npm - jbrowse-plugin-msaview - Versions diffs - 2.4.2 → 2.4.3 - Mend

jbrowse-plugin-msaview 2.4.2 → 2.4.3

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.

Files changed (71) hide show

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

@@ -1,13 +1,13 @@
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if(m>0){if(!Ne.compareByGeneratedPositionsInflated(l,d[m-1]))continue;c+=","}c+=Ji.encode(l.generatedColumn-t),t=l.generatedColumn,l.source!=null&&(u=this._sources.indexOf(l.source),c+=Ji.encode(u-s),s=u,c+=Ji.encode(l.originalLine-1-o),o=l.originalLine-1,c+=Ji.encode(l.originalColumn-n),n=l.originalColumn,l.name!=null&&(A=this._names.indexOf(l.name),c+=Ji.encode(A-i),i=A)),a+=c}return a};tr.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)};tr.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};tr.prototype.toString=function(){return JSON.stringify(this.toJSON())};eE.SourceMapGenerator=tr});var tE=H(Vn=>{Vn.GREATEST_LOWER_BOUND=1;Vn.LEAST_UPPER_BOUND=2;function Ou(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?Ou(s,t,r,n,o,i):i==Vn.LEAST_UPPER_BOUND?t<n.length?t:-1:s:s-e>1?Ou(e,s,r,n,o,i):i==Vn.LEAST_UPPER_BOUND?s:e<0?-1:e}Vn.search=function(t,r,n,o){if(r.length===0)return-1;var i=Ou(-1,r.length,t,r,n,o||Vn.GREATEST_LOWER_BOUND);if(i<0)return-1;for(;i-1>=0&&n(r[i],r[i-1],!0)===0;)--i;return i}});var oE=H(nE=>{function Av(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 uv(e){let t=Av.toString();return new Function(`return ${t}`)()(e)}var rE=new WeakMap;nE.quickSort=function(e,t,r=0){let n=rE.get(t);n===void 0&&(n=uv(t),rE.set(t,n)),n(e,t,r,e.length-1)}});var aE=H(sc=>{var D=Ko(),Hu=tE(),Xo=Ru().ArraySet,fv=ku(),Vi=oE().quickSort;function he(e,t){var r=e;return typeof e=="string"&&(r=D.parseSourceMapInput(e)),r.sections!=null?new Er(r,t):new it(r,t)}he.fromSourceMap=function(e,t){return it.fromSourceMap(e,t)};he.prototype._version=3;he.prototype.__generatedMappings=null;Object.defineProperty(he.prototype,"_generatedMappings",{configurable:!0,enumerable:!0,get:function(){return this.__generatedMappings||this._parseMappings(this._mappings,this.sourceRoot),this.__generatedMappings}});he.prototype.__originalMappings=null;Object.defineProperty(he.prototype,"_originalMappings",{configurable:!0,enumerable:!0,get:function(){return this.__originalMappings||this._parseMappings(this._mappings,this.sourceRoot),this.__originalMappings}});he.prototype._charIsMappingSeparator=function(t,r){var n=t.charAt(r);return n===";"||n===","};he.prototype._parseMappings=function(t,r){throw new Error("Subclasses must implement _parseMappings")};he.GENERATED_ORDER=1;he.ORIGINAL_ORDER=2;he.GREATEST_LOWER_BOUND=1;he.LEAST_UPPER_BOUND=2;he.prototype.eachMapping=function(t,r,n){var o=r||null,i=n||he.GENERATED_ORDER,s;switch(i){case he.GENERATED_ORDER:s=this._generatedMappings;break;case he.ORIGINAL_ORDER:s=this._originalMappings;break;default:throw new Error("Unknown order of iteration.")}for(var a=this.sourceRoot,c=t.bind(o),l=this._names,A=this._sources,u=this._sourceMapURL,d=0,m=s.length;d<m;d++){var p=s[d],C=p.source===null?null:A.at(p.source);C!==null&&(C=D.computeSourceURL(a,C,u)),c({source:C,generatedLine:p.generatedLine,generatedColumn:p.generatedColumn,originalLine:p.originalLine,originalColumn:p.originalColumn,name:p.name===null?null:l.at(p.name)})}};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,Hu.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};sc.SourceMapConsumer=he;function it(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=Xo.fromArray(i.map(String),!0),this._sources=Xo.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}it.prototype=Object.create(he.prototype);it.prototype.consumer=he;it.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};it.fromSourceMap=function(t,r){var n=Object.create(it.prototype),o=n._names=Xo.fromArray(t._names.toArray(),!0),i=n._sources=Xo.fromArray(t._sources.toArray(),!0);n.sourceRoot=t._sourceRoot,n.sourcesContent=t._generateSourcesContent(n._sources.toArray(),n.sourceRoot),n.file=t._file,n._sourceMapURL=r,n._absoluteSources=n._sources.toArray().map(function(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 sE;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 Vi(n.__originalMappings,D.compareByOriginalPositions),n};it.prototype._version=3;Object.defineProperty(it.prototype,"sources",{get:function(){return this._absoluteSources.slice()}});function sE(){this.generatedLine=0,this.generatedColumn=0,this.source=null,this.originalLine=null,this.originalColumn=null,this.name=null}var Gu=D.compareByGeneratedPositionsDeflatedNoLine;function iE(e,t){let r=e.length,n=e.length-t;if(!(n<=1))if(n==2){let o=e[t],i=e[t+1];Gu(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(Gu(s,a)<=0)break;e[i-1]=a,e[i]=s}else Vi(e,Gu,t)}it.prototype._parseMappings=function(t,r){var n=1,o=0,i=0,s=0,a=0,c=0,l=t.length,A=0,u={},d={},m=[],p=[],C,x,I,h,y;let w=0;for(;A<l;)if(t.charAt(A)===";")n++,A++,o=0,iE(p,w),w=p.length;else if(t.charAt(A)===",")A++;else{for(C=new sE,C.generatedLine=n,h=A;h<l&&!this._charIsMappingSeparator(t,h);h++);for(x=t.slice(A,h),I=[];A<h;)fv.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])),p.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)}}iE(p,w),this.__generatedMappings=p;for(var S=0;S<m.length;S++)m[S]!=null&&Vi(m[S],D.compareByOriginalPositionsNoSource);this.__originalMappings=[].concat(...m)};it.prototype._findMapping=function(t,r,n,o,i,s){if(t[n]<=0)throw new TypeError("Line must be greater than or equal to 1, got "+t[n]);if(t[o]<0)throw new TypeError("Column must be greater than or equal to 0, got "+t[o]);return Hu.search(t,r,i,s)};it.prototype.computeColumnSpans=function(){for(var t=0;t<this._generatedMappings.length;++t){var r=this._generatedMappings[t];if(t+1<this._generatedMappings.length){var n=this._generatedMappings[t+1];if(r.generatedLine===n.generatedLine){r.lastGeneratedColumn=n.generatedColumn-1;continue}}r.lastGeneratedColumn=1/0}};it.prototype.originalPositionFor=function(t){var r={generatedLine: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}};it.prototype.hasContentsOfAllSources=function(){return this.sourcesContent?this.sourcesContent.length>=this._sources.size()&&!this.sourcesContent.some(function(t){return t==null}):!1};it.prototype.sourceContentFor=function(t,r){if(!this.sourcesContent)return null;var n=this._findSourceIndex(t);if(n>=0)return this.sourcesContent[n];var o=t;this.sourceRoot!=null&&(o=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.')};it.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}};sc.BasicSourceMapConsumer=it;function Er(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 Xo,this._names=new Xo;var i={line:-1,column:0};this._sections=o.map(function(s){if(s.url)throw new Error("Support for url field in sections not implemented.");var a=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)}})}Er.prototype=Object.create(he.prototype);Er.prototype.constructor=he;Er.prototype._version=3;Object.defineProperty(Er.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}});Er.prototype.originalPositionFor=function(t){var r={generatedLine:D.getArg(t,"line"),generatedColumn:D.getArg(t,"column")},n=Hu.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}};Er.prototype.hasContentsOfAllSources=function(){return this._sections.every(function(t){return t.consumer.hasContentsOfAllSources()})};Er.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.')};Er.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}};Er.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)}Vi(this.__generatedMappings,D.compareByGeneratedPositionsDeflated),Vi(this.__originalMappings,D.compareByOriginalPositions)};sc.IndexedSourceMapConsumer=Er});var lE=H(cE=>{var dv=Pu().SourceMapGenerator,ac=Ko(),mv=/(\r?\n)/,gv=10,Zo="$$$isSourceNode$$$";function Pt(e,t,r,n,o){this.children=[],this.sourceContents={},this.line=e??null,this.column=t??null,this.source=r??null,this.name=o??null,this[Zo]=!0,n!=null&&this.add(n)}Pt.fromStringWithSourceMap=function(t,r,n){var o=new Pt,i=t.split(mv),s=0,a=function(){var d=p(),m=p()||"";return d+m;function p(){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]||"",p=m.substr(0,d.generatedColumn-l);i[s]=m.substr(d.generatedColumn-l),l=d.generatedColumn,u(A,p),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=ac.join(n,d)),o.setSourceContent(d,m))}),o;function u(d,m){if(d===null||d.source===void 0)o.add(m);else{var p=n?ac.join(n,d.source):d.source;o.add(new Pt(d.originalLine,d.originalColumn,p,m,d.name))}}};Pt.prototype.add=function(t){if(Array.isArray(t))t.forEach(function(r){this.add(r)},this);else if(t[Zo]||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};Pt.prototype.prepend=function(t){if(Array.isArray(t))for(var r=t.length-1;r>=0;r--)this.prepend(t[r]);else if(t[Zo]||typeof t=="string")this.children.unshift(t);else throw new TypeError("Expected a SourceNode, string, or an array of SourceNodes and strings. Got "+t);return this};Pt.prototype.walk=function(t){for(var r,n=0,o=this.children.length;n<o;n++)r=this.children[n],r[Zo]?r.walk(t):r!==""&&t(r,{source:this.source,line:this.line,column:this.column,name:this.name})};Pt.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};Pt.prototype.replaceRight=function(t,r){var n=this.children[this.children.length-1];return n[Zo]?n.replaceRight(t,r):typeof n=="string"?this.children[this.children.length-1]=n.replace(t,r):this.children.push("".replace(t,r)),this};Pt.prototype.setSourceContent=function(t,r){this.sourceContents[ac.toSetString(t)]=r};Pt.prototype.walkSourceContents=function(t){for(var r=0,n=this.children.length;r<n;r++)this.children[r][Zo]&&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]])};Pt.prototype.toString=function(){var t="";return this.walk(function(r){t+=r}),t};Pt.prototype.toStringWithSourceMap=function(t){var r={code:"",line:1,column:0},n=new dv(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)===gv?(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}};cE.SourceNode=Pt});var AE=H(cc=>{cc.SourceMapGenerator=Pu().SourceMapGenerator;cc.SourceMapConsumer=aE().SourceMapConsumer;cc.SourceNode=lE().SourceNode});function Ac(e){let{children:t,...r}=e;return(0,lc.jsxs)(uE.Link,{...r,target:"_blank",rel:"noopener noreferrer",children:[t," ",(0,lc.jsx)(pa,{fontSize:"small"})]})}var lc,uE,fE=g(()=>{lc=f(L(),1);bA();uE=f(N(),1)});function Uu({text:e,extra:t}){let{classes:r}=pv(),n=t?`supporting data: ${JSON.stringify(t,null,2)}`:"",o=[e,n].filter(Boolean).join(`
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JSON.parse(e.replace(/^\)]}'[^\n]*\n/,""))}ze.parseSourceMapInput=gv;function pv(e,t,r){if(t=t||"",e&&(e[e.length-1]!=="/"&&t[0]!=="/"&&(e+="/"),t=e+t),r){var n=Vi(r);if(!n)throw new Error("sourceMapURL could not be parsed");if(n.path){var o=n.path.lastIndexOf("/");o>=0&&(n.path=n.path.substring(0,o+1))}t=tE(zo(n),t)}return Gu(t)}ze.computeSourceURL=pv});var qu=G(iE=>{var Hu=$o(),Uu=Object.prototype.hasOwnProperty,jn=typeof Map<"u";function Zr(){this._array=[],this._set=jn?new Map:Object.create(null)}Zr.fromArray=function(t,r){for(var n=new Zr,o=0,i=t.length;o<i;o++)n.add(t[o],r);return n};Zr.prototype.size=function(){return jn?this._set.size:Object.getOwnPropertyNames(this._set).length};Zr.prototype.add=function(t,r){var n=jn?t:Hu.toSetString(t),o=jn?this.has(t):Uu.call(this._set,n),i=this._array.length;(!o||r)&&this._array.push(t),o||(jn?this._set.set(t,i):this._set[n]=i)};Zr.prototype.has=function(t){if(jn)return this._set.has(t);var r=Hu.toSetString(t);return Uu.call(this._set,r)};Zr.prototype.indexOf=function(t){if(jn){var r=this._set.get(t);if(r>=0)return r}else{var n=Hu.toSetString(t);if(Uu.call(this._set,n))return this._set[n]}throw new Error('"'+t+'" is not in the set.')};Zr.prototype.at=function(t){if(t>=0&&t<this._array.length)return this._array[t];throw new Error("No element indexed by "+t)};Zr.prototype.toArray=function(){return this._array.slice()};iE.ArraySet=Zr});var cE=G(aE=>{var sE=$o();function hv(e,t){var r=e.generatedLine,n=t.generatedLine,o=e.generatedColumn,i=t.generatedColumn;return n>r||n==r&&i>=o||sE.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){hv(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(sE.compareByGeneratedPositionsInflated),this._sorted=!0),this._array};aE.MappingList=ac});var ju=G(lE=>{var Yi=Ou(),ke=$o(),cc=qu().ArraySet,Cv=cE().MappingList;function tr(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 Cv,this._sourcesContents=null}tr.prototype._version=3;tr.fromSourceMap=function(t,r){var n=t.sourceRoot,o=new tr(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};tr.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}))};tr.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))};tr.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)};tr.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)}};tr.prototype._serializeMappings=function(){for(var t=0,r=1,n=0,o=0,i=0,s=0,a="",c,l,A,u,m=this._mappings.toArray(),d=0,p=m.length;d<p;d++){if(l=m[d],c="",l.generatedLine!==r)for(t=0;l.generatedLine!==r;)c+=";",r++;else if(d>0){if(!ke.compareByGeneratedPositionsInflated(l,m[d-1]))continue;c+=","}c+=Yi.encode(l.generatedColumn-t),t=l.generatedColumn,l.source!=null&&(u=this._sources.indexOf(l.source),c+=Yi.encode(u-s),s=u,c+=Yi.encode(l.originalLine-1-o),o=l.originalLine-1,c+=Yi.encode(l.originalColumn-n),n=l.originalColumn,l.name!=null&&(A=this._names.indexOf(l.name),c+=Yi.encode(A-i),i=A)),a+=c}return a};tr.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)};tr.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};tr.prototype.toString=function(){return JSON.stringify(this.toJSON())};lE.SourceMapGenerator=tr});var AE=G(Jn=>{Jn.GREATEST_LOWER_BOUND=1;Jn.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==Jn.LEAST_UPPER_BOUND?t<n.length?t:-1:s:s-e>1?Ju(e,s,r,n,o,i):i==Jn.LEAST_UPPER_BOUND?s:e<0?-1:e}Jn.search=function(t,r,n,o){if(r.length===0)return-1;var i=Ju(-1,r.length,t,r,n,o||Jn.GREATEST_LOWER_BOUND);if(i<0)return-1;for(;i-1>=0&&n(r[i],r[i-1],!0)===0;)--i;return i}});var mE=G(fE=>{function Ev(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 m=l+1;n(o,i,s,m-1),n(o,i,m+1,a)}}return n}function Iv(e){let t=Ev.toString();return new Function(`return ${t}`)()(e)}var uE=new WeakMap;fE.quickSort=function(e,t,r=0){let n=uE.get(t);n===void 0&&(n=Iv(t),uE.set(t,n)),n(e,t,r,e.length-1)}});var pE=G(lc=>{var k=$o(),Yu=AE(),Ko=qu().ArraySet,xv=Ou(),Wi=mE().quickSort;function pe(e,t){var r=e;return typeof e=="string"&&(r=k.parseSourceMapInput(e)),r.sections!=null?new Er(r,t):new tt(r,t)}pe.fromSourceMap=function(e,t){return tt.fromSourceMap(e,t)};pe.prototype._version=3;pe.prototype.__generatedMappings=null;Object.defineProperty(pe.prototype,"_generatedMappings",{configurable:!0,enumerable:!0,get:function(){return this.__generatedMappings||this._parseMappings(this._mappings,this.sourceRoot),this.__generatedMappings}});pe.prototype.__originalMappings=null;Object.defineProperty(pe.prototype,"_originalMappings",{configurable:!0,enumerable:!0,get:function(){return this.__originalMappings||this._parseMappings(this._mappings,this.sourceRoot),this.__originalMappings}});pe.prototype._charIsMappingSeparator=function(t,r){var n=t.charAt(r);return n===";"||n===","};pe.prototype._parseMappings=function(t,r){throw new Error("Subclasses must implement _parseMappings")};pe.GENERATED_ORDER=1;pe.ORIGINAL_ORDER=2;pe.GREATEST_LOWER_BOUND=1;pe.LEAST_UPPER_BOUND=2;pe.prototype.eachMapping=function(t,r,n){var o=r||null,i=n||pe.GENERATED_ORDER,s;switch(i){case pe.GENERATED_ORDER:s=this._generatedMappings;break;case pe.ORIGINAL_ORDER:s=this._originalMappings;break;default:throw new Error("Unknown order of iteration.")}for(var a=this.sourceRoot,c=t.bind(o),l=this._names,A=this._sources,u=this._sourceMapURL,m=0,d=s.length;m<d;m++){var p=s[m],C=p.source===null?null:A.at(p.source);C!==null&&(C=k.computeSourceURL(a,C,u)),c({source:C,generatedLine:p.generatedLine,generatedColumn:p.generatedColumn,originalLine:p.originalLine,originalColumn:p.originalColumn,name:p.name===null?null:l.at(p.name)})}};pe.prototype.allGeneratedPositionsFor=function(t){var r=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,Yu.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=pe;function tt(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=Ko.fromArray(i.map(String),!0),this._sources=Ko.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}tt.prototype=Object.create(pe.prototype);tt.prototype.consumer=pe;tt.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};tt.fromSourceMap=function(t,r){var n=Object.create(tt.prototype),o=n._names=Ko.fromArray(t._names.toArray(),!0),i=n._sources=Ko.fromArray(t._sources.toArray(),!0);n.sourceRoot=t._sourceRoot,n.sourcesContent=t._generateSourcesContent(n._sources.toArray(),n.sourceRoot),n.file=t._file,n._sourceMapURL=r,n._absoluteSources=n._sources.toArray().map(function(d){return k.computeSourceURL(n.sourceRoot,d,r)});for(var s=t._mappings.toArray().slice(),a=n.__generatedMappings=[],c=n.__originalMappings=[],l=0,A=s.length;l<A;l++){var u=s[l],m=new gE;m.generatedLine=u.generatedLine,m.generatedColumn=u.generatedColumn,u.source&&(m.source=i.indexOf(u.source),m.originalLine=u.originalLine,m.originalColumn=u.originalColumn,u.name&&(m.name=o.indexOf(u.name)),c.push(m)),a.push(m)}return Wi(n.__originalMappings,k.compareByOriginalPositions),n};tt.prototype._version=3;Object.defineProperty(tt.prototype,"sources",{get:function(){return this._absoluteSources.slice()}});function gE(){this.generatedLine=0,this.generatedColumn=0,this.source=null,this.originalLine=null,this.originalColumn=null,this.name=null}var Vu=k.compareByGeneratedPositionsDeflatedNoLine;function dE(e,t){let r=e.length,n=e.length-t;if(!(n<=1))if(n==2){let o=e[t],i=e[t+1];Vu(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(Vu(s,a)<=0)break;e[i-1]=a,e[i]=s}else Wi(e,Vu,t)}tt.prototype._parseMappings=function(t,r){var n=1,o=0,i=0,s=0,a=0,c=0,l=t.length,A=0,u={},m={},d=[],p=[],C,y,I,h,x;let w=0;for(;A<l;)if(t.charAt(A)===";")n++,A++,o=0,dE(p,w),w=p.length;else if(t.charAt(A)===",")A++;else{for(C=new gE,C.generatedLine=n,h=A;h<l&&!this._charIsMappingSeparator(t,h);h++);for(y=t.slice(A,h),I=[];A<h;)xv.decode(t,A,m),x=m.value,A=m.rest,I.push(x);if(I.length===2)throw new Error("Found a source, but no line and column");if(I.length===3)throw new Error("Found a source and line, but no column");if(C.generatedColumn=o+I[0],o=C.generatedColumn,I.length>1&&(C.source=a+I[1],a+=I[1],C.originalLine=i+I[2],i=C.originalLine,C.originalLine+=1,C.originalColumn=s+I[3],s=C.originalColumn,I.length>4&&(C.name=c+I[4],c+=I[4])),p.push(C),typeof C.originalLine=="number"){let S=C.source;for(;d.length<=S;)d.push(null);d[S]===null&&(d[S]=[]),d[S].push(C)}}dE(p,w),this.__generatedMappings=p;for(var Q=0;Q<d.length;Q++)d[Q]!=null&&Wi(d[Q],k.compareByOriginalPositionsNoSource);this.__originalMappings=[].concat(...d)};tt.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 Yu.search(t,r,i,s)};tt.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}};tt.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",pe.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}};tt.prototype.hasContentsOfAllSources=function(){return this.sourcesContent?this.sourcesContent.length>=this._sources.size()&&!this.sourcesContent.some(function(t){return t==null}):!1};tt.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.')};tt.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",pe.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=tt;function Er(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 Ko,this._names=new Ko;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 pe(k.getArg(s,"map"),t)}})}Er.prototype=Object.create(pe.prototype);Er.prototype.constructor=pe;Er.prototype._version=3;Object.defineProperty(Er.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}});Er.prototype.originalPositionFor=function(t){var r={generatedLine:k.getArg(t,"line"),generatedColumn:k.getArg(t,"column")},n=Yu.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 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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-------------------------------------
-`,Xb=`CLUSTAL O(1.2.4) multiple sequence alignment
+`,aB=`CLUSTAL O(1.2.4) multiple sequence alignment
 sp|P69905|HBA_HUMAN       MVLSPADKTNVKAAWGKVGAHAGEYGAEALERMFLSFPTTKTYFPHFDLSHGSAQVKGHG	60
@@ -57,21 +57,21 @@ 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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mouseOverRowName(){let{mouseRow:t}=e;return t===void 0?void 0:this.rowNames[t]},get hoveredInsertion(){let{mouseCol:t,mouseRow:r}=e;if(t===void 0||r===void 0)return;let n=this.rowNames[r];if(!n)return;let o=this.insertionPositions.get(n);if(!o)return;let i=o.find(s=>s.pos===t);if(i)return{rowName:n,col:t,letters:i.letters}},get root(){let t=kb(this.tree,r=>r.children);if(Nb(t,r=>r.children.length>0?0:1),Lb(t,(r,n)=>(r.data.length??1)-(n.data.length??1)),e.showOnly){let r=ps(t,n=>n.data.id===e.showOnly);r&&(t=r)}for(let r of e.collapsed){let n=ps(t,o=>o.data.id===r);n&&(n.children?Pb(n):n.parent?.children&&(n.parent.children=n.parent.children.filter(o=>o.data.id!==r)))}return t},get msaAreaWidth(){return e.width-e.treeAreaWidth},get treeAreaWidthMinusMargin(){return e.treeAreaWidth-e.marginLeft},get blanks(){let{hideGapsEffective:t,realAllowedGappyness:r}=e;if(!t)return[];let n=this.leaves.map(l=>this.MSA?.getRow(l.data.name)).filter(qe.notEmpty);if(n.length===0)return[];let 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Jk="jbrowse-msaview-data",Vk=1,bs="msa-data";async function Fd(){return Rn(Jk,Vk,{upgrade(e){e.objectStoreNames.contains(bs)||e.createObjectStore(bs,{keyPath:"id"}).createIndex("timestamp","timestamp",{unique:!1})}})}function KS(){return`msa-${Date.now()}-${Math.random().toString(36).slice(2,11)}`}async function XS(e,t){try{let r=await Fd(),n={id:e,msa:t.msa,tree:t.tree,treeMetadata:t.treeMetadata,timestamp:Date.now()};return await r.put(bs,n),!0}catch(r){return console.warn("Failed to store MSA data:",r),!1}}async function ZS(e){try{let r=await(await Fd()).get(bs,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 eQ(e=10080*60*1e3){try{let t=await Fd(),r=Date.now()-e,i=await t.transaction(bs,"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}}ys();function tQ(e){let{dataStoreId:t,rows:r}=e;t&&r.length===0&&(async()=>{try{e.setLoadingStoredData(!0);let n=await ZS(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 rQ(e){let{rows:t,dataStoreId:r,isStoringData:n}=e;if(t.length>0&&!r&&!n){if(e.msaFilehandle||e.treeFilehandle)return;let o=e.data.msa,i=e.data.tree;(o||i)&&(e.setIsStoringData(!0),(async()=>{try{let s=KS();await XS(s,{msa:o,tree:i,treeMetadata:e.data.treeMetadata})&&e.setDataStoreId(s)}catch(s){console.error("Failed to store MSA data to IndexedDB:",s)}finally{e.setIsStoringData(!1)}})())}}function nQ(e){e.blastParams&&(async()=>{try{e.setProgress("Submitting query"),e.setError(void 0);let t=await zS({self:e});e.setData(t),e.setBlastParams(void 0)}catch(t){e.setError(t),console.error(t)}finally{e.setProgress("")}})()}function oQ(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=xm(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 iQ(e){let{mouseCol:t,mouseClickCol:r}=e,n=t===void 0?void 0:ws({model:e,coord:t}),o=r===void 0?void 0:ws({model:e,coord:r});e.setConnectedHighlights([n,o].filter(i=>!!i))}function sQ(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=dl(i,t);if(s===void 0){o.clearHighlightFromExternal?.();continue}let a=n.msaToStructure[s];a===void 0?o.clearHighlightFromExternal?.():o.highlightFromExternal?.(a)}}function aQ(e){let{connectedViewId:t,uniprotId:r,rows:n,connectedStructures:o}=e;if(!(!r||n.length===0))for(let i of vn((0,Rd.getSession)(e).views))for(let s=0;s<i.structures.length;s++){let a=i.structures[s];if(!(!a||a.connectedViewId!==t||a.uniprotId!==r||o.some(l=>l.proteinViewId===i.id&&l.structureIdx===s))&&a.structureSequences?.[0])try{e.connectToStructure(i.id,s)}catch(l){console.error("Failed to auto-connect to ProteinView:",l)}}}function cQ(e){let{connectedViewId:t,transcriptToMsaMap:r,querySeqName:n}=e;if(!t||!r)return;let o=new Set;for(let s of vn((0,Rd.getSession)(e).views))for(let a of s.structures){if(a.connectedViewId!==t)continue;let c=a.hoverGenomeHighlights;if(!c||c.length===0)continue;let{g2p:l}=r;for(let A of c)for(let u=A.start;u<A.end;u++){let d=l[u];if(d!==void 0){let m=e.seqPosToGlobalCol(n,d);o.add(m)}}}let i=Array.from(o).map(s=>e.globalColToVisibleCol(s)).filter(s=>s!==void 0);e.setHighlightedColumns(i.length>0?i:void 0)}function lQ(){eQ().catch(e=>{console.error("Failed to cleanup old MSA data:",e)})}var AQ=f(ie());function uQ({model:e}){let{hovered:t}=(0,AQ.getSession)(e),{querySeqName:r,transcriptToMsaMap:n,connectedView:o,mafRegion:i}=e;if(!o?.initialized||!Im(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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dQ(e,t){return fQ[e.toUpperCase()]?.[t.toUpperCase()]??-4}var Wk=-10,zk=-.5;function $k(e,t,r=Wk,n=zk){let o=e.length,i=t.length,s=[],a=[],c=[];for(let h=0;h<=o;h++){s[h]=[],a[h]=[],c[h]=[];for(let y=0;y<=i;y++)s[h][y]=-1/0,a[h][y]=-1/0,c[h][y]=-1/0}s[0][0]=0;for(let h=1;h<=o;h++)a[h][0]=r+(h-1)*n;for(let h=1;h<=i;h++)c[0][h]=r+(h-1)*n;for(let h=1;h<=o;h++)for(let y=1;y<=i;y++){let w=dQ(e[h-1],t[y-1]);s[h][y]=Math.max(s[h-1][y-1],a[h-1][y-1],c[h-1][y-1])+w,a[h][y]=Math.max(s[h-1][y]+r,a[h-1][y]+n),c[h][y]=Math.max(s[h][y-1]+r,c[h][y-1]+n)}let l="",A="",u=o,d=i,m=s[o][i],p=a[o][i],C=c[o][i],x=Math.max(m,p,C),I=x===m?"M":x===p?"Ix":"Iy";for(;u>0||d>0;)if(I==="M"&&u>0&&d>0){l=e[u-1]+l,A=t[d-1]+A;let h=dQ(e[u-1],t[d-1]),y=s[u-1][d-1],w=a[u-1][d-1],S=s[u][d];S===y+h?I="M":S===w+h?I="Ix":I="Iy",u--,d--}else if(I==="Ix"&&u>0){l=e[u-1]+l,A="-"+A;let h=a[u][d],y=s[u-1][d]+r;I=h===y?"M":"Ix",u--}else if(d>0){l="-"+l,A=t[d-1]+A;let h=c[u][d],y=s[u][d-1]+r;I=h===y?"M":"Iy",d--}else break;return{alignedSeq1:l,alignedSeq2:A,score:x}}function Kk(e,t){let r="";for(let n=0;n<e.length;n++){let o=e[n],i=t[n];o==="-"||i==="-"?r+=" ":o.toUpperCase()===i.toUpperCase()?r+="|":r+=" "}return r}function mQ(e,t){let{alignedSeq1:r,alignedSeq2:n}=$k(e,t);return{consensus:Kk(r,n),alns:[{id:"msa",seq:r},{id:"structure",seq:n}]}}function gQ(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}}ys();var tN=(0,xQ.lazy)(()=>Promise.resolve().then(()=>(IQ(),EQ)));function Pd(){return xe.types.compose(yQ.BaseViewModel,Al(),xe.types.model("MsaView",{connectedViewId:xe.types.maybe(xe.types.string),connectedFeature:xe.types.frozen(),connectedHighlights:xe.types.array(xe.types.model({refName:xe.types.string,start:xe.types.number,end:xe.types.number})),blastParams:xe.types.frozen(),querySeqName:"QUERY",uniprotId:xe.types.maybe(xe.types.string),zoomToBaseLevel:!1,init:xe.types.frozen(),connectedStructures:xe.types.array(xe.types.frozen()),dataStoreId:xe.types.maybe(xe.types.string),mafRegion:xe.types.frozen()})).volatile(()=>({rid:void 0,progress:"",error:void 0,loadingStoredData:!1,isStoringData:!1})).views(e=>({getRowByName(t){return e.rows.find(r=>r[0]===t)},getSequenceByRowName(t){return e.rows.find(r=>r[0]===t)?.[1]}})).views(e=>({get transcriptToMsaMap(){return e.connectedFeature?Gh(e.connectedFeature):void 0},get connectedView(){let{views:t}=(0,xi.getSession)(e);return t.find(r=>r.id===e.connectedViewId)},get connectedProteinViews(){let t=vn((0,xi.getSession)(e).views),r=[];for(let n of e.connectedStructures){let o=t.find(i=>i.id===n.proteinViewId);o&&r.push({...n,proteinView:o})}return r}})).views(e=>({get structureHoverCol(){for(let t of e.connectedProteinViews){let n=t.proteinView.structures[t.structureIdx]?.hoverPosition?.structureSeqPos;if(n!==void 0){let o=t.structureToMsa[n];if(o!==void 0){let i=e.getSequenceByRowName(t.msaRowName);if(i){let s=$S(i,o);if(s!==void 0)return e.globalColToVisibleCol(s)}}}}}})).views(e=>({get mouseCol2(){let t=e.structureHoverCol;return t!==void 0?t:uQ({model:e})}})).actions(e=>({setZoomToBaseLevel(t){e.zoomToBaseLevel=t},setError(t){e.error=t},setProgress(t){e.progress=t},setRid(t){e.rid=t},setConnectedHighlights(t){e.connectedHighlights=(0,xe.cast)(t)},addToConnectedHighlights(t){e.connectedHighlights.push(t)},clearConnectedHighlights(){e.connectedHighlights=(0,xe.cast)([])},setBlastParams(t){e.blastParams=t},setInit(t){e.init=t},setQuerySeqName(t){e.querySeqName=t},setUniprotId(t){e.uniprotId=t},setDataStoreId(t){e.dataStoreId=t},setMafRegion(t){e.mafRegion=t},setLoadingStoredData(t){e.loadingStoredData=t},setIsStoringData(t){e.isStoringData=t},handleMsaClick(t){let{connectedView:r,zoomToBaseLevel:n}=e,{assemblyManager:o}=(0,xi.getSession)(e),i=ws({model:e,coord:t});if(!(!i||!r))if(n)r.navTo(i);else{let s=Ls({assemblyManager:o,assemblyNames:r.assemblyNames,refName:i.refName});r.centerAt(i.start,s)}},connectToStructure(t,r,n){let o=n??e.querySeqName,i=e.getSequenceByRowName(o);if(!i)throw new Error(`MSA row "${o}" not found`);let s=i.replaceAll("-",""),a=vn((0,xi.getSession)(e).views).find(p=>p.id===t);if(!a)throw new Error(`ProteinView "${t}" not found`);let c=a.structures[r];if(!c)throw new Error(`Structure at index ${r} not found`);let l=c.structureSequences?.[0];if(!l)throw new Error("Structure sequence not available");let A=mQ(s,l),{seq1ToSeq2:u,seq2ToSeq1:d}=gQ(A),m={proteinViewId:t,structureIdx:r,msaRowName:o,msaToStructure:Object.fromEntries(u),structureToMsa:Object.fromEntries(d)};e.connectedStructures.push(m)},disconnectFromStructure(t,r){let n=e.connectedStructures.findIndex(o=>o.proteinViewId===t&&o.structureIdx===r);n!==-1&&e.connectedStructures.splice(n,1)},disconnectAllStructures(){e.connectedStructures.clear()}})).actions(e=>{let t=e.setMouseClickPos.bind(e);return{setMouseClickPos(r,n){t(r,n),r!==void 0&&e.handleMsaClick(r)}}}).views(e=>({extraViewMenuItems(){return[{label:"Zoom to base level on click?",checked:e.zoomToBaseLevel,type:"checkbox",onClick:()=>{e.setZoomToBaseLevel(!e.zoomToBaseLevel)}},{label:"Connect to protein structure...",onClick:()=>{(0,xi.getSession)(e).queueDialog(t=>[tN,{model:e,handleClose:t}])}},...e.connectedStructures.length>0?[{label:"Disconnect from protein structures",onClick:()=>{e.disconnectAllStructures()}}]:[]]}})).actions(e=>({afterCreate(){lQ();for(let t of[tQ,rQ,nQ,oQ,iQ,sQ,aQ,cQ])(0,xe.addDisposer)(e,(0,wQ.autorun)(()=>{t(e)}))}}))}var lN=(0,PQ.lazy)(()=>Promise.resolve().then(()=>(RQ(),FQ)));function Ud(e){e.addViewType(()=>new OQ.default({name:"MsaView",stateModel:Pd(),ReactComponent:lN}))}var GQ="2.4.2";var hl=class extends HQ.default{constructor(){super(...arguments);this.name="MsaViewPlugin";this.version=GQ;this.rootConfigurationSchema=r=>({msa:(0,qd.ConfigurationSchema)("MSA",{datasets:jd.types.maybe(jd.types.array((0,qd.ConfigurationSchema)("MSAEntry",{datasetId:{type:"string",defaultValue:""},description:{type:"string",defaultValue:""},name:{type:"string",defaultValue:""},adapter:r.pluggableConfigSchemaType("adapter")})))})})}install(r){Ud(r),$A(r),KA(r),Tl(r),zl(r)}configure(r){(0,UQ.isAbstractMenuManager)(r.rootModel)&&r.rootModel.appendToSubMenu(["Add"],{label:"Multiple sequence alignment view",icon:dm,onClick:n=>{n.addView("MsaView",{})}})}};return t1(AN);})();
+`),onProgress:I=>{e.setProgress(I)}}),y=JSON.stringify(d);return await hp({proteinSequence:c,blastDatabase:r,blastProgram:n,msaAlgorithm:o,msa:C.msa,tree:C.tree,treeMetadata:y,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:y}}function Xk(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}bs();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=pl(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}}}_i();var eN="jbrowse-msaview-data",tN=1,Ss="msa-data";async function Um(){return Rn(eN,tN,{upgrade(e){e.objectStoreNames.contains(Ss)||e.createObjectStore(Ss,{keyPath:"id"}).createIndex("timestamp","timestamp",{unique:!1})}})}function sQ(){return`msa-${Date.now()}-${Math.random().toString(36).slice(2,11)}`}async function aQ(e,t){try{let r=await Um(),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 cQ(e){try{let r=await(await Um()).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 lQ(e=10080*60*1e3){try{let t=await Um(),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}}bs();function AQ(e){let{dataStoreId:t,rows:r}=e;t&&r.length===0&&(async()=>{try{e.setLoadingStoredData(!0);let n=await cQ(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 uQ(e){let{rows:t,dataStoreId:r,isStoringData:n}=e;if(t.length>0&&!r&&!n){if(e.msaFilehandle||e.treeFilehandle)return;let o=e.data.msa,i=e.data.tree;(o||i)&&(e.setIsStoringData(!0),(async()=>{try{let s=sQ();await aQ(s,{msa:o,tree:i,treeMetadata:e.data.treeMetadata})&&e.setDataStoreId(s)}catch(s){console.error("Failed to store MSA data to IndexedDB:",s)}finally{e.setIsStoringData(!1)}})())}}function fQ(e){e.blastParams&&(async()=>{try{e.setProgress("Submitting query"),e.setError(void 0);let t=await oQ({self:e});e.setData(t),e.setBlastParams(void 0)}catch(t){e.setError(t),console.error(t)}finally{e.setProgress("")}})()}function mQ(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=Qd(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 dQ(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 gQ(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=pl(i,t);if(s===void 0){o.clearHighlightFromExternal?.();continue}let a=n.msaToStructure[s];a===void 0?o.clearHighlightFromExternal?.():o.highlightFromExternal?.(a)}}function pQ(e){let{connectedViewId:t,uniprotId:r,rows:n,connectedStructures:o}=e;if(!(!r||n.length===0))for(let i of Mn((0,qm.getSession)(e).views))for(let s=0;s<i.structures.length;s++){let a=i.structures[s];if(!(!a||a.connectedViewId!==t||a.uniprotId!==r||o.some(l=>l.proteinViewId===i.id&&l.structureIdx===s))&&a.structureSequences?.[0])try{e.connectToStructure(i.id,s)}catch(l){console.error("Failed to auto-connect to ProteinView:",l)}}}function hQ(e){let{connectedViewId:t,transcriptToMsaMap:r,querySeqName:n}=e;if(!t||!r)return;let o=new Set;for(let s of Mn((0,qm.getSession)(e).views))for(let a of s.structures){if(a.connectedViewId!==t)continue;let c=a.hoverGenomeHighlights;if(!c||c.length===0)continue;let{g2p:l}=r;for(let A of c)for(let u=A.start;u<A.end;u++){let m=l[u];if(m!==void 0){let d=e.seqPosToGlobalCol(n,m);o.add(d)}}}let i=Array.from(o).map(s=>e.globalColToVisibleCol(s)).filter(s=>s!==void 0);e.setHighlightedColumns(i.length>0?i:void 0)}function CQ(){lQ().catch(e=>{console.error("Failed to cleanup old MSA data:",e)})}var EQ=f(ge());function IQ({model:e}){let{hovered:t}=(0,EQ.getSession)(e),{querySeqName:r,transcriptToMsaMap:n,connectedView:o,mafRegion:i}=e;if(!o?.initialized||!Sd(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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yQ(e,t){return xQ[e.toUpperCase()]?.[t.toUpperCase()]??-4}var nN=-10,oN=-.5;function iN(e,t,r=nN,n=oN){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 x=0;x<=i;x++)s[h][x]=-1/0,a[h][x]=-1/0,c[h][x]=-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 x=1;x<=i;x++){let w=yQ(e[h-1],t[x-1]);s[h][x]=Math.max(s[h-1][x-1],a[h-1][x-1],c[h-1][x-1])+w,a[h][x]=Math.max(s[h-1][x]+r,a[h-1][x]+n),c[h][x]=Math.max(s[h][x-1]+r,c[h][x-1]+n)}let l="",A="",u=o,m=i,d=s[o][i],p=a[o][i],C=c[o][i],y=Math.max(d,p,C),I=y===d?"M":y===p?"Ix":"Iy";for(;u>0||m>0;)if(I==="M"&&u>0&&m>0){l=e[u-1]+l,A=t[m-1]+A;let h=yQ(e[u-1],t[m-1]),x=s[u-1][m-1],w=a[u-1][m-1],Q=s[u][m];Q===x+h?I="M":Q===w+h?I="Ix":I="Iy",u--,m--}else if(I==="Ix"&&u>0){l=e[u-1]+l,A="-"+A;let h=a[u][m],x=s[u-1][m]+r;I=h===x?"M":"Ix",u--}else if(m>0){l="-"+l,A=t[m-1]+A;let h=c[u][m],x=s[u][m-1]+r;I=h===x?"M":"Iy",m--}else break;return{alignedSeq1:l,alignedSeq2:A,score:y}}function sN(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 wQ(e,t){let{alignedSeq1:r,alignedSeq2:n}=iN(e,t);return{consensus:sN(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}}bs();var AN=(0,TQ.lazy)(()=>Promise.resolve().then(()=>(vQ(),MQ)));function jm(){return Ie.types.compose(_Q.BaseViewModel,ml(),Ie.types.model("MsaView",{connectedViewId:Ie.types.maybe(Ie.types.string),connectedFeature:Ie.types.frozen(),connectedHighlights:Ie.types.array(Ie.types.model({refName:Ie.types.string,start:Ie.types.number,end:Ie.types.number})),blastParams:Ie.types.frozen(),querySeqName:"QUERY",uniprotId:Ie.types.maybe(Ie.types.string),zoomToBaseLevel:!1,init:Ie.types.frozen(),connectedStructures:Ie.types.array(Ie.types.frozen()),dataStoreId:Ie.types.maybe(Ie.types.string),mafRegion:Ie.types.frozen()})).volatile(()=>({rid:void 0,progress:"",error:void 0,loadingStoredData:!1,isStoringData:!1})).views(e=>({getRowByName(t){return e.rows.find(r=>r[0]===t)},getSequenceByRowName(t){return e.rows.find(r=>r[0]===t)?.[1]}})).views(e=>({get transcriptToMsaMap(){return e.connectedFeature?zh(e.connectedFeature):void 0},get connectedView(){let{views:t}=(0,Ii.getSession)(e);return t.find(r=>r.id===e.connectedViewId)},get connectedProteinViews(){let t=Mn((0,Ii.getSession)(e).views),r=[];for(let n of e.connectedStructures){let o=t.find(i=>i.id===n.proteinViewId);o&&r.push({...n,proteinView:o})}return r}})).views(e=>({get structureHoverCol(){for(let t of e.connectedProteinViews){let n=t.proteinView.structures[t.structureIdx]?.hoverPosition?.structureSeqPos;if(n!==void 0){let o=t.structureToMsa[n];if(o!==void 0){let i=e.getSequenceByRowName(t.msaRowName);if(i){let s=iQ(i,o);if(s!==void 0)return e.globalColToVisibleCol(s)}}}}}})).views(e=>({get mouseCol2(){let t=e.structureHoverCol;return t!==void 0?t:IQ({model:e})}})).actions(e=>({setZoomToBaseLevel(t){e.zoomToBaseLevel=t},setError(t){e.error=t},setProgress(t){e.progress=t},setRid(t){e.rid=t},setConnectedHighlights(t){e.connectedHighlights=(0,Ie.cast)(t)},addToConnectedHighlights(t){e.connectedHighlights.push(t)},clearConnectedHighlights(){e.connectedHighlights=(0,Ie.cast)([])},setBlastParams(t){e.blastParams=t},setInit(t){e.init=t},setQuerySeqName(t){e.querySeqName=t},setUniprotId(t){e.uniprotId=t},setDataStoreId(t){e.dataStoreId=t},setMafRegion(t){e.mafRegion=t},setLoadingStoredData(t){e.loadingStoredData=t},setIsStoringData(t){e.isStoringData=t},handleMsaClick(t){let{connectedView:r,zoomToBaseLevel:n}=e,{assemblyManager:o}=(0,Ii.getSession)(e),i=Bs({model:e,coord:t});if(!(!i||!r))if(n)r.navTo(i);else{let s=Rs({assemblyManager:o,assemblyNames:r.assemblyNames,refName:i.refName});r.centerAt(i.start,s)}},connectToStructure(t,r,n){let o=n??e.querySeqName,i=e.getSequenceByRowName(o);if(!i)throw new Error(`MSA row "${o}" not found`);let s=i.replaceAll("-",""),a=Mn((0,Ii.getSession)(e).views).find(p=>p.id===t);if(!a)throw new Error(`ProteinView "${t}" not found`);let c=a.structures[r];if(!c)throw new Error(`Structure at index ${r} not found`);let l=c.structureSequences?.[0];if(!l)throw new Error("Structure sequence not available");let A=wQ(s,l),{seq1ToSeq2:u,seq2ToSeq1:m}=bQ(A),d={proteinViewId:t,structureIdx:r,msaRowName:o,msaToStructure:Object.fromEntries(u),structureToMsa:Object.fromEntries(m)};e.connectedStructures.push(d)},disconnectFromStructure(t,r){let n=e.connectedStructures.findIndex(o=>o.proteinViewId===t&&o.structureIdx===r);n!==-1&&e.connectedStructures.splice(n,1)},disconnectAllStructures(){e.connectedStructures.clear()}})).actions(e=>{let t=e.setMouseClickPos.bind(e);return{setMouseClickPos(r,n){t(r,n),r!==void 0&&e.handleMsaClick(r)}}}).views(e=>({extraViewMenuItems(){return[{label:"Zoom to base level on click?",checked:e.zoomToBaseLevel,type:"checkbox",onClick:()=>{e.setZoomToBaseLevel(!e.zoomToBaseLevel)}},{label:"Connect to protein structure...",onClick:()=>{(0,Ii.getSession)(e).queueDialog(t=>[AN,{model:e,handleClose:t}])}},...e.connectedStructures.length>0?[{label:"Disconnect from protein structures",onClick:()=>{e.disconnectAllStructures()}}]:[]]}})).actions(e=>({afterCreate(){CQ();for(let t of[AQ,uQ,fQ,mQ,dQ,gQ,pQ,hQ])(0,Ie.addDisposer)(e,(0,DQ.autorun)(()=>{t(e)}))}}))}var CN=(0,YQ.lazy)(()=>Promise.resolve().then(()=>(VQ(),JQ)));function Wm(e){e.addViewType(()=>new WQ.default({name:"MsaView",stateModel:jm(),ReactComponent:CN}))}var zQ="2.4.3";var Il=class extends $Q.default{constructor(){super(...arguments);this.name="MsaViewPlugin";this.version=zQ;this.rootConfigurationSchema=r=>({msa:(0,zm.ConfigurationSchema)("MSA",{datasets:$m.types.maybe($m.types.array((0,zm.ConfigurationSchema)("MSAEntry",{datasetId:{type:"string",defaultValue:""},description:{type:"string",defaultValue:""},name:{type:"string",defaultValue:""},adapter:r.pluggableConfigSchemaType("adapter")})))})})}install(r){Wm(r),ru(r),nu(r),kl(r),Xl(r)}configure(r){(0,KQ.isAbstractMenuManager)(r.rootModel)&&r.rootModel.appendToSubMenu(["Add"],{label:"Multiple sequence alignment view",icon:Ed,onClick:n=>{n.addView("MsaView",{})}})}};return A1(EN);})();
 /*! Bundled license information:
 use-sync-external-store/cjs/use-sync-external-store-shim.production.js: