=_e.join(n,c.source)),i!=null&&(c.source=_e.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=_e.join(n,c)),i!=null&&(c=_e.relative(i,c)),this.setSourceContent(c,l))},this)};Xt.prototype._validateMapping=function(t,r,n,o){if(r&&typeof r.line!="number"&&typeof r.column!="number"){var i="original.line and original.column are not numbers -- you probably meant to omit the original mapping entirely and only map the generated position. If so, pass null for the original mapping instead of an object with empty or null values.";if(this._ignoreInvalidMapping)return typeof console<"u"&&console.warn&&console.warn(i),!1;throw new Error(i)}if(!(t&&"line"in t&&"column"in t&&t.line>0&&t.column>=0&&!r&&!n&&!o)){if(t&&"line"in t&&"column"in t&&r&&"line"in r&&"column"in r&&t.line>0&&t.column>=0&&r.line>0&&r.column>=0&&n)return;var i="Invalid mapping: "+JSON.stringify({generated:t,source:n,original:r,name:o});if(this._ignoreInvalidMapping)return typeof console<"u"&&console.warn&&console.warn(i),!1;throw new Error(i)}};Xt.prototype._serializeMappings=function(){for(var t=0,r=1,n=0,o=0,i=0,s=0,a="",c,l,A,u,f=this._mappings.toArray(),m=0,p=f.length;m<p;m++){if(l=f[m],c="",l.generatedLine!==r)for(t=0;l.generatedLine!==r;)c+=";",r++;else if(m>0){if(!_e.compareByGeneratedPositionsInflated(l,f[m-1]))continue;c+=","}c+=Hi.encode(l.generatedColumn-t),t=l.generatedColumn,l.source!=null&&(u=this._sources.indexOf(l.source),c+=Hi.encode(u-s),s=u,c+=Hi.encode(l.originalLine-1-o),o=l.originalLine-1,c+=Hi.encode(l.originalColumn-n),n=l.originalColumn,l.name!=null&&(A=this._names.indexOf(l.name),c+=Hi.encode(A-i),i=A)),a+=c}return a};Xt.prototype._generateSourcesContent=function(t,r){return t.map(function(n){if(!this._sourcesContents)return null;r!=null&&(n=_e.relative(r,n));var o=_e.toSetString(n);return Object.prototype.hasOwnProperty.call(this._sourcesContents,o)?this._sourcesContents[o]:null},this)};Xt.prototype.toJSON=function(){var t={version:this._version,sources:this._sources.toArray(),names:this._names.toArray(),mappings:this._serializeMappings()};return this._file!=null&&(t.file=this._file),this._sourceRoot!=null&&(t.sourceRoot=this._sourceRoot),this._sourcesContents&&(t.sourcesContent=this._generateSourcesContent(t.sources,t.sourceRoot)),t};Xt.prototype.toString=function(){return JSON.stringify(this.toJSON())};HC.SourceMapGenerator=Xt});var JC=O(jn=>{jn.GREATEST_LOWER_BOUND=1;jn.LEAST_UPPER_BOUND=2;function Eu(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?Eu(s,t,r,n,o,i):i==jn.LEAST_UPPER_BOUND?t<n.length?t:-1:s:s-e>1?Eu(e,s,r,n,o,i):i==jn.LEAST_UPPER_BOUND?s:e<0?-1:e}jn.search=function(t,r,n,o){if(r.length===0)return-1;var i=Eu(-1,r.length,t,r,n,o||jn.GREATEST_LOWER_BOUND);if(i<0)return-1;for(;i-1>=0&&n(r[i],r[i-1],!0)===0;)--i;return i}});var qC=O(YC=>{function kv(e){function t(o,i,s){var a=o[i];o[i]=o[s],o[s]=a}function r(o,i){return Math.round(o+Math.random()*(i-o))}function n(o,i,s,a){if(s<a){var c=r(s,a),l=s-1;t(o,c,a);for(var A=o[a],u=s;u<a;u++)i(o[u],A,!1)<=0&&(l+=1,t(o,l,u));t(o,l+1,u);var f=l+1;n(o,i,s,f-1),n(o,i,f+1,a)}}return n}function Nv(e){let t=kv.toString();return new Function(`return ${t}`)()(e)}var UC=new WeakMap;YC.quickSort=function(e,t,r=0){let n=UC.get(t);n===void 0&&(n=Nv(t),UC.set(t,n)),n(e,t,r,e.length-1)}});var WC=O(Va=>{var k=qo(),xu=JC(),jo=hu().ArraySet,Lv=du(),Ji=qC().quickSort;function he(e,t){var r=e;return typeof e=="string"&&(r=k.parseSourceMapInput(e)),r.sections!=null?new dr(r,t):new it(r,t)}he.fromSourceMap=function(e,t){return it.fromSourceMap(e,t)};he.prototype._version=3;he.prototype.__generatedMappings=null;Object.defineProperty(he.prototype,"_generatedMappings",{configurable:!0,enumerable:!0,get:function(){return this.__generatedMappings||this._parseMappings(this._mappings,this.sourceRoot),this.__generatedMappings}});he.prototype.__originalMappings=null;Object.defineProperty(he.prototype,"_originalMappings",{configurable:!0,enumerable:!0,get:function(){return this.__originalMappings||this._parseMappings(this._mappings,this.sourceRoot),this.__originalMappings}});he.prototype._charIsMappingSeparator=function(t,r){var n=t.charAt(r);return n===";"||n===","};he.prototype._parseMappings=function(t,r){throw new Error("Subclasses must implement _parseMappings")};he.GENERATED_ORDER=1;he.ORIGINAL_ORDER=2;he.GREATEST_LOWER_BOUND=1;he.LEAST_UPPER_BOUND=2;he.prototype.eachMapping=function(t,r,n){var o=r||null,i=n||he.GENERATED_ORDER,s;switch(i){case he.GENERATED_ORDER:s=this._generatedMappings;break;case he.ORIGINAL_ORDER:s=this._originalMappings;break;default:throw new Error("Unknown order of iteration.")}for(var a=this.sourceRoot,c=t.bind(o),l=this._names,A=this._sources,u=this._sourceMapURL,f=0,m=s.length;f<m;f++){var p=s[f],h=p.source===null?null:A.at(p.source);h!==null&&(h=k.computeSourceURL(a,h,u)),c({source:h,generatedLine:p.generatedLine,generatedColumn:p.generatedColumn,originalLine:p.originalLine,originalColumn:p.originalColumn,name:p.name===null?null:l.at(p.name)})}};he.prototype.allGeneratedPositionsFor=function(t){var r=k.getArg(t,"line"),n={source:k.getArg(t,"source"),originalLine:r,originalColumn:k.getArg(t,"column",0)};if(n.source=this._findSourceIndex(n.source),n.source<0)return[];var o=[],i=this._findMapping(n,this._originalMappings,"originalLine","originalColumn",k.compareByOriginalPositions,xu.LEAST_UPPER_BOUND);if(i>=0){var s=this._originalMappings[i];if(t.column===void 0)for(var a=s.originalLine;s&&s.originalLine===a;)o.push({line:k.getArg(s,"generatedLine",null),column:k.getArg(s,"generatedColumn",null),lastColumn:k.getArg(s,"lastGeneratedColumn",null)}),s=this._originalMappings[++i];else for(var c=s.originalColumn;s&&s.originalLine===r&&s.originalColumn==c;)o.push({line:k.getArg(s,"generatedLine",null),column:k.getArg(s,"generatedColumn",null),lastColumn:k.getArg(s,"lastGeneratedColumn",null)}),s=this._originalMappings[++i]}return o};Va.SourceMapConsumer=he;function it(e,t){var r=e;typeof e=="string"&&(r=k.parseSourceMapInput(e));var n=k.getArg(r,"version"),o=k.getArg(r,"sources"),i=k.getArg(r,"names",[]),s=k.getArg(r,"sourceRoot",null),a=k.getArg(r,"sourcesContent",null),c=k.getArg(r,"mappings"),l=k.getArg(r,"file",null);if(n!=this._version)throw new Error("Unsupported version: "+n);s&&(s=k.normalize(s)),o=o.map(String).map(k.normalize).map(function(A){return s&&k.isAbsolute(s)&&k.isAbsolute(A)?k.relative(s,A):A}),this._names=jo.fromArray(i.map(String),!0),this._sources=jo.fromArray(o,!0),this._absoluteSources=this._sources.toArray().map(function(A){return k.computeSourceURL(s,A,t)}),this.sourceRoot=s,this.sourcesContent=a,this._mappings=c,this._sourceMapURL=t,this.file=l}it.prototype=Object.create(he.prototype);it.prototype.consumer=he;it.prototype._findSourceIndex=function(e){var t=e;if(this.sourceRoot!=null&&(t=k.relative(this.sourceRoot,t)),this._sources.has(t))return this._sources.indexOf(t);var r;for(r=0;r<this._absoluteSources.length;++r)if(this._absoluteSources[r]==e)return r;return-1};it.fromSourceMap=function(t,r){var n=Object.create(it.prototype),o=n._names=jo.fromArray(t._names.toArray(),!0),i=n._sources=jo.fromArray(t._sources.toArray(),!0);n.sourceRoot=t._sourceRoot,n.sourcesContent=t._generateSourcesContent(n._sources.toArray(),n.sourceRoot),n.file=t._file,n._sourceMapURL=r,n._absoluteSources=n._sources.toArray().map(function(m){return k.computeSourceURL(n.sourceRoot,m,r)});for(var s=t._mappings.toArray().slice(),a=n.__generatedMappings=[],c=n.__originalMappings=[],l=0,A=s.length;l<A;l++){var u=s[l],f=new VC;f.generatedLine=u.generatedLine,f.generatedColumn=u.generatedColumn,u.source&&(f.source=i.indexOf(u.source),f.originalLine=u.originalLine,f.originalColumn=u.originalColumn,u.name&&(f.name=o.indexOf(u.name)),c.push(f)),a.push(f)}return Ji(n.__originalMappings,k.compareByOriginalPositions),n};it.prototype._version=3;Object.defineProperty(it.prototype,"sources",{get:function(){return this._absoluteSources.slice()}});function VC(){this.generatedLine=0,this.generatedColumn=0,this.source=null,this.originalLine=null,this.originalColumn=null,this.name=null}var Iu=k.compareByGeneratedPositionsDeflatedNoLine;function jC(e,t){let r=e.length,n=e.length-t;if(!(n<=1))if(n==2){let o=e[t],i=e[t+1];Iu(o,i)>0&&(e[t]=i,e[t+1]=o)}else if(n<20)for(let o=t;o<r;o++)for(let i=o;i>t;i--){let s=e[i-1],a=e[i];if(Iu(s,a)<=0)break;e[i-1]=a,e[i]=s}else Ji(e,Iu,t)}it.prototype._parseMappings=function(t,r){var n=1,o=0,i=0,s=0,a=0,c=0,l=t.length,A=0,u={},f={},m=[],p=[],h,C,E,x,y;let w=0;for(;A<l;)if(t.charAt(A)===";")n++,A++,o=0,jC(p,w),w=p.length;else if(t.charAt(A)===",")A++;else{for(h=new VC,h.generatedLine=n,x=A;x<l&&!this._charIsMappingSeparator(t,x);x++);for(C=t.slice(A,x),E=[];A<x;)Lv.decode(t,A,f),y=f.value,A=f.rest,E.push(y);if(E.length===2)throw new Error("Found a source, but no line and column");if(E.length===3)throw new Error("Found a source and line, but no column");if(h.generatedColumn=o+E[0],o=h.generatedColumn,E.length>1&&(h.source=a+E[1],a+=E[1],h.originalLine=i+E[2],i=h.originalLine,h.originalLine+=1,h.originalColumn=s+E[3],s=h.originalColumn,E.length>4&&(h.name=c+E[4],c+=E[4])),p.push(h),typeof h.originalLine=="number"){let v=h.source;for(;m.length<=v;)m.push(null);m[v]===null&&(m[v]=[]),m[v].push(h)}}jC(p,w),this.__generatedMappings=p;for(var S=0;S<m.length;S++)m[S]!=null&&Ji(m[S],k.compareByOriginalPositionsNoSource);this.__originalMappings=[].concat(...m)};it.prototype._findMapping=function(t,r,n,o,i,s){if(t[n]<=0)throw new TypeError("Line must be greater than or equal to 1, got "+t[n]);if(t[o]<0)throw new TypeError("Column must be greater than or equal to 0, got "+t[o]);return xu.search(t,r,i,s)};it.prototype.computeColumnSpans=function(){for(var t=0;t<this._generatedMappings.length;++t){var r=this._generatedMappings[t];if(t+1<this._generatedMappings.length){var n=this._generatedMappings[t+1];if(r.generatedLine===n.generatedLine){r.lastGeneratedColumn=n.generatedColumn-1;continue}}r.lastGeneratedColumn=1/0}};it.prototype.originalPositionFor=function(t){var r={generatedLine:k.getArg(t,"line"),generatedColumn:k.getArg(t,"column")},n=this._findMapping(r,this._generatedMappings,"generatedLine","generatedColumn",k.compareByGeneratedPositionsDeflated,k.getArg(t,"bias",he.GREATEST_LOWER_BOUND));if(n>=0){var o=this._generatedMappings[n];if(o.generatedLine===r.generatedLine){var i=k.getArg(o,"source",null);i!==null&&(i=this._sources.at(i),i=k.computeSourceURL(this.sourceRoot,i,this._sourceMapURL));var s=k.getArg(o,"name",null);return s!==null&&(s=this._names.at(s)),{source:i,line:k.getArg(o,"originalLine",null),column:k.getArg(o,"originalColumn",null),name:s}}}return{source:null,line:null,column:null,name:null}};it.prototype.hasContentsOfAllSources=function(){return this.sourcesContent?this.sourcesContent.length>=this._sources.size()&&!this.sourcesContent.some(function(t){return t==null}):!1};it.prototype.sourceContentFor=function(t,r){if(!this.sourcesContent)return null;var n=this._findSourceIndex(t);if(n>=0)return this.sourcesContent[n];var o=t;this.sourceRoot!=null&&(o=k.relative(this.sourceRoot,o));var i;if(this.sourceRoot!=null&&(i=k.urlParse(this.sourceRoot))){var s=o.replace(/^file:\/\//,"");if(i.scheme=="file"&&this._sources.has(s))return this.sourcesContent[this._sources.indexOf(s)];if((!i.path||i.path=="/")&&this._sources.has("/"+o))return this.sourcesContent[this._sources.indexOf("/"+o)]}if(r)return null;throw new Error('"'+o+'" is not in the SourceMap.')};it.prototype.generatedPositionFor=function(t){var r=k.getArg(t,"source");if(r=this._findSourceIndex(r),r<0)return{line:null,column:null,lastColumn:null};var n={source:r,originalLine:k.getArg(t,"line"),originalColumn:k.getArg(t,"column")},o=this._findMapping(n,this._originalMappings,"originalLine","originalColumn",k.compareByOriginalPositions,k.getArg(t,"bias",he.GREATEST_LOWER_BOUND));if(o>=0){var i=this._originalMappings[o];if(i.source===n.source)return{line:k.getArg(i,"generatedLine",null),column:k.getArg(i,"generatedColumn",null),lastColumn:k.getArg(i,"lastGeneratedColumn",null)}}return{line:null,column:null,lastColumn:null}};Va.BasicSourceMapConsumer=it;function dr(e,t){var r=e;typeof e=="string"&&(r=k.parseSourceMapInput(e));var n=k.getArg(r,"version"),o=k.getArg(r,"sections");if(n!=this._version)throw new Error("Unsupported version: "+n);this._sources=new jo,this._names=new jo;var i={line:-1,column:0};this._sections=o.map(function(s){if(s.url)throw new Error("Support for url field in sections not implemented.");var a=k.getArg(s,"offset"),c=k.getArg(a,"line"),l=k.getArg(a,"column");if(c<i.line||c===i.line&&l<i.column)throw new Error("Section offsets must be ordered and non-overlapping.");return i=a,{generatedOffset:{generatedLine:c+1,generatedColumn:l+1},consumer:new he(k.getArg(s,"map"),t)}})}dr.prototype=Object.create(he.prototype);dr.prototype.constructor=he;dr.prototype._version=3;Object.defineProperty(dr.prototype,"sources",{get:function(){for(var e=[],t=0;t<this._sections.length;t++)for(var r=0;r<this._sections[t].consumer.sources.length;r++)e.push(this._sections[t].consumer.sources[r]);return e}});dr.prototype.originalPositionFor=function(t){var r={generatedLine:k.getArg(t,"line"),generatedColumn:k.getArg(t,"column")},n=xu.search(r,this._sections,function(i,s){var a=i.generatedLine-s.generatedOffset.generatedLine;return a||i.generatedColumn-s.generatedOffset.generatedColumn}),o=this._sections[n];return o?o.consumer.originalPositionFor({line:r.generatedLine-(o.generatedOffset.generatedLine-1),column:r.generatedColumn-(o.generatedOffset.generatedLine===r.generatedLine?o.generatedOffset.generatedColumn-1:0),bias:t.bias}):{source:null,line:null,column:null,name:null}};dr.prototype.hasContentsOfAllSources=function(){return this._sections.every(function(t){return t.consumer.hasContentsOfAllSources()})};dr.prototype.sourceContentFor=function(t,r){for(var n=0;n<this._sections.length;n++){var o=this._sections[n],i=o.consumer.sourceContentFor(t,!0);if(i||i==="")return i}if(r)return null;throw new Error('"'+t+'" is not in the SourceMap.')};dr.prototype.generatedPositionFor=function(t){for(var r=0;r<this._sections.length;r++){var n=this._sections[r];if(n.consumer._findSourceIndex(k.getArg(t,"source"))!==-1){var o=n.consumer.generatedPositionFor(t);if(o){var i={line:o.line+(n.generatedOffset.generatedLine-1),column:o.column+(n.generatedOffset.generatedLine===o.line?n.generatedOffset.generatedColumn-1:0)};return i}}}return{line:null,column:null}};dr.prototype._parseMappings=function(t,r){this.__generatedMappings=[],this.__originalMappings=[];for(var n=0;n<this._sections.length;n++)for(var o=this._sections[n],i=o.consumer._generatedMappings,s=0;s<i.length;s++){var a=i[s],c=o.consumer._sources.at(a.source);c!==null&&(c=k.computeSourceURL(o.consumer.sourceRoot,c,this._sourceMapURL)),this._sources.add(c),c=this._sources.indexOf(c);var l=null;a.name&&(l=o.consumer._names.at(a.name),this._names.add(l),l=this._names.indexOf(l));var A={source:c,generatedLine:a.generatedLine+(o.generatedOffset.generatedLine-1),generatedColumn:a.generatedColumn+(o.generatedOffset.generatedLine===a.generatedLine?o.generatedOffset.generatedColumn-1:0),originalLine:a.originalLine,originalColumn:a.originalColumn,name:l};this.__generatedMappings.push(A),typeof A.originalLine=="number"&&this.__originalMappings.push(A)}Ji(this.__generatedMappings,k.compareByGeneratedPositionsDeflated),Ji(this.__originalMappings,k.compareByOriginalPositions)};Va.IndexedSourceMapConsumer=dr});var zC=O(KC=>{var Fv=Cu().SourceMapGenerator,Wa=qo(),Rv=/(\r?\n)/,Pv=10,Vo="$$$isSourceNode$$$";function Rt(e,t,r,n,o){this.children=[],this.sourceContents={},this.line=e??null,this.column=t??null,this.source=r??null,this.name=o??null,this[Vo]=!0,n!=null&&this.add(n)}Rt.fromStringWithSourceMap=function(t,r,n){var o=new Rt,i=t.split(Rv),s=0,a=function(){var f=p(),m=p()||"";return f+m;function p(){return s<i.length?i[s++]:void 0}},c=1,l=0,A=null;return r.eachMapping(function(f){if(A!==null)if(c<f.generatedLine)u(A,a()),c++,l=0;else{var m=i[s]||"",p=m.substr(0,f.generatedColumn-l);i[s]=m.substr(f.generatedColumn-l),l=f.generatedColumn,u(A,p),A=f;return}for(;c<f.generatedLine;)o.add(a()),c++;if(l<f.generatedColumn){var m=i[s]||"";o.add(m.substr(0,f.generatedColumn)),i[s]=m.substr(f.generatedColumn),l=f.generatedColumn}A=f},this),s<i.length&&(A&&u(A,a()),o.add(i.splice(s).join(""))),r.sources.forEach(function(f){var m=r.sourceContentFor(f);m!=null&&(n!=null&&(f=Wa.join(n,f)),o.setSourceContent(f,m))}),o;function u(f,m){if(f===null||f.source===void 0)o.add(m);else{var p=n?Wa.join(n,f.source):f.source;o.add(new Rt(f.originalLine,f.originalColumn,p,m,f.name))}}};Rt.prototype.add=function(t){if(Array.isArray(t))t.forEach(function(r){this.add(r)},this);else if(t[Vo]||typeof t=="string")t&&this.children.push(t);else throw new TypeError("Expected a SourceNode, string, or an array of SourceNodes and strings. Got "+t);return this};Rt.prototype.prepend=function(t){if(Array.isArray(t))for(var r=t.length-1;r>=0;r--)this.prepend(t[r]);else if(t[Vo]||typeof t=="string")this.children.unshift(t);else throw new TypeError("Expected a SourceNode, string, or an array of SourceNodes and strings. Got "+t);return this};Rt.prototype.walk=function(t){for(var r,n=0,o=this.children.length;n<o;n++)r=this.children[n],r[Vo]?r.walk(t):r!==""&&t(r,{source:this.source,line:this.line,column:this.column,name:this.name})};Rt.prototype.join=function(t){var r,n,o=this.children.length;if(o>0){for(r=[],n=0;n<o-1;n++)r.push(this.children[n]),r.push(t);r.push(this.children[n]),this.children=r}return this};Rt.prototype.replaceRight=function(t,r){var n=this.children[this.children.length-1];return n[Vo]?n.replaceRight(t,r):typeof n=="string"?this.children[this.children.length-1]=n.replace(t,r):this.children.push("".replace(t,r)),this};Rt.prototype.setSourceContent=function(t,r){this.sourceContents[Wa.toSetString(t)]=r};Rt.prototype.walkSourceContents=function(t){for(var r=0,n=this.children.length;r<n;r++)this.children[r][Vo]&&this.children[r].walkSourceContents(t);for(var o=Object.keys(this.sourceContents),r=0,n=o.length;r<n;r++)t(Wa.fromSetString(o[r]),this.sourceContents[o[r]])};Rt.prototype.toString=function(){var t="";return this.walk(function(r){t+=r}),t};Rt.prototype.toStringWithSourceMap=function(t){var r={code:"",line:1,column:0},n=new Fv(t),o=!1,i=null,s=null,a=null,c=null;return this.walk(function(l,A){r.code+=l,A.source!==null&&A.line!==null&&A.column!==null?((i!==A.source||s!==A.line||a!==A.column||c!==A.name)&&n.addMapping({source:A.source,original:{line:A.line,column:A.column},generated:{line:r.line,column:r.column},name:A.name}),i=A.source,s=A.line,a=A.column,c=A.name,o=!0):o&&(n.addMapping({generated:{line:r.line,column:r.column}}),i=null,o=!1);for(var u=0,f=l.length;u<f;u++)l.charCodeAt(u)===Pv?(r.line++,r.column=0,u+1===f?(i=null,o=!1):o&&n.addMapping({source:A.source,original:{line:A.line,column:A.column},generated:{line:r.line,column:r.column},name:A.name})):r.column++}),this.walkSourceContents(function(l,A){n.setSourceContent(l,A)}),{code:r.code,map:n}};KC.SourceNode=Rt});var $C=O(Ka=>{Ka.SourceMapGenerator=Cu().SourceMapGenerator;Ka.SourceMapConsumer=WC().SourceMapConsumer;Ka.SourceNode=zC().SourceNode});function $a(e){let{children:t,...r}=e;return(0,za.jsxs)(XC.Link,{...r,target:"_blank",rel:"noopener noreferrer",children:[t," ",(0,za.jsx)(na,{fontSize:"small"})]})}var za,XC,ZC=g(()=>{za=d(F(),1);oA();XC=d(N(),1)});function yu({text:e,extra:t}){let{classes:r}=Gv(),n=t?`supporting data: ${JSON.stringify(t,null,2)}`:"",o=[e,n].filter(Boolean).join(`
4
4
  `),i=encodeURIComponent(`I got this error from JBrowse, here is the stack trace:
5
5
 
6
6
  \`\`\`
7
7
  ${e}
8
8
  \`\`\`
9
9
  ${n}
10
- `),s=`https://github.com/GMOD/jbrowse-components/issues/new?labels=bug&title=JBrowse+issue&body=${i}`,a=`mailto:${eE}?subject=JBrowse%202%20error&body=${i}`;return(0,Kr.jsxs)(Kr.Fragment,{children:[(0,Kr.jsxs)(Xa.Typography,{children:["Post a new issue at"," ",(0,Kr.jsx)($a,{href:s,children:"GitHub"})," or send an email to ",(0,Kr.jsx)($a,{href:a,children:eE})]}),(0,Kr.jsx)("pre",{className:r.pre,children:o})]})}var Kr,Xa,eE,Pv,tE=g(()=>{Kr=d(F(),1),Xa=d(N(),1);ZC();xt();eE="jbrowse2@berkeley.edu",Pv=te()(e=>({pre:{background:(0,Xa.alpha)(e.palette.error.main,.2),border:`1px solid ${e.palette.divider}`,overflow:"auto",margin:20,maxHeight:300}}))});function wu({message:e,children:t,variant:r="body2",...n}){let{classes:o}=Gv();return(0,rE.jsx)(nE.Typography,{className:Ya(o.dots,n.className),...n,variant:r,children:e||"Loading"})}var rE,nE,Gv,oE=g(()=>{rE=d(F(),1),nE=d(N(),1);xt();Gv=te()({dots:{"&::after":{display:"inline-block",content:'""',width:"1em",textAlign:"left",animation:`${iu`
10
+ `),s=`https://github.com/GMOD/jbrowse-components/issues/new?labels=bug&title=JBrowse+issue&body=${i}`,a=`mailto:${eE}?subject=JBrowse%202%20error&body=${i}`;return(0,Kr.jsxs)(Kr.Fragment,{children:[(0,Kr.jsxs)(Xa.Typography,{children:["Post a new issue at"," ",(0,Kr.jsx)($a,{href:s,children:"GitHub"})," or send an email to ",(0,Kr.jsx)($a,{href:a,children:eE})]}),(0,Kr.jsx)("pre",{className:r.pre,children:o})]})}var Kr,Xa,eE,Gv,tE=g(()=>{Kr=d(F(),1),Xa=d(N(),1);ZC();xt();eE="jbrowse2@berkeley.edu",Gv=te()(e=>({pre:{background:(0,Xa.alpha)(e.palette.error.main,.2),border:`1px solid ${e.palette.divider}`,overflow:"auto",margin:20,maxHeight:300}}))});function wu({message:e,children:t,variant:r="body2",...n}){let{classes:o}=Ov();return(0,rE.jsx)(nE.Typography,{className:Ya(o.dots,n.className),...n,variant:r,children:e||"Loading"})}var rE,nE,Ov,oE=g(()=>{rE=d(F(),1),nE=d(N(),1);xt();Ov=te()({dots:{"&::after":{display:"inline-block",content:'""',width:"1em",textAlign:"left",animation:`${iu`
11
11
  0% {
12
12
  content: '';
13
13
  }
@@ -20,15 +20,15 @@ ${n}
20
20
  75% {
21
21
  content: '...';
22
22
  }
23
- `} 1.2s infinite ease-in-out`}}})});var sE=O((r8,iE)=>{iE.exports=function(){var e=document.getSelection();if(!e.rangeCount)return function(){};for(var t=document.activeElement,r=[],n=0;n<e.rangeCount;n++)r.push(e.getRangeAt(n));switch(t.tagName.toUpperCase()){case"INPUT":case"TEXTAREA":t.blur();break;default:t=null;break}return e.removeAllRanges(),function(){e.type==="Caret"&&e.removeAllRanges(),e.rangeCount||r.forEach(function(o){e.addRange(o)}),t&&t.focus()}}});var lE=O((n8,cE)=>{"use strict";var Ov=sE(),aE={"text/plain":"Text","text/html":"Url",default:"Text"},Hv="Copy to clipboard: #{key}, Enter";function Jv(e){var t=(/mac os x/i.test(navigator.userAgent)?"\u2318":"Ctrl")+"+C";return e.replace(/#{\s*key\s*}/g,t)}function Uv(e,t){var r,n,o,i,s,a,c=!1;t||(t={}),r=t.debug||!1;try{o=Ov(),i=document.createRange(),s=document.getSelection(),a=document.createElement("span"),a.textContent=e,a.ariaHidden="true",a.style.all="unset",a.style.position="fixed",a.style.top=0,a.style.clip="rect(0, 0, 0, 0)",a.style.whiteSpace="pre",a.style.webkitUserSelect="text",a.style.MozUserSelect="text",a.style.msUserSelect="text",a.style.userSelect="text",a.addEventListener("copy",function(A){if(A.stopPropagation(),t.format)if(A.preventDefault(),typeof A.clipboardData>"u"){r&&console.warn("unable to use e.clipboardData"),r&&console.warn("trying IE specific stuff"),window.clipboardData.clearData();var u=aE[t.format]||aE.default;window.clipboardData.setData(u,e)}else A.clipboardData.clearData(),A.clipboardData.setData(t.format,e);t.onCopy&&(A.preventDefault(),t.onCopy(A.clipboardData))}),document.body.appendChild(a),i.selectNodeContents(a),s.addRange(i);var l=document.execCommand("copy");if(!l)throw new Error("copy command was unsuccessful");c=!0}catch(A){r&&console.error("unable to copy using execCommand: ",A),r&&console.warn("trying IE specific stuff");try{window.clipboardData.setData(t.format||"text",e),t.onCopy&&t.onCopy(window.clipboardData),c=!0}catch(u){r&&console.error("unable to copy using clipboardData: ",u),r&&console.error("falling back to prompt"),n=Jv("message"in t?t.message:Hv),window.prompt(n,e)}}finally{s&&(typeof s.removeRange=="function"?s.removeRange(i):s.removeAllRanges()),a&&document.body.removeChild(a),o()}return c}cE.exports=Uv});var mE={};et(mE,{default:()=>dE});async function fE(e){let t=await fetch(e);if(!t.ok)throw new Error(`HTTP ${t.status} fetching ${e}: ${await t.text()}`);return t.text()}async function Yv(e){return JSON.parse(await fE(e))}async function Vv(e){if(Bu[e])return Bu[e];let t=new URL(e).search,r=await fE(e),n=qv.exec(r)?.[1]??"",o=await Yv(new URL(n,e).href+t),i=new uE.SourceMapConsumer(o);return Bu[e]=i,i}async function Wv(e){let t=[];for(let r of e.split(`
24
- `)){let n=jv.exec(r);if(!n){t.push(r);continue}let o=n[2],s=(await Vv(o)).originalPositionFor({line:+n[3],column:+n[4]});if(!s.source||!s.line||!s.column){t.push(r);continue}t.push(`${s.source}:${s.line}:${s.column+1} (${n[1].trim()})`)}return t.join(`
25
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26
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32
32
  UniProt/Swiss-Prot|P26898|IL2RA_SHEEP MEPSLLMWRFFVFIVVPGCVTEACHDDPPSLRNA----------MFKVLRYE----VGTM
33
33
  UniProt/Swiss-Prot|P01590|IL2RA_MOUSE MEPRLLMLGFLSLTIVPSCRAELCLYDPPEVPNA----------TFKALSYK----NGTI
34
34
  UniProt/Swiss-Prot|P41690|IL2RA_FELCA MEPSLLLWGILTFVVVHGHVTELCDENPPDIQHA----------TFKALTYK----TGTM
@@ -57,23 +57,23 @@ sp|P13786|HBAZ_CAPHI SKVVAAVGDAVKSIDNVTSALSKLSELHAYVLRVDPVNFKFLSHCLLVTLASHF
57
57
  sp|P69905|HBA_HUMAN AVHASLDKFLASVSTVLTSKYR 142
58
58
  sp|P01942|HBA_MOUSE AVHASLDKFLASVSTVLTSKYR 142
59
59
  sp|P13786|HBAZ_CAPHI DAHAAWDKFLSIVSGVLTEKYR 142
60
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- `);if(a===-1)continue;let c=s.slice(a+1).replaceAll(/\s/g,"");c&&r.push(c)}if(r.length<2)return!1;let n=!1,o=-1,i=!0;for(let s of r){let a=0;for(let c=0;c<s.length;c++){let l=s.charCodeAt(c);li(l)?n=!0:l>=65&&l<=90&&a++}o===-1?o=a:a!==o&&(i=!1)}return n&&i}expandA3M(t,r){let n=r.length;if(n===0)return{};let o=[],i=[];for(let l=0;l<n;l++){let A=t[l],u=[],f=[],m=0;for(;m<A.length;){let p=A.charCodeAt(m);if(p>=65&&p<=90){u.push(A[m]);let h="",C=m+1;for(;C<A.length;){let E=A.charCodeAt(C);if(li(E)||E===45||E===46)h+=A[C],C++;else break}f.push(h),m=C}else if(p===45||p===46)m++;else if(li(p)){let h="";for(;m<A.length&&li(A.charCodeAt(m));)h+=A[m],m++;u.push(""),f.push(h)}else m++}o.push(u),i.push(f)}let s=Math.max(...o.map(l=>l.length),0),a=new Array(s).fill(0);for(let l=0;l<n;l++){let A=i[l];for(let u=0;u<A.length;u++){let f=0;for(let m of A[u])li(m.charCodeAt(0))&&f++;f>a[u]&&(a[u]=f)}}let c={};for(let l=0;l<n;l++){let A=o[l],u=i[l],f=[];for(let m=0;m<s;m++){let p=a[m];if(m<A.length){let h=A[m],C=u[m]||"";f.push(h||"-");let E="";for(let y of C)li(y.charCodeAt(0))&&(E+=y.toUpperCase());f.push(E);let x=p-E.length;x>0&&f.push(".".repeat(x))}else f.push("-"),p>0&&f.push(".".repeat(p))}c[r[l]]=f.join("")}return c}getMSA(){return this.MSA}getRowData(){}getNames(){return this.orderedNames}getRow(t){return this.MSA.seqdata[t]||""}getWidth(){let t=Object.keys(this.MSA.seqdata)[0];return t?this.getRow(t).length:0}getStructures(){return{}}get alignmentNames(){return[]}getHeader(){return{}}getTree(){return{id:"root",name:"root",noTree:!0,children:this.getNames().map(t=>({id:t,children:[],name:t}))}}get seqConsensus(){}get secondaryStructureConsensus(){}get tracks(){return[]}}});function mD(e){let t=/\(?(\d+(\.\d+)+)\)?/.exec(e);return t&&t.length>1?t[1]:""}function tb(e){let t=["CLUSTAL","PROBCONS","MUSCLE","MSAPROBS","Kalign"];t.some(n=>e.startsWith(n))||console.warn(`${e} is not a known CLUSTAL header: ${t.join(",")}, proceeding but could indicate an issue`);let r=mD(e);return{info:e,version:r}}function Oc(e){let t=e.next();for(;!t.done&&t.value.trim()==="";)t=e.next();return t.value}function gD(e){let t=e.split(/\s+/),r=e.slice(t[0].length),n=t[0].length+r.indexOf(t[1]),o=n+t[1].length;return[n,o]}function eb(e){let t=Oc(e),r=[],n="";if(!t)return;for(;t;)t.startsWith(" ")?n=t:r.push(t),t=e.next().value;let[o,i]=gD(r[0]),a=r.map(u=>u.split(/\s+/)).map(u=>u[0]),c=r.map(u=>u.slice(o,i)),l=n.slice(o,i),A=c[0].length-l.length;return A&&(l+=" ".repeat(A)),{ids:a,seqs:c,consensus:l}}function rb(e){let t,r=eb(e);if(r!==void 0)for(;t=eb(e);){for(let n=0;n<t.seqs.length;n++)r.seqs[n]+=t.seqs[n];r.consensus+=t.consensus}return r}var Of=g(()=>{});var nb=g(()=>{Of()});function pD(e){let t=Oc(e);if(!t)throw new Error("Empty file received");let r=tb(t),n=rb(e);if(n===void 0)throw new Error("No blocks parsed");let o=n.seqs.map((s,a)=>({id:n.ids[a],seq:s})),{consensus:i}=n;if(i.length!=o[0].seq.length)throw new Error(`Consensus length != sequence length. Con ${i.length} seq ${o[0].seq.length}`);return{consensus:i,alns:o,header:r}}function ob(e){let t=e.split(`
63
- `)[Symbol.iterator]();return pD(t)}var ib=g(()=>{nb();Of()});var wn,Hf=g(()=>{ib();wn=class{MSA;constructor(t){this.MSA=ob(t)}getMSA(){return this.MSA}getRow(t){return this.MSA.alns.find(r=>r.id===t)?.seq||""}getWidth(){return this.MSA.alns[0].seq.length}getRowData(){}getHeader(){return this.MSA.header}getNames(){return this.MSA.alns.map(t=>t.id)}getStructures(){return{}}get alignmentNames(){return[]}getTree(){return{id:"root",name:"root",noTree:!0,children:this.getNames().map(t=>({id:t,name:t,children:[]}))}}get seqConsensus(){return this.MSA.consensus}get secondaryStructureConsensus(){}get tracks(){return[]}}});function sb(e){let t=e.split(`
62
+ `);if(a===-1)continue;let c=s.slice(a+1).replaceAll(/\s/g,"");c&&r.push(c)}if(r.length<2)return!1;let n=!1,o=-1,i=!0;for(let s of r){let a=0;for(let c=0;c<s.length;c++){let l=s.charCodeAt(c);li(l)?n=!0:(l>=65&&l<=90||l===45)&&a++}o===-1?o=a:a!==o&&(i=!1)}return n&&i}expandA3M(t,r){let n=r.length;if(n===0)return{};let o=[],i=[];for(let l=0;l<n;l++){let A=t[l],u=[],f=[],m=0;for(;m<A.length;){let p=A.charCodeAt(m);if(p>=65&&p<=90||p===45){u.push(A[m]);let h="",C=m+1;for(;C<A.length;){let E=A.charCodeAt(C);if(li(E)||E===46)h+=A[C],C++;else break}f.push(h),m=C}else if(p===46)m++;else if(li(p)){let h="";for(;m<A.length&&li(A.charCodeAt(m));)h+=A[m],m++;u.push(""),f.push(h)}else m++}o.push(u),i.push(f)}let s=Math.max(...o.map(l=>l.length),0),a=new Array(s).fill(0);for(let l=0;l<n;l++){let A=i[l];for(let u=0;u<A.length;u++){let f=0;for(let m of A[u])li(m.charCodeAt(0))&&f++;f>a[u]&&(a[u]=f)}}let c={};for(let l=0;l<n;l++){let A=o[l],u=i[l],f=[];for(let m=0;m<s;m++){let p=a[m];if(m<A.length){let h=A[m],C=u[m]||"";f.push(h||"-");let E="";for(let y of C)li(y.charCodeAt(0))&&(E+=y.toUpperCase());f.push(E);let x=p-E.length;x>0&&f.push(".".repeat(x))}else f.push("-"),p>0&&f.push(".".repeat(p))}c[r[l]]=f.join("")}return c}getMSA(){return this.MSA}getRowData(){}getNames(){return this.orderedNames}getRow(t){return this.MSA.seqdata[t]||""}getWidth(){let t=Object.keys(this.MSA.seqdata)[0];return t?this.getRow(t).length:0}getStructures(){return{}}get alignmentNames(){return[]}getHeader(){return{}}getTree(){return{id:"root",name:"root",noTree:!0,children:this.getNames().map(t=>({id:t,children:[],name:t}))}}get seqConsensus(){}get secondaryStructureConsensus(){}get tracks(){return[]}}});function gD(e){let t=/\(?(\d+(\.\d+)+)\)?/.exec(e);return t&&t.length>1?t[1]:""}function tb(e){let t=["CLUSTAL","PROBCONS","MUSCLE","MSAPROBS","Kalign"];t.some(n=>e.startsWith(n))||console.warn(`${e} is not a known CLUSTAL header: ${t.join(",")}, proceeding but could indicate an issue`);let r=gD(e);return{info:e,version:r}}function Oc(e){let t=e.next();for(;!t.done&&t.value.trim()==="";)t=e.next();return t.value}function pD(e){let t=e.split(/\s+/),r=e.slice(t[0].length),n=t[0].length+r.indexOf(t[1]),o=n+t[1].length;return[n,o]}function eb(e){let t=Oc(e),r=[],n="";if(!t)return;for(;t;)t.startsWith(" ")?n=t:r.push(t),t=e.next().value;let[o,i]=pD(r[0]),a=r.map(u=>u.split(/\s+/)).map(u=>u[0]),c=r.map(u=>u.slice(o,i)),l=n.slice(o,i),A=c[0].length-l.length;return A&&(l+=" ".repeat(A)),{ids:a,seqs:c,consensus:l}}function rb(e){let t,r=eb(e);if(r!==void 0)for(;t=eb(e);){for(let n=0;n<t.seqs.length;n++)r.seqs[n]+=t.seqs[n];r.consensus+=t.consensus}return r}var Of=g(()=>{});var nb=g(()=>{Of()});function hD(e){let t=Oc(e);if(!t)throw new Error("Empty file received");let r=tb(t),n=rb(e);if(n===void 0)throw new Error("No blocks parsed");let o=n.seqs.map((s,a)=>({id:n.ids[a],seq:s})),{consensus:i}=n;if(i.length!=o[0].seq.length)throw new Error(`Consensus length != sequence length. Con ${i.length} seq ${o[0].seq.length}`);return{consensus:i,alns:o,header:r}}function ob(e){let t=e.split(`
63
+ `)[Symbol.iterator]();return hD(t)}var ib=g(()=>{nb();Of()});var Bn,Hf=g(()=>{ib();Bn=class{MSA;constructor(t){this.MSA=ob(t)}getMSA(){return this.MSA}getRow(t){return this.MSA.alns.find(r=>r.id===t)?.seq||""}getWidth(){return this.MSA.alns[0].seq.length}getRowData(){}getHeader(){return this.MSA.header}getNames(){return this.MSA.alns.map(t=>t.id)}getStructures(){return{}}get alignmentNames(){return[]}getTree(){return{id:"root",name:"root",noTree:!0,children:this.getNames().map(t=>({id:t,name:t,children:[]}))}}get seqConsensus(){return this.MSA.consensus}get secondaryStructureConsensus(){}get tracks(){return[]}}});function sb(e){let t=e.split(`
64
64
  `).map(i=>i.trim()).filter(i=>!!i),r=[],n=[];for(let i of t)if(i.startsWith("SEQ"))r.push(i);else{if(i.startsWith("DATA"))continue;if(i.startsWith("//"))break;n.push(i)}let o=r.map(i=>{let[,s,a,c,l,A,u,f,m]=i.split(" ");return{species:s,protein:a,chr:c,start:+l,end:+A,strand:+u,geneId:f,unknown:m,seq:""}});for(let i of n)for(let s=0;s<r.length;s++)o[s].seq+=i[s];return o}function Hc(e){let t=e.split(`
65
- `).map(i=>i.trim()).filter(i=>!!i),r=[],n="";for(let i of t)if(i.startsWith("SEQ"))r.push(i);else{if(i.startsWith("DATA"))continue;if(i.startsWith("//"))break;n=i}let o=r.map(i=>{let[,s,a,c,l,A,u,f,m]=i.split(" ");return{species:s,protein:a,chr:c,start:+l,end:+A,strand:+u,geneId:f,unknown:m}});return{tree:n,seqs:o}}var Jf=g(()=>{});var Bn,Uf=g(()=>{Jf();Bn=class{MSA;constructor(t){this.MSA=sb(t)}getMSA(){return this.MSA}getRow(t){return this.MSA.find(r=>r.protein===t)?.seq||""}getWidth(){return this.MSA[0].seq.length}getRowData(){}getHeader(){return""}getNames(){return this.MSA.map(t=>t.protein)}getStructures(){return{}}get alignmentNames(){return[]}getTree(){return{id:"root",name:"root",noTree:!0,children:this.getNames().map(t=>({id:t,name:t,children:[]}))}}get seqConsensus(){}get secondaryStructureConsensus(){}get tracks(){return[]}}});var bn,Yf=g(()=>{bn=class{MSA;constructor(t){let r={};for(let n of t.split(">")){if(!/\S/.test(n))continue;let o=n.indexOf(`
65
+ `).map(i=>i.trim()).filter(i=>!!i),r=[],n="";for(let i of t)if(i.startsWith("SEQ"))r.push(i);else{if(i.startsWith("DATA"))continue;if(i.startsWith("//"))break;n=i}let o=r.map(i=>{let[,s,a,c,l,A,u,f,m]=i.split(" ");return{species:s,protein:a,chr:c,start:+l,end:+A,strand:+u,geneId:f,unknown:m}});return{tree:n,seqs:o}}var Jf=g(()=>{});var bn,Uf=g(()=>{Jf();bn=class{MSA;constructor(t){this.MSA=sb(t)}getMSA(){return this.MSA}getRow(t){return this.MSA.find(r=>r.protein===t)?.seq||""}getWidth(){return this.MSA[0].seq.length}getRowData(){}getHeader(){return""}getNames(){return this.MSA.map(t=>t.protein)}getStructures(){return{}}get alignmentNames(){return[]}getTree(){return{id:"root",name:"root",noTree:!0,children:this.getNames().map(t=>({id:t,name:t,children:[]}))}}get seqConsensus(){}get secondaryStructureConsensus(){}get tracks(){return[]}}});var Sn,Yf=g(()=>{Sn=class{MSA;constructor(t){let r={};for(let n of t.split(">")){if(!/\S/.test(n))continue;let o=n.indexOf(`
66
66
  `);if(o===-1)continue;let i=n.slice(0,o),s=i.indexOf(" "),a=s===-1?i:i.slice(0,s);a&&(r[a]=n.slice(o+1).replaceAll(/\s/g,""))}this.MSA={seqdata:r}}getMSA(){return this.MSA}getRowData(){}getNames(){return Object.keys(this.MSA.seqdata)}getRow(t){return this.MSA.seqdata[t]||""}getWidth(){let t=Object.keys(this.MSA.seqdata)[0];return this.getRow(t).length}getStructures(){return{}}get alignmentNames(){return[]}getHeader(){return{}}getTree(){return{id:"root",name:"root",noTree:!0,children:this.getNames().map(t=>({id:t,children:[],name:t}))}}get seqConsensus(){}get secondaryStructureConsensus(){}get tracks(){return[]}}});function eo(e){let t=[],r={},n=e.split(/\s*(;|\(|\)|,|:)\s*/);for(let o=0;o<n.length;o++){let i=n[o],s={};switch(i){case"(":r.children=[s],t.push(r),r=s;break;case",":t.at(-1)?.children.push(s),r=s;break;case")":r=t.pop();break;case":":break;default:{let a=n[o-1];a===")"||a==="("||a===","?r.name=i:a===":"&&(r.length=Number.parseFloat(i))}}}return r}var qf=g(()=>{});function Ai(){return{gf:{},gc:{},gs:{},gr:{},seqname:[],seqdata:{}}}function ui(e){return ab.test(e)}function cb(e,t){let r=t??{},n=[],o=null,i=e.split(`
67
- `);for(let s of i){let a;if(ab.test(s))o=Ai();else if(hD.test(s))o&&n.push(o),o=null;else if(a=CD.exec(s)){if(!o){if(r.strict)throw new Error("No format header: # STOCKHOLM 1.0");o=Ai()}let c=a[1];o.gf[c]||(o.gf[c]=[]),o.gf[c].push(a[2])}else if(a=ED.exec(s)){if(!o){if(r.strict)throw new Error("No format header: # STOCKHOLM 1.0");o=Ai()}let c=a[1];o.gc[c]||(o.gc[c]=""),o.gc[c]+=a[2]}else if(a=ID.exec(s)){if(!o){if(r.strict)throw new Error("No format header: # STOCKHOLM 1.0");o=Ai()}let c=a[1],l=a[2],A=a[3];o.gs[l]||(o.gs[l]={}),o.gs[l][c]||(o.gs[l][c]=[]),o.gs[l][c].push(A)}else if(a=xD.exec(s)){if(!o){if(r.strict)throw new Error("No format header: # STOCKHOLM 1.0");o=Ai()}let c=a[1],l=a[2],A=a[3];o.gr[l]||(o.gr[l]={}),o.gr[l][c]||(o.gr[l][c]=""),o.gr[l][c]+=A}else if(a=yD.exec(s)){if(!o){if(r.strict)throw new Error("No format header: # STOCKHOLM 1.0");o=Ai()}let c=a[1],l=a[2];o.seqdata[c]||(o.seqdata[c]="",o.seqname.push(c)),o.seqdata[c]+=l}else if(wD.test(s)&&r.strict)throw new Error("Malformed line")}return o&&n.push(o),n}var ab,hD,CD,ED,ID,xD,yD,wD,jf=g(()=>{ab=/^# STOCKHOLM 1.0/,hD=/^\/\/\s*$/,CD=/^#=GF\s+(\S+)\s+(.*?)\s*$/,ED=/^#=GC\s+(\S+)\s+(.*?)\s*$/,ID=/^#=GS\s+(\S+)\s+(\S+)\s+(.*?)\s*$/,xD=/^#=GR\s+(\S+)\s+(\S+)\s+(.*?)\s*$/,yD=/^\s*(\S+)\s+(\S+)\s*$/,wD=/\S/});var Sn,Vf=g(()=>{qf();jf();Pf();jf();Sn=class{data;MSA;constructor(t,r){let n=cb(t);this.data=n,this.MSA=n[r]}getMSA(){return this.MSA}getRow(t){return this.MSA.seqdata[t]||""}getWidth(){let t=Object.keys(this.MSA.seqdata)[0];return this.getRow(t).length}get alignmentNames(){return this.data.map((t,r)=>t.gf.DE?.[0]??`Alignment ${r+1}`)}getHeader(){let t=this.MSA.gs.AC??{},r=this.MSA.gs.DR??{};return{General:this.MSA.gf,Accessions:Object.fromEntries(Object.entries(t).map(([n,o])=>[n,o[0]])),Dbxref:Object.fromEntries(Object.entries(r).map(([n,o])=>[n,o.join("; ")]))}}getRowData(t){return{name:t,accession:this.MSA.gs.AC?.[t]?.[0],dbxref:this.MSA.gs.DR?.[t]?.join("; ")}}getNames(){return Object.keys(this.MSA.seqdata)}getSeqCoords(){}getStructures(){let t=/PDB; +(\S+) +(\S); ([0-9]+)-([0-9]+)/,r=this.MSA.gs.DR??{},n=Object.entries(r).flatMap(([i,s])=>s.map(a=>{let c=t.exec(a);return c?{id:i,match:c}:null})).filter(i=>!!i).map(({id:i,match:s})=>({id:i,pdb:s[1].toLowerCase(),chain:s[2],startPos:+s[3],endPos:+s[4]})),o={};for(let i of n){let{id:s,...a}=i;o[s]||(o[s]=[]),o[s].push(a)}return o}getTree(){let t=this.MSA.gf.NH?.[0];return t?ci(eo(t)):{id:"root",name:"root",noTree:!0,children:this.getNames().map(r=>({id:r,children:[],name:r}))}}get seqConsensus(){return this.MSA.gc.seq_cons}get secondaryStructureConsensus(){return this.MSA.gc.SS_cons}get tracks(){return[{id:"seqConsensus",name:"Sequence consensus",data:this.seqConsensus,customColorScheme:{}},{id:"secondaryStruct",name:"Secondary-structure",data:this.secondaryStructureConsensus,customColorScheme:{">":"pink","<":"lightblue"}}]}}});var lb=g(()=>{Gf();Hf();Uf();Yf();Vf();Jf();qf();Gf();Hf();Uf();Yf();Vf()});function BD(e){return e?Object.fromEntries(e.split(";").map(t=>t.trim()).filter(t=>!!t).map(t=>t.split("=")).map(([t,r])=>[t?.trim()??"",r?decodeURIComponent(r).trim().split(",").join(" "):void 0]).filter(([t])=>t!=="")):{}}function Jc(e){return e?e.split(`
68
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colConsensus(){let{colStats:t,colStatsSums:r}=this;return t.map((n,o)=>{let i=r[o],s=0,a="";for(let l in n){let A=n[l];A>s&&l!=="-"&&l!=="."&&(s=A,a=l)}let c=s/i;return{letter:a,color:c>.4?`hsl(240, 30%, ${100*Math.max(1-c/3,.3)}%)`:void 0}})},get colClustalX(){let{colStats:t,colStatsSums:r}=this;return t.map((n,o)=>{let i=r[o],s={},a=n.W??0,c=n.L??0,l=n.V??0,A=n.I??0,u=n.M??0,f=n.A??0,m=n.F??0,p=n.C??0,h=n.H??0,C=n.P??0,E=n.R??0,x=n.K??0,y=n.Q??0,w=n.E??0,S=n.D??0,v=n.T??0,M=n.S??0,T=n.G??0,_=n.Y??0,P=n.N??0,B=a+c+l+A+u+f+m+p+h+C+_,J=x+E,X=y+w,H=w+S,we=v+M;return B/i>.6&&(s.W="rgb(128,179,230)",s.L="rgb(128,179,230)",s.V="rgb(128,179,230)",s.A="rgb(128,179,230)",s.I="rgb(128,179,230)",s.M="rgb(128,179,230)",s.F="rgb(128,179,230)",s.C="rgb(128,179,230)"),(J/i>.6||x/i>.8||E/i>.8||y/i>.8)&&(s.K="#d88",s.R="#d88"),(J/i>.6||X/i>.5||w/i>.8||y/i>.8||S/i>.8)&&(s.E="rgb(192, 72, 192)"),(J/i>.6||H/i>.5||x/i>.8||E/i>.8||y/i>.8)&&(s.D="rgb(204, 77, 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ce,lS,AS,fS=g(()=>{ce=d(b(),1),lS=d(se(),1),AS=d(Yr(),1);nS();Mf();vf();Yc();Fc();yn()});function ok(){return K.types.compose(Nb(),Gb(),Rb(),K.types.model("MsaView",{id:ro.ElementId,showDomains:!1,hideGaps:!0,allowedGappyness:100,contrastLettering:!0,subFeatureRows:!1,type:K.types.literal("MsaView"),drawMsaLetters:!0,height:K.types.optional(K.types.number,550),rowHeight:16,scrollY:0,scrollX:0,colWidth:12,treeFilehandle:K.types.maybe(ro.FileLocation),msaFilehandle:K.types.maybe(ro.FileLocation),treeMetadataFilehandle:K.types.maybe(ro.FileLocation),gffFilehandle:K.types.maybe(ro.FileLocation),currentAlignment:0,collapsed:K.types.array(K.types.string),collapsedLeaves:K.types.array(K.types.string),showOnly:K.types.maybe(K.types.string),turnedOffTracks:K.types.map(K.types.boolean),data:K.types.optional(_b(),{tree:"",msa:"",treeMetadata:""}),featureFilters:K.types.map(K.types.boolean),relativeTo:K.types.maybe(K.types.string)})).volatile(()=>({headerHeight:0,status:void 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Le(`${Yt}/mafft/run`,{method:"POST",body:new URLSearchParams({email:"colin.diesh@gmail.com",stype:"protein",sequence:e})});return await Vc({jobId:r,algorithm:"mafft",onProgress:t}),{msa:await Le(`${Yt}/mafft/result/${r}/fa`),tree:await Le(`${Yt}/mafft/result/${r}/phylotree`)}}async function Vc({onProgress:e,jobId:t,algorithm:r}){for(;;){for(let o=0;o<10;o++)await Us(1e3),e(`Re-checking MSA status in... ${10-o}`);let n=await Le(`${Yt}/${r}/status/${t}`);if(n==="FINISHED")break;if(n.includes("FAILURE"))throw new Error(`Failed to run: jobId ${t}`)}}async function SS({algorithm:e,sequence:t,onProgress:r}){switch(r(`Launching ${e} MSA...`),e){case"clustalo":return ok({sequence:t,onProgress:r});case"muscle":return ik({sequence:t,onProgress:r});case"kalign":return sk({sequence:t,onProgress:r});case"mafft":return ak({sequence:t,onProgress:r});default:throw new Error("unknown algorithm")}}async function QS({query:e,blastDatabase:t,blastProgram:r,baseUrl:n,onProgress:o,onRid:i}){o("Submitting to 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Le(`${r}?CMD=Get&FORMAT_OBJECT=SearchInfo&RID=${e}`),i=/\s+Status=WAITING/m.test(o),s=/\s+Status=FAILED/m.test(o),a=/\s+Status=READY/m.test(o),c=/\s+ThereAreHits=yes/m.test(o);if(!i){if(s)throw new Error(`BLAST ${e} failed`);if(a){if(c)return!0;throw new Error("No hits found")}}}}ea();var Ak="jbrowse-msaview-taxonomy-cache",Wc="common-names",uk=1;async function MS(){return Qi(Ak,uk,{upgrade(e){e.objectStoreNames.contains(Wc)||e.createObjectStore(Wc,{keyPath:"taxid"})}})}async function fk(e){return(await MS()).get(Wc,e)}async function dk(e){let r=(await MS()).transaction(Wc,"readwrite");for(let n of e)await r.store.put(n);await r.done}async function vS(e){let t=new Map,r=[];for(let i of e){let s=await fk(i);s?t.set(i,{sciname:s.sciname,commonName:s.commonName}):r.push(i)}if(r.length===0)return t;let n=100,o=[];for(let i=0;i<r.length;i+=n){let s=r.slice(i,i+n),a=s.join(",");try{let l=await(await fetch(`https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=taxonomy&id=${a}&retmode=xml`)).text();for(let A of s){let f=new RegExp(`<Taxon>.*?<TaxId>${A}</TaxId>.*?</Taxon>`,"s").exec(l);if(f){let m=f[0],p=/<GenbankCommonName>(.*?)<\/GenbankCommonName>/.exec(m),h=/<CommonName>(.*?)<\/CommonName>/.exec(m),C=/<ScientificName>(.*?)<\/ScientificName>/.exec(m),E=p?.[1]??h?.[1],x=C?.[1]??"";t.set(A,{sciname:x,commonName:E}),o.push({taxid:A,sciname:x,commonName:E})}else o.push({taxid:A,sciname:"",commonName:void 0})}}catch(c){console.error("Failed to fetch taxonomy data:",c)}}return o.length>0&&await dk(o),t}async function TS({self:e}){let{baseUrl:t,blastDatabase:r,blastProgram:n,msaAlgorithm:o,proteinSequence:i,selectedTranscript:s}=e.blastParams,a=qs(i),{hits:c,rid:l}=await QS({query:a,blastDatabase:r,blastProgram:n,baseUrl:t,onProgress:C=>{e.setProgress(C)},onRid:C=>{e.setRid(C)}});e.setProgress("Fetching species taxonomy info...");let A=c.map(C=>C.description[0]?.taxid).filter(C=>C!==void 0),u=await vS(A),f={},m=c.map(C=>{let E=C.description[0]??{accession:"unknown",id:"unknown",sciname:"unknown"},x=BS(E,u),y=bS(C.hsps[0]?.hseq??"");return f[x]=mk(E,u),`>${x}
74
- ${y}`}),p=await SS({algorithm:o,sequence:[`>QUERY
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+ `),treeMetadata:JSON.stringify(Object.fromEntries(s.map(a=>[a.id,{genome:a.species}])))}}function Cg(e){let{data:t,error:r,isLoading:n}=Ln(()=>e?["geneTree",e]:null,([,o])=>hg(o),{revalidateOnFocus:!1,revalidateOnReconnect:!1,revalidateIfStale:!1});return{treeData:t,isTreeLoading:n,treeError:r}}var Eg=d(se());function A1(e){let r=(e.get("subfeatures")??[]).filter(n=>(n.get("type")==="mRNA"||n.get("type")==="transcript")&&n.get("subfeatures")?.some(o=>o.get("type")==="CDS"));return r.length>0?r:[e]}function Ys(e){let t=(0,Eg.sum)(e.get("subfeatures")?.filter(r=>r.get("type")?.toLowerCase()==="cds").map(r=>r.get("end")-r.get("start"))??[]);return{len:Math.floor(t/3),mod:t%3}}function Or(e){return e?.get("name")??e?.get("id")??""}function bi(e){return e===void 0?"":[e.get("name"),e.get("id")].filter(t=>!!t).join(" ")}function yr(e){return e===void 0?"":[e.get("gene_name")??e.get("name"),e.get("id")?`(${e.get("id")})`:""].filter(t=>!!t).join(" ")}function Ig(e){return A1(e).toSorted((t,r)=>Ys(r).len-Ys(t).len)}function qs(e){return e.replaceAll("*","").replaceAll("&","")}var lr=d(b()),js=d(N()),Bg=d(tt());var yg=d(b()),wg=d(tt());var jl=d(b()),xg=d(N());function u1({children:e,...t}){return jl.default.createElement("div",null,jl.default.createElement(xg.TextField,{...t},e))}var At=u1;var f1=(0,wg.makeStyles)()({textAreaFont:{fontFamily:"Courier New"}});function Vl({value:e}){let{classes:t}=f1();return yg.default.createElement(At,{variant:"outlined",multiline:!0,minRows:5,maxRows:10,fullWidth:!0,value:e,slotProps:{input:{readOnly:!0,classes:{input:t.textAreaFont}}}})}var d1=(0,Bg.makeStyles)()({flex:{display:"flex"},minWidth:{minWidth:300}});function Ar({feature:e,options:t,selectedTranscript:r,onTranscriptChange:n,proteinSequence:o,validSet:i}){let{classes:s}=d1(),[a,c]=(0,lr.useState)(!1);return lr.default.createElement(lr.default.Fragment,null,lr.default.createElement("div",{className:s.flex},lr.default.createElement(At,{variant:"outlined",label:`Choose isoform of ${yr(e)}`,select:!0,className:s.minWidth,value:Or(r),onChange:l=>{n(l.target.value)}},t.map(l=>{let A=i?i.has(Or(l)):!0,{len:u,mod:f}=Ys(l);return lr.default.createElement(js.MenuItem,{value:Or(l),key:l.id(),disabled:!A},bi(l)," (",u," aa)"," ",f?" (possible fragment)":"",i?A?" (has data)":" (no data)":"")})),lr.default.createElement("div",{style:{alignContent:"center",marginLeft:20}},lr.default.createElement(js.Button,{variant:"contained",color:"primary",onClick:()=>{c(!a)}},a?"Hide sequence":"Show sequence"))),a&&lr.default.createElement(Vl,{value:o?`>${bi(r)}
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+ ${o}`:"Loading..."}))}var Io=d(b());var dn=d(se());function m1(e,t){return e.map(r=>t.slice(r.start,r.end)).join("")}function g1({cds:e,sequence:t,codonTable:r}){let n=m1(e,t),o="";for(let i=0;i<n.length;i+=3)o+=r[n.slice(i,i+3)]??"&";return o}function p1(e,t){return e.map(r=>({...r,start:t-r.end,end:t-r.start})).toSorted((r,n)=>r.start-n.start)}function bg({feature:e,seq:t}){let{subfeatures:r,start:n,strand:o}=e.toJSON(),i=(0,dn.dedupe)(r?.toSorted((s,a)=>s.start-a.start).map(s=>({...s,start:s.start-n,end:s.end-n})).filter(s=>s.type==="CDS")??[],s=>`${s.start}-${s.end}`);return g1({cds:o===-1?p1(i,t.length):i,sequence:o===-1?(0,dn.revcom)(t):t,codonTable:(0,dn.generateCodonTable)(dn.defaultCodonTable)})}var Qg=d(se());var Sg=d(Nn());async function Vs({start:e,end:t,refName:r,session:n,assemblyName:o}){let{assemblyManager:i,rpcManager:s}=n,a=await i.waitForAssembly(o);if(!a)throw new Error("assembly not found");let c="getSequence";return(await 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fr.default.createElement(fr.default.Fragment,null,fr.default.createElement(mp.IconButton,{style:{float:"right"},size:"small",onClick:()=>{c(!0)}},fr.default.createElement($s,null)),fr.default.createElement(n==="automatic"?sp:fp,{model:t,feature:r,handleClose:e,baseUrl:i},fr.default.createElement(aA,{lookupMethod:n,setLookupMethod:o})),a?fr.default.createElement(cA,{baseUrl:i,handleClose:A=>{A&&s(A),c(!1)}}):null)}var Ue=d(b()),ch=d(Nn()),Gn=d(xe()),Qo=d(se()),qr=d(N()),lh=d(G());var Ah=d(tt());var AA={revalidateOnFocus:!1,revalidateOnReconnect:!1,revalidateIfStale:!1,refreshWhenHidden:!1,refreshWhenOffline:!1,shouldRetryOnError:!1};gn();function MA(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 bA(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-${bA(t)}`}function nh(e={}){return`${MA(e)}`}var oh={};async function dM(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 ${n}`);let i=o.configSchema.create(r,{pluginManager:e}),s=ga.bind(null,e,t),a=await o.getAdapterClass();return{dataAdapter:new a(i,s,e),sessionIds:new Set([t])}}async function ga(e,t,r){let n=nh(r);oh[n]??=dM(e,t,r);let o=await oh[n];return o.sessionIds.add(t),o}async function ih({config:e,pluginManager:t}){return(await ga(t,"msa",e)).dataAdapter.getMSAList()}async function sh({config:e,pluginManager:t,msaId:r}){return(await ga(t,"msa",e)).dataAdapter.getMSA(r)}function ah({session:e,newViewTitle:t,view:r,feature:n,data:o,querySeqName:i}){e.addView("MsaView",{type:"MsaView",displayName:t,treeAreaWidth:200,querySeqName:i,treeWidth:100,drawNodeBubbles:!1,labelsAlignRight:!0,showBranchLen:!1,colWidth:10,rowHeight:12,colorSchemeName:"percent_identity_dynamic",data:o,connectedViewId:r.id,connectedFeature:n.toJSON()})}var mM=(0,Ah.makeStyles)()({dialogContent:{width:"80em"}}),gM=(0,lh.observer)(function({model:t,feature:r,handleClose:n}){let o=(0,Qo.getSession)(t),i=(0,Qo.getContainingView)(t),{classes:s}=mM(),{pluginManager:a}=(0,Qo.getEnv)(t),{assemblyNames:c}=i,[l,A]=(0,Ue.useState)(),{jbrowse:u}=o,f=(0,ch.readConfObject)(u,["msa","datasets"]),[m,p]=(0,Ue.useState)(f?.[0]?.datasetId),h=f?.find(H=>H.datasetId===m),{data:C,isLoading:E,error:x}=Ln(m?`${m}-msa-list`:"none-msa-list",()=>h?ih({config:h.adapter,pluginManager:a}):void 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72
+ ${Be.get("seq")}`).join(`
73
+ `)}}),n()}catch(H){A(H)}}},"Submit"),Ue.default.createElement(qr.Button,{color:"secondary",variant:"contained",onClick:()=>{n()}},"Cancel")))}),uh=gM;var vA=d(b());function Mo({children:e,value:t,index:r,...n}){return vA.default.createElement("div",{role:"tabpanel",hidden:t!==r,...n},t===r&&vA.default.createElement("div",null,e))}function TA({handleClose:e,feature:t,model:r}){let n=(0,mh.getSession)(r),{jbrowse:o}=n,i=(0,fh.readConfObject)(o,["msa","datasets"]),s=i&&i.length>0,[a,c]=(0,nt.useState)("ncbi_blast");return nt.default.createElement(dh.Dialog,{maxWidth:"xl",title:"Launch MSA view",open:!0,onClose:e},nt.default.createElement(On.Tabs,{value:a,onChange:(A,u)=>{c(u)}},nt.default.createElement(On.Tab,{label:"NCBI BLAST query",value:"ncbi_blast"}),s?nt.default.createElement(On.Tab,{label:"Pre-loaded MSA datasets",value:"preloaded_msa"}):null,nt.default.createElement(On.Tab,{label:"Ensembl GeneTree",value:"ensembl_genetree"}),nt.default.createElement(On.Tab,{label:"Manual upload",value:"manual_msa"})),nt.default.createElement(Mo,{value:a,index:"ncbi_blast"},nt.default.createElement(lA,{handleClose:e,feature:t,model:r})),s?nt.default.createElement(Mo,{value:a,index:"preloaded_msa"},nt.default.createElement(uh,{model:r,feature:t,handleClose:e})):null,nt.default.createElement(Mo,{value:a,index:"ensembl_genetree"},nt.default.createElement(Dg,{model:r,feature:t,handleClose:e})),nt.default.createElement(Mo,{value:a,index:"manual_msa"},nt.default.createElement(Fg,{model:r,feature:t,handleClose:e})))}function pM(e){return e.name==="LinearBasicDisplay"}function hM(e){return e.views(t=>{let r=t.contextMenuItems;return{contextMenuItems(){let n=t.contextMenuFeature,o=(0,pa.getContainingTrack)(t),i=n?.get("type"),s=n&&["gene","mRNA","transcript"].includes(i);return[...r(),...s?[{label:"Launch MSA view",icon:qm,onClick:()=>{(0,pa.getSession)(o).queueDialog(a=>[TA,{model:o,handleClose:a,feature:n}])}}]:[]]}}})}function _A(e){e.addToExtensionPoint("Core-extendPluggableElement",t=>(pM(t)&&(t.stateModel=hM(t.stateModel)),t))}function DA(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:f,drawNodeBubbles:m,labelsAlignRight:p,showBranchLen:h,querySeqName:C})=>{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:f,drawNodeBubbles:m,labelsAlignRight:p,showBranchLen:h,init:{msaData:r?.msa,treeData:r?.tree,msaUrl:n?.uri,treeUrl:o?.uri,querySeqName:C}})})}var cQ=d(b()),lQ=d(ph());var KS=d(b()),zS=d(Al()),Tn=d(se()),ee=d(Nt());function*CM(e,t){if(t!==-1)for(let r=e.start;r<e.end;r++)yield r;else for(let r=e.end-1;r>=e.start;r--)yield r}function hh(e){let t=e.strand,r=e.refName;if(t!==-1&&t!==1)throw new Error(`Invalid strand value: ${t}. Expected 1 or -1.`);if(!r)throw new Error("refName is required");let n=e.subfeatures?.filter(u=>u.type==="CDS")??[],o=new Set,i=n.filter(u=>{if(u.start>=u.end)return!1;let f=`${u.start}-${u.end}`;return o.has(f)?!1:(o.add(f),!0)}).sort((u,f)=>t*(u.start-f.start)),s={},a={};if(i.length===0)return{g2p:s,p2g:a,refName:r,strand:t};let l=(3-(i[0]?.phase??0))%3,A=-1;for(let u of i)for(let f of CM(u,t)){let m=Math.floor(l++/3);s[f]=m,m!==A&&(a[m]=f,A=m)}return{g2p:s,p2g:a,refName:r,strand:t}}var nn=d(Yr());Cd();function bS(e,t){let r=e.sciname.replaceAll(" ","_");if(e.taxid&&t?.has(e.taxid)){let n=t.get(e.taxid);n.commonName&&(r=n.commonName.split(" ").map(o=>o.charAt(0).toUpperCase()+o.slice(1).toLowerCase()).join("_"))}return`${e.accession}-${r}`}function SS(e){return e.replace("-","")}var Yt="https://www.ebi.ac.uk/Tools/services/rest";async function ik({sequence:e,onProgress:t}){let r=await Le(`${Yt}/clustalo/run`,{method:"POST",body:new URLSearchParams({email:"colin.diesh@gmail.com",sequence:e})});return await Vc({jobId:r,algorithm:"clustalo",onProgress:t}),{msa:await Le(`${Yt}/clustalo/result/${r}/aln-clustal_num`),tree:await Le(`${Yt}/clustalo/result/${r}/phylotree`)}}async function sk({sequence:e,onProgress:t}){let r=await Le(`${Yt}/muscle/run`,{method:"POST",body:new URLSearchParams({email:"colin.diesh@gmail.com",format:"clw",tree:"tree1",sequence:e})});return await Vc({jobId:r,algorithm:"muscle",onProgress:t}),{msa:await Le(`${Yt}/muscle/result/${r}/fa`),tree:await Le(`${Yt}/muscle/result/${r}/phylotree`)}}async function ak({sequence:e,onProgress:t}){let r=await Le(`${Yt}/kalign/run`,{method:"POST",body:new URLSearchParams({email:"colin.diesh@gmail.com",stype:"protein",sequence:e})});return await Vc({jobId:r,algorithm:"kalign",onProgress:t}),{msa:await Le(`${Yt}/kalign/result/${r}/fa`),tree:await Le(`${Yt}/kalign/result/${r}/phylotree`)}}async function ck({sequence:e,onProgress:t}){let r=await Le(`${Yt}/mafft/run`,{method:"POST",body:new URLSearchParams({email:"colin.diesh@gmail.com",stype:"protein",sequence:e})});return await Vc({jobId:r,algorithm:"mafft",onProgress:t}),{msa:await Le(`${Yt}/mafft/result/${r}/fa`),tree:await Le(`${Yt}/mafft/result/${r}/phylotree`)}}async function Vc({onProgress:e,jobId:t,algorithm:r}){for(;;){for(let o=0;o<10;o++)await Us(1e3),e(`Re-checking MSA status in... ${10-o}`);let n=await Le(`${Yt}/${r}/status/${t}`);if(n==="FINISHED")break;if(n.includes("FAILURE"))throw new Error(`Failed to run: jobId ${t}`)}}async function QS({algorithm:e,sequence:t,onProgress:r}){switch(r(`Launching ${e} MSA...`),e){case"clustalo":return ik({sequence:t,onProgress:r});case"muscle":return sk({sequence:t,onProgress:r});case"kalign":return ak({sequence:t,onProgress:r});case"mafft":return ck({sequence:t,onProgress:r});default:throw new Error("unknown algorithm")}}async function MS({query:e,blastDatabase:t,blastProgram:r,baseUrl:n,onProgress:o,onRid:i}){o("Submitting to NCBI BLAST...");let{rid:s}=await lk({query:e,blastDatabase:t,blastProgram:r,baseUrl:n});i(s),await Ak({rid:s,onProgress:o,baseUrl:n});let a=await Eo(`${n}?CMD=Get&RID=${s}&FORMAT_TYPE=JSON2_S&FORMAT_OBJECT=Alignment`);return{rid:s,hits:a.BlastOutput2[0]?.report.results.search.hits??[]}}async function lk({query:e,blastProgram:t,blastDatabase:r,baseUrl:n}){let o=await Le(n,{method:"POST",body:new URLSearchParams({CMD:"Put",PROGRAM:t==="quick-blastp"?"blastp":t,DATABASE:r,QUERY:e,...r==="nr_clustered_seq"?{CLUSTERED_DB:"on",DB_TYPE:"Experimental Databases"}:{},...t==="quick-blastp"?{BLAST_PROGRAMS:"kmerBlastp"}:{}})}),i=/^ {4}RID = (.*$)/m.exec(o)?.[1],s=/^ {4}RTOE = (.*$)/m.exec(o)?.[1];if(!i)throw new Error("Failed to get RID from BLAST request");return{rid:i,rtoe:s}}async function Ak({rid:e,onProgress:t,baseUrl:r}){for(;;){for(let l=0;l<20;l++)await Us(1e3),t(`Re-checking BLAST status in... ${20-l}`);let o=await Le(`${r}?CMD=Get&FORMAT_OBJECT=SearchInfo&RID=${e}`),i=/\s+Status=WAITING/m.test(o),s=/\s+Status=FAILED/m.test(o),a=/\s+Status=READY/m.test(o),c=/\s+ThereAreHits=yes/m.test(o);if(!i){if(s)throw new Error(`BLAST ${e} failed`);if(a){if(c)return!0;throw new Error("No hits found")}}}}ea();var uk="jbrowse-msaview-taxonomy-cache",Wc="common-names",fk=1;async function vS(){return Qi(uk,fk,{upgrade(e){e.objectStoreNames.contains(Wc)||e.createObjectStore(Wc,{keyPath:"taxid"})}})}async function dk(e){return(await vS()).get(Wc,e)}async function mk(e){let r=(await vS()).transaction(Wc,"readwrite");for(let n of e)await r.store.put(n);await r.done}async function TS(e){let t=new Map,r=[];for(let i of e){let s=await dk(i);s?t.set(i,{sciname:s.sciname,commonName:s.commonName}):r.push(i)}if(r.length===0)return t;let n=100,o=[];for(let i=0;i<r.length;i+=n){let s=r.slice(i,i+n),a=s.join(",");try{let l=await(await fetch(`https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=taxonomy&id=${a}&retmode=xml`)).text();for(let A of s){let f=new RegExp(`<Taxon>.*?<TaxId>${A}</TaxId>.*?</Taxon>`,"s").exec(l);if(f){let m=f[0],p=/<GenbankCommonName>(.*?)<\/GenbankCommonName>/.exec(m),h=/<CommonName>(.*?)<\/CommonName>/.exec(m),C=/<ScientificName>(.*?)<\/ScientificName>/.exec(m),E=p?.[1]??h?.[1],x=C?.[1]??"";t.set(A,{sciname:x,commonName:E}),o.push({taxid:A,sciname:x,commonName:E})}else o.push({taxid:A,sciname:"",commonName:void 0})}}catch(c){console.error("Failed to fetch taxonomy data:",c)}}return o.length>0&&await mk(o),t}async function _S({self:e}){let{baseUrl:t,blastDatabase:r,blastProgram:n,msaAlgorithm:o,proteinSequence:i,selectedTranscript:s}=e.blastParams,a=qs(i),{hits:c,rid:l}=await MS({query:a,blastDatabase:r,blastProgram:n,baseUrl:t,onProgress:C=>{e.setProgress(C)},onRid:C=>{e.setRid(C)}});e.setProgress("Fetching species taxonomy info...");let A=c.map(C=>C.description[0]?.taxid).filter(C=>C!==void 0),u=await TS(A),f={},m=c.map(C=>{let E=C.description[0]??{accession:"unknown",id:"unknown",sciname:"unknown"},x=bS(E,u),y=SS(C.hsps[0]?.hseq??"");return f[x]=gk(E,u),`>${x}
74
+ ${y}`}),p=await QS({algorithm:o,sequence:[`>QUERY
75
75
  ${a}`,...m].join(`
76
- `),onProgress:C=>{e.setProgress(C)}}),h=JSON.stringify(f);return await zg({proteinSequence:a,blastDatabase:r,blastProgram:n,msaAlgorithm:o,msa:p.msa,tree:p.tree,treeMetadata:h,rid:l,geneId:s?.get("parentId"),transcriptId:s?.get("id")}),{...p,treeMetadata:h}}function mk(e,t){let r={},n=e.taxid?t.get(e.taxid):void 0;return n?.sciname&&(r["Scientific name"]=n.sciname),n?.commonName&&(r["Common name"]=n.commonName),e.accession&&(r.Accession=e.accession),e.id&&(r.ID=e.id),e.title&&(r.Description=e.title),r}var kS=d(se());function _S(e){return typeof e=="object"&&e!==null&&"hoverFeature"in e&&"hoverPosition"in e}function DS(e){return/AF-([A-Z0-9]+)-F\d+/.exec(e)?.[1]}function NS({model:e}){let{hovered:t}=(0,kS.getSession)(e),{querySeqName:r,transcriptToMsaMap:n,connectedView:o,mafRegion:i}=e;if(!o?.initialized||!_S(t))return;let{coord:s,refName:a}=t.hoverPosition;if(i){if(a!==i.refName||!o.assemblyNames.includes(i.assemblyName)||s<i.start||s>=i.end)return;let l=s-i.start;return e.seqPosToVisibleCol(r,l)}if(n){let{g2p:c}=n,l=c[s];if(l!==void 0)return e.seqPosToVisibleCol(r,l)}}function Kc(e,t){if(t<0||t>=e.length)return;let r=0;for(let n=0;n<t;n++)e[n]!=="-"&&r++;if(e[t]!=="-")return r}function LS(e,t){let r=0;for(let n=0;n<e.length;n++)if(e[n]!=="-"){if(r===t)return n;r++}}function Ed(e){let t={};for(let[r,n]of e)t[r]=n;return t}function zc({model:e,coord:t}){let{querySeqName:r,transcriptToMsaMap:n,mafRegion:o}=e,s=e.rows.find(c=>c[0]===r)?.[1];if(!s)return;let a=Kc(s,t);if(a!==void 0){if(o){let c=o.start+a;return c>=o.end?void 0:{refName:o.refName,start:c,end:c+1}}if(n){let{refName:c,p2g:l}=n,A=l[a],u=l[a+1];return A!==void 0&&u!==void 0?{refName:c,start:Math.min(A,u),end:Math.max(A,u)}:void 0}}}var gk="jbrowse-msaview-data";var vn="msa-data",$c,no;function pk(){if(no!==void 0)return no;try{return typeof indexedDB>"u"?(no=!1,!1):(no=!0,!0)}catch{return no=!1,!1}}async function Id(){if(pk())return $c||($c=new Promise(e=>{try{let t=indexedDB.open(gk,1);t.addEventListener("error",()=>{console.warn("IndexedDB unavailable - MSA data will not persist across page refreshes"),no=!1,e(void 0)}),t.onsuccess=()=>{e(t.result)},t.onupgradeneeded=r=>{let n=r.target.result;n.objectStoreNames.contains(vn)||n.createObjectStore(vn,{keyPath:"id"}).createIndex("timestamp","timestamp",{unique:!1})}}catch(t){console.warn("Failed to open IndexedDB:",t),no=!1,e(void 0)}}),$c)}function FS(){return`msa-${Date.now()}-${Math.random().toString(36).slice(2,11)}`}async function RS(e,t){let r=await Id();return r?new Promise(n=>{try{let i=r.transaction(vn,"readwrite").objectStore(vn),s={id:e,msa:t.msa,tree:t.tree,treeMetadata:t.treeMetadata,timestamp:Date.now()},a=i.put(s);a.addEventListener("error",()=>{console.warn("Failed to store MSA data:",a.error),n(!1)}),a.onsuccess=()=>{n(!0)}}catch(o){console.warn("Failed to store MSA data:",o),n(!1)}}):!1}async function PS(e){let t=await Id();if(t)return new Promise(r=>{try{let i=t.transaction(vn,"readonly").objectStore(vn).get(e);i.addEventListener("error",()=>{console.warn("Failed to retrieve MSA data:",i.error),r(void 0)}),i.onsuccess=()=>{let s=i.result;r(s?{msa:s.msa,tree:s.tree,treeMetadata:s.treeMetadata}:void 0)}}catch(n){console.warn("Failed to retrieve MSA data:",n),r(void 0)}})}async function GS(e=10080*60*1e3){let t=await Id();if(!t)return 0;let r=Date.now()-e;return new Promise(n=>{try{let s=t.transaction(vn,"readwrite").objectStore(vn).index("timestamp"),a=IDBKeyRange.upperBound(r),c=s.openCursor(a),l=0;c.addEventListener("error",()=>{console.warn("Failed to cleanup old MSA data:",c.error),n(l)}),c.onsuccess=A=>{let u=A.target.result;u?(u.delete(),l++,u.continue()):n(l)}}catch(o){console.warn("Failed to cleanup old MSA data:",o),n(0)}})}var 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OS(e,t){let r=e.toUpperCase(),n=t.toUpperCase();return hk[r]?.[n]??-4}var Ck=-10,Ek=-.5;function Ik(e,t,r=Ck,n=Ek){let o=e.length,i=t.length,s=[],a=[],c=[];for(let C=0;C<=o;C++){s[C]=[],a[C]=[],c[C]=[];for(let E=0;E<=i;E++)s[C][E]=-1/0,a[C][E]=-1/0,c[C][E]=-1/0}s[0][0]=0;for(let C=1;C<=o;C++)a[C][0]=r+(C-1)*n;for(let C=1;C<=i;C++)c[0][C]=r+(C-1)*n;for(let C=1;C<=o;C++)for(let E=1;E<=i;E++){let x=OS(e[C-1],t[E-1]);s[C][E]=Math.max(s[C-1][E-1],a[C-1][E-1],c[C-1][E-1])+x,a[C][E]=Math.max(s[C-1][E]+r,a[C-1][E]+n),c[C][E]=Math.max(s[C][E-1]+r,c[C][E-1]+n)}let l="",A="",u=o,f=i,m=[s[o][i],a[o][i],c[o][i]],p=Math.max(...m),h=p===s[o][i]?"M":p===a[o][i]?"Ix":"Iy";for(;u>0||f>0;)if(h==="M"&&u>0&&f>0){l=e[u-1]+l,A=t[f-1]+A;let C=OS(e[u-1],t[f-1]),E=s[u-1][f-1],x=a[u-1][f-1];s[u][f]===E+C?h="M":s[u][f]===x+C?h="Ix":h="Iy",u--,f--}else if(h==="Ix"&&u>0)l=e[u-1]+l,A="-"+A,h=a[u][f]===s[u-1][f]+r?"M":"Ix",u--;else if(f>0)l="-"+l,A=t[f-1]+A,h=c[u][f]===s[u][f-1]+r?"M":"Iy",f--;else break;return{alignedSeq1:l,alignedSeq2:A,score:p}}function xk(e,t){let r="";for(let n=0;n<e.length;n++){let o=e[n],i=t[n];o==="-"||i==="-"?r+=" ":o.toUpperCase()===i.toUpperCase()?r+="|":r+=" "}return r}function HS(e,t){let{alignedSeq1:r,alignedSeq2:n}=Ik(e,t);return{consensus:xk(r,n),alns:[{id:"msa",seq:r},{id:"structure",seq:n}]}}function JS(e){let t=e.alns[0].seq,r=e.alns[1].seq;if(t.length!==r.length)throw new Error("Aligned sequences must have same length");let n=0,o=0,i=new Map,s=new Map;for(let a=0;a<t.length;a++){let c=t[a],l=r[a];c!=="-"&&l!=="-"?(i.set(n,o),s.set(o,n),n++,o++):c==="-"?o++:n++}return{seq1ToSeq2:i,seq2ToSeq1:s}}var Bk=(0,WS.lazy)(()=>Promise.resolve().then(()=>(VS(),jS)));function bk(e){let{mouseCol:t,connectedProteinViews:r}=e;if(r.length!==0)for(let n of r){let o=n.proteinView?.structures?.[n.structureIdx];if(!o)continue;if(t===void 0){o.clearHighlightFromExternal?.();continue}let i=e.getSequenceByRowName(n.msaRowName);if(!i)continue;let s=Kc(i,t);if(s===void 0){o.clearHighlightFromExternal?.();continue}let a=n.msaToStructure[s];a===void 0?o.clearHighlightFromExternal?.():o.highlightFromExternal?.(a)}}function xd(){return ee.types.compose(KS.BaseViewModel,hd(),ee.types.model("MsaView",{connectedViewId:ee.types.maybe(ee.types.string),connectedFeature:ee.types.frozen(),connectedHighlights:ee.types.array(ee.types.model({refName:ee.types.string,start:ee.types.number,end:ee.types.number})),blastParams:ee.types.frozen(),querySeqName:"QUERY",uniprotId:ee.types.maybe(ee.types.string),zoomToBaseLevel:!1,init:ee.types.frozen(),connectedStructures:ee.types.array(ee.types.frozen()),dataStoreId:ee.types.maybe(ee.types.string),mafRegion:ee.types.frozen()})).volatile(()=>({rid:void 0,progress:"",error:void 0,loadingStoredData:!1})).views(e=>({getRowByName(t){return e.rows.find(r=>r[0]===t)},getSequenceByRowName(t){return e.rows.find(r=>r[0]===t)?.[1]}})).views(e=>({get transcriptToMsaMap(){return e.connectedFeature?hh(e.connectedFeature):void 0},get 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s=i.replaceAll("-",""),{views:a}=(0,Tn.getSession)(e),c=a.find(h=>h.id===t);if(!c)throw new Error(`ProteinView "${t}" not found`);let l=c.structures?.[r];if(!l)throw new Error(`Structure at index ${r} not found`);let A=l.structureSequences?.[0];if(!A)throw new Error("Structure sequence not available");let u=HS(s,A),{seq1ToSeq2:f,seq2ToSeq1:m}=JS(u),p={proteinViewId:t,structureIdx:r,msaRowName:o,msaToStructure:Ed(f),structureToMsa:Ed(m)};e.connectedStructures.push(p)},disconnectFromStructure(t,r){let n=e.connectedStructures.findIndex(o=>o.proteinViewId===t&&o.structureIdx===r);n!==-1&&e.connectedStructures.splice(n,1)},disconnectAllStructures(){e.connectedStructures.clear()}})).actions(e=>{let t=e.setMouseClickPos.bind(e);return{setMouseClickPos(r,n){t(r,n),r!==void 0&&e.handleMsaClick(r)}}}).views(e=>({extraViewMenuItems(){return[{label:"Zoom to base level on click?",checked:e.zoomToBaseLevel,type:"checkbox",onClick:()=>{e.setZoomToBaseLevel(!e.zoomToBaseLevel)}},{label:"Connect to protein structure...",onClick:()=>{(0,Tn.getSession)(e).queueDialog(t=>[Bk,{model:e,handleClose:t}])}},...e.connectedStructures.length>0?[{label:"Disconnect from protein structures",onClick:()=>{e.disconnectAllStructures()}}]:[]]}})).actions(e=>({afterCreate(){GS().catch(t=>{console.error("Failed to cleanup old MSA data:",t)}),(0,ee.addDisposer)(e,(0,rn.autorun)(async()=>{let{dataStoreId:t,rows:r}=e;if(t&&r.length===0)try{e.setLoadingStoredData(!0);let n=await PS(t);n&&(n.msa&&e.setMSA(n.msa),n.tree&&e.setTree(n.tree))}catch(n){console.error("Failed to load MSA data from IndexedDB:",n)}finally{e.setLoadingStoredData(!1)}})),(0,ee.addDisposer)(e,(0,rn.autorun)(async()=>{let{rows:t,dataStoreId:r}=e;if(t.length>0&&!r){if(!!(e.msaFilehandle??e.treeFilehandle))return;let o=e.data.msa,i=e.data.tree;if(o||i)try{let s=FS();await RS(s,{msa:o,tree:i,treeMetadata:e.data.treeMetadata})&&e.setDataStoreId(s)}catch(s){console.error("Failed to store MSA data to 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0:zc({model:e,coord:r});e.setConnectedHighlights([n,o].filter(i=>!!i))})),(0,ee.addDisposer)(e,(0,rn.autorun)(()=>{bk(e)})),(0,ee.addDisposer)(e,(0,rn.autorun)(()=>{let{views:t}=(0,Tn.getSession)(e),{connectedViewId:r,uniprotId:n,rows:o,connectedStructures:i}=e;if(!(!n||o.length===0))for(let s of t){let a=s;if(!(a.type!=="ProteinView"||!a.structures))for(let c=0;c<a.structures.length;c++){let l=a.structures[c];if(!(l.connectedViewId!==r||l.uniprotId!==n||i.some(u=>u.proteinViewId===a.id&&u.structureIdx===c))&&l.structureSequences?.[0])try{e.connectToStructure(a.id,c)}catch(u){console.error("Failed to auto-connect to ProteinView:",u)}}}})),(0,ee.addDisposer)(e,(0,rn.autorun)(()=>{let{views:t}=(0,Tn.getSession)(e),{connectedViewId:r,transcriptToMsaMap:n,querySeqName:o}=e;if(!r||!n)return;let i=[];for(let a of t){let c=a;if(!(c.type!=="ProteinView"||!c.structures))for(let l of c.structures){if(l.connectedViewId!==r)continue;let A=l.hoverGenomeHighlights;if(!A||A.length===0)continue;let{g2p:u}=n;for(let f of A)for(let m=f.start;m<f.end;m++){let p=u[m];if(p!==void 0){let h=e.seqPosToGlobalCol(o,p);i.includes(h)||i.push(h)}}}}let s=i.map(a=>e.globalColToVisibleCol(a)).filter(a=>a!==void 0);e.setHighlightedColumns(s.length>0?s:void 0)}))}}))}var Dk=(0,aQ.lazy)(()=>Promise.resolve().then(()=>(sQ(),iQ)));function bd(e){e.addViewType(()=>new cQ.default({name:"MsaView",stateModel:xd(),ReactComponent:Dk}))}var Zc=class extends lQ.default{constructor(){super(...arguments);this.name="MsaViewPlugin";this.version=$d}install(r){bd(r),_A(r),DA(r),ll(r),Ml(r)}configure(r){(0,AQ.isAbstractMenuManager)(r.rootModel)&&r.rootModel.appendToSubMenu(["Add"],{label:"Multiple sequence alignment view",icon:zd,onClick:n=>{n.addView("MsaView",{})}})}rootConfigurationSchema(r){return{msa:(0,Sd.ConfigurationSchema)("MSA",{datasets:Qd.types.maybe(Qd.types.array((0,Sd.ConfigurationSchema)("MSAEntry",{datasetId:{type:"string",defaultValue:""},description:{type:"string",defaultValue:""},name:{type:"string",defaultValue:""},adapter:r.pluggableConfigSchemaType("adapter")})))})}}};return wQ(kk);})();
76
+ `),onProgress:C=>{e.setProgress(C)}}),h=JSON.stringify(f);return await zg({proteinSequence:a,blastDatabase:r,blastProgram:n,msaAlgorithm:o,msa:p.msa,tree:p.tree,treeMetadata:h,rid:l,geneId:s?.get("parentId"),transcriptId:s?.get("id")}),{...p,treeMetadata:h}}function gk(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 NS=d(se());function DS(e){return typeof e=="object"&&e!==null&&"hoverFeature"in e&&"hoverPosition"in e}function kS(e){return/AF-([A-Z0-9]+)-F\d+/.exec(e)?.[1]}function LS({model:e}){let{hovered:t}=(0,NS.getSession)(e),{querySeqName:r,transcriptToMsaMap:n,connectedView:o,mafRegion:i}=e;if(!o?.initialized||!DS(t))return;let{coord:s,refName:a}=t.hoverPosition;if(i){if(a!==i.refName||!o.assemblyNames.includes(i.assemblyName)||s<i.start||s>=i.end)return;let l=s-i.start;return e.seqPosToVisibleCol(r,l)}if(n){let{g2p:c}=n,l=c[s];if(l!==void 0)return e.seqPosToVisibleCol(r,l)}}function Kc(e,t){if(t<0||t>=e.length)return;let r=0;for(let n=0;n<t;n++)e[n]!=="-"&&r++;if(e[t]!=="-")return r}function FS(e,t){let r=0;for(let n=0;n<e.length;n++)if(e[n]!=="-"){if(r===t)return n;r++}}function Ed(e){let t={};for(let[r,n]of e)t[r]=n;return t}function zc({model:e,coord:t}){let{querySeqName:r,transcriptToMsaMap:n,mafRegion:o}=e,s=e.rows.find(c=>c[0]===r)?.[1];if(!s)return;let a=Kc(s,t);if(a!==void 0){if(o){let c=o.start+a;return c>=o.end?void 0:{refName:o.refName,start:c,end:c+1}}if(n){let{refName:c,p2g:l}=n,A=l[a],u=l[a+1];return A!==void 0&&u!==void 0?{refName:c,start:Math.min(A,u),end:Math.max(A,u)}:void 0}}}var pk="jbrowse-msaview-data";var vn="msa-data",$c,no;function hk(){if(no!==void 0)return no;try{return typeof indexedDB>"u"?(no=!1,!1):(no=!0,!0)}catch{return no=!1,!1}}async function Id(){if(hk())return $c||($c=new Promise(e=>{try{let t=indexedDB.open(pk,1);t.addEventListener("error",()=>{console.warn("IndexedDB unavailable - MSA data will not persist across page refreshes"),no=!1,e(void 0)}),t.onsuccess=()=>{e(t.result)},t.onupgradeneeded=r=>{let n=r.target.result;n.objectStoreNames.contains(vn)||n.createObjectStore(vn,{keyPath:"id"}).createIndex("timestamp","timestamp",{unique:!1})}}catch(t){console.warn("Failed to open IndexedDB:",t),no=!1,e(void 0)}}),$c)}function RS(){return`msa-${Date.now()}-${Math.random().toString(36).slice(2,11)}`}async function PS(e,t){let r=await Id();return r?new Promise(n=>{try{let i=r.transaction(vn,"readwrite").objectStore(vn),s={id:e,msa:t.msa,tree:t.tree,treeMetadata:t.treeMetadata,timestamp:Date.now()},a=i.put(s);a.addEventListener("error",()=>{console.warn("Failed to store MSA data:",a.error),n(!1)}),a.onsuccess=()=>{n(!0)}}catch(o){console.warn("Failed to store MSA data:",o),n(!1)}}):!1}async function GS(e){let t=await Id();if(t)return new Promise(r=>{try{let i=t.transaction(vn,"readonly").objectStore(vn).get(e);i.addEventListener("error",()=>{console.warn("Failed to retrieve MSA data:",i.error),r(void 0)}),i.onsuccess=()=>{let s=i.result;r(s?{msa:s.msa,tree:s.tree,treeMetadata:s.treeMetadata}:void 0)}}catch(n){console.warn("Failed to retrieve MSA data:",n),r(void 0)}})}async function OS(e=10080*60*1e3){let t=await Id();if(!t)return 0;let r=Date.now()-e;return new Promise(n=>{try{let s=t.transaction(vn,"readwrite").objectStore(vn).index("timestamp"),a=IDBKeyRange.upperBound(r),c=s.openCursor(a),l=0;c.addEventListener("error",()=>{console.warn("Failed to cleanup old MSA data:",c.error),n(l)}),c.onsuccess=A=>{let u=A.target.result;u?(u.delete(),l++,u.continue()):n(l)}}catch(o){console.warn("Failed to cleanup old MSA data:",o),n(0)}})}var Ck={A:{A:4,R:-1,N:-2,D:-2,C:0,Q:-1,E:-1,G:0,H:-2,I:-1,L:-1,K:-1,M:-1,F:-2,P:-1,S:1,T:0,W:-3,Y:-2,V:0,B:-2,Z:-1,X:0,"*":-4},R:{A:-1,R:5,N:0,D:-2,C:-3,Q:1,E:0,G:-2,H:0,I:-3,L:-2,K:2,M:-1,F:-3,P:-2,S:-1,T:-1,W:-3,Y:-2,V:-3,B:-1,Z:0,X:-1,"*":-4},N:{A:-2,R:0,N:6,D:1,C:-3,Q:0,E:0,G:0,H:1,I:-3,L:-3,K:0,M:-2,F:-3,P:-2,S:1,T:0,W:-4,Y:-2,V:-3,B:3,Z:0,X:-1,"*":-4},D:{A:-2,R:-2,N:1,D:6,C:-3,Q:0,E:2,G:-1,H:-1,I:-3,L:-4,K:-1,M:-3,F:-3,P:-1,S:0,T:-1,W:-4,Y:-3,V:-3,B:4,Z:1,X:-1,"*":-4},C:{A:0,R:-3,N:-3,D:-3,C:9,Q:-3,E:-4,G:-3,H:-3,I:-1,L:-1,K:-3,M:-1,F:-2,P:-3,S:-1,T:-1,W:-2,Y:-2,V:-1,B:-3,Z:-3,X:-2,"*":-4},Q:{A:-1,R:1,N:0,D:0,C:-3,Q:5,E:2,G:-2,H:0,I:-3,L:-2,K:1,M:0,F:-3,P:-1,S:0,T:-1,W:-2,Y:-1,V:-2,B:0,Z:3,X:-1,"*":-4},E:{A:-1,R:0,N:0,D:2,C:-4,Q:2,E:5,G:-2,H:0,I:-3,L:-3,K:1,M:-2,F:-3,P:-1,S:0,T:-1,W:-3,Y:-2,V:-2,B:1,Z:4,X:-1,"*":-4},G:{A:0,R:-2,N:0,D:-1,C:-3,Q:-2,E:-2,G:6,H:-2,I:-4,L:-4,K:-2,M:-3,F:-3,P:-2,S:0,T:-2,W:-2,Y:-3,V:-3,B:-1,Z:-2,X:-1,"*":-4},H:{A:-2,R:0,N:1,D:-1,C:-3,Q:0,E:0,G:-2,H:8,I:-3,L:-3,K:-1,M:-2,F:-1,P:-2,S:-1,T:-2,W:-2,Y:2,V:-3,B:0,Z:0,X:-1,"*":-4},I:{A:-1,R:-3,N:-3,D:-3,C:-1,Q:-3,E:-3,G:-4,H:-3,I:4,L:2,K:-3,M:1,F:0,P:-3,S:-2,T:-1,W:-3,Y:-1,V:3,B:-3,Z:-3,X:-1,"*":-4},L:{A:-1,R:-2,N:-3,D:-4,C:-1,Q:-2,E:-3,G:-4,H:-3,I:2,L:4,K:-2,M:2,F:0,P:-3,S:-2,T:-1,W:-2,Y:-1,V:1,B:-4,Z:-3,X:-1,"*":-4},K:{A:-1,R:2,N:0,D:-1,C:-3,Q:1,E:1,G:-2,H:-1,I:-3,L:-2,K:5,M:-1,F:-3,P:-1,S:0,T:-1,W:-3,Y:-2,V:-2,B:0,Z:1,X:-1,"*":-4},M:{A:-1,R:-1,N:-2,D:-3,C:-1,Q:0,E:-2,G:-3,H:-2,I:1,L:2,K:-1,M:5,F:0,P:-2,S:-1,T:-1,W:-1,Y:-1,V:1,B:-3,Z:-1,X:-1,"*":-4},F:{A:-2,R:-3,N:-3,D:-3,C:-2,Q:-3,E:-3,G:-3,H:-1,I:0,L:0,K:-3,M:0,F:6,P:-4,S:-2,T:-2,W:1,Y:3,V:-1,B:-3,Z:-3,X:-1,"*":-4},P:{A:-1,R:-2,N:-2,D:-1,C:-3,Q:-1,E:-1,G:-2,H:-2,I:-3,L:-3,K:-1,M:-2,F:-4,P:7,S:-1,T:-1,W:-4,Y:-3,V:-2,B:-2,Z:-1,X:-2,"*":-4},S:{A:1,R:-1,N:1,D:0,C:-1,Q:0,E:0,G:0,H:-1,I:-2,L:-2,K:0,M:-1,F:-2,P:-1,S:4,T:1,W:-3,Y:-2,V:-2,B:0,Z:0,X:0,"*":-4},T:{A:0,R:-1,N:0,D:-1,C:-1,Q:-1,E:-1,G:-2,H:-2,I:-1,L:-1,K:-1,M:-1,F:-2,P:-1,S:1,T:5,W:-2,Y:-2,V:0,B:-1,Z:-1,X:0,"*":-4},W:{A:-3,R:-3,N:-4,D:-4,C:-2,Q:-2,E:-3,G:-2,H:-2,I:-3,L:-2,K:-3,M:-1,F:1,P:-4,S:-3,T:-2,W:11,Y:2,V:-3,B:-4,Z:-3,X:-2,"*":-4},Y:{A:-2,R:-2,N:-2,D:-3,C:-2,Q:-1,E:-2,G:-3,H:2,I:-1,L:-1,K:-2,M:-1,F:3,P:-3,S:-2,T:-2,W:2,Y:7,V:-1,B:-3,Z:-2,X:-1,"*":-4},V:{A:0,R:-3,N:-3,D:-3,C:-1,Q:-2,E:-2,G:-3,H:-3,I:3,L:1,K:-2,M:1,F:-1,P:-2,S:-2,T:0,W:-3,Y:-1,V:4,B:-3,Z:-2,X:-1,"*":-4},B:{A:-2,R:-1,N:3,D:4,C:-3,Q:0,E:1,G:-1,H:0,I:-3,L:-4,K:0,M:-3,F:-3,P:-2,S:0,T:-1,W:-4,Y:-3,V:-3,B:4,Z:1,X:-1,"*":-4},Z:{A:-1,R:0,N:0,D:1,C:-3,Q:3,E:4,G:-2,H:0,I:-3,L:-3,K:1,M:-1,F:-3,P:-1,S:0,T:-1,W:-3,Y:-2,V:-2,B:1,Z:4,X:-1,"*":-4},X:{A:0,R:-1,N:-1,D:-1,C:-2,Q:-1,E:-1,G:-1,H:-1,I:-1,L:-1,K:-1,M:-1,F:-1,P:-2,S:0,T:0,W:-2,Y:-1,V:-1,B:-1,Z:-1,X:-1,"*":-4},"*":{A:-4,R:-4,N:-4,D:-4,C:-4,Q:-4,E:-4,G:-4,H:-4,I:-4,L:-4,K:-4,M:-4,F:-4,P:-4,S:-4,T:-4,W:-4,Y:-4,V:-4,B:-4,Z:-4,X:-4,"*":1}};function HS(e,t){let r=e.toUpperCase(),n=t.toUpperCase();return Ck[r]?.[n]??-4}var Ek=-10,Ik=-.5;function xk(e,t,r=Ek,n=Ik){let o=e.length,i=t.length,s=[],a=[],c=[];for(let C=0;C<=o;C++){s[C]=[],a[C]=[],c[C]=[];for(let E=0;E<=i;E++)s[C][E]=-1/0,a[C][E]=-1/0,c[C][E]=-1/0}s[0][0]=0;for(let C=1;C<=o;C++)a[C][0]=r+(C-1)*n;for(let C=1;C<=i;C++)c[0][C]=r+(C-1)*n;for(let C=1;C<=o;C++)for(let E=1;E<=i;E++){let x=HS(e[C-1],t[E-1]);s[C][E]=Math.max(s[C-1][E-1],a[C-1][E-1],c[C-1][E-1])+x,a[C][E]=Math.max(s[C-1][E]+r,a[C-1][E]+n),c[C][E]=Math.max(s[C][E-1]+r,c[C][E-1]+n)}let l="",A="",u=o,f=i,m=[s[o][i],a[o][i],c[o][i]],p=Math.max(...m),h=p===s[o][i]?"M":p===a[o][i]?"Ix":"Iy";for(;u>0||f>0;)if(h==="M"&&u>0&&f>0){l=e[u-1]+l,A=t[f-1]+A;let C=HS(e[u-1],t[f-1]),E=s[u-1][f-1],x=a[u-1][f-1];s[u][f]===E+C?h="M":s[u][f]===x+C?h="Ix":h="Iy",u--,f--}else if(h==="Ix"&&u>0)l=e[u-1]+l,A="-"+A,h=a[u][f]===s[u-1][f]+r?"M":"Ix",u--;else if(f>0)l="-"+l,A=t[f-1]+A,h=c[u][f]===s[u][f-1]+r?"M":"Iy",f--;else break;return{alignedSeq1:l,alignedSeq2:A,score:p}}function yk(e,t){let r="";for(let n=0;n<e.length;n++){let o=e[n],i=t[n];o==="-"||i==="-"?r+=" ":o.toUpperCase()===i.toUpperCase()?r+="|":r+=" "}return r}function JS(e,t){let{alignedSeq1:r,alignedSeq2:n}=xk(e,t);return{consensus:yk(r,n),alns:[{id:"msa",seq:r},{id:"structure",seq:n}]}}function US(e){let t=e.alns[0].seq,r=e.alns[1].seq;if(t.length!==r.length)throw new Error("Aligned sequences must have same length");let n=0,o=0,i=new Map,s=new Map;for(let a=0;a<t.length;a++){let c=t[a],l=r[a];c!=="-"&&l!=="-"?(i.set(n,o),s.set(o,n),n++,o++):c==="-"?o++:n++}return{seq1ToSeq2:i,seq2ToSeq1:s}}var bk=(0,KS.lazy)(()=>Promise.resolve().then(()=>(WS(),VS)));function Sk(e){let{mouseCol:t,connectedProteinViews:r}=e;if(r.length!==0)for(let n of r){let o=n.proteinView?.structures?.[n.structureIdx];if(!o)continue;if(t===void 0){o.clearHighlightFromExternal?.();continue}let i=e.getSequenceByRowName(n.msaRowName);if(!i)continue;let s=Kc(i,t);if(s===void 0){o.clearHighlightFromExternal?.();continue}let a=n.msaToStructure[s];a===void 0?o.clearHighlightFromExternal?.():o.highlightFromExternal?.(a)}}function xd(){return ee.types.compose(zS.BaseViewModel,hd(),ee.types.model("MsaView",{connectedViewId:ee.types.maybe(ee.types.string),connectedFeature:ee.types.frozen(),connectedHighlights:ee.types.array(ee.types.model({refName:ee.types.string,start:ee.types.number,end:ee.types.number})),blastParams:ee.types.frozen(),querySeqName:"QUERY",uniprotId:ee.types.maybe(ee.types.string),zoomToBaseLevel:!1,init:ee.types.frozen(),connectedStructures:ee.types.array(ee.types.frozen()),dataStoreId:ee.types.maybe(ee.types.string),mafRegion:ee.types.frozen()})).volatile(()=>({rid:void 0,progress:"",error:void 0,loadingStoredData:!1})).views(e=>({getRowByName(t){return e.rows.find(r=>r[0]===t)},getSequenceByRowName(t){return e.rows.find(r=>r[0]===t)?.[1]}})).views(e=>({get transcriptToMsaMap(){return e.connectedFeature?hh(e.connectedFeature):void 0},get processing(){return!!e.progress},get connectedView(){let{views:t}=(0,Tn.getSession)(e);return t.find(r=>r.id===e.connectedViewId)},get connectedProteinViews(){let{views:t}=(0,Tn.getSession)(e);return e.connectedStructures.map(r=>{let n=t.find(o=>o.id===r.proteinViewId);return n?{...r,proteinView:n}:void 0}).filter(r=>!!r)}})).views(e=>({get structureHoverCol(){for(let t of e.connectedProteinViews){let n=t.proteinView?.structures?.[t.structureIdx]?.hoverPosition?.structureSeqPos;if(n!==void 0){let o=t.structureToMsa[n];if(o!==void 0){let i=e.getSequenceByRowName(t.msaRowName);if(i){let s=FS(i,o);if(s!==void 0)return e.globalColToVisibleCol(s)}}}}}})).views(e=>({get mouseCol2(){let t=e.structureHoverCol;return t!==void 0?t:LS({model:e})},get clickCol2(){}})).actions(e=>({setZoomToBaseLevel(t){e.zoomToBaseLevel=t},setError(t){e.error=t},setProgress(t){e.progress=t},setRid(t){e.rid=t},setConnectedHighlights(t){e.connectedHighlights=(0,ee.cast)(t)},addToConnectedHighlights(t){e.connectedHighlights.push(t)},clearConnectedHighlights(){e.connectedHighlights=(0,ee.cast)([])},setBlastParams(t){e.blastParams=t},setInit(t){e.init=t},setQuerySeqName(t){e.querySeqName=t},setUniprotId(t){e.uniprotId=t},setDataStoreId(t){e.dataStoreId=t},setMafRegion(t){e.mafRegion=t},setLoadingStoredData(t){e.loadingStoredData=t},handleMsaClick(t){let{connectedView:r,zoomToBaseLevel:n}=e,{assemblyManager:o}=(0,Tn.getSession)(e),i=zc({model:e,coord:t});if(!(!i||!r))if(n)r.navTo(i);else{let s=o.get(r.assemblyNames[0])?.getCanonicalRefName(i.refName)??i.refName;r.centerAt(i.start,s)}},connectToStructure(t,r,n){let o=n??e.querySeqName,i=e.getSequenceByRowName(o);if(!i)throw new Error(`MSA row "${o}" not found`);let s=i.replaceAll("-",""),{views:a}=(0,Tn.getSession)(e),c=a.find(h=>h.id===t);if(!c)throw new Error(`ProteinView "${t}" not found`);let l=c.structures?.[r];if(!l)throw new Error(`Structure at index ${r} not found`);let A=l.structureSequences?.[0];if(!A)throw new Error("Structure sequence not available");let u=JS(s,A),{seq1ToSeq2:f,seq2ToSeq1:m}=US(u),p={proteinViewId:t,structureIdx:r,msaRowName:o,msaToStructure:Ed(f),structureToMsa:Ed(m)};e.connectedStructures.push(p)},disconnectFromStructure(t,r){let n=e.connectedStructures.findIndex(o=>o.proteinViewId===t&&o.structureIdx===r);n!==-1&&e.connectedStructures.splice(n,1)},disconnectAllStructures(){e.connectedStructures.clear()}})).actions(e=>{let t=e.setMouseClickPos.bind(e);return{setMouseClickPos(r,n){t(r,n),r!==void 0&&e.handleMsaClick(r)}}}).views(e=>({extraViewMenuItems(){return[{label:"Zoom to base level on click?",checked:e.zoomToBaseLevel,type:"checkbox",onClick:()=>{e.setZoomToBaseLevel(!e.zoomToBaseLevel)}},{label:"Connect to protein structure...",onClick:()=>{(0,Tn.getSession)(e).queueDialog(t=>[bk,{model:e,handleClose:t}])}},...e.connectedStructures.length>0?[{label:"Disconnect from protein structures",onClick:()=>{e.disconnectAllStructures()}}]:[]]}})).actions(e=>({afterCreate(){OS().catch(t=>{console.error("Failed to cleanup old MSA data:",t)}),(0,ee.addDisposer)(e,(0,nn.autorun)(async()=>{let{dataStoreId:t,rows:r}=e;if(t&&r.length===0)try{e.setLoadingStoredData(!0);let n=await GS(t);n&&(n.msa&&e.setMSA(n.msa),n.tree&&e.setTree(n.tree))}catch(n){console.error("Failed to load MSA data from IndexedDB:",n)}finally{e.setLoadingStoredData(!1)}})),(0,ee.addDisposer)(e,(0,nn.autorun)(async()=>{let{rows:t,dataStoreId:r}=e;if(t.length>0&&!r){if(!!(e.msaFilehandle??e.treeFilehandle))return;let o=e.data.msa,i=e.data.tree;if(o||i)try{let s=RS();await PS(s,{msa:o,tree:i,treeMetadata:e.data.treeMetadata})&&e.setDataStoreId(s)}catch(s){console.error("Failed to store MSA data to IndexedDB:",s)}}})),(0,ee.addDisposer)(e,(0,nn.autorun)(async()=>{if(e.blastParams)try{e.setProgress("Submitting query"),e.setError(void 0);let t=await _S({self:e});e.setData(t),e.setBlastParams(void 0)}catch(t){e.setError(t),console.error(t)}finally{e.setProgress("")}})),(0,ee.addDisposer)(e,(0,nn.autorun)(async()=>{let{init:t}=e;if(t)try{e.setError(void 0);let{msaData:r,msaUrl:n,treeData:o,treeUrl:i,querySeqName:s}=t;if(n){let a=kS(n);a&&(e.setUniprotId(a),e.setQuerySeqName("query"))}if(s&&e.setQuerySeqName(s),r)e.setMSA(r);else if(n){let a=await fetch(n);if(!a.ok)throw new Error(`Failed to fetch MSA: ${a.status}`);let c=await a.text();e.setMSA(c)}if(o)e.setTree(o);else if(i){let a=await fetch(i);if(!a.ok)throw new Error(`Failed to fetch tree: ${a.status}`);let c=await a.text();e.setTree(c)}e.setInit(void 0)}catch(r){e.setError(r),console.error(r)}})),(0,ee.addDisposer)(e,(0,nn.autorun)(()=>{let{mouseCol:t,mouseClickCol:r}=e,n=t===void 0?void 0:zc({model:e,coord:t}),o=r===void 0?void 0:zc({model:e,coord:r});e.setConnectedHighlights([n,o].filter(i=>!!i))})),(0,ee.addDisposer)(e,(0,nn.autorun)(()=>{Sk(e)})),(0,ee.addDisposer)(e,(0,nn.autorun)(()=>{let{views:t}=(0,Tn.getSession)(e),{connectedViewId:r,uniprotId:n,rows:o,connectedStructures:i}=e;if(!(!n||o.length===0))for(let s of t){let a=s;if(!(a.type!=="ProteinView"||!a.structures))for(let c=0;c<a.structures.length;c++){let l=a.structures[c];if(!(l.connectedViewId!==r||l.uniprotId!==n||i.some(u=>u.proteinViewId===a.id&&u.structureIdx===c))&&l.structureSequences?.[0])try{e.connectToStructure(a.id,c)}catch(u){console.error("Failed to auto-connect to ProteinView:",u)}}}})),(0,ee.addDisposer)(e,(0,nn.autorun)(()=>{let{views:t}=(0,Tn.getSession)(e),{connectedViewId:r,transcriptToMsaMap:n,querySeqName:o}=e;if(!r||!n)return;let i=[];for(let a of t){let c=a;if(!(c.type!=="ProteinView"||!c.structures))for(let l of c.structures){if(l.connectedViewId!==r)continue;let A=l.hoverGenomeHighlights;if(!A||A.length===0)continue;let{g2p:u}=n;for(let f of A)for(let m=f.start;m<f.end;m++){let p=u[m];if(p!==void 0){let h=e.seqPosToGlobalCol(o,p);i.includes(h)||i.push(h)}}}}let s=i.map(a=>e.globalColToVisibleCol(a)).filter(a=>a!==void 0);e.setHighlightedColumns(s.length>0?s:void 0)}))}}))}var kk=(0,cQ.lazy)(()=>Promise.resolve().then(()=>(aQ(),sQ)));function bd(e){e.addViewType(()=>new lQ.default({name:"MsaView",stateModel:xd(),ReactComponent:kk}))}var Zc=class extends AQ.default{constructor(){super(...arguments);this.name="MsaViewPlugin";this.version=$d}install(r){bd(r),_A(r),DA(r),ll(r),Ml(r)}configure(r){(0,uQ.isAbstractMenuManager)(r.rootModel)&&r.rootModel.appendToSubMenu(["Add"],{label:"Multiple sequence alignment view",icon:zd,onClick:n=>{n.addView("MsaView",{})}})}rootConfigurationSchema(r){return{msa:(0,Sd.ConfigurationSchema)("MSA",{datasets:Qd.types.maybe(Qd.types.array((0,Sd.ConfigurationSchema)("MSAEntry",{datasetId:{type:"string",defaultValue:""},description:{type:"string",defaultValue:""},name:{type:"string",defaultValue:""},adapter:r.pluggableConfigSchemaType("adapter")})))})}}};return BQ(Nk);})();
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  use-sync-external-store/cjs/use-sync-external-store-shim.production.js: