higlass-transcripts.js

/*! For license information please see higlass-transcripts.js.LICENSE.txt */
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m=8+(i.w_bits-8<<4)<<8;m|=(i.strategy>=2||i.level<2?0:i.level<6?1:6===i.level?2:3)<<6,0!==i.strstart&&(m|=32),m+=31-m%31,i.status=113,g(i,m),0!==i.strstart&&(g(i,t.adler>>>16),g(i,65535&t.adler)),t.adler=1}if(69===i.status)if(i.gzhead.extra){for(s=i.pending;i.gzindex<(65535&i.gzhead.extra.length)&&(i.pending!==i.pending_buf_size||(i.gzhead.hcrc&&i.pending>s&&(t.adler=o(t.adler,i.pending_buf,i.pending-s,s)),f(t),s=i.pending,i.pending!==i.pending_buf_size));)p(i,255&i.gzhead.extra[i.gzindex]),i.gzindex++;i.gzhead.hcrc&&i.pending>s&&(t.adler=o(t.adler,i.pending_buf,i.pending-s,s)),i.gzindex===i.gzhead.extra.length&&(i.gzindex=0,i.status=73)}else 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n,r,i,a=e.dyn_tree,s=e.stat_desc.static_tree,o=e.stat_desc.has_stree,h=e.stat_desc.elems,l=-1;for(t.heap_len=0,t.heap_max=573,n=0;n<h;n++)0!==a[2*n]?(t.heap[++t.heap_len]=l=n,t.depth[n]=0):a[2*n+1]=0;for(;t.heap_len<2;)a[2*(i=t.heap[++t.heap_len]=l<2?++l:0)]=1,t.depth[i]=0,t.opt_len--,o&&(t.static_len-=s[2*i+1]);for(e.max_code=l,n=t.heap_len>>1;n>=1;n--)I(t,a,n);i=h;do{n=t.heap[1],t.heap[1]=t.heap[t.heap_len--],I(t,a,1),r=t.heap[1],t.heap[--t.heap_max]=n,t.heap[--t.heap_max]=r,a[2*i]=a[2*n]+a[2*r],t.depth[i]=(t.depth[n]>=t.depth[r]?t.depth[n]:t.depth[r])+1,a[2*n+1]=a[2*r+1]=i,t.heap[1]=i++,I(t,a,1)}while(t.heap_len>=2);t.heap[--t.heap_max]=t.heap[1],function(t,e){var n,r,i,a,s,o,h=e.dyn_tree,l=e.max_code,u=e.stat_desc.static_tree,c=e.stat_desc.has_stree,f=e.stat_desc.extra_bits,d=e.stat_desc.extra_base,p=e.stat_desc.max_length,g=0;for(a=0;a<=15;a++)t.bl_count[a]=0;for(h[2*t.heap[t.heap_max]+1]=0,n=t.heap_max+1;n<573;n++)(a=h[2*h[2*(r=t.heap[n])+1]+1]+1)>p&&(a=p,g++),h[2*r+1]=a,r>l||(t.bl_count[a]++,s=0,r>=d&&(s=f[r-d]),o=h[2*r],t.opt_len+=o*(a+s),c&&(t.static_len+=o*(u[2*r+1]+s)));if(0!==g){do{for(a=p-1;0===t.bl_count[a];)a--;t.bl_count[a]--,t.bl_count[a+1]+=2,t.bl_count[p]--,g-=2}while(g>0);for(a=p;0!==a;a--)for(r=t.bl_count[a];0!==r;)(i=t.heap[--n])>l||(h[2*i+1]!==a&&(t.opt_len+=(a-h[2*i+1])*h[2*i],h[2*i+1]=a),r--)}}(t,e),T(a,l,t.bl_count)}function z(t,e,n){var r,i,a=-1,s=e[1],o=0,h=7,l=4;for(0===s&&(h=138,l=3),e[2*(n+1)+1]=65535,r=0;r<=n;r++)i=s,s=e[2*(r+1)+1],++o<h&&i===s||(o<l?t.bl_tree[2*i]+=o:0!==i?(i!==a&&t.bl_tree[2*i]++,t.bl_tree[32]++):o<=10?t.bl_tree[34]++:t.bl_tree[36]++,o=0,a=i,0===s?(h=138,l=3):i===s?(h=6,l=3):(h=7,l=4))}function P(t,e,n){var r,i,a=-1,s=e[1],o=0,h=7,l=4;for(0===s&&(h=138,l=3),r=0;r<=n;r++)if(i=s,s=e[2*(r+1)+1],!(++o<h&&i===s)){if(o<l)do{x(t,i,t.bl_tree)}while(0!=--o);else 0!==i?(i!==a&&(x(t,i,t.bl_tree),o--),x(t,16,t.bl_tree),k(t,o-3,2)):o<=10?(x(t,17,t.bl_tree),k(t,o-3,3)):(x(t,18,t.bl_tree),k(t,o-11,7));o=0,a=i,0===s?(h=138,l=3):i===s?(h=6,l=3):(h=7,l=4)}}i(v);var R=!1;function O(t,e,n,i){k(t,0+(i?1:0),3),function(t,e,n,i){E(t),i&&(y(t,n),y(t,~n)),r.arraySet(t.pending_buf,t.window,e,n,t.pending),t.pending+=n}(t,e,n,!0)}e._tr_init=function(t){R||(!function(){var t,e,n,r,i,h=new 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t.pending_buf[t.d_buf+2*t.last_lit]=e>>>8&255,t.pending_buf[t.d_buf+2*t.last_lit+1]=255&e,t.pending_buf[t.l_buf+t.last_lit]=255&n,t.last_lit++,0===e?t.dyn_ltree[2*n]++:(t.matches++,e--,t.dyn_ltree[2*(f[n]+256+1)]++,t.dyn_dtree[2*_(e)]++),t.last_lit===t.lit_bufsize-1},e._tr_align=function(t){k(t,2,3),x(t,256,l),function(t){16===t.bi_valid?(y(t,t.bi_buf),t.bi_buf=0,t.bi_valid=0):t.bi_valid>=8&&(t.pending_buf[t.pending++]=255&t.bi_buf,t.bi_buf>>=8,t.bi_valid-=8)}(t)}},function(t,e,n){"use strict";var r=n(30),i=n(2),a=n(13),s=n(15),o=n(6),h=n(14),l=n(33),u=Object.prototype.toString;function c(t){if(!(this instanceof c))return new c(t);this.options=i.assign({chunkSize:16384,windowBits:0,to:""},t||{});var 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13:if(n.last){g>>>=7&m,m-=7&m,n.mode=27;break}for(;m<3;){if(0===d)break t;d--,g+=l[c++]<<m,m+=8}switch(n.last=1&g,m-=1,3&(g>>>=1)){case 0:n.mode=14;break;case 1:if(v(n),n.mode=20,6===e){g>>>=2,m-=2;break t}break;case 2:n.mode=17;break;case 3:t.msg="invalid block type",n.mode=30}g>>>=2,m-=2;break;case 14:for(g>>>=7&m,m-=7&m;m<32;){if(0===d)break t;d--,g+=l[c++]<<m,m+=8}if((65535&g)!=(g>>>16^65535)){t.msg="invalid stored block lengths",n.mode=30;break}if(n.length=65535&g,g=0,m=0,n.mode=15,6===e)break t;case 15:n.mode=16;case 16:if(y=n.length){if(y>d&&(y=d),y>p&&(y=p),0===y)break t;r.arraySet(u,l,c,y,f),d-=y,c+=y,p-=y,f+=y,n.length-=y;break}n.mode=12;break;case 17:for(;m<14;){if(0===d)break t;d--,g+=l[c++]<<m,m+=8}if(n.nlen=257+(31&g),g>>>=5,m-=5,n.ndist=1+(31&g),g>>>=5,m-=5,n.ncode=4+(15&g),g>>>=4,m-=4,n.nlen>286||n.ndist>30){t.msg="too many length or distance symbols",n.mode=30;break}n.have=0,n.mode=18;case 18:for(;n.have<n.ncode;){for(;m<3;){if(0===d)break t;d--,g+=l[c++]<<m,m+=8}n.lens[N[n.have++]]=7&g,g>>>=3,m-=3}for(;n.have<19;)n.lens[N[n.have++]]=0;if(n.lencode=n.lendyn,n.lenbits=7,z={bits:n.lenbits},M=o(0,n.lens,0,19,n.lencode,0,n.work,z),n.lenbits=z.bits,M){t.msg="invalid code lengths set",n.mode=30;break}n.have=0,n.mode=19;case 19:for(;n.have<n.nlen+n.ndist;){for(;T=(R=n.lencode[g&(1<<n.lenbits)-1])>>>16&255,S=65535&R,!((A=R>>>24)<=m);){if(0===d)break t;d--,g+=l[c++]<<m,m+=8}if(S<16)g>>>=A,m-=A,n.lens[n.have++]=S;else{if(16===S){for(P=A+2;m<P;){if(0===d)break t;d--,g+=l[c++]<<m,m+=8}if(g>>>=A,m-=A,0===n.have){t.msg="invalid bit length repeat",n.mode=30;break}B=n.lens[n.have-1],y=3+(3&g),g>>>=2,m-=2}else if(17===S){for(P=A+3;m<P;){if(0===d)break t;d--,g+=l[c++]<<m,m+=8}m-=A,B=0,y=3+(7&(g>>>=A)),g>>>=3,m-=3}else{for(P=A+7;m<P;){if(0===d)break t;d--,g+=l[c++]<<m,m+=8}m-=A,B=0,y=11+(127&(g>>>=A)),g>>>=7,m-=7}if(n.have+y>n.nlen+n.ndist){t.msg="invalid bit length 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a.libraries.PIXI.Sprite(n[o].texture);g.width=n[o].width,g.height=n[o].height;var m=new a.libraries.PIXI.Sprite(n[o].textureAbbrev);m.width=n[o].widthAbbrev,m.height=n[o].heightAbbrev;var v={posStart:"+"===r?e+t[1].pos:Wt(e+t[2].pos+1,i),posEnd:"+"===r?e+t[2].pos:Wt(e+t[1].pos+1,i),aminoAcid:h,width:g.width,height:g.height,sprite:g,widthAbbrev:m.width,heightAbbrev:m.height,spriteAbbrev:m};s.push(v)}else if(t[2].pos-t[1].pos>1){var w=new a.libraries.PIXI.Sprite(n[o].texture);w.width=n[o].width,w.height=n[o].height;var b=new a.libraries.PIXI.Sprite(n[o].textureAbbrev);b.width=n[o].widthAbbrev,b.height=n[o].heightAbbrev;var _={posStart:"+"===r?e+t[0].pos:Wt(e+t[1].pos+1,i),posEnd:"+"===r?e+t[1].pos:Wt(e+t[0].pos+1,i),aminoAcid:h,width:w.width,height:w.height,sprite:w,widthAbbrev:b.width,heightAbbrev:b.height,spriteAbbrev:b};s.push(_);var y=new a.libraries.PIXI.Sprite(n[o].texture);y.width=n[o].width,y.height=n[o].height;var k=new 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r=+n.max_width/Math.pow(2,+t),i=n.min_pos[0]+e*r,a=n.min_pos[0]+(e+1)*r,s=n.chrom_sizes.split("\t").map((function(t){return+t})),o=n.chrom_names.split("\t"),h=[];this.chromInfo=this.parseChromsizes(o,s);for(var l=this.chromInfo,u=l.chromLengths,c=l.cumPositions,f=0;f<c.length;f++){var d=c[f].chr,p=c[f].pos,g=c[f].pos+u[d];if(p<=i&&i<g){if(!(a>g)){var m=Math.ceil(a-p),v=Math.floor(i-p);h.push(this.sequenceFile.getSequence(d,v,m).then((function(t){return t})));break}h.push(this.sequenceFile.getSequence(d,i-p,g-p).then((function(t){return t}))),i=g}}return Promise.all(h).then((function(t){return t}))}},{key:"parseChromsizes",value:function(t,e){for(var n=[],r={},i={},a=0,s=0;s<e.length;s++){var o=Number(e[s]);a+=o;var h={id:s,chr:t[s],pos:a-o};n.push(h),i[h.chr]=h,r[t[s]]=o}return{cumPositions:n,chrPositions:i,totalLength:a,chromLengths:r}}}]),t}(),ne=function(t,e){if(Array.isArray(t))return t;if(Symbol.iterator in Object(t))return function(t,e){var n=[],r=!0,i=!1,a=void 0;try{for(var 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e.libraries.PIXI.Graphics,n.labelBgGraphics=new e.libraries.PIXI.Graphics,n.labelGraphics=new e.libraries.PIXI.Graphics,n.graphics.addChild(n.rectGraphics),n.graphics.addChild(n.rectMaskGraphics),n.graphics.addChild(n.codonSeparatorGraphics),n.graphics.addChild(n.codonTextGraphics),n.graphics.addChild(n.labelBgGraphics),n.graphics.addChild(n.labelGraphics),n.rectGraphics.mask=n.rectMaskGraphics,n.tileData.sort&&(n.tileData.sort((function(t,e){return e.importance-t.importance})),n.tileData.forEach((function(r,h){var l=r.fields,u=t.formatTranscriptData(l),c=u.transcriptName,f=u.transcriptId,d=u.strand;if(r.transcriptId=f,!(h>=o)){var p=new e.libraries.PIXI.Text(c,{fontSize:a+"px",fontFamily:s,fill:t.colors.labelFont});p.interactive=!0,i&&(p.scale.x=-1),p.anchor.x=0,p.anchor.y=.5,p.visible=!1,n.texts[f]=p,n.texts[f].strand=d,n.labelGraphics.addChild(p)}})),f(t,n),n.initialized=!0)}function f(t,n){if(t.zoomLevel===t.tilesetInfo.max_zoom&&void 0!==t.sequenceLoader){n.aaInfo={},n.aaInfo.exonOffsets={},n.aaInfo.nucSequences={},n.aaInfo.aminoAcids={},n.aaInfo.tileOffset=0;var r=t.tilesetInfo.chrom_sizes.split("\t").map((function(t){return+t})),i=t.tilesetInfo.chrom_names.split("\t"),a=t.sequenceLoader.parseChromsizes(i,r),s=+n.tileId.split(".")[1],o=+n.tileId.split(".")[0],h=t.sequenceLoader.getTile(o,s,t.tilesetInfo),u=+t.tilesetInfo.max_width/Math.pow(2,o),c=t.tilesetInfo.min_pos[0]+s*u,f=t.tilesetInfo.min_pos[0]+(s+1)*u,d=+l(c,a)[1],p=+l(f,a)[1];n.tileData.forEach((function(r){var i=r.fields,s=t.formatTranscriptData(i),o=s.transcriptId,l=a.chromLengths[s.chromName],u=d,c=p;if("."!==s.startCodonPos&&"."!==s.stopCodonPos){var f=s.strand;n.aaInfo.exonOffsets[o]=[],n.aaInfo.nucSequences[o]=[],n.aaInfo.aminoAcids[o]=[];var g=s.exonStarts,m=s.exonEnds,v=g,w=m,b=s.startCodonPos,_=s.stopCodonPos;"-"===f&&(u=Wt(c,l),c=Wt(u,l),v=Wt(m,l),w=Wt(g,l),b=Wt(b,l),_=Wt(_,l));for(var y=0,k=0;k<v.length;k++)if(v[k]<=b)n.aaInfo.exonOffsets[o].push(0);else{var x=(y+=(3-(w[k-1]-Math.max(v[k-1],b))%3)%3)%3;n.aaInfo.exonOffsets[o].push(x)}h.then((function(r){var i=r[0];"-"===f&&(i=Vt(i));var a=Yt(v,w,b,_,u,i);if(0!==a.filter((function(t){return"."!==t})).length){n.aaInfo.nucSequences[o].push(a);var h=null;if("."!==a[0]){h=$t(v,w,u).exon;var c=Math.max(b,v[h]),d=n.aaInfo.exonOffsets[o][h];n.aaInfo.tileOffset=Zt(c,d,u)}else if(u<b)n.aaInfo.tileOffset=0;else{var p=Xt(v,w,u);n.aaInfo.tileOffset=null!==p&&u>b?n.aaInfo.exonOffsets[o][p.exon]:0}Kt(e,a,n.aaInfo.tileOffset,s.chromName,l,f,v,w,u,t.pixiTexts,t.sequenceLoader).then((function(e){n.aaInfo.aminoAcids[o]=e,t.draw()}))}}))}}))}}function d(t,e,n,r,i,a,s,o){var h=a-s/2,l=+e.tileId.split(".")[1],u=+e.tileId.split(".")[0],c=+t.tilesetInfo.max_width/Math.pow(2,u),f=t.tilesetInfo.min_pos[0]+l*c,d=t.tilesetInfo.min_pos[0]+(l+1)*c,p=t.transcriptInfo[n].exonStarts,g=t.transcriptInfo[n].exonEnds,m="."!==t.transcriptInfo[n].startCodonPos&&"."!==t.transcriptInfo[n].stopCodonPos,v=m?t.transcriptInfo[n].startCodonPos+i:-1,w=m?t.transcriptInfo[n].stopCodonPos+i:-1,b=t.transcriptInfo[n].txStart+i,_=t.transcriptInfo[n].txEnd+i,y=p.map((function(t){return+t+i})),k=g.map((function(t){return+t+i}));m&&(y.push(v,w),k.push(v,w),y.sort(),k.sort());var x=t._xScale(b+1),A=t._xScale(_+1),T=A-x,S=a,E=[],C=[];r.beginFill(t.colors.intron);var I=[x,S-1,x+T,S-1,x+T,S+1,x,S+1];r.drawPolygon(I),E.push([x,x+T,h,h+s]),C.push({rect:I,color:t.colors.intronHEX,paintOrder:0});for(var B=0;B<y.length;B++){var M=y[B],z=k[B];if(!(z<f||M>d)){var P=!m||"+"===o&&(z<=v||M>=w)||"-"===o&&(M>=v||z<=w),R=P?t.colors.utr:t.colors[o],O=P?t.options.utrColor:t.colors[o+"HEX"];r.beginFill(R);var N=t._xScale(M+1),G=Math.max(2,t._xScale(z+1)-t._xScale(M+1)),F=x,L=A,U=null,H=null;if("+"===o){var D=Math.min(N,L),j=Math.max(D-5,x),q=Math.min(N+G,L),$=Math.max(q-5,x);U=[D,h,$,h,q,h+s/2,$,h+s,j,h+s,D,h+s/2,j,h],H=[D,q,h,h+s]}else{var Z=Math.max(N,F),Y=Math.min(Z+5,A),X=Math.min(Math.max(N+G,F),A),W=Math.min(X+5,A);U=[Z,h+s/2,Y,h,W,h,X,h+s/2,W,h+s,Y,h+s,Z,h+s/2],H=[Z,X,h,h+s]}r.drawPolygon(U),E.push(H),C.push({rect:U,color:O,paintOrder:1})}}var V=E.map((function(e){return[e,t.transcriptInfo[n]]}));e.allExonsForMouseOver=e.allExonsForMouseOver.concat(V),e.allExonsForSVG=e.allExonsForSVG.concat(C)}function p(t,e,n,r,i,a){t.forEach((function(t){var s=t.fields,o=+t.chrOffset,h=e.transcriptId(s);if((!e.areTranscriptsHidden||0===e.transcriptInfo[h].displayOrder)&&e.transcriptInfo[h]){var l=e.transcriptInfo[h].displayOrder*(i+a);e.options.showToggleTranscriptsButton&&(l+=e.toggleButtonHeight),d(e,n,h,n.rectGraphics,o,r+l,i,t.strand||t.fields[5])}}))}function g(t,e){var n=h.getTilePosAndDimensions(t.tilesetInfo,e.tileId),r=n.tileX,i=n.tileWidth;e.rectMaskGraphics.clear();var a=Math.floor(Math.random()*Math.pow(16,6));e.rectMaskGraphics.beginFill(a,.3);var s=t._xScale(r),o=t._xScale(r+i)-t._xScale(r),l=t.dimensions[1];e.rectMaskGraphics.drawRect(s,0,o,l)}var m=function(t,e,n){"over"===n?(e.buttons.pToggleButton.children[0].alpha=.8,document.body.style.cursor="pointer"):"out"===n&&(e.buttons.pToggleButton.children[0].alpha=.5,document.body.style.cursor="default"),requestAnimationFrame(e.animate)},v=function(t,e){if(e.areTranscriptsHidden)e.buttons.pToggleButton.children[0].text="SHOW FEWER TRANSCRIPTS...",e.areTranscriptsHidden=!1;else{var n=Object.keys(e.transcriptInfo).length-e.transcriptPositionInfo[0].length,r=Math.max(0,n);e.buttons.pToggleButton.children[0].text="SHOW "+r+" MORE TRANSCRIPTS...",e.areTranscriptsHidden=!0}e.pubSub.publish("trackDimensionsModified",{height:e.computeTrackHeight(),resizeParentDiv:!0,trackId:e.trackId,viewId:e.viewId})};function w(t){if(t.options.showToggleTranscriptsButton&&!t.hasToggleBtnBeenRendered){var n=t.buttons.pToggleButton;t.pForeground.removeChildren(),t.pForeground.addChild(n),n.clear(),n.removeChildren();var r=new e.libraries.PIXI.Text("SHOW FEWER TRANSCRIPTS...",{fontSize:"10px",fontFamily:t.options.fontFamily,fontWeight:"500",fill:t.colors.black});r.interactive=!0,r.buttonMode=!0,r.mouseover=function(e){return m(e,t,"over")},r.mouseout=function(e){return m(e,t,"out")},r.pointerup=function(e){return v(e,t)},r.alpha=.5,r.anchor.x=.5,r.anchor.y=.5,r.position.x=t.dimensions[0]/2,r.position.y=t.toggleButtonHeight/2,n.addChild(r),t.hasToggleBtnBeenRendered=!0}}var b=function(n){function r(t,n){ae(this,r);var i=se(this,(r.__proto__||Object.getPrototypeOf(r)).call(this,t,n)),a=t.animate,s=t.viewUid;i.trackId=i.id,i.viewId=s,i.animate=a,i.options=n,i.initOptions(),i.numTranscriptRows=0,i.trackHeight=0,i.trackHeightOld=0,i.areTranscriptsHidden=i.options.startCollapsed,i.areCodonsShown=!1,i.transcriptInfo={},i.transcriptSequences={},i.buttons={};var o=new e.libraries.PIXI.Graphics;return o.interactive=!0,o.buttonMode=!0,i.buttons.pToggleButton=o,i}return oe(r,n),re(r,[{key:"initOptions",value:function(){this.fontSize=+this.options.fontSize,this.transcriptHeight=+this.options.transcriptHeight,this.transcriptSpacing=+this.options.transcriptSpacing,this.geneStrandHSpacing=this.transcriptSpacing/2,this.transcriptHHeight=this.transcriptHeight/2,this.trackHeightAdjustment="automatic"===this.options.trackHeightAdjustment,this.toggleButtonHeight=26,this.minCodonDistance=15,this.codonTextOptions={fontSize:2*this.fontSize+"px",fontFamily:this.options.fontFamily,fill:u,fontWeight:"bold"},void 0!==this.options.sequenceData&&(this.sequenceLoader=new ee(this.options.sequenceData.fastaUrl,this.options.sequenceData.faiUrl),this.pixiTexts||(this.pixiTexts=qt(this.codonTextOptions,e))),this.colors={},this.colors["+"]=o(this.options.plusStrandColor),this.colors["-"]=o(this.options.minusStrandColor),this.colors["+HEX"]=this.options.plusStrandColor,this.colors["-HEX"]=this.options.minusStrandColor,this.colors.utr=o(this.options.utrColor),this.colors.labelFont=o(this.options.labelFontColor),this.colors.black=o("#000000"),this.colors.intron=o("#CFCFCF"),this.colors.intronHEX="#CFCFCF",this.colors.labelBackgroundPlus=o(this.options.labelBackgroundPlusStrandColor),this.colors.labelBackgroundMinus=o(this.options.labelBackgroundMinusStrandColor),this.colors.labelStrokePlus=o(this.options.labelStrokePlusStrandColor),this.colors.labelStrokeMinus=o(this.options.labelStrokeMinusStrandColor),this.colors.background=o(this.options.backgroundColor)}},{key:"initTile",value:function(t){t.initialized||(c(this,t,{flipText:this.flipText,fontSize:this.fontSize,fontFamily:this.options.fontFamily,maxTexts:this.options.maxTexts}),this.rerender(this.options,!0))}},{key:"destroyTile",value:function(t){for(var e in t.rectGraphics.destroy(),t.rectMaskGraphics.destroy(),t.labelGraphics.removeChildren(),t.texts)t.texts[e].destroy();t.texts=[],t.labelGraphics.destroy(),t.labelBgGraphics.destroy(),t.codonSeparatorGraphics.destroy(),t.codonTextGraphics.removeChildren(),t.codonTextGraphics.destroy(),t.graphics.destroy(),t.tileData.length=0,t=null}},{key:"computeTrackHeight",value:function(){var t=0;if(this.areTranscriptsHidden)t=this.toggleButtonHeight+Math.min(1,this.numTranscriptRows)*(this.transcriptHeight+this.transcriptSpacing)+10;else{var e=this.options.showToggleTranscriptsButton?this.toggleButtonHeight:0;t=this.numTranscriptRows*(this.transcriptHeight+this.transcriptSpacing)+e+10}return this.trackHeightOld=this.trackHeight,this.trackHeight=t,t}},{key:"adjustTrackHeight",value:function(){return this.computeTrackHeight(),this.trackHeightOld!==this.trackHeight&&(this.pubSub.publish("trackDimensionsModified",{height:this.trackHeight,resizeParentDiv:!0,trackId:this.trackId,viewId:this.viewId}),!0)}},{key:"formatTranscriptData",value:function(t){var e=t[5],n="."===t[12]?".":"+"===e?+t[12]+2:+t[12]-1,r="."===t[11]?".":"+"===e?+t[11]-1:+t[11]+2,i=t[9].split(",").map((function(t){return+t-1})),a=t[10].split(",").map((function(t){return+t})),s=+t[1]-1,o=+t[2]-1;return{transcriptId:this.transcriptId(t),transcriptName:t[3],txStart:s,txEnd:o,strand:e,chromName:t[0],codingType:t[8],exonStarts:i,exonEnds:a,startCodonPos:r,stopCodonPos:n,importance:+t[4]}}},{key:"updateTranscriptInfo",value:function(){var t=this,e={};this.visibleAndFetchedTiles().forEach((function(t){t.tileData.forEach((function(t){e[t.transcriptId]=t.fields}))}));var n=[];for(var r in e)n.push(e[r]);if(this.transcriptInfo={},this.transcriptPositionInfo={},this.numTranscriptRows=0,n.sort((function(t,e){return+t[1]-e[1]})).forEach((function(e){var n=t.calculateTranscriptRowNumber(t.transcriptPositionInfo,+e[1],+e[2]);void 0===t.transcriptPositionInfo[n]&&(t.transcriptPositionInfo[n]=[]),t.transcriptPositionInfo[n].push([+e[1],+e[2],e[3]]);var r=t.formatTranscriptData(e),i={transcriptId:r.transcriptId,transcriptName:r.transcriptName,txStart:r.txStart,txEnd:r.txEnd,strand:r.strand,chromName:r.chromName,codingType:r.codingType,exonStarts:r.exonStarts,exonEnds:r.exonEnds,startCodonPos:r.startCodonPos,stopCodonPos:r.stopCodonPos,displayOrder:n,importance:r.importance};t.transcriptInfo[i.transcriptId]=i})),this.numTranscriptRows=Object.keys(this.transcriptPositionInfo).length,this.areTranscriptsHidden&&this.buttons.pToggleButton.children[0]&&this.transcriptPositionInfo[0]){var i=Object.keys(this.transcriptInfo).length-this.transcriptPositionInfo[0].length,a=Math.max(0,i);this.buttons.pToggleButton.children[0].text="SHOW "+a+" MORE TRANSCRIPTS..."}}},{key:"calculateTranscriptRowNumber",value:function(t,e,n){for(var r=Object.keys(t).length,i=0;i<r;i++){var a=!0;if(t[i].forEach((function(t){var r=t[0],i=t[1];(r<=e&&e<=i||r<=n&&n<=i)&&(a=!1)})),a)return i}return r}},{key:"rerender",value:function(t,e){var n=this,r=JSON.stringify(t);(e||r!==this.prevOptions)&&(this.options=t,this.initOptions(),this.prevOptions=r,w(this),this.updateTranscriptInfo(),this.trackHeightAdjustment&&this.adjustTrackHeight()||this.visibleAndFetchedTiles().forEach((function(t){n.renderTile(t)})))}},{key:"drawTile",value:function(){}},{key:"transcriptId",value:function(t){return t[7]+"_"+t[0]+"_"+t[1]+"_"+t[2]}},{key:"exonId",value:function(t,e,n){return t[7]+"_"+t[0]+"_"+t[1]+"_"+t[2]+"_"+e+"_"+n}},{key:"renderTile",value:function(t){if(t.initialized){t.allExonsForMouseOver=[],t.allExonsForSVG=[],t.drawnAtScale=this._xScale.copy(),t.rectGraphics.removeChildren(),t.rectGraphics.clear(),t.labelBgGraphics.clear();var e=t.tileData.filter((function(t){return"filler"!==t.type&&("+"===t.strand||"+"===t.fields[5])})),n=t.tileData.filter((function(t){return"filler"!==t.type&&("-"===t.strand||"-"===t.fields[5])})),r=[this,t,this.transcriptHeight/2+this.transcriptSpacing/2,this.transcriptHeight,this.transcriptSpacing];p.apply(void 0,[e].concat(r)),p.apply(void 0,[n].concat(r)),g(this,t),h.stretchRects(this,[function(t){return t.rectGraphics},function(t){return t.rectMaskGraphics}])}}},{key:"calculateZoomLevel",value:function(){var t=a.calculateZoomLevel(this._xScale,this.tilesetInfo.min_pos[0],this.tilesetInfo.max_pos[0]),e=Math.min(t,this.maxZoom);return e=Math.max(e,0)}},{key:"draw",value:function(){h.stretchRects(this,[function(t){return t.rectGraphics},function(t){return t.rectMaskGraphics}]),this.areCodonsShown=!1,this.drawLabels(),this.drawCodonSeparators(),this.drawCodonTexts(),requestAnimationFrame(this.animate)}},{key:"drawCodonTexts",value:function(){var t=this;Object.values(this.fetchedTiles).filter((function(t){return t.drawnAtScale})).forEach((function(e){if(e.initialized&&e.aaInfo&&e.aaInfo.aminoAcids){e.codonTextGraphics.clear(),e.codonTextGraphics.removeChildren();var n=1,r=t._xScale(3)-t._xScale(0);if(!(r<t.minCodonDistance)){r<t.minCodonDistance+3&&r>=t.minCodonDistance&&(n=Lt().domain([t.minCodonDistance,t.minCodonDistance+3]).range([0,1]).clamp(!0)(r));var i=e.codonTextGraphics;i.beginFill(u),i.alpha=n,e.tileData.forEach((function(n){var a=n.transcriptId;if(t.transcriptInfo[a]&&e.aaInfo.aminoAcids[a]){var s=t.transcriptInfo[a];if(!t.areTranscriptsHidden||0===s.displayOrder){var o=+n.chrOffset,h=e.aaInfo.aminoAcids[a],l=s.displayOrder*(t.transcriptHeight+t.transcriptSpacing)+t.transcriptHeight/2+t.transcriptSpacing/2-t.fontSize/2-1;t.options.showToggleTranscriptsButton&&(l+=t.toggleButtonHeight);for(var u=0,c=h.length;u<c;++u){var f=h[u],d=t._xScale(f.posStart+o+1);if(!(t._xScale(f.posEnd+o+1)<0||d>t.dimensions[0]))if(r<t.minCodonDistance+10){var p=t._xScale((f.posStart+f.posEnd+1)/2+o+1)-f.widthAbbrev/2;f.spriteAbbrev.position.x=p,f.spriteAbbrev.position.y=l,i.addChild(f.spriteAbbrev)}else{var g=t._xScale((f.posStart+f.posEnd+1)/2+o+1)-f.width/2;f.sprite.position.x=g,f.sprite.position.y=l,i.addChild(f.sprite)}}}}}))}}}))}},{key:"drawCodonSeparators",value:function(){var t=this;Object.values(this.fetchedTiles).filter((function(t){return t.drawnAtScale})).forEach((function(e){if(e.initialized&&e.aaInfo&&e.aaInfo.aminoAcids){e.allCodonsForMouseOver=[],e.codonSeparatorGraphics.clear();var n=1,r=t._xScale(3)-t._xScale(0);if(!(r<t.minCodonDistance)){r<t.minCodonDistance+3&&r>=t.minCodonDistance&&(n=Lt().domain([t.minCodonDistance,t.minCodonDistance+3]).range([0,1]).clamp(!0)(r)),t.areCodonsShown=!0;var i=e.codonSeparatorGraphics;i.beginFill(u),i.alpha=n,e.tileData.forEach((function(n){var r=n.transcriptId;if(t.transcriptInfo[r]&&e.aaInfo.aminoAcids[r]){var a=t.transcriptInfo[r];if(!t.areTranscriptsHidden||0===a.displayOrder){var s=+n.chrOffset,o=e.aaInfo.aminoAcids[r],h=a.displayOrder*(t.transcriptHeight+t.transcriptSpacing)+t.transcriptHeight/2+t.transcriptSpacing/2;t.options.showToggleTranscriptsButton&&(h+=t.toggleButtonHeight);for(var l=h-t.transcriptHeight/2,u=h+t.transcriptHeight/2,c=0,f=o.length;c<f;++c){var d=o[c],p=t._xScale(d.posStart+s+1),g=t._xScale(d.posEnd+s+2);if(!(g<0||p>t.dimensions[0])){var m=[[p,g,l,u],d.aminoAcid];if(e.allCodonsForMouseOver.push(m),!("+"===a.strand&&d.posStart===a.startCodonPos||"+"===a.strand&&a.exonStarts.includes(d.posStart)||"-"===a.strand&&d.posEnd+1===a.startCodonPos||"-"===a.strand&&a.exonEnds.includes(d.posEnd+1))){var v="+"===a.strand?p:g,w=v,b=v,_=v;"+"===a.strand?(w-=5,b+=2,_-=3):(w+=5,b-=2,_+=3);var y=[v,l,_,l,b,h,_,u,w,u,v,h,w,l];i.drawPolygon(y)}}}}}}))}}}))}},{key:"drawLabels",value:function(){var t=this;this.allTexts=[],this.allBoxes=[];var e=[];Object.values(this.fetchedTiles).filter((function(t){return t.drawnAtScale})).forEach((function(n){try{if(n.labelBgGraphics.clear(),!n.initialized)return;n.tileData.forEach((function(r){if(n.texts){var i=r.transcriptId;if(void 0!==t.transcriptInfo[i]){var a=t.transcriptInfo[i],s=n.texts[i];if(s)if(t.areTranscriptsHidden&&0!==a.displayOrder)s.visible=!1;else{try{if(!n.textWidths[i]){var o=s.getBounds().width,h=s.getBounds().height;n.textHeights[i]=h,n.textWidths[i]=o}}catch(t){return}var l=+r.chrOffset,u=a.txStart+l,c=a.txEnd+l,f=a.displayOrder*(t.transcriptHeight+t.transcriptSpacing);t.options.showToggleTranscriptsButton&&(f+=t.toggleButtonHeight);var d=t.transcriptHeight/2+t.transcriptSpacing/2+f;"+"===a.strand?s.position.x=Math.max(t._xScale(t.xScale().domain()[0])+3,t._xScale(u+1)-n.textWidths[i]-6-3):s.position.x=Math.max(t._xScale(t.xScale().domain()[0])+3+5,t._xScale(u+1)-n.textWidths[i]-6);var p="+"===a.strand?n.textWidths[i]+t.transcriptHeight/2+6-3:n.textWidths[i]+3;s.position.x=Math.min(s.position.x,t._xScale(c+1)-p),s.position.y=d;var g=!0,m=a.displayOrder;t.transcriptPositionInfo[m].filter((function(t){return t[1]<a.txStart})).forEach((function(e){t._xScale(e[1]+l+1)>s.position.x-12&&(g=!1)})),g?(s.visible=!0,t.allBoxes.push([s.position.x-3,d,n.textWidths[i]+6,t.transcriptHeight,a.transcriptName]),t.allTexts.push({importance:a.importance,text:s,caption:a.transcriptName,strand:a.strand}),e.push(n.labelBgGraphics)):s.visible=!1}}}}))}catch(t){return}})),this.renderTextBg(this.allBoxes,this.allTexts,e)}},{key:"renderTextBg",value:function(t,e,n){var r=this;e.forEach((function(e,i){if(e.text.visible&&t[i]&&n[i]){var a=ne(t[i],4),s=a[0],o=a[1],h=a[2],l=a[3],u=s,c=u+1,f=s+h,d=f-1,p=o-l/2,g=p+1,m=o+l/2,v=m-1;if("+"===e.strand){n[i].beginFill(r.colors.labelStrokePlus);var w=[u,p,f,p,f+5,o,f,m,u,m];n[i].drawPolygon(w),n[i].beginFill(r.colors.labelBackgroundPlus);var b=[c,g,f,g,d+3,o,f,v,c,v];n[i].drawPolygon(b)}else{n[i].beginFill(r.colors.background);var _=[u-5,p,f,p,f,m,u-5,m];n[i].drawPolygon(_),n[i].beginFill(r.colors.labelStrokeMinus);var y=[u-5,o,u,p,f,p,f,m,s,m];n[i].drawPolygon(y),n[i].beginFill(r.colors.labelBackgroundMinus);var k=[c-3,o,s,g,d,g,d,v,s,v];n[i].drawPolygon(k)}}}))}},{key:"hideTexts",value:function(t){t.forEach((function(t,e){t.visible=!1}))}},{key:"setPosition",value:function(t){ie(r.prototype.__proto__||Object.getPrototypeOf(r.prototype),"setPosition",this).call(this,t);var e=ne(this.position,2);this.pMain.position.x=e[0],this.pMain.position.y=e[1]}},{key:"setDimensions",value:function(t){this.updateTranscriptInfo(),ie(r.prototype.__proto__||Object.getPrototypeOf(r.prototype),"setDimensions",this).call(this,t),this.rerender(this.options,!0)}},{key:"zoomed",value:function(t,e){this.xScale(t),this.yScale(e),this.refreshTiles(),this.draw()}},{key:"isPointInRectangle",value:function(t,e){return t[0]<e[0]&&t[1]>e[0]&&t[2]<e[1]&&t[3]>e[1]}},{key:"getMouseOverHtml",value:function(t,e,n){if(!this.tilesetInfo||!this.options||!this.options.showTooltip&&!n)return"";var r=[t,e],i=!0,a=!1,s=void 0;try{for(var o,h=this.visibleAndFetchedTiles()[Symbol.iterator]();!(i=(o=h.next()).done);i=!0){var l=o.value;if(!l.allExonsForMouseOver)return;for(var u=0;u<l.allExonsForMouseOver.length;u++){var c=l.allExonsForMouseOver[u][0];if(this.isPointInRectangle(c,r)){var f=l.allExonsForMouseOver[u][1];if(!this.areCodonsShown){var d='<div class="track-mouseover-menu-table">';return d+='\n                <div class="track-mouseover-menu-table-item">\n                  <label for="name" class="track-mouseover-menu-table-item-label">Transcript</label>\n                  <div name="name" class="track-mouseover-menu-table-item-value">'+f.transcriptName+"</div>\n                </div>\n                ",d+='\n                <div class="track-mouseover-menu-table-item">\n                  <label for="position" class="track-mouseover-menu-table-item-label">Interval</label>\n                  <div name="position" class="track-mouseover-menu-table-item-value">'+f.chromName+":"+f.txStart+"-"+f.txEnd+" ("+f.strand+")</div>\n                </div>\n                ",d+="</div>"}for(var p=0;p<l.allCodonsForMouseOver.length;p++){var g=l.allCodonsForMouseOver[p][0];if(this.isPointInRectangle(g,r)){var m=l.allCodonsForMouseOver[p][1];if("X"===m.key)return'\n                      <div style="text-align: center; padding:10px;">\n                        <div style="text-transform: uppercase;">\n                          <b>'+m.name+'</b>\n                        </div>\n                        <div style="font-size: 10px;">\n                          '+m.codons.join(", ")+"\n                        </div>\n                      </div>\n                    ";var v=m.essential?"essential":"non-essential";return'\n                    <div style="text-align: center; padding:10px;">\n                      <div>\n                        <img class="fit-picture" \n                             src="'+m.image+'" \n                             style="width:125px;height:125px"\n                             alt="'+m.name+'">\n                      </div>\n                      <div style="text-transform: uppercase; padding-top:6px;">\n                        <b>'+m.name+'</b>\n                      </div>\n                      <div style="padding-top:0px;">\n                        <i>'+m.property+", "+v+'</i>\n                      </div>\n                      <div style="font-size: 10px;">\n                        '+m.codons.join(", ")+"\n                      </div>\n                    </div>\n                  "}}}}}}catch(t){a=!0,s=t}finally{try{!i&&h.return&&h.return()}finally{if(a)throw s}}return""}},{key:"exportSVG",value:function(){var e,n=this,r=null;r=e=document.createElement("g");var i=Ht.a.nice(),a=document.createElement("g");a.setAttribute("style","clip-path:url(#"+i+");"),r.appendChild(a);var s=document.createElementNS("http://www.w3.org/2000/svg","clipPath");s.setAttribute("id",i),r.appendChild(s);var o=document.createElementNS("http://www.w3.org/2000/svg","polygon");s.appendChild(o),o.setAttribute("points",this.position[0]+","+this.position[1]+" "+(this.position[0]+this.dimensions[0])+","+this.position[1]+" "+(this.position[0]+this.dimensions[0])+","+(this.position[1]+this.dimensions[1])+" "+this.position[0]+","+(this.position[1]+this.dimensions[1])+" ");var h=document.createElement("g");h.setAttribute("transform","translate("+this.position[0]+","+this.position[1]+")"),a.appendChild(h);var l=document.createElement("rect");l.setAttribute("fill",this.options.backgroundColor),l.setAttribute("fill-opacity","1"),l.setAttribute("stroke-opacity","0"),l.setAttribute("width",this.dimensions[0]),l.setAttribute("height",this.dimensions[1]),l.setAttribute("x","0"),l.setAttribute("y","0"),h.appendChild(l);[0,1].forEach((function(t){n.visibleAndFetchedTiles().filter((function(t){return t.allExonsForSVG})).forEach((function(e){var n=document.createElement("g");n.setAttribute("transform","translate("+e.rectGraphics.position.x+",\n              "+e.rectGraphics.position.y+")\n              scale("+e.rectGraphics.scale.x+",\n              "+e.rectGraphics.scale.y+")"),e.allExonsForSVG.filter((function(e){return e.paintOrder===t})).forEach((function(t){for(var e=document.createElement("path"),r=t.rect,i="M "+r[0]+" "+r[1],a=2;a<r.length;a+=2)i+=" L "+r[a]+" "+r[a+1];e.setAttribute("d",i),e.setAttribute("fill",t.color),e.setAttribute("opacity","1"),n.appendChild(e)})),h.appendChild(n)}))}));var u=[],c=2,f=2,d=1,p=1;return this.allTexts.filter((function(t){return t.text.visible})).forEach((function(e){if(!u.includes(e.text.text)){var r=document.createElement("polygon");r.setAttribute("stroke-width","1"),r.setAttribute("stroke-opacity","1");var i=-c+","+d,a=e.text.width+f+","+d,s=e.text.width+f+","+(.75*-n.transcriptHeight-p),o=-c+","+(.75*-n.transcriptHeight-p);switch(e.strand){case"-":var l=void 0!==n.options.labelStrokeMinusStrandColor?n.options.labelStrokeMinusStrandColor:t.config.defaultOptions.labelStrokeMinusStrandColor;r.setAttribute("stroke",l);var g=void 0!==n.options.labelBackgroundMinusStrandColor?n.options.labelBackgroundMinusStrandColor:t.config.defaultOptions.labelBackgroundMinusStrandColor;r.setAttribute("fill",g);var m=-c-5+","+.75*-n.transcriptHeight/2;r.setAttribute("points",m+" "+i+" "+a+" "+s+" "+o);break;case"+":default:var v=void 0!==n.options.labelStrokeMinusStrandColor?n.options.labelStrokeMinusStrandColor:t.config.defaultOptions.labelStrokeMinusStrandColor;r.setAttribute("stroke",v);var w=void 0!==n.options.labelBackgroundPlusStrandColor?n.options.labelBackgroundPlusStrandColor:t.config.defaultOptions.labelBackgroundPlusStrandColor;r.setAttribute("fill",w);var b=e.text.width+f+5+","+.75*-n.transcriptHeight/2;r.setAttribute("points",i+" "+a+" "+b+" "+s+" "+o)}var _=document.createElement("text");_.setAttribute("text-anchor","start"),_.setAttribute("font-family",n.options.fontFamily),_.setAttribute("font-size",n.fontSize+"px"),_.setAttribute("fill",n.options.labelFontColor),_.innerHTML=e.text.text,u.push(e.text.text);var y=document.createElement("g");y.setAttribute("transform","scale("+e.text.scale.x+",1)"),y.appendChild(r),y.appendChild(_),y.setAttribute("transform","translate("+e.text.x+","+(e.text.y+n.transcriptHeight/4+1)+")scale("+e.text.scale.x+",1)"),h.appendChild(y)}})),[e,e]}}]),r}(e.tracks.HorizontalGeneAnnotationsTrack);return new(Function.prototype.bind.apply(b,[null].concat(r)))};he.config={type:"horizontal-transcripts",datatype:["gene-annotation"],local:!1,orientation:"1d-horizontal",thumbnail:(new DOMParser).parseFromString('<svg width="20" height="20" xmlns="http://www.w3.org/2000/svg"> <g> <title>background</title> <rect fill="#fff" id="canvas_background" height="3.24996" width="3.24996" y="-1" x="-1"/> <g display="none" id="canvasGrid"> <rect fill="url(#gridpattern)" stroke-width="0" y="0" x="0" height="100%" width="100%" id="svg_2"/> </g> </g> <g> <title>Layer 1</title> <rect id="svg_1" height="20" width="20" stroke-width="0" stroke="#000" fill="#C0EAAF"/> <path stroke="#bdbfff" id="svg_4" d="m11.42795,10.0119l-4.10746,-6.99997l2.70509,0l4.10746,6.99997l-4.10746,6.99997l-2.70509,0l4.10746,-6.99997z" stroke-width="6" fill="#bdbfff"/> </g> </svg>',"text/xml").documentElement,availableOptions:["fontSize","fontFamily","transcriptSpacing","transcriptHeight","maxTexts","plusStrandColor","minusStrandColor","utrColor","labelBackgroundPlusStrandColor","labelBackgroundMinusStrandColor","labelFontColor","labelStrokePlusStrandColor","labelStrokeMinusStrandColor","startCollapsed","showToggleTranscriptsButton","trackHeightAdjustment","sequenceData","backgroundColor","showTooltip"],defaultOptions:{fontSize:9,fontFamily:"Helvetica",transcriptSpacing:2,transcriptHeight:11,maxTexts:20,plusStrandColor:"#bdbfff",minusStrandColor:"#fabec2",utrColor:"#C0EAAF",labelBackgroundPlusStrandColor:"#ffffff",labelBackgroundMinusStrandColor:"#ffffff",labelFontColor:"#333333",labelStrokePlusStrandColor:"#999999",labelStrokeMinusStrandColor:"#999999",startCollapsed:!1,trackHeightAdjustment:"automatic",showToggleTranscriptsButton:!0,backgroundColor:"#ffffff",showTooltip:!0}};var le=he;i({name:"TranscriptsTrack",track:le,config:le.config});e.default=le},function(t,e,n){"use strict";n.r(e),n.d(e,"parseSmallFasta",(function(){return o})),n.d(e,"FetchableSmallFasta",(function(){return h})),n.d(e,"IndexedFasta",(function(){return a.a})),n.d(e,"BgzipIndexedFasta",(function(){return s}));var r=n(0),i=n(10),a=(n(4),n(5));class s extends a.a{constructor({fasta:t,path:e,fai:n,faiPath:r,gzi:a,gziPath:s,chunkSizeLimit:o}){super({fasta:t,path:e,fai:n,faiPath:r,chunkSizeLimit:o}),t&&a?this.fasta=new i.a({filehandle:t,gziFilehandle:a}):e&&s&&(this.fasta=new i.a({path:e,gziPath:s}))}}function o(t){return t.split(">").filter(t=>/\S/.test(t)).map(t=>{const[e,...n]=t.split("\n"),[r,...i]=e.split(" "),a=n.join("").replace(/\s/g,"");return{id:r,description:i.join(" "),sequence:a}})}class h{constructor({fasta:t,path:e}){if(t)this.fasta=t;else{if(!e)throw new Error("Need to pass fasta or path");this.fasta=new r.a(e)}this.data=this.fasta.readFile().then(t=>o(t.toString("utf8")))}async fetch(t,e,n){const r=(await this.data).find(e=>e.id===t),i=n-e;if(!r)throw new Error(`no sequence with id ${t} exists`);return r.sequence.substr(e,i)}async getSequenceNames(){return(await this.data).map(t=>t.id)}}}])}));