@realsee/dnalogel 3.40.0 → 3.40.2

package/docs/assets/highlight.css

@@ -1,127 +0,0 @@
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-    --dark-hl-0: #DCDCAA;
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-    --dark-hl-5: #569CD6;
-    --light-hl-6: #0070C1;
-    --dark-hl-6: #4FC1FF;
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-    --hl-13: var(--light-hl-13);
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-    --hl-13: var(--dark-hl-13);
-    --hl-14: var(--dark-hl-14);
-    --code-background: var(--dark-code-background);
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-.hl-3 { color: var(--hl-3); }
-.hl-4 { color: var(--hl-4); }
-.hl-5 { color: var(--hl-5); }
-.hl-6 { color: var(--hl-6); }
-.hl-7 { color: var(--hl-7); }
-.hl-8 { color: var(--hl-8); }
-.hl-9 { color: var(--hl-9); }
-.hl-10 { color: var(--hl-10); }
-.hl-11 { color: var(--hl-11); }
-.hl-12 { color: var(--hl-12); }
-.hl-13 { color: var(--hl-13); }
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package/docs/assets/main.js

@@ -1,58 +0,0 @@
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this.minimizedNodes?n.parent.edges[n.char]=this.minimizedNodes[i]:(n.child._str=i,this.minimizedNodes[i]=n.child),this.uncheckedNodes.pop()}};t.Index=function(e){this.invertedIndex=e.invertedIndex,this.fieldVectors=e.fieldVectors,this.tokenSet=e.tokenSet,this.fields=e.fields,this.pipeline=e.pipeline},t.Index.prototype.search=function(e){return this.query(function(r){var n=new t.QueryParser(e,r);n.parse()})},t.Index.prototype.query=function(e){for(var r=new t.Query(this.fields),n=Object.create(null),i=Object.create(null),s=Object.create(null),o=Object.create(null),a=Object.create(null),l=0;l<this.fields.length;l++)i[this.fields[l]]=new t.Vector;e.call(r,r);for(var l=0;l<r.clauses.length;l++){var u=r.clauses[l],d=null,m=t.Set.empty;u.usePipeline?d=this.pipeline.runString(u.term,{fields:u.fields}):d=[u.term];for(var y=0;y<d.length;y++){var b=d[y];u.term=b;var g=t.TokenSet.fromClause(u),E=this.tokenSet.intersect(g).toArray();if(E.length===0&&u.presence===t.Query.presence.REQUIRED){for(var f=0;f<u.fields.length;f++){var p=u.fields[f];o[p]=t.Set.empty}break}for(var w=0;w<E.length;w++)for(var S=E[w],k=this.invertedIndex[S],_=k._index,f=0;f<u.fields.length;f++){var p=u.fields[f],B=k[p],A=Object.keys(B),j=S+"/"+p,q=new t.Set(A);if(u.presence==t.Query.presence.REQUIRED&&(m=m.union(q),o[p]===void 0&&(o[p]=t.Set.complete)),u.presence==t.Query.presence.PROHIBITED){a[p]===void 0&&(a[p]=t.Set.empty),a[p]=a[p].union(q);continue}if(i[p].upsert(_,u.boost,function(Ee,be){return Ee+be}),!s[j]){for(var V=0;V<A.length;V++){var $=A[V],I=new t.FieldRef($,p),z=B[$],W;(W=n[I])===void 0?n[I]=new t.MatchData(S,p,z):W.add(S,p,z)}s[j]=!0}}}if(u.presence===t.Query.presence.REQUIRED)for(var f=0;f<u.fields.length;f++){var p=u.fields[f];o[p]=o[p].intersect(m)}}for(var H=t.Set.complete,R=t.Set.empty,l=0;l<this.fields.length;l++){var p=this.fields[l];o[p]&&(H=H.intersect(o[p])),a[p]&&(R=R.union(a[p]))}var c=Object.keys(n),v=[],C=Object.create(null);if(r.isNegated()){c=Object.keys(this.fieldVectors);for(var l=0;l<c.length;l++){var I=c[l],T=t.FieldRef.fromString(I);n[I]=new t.MatchData}}for(var l=0;l<c.length;l++){var T=t.FieldRef.fromString(c[l]),h=T.docRef;if(H.contains(h)&&!R.contains(h)){var x=this.fieldVectors[T],O=i[T.fieldName].similarity(x),F;if((F=C[h])!==void 0)F.score+=O,F.matchData.combine(n[T]);else{var L={ref:h,score:O,matchData:n[T]};C[h]=L,v.push(L)}}}return v.sort(function(xe,Le){return Le.score-xe.score})},t.Index.prototype.toJSON=function(){var e=Object.keys(this.invertedIndex).sort().map(function(n){return[n,this.invertedIndex[n]]},this),r=Object.keys(this.fieldVectors).map(function(n){return[n,this.fieldVectors[n].toJSON()]},this);return{version:t.version,fields:this.fields,fieldVectors:r,invertedIndex:e,pipeline:this.pipeline.toJSON()}},t.Index.load=function(e){var r={},n={},i=e.fieldVectors,s=Object.create(null),o=e.invertedIndex,a=new t.TokenSet.Builder,l=t.Pipeline.load(e.pipeline);e.version!=t.version&&t.utils.warn("Version mismatch when loading serialised index. Current version of lunr '"+t.version+"' does not match serialized index '"+e.version+"'");for(var u=0;u<i.length;u++){var d=i[u],m=d[0],y=d[1];n[m]=new t.Vector(y)}for(var u=0;u<o.length;u++){var d=o[u],b=d[0],g=d[1];a.insert(b),s[b]=g}return a.finish(),r.fields=e.fields,r.fieldVectors=n,r.invertedIndex=s,r.tokenSet=a.root,r.pipeline=l,new t.Index(r)};t.Builder=function(){this._ref="id",this._fields=Object.create(null),this._documents=Object.create(null),this.invertedIndex=Object.create(null),this.fieldTermFrequencies={},this.fieldLengths={},this.tokenizer=t.tokenizer,this.pipeline=new t.Pipeline,this.searchPipeline=new t.Pipeline,this.documentCount=0,this._b=.75,this._k1=1.2,this.termIndex=0,this.metadataWhitelist=[]},t.Builder.prototype.ref=function(e){this._ref=e},t.Builder.prototype.field=function(e,r){if(/\//.test(e))throw new RangeError("Field '"+e+"' contains illegal character '/'");this._fields[e]=r||{}},t.Builder.prototype.b=function(e){e<0?this._b=0:e>1?this._b=1:this._b=e},t.Builder.prototype.k1=function(e){this._k1=e},t.Builder.prototype.add=function(e,r){var n=e[this._ref],i=Object.keys(this._fields);this._documents[n]=r||{},this.documentCount+=1;for(var s=0;s<i.length;s++){var o=i[s],a=this._fields[o].extractor,l=a?a(e):e[o],u=this.tokenizer(l,{fields:[o]}),d=this.pipeline.run(u),m=new t.FieldRef(n,o),y=Object.create(null);this.fieldTermFrequencies[m]=y,this.fieldLengths[m]=0,this.fieldLengths[m]+=d.length;for(var b=0;b<d.length;b++){var g=d[b];if(y[g]==null&&(y[g]=0),y[g]+=1,this.invertedIndex[g]==null){var E=Object.create(null);E._index=this.termIndex,this.termIndex+=1;for(var f=0;f<i.length;f++)E[i[f]]=Object.create(null);this.invertedIndex[g]=E}this.invertedIndex[g][o][n]==null&&(this.invertedIndex[g][o][n]=Object.create(null));for(var p=0;p<this.metadataWhitelist.length;p++){var w=this.metadataWhitelist[p],S=g.metadata[w];this.invertedIndex[g][o][n][w]==null&&(this.invertedIndex[g][o][n][w]=[]),this.invertedIndex[g][o][n][w].push(S)}}}},t.Builder.prototype.calculateAverageFieldLengths=function(){for(var e=Object.keys(this.fieldLengths),r=e.length,n={},i={},s=0;s<r;s++){var o=t.FieldRef.fromString(e[s]),a=o.fieldName;i[a]||(i[a]=0),i[a]+=1,n[a]||(n[a]=0),n[a]+=this.fieldLengths[o]}for(var l=Object.keys(this._fields),s=0;s<l.length;s++){var u=l[s];n[u]=n[u]/i[u]}this.averageFieldLength=n},t.Builder.prototype.createFieldVectors=function(){for(var e={},r=Object.keys(this.fieldTermFrequencies),n=r.length,i=Object.create(null),s=0;s<n;s++){for(var o=t.FieldRef.fromString(r[s]),a=o.fieldName,l=this.fieldLengths[o],u=new t.Vector,d=this.fieldTermFrequencies[o],m=Object.keys(d),y=m.length,b=this._fields[a].boost||1,g=this._documents[o.docRef].boost||1,E=0;E<y;E++){var f=m[E],p=d[f],w=this.invertedIndex[f]._index,S,k,_;i[f]===void 0?(S=t.idf(this.invertedIndex[f],this.documentCount),i[f]=S):S=i[f],k=S*((this._k1+1)*p)/(this._k1*(1-this._b+this._b*(l/this.averageFieldLength[a]))+p),k*=b,k*=g,_=Math.round(k*1e3)/1e3,u.insert(w,_)}e[o]=u}this.fieldVectors=e},t.Builder.prototype.createTokenSet=function(){this.tokenSet=t.TokenSet.fromArray(Object.keys(this.invertedIndex).sort())},t.Builder.prototype.build=function(){return this.calculateAverageFieldLengths(),this.createFieldVectors(),this.createTokenSet(),new t.Index({invertedIndex:this.invertedIndex,fieldVectors:this.fieldVectors,tokenSet:this.tokenSet,fields:Object.keys(this._fields),pipeline:this.searchPipeline})},t.Builder.prototype.use=function(e){var r=Array.prototype.slice.call(arguments,1);r.unshift(this),e.apply(this,r)},t.MatchData=function(e,r,n){for(var i=Object.create(null),s=Object.keys(n||{}),o=0;o<s.length;o++){var a=s[o];i[a]=n[a].slice()}this.metadata=Object.create(null),e!==void 0&&(this.metadata[e]=Object.create(null),this.metadata[e][r]=i)},t.MatchData.prototype.combine=function(e){for(var r=Object.keys(e.metadata),n=0;n<r.length;n++){var i=r[n],s=Object.keys(e.metadata[i]);this.metadata[i]==null&&(this.metadata[i]=Object.create(null));for(var o=0;o<s.length;o++){var a=s[o],l=Object.keys(e.metadata[i][a]);this.metadata[i][a]==null&&(this.metadata[i][a]=Object.create(null));for(var u=0;u<l.length;u++){var d=l[u];this.metadata[i][a][d]==null?this.metadata[i][a][d]=e.metadata[i][a][d]:this.metadata[i][a][d]=this.metadata[i][a][d].concat(e.metadata[i][a][d])}}}},t.MatchData.prototype.add=function(e,r,n){if(!(e in this.metadata)){this.metadata[e]=Object.create(null),this.metadata[e][r]=n;return}if(!(r in this.metadata[e])){this.metadata[e][r]=n;return}for(var i=Object.keys(n),s=0;s<i.length;s++){var o=i[s];o in this.metadata[e][r]?this.metadata[e][r][o]=this.metadata[e][r][o].concat(n[o]):this.metadata[e][r][o]=n[o]}},t.Query=function(e){this.clauses=[],this.allFields=e},t.Query.wildcard=new String("*"),t.Query.wildcard.NONE=0,t.Query.wildcard.LEADING=1,t.Query.wildcard.TRAILING=2,t.Query.presence={OPTIONAL:1,REQUIRED:2,PROHIBITED:3},t.Query.prototype.clause=function(e){return"fields"in e||(e.fields=this.allFields),"boost"in e||(e.boost=1),"usePipeline"in e||(e.usePipeline=!0),"wildcard"in e||(e.wildcard=t.Query.wildcard.NONE),e.wildcard&t.Query.wildcard.LEADING&&e.term.charAt(0)!=t.Query.wildcard&&(e.term="*"+e.term),e.wildcard&t.Query.wildcard.TRAILING&&e.term.slice(-1)!=t.Query.wildcard&&(e.term=""+e.term+"*"),"presence"in e||(e.presence=t.Query.presence.OPTIONAL),this.clauses.push(e),this},t.Query.prototype.isNegated=function(){for(var e=0;e<this.clauses.length;e++)if(this.clauses[e].presence!=t.Query.presence.PROHIBITED)return!1;return!0},t.Query.prototype.term=function(e,r){if(Array.isArray(e))return e.forEach(function(i){this.term(i,t.utils.clone(r))},this),this;var n=r||{};return n.term=e.toString(),this.clause(n),this},t.QueryParseError=function(e,r,n){this.name="QueryParseError",this.message=e,this.start=r,this.end=n},t.QueryParseError.prototype=new Error,t.QueryLexer=function(e){this.lexemes=[],this.str=e,this.length=e.length,this.pos=0,this.start=0,this.escapeCharPositions=[]},t.QueryLexer.prototype.run=function(){for(var e=t.QueryLexer.lexText;e;)e=e(this)},t.QueryLexer.prototype.sliceString=function(){for(var e=[],r=this.start,n=this.pos,i=0;i<this.escapeCharPositions.length;i++)n=this.escapeCharPositions[i],e.push(this.str.slice(r,n)),r=n+1;return e.push(this.str.slice(r,this.pos)),this.escapeCharPositions.length=0,e.join("")},t.QueryLexer.prototype.emit=function(e){this.lexemes.push({type:e,str:this.sliceString(),start:this.start,end:this.pos}),this.start=this.pos},t.QueryLexer.prototype.escapeCharacter=function(){this.escapeCharPositions.push(this.pos-1),this.pos+=1},t.QueryLexer.prototype.next=function(){if(this.pos>=this.length)return t.QueryLexer.EOS;var e=this.str.charAt(this.pos);return this.pos+=1,e},t.QueryLexer.prototype.width=function(){return this.pos-this.start},t.QueryLexer.prototype.ignore=function(){this.start==this.pos&&(this.pos+=1),this.start=this.pos},t.QueryLexer.prototype.backup=function(){this.pos-=1},t.QueryLexer.prototype.acceptDigitRun=function(){var e,r;do e=this.next(),r=e.charCodeAt(0);while(r>47&&r<58);e!=t.QueryLexer.EOS&&this.backup()},t.QueryLexer.prototype.more=function(){return this.pos<this.length},t.QueryLexer.EOS="EOS",t.QueryLexer.FIELD="FIELD",t.QueryLexer.TERM="TERM",t.QueryLexer.EDIT_DISTANCE="EDIT_DISTANCE",t.QueryLexer.BOOST="BOOST",t.QueryLexer.PRESENCE="PRESENCE",t.QueryLexer.lexField=function(e){return e.backup(),e.emit(t.QueryLexer.FIELD),e.ignore(),t.QueryLexer.lexText},t.QueryLexer.lexTerm=function(e){if(e.width()>1&&(e.backup(),e.emit(t.QueryLexer.TERM)),e.ignore(),e.more())return t.QueryLexer.lexText},t.QueryLexer.lexEditDistance=function(e){return e.ignore(),e.acceptDigitRun(),e.emit(t.QueryLexer.EDIT_DISTANCE),t.QueryLexer.lexText},t.QueryLexer.lexBoost=function(e){return e.ignore(),e.acceptDigitRun(),e.emit(t.QueryLexer.BOOST),t.QueryLexer.lexText},t.QueryLexer.lexEOS=function(e){e.width()>0&&e.emit(t.QueryLexer.TERM)},t.QueryLexer.termSeparator=t.tokenizer.separator,t.QueryLexer.lexText=function(e){for(;;){var r=e.next();if(r==t.QueryLexer.EOS)return t.QueryLexer.lexEOS;if(r.charCodeAt(0)==92){e.escapeCharacter();continue}if(r==":")return t.QueryLexer.lexField;if(r=="~")return e.backup(),e.width()>0&&e.emit(t.QueryLexer.TERM),t.QueryLexer.lexEditDistance;if(r=="^")return e.backup(),e.width()>0&&e.emit(t.QueryLexer.TERM),t.QueryLexer.lexBoost;if(r=="+"&&e.width()===1||r=="-"&&e.width()===1)return e.emit(t.QueryLexer.PRESENCE),t.QueryLexer.lexText;if(r.match(t.QueryLexer.termSeparator))return t.QueryLexer.lexTerm}},t.QueryParser=function(e,r){this.lexer=new t.QueryLexer(e),this.query=r,this.currentClause={},this.lexemeIdx=0},t.QueryParser.prototype.parse=function(){this.lexer.run(),this.lexemes=this.lexer.lexemes;for(var e=t.QueryParser.parseClause;e;)e=e(this);return this.query},t.QueryParser.prototype.peekLexeme=function(){return this.lexemes[this.lexemeIdx]},t.QueryParser.prototype.consumeLexeme=function(){var e=this.peekLexeme();return this.lexemeIdx+=1,e},t.QueryParser.prototype.nextClause=function(){var e=this.currentClause;this.query.clause(e),this.currentClause={}},t.QueryParser.parseClause=function(e){var r=e.peekLexeme();if(r!=null)switch(r.type){case t.QueryLexer.PRESENCE:return t.QueryParser.parsePresence;case t.QueryLexer.FIELD:return t.QueryParser.parseField;case t.QueryLexer.TERM:return t.QueryParser.parseTerm;default:var n="expected either a field or a term, found "+r.type;throw r.str.length>=1&&(n+=" with value '"+r.str+"'"),new t.QueryParseError(n,r.start,r.end)}},t.QueryParser.parsePresence=function(e){var r=e.consumeLexeme();if(r!=null){switch(r.str){case"-":e.currentClause.presence=t.Query.presence.PROHIBITED;break;case"+":e.currentClause.presence=t.Query.presence.REQUIRED;break;default:var n="unrecognised presence operator'"+r.str+"'";throw new t.QueryParseError(n,r.start,r.end)}var i=e.peekLexeme();if(i==null){var n="expecting term or field, found nothing";throw new t.QueryParseError(n,r.start,r.end)}switch(i.type){case t.QueryLexer.FIELD:return t.QueryParser.parseField;case t.QueryLexer.TERM:return t.QueryParser.parseTerm;default:var n="expecting term or field, found '"+i.type+"'";throw new t.QueryParseError(n,i.start,i.end)}}},t.QueryParser.parseField=function(e){var r=e.consumeLexeme();if(r!=null){if(e.query.allFields.indexOf(r.str)==-1){var n=e.query.allFields.map(function(o){return"'"+o+"'"}).join(", "),i="unrecognised field '"+r.str+"', possible fields: "+n;throw new t.QueryParseError(i,r.start,r.end)}e.currentClause.fields=[r.str];var s=e.peekLexeme();if(s==null){var i="expecting term, found nothing";throw new t.QueryParseError(i,r.start,r.end)}switch(s.type){case t.QueryLexer.TERM:return t.QueryParser.parseTerm;default:var i="expecting term, found '"+s.type+"'";throw new t.QueryParseError(i,s.start,s.end)}}},t.QueryParser.parseTerm=function(e){var r=e.consumeLexeme();if(r!=null){e.currentClause.term=r.str.toLowerCase(),r.str.indexOf("*")!=-1&&(e.currentClause.usePipeline=!1);var n=e.peekLexeme();if(n==null){e.nextClause();return}switch(n.type){case t.QueryLexer.TERM:return e.nextClause(),t.QueryParser.parseTerm;case t.QueryLexer.FIELD:return e.nextClause(),t.QueryParser.parseField;case t.QueryLexer.EDIT_DISTANCE:return t.QueryParser.parseEditDistance;case t.QueryLexer.BOOST:return t.QueryParser.parseBoost;case t.QueryLexer.PRESENCE:return e.nextClause(),t.QueryParser.parsePresence;default:var i="Unexpected lexeme type '"+n.type+"'";throw new t.QueryParseError(i,n.start,n.end)}}},t.QueryParser.parseEditDistance=function(e){var r=e.consumeLexeme();if(r!=null){var n=parseInt(r.str,10);if(isNaN(n)){var i="edit distance must be numeric";throw new t.QueryParseError(i,r.start,r.end)}e.currentClause.editDistance=n;var s=e.peekLexeme();if(s==null){e.nextClause();return}switch(s.type){case t.QueryLexer.TERM:return e.nextClause(),t.QueryParser.parseTerm;case t.QueryLexer.FIELD:return e.nextClause(),t.QueryParser.parseField;case t.QueryLexer.EDIT_DISTANCE:return t.QueryParser.parseEditDistance;case t.QueryLexer.BOOST:return t.QueryParser.parseBoost;case t.QueryLexer.PRESENCE:return e.nextClause(),t.QueryParser.parsePresence;default:var i="Unexpected lexeme type '"+s.type+"'";throw new t.QueryParseError(i,s.start,s.end)}}},t.QueryParser.parseBoost=function(e){var r=e.consumeLexeme();if(r!=null){var n=parseInt(r.str,10);if(isNaN(n)){var i="boost must be numeric";throw new t.QueryParseError(i,r.start,r.end)}e.currentClause.boost=n;var s=e.peekLexeme();if(s==null){e.nextClause();return}switch(s.type){case t.QueryLexer.TERM:return e.nextClause(),t.QueryParser.parseTerm;case t.QueryLexer.FIELD:return e.nextClause(),t.QueryParser.parseField;case t.QueryLexer.EDIT_DISTANCE:return t.QueryParser.parseEditDistance;case t.QueryLexer.BOOST:return t.QueryParser.parseBoost;case t.QueryLexer.PRESENCE:return e.nextClause(),t.QueryParser.parsePresence;default:var i="Unexpected lexeme type '"+s.type+"'";throw new t.QueryParseError(i,s.start,s.end)}}},function(e,r){typeof define=="function"&&define.amd?define(r):typeof se=="object"?oe.exports=r():e.lunr=r()}(this,function(){return 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-/*! Bundled license information:
-
-lunr/lunr.js:
-  (**
-   * lunr - http://lunrjs.com - A bit like Solr, but much smaller and not as bright - 2.3.9
-   * Copyright (C) 2020 Oliver Nightingale
-   * @license MIT
-   *)
-  (*!
-   * lunr.utils
-   * Copyright (C) 2020 Oliver Nightingale
-   *)
-  (*!
-   * lunr.Set
-   * Copyright (C) 2020 Oliver Nightingale
-   *)
-  (*!
-   * lunr.tokenizer
-   * Copyright (C) 2020 Oliver Nightingale
-   *)
-  (*!
-   * lunr.Pipeline
-   * Copyright (C) 2020 Oliver Nightingale
-   *)
-  (*!
-   * lunr.Vector
-   * Copyright (C) 2020 Oliver Nightingale
-   *)
-  (*!
-   * lunr.stemmer
-   * Copyright (C) 2020 Oliver Nightingale
-   * Includes code from - http://tartarus.org/~martin/PorterStemmer/js.txt
-   *)
-  (*!
-   * lunr.stopWordFilter
-   * Copyright (C) 2020 Oliver Nightingale
-   *)
-  (*!
-   * lunr.trimmer
-   * Copyright (C) 2020 Oliver Nightingale
-   *)
-  (*!
-   * lunr.TokenSet
-   * Copyright (C) 2020 Oliver Nightingale
-   *)
-  (*!
-   * lunr.Index
-   * Copyright (C) 2020 Oliver Nightingale
-   *)
-  (*!
-   * lunr.Builder
-   * Copyright (C) 2020 Oliver Nightingale
-   *)
-*/