jbrowse-plugin-msaview 2.3.2 → 2.3.5
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- package/dist/BgzipFastaMsaAdapter/BgzipFastaMsaAdapter.js +2 -11
- package/dist/BgzipFastaMsaAdapter/BgzipFastaMsaAdapter.js.map +1 -1
- package/dist/LaunchMsaView/components/NCBIBlastQuery/CachedBlastResults.js +24 -47
- package/dist/LaunchMsaView/components/NCBIBlastQuery/CachedBlastResults.js.map +1 -1
- package/dist/LaunchMsaView/components/NCBIBlastQuery/NCBIBlastAutomaticPanel.js +5 -20
- package/dist/LaunchMsaView/components/NCBIBlastQuery/NCBIBlastAutomaticPanel.js.map +1 -1
- package/dist/LaunchMsaView/components/NCBIBlastQuery/useCachedBlastResults.d.ts +7 -0
- package/dist/LaunchMsaView/components/NCBIBlastQuery/useCachedBlastResults.js +29 -0
- package/dist/LaunchMsaView/components/NCBIBlastQuery/useCachedBlastResults.js.map +1 -0
- package/dist/LaunchMsaView/components/useTranscriptSelection.js +15 -14
- package/dist/LaunchMsaView/components/useTranscriptSelection.js.map +1 -1
- package/dist/MsaViewPanel/afterCreateAutoruns.js +14 -9
- package/dist/MsaViewPanel/afterCreateAutoruns.js.map +1 -1
- package/dist/MsaViewPanel/components/ErrorBoundary.d.ts +19 -0
- package/dist/MsaViewPanel/components/ErrorBoundary.js +22 -0
- package/dist/MsaViewPanel/components/ErrorBoundary.js.map +1 -0
- package/dist/MsaViewPanel/components/MsaViewPanel.js +4 -2
- package/dist/MsaViewPanel/components/MsaViewPanel.js.map +1 -1
- package/dist/MsaViewPanel/model.d.ts +0 -12
- package/dist/MsaViewPanel/model.js +1 -1
- package/dist/MsaViewPanel/model.js.map +1 -1
- package/dist/MsaViewPanel/pairwiseAlignment.js +9 -4
- package/dist/MsaViewPanel/pairwiseAlignment.js.map +1 -1
- package/dist/jbrowse-plugin-msaview.umd.production.min.js +26 -26
- package/dist/jbrowse-plugin-msaview.umd.production.min.js.map +4 -4
- package/dist/utils/blastCache.js +2 -3
- package/dist/utils/blastCache.js.map +1 -1
- package/dist/version.d.ts +1 -1
- package/dist/version.js +1 -1
- package/dist/version.js.map +1 -1
- package/package.json +35 -34
- package/src/BgzipFastaMsaAdapter/BgzipFastaMsaAdapter.ts +2 -11
- package/src/LaunchMsaView/components/NCBIBlastQuery/CachedBlastResults.tsx +23 -49
- package/src/LaunchMsaView/components/NCBIBlastQuery/NCBIBlastAutomaticPanel.tsx +6 -20
- package/src/LaunchMsaView/components/NCBIBlastQuery/useCachedBlastResults.ts +49 -0
- package/src/LaunchMsaView/components/useTranscriptSelection.ts +25 -17
- package/src/MsaViewPanel/afterCreateAutoruns.ts +26 -9
- package/src/MsaViewPanel/components/ErrorBoundary.tsx +40 -0
- package/src/MsaViewPanel/components/MsaViewPanel.tsx +14 -11
- package/src/MsaViewPanel/model.ts +32 -21
- package/src/MsaViewPanel/pairwiseAlignment.ts +9 -4
- package/src/utils/blastCache.ts +2 -3
- package/src/version.ts +1 -1
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"use strict";var JBrowsePluginMsaView=(()=>{var
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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,d=0,m=s.length;d<m;d++){var g=s[d],h=g.source===null?null:A.at(g.source);h!==null&&(h=D.computeSourceURL(a,h,u)),c({source:h,generatedLine:g.generatedLine,generatedColumn:g.generatedColumn,originalLine:g.originalLine,originalColumn:g.originalColumn,name:g.name===null?null:l.at(g.name)})}};he.prototype.allGeneratedPositionsFor=function(t){var r=D.getArg(t,"line"),n={source:D.getArg(t,"source"),originalLine:r,originalColumn:D.getArg(t,"column",0)};if(n.source=this._findSourceIndex(n.source),n.source<0)return[];var o=[],i=this._findMapping(n,this._originalMappings,"originalLine","originalColumn",D.compareByOriginalPositions,Lu.LEAST_UPPER_BOUND);if(i>=0){var s=this._originalMappings[i];if(t.column===void 0)for(var a=s.originalLine;s&&s.originalLine===a;)o.push({line:D.getArg(s,"generatedLine",null),column:D.getArg(s,"generatedColumn",null),lastColumn:D.getArg(s,"lastGeneratedColumn",null)}),s=this._originalMappings[++i];else for(var c=s.originalColumn;s&&s.originalLine===r&&s.originalColumn==c;)o.push({line:D.getArg(s,"generatedLine",null),column:D.getArg(s,"generatedColumn",null),lastColumn:D.getArg(s,"lastGeneratedColumn",null)}),s=this._originalMappings[++i]}return o};ic.SourceMapConsumer=he;function ot(e,t){var r=e;typeof e=="string"&&(r=D.parseSourceMapInput(e));var n=D.getArg(r,"version"),o=D.getArg(r,"sources"),i=D.getArg(r,"names",[]),s=D.getArg(r,"sourceRoot",null),a=D.getArg(r,"sourcesContent",null),c=D.getArg(r,"mappings"),l=D.getArg(r,"file",null);if(n!=this._version)throw new Error("Unsupported version: "+n);s&&(s=D.normalize(s)),o=o.map(String).map(D.normalize).map(function(A){return s&&D.isAbsolute(s)&&D.isAbsolute(A)?D.relative(s,A):A}),this._names=ei.fromArray(i.map(String),!0),this._sources=ei.fromArray(o,!0),this._absoluteSources=this._sources.toArray().map(function(A){return D.computeSourceURL(s,A,t)}),this.sourceRoot=s,this.sourcesContent=a,this._mappings=c,this._sourceMapURL=t,this.file=l}ot.prototype=Object.create(he.prototype);ot.prototype.consumer=he;ot.prototype._findSourceIndex=function(e){var t=e;if(this.sourceRoot!=null&&(t=D.relative(this.sourceRoot,t)),this._sources.has(t))return this._sources.indexOf(t);var r;for(r=0;r<this._absoluteSources.length;++r)if(this._absoluteSources[r]==e)return r;return-1};ot.fromSourceMap=function(t,r){var n=Object.create(ot.prototype),o=n._names=ei.fromArray(t._names.toArray(),!0),i=n._sources=ei.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 D.computeSourceURL(n.sourceRoot,m,r)});for(var s=t._mappings.toArray().slice(),a=n.__generatedMappings=[],c=n.__originalMappings=[],l=0,A=s.length;l<A;l++){var u=s[l],d=new rE;d.generatedLine=u.generatedLine,d.generatedColumn=u.generatedColumn,u.source&&(d.source=i.indexOf(u.source),d.originalLine=u.originalLine,d.originalColumn=u.originalColumn,u.name&&(d.name=o.indexOf(u.name)),c.push(d)),a.push(d)}return ji(n.__originalMappings,D.compareByOriginalPositions),n};ot.prototype._version=3;Object.defineProperty(ot.prototype,"sources",{get:function(){return this._absoluteSources.slice()}});function rE(){this.generatedLine=0,this.generatedColumn=0,this.source=null,this.originalLine=null,this.originalColumn=null,this.name=null}var Nu=D.compareByGeneratedPositionsDeflatedNoLine;function tE(e,t){let r=e.length,n=e.length-t;if(!(n<=1))if(n==2){let o=e[t],i=e[t+1];Nu(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(Nu(s,a)<=0)break;e[i-1]=a,e[i]=s}else ji(e,Nu,t)}ot.prototype._parseMappings=function(t,r){var n=1,o=0,i=0,s=0,a=0,c=0,l=t.length,A=0,u={},d={},m=[],g=[],h,I,C,x,y;let b=0;for(;A<l;)if(t.charAt(A)===";")n++,A++,o=0,tE(g,b),b=g.length;else if(t.charAt(A)===",")A++;else{for(h=new rE,h.generatedLine=n,x=A;x<l&&!this._charIsMappingSeparator(t,x);x++);for(I=t.slice(A,x),C=[];A<x;)ev.decode(t,A,d),y=d.value,A=d.rest,C.push(y);if(C.length===2)throw new Error("Found a source, but no line and column");if(C.length===3)throw new Error("Found a source and line, but no column");if(h.generatedColumn=o+C[0],o=h.generatedColumn,C.length>1&&(h.source=a+C[1],a+=C[1],h.originalLine=i+C[2],i=h.originalLine,h.originalLine+=1,h.originalColumn=s+C[3],s=h.originalColumn,C.length>4&&(h.name=c+C[4],c+=C[4])),g.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)}}tE(g,b),this.__generatedMappings=g;for(var S=0;S<m.length;S++)m[S]!=null&&ji(m[S],D.compareByOriginalPositionsNoSource);this.__originalMappings=[].concat(...m)};ot.prototype._findMapping=function(t,r,n,o,i,s){if(t[n]<=0)throw new TypeError("Line must be greater than or equal to 1, got "+t[n]);if(t[o]<0)throw new TypeError("Column must be greater than or equal to 0, got "+t[o]);return Lu.search(t,r,i,s)};ot.prototype.computeColumnSpans=function(){for(var t=0;t<this._generatedMappings.length;++t){var r=this._generatedMappings[t];if(t+1<this._generatedMappings.length){var n=this._generatedMappings[t+1];if(r.generatedLine===n.generatedLine){r.lastGeneratedColumn=n.generatedColumn-1;continue}}r.lastGeneratedColumn=1/0}};ot.prototype.originalPositionFor=function(t){var r={generatedLine:D.getArg(t,"line"),generatedColumn:D.getArg(t,"column")},n=this._findMapping(r,this._generatedMappings,"generatedLine","generatedColumn",D.compareByGeneratedPositionsDeflated,D.getArg(t,"bias",he.GREATEST_LOWER_BOUND));if(n>=0){var o=this._generatedMappings[n];if(o.generatedLine===r.generatedLine){var i=D.getArg(o,"source",null);i!==null&&(i=this._sources.at(i),i=D.computeSourceURL(this.sourceRoot,i,this._sourceMapURL));var s=D.getArg(o,"name",null);return s!==null&&(s=this._names.at(s)),{source:i,line:D.getArg(o,"originalLine",null),column:D.getArg(o,"originalColumn",null),name:s}}}return{source:null,line:null,column:null,name:null}};ot.prototype.hasContentsOfAllSources=function(){return this.sourcesContent?this.sourcesContent.length>=this._sources.size()&&!this.sourcesContent.some(function(t){return t==null}):!1};ot.prototype.sourceContentFor=function(t,r){if(!this.sourcesContent)return null;var n=this._findSourceIndex(t);if(n>=0)return this.sourcesContent[n];var o=t;this.sourceRoot!=null&&(o=D.relative(this.sourceRoot,o));var i;if(this.sourceRoot!=null&&(i=D.urlParse(this.sourceRoot))){var s=o.replace(/^file:\/\//,"");if(i.scheme=="file"&&this._sources.has(s))return this.sourcesContent[this._sources.indexOf(s)];if((!i.path||i.path=="/")&&this._sources.has("/"+o))return this.sourcesContent[this._sources.indexOf("/"+o)]}if(r)return null;throw new Error('"'+o+'" is not in the SourceMap.')};ot.prototype.generatedPositionFor=function(t){var r=D.getArg(t,"source");if(r=this._findSourceIndex(r),r<0)return{line:null,column:null,lastColumn:null};var n={source:r,originalLine:D.getArg(t,"line"),originalColumn:D.getArg(t,"column")},o=this._findMapping(n,this._originalMappings,"originalLine","originalColumn",D.compareByOriginalPositions,D.getArg(t,"bias",he.GREATEST_LOWER_BOUND));if(o>=0){var i=this._originalMappings[o];if(i.source===n.source)return{line:D.getArg(i,"generatedLine",null),column:D.getArg(i,"generatedColumn",null),lastColumn:D.getArg(i,"lastGeneratedColumn",null)}}return{line:null,column:null,lastColumn:null}};ic.BasicSourceMapConsumer=ot;function hr(e,t){var r=e;typeof e=="string"&&(r=D.parseSourceMapInput(e));var n=D.getArg(r,"version"),o=D.getArg(r,"sections");if(n!=this._version)throw new Error("Unsupported version: "+n);this._sources=new ei,this._names=new ei;var i={line:-1,column:0};this._sections=o.map(function(s){if(s.url)throw new Error("Support for url field in sections not implemented.");var a=D.getArg(s,"offset"),c=D.getArg(a,"line"),l=D.getArg(a,"column");if(c<i.line||c===i.line&&l<i.column)throw new Error("Section offsets must be ordered and non-overlapping.");return i=a,{generatedOffset:{generatedLine:c+1,generatedColumn:l+1},consumer:new he(D.getArg(s,"map"),t)}})}hr.prototype=Object.create(he.prototype);hr.prototype.constructor=he;hr.prototype._version=3;Object.defineProperty(hr.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}});hr.prototype.originalPositionFor=function(t){var r={generatedLine:D.getArg(t,"line"),generatedColumn:D.getArg(t,"column")},n=Lu.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}};hr.prototype.hasContentsOfAllSources=function(){return this._sections.every(function(t){return t.consumer.hasContentsOfAllSources()})};hr.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.')};hr.prototype.generatedPositionFor=function(t){for(var r=0;r<this._sections.length;r++){var n=this._sections[r];if(n.consumer._findSourceIndex(D.getArg(t,"source"))!==-1){var o=n.consumer.generatedPositionFor(t);if(o){var i={line:o.line+(n.generatedOffset.generatedLine-1),column:o.column+(n.generatedOffset.generatedLine===o.line?n.generatedOffset.generatedColumn-1:0)};return i}}}return{line:null,column:null}};hr.prototype._parseMappings=function(t,r){this.__generatedMappings=[],this.__originalMappings=[];for(var n=0;n<this._sections.length;n++)for(var o=this._sections[n],i=o.consumer._generatedMappings,s=0;s<i.length;s++){var a=i[s],c=o.consumer._sources.at(a.source);c!==null&&(c=D.computeSourceURL(o.consumer.sourceRoot,c,this._sourceMapURL)),this._sources.add(c),c=this._sources.indexOf(c);var l=null;a.name&&(l=o.consumer._names.at(a.name),this._names.add(l),l=this._names.indexOf(l));var A={source:c,generatedLine:a.generatedLine+(o.generatedOffset.generatedLine-1),generatedColumn:a.generatedColumn+(o.generatedOffset.generatedLine===a.generatedLine?o.generatedOffset.generatedColumn-1:0),originalLine:a.originalLine,originalColumn:a.originalColumn,name:l};this.__generatedMappings.push(A),typeof A.originalLine=="number"&&this.__originalMappings.push(A)}ji(this.__generatedMappings,D.compareByGeneratedPositionsDeflated),ji(this.__originalMappings,D.compareByOriginalPositions)};ic.IndexedSourceMapConsumer=hr});var iE=H(oE=>{var tv=Du().SourceMapGenerator,sc=Zo(),rv=/(\r?\n)/,nv=10,ti="$$$isSourceNode$$$";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[ti]=!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 d=g(),m=g()||"";return d+m;function g(){return s<i.length?i[s++]:void 0}},c=1,l=0,A=null;return r.eachMapping(function(d){if(A!==null)if(c<d.generatedLine)u(A,a()),c++,l=0;else{var m=i[s]||"",g=m.substr(0,d.generatedColumn-l);i[s]=m.substr(d.generatedColumn-l),l=d.generatedColumn,u(A,g),A=d;return}for(;c<d.generatedLine;)o.add(a()),c++;if(l<d.generatedColumn){var m=i[s]||"";o.add(m.substr(0,d.generatedColumn)),i[s]=m.substr(d.generatedColumn),l=d.generatedColumn}A=d},this),s<i.length&&(A&&u(A,a()),o.add(i.splice(s).join(""))),r.sources.forEach(function(d){var m=r.sourceContentFor(d);m!=null&&(n!=null&&(d=sc.join(n,d)),o.setSourceContent(d,m))}),o;function u(d,m){if(d===null||d.source===void 0)o.add(m);else{var g=n?sc.join(n,d.source):d.source;o.add(new Rt(d.originalLine,d.originalColumn,g,m,d.name))}}};Rt.prototype.add=function(t){if(Array.isArray(t))t.forEach(function(r){this.add(r)},this);else if(t[ti]||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[ti]||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[ti]?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[ti]?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[sc.toSetString(t)]=r};Rt.prototype.walkSourceContents=function(t){for(var r=0,n=this.children.length;r<n;r++)this.children[r][ti]&&this.children[r].walkSourceContents(t);for(var o=Object.keys(this.sourceContents),r=0,n=o.length;r<n;r++)t(sc.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 tv(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,d=l.length;u<d;u++)l.charCodeAt(u)===nv?(r.line++,r.column=0,u+1===d?(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}};oE.SourceNode=Rt});var sE=H(ac=>{ac.SourceMapGenerator=Du().SourceMapGenerator;ac.SourceMapConsumer=nE().SourceMapConsumer;ac.SourceNode=iE().SourceNode});function lc(e){let{children:t,...r}=e;return(0,cc.jsxs)(aE.Link,{...r,target:"_blank",rel:"noopener noreferrer",children:[t," ",(0,cc.jsx)(pa,{fontSize:"small"})]})}var cc,aE,cE=p(()=>{cc=f(L(),1);CA();aE=f(k(),1)});function Fu({text:e,extra:t}){let{classes:r}=ov(),n=t?`supporting data: ${JSON.stringify(t,null,2)}`:"",o=[e,n].filter(Boolean).join(`
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Pu.call(this._set,r)};on.prototype.indexOf=function(t){if(Wn){var r=this._set.get(t);if(r>=0)return r}else{var n=Ru.toSetString(t);if(Pu.call(this._set,n))return this._set[n]}throw new Error('"'+t+'" is not in the set.')};on.prototype.at=function(t){if(t>=0&&t<this._array.length)return this._array[t];throw new Error("No element indexed by "+t)};on.prototype.toArray=function(){return this._array.slice()};eE.ArraySet=on});var nE=U(rE=>{var tE=ei();function dv(e,t){var r=e.generatedLine,n=t.generatedLine,o=e.generatedColumn,i=t.generatedColumn;return n>r||n==r&&i>=o||tE.compareByGeneratedPositionsInflated(e,t)<=0}function ac(){this._array=[],this._sorted=!0,this._last={generatedLine:-1,generatedColumn:0}}ac.prototype.unsortedForEach=function(t,r){this._array.forEach(t,r)};ac.prototype.add=function(t){dv(this._last,t)?(this._last=t,this._array.push(t)):(this._sorted=!1,this._array.push(t))};ac.prototype.toArray=function(){return this._sorted||(this._array.sort(tE.compareByGeneratedPositionsInflated),this._sorted=!0),this._array};rE.MappingList=ac});var Gu=U(oE=>{var Wi=Lu(),ke=ei(),cc=Ou().ArraySet,mv=nE().MappingList;function sr(e){e||(e={}),this._file=ke.getArg(e,"file",null),this._sourceRoot=ke.getArg(e,"sourceRoot",null),this._skipValidation=ke.getArg(e,"skipValidation",!1),this._ignoreInvalidMapping=ke.getArg(e,"ignoreInvalidMapping",!1),this._sources=new cc,this._names=new cc,this._mappings=new mv,this._sourcesContents=null}sr.prototype._version=3;sr.fromSourceMap=function(t,r){var n=t.sourceRoot,o=new sr(Object.assign(r||{},{file:t.file,sourceRoot:n}));return t.eachMapping(function(i){var s={generated:{line:i.generatedLine,column:i.generatedColumn}};i.source!=null&&(s.source=i.source,n!=null&&(s.source=ke.relative(n,s.source)),s.original={line:i.originalLine,column:i.originalColumn},i.name!=null&&(s.name=i.name)),o.addMapping(s)}),t.sources.forEach(function(i){var s=i;n!==null&&(s=ke.relative(n,i)),o._sources.has(s)||o._sources.add(s);var a=t.sourceContentFor(i);a!=null&&o.setSourceContent(i,a)}),o};sr.prototype.addMapping=function(t){var r=ke.getArg(t,"generated"),n=ke.getArg(t,"original",null),o=ke.getArg(t,"source",null),i=ke.getArg(t,"name",null);!this._skipValidation&&this._validateMapping(r,n,o,i)===!1||(o!=null&&(o=String(o),this._sources.has(o)||this._sources.add(o)),i!=null&&(i=String(i),this._names.has(i)||this._names.add(i)),this._mappings.add({generatedLine:r.line,generatedColumn:r.column,originalLine:n!=null&&n.line,originalColumn:n!=null&&n.column,source:o,name:i}))};sr.prototype.setSourceContent=function(t,r){var n=t;this._sourceRoot!=null&&(n=ke.relative(this._sourceRoot,n)),r!=null?(this._sourcesContents||(this._sourcesContents=Object.create(null)),this._sourcesContents[ke.toSetString(n)]=r):this._sourcesContents&&(delete this._sourcesContents[ke.toSetString(n)],Object.keys(this._sourcesContents).length===0&&(this._sourcesContents=null))};sr.prototype.applySourceMap=function(t,r,n){var o=r;if(r==null){if(t.file==null)throw new Error(`SourceMapGenerator.prototype.applySourceMap requires either an explicit source file, or the source map's "file" property. Both were omitted.`);o=t.file}var i=this._sourceRoot;i!=null&&(o=ke.relative(i,o));var s=new cc,a=new cc;this._mappings.unsortedForEach(function(c){if(c.source===o&&c.originalLine!=null){var l=t.originalPositionFor({line:c.originalLine,column:c.originalColumn});l.source!=null&&(c.source=l.source,n!=null&&(c.source=ke.join(n,c.source)),i!=null&&(c.source=ke.relative(i,c.source)),c.originalLine=l.line,c.originalColumn=l.column,l.name!=null&&(c.name=l.name))}var A=c.source;A!=null&&!s.has(A)&&s.add(A);var u=c.name;u!=null&&!a.has(u)&&a.add(u)},this),this._sources=s,this._names=a,t.sources.forEach(function(c){var l=t.sourceContentFor(c);l!=null&&(n!=null&&(c=ke.join(n,c)),i!=null&&(c=ke.relative(i,c)),this.setSourceContent(c,l))},this)};sr.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)}};sr.prototype._serializeMappings=function(){for(var t=0,r=1,n=0,o=0,i=0,s=0,a="",c,l,A,u,d=this._mappings.toArray(),m=0,g=d.length;m<g;m++){if(l=d[m],c="",l.generatedLine!==r)for(t=0;l.generatedLine!==r;)c+=";",r++;else if(m>0){if(!ke.compareByGeneratedPositionsInflated(l,d[m-1]))continue;c+=","}c+=Wi.encode(l.generatedColumn-t),t=l.generatedColumn,l.source!=null&&(u=this._sources.indexOf(l.source),c+=Wi.encode(u-s),s=u,c+=Wi.encode(l.originalLine-1-o),o=l.originalLine-1,c+=Wi.encode(l.originalColumn-n),n=l.originalColumn,l.name!=null&&(A=this._names.indexOf(l.name),c+=Wi.encode(A-i),i=A)),a+=c}return a};sr.prototype._generateSourcesContent=function(t,r){return t.map(function(n){if(!this._sourcesContents)return null;r!=null&&(n=ke.relative(r,n));var o=ke.toSetString(n);return Object.prototype.hasOwnProperty.call(this._sourcesContents,o)?this._sourcesContents[o]:null},this)};sr.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};sr.prototype.toString=function(){return JSON.stringify(this.toJSON())};oE.SourceMapGenerator=sr});var iE=U(zn=>{zn.GREATEST_LOWER_BOUND=1;zn.LEAST_UPPER_BOUND=2;function Hu(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?Hu(s,t,r,n,o,i):i==zn.LEAST_UPPER_BOUND?t<n.length?t:-1:s:s-e>1?Hu(e,s,r,n,o,i):i==zn.LEAST_UPPER_BOUND?s:e<0?-1:e}zn.search=function(t,r,n,o){if(r.length===0)return-1;var i=Hu(-1,r.length,t,r,n,o||zn.GREATEST_LOWER_BOUND);if(i<0)return-1;for(;i-1>=0&&n(r[i],r[i-1],!0)===0;)--i;return i}});var cE=U(aE=>{function gv(e){function t(o,i,s){var a=o[i];o[i]=o[s],o[s]=a}function r(o,i){return Math.round(o+Math.random()*(i-o))}function n(o,i,s,a){if(s<a){var c=r(s,a),l=s-1;t(o,c,a);for(var A=o[a],u=s;u<a;u++)i(o[u],A,!1)<=0&&(l+=1,t(o,l,u));t(o,l+1,u);var d=l+1;n(o,i,s,d-1),n(o,i,d+1,a)}}return n}function pv(e){let t=gv.toString();return new Function(`return ${t}`)()(e)}var sE=new WeakMap;aE.quickSort=function(e,t,r=0){let n=sE.get(t);n===void 0&&(n=pv(t),sE.set(t,n)),n(e,t,r,e.length-1)}});var uE=U(lc=>{var k=ei(),qu=iE(),ti=Ou().ArraySet,hv=Lu(),zi=cE().quickSort;function Ce(e,t){var r=e;return typeof e=="string"&&(r=k.parseSourceMapInput(e)),r.sections!=null?new wr(r,t):new st(r,t)}Ce.fromSourceMap=function(e,t){return st.fromSourceMap(e,t)};Ce.prototype._version=3;Ce.prototype.__generatedMappings=null;Object.defineProperty(Ce.prototype,"_generatedMappings",{configurable:!0,enumerable:!0,get:function(){return this.__generatedMappings||this._parseMappings(this._mappings,this.sourceRoot),this.__generatedMappings}});Ce.prototype.__originalMappings=null;Object.defineProperty(Ce.prototype,"_originalMappings",{configurable:!0,enumerable:!0,get:function(){return this.__originalMappings||this._parseMappings(this._mappings,this.sourceRoot),this.__originalMappings}});Ce.prototype._charIsMappingSeparator=function(t,r){var n=t.charAt(r);return n===";"||n===","};Ce.prototype._parseMappings=function(t,r){throw new Error("Subclasses must implement _parseMappings")};Ce.GENERATED_ORDER=1;Ce.ORIGINAL_ORDER=2;Ce.GREATEST_LOWER_BOUND=1;Ce.LEAST_UPPER_BOUND=2;Ce.prototype.eachMapping=function(t,r,n){var o=r||null,i=n||Ce.GENERATED_ORDER,s;switch(i){case Ce.GENERATED_ORDER:s=this._generatedMappings;break;case Ce.ORIGINAL_ORDER:s=this._originalMappings;break;default:throw new Error("Unknown order of iteration.")}for(var a=this.sourceRoot,c=t.bind(o),l=this._names,A=this._sources,u=this._sourceMapURL,d=0,m=s.length;d<m;d++){var g=s[d],h=g.source===null?null:A.at(g.source);h!==null&&(h=k.computeSourceURL(a,h,u)),c({source:h,generatedLine:g.generatedLine,generatedColumn:g.generatedColumn,originalLine:g.originalLine,originalColumn:g.originalColumn,name:g.name===null?null:l.at(g.name)})}};Ce.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,qu.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};lc.SourceMapConsumer=Ce;function st(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=ti.fromArray(i.map(String),!0),this._sources=ti.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}st.prototype=Object.create(Ce.prototype);st.prototype.consumer=Ce;st.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};st.fromSourceMap=function(t,r){var n=Object.create(st.prototype),o=n._names=ti.fromArray(t._names.toArray(),!0),i=n._sources=ti.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],d=new AE;d.generatedLine=u.generatedLine,d.generatedColumn=u.generatedColumn,u.source&&(d.source=i.indexOf(u.source),d.originalLine=u.originalLine,d.originalColumn=u.originalColumn,u.name&&(d.name=o.indexOf(u.name)),c.push(d)),a.push(d)}return zi(n.__originalMappings,k.compareByOriginalPositions),n};st.prototype._version=3;Object.defineProperty(st.prototype,"sources",{get:function(){return this._absoluteSources.slice()}});function AE(){this.generatedLine=0,this.generatedColumn=0,this.source=null,this.originalLine=null,this.originalColumn=null,this.name=null}var Uu=k.compareByGeneratedPositionsDeflatedNoLine;function lE(e,t){let r=e.length,n=e.length-t;if(!(n<=1))if(n==2){let o=e[t],i=e[t+1];Uu(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(Uu(s,a)<=0)break;e[i-1]=a,e[i]=s}else zi(e,Uu,t)}st.prototype._parseMappings=function(t,r){var n=1,o=0,i=0,s=0,a=0,c=0,l=t.length,A=0,u={},d={},m=[],g=[],h,I,C,y,x;let S=0;for(;A<l;)if(t.charAt(A)===";")n++,A++,o=0,lE(g,S),S=g.length;else if(t.charAt(A)===",")A++;else{for(h=new AE,h.generatedLine=n,y=A;y<l&&!this._charIsMappingSeparator(t,y);y++);for(I=t.slice(A,y),C=[];A<y;)hv.decode(t,A,d),x=d.value,A=d.rest,C.push(x);if(C.length===2)throw new Error("Found a source, but no line and column");if(C.length===3)throw new Error("Found a source and line, but no column");if(h.generatedColumn=o+C[0],o=h.generatedColumn,C.length>1&&(h.source=a+C[1],a+=C[1],h.originalLine=i+C[2],i=h.originalLine,h.originalLine+=1,h.originalColumn=s+C[3],s=h.originalColumn,C.length>4&&(h.name=c+C[4],c+=C[4])),g.push(h),typeof h.originalLine=="number"){let M=h.source;for(;m.length<=M;)m.push(null);m[M]===null&&(m[M]=[]),m[M].push(h)}}lE(g,S),this.__generatedMappings=g;for(var B=0;B<m.length;B++)m[B]!=null&&zi(m[B],k.compareByOriginalPositionsNoSource);this.__originalMappings=[].concat(...m)};st.prototype._findMapping=function(t,r,n,o,i,s){if(t[n]<=0)throw new TypeError("Line must be greater than or equal to 1, got "+t[n]);if(t[o]<0)throw new TypeError("Column must be greater than or equal to 0, got "+t[o]);return qu.search(t,r,i,s)};st.prototype.computeColumnSpans=function(){for(var t=0;t<this._generatedMappings.length;++t){var r=this._generatedMappings[t];if(t+1<this._generatedMappings.length){var n=this._generatedMappings[t+1];if(r.generatedLine===n.generatedLine){r.lastGeneratedColumn=n.generatedColumn-1;continue}}r.lastGeneratedColumn=1/0}};st.prototype.originalPositionFor=function(t){var r={generatedLine:k.getArg(t,"line"),generatedColumn:k.getArg(t,"column")},n=this._findMapping(r,this._generatedMappings,"generatedLine","generatedColumn",k.compareByGeneratedPositionsDeflated,k.getArg(t,"bias",Ce.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}};st.prototype.hasContentsOfAllSources=function(){return this.sourcesContent?this.sourcesContent.length>=this._sources.size()&&!this.sourcesContent.some(function(t){return t==null}):!1};st.prototype.sourceContentFor=function(t,r){if(!this.sourcesContent)return null;var n=this._findSourceIndex(t);if(n>=0)return this.sourcesContent[n];var o=t;this.sourceRoot!=null&&(o=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.')};st.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",Ce.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}};lc.BasicSourceMapConsumer=st;function wr(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 ti,this._names=new ti;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 Ce(k.getArg(s,"map"),t)}})}wr.prototype=Object.create(Ce.prototype);wr.prototype.constructor=Ce;wr.prototype._version=3;Object.defineProperty(wr.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}});wr.prototype.originalPositionFor=function(t){var r={generatedLine:k.getArg(t,"line"),generatedColumn:k.getArg(t,"column")},n=qu.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}};wr.prototype.hasContentsOfAllSources=function(){return this._sections.every(function(t){return t.consumer.hasContentsOfAllSources()})};wr.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.')};wr.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}};wr.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)}zi(this.__generatedMappings,k.compareByGeneratedPositionsDeflated),zi(this.__originalMappings,k.compareByOriginalPositions)};lc.IndexedSourceMapConsumer=wr});var dE=U(fE=>{var Cv=Gu().SourceMapGenerator,Ac=ei(),Ev=/(\r?\n)/,Iv=10,ri="$$$isSourceNode$$$";function Gt(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[ri]=!0,n!=null&&this.add(n)}Gt.fromStringWithSourceMap=function(t,r,n){var o=new Gt,i=t.split(Ev),s=0,a=function(){var d=g(),m=g()||"";return d+m;function g(){return s<i.length?i[s++]:void 0}},c=1,l=0,A=null;return r.eachMapping(function(d){if(A!==null)if(c<d.generatedLine)u(A,a()),c++,l=0;else{var m=i[s]||"",g=m.substr(0,d.generatedColumn-l);i[s]=m.substr(d.generatedColumn-l),l=d.generatedColumn,u(A,g),A=d;return}for(;c<d.generatedLine;)o.add(a()),c++;if(l<d.generatedColumn){var 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Got "+t);return this};Gt.prototype.prepend=function(t){if(Array.isArray(t))for(var r=t.length-1;r>=0;r--)this.prepend(t[r]);else if(t[ri]||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};Gt.prototype.walk=function(t){for(var r,n=0,o=this.children.length;n<o;n++)r=this.children[n],r[ri]?r.walk(t):r!==""&&t(r,{source:this.source,line:this.line,column:this.column,name:this.name})};Gt.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};Gt.prototype.replaceRight=function(t,r){var n=this.children[this.children.length-1];return n[ri]?n.replaceRight(t,r):typeof n=="string"?this.children[this.children.length-1]=n.replace(t,r):this.children.push("".replace(t,r)),this};Gt.prototype.setSourceContent=function(t,r){this.sourceContents[Ac.toSetString(t)]=r};Gt.prototype.walkSourceContents=function(t){for(var r=0,n=this.children.length;r<n;r++)this.children[r][ri]&&this.children[r].walkSourceContents(t);for(var o=Object.keys(this.sourceContents),r=0,n=o.length;r<n;r++)t(Ac.fromSetString(o[r]),this.sourceContents[o[r]])};Gt.prototype.toString=function(){var t="";return this.walk(function(r){t+=r}),t};Gt.prototype.toStringWithSourceMap=function(t){var r={code:"",line:1,column:0},n=new Cv(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,d=l.length;u<d;u++)l.charCodeAt(u)===Iv?(r.line++,r.column=0,u+1===d?(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}};fE.SourceNode=Gt});var mE=U(uc=>{uc.SourceMapGenerator=Gu().SourceMapGenerator;uc.SourceMapConsumer=uE().SourceMapConsumer;uc.SourceNode=dE().SourceNode});function dc(e){let{children:t,...r}=e;return(0,fc.jsxs)(gE.Link,{...r,target:"_blank",rel:"noopener noreferrer",children:[t," ",(0,fc.jsx)(Ia,{fontSize:"small"})]})}var fc,gE,pE=p(()=>{fc=f(F(),1);SA();gE=f(L(),1)});function ju({text:e,extra:t}){let{classes:r}=yv(),n=t?`supporting data: ${JSON.stringify(t,null,2)}`:"",o=[e,n].filter(Boolean).join(`
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4
4
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`),i=encodeURIComponent(`I got this error from JBrowse, here is the stack trace:
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\`\`\`
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${e}
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${n}
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`),s=`https://github.com/GMOD/jbrowse-components/issues/new?labels=bug&title=JBrowse+issue&body=${i}`,a=`mailto:${
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+
`),s=`https://github.com/GMOD/jbrowse-components/issues/new?labels=bug&title=JBrowse+issue&body=${i}`,a=`mailto:${hE}?subject=JBrowse%202%20error&body=${i}`;return(0,sn.jsxs)(sn.Fragment,{children:[(0,sn.jsxs)(mc.Typography,{children:["Post a new issue at"," ",(0,sn.jsx)(dc,{href:s,children:"GitHub"})," or send an email to ",(0,sn.jsx)(dc,{href:a,children:hE})]}),(0,sn.jsx)("pre",{className:r.pre,children:o})]})}var sn,mc,hE,yv,CE=p(()=>{sn=f(F(),1),mc=f(L(),1);pE();yt();hE="jbrowse2@berkeley.edu",yv=te()(e=>({pre:{background:(0,mc.alpha)(e.palette.error.main,.2),border:`1px solid ${e.palette.divider}`,overflow:"auto",margin:20,maxHeight:300}}))});function Ju({message:e,children:t,variant:r="body2",...n}){let{classes:o}=xv();return(0,EE.jsx)(IE.Typography,{className:sc(o.dots,n.className),...n,variant:r,children:e||"Loading"})}var EE,IE,xv,yE=p(()=>{EE=f(F(),1),IE=f(L(),1);yt();xv=te()({dots:{"&::after":{display:"inline-block",content:'""',width:"1em",textAlign:"left",animation:`${Su`
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}
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@@ -20,15 +20,15 @@ ${n}
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`} 1.2s infinite ease-in-out`}}})});var
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`);return(0,or.jsxs)(Pt.Dialog,{open:!0,onClose:t,maxWidth:"xl",children:[(0,or.jsxs)(Pt.DialogTitle,{children:["Stack trace",(0,or.jsx)(Pt.IconButton,{onClick:t,sx:{position:"absolute",right:8,top:8},children:(0,or.jsx)(_a,{})})]}),(0,or.jsx)(Pt.DialogContent,{children:n===void 0?(0,or.jsx)(Ru,{variant:"h6"}):(0,or.jsx)(Fu,{text:d,extra:r})}),(0,or.jsxs)(Pt.DialogActions,{children:[(0,or.jsx)(Pt.Button,{variant:"contained",color:"secondary",onClick:async()=>{let{default:m}=await Promise.resolve().then(()=>f(CE(),1));m(d),c(!0),setTimeout(()=>{c(!1)},1e3)},children:a?"Copied!":"Copy stack trace to clipboard"}),(0,or.jsx)(Pt.Button,{variant:"contained",color:"primary",onClick:t,children:"Close"})]})]})}var or,ri,Pt,IE,Pu,uv,fv,EE,BE=p(()=>{or=f(L(),1),ri=f(B(),1);$A();Pt=f(k(),1),IE=f(sE(),1);AE();dE();Pu={},uv=/\/\/# sourceMappingURL=(.*)/,fv=/(.*)((?:https?|file):\/\/.*):(\d+):(\d+)/;EE=1e4});function Cv(e){let t="",r="is not assignable",n=e.indexOf(r);if(n!==-1){let 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UniProt/Swiss-Prot|P26898|IL2RA_SHEEP MEPSLLMWRFFVFIVVPGCVTEACHDDPPSLRNA----------MFKVLRYE----VGTM
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UniProt/Swiss-Prot|P01590|IL2RA_MOUSE MEPRLLMLGFLSLTIVPSCRAELCLYDPPEVPNA----------TFKALSYK----NGTI
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UniProt/Swiss-Prot|P41690|IL2RA_FELCA MEPSLLLWGILTFVVVHGHVTELCDENPPDIQHA----------TFKALTYK----TGTM
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@@ -41,7 +41,7 @@ UniProt/Swiss-Prot|Q8BZM1|GLMN_MOUSE PLPLRSLLFLQLPLLGVGLNP----------------
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UniProt/Swiss-Prot|P36835|IL2_CAPHI -----------LLGVGLNPKFLTP------------------------------------
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UniProt/Swiss-Prot|Q7JFM4|IL2_AOTVO MLKPPLPLRSLLFLQLPLLGVGLNPKFLTPSGNEDIGGKPGTGGDFFLTSTPAGTLDVST
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UniProt/Swiss-Prot|Q29416|IL2_CANFA --------------LFLQLSLLG-------------------------------------
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`,
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`,rB=`CLUSTAL O(1.2.4) multiple sequence alignment
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sp|P69905|HBA_HUMAN MVLSPADKTNVKAAWGKVGAHAGEYGAEALERMFLSFPTTKTYFPHFDLSHGSAQVKGHG 60
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@@ -57,23 +57,23 @@ sp|P13786|HBAZ_CAPHI SKVVAAVGDAVKSIDNVTSALSKLSELHAYVLRVDPVNFKFLSHCLLVTLASHF
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sp|P69905|HBA_HUMAN AVHASLDKFLASVSTVLTSKYR 142
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sp|P01942|HBA_MOUSE AVHASLDKFLASVSTVLTSKYR 142
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sp|P13786|HBAZ_CAPHI DAHAAWDKFLSIVSGVLTEKYR 142
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.**: ****: ** ***.***`,
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+
.**: ****: ** ***.***`,nB="(((UniProt/Swiss-Prot|P26898|IL2RA_SHEEP:0.24036,(UniProt/Swiss-Prot|P41690|IL2RA_FELCA:0.17737,(UniProt/Swiss-Prot|P01589|IL2RA_HUMAN:0.03906,UniProt/Swiss-Prot|Q5MNY4|IL2RA_MACMU:0.03787):0.13033):0.04964):0.02189,UniProt/Swiss-Prot|P01590|IL2RA_MOUSE:0.23072):0.06814,(((UniProt/Swiss-Prot|Q95118|IL2RG_BOVIN:0.09600,UniProt/Swiss-Prot|P40321|IL2RG_CANFA:0.09845):0.25333,UniProt/Swiss-Prot|Q29416|IL2_CANFA:-0.35055):0.10231,(UniProt/Swiss-Prot|P26896|IL2RB_RAT:0.33631,UniProt/Swiss-Prot|Q7JFM4|IL2_AOTVO:-0.33631):0.10166):0.01607,(UniProt/Swiss-Prot|Q8BZM1|GLMN_MOUSE:0.32378,UniProt/Swiss-Prot|P36835|IL2_CAPHI:-0.32378):0.09999)"});async function tl(e,t,r,n){e.setError(void 0),t&&e.setMSAFilehandle(t),r&&e.setTreeFilehandle(r),n&&e.setGFFFilehandle(n)}var Xf=p(()=>{});function Hr({onClick:e,model:t,children:r}){return Mt.default.createElement("li",null,Mt.default.createElement(rl.Link,{onClick:n=>{t.setError(void 0),n.preventDefault(),e()},href:"#"},Mt.default.createElement(rl.Typography,{component:"span"},r)))}var Mt,rl,iB,Tn,jD,sB,aB=p(()=>{Mt=f(b(),1),rl=f(L(),1),iB=f(P(),1);oB();Xf();Tn="https://jbrowse.org/genomes/multiple_sequence_alignments",jD=(0,iB.observer)(function({model:e}){function t({msa:r,tree:n,gff:o}){(async()=>{try{await tl(e,r?{uri:r,locationType:"UriLocation"}:void 0,n?{uri:n,locationType:"UriLocation"}:void 0,o?{uri:o,locationType:"UriLocation"}:void 0)}catch(i){console.error(i),e.setError(i)}})()}return Mt.default.createElement("ul",null,Mt.default.createElement(Hr,{model:e,onClick:()=>{t({tree:"https://jbrowse.org/genomes/newicktrees/sarscov2phylo.pub.ft.nh"})}},"230k COVID-19 samples (tree only)"),Mt.default.createElement(Hr,{model:e,onClick:()=>{e.setData({msa:tB,tree:nB})}},"Small protein MSA+tree"),Mt.default.createElement(Hr,{model:e,onClick:()=>{e.setData({msa:rB})}},"Small MSA only"),Mt.default.createElement(Hr,{model:e,onClick:()=>{t({msa:`${Tn}/pfam-cov2.stock`})}},"PFAM SARS-CoV2 multi-stockholm"),Mt.default.createElement(Hr,{model:e,onClick:()=>{t({msa:`${Tn}/pfam-cov2.stock`,gff:`${Tn}/pfam-cov2-domains.gff`})}},"PFAM SARS-CoV2 multi-stockholm w/ domains loaded"),Mt.default.createElement(Hr,{model:e,onClick:()=>{t({msa:`${Tn}/Lysine.stock`})}},"Lysine stockholm file"),Mt.default.createElement(Hr,{model:e,onClick:()=>{t({msa:`${Tn}/PF01601_full.txt`})}},"PF01601 stockholm file (SARS-CoV2 spike protein)"),Mt.default.createElement(Hr,{model:e,onClick:()=>{t({msa:`${Tn}/europe_covid.fa`})}},"Europe COVID full genomes (LR883044.1 and 199 other sequences)"),Mt.default.createElement(Hr,{model:e,onClick:()=>{t({msa:`${Tn}/rhv_test-only.aligned_with_mafft_auto.fa`,tree:`${Tn}/rhv_test-only.aligned_with_mafft_auto.nh`})}},"MAFFT+VeryFastTree(17.9k samples)"),Mt.default.createElement(Hr,{model:e,onClick:()=>{t({msa:"https://jbrowse.org/demos/ttc39a.mfa"})}},"Human BLAST results mfa"))}),sB=jD});var me,Ci,Qr,cB,JD,lB,AB=p(()=>{me=f(b(),1),Ci=f(se(),1),Qr=f(L(),1),cB=f(P(),1);aB();Xf();JD=(0,cB.observer)(function({model:e}){let[t,r]=(0,me.useState)(),[n,o]=(0,me.useState)(),[i,s]=(0,me.useState)(),{error:a}=e;return me.default.createElement(Qr.Container,null,me.default.createElement("div",{style:{width:"50%"}},a?me.default.createElement(Ci.ErrorMessage,{error:a}):null,me.default.createElement(Qr.Typography,null,"Open an MSA file (stockholm or clustal format) and/or a tree file (newick format)."),me.default.createElement(Qr.Typography,{color:"error"},"Note: you can open up just an MSA or just a tree, both are not required. 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`);if(i===-1)continue;let s=o.slice(0,i),a=s.indexOf(" "),c=a===-1?s:s.slice(0,a);c&&(r.push(o.slice(i+1).replaceAll(/\s/g,"")),n.push(c))}this.orderedNames=n,this.MSA={seqdata:this.expandA3M(r,n)}}static sniff(t){if(!t.startsWith(">"))return!1;let r=[];for(let s of t.split(">")){if(!/\S/.test(s))continue;let a=s.indexOf(`
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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);
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`)[Symbol.iterator]();return
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`).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,d,m]=i.split(" ");return{species:s,protein:a,chr:c,start:+l,end:+A,strand:+u,geneId:d,unknown:m,seq:""}});for(let i of n)for(let s=0;s<r.length;s++)o[s].seq+=i[s];return o}function
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`).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,d,m]=i.split(" ");return{species:s,protein:a,chr:c,start:+l,end:+A,strand:+u,geneId:d,unknown:m}});return{tree:n,seqs:o}}var
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`);if(i===-1)continue;let s=o.slice(0,i),a=s.indexOf(" "),c=a===-1?s:s.slice(0,a);c&&(r[c]=o.slice(i+1).replaceAll(/\s/g,""),c.includes(":")&&(n[c.replaceAll(":","_")]=c))}this.MSA={seqdata:r,colonNormalized:n}}getMSA(){return this.MSA}getNames(){return Object.keys(this.MSA.seqdata)}getRow(t){return this.MSA.seqdata[t]??this.MSA.seqdata[this.MSA.colonNormalized[t]??""]??""}getWidth(){let t=Object.keys(this.MSA.seqdata)[0];return this.getRow(t).length}}});function
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`);for(let s of i){let a;if(
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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);yi(l)?n=!0:(l>=IB&&l<=yB||l===xB)&&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=[],d=[],m=0;for(;m<A.length;){let g=A.charCodeAt(m);if(g>=IB&&g<=yB||g===xB){u.push(A[m]);let h="",I=m+1;for(;I<A.length;){let C=A.charCodeAt(I);if(yi(C)||C===wB)h+=A[I],I++;else break}d.push(h),m=I}else if(g===wB)m++;else if(yi(g)){let h="";for(;m<A.length&&yi(A.charCodeAt(m));)h+=A[m],m++;u.push(""),d.push(h)}else m++}o.push(u),i.push(d)}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 d=0;for(let m of A[u])yi(m.charCodeAt(0))&&d++;d>a[u]&&(a[u]=d)}}let c={};for(let l=0;l<n;l++){let A=o[l],u=i[l],d=[];for(let m=0;m<s;m++){let g=a[m];if(m<A.length){let h=A[m],I=u[m]||"";d.push(h||"-");let C="";for(let x of I)yi(x.charCodeAt(0))&&(C+=x.toUpperCase());d.push(C);let y=g-C.length;y>0&&d.push(".".repeat(y))}else d.push("-"),g>0&&d.push(".".repeat(g))}c[r[l]]=d.join("")}return c}getMSA(){return this.MSA}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}}});function $D(e){let t=/\(?(\d+(\.\d+)+)\)?/.exec(e);return t&&t.length>1?t[1]:""}function BB(e){let t=["CLUSTAL","PROBCONS","MUSCLE","MSAPROBS","Kalign"];t.some(n=>e.startsWith(n))||console.warn(`${e} is not a known CLUSTAL header: ${t.join(",")}, proceeding but could indicate an issue`);let r=$D(e);return{info:e,version:r}}function il(e){let t=e.next();for(;!t.done&&t.value.trim()==="";)t=e.next();return t.value}function KD(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 bB(e){let t=il(e),r=[],n="";if(!t)return;for(;t;)t.startsWith(" ")?n=t:r.push(t),t=e.next().value;let[o,i]=KD(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 SB(e){let t,r=bB(e);if(r!==void 0)for(;t=bB(e);){for(let n=0;n<t.seqs.length;n++)r.seqs[n]+=t.seqs[n];r.consensus+=t.consensus}return r}var nd=p(()=>{});var QB=p(()=>{nd()});function XD(e){let t=il(e);if(!t)throw new Error("Empty file received");let r=BB(t),n=SB(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 MB(e){let t=e.split(`
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63
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+
`)[Symbol.iterator]();return XD(t)}var vB=p(()=>{QB();nd()});var so,od=p(()=>{vB();Ii();so=class extends Vt{MSA;constructor(t){super(),this.MSA=MB(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}getHeader(){return this.MSA.header}getNames(){return this.MSA.alns.map(t=>t.id)}get seqConsensus(){return this.MSA.consensus}}});function TB(e){let t=e.split(`
|
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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,d,m]=i.split(" ");return{species:s,protein:a,chr:c,start:+l,end:+A,strand:+u,geneId:d,unknown:m,seq:""}});for(let i of n)for(let s=0;s<r.length;s++)o[s].seq+=i[s];return o}function sl(e){let t=e.split(`
|
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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,d,m]=i.split(" ");return{species:s,protein:a,chr:c,start:+l,end:+A,strand:+u,geneId:d,unknown:m}});return{tree:n,seqs:o}}var id=p(()=>{});var ao,sd=p(()=>{id();Ii();ao=class extends Vt{MSA;constructor(t){super(),this.MSA=TB(t)}getMSA(){return this.MSA}getRow(t){return this.MSA.find(r=>r.protein===t)?.seq||""}getWidth(){return this.MSA[0].seq.length}getHeader(){return""}getNames(){return this.MSA.map(t=>t.protein)}}});var co,ad=p(()=>{Ii();co=class extends Vt{MSA;constructor(t){super();let r={},n={};for(let o of t.split(">")){if(!/\S/.test(o))continue;let i=o.indexOf(`
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+
`);if(i===-1)continue;let s=o.slice(0,i),a=s.indexOf(" "),c=a===-1?s:s.slice(0,a);c&&(r[c]=o.slice(i+1).replaceAll(/\s/g,""),c.includes(":")&&(n[c.replaceAll(":","_")]=c))}this.MSA={seqdata:r,colonNormalized:n}}getMSA(){return this.MSA}getNames(){return Object.keys(this.MSA.seqdata)}getRow(t){return this.MSA.seqdata[t]??this.MSA.seqdata[this.MSA.colonNormalized[t]??""]??""}getWidth(){let t=Object.keys(this.MSA.seqdata)[0];return this.getRow(t).length}}});function lo(e){let t=[],r=[],n=e.replace(/'((?:[^']|'')*)'/g,(s,a)=>{let c=r.length;return r.push(a.replaceAll("''","'")),`__Q${c}__`}),o={},i=n.split(/\s*(;|\(|\)|,|:)\s*/);for(let s=0;s<i.length;s++){let c=i[s].replace(/^__Q(\d+)__$/,(A,u)=>r[Number(u)]),l={};switch(c){case"(":o.children=[l],t.push(o),o=l;break;case",":t.at(-1)?.children.push(l),o=l;break;case")":o=t.pop();break;case":":break;default:{let A=i[s-1];A===")"||A==="("||A===","?o.name=c:A===":"&&(o.length=Number.parseFloat(c))}}}return o}var cd=p(()=>{});function xi(){return{gf:{},gc:{},gs:{},gr:{},seqname:[],seqdata:{}}}function Is(e){return _B.test(e)}function DB(e,t){let r=t??{},n=[],o=null,i=e.split(`
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e.type&&e.adapterId?`${e.type}-${e.adapterId}`:`${JA(e)}`}var wh={};async function FM(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 ${n}`);let i=o.configSchema.create(r,{pluginManager:e}),s=Ma.bind(null,e,t),a=await o.getAdapterClass();return{dataAdapter:new a(i,s,e),sessionIds:new Set([t])}}async function Ma(e,t,r){let n=yh(r);wh[n]??=FM(e,t,r);let o=await wh[n];return o.sessionIds.add(t),o}async function Bh({config:e,pluginManager:t}){return(await Ma(t,"msa",e)).dataAdapter.getMSAList()}async function bh({config:e,pluginManager:t,msaId:r}){return(await Ma(t,"msa",e)).dataAdapter.getMSA(r)}function Sh({session:e,newViewTitle:t,view:r,feature:n,data:o,querySeqName:i}){e.addView("MsaView",{type:"MsaView",displayName:t,treeAreaWidth:200,querySeqName:i,treeWidth:100,drawNodeBubbles:!1,labelsAlignRight:!0,showBranchLen:!1,colWidth:10,rowHeight:12,colorSchemeName:"percent_identity_dynamic",data:o,connectedViewId:r.id,connectedFeature:n.toJSON()})}var RM=(0,vh.makeStyles)()({dialogContent:{width:"80em"}}),PM=(0,Mh.observer)(function({model:e,feature:t,handleClose:r}){let n=(0,No.getSession)(e),o=(0,No.getContainingView)(e),{classes:i}=RM(),{pluginManager:s}=(0,No.getEnv)(e),{assemblyNames:a}=o,[c,l]=(0,Ue.useState)(),{jbrowse:A}=n,u=(0,Qh.readConfObject)(A,["msa","datasets"]),[d,m]=(0,Ue.useState)(u?.[0]?.datasetId),g=u?.find(T=>T.datasetId===d),{data:h,isLoading:I,error:C}=kn(d?`${d}-msa-list`:"none-msa-list",()=>g?Bh({config:g.adapter,pluginManager:s}):void 0,wA),{options:x,selectedId:y,setSelectedId:b,selectedTranscript:S,proteinSequence:v,error:M}=$t({feature:t,view:o,validIds:h}),{data:F,isLoading:O,error:q}=kn(y&&d?`${d}-${y}-${h?.length}-msa`:"none-msa",()=>y&&g&&h?bh({msaId:y,config:g.adapter,pluginManager:s}):void 0,wA),w=C??q??M??c;return w&&console.error(w),Ue.default.createElement(Ue.default.Fragment,null,Ue.default.createElement(Kr.DialogContent,{className:i.dialogContent},w?Ue.default.createElement(Gn.ErrorMessage,{error:w}):null,Ue.default.createElement(tt,{select:!0,label:"Select MSA dataset",value:d,onChange:T=>{m(T.target.value)}},u?.map(T=>Ue.default.createElement(Kr.MenuItem,{key:T.datasetId,value:T.datasetId},T.name))),g?Ue.default.createElement("div",{style:{marginTop:50}},!I&&O?Ue.default.createElement(Gn.LoadingEllipses,{variant:"h6",message:`Loading MSA for (${y})`}):null,I?Ue.default.createElement(Gn.LoadingEllipses,{variant:"h6",message:`Loading available MSAs for (${g.name})`}):null,h?Ue.default.createElement("div",null,Ue.default.createElement(Gn.SanitizedHTML,{html:g.description}),Ue.default.createElement(Nt,{feature:t,options:x,selectedId:y,selectedTranscript:S,onTranscriptChange:b,proteinSequence:v,validIds:h})):null):null),Ue.default.createElement(Kr.DialogActions,null,Ue.default.createElement(Kr.Button,{color:"primary",variant:"contained",disabled:!S||!F?.length,onClick:()=>{try{if(!S||!F)return;let T=`${y}_${a[0]}`;Sh({session:n,newViewTitle:zt(S),view:o,querySeqName:T,feature:S,data:{msa:F.map(J=>`>${J.get("refName")}
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72
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-
${
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73
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-
`)}}),r()}catch(
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74
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-
${
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70
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+
`),treeMetadata:JSON.stringify(Object.fromEntries(s.map(a=>[a.id,{genome:a.species}])))}}function Rg(e){let{data:t,error:r,isLoading:n}=zr(()=>e?["geneTree",e]:null,([,o])=>Fg(o),{revalidateOnFocus:!1,revalidateOnReconnect:!1,revalidateIfStale:!1});return{treeData:t,isTreeLoading:n,treeError:r}}var Pg=f(ne());function J1(e){let r=(e.get("subfeatures")??[]).filter(n=>(n.get("type")==="mRNA"||n.get("type")==="transcript")&&n.get("subfeatures")?.some(o=>o.get("type")==="CDS"));return r.length>0?r:[e]}function na(e){let t=(0,Pg.sum)(e.get("subfeatures")?.filter(r=>r.get("type")?.toLowerCase()==="cds").map(r=>r.get("end")-r.get("start"))??[]);return{len:Math.floor(t/3),mod:t%3}}function Fn(e){return e?.id()??""}function V1(e){if(!e)return[];let t=[e.id(),e.get("name"),e.get("id"),e.get("transcript_id")].filter(r=>!!r);return[...new Set(t)]}function oa(e,t){return V1(e).includes(t)}function Rn(e){return e===void 0?"":[e.get("name"),e.get("id")].filter(t=>!!t).join(" ")}function Xt(e){return e===void 0?"":[e.get("gene_name")??e.get("name"),e.get("id")?`(${e.get("id")})`:""].filter(t=>!!t).join(" ")}function Og(e){return J1(e).toSorted((r,n)=>na(n).len-na(r).len)}function ia(e){return e.replaceAll("*","").replaceAll("&","")}function sa(e){let t=[e.id(),e.get("id"),e.get("name"),e.get("gene_id"),e.get("gene_name")].filter(r=>!!r);return[...new Set(t)]}var Er=f(b()),Mo=f(L()),qg=f(ze());var Hg=f(b()),Ug=f(ze());var mA=f(b()),Gg=f(L());function Y1({children:e,...t}){return mA.default.createElement("div",null,mA.default.createElement(Gg.TextField,{...t},e))}var nt=Y1;var W1=(0,Ug.makeStyles)()({textAreaFont:{fontFamily:"Courier New"}});function gA({value:e}){let{classes:t}=W1();return Hg.default.createElement(nt,{variant:"outlined",multiline:!0,minRows:5,maxRows:10,fullWidth:!0,value:e,slotProps:{input:{readOnly:!0,classes:{input:t.textAreaFont}}}})}var z1=(0,qg.makeStyles)()({flex:{display:"flex"},minWidth:{minWidth:300}});function Rt({feature:e,options:t,selectedId:r,selectedTranscript:n,onTranscriptChange:o,proteinSequence:i,validIds:s}){let{classes:a}=z1(),[c,l]=(0,Er.useState)(!1);return Er.default.createElement(Er.default.Fragment,null,Er.default.createElement("div",{className:a.flex},Er.default.createElement(Mo.TextField,{variant:"outlined",label:`Choose isoform of ${Xt(e)}`,select:!0,className:a.minWidth,value:r,onChange:A=>{o(A.target.value)}},t.map(A=>{let u=s?s.some(g=>oa(A,g)):!0,{len:d,mod:m}=na(A);return Er.default.createElement(Mo.MenuItem,{value:Fn(A),key:A.id(),disabled:!u},Rn(A)," (",d," aa)"," ",m?" (possible fragment)":"",s?u?" (has data)":" (no data)":"")})),Er.default.createElement("div",{style:{alignContent:"center",marginLeft:20}},Er.default.createElement(Mo.Button,{variant:"contained",color:"primary",onClick:()=>{l(!c)}},c?"Hide sequence":"Show sequence"))),c&&Er.default.createElement(gA,{value:i?`>${Rn(n)}
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${i}`:"Loading..."}))}var ca=f(b());var Cn=f(ne());function $1(e,t){return e.map(r=>t.slice(r.start,r.end)).join("")}function K1({cds:e,sequence:t,codonTable:r}){let n=$1(e,t),o="";for(let i=0;i<n.length;i+=3)o+=r[n.slice(i,i+3)]??"&";return o}function X1(e,t){return e.map(r=>({...r,start:t-r.end,end:t-r.start})).toSorted((r,n)=>r.start-n.start)}function jg({feature:e,seq:t}){let{subfeatures:r,start:n,strand:o}=e.toJSON(),i=(0,Cn.dedupe)(r?.toSorted((s,a)=>s.start-a.start).map(s=>({...s,start:s.start-n,end:s.end-n})).filter(s=>s.type==="CDS")??[],s=>`${s.start}-${s.end}`);return K1({cds:o===-1?X1(i,t.length):i,sequence:o===-1?(0,Cn.revcom)(t):t,codonTable:(0,Cn.generateCodonTable)(Cn.defaultCodonTable)})}var Vg=f(ne());var Jg=f(Ln());async function aa({start:e,end:t,refName:r,session:n,assemblyName:o}){let{assemblyManager:i,rpcManager:s}=n,a=await i.waitForAssembly(o);if(!a)throw new Error("assembly not found");let c="getSequence";return(await 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(${g.name})`}):null,h?je.default.createElement("div",null,je.default.createElement(Un.SanitizedHTML,{html:g.description}),je.default.createElement(Rt,{feature:t,options:y,selectedId:x,selectedTranscript:B,onTranscriptChange:S,proteinSequence:M,validIds:h})):null):null),je.default.createElement(tn.DialogActions,null,je.default.createElement(tn.Button,{color:"primary",variant:"contained",disabled:!B||!R?.length,onClick:()=>{try{if(!B||!R)return;let D=`${x}_${a[0]}`;Nh({session:n,newViewTitle:Xt(B),view:o,querySeqName:D,feature:B,data:{msa:R.map(H=>`>${H.get("refName")}
|
|
72
|
+
${H.get("seq")}`).join(`
|
|
73
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+
`)}}),r()}catch(D){l(D)}}},"Submit"),je.default.createElement(tn.Button,{color:"secondary",variant:"contained",onClick:r},"Cancel")))}),Ph=tM;var $A=f(b());function Fo({children:e,value:t,index:r,...n}){return $A.default.createElement("div",{role:"tabpanel",hidden:t!==r,...n},t===r&&$A.default.createElement("div",null,e))}function KA({handleClose:e,feature:t,model:r}){let n=(0,Hh.getSession)(r),{jbrowse:o}=n,i=(0,Oh.readConfObject)(o,["msa","datasets"]),s=i&&i.length>0,[a,c]=(0,ot.useState)("ncbi_blast");return ot.default.createElement(Gh.Dialog,{maxWidth:"xl",title:"Launch MSA view",open:!0,onClose:e},ot.default.createElement(qn.Tabs,{value:a,onChange:(A,u)=>{c(u)}},ot.default.createElement(qn.Tab,{label:"NCBI BLAST query",value:"ncbi_blast"}),s?ot.default.createElement(qn.Tab,{label:"Pre-loaded MSA datasets",value:"preloaded_msa"}):null,ot.default.createElement(qn.Tab,{label:"Ensembl GeneTree",value:"ensembl_genetree"}),ot.default.createElement(qn.Tab,{label:"Manual upload",value:"manual_msa"})),ot.default.createElement(Fo,{value:a,index:"ncbi_blast"},ot.default.createElement(TA,{handleClose:e,feature:t,model:r})),s?ot.default.createElement(Fo,{value:a,index:"preloaded_msa"},ot.default.createElement(Ph,{model:r,feature:t,handleClose:e})):null,ot.default.createElement(Fo,{value:a,index:"ensembl_genetree"},ot.default.createElement(Xg,{model:r,feature:t,handleClose:e})),ot.default.createElement(Fo,{value:a,index:"manual_msa"},ot.default.createElement(rp,{model:r,feature:t,handleClose:e})))}function rM(e){return e.name==="LinearBasicDisplay"}function nM(e){return e.views(t=>{let r=t.contextMenuItems;return{contextMenuItems(){let n=t.contextMenuFeature,o=(0,ka.getContainingTrack)(t),i=n?.get("type"),s=n&&["gene","mRNA","transcript"].includes(i);return[...r(),...s?[{label:"Launch MSA view",icon:Ag,onClick:()=>{(0,ka.getSession)(o).queueDialog(a=>[KA,{model:o,handleClose:a,feature:n}])}}]:[]]}}})}function XA(e){e.addToExtensionPoint("Core-extendPluggableElement",t=>(rM(t)&&(t.stateModel=nM(t.stateModel)),t))}function ZA(e){e.addToExtensionPoint("LaunchView-MsaView",({session:t,data:r,msaFileLocation:n,treeFileLocation:o,connectedViewId:i,connectedFeature:s,displayName:a,colorSchemeName:c,colWidth:l,rowHeight:A,treeAreaWidth:u,treeWidth:d,drawNodeBubbles:m,labelsAlignRight:g,showBranchLen:h,querySeqName:I})=>{if(!r&&!n)throw new Error("No MSA data or file location provided when launching MSA view");t.addView("MsaView",{type:"MsaView",displayName:a,connectedViewId:i,connectedFeature:s,colorSchemeName:c,colWidth:l,rowHeight:A,treeAreaWidth:u,treeWidth:d,drawNodeBubbles:m,labelsAlignRight:g,showBranchLen:h,init:{msaData:r?.msa,treeData:r?.tree,msaUrl:n?.uri,treeUrl:o?.uri,querySeqName:I}})})}var UQ=f(b()),qQ=f(qh());var SQ=f(b()),QQ=f(Dl()),bi=f(ne()),ye=f(Lt());function*oM(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 jh(e){let t=e.strand,r=e.refName;if(t!==-1&&t!==1)throw new Error(`Invalid strand value: ${t}. 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ml="https://www.ebi.ac.uk/Tools/services/rest",Gk={clustalo:{params:{email:"colin.diesh@gmail.com"},msaResult:"aln-clustal_num",treeResult:"phylotree"},muscle:{params:{email:"colin.diesh@gmail.com",format:"clw",tree:"tree1"},msaResult:"fa",treeResult:"phylotree"},kalign:{params:{email:"colin.diesh@gmail.com",stype:"protein"},msaResult:"fa",treeResult:"phylotree"},mafft:{params:{email:"colin.diesh@gmail.com",stype:"protein"},msaResult:"fa",treeResult:"phylotree"}};async function Hk({onProgress:e,jobId:t,algorithm:r}){for(;;){for(let o=0;o<10;o++)await ra(1e3),e(`Re-checking MSA status in... ${10-o}`);let n=await Cr(`${ml}/${r}/status/${t}`);if(n==="FINISHED")break;if(n.includes("FAILURE"))throw new Error(`Failed to run: jobId ${t}`)}}async function YS({algorithm:e,sequence:t,onProgress:r}){let n=Gk[e];if(!n)throw new Error(`unknown algorithm: ${e}`);r(`Launching ${e} MSA...`);let o=await Cr(`${ml}/${e}/run`,{method:"POST",body:new URLSearchParams({...n.params,sequence:t})});return await Hk({jobId:o,algorithm:e,onProgress:r}),{msa:await Cr(`${ml}/${e}/result/${o}/${n.msaResult}`),tree:await Cr(`${ml}/${e}/result/${o}/${n.treeResult}`)}}async function Rd({rid:e,baseUrl:t,onProgress:r}){r(`Checking BLAST status for RID: ${e}...`),await qk({rid:e,onProgress:r,baseUrl:t});let n=await Qo(`${t}?CMD=Get&RID=${e}&FORMAT_TYPE=JSON2_S&FORMAT_OBJECT=Alignment`);return{rid:e,hits:n.BlastOutput2[0]?.report.results.search.hits??[]}}async function WS({query:e,blastDatabase:t,blastProgram:r,baseUrl:n,onProgress:o,onRid:i}){o("Submitting to NCBI BLAST...");let{rid:s}=await Uk({query:e,blastDatabase:t,blastProgram:r,baseUrl:n});return i(s),Rd({rid:s,baseUrl:n,onProgress:o})}async function Uk({query:e,blastProgram:t,blastDatabase:r,baseUrl:n}){let o=await Cr(n,{method:"POST",body:new URLSearchParams({CMD:"Put",PROGRAM:t==="quick-blastp"?"blastp":t,DATABASE:r,QUERY:e,...r==="nr_clustered_seq"?{CLUSTERED_DB:"on",DB_TYPE:"Experimental Databases"}:{},...t==="quick-blastp"?{BLAST_PROGRAMS:"kmerBlastp"}:{}})}),i=/^ {4}RID = (.*$)/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 qk({rid:e,onProgress:t,baseUrl:r}){for(;;){for(let l=0;l<20;l++)await ra(1e3),t(`Re-checking BLAST status in... ${20-l}`);let o=await Cr(`${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")}}}}Li();var jk="jbrowse-msaview-taxonomy-cache",bs="common-names",Jk=2;async function zS(){return On(jk,Jk,{upgrade(e){e.objectStoreNames.contains(bs)&&e.deleteObjectStore(bs),e.createObjectStore(bs,{keyPath:"taxid"})}})}async function Vk(e){return(await zS()).get(bs,e)}async function Yk(e){let r=(await zS()).transaction(bs,"readwrite");for(let n of e)await r.store.put(n);await r.done}async function $S(e){let t=new Map,r=[];for(let i of e){let s=await Vk(i);s?t.set(i,{sciname:s.sciname,commonName:s.commonName}):r.push(i)}if(r.length===0)return t;let n=100,o=[];for(let i=0;i<r.length;i+=n){let s=r.slice(i,i+n),a=s.join(",");try{let l=await(await fetch(`https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=taxonomy&id=${a}&retmode=xml`)).text(),A=new Map,u=/<Taxon>\s*<TaxId>(\d+)<\/TaxId>/g,d;for(;(d=u.exec(l))!==null;){let m=Number(d[1]),g=d.index,h=1,I=g+d[0].length;for(;h>0&&I<l.length;){let B=l.indexOf("<Taxon>",I),M=l.indexOf("</Taxon>",I);if(M===-1)break;B!==-1&&B<M?(h++,I=B+7):(h--,I=M+8)}let C=l.slice(g,I),y=A.get(m),x=C.includes("<LineageEx>"),S=y?.includes("<LineageEx>");(!y||x&&!S)&&A.set(m,C)}for(let m of s){let g=A.get(m);if(g){let h=/<GenbankCommonName>(.*?)<\/GenbankCommonName>/.exec(g),I=/<CommonName>(.*?)<\/CommonName>/.exec(g),C=/<ScientificName>(.*?)<\/ScientificName>/.exec(g),y=h?.[1]??I?.[1],x=C?.[1]??"";t.set(m,{sciname:x,commonName:y}),o.push({taxid:m,sciname:x,commonName:y})}else o.push({taxid:m,sciname:"",commonName:void 0})}}catch(c){console.error("Failed to fetch taxonomy data:",c)}}return o.length>0&&await Yk(o),t}async function KS({self:e}){let{baseUrl:t,blastDatabase:r,blastProgram:n,msaAlgorithm:o,proteinSequence:i,selectedTranscript:s,rid:a}=e.blastParams,c=ia(i),l,A;if(a){e.setRid(a);let C=await Rd({rid:a,baseUrl:t,onProgress:y=>{e.setProgress(y)}});l=C.hits,A=C.rid}else{let C=await WS({query:c,blastDatabase:r,blastProgram:n,baseUrl:t,onProgress:y=>{e.setProgress(y)},onRid:y=>{e.setRid(y)}});l=C.hits,A=C.rid}e.setProgress("Fetching species taxonomy info...");let u=l.map(C=>C.description[0]?.taxid).filter(C=>C!==void 0),d=await $S(u),m={},g=l.map(C=>{let y=C.description[0]??{accession:"unknown",id:"unknown",sciname:"unknown"},x=JS(y,d),S=VS(C.hsps[0]?.hseq??"");return m[x]=Wk(y,d),`>${x}
|
|
74
|
+
${S}`}),h=await YS({algorithm:o,sequence:[`>QUERY
|
|
75
75
|
${c}`,...g].join(`
|
|
76
|
-
`),onProgress:C=>{e.setProgress(C)}}),I=JSON.stringify(m);return await cp({proteinSequence:c,blastDatabase:r,blastProgram:n,msaAlgorithm:o,msa:h.msa,tree:h.tree,treeMetadata:I,rid:A,geneId:s?.get("parentId"),transcriptId:s?.id(),transcriptName:s?.get("name")??s?.get("id"),geneName:s?.get("gene_name")??s?.get("parentId")}),{...h,treeMetadata:I}}function Mk(e,t){let r={},n=e.taxid?t.get(e.taxid):void 0;return n?.sciname&&(r["Scientific name"]=n.sciname),n?.commonName&&(r["Common name"]=n.commonName),e.accession&&(r.Accession=e.accession),e.id&&(r.ID=e.id),e.title&&(r.Description=e.title),r}function ul(e,t){if(t<0||t>=e.length)return;let r=0;for(let n=0;n<t;n++)e[n]!=="-"&&r++;if(e[t]!=="-")return r}function GS(e,t){let r=0;for(let n=0;n<e.length;n++)if(e[n]!=="-"){if(r===t)return n;r++}}function _d(e){return Object.fromEntries(e)}function xs({model:e,coord:t}){let{querySeqName:r,transcriptToMsaMap:n,mafRegion:o}=e,s=e.rows.find(c=>c[0]===r)?.[1];if(!s)return;let a=ul(s,t);if(a!==void 0){if(o){let c=o.start+a;return c>=o.end?void 0:{refName:o.refName,start:c,end:c+1}}if(n){let{refName:c,p2g:l}=n,A=l[a],u=l[a+1];return A!==void 0&&u!==void 0?{refName:c,start:Math.min(A,u),end:Math.max(A,u)}:void 0}}}Di();var vk="jbrowse-msaview-data",Tk=1,ys="msa-data";async function Dd(){return Rn(vk,Tk,{upgrade(e){e.objectStoreNames.contains(ys)||e.createObjectStore(ys,{keyPath:"id"}).createIndex("timestamp","timestamp",{unique:!1})}})}function JS(){return`msa-${Date.now()}-${Math.random().toString(36).slice(2,11)}`}async function HS(e,t){try{let r=await Dd(),n={id:e,msa:t.msa,tree:t.tree,treeMetadata:t.treeMetadata,timestamp:Date.now()};return await r.put(ys,n),!0}catch(r){return console.warn("Failed to store MSA data:",r),!1}}async function US(e){try{let r=await(await Dd()).get(ys,e);return r?{msa:r.msa,tree:r.tree,treeMetadata:r.treeMetadata}:void 0}catch(t){console.warn("Failed to retrieve MSA data:",t);return}}async function qS(e=10080*60*1e3){try{let t=await Dd(),r=Date.now()-e,i=await t.transaction(ys,"readwrite").store.index("timestamp").openCursor(IDBKeyRange.upperBound(r)),s=0;for(;i;)await i.delete(),s++,i=await i.continue();return s}catch(t){return console.warn("Failed to cleanup old MSA data:",t),0}}function YS(e){return typeof e=="object"&&e!==null&&"hoverFeature"in e&&"hoverPosition"in e}function jS(e){return/AF-([A-Z0-9]+)-F\d+/.exec(e)?.[1]}function VS(e){let{dataStoreId:t,rows:r}=e;t&&r.length===0&&(async()=>{try{e.setLoadingStoredData(!0);let n=await US(t);n&&(n.msa&&e.setMSA(n.msa),n.tree&&e.setTree(n.tree))}catch(n){console.error("Failed to load MSA data from IndexedDB:",n)}finally{e.setLoadingStoredData(!1)}})()}function WS(e){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;(o||i)&&(async()=>{try{let s=JS();await HS(s,{msa:o,tree:i,treeMetadata:e.data.treeMetadata})&&e.setDataStoreId(s)}catch(s){console.error("Failed to store MSA data to IndexedDB:",s)}})()}}function zS(e){e.blastParams&&(async()=>{try{e.setProgress("Submitting query"),e.setError(void 0);let t=await OS({self:e});e.setData(t),e.setBlastParams(void 0)}catch(t){e.setError(t),console.error(t)}finally{e.setProgress("")}})()}function $S(e){let{init:t}=e;t&&(async()=>{try{e.setError(void 0);let{msaData:r,msaUrl:n,treeData:o,treeUrl:i,querySeqName:s}=t;if(n){let a=jS(n);a&&(e.setUniprotId(a),e.setQuerySeqName("query"))}if(s&&e.setQuerySeqName(s),r)e.setMSA(r);else if(n){let a=await fetch(n);if(!a.ok)throw new Error(`Failed to fetch MSA: ${a.status}`);let c=await a.text();e.setMSA(c)}if(o)e.setTree(o);else if(i){let a=await fetch(i);if(!a.ok)throw new Error(`Failed to fetch tree: ${a.status}`);let c=await a.text();e.setTree(c)}e.setInit(void 0)}catch(r){e.setError(r),console.error(r)}})()}function KS(e){let{mouseCol:t,mouseClickCol:r}=e,n=t===void 0?void 0:xs({model:e,coord:t}),o=r===void 0?void 0:xs({model:e,coord:r});e.setConnectedHighlights([n,o].filter(i=>!!i))}function XS(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=ul(i,t);if(s===void 0){o.clearHighlightFromExternal?.();continue}let a=n.msaToStructure[s];a===void 0?o.clearHighlightFromExternal?.():o.highlightFromExternal?.(a)}}function ZS(e){let{views:t}=(0,kd.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 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break;return{alignedSeq1:l,alignedSeq2:A,score:g}}function Lk(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 sQ(e,t){let{alignedSeq1:r,alignedSeq2:n}=Nk(e,t);return{consensus:Lk(r,n),alns:[{id:"msa",seq:r},{id:"structure",seq:n}]}}function aQ(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 Pk=(0,dQ.lazy)(()=>Promise.resolve().then(()=>(fQ(),uQ)));function Nd(){return Ie.types.compose(mQ.BaseViewModel,ll(),Ie.types.model("MsaView",{connectedViewId:Ie.types.maybe(Ie.types.string),connectedFeature:Ie.types.frozen(),connectedHighlights:Ie.types.array(Ie.types.model({refName:Ie.types.string,start:Ie.types.number,end:Ie.types.number})),blastParams:Ie.types.frozen(),querySeqName:"QUERY",uniprotId:Ie.types.maybe(Ie.types.string),zoomToBaseLevel:!1,init:Ie.types.frozen(),connectedStructures:Ie.types.array(Ie.types.frozen()),dataStoreId:Ie.types.maybe(Ie.types.string),mafRegion:Ie.types.frozen()})).volatile(()=>({rid:void 0,progress:"",error:void 0,loadingStoredData:!1})).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?Fh(e.connectedFeature):void 0},get processing(){return!!e.progress},get connectedView(){let{views:t}=(0,Ii.getSession)(e);return t.find(r=>r.id===e.connectedViewId)},get connectedProteinViews(){let{views:t}=(0,Ii.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=GS(i,o);if(s!==void 0)return e.globalColToVisibleCol(s)}}}}}})).views(e=>({get mouseCol2(){let t=e.structureHoverCol;return t!==void 0?t:nQ({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,Ie.cast)(t)},addToConnectedHighlights(t){e.connectedHighlights.push(t)},clearConnectedHighlights(){e.connectedHighlights=(0,Ie.cast)([])},setBlastParams(t){e.blastParams=t},setInit(t){e.init=t},setQuerySeqName(t){e.querySeqName=t},setUniprotId(t){e.uniprotId=t},setDataStoreId(t){e.dataStoreId=t},setMafRegion(t){e.mafRegion=t},setLoadingStoredData(t){e.loadingStoredData=t},handleMsaClick(t){let{connectedView:r,zoomToBaseLevel:n}=e,{assemblyManager:o}=(0,Ii.getSession)(e),i=xs({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,Ii.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 ${r} not found`);let A=l.structureSequences?.[0];if(!A)throw new Error("Structure sequence not available");let u=sQ(s,A),{seq1ToSeq2:d,seq2ToSeq1:m}=aQ(u),g={proteinViewId:t,structureIdx:r,msaRowName:o,msaToStructure:_d(d),structureToMsa:_d(m)};e.connectedStructures.push(g)},disconnectFromStructure(t,r){let n=e.connectedStructures.findIndex(o=>o.proteinViewId===t&&o.structureIdx===r);n!==-1&&e.connectedStructures.splice(n,1)},disconnectAllStructures(){e.connectedStructures.clear()}})).actions(e=>{let t=e.setMouseClickPos.bind(e);return{setMouseClickPos(r,n){t(r,n),r!==void 0&&e.handleMsaClick(r)}}}).views(e=>({extraViewMenuItems(){return[{label:"Zoom to base level on click?",checked:e.zoomToBaseLevel,type:"checkbox",onClick:()=>{e.setZoomToBaseLevel(!e.zoomToBaseLevel)}},{label:"Connect to protein structure...",onClick:()=>{(0,Ii.getSession)(e).queueDialog(t=>[Pk,{model:e,handleClose:t}])}},...e.connectedStructures.length>0?[{label:"Disconnect from protein structures",onClick:()=>{e.disconnectAllStructures()}}]:[]]}})).actions(e=>({afterCreate(){tQ();for(let t of[VS,WS,zS,$S,KS,XS,ZS,eQ])(0,Ie.addDisposer)(e,(0,gQ.autorun)(()=>{t(e)}))}}))}var Yk=(0,QQ.lazy)(()=>Promise.resolve().then(()=>(SQ(),bQ)));function Pd(e){e.addViewType(()=>new MQ.default({name:"MsaView",stateModel:Nd(),ReactComponent:Yk}))}var vQ="2.2.11";var dl=class extends TQ.default{constructor(){super(...arguments);this.name="MsaViewPlugin";this.version=vQ;this.rootConfigurationSchema=r=>({msa:(0,Od.ConfigurationSchema)("MSA",{datasets:Gd.types.maybe(Gd.types.array((0,Od.ConfigurationSchema)("MSAEntry",{datasetId:{type:"string",defaultValue:""},description:{type:"string",defaultValue:""},name:{type:"string",defaultValue:""},adapter:r.pluggableConfigSchemaType("adapter")})))})})}install(r){Pd(r),qA(r),YA(r),wl(r),Hl(r)}configure(r){(0,_Q.isAbstractMenuManager)(r.rootModel)&&r.rootModel.appendToSubMenu(["Add"],{label:"Multiple sequence alignment view",icon:lm,onClick:n=>{n.addView("MsaView",{})}})}};return qQ(jk);})();
|
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76
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+
`),onProgress:C=>{e.setProgress(C)}}),I=JSON.stringify(m);return await gp({proteinSequence:c,blastDatabase:r,blastProgram:n,msaAlgorithm:o,msa:h.msa,tree:h.tree,treeMetadata:I,rid:A,geneId:s?.get("parentId"),transcriptId:s?.id(),transcriptName:s?.get("name")??s?.get("id"),geneName:s?.get("gene_name")??s?.get("parentId")}),{...h,treeMetadata:I}}function Wk(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}function gl(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 XS(e,t){let r=0;for(let n=0;n<e.length;n++)if(e[n]!=="-"){if(r===t)return n;r++}}function Pd(e){return Object.fromEntries(e)}function Bs({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=gl(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}}}Li();var zk="jbrowse-msaview-data",$k=1,Ss="msa-data";async function Od(){return On(zk,$k,{upgrade(e){e.objectStoreNames.contains(Ss)||e.createObjectStore(Ss,{keyPath:"id"}).createIndex("timestamp","timestamp",{unique:!1})}})}function ZS(){return`msa-${Date.now()}-${Math.random().toString(36).slice(2,11)}`}async function eQ(e,t){try{let r=await Od(),n={id:e,msa:t.msa,tree:t.tree,treeMetadata:t.treeMetadata,timestamp:Date.now()};return await r.put(Ss,n),!0}catch(r){return console.warn("Failed to store MSA data:",r),!1}}async function tQ(e){try{let r=await(await Od()).get(Ss,e);return r?{msa:r.msa,tree:r.tree,treeMetadata:r.treeMetadata}:void 0}catch(t){console.warn("Failed to retrieve MSA data:",t);return}}async function rQ(e=10080*60*1e3){try{let t=await Od(),r=Date.now()-e,i=await t.transaction(Ss,"readwrite").store.index("timestamp").openCursor(IDBKeyRange.upperBound(r)),s=0;for(;i;)await i.delete(),s++,i=await i.continue();return s}catch(t){return console.warn("Failed to cleanup old MSA data:",t),0}}function nQ(e){return typeof e=="object"&&e!==null&&"hoverFeature"in e&&"hoverPosition"in e}function oQ(e){return/AF-([A-Z0-9]+)-F\d+/.exec(e)?.[1]}function iQ(e){let t=e;return t.type==="ProteinView"&&Array.isArray(t.structures)}function sQ(e){let{dataStoreId:t,rows:r}=e;t&&r.length===0&&(async()=>{try{e.setLoadingStoredData(!0);let n=await tQ(t);n&&(n.msa&&e.setMSA(n.msa),n.tree&&e.setTree(n.tree))}catch(n){console.error("Failed to load MSA data from IndexedDB:",n)}finally{e.setLoadingStoredData(!1)}})()}function aQ(e){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;(o||i)&&(async()=>{try{let s=ZS();await eQ(s,{msa:o,tree:i,treeMetadata:e.data.treeMetadata})&&e.setDataStoreId(s)}catch(s){console.error("Failed to store MSA data to IndexedDB:",s)}})()}}function cQ(e){e.blastParams&&(async()=>{try{e.setProgress("Submitting query"),e.setError(void 0);let t=await KS({self:e});e.setData(t),e.setBlastParams(void 0)}catch(t){e.setError(t),console.error(t)}finally{e.setProgress("")}})()}function lQ(e){let{init:t}=e;t&&(async()=>{try{e.setError(void 0);let{msaData:r,msaUrl:n,treeData:o,treeUrl:i,querySeqName:s}=t;if(n){let a=oQ(n);a&&(e.setUniprotId(a),e.setQuerySeqName("query"))}if(s&&e.setQuerySeqName(s),r)e.setMSA(r);else if(n){let a=await fetch(n);if(!a.ok)throw new Error(`Failed to fetch MSA: ${a.status}`);let c=await a.text();e.setMSA(c)}if(o)e.setTree(o);else if(i){let a=await fetch(i);if(!a.ok)throw new Error(`Failed to fetch tree: ${a.status}`);let c=await a.text();e.setTree(c)}e.setInit(void 0)}catch(r){e.setError(r),console.error(r)}})()}function AQ(e){let{mouseCol:t,mouseClickCol:r}=e,n=t===void 0?void 0:Bs({model:e,coord:t}),o=r===void 0?void 0:Bs({model:e,coord:r});e.setConnectedHighlights([n,o].filter(i=>!!i))}function uQ(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=gl(i,t);if(s===void 0){o.clearHighlightFromExternal?.();continue}let a=n.msaToStructure[s];a===void 0?o.clearHighlightFromExternal?.():o.highlightFromExternal?.(a)}}function fQ(e){let{views:t}=(0,Gd.getSession)(e),{connectedViewId:r,uniprotId:n,rows:o,connectedStructures:i}=e;if(!(!n||o.length===0))for(let s of t){if(!iQ(s))continue;let a=s;for(let c=0;c<a.structures.length;c++){let l=a.structures[c];if(!(!l||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)}}}}function dQ(e){let{views:t}=(0,Gd.getSession)(e),{connectedViewId:r,transcriptToMsaMap:n,querySeqName:o}=e;if(!r||!n)return;let i=new Set;for(let a of t){if(!iQ(a))continue;let c=a;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 d of A)for(let m=d.start;m<d.end;m++){let g=u[m];if(g!==void 0){let h=e.seqPosToGlobalCol(o,g);i.add(h)}}}}let s=Array.from(i).map(a=>e.globalColToVisibleCol(a)).filter(a=>a!==void 0);e.setHighlightedColumns(s.length>0?s:void 0)}function mQ(){rQ().catch(e=>{console.error("Failed to cleanup old MSA data:",e)})}var gQ=f(ne());function pQ({model:e}){let{hovered:t}=(0,gQ.getSession)(e),{querySeqName:r,transcriptToMsaMap:n,connectedView:o,mafRegion:i}=e;if(!o?.initialized||!nQ(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)}}var 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CQ(e,t){let r=e.toUpperCase(),n=t.toUpperCase();return hQ[r]?.[n]??-4}var Xk=-10,Zk=-.5;function eN(e,t,r=Xk,n=Zk){let o=e.length,i=t.length,s=[],a=[],c=[];for(let I=0;I<=o;I++){s[I]=[],a[I]=[],c[I]=[];for(let C=0;C<=i;C++)s[I][C]=-1/0,a[I][C]=-1/0,c[I][C]=-1/0}s[0][0]=0;for(let I=1;I<=o;I++)a[I][0]=r+(I-1)*n;for(let I=1;I<=i;I++)c[0][I]=r+(I-1)*n;for(let I=1;I<=o;I++)for(let C=1;C<=i;C++){let y=CQ(e[I-1],t[C-1]);s[I][C]=Math.max(s[I-1][C-1],a[I-1][C-1],c[I-1][C-1])+y,a[I][C]=Math.max(s[I-1][C]+r,a[I-1][C]+n),c[I][C]=Math.max(s[I][C-1]+r,c[I][C-1]+n)}let l="",A="",u=o,d=i,m=[s[o][i],a[o][i],c[o][i]],g=Math.max(...m),h=g===s[o][i]?"M":g===a[o][i]?"Ix":"Iy";for(;u>0||d>0;)if(h==="M"&&u>0&&d>0){l=e[u-1]+l,A=t[d-1]+A;let I=CQ(e[u-1],t[d-1]),C=s[u-1][d-1],y=a[u-1][d-1],x=s[u][d];x===C+I?h="M":x===y+I?h="Ix":h="Iy",u--,d--}else if(h==="Ix"&&u>0){l=e[u-1]+l,A="-"+A;let I=a[u][d],C=s[u-1][d]+r;h=I===C?"M":"Ix",u--}else if(d>0){l="-"+l,A=t[d-1]+A;let I=c[u][d],C=s[u][d-1]+r;h=I===C?"M":"Iy",d--}else break;return{alignedSeq1:l,alignedSeq2:A,score:g}}function tN(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 EQ(e,t){let{alignedSeq1:r,alignedSeq2:n}=eN(e,t);return{consensus:tN(r,n),alns:[{id:"msa",seq:r},{id:"structure",seq:n}]}}function IQ(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 oN=(0,SQ.lazy)(()=>Promise.resolve().then(()=>(BQ(),bQ)));function Hd(){return ye.types.compose(QQ.BaseViewModel,dl(),ye.types.model("MsaView",{connectedViewId:ye.types.maybe(ye.types.string),connectedFeature:ye.types.frozen(),connectedHighlights:ye.types.array(ye.types.model({refName:ye.types.string,start:ye.types.number,end:ye.types.number})),blastParams:ye.types.frozen(),querySeqName:"QUERY",uniprotId:ye.types.maybe(ye.types.string),zoomToBaseLevel:!1,init:ye.types.frozen(),connectedStructures:ye.types.array(ye.types.frozen()),dataStoreId:ye.types.maybe(ye.types.string),mafRegion:ye.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?jh(e.connectedFeature):void 0},get processing(){return!!e.progress},get connectedView(){let{views:t}=(0,bi.getSession)(e);return t.find(r=>r.id===e.connectedViewId)},get connectedProteinViews(){let{views:t}=(0,bi.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!==void 0)}})).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=XS(i,o);if(s!==void 0)return e.globalColToVisibleCol(s)}}}}}})).views(e=>({get mouseCol2(){let t=e.structureHoverCol;return t!==void 0?t:pQ({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,ye.cast)(t)},addToConnectedHighlights(t){e.connectedHighlights.push(t)},clearConnectedHighlights(){e.connectedHighlights=(0,ye.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,bi.getSession)(e),i=Bs({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,bi.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 ${r} not found`);let A=l.structureSequences?.[0];if(!A)throw new Error("Structure sequence not available");let u=EQ(s,A),{seq1ToSeq2:d,seq2ToSeq1:m}=IQ(u),g={proteinViewId:t,structureIdx:r,msaRowName:o,msaToStructure:Pd(d),structureToMsa:Pd(m)};e.connectedStructures.push(g)},disconnectFromStructure(t,r){let n=e.connectedStructures.findIndex(o=>o.proteinViewId===t&&o.structureIdx===r);n!==-1&&e.connectedStructures.splice(n,1)},disconnectAllStructures(){e.connectedStructures.clear()}})).actions(e=>{let t=e.setMouseClickPos.bind(e);return{setMouseClickPos(r,n){t(r,n),r!==void 0&&e.handleMsaClick(r)}}}).views(e=>({extraViewMenuItems(){return[{label:"Zoom to base level on click?",checked:e.zoomToBaseLevel,type:"checkbox",onClick:()=>{e.setZoomToBaseLevel(!e.zoomToBaseLevel)}},{label:"Connect to protein structure...",onClick:()=>{(0,bi.getSession)(e).queueDialog(t=>[oN,{model:e,handleClose:t}])}},...e.connectedStructures.length>0?[{label:"Disconnect from protein structures",onClick:()=>{e.disconnectAllStructures()}}]:[]]}})).actions(e=>({afterCreate(){mQ();for(let t of[sQ,aQ,cQ,lQ,AQ,uQ,fQ,dQ])(0,ye.addDisposer)(e,(0,MQ.autorun)(()=>{t(e)}))}}))}var uN=(0,UQ.lazy)(()=>Promise.resolve().then(()=>(HQ(),GQ)));function Jd(e){e.addViewType(()=>new qQ.default({name:"MsaView",stateModel:Hd(),ReactComponent:uN}))}var jQ="2.3.5";var Cl=class extends JQ.default{constructor(){super(...arguments);this.name="MsaViewPlugin";this.version=jQ;this.rootConfigurationSchema=r=>({msa:(0,Vd.ConfigurationSchema)("MSA",{datasets:Yd.types.maybe(Yd.types.array((0,Vd.ConfigurationSchema)("MSAEntry",{datasetId:{type:"string",defaultValue:""},description:{type:"string",defaultValue:""},name:{type:"string",defaultValue:""},adapter:r.pluggableConfigSchemaType("adapter")})))})})}install(r){Jd(r),XA(r),ZA(r),_l(r),$l(r)}configure(r){(0,VQ.isAbstractMenuManager)(r.rootModel)&&r.rootModel.appendToSubMenu(["Add"],{label:"Multiple sequence alignment view",icon:pm,onClick:n=>{n.addView("MsaView",{})}})}};return i1(fN);})();
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(*! @license DOMPurify 3.4.2 | (c) Cure53 and other contributors | Released under the Apache license 2.0 and Mozilla Public License 2.0 | github.com/cure53/DOMPurify/blob/3.4.2/LICENSE *)
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