npm - jbrowse-plugin-mafviewer - Versions diffs - 1.4.5 → 1.4.6 - Mend

jbrowse-plugin-mafviewer 1.4.5 → 1.4.6

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 (169) hide show

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

@@ -1,31 +1,19 @@
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r=t.dyn_tree,n=t.max_code,i=t.stat_desc.static_tree,o=t.stat_desc.has_stree,a=t.stat_desc.extra_bits,u=t.stat_desc.extra_base,f=t.stat_desc.max_length,s,c,l,d,p,h,m=0;for(d=0;d<=yi;d++)e.bl_count[d]=0;for(r[e.heap[e.heap_max]*2+1]=0,s=e.heap_max+1;s<Ex;s++)c=e.heap[s],d=r[r[c*2+1]*2+1]+1,d>f&&(d=f,m++),r[c*2+1]=d,!(c>n)&&(e.bl_count[d]++,p=0,c>=u&&(p=a[c-u]),h=r[c*2],e.opt_len+=h*(d+p),o&&(e.static_len+=h*(i[c*2+1]+p)));if(m!==0){do{for(d=f-1;e.bl_count[d]===0;)d--;e.bl_count[d]--,e.bl_count[d+1]+=2,e.bl_count[f]--,m-=2}while(m>0);for(d=f;d!==0;d--)for(c=e.bl_count[d];c!==0;)l=e.heap[--s],!(l>n)&&(r[l*2+1]!==d&&(e.opt_len+=(d-r[l*2+1])*r[l*2],r[l*2+1]=d),c--)}}function jx(e,t,r){var n=new Array(yi+1),i=0,o,a;for(o=1;o<=yi;o++)n[o]=i=i+r[o-1]<<1;for(a=0;a<=t;a++){var u=e[a*2+1];u!==0&&(e[a*2]=qx(n[u]++,u))}}function Fk(){var e,t,r,n,i,o=new Array(yi+1);for(Ar=new Array((Za+2)*2),go(Ar),yo=new Array(_o*2),go(yo),xo=new Array(kk),go(xo),So=new Array(Mk-Pk+1),go(So),oc=new 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Nx(e,t,r,n){Ct(e,(Rk<<1)+(n?1:0),3),Lk(e,t,r,!0)}function Uk(e){Ct(e,Ox<<1,3),Rr(e,Wh,Ar),qk(e)}function Wk(e,t,r,n){var i,o,a=0;e.level>0?(e.strm.data_type===wo.Z_UNKNOWN&&(e.strm.data_type=Bk(e)),zh(e,e.l_desc),zh(e,e.d_desc),a=Nk(e),i=e.opt_len+3+7>>>3,o=e.static_len+3+7>>>3,o<=i&&(i=o)):i=o=r+5,r+4<=i&&t!==-1?Nx(e,t,r,n):e.strategy===wo.Z_FIXED||o===i?(Ct(e,(Ox<<1)+(n?1:0),3),yx(e,Ar,yo)):(Ct(e,(Tk<<1)+(n?1:0),3),Dk(e,e.l_desc.max_code+1,e.d_desc.max_code+1,a+1),yx(e,e.dyn_ltree,e.dyn_dtree)),Fx(e),n&&Lx(e)}function Hk(e,t,r){return e.pending_buf[e.d_buf+e.last_lit*2]=t>>>8&255,e.pending_buf[e.d_buf+e.last_lit*2+1]=t&255,e.pending_buf[e.l_buf+e.last_lit]=r&255,e.last_lit++,t===0?e.dyn_ltree[r*2]++:(e.matches++,t--,e.dyn_ltree[(So[r]+Ya+1)*2]++,e.dyn_dtree[kx(t)*2]++),e.last_lit===e.lit_bufsize-1}});var Gx=g(It=>{"use strict";var $h=It&&It.__importDefault||function(e){return e&&e.__esModule?e:{default:e}};Object.defineProperty(It,"__esModule",{value:!0});It.deflateInfo=void 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e.strstart++,e.ins_h=(e.ins_h<<e.hash_shift^e.window[e.strstart+xe-1])&e.hash_mask,r=e.prev[e.strstart&e.w_mask]=e.head[e.ins_h],e.head[e.ins_h]=e.strstart;while(--e.match_length!==0);e.strstart++}else e.strstart+=e.match_length,e.match_length=0,e.ins_h=e.window[e.strstart],e.ins_h=(e.ins_h<<e.hash_shift^e.window[e.strstart+1])&e.hash_mask;else n=(0,Yt._tr_tally)(e,0,e.window[e.strstart]),e.lookahead--,e.strstart++;if(n&&(st(e,!1),e.strm.avail_out===0))return Qe}return e.insert=e.strstart<xe-1?e.strstart:xe-1,t===Y.Z_FINISH?(st(e,!0),e.strm.avail_out===0?Si:Eo):e.last_lit&&(st(e,!1),e.strm.avail_out===0)?Qe:Qa}function Oo(e,t){for(var r,n,i;;){if(e.lookahead<cr){if(Oi(e),e.lookahead<cr&&t===Y.Z_NO_FLUSH)return 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a.forEach(function(f,s){f&&u.push(r[s])}),u})}},{key:"_filterStatic",value:function(r,n){return this.eval(n).then(function(i){return typeof i=="boolean"?i?r:void 0:r[i]})}}]),e})();H1.exports=Oj});var K1=g((ZQ,Z1)=>{"use strict";var $1=Sn(),Ej=$1(Ai()),Aj=$1(Ri()),Rj=/^-?(?:(?:[0-9]*\.[0-9]+)|[0-9]+)$/,G1=/^[a-zA-Zа-яА-Я_\u00C0-\u00D6\u00D8-\u00F6\u00F8-\u00FF$][a-zA-Zа-яА-Я0-9_\u00C0-\u00D6\u00D8-\u00F6\u00F8-\u00FF$]*$/,Tj=/\\\\/,Pj=/^\s*$/,Mj=["'(?:(?:\\\\')|[^'])*'",'"(?:(?:\\\\")|[^"])*"',"\\s+","\\btrue\\b","\\bfalse\\b"],Cj=["[a-zA-Z\u0430-\u044F\u0410-\u042F_\xC0-\xD6\xD8-\xF6\xF8-\xFF\\$][a-zA-Z0-9\u0430-\u044F\u0410-\u042F_\xC0-\xD6\xD8-\xF6\xF8-\xFF\\$]*","(?:(?:[0-9]*\\.[0-9]+)|[0-9]+)"],Ij=["binaryOp","unaryOp","openParen","openBracket","question","colon"],kj=(function(){function e(t){(0,Ej.default)(this,e),this._grammar=t}return(0,Aj.default)(e,[{key:"getElements",value:function(r){var n=this._getSplitRegex();return r.split(n).filter(function(i){return 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n=Object.keys(this._grammar.elements).sort(function(i,o){return o.length-i.length}).map(function(i){return r._escapeRegExp(i)},this);this._splitRegex=new RegExp("("+[Mj.join("|"),n.join("|"),Cj.join("|")].join("|")+")")}return this._splitRegex}},{key:"_isNegative",value:function(r){return r.length?Ij.some(function(n){return n===r[r.length-1].type}):!0}},{key:"_isWhitespace",value:function(r){return!!r.match(Pj)}},{key:"_unquote",value:function(r){var n=r[0],i=new RegExp("\\\\"+n,"g");return r.substr(1,r.length-2).replace(i,n).replace(Tj,"\\")}}]),e})();Z1.exports=kj});var xm=g(et=>{"use strict";et.argVal=function(e){e&&this._cursor.args.push(e)};et.arrayStart=function(){this._placeAtCursor({type:"ArrayLiteral",value:[]})};et.arrayVal=function(e){e&&this._cursor.value.push(e)};et.binaryOp=function(e){for(var t=this._grammar.elements[e.value].precedence||0,r=this._cursor._parent;r&&r.operator&&this._grammar.elements[r.operator].precedence>=t;)this._cursor=r,r=r._parent;var n={type:"BinaryExpression",operator:e.value,left:this._cursor};this._setParent(this._cursor,n),this._cursor=r,this._placeAtCursor(n)};et.dot=function(){this._nextIdentEncapsulate=this._cursor&&this._cursor.type!=="UnaryExpression"&&(this._cursor.type!=="BinaryExpression"||this._cursor.type==="BinaryExpression"&&this._cursor.right),this._nextIdentRelative=!this._cursor||this._cursor&&!this._nextIdentEncapsulate,this._nextIdentRelative&&(this._relative=!0)};et.filter=function(e){this._placeBeforeCursor({type:"FilterExpression",expr:e,relative:this._subParser.isRelative(),subject:this._cursor})};et.functionCall=function(){this._placeBeforeCursor({type:"FunctionCall",name:this._cursor.value,args:[],pool:"functions"})};et.identifier=function(e){var t={type:"Identifier",value:e.value};this._nextIdentEncapsulate?(t.from=this._cursor,this._placeBeforeCursor(t),this._nextIdentEncapsulate=!1):(this._nextIdentRelative&&(t.relative=!0,this._nextIdentRelative=!1),this._placeAtCursor(t))};et.literal=function(e){this._placeAtCursor({type:"Literal",value:e.value})};et.objKey=function(e){this._curObjKey=e.value};et.objStart=function(){this._placeAtCursor({type:"ObjectLiteral",value:{}})};et.objVal=function(e){this._cursor.value[this._curObjKey]=e};et.subExpression=function(e){this._placeAtCursor(e)};et.ternaryEnd=function(e){this._cursor.alternate=e};et.ternaryMid=function(e){this._cursor.consequent=e};et.ternaryStart=function(){this._tree={type:"ConditionalExpression",test:this._tree},this._cursor=this._tree};et.transform=function(e){this._placeBeforeCursor({type:"FunctionCall",name:e.value,args:[this._cursor],pool:"transforms"})};et.unaryOp=function(e){this._placeAtCursor({type:"UnaryExpression",operator:e.value})}});var X1=g(Y1=>{"use 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kt=xm();Y1.states={expectOperand:{tokenTypes:{literal:{toState:"expectBinOp"},identifier:{toState:"identifier"},unaryOp:{},openParen:{toState:"subExpression"},openCurl:{toState:"expectObjKey",handler:kt.objStart},dot:{toState:"traverse"},openBracket:{toState:"arrayVal",handler:kt.arrayStart}}},expectBinOp:{tokenTypes:{binaryOp:{toState:"expectOperand"},pipe:{toState:"expectTransform"},dot:{toState:"traverse"},question:{toState:"ternaryMid",handler:kt.ternaryStart}},completable:!0},expectTransform:{tokenTypes:{identifier:{toState:"postTransform",handler:kt.transform}}},expectObjKey:{tokenTypes:{identifier:{toState:"expectKeyValSep",handler:kt.objKey},closeCurl:{toState:"expectBinOp"}}},expectKeyValSep:{tokenTypes:{colon:{toState:"objVal"}}},postTransform:{tokenTypes:{openParen:{toState:"argVal"},binaryOp:{toState:"expectOperand"},dot:{toState:"traverse"},openBracket:{toState:"filter"},pipe:{toState:"expectTransform"}},completable:!0},postArgs:{tokenTypes:{binaryOp:{toState:"expectOperand"},dot:{toState:"traverse"},openBracket:{toState:"filter"},pipe:{toState:"expectTransform"}},completable:!0},identifier:{tokenTypes:{binaryOp:{toState:"expectOperand"},dot:{toState:"traverse"},openBracket:{toState:"filter"},openParen:{toState:"argVal",handler:kt.functionCall},pipe:{toState:"expectTransform"},question:{toState:"ternaryMid",handler:kt.ternaryStart}},completable:!0},traverse:{tokenTypes:{identifier:{toState:"identifier"}}},filter:{subHandler:kt.filter,endStates:{closeBracket:"identifier"}},subExpression:{subHandler:kt.subExpression,endStates:{closeParen:"expectBinOp"}},argVal:{subHandler:kt.argVal,endStates:{comma:"argVal",closeParen:"postArgs"}},objVal:{subHandler:kt.objVal,endStates:{comma:"expectObjKey",closeCurl:"expectBinOp"}},arrayVal:{subHandler:kt.arrayVal,endStates:{comma:"arrayVal",closeBracket:"expectBinOp"}},ternaryMid:{subHandler:kt.ternaryMid,endStates:{colon:"ternaryEnd"}},ternaryEnd:{subHandler:kt.ternaryEnd,completable:!0}}});var eS=g((XQ,Q1)=>{"use strict";var J1=Sn(),qj=J1(Ai()),jj=J1(Ri()),Fj=xm(),mc=X1().states,Lj=(function(){function e(t,r,n){(0,qj.default)(this,e),this._grammar=t,this._state="expectOperand",this._tree=null,this._exprStr=r||"",this._relative=!1,this._stopMap=n||{}}return(0,jj.default)(e,[{key:"addToken",value:function(r){if(this._state==="complete")throw new Error("Cannot add a new token to a completed Parser");var n=mc[this._state],i=this._exprStr;if(this._exprStr+=r.raw,n.subHandler){this._subParser||this._startSubExpression(i);var o=this._subParser.addToken(r);if(o){if(this._endSubExpression(),this._parentStop)return o;this._state=o}}else if(n.tokenTypes[r.type]){var a=n.tokenTypes[r.type],u=Fj[r.type];a.handler&&(u=a.handler),u&&u.call(this,r),a.toState&&(this._state=a.toState)}else{if(this._stopMap[r.type])return this._stopMap[r.type];throw new Error("Token ".concat(r.raw," (").concat(r.type,") unexpected in expression: 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n=mc[this._state].endStates;n||(this._parentStop=!0,n=this._stopMap),this._subParser=new e(this._grammar,r,n)}}]),e})();Q1.exports=Lj});var nS=g((JQ,rS)=>{"use strict";var tS=Sn(),Nj=tS(Ai()),Dj=tS(Ri()),On=(function(){function e(t){(0,Nj.default)(this,e),t(this._resolve.bind(this),this._reject.bind(this))}return(0,Dj.default)(e,[{key:"catch",value:function(r){if(this.error)try{this._resolve(r(this.error))}catch(n){this._reject(n)}return this}},{key:"then",value:function(r,n){if(!this.error)try{this._resolve(r(this.value))}catch(i){this._reject(i)}return n&&this.catch(n),this}},{key:"_reject",value:function(r){this.value=void 0,this.error=r}},{key:"_resolve",value:function(r){r instanceof e?r.error?this._reject(r.error):this._resolve(r.value):(this.value=r,this.error=void 0)}}]),e})();On.all=function(e){return new On(function(t){var r=e.map(function(n){for(;n instanceof On;){if(n.error)throw Error(n.error);n=n.value}return n});t(r)})};On.resolve=function(e){return new 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this._ast||this.compile(),this._ast}}]),e})();oS.exports=Gj});var sS=g(uS=>{"use strict";uS.getGrammar=function(){return{elements:{".":{type:"dot"},"[":{type:"openBracket"},"]":{type:"closeBracket"},"|":{type:"pipe"},"{":{type:"openCurl"},"}":{type:"closeCurl"},":":{type:"colon"},",":{type:"comma"},"(":{type:"openParen"},")":{type:"closeParen"},"?":{type:"question"},"+":{type:"binaryOp",precedence:30,eval:function(t,r){return t+r}},"-":{type:"binaryOp",precedence:30,eval:function(t,r){return t-r}},"*":{type:"binaryOp",precedence:40,eval:function(t,r){return t*r}},"/":{type:"binaryOp",precedence:40,eval:function(t,r){return t/r}},"//":{type:"binaryOp",precedence:40,eval:function(t,r){return Math.floor(t/r)}},"%":{type:"binaryOp",precedence:50,eval:function(t,r){return t%r}},"^":{type:"binaryOp",precedence:50,eval:function(t,r){return Math.pow(t,r)}},"==":{type:"binaryOp",precedence:20,eval:function(t,r){return t==r}},"!=":{type:"binaryOp",precedence:20,eval:function(t,r){return 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this._grammar.transforms[r]}},{key:"eval",value:function(r){var n=arguments.length>1&&arguments[1]!==void 0?arguments[1]:{},i=this.createExpression(r);return i.eval(n)}},{key:"evalSync",value:function(r){var n=arguments.length>1&&arguments[1]!==void 0?arguments[1]:{},i=this.createExpression(r);return i.evalSync(n)}},{key:"expr",value:function(r){for(var n=arguments.length,i=new Array(n>1?n-1:0),o=1;o<n;o++)i[o-1]=arguments[o];var a=r.reduce(function(u,f,s){var c=s<i.length?i[s]:"";return u+=f+c,u},"");return this.createExpression(a)}},{key:"removeOp",value:function(r){this._grammar.elements[r]&&(this._grammar.elements[r].type==="binaryOp"||this._grammar.elements[r].type==="unaryOp")&&delete this._grammar.elements[r]}},{key:"_addGrammarElement",value:function(r,n){this._grammar.elements[r]=n}}]),e})();Om.exports=new cS;Om.exports.Jexl=cS});var fS=g(_u=>{"use strict";var Qj=_u&&_u.__importDefault||function(e){return 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The file "${f.name}" may need to be reopened.`);let l=`fh-blob-${f.handleId}`;return t[l]=n,{locationType:"BlobLocation",name:f.name,blobId:l}},a=f=>{if(!(!f||typeof f!="object"||o.has(f)))if(o.add(f),Array.isArray(f))for(let n=0;n<f.length;n++){let l=f[n];wf(l)?f[n]=r(l):a(l)}else{let n=f;for(let l of Object.keys(n)){let d=n[l];wf(d)?n[l]=r(d):a(d)}}};a(e)}var wo=class e extends So{pluginManager;constructor(t){super(),this.pluginManager=t}async serializeArguments(t,o){return await this.augmentLocationObjects(t,o),{...t,blobMap:Cf()}}async serializeNewAuthArguments(t,o){let r=this.pluginManager.rootModel;if(!Tf(r)||t.internetAccountPreAuthorization)return t;let a=r.findAppropriateInternetAccount(t);return a&&(t.internetAccountPreAuthorization=await a.getPreAuthorizationInformation(t)),t}async deserializeArguments(t,o){return t.blobMap&&Fu(t.blobMap),t}async executeDirect(t){}supportsDirectExecution(){return this.executeDirect!==e.prototype.executeDirect}async serializeReturn(t,o,r){return t}async deserializeReturn(t,o,r){let a;try{a=await t}catch(f){if(Eu(f)){let n=this.pluginManager.rootModel?.createEphemeralInternetAccount(`HTTPBasicInternetAccount-${new URL(f.url).origin}`,{},f.url);throw new Fr("Retrying with created internet account",n.internetAccountId)}throw f}return bu(a)?a.value:a}async augmentLocationObjects(t,o){let r=this.pluginManager.rootModel,a=[],f=Cf(),{renderingProps:n,...l}=t;if(Oc(l,f),Of(l,(d,s)=>{if(Sf(s)&&a.push(s),Array.isArray(s))for(let u of s)Sf(u)&&a.push(u);return[d,s]},{deep:!0}),Tf(r)&&r.internetAccounts.length===0)return t;for(let d of a)await this.serializeNewAuthArguments(d,o);return t}};var Co=class e{filterChain;constructor({filters:t,jexl:o}){this.filterChain=t.map(r=>r.trim()).filter(r=>!!r).map(r=>{if(typeof r=="string")return{expr:Ou(r,o),string:r};throw new Error(`invalid inputFilter string "${r}"`)})}passes(...t){for(let o of this.filterChain)if(!o.expr.eval({feature:t[0]}))return!1;return!0}toJSON(){return{filters:this.filterChain.map(t=>t.string)}}static fromJSON(t){return new e(t)}};var nt=class extends wo{async deserializeArguments(t,o){return{...await super.deserializeArguments(t,o),filters:t.filters?new Co({filters:t.filters,jexl:this.pluginManager.jexl}):void 0}}async serializeArguments(t,o){let a=this.pluginManager.rootModel?.session?.assemblyManager;if(!a)throw new Error("no assembly manager");let f=await vu(a,{...t,filters:t.filters?.toJSON().filters});return super.serializeArguments(f,o)}};var Ro=class extends nt{name="MafGetSamples";async execute(t,o){let r=this.pluginManager,a=await this.deserializeArguments(t,o),{regions:f,adapterConfig:n,sessionId:l}=a,{dataAdapter:d}=await To(r,l,n);return d.getSamples(f,a)}};function Ef(e){e.addRpcMethod(()=>new Ro(e))}function Nu({regions:e,showAllLetters:t,samples:o,features:r,includeInsertions:a}){let f=e[0],n=new Map(o.map((u,i)=>[u.id,i])),l=f.end-f.start,d=o.map(()=>new Array(l).fill("-")),s=new Map;for(let u of r.values()){let i=u.get("start"),p=u.get("alignments"),m=u.get("seq");for(let[h,c]of Object.entries(p)){let w=c.seq,T=n.get(h);if(T===void 0)continue;let g=d[T];for(let x=0,C=0,y=w.length;x<y;x++)if(m[x]!=="-"){let R=w[x],S=i+C-f.start;S>=0&&S<l&&(R==="-"?g[S]="-":R!==" "&&(t?g[S]=R:m[x]===R?g[S]=".":g[S]=R)),C++}else if(a){let R="";for(;x<w.length&&m[x]==="-";){let S=w[x];R+=S!=="-"&&S!==" "?S:"-",x++}if(x--,R.length>0){let S=i+C-f.start;if(S>=0&&S<=l){let B=s.get(S)||[];B.push({sequence:R,sampleIndex:T}),s.set(S,B)}}}}}return a&&s.size>0?Ec(d,s,o.length):d.map(u=>u.join(""))}function Ec(e,t,o){let r=[...t.keys()].sort((a,f)=>f-a);for(let a of r){let f=t.get(a),n=0;for(let d of f)d.sequence.length>n&&(n=d.sequence.length);let l=new Map;for(let d of f)l.set(d.sampleIndex,d.sequence);for(let d=0;d<o;d++){let s=e[d],u=l.get(d);if(u){let i=u.padEnd(n,"-");s.splice(a,0,...i.split(""))}else{let i=new Array(n).fill("-");s.splice(a,0,...i)}}}return e.map(a=>a.join(""))}var yo=class extends nt{name="MafGetSequences";async execute(t,o){let r=await this.deserializeArguments(t,o),{samples:a,regions:f,adapterConfig:n,sessionId:l,showAllLetters:d,includeInsertions:s}=r,u=(await To(this.pluginManager,l,n)).dataAdapter,i=await Xe(u.getFeatures(f[0],r).pipe($e()));return Nu({features:new Map(i.map(p=>[p.id(),p])),samples:a,regions:f,showAllLetters:d,includeInsertions:s})}};function bf(e){e.addRpcMethod(()=>new yo(e))}var Ni=A(Q()),Hi=A(Wu());var Vu=A(Q());var vr=A(Q()),Gu=A(X());var _u=A(re()),Uu=A(De()),bc=(0,Uu.makeStyles)()(e=>({highlight:{height:"100%",position:"absolute",background:Ru(e.palette.primary.main).alpha(.4).toRgbString(),borderLeft:`2px solid ${e.palette.primary.main}`,borderRight:`2px solid ${e.palette.primary.main}`,pointerEvents:"none",zIndex:10}})),Qc=(0,_u.observer)(function({model:t}){let{classes:o}=bc(),r=(0,Gu.getSession)(t),{assemblyManager:a}=r,f="widgets"in r?r.widgets:void 0;if(!f)return null;let n=[];for(let[,l]of f){let d=l;if(d.type==="MafSequenceWidget"&&d.connectedViewId===t.id){let s=l,{hoverHighlight:u}=s;if(u){let{refName:i,start:p,end:m,assemblyName:h}=u,w=a.get(h)?.getCanonicalRefName(i)??i,T=t.bpToPx({refName:w,coord:p}),g=t.bpToPx({refName:w,coord:m});if(T&&g){let x=Math.min(T.offsetPx,g.offsetPx)-t.offsetPx,C=Math.max(Math.abs(g.offsetPx-T.offsetPx),3);n.push(vr.default.createElement("div",{key:`maf-hover-${s.id}`,className:o.highlight,style:{left:x,width:C}}))}}}}return vr.default.createElement(vr.default.Fragment,null,n)}),Ju=Qc;function Qf(e){e.addToExtensionPoint("LinearGenomeView-TracksContainerComponent",(t,o)=>{let r=o.model;return[...t,Vu.default.createElement(Ju,{key:"maf-sequence-hover-highlight",model:r})]})}var Ku=A(He()),Yu=(0,Ku.ConfigurationSchema)("MafSequenceWidget",{});var Pe=A(Te());function qu(){return Pe.types.model("MafSequenceWidget",{id:Pe.types.identifier,type:Pe.types.literal("MafSequenceWidget"),adapterConfig:Pe.types.frozen(void 0),samples:Pe.types.frozen(void 0),regions:Pe.types.frozen(void 0),connectedViewId:Pe.types.maybe(Pe.types.string)}).volatile(()=>({hoverHighlight:void 0})).actions(e=>({setHoverHighlight(t){e.hoverHighlight=t}}))}function Vf(e){e.addWidgetType(()=>new Hi.default({name:"MafSequenceWidget",heading:"MAF Sequence",configSchema:Yu,stateModel:qu(),ReactComponent:(0,Ni.lazy)(()=>Promise.resolve().then(()=>(Li(),Pi)))})),Qf(e)}var Vi=A(Le());var Wi=A(Nr()),Wt=A(X()),Gi=A(Hr()),_i=A(Wr()),Ui=A(Te());var Io=class extends Wi.BaseFeatureDataAdapter{setupP;async setupPre(){if(!this.getSubAdapter)throw new Error("no getSubAdapter available");return{adapter:(await this.getSubAdapter({...(0,Ui.getSnapshot)(this.config),type:"BedTabixAdapter"})).dataAdapter}}async setupPre2(){return this.setupP||(this.setupP=this.setupPre().catch(t=>{throw this.setupP=void 0,t})),this.setupP}async setup(t){let{statusCallback:o=()=>{}}=t||{};return(0,Wt.updateStatus)("Downloading index",o,()=>this.setupPre2())}async getRefNames(t){let{adapter:o}=await this.setup(t);return o.getRefNames()}async getHeader(t){let{adapter:o}=await this.setup(t);return o.getHeader()}getFeatures(t,o){let{statusCallback:r=()=>{}}=o||{};return(0,_i.ObservableCreate)(async a=>{let{adapter:f}=await this.setup(o),n=await(0,Wt.updateStatus)("Downloading alignments",r,()=>Xe(f.getFeatures(t).pipe($e())));await(0,Wt.updateStatus)("Processing alignments",r,()=>{let l="",d=this.getConf("refAssemblyName");for(let s of n){let u=s.get("field5").split(","),i={},p=u.length;for(let m=0;m<p;m++){let c=u[m].split(":"),[w,T,g,x,C,y]=c;if(!w||!y)continue;let{assemblyName:R,chr:S}=gn(w);R&&(l||(l=R),i[R]={chr:S,start:+T,srcSize:+g,strand:x==="-"?-1:1,unknown:+C,seq:y})}a.next(new Wt.SimpleFeature({id:s.id(),data:{start:s.get("start"),end:s.get("end"),refName:s.get("refName"),name:s.get("name"),score:s.get("score"),alignments:i,seq:Sn(i,d,t.assemblyName,l)}}))}}),a.complete()})}async getSamples(t){let o=this.getConf("nhLocation"),r=o.uri==="/path/to/my.nh"?void 0:await(0,Gi.openLocation)(o).readFile("utf8");return{samples:mt(this.getConf("samples")),tree:r?Ut(r):void 0}}freeResources(){}};var Kf=A(He());var Nc=(0,Kf.ConfigurationSchema)("MafTabixAdapter",{samples:{type:"frozen",description:"string[] or {id:string,label:string,color?:string}[]",defaultValue:[]},bedGzLocation:{type:"fileLocation",defaultValue:{uri:"/path/to/my.bed.gz.tbi",locationType:"UriLocation"}},refAssemblyName:{type:"string",defaultValue:""},index:(0,Kf.ConfigurationSchema)("Index",{location:{type:"fileLocation",defaultValue:{uri:"/path/to/my.bed.gz.tbi"}},indexType:{type:"string",defaultValue:"TBI"}}),nhLocation:{type:"fileLocation",description:"newick tree",defaultValue:{uri:"/path/to/my.nh",locationType:"UriLocation"}}},{explicitlyTyped:!0,preProcessSnapshot:e=>e.uri?{...e,...e.nhUri?{nhLocation:{uri:e.nhUri,baseUri:e.baseUri}}:{},bedGzLocation:{uri:e.uri,baseUri:e.baseUri},index:{location:{uri:`${e.uri}.tbi`,baseUri:e.baseUri}}}:e}),Ji=Nc;function Yf(e){return e.addAdapterType(()=>new Vi.AdapterType({name:"MafTabixAdapter",AdapterClass:Io,configSchema:Ji}))}var Pr=A(Le());var Ki=A(He()),Yi=A(Le());function qf(e){return(0,Ki.ConfigurationSchema)("MafTrack",{},{baseConfiguration:(0,Yi.createBaseTrackConfig)(e),explicitIdentifier:"trackId"})}function jf(e){return e.addTrackType(()=>{let t=qf(e);return new Pr.TrackType({name:"MafTrack",configSchema:t,displayName:"MAF track",stateModel:(0,Pr.createBaseTrackModel)(e,"MafTrack",t)})})}var Lr=class extends qi.default{name="MafViewerPlugin";version=Zf;install(t){Xr(t),jf(t),Ma(t),Ga(t),Yf(t),Ua(t),bf(t),Ef(t),Vf(t)}configure(t){}};return ep(Hc);})();
 /*! Bundled license information:
-tabbable/dist/index.esm.js:
-  (*!
-  * tabbable 6.3.0
-  * @license MIT, https://github.com/focus-trap/tabbable/blob/master/LICENSE
-  *)
-canvas2svg/canvas2svg.js:
-  (*!!
-   *  Canvas 2 Svg v1.0.15
-   *  A low level canvas to SVG converter. Uses a mock canvas context to build an SVG document.
-   *
-   *  Licensed under the MIT license:
-   *  http://www.opensource.org/licenses/mit-license.php
+react-is/cjs/react-is.production.min.js:
+  (** @license React v16.13.1
+   * react-is.production.min.js
    *
-   *  Author:
-   *  Kerry Liu
+   * Copyright (c) Facebook, Inc. and its affiliates.
    *
-   *  Copyright (c) 2014 Gliffy Inc.
+   * This source code is licensed under the MIT license found in the
+   * LICENSE file in the root directory of this source tree.
    *)
 */
 //# sourceMappingURL=jbrowse-plugin-mafviewer.umd.production.min.js.map