npm - jbrowse-plugin-msaview - Versions diffs - 2.3.5 → 2.3.8 - Mend

jbrowse-plugin-msaview 2.3.5 → 2.3.8

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Files changed (62) hide show

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

@@ -1,13 +1,13 @@
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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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s=i;n!==null&&(s=Ne.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=Ne.getArg(t,"generated"),n=Ne.getArg(t,"original",null),o=Ne.getArg(t,"source",null),i=Ne.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=Ne.relative(this._sourceRoot,n)),r!=null?(this._sourcesContents||(this._sourcesContents=Object.create(null)),this._sourcesContents[Ne.toSetString(n)]=r):this._sourcesContents&&(delete this._sourcesContents[Ne.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=Ne.relative(i,o));var s=new Ac,a=new Ac;this._mappings.unsortedForEach(function(c){if(c.source===o&&c.originalLine!=null){var l=t.originalPositionFor({line:c.originalLine,column:c.originalColumn});l.source!=null&&(c.source=l.source,n!=null&&(c.source=Ne.join(n,c.source)),i!=null&&(c.source=Ne.relative(i,c.source)),c.originalLine=l.line,c.originalColumn=l.column,l.name!=null&&(c.name=l.name))}var A=c.source;A!=null&&!s.has(A)&&s.add(A);var u=c.name;u!=null&&!a.has(u)&&a.add(u)},this),this._sources=s,this._names=a,t.sources.forEach(function(c){var l=t.sourceContentFor(c);l!=null&&(n!=null&&(c=Ne.join(n,c)),i!=null&&(c=Ne.relative(i,c)),this.setSourceContent(c,l))},this)};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(!Ne.compareByGeneratedPositionsInflated(l,d[m-1]))continue;c+=","}c+=zi.encode(l.generatedColumn-t),t=l.generatedColumn,l.source!=null&&(u=this._sources.indexOf(l.source),c+=zi.encode(u-s),s=u,c+=zi.encode(l.originalLine-1-o),o=l.originalLine-1,c+=zi.encode(l.originalColumn-n),n=l.originalColumn,l.name!=null&&(A=this._names.indexOf(l.name),c+=zi.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=Ne.relative(r,n));var o=Ne.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())};AE.SourceMapGenerator=sr});var uE=U($n=>{$n.GREATEST_LOWER_BOUND=1;$n.LEAST_UPPER_BOUND=2;function ju(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?ju(s,t,r,n,o,i):i==$n.LEAST_UPPER_BOUND?t<n.length?t:-1:s:s-e>1?ju(e,s,r,n,o,i):i==$n.LEAST_UPPER_BOUND?s:e<0?-1:e}$n.search=function(t,r,n,o){if(r.length===0)return-1;var i=ju(-1,r.length,t,r,n,o||$n.GREATEST_LOWER_BOUND);if(i<0)return-1;for(;i-1>=0&&n(r[i],r[i-1],!0)===0;)--i;return i}});var mE=U(dE=>{function bv(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 Bv(e){let t=bv.toString();return new Function(`return ${t}`)()(e)}var fE=new WeakMap;dE.quickSort=function(e,t,r=0){let n=fE.get(t);n===void 0&&(n=Bv(t),fE.set(t,n)),n(e,t,r,e.length-1)}});var hE=U(uc=>{var k=ti(),Vu=uE(),ri=Uu().ArraySet,Sv=Pu(),$i=mE().quickSort;function he(e,t){var r=e;return typeof e=="string"&&(r=k.parseSourceMapInput(e)),r.sections!=null?new wr(r,t):new st(r,t)}he.fromSourceMap=function(e,t){return st.fromSourceMap(e,t)};he.prototype._version=3;he.prototype.__generatedMappings=null;Object.defineProperty(he.prototype,"_generatedMappings",{configurable:!0,enumerable:!0,get:function(){return this.__generatedMappings||this._parseMappings(this._mappings,this.sourceRoot),this.__generatedMappings}});he.prototype.__originalMappings=null;Object.defineProperty(he.prototype,"_originalMappings",{configurable:!0,enumerable:!0,get:function(){return this.__originalMappings||this._parseMappings(this._mappings,this.sourceRoot),this.__originalMappings}});he.prototype._charIsMappingSeparator=function(t,r){var n=t.charAt(r);return n===";"||n===","};he.prototype._parseMappings=function(t,r){throw new Error("Subclasses must implement _parseMappings")};he.GENERATED_ORDER=1;he.ORIGINAL_ORDER=2;he.GREATEST_LOWER_BOUND=1;he.LEAST_UPPER_BOUND=2;he.prototype.eachMapping=function(t,r,n){var o=r||null,i=n||he.GENERATED_ORDER,s;switch(i){case he.GENERATED_ORDER:s=this._generatedMappings;break;case he.ORIGINAL_ORDER:s=this._originalMappings;break;default:throw new Error("Unknown order of iteration.")}for(var a=this.sourceRoot,c=t.bind(o),l=this._names,A=this._sources,u=this._sourceMapURL,d=0,m=s.length;d<m;d++){var g=s[d],C=g.source===null?null:A.at(g.source);C!==null&&(C=k.computeSourceURL(a,C,u)),c({source:C,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=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,Vu.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};uc.SourceMapConsumer=he;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=ri.fromArray(i.map(String),!0),this._sources=ri.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(he.prototype);st.prototype.consumer=he;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=ri.fromArray(t._names.toArray(),!0),i=n._sources=ri.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 pE;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 $i(n.__originalMappings,k.compareByOriginalPositions),n};st.prototype._version=3;Object.defineProperty(st.prototype,"sources",{get:function(){return this._absoluteSources.slice()}});function pE(){this.generatedLine=0,this.generatedColumn=0,this.source=null,this.originalLine=null,this.originalColumn=null,this.name=null}var Ju=k.compareByGeneratedPositionsDeflatedNoLine;function gE(e,t){let r=e.length,n=e.length-t;if(!(n<=1))if(n==2){let o=e[t],i=e[t+1];Ju(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(Ju(s,a)<=0)break;e[i-1]=a,e[i]=s}else $i(e,Ju,t)}st.prototype._parseMappings=function(t,r){var n=1,o=0,i=0,s=0,a=0,c=0,l=t.length,A=0,u={},d={},m=[],g=[],C,x,I,h,y;let b=0;for(;A<l;)if(t.charAt(A)===";")n++,A++,o=0,gE(g,b),b=g.length;else if(t.charAt(A)===",")A++;else{for(C=new pE,C.generatedLine=n,h=A;h<l&&!this._charIsMappingSeparator(t,h);h++);for(x=t.slice(A,h),I=[];A<h;)Sv.decode(t,A,d),y=d.value,A=d.rest,I.push(y);if(I.length===2)throw new Error("Found a source, but no line and column");if(I.length===3)throw new Error("Found a source and line, but no column");if(C.generatedColumn=o+I[0],o=C.generatedColumn,I.length>1&&(C.source=a+I[1],a+=I[1],C.originalLine=i+I[2],i=C.originalLine,C.originalLine+=1,C.originalColumn=s+I[3],s=C.originalColumn,I.length>4&&(C.name=c+I[4],c+=I[4])),g.push(C),typeof C.originalLine=="number"){let v=C.source;for(;m.length<=v;)m.push(null);m[v]===null&&(m[v]=[]),m[v].push(C)}}gE(g,b),this.__generatedMappings=g;for(var w=0;w<m.length;w++)m[w]!=null&&$i(m[w],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 Vu.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",he.GREATEST_LOWER_BOUND));if(n>=0){var o=this._generatedMappings[n];if(o.generatedLine===r.generatedLine){var i=k.getArg(o,"source",null);i!==null&&(i=this._sources.at(i),i=k.computeSourceURL(this.sourceRoot,i,this._sourceMapURL));var s=k.getArg(o,"name",null);return s!==null&&(s=this._names.at(s)),{source:i,line:k.getArg(o,"originalLine",null),column:k.getArg(o,"originalColumn",null),name:s}}}return{source:null,line:null,column:null,name:null}};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",he.GREATEST_LOWER_BOUND));if(o>=0){var i=this._originalMappings[o];if(i.source===n.source)return{line:k.getArg(i,"generatedLine",null),column:k.getArg(i,"generatedColumn",null),lastColumn:k.getArg(i,"lastGeneratedColumn",null)}}return{line:null,column:null,lastColumn:null}};uc.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 ri,this._names=new ri;var i={line:-1,column:0};this._sections=o.map(function(s){if(s.url)throw new Error("Support for url field in sections not implemented.");var a=k.getArg(s,"offset"),c=k.getArg(a,"line"),l=k.getArg(a,"column");if(c<i.line||c===i.line&&l<i.column)throw new Error("Section offsets must be ordered and non-overlapping.");return i=a,{generatedOffset:{generatedLine:c+1,generatedColumn:l+1},consumer:new he(k.getArg(s,"map"),t)}})}wr.prototype=Object.create(he.prototype);wr.prototype.constructor=he;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=Vu.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 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 UniProt/Swiss-Prot|P26898|IL2RA_SHEEP      MEPSLLMWRFFVFIVVPGCVTEACHDDPPSLRNA----------MFKVLRYE----VGTM
 UniProt/Swiss-Prot|P01590|IL2RA_MOUSE      MEPRLLMLGFLSLTIVPSCRAELCLYDPPEVPNA----------TFKALSYK----NGTI
 UniProt/Swiss-Prot|P41690|IL2RA_FELCA      MEPSLLLWGILTFVVVHGHVTELCDENPPDIQHA----------TFKALTYK----TGTM
@@ -41,7 +41,7 @@ UniProt/Swiss-Prot|Q8BZM1|GLMN_MOUSE       PLPLRSLLFLQLPLLGVGLNP----------------
 UniProt/Swiss-Prot|P36835|IL2_CAPHI        -----------LLGVGLNPKFLTP------------------------------------
 UniProt/Swiss-Prot|Q7JFM4|IL2_AOTVO        MLKPPLPLRSLLFLQLPLLGVGLNPKFLTPSGNEDIGGKPGTGGDFFLTSTPAGTLDVST
 UniProt/Swiss-Prot|Q29416|IL2_CANFA        --------------LFLQLSLLG-------------------------------------
-`,rB=`CLUSTAL O(1.2.4) multiple sequence alignment
+`,cB=`CLUSTAL O(1.2.4) multiple sequence alignment
 sp|P69905|HBA_HUMAN       MVLSPADKTNVKAAWGKVGAHAGEYGAEALERMFLSFPTTKTYFPHFDLSHGSAQVKGHG	60
@@ -57,23 +57,23 @@ sp|P13786|HBAZ_CAPHI      SKVVAAVGDAVKSIDNVTSALSKLSELHAYVLRVDPVNFKFLSHCLLVTLASHF
 sp|P69905|HBA_HUMAN       AVHASLDKFLASVSTVLTSKYR	142
 sp|P01942|HBA_MOUSE       AVHASLDKFLASVSTVLTSKYR	142
 sp|P13786|HBAZ_CAPHI      DAHAAWDKFLSIVSGVLTEKYR	142
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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}
-${S}`}),h=await YS({algorithm:o,sequence:[`>QUERY
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Expected 1 or -1.`);if(!r)throw new Error("refName is required");let n=e.subfeatures?.filter(u=>u.type==="CDS")??[],o=new Set,i=n.filter(u=>{if(u.start>=u.end)return!1;let d=`${u.start}-${u.end}`;return o.has(d)?!1:(o.add(d),!0)}).sort((u,d)=>t*(u.start-d.start)),s={},a={};if(i.length===0)return{g2p:s,p2g:a,refName:r,strand:t};let l=(3-(i[0]?.phase??0))%3,A=-1;for(let u of i)for(let d of dM(u,t)){let m=Math.floor(l++/3);s[d]=m,m!==A&&(a[m]=d,A=m)}return{g2p:s,p2g:a,refName:r,strand:t}}var kQ=f(en());Od();var qd=f(ne());function KS(e,t){let r=e.sciname.replaceAll(" ","_");if(e.taxid&&t?.has(e.taxid)){let n=t.get(e.taxid);n.commonName&&(r=n.commonName.split(" ").map(o=>o.charAt(0).toUpperCase()+o.slice(1).toLowerCase()).join("_"))}return`${e.accession}-${r}`}function XS(e){return e.replaceAll("-","")}var pl="https://www.ebi.ac.uk/Tools/services/rest",zk={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 $k({onProgress:e,jobId:t,algorithm:r}){for(;;){for(let o=0;o<10;o++)await oa(1e3),e(`Re-checking MSA status in... ${10-o}`);let n=await Cr(`${pl}/${r}/status/${t}`);if(n==="FINISHED")break;if(n.includes("FAILURE"))throw new Error(`Failed to run: jobId ${t}`)}}async function ZS({algorithm:e,sequence:t,onProgress:r}){let n=zk[e];if(!n)throw new Error(`unknown algorithm: ${e}`);r(`Launching ${e} MSA...`);let o=await Cr(`${pl}/${e}/run`,{method:"POST",body:new URLSearchParams({...n.params,sequence:t})});return await $k({jobId:o,algorithm:e,onProgress:r}),{msa:await Cr(`${pl}/${e}/result/${o}/${n.msaResult}`),tree:await Cr(`${pl}/${e}/result/${o}/${n.treeResult}`)}}async function Gd({rid:e,baseUrl:t,onProgress:r}){r(`Checking BLAST status for RID: ${e}...`),await Xk({rid:e,onProgress:r,baseUrl:t});let n=await Mo(`${t}?CMD=Get&RID=${e}&FORMAT_TYPE=JSON2_S&FORMAT_OBJECT=Alignment`);return{rid:e,hits:n.BlastOutput2[0]?.report.results.search.hits??[]}}async function eQ({query:e,blastDatabase:t,blastProgram:r,baseUrl:n,onProgress:o,onRid:i}){o("Submitting to NCBI BLAST...");let{rid:s}=await Kk({query:e,blastDatabase:t,blastProgram:r,baseUrl:n});return i(s),Gd({rid:s,baseUrl:n,onProgress:o})}async function Kk({query:e,blastProgram:t,blastDatabase:r,baseUrl:n}){let o=await Cr(n,{method:"POST",body:new URLSearchParams({CMD:"Put",PROGRAM:t==="quick-blastp"?"blastp":t,DATABASE:r,QUERY:e,...r==="nr_clustered_seq"?{CLUSTERED_DB:"on",DB_TYPE:"Experimental Databases"}:{},...t==="quick-blastp"?{BLAST_PROGRAMS:"kmerBlastp"}:{}})}),i=/^ {4}RID = (.*$)/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 Xk({rid:e,onProgress:t,baseUrl:r}){for(;;){for(let l=0;l<20;l++)await oa(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 ${e} failed`);if(a){if(c)return!0;throw new Error("No hits found")}}}}Fi();var Zk="jbrowse-msaview-taxonomy-cache",Bs="common-names",eN=2;async function tQ(){return Gn(Zk,eN,{upgrade(e){e.objectStoreNames.contains(Bs)&&e.deleteObjectStore(Bs),e.createObjectStore(Bs,{keyPath:"taxid"})}})}async function tN(e){return(await tQ()).get(Bs,e)}async function rN(e){let r=(await tQ()).transaction(Bs,"readwrite");for(let n of e)await r.store.put(n);await r.done}async function rQ(e){let t=new Map,r=[];for(let i of e){let s=await tN(i);s?t.set(i,{sciname:s.sciname,commonName:s.commonName}):r.push(i)}if(r.length===0)return t;let n=100,o=[];for(let i=0;i<r.length;i+=n){let s=r.slice(i,i+n),a=s.join(",");try{let l=await(await fetch(`https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=taxonomy&id=${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,C=1,x=g+d[0].length;for(;C>0&&x<l.length;){let w=l.indexOf("<Taxon>",x),v=l.indexOf("</Taxon>",x);if(v===-1)break;w!==-1&&w<v?(C++,x=w+7):(C--,x=v+8)}let I=l.slice(g,x),h=A.get(m),y=I.includes("<LineageEx>"),b=h?.includes("<LineageEx>");(!h||y&&!b)&&A.set(m,I)}for(let m of s){let g=A.get(m);if(g){let C=/<GenbankCommonName>(.*?)<\/GenbankCommonName>/.exec(g),x=/<CommonName>(.*?)<\/CommonName>/.exec(g),I=/<ScientificName>(.*?)<\/ScientificName>/.exec(g),h=C?.[1]??x?.[1],y=I?.[1]??"";t.set(m,{sciname:y,commonName:h}),o.push({taxid:m,sciname:y,commonName:h})}else o.push({taxid:m,sciname:"",commonName:void 0})}}catch(c){console.error("Failed to fetch taxonomy data:",c)}}return o.length>0&&await rN(o),t}async function nQ({self:e}){let{baseUrl:t,blastDatabase:r,blastProgram:n,msaAlgorithm:o,proteinSequence:i,selectedTranscript:s,rid:a}=e.blastParams,c=aa(i),l,A;if(a){e.setRid(a);let I=await Gd({rid:a,baseUrl:t,onProgress:h=>{e.setProgress(h)}});l=I.hits,A=I.rid}else{let I=await eQ({query:c,blastDatabase:r,blastProgram:n,baseUrl:t,onProgress:h=>{e.setProgress(h)},onRid:h=>{e.setRid(h)}});l=I.hits,A=I.rid}e.setProgress("Fetching species taxonomy info...");let u=l.map(I=>I.description[0]?.taxid).filter(I=>I!==void 0),d=await rQ(u),m={},g=l.map(I=>{let h=I.description[0]??{accession:"unknown",id:"unknown",sciname:"unknown"},y=KS(h,d),b=XS(I.hsps[0]?.hseq??"");return m[y]=nN(h,d),`>${y}
+${b}`}),C=await ZS({algorithm:o,sequence:[`>QUERY
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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 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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);})();
+`),onProgress:I=>{e.setProgress(I)}}),x=JSON.stringify(m);return await Cp({proteinSequence:c,blastDatabase:r,blastProgram:n,msaAlgorithm:o,msa:C.msa,tree:C.tree,treeMetadata:x,rid:A,geneId:s?.get("parentId"),transcriptId:s?.id(),transcriptName:s?.get("name")??s?.get("id"),geneName:s?.get("gene_name")??s?.get("parentId")}),{...C,treeMetadata:x}}function nN(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}Ss();function Qs({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=hl(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}}}Fi();var oN="jbrowse-msaview-data",iN=1,Ms="msa-data";async function Ud(){return Gn(oN,iN,{upgrade(e){e.objectStoreNames.contains(Ms)||e.createObjectStore(Ms,{keyPath:"id"}).createIndex("timestamp","timestamp",{unique:!1})}})}function iQ(){return`msa-${Date.now()}-${Math.random().toString(36).slice(2,11)}`}async function sQ(e,t){try{let r=await Ud(),n={id:e,msa:t.msa,tree:t.tree,treeMetadata:t.treeMetadata,timestamp:Date.now()};return await r.put(Ms,n),!0}catch(r){return console.warn("Failed to store MSA data:",r),!1}}async function aQ(e){try{let r=await(await Ud()).get(Ms,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 cQ(e=10080*60*1e3){try{let t=await Ud(),r=Date.now()-e,i=await t.transaction(Ms,"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}}Ss();function lQ(e){return typeof e=="object"&&e!==null&&"hoverFeature"in e&&"hoverPosition"in e}function AQ(e){return/AF-([A-Z0-9]+)-F\d+/.exec(e)?.[1]}function uQ(e){let{dataStoreId:t,rows:r}=e;t&&r.length===0&&(async()=>{try{e.setLoadingStoredData(!0);let n=await aQ(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 fQ(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=iQ();await sQ(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 dQ(e){e.blastParams&&(async()=>{try{e.setProgress("Submitting query"),e.setError(void 0);let t=await nQ({self:e});e.setData(t),e.setBlastParams(void 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wQ(e,t){return xQ[e.toUpperCase()]?.[t.toUpperCase()]??-4}var aN=-10,cN=-.5;function lN(e,t,r=aN,n=cN){let o=e.length,i=t.length,s=[],a=[],c=[];for(let h=0;h<=o;h++){s[h]=[],a[h]=[],c[h]=[];for(let y=0;y<=i;y++)s[h][y]=-1/0,a[h][y]=-1/0,c[h][y]=-1/0}s[0][0]=0;for(let h=1;h<=o;h++)a[h][0]=r+(h-1)*n;for(let h=1;h<=i;h++)c[0][h]=r+(h-1)*n;for(let h=1;h<=o;h++)for(let y=1;y<=i;y++){let b=wQ(e[h-1],t[y-1]);s[h][y]=Math.max(s[h-1][y-1],a[h-1][y-1],c[h-1][y-1])+b,a[h][y]=Math.max(s[h-1][y]+r,a[h-1][y]+n),c[h][y]=Math.max(s[h][y-1]+r,c[h][y-1]+n)}let l="",A="",u=o,d=i,m=s[o][i],g=a[o][i],C=c[o][i],x=Math.max(m,g,C),I=x===m?"M":x===g?"Ix":"Iy";for(;u>0||d>0;)if(I==="M"&&u>0&&d>0){l=e[u-1]+l,A=t[d-1]+A;let h=wQ(e[u-1],t[d-1]),y=s[u-1][d-1],b=a[u-1][d-1],w=s[u][d];w===y+h?I="M":w===b+h?I="Ix":I="Iy",u--,d--}else if(I==="Ix"&&u>0){l=e[u-1]+l,A="-"+A;let h=a[u][d],y=s[u-1][d]+r;I=h===y?"M":"Ix",u--}else if(d>0){l="-"+l,A=t[d-1]+A;let h=c[u][d],y=s[u][d-1]+r;I=h===y?"M":"Iy",d--}else break;return{alignedSeq1:l,alignedSeq2:A,score:x}}function AN(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 bQ(e,t){let{alignedSeq1:r,alignedSeq2:n}=lN(e,t);return{consensus:AN(r,n),alns:[{id:"msa",seq:r},{id:"structure",seq:n}]}}function BQ(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}}Ss();var mN=(0,_Q.lazy)(()=>Promise.resolve().then(()=>(TQ(),vQ)));function jd(){return ye.types.compose(DQ.BaseViewModel,gl(),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?$h(e.connectedFeature):void 0},get processing(){return!!e.progress},get connectedView(){let{views:t}=(0,Bi.getSession)(e);return t.find(r=>r.id===e.connectedViewId)},get connectedProteinViews(){let{views:t}=(0,Bi.getSession)(e),r=t,n=[];for(let o of e.connectedStructures){let i=r.find(s=>Dn(s)&&s.id===o.proteinViewId);i&&n.push({...o,proteinView:i})}return n}})).views(e=>({get structureHoverCol(){for(let t of e.connectedProteinViews){let n=t.proteinView.structures[t.structureIdx]?.hoverPosition?.structureSeqPos;if(n!==void 0){let o=t.structureToMsa[n];if(o!==void 0){let i=e.getSequenceByRowName(t.msaRowName);if(i){let s=oQ(i,o);if(s!==void 0)return e.globalColToVisibleCol(s)}}}}}})).views(e=>({get mouseCol2(){let t=e.structureHoverCol;return t!==void 0?t:yQ({model:e})},get clickCol2(){}})).actions(e=>({setZoomToBaseLevel(t){e.zoomToBaseLevel=t},setError(t){e.error=t},setProgress(t){e.progress=t},setRid(t){e.rid=t},setConnectedHighlights(t){e.connectedHighlights=(0,ye.cast)(t)},addToConnectedHighlights(t){e.connectedHighlights.push(t)},clearConnectedHighlights(){e.connectedHighlights=(0,ye.cast)([])},setBlastParams(t){e.blastParams=t},setInit(t){e.init=t},setQuerySeqName(t){e.querySeqName=t},setUniprotId(t){e.uniprotId=t},setDataStoreId(t){e.dataStoreId=t},setMafRegion(t){e.mafRegion=t},setLoadingStoredData(t){e.loadingStoredData=t},handleMsaClick(t){let{connectedView:r,zoomToBaseLevel:n}=e,{assemblyManager:o}=(0,Bi.getSession)(e),i=Qs({model:e,coord:t});if(!(!i||!r))if(n)r.navTo(i);else{let s=o.get(r.assemblyNames[0])?.getCanonicalRefName(i.refName)??i.refName;r.centerAt(i.start,s)}},connectToStructure(t,r,n){let o=n??e.querySeqName,i=e.getSequenceByRowName(o);if(!i)throw new Error(`MSA row "${o}" not found`);let s=i.replaceAll("-",""),{views:a}=(0,Bi.getSession)(e),c=a.find(C=>Dn(C)&&C.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=bQ(s,A),{seq1ToSeq2:d,seq2ToSeq1:m}=BQ(u),g={proteinViewId:t,structureIdx:r,msaRowName:o,msaToStructure:Hd(d),structureToMsa:Hd(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=>[mN,{model:e,handleClose:t}])}},...e.connectedStructures.length>0?[{label:"Disconnect from protein structures",onClick:()=>{e.disconnectAllStructures()}}]:[]]}})).actions(e=>({afterCreate(){EQ();for(let t of[uQ,fQ,dQ,mQ,gQ,pQ,hQ,CQ])(0,ye.addDisposer)(e,(0,kQ.autorun)(()=>{t(e)}))}}))}var xN=(0,WQ.lazy)(()=>Promise.resolve().then(()=>(YQ(),VQ)));function Wd(e){e.addViewType(()=>new zQ.default({name:"MsaView",stateModel:jd(),ReactComponent:xN}))}var $Q="2.3.8";var yl=class extends KQ.default{constructor(){super(...arguments);this.name="MsaViewPlugin";this.version=$Q;this.rootConfigurationSchema=r=>({msa:(0,zd.ConfigurationSchema)("MSA",{datasets:$d.types.maybe($d.types.array((0,zd.ConfigurationSchema)("MSAEntry",{datasetId:{type:"string",defaultValue:""},description:{type:"string",defaultValue:""},name:{type:"string",defaultValue:""},adapter:r.pluggableConfigSchemaType("adapter")})))})})}install(r){Wd(r),tu(r),ru(r),Nl(r),Zl(r)}configure(r){(0,XQ.isAbstractMenuManager)(r.rootModel)&&r.rootModel.appendToSubMenu(["Add"],{label:"Multiple sequence alignment view",icon:Em,onClick:n=>{n.addView("MsaView",{})}})}};return u1(wN);})();
 /*! Bundled license information:
 use-sync-external-store/cjs/use-sync-external-store-shim.production.js: