diff --git a/README.md b/README.md index 94d787e..1d96b6e 100644 --- a/README.md +++ b/README.md @@ -11,7 +11,7 @@ to display. Below is an example of a simple web page which uses a `FornaContainer` to show a simple RNA molecule: -![blah blah](https://raw.githubusercontent.com/pkerpedjiev/fornac/develop/doc/img/forna-container-screenshot.png "An example of the FornaContainer") + The code for creating this web page is rather straightforward. After importing some necessary javascript files, we create a container using `new @@ -44,7 +44,7 @@ This after the RNA container. Display two cofolded sequences using the format of [RNAcofold](http://rna.tbi.univie.ac.at/cgi-bin/RNAcofold.cgi): -![Cofolded sequences](https://raw.githubusercontent.com/pkerpedjiev/fornac/master/doc/img/cofold_example.png "An example of cofolded sequences displayed using the FornaContainer") + ```javascript var container = new fornac.FornaContainer("#cofold_ss", @@ -91,7 +91,7 @@ This only makes sense in connection with the `animation` argument. If it's true, the external loops will be arranged in a nice circle. 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n=e.rna,r=h.pairtableToDotbracket(n.pairtable),i=n.getPositions("nucleotide"),s=n.seq,u=n.getUids(),l=e.num,c=r,f=s.slice(0,l-1)+t+s.slice(l);console.log("newSequence:",f),console.log("uids:",u),u.splice(l-1,1,a.nice());var d=i;delete o.rnas[n.uid],o.addRNA(c,{sequence:f,positions:d,uids:u,centerView:!1})},K=function(t,e,n){var r=e.rna,i=h.pairtableToDotbracket(r.pairtable),s=r.getPositions("nucleotide"),u=r.seq,l=r.getUids(),c=e.num+n,f=i.slice(0,c)+"."+i.slice(c),d=u.slice(0,c)+t+u.slice(c);console.log("newSequence:",d),l.splice(c,0,a.nice()),s.splice(c,0,s[c-n-1]);var p=l,g=s;console.log("positions:",s),console.log("new node positions:",g),delete o.rnas[r.uid],o.addRNA(f,{sequence:d,positions:g,uids:p,centerView:!1})},Z=function(t){console.log("deleting...",t);var e=t.rna,n=e.pairtable[t.num];0!=n&&(e.pairtable[t.num]=0,e.pairtable[n]=0);var r=h.pairtableToDotbracket(e.pairtable),i=e.getPositions("nucleotide"),s=e.seq,a=e.getUids(),u=r.slice(0,t.num-1)+r.slice(t.num),l=i.slice(0,t.num-1).concat(i.slice(t.num)),c=s.slice(0,t.num-1)+s.slice(t.num),f=a.slice(0,t.num-1).concat(a.slice(t.num));delete o.rnas[e.uid],o.addRNA(u,{sequence:c,positions:l,uids:f,centerView:!1}),console.log("new dotbracket:",u)},Q=function(t){return t.uid},tt=function(t){var e=t.getPositions("nucleotide"),n=t.getPositions("label"),r=t.getUids();t.recalculateElements().elementsToJson().addPseudoknots().addPositions("nucleotide",e).addUids(r).addLabels(1,o.options.labelInterval).addPositions("label",n).reinforceStems().reinforceLoops().updateLinkUids()},et=function(t){if(t.target.num-t.source.num==1){for(var e=t.target.rna,n=[],r=0;r=t.target.num&&(console.log("crossing basepair",i),n.push(i))}console.log("toRemove:",n);for(var s=0;s-1){if(t.source.rna==t.target.rna){if("backbone"==t.linkType)return console.log("trying to remove a backbone link",t.source.num,t.target.num),void et(t);var n=t.source.rna;n.addPseudoknots(),n.pairtable[t.source.num]=0,n.pairtable[t.target.num]=0,tt(n)}else{var r=o.extraLinks.indexOf(t);o.extraLinks.splice(r,1)}W()}o.update()},rt=function(t){var e=t.target.rna,n=t.source.rna;1==t.target.num&&(e=t.source.rna,n=t.target.rna);for(var r=h.pairtableToDotbracket(e.pairtable),i=h.pairtableToDotbracket(n.pairtable),s=e.seq,u=n.seq,l=e.getPositions("nucleotide"),c=n.getPositions("nucleotide"),f=r+i,d=s+u,p=l.concat(c),g=[],y={},m=0;m1&&void 0!==arguments[1]?arguments[1]:{},n=F(t,e);if("extraLinks"in e){var r=o.addExternalLinks(n,e.extraLinks);o.extraLinks=o.extraLinks.concat(r)}return"centerPos"in e?o.addRNAJSON(n,{centerPos:e.centerPos,centerView:!1}):"avoidOthers"in e?o.addRNAJSON(n,{avoidOthers:e.avoidOthers}):o.addRNAJSON(n,{centerView:e.centerView}),n},o.addRNAJSON=function(t,e){var n,r,i=e.avoidOthers,a=void 0!==i&&i,u=e.centerPos,l=void 0===u?null:u,c=e.centerView,f=void 0===c||c;if(null!=l){var d=0,h=0,p=0;t.nodes.forEach((function(t){d+=t.x,h+=t.y,p+=1})),p>0&&t.nodes.forEach((function(t){t.x=t.x+l[0]-d/p,t.y=t.y+l[1]-h/p,t.px=t.x,t.py=t.y}))}return a&&(n=o.graph.nodes.length>0?s().max(o.graph.nodes.map((function(t){return t.x}))):0,r=s().min(t.nodes.map((function(t){return t.x}))),t.nodes.forEach((function(t){t.x+=n-r+20,t.px+=n-r}))),t.nodes.forEach((function(e){e.rna=t})),o.rnas[t.uid]=t,W(),o.update(),f&&o.centerView(),t},o.addNodes=function(t){t.links.forEach((function(e){"number"==typeof e.source&&(e.source=t.nodes[e.source]),"number"==typeof e.target&&(e.target=t.nodes[e.target])})),o.graph.nodes.length>0?(maxX=s().max(o.graph.nodes.map((function(t){return t.x}))),maxY=s().max(o.graph.nodes.map((function(t){return t.y})))):(maxX=0,maxY=0),t.nodes.forEach((function(t){t.rna.uid in o.rnas||(o.rnas[t.rna.uid]=t.rna),t.x+=maxX,t.px+=maxX})),r=new y("",""),r.nodes=t.nodes,r.links=t.links,W(),o.update(),o.centerView()},o.clearNodes=function(){o.graph.nodes=[],o.graph.links=[],o.rnas={},o.extraLinks=[],o.update()},o.addLink=function(t){if(console.log("adding new link"),t.source.rna==t.target.rna){var e=t.source.rna;e.pairtable[t.source.num]=t.target.num,e.pairtable[t.target.num]=t.source.num,tt(e)}else console.log("intermolecule"),t.linkType="intermolecule",o.extraLinks.push(t);W(),o.update()},o.addExternalLinks=function(t,e){for(var n=[],r=0;r0&&void 0!==arguments[0]?arguments[0]:{},o={width:300,height:300,nucleotideRadius:5,rnaEdgePadding:1,labelInterval:10,showNucleotideLabels:!0,startNucleotideNumber:1,bundleExternalLinks:!1,rnaLayout:"simple",namePosition:"0 0"};function i(e,r){var i=d3.extent(e),s=d3.extent(r);i[0]-=o.nucleotideRadius+o.rnaEdgePadding,s[0]-=o.nucleotideRadius+o.rnaEdgePadding,i[1]+=o.nucleotideRadius+o.rnaEdgePadding,s[1]+=o.nucleotideRadius+o.rnaEdgePadding;var a,u=i[1]-i[0],l=s[1]-s[0];function c(t,e,n){var r=(t.range()[1]-t.range()[0])/(t.domain()[1]-t.domain()[0]),o=(e[1]-e[0])*r,i=(n[1]-n[0]-o)/2;return{scaleFactor:r,scale:d3.scale.linear().domain(e).range([n[0]+i,n[1]-i])}}return u-o.width>l-o.height?(a=c(t=d3.scale.linear().domain(i).range([0,o.width]),s,[0,o.height]),n=a.scale):(a=c(n=d3.scale.linear().domain(s).range([0,o.height]),i,[0,o.width]),t=a.scale),t.range()[0],t.domain()[0],n.range()[0],n.domain()[0],"translate("+-(t.domain()[0]*a.scaleFactor-t.range()[0])+","+-(n.domain()[0]*a.scaleFactor-n.range()[0])+")scale("+a.scaleFactor+")"}function s(t,n){var r=t.selectAll(".gnode").data(n).enter().append("svg:g").classed("gnode",!0).attr("transform",(function(t){return"translate("+t.x+","+t.y+")"}));r.append("svg:circle").classed(e().node,!0).attr("node_type","nucleotide").attr("base_type",(function(t){if(t.name)return t.name.toLowerCase()})).attr("r",o.nucleotideRadius),o.showNucleotideLabels&&r.append("svg:text").text((function(t){return t.name})).classed(e().nodeLabel,!0).append("svg:title").text((function(t){return t.struct_name+":"+t.num}))}function a(t,n){var r=t.selectAll().data(n).enter().append("svg:g").classed("gnode",!0).attr("transform",(function(t){return"translate("+t.x+","+t.y+")"}));r.append("svg:circle").classed(e().node,!0).attr("node_type","label").attr("r",o.nucleotideRadius),r.append("svg:text").classed(e().nodeLabel,!0).text((function(t){return t.name}))}function u(t,n){var r=t.append("svg:text").classed(e().plotLabel,!0).text(n),i=o.namePosition.split(" ",2),s=[],a=r.node().getBBox(),u=[a.width,a.height],l=[o.width,o.height];for(var c in[0,1])switch(i[c]){case"0":s[c]=u[c]/2;break;case"1":s[c]=l[c]-u[c]/2;break;case"0.5":s[c]=l[c]/2}r.attr("x",s[0]).attr("y",s[1])}function l(t,e){var n={},r=[];e=e.filter((function(t){return"correct"==t.linkType||"incorrect"==t.linkType||"extra"==t.linkType})),t.selectAll("[link-type=extra]").remove();for(var o=0;o0&&void 0!==arguments[0]?arguments[0]:{},e={width:300,height:300,nucleotideRadius:5,rnaEdgePadding:1,labelInterval:10,showNucleotideLabels:!0,startNucleotideNumber:1,bundleExternalLinks:!1,rnaLayout:"simple",namePosition:"0 0"};function n(t){t.each((function(t){d3.select(this).attr("transform",(function(t){return"translate("+t.x+","+t.y+")"})).append("rect").attr("fill","transparent").attr("width",(function(t){return Math.max(0,t.dx)})).attr("height",(function(t){return Math.max(0,t.dy)}));var n=T(e).width(Math.max(0,t.dx)).height(Math.max(0,t.dy));"structure"in t&&d3.select(this).call(n)}))}e=Object.assign(e,t);var r=function(t){t.each((function(t){console.log("data:",t);var r=d3.layout.treemap().size([e.width,e.height]).sticky(!1).value((function(t){return t.size}));d3.select(this).append("g").classed("rnatreemap",!0).datum(t).selectAll(".treemapnode").data(r.nodes).enter().append("g").classed("treemapnode",!0).call(n)}))};return r.width=function(t){return arguments.length?(e.width=t,r):e.width},r.height=function(t){return arguments.length?(e.height=t,r):e.height},r.showNucleotideLabels=function(t){return arguments.length?(e.showNucleotideLabels=t,r):e.showNucleotideLabels},r.rnaEdgePadding=function(t){return arguments.length?(e.rnaEdgePadding=t,r):e.rnaEdgePadding},r.nucleotideRadius=function(t){return arguments.length?(e.nucleotideRadius=t,r):e.nucleotideRadius},r.labelInterval=function(t){return arguments.length?(e.labelInterval=t,r):e.labelInterval},r.showNucleotideLabels=function(t){return arguments.length?(e.showNucleotideLabels=t,r):e.showNucleotideLabels},r.startNucleotideNumber=function(t){return arguments.length?(e.startNucleotideNumber=t,r):e.startNucleotideNumber},r.bundleExternalLinks=function(t){return arguments.length?(e.bundleExternalLinks=t,r):e.bundleExternalLinks},r.rnaLayout=function(t){return arguments.length?(e.rnaLayout=t,r):e.rnaLayout},r.namePosition=function(t){return arguments.length?(e.namePosition=t,r):e.namePosition},r.zoom=function(t){return arguments.length?(e.zoom=t,r):e.zoom},r}E.prototype.naview_xy_coordinates=function(t){var e,n=[],r=[];if(0===t.length||0===t[0])return 0;this.nbase=t[0],this.bases=[];for(var o=0;oe&&n++;0==n&&(this.bases[1].setMate(this.nbase),this.bases[this.nbase].setMate(1))},E.prototype.find_regions=function(){var t,e=null,n=null;t=this.nbase+1;var r=[];for(e=0;ethis.nbase&&(e=0)}while(e!=t);return r},E.prototype.find_central_loop=function(){var t=new w.r,e=null,n=null,r=null;for(A.bind(this)(),e=0,n=-1,r=0;re?(n=t.getDepth(),e=t.getNconnection(),this.root=t):t.getDepth()>n&&t.getNconnection()==e&&(n=t.getDepth(),this.root=t)},E.prototype.traverse_loop=function(t,e){var n,r,o,i,s,a,u,l,c,f,d,h,p,g,y,m,b,v,k,x,w,E,A,N,L,T,_,M,S,B,I,P,R,C,U,O,X,Y,q,D,F,z,V,j,$,W,G,J,H,K,Z,Q,tt,et,nt,rt,ot,it,st,at,ut,lt,ct,ft,dt,ht,pt,gt,yt,mt=0;a=2*Math.PI/(this.nbase+1),v=null,B=-1;var bt=0;for(A=0;null!=(m=t.getConnection(bt));bt++,A++)n=-Math.sin(a*m.getStart()),r=Math.cos(a*m.getStart()),o=-Math.sin(a*m.getEnd()),i=Math.cos(a*m.getEnd())-r,s=n-o,u=Math.sqrt(i*i+s*s),m.setXrad(i/u),m.setYrad(s/u),m.setAngle(Math.atan2(s,i)),m.getAngle()<0&&m.setAngle(m.getAngle()+2*Math.PI),null!=e&&e.getRegion()==m.getRegion()&&(v=m,B=A);t:for(;;){this.determine_radius(t,this.lencut),l=t.getRadius()/this.RADIUS_REDUCTION_FACTOR,null==e?c=f=0:(d=(this.bases[v.getStart()].getX()+this.bases[v.getEnd()].getX())/2,h=(this.bases[v.getStart()].getY()+this.bases[v.getEnd()].getY())/2,c=d-l*v.getXrad(),f=h-l*v.getYrad()),_=-1==B?0:B,m=t.getConnection(_),T=0,I=!1;do{if((w=_-1)<0&&(w=t.getNconnection()-1),k=t.getConnection(w),this.connected_connection(k,m)?(_=w,m=k):I=!0,++T>t.getNconnection()){for(L=-1,A=0;A=t.getNconnection()&&(w=0),m=t.getConnection(A),(dt=(b=t.getConnection(w)).getAngle()-m.getAngle())<0&&(dt+=2*Math.PI),dt>L&&(L=dt,mt=A);M=mt,(_=mt+1)>=t.getNconnection()&&(_=0),(m=t.getConnection(M)).setBroken(!0),I=!0}}while(!I);for(P=!1,W=_;!P;){for(T=0,I=!1,M=_,R=!1;!I;)if(m=t.getConnection(M),M==B&&(R=!0),(w=M+1)>=t.getNconnection()&&(w=0),b=t.getConnection(w),this.connected_connection(m,b)){if(++T>=t.getNconnection())break;M=w}else I=!0;for(A=G=J=S=this.find_ic_middle(_,M,e,v,t),I=!1,K=0;!I;)(A=K<0?G:0==K?S:J)>=0&&(m=t.getConnection(A),null!=e&&v==m||(0==K?(p=m.getAngle()-Math.asin(.5/l),g=m.getAngle()+Math.asin(.5/l),this.bases[m.getStart()].setX(c+l*Math.cos(p)),this.bases[m.getStart()].setY(f+l*Math.sin(p)),this.bases[m.getEnd()].setX(c+l*Math.cos(g)),this.bases[m.getEnd()].setY(f+l*Math.sin(g))):K<0?((w=A+1)>=t.getNconnection()&&(w=0),m=t.getConnection(A),b=t.getConnection(w),nt=m.getXrad(),rt=m.getYrad(),dt=(m.getAngle()+b.getAngle())/2,m.getAngle()>b.getAngle()&&(dt-=Math.PI),st=Math.cos(dt),lt=Math.sin(dt),ct=-st,(N=b.getAngle()-m.getAngle())<0&&(N+=2*Math.PI),ft=m.isExtruded()?N<=Math.PI/2?2:1.5:1,this.bases[m.getEnd()].setX(this.bases[b.getStart()].getX()+ft*lt),this.bases[m.getEnd()].setY(this.bases[b.getStart()].getY()+ft*ct),this.bases[m.getStart()].setX(this.bases[m.getEnd()].getX()+rt),this.bases[m.getStart()].setY(this.bases[m.getEnd()].getY()-nt)):((w=A-1)<0&&(w=t.getNconnection()-1),m=t.getConnection(w),ot=(b=t.getConnection(A)).getXrad(),it=b.getYrad(),dt=(m.getAngle()+b.getAngle())/2,m.getAngle()>b.getAngle()&&(dt-=Math.PI),st=Math.cos(dt),lt=-Math.sin(dt),ct=st,(N=b.getAngle()-m.getAngle())<0&&(N+=2*Math.PI),ft=m.isExtruded()?N<=Math.PI/2?2:1.5:1,this.bases[b.getStart()].setX(this.bases[m.getEnd()].getX()+ft*lt),this.bases[b.getStart()].setY(this.bases[m.getEnd()].getY()+ft*ct),this.bases[b.getEnd()].setX(this.bases[b.getStart()].getX()-it),this.bases[b.getEnd()].setY(this.bases[b.getStart()].getY()+ot)))),K<0?(J==M?J=-1:J>=0&&++J>=t.getNconnection()&&(J=0),K=1):(G==_?G=-1:G>=0&&--G<0&&(G=t.getNconnection()-1),K=-1),I=-1==G&&-1==J;if((H=M+1)>=t.getNconnection()&&(H=0),M!=_&&(_!=W||H!=W))if(m=t.getConnection(_),b=t.getConnection(M),Q=this.bases[b.getEnd()].getX()-this.bases[m.getStart()].getX(),tt=this.bases[b.getEnd()].getY()-this.bases[m.getStart()].getY(),U=this.bases[m.getStart()].getX()+Q/2,O=this.bases[m.getStart()].getY()+tt/2,q=Q/(et=Math.sqrt(Q*Q+tt*tt)),D=tt/et,F=c-U,z=f-O,X=(V=(F/=et=Math.sqrt(Q*Q+tt*tt))*q+(z/=et)*D)*q-F,Y=V*D-z,X/=et=Math.sqrt(X*X+Y*Y),Y/=et,Q=this.bases[m.getStart()].getX()-c,tt=this.bases[m.getStart()].getY()-f,(dt=Math.atan2(tt,Q))<0&&(dt+=2*Math.PI),Q=this.bases[b.getEnd()].getX()-c,tt=this.bases[b.getEnd()].getY()-f,(ht=Math.atan2(tt,Q))<0&&(ht+=2*Math.PI),htMath.PI?-1:1)*l*X,$=f+C*l*Y,R)c-=j-U,f-=$-O;else for(A=_;x=(m=t.getConnection(A)).getStart(),this.bases[x].setX(this.bases[x].getX()+j-U),this.bases[x].setY(this.bases[x].getY()+$-O),x=m.getEnd(),this.bases[x].setX(this.bases[x].getX()+j-U),this.bases[x].setY(this.bases[x].getY()+$-O),A!=M;)++A>=t.getNconnection()&&(A=0);P=(_=H)==W}for(A=0;A=t.getNconnection()&&(w=0),b=t.getConnection(w),Q=this.bases[m.getEnd()].getX()-c,tt=this.bases[m.getEnd()].getY()-f,ut=Math.sqrt(Q*Q+tt*tt),(dt=Math.atan2(tt,Q))<0&&(dt+=2*Math.PI),Q=this.bases[b.getStart()].getX()-c,tt=this.bases[b.getStart()].getY()-f,at=Math.sqrt(Q*Q+tt*tt),(ht=Math.atan2(tt,Q))<0&&(ht+=2*Math.PI),htMath.PI)if(m.isExtruded())console.log("Warning from traverse_loop. Loop "+t.getNumber()+" has crossed regions\n");else if(b.getStart()-m.getEnd()!=1){m.setExtruded(!0);continue t}if(m.isExtruded())this.construct_extruded_segment(m,b);else for((E=b.getStart()-m.getEnd())<0&&(E+=this.nbase+1),a=Z/E,w=1;wthis.nbase&&(x-=this.nbase+1),et=ut+(at-ut)*((y=dt+w*a)-dt)/Z,this.bases[x].setX(c+et*Math.cos(y)),this.bases[x].setY(f+et*Math.sin(y))}break}for(A=0;A=t.getNconnection()&&(w=0),m=t.getConnection(A),b=t.getConnection(w),E+=2,pt+=this.bases[m.getStart()].getX()+this.bases[m.getEnd()].getX(),gt+=this.bases[m.getStart()].getY()+this.bases[m.getEnd()].getY(),!m.isExtruded())for(w=m.getEnd()+1;w!=b.getStart();w++)w>this.nbase&&(w-=this.nbase+1),E++,pt+=this.bases[w].getX(),gt+=this.bases[w].getY();t.setX(pt/E),t.setY(gt/E)},E.prototype.determine_radius=function(t,e){var n,r,o,i,s,a,u,l,c,f,d,h=0,p=new v.Connection,g=new v.Connection,y=.7071068;do{for(n=1e10,s=0,i=0,l=0;l=t.getNconnection()&&(c=0),g=t.getConnection(c),f=p.getEnd(),(d=g.getStart())1&&(n=u,h=l);(a=i/s)0?a=t.getRadius():t.setRadius(a)},E.prototype.find_ic_middle=function(t,e,n,r,o){var i,s,a,u,l;for(i=0,s=-1,a=t,l=!1;!l;)i++>2*o.getNconnection()&&console.log("Infinite loop in 'find_ic_middle'"),null!=n&&o.getConnection(a)==r&&(s=a),l=a==e,++a>=o.getNconnection()&&(a=0);if(-1==s){for(u=1,a=t;u<(i+1)/2;u++)++a>=o.getNconnection()&&(a=0);s=a}return s},E.prototype.construct_extruded_segment=function(t,e){var n,r,o,i,s,a,u,l,c,f,d,h,p,g,y,m,b,v;if(n=t.getAngle(),(o=r=e.getAngle())=1.5&&d<=Math.PI/2&&((m=p+1)>this.nbase&&(m-=this.nbase+1),(b=g-1)<0&&(b+=this.nbase+1),this.bases[m].setX(this.bases[p].getX()+.5*s),this.bases[m].setY(this.bases[p].getY()+.5*a),this.bases[b].setX(this.bases[g].getX()-.5*s),this.bases[b].setY(this.bases[g].getY()-.5*a),p=m,g=b);do{v=!1,this.construct_circle_segment(p,g),(m=p+1)>this.nbase&&(m-=this.nbase+1),s=this.bases[m].getX()-this.bases[p].getX(),a=this.bases[m].getY()-this.bases[p].getY(),(u=Math.atan2(a,s))<0&&(u+=2*Math.PI),(h=u-n)<0&&(h+=2*Math.PI),h>Math.PI&&(v=!0),(b=g-1)<0&&(b+=this.nbase+1),s=this.bases[b].getX()-this.bases[g].getX(),a=this.bases[b].getY()-this.bases[g].getY(),(l=Math.atan2(a,s))<0&&(l+=2*Math.PI),(h=r-l)<0&&(h+=2*Math.PI),h>Math.PI&&(v=!0),v&&(c=this.minf2(i,n+.5),this.bases[m].setX(this.bases[p].getX()+Math.cos(c)),this.bases[m].setY(this.bases[p].getY()+Math.sin(c)),p=m,c=this.maxf2(i,o-.5),this.bases[b].setX(this.bases[g].getX()+Math.cos(c)),this.bases[b].setY(this.bases[g].getY()+Math.sin(c)),g=b,y-=2)}while(v&&y>1)}},E.prototype.construct_circle_segment=function(t,e){var n,r,o,i,s,a,u,l,c,f,d,h,p,g,y;if(n=this.bases[e].getX()-this.bases[t].getX(),r=this.bases[e].getY()-this.bases[t].getY(),o=Math.sqrt(n*n+r*r),(p=e-t)<0&&(p+=this.nbase+1),o>=p)for(n/=o,r/=o,g=1;gthis.nbase&&(y-=this.nbase+1),this.bases[y].setX(this.bases[t].getX()+n*g/p),this.bases[y].setY(this.bases[t].getY()+r*g/p);else for(this.find_center_for_arc(p-1,o),n/=o,r/=o,i=this.bases[t].getX()+n*o/2,s=this.bases[t].getY()+r*o/2,a=r,u=-n,l=i+this._h*a,c=s+this._h*u,f=this.bases[t].getX()-l,d=this.bases[t].getY()-c,o=Math.sqrt(f*f+d*d),h=Math.atan2(d,f),g=1;gthis.nbase&&(y-=this.nbase+1),this.bases[y].setX(l+o*Math.cos(h+g*this.angleinc)),this.bases[y].setY(c+o*Math.sin(h+g*this.angleinc))},E.prototype.find_center_for_arc=function(t,e){var n,r,o,i,s,a,u,l;o=-(r=(t+1)/Math.PI)-e/(t+1.000001-e),e<1&&(o=0),l=0;do{n=(r+o)/2,s=1-.5/((i=Math.sqrt(n*n+e*e/4))*i),Math.abs(s)>1&&console.log("Unexpected large magnitude discriminant = "+s+" "+i),(u=(a=Math.acos(s))*(t+1)+2*Math.acos(n/i)-2*Math.PI)>0?o=n:r=n}while(Math.abs(u)>1e-4&&++l=this.MAXITER&&(noIterationFailureYet&&(console.log("Iteration failed in find_center_for_arc"),noIterationFailureYet=!1),n=0,a=0),this._h=n,this.angleinc=a},E.prototype.generate_region=function(t){var e,n,r,o,i,s;for(s=t.getRegion(),e=0,t.getStart()==s.getStart1()?(n=s.getStart1(),r=s.getEnd1()):(n=s.getStart2(),r=s.getEnd2()),(this.bases[t.getStart()].getX()>this.ANUM-100||this.bases[t.getEnd()].getX()>this.ANUM-100)&&console.log("Bad region passed to generate_region. Coordinates not defined."),o=n+1;o<=r;o++)e++,this.bases[o].setX(this.bases[t.getStart()].getX()+this.HELIX_FACTOR*e*t.getXrad()),this.bases[o].setY(this.bases[t.getStart()].getY()+this.HELIX_FACTOR*e*t.getYrad()),i=this.bases[o].getMate(),this.bases[i].setX(this.bases[t.getEnd()].getX()+this.HELIX_FACTOR*e*t.getXrad()),this.bases[i].setY(this.bases[t.getEnd()].getY()+this.HELIX_FACTOR*e*t.getYrad())},E.prototype.minf2=function(t,e){return te?t:e},E.prototype.connected_connection=function(t,e){return!!t.isExtruded()||t.getEnd()+1==e.getStart()}})(),i})()})); +!function(t,e){"object"==typeof exports&&"object"==typeof module?module.exports=e(require("d3")):"function"==typeof define&&define.amd?define(["d3"],e):"object"==typeof exports?exports.fornac=e(require("d3")):t.fornac=e(t.d3)}(self,(t=>(()=>{var e={332:(t,e,n)=>{"use strict";n.r(e),n.d(e,{Connection:()=>i});var r=n(326),o=n(980);function i(){this.loop=new r.F,this.region=new o.T,this.start=null,this.end=null,this.xrad=null,this.yrad=null,this.angle=null,this.extruded=null,this.broken=null,this._isNull=!1}i.prototype.isNull=function(){return this._isNull},i.prototype.setNull=function(t){this._isNull=t},i.prototype.getLoop=function(){return this.loop},i.prototype.setLoop=function(t){this.loop=t},i.prototype.getRegion=function(){return this.region},i.prototype.setRegion=function(t){this.region=t},i.prototype.getStart=function(){return this.start},i.prototype.setStart=function(t){this.start=t},i.prototype.getEnd=function(){return this.end},i.prototype.setEnd=function(t){this.end=t},i.prototype.getXrad=function(){return this.xrad},i.prototype.setXrad=function(t){this.xrad=t},i.prototype.getYrad=function(){return this.yrad},i.prototype.setYrad=function(t){this.yrad=t},i.prototype.getAngle=function(){return this.angle},i.prototype.setAngle=function(t){this.angle=t},i.prototype.isExtruded=function(){return this.extruded},i.prototype.setExtruded=function(t){this.extruded=t},i.prototype.isBroken=function(){return this.broken},i.prototype.setBroken=function(t){this.broken=t}},326:(t,e,n)=>{"use strict";n.d(e,{F:()=>o});var r=n(332);function o(){this.nconnection=null,this.connections=[],this._connections=[],this.number=null,this.depth=null,this.mark=null,this.x=null,this.y=null,this.radius=null}o.prototype.getNconnection=function(){return this.nconnection},o.prototype.setNconnection=function(t){this.nconnection=t},o.prototype.setConnection=function(t,e){null!=e?this._connections[t]=e:(this._connections[t]||(this._connections[t]=new r.Connection),this._connections[t].setNull(!0))},o.prototype.getConnection=function(t){var e=n(332);this._connections[t]||(this._connections[t]=new e);var r=this._connections[t];return r.isNull()?null:r},o.prototype.addConnection=function(t,e){this._connections.push(e)},o.prototype.getNumber=function(){return this.number},o.prototype.setNumber=function(t){this.number=t},o.prototype.getDepth=function(){return this.depth},o.prototype.setDepth=function(t){this.depth=t},o.prototype.isMark=function(){return this.mark},o.prototype.setMark=function(t){this.mark=t},o.prototype.getX=function(){return this.x},o.prototype.setX=function(t){this.x=t},o.prototype.getY=function(){return this.y},o.prototype.setY=function(t){this.y=t},o.prototype.getRadius=function(){return this.radius},o.prototype.setRadius=function(t){this.radius=t}},980:(t,e,n)=>{"use strict";function r(){this._start1=null,this._end1=null,this._start2=null,this._end2=null}n.d(e,{T:()=>r}),r.prototype.getStart1=function(){return this._start1},r.prototype.setStart1=function(t){this._start1=t},r.prototype.getEnd1=function(){return this._end1},r.prototype.setEnd1=function(t){this._end1=t},r.prototype.getStart2=function(){return this._start2},r.prototype.setStart2=function(t){this._start2=t},r.prototype.getEnd2=function(){return this._end2},r.prototype.setEnd2=function(t){this._end2=t}},526:(t,e)=>{"use strict";e.byteLength=function(t){var e=a(t),n=e[0],r=e[1];return 3*(n+r)/4-r},e.toByteArray=function(t){var e,n,i=a(t),s=i[0],u=i[1],l=new o(function(t,e,n){return 3*(e+n)/4-n}(0,s,u)),c=0,f=u>0?s-4:s;for(n=0;n>16&255,l[c++]=e>>8&255,l[c++]=255&e;return 2===u&&(e=r[t.charCodeAt(n)]<<2|r[t.charCodeAt(n+1)]>>4,l[c++]=255&e),1===u&&(e=r[t.charCodeAt(n)]<<10|r[t.charCodeAt(n+1)]<<4|r[t.charCodeAt(n+2)]>>2,l[c++]=e>>8&255,l[c++]=255&e),l},e.fromByteArray=function(t){for(var e,r=t.length,o=r%3,i=[],s=16383,a=0,l=r-o;al?l:a+s));return 1===o?(e=t[r-1],i.push(n[e>>2]+n[e<<4&63]+"==")):2===o&&(e=(t[r-2]<<8)+t[r-1],i.push(n[e>>10]+n[e>>4&63]+n[e<<2&63]+"=")),i.join("")};for(var n=[],r=[],o="undefined"!=typeof Uint8Array?Uint8Array:Array,i="ABCDEFGHIJKLMNOPQRSTUVWXYZabcdefghijklmnopqrstuvwxyz0123456789+/",s=0;s<64;++s)n[s]=i[s],r[i.charCodeAt(s)]=s;function a(t){var e=t.length;if(e%4>0)throw new Error("Invalid string. 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t.linkType})).attr("extra-link-type",(function(t){return t.extraLinkType})).classed("link",!0).classed(e().link,!0)}(i,h),function(t,n){var r=t.selectAll(".gnode").data(n).enter().append("svg:g").classed("gnode",!0).attr("transform",(function(t){return"translate("+t.x+","+t.y+")"}));r.append("svg:circle").classed(e().node,!0).attr("node_type","nucleotide").attr("base_type",(function(t){if(t.name)return t.name.toLowerCase()})).attr("r",o.nucleotideRadius),o.showNucleotideLabels&&r.append("svg:text").text((function(t){return t.name})).classed(e().nodeLabel,!0).append("svg:title").text((function(t){return t.struct_name+":"+t.num}))}(i,f),function(t,n){var r=t.selectAll().data(n).enter().append("svg:g").classed("gnode",!0).attr("transform",(function(t){return"translate("+t.x+","+t.y+")"}));r.append("svg:circle").classed(e().node,!0).attr("node_type","label").attr("r",o.nucleotideRadius),r.append("svg:text").classed(e().nodeLabel,!0).text((function(t){return t.name}))}(i,d),function(t,n){var r=t.append("svg:text").classed(e().plotLabel,!0).text(n),i=o.namePosition.split(" ",2),s=[],a=r.node().getBBox(),u=[a.width,a.height],l=[o.width,o.height];for(var c in[0,1])switch(i[c]){case"0":s[c]=u[c]/2;break;case"1":s[c]=l[c]-u[c]/2;break;case"0.5":s[c]=l[c]/2}r.attr("x",s[0]).attr("y",s[1])}(d3.select(this),r.name),o.bundleExternalLinks&&function(t,e){var n={},r=[];e=e.filter((function(t){return"correct"==t.linkType||"incorrect"==t.linkType||"extra"==t.linkType})),t.selectAll("[link-type=extra]").remove();for(var o=0;o0&&void 0!==arguments[0]?arguments[0]:{},e={width:300,height:300,nucleotideRadius:5,rnaEdgePadding:1,labelInterval:10,showNucleotideLabels:!0,startNucleotideNumber:1,bundleExternalLinks:!1,rnaLayout:"simple",namePosition:"0 0"};function n(t){t.each((function(t){d3.select(this).attr("transform",(function(t){return"translate("+t.x+","+t.y+")"})).append("rect").attr("fill","transparent").attr("width",(function(t){return Math.max(0,t.dx)})).attr("height",(function(t){return Math.max(0,t.dy)}));var n=N(e).width(Math.max(0,t.dx)).height(Math.max(0,t.dy));"structure"in t&&d3.select(this).call(n)}))}e=Object.assign(e,t);var r=function(t){t.each((function(t){console.log("data:",t);var r=d3.layout.treemap().size([e.width,e.height]).sticky(!1).value((function(t){return t.size}));d3.select(this).append("g").classed("rnatreemap",!0).datum(t).selectAll(".treemapnode").data(r.nodes).enter().append("g").classed("treemapnode",!0).call(n)}))};return r.width=function(t){return arguments.length?(e.width=t,r):e.width},r.height=function(t){return arguments.length?(e.height=t,r):e.height},r.showNucleotideLabels=function(t){return arguments.length?(e.showNucleotideLabels=t,r):e.showNucleotideLabels},r.rnaEdgePadding=function(t){return arguments.length?(e.rnaEdgePadding=t,r):e.rnaEdgePadding},r.nucleotideRadius=function(t){return arguments.length?(e.nucleotideRadius=t,r):e.nucleotideRadius},r.labelInterval=function(t){return arguments.length?(e.labelInterval=t,r):e.labelInterval},r.showNucleotideLabels=function(t){return arguments.length?(e.showNucleotideLabels=t,r):e.showNucleotideLabels},r.startNucleotideNumber=function(t){return arguments.length?(e.startNucleotideNumber=t,r):e.startNucleotideNumber},r.bundleExternalLinks=function(t){return arguments.length?(e.bundleExternalLinks=t,r):e.bundleExternalLinks},r.rnaLayout=function(t){return arguments.length?(e.rnaLayout=t,r):e.rnaLayout},r.namePosition=function(t){return arguments.length?(e.namePosition=t,r):e.namePosition},r.zoom=function(t){return arguments.length?(e.zoom=t,r):e.zoom},r}w.prototype.naview_xy_coordinates=function(t){var e,n=[],r=[];if(0===t.length||0===t[0])return 0;this.nbase=t[0],this.bases=[];for(var o=0;oe&&n++;0==n&&(this.bases[1].setMate(this.nbase),this.bases[this.nbase].setMate(1))},w.prototype.find_regions=function(){var t,e=null,n=null;t=this.nbase+1;var r=[];for(e=0;ethis.nbase&&(e=0)}while(e!=t);return r},w.prototype.find_central_loop=function(){var t=new x.F,e=null,n=null,r=null;for(E.bind(this)(),e=0,n=-1,r=0;re?(n=t.getDepth(),e=t.getNconnection(),this.root=t):t.getDepth()>n&&t.getNconnection()==e&&(n=t.getDepth(),this.root=t)},w.prototype.traverse_loop=function(t,e){var n,r,o,i,s,a,u,l,c,f,d,h,p,g,y,m,b,v,k,x,w,E,A,L,N,T,_,M,I,S,P,R,C,B,U,O,X,Y,F,q,D,z,V,j,$,J,H,W,G,K,Z,Q,tt,et,nt,rt,ot,it,st,at,ut,lt,ct,ft,dt,ht,pt,gt,yt,mt=0;a=2*Math.PI/(this.nbase+1),v=null,S=-1;var bt=0;for(A=0;null!=(m=t.getConnection(bt));bt++,A++)n=-Math.sin(a*m.getStart()),r=Math.cos(a*m.getStart()),o=-Math.sin(a*m.getEnd()),i=Math.cos(a*m.getEnd())-r,s=n-o,u=Math.sqrt(i*i+s*s),m.setXrad(i/u),m.setYrad(s/u),m.setAngle(Math.atan2(s,i)),m.getAngle()<0&&m.setAngle(m.getAngle()+2*Math.PI),null!=e&&e.getRegion()==m.getRegion()&&(v=m,S=A);t:for(;;){this.determine_radius(t,this.lencut),l=t.getRadius()/this.RADIUS_REDUCTION_FACTOR,null==e?c=f=0:(d=(this.bases[v.getStart()].getX()+this.bases[v.getEnd()].getX())/2,h=(this.bases[v.getStart()].getY()+this.bases[v.getEnd()].getY())/2,c=d-l*v.getXrad(),f=h-l*v.getYrad()),_=-1==S?0:S,m=t.getConnection(_),T=0,P=!1;do{if((w=_-1)<0&&(w=t.getNconnection()-1),k=t.getConnection(w),this.connected_connection(k,m)?(_=w,m=k):P=!0,++T>t.getNconnection()){for(N=-1,A=0;A=t.getNconnection()&&(w=0),m=t.getConnection(A),(dt=(b=t.getConnection(w)).getAngle()-m.getAngle())<0&&(dt+=2*Math.PI),dt>N&&(N=dt,mt=A);M=mt,(_=mt+1)>=t.getNconnection()&&(_=0),(m=t.getConnection(M)).setBroken(!0),P=!0}}while(!P);for(R=!1,J=_;!R;){for(T=0,P=!1,M=_,C=!1;!P;)if(m=t.getConnection(M),M==S&&(C=!0),(w=M+1)>=t.getNconnection()&&(w=0),b=t.getConnection(w),this.connected_connection(m,b)){if(++T>=t.getNconnection())break;M=w}else P=!0;for(A=H=W=I=this.find_ic_middle(_,M,e,v,t),P=!1,K=0;!P;)(A=K<0?H:0==K?I:W)>=0&&(m=t.getConnection(A),null!=e&&v==m||(0==K?(p=m.getAngle()-Math.asin(.5/l),g=m.getAngle()+Math.asin(.5/l),this.bases[m.getStart()].setX(c+l*Math.cos(p)),this.bases[m.getStart()].setY(f+l*Math.sin(p)),this.bases[m.getEnd()].setX(c+l*Math.cos(g)),this.bases[m.getEnd()].setY(f+l*Math.sin(g))):K<0?((w=A+1)>=t.getNconnection()&&(w=0),m=t.getConnection(A),b=t.getConnection(w),nt=m.getXrad(),rt=m.getYrad(),dt=(m.getAngle()+b.getAngle())/2,m.getAngle()>b.getAngle()&&(dt-=Math.PI),st=Math.cos(dt),lt=Math.sin(dt),ct=-st,(L=b.getAngle()-m.getAngle())<0&&(L+=2*Math.PI),ft=m.isExtruded()?L<=Math.PI/2?2:1.5:1,this.bases[m.getEnd()].setX(this.bases[b.getStart()].getX()+ft*lt),this.bases[m.getEnd()].setY(this.bases[b.getStart()].getY()+ft*ct),this.bases[m.getStart()].setX(this.bases[m.getEnd()].getX()+rt),this.bases[m.getStart()].setY(this.bases[m.getEnd()].getY()-nt)):((w=A-1)<0&&(w=t.getNconnection()-1),m=t.getConnection(w),ot=(b=t.getConnection(A)).getXrad(),it=b.getYrad(),dt=(m.getAngle()+b.getAngle())/2,m.getAngle()>b.getAngle()&&(dt-=Math.PI),st=Math.cos(dt),lt=-Math.sin(dt),ct=st,(L=b.getAngle()-m.getAngle())<0&&(L+=2*Math.PI),ft=m.isExtruded()?L<=Math.PI/2?2:1.5:1,this.bases[b.getStart()].setX(this.bases[m.getEnd()].getX()+ft*lt),this.bases[b.getStart()].setY(this.bases[m.getEnd()].getY()+ft*ct),this.bases[b.getEnd()].setX(this.bases[b.getStart()].getX()-it),this.bases[b.getEnd()].setY(this.bases[b.getStart()].getY()+ot)))),K<0?(W==M?W=-1:W>=0&&++W>=t.getNconnection()&&(W=0),K=1):(H==_?H=-1:H>=0&&--H<0&&(H=t.getNconnection()-1),K=-1),P=-1==H&&-1==W;if((G=M+1)>=t.getNconnection()&&(G=0),M!=_&&(_!=J||G!=J))if(m=t.getConnection(_),b=t.getConnection(M),Q=this.bases[b.getEnd()].getX()-this.bases[m.getStart()].getX(),tt=this.bases[b.getEnd()].getY()-this.bases[m.getStart()].getY(),U=this.bases[m.getStart()].getX()+Q/2,O=this.bases[m.getStart()].getY()+tt/2,F=Q/(et=Math.sqrt(Q*Q+tt*tt)),q=tt/et,D=c-U,z=f-O,X=(V=(D/=et=Math.sqrt(Q*Q+tt*tt))*F+(z/=et)*q)*F-D,Y=V*q-z,X/=et=Math.sqrt(X*X+Y*Y),Y/=et,Q=this.bases[m.getStart()].getX()-c,tt=this.bases[m.getStart()].getY()-f,(dt=Math.atan2(tt,Q))<0&&(dt+=2*Math.PI),Q=this.bases[b.getEnd()].getX()-c,tt=this.bases[b.getEnd()].getY()-f,(ht=Math.atan2(tt,Q))<0&&(ht+=2*Math.PI),htMath.PI?-1:1)*l*X,$=f+B*l*Y,C)c-=j-U,f-=$-O;else for(A=_;x=(m=t.getConnection(A)).getStart(),this.bases[x].setX(this.bases[x].getX()+j-U),this.bases[x].setY(this.bases[x].getY()+$-O),x=m.getEnd(),this.bases[x].setX(this.bases[x].getX()+j-U),this.bases[x].setY(this.bases[x].getY()+$-O),A!=M;)++A>=t.getNconnection()&&(A=0);R=(_=G)==J}for(A=0;A=t.getNconnection()&&(w=0),b=t.getConnection(w),Q=this.bases[m.getEnd()].getX()-c,tt=this.bases[m.getEnd()].getY()-f,ut=Math.sqrt(Q*Q+tt*tt),(dt=Math.atan2(tt,Q))<0&&(dt+=2*Math.PI),Q=this.bases[b.getStart()].getX()-c,tt=this.bases[b.getStart()].getY()-f,at=Math.sqrt(Q*Q+tt*tt),(ht=Math.atan2(tt,Q))<0&&(ht+=2*Math.PI),htMath.PI)if(m.isExtruded())console.log("Warning from traverse_loop. Loop "+t.getNumber()+" has crossed regions\n");else if(b.getStart()-m.getEnd()!=1){m.setExtruded(!0);continue t}if(m.isExtruded())this.construct_extruded_segment(m,b);else for((E=b.getStart()-m.getEnd())<0&&(E+=this.nbase+1),a=Z/E,w=1;wthis.nbase&&(x-=this.nbase+1),et=ut+(at-ut)*((y=dt+w*a)-dt)/Z,this.bases[x].setX(c+et*Math.cos(y)),this.bases[x].setY(f+et*Math.sin(y))}break}for(A=0;A=t.getNconnection()&&(w=0),m=t.getConnection(A),b=t.getConnection(w),E+=2,pt+=this.bases[m.getStart()].getX()+this.bases[m.getEnd()].getX(),gt+=this.bases[m.getStart()].getY()+this.bases[m.getEnd()].getY(),!m.isExtruded())for(w=m.getEnd()+1;w!=b.getStart();w++)w>this.nbase&&(w-=this.nbase+1),E++,pt+=this.bases[w].getX(),gt+=this.bases[w].getY();t.setX(pt/E),t.setY(gt/E)},w.prototype.determine_radius=function(t,e){var n,r,o,i,s,a,u,l,c,f,d,h=0,p=new b.Connection,g=new b.Connection,y=.7071068;do{for(n=1e10,s=0,i=0,l=0;l=t.getNconnection()&&(c=0),g=t.getConnection(c),f=p.getEnd(),(d=g.getStart())1&&(n=u,h=l);(a=i/s)0?a=t.getRadius():t.setRadius(a)},w.prototype.find_ic_middle=function(t,e,n,r,o){var i,s,a,u,l;for(i=0,s=-1,a=t,l=!1;!l;)i++>2*o.getNconnection()&&console.log("Infinite loop in 'find_ic_middle'"),null!=n&&o.getConnection(a)==r&&(s=a),l=a==e,++a>=o.getNconnection()&&(a=0);if(-1==s){for(u=1,a=t;u<(i+1)/2;u++)++a>=o.getNconnection()&&(a=0);s=a}return s},w.prototype.construct_extruded_segment=function(t,e){var n,r,o,i,s,a,u,l,c,f,d,h,p,g,y,m,b,v;if(n=t.getAngle(),(o=r=e.getAngle())=1.5&&d<=Math.PI/2&&((m=p+1)>this.nbase&&(m-=this.nbase+1),(b=g-1)<0&&(b+=this.nbase+1),this.bases[m].setX(this.bases[p].getX()+.5*s),this.bases[m].setY(this.bases[p].getY()+.5*a),this.bases[b].setX(this.bases[g].getX()-.5*s),this.bases[b].setY(this.bases[g].getY()-.5*a),p=m,g=b);do{v=!1,this.construct_circle_segment(p,g),(m=p+1)>this.nbase&&(m-=this.nbase+1),s=this.bases[m].getX()-this.bases[p].getX(),a=this.bases[m].getY()-this.bases[p].getY(),(u=Math.atan2(a,s))<0&&(u+=2*Math.PI),(h=u-n)<0&&(h+=2*Math.PI),h>Math.PI&&(v=!0),(b=g-1)<0&&(b+=this.nbase+1),s=this.bases[b].getX()-this.bases[g].getX(),a=this.bases[b].getY()-this.bases[g].getY(),(l=Math.atan2(a,s))<0&&(l+=2*Math.PI),(h=r-l)<0&&(h+=2*Math.PI),h>Math.PI&&(v=!0),v&&(c=this.minf2(i,n+.5),this.bases[m].setX(this.bases[p].getX()+Math.cos(c)),this.bases[m].setY(this.bases[p].getY()+Math.sin(c)),p=m,c=this.maxf2(i,o-.5),this.bases[b].setX(this.bases[g].getX()+Math.cos(c)),this.bases[b].setY(this.bases[g].getY()+Math.sin(c)),g=b,y-=2)}while(v&&y>1)}},w.prototype.construct_circle_segment=function(t,e){var n,r,o,i,s,a,u,l,c,f,d,h,p,g,y;if(n=this.bases[e].getX()-this.bases[t].getX(),r=this.bases[e].getY()-this.bases[t].getY(),o=Math.sqrt(n*n+r*r),(p=e-t)<0&&(p+=this.nbase+1),o>=p)for(n/=o,r/=o,g=1;gthis.nbase&&(y-=this.nbase+1),this.bases[y].setX(this.bases[t].getX()+n*g/p),this.bases[y].setY(this.bases[t].getY()+r*g/p);else for(this.find_center_for_arc(p-1,o),n/=o,r/=o,i=this.bases[t].getX()+n*o/2,s=this.bases[t].getY()+r*o/2,a=r,u=-n,l=i+this._h*a,c=s+this._h*u,f=this.bases[t].getX()-l,d=this.bases[t].getY()-c,o=Math.sqrt(f*f+d*d),h=Math.atan2(d,f),g=1;gthis.nbase&&(y-=this.nbase+1),this.bases[y].setX(l+o*Math.cos(h+g*this.angleinc)),this.bases[y].setY(c+o*Math.sin(h+g*this.angleinc))},w.prototype.find_center_for_arc=function(t,e){var n,r,o,i,s,a,u,l;o=-(r=(t+1)/Math.PI)-e/(t+1.000001-e),e<1&&(o=0),l=0;do{n=(r+o)/2,s=1-.5/((i=Math.sqrt(n*n+e*e/4))*i),Math.abs(s)>1&&console.log("Unexpected large magnitude discriminant = "+s+" "+i),(u=(a=Math.acos(s))*(t+1)+2*Math.acos(n/i)-2*Math.PI)>0?o=n:r=n}while(Math.abs(u)>1e-4&&++l=this.MAXITER&&(noIterationFailureYet&&(console.log("Iteration failed in find_center_for_arc"),noIterationFailureYet=!1),n=0,a=0),this._h=n,this.angleinc=a},w.prototype.generate_region=function(t){var e,n,r,o,i,s;for(s=t.getRegion(),e=0,t.getStart()==s.getStart1()?(n=s.getStart1(),r=s.getEnd1()):(n=s.getStart2(),r=s.getEnd2()),(this.bases[t.getStart()].getX()>this.ANUM-100||this.bases[t.getEnd()].getX()>this.ANUM-100)&&console.log("Bad region passed to generate_region. Coordinates not defined."),o=n+1;o<=r;o++)e++,this.bases[o].setX(this.bases[t.getStart()].getX()+this.HELIX_FACTOR*e*t.getXrad()),this.bases[o].setY(this.bases[t.getStart()].getY()+this.HELIX_FACTOR*e*t.getYrad()),i=this.bases[o].getMate(),this.bases[i].setX(this.bases[t.getEnd()].getX()+this.HELIX_FACTOR*e*t.getXrad()),this.bases[i].setY(this.bases[t.getEnd()].getY()+this.HELIX_FACTOR*e*t.getYrad())},w.prototype.minf2=function(t,e){return te?t:e},w.prototype.connected_connection=function(t,e){return!!t.isExtruded()||t.getEnd()+1==e.getStart()}})(),i})())); //# sourceMappingURL=fornac.js.map \ No newline at end of file diff --git a/dist/fornac.js.LICENSE.txt b/dist/fornac.js.LICENSE.txt new file mode 100644 index 0000000..df537c5 --- /dev/null +++ b/dist/fornac.js.LICENSE.txt @@ -0,0 +1,8 @@ +/*! + * The buffer module from node.js, for the browser. + * + * @author Feross Aboukhadijeh + * @license MIT + */ + +/*! ieee754. BSD-3-Clause License. Feross Aboukhadijeh */ diff --git a/dist/fornac.js.map b/dist/fornac.js.map index f2bd86d..37ffdbf 100644 --- a/dist/fornac.js.map +++ b/dist/fornac.js.map @@ -1 +1 @@ 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umd \"d3\"","webpack://[name]/webpack/bootstrap","webpack://[name]/webpack/runtime/compat get default export","webpack://[name]/webpack/runtime/define property getters","webpack://[name]/webpack/runtime/global","webpack://[name]/webpack/runtime/hasOwnProperty shorthand","webpack://[name]/webpack/runtime/make namespace object","webpack://[name]/webpack/runtime/publicPath","webpack://[name]/./src/img/play.svg","webpack://[name]/./src/d3-context-menu.js","webpack://[name]/./src/rnautils.js","webpack://[name]/./src/rnagraph.js","webpack://[name]/./src/simplernaplot.js","webpack://[name]/./src/naview/radloop.js","webpack://[name]/./src/naview/base.js","webpack://[name]/./src/naview/naview.js","webpack://[name]/./src/fornac.js","webpack://[name]/./src/rnaplot.js","webpack://[name]/./src/rnatreemap.js"],"sourcesContent":["(function webpackUniversalModuleDefinition(root, factory) {\n\tif(typeof exports === 'object' && typeof module === 'object')\n\t\tmodule.exports = factory(require(\"d3\"));\n\telse if(typeof define === 'function' && define.amd)\n\t\tdefine([\"d3\"], factory);\n\telse if(typeof exports === 'object')\n\t\texports[\"fornac\"] = factory(require(\"d3\"));\n\telse\n\t\troot[\"fornac\"] = factory(root[\"d3\"]);\n})(self, function(__WEBPACK_EXTERNAL_MODULE__990__) {\nreturn ","import {Loop} from './loop.js';\nimport {Region} from './region.js';\n\nexport function Connection() {\n\tthis.loop = new Loop();\n\tthis.region = new Region();\n\t// Start and end form the 1st base pair of the region.\n\tthis.start = null;\n this.end = null;\n\tthis.xrad = null;\n this.yrad = null;\n this.angle = null;\n\t// True if segment between this connection and the\n\t// next must be extruded out of the circle\n\tthis.extruded = null;\n\t// True if the extruded segment must be drawn long.\n\tthis.broken = null;\n\n\tthis._isNull = false;\n}\n\nConnection.prototype.isNull = function(){\n\treturn this._isNull;\n}\n\nConnection.prototype.setNull = function(isNull){\n\tthis._isNull = isNull;\n}\n\nConnection.prototype.getLoop = function(){\n\treturn this.loop;\n}\n\nConnection.prototype.setLoop = function(loop) {\n\tthis.loop = loop;\n}\n\nConnection.prototype.getRegion = function(){\n\treturn this.region;\n}\n\nConnection.prototype.setRegion = function(region){\n\tthis.region = region;\n}\n\nConnection.prototype.getStart = function(){\n\treturn this.start;\n}\n\nConnection.prototype.setStart = function(start) {\n\tthis.start = start;\n}\n\nConnection.prototype.getEnd = function(){\n\treturn this.end;\n}\n\nConnection.prototype.setEnd = function(end){\n\tthis.end = end;\n}\n\nConnection.prototype.getXrad = function(){\n\treturn this.xrad;\n}\n\nConnection.prototype.setXrad = function(xrad){\n\tthis.xrad = xrad;\n}\n\nConnection.prototype.getYrad = function(){\n\treturn this.yrad;\n}\n\nConnection.prototype.setYrad = function(yrad) {\n\tthis.yrad = yrad;\n}\n\nConnection.prototype.getAngle = function(){\n\treturn this.angle;\n}\n\nConnection.prototype.setAngle = function(angle){\n\tthis.angle = angle;\n}\n\nConnection.prototype.isExtruded = function(){\n\treturn this.extruded;\n}\n\nConnection.prototype.setExtruded = function(extruded){\n\tthis.extruded = extruded;\n}\n\nConnection.prototype.isBroken = function(){\n\treturn this.broken;\n}\n\nConnection.prototype.setBroken = function(broken){\n\tthis.broken = broken;\n}\n","import {Connection} from './connection.js';\n\nexport function Loop() {\n\tthis.nconnection = null;\n\tthis.connections = [];\n\tthis._connections = [];\n\tthis.number = null;\n\tthis.depth = null;\n\tthis.mark = null;\n\tthis.x = null;\n this.y = null;\n this.radius = null;\n}\n\nLoop.prototype.getNconnection = function() {\n\treturn this.nconnection;\n}\n\nLoop.prototype.setNconnection = function(nconnection) {\n\tthis.nconnection = nconnection;\n}\n\nLoop.prototype.setConnection = function(i, c){\n\tif (c != null){\n\t\tthis._connections[i] = c;\n }\n\telse {\n\t\tif (!this._connections[i]){\n\t\t\tthis._connections[i] = new Connection();\n\t\t}\n\t\tthis._connections[i].setNull(true);\n\t}\n}\n\nLoop.prototype.getConnection = function(i){\n\tvar Connection = require(\"./connection\");\n\tif (!this._connections[i]){\n this._connections[i] = new Connection();\n }\n\tvar c = this._connections[i];\n\tif (c.isNull()){\n\t\treturn null;\n }\n\telse {\n\t\treturn c;\n }\n}\n\nLoop.prototype.addConnection = function(i, c){\n\tthis._connections.push(c);\n}\n\nLoop.prototype.getNumber = function(){\n\treturn this.number;\n}\n\nLoop.prototype.setNumber = function(number){\n\tthis.number = number;\n}\n\nLoop.prototype.getDepth = function(){\n\treturn this.depth;\n}\n\nLoop.prototype.setDepth = function(depth){\n\tthis.depth = depth;\n}\n\nLoop.prototype.isMark = function(){\n\treturn this.mark;\n}\n\nLoop.prototype.setMark = function(mark){\n\tthis.mark = mark;\n}\n\nLoop.prototype.getX = function(){\n\treturn this.x;\n}\n\nLoop.prototype.setX = function(x){\n\tthis.x = x;\n}\n\nLoop.prototype.getY = function(){\n\treturn this.y;\n}\n\nLoop.prototype.setY = function(y){\n\tthis.y = y;\n}\n\nLoop.prototype.getRadius = function(){\n\treturn this.radius;\n}\n\nLoop.prototype.setRadius = function(radius){\n\tthis.radius = radius;\n}\n","export function Region() {\n\tthis._start1 = null;\n this._end1 = null;\n this._start2 = null;\n this._end2 = null;\n}\n\nRegion.prototype.getStart1 = function(){\n\treturn this._start1;\n}\n\nRegion.prototype.setStart1 = function(start1){\n\tthis._start1 = start1;\n}\n\nRegion.prototype.getEnd1 = function(){\n\treturn this._end1;\n}\n\nRegion.prototype.setEnd1 = function(end1){\n\tthis._end1 = end1;\n}\n\nRegion.prototype.getStart2 = function(){\n\treturn this._start2;\n}\n\nRegion.prototype.setStart2 = function(start2){\n\tthis._start2 = start2;\n}\n\nRegion.prototype.getEnd2 = function(){\n\treturn this._end2;\n}\n\nRegion.prototype.setEnd2 = function(end2){\n\tthis._end2 = end2;\n}\n","'use strict'\n\nexports.byteLength = byteLength\nexports.toByteArray = toByteArray\nexports.fromByteArray = fromByteArray\n\nvar lookup = []\nvar revLookup = []\nvar Arr = typeof Uint8Array !== 'undefined' ? Uint8Array : Array\n\nvar code = 'ABCDEFGHIJKLMNOPQRSTUVWXYZabcdefghijklmnopqrstuvwxyz0123456789+/'\nfor (var i = 0, len = code.length; i < len; ++i) {\n lookup[i] = code[i]\n revLookup[code.charCodeAt(i)] = i\n}\n\n// Support decoding URL-safe base64 strings, as Node.js does.\n// See: https://en.wikipedia.org/wiki/Base64#URL_applications\nrevLookup['-'.charCodeAt(0)] = 62\nrevLookup['_'.charCodeAt(0)] = 63\n\nfunction getLens (b64) {\n var len = b64.length\n\n if (len % 4 > 0) {\n throw new Error('Invalid string. Length must be a multiple of 4')\n }\n\n // Trim off extra bytes after placeholder bytes are found\n // See: https://github.com/beatgammit/base64-js/issues/42\n var validLen = b64.indexOf('=')\n if (validLen === -1) validLen = len\n\n var placeHoldersLen = validLen === len\n ? 0\n : 4 - (validLen % 4)\n\n return [validLen, placeHoldersLen]\n}\n\n// base64 is 4/3 + up to two characters of the original data\nfunction byteLength (b64) {\n var lens = getLens(b64)\n var validLen = lens[0]\n var placeHoldersLen = lens[1]\n return ((validLen + placeHoldersLen) * 3 / 4) - placeHoldersLen\n}\n\nfunction _byteLength (b64, validLen, placeHoldersLen) {\n return ((validLen + placeHoldersLen) * 3 / 4) - placeHoldersLen\n}\n\nfunction toByteArray (b64) {\n var tmp\n var lens = getLens(b64)\n var validLen = lens[0]\n var placeHoldersLen = lens[1]\n\n var arr = new Arr(_byteLength(b64, validLen, placeHoldersLen))\n\n var curByte = 0\n\n // if there are placeholders, only get up to the last complete 4 chars\n var len = placeHoldersLen > 0\n ? validLen - 4\n : validLen\n\n var i\n for (i = 0; i < len; i += 4) {\n tmp =\n (revLookup[b64.charCodeAt(i)] << 18) |\n (revLookup[b64.charCodeAt(i + 1)] << 12) |\n (revLookup[b64.charCodeAt(i + 2)] << 6) |\n revLookup[b64.charCodeAt(i + 3)]\n arr[curByte++] = (tmp >> 16) & 0xFF\n arr[curByte++] = (tmp >> 8) & 0xFF\n arr[curByte++] = tmp & 0xFF\n }\n\n if (placeHoldersLen === 2) {\n tmp =\n (revLookup[b64.charCodeAt(i)] << 2) |\n (revLookup[b64.charCodeAt(i + 1)] >> 4)\n arr[curByte++] = tmp & 0xFF\n }\n\n if (placeHoldersLen === 1) {\n tmp =\n (revLookup[b64.charCodeAt(i)] << 10) |\n (revLookup[b64.charCodeAt(i + 1)] << 4) |\n (revLookup[b64.charCodeAt(i + 2)] >> 2)\n arr[curByte++] = (tmp >> 8) & 0xFF\n arr[curByte++] = tmp & 0xFF\n }\n\n return arr\n}\n\nfunction tripletToBase64 (num) {\n return lookup[num >> 18 & 0x3F] +\n lookup[num >> 12 & 0x3F] +\n lookup[num >> 6 & 0x3F] +\n lookup[num & 0x3F]\n}\n\nfunction encodeChunk (uint8, start, end) {\n var tmp\n var output = []\n for (var i = start; i < end; i += 3) {\n tmp =\n ((uint8[i] << 16) & 0xFF0000) +\n ((uint8[i + 1] << 8) & 0xFF00) +\n (uint8[i + 2] & 0xFF)\n output.push(tripletToBase64(tmp))\n }\n return output.join('')\n}\n\nfunction fromByteArray (uint8) {\n var tmp\n var len = uint8.length\n var extraBytes = len % 3 // if we have 1 byte left, pad 2 bytes\n var parts = []\n var maxChunkLength = 16383 // must be multiple of 3\n\n // go through the array every three bytes, we'll deal with trailing stuff later\n for (var i = 0, len2 = len - extraBytes; i < len2; i += maxChunkLength) {\n parts.push(encodeChunk(uint8, i, (i + maxChunkLength) > len2 ? len2 : (i + maxChunkLength)))\n }\n\n // pad the end with zeros, but make sure to not forget the extra bytes\n if (extraBytes === 1) {\n tmp = uint8[len - 1]\n parts.push(\n lookup[tmp >> 2] +\n lookup[(tmp << 4) & 0x3F] +\n '=='\n )\n } else if (extraBytes === 2) {\n tmp = (uint8[len - 2] << 8) + uint8[len - 1]\n parts.push(\n lookup[tmp >> 10] +\n lookup[(tmp >> 4) & 0x3F] +\n lookup[(tmp << 2) & 0x3F] +\n '='\n )\n }\n\n return parts.join('')\n}\n","/*!\n * The buffer module from node.js, for the browser.\n *\n * @author Feross Aboukhadijeh \n * @license MIT\n */\n/* eslint-disable no-proto */\n\n'use strict'\n\nconst base64 = require('base64-js')\nconst ieee754 = require('ieee754')\nconst customInspectSymbol =\n (typeof Symbol === 'function' && typeof Symbol['for'] === 'function') // eslint-disable-line dot-notation\n ? Symbol['for']('nodejs.util.inspect.custom') // eslint-disable-line dot-notation\n : null\n\nexports.Buffer = Buffer\nexports.SlowBuffer = SlowBuffer\nexports.INSPECT_MAX_BYTES = 50\n\nconst K_MAX_LENGTH = 0x7fffffff\nexports.kMaxLength = K_MAX_LENGTH\n\n/**\n * If `Buffer.TYPED_ARRAY_SUPPORT`:\n * === true Use Uint8Array implementation (fastest)\n * === false Print warning and recommend using `buffer` v4.x which has an Object\n * implementation (most compatible, even IE6)\n *\n * Browsers that support typed arrays are IE 10+, Firefox 4+, Chrome 7+, Safari 5.1+,\n * Opera 11.6+, iOS 4.2+.\n *\n * We report that the browser does not support typed arrays if the are not subclassable\n * using __proto__. Firefox 4-29 lacks support for adding new properties to `Uint8Array`\n * (See: https://bugzilla.mozilla.org/show_bug.cgi?id=695438). IE 10 lacks support\n * for __proto__ and has a buggy typed array implementation.\n */\nBuffer.TYPED_ARRAY_SUPPORT = typedArraySupport()\n\nif (!Buffer.TYPED_ARRAY_SUPPORT && typeof console !== 'undefined' &&\n typeof console.error === 'function') {\n console.error(\n 'This browser lacks typed array (Uint8Array) support which is required by ' +\n '`buffer` v5.x. Use `buffer` v4.x if you require old browser support.'\n )\n}\n\nfunction typedArraySupport () {\n // Can typed array instances can be augmented?\n try {\n const arr = new Uint8Array(1)\n const proto = { foo: function () { return 42 } }\n Object.setPrototypeOf(proto, Uint8Array.prototype)\n Object.setPrototypeOf(arr, proto)\n return arr.foo() === 42\n } catch (e) {\n return false\n }\n}\n\nObject.defineProperty(Buffer.prototype, 'parent', {\n enumerable: true,\n get: function () {\n if (!Buffer.isBuffer(this)) return undefined\n return this.buffer\n }\n})\n\nObject.defineProperty(Buffer.prototype, 'offset', {\n enumerable: true,\n get: function () {\n if (!Buffer.isBuffer(this)) return undefined\n return this.byteOffset\n }\n})\n\nfunction createBuffer (length) {\n if (length > K_MAX_LENGTH) {\n throw new RangeError('The value \"' + length + '\" is invalid for option \"size\"')\n }\n // Return an augmented `Uint8Array` instance\n const buf = new Uint8Array(length)\n Object.setPrototypeOf(buf, Buffer.prototype)\n return buf\n}\n\n/**\n * The Buffer constructor returns instances of `Uint8Array` that have their\n * prototype changed to `Buffer.prototype`. Furthermore, `Buffer` is a subclass of\n * `Uint8Array`, so the returned instances will have all the node `Buffer` methods\n * and the `Uint8Array` methods. Square bracket notation works as expected -- it\n * returns a single octet.\n *\n * The `Uint8Array` prototype remains unmodified.\n */\n\nfunction Buffer (arg, encodingOrOffset, length) {\n // Common case.\n if (typeof arg === 'number') {\n if (typeof encodingOrOffset === 'string') {\n throw new TypeError(\n 'The \"string\" argument must be of type string. Received type number'\n )\n }\n return allocUnsafe(arg)\n }\n return from(arg, encodingOrOffset, length)\n}\n\nBuffer.poolSize = 8192 // not used by this implementation\n\nfunction from (value, encodingOrOffset, length) {\n if (typeof value === 'string') {\n return fromString(value, encodingOrOffset)\n }\n\n if (ArrayBuffer.isView(value)) {\n return fromArrayView(value)\n }\n\n if (value == null) {\n throw new TypeError(\n 'The first argument must be one of type string, Buffer, ArrayBuffer, Array, ' +\n 'or Array-like Object. Received type ' + (typeof value)\n )\n }\n\n if (isInstance(value, ArrayBuffer) ||\n (value && isInstance(value.buffer, ArrayBuffer))) {\n return fromArrayBuffer(value, encodingOrOffset, length)\n }\n\n if (typeof SharedArrayBuffer !== 'undefined' &&\n (isInstance(value, SharedArrayBuffer) ||\n (value && isInstance(value.buffer, SharedArrayBuffer)))) {\n return fromArrayBuffer(value, encodingOrOffset, length)\n }\n\n if (typeof value === 'number') {\n throw new TypeError(\n 'The \"value\" argument must not be of type number. Received type number'\n )\n }\n\n const valueOf = value.valueOf && value.valueOf()\n if (valueOf != null && valueOf !== value) {\n return Buffer.from(valueOf, encodingOrOffset, length)\n }\n\n const b = fromObject(value)\n if (b) return b\n\n if (typeof Symbol !== 'undefined' && Symbol.toPrimitive != null &&\n typeof value[Symbol.toPrimitive] === 'function') {\n return Buffer.from(value[Symbol.toPrimitive]('string'), encodingOrOffset, length)\n }\n\n throw new TypeError(\n 'The first argument must be one of type string, Buffer, ArrayBuffer, Array, ' +\n 'or Array-like Object. Received type ' + (typeof value)\n )\n}\n\n/**\n * Functionally equivalent to Buffer(arg, encoding) but throws a TypeError\n * if value is a number.\n * Buffer.from(str[, encoding])\n * Buffer.from(array)\n * Buffer.from(buffer)\n * Buffer.from(arrayBuffer[, byteOffset[, length]])\n **/\nBuffer.from = function (value, encodingOrOffset, length) {\n return from(value, encodingOrOffset, length)\n}\n\n// Note: Change prototype *after* Buffer.from is defined to workaround Chrome bug:\n// https://github.com/feross/buffer/pull/148\nObject.setPrototypeOf(Buffer.prototype, Uint8Array.prototype)\nObject.setPrototypeOf(Buffer, Uint8Array)\n\nfunction assertSize (size) {\n if (typeof size !== 'number') {\n throw new TypeError('\"size\" argument must be of type number')\n } else if (size < 0) {\n throw new RangeError('The value \"' + size + '\" is invalid for option \"size\"')\n }\n}\n\nfunction alloc (size, fill, encoding) {\n assertSize(size)\n if (size <= 0) {\n return createBuffer(size)\n }\n if (fill !== undefined) {\n // Only pay attention to encoding if it's a string. This\n // prevents accidentally sending in a number that would\n // be interpreted as a start offset.\n return typeof encoding === 'string'\n ? createBuffer(size).fill(fill, encoding)\n : createBuffer(size).fill(fill)\n }\n return createBuffer(size)\n}\n\n/**\n * Creates a new filled Buffer instance.\n * alloc(size[, fill[, encoding]])\n **/\nBuffer.alloc = function (size, fill, encoding) {\n return alloc(size, fill, encoding)\n}\n\nfunction allocUnsafe (size) {\n assertSize(size)\n return createBuffer(size < 0 ? 0 : checked(size) | 0)\n}\n\n/**\n * Equivalent to Buffer(num), by default creates a non-zero-filled Buffer instance.\n * */\nBuffer.allocUnsafe = function (size) {\n return allocUnsafe(size)\n}\n/**\n * Equivalent to SlowBuffer(num), by default creates a non-zero-filled Buffer instance.\n */\nBuffer.allocUnsafeSlow = function (size) {\n return allocUnsafe(size)\n}\n\nfunction fromString (string, encoding) {\n if (typeof encoding !== 'string' || encoding === '') {\n encoding = 'utf8'\n }\n\n if (!Buffer.isEncoding(encoding)) {\n throw new TypeError('Unknown encoding: ' + encoding)\n }\n\n const length = byteLength(string, encoding) | 0\n let buf = createBuffer(length)\n\n const actual = buf.write(string, encoding)\n\n if (actual !== length) {\n // Writing a hex string, for example, that contains invalid characters will\n // cause everything after the first invalid character to be ignored. (e.g.\n // 'abxxcd' will be treated as 'ab')\n buf = buf.slice(0, actual)\n }\n\n return buf\n}\n\nfunction fromArrayLike (array) {\n const length = array.length < 0 ? 0 : checked(array.length) | 0\n const buf = createBuffer(length)\n for (let i = 0; i < length; i += 1) {\n buf[i] = array[i] & 255\n }\n return buf\n}\n\nfunction fromArrayView (arrayView) {\n if (isInstance(arrayView, Uint8Array)) {\n const copy = new Uint8Array(arrayView)\n return fromArrayBuffer(copy.buffer, copy.byteOffset, copy.byteLength)\n }\n return fromArrayLike(arrayView)\n}\n\nfunction fromArrayBuffer (array, byteOffset, length) {\n if (byteOffset < 0 || array.byteLength < byteOffset) {\n throw new RangeError('\"offset\" is outside of buffer bounds')\n }\n\n if (array.byteLength < byteOffset + (length || 0)) {\n throw new RangeError('\"length\" is outside of buffer bounds')\n }\n\n let buf\n if (byteOffset === undefined && length === undefined) {\n buf = new Uint8Array(array)\n } else if (length === undefined) {\n buf = new Uint8Array(array, byteOffset)\n } else {\n buf = new Uint8Array(array, byteOffset, length)\n }\n\n // Return an augmented `Uint8Array` instance\n Object.setPrototypeOf(buf, Buffer.prototype)\n\n return buf\n}\n\nfunction fromObject (obj) {\n if (Buffer.isBuffer(obj)) {\n const len = checked(obj.length) | 0\n const buf = createBuffer(len)\n\n if (buf.length === 0) {\n return buf\n }\n\n obj.copy(buf, 0, 0, len)\n return buf\n }\n\n if (obj.length !== undefined) {\n if (typeof obj.length !== 'number' || numberIsNaN(obj.length)) {\n return createBuffer(0)\n }\n return fromArrayLike(obj)\n }\n\n if (obj.type === 'Buffer' && Array.isArray(obj.data)) {\n return fromArrayLike(obj.data)\n }\n}\n\nfunction checked (length) {\n // Note: cannot use `length < K_MAX_LENGTH` here because that fails when\n // length is NaN (which is otherwise coerced to zero.)\n if (length >= K_MAX_LENGTH) {\n throw new RangeError('Attempt to allocate Buffer larger than maximum ' +\n 'size: 0x' + K_MAX_LENGTH.toString(16) + ' bytes')\n }\n return length | 0\n}\n\nfunction SlowBuffer (length) {\n if (+length != length) { // eslint-disable-line eqeqeq\n length = 0\n }\n return Buffer.alloc(+length)\n}\n\nBuffer.isBuffer = function isBuffer (b) {\n return b != null && b._isBuffer === true &&\n b !== Buffer.prototype // so Buffer.isBuffer(Buffer.prototype) will be false\n}\n\nBuffer.compare = function compare (a, b) {\n if (isInstance(a, Uint8Array)) a = Buffer.from(a, a.offset, a.byteLength)\n if (isInstance(b, Uint8Array)) b = Buffer.from(b, b.offset, b.byteLength)\n if (!Buffer.isBuffer(a) || !Buffer.isBuffer(b)) {\n throw new TypeError(\n 'The \"buf1\", \"buf2\" arguments must be one of type Buffer or Uint8Array'\n )\n }\n\n if (a === b) return 0\n\n let x = a.length\n let y = b.length\n\n for (let i = 0, len = Math.min(x, y); i < len; ++i) {\n if (a[i] !== b[i]) {\n x = a[i]\n y = b[i]\n break\n }\n }\n\n if (x < y) return -1\n if (y < x) return 1\n return 0\n}\n\nBuffer.isEncoding = function isEncoding (encoding) {\n switch (String(encoding).toLowerCase()) {\n case 'hex':\n case 'utf8':\n case 'utf-8':\n case 'ascii':\n case 'latin1':\n case 'binary':\n case 'base64':\n case 'ucs2':\n case 'ucs-2':\n case 'utf16le':\n case 'utf-16le':\n return true\n default:\n return false\n }\n}\n\nBuffer.concat = function concat (list, length) {\n if (!Array.isArray(list)) {\n throw new TypeError('\"list\" argument must be an Array of Buffers')\n }\n\n if (list.length === 0) {\n return Buffer.alloc(0)\n }\n\n let i\n if (length === undefined) {\n length = 0\n for (i = 0; i < list.length; ++i) {\n length += list[i].length\n }\n }\n\n const buffer = Buffer.allocUnsafe(length)\n let pos = 0\n for (i = 0; i < list.length; ++i) {\n let buf = list[i]\n if (isInstance(buf, Uint8Array)) {\n if (pos + buf.length > buffer.length) {\n if (!Buffer.isBuffer(buf)) buf = Buffer.from(buf)\n buf.copy(buffer, pos)\n } else {\n Uint8Array.prototype.set.call(\n buffer,\n buf,\n pos\n )\n }\n } else if (!Buffer.isBuffer(buf)) {\n throw new TypeError('\"list\" argument must be an Array of Buffers')\n } else {\n buf.copy(buffer, pos)\n }\n pos += buf.length\n }\n return buffer\n}\n\nfunction byteLength (string, encoding) {\n if (Buffer.isBuffer(string)) {\n return string.length\n }\n if (ArrayBuffer.isView(string) || isInstance(string, ArrayBuffer)) {\n return string.byteLength\n }\n if (typeof string !== 'string') {\n throw new TypeError(\n 'The \"string\" argument must be one of type string, Buffer, or ArrayBuffer. ' +\n 'Received type ' + typeof string\n )\n }\n\n const len = string.length\n const mustMatch = (arguments.length > 2 && arguments[2] === true)\n if (!mustMatch && len === 0) return 0\n\n // Use a for loop to avoid recursion\n let loweredCase = false\n for (;;) {\n switch (encoding) {\n case 'ascii':\n case 'latin1':\n case 'binary':\n return len\n case 'utf8':\n case 'utf-8':\n return utf8ToBytes(string).length\n case 'ucs2':\n case 'ucs-2':\n case 'utf16le':\n case 'utf-16le':\n return len * 2\n case 'hex':\n return len >>> 1\n case 'base64':\n return base64ToBytes(string).length\n default:\n if (loweredCase) {\n return mustMatch ? -1 : utf8ToBytes(string).length // assume utf8\n }\n encoding = ('' + encoding).toLowerCase()\n loweredCase = true\n }\n }\n}\nBuffer.byteLength = byteLength\n\nfunction slowToString (encoding, start, end) {\n let loweredCase = false\n\n // No need to verify that \"this.length <= MAX_UINT32\" since it's a read-only\n // property of a typed array.\n\n // This behaves neither like String nor Uint8Array in that we set start/end\n // to their upper/lower bounds if the value passed is out of range.\n // undefined is handled specially as per ECMA-262 6th Edition,\n // Section 13.3.3.7 Runtime Semantics: KeyedBindingInitialization.\n if (start === undefined || start < 0) {\n start = 0\n }\n // Return early if start > this.length. Done here to prevent potential uint32\n // coercion fail below.\n if (start > this.length) {\n return ''\n }\n\n if (end === undefined || end > this.length) {\n end = this.length\n }\n\n if (end <= 0) {\n return ''\n }\n\n // Force coercion to uint32. This will also coerce falsey/NaN values to 0.\n end >>>= 0\n start >>>= 0\n\n if (end <= start) {\n return ''\n }\n\n if (!encoding) encoding = 'utf8'\n\n while (true) {\n switch (encoding) {\n case 'hex':\n return hexSlice(this, start, end)\n\n case 'utf8':\n case 'utf-8':\n return utf8Slice(this, start, end)\n\n case 'ascii':\n return asciiSlice(this, start, end)\n\n case 'latin1':\n case 'binary':\n return latin1Slice(this, start, end)\n\n case 'base64':\n return base64Slice(this, start, end)\n\n case 'ucs2':\n case 'ucs-2':\n case 'utf16le':\n case 'utf-16le':\n return utf16leSlice(this, start, end)\n\n default:\n if (loweredCase) throw new TypeError('Unknown encoding: ' + encoding)\n encoding = (encoding + '').toLowerCase()\n loweredCase = true\n }\n }\n}\n\n// This property is used by `Buffer.isBuffer` (and the `is-buffer` npm package)\n// to detect a Buffer instance. It's not possible to use `instanceof Buffer`\n// reliably in a browserify context because there could be multiple different\n// copies of the 'buffer' package in use. This method works even for Buffer\n// instances that were created from another copy of the `buffer` package.\n// See: https://github.com/feross/buffer/issues/154\nBuffer.prototype._isBuffer = true\n\nfunction swap (b, n, m) {\n const i = b[n]\n b[n] = b[m]\n b[m] = i\n}\n\nBuffer.prototype.swap16 = function swap16 () {\n const len = this.length\n if (len % 2 !== 0) {\n throw new RangeError('Buffer size must be a multiple of 16-bits')\n }\n for (let i = 0; i < len; i += 2) {\n swap(this, i, i + 1)\n }\n return this\n}\n\nBuffer.prototype.swap32 = function swap32 () {\n const len = this.length\n if (len % 4 !== 0) {\n throw new RangeError('Buffer size must be a multiple of 32-bits')\n }\n for (let i = 0; i < len; i += 4) {\n swap(this, i, i + 3)\n swap(this, i + 1, i + 2)\n }\n return this\n}\n\nBuffer.prototype.swap64 = function swap64 () {\n const len = this.length\n if (len % 8 !== 0) {\n throw new RangeError('Buffer size must be a multiple of 64-bits')\n }\n for (let i = 0; i < len; i += 8) {\n swap(this, i, i + 7)\n swap(this, i + 1, i + 6)\n swap(this, i + 2, i + 5)\n swap(this, i + 3, i + 4)\n }\n return this\n}\n\nBuffer.prototype.toString = function toString () {\n const length = this.length\n if (length === 0) return ''\n if (arguments.length === 0) return utf8Slice(this, 0, length)\n return slowToString.apply(this, arguments)\n}\n\nBuffer.prototype.toLocaleString = Buffer.prototype.toString\n\nBuffer.prototype.equals = function equals (b) {\n if (!Buffer.isBuffer(b)) throw new TypeError('Argument must be a Buffer')\n if (this === b) return true\n return Buffer.compare(this, b) === 0\n}\n\nBuffer.prototype.inspect = function inspect () {\n let str = ''\n const max = exports.INSPECT_MAX_BYTES\n str = this.toString('hex', 0, max).replace(/(.{2})/g, '$1 ').trim()\n if (this.length > max) str += ' ... '\n return ''\n}\nif (customInspectSymbol) {\n Buffer.prototype[customInspectSymbol] = Buffer.prototype.inspect\n}\n\nBuffer.prototype.compare = function compare (target, start, end, thisStart, thisEnd) {\n if (isInstance(target, Uint8Array)) {\n target = Buffer.from(target, target.offset, target.byteLength)\n }\n if (!Buffer.isBuffer(target)) {\n throw new TypeError(\n 'The \"target\" argument must be one of type Buffer or Uint8Array. ' +\n 'Received type ' + (typeof target)\n )\n }\n\n if (start === undefined) {\n start = 0\n }\n if (end === undefined) {\n end = target ? target.length : 0\n }\n if (thisStart === undefined) {\n thisStart = 0\n }\n if (thisEnd === undefined) {\n thisEnd = this.length\n }\n\n if (start < 0 || end > target.length || thisStart < 0 || thisEnd > this.length) {\n throw new RangeError('out of range index')\n }\n\n if (thisStart >= thisEnd && start >= end) {\n return 0\n }\n if (thisStart >= thisEnd) {\n return -1\n }\n if (start >= end) {\n return 1\n }\n\n start >>>= 0\n end >>>= 0\n thisStart >>>= 0\n thisEnd >>>= 0\n\n if (this === target) return 0\n\n let x = thisEnd - thisStart\n let y = end - start\n const len = Math.min(x, y)\n\n const thisCopy = this.slice(thisStart, thisEnd)\n const targetCopy = target.slice(start, end)\n\n for (let i = 0; i < len; ++i) {\n if (thisCopy[i] !== targetCopy[i]) {\n x = thisCopy[i]\n y = targetCopy[i]\n break\n }\n }\n\n if (x < y) return -1\n if (y < x) return 1\n return 0\n}\n\n// Finds either the first index of `val` in `buffer` at offset >= `byteOffset`,\n// OR the last index of `val` in `buffer` at offset <= `byteOffset`.\n//\n// Arguments:\n// - buffer - a Buffer to search\n// - val - a string, Buffer, or number\n// - byteOffset - an index into `buffer`; will be clamped to an int32\n// - encoding - an optional encoding, relevant is val is a string\n// - dir - true for indexOf, false for lastIndexOf\nfunction bidirectionalIndexOf (buffer, val, byteOffset, encoding, dir) {\n // Empty buffer means no match\n if (buffer.length === 0) return -1\n\n // Normalize byteOffset\n if (typeof byteOffset === 'string') {\n encoding = byteOffset\n byteOffset = 0\n } else if (byteOffset > 0x7fffffff) {\n byteOffset = 0x7fffffff\n } else if (byteOffset < -0x80000000) {\n byteOffset = -0x80000000\n }\n byteOffset = +byteOffset // Coerce to Number.\n if (numberIsNaN(byteOffset)) {\n // byteOffset: it it's undefined, null, NaN, \"foo\", etc, search whole buffer\n byteOffset = dir ? 0 : (buffer.length - 1)\n }\n\n // Normalize byteOffset: negative offsets start from the end of the buffer\n if (byteOffset < 0) byteOffset = buffer.length + byteOffset\n if (byteOffset >= buffer.length) {\n if (dir) return -1\n else byteOffset = buffer.length - 1\n } else if (byteOffset < 0) {\n if (dir) byteOffset = 0\n else return -1\n }\n\n // Normalize val\n if (typeof val === 'string') {\n val = Buffer.from(val, encoding)\n }\n\n // Finally, search either indexOf (if dir is true) or lastIndexOf\n if (Buffer.isBuffer(val)) {\n // Special case: looking for empty string/buffer always fails\n if (val.length === 0) {\n return -1\n }\n return arrayIndexOf(buffer, val, byteOffset, encoding, dir)\n } else if (typeof val === 'number') {\n val = val & 0xFF // Search for a byte value [0-255]\n if (typeof Uint8Array.prototype.indexOf === 'function') {\n if (dir) {\n return Uint8Array.prototype.indexOf.call(buffer, val, byteOffset)\n } else {\n return Uint8Array.prototype.lastIndexOf.call(buffer, val, byteOffset)\n }\n }\n return arrayIndexOf(buffer, [val], byteOffset, encoding, dir)\n }\n\n throw new TypeError('val must be string, number or Buffer')\n}\n\nfunction arrayIndexOf (arr, val, byteOffset, encoding, dir) {\n let indexSize = 1\n let arrLength = arr.length\n let valLength = val.length\n\n if (encoding !== undefined) {\n encoding = String(encoding).toLowerCase()\n if (encoding === 'ucs2' || encoding === 'ucs-2' ||\n encoding === 'utf16le' || encoding === 'utf-16le') {\n if (arr.length < 2 || val.length < 2) {\n return -1\n }\n indexSize = 2\n arrLength /= 2\n valLength /= 2\n byteOffset /= 2\n }\n }\n\n function read (buf, i) {\n if (indexSize === 1) {\n return buf[i]\n } else {\n return buf.readUInt16BE(i * indexSize)\n }\n }\n\n let i\n if (dir) {\n let foundIndex = -1\n for (i = byteOffset; i < arrLength; i++) {\n if (read(arr, i) === read(val, foundIndex === -1 ? 0 : i - foundIndex)) {\n if (foundIndex === -1) foundIndex = i\n if (i - foundIndex + 1 === valLength) return foundIndex * indexSize\n } else {\n if (foundIndex !== -1) i -= i - foundIndex\n foundIndex = -1\n }\n }\n } else {\n if (byteOffset + valLength > arrLength) byteOffset = arrLength - valLength\n for (i = byteOffset; i >= 0; i--) {\n let found = true\n for (let j = 0; j < valLength; j++) {\n if (read(arr, i + j) !== read(val, j)) {\n found = false\n break\n }\n }\n if (found) return i\n }\n }\n\n return -1\n}\n\nBuffer.prototype.includes = function includes (val, byteOffset, encoding) {\n return this.indexOf(val, byteOffset, encoding) !== -1\n}\n\nBuffer.prototype.indexOf = function indexOf (val, byteOffset, encoding) {\n return bidirectionalIndexOf(this, val, byteOffset, encoding, true)\n}\n\nBuffer.prototype.lastIndexOf = function lastIndexOf (val, byteOffset, encoding) {\n return bidirectionalIndexOf(this, val, byteOffset, encoding, false)\n}\n\nfunction hexWrite (buf, string, offset, length) {\n offset = Number(offset) || 0\n const remaining = buf.length - offset\n if (!length) {\n length = remaining\n } else {\n length = Number(length)\n if (length > remaining) {\n length = remaining\n }\n }\n\n const strLen = string.length\n\n if (length > strLen / 2) {\n length = strLen / 2\n }\n let i\n for (i = 0; i < length; ++i) {\n const parsed = parseInt(string.substr(i * 2, 2), 16)\n if (numberIsNaN(parsed)) return i\n buf[offset + i] = parsed\n }\n return i\n}\n\nfunction utf8Write (buf, string, offset, length) {\n return blitBuffer(utf8ToBytes(string, buf.length - offset), buf, offset, length)\n}\n\nfunction asciiWrite (buf, string, offset, length) {\n return blitBuffer(asciiToBytes(string), buf, offset, length)\n}\n\nfunction base64Write (buf, string, offset, length) {\n return blitBuffer(base64ToBytes(string), buf, offset, length)\n}\n\nfunction ucs2Write (buf, string, offset, length) {\n return blitBuffer(utf16leToBytes(string, buf.length - offset), buf, offset, length)\n}\n\nBuffer.prototype.write = function write (string, offset, length, encoding) {\n // Buffer#write(string)\n if (offset === undefined) {\n encoding = 'utf8'\n length = this.length\n offset = 0\n // Buffer#write(string, encoding)\n } else if (length === undefined && typeof offset === 'string') {\n encoding = offset\n length = this.length\n offset = 0\n // Buffer#write(string, offset[, length][, encoding])\n } else if (isFinite(offset)) {\n offset = offset >>> 0\n if (isFinite(length)) {\n length = length >>> 0\n if (encoding === undefined) encoding = 'utf8'\n } else {\n encoding = length\n length = undefined\n }\n } else {\n throw new Error(\n 'Buffer.write(string, encoding, offset[, length]) is no longer supported'\n )\n }\n\n const remaining = this.length - offset\n if (length === undefined || length > remaining) length = remaining\n\n if ((string.length > 0 && (length < 0 || offset < 0)) || offset > this.length) {\n throw new RangeError('Attempt to write outside buffer bounds')\n }\n\n if (!encoding) encoding = 'utf8'\n\n let loweredCase = false\n for (;;) {\n switch (encoding) {\n case 'hex':\n return hexWrite(this, string, offset, length)\n\n case 'utf8':\n case 'utf-8':\n return utf8Write(this, string, offset, length)\n\n case 'ascii':\n case 'latin1':\n case 'binary':\n return asciiWrite(this, string, offset, length)\n\n case 'base64':\n // Warning: maxLength not taken into account in base64Write\n return base64Write(this, string, offset, length)\n\n case 'ucs2':\n case 'ucs-2':\n case 'utf16le':\n case 'utf-16le':\n return ucs2Write(this, string, offset, length)\n\n default:\n if (loweredCase) throw new TypeError('Unknown encoding: ' + encoding)\n encoding = ('' + encoding).toLowerCase()\n loweredCase = true\n }\n }\n}\n\nBuffer.prototype.toJSON = function toJSON () {\n return {\n type: 'Buffer',\n data: Array.prototype.slice.call(this._arr || this, 0)\n }\n}\n\nfunction base64Slice (buf, start, end) {\n if (start === 0 && end === buf.length) {\n return base64.fromByteArray(buf)\n } else {\n return base64.fromByteArray(buf.slice(start, end))\n }\n}\n\nfunction utf8Slice (buf, start, end) {\n end = Math.min(buf.length, end)\n const res = []\n\n let i = start\n while (i < end) {\n const firstByte = buf[i]\n let codePoint = null\n let bytesPerSequence = (firstByte > 0xEF)\n ? 4\n : (firstByte > 0xDF)\n ? 3\n : (firstByte > 0xBF)\n ? 2\n : 1\n\n if (i + bytesPerSequence <= end) {\n let secondByte, thirdByte, fourthByte, tempCodePoint\n\n switch (bytesPerSequence) {\n case 1:\n if (firstByte < 0x80) {\n codePoint = firstByte\n }\n break\n case 2:\n secondByte = buf[i + 1]\n if ((secondByte & 0xC0) === 0x80) {\n tempCodePoint = (firstByte & 0x1F) << 0x6 | (secondByte & 0x3F)\n if (tempCodePoint > 0x7F) {\n codePoint = tempCodePoint\n }\n }\n break\n case 3:\n secondByte = buf[i + 1]\n thirdByte = buf[i + 2]\n if ((secondByte & 0xC0) === 0x80 && (thirdByte & 0xC0) === 0x80) {\n tempCodePoint = (firstByte & 0xF) << 0xC | (secondByte & 0x3F) << 0x6 | (thirdByte & 0x3F)\n if (tempCodePoint > 0x7FF && (tempCodePoint < 0xD800 || tempCodePoint > 0xDFFF)) {\n codePoint = tempCodePoint\n }\n }\n break\n case 4:\n secondByte = buf[i + 1]\n thirdByte = buf[i + 2]\n fourthByte = buf[i + 3]\n if ((secondByte & 0xC0) === 0x80 && (thirdByte & 0xC0) === 0x80 && (fourthByte & 0xC0) === 0x80) {\n tempCodePoint = (firstByte & 0xF) << 0x12 | (secondByte & 0x3F) << 0xC | (thirdByte & 0x3F) << 0x6 | (fourthByte & 0x3F)\n if (tempCodePoint > 0xFFFF && tempCodePoint < 0x110000) {\n codePoint = tempCodePoint\n }\n }\n }\n }\n\n if (codePoint === null) {\n // we did not generate a valid codePoint so insert a\n // replacement char (U+FFFD) and advance only 1 byte\n codePoint = 0xFFFD\n bytesPerSequence = 1\n } else if (codePoint > 0xFFFF) {\n // encode to utf16 (surrogate pair dance)\n codePoint -= 0x10000\n res.push(codePoint >>> 10 & 0x3FF | 0xD800)\n codePoint = 0xDC00 | codePoint & 0x3FF\n }\n\n res.push(codePoint)\n i += bytesPerSequence\n }\n\n return decodeCodePointsArray(res)\n}\n\n// Based on http://stackoverflow.com/a/22747272/680742, the browser with\n// the lowest limit is Chrome, with 0x10000 args.\n// We go 1 magnitude less, for safety\nconst MAX_ARGUMENTS_LENGTH = 0x1000\n\nfunction decodeCodePointsArray (codePoints) {\n const len = codePoints.length\n if (len <= MAX_ARGUMENTS_LENGTH) {\n return String.fromCharCode.apply(String, codePoints) // avoid extra slice()\n }\n\n // Decode in chunks to avoid \"call stack size exceeded\".\n let res = ''\n let i = 0\n while (i < len) {\n res += String.fromCharCode.apply(\n String,\n codePoints.slice(i, i += MAX_ARGUMENTS_LENGTH)\n )\n }\n return res\n}\n\nfunction asciiSlice (buf, start, end) {\n let ret = ''\n end = Math.min(buf.length, end)\n\n for (let i = start; i < end; ++i) {\n ret += String.fromCharCode(buf[i] & 0x7F)\n }\n return ret\n}\n\nfunction latin1Slice (buf, start, end) {\n let ret = ''\n end = Math.min(buf.length, end)\n\n for (let i = start; i < end; ++i) {\n ret += String.fromCharCode(buf[i])\n }\n return ret\n}\n\nfunction hexSlice (buf, start, end) {\n const len = buf.length\n\n if (!start || start < 0) start = 0\n if (!end || end < 0 || end > len) end = len\n\n let out = ''\n for (let i = start; i < end; ++i) {\n out += hexSliceLookupTable[buf[i]]\n }\n return out\n}\n\nfunction utf16leSlice (buf, start, end) {\n const bytes = buf.slice(start, end)\n let res = ''\n // If bytes.length is odd, the last 8 bits must be ignored (same as node.js)\n for (let i = 0; i < bytes.length - 1; i += 2) {\n res += String.fromCharCode(bytes[i] + (bytes[i + 1] * 256))\n }\n return res\n}\n\nBuffer.prototype.slice = function slice (start, end) {\n const len = this.length\n start = ~~start\n end = end === undefined ? len : ~~end\n\n if (start < 0) {\n start += len\n if (start < 0) start = 0\n } else if (start > len) {\n start = len\n }\n\n if (end < 0) {\n end += len\n if (end < 0) end = 0\n } else if (end > len) {\n end = len\n }\n\n if (end < start) end = start\n\n const newBuf = this.subarray(start, end)\n // Return an augmented `Uint8Array` instance\n Object.setPrototypeOf(newBuf, Buffer.prototype)\n\n return newBuf\n}\n\n/*\n * Need to make sure that buffer isn't trying to write out of bounds.\n */\nfunction checkOffset (offset, ext, length) {\n if ((offset % 1) !== 0 || offset < 0) throw new RangeError('offset is not uint')\n if (offset + ext > length) throw new RangeError('Trying to access beyond buffer length')\n}\n\nBuffer.prototype.readUintLE =\nBuffer.prototype.readUIntLE = function readUIntLE (offset, byteLength, noAssert) {\n offset = offset >>> 0\n byteLength = byteLength >>> 0\n if (!noAssert) checkOffset(offset, byteLength, this.length)\n\n let val = this[offset]\n let mul = 1\n let i = 0\n while (++i < byteLength && (mul *= 0x100)) {\n val += this[offset + i] * mul\n }\n\n return val\n}\n\nBuffer.prototype.readUintBE =\nBuffer.prototype.readUIntBE = function readUIntBE (offset, byteLength, noAssert) {\n offset = offset >>> 0\n byteLength = byteLength >>> 0\n if (!noAssert) {\n checkOffset(offset, byteLength, this.length)\n }\n\n let val = this[offset + --byteLength]\n let mul = 1\n while (byteLength > 0 && (mul *= 0x100)) {\n val += this[offset + --byteLength] * mul\n }\n\n return val\n}\n\nBuffer.prototype.readUint8 =\nBuffer.prototype.readUInt8 = function readUInt8 (offset, noAssert) {\n offset = offset >>> 0\n if (!noAssert) checkOffset(offset, 1, this.length)\n return this[offset]\n}\n\nBuffer.prototype.readUint16LE =\nBuffer.prototype.readUInt16LE = function readUInt16LE (offset, noAssert) {\n offset = offset >>> 0\n if (!noAssert) checkOffset(offset, 2, this.length)\n return this[offset] | (this[offset + 1] << 8)\n}\n\nBuffer.prototype.readUint16BE =\nBuffer.prototype.readUInt16BE = function readUInt16BE (offset, noAssert) {\n offset = offset >>> 0\n if (!noAssert) checkOffset(offset, 2, this.length)\n return (this[offset] << 8) | this[offset + 1]\n}\n\nBuffer.prototype.readUint32LE =\nBuffer.prototype.readUInt32LE = function readUInt32LE (offset, noAssert) {\n offset = offset >>> 0\n if (!noAssert) checkOffset(offset, 4, this.length)\n\n return ((this[offset]) |\n (this[offset + 1] << 8) |\n (this[offset + 2] << 16)) +\n (this[offset + 3] * 0x1000000)\n}\n\nBuffer.prototype.readUint32BE =\nBuffer.prototype.readUInt32BE = function readUInt32BE (offset, noAssert) {\n offset = offset >>> 0\n if (!noAssert) checkOffset(offset, 4, this.length)\n\n return (this[offset] * 0x1000000) +\n ((this[offset + 1] << 16) |\n (this[offset + 2] << 8) |\n this[offset + 3])\n}\n\nBuffer.prototype.readBigUInt64LE = defineBigIntMethod(function readBigUInt64LE (offset) {\n offset = offset >>> 0\n validateNumber(offset, 'offset')\n const first = this[offset]\n const last = this[offset + 7]\n if (first === undefined || last === undefined) {\n boundsError(offset, this.length - 8)\n }\n\n const lo = first +\n this[++offset] * 2 ** 8 +\n this[++offset] * 2 ** 16 +\n this[++offset] * 2 ** 24\n\n const hi = this[++offset] +\n this[++offset] * 2 ** 8 +\n this[++offset] * 2 ** 16 +\n last * 2 ** 24\n\n return BigInt(lo) + (BigInt(hi) << BigInt(32))\n})\n\nBuffer.prototype.readBigUInt64BE = defineBigIntMethod(function readBigUInt64BE (offset) {\n offset = offset >>> 0\n validateNumber(offset, 'offset')\n const first = this[offset]\n const last = this[offset + 7]\n if (first === undefined || last === undefined) {\n boundsError(offset, this.length - 8)\n }\n\n const hi = first * 2 ** 24 +\n this[++offset] * 2 ** 16 +\n this[++offset] * 2 ** 8 +\n this[++offset]\n\n const lo = this[++offset] * 2 ** 24 +\n this[++offset] * 2 ** 16 +\n this[++offset] * 2 ** 8 +\n last\n\n return (BigInt(hi) << BigInt(32)) + BigInt(lo)\n})\n\nBuffer.prototype.readIntLE = function readIntLE (offset, byteLength, noAssert) {\n offset = offset >>> 0\n byteLength = byteLength >>> 0\n if (!noAssert) checkOffset(offset, byteLength, this.length)\n\n let val = this[offset]\n let mul = 1\n let i = 0\n while (++i < byteLength && (mul *= 0x100)) {\n val += this[offset + i] * mul\n }\n mul *= 0x80\n\n if (val >= mul) val -= Math.pow(2, 8 * byteLength)\n\n return val\n}\n\nBuffer.prototype.readIntBE = function readIntBE (offset, byteLength, noAssert) {\n offset = offset >>> 0\n byteLength = byteLength >>> 0\n if (!noAssert) checkOffset(offset, byteLength, this.length)\n\n let i = byteLength\n let mul = 1\n let val = this[offset + --i]\n while (i > 0 && (mul *= 0x100)) {\n val += this[offset + --i] * mul\n }\n mul *= 0x80\n\n if (val >= mul) val -= Math.pow(2, 8 * byteLength)\n\n return val\n}\n\nBuffer.prototype.readInt8 = function readInt8 (offset, noAssert) {\n offset = offset >>> 0\n if (!noAssert) checkOffset(offset, 1, this.length)\n if (!(this[offset] & 0x80)) return (this[offset])\n return ((0xff - this[offset] + 1) * -1)\n}\n\nBuffer.prototype.readInt16LE = function readInt16LE (offset, noAssert) {\n offset = offset >>> 0\n if (!noAssert) checkOffset(offset, 2, this.length)\n const val = this[offset] | (this[offset + 1] << 8)\n return (val & 0x8000) ? val | 0xFFFF0000 : val\n}\n\nBuffer.prototype.readInt16BE = function readInt16BE (offset, noAssert) {\n offset = offset >>> 0\n if (!noAssert) checkOffset(offset, 2, this.length)\n const val = this[offset + 1] | (this[offset] << 8)\n return (val & 0x8000) ? val | 0xFFFF0000 : val\n}\n\nBuffer.prototype.readInt32LE = function readInt32LE (offset, noAssert) {\n offset = offset >>> 0\n if (!noAssert) checkOffset(offset, 4, this.length)\n\n return (this[offset]) |\n (this[offset + 1] << 8) |\n (this[offset + 2] << 16) |\n (this[offset + 3] << 24)\n}\n\nBuffer.prototype.readInt32BE = function readInt32BE (offset, noAssert) {\n offset = offset >>> 0\n if (!noAssert) checkOffset(offset, 4, this.length)\n\n return (this[offset] << 24) |\n (this[offset + 1] << 16) |\n (this[offset + 2] << 8) |\n (this[offset + 3])\n}\n\nBuffer.prototype.readBigInt64LE = defineBigIntMethod(function readBigInt64LE (offset) {\n offset = offset >>> 0\n validateNumber(offset, 'offset')\n const first = this[offset]\n const last = this[offset + 7]\n if (first === undefined || last === undefined) {\n boundsError(offset, this.length - 8)\n }\n\n const val = this[offset + 4] +\n this[offset + 5] * 2 ** 8 +\n this[offset + 6] * 2 ** 16 +\n (last << 24) // Overflow\n\n return (BigInt(val) << BigInt(32)) +\n BigInt(first +\n this[++offset] * 2 ** 8 +\n this[++offset] * 2 ** 16 +\n this[++offset] * 2 ** 24)\n})\n\nBuffer.prototype.readBigInt64BE = defineBigIntMethod(function readBigInt64BE (offset) {\n offset = offset >>> 0\n validateNumber(offset, 'offset')\n const first = this[offset]\n const last = this[offset + 7]\n if (first === undefined || last === undefined) {\n boundsError(offset, this.length - 8)\n }\n\n const val = (first << 24) + // Overflow\n this[++offset] * 2 ** 16 +\n this[++offset] * 2 ** 8 +\n this[++offset]\n\n return (BigInt(val) << BigInt(32)) +\n BigInt(this[++offset] * 2 ** 24 +\n this[++offset] * 2 ** 16 +\n this[++offset] * 2 ** 8 +\n last)\n})\n\nBuffer.prototype.readFloatLE = function readFloatLE (offset, noAssert) {\n offset = offset >>> 0\n if (!noAssert) checkOffset(offset, 4, this.length)\n return ieee754.read(this, offset, true, 23, 4)\n}\n\nBuffer.prototype.readFloatBE = function readFloatBE (offset, noAssert) {\n offset = offset >>> 0\n if (!noAssert) checkOffset(offset, 4, this.length)\n return ieee754.read(this, offset, false, 23, 4)\n}\n\nBuffer.prototype.readDoubleLE = function readDoubleLE (offset, noAssert) {\n offset = offset >>> 0\n if (!noAssert) checkOffset(offset, 8, this.length)\n return ieee754.read(this, offset, true, 52, 8)\n}\n\nBuffer.prototype.readDoubleBE = function readDoubleBE (offset, noAssert) {\n offset = offset >>> 0\n if (!noAssert) checkOffset(offset, 8, this.length)\n return ieee754.read(this, offset, false, 52, 8)\n}\n\nfunction checkInt (buf, value, offset, ext, max, min) {\n if (!Buffer.isBuffer(buf)) throw new TypeError('\"buffer\" argument must be a Buffer instance')\n if (value > max || value < min) throw new RangeError('\"value\" argument is out of bounds')\n if (offset + ext > buf.length) throw new RangeError('Index out of range')\n}\n\nBuffer.prototype.writeUintLE =\nBuffer.prototype.writeUIntLE = function writeUIntLE (value, offset, byteLength, noAssert) {\n value = +value\n offset = offset >>> 0\n byteLength = byteLength >>> 0\n if (!noAssert) {\n const maxBytes = Math.pow(2, 8 * byteLength) - 1\n checkInt(this, value, offset, byteLength, maxBytes, 0)\n }\n\n let mul = 1\n let i = 0\n this[offset] = value & 0xFF\n while (++i < byteLength && (mul *= 0x100)) {\n this[offset + i] = (value / mul) & 0xFF\n }\n\n return offset + byteLength\n}\n\nBuffer.prototype.writeUintBE =\nBuffer.prototype.writeUIntBE = function writeUIntBE (value, offset, byteLength, noAssert) {\n value = +value\n offset = offset >>> 0\n byteLength = byteLength >>> 0\n if (!noAssert) {\n const maxBytes = Math.pow(2, 8 * byteLength) - 1\n checkInt(this, value, offset, byteLength, maxBytes, 0)\n }\n\n let i = byteLength - 1\n let mul = 1\n this[offset + i] = value & 0xFF\n while (--i >= 0 && (mul *= 0x100)) {\n this[offset + i] = (value / mul) & 0xFF\n }\n\n return offset + byteLength\n}\n\nBuffer.prototype.writeUint8 =\nBuffer.prototype.writeUInt8 = function writeUInt8 (value, offset, noAssert) {\n value = +value\n offset = offset >>> 0\n if (!noAssert) checkInt(this, value, offset, 1, 0xff, 0)\n this[offset] = (value & 0xff)\n return offset + 1\n}\n\nBuffer.prototype.writeUint16LE =\nBuffer.prototype.writeUInt16LE = function writeUInt16LE (value, offset, noAssert) {\n value = +value\n offset = offset >>> 0\n if (!noAssert) checkInt(this, value, offset, 2, 0xffff, 0)\n this[offset] = (value & 0xff)\n this[offset + 1] = (value >>> 8)\n return offset + 2\n}\n\nBuffer.prototype.writeUint16BE =\nBuffer.prototype.writeUInt16BE = function writeUInt16BE (value, offset, noAssert) {\n value = +value\n offset = offset >>> 0\n if (!noAssert) checkInt(this, value, offset, 2, 0xffff, 0)\n this[offset] = (value >>> 8)\n this[offset + 1] = (value & 0xff)\n return offset + 2\n}\n\nBuffer.prototype.writeUint32LE =\nBuffer.prototype.writeUInt32LE = function writeUInt32LE (value, offset, noAssert) {\n value = +value\n offset = offset >>> 0\n if (!noAssert) checkInt(this, value, offset, 4, 0xffffffff, 0)\n this[offset + 3] = (value >>> 24)\n this[offset + 2] = (value >>> 16)\n this[offset + 1] = (value >>> 8)\n this[offset] = (value & 0xff)\n return offset + 4\n}\n\nBuffer.prototype.writeUint32BE =\nBuffer.prototype.writeUInt32BE = function writeUInt32BE (value, offset, noAssert) {\n value = +value\n offset = offset >>> 0\n if (!noAssert) checkInt(this, value, offset, 4, 0xffffffff, 0)\n this[offset] = (value >>> 24)\n this[offset + 1] = (value >>> 16)\n this[offset + 2] = (value >>> 8)\n this[offset + 3] = (value & 0xff)\n return offset + 4\n}\n\nfunction wrtBigUInt64LE (buf, value, offset, min, max) {\n checkIntBI(value, min, max, buf, offset, 7)\n\n let lo = Number(value & BigInt(0xffffffff))\n buf[offset++] = lo\n lo = lo >> 8\n buf[offset++] = lo\n lo = lo >> 8\n buf[offset++] = lo\n lo = lo >> 8\n buf[offset++] = lo\n let hi = Number(value >> BigInt(32) & BigInt(0xffffffff))\n buf[offset++] = hi\n hi = hi >> 8\n buf[offset++] = hi\n hi = hi >> 8\n buf[offset++] = hi\n hi = hi >> 8\n buf[offset++] = hi\n return offset\n}\n\nfunction wrtBigUInt64BE (buf, value, offset, min, max) {\n checkIntBI(value, min, max, buf, offset, 7)\n\n let lo = Number(value & BigInt(0xffffffff))\n buf[offset + 7] = lo\n lo = lo >> 8\n buf[offset + 6] = lo\n lo = lo >> 8\n buf[offset + 5] = lo\n lo = lo >> 8\n buf[offset + 4] = lo\n let hi = Number(value >> BigInt(32) & BigInt(0xffffffff))\n buf[offset + 3] = hi\n hi = hi >> 8\n buf[offset + 2] = hi\n hi = hi >> 8\n buf[offset + 1] = hi\n hi = hi >> 8\n buf[offset] = hi\n return offset + 8\n}\n\nBuffer.prototype.writeBigUInt64LE = defineBigIntMethod(function writeBigUInt64LE (value, offset = 0) {\n return wrtBigUInt64LE(this, value, offset, BigInt(0), BigInt('0xffffffffffffffff'))\n})\n\nBuffer.prototype.writeBigUInt64BE = defineBigIntMethod(function writeBigUInt64BE (value, offset = 0) {\n return wrtBigUInt64BE(this, value, offset, BigInt(0), BigInt('0xffffffffffffffff'))\n})\n\nBuffer.prototype.writeIntLE = function writeIntLE (value, offset, byteLength, noAssert) {\n value = +value\n offset = offset >>> 0\n if (!noAssert) {\n const limit = Math.pow(2, (8 * byteLength) - 1)\n\n checkInt(this, value, offset, byteLength, limit - 1, -limit)\n }\n\n let i = 0\n let mul = 1\n let sub = 0\n this[offset] = value & 0xFF\n while (++i < byteLength && (mul *= 0x100)) {\n if (value < 0 && sub === 0 && this[offset + i - 1] !== 0) {\n sub = 1\n }\n this[offset + i] = ((value / mul) >> 0) - sub & 0xFF\n }\n\n return offset + byteLength\n}\n\nBuffer.prototype.writeIntBE = function writeIntBE (value, offset, byteLength, noAssert) {\n value = +value\n offset = offset >>> 0\n if (!noAssert) {\n const limit = Math.pow(2, (8 * byteLength) - 1)\n\n checkInt(this, value, offset, byteLength, limit - 1, -limit)\n }\n\n let i = byteLength - 1\n let mul = 1\n let sub = 0\n this[offset + i] = value & 0xFF\n while (--i >= 0 && (mul *= 0x100)) {\n if (value < 0 && sub === 0 && this[offset + i + 1] !== 0) {\n sub = 1\n }\n this[offset + i] = ((value / mul) >> 0) - sub & 0xFF\n }\n\n return offset + byteLength\n}\n\nBuffer.prototype.writeInt8 = function writeInt8 (value, offset, noAssert) {\n value = +value\n offset = offset >>> 0\n if (!noAssert) checkInt(this, value, offset, 1, 0x7f, -0x80)\n if (value < 0) value = 0xff + value + 1\n this[offset] = (value & 0xff)\n return offset + 1\n}\n\nBuffer.prototype.writeInt16LE = function writeInt16LE (value, offset, noAssert) {\n value = +value\n offset = offset >>> 0\n if (!noAssert) checkInt(this, value, offset, 2, 0x7fff, -0x8000)\n this[offset] = (value & 0xff)\n this[offset + 1] = (value >>> 8)\n return offset + 2\n}\n\nBuffer.prototype.writeInt16BE = function writeInt16BE (value, offset, noAssert) {\n value = +value\n offset = offset >>> 0\n if (!noAssert) checkInt(this, value, offset, 2, 0x7fff, -0x8000)\n this[offset] = (value >>> 8)\n this[offset + 1] = (value & 0xff)\n return offset + 2\n}\n\nBuffer.prototype.writeInt32LE = function writeInt32LE (value, offset, noAssert) {\n value = +value\n offset = offset >>> 0\n if (!noAssert) checkInt(this, value, offset, 4, 0x7fffffff, -0x80000000)\n this[offset] = (value & 0xff)\n this[offset + 1] = (value >>> 8)\n this[offset + 2] = (value >>> 16)\n this[offset + 3] = (value >>> 24)\n return offset + 4\n}\n\nBuffer.prototype.writeInt32BE = function writeInt32BE (value, offset, noAssert) {\n value = +value\n offset = offset >>> 0\n if (!noAssert) checkInt(this, value, offset, 4, 0x7fffffff, -0x80000000)\n if (value < 0) value = 0xffffffff + value + 1\n this[offset] = (value >>> 24)\n this[offset + 1] = (value >>> 16)\n this[offset + 2] = (value >>> 8)\n this[offset + 3] = (value & 0xff)\n return offset + 4\n}\n\nBuffer.prototype.writeBigInt64LE = defineBigIntMethod(function writeBigInt64LE (value, offset = 0) {\n return wrtBigUInt64LE(this, value, offset, -BigInt('0x8000000000000000'), BigInt('0x7fffffffffffffff'))\n})\n\nBuffer.prototype.writeBigInt64BE = defineBigIntMethod(function writeBigInt64BE (value, offset = 0) {\n return wrtBigUInt64BE(this, value, offset, -BigInt('0x8000000000000000'), BigInt('0x7fffffffffffffff'))\n})\n\nfunction checkIEEE754 (buf, value, offset, ext, max, min) {\n if (offset + ext > buf.length) throw new RangeError('Index out of range')\n if (offset < 0) throw new RangeError('Index out of range')\n}\n\nfunction writeFloat (buf, value, offset, littleEndian, noAssert) {\n value = +value\n offset = offset >>> 0\n if (!noAssert) {\n checkIEEE754(buf, value, offset, 4, 3.4028234663852886e+38, -3.4028234663852886e+38)\n }\n ieee754.write(buf, value, offset, littleEndian, 23, 4)\n return offset + 4\n}\n\nBuffer.prototype.writeFloatLE = function writeFloatLE (value, offset, noAssert) {\n return writeFloat(this, value, offset, true, noAssert)\n}\n\nBuffer.prototype.writeFloatBE = function writeFloatBE (value, offset, noAssert) {\n return writeFloat(this, value, offset, false, noAssert)\n}\n\nfunction writeDouble (buf, value, offset, littleEndian, noAssert) {\n value = +value\n offset = offset >>> 0\n if (!noAssert) {\n checkIEEE754(buf, value, offset, 8, 1.7976931348623157E+308, -1.7976931348623157E+308)\n }\n ieee754.write(buf, value, offset, littleEndian, 52, 8)\n return offset + 8\n}\n\nBuffer.prototype.writeDoubleLE = function writeDoubleLE (value, offset, noAssert) {\n return writeDouble(this, value, offset, true, noAssert)\n}\n\nBuffer.prototype.writeDoubleBE = function writeDoubleBE (value, offset, noAssert) {\n return writeDouble(this, value, offset, false, noAssert)\n}\n\n// copy(targetBuffer, targetStart=0, sourceStart=0, sourceEnd=buffer.length)\nBuffer.prototype.copy = function copy (target, targetStart, start, end) {\n if (!Buffer.isBuffer(target)) throw new TypeError('argument should be a Buffer')\n if (!start) start = 0\n if (!end && end !== 0) end = this.length\n if (targetStart >= target.length) targetStart = target.length\n if (!targetStart) targetStart = 0\n if (end > 0 && end < start) end = start\n\n // Copy 0 bytes; we're done\n if (end === start) return 0\n if (target.length === 0 || this.length === 0) return 0\n\n // Fatal error conditions\n if (targetStart < 0) {\n throw new RangeError('targetStart out of bounds')\n }\n if (start < 0 || start >= this.length) throw new RangeError('Index out of range')\n if (end < 0) throw new RangeError('sourceEnd out of bounds')\n\n // Are we oob?\n if (end > this.length) end = this.length\n if (target.length - targetStart < end - start) {\n end = target.length - targetStart + start\n }\n\n const len = end - start\n\n if (this === target && typeof Uint8Array.prototype.copyWithin === 'function') {\n // Use built-in when available, missing from IE11\n this.copyWithin(targetStart, start, end)\n } else {\n Uint8Array.prototype.set.call(\n target,\n this.subarray(start, end),\n targetStart\n )\n }\n\n return len\n}\n\n// Usage:\n// buffer.fill(number[, offset[, end]])\n// buffer.fill(buffer[, offset[, end]])\n// buffer.fill(string[, offset[, end]][, encoding])\nBuffer.prototype.fill = function fill (val, start, end, encoding) {\n // Handle string cases:\n if (typeof val === 'string') {\n if (typeof start === 'string') {\n encoding = start\n start = 0\n end = this.length\n } else if (typeof end === 'string') {\n encoding = end\n end = this.length\n }\n if (encoding !== undefined && typeof encoding !== 'string') {\n throw new TypeError('encoding must be a string')\n }\n if (typeof encoding === 'string' && !Buffer.isEncoding(encoding)) {\n throw new TypeError('Unknown encoding: ' + encoding)\n }\n if (val.length === 1) {\n const code = val.charCodeAt(0)\n if ((encoding === 'utf8' && code < 128) ||\n encoding === 'latin1') {\n // Fast path: If `val` fits into a single byte, use that numeric value.\n val = code\n }\n }\n } else if (typeof val === 'number') {\n val = val & 255\n } else if (typeof val === 'boolean') {\n val = Number(val)\n }\n\n // Invalid ranges are not set to a default, so can range check early.\n if (start < 0 || this.length < start || this.length < end) {\n throw new RangeError('Out of range index')\n }\n\n if (end <= start) {\n return this\n }\n\n start = start >>> 0\n end = end === undefined ? this.length : end >>> 0\n\n if (!val) val = 0\n\n let i\n if (typeof val === 'number') {\n for (i = start; i < end; ++i) {\n this[i] = val\n }\n } else {\n const bytes = Buffer.isBuffer(val)\n ? val\n : Buffer.from(val, encoding)\n const len = bytes.length\n if (len === 0) {\n throw new TypeError('The value \"' + val +\n '\" is invalid for argument \"value\"')\n }\n for (i = 0; i < end - start; ++i) {\n this[i + start] = bytes[i % len]\n }\n }\n\n return this\n}\n\n// CUSTOM ERRORS\n// =============\n\n// Simplified versions from Node, changed for Buffer-only usage\nconst errors = {}\nfunction E (sym, getMessage, Base) {\n errors[sym] = class NodeError extends Base {\n constructor () {\n super()\n\n Object.defineProperty(this, 'message', {\n value: getMessage.apply(this, arguments),\n writable: true,\n configurable: true\n })\n\n // Add the error code to the name to include it in the stack trace.\n this.name = `${this.name} [${sym}]`\n // Access the stack to generate the error message including the error code\n // from the name.\n this.stack // eslint-disable-line no-unused-expressions\n // Reset the name to the actual name.\n delete this.name\n }\n\n get code () {\n return sym\n }\n\n set code (value) {\n Object.defineProperty(this, 'code', {\n configurable: true,\n enumerable: true,\n value,\n writable: true\n })\n }\n\n toString () {\n return `${this.name} [${sym}]: ${this.message}`\n }\n }\n}\n\nE('ERR_BUFFER_OUT_OF_BOUNDS',\n function (name) {\n if (name) {\n return `${name} is outside of buffer bounds`\n }\n\n return 'Attempt to access memory outside buffer bounds'\n }, RangeError)\nE('ERR_INVALID_ARG_TYPE',\n function (name, actual) {\n return `The \"${name}\" argument must be of type number. Received type ${typeof actual}`\n }, TypeError)\nE('ERR_OUT_OF_RANGE',\n function (str, range, input) {\n let msg = `The value of \"${str}\" is out of range.`\n let received = input\n if (Number.isInteger(input) && Math.abs(input) > 2 ** 32) {\n received = addNumericalSeparator(String(input))\n } else if (typeof input === 'bigint') {\n received = String(input)\n if (input > BigInt(2) ** BigInt(32) || input < -(BigInt(2) ** BigInt(32))) {\n received = addNumericalSeparator(received)\n }\n received += 'n'\n }\n msg += ` It must be ${range}. Received ${received}`\n return msg\n }, RangeError)\n\nfunction addNumericalSeparator (val) {\n let res = ''\n let i = val.length\n const start = val[0] === '-' ? 1 : 0\n for (; i >= start + 4; i -= 3) {\n res = `_${val.slice(i - 3, i)}${res}`\n }\n return `${val.slice(0, i)}${res}`\n}\n\n// CHECK FUNCTIONS\n// ===============\n\nfunction checkBounds (buf, offset, byteLength) {\n validateNumber(offset, 'offset')\n if (buf[offset] === undefined || buf[offset + byteLength] === undefined) {\n boundsError(offset, buf.length - (byteLength + 1))\n }\n}\n\nfunction checkIntBI (value, min, max, buf, offset, byteLength) {\n if (value > max || value < min) {\n const n = typeof min === 'bigint' ? 'n' : ''\n let range\n if (byteLength > 3) {\n if (min === 0 || min === BigInt(0)) {\n range = `>= 0${n} and < 2${n} ** ${(byteLength + 1) * 8}${n}`\n } else {\n range = `>= -(2${n} ** ${(byteLength + 1) * 8 - 1}${n}) and < 2 ** ` +\n `${(byteLength + 1) * 8 - 1}${n}`\n }\n } else {\n range = `>= ${min}${n} and <= ${max}${n}`\n }\n throw new errors.ERR_OUT_OF_RANGE('value', range, value)\n }\n checkBounds(buf, offset, byteLength)\n}\n\nfunction validateNumber (value, name) {\n if (typeof value !== 'number') {\n throw new errors.ERR_INVALID_ARG_TYPE(name, 'number', value)\n }\n}\n\nfunction boundsError (value, length, type) {\n if (Math.floor(value) !== value) {\n validateNumber(value, type)\n throw new errors.ERR_OUT_OF_RANGE(type || 'offset', 'an integer', value)\n }\n\n if (length < 0) {\n throw new errors.ERR_BUFFER_OUT_OF_BOUNDS()\n }\n\n throw new errors.ERR_OUT_OF_RANGE(type || 'offset',\n `>= ${type ? 1 : 0} and <= ${length}`,\n value)\n}\n\n// HELPER FUNCTIONS\n// ================\n\nconst INVALID_BASE64_RE = /[^+/0-9A-Za-z-_]/g\n\nfunction base64clean (str) {\n // Node takes equal signs as end of the Base64 encoding\n str = str.split('=')[0]\n // Node strips out invalid characters like \\n and \\t from the string, base64-js does not\n str = str.trim().replace(INVALID_BASE64_RE, '')\n // Node converts strings with length < 2 to ''\n if (str.length < 2) return ''\n // Node allows for non-padded base64 strings (missing trailing ===), base64-js does not\n while (str.length % 4 !== 0) {\n str = str + '='\n }\n return str\n}\n\nfunction utf8ToBytes (string, units) {\n units = units || Infinity\n let codePoint\n const length = string.length\n let leadSurrogate = null\n const bytes = []\n\n for (let i = 0; i < length; ++i) {\n codePoint = string.charCodeAt(i)\n\n // is surrogate component\n if (codePoint > 0xD7FF && codePoint < 0xE000) {\n // last char was a lead\n if (!leadSurrogate) {\n // no lead yet\n if (codePoint > 0xDBFF) {\n // unexpected trail\n if ((units -= 3) > -1) bytes.push(0xEF, 0xBF, 0xBD)\n continue\n } else if (i + 1 === length) {\n // unpaired lead\n if ((units -= 3) > -1) bytes.push(0xEF, 0xBF, 0xBD)\n continue\n }\n\n // valid lead\n leadSurrogate = codePoint\n\n continue\n }\n\n // 2 leads in a row\n if (codePoint < 0xDC00) {\n if ((units -= 3) > -1) bytes.push(0xEF, 0xBF, 0xBD)\n leadSurrogate = codePoint\n continue\n }\n\n // valid surrogate pair\n codePoint = (leadSurrogate - 0xD800 << 10 | codePoint - 0xDC00) + 0x10000\n } else if (leadSurrogate) {\n // valid bmp char, but last char was a lead\n if ((units -= 3) > -1) bytes.push(0xEF, 0xBF, 0xBD)\n }\n\n leadSurrogate = null\n\n // encode utf8\n if (codePoint < 0x80) {\n if ((units -= 1) < 0) break\n bytes.push(codePoint)\n } else if (codePoint < 0x800) {\n if ((units -= 2) < 0) break\n bytes.push(\n codePoint >> 0x6 | 0xC0,\n codePoint & 0x3F | 0x80\n )\n } else if (codePoint < 0x10000) {\n if ((units -= 3) < 0) break\n bytes.push(\n codePoint >> 0xC | 0xE0,\n codePoint >> 0x6 & 0x3F | 0x80,\n codePoint & 0x3F | 0x80\n )\n } else if (codePoint < 0x110000) {\n if ((units -= 4) < 0) break\n bytes.push(\n codePoint >> 0x12 | 0xF0,\n codePoint >> 0xC & 0x3F | 0x80,\n codePoint >> 0x6 & 0x3F | 0x80,\n codePoint & 0x3F | 0x80\n )\n } else {\n throw new Error('Invalid code point')\n }\n }\n\n return bytes\n}\n\nfunction asciiToBytes (str) {\n const byteArray = []\n for (let i = 0; i < str.length; ++i) {\n // Node's code seems to be doing this and not & 0x7F..\n byteArray.push(str.charCodeAt(i) & 0xFF)\n }\n return byteArray\n}\n\nfunction utf16leToBytes (str, units) {\n let c, hi, lo\n const byteArray = []\n for (let i = 0; i < str.length; ++i) {\n if ((units -= 2) < 0) break\n\n c = str.charCodeAt(i)\n hi = c >> 8\n lo = c % 256\n byteArray.push(lo)\n byteArray.push(hi)\n }\n\n return byteArray\n}\n\nfunction base64ToBytes (str) {\n return base64.toByteArray(base64clean(str))\n}\n\nfunction blitBuffer (src, dst, offset, length) {\n let i\n for (i = 0; i < length; ++i) {\n if ((i + offset >= dst.length) || (i >= src.length)) break\n dst[i + offset] = src[i]\n }\n return i\n}\n\n// ArrayBuffer or Uint8Array objects from other contexts (i.e. iframes) do not pass\n// the `instanceof` check but they should be treated as of that type.\n// See: https://github.com/feross/buffer/issues/166\nfunction isInstance (obj, type) {\n return obj instanceof type ||\n (obj != null && obj.constructor != null && obj.constructor.name != null &&\n obj.constructor.name === type.name)\n}\nfunction numberIsNaN (obj) {\n // For IE11 support\n return obj !== obj // eslint-disable-line no-self-compare\n}\n\n// Create lookup table for `toString('hex')`\n// See: https://github.com/feross/buffer/issues/219\nconst hexSliceLookupTable = (function () {\n const alphabet = '0123456789abcdef'\n const table = new Array(256)\n for (let i = 0; i < 16; ++i) {\n const i16 = i * 16\n for (let j = 0; j < 16; ++j) {\n table[i16 + j] = alphabet[i] + alphabet[j]\n }\n }\n return table\n})()\n\n// Return not function with Error if BigInt not supported\nfunction defineBigIntMethod (fn) {\n return typeof BigInt === 'undefined' ? BufferBigIntNotDefined : fn\n}\n\nfunction BufferBigIntNotDefined () {\n throw new Error('BigInt not supported')\n}\n","// extracted by extract-css-chunks-webpack-plugin\nmodule.exports = {};","// extracted by extract-css-chunks-webpack-plugin\nmodule.exports = {\"nodeStrokeWidth\":\"0.8\",\"directionArrowSize\":\"6\",\"directionArrowWidth\":\"0.7\",\"node\":\"fornac-node\",\"directionArrow\":\"fornac-directionArrow\",\"plot\":\"fornac-plot\",\"selectedNode\":\"fornac-selectedNode\",\"nodeLabel\":\"fornac-nodeLabel\",\"link\":\"fornac-link\",\"plotLabel\":\"fornac-plotLabel\",\"transparent\":\"fornac-transparent\",\"dragLine\":\"fornac-dragLine\",\"mouseEventHelper\":\"fornac-mouseEventHelper\"};","/*! ieee754. BSD-3-Clause License. Feross Aboukhadijeh */\nexports.read = function (buffer, offset, isLE, mLen, nBytes) {\n var e, m\n var eLen = (nBytes * 8) - mLen - 1\n var eMax = (1 << eLen) - 1\n var eBias = eMax >> 1\n var nBits = -7\n var i = isLE ? (nBytes - 1) : 0\n var d = isLE ? -1 : 1\n var s = buffer[offset + i]\n\n i += d\n\n e = s & ((1 << (-nBits)) - 1)\n s >>= (-nBits)\n nBits += eLen\n for (; nBits > 0; e = (e * 256) + buffer[offset + i], i += d, nBits -= 8) {}\n\n m = e & ((1 << (-nBits)) - 1)\n e >>= (-nBits)\n nBits += mLen\n for (; nBits > 0; m = (m * 256) + buffer[offset + i], i += d, nBits -= 8) {}\n\n if (e === 0) {\n e = 1 - eBias\n } else if (e === eMax) {\n return m ? NaN : ((s ? -1 : 1) * Infinity)\n } else {\n m = m + Math.pow(2, mLen)\n e = e - eBias\n }\n return (s ? -1 : 1) * m * Math.pow(2, e - mLen)\n}\n\nexports.write = function (buffer, value, offset, isLE, mLen, nBytes) {\n var e, m, c\n var eLen = (nBytes * 8) - mLen - 1\n var eMax = (1 << eLen) - 1\n var eBias = eMax >> 1\n var rt = (mLen === 23 ? Math.pow(2, -24) - Math.pow(2, -77) : 0)\n var i = isLE ? 0 : (nBytes - 1)\n var d = isLE ? 1 : -1\n var s = value < 0 || (value === 0 && 1 / value < 0) ? 1 : 0\n\n value = Math.abs(value)\n\n if (isNaN(value) || value === Infinity) {\n m = isNaN(value) ? 1 : 0\n e = eMax\n } else {\n e = Math.floor(Math.log(value) / Math.LN2)\n if (value * (c = Math.pow(2, -e)) < 1) {\n e--\n c *= 2\n }\n if (e + eBias >= 1) {\n value += rt / c\n } else {\n value += rt * Math.pow(2, 1 - eBias)\n }\n if (value * c >= 2) {\n e++\n c /= 2\n }\n\n if (e + eBias >= eMax) {\n m = 0\n e = eMax\n } else if (e + eBias >= 1) {\n m = ((value * c) - 1) * Math.pow(2, mLen)\n e = e + eBias\n } else {\n m = value * Math.pow(2, eBias - 1) * Math.pow(2, mLen)\n e = 0\n }\n }\n\n for (; mLen >= 8; buffer[offset + i] = m & 0xff, i += d, m /= 256, mLen -= 8) {}\n\n e = (e << mLen) | m\n eLen += mLen\n for (; eLen > 0; buffer[offset + i] = e & 0xff, i += d, e /= 256, eLen -= 8) {}\n\n buffer[offset + i - d] |= s * 128\n}\n","// The MIT License (MIT)\n//\n// Copyright (c) 2014 Jonas Finnemann Jensen\n//\n// Permission is hereby granted, free of charge, to any person obtaining a copy\n// of this software and associated documentation files (the \"Software\"), to deal\n// in the Software without restriction, including without limitation the rights\n// to use, copy, modify, merge, publish, distribute, sublicense, and/or sell\n// copies of the Software, and to permit persons to whom the Software is\n// furnished to do so, subject to the following conditions:\n//\n// The above copyright notice and this permission notice shall be included in\n// all copies or substantial portions of the Software.\n//\n// THE SOFTWARE IS PROVIDED \"AS IS\", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR\n// IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,\n// FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE\n// AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER\n// LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,\n// OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN\n// THE SOFTWARE.\n\nmodule.exports = require('./slugid');\n","// The MIT License (MIT)\n//\n// Copyright (c) 2014 Jonas Finnemann Jensen\n//\n// Permission is hereby granted, free of charge, to any person obtaining a copy\n// of this software and associated documentation files (the \"Software\"), to deal\n// in the Software without restriction, including without limitation the rights\n// to use, copy, modify, merge, publish, distribute, sublicense, and/or sell\n// copies of the Software, and to permit persons to whom the Software is\n// furnished to do so, subject to the following conditions:\n//\n// The above copyright notice and this permission notice shall be included in\n// all copies or substantial portions of the Software.\n//\n// THE SOFTWARE IS PROVIDED \"AS IS\", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR\n// IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,\n// FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE\n// AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER\n// LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,\n// OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN\n// THE SOFTWARE.\n\nvar uuid = require('uuid');\n\n/**\n * Returns the given uuid as a 22 character slug. This can be a regular v4\n * slug or a \"nice\" slug.\n */\nexports.encode = function(uuid_) {\n var bytes = uuid.parse(uuid_);\n var base64 = Buffer.from(bytes).toString('base64');\n var slug = base64\n .replace(/\\+/g, '-') // Replace + with - (see RFC 4648, sec. 5)\n .replace(/\\//g, '_') // Replace / with _ (see RFC 4648, sec. 5)\n .substring(0, 22); // Drop '==' padding\n return slug;\n};\n\n/**\n * Returns the uuid represented by the given v4 or \"nice\" slug\n */\nexports.decode = function(slug) {\n var base64 = slug\n .replace(/-/g, '+')\n .replace(/_/g, '/')\n + '==';\n return uuid.stringify(Buffer.from(base64, 'base64'));\n};\n\n/**\n * Returns a randomly generated uuid v4 compliant slug\n */\nexports.v4 = function() {\n var bytes = uuid.v4(null, Buffer.alloc(16));\n var base64 = bytes.toString('base64');\n var slug = base64\n .replace(/\\+/g, '-') // Replace + with - (see RFC 4648, sec. 5)\n .replace(/\\//g, '_') // Replace / with _ (see RFC 4648, sec. 5)\n .substring(0, 22); // Drop '==' padding\n return slug;\n};\n\n/**\n * Returns a randomly generated uuid v4 compliant slug which conforms to a set\n * of \"nice\" properties, at the cost of some entropy. Currently this means one\n * extra fixed bit (the first bit of the uuid is set to 0) which guarantees the\n * slug will begin with [A-Za-f]. For example such slugs don't require special\n * handling when used as command line parameters (whereas non-nice slugs may\n * start with `-` which can confuse command line tools).\n *\n * Potentially other \"nice\" properties may be added in future to further\n * restrict the range of potential uuids that may be generated.\n */\nexports.nice = function() {\n var bytes = uuid.v4(null, Buffer.alloc(16));\n bytes[0] = bytes[0] & 0x7f; // unset first bit to ensure [A-Za-f] first char\n var base64 = bytes.toString('base64');\n var slug = base64\n .replace(/\\+/g, '-') // Replace + with - (see RFC 4648, sec. 5)\n .replace(/\\//g, '_') // Replace / with _ (see RFC 4648, sec. 5)\n .substring(0, 22); // Drop '==' padding\n return slug;\n};\n","// Unique ID creation requires a high quality random # generator. In the browser we therefore\n// require the crypto API and do not support built-in fallback to lower quality random number\n// generators (like Math.random()).\nvar getRandomValues;\nvar rnds8 = new Uint8Array(16);\nexport default function rng() {\n // lazy load so that environments that need to polyfill have a chance to do so\n if (!getRandomValues) {\n // getRandomValues needs to be invoked in a context where \"this\" is a Crypto implementation. Also,\n // find the complete implementation of crypto (msCrypto) on IE11.\n getRandomValues = typeof crypto !== 'undefined' && crypto.getRandomValues && crypto.getRandomValues.bind(crypto) || typeof msCrypto !== 'undefined' && typeof msCrypto.getRandomValues === 'function' && msCrypto.getRandomValues.bind(msCrypto);\n\n if (!getRandomValues) {\n throw new Error('crypto.getRandomValues() not supported. See https://github.com/uuidjs/uuid#getrandomvalues-not-supported');\n }\n }\n\n return getRandomValues(rnds8);\n}","export default /^(?:[0-9a-f]{8}-[0-9a-f]{4}-[1-5][0-9a-f]{3}-[89ab][0-9a-f]{3}-[0-9a-f]{12}|00000000-0000-0000-0000-000000000000)$/i;","import REGEX from './regex.js';\n\nfunction validate(uuid) {\n return typeof uuid === 'string' && REGEX.test(uuid);\n}\n\nexport default validate;","import validate from './validate.js';\n/**\n * Convert array of 16 byte values to UUID string format of the form:\n * XXXXXXXX-XXXX-XXXX-XXXX-XXXXXXXXXXXX\n */\n\nvar byteToHex = [];\n\nfor (var i = 0; i < 256; ++i) {\n byteToHex.push((i + 0x100).toString(16).substr(1));\n}\n\nfunction stringify(arr) {\n var offset = arguments.length > 1 && arguments[1] !== undefined ? arguments[1] : 0;\n // Note: Be careful editing this code! It's been tuned for performance\n // and works in ways you may not expect. See https://github.com/uuidjs/uuid/pull/434\n var uuid = (byteToHex[arr[offset + 0]] + byteToHex[arr[offset + 1]] + byteToHex[arr[offset + 2]] + byteToHex[arr[offset + 3]] + '-' + byteToHex[arr[offset + 4]] + byteToHex[arr[offset + 5]] + '-' + byteToHex[arr[offset + 6]] + byteToHex[arr[offset + 7]] + '-' + byteToHex[arr[offset + 8]] + byteToHex[arr[offset + 9]] + '-' + byteToHex[arr[offset + 10]] + byteToHex[arr[offset + 11]] + byteToHex[arr[offset + 12]] + byteToHex[arr[offset + 13]] + byteToHex[arr[offset + 14]] + byteToHex[arr[offset + 15]]).toLowerCase(); // Consistency check for valid UUID. If this throws, it's likely due to one\n // of the following:\n // - One or more input array values don't map to a hex octet (leading to\n // \"undefined\" in the uuid)\n // - Invalid input values for the RFC `version` or `variant` fields\n\n if (!validate(uuid)) {\n throw TypeError('Stringified UUID is invalid');\n }\n\n return uuid;\n}\n\nexport default stringify;","import rng from './rng.js';\nimport stringify from './stringify.js'; // **`v1()` - Generate time-based UUID**\n//\n// Inspired by https://github.com/LiosK/UUID.js\n// and http://docs.python.org/library/uuid.html\n\nvar _nodeId;\n\nvar _clockseq; // Previous uuid creation time\n\n\nvar _lastMSecs = 0;\nvar _lastNSecs = 0; // See https://github.com/uuidjs/uuid for API details\n\nfunction v1(options, buf, offset) {\n var i = buf && offset || 0;\n var b = buf || new Array(16);\n options = options || {};\n var node = options.node || _nodeId;\n var clockseq = options.clockseq !== undefined ? options.clockseq : _clockseq; // node and clockseq need to be initialized to random values if they're not\n // specified. We do this lazily to minimize issues related to insufficient\n // system entropy. See #189\n\n if (node == null || clockseq == null) {\n var seedBytes = options.random || (options.rng || rng)();\n\n if (node == null) {\n // Per 4.5, create and 48-bit node id, (47 random bits + multicast bit = 1)\n node = _nodeId = [seedBytes[0] | 0x01, seedBytes[1], seedBytes[2], seedBytes[3], seedBytes[4], seedBytes[5]];\n }\n\n if (clockseq == null) {\n // Per 4.2.2, randomize (14 bit) clockseq\n clockseq = _clockseq = (seedBytes[6] << 8 | seedBytes[7]) & 0x3fff;\n }\n } // UUID timestamps are 100 nano-second units since the Gregorian epoch,\n // (1582-10-15 00:00). JSNumbers aren't precise enough for this, so\n // time is handled internally as 'msecs' (integer milliseconds) and 'nsecs'\n // (100-nanoseconds offset from msecs) since unix epoch, 1970-01-01 00:00.\n\n\n var msecs = options.msecs !== undefined ? options.msecs : Date.now(); // Per 4.2.1.2, use count of uuid's generated during the current clock\n // cycle to simulate higher resolution clock\n\n var nsecs = options.nsecs !== undefined ? options.nsecs : _lastNSecs + 1; // Time since last uuid creation (in msecs)\n\n var dt = msecs - _lastMSecs + (nsecs - _lastNSecs) / 10000; // Per 4.2.1.2, Bump clockseq on clock regression\n\n if (dt < 0 && options.clockseq === undefined) {\n clockseq = clockseq + 1 & 0x3fff;\n } // Reset nsecs if clock regresses (new clockseq) or we've moved onto a new\n // time interval\n\n\n if ((dt < 0 || msecs > _lastMSecs) && options.nsecs === undefined) {\n nsecs = 0;\n } // Per 4.2.1.2 Throw error if too many uuids are requested\n\n\n if (nsecs >= 10000) {\n throw new Error(\"uuid.v1(): Can't create more than 10M uuids/sec\");\n }\n\n _lastMSecs = msecs;\n _lastNSecs = nsecs;\n _clockseq = clockseq; // Per 4.1.4 - Convert from unix epoch to Gregorian epoch\n\n msecs += 12219292800000; // `time_low`\n\n var tl = ((msecs & 0xfffffff) * 10000 + nsecs) % 0x100000000;\n b[i++] = tl >>> 24 & 0xff;\n b[i++] = tl >>> 16 & 0xff;\n b[i++] = tl >>> 8 & 0xff;\n b[i++] = tl & 0xff; // `time_mid`\n\n var tmh = msecs / 0x100000000 * 10000 & 0xfffffff;\n b[i++] = tmh >>> 8 & 0xff;\n b[i++] = tmh & 0xff; // `time_high_and_version`\n\n b[i++] = tmh >>> 24 & 0xf | 0x10; // include version\n\n b[i++] = tmh >>> 16 & 0xff; // `clock_seq_hi_and_reserved` (Per 4.2.2 - include variant)\n\n b[i++] = clockseq >>> 8 | 0x80; // `clock_seq_low`\n\n b[i++] = clockseq & 0xff; // `node`\n\n for (var n = 0; n < 6; ++n) {\n b[i + n] = node[n];\n }\n\n return buf || stringify(b);\n}\n\nexport default v1;","import validate from './validate.js';\n\nfunction parse(uuid) {\n if (!validate(uuid)) {\n throw TypeError('Invalid UUID');\n }\n\n var v;\n var arr = new Uint8Array(16); // Parse ########-....-....-....-............\n\n arr[0] = (v = parseInt(uuid.slice(0, 8), 16)) >>> 24;\n arr[1] = v >>> 16 & 0xff;\n arr[2] = v >>> 8 & 0xff;\n arr[3] = v & 0xff; // Parse ........-####-....-....-............\n\n arr[4] = (v = parseInt(uuid.slice(9, 13), 16)) >>> 8;\n arr[5] = v & 0xff; // Parse ........-....-####-....-............\n\n arr[6] = (v = parseInt(uuid.slice(14, 18), 16)) >>> 8;\n arr[7] = v & 0xff; // Parse ........-....-....-####-............\n\n arr[8] = (v = parseInt(uuid.slice(19, 23), 16)) >>> 8;\n arr[9] = v & 0xff; // Parse ........-....-....-....-############\n // (Use \"/\" to avoid 32-bit truncation when bit-shifting high-order bytes)\n\n arr[10] = (v = parseInt(uuid.slice(24, 36), 16)) / 0x10000000000 & 0xff;\n arr[11] = v / 0x100000000 & 0xff;\n arr[12] = v >>> 24 & 0xff;\n arr[13] = v >>> 16 & 0xff;\n arr[14] = v >>> 8 & 0xff;\n arr[15] = v & 0xff;\n return arr;\n}\n\nexport default parse;","import stringify from './stringify.js';\nimport parse from './parse.js';\n\nfunction stringToBytes(str) {\n str = unescape(encodeURIComponent(str)); // UTF8 escape\n\n var bytes = [];\n\n for (var i = 0; i < str.length; ++i) {\n bytes.push(str.charCodeAt(i));\n }\n\n return bytes;\n}\n\nexport var DNS = '6ba7b810-9dad-11d1-80b4-00c04fd430c8';\nexport var URL = '6ba7b811-9dad-11d1-80b4-00c04fd430c8';\nexport default function (name, version, hashfunc) {\n function generateUUID(value, namespace, buf, offset) {\n if (typeof value === 'string') {\n value = stringToBytes(value);\n }\n\n if (typeof namespace === 'string') {\n namespace = parse(namespace);\n }\n\n if (namespace.length !== 16) {\n throw TypeError('Namespace must be array-like (16 iterable integer values, 0-255)');\n } // Compute hash of namespace and value, Per 4.3\n // Future: Use spread syntax when supported on all platforms, e.g. `bytes =\n // hashfunc([...namespace, ... value])`\n\n\n var bytes = new Uint8Array(16 + value.length);\n bytes.set(namespace);\n bytes.set(value, namespace.length);\n bytes = hashfunc(bytes);\n bytes[6] = bytes[6] & 0x0f | version;\n bytes[8] = bytes[8] & 0x3f | 0x80;\n\n if (buf) {\n offset = offset || 0;\n\n for (var i = 0; i < 16; ++i) {\n buf[offset + i] = bytes[i];\n }\n\n return buf;\n }\n\n return stringify(bytes);\n } // Function#name is not settable on some platforms (#270)\n\n\n try {\n generateUUID.name = name; // eslint-disable-next-line no-empty\n } catch (err) {} // For CommonJS default export support\n\n\n generateUUID.DNS = DNS;\n generateUUID.URL = URL;\n return generateUUID;\n}","/*\n * Browser-compatible JavaScript MD5\n *\n * Modification of JavaScript MD5\n * https://github.com/blueimp/JavaScript-MD5\n *\n * Copyright 2011, Sebastian Tschan\n * https://blueimp.net\n *\n * Licensed under the MIT license:\n * https://opensource.org/licenses/MIT\n *\n * Based on\n * A JavaScript implementation of the RSA Data Security, Inc. MD5 Message\n * Digest Algorithm, as defined in RFC 1321.\n * Version 2.2 Copyright (C) Paul Johnston 1999 - 2009\n * Other contributors: Greg Holt, Andrew Kepert, Ydnar, Lostinet\n * Distributed under the BSD License\n * See http://pajhome.org.uk/crypt/md5 for more info.\n */\nfunction md5(bytes) {\n if (typeof bytes === 'string') {\n var msg = unescape(encodeURIComponent(bytes)); // UTF8 escape\n\n bytes = new Uint8Array(msg.length);\n\n for (var i = 0; i < msg.length; ++i) {\n bytes[i] = msg.charCodeAt(i);\n }\n }\n\n return md5ToHexEncodedArray(wordsToMd5(bytesToWords(bytes), bytes.length * 8));\n}\n/*\n * Convert an array of little-endian words to an array of bytes\n */\n\n\nfunction md5ToHexEncodedArray(input) {\n var output = [];\n var length32 = input.length * 32;\n var hexTab = '0123456789abcdef';\n\n for (var i = 0; i < length32; i += 8) {\n var x = input[i >> 5] >>> i % 32 & 0xff;\n var hex = parseInt(hexTab.charAt(x >>> 4 & 0x0f) + hexTab.charAt(x & 0x0f), 16);\n output.push(hex);\n }\n\n return output;\n}\n/**\n * Calculate output length with padding and bit length\n */\n\n\nfunction getOutputLength(inputLength8) {\n return (inputLength8 + 64 >>> 9 << 4) + 14 + 1;\n}\n/*\n * Calculate the MD5 of an array of little-endian words, and a bit length.\n */\n\n\nfunction wordsToMd5(x, len) {\n /* append padding */\n x[len >> 5] |= 0x80 << len % 32;\n x[getOutputLength(len) - 1] = len;\n var a = 1732584193;\n var b = -271733879;\n var c = -1732584194;\n var d = 271733878;\n\n for (var i = 0; i < x.length; i += 16) {\n var olda = a;\n var oldb = b;\n var oldc = c;\n var oldd = d;\n a = md5ff(a, b, c, d, x[i], 7, -680876936);\n d = md5ff(d, a, b, c, x[i + 1], 12, -389564586);\n c = md5ff(c, d, a, b, x[i + 2], 17, 606105819);\n b = md5ff(b, c, d, a, x[i + 3], 22, -1044525330);\n a = md5ff(a, b, c, d, x[i + 4], 7, -176418897);\n d = md5ff(d, a, b, c, x[i + 5], 12, 1200080426);\n c = md5ff(c, d, a, b, x[i + 6], 17, -1473231341);\n b = md5ff(b, c, d, a, x[i + 7], 22, -45705983);\n a = md5ff(a, b, c, d, x[i + 8], 7, 1770035416);\n d = md5ff(d, a, b, c, x[i + 9], 12, -1958414417);\n c = md5ff(c, d, a, b, x[i + 10], 17, -42063);\n b = md5ff(b, c, d, a, x[i + 11], 22, -1990404162);\n a = md5ff(a, b, c, d, x[i + 12], 7, 1804603682);\n d = md5ff(d, a, b, c, x[i + 13], 12, -40341101);\n c = md5ff(c, d, a, b, x[i + 14], 17, -1502002290);\n b = md5ff(b, c, d, a, x[i + 15], 22, 1236535329);\n a = md5gg(a, b, c, d, x[i + 1], 5, -165796510);\n d = md5gg(d, a, b, c, x[i + 6], 9, -1069501632);\n c = md5gg(c, d, a, b, x[i + 11], 14, 643717713);\n b = md5gg(b, c, d, a, x[i], 20, -373897302);\n a = md5gg(a, b, c, d, x[i + 5], 5, -701558691);\n d = md5gg(d, a, b, c, x[i + 10], 9, 38016083);\n c = md5gg(c, d, a, b, x[i + 15], 14, -660478335);\n b = md5gg(b, c, d, a, x[i + 4], 20, -405537848);\n a = md5gg(a, b, c, d, x[i + 9], 5, 568446438);\n d = md5gg(d, a, b, c, x[i + 14], 9, -1019803690);\n c = md5gg(c, d, a, b, x[i + 3], 14, -187363961);\n b = md5gg(b, c, d, a, x[i + 8], 20, 1163531501);\n a = md5gg(a, b, c, d, x[i + 13], 5, -1444681467);\n d = md5gg(d, a, b, c, x[i + 2], 9, -51403784);\n c = md5gg(c, d, a, b, x[i + 7], 14, 1735328473);\n b = md5gg(b, c, d, a, x[i + 12], 20, -1926607734);\n a = md5hh(a, b, c, d, x[i + 5], 4, -378558);\n d = md5hh(d, a, b, c, x[i + 8], 11, -2022574463);\n c = md5hh(c, d, a, b, x[i + 11], 16, 1839030562);\n b = md5hh(b, c, d, a, x[i + 14], 23, -35309556);\n a = md5hh(a, b, c, d, x[i + 1], 4, -1530992060);\n d = md5hh(d, a, b, c, x[i + 4], 11, 1272893353);\n c = md5hh(c, d, a, b, x[i + 7], 16, -155497632);\n b = md5hh(b, c, d, a, x[i + 10], 23, -1094730640);\n a = md5hh(a, b, c, d, x[i + 13], 4, 681279174);\n d = md5hh(d, a, b, c, x[i], 11, -358537222);\n c = md5hh(c, d, a, b, x[i + 3], 16, -722521979);\n b = md5hh(b, c, d, a, x[i + 6], 23, 76029189);\n a = md5hh(a, b, c, d, x[i + 9], 4, -640364487);\n d = md5hh(d, a, b, c, x[i + 12], 11, -421815835);\n c = md5hh(c, d, a, b, x[i + 15], 16, 530742520);\n b = md5hh(b, c, d, a, x[i + 2], 23, -995338651);\n a = md5ii(a, b, c, d, x[i], 6, -198630844);\n d = md5ii(d, a, b, c, x[i + 7], 10, 1126891415);\n c = md5ii(c, d, a, b, x[i + 14], 15, -1416354905);\n b = md5ii(b, c, d, a, x[i + 5], 21, -57434055);\n a = md5ii(a, b, c, d, x[i + 12], 6, 1700485571);\n d = md5ii(d, a, b, c, x[i + 3], 10, -1894986606);\n c = md5ii(c, d, a, b, x[i + 10], 15, -1051523);\n b = md5ii(b, c, d, a, x[i + 1], 21, -2054922799);\n a = md5ii(a, b, c, d, x[i + 8], 6, 1873313359);\n d = md5ii(d, a, b, c, x[i + 15], 10, -30611744);\n c = md5ii(c, d, a, b, x[i + 6], 15, -1560198380);\n b = md5ii(b, c, d, a, x[i + 13], 21, 1309151649);\n a = md5ii(a, b, c, d, x[i + 4], 6, -145523070);\n d = md5ii(d, a, b, c, x[i + 11], 10, -1120210379);\n c = md5ii(c, d, a, b, x[i + 2], 15, 718787259);\n b = md5ii(b, c, d, a, x[i + 9], 21, -343485551);\n a = safeAdd(a, olda);\n b = safeAdd(b, oldb);\n c = safeAdd(c, oldc);\n d = safeAdd(d, oldd);\n }\n\n return [a, b, c, d];\n}\n/*\n * Convert an array bytes to an array of little-endian words\n * Characters >255 have their high-byte silently ignored.\n */\n\n\nfunction bytesToWords(input) {\n if (input.length === 0) {\n return [];\n }\n\n var length8 = input.length * 8;\n var output = new Uint32Array(getOutputLength(length8));\n\n for (var i = 0; i < length8; i += 8) {\n output[i >> 5] |= (input[i / 8] & 0xff) << i % 32;\n }\n\n return output;\n}\n/*\n * Add integers, wrapping at 2^32. This uses 16-bit operations internally\n * to work around bugs in some JS interpreters.\n */\n\n\nfunction safeAdd(x, y) {\n var lsw = (x & 0xffff) + (y & 0xffff);\n var msw = (x >> 16) + (y >> 16) + (lsw >> 16);\n return msw << 16 | lsw & 0xffff;\n}\n/*\n * Bitwise rotate a 32-bit number to the left.\n */\n\n\nfunction bitRotateLeft(num, cnt) {\n return num << cnt | num >>> 32 - cnt;\n}\n/*\n * These functions implement the four basic operations the algorithm uses.\n */\n\n\nfunction md5cmn(q, a, b, x, s, t) {\n return safeAdd(bitRotateLeft(safeAdd(safeAdd(a, q), safeAdd(x, t)), s), b);\n}\n\nfunction md5ff(a, b, c, d, x, s, t) {\n return md5cmn(b & c | ~b & d, a, b, x, s, t);\n}\n\nfunction md5gg(a, b, c, d, x, s, t) {\n return md5cmn(b & d | c & ~d, a, b, x, s, t);\n}\n\nfunction md5hh(a, b, c, d, x, s, t) {\n return md5cmn(b ^ c ^ d, a, b, x, s, t);\n}\n\nfunction md5ii(a, b, c, d, x, s, t) {\n return md5cmn(c ^ (b | ~d), a, b, x, s, t);\n}\n\nexport default md5;","import v35 from './v35.js';\nimport md5 from './md5.js';\nvar v3 = v35('v3', 0x30, md5);\nexport default v3;","import rng from './rng.js';\nimport stringify from './stringify.js';\n\nfunction v4(options, buf, offset) {\n options = options || {};\n var rnds = options.random || (options.rng || rng)(); // Per 4.4, set bits for version and `clock_seq_hi_and_reserved`\n\n rnds[6] = rnds[6] & 0x0f | 0x40;\n rnds[8] = rnds[8] & 0x3f | 0x80; // Copy bytes to buffer, if provided\n\n if (buf) {\n offset = offset || 0;\n\n for (var i = 0; i < 16; ++i) {\n buf[offset + i] = rnds[i];\n }\n\n return buf;\n }\n\n return stringify(rnds);\n}\n\nexport default v4;","// Adapted from Chris Veness' SHA1 code at\n// http://www.movable-type.co.uk/scripts/sha1.html\nfunction f(s, x, y, z) {\n switch (s) {\n case 0:\n return x & y ^ ~x & z;\n\n case 1:\n return x ^ y ^ z;\n\n case 2:\n return x & y ^ x & z ^ y & z;\n\n case 3:\n return x ^ y ^ z;\n }\n}\n\nfunction ROTL(x, n) {\n return x << n | x >>> 32 - n;\n}\n\nfunction sha1(bytes) {\n var K = [0x5a827999, 0x6ed9eba1, 0x8f1bbcdc, 0xca62c1d6];\n var H = [0x67452301, 0xefcdab89, 0x98badcfe, 0x10325476, 0xc3d2e1f0];\n\n if (typeof bytes === 'string') {\n var msg = unescape(encodeURIComponent(bytes)); // UTF8 escape\n\n bytes = [];\n\n for (var i = 0; i < msg.length; ++i) {\n bytes.push(msg.charCodeAt(i));\n }\n } else if (!Array.isArray(bytes)) {\n // Convert Array-like to Array\n bytes = Array.prototype.slice.call(bytes);\n }\n\n bytes.push(0x80);\n var l = bytes.length / 4 + 2;\n var N = Math.ceil(l / 16);\n var M = new Array(N);\n\n for (var _i = 0; _i < N; ++_i) {\n var arr = new Uint32Array(16);\n\n for (var j = 0; j < 16; ++j) {\n arr[j] = bytes[_i * 64 + j * 4] << 24 | bytes[_i * 64 + j * 4 + 1] << 16 | bytes[_i * 64 + j * 4 + 2] << 8 | bytes[_i * 64 + j * 4 + 3];\n }\n\n M[_i] = arr;\n }\n\n M[N - 1][14] = (bytes.length - 1) * 8 / Math.pow(2, 32);\n M[N - 1][14] = Math.floor(M[N - 1][14]);\n M[N - 1][15] = (bytes.length - 1) * 8 & 0xffffffff;\n\n for (var _i2 = 0; _i2 < N; ++_i2) {\n var W = new Uint32Array(80);\n\n for (var t = 0; t < 16; ++t) {\n W[t] = M[_i2][t];\n }\n\n for (var _t = 16; _t < 80; ++_t) {\n W[_t] = ROTL(W[_t - 3] ^ W[_t - 8] ^ W[_t - 14] ^ W[_t - 16], 1);\n }\n\n var a = H[0];\n var b = H[1];\n var c = H[2];\n var d = H[3];\n var e = H[4];\n\n for (var _t2 = 0; _t2 < 80; ++_t2) {\n var s = Math.floor(_t2 / 20);\n var T = ROTL(a, 5) + f(s, b, c, d) + e + K[s] + W[_t2] >>> 0;\n e = d;\n d = c;\n c = ROTL(b, 30) >>> 0;\n b = a;\n a = T;\n }\n\n H[0] = H[0] + a >>> 0;\n H[1] = H[1] + b >>> 0;\n H[2] = H[2] + c >>> 0;\n H[3] = H[3] + d >>> 0;\n H[4] = H[4] + e >>> 0;\n }\n\n return [H[0] >> 24 & 0xff, H[0] >> 16 & 0xff, H[0] >> 8 & 0xff, H[0] & 0xff, H[1] >> 24 & 0xff, H[1] >> 16 & 0xff, H[1] >> 8 & 0xff, H[1] & 0xff, H[2] >> 24 & 0xff, H[2] >> 16 & 0xff, H[2] >> 8 & 0xff, H[2] & 0xff, H[3] >> 24 & 0xff, H[3] >> 16 & 0xff, H[3] >> 8 & 0xff, H[3] & 0xff, H[4] >> 24 & 0xff, H[4] >> 16 & 0xff, H[4] >> 8 & 0xff, H[4] & 0xff];\n}\n\nexport default sha1;","import v35 from './v35.js';\nimport sha1 from './sha1.js';\nvar v5 = v35('v5', 0x50, sha1);\nexport default v5;","export default '00000000-0000-0000-0000-000000000000';","import validate from './validate.js';\n\nfunction version(uuid) {\n if (!validate(uuid)) {\n throw TypeError('Invalid UUID');\n }\n\n return parseInt(uuid.substr(14, 1), 16);\n}\n\nexport default version;","module.exports = __WEBPACK_EXTERNAL_MODULE__990__;","// The module cache\nvar __webpack_module_cache__ = {};\n\n// The require function\nfunction __webpack_require__(moduleId) {\n\t// Check if module is in cache\n\tvar cachedModule = __webpack_module_cache__[moduleId];\n\tif (cachedModule !== undefined) {\n\t\treturn cachedModule.exports;\n\t}\n\t// Create a new module (and put it into the cache)\n\tvar module = __webpack_module_cache__[moduleId] = {\n\t\t// no module.id needed\n\t\t// no module.loaded needed\n\t\texports: {}\n\t};\n\n\t// Execute the module function\n\t__webpack_modules__[moduleId](module, module.exports, __webpack_require__);\n\n\t// Return the exports of the module\n\treturn module.exports;\n}\n\n","// getDefaultExport function for compatibility with non-harmony modules\n__webpack_require__.n = (module) => {\n\tvar getter = module && module.__esModule ?\n\t\t() => (module['default']) :\n\t\t() => (module);\n\t__webpack_require__.d(getter, { a: getter });\n\treturn getter;\n};","// define getter functions for harmony exports\n__webpack_require__.d = (exports, definition) => {\n\tfor(var key in definition) {\n\t\tif(__webpack_require__.o(definition, key) && !__webpack_require__.o(exports, key)) {\n\t\t\tObject.defineProperty(exports, key, { enumerable: true, get: definition[key] });\n\t\t}\n\t}\n};","__webpack_require__.g = (function() {\n\tif (typeof globalThis === 'object') return globalThis;\n\ttry {\n\t\treturn this || new Function('return this')();\n\t} catch (e) {\n\t\tif (typeof window === 'object') return window;\n\t}\n})();","__webpack_require__.o = (obj, prop) => (Object.prototype.hasOwnProperty.call(obj, prop))","// define __esModule on exports\n__webpack_require__.r = (exports) => {\n\tif(typeof Symbol !== 'undefined' && Symbol.toStringTag) {\n\t\tObject.defineProperty(exports, Symbol.toStringTag, { value: 'Module' });\n\t}\n\tObject.defineProperty(exports, '__esModule', { value: true });\n};","var scriptUrl;\nif (__webpack_require__.g.importScripts) scriptUrl = __webpack_require__.g.location + \"\";\nvar document = __webpack_require__.g.document;\nif (!scriptUrl && document) {\n\tif (document.currentScript)\n\t\tscriptUrl = document.currentScript.src\n\tif (!scriptUrl) {\n\t\tvar scripts = document.getElementsByTagName(\"script\");\n\t\tif(scripts.length) scriptUrl = scripts[scripts.length - 1].src\n\t}\n}\n// When supporting browsers where an automatic publicPath is not supported you must specify an output.publicPath manually via configuration\n// or pass an empty string (\"\") and set the __webpack_public_path__ variable from your code to use your own logic.\nif (!scriptUrl) throw new Error(\"Automatic publicPath is not supported in this browser\");\nscriptUrl = scriptUrl.replace(/#.*$/, \"\").replace(/\\?.*$/, \"\").replace(/\\/[^\\/]+$/, \"/\");\n__webpack_require__.p = scriptUrl;","export default __webpack_public_path__ + \"02188894d5236b1517df3210b79c2a7f.svg\";","import './d3-context-menu.css';\nimport ArrowIcon from './img/play.svg';\n\nimport d3 from 'd3';\nimport slugid from 'slugid';\n\nexport function contextMenu(menu, opts) {\n let previouslyMouseUp = false;\n let clickAway = () => {};\n let uid = slugid.nice();\n let rootElement = null;\n let orientation = 'right'; // display the menu to the right of the mouse click\n // or parent elemement\n let initialPos = null;\n let parentStart = null;\n\n var openCallback,\n closeCallback;\n\n if (typeof opts === 'function') {\n openCallback = opts;\n } else {\n opts = opts || {};\n openCallback = opts.onOpen;\n closeCallback = opts.onClose;\n }\n\n if ('rootElement' in opts)\n rootElement = opts['rootElement']\n\n if ('pos' in opts) {\n // do we want to place this menu somewhere specific?\n initialPos = opts.pos;\n }\n\n if ('orientation' in opts) {\n orientation = opts.orientation;\n }\n\n if ('parentStart' in opts) {\n parentStart = opts.parentStart;\n }\n\n // create the div element that will hold the context menu\n d3.selectAll('.d3-context-menu-' + uid).data([1])\n .enter()\n .append('div')\n .classed('d3-context-menu', true)\n .classed('d3-context-menu-' + uid, true)\n\n // close menu\n d3.select('body').on('click.d3-context-menu-' + uid, function() {\n if (previouslyMouseUp) {\n previouslyMouseUp = false;\n return;\n }\n console.log('body click close');\n\n d3.select('.d3-context-menu-' + uid).style('display', 'none');\n orientation = 'right';\n\n if (closeCallback) {\n closeCallback();\n }\n });\n\n // this gets executed when a contextmenu event occurs\n return function(data, index, pMouseUp=false,\n clickAwayFunc = function() { } ) {\n var elm = this;\n var contextMenuPos = null;\n let mousePos = null;\n let currentThis = this;\n\n if (rootElement == null)\n mousePos = d3.mouse(this);\n else\n mousePos = d3.mouse(rootElement); // for recursive menus, we need the mouse\n // position relative to another element\n\n clickAway = clickAwayFunc;\n let openChildMenuUid = null;\n\n previouslyMouseUp = pMouseUp;\n\n d3.selectAll('.d3-context-menu-' + uid).html('');\n var list = d3.selectAll('.d3-context-menu-' + uid)\n .on('contextmenu', function(d) {\n console.log('context-menu close');\n d3.select('.d3-context-menu-' + uid).style('display', 'none'); \n orientation = 'right';\n\n d3.event.preventDefault();\n d3.event.stopPropagation();\n })\n .append('ul');\n\n list.selectAll('li').data(typeof menu === 'function' ? menu(data) : menu).enter()\n .append('li')\n .attr('class', function(d) {\n console.log('d:', d);\n var ret = '';\n if (d.divider) {\n ret += ' is-divider';\n }\n if (d.disabled) {\n ret += ' is-disabled';\n }\n if (!d.action) {\n ret += ' is-header';\n }\n if ('children' in d) {\n ret += ' d3-context-menu-recursive';\n }\n return ret;\n })\n .html(function(d) {\n if (d.divider) {\n return '
';\n }\n if (!d.title) {\n console.error('No title attribute set. Check the spelling of your options.');\n }\n return (typeof d.title === 'string') ? d.title : d.title(data);\n })\n .on('click', function(d, i) {\n if (d.disabled) return; // do nothing if disabled\n if (!d.action) return; // headers have no \"action\"\n d.action(elm, data, index, mousePos);\n console.log('click close');\n\n // close all context menus\n d3.selectAll('.d3-context-menu').style('display', 'none');\n orientation = 'right';\n\n if (closeCallback) {\n closeCallback();\n }\n })\n .on('mouseenter', function(d, i) {\n d3.select(this)\n .classed('d3-context-menu-selected', true)\n\n if (openChildMenuUid != null) {\n // there's a child menu open\n\n // unselect all items\n d3.select('.d3-context-menu-' + uid)\n .selectAll('li')\n .classed('d3-context-menu-selected', false);\n\n if (typeof d.children == 'undefined') {\n console.log(\"no children close\");\n // no children, so hide any open child menus\n d3.select('.d3-context-menu-' + openChildMenuUid)\n .style('display', 'none');\n\n openChildMenuUid = null;\n return;\n }\n\n if (d.childUid == openChildMenuUid) {\n // the correct child menu is already open\n return;\n\n } else {\n // need to open a different child menu\n console.log('open different child menu close');\n \n // close the already open one\n d3.select('.d3-context-menu-' + openChildMenuUid)\n .style('display', 'none');\n\n openChildMenuUid = null;\n\n }\n } \n\n // there should be no menu open right now\n if (typeof d.children != 'undefined') {\n let boundingRect = this.getBoundingClientRect();\n\n let childrenContextMenu = null\n if (orientation == 'left') {\n childrenContextMenu = contextMenu(d.children, {'rootElement': currentThis,\n 'pos': [ boundingRect.left + window.pageXOffset,\n boundingRect.top - 2 + window.pageYOffset],\n 'orientation': 'left'});\n } else {\n childrenContextMenu = contextMenu(d.children, \n {\n 'pos': [ boundingRect.left + boundingRect.width + window.pageXOffset,\n boundingRect.top - 2 + window.pageYOffset],\n 'rootElement': currentThis,\n 'parentStart': [boundingRect.left + window.pageXOffset,\n boundingRect.top - 2 + window.pageYOffset]});\n }\n\n d.childUid = childrenContextMenu.apply(this, [data,i,true,\n function() { }]);\n openChildMenuUid = d.childUid;\n }\n\n\n d3.select(this)\n .classed('d3-context-menu-selected', true)\n \n })\n .on('mouseleave', function(d, i) {\n\n if (openChildMenuUid == null) {\n d3.select(this)\n .classed('d3-context-menu-selected', false);\n }\n });\n\n list.selectAll('.d3-context-menu-recursive')\n .append('img')\n .attr('src', ArrowIcon)\n .attr('width', '14px')\n .attr('height', '14px')\n .style('position', 'absolute')\n .style('right', '5px')\n ;\n\n // the openCallback allows an action to fire before the menu is displayed\n // an example usage would be closing a tooltip\n if (openCallback) {\n if (openCallback(data, index) === false) {\n return uid;\n }\n }\n\n let contextMenuSelection = d3.select('.d3-context-menu-' + uid)\n .style('display', 'block');\n\n if (initialPos == null) {\n d3.select('.d3-context-menu-' + uid)\n .style('left', (d3.event.pageX - 2) + 'px')\n .style('top', (d3.event.pageY - 2) + 'px')\n } else {\n d3.select('.d3-context-menu-' + uid)\n .style('left', initialPos[0] + 'px')\n .style('top', initialPos[1] + 'px')\n }\n\n // check if the menu disappears off the side of the window\n let boundingRect = contextMenuSelection.node().getBoundingClientRect();\n\n if (boundingRect.left + boundingRect.width > window.innerWidth || orientation == 'left') {\n orientation = 'left';\n\n // menu goes of the end of the window, position it the other way\n if (initialPos == null) {\n // place the menu where the user clicked\n d3.select('.d3-context-menu-' + uid)\n .style('left', (d3.event.pageX - 2 - boundingRect.width) + 'px')\n .style('top', (d3.event.pageY - 2) + 'px')\n } else {\n if (parentStart != null) {\n d3.select('.d3-context-menu-' + uid)\n .style('left', (parentStart[0] - boundingRect.width) + 'px')\n .style('top', parentStart[1] + 'px')\n } else {\n d3.select('.d3-context-menu-' + uid)\n .style('left', (initialPos[0] - boundingRect.width) + 'px')\n .style('top', initialPos[1] + 'px')\n }\n }\n \n }\n\n // display context menu\n\n if (previouslyMouseUp)\n return uid;\n\n d3.event.preventDefault();\n d3.event.stopPropagation();\n //d3.event.stopImmediatePropagation();\n //\n return uid;\n };\n};\n","var numberSort = function(a,b) { return a - b; };\n\nexport function arraysEqual(a, b) {\n // courtesy of \n // http://stackoverflow.com/questions/3115982/how-to-check-if-two-arrays-are-equal-with-javascript\n if (a === b) return true;\n if (a === null || b === null) return false;\n if (a.length != b.length) return false;\n\n // If you don't care about the order of the elements inside\n // the array, you should sort both arrays here.\n\n for (var i = 0; i < a.length; ++i) {\n if (a[i] !== b[i]) return false;\n }\n return true;\n}\n\nexport function RNAUtilities() {\n var self = this;\n\n // the brackets to use when constructing dotbracket strings\n // with pseudoknots\n self.bracketLeft = \"([{abcdefghijklmnopqrstuvwxyz\".split(\"\");\n\n self.inverseBrackets = function(bracket) {\n var res = {};\n for (var i = 0; i < bracket.length; i++) {\n res[bracket[i]] = i;\n }\n return res;\n };\n\n self.maximumMatching = function maximumMatching(pt){\n // Courtesy of the great Ronny Lorenz\n\n var n = pt[0];\n var TURN = 0; //minimal number of nucleotides in the hairpin\n\n /* array init */\n var mm = new Array(n + 1);\n for(var i = 0; i <= n; i++){\n mm[i] = new Array(n + 1);\n for(var j = i; j <= n; j++)\n mm[i][j] = 0;\n }\n var maximum = 0;\n\n /* actual computation */\n for(var i = n - TURN - 1; i > 0; i--)\n\n for(var j = i + TURN + 1; j <= n; j++){\n maximum = mm[i][j-1];\n\n for(var l = j - TURN - 1; l >= i; l--) {\n if(pt[l] === j) {\n\n // we have a base pair here\n maximum = Math.max(maximum, ((l > i) ? mm[i][l-1] : 0) + 1 + ((j - l - 1 > 0) ? mm[l+1][j-1] : 0));\n }\n }\n\n mm[i][j] = maximum;\n }\n\n maximum = mm[1][n];\n\n return mm;\n };\n\n self.backtrackMaximumMatching = function(mm, oldPt) {\n var pt = Array.apply(null, \n Array(mm.length)).map(function() { return 0 }); \n //create an array containing zeros\n\n self.mmBt(mm, pt, oldPt, 1, mm.length-1);\n return pt;\n }\n\n self.mmBt = function(mm, pt, oldPt, i, j){\n // Create a pairtable from the backtracking\n var maximum = mm[i][j];\n var TURN = 0;\n\n if(j - i - 1 < TURN) return; /* no more pairs */\n\n if(mm[i][j-1] == maximum){ /* j is unpaired */\n self.mmBt(mm, pt, oldPt, i, j-1);\n return;\n }\n\n for(var q = j - TURN - 1; q >= i; q--){ /* j is paired with some q */\n if (oldPt[j] !== q)\n continue;\n\n var leftPart = (q > i) ? mm[i][q-1] : 0;\n var enclosedPart = (j - q - 1 > 0) ? mm[q+1][j-1] : 0;\n\n if(leftPart + enclosedPart + 1 == maximum) {\n // there's a base pair between j and q\n pt[q] = j;\n pt[j] = q;\n\n if(i < q) \n self.mmBt(mm, pt, oldPt, i, q - 1);\n\n self.mmBt(mm, pt, oldPt, q + 1, j - 1);\n return;\n }\n }\n\n //alert(i + \",\" + j + \": backtracking failed!\");\n console.log('FAILED!!!' + i + ',' + j + ': backtracking failed!');\n\n };\n\n self.dotbracketToPairtable = function(dotbracket) {\n // create an array and initialize it to 0\n var pt = Array.apply(null, new Array(dotbracket.length + 1)).map(Number.prototype.valueOf,0);\n \n // the first element is always the length of the RNA molecule\n pt[0] = dotbracket.length;\n\n // store the pairing partners for each symbol\n var stack = {};\n for (var i = 0; i < self.bracketLeft.length; i++) {\n stack[i] = [];\n }\n\n // lookup the index of each symbol in the bracket array\n var inverseBracketLeft = self.inverseBrackets(self.bracketLeft);\n var inverseBracketRight = self.inverseBrackets(self.bracketRight);\n\n for (var i = 0; i < dotbracket.length; i++) {\n var a = dotbracket[i];\n var ni = i + 1;\n\n if (a == '.' || a == 'o') {\n // unpaired\n pt[ni] = 0;\n } else {\n if (a in inverseBracketLeft) {\n // open pair?\n stack[inverseBracketLeft[a]].push(ni);\n } else if (a in inverseBracketRight){\n // close pair?\n var j = stack[inverseBracketRight[a]].pop();\n\n pt[ni] = j;\n pt[j] = ni;\n } else {\n throw \"Unknown symbol in dotbracket string\";\n }\n }\n }\n\n for (var key in stack) {\n if (stack[key].length > 0) {\n throw \"Unmatched base at position \" + stack[key][0];\n }\n }\n\n return pt;\n };\n\n self.insertIntoStack = function(stack, i, j) {\n var k = 0;\n while (stack[k].length > 0 && stack[k][stack[k].length - 1] < j) {\n k += 1;\n }\n\n stack[k].push(j);\n return k;\n };\n\n self.deleteFromStack = function(stack, j) {\n var k = 0;\n while (stack[k].length === 0 || stack[k][stack[k].length-1] != j) {\n k += 1;\n }\n stack[k].pop();\n return k;\n };\n\n self.pairtableToDotbracket = function(pt) {\n // store the pairing partners for each symbol\n var stack = {};\n for (var i = 0; i < pt[0]; i++) {\n stack[i] = [];\n }\n\n var seen = {};\n var res = \"\";\n var i;\n for (var i = 1; i < pt[0] + 1; i++) {\n if (pt[i] !== 0 && pt[i] in seen) {\n throw \"Invalid pairtable contains duplicate entries\";\n }\n seen[pt[i]] = true;\n\n if (pt[i] === 0) {\n res += '.';\n } else {\n if (pt[i] > i) {\n res += self.bracketLeft[self.insertIntoStack(stack, i, pt[i])];\n } else {\n res += self.bracketRight[self.deleteFromStack(stack, i)];\n }\n }\n }\n\n return res;\n };\n\n self.findUnmatched = function(pt, from, to) {\n /*\n * Find unmatched nucleotides in this molecule.\n */\n var toRemove = [];\n var unmatched = [];\n\n var origFrom = from;\n var origTo = to;\n var i;\n\n for (var i = from; i <= to; i++)\n if (pt[i] !== 0 && (pt[i] < from || pt[i] > to))\n unmatched.push([i,pt[i]]);\n\n for (var i = origFrom; i <= origTo; i++) {\n while (pt[i] === 0 && i <= origTo) i++;\n\n to = pt[i];\n\n while (pt[i] === to) {\n i++;\n to--;\n }\n \n toRemove = toRemove.concat(self.findUnmatched(pt, i, to));\n }\n\n if (unmatched.length > 0)\n toRemove.push(unmatched);\n\n return toRemove;\n };\n\n self.removePseudoknotsFromPairtable = function(pt) {\n /* Remove the pseudoknots from this structure in such a fashion\n * that the least amount of base-pairs need to be broken\n *\n * The pairtable is manipulated in place and a list of tuples\n * indicating the broken base pairs is returned.\n */\n\n var mm = self.maximumMatching(pt);\n var newPt = self.backtrackMaximumMatching(mm, pt);\n var removed = [];\n\n for (var i = 1; i < pt.length; i++) {\n if (pt[i] < i)\n continue;\n\n if (newPt[i] != pt[i]) {\n removed.push([i, pt[i]]);\n pt[pt[i]] = 0;\n pt[i] = 0;\n }\n }\n\n return removed;\n };\n\n self.ptToElements = function(pt, level, i, j, dotBracketBreaks) {\n /* Convert a pair table to a list of secondary structure \n * elements:\n *\n * [['s',1,[2,3]]\n *\n * The 's' indicates that an element can be a stem. It can also be\n * an interior loop ('i'), a hairpin loop ('h') or a multiloop ('m')\n *\n * The second number (1 in this case) indicates the depth or\n * how many base pairs have to be broken to get to this element.\n *\n * Finally, there is the list of nucleotides which are part of\n * of this element.\n */\n var elements = [];\n var u5 = [i-1];\n var u3 = [j+1];\n\n if (arguments.length < 5)\n dotBracketBreaks = [];\n\n if (i > j)\n return [];\n \n //iterate over the unpaired regions on either side\n //this is either 5' and 3' unpaired if level == 0\n //or an interior loop or a multiloop\n for (; pt[i] === 0; i++) { u5.push(i); }\n for (; pt[j] === 0; j--) { u3.push(j); }\n\n if (i > j) {\n //hairpin loop or one large unpaired molecule\n u5.push(i);\n if (level === 0)\n return [['e',level, u5.sort(numberSort)]];\n else {\n // check to see if we have chain breaks due\n // to multiple strands in the input\n var external = false;\n var left = [];\n var right = [];\n for (var k = 0; k < u5.length; k++) {\n if (external)\n right.push(u5[k]);\n else\n left.push(u5[k]);\n\n if (dotBracketBreaks.indexOf(u5[k]) >= 0)\n external = true;\n }\n\n if (external) {\n return [['h',level, u5.sort(numberSort)]];\n }\n else\n // if not, this is a simple hairpin loop\n return [['h',level, u5.sort(numberSort)]];\n }\n }\n\n if (pt[i] != j) {\n //multiloop\n var m = u5;\n var k = i;\n\n // the nucleotide before and the starting nucleotide\n m.push(k);\n while (k <= j) {\n // recurse into a stem\n elements = elements.concat(self.ptToElements(pt, level, k, pt[k], dotBracketBreaks));\n\n // add the nucleotides between stems\n m.push(pt[k]);\n k = pt[k] + 1;\n for (; pt[k] === 0 && k <= j; k++) { m.push(k);}\n m.push(k);\n }\n m.pop();\n m = m.concat(u3);\n \n if (m.length > 0) {\n if (level === 0)\n elements.push(['e', level, m.sort(numberSort)]);\n else\n elements.push(['m', level, m.sort(numberSort)]);\n }\n \n return elements;\n }\n\n if (pt[i] === j) {\n //interior loop\n u5.push(i);\n u3.push(j);\n\n var combined = u5.concat(u3);\n if (combined.length > 4) {\n if (level === 0)\n elements.push(['e',level, u5.concat(u3).sort(numberSort)]);\n else\n elements.push(['i',level, u5.concat(u3).sort(numberSort)]);\n }\n } \n\n var s = [];\n //go through the stem\n while (pt[i] === j && i < j) {\n //one stem\n s.push(i);\n s.push(j);\n\n i += 1;\n j -= 1;\n\n level += 1;\n }\n\n u5 = [i-1];\n u3 = [j+1];\n elements.push(['s', level, s.sort(numberSort)]);\n\n return elements.concat(self.ptToElements(pt, level, i, j, dotBracketBreaks));\n };\n\n}\n\nexport var rnaUtilities = new RNAUtilities();\n\nexport function ColorScheme(colorsText) {\n var self = this;\n self.colorsText = colorsText;\n\n self.parseRange = function(rangeText) {\n //parse a number range such as 1-10 or 3,7,9 or just 7\n var parts = rangeText.split(',')\n var nums = [];\n\n for (var i = 0; i < parts.length; i++) {\n //could be 1 or 10-11 or something like that\n var parts1 = parts[i].split('-');\n\n if (parts1.length == 1)\n nums.push(parseInt(parts1[0]));\n else if (parts1.length == 2) {\n var from = parseInt(parts1[0]);\n var to = parseInt(parts1[1]);\n\n // add each number in this range\n for (var j = from; j <= to; j++) \n nums.push(j)\n } else {\n console.log('Malformed range (too many dashes):', rangeText);\n }\n }\n\n return nums;\n }\n\n self.parseColorText = function(colorText) {\n /* Parse the text of an RNA color string. Instructions and description\n * of the format are given below.\n *\n * The return is a json double dictionary indexed first by the \n * molecule name, then by the nucleotide. This is then applied\n * by force.js to the RNAs it is displaying. When no molecule\n * name is specified, the color is applied to all molecules*/\n var lines = colorText.split('\\n');\n var currMolecule = '';\n var counter = 1;\n var colorsJson = {colorValues: {'':{}}, range:['white', 'steelblue']};\n var domainValues = [];\n\n\n for (var i = 0; i < lines.length; i++) {\n\n if (lines[i][0] == '>') {\n // new molecule\n currMolecule = lines[i].trim().slice(1);\n counter = 1;\n\n colorsJson.colorValues[currMolecule] = {};\n continue;\n }\n\n let words = lines[i].trim().split(/[\\s]+/);\n\n for (var j = 0; j < words.length; j++) {\n if (isNaN(words[j])) {\n if (words[j].search('range') === 0) {\n //there's a color scale in this entry\n let parts = words[j].split('=');\n let partsRight = parts[1].split(':')\n colorsJson.range = [partsRight[0], partsRight[1]];\n continue;\n }\n\n if (words[j].search('domain') == 0) {\n //there's a color scale in this entry\n let parts = words[j].split('=');\n let partsRight = parts[1].split(':')\n colorsJson.domain = [partsRight[0], partsRight[1]];\n continue;\n }\n\n // it's not a number, should be a combination \n // of a number (nucleotide #) and a color\n let parts = words[j].split(':');\n let nums = self.parseRange(parts[0]);\n let color = parts[1]\n\n for (var k = 0; k < nums.length; k++) {\n if (isNaN(color)) {\n colorsJson.colorValues[currMolecule][nums[k]] = color;\n } else {\n colorsJson.colorValues[currMolecule][nums[k]] = +color;\n domainValues.push(Number(color));\n }\n }\n } else {\n //it's a number, so we add it to the list of values\n //seen for this molecule\n colorsJson.colorValues[currMolecule][counter] = Number(words[j]);\n counter += 1;\n\n domainValues.push(Number(words[j]));\n }\n }\n }\n\n if (!('domain' in colorsJson))\n colorsJson.domain = [Math.min.apply(null, domainValues), Math.max.apply(null, domainValues)];\n\n self.colorsJson = colorsJson;\n\n return self;\n };\n\n self.normalizeColors = function() {\n /* \n * Normalize the passed in values so that they range from\n * 0 to 1\n */\n var value;\n\n for (var moleculeName in self.colorsJson) {\n var minNum = Number.MAX_VALUE;\n var maxNum = Number.MIN_VALUE;\n\n // iterate once to find the min and max values;\n for (var resnum in self.colorsJson.colorValues[moleculeName]) {\n value = self.colorsJson.colorValues[moleculeName][resnum];\n if (typeof value == 'number') {\n if (value < minNum)\n minNum = value;\n if (value > maxNum)\n maxNum = value;\n }\n }\n\n // iterate again to normalize\n for (resnum in self.colorsJson.colorValues[moleculeName]) {\n value = self.colorsJson.colorValues[moleculeName][resnum];\n if (typeof value == 'number') {\n self.colorsJson.colorValues[moleculeName][resnum] = (value - minNum ) / (maxNum - minNum);\n }\n }\n }\n\n return self;\n };\n\n self.parseColorText(self.colorsText);\n return self;\n}\n","import {arraysEqual,RNAUtilities,rnaUtilities} from './rnautils.js';\nimport slugid from 'slugid';\n\nvar numberSort = function(a,b) { return a - b; };\n\nif (typeof(String.prototype.trim) === 'undefined') {\n String.prototype.trim = function() {\n return String(this).replace(/^\\s+|\\s+$/g, '');\n };\n}\n\nexport function ProteinGraph(structName, size, uid) {\n var self = this;\n\n self.type = 'protein';\n self.size = size;\n self.nodes = [{'name': 'P',\n 'num': 1,\n 'radius': 3 * Math.sqrt(size),\n 'rna': self,\n 'nodeType': 'protein',\n 'structName': structName,\n 'elemType': 'p',\n 'size': size,\n 'uid': slugid.nice()}];\n\n self.links = [];\n self.uid = slugid.nice();\n\n self.addUids = function(uids) {\n for (let i = 0; i < uids.length; i++)\n self.nodes[i].uid = uids[i];\n\n return self;\n };\n\n self.getUids = function() {\n /* Get the positions of each node so that they\n * can be passed to elementsToJson later\n */\n uids = [];\n for (let i = 0; i < self.dotbracket.length; i++)\n uids.push(self.nodes[i].uid);\n\n return uids;\n };\n\n}\n\nexport function RNAGraph(seq = '', dotbracket = '', structName = '', startNumber = 1) {\n var self = this;\n\n self.type = 'rna';\n self.circularizeExternal = false;\n self.seq = seq;\n self.dotbracket = dotbracket; //i.e. ..((..))..\n self.structName = structName;\n self.circular = false;\n\n if (self.dotbracket.slice(-1) == '*') {\n //circular RNA\n self.dotbracket = self.dotbracket.slice(0, -1);\n self.circular = true;\n }\n\n self.uid = slugid.nice();\n\n self.elements = []; //store the elements and the\n //nucleotides they contain\n self.pseudoknotPairs = [];\n self.nucsToNodes = {};\n\n self.addUids = function(uids) {\n let nucleotideNodes = self.nodes.filter(function(d) { return d.nodeType == 'nucleotide'; });\n\n for (let i = 0; i < uids.length && i < nucleotideNodes.length; i++) {\n nucleotideNodes[i].uid = uids[i];\n }\n\n return self;\n };\n\n self.computePairtable = function() {\n self.pairtable = rnaUtilities.dotbracketToPairtable(self.dotbracket);\n };\n\n self.removeBreaks = function(targetString) {\n // Remove all chain breaks (denoted with a '&', which indicate\n // that the input represents more than one strand)\n var breaks = [];\n var breakIndex = -1;\n\n while ((breakIndex = targetString.indexOf('&')) >= 0) {\n breaks.push(breakIndex);\n targetString = targetString.substring(0, breakIndex) + targetString.substring(breakIndex+1, targetString.length);\n\n }\n\n return {targetString: targetString, breaks: breaks};\n };\n\n var ret = self.removeBreaks(self.dotbracket);\n self.dotbracket = ret.targetString;\n self.dotBracketBreaks = ret.breaks;\n\n ret = self.removeBreaks(self.seq);\n self.seq = ret.targetString;\n self.seqBreaks = ret.breaks;\n\n self.rnaLength = self.dotbracket.length;\n\n if (!arraysEqual(self.dotBracketBreaks, self.seqBreaks)) {\n console.log('WARNING: Sequence and structure breaks not equal');\n console.log('WARNING: Using the breaks in the structure');\n }\n\n self.computePairtable();\n\n self.addPositions = function(nodeType, positions) {\n let labelNodes = self.nodes.filter(function(d) { return d.nodeType == nodeType; });\n\n for (let i = 0; i < labelNodes.length; i++) {\n labelNodes[i].x = positions[i][0];\n labelNodes[i].y = positions[i][1];\n }\n\n return self;\n };\n\n self.breakNodesToFakeNodes = function() {\n // convert all the nodes following breaks to fake nodes\n let labelNodes = self.nodes.filter(function(d) { return d.nodeType == 'nucleotide'; });\n\n // if a node was an artifical break node, convert it to a middle\n for (let i = 0; i < labelNodes.length; i++) {\n if (self.dotBracketBreaks.indexOf(i) >= 0) {\n labelNodes[i].nodeType = 'middle';\n labelNodes[i+1].nodeType = 'middle';\n }\n }\n\n for (let i = 0; i < self.elements.length; i++) {\n var broken = false;\n\n // change the elemType of the other nodes in the element containing\n // the break\n for (let j = 0; j < self.elements[i][2].length; j++) {\n if (self.dotBracketBreaks.indexOf(self.elements[i][2][j]) >= 0)\n broken = true;\n }\n\n if (broken) {\n self.elements[i][2].map(function(x) {\n if (x == 0)\n return;\n self.nodes[x-1].elemType = 'e';\n });\n } else {\n self.elements[i][2].map(function(x) {\n if (x == 0)\n return;\n self.nodes[x-1].elemType = self.elements[i][0];\n });\n }\n }\n return self;\n };\n\n self.getPositions = function(nodeType) {\n var positions = [];\n let nucleotideNodes = self.nodes.filter(function(d) { return d.nodeType == nodeType; });\n\n for (let i = 0; i < nucleotideNodes.length; i++)\n positions.push([nucleotideNodes[i].x, nucleotideNodes[i].y]);\n\n return positions;\n };\n\n self.getUids = function() {\n /* Get the positions of each node so that they\n * can be passed to elementsToJson later\n */\n var uids = [];\n for (let i = 0; i < self.dotbracket.length; i++)\n uids.push(self.nodes[i].uid);\n\n return uids;\n };\n\n self.reinforceStems = function() {\n var pt = self.pairtable;\n let relevantElements = self.elements.filter( function(d) {\n return d[0] == 's' && d[2].length >= 4;\n });\n\n for (let i = 0; i < relevantElements.length; i++) {\n let allNucs = relevantElements[i][2];\n let nucs = allNucs.slice(0, allNucs.length / 2);\n\n for (let j = 0; j < nucs.length-1; j++) {\n self.addFakeNode([nucs[j], nucs[j+1], pt[nucs[j+1]], pt[nucs[j]]]);\n }\n }\n\n return self;\n };\n\n self.reinforceLoops = function() {\n /*\n * Add a set of fake nodes to enforce the structure\n */\n var filterNucs = function(d) {\n return d !== 0 && d <= self.dotbracket.length;\n };\n\n for (let i = 0; i < self.elements.length; i++) {\n if (self.elements[i][0] == 's' || (!self.circularizeExternal && self.elements[i][0] == 'e'))\n continue;\n\n var nucs = self.elements[i][2].filter(filterNucs);\n\n if (self.elements[i][0] == 'e') {\n var newNode1 = {'name': '',\n 'num': -3,\n //'radius': 18 * radius -6,\n 'radius': 0,\n 'rna': self,\n 'nodeType': 'middle',\n 'elemType': 'f',\n 'nucs': [],\n 'x': self.nodes[self.rnaLength-1].x,\n 'y': self.nodes[self.rnaLength-1].y,\n 'px': self.nodes[self.rnaLength-1].px,\n 'py': self.nodes[self.rnaLength-1].py,\n 'uid': slugid.nice() };\n var newNode2 = {'name': '',\n 'num': -2,\n //'radius': 18 * radius -6,\n 'radius': 0,\n 'rna': self,\n 'nodeType': 'middle',\n 'elemType': 'f',\n 'nucs': [],\n 'x': self.nodes[0].x,\n 'y': self.nodes[0].y,\n 'px': self.nodes[0].px,\n 'py': self.nodes[0].py,\n 'uid': slugid.nice() };\n\n nucs.push(self.nodes.length+1);\n nucs.push(self.nodes.length+2);\n self.nodes.push(newNode1);\n self.nodes.push(newNode2);\n }\n\n\n self.addFakeNode(nucs);\n }\n\n return self;\n };\n\n self.updateLinkUids = function() {\n for (let i = 0; i < self.links.length; i++) {\n self.links[i].uid = self.links[i].source.uid + self.links[i].target.uid;\n }\n\n return self;\n };\n\n self.addFakeNode = function(nucs) {\n var linkLength = 18; //make sure this is consistent with the value in force.js\n var nodeWidth = 6;\n var angle = (3.1415 * 2) / (2 * nucs.length);\n var radius = linkLength / (2 * Math.tan(angle));\n\n var fakeNodeUid = '';\n\n for (let i = 0; i < nucs.length; i++)\n fakeNodeUid += self.nodes[nucs[i]-1].uid;\n\n var newNode = {'name': '',\n 'num': -1,\n //'radius': 18 * radius -6,\n 'radius': radius,\n 'rna': self,\n 'nodeType': 'middle',\n 'elemType': 'f',\n 'nucs': nucs,\n 'uid': fakeNodeUid };\n self.nodes.push(newNode);\n\n var newX = 0;\n var newY = 0;\n var coordsCounted = 0;\n\n angle = (nucs.length - 2) * 3.14159 / (2 * nucs.length);\n radius = 0.5 / Math.cos(angle);\n\n for (let j = 0; j < nucs.length; j++) {\n if (nucs[j] === 0 || nucs[j] > self.dotbracket.length)\n continue;\n\n //link to the center node\n self.links.push({'source': self.nodes[nucs[j] - 1],\n 'target': self.nodes[self.nodes.length-1],\n 'linkType': 'fake',\n 'value': radius,\n 'uid': slugid.nice() });\n\n if (nucs.length > 4) {\n //link across the loop\n self.links.push({'source': self.nodes[nucs[j] - 1],\n 'target': self.nodes[nucs[(j + Math.floor(nucs.length / 2)) % nucs.length] - 1],\n 'linkType': 'fake',\n 'value': radius * 2,\n 'uid': slugid.nice() });\n }\n\n var ia = ((nucs.length - 2) * 3.14159) / nucs.length;\n var c = 2 * Math.cos(3.14159 / 2 - ia / 2);\n //link to over-neighbor\n self.links.push({'source': self.nodes[nucs[j] - 1],\n 'target': self.nodes[nucs[(j + 2) % nucs.length] - 1],\n 'linkType': 'fake',\n 'value': c});\n\n // calculate the mean of the coordinats in this loop\n // and place the fake node there\n var fromNode = self.nodes[nucs[j]-1];\n if ('x' in fromNode) {\n newX += fromNode.x;\n newY += fromNode.y;\n\n coordsCounted += 1;\n }\n }\n\n if (coordsCounted > 0) {\n // the nucleotides had set positions so we can calculate the position\n // of the fake node\n newNode.x = newX / coordsCounted;\n newNode.y = newY / coordsCounted;\n newNode.px = newNode.x;\n newNode.py = newNode.y;\n }\n\n return self;\n };\n\n self.connectFakeNodes = function() {\n var linkLength = 18;\n\n // We want to be able to connect all of the fake nodes\n // and create a structure consisting of just them\n var filterOutNonFakeNodes = function(d) {\n return d.nodeType == 'middle';\n }\n\n var nucsToNodes = {};\n var fakeNodes = self.nodes.filter(filterOutNonFakeNodes);\n var linked = {};\n\n // initialize the nucleotides to nodes\n for (var i = 1; i <= self.nodes.length; i++)\n nucsToNodes[i] = [];\n\n for (var i = 0; i < fakeNodes.length; i++) {\n var thisNode = fakeNodes[i];\n\n // each fake node represents a certain set of nucleotides (thisNode.nucs)\n for (var j = 0; j < thisNode.nucs.length; j++) {\n var thisNuc = thisNode.nucs[j];\n\n // check to see if this nucleotide has been seen in another fake node\n // if it has, then we add a link between the two nodes\n for (var k = 0; k < nucsToNodes[thisNuc].length; k++) {\n if (JSON.stringify([nucsToNodes[thisNuc][k].uid, thisNode.uid].sort()) in linked)\n continue; //already linked\n\n var distance = nucsToNodes[thisNuc][k].radius + thisNode.radius;\n\n self.links.push({'source': nucsToNodes[thisNuc][k],\n 'target': thisNode,\n 'value': distance / linkLength,\n 'linkType': 'fake_fake'});\n\n // note that we've already seen this link\n linked[JSON.stringify([nucsToNodes[thisNuc][k].uid, thisNode.uid].sort())] = true;\n }\n\n nucsToNodes[thisNuc].push(thisNode);\n }\n }\n\n return self;\n\n };\n\n self.addExtraLinks = function(extraLinks) {\n if (typeof extraLinks == 'undefined')\n return self;\n\n for (var i = 0; i < extraLinks.length; i++) {\n var source = self.getNodeFromNucleotides(extraLinks[i].from);\n var target = self.getNodeFromNucleotides(extraLinks[i].to);\n\n var newLink = {'source': source, 'target': target, 'linkType': 'extra',\n 'extraLinkType': extraLinks[i].linkType, 'uid': slugid.nice() };\n\n self.links.push(newLink);\n }\n\n return self;\n }\n\n\n self.elementsToJson = function() {\n /* Convert a set of secondary structure elements to a json\n * representation of the graph that can be used with d3's\n * force-directed layout to generate a visualization of\n * the structure.\n */\n var pt = self.pairtable;\n var elements = self.elements;\n\n self.nodes = [];\n self.links = [];\n\n //create a reverse lookup so we can find out the type\n //of element that a node is part of\n var elemTypes = {};\n\n //sort so that we count stems last\n self.elements.sort();\n\n for (let i = 0; i < self.elements.length; i++) {\n var nucs = self.elements[i][2];\n for (let j = 0; j < nucs.length; j++) {\n elemTypes[nucs[j]] = self.elements[i][0];\n }\n }\n\n for (let i = 1; i <= pt[0]; i++) {\n var nodeName = self.seq[i-1];\n\n if (self.dotBracketBreaks.indexOf(i-1) >= 0 ||\n self.dotBracketBreaks.indexOf(i-2) >= 0) {\n nodeName = '';\n }\n\n //create a node for each nucleotide\n self.nodes.push({'name': nodeName,\n 'num': startNumber + i - 1,\n 'radius': 5,\n 'rna': self,\n 'nodeType': 'nucleotide',\n 'structName': self.structName,\n 'elemType': elemTypes[i],\n 'uid': slugid.nice(),\n 'linked': false});\n }\n\n for (let i = 0; i < self.nodes.length; i++) {\n if (i === 0)\n self.nodes[i].prevNode = null;\n else {\n self.nodes[i].prevNode = self.nodes[i-1];\n }\n\n if (i == self.nodes.length-1)\n self.nodes[i].nextNode = null;\n else {\n self.nodes[i].nextNode = self.nodes[i+1];\n }\n }\n\n for (let i = 1; i <= pt[0]; i++) {\n\n if (pt[i] !== 0) {\n // base-pair links\n self.links.push({'source': self.nodes[i-1],\n 'target': self.nodes[pt[i]-1],\n 'linkType': 'basepair',\n 'value': 1,\n 'uid': slugid.nice() });\n }\n\n if (i > 1) {\n // backbone links\n if (self.dotBracketBreaks.indexOf(i-1) === -1 &&\n self.dotBracketBreaks.indexOf(i-2) == -1 &&\n self.dotBracketBreaks.indexOf(i-3) == -1) {\n // there is no break in the strands here\n // we can add a backbone link\n self.links.push({'source': self.nodes[i-2],\n 'target': self.nodes[i-1],\n 'linkType': 'backbone',\n 'value': 1,\n 'uid': slugid.nice() });\n self.nodes[i-1].linked = true;\n }\n }\n }\n\n //add the pseudoknot links\n for (let i = 0; i < self.pseudoknotPairs.length; i++) {\n self.links.push({'source': self.nodes[self.pseudoknotPairs[i][0]-1],\n 'target': self.nodes[self.pseudoknotPairs[i][1]-1],\n 'linkType': 'pseudoknot',\n 'value': 1,\n 'uid': slugid.nice()});\n }\n\n if (self.circular) {\n self.links.push({'source': self.nodes[0],\n 'target': self.nodes[self.rnaLength-1],\n 'linkType': 'backbone',\n 'value': 1,\n 'uid': slugid.nice() });\n\n }\n\n return self;\n };\n\n self.ptToElements = function(pt, level, i, j) {\n /* Convert a pair table to a list of secondary structure\n * elements:\n *\n * [['s',1,[2,3]]\n *\n * The 's' indicates that an element can be a stem. It can also be\n * an interior loop ('i'), a hairpin loop ('h') or a multiloop ('m')\n *\n * The second number (1 in this case) indicates the depth or\n * how many base pairs have to be broken to get to this element.\n *\n * Finally, there is the list of nucleotides which are part of\n * of this element.\n */\n var elements = [];\n var u5 = [i-1];\n var u3 = [j+1];\n\n if (i > j)\n return [];\n\n //iterate over the unpaired regions on either side\n //this is either 5' and 3' unpaired if level == 0\n //or an interior loop or a multiloop\n for (; pt[i] === 0; i++) { u5.push(i); }\n for (; pt[j] === 0; j--) { u3.push(j); }\n\n if (i > j) {\n //hairpin loop or one large unpaired molecule\n u5.push(i);\n if (level === 0)\n return [['e',level, u5.sort(numberSort)]];\n else {\n // check to see if we have chain breaks due\n // to multiple strands in the input\n var external = false;\n var left = [];\n var right = [];\n for (var k = 0; k < u5.length; k++) {\n if (external)\n right.push(u5[k]);\n else\n left.push(u5[k]);\n\n if (self.dotBracketBreaks.indexOf(u5[k]) >= 0)\n external = true;\n }\n\n if (external) {\n return [['h',level, u5.sort(numberSort)]];\n }\n else\n // if not, this is a simple hairpin loop\n return [['h',level, u5.sort(numberSort)]];\n }\n }\n\n if (pt[i] != j) {\n //multiloop\n var m = u5;\n var k = i;\n\n // the nucleotide before and the starting nucleotide\n m.push(k);\n while (k <= j) {\n // recurse into a stem\n elements = elements.concat(self.ptToElements(pt, level, k, pt[k]));\n\n // add the nucleotides between stems\n m.push(pt[k]);\n k = pt[k] + 1;\n for (; pt[k] === 0 && k <= j; k++) { m.push(k);}\n m.push(k);\n }\n m.pop();\n m = m.concat(u3);\n\n if (m.length > 0) {\n if (level === 0)\n elements.push(['e', level, m.sort(numberSort)]);\n else\n elements.push(['m', level, m.sort(numberSort)]);\n }\n\n return elements;\n }\n\n if (pt[i] === j) {\n //interior loop\n u5.push(i);\n u3.push(j);\n\n var combined = u5.concat(u3);\n if (combined.length > 4) {\n if (level === 0)\n elements.push(['e',level, u5.concat(u3).sort(numberSort)]);\n else\n elements.push(['i',level, u5.concat(u3).sort(numberSort)]);\n }\n }\n\n var s = [];\n //go through the stem\n while (pt[i] === j && i < j) {\n //one stem\n s.push(i);\n s.push(j);\n\n i += 1;\n j -= 1;\n\n level += 1;\n }\n\n u5 = [i-1];\n u3 = [j+1];\n elements.push(['s', level, s.sort(numberSort)]);\n\n return elements.concat(self.ptToElements(pt, level, i, j));\n };\n\n self.addLabels = function(startNumber = 1, labelInterval = 10) {\n if (labelInterval === 0)\n return self;\n\n for (let i = 1; i <= self.rnaLength; i++) {\n // add labels\n if (i % labelInterval === 0) {\n //create a node for each label\n let newX, newY;\n\n let thisNode = self.nodes[i-1];\n let prevNode, nextNode;\n let prevVec, nextVec;\n\n if (self.rnaLength == 1) {\n nextVec = [thisNode.x - 15, thisNode.y];\n prevVec = [thisNode.x - 15, thisNode.y];\n } else {\n // if we're labelling the first node, then label it in relation to the last\n if (i == 1)\n prevNode = self.nodes[self.rnaLength - 1];\n else\n prevNode = self.nodes[i - 2];\n\n // if we're labelling the last node, then label it in relation to the first\n if (i == self.rnaLength)\n nextNode = self.nodes[0];\n else\n nextNode = self.nodes[i];\n\n // this nucleotide and its neighbors are paired\n if (self.pairtable[nextNode.num - startNumber+1] !== 0 &&\n self.pairtable[prevNode.num - startNumber+1] !== 0 &&\n self.pairtable[thisNode.num - startNumber+1] !== 0) {\n\n prevNode = nextNode = self.nodes[self.pairtable[thisNode.num - startNumber+1]-1];\n }\n\n // this node is paired but at least one of its neighbors is unpaired\n // place the label in the direction of the two neighbors\n if (self.pairtable[thisNode.num - startNumber+1] !== 0 && (\n self.pairtable[nextNode.num - startNumber+1] === 0 ||\n self.pairtable[prevNode.num - startNumber+1] === 0)) {\n nextVec = [thisNode.x - nextNode.x, thisNode.y - nextNode.y];\n prevVec = [thisNode.x - prevNode.x, thisNode.y - prevNode.y];\n\n } else {\n nextVec = [nextNode.x - thisNode.x, nextNode.y - thisNode.y];\n prevVec = [prevNode.x - thisNode.x, prevNode.y - thisNode.y];\n }\n }\n\n var combinedVec = [nextVec[0] + prevVec[0], nextVec[1] + prevVec[1]];\n var vecLength = Math.sqrt(combinedVec[0] * combinedVec[0] + combinedVec[1] * combinedVec[1]);\n var normedVec = [combinedVec[0] / vecLength, combinedVec[1] / vecLength];\n var offsetVec = [-15 * normedVec[0], -15 * normedVec[1]];\n\n newX = self.nodes[i-1].x + offsetVec[0];\n newY = self.nodes[i-1].y + offsetVec[1];\n\n var newNode = {'name': i + startNumber -1,\n 'num': -1,\n 'radius': 6,\n 'rna': self,\n 'nodeType': 'label',\n 'structName': self.structName,\n 'elemType': 'l',\n 'x': newX,\n 'y': newY,\n 'px': newX,\n 'py': newY,\n 'uid': slugid.nice() };\n var newLink = {'source': self.nodes[i-1],\n 'target': newNode,\n 'value': 1,\n 'linkType': 'label_link',\n 'uid': slugid.nice() };\n\n self.nodes.push(newNode);\n self.links.push(newLink);\n }\n }\n\n return self;\n };\n\n self.recalculateElements = function() {\n self.removePseudoknots();\n self.elements = self.ptToElements(self.pairtable, 0, 1, self.dotbracket.length);\n\n if (self.circular) {\n //check to see if the external loop is a hairpin or a multiloop\n let externalLoop = self.elements.filter(function(d) { if (d[0] == 'e') return true; });\n\n if (externalLoop.length > 0) {\n eloop = externalLoop[0];\n nucs = eloop[2].sort(numberSort);\n\n prev = nucs[0];\n hloop = true;\n numGreater = 0;\n for (let i = 1; i < nucs.length; i++) {\n if (nucs[i] - prev > 1) {\n numGreater += 1;\n }\n prev = nucs[i];\n }\n\n if (numGreater == 1) {\n eloop[0] = 'h';\n } else if (numGreater == 2) {\n eloop[0] = 'i';\n } else {\n eloop[0] = 'm';\n }\n }\n }\n\n return self;\n };\n\n self.reassignLinkUids = function() {\n // reassign uids to the links, corresponding to the uids of the two nodes\n // they connect\n var i;\n\n for (var i = 0; i < self.links.length; i++) {\n self.links[i].uid = self.links[i].source.uid + self.links[i].target.uid;\n }\n\n return self;\n }\n\n self.removePseudoknots = function() {\n if (self.pairtable.length > 1)\n self.pseudoknotPairs = self.pseudoknotPairs.concat(rnaUtilities.removePseudoknotsFromPairtable(self.pairtable));\n\n return self;\n };\n\n self.addPseudoknots = function() {\n /* Add all of the pseudoknot pairs which are stored outside\n * of the pairtable back to the pairtable\n */\n var pt = self.pairtable;\n var pseudoknotPairs = self.pseudoknotPairs;\n\n for (var i = 0; i < pseudoknotPairs.length; i++) {\n pt[pseudoknotPairs[i][0]] = pseudoknotPairs[i][1];\n pt[pseudoknotPairs[i][1]] = pseudoknotPairs[i][0];\n }\n\n self.pseudoknotPairs = [];\n return self;\n };\n\n self.addName = function(name) {\n if (typeof name == 'undefined') {\n self.name = '';\n return self;\n } else {\n self.name = name;\n return self;\n }\n };\n\n\n if (self.rnaLength > 0)\n self.recalculateElements();\n\n self.getNodeFromNucleotides = function(nucs) {\n /* Get a node given a nucleotide number or an array of nucleotide\n * numbers indicating an element node */\n if (Object.prototype.toString.call(nucs) === '[object Array]') {\n for (let j = 0; j < self.nodes.length; j++) {\n if ('nucs' in self.nodes[j]) {\n if (self.nodes[j].nucs.equals(nucs)) {\n return self.nodes[j];\n }\n }\n }\n } else {\n for (let j = 0; j < self.nodes.length; j++) {\n if (self.nodes[j].num == nucs) {\n return self.nodes[j];\n }\n }\n }\n\n console.log('ERROR: No node found for nucs:', nucs);\n return null;\n }\n}\n\nexport function moleculesToJson(moleculesJson) {\n /* Convert a list of RNA and protein molecules to a list of RNAGraph\n * ProteinGraph and extraLinks structure */\n\n var nodes = {}; //index the nodes by uid\n var graphs = [];\n var extraLinks = [];\n\n\n // Create the graphs for each molecule\n for (var i = 0; i < moleculesJson.molecules.length; i++) {\n var molecule = moleculesJson.molecules[i];\n var rg;\n\n if (molecule.type == 'rna') {\n rg = new RNAGraph(molecule.seq, molecule.ss, molecule.header);\n rg.circularizeExternal = true;\n rg.elementsToJson()\n .addPositions('nucleotide', molecule.positions)\n .addLabels()\n .reinforceStems()\n .reinforceLoops();\n\n\n } else if (molecule.type == 'protein') {\n rg = new ProteinGraph(molecule.header, molecule.size);\n\n }\n\n rg.addUids(molecule.uids);\n\n for (var j = 0; j < rg.nodes.length; j++) {\n nodes[rg.nodes[j].uid] = rg.nodes[j];\n }\n\n graphs.push(rg);\n }\n\n //Add the extra links\n for (var i = 0; i < moleculesJson.extraLinks.length; i++) {\n link = moleculesJson.extraLinks[i];\n\n link.source = nodes[link.source];\n link.target = nodes[link.target];\n link.uid = slugid.nice();\n\n extraLinks.push(link);\n }\n\n return {'graphs': graphs, 'extraLinks': extraLinks};\n};\n","export function simpleXyCoordinates (pair_table) {\n var INIT_ANGLE=0.; /* initial bending angle */\n var INIT_X = 100.; /* coordinate of first digit */\n var INIT_Y = 100.; /* see above */\n var RADIUS = 15.;\n\n var x = [], y = [];\n\n var i, len;\n var alpha;\n\n len = pair_table[0];\n var angle = Array.apply(null, new Array(len+5)).map(Number.prototype.valueOf,0); \n var loop_size = Array.apply(null, new Array(16+Math.floor(len/5)))\n .map(Number.prototype.valueOf, 0); \n var stack_size = Array.apply(null, new Array(16+Math.floor(len/5)))\n .map(Number.prototype.valueOf, 0); \n\n var lp = 0;\n var stk = 0;\n var PIHALF = Math.PI / 2;\n\n\n var loop = function(i, j, pair_table)\n /* i, j are the positions AFTER the last pair of a stack; i.e\n i-1 and j+1 are paired. */\n {\n var count = 2; /* counts the VERTICES of a loop polygon; that's\n NOT necessarily the number of unpaired bases!\n Upon entry the loop has already 2 vertices, namely\n the pair i-1/j+1. */\n\n var r = 0, bubble = 0; /* bubble counts the unpaired digits in loops */\n\n var i_old, partner, k, l, start_k, start_l, fill, ladder;\n var begin, v, diff;\n var polygon;\n\n var remember = Array.apply(null, new Array((3+Math.floor((j-i)/5)*2))).map(Number.prototype.valueOf, 0);\n\n i_old = i-1, j++; /* j has now been set to the partner of the\n previous pair for correct while-loop\n termination. */\n while (i != j) {\n partner = pair_table[i];\n if ((!partner) || (i==0))\n i++, count++, bubble++;\n else {\n count += 2;\n k = i, l = partner; /* beginning of stack */\n remember[++r] = k;\n remember[++r] = l;\n i = partner+1; /* next i for the current loop */\n\n start_k = k, start_l = l;\n ladder = 0;\n do {\n k++, l--, ladder++; /* go along the stack region */\n }\n while ((pair_table[k] == l) && (pair_table[k] > k));\n\n fill = ladder-2;\n if (ladder >= 2) {\n angle[start_k+1+fill] += PIHALF; /* Loop entries and */\n angle[start_l-1-fill] += PIHALF; /* exits get an */\n angle[start_k] += PIHALF; /* additional PI/2. */\n angle[start_l] += PIHALF; /* Why ? (exercise) */\n if (ladder > 2) {\n for (; fill >= 1; fill--) {\n angle[start_k+fill] = Math.PI; /* fill in the angles */\n angle[start_l-fill] = Math.PI; /* for the backbone */\n }\n }\n }\n stack_size[++stk] = ladder;\n if (k <= l)\n loop(k, l, pair_table);\n }\n }\n\n polygon = Math.PI*(count-2)/count; /* bending angle in loop polygon */\n remember[++r] = j;\n begin = i_old < 0 ? 0 : i_old;\n for (v = 1; v <= r; v++) {\n diff = remember[v]-begin;\n for (fill = 0; fill <= diff; fill++)\n angle[begin+fill] += polygon;\n if (v > r)\n break;\n begin = remember[++v];\n }\n loop_size[++lp] = bubble;\n }\n\n loop(0, len+1, pair_table);\n loop_size[lp] -= 2; /* correct for cheating with function loop */\n\n alpha = INIT_ANGLE;\n x[0] = INIT_X;\n y[0] = INIT_Y;\n\n var poss = [];\n\n poss.push([x[0], y[0]]);\n for (i = 1; i < len; i++) {\n x[i] = x[i-1]+RADIUS*Math.cos(alpha);\n y[i] = y[i-1]+RADIUS*Math.sin(alpha);\n\n poss.push([x[i], y[i]]);\n alpha += Math.PI-angle[i+1];\n }\n\n return poss;\n}\n","export function Radloop() {\n\tthis.radius = null;\n\tthis.loopnumber = null;\n\tthis.next = null;\n this.prev = null;\n}\n\nRadloop.prototype.getRadius = function(){\n\treturn this.radius;\n}\n\nRadloop.prototype.setRadius = function(radius){\n\tthis.radius = radius;\n}\n\nRadloop.prototype.getLoopnumber = function(){\n\treturn this.loopnumber;\n}\n\nRadloop.prototype.setLoopnumber = function(loopnumber){\n\tthis.loopnumber = loopnumber;\n}\n\nRadloop.prototype.getNext = function(){\n\treturn this.next;\n}\n\nRadloop.prototype.setNext = function(next){\n\tthis.next = next;\n}\n\nRadloop.prototype.getPrev = function(){\n\treturn this.prev;\n}\n\nRadloop.prototype.setPrev = function(prev){\n\tthis.prev = prev;\n}\n","import {Region} from './region.js';\n\nexport function Base() {\n\tthis.mate = null;\n\tthis.x = null;\n this.y = null;\n\tthis.extracted = null;\n\tthis.region = new Region();\n}\n\nBase.prototype.getMate = function(){\n\treturn this.mate;\n}\n\nBase.prototype.setMate = function(mate){\n\tthis.mate = mate;\n}\n\nBase.prototype.getX = function(){\n\treturn this.x;\n}\n\nBase.prototype.setX = function(x){\n\tthis.x = x;\n}\n\nBase.prototype.getY = function(){\n\treturn this.y;\n}\n\nBase.prototype.setY = function(y){\n\tthis.y = y;\n}\n\nBase.prototype.isExtracted = function(){\n\treturn this.extracted;\n}\n\nBase.prototype.setExtracted = function(extracted){\n\tthis.extracted = extracted;\n}\n\nBase.prototype.getRegion = function(){\n\treturn this.region;\n}\n\nBase.prototype.setRegion = function(region){\n\tthis.region = region;\n}\n","import {Radloop} from './radloop.js';\nimport {Connection} from './connection.js';\nimport {Region} from './region.js';\nimport {Base} from './base.js';\nimport {Loop} from './loop.js';\n\nexport function NAView(){\n this.ANUM = 9999.0;\n\tthis.MAXITER = 500;\n\n\tthis.bases = [];\n\tthis.nbase = null;\n this.nregion = null;\n this.loop_count = null;\n\n\tthis.root = new Loop();\n\tthis.loops = [];\n\n\tthis.regions = [];\n\n\tthis.rlphead = new Radloop();\n\n\tthis.lencut = 0.8;\n\tthis.RADIUS_REDUCTION_FACTOR = 1.4;\n\n\t// show algorithm step by step\n\tthis.angleinc = null;\n\n\tthis._h = null;\n\n\t// private boolean noIterationFailureYet = true;\n\n\tthis.HELIX_FACTOR = 0.6;\n\tthis.BACKBONE_DISTANCE = 27;\n}\n\nNAView.prototype.naview_xy_coordinates = function(pair_table){\n var x = [];\n\tvar y = [];\n if (pair_table.length === 0 || pair_table[0] === 0){\n return 0;\n }\n var i;\n this.nbase = pair_table[0];\n this.bases = [];\n for (var index = 0; index < this.nbase + 1; index++){\n this.bases.push(new Base());\n }\n this.regions = [];\n for (var index = 0; index < this.nbase + 1; index++){\n this.regions.push(new Region());\n }\n this.read_in_bases(pair_table);\n this.rlphead = null;\n this.find_regions();\n this.loop_count = 0;\n this.loops = [];\n for (var index = 0; index < this.nbase + 1; index++){\n this.loops.push(new Loop());\n }\n this.construct_loop(0);\n this.find_central_loop();\n this.traverse_loop(this.root, null);\n\n for (i = 0; i < this.nbase; i++){\n x.push(100 + this.BACKBONE_DISTANCE * this.bases[i + 1].getX());\n y.push(100 + this.BACKBONE_DISTANCE * this.bases[i + 1].getY());\n }\n\n return {\n nbase: this.nbase,\n x: x,\n y: y\n }\n}\n\nNAView.prototype.read_in_bases = function read_in_bases(pair_table){\n var i = null;\n var npairs = null;\n\n // Set up an origin.\n this.bases.push(new Base());\n this.bases[0].setMate(0);\n this.bases[0].setExtracted(false);\n this.bases[0].setX(this.ANUM);\n this.bases[0].setY(this.ANUM);\n\n for (npairs = 0, i = 1; i <= this.nbase; i++){\n this.bases.push(new Base());\n this.bases[i].setExtracted(false);\n this.bases[i].setX(this.ANUM);\n this.bases[i].setY(this.ANUM);\n this.bases[i].setMate(pair_table[i]);\n if (pair_table[i] > i)\n npairs++;\n }\n // must have at least 1 pair to avoid segfault\n if (npairs == 0){\n this.bases[1].setMate(this.nbase);\n this.bases[this.nbase].setMate(1);\n }\n}\n\nNAView.prototype.find_regions = function find_regions(){\n var i = null;\n var mate = null;\n var nb1 = null;\n\n nb1 = this.nbase + 1;\n var mark = [];\n for (i = 0; i < nb1; i++){\n mark.push(false);\n }\n this.nregion = 0;\n for (i = 0; i <= this.nbase; i++) {\n if ((mate = this.bases[i].getMate()) != 0 && !mark[i]) {\n this.regions[this.nregion].setStart1(i);\n this.regions[this.nregion].setEnd2(mate);\n mark[i] = true;\n mark[mate] = true;\n this.bases[i].setRegion(this.regions[this.nregion]);\n this.bases[mate].setRegion(this.regions[this.nregion]);\n for (i++, mate--; i < mate && this.bases[i].getMate() == mate; i++, mate--) {\n mark[mate] = true;\n mark[i]= true;\n this.bases[i].setRegion(this.regions[this.nregion]);\n this.bases[mate].setRegion(this.regions[this.nregion]);\n }\n this.regions[this.nregion].setEnd1(--i);\n this.regions[this.nregion].setStart2(mate + 1);\n\n this.nregion++;\n }\n }\n}\n\nNAView.prototype.construct_loop = function construct_loop(ibase){\n var i = null;\n var mate = null;\n var retloop = new Loop();\n var lp = new Loop();\n var cp = new Connection();\n var rp = new Region();\n var rlp = new Radloop();\n retloop = this.loops[this.loop_count++];\n retloop.setNconnection(0);\n retloop.setDepth(0);\n retloop.setNumber(this.loop_count);\n retloop.setRadius(0.0);\n\n for (rlp = this.rlphead; rlp != null; rlp = rlp.getNext())\n if (rlp.getLoopnumber() == this.loop_count)\n retloop.setRadius(rlp.getRadius());\n i = ibase;\n do {\n if ((mate = this.bases[i].getMate()) != 0) {\n rp = this.bases[i].getRegion();\n if (!this.bases[rp.getStart1()].isExtracted()) {\n if (i == rp.getStart1()) {\n this.bases[rp.getStart1()].setExtracted(true);\n this.bases[rp.getEnd1()].setExtracted(true);\n this.bases[rp.getStart2()].setExtracted(true);\n this.bases[rp.getEnd2()].setExtracted(true);\n lp = this.construct_loop(rp.getEnd1() < this.nbase ? rp.getEnd1() + 1\n : 0);\n } else if (i == rp.getStart2()) {\n this.bases[rp.getStart2()].setExtracted(true);\n this.bases[rp.getEnd2()].setExtracted(true);\n this.bases[rp.getStart1()].setExtracted(true);\n this.bases[rp.getEnd1()].setExtracted(true);\n lp = this.construct_loop(rp.getEnd2() < this.nbase ? rp.getEnd2() + 1\n : 0);\n } else {\n console.log(\"Something went terribly wrong ....\");\n }\n retloop.setNconnection(retloop.getNconnection() + 1);\n cp = new Connection();\n retloop.setConnection(retloop.getNconnection() - 1,\tcp);\n retloop.setConnection(retloop.getNconnection(), null);\n cp.setLoop(lp);\n cp.setRegion(rp);\n if(i == rp.getStart1()) {\n cp.setStart(rp.getStart1());\n cp.setEnd(rp.getEnd2());\n } else {\n cp.setStart(rp.getStart2());\n cp.setEnd(rp.getEnd1());\n }\n cp.setExtruded(false);\n cp.setBroken(false);\n lp.setNconnection(lp.getNconnection() + 1);\n cp = new Connection();\n lp.setConnection(lp.getNconnection() - 1, cp);\n lp.setConnection(lp.getNconnection(), null);\n cp.setLoop(retloop);\n cp.setRegion(rp);\n if (i == rp.getStart1()) {\n cp.setStart(rp.getStart2());\n cp.setEnd(rp.getEnd1());\n } else {\n cp.setStart(rp.getStart1());\n cp.setEnd(rp.getEnd2());\n }\n cp.setExtruded(false);\n cp.setBroken(false);\n }\n i = mate;\n }\n if (++i > this.nbase)\n i = 0;\n } while (i != ibase);\n return retloop;\n}\n\nNAView.prototype.find_central_loop = function find_central_loop(){\n var lp = new Loop();\n var maxconn = null;\n var maxdepth = null;\n var i = null;\n\n determine_depths.bind(this)();\n maxconn = 0;\n maxdepth = -1;\n for (i = 0; i < this.loop_count; i++) {\n lp = this.loops[i];\n if (lp.getNconnection() > maxconn) {\n maxdepth = lp.getDepth();\n maxconn = lp.getNconnection();\n this.root = lp;\n } else if (lp.getDepth() > maxdepth\n && lp.getNconnection() == maxconn) {\n maxdepth = lp.getDepth();\n this.root = lp;\n }\n }\n}\n\nfunction determine_depths() {\n var lp = new Loop();\n var i = null;\n var j = null;\n\n for (i = 0; i < this.loop_count; i++) {\n lp = this.loops[i];\n for (j = 0; j < this.loop_count; j++){\n this.loops[j].setMark(false);\n }\n lp.setDepth(depth(lp));\n }\n}\n\nfunction depth(lp){\n var count = null;\n var ret = null;\n var d = null;\n\n if (lp.getNconnection() <= 1){\n return 0;\n }\n if (lp.isMark()){\n return -1;\n }\n lp.setMark(true);\n count = 0;\n ret = 0;\n for (var i = 0; lp.getConnection(i) != null; i++) {\n d = depth(lp.getConnection(i).getLoop());\n if (d >= 0) {\n if (++count == 1){\n ret = d;\n }\n else if (ret > d){\n ret = d;\n }\n }\n }\n lp.setMark(false);\n return ret + 1;\n}\n\nNAView.prototype.traverse_loop = function traverse_loop(lp, anchor_connection){\n var xs, ys, xe, ye, xn, yn, angleinc, r;\n var radius, xc, yc, xo, yo, astart, aend, a;\n var cp, cpnext, acp, cpprev;\n var i, j, n, ic;\n var da, maxang;\n var count, icstart, icend, icmiddle, icroot;\n var done, done_all_connections, rooted;\n var sign;\n var midx, midy, nrx, nry, mx, my, vx, vy, dotmv, nmidx, nmidy;\n var icstart1, icup, icdown, icnext, direction;\n var dan, dx, dy, rr;\n var cpx, cpy, cpnextx, cpnexty, cnx, cny, rcn, rc, lnx, lny, rl, ac, acn, sx, sy, dcp;\n var imaxloop = 0;\n\n angleinc = 2 * Math.PI / (this.nbase + 1);\n acp = null;\n icroot = -1;\n var indice = 0;\n\n for (ic = 0; (cp = lp.getConnection(indice)) != null; indice++, ic++) {\n xs = -Math.sin(angleinc * cp.getStart());\n ys = Math.cos(angleinc * cp.getStart());\n xe = -Math.sin(angleinc * cp.getEnd());\n ye = Math.cos(angleinc * cp.getEnd());\n xn = ye - ys;\n yn = xs - xe;\n r = Math.sqrt(xn * xn + yn * yn);\n cp.setXrad(xn / r);\n cp.setYrad(yn / r);\n cp.setAngle(Math.atan2(yn, xn));\n if (cp.getAngle() < 0.0){\n cp.setAngle(cp.getAngle() + 2 * Math.PI);\n }\n if (anchor_connection != null\n && anchor_connection.getRegion() == cp.getRegion()) {\n acp = cp;\n icroot = ic;\n }\n }\n set_radius: while (true) {\n this.determine_radius(lp, this.lencut);\n radius = lp.getRadius()/this.RADIUS_REDUCTION_FACTOR;\n if (anchor_connection == null){\n xc = yc = 0.0;\n }\n else {\n xo = (this.bases[acp.getStart()].getX() + this.bases\n [acp.getEnd()].getX()) / 2.0;\n yo = (this.bases[acp.getStart()].getY() + this.bases\n [acp.getEnd()].getY()) / 2.0;\n xc = xo - radius * acp.getXrad();\n yc = yo - radius * acp.getYrad();\n }\n\n // The construction of the connectors will proceed in blocks of\n // connected connectors, where a connected connector pairs means two\n // connectors that are forced out of the drawn circle because they\n // are too close together in angle.\n\n // First, find the start of a block of connected connectors\n\n if (icroot == -1){\n icstart = 0;\n }\n else {\n icstart = icroot;\n }\n cp = lp.getConnection(icstart);\n count = 0;\n done = false;\n do {\n j = icstart - 1;\n if (j < 0){\n j = lp.getNconnection() - 1;\n }\n cpprev = lp.getConnection(j);\n if (!this.connected_connection(cpprev, cp)) {\n done = true;\n }\n else {\n icstart = j;\n cp = cpprev;\n }\n if (++count > lp.getNconnection()) {\n // Here everything is connected. Break on maximum angular\n // separation between connections.\n maxang = -1.0;\n for (ic = 0; ic < lp.getNconnection(); ic++) {\n j = ic + 1;\n if (j >= lp.getNconnection()){\n j = 0;\n }\n cp = lp.getConnection(ic);\n cpnext = lp.getConnection(j);\n ac = cpnext.getAngle() - cp.getAngle();\n if (ac < 0.0){\n ac += 2 * Math.PI;\n }\n if (ac > maxang) {\n maxang = ac;\n imaxloop = ic;\n }\n }\n icend = imaxloop;\n icstart = imaxloop + 1;\n if (icstart >= lp.getNconnection()){\n icstart = 0;\n }\n cp = lp.getConnection(icend);\n cp.setBroken(true);\n done = true;\n }\n } while (!done);\n done_all_connections = false;\n icstart1 = icstart;\n while (!done_all_connections) {\n count = 0;\n done = false;\n icend = icstart;\n rooted = false;\n while (!done) {\n cp = lp.getConnection(icend);\n if (icend == icroot){\n rooted = true;\n }\n j = icend + 1;\n if (j >= lp.getNconnection()) {\n j = 0;\n }\n cpnext = lp.getConnection(j);\n if (this.connected_connection(cp, cpnext)) {\n if (++count >= lp.getNconnection()){\n break;\n }\n icend = j;\n }\n else {\n done = true;\n }\n }\n icmiddle = this.find_ic_middle(icstart, icend, anchor_connection,\n acp, lp);\n ic = icup = icdown = icmiddle;\n done = false;\n direction = 0;\n while (!done) {\n if (direction < 0) {\n ic = icup;\n }\n else if (direction == 0) {\n ic = icmiddle;\n }\n else {\n ic = icdown;\n }\n if (ic >= 0) {\n cp = lp.getConnection(ic);\n if (anchor_connection == null || acp != cp) {\n if (direction == 0) {\n astart = cp.getAngle()\n - Math.asin(1.0 / 2.0 / radius);\n aend = cp.getAngle()\n + Math.asin(1.0 / 2.0 / radius);\n this.bases[cp.getStart()].setX(\n xc + radius * Math.cos(astart));\n this.bases[cp.getStart()].setY(\n yc + radius * Math.sin(astart));\n this.bases[cp.getEnd()].setX(\n xc + radius * Math.cos(aend));\n this.bases[cp.getEnd()].setY(\n yc + radius * Math.sin(aend));\n }\n else if (direction < 0) {\n j = ic + 1;\n if (j >= lp.getNconnection()){\n j = 0;\n }\n cp = lp.getConnection(ic);\n cpnext = lp.getConnection(j);\n cpx = cp.getXrad();\n cpy = cp.getYrad();\n ac = (cp.getAngle() + cpnext.getAngle()) / 2.0;\n if (cp.getAngle() > cpnext.getAngle()){\n ac -= Math.PI;\n }\n cnx = Math.cos(ac);\n cny = Math.sin(ac);\n lnx = cny;\n lny = -cnx;\n da = cpnext.getAngle() - cp.getAngle();\n if (da < 0.0){\n da += 2 * Math.PI;\n }\n if (cp.isExtruded()) {\n if (da <= Math.PI / 2){\n rl = 2.0;\n }\n else {\n rl = 1.5;\n }\n }\n else {\n rl = 1.0;\n }\n this.bases[cp.getEnd()].setX(\n this.bases[cpnext.getStart()].getX()\n + rl * lnx);\n this.bases[cp.getEnd()].setY(\n this.bases[cpnext.getStart()].getY()\n + rl * lny);\n this.bases[cp.getStart()].setX(\n this.bases[cp.getEnd()].getX() + cpy);\n this.bases[cp.getStart()].setY(\n this.bases[cp.getEnd()].getY() - cpx);\n } else {\n j = ic - 1;\n if (j < 0){\n j = lp.getNconnection() - 1;\n }\n cp = lp.getConnection(j);\n cpnext = lp.getConnection(ic);\n cpnextx = cpnext.getXrad();\n cpnexty = cpnext.getYrad();\n ac = (cp.getAngle() + cpnext.getAngle()) / 2.0;\n if (cp.getAngle() > cpnext.getAngle()){\n ac -= Math.PI;\n }\n cnx = Math.cos(ac);\n cny = Math.sin(ac);\n lnx = -cny;\n lny = cnx;\n da = cpnext.getAngle() - cp.getAngle();\n if (da < 0.0){\n da += 2 * Math.PI;\n }\n if (cp.isExtruded()) {\n if (da <= Math.PI / 2){\n rl = 2.0;\n }\n else {\n rl = 1.5;\n }\n }\n else {\n rl = 1.0;\n }\n this.bases[cpnext.getStart()].setX(\n this.bases[cp.getEnd()].getX() + rl\n * lnx);\n this.bases[cpnext.getStart()].setY(\n this.bases[cp.getEnd()].getY() + rl\n * lny);\n this.bases[cpnext.getEnd()].setX(\n this.bases[cpnext.getStart()].getX()\n - cpnexty);\n this.bases[cpnext.getEnd()].setY(\n this.bases[cpnext.getStart()].getY()\n + cpnextx);\n }\n }\n }\n if (direction < 0) {\n if (icdown == icend) {\n icdown = -1;\n }\n else if (icdown >= 0) {\n if (++icdown >= lp.getNconnection()) {\n icdown = 0;\n }\n }\n direction = 1;\n }\n else {\n if (icup == icstart){\n icup = -1;\n }\n else if (icup >= 0) {\n if (--icup < 0) {\n icup = lp.getNconnection() - 1;\n }\n }\n direction = -1;\n }\n done = icup == -1 && icdown == -1;\n }\n icnext = icend + 1;\n if (icnext >= lp.getNconnection()){\n icnext = 0;\n }\n if (icend != icstart\n && (!(icstart == icstart1 && icnext == icstart1))) {\n\n // Move the bases just constructed (or the radius) so that\n // the bisector of the end points is radius distance away\n // from the loop center.\n\n cp = lp.getConnection(icstart);\n cpnext = lp.getConnection(icend);\n dx = this.bases[cpnext.getEnd()].getX()\n - this.bases[cp.getStart()].getX();\n dy = this.bases[cpnext.getEnd()].getY()\n - this.bases[cp.getStart()].getY();\n midx = this.bases[cp.getStart()].getX() + dx / 2.0;\n midy = this.bases[cp.getStart()].getY() + dy / 2.0;\n rr = Math.sqrt(dx * dx + dy * dy);\n mx = dx / rr;\n my = dy / rr;\n vx = xc - midx;\n vy = yc - midy;\n rr = Math.sqrt(dx * dx + dy * dy);\n vx /= rr;\n vy /= rr;\n dotmv = vx * mx + vy * my;\n nrx = dotmv * mx - vx;\n nry = dotmv * my - vy;\n rr = Math.sqrt(nrx * nrx + nry * nry);\n nrx /= rr;\n nry /= rr;\n\n // Determine which side of the bisector the center should\n // be.\n\n dx = this.bases[cp.getStart()].getX() - xc;\n dy = this.bases[cp.getStart()].getY() - yc;\n ac = Math.atan2(dy, dx);\n if (ac < 0.0){\n ac += 2 * Math.PI;\n }\n dx = this.bases[cpnext.getEnd()].getX() - xc;\n dy = this.bases[cpnext.getEnd()].getY() - yc;\n acn = Math.atan2(dy, dx);\n if (acn < 0.0){\n acn += 2 * Math.PI;\n }\n if (acn < ac){\n acn += 2 * Math.PI;\n }\n if (acn - ac > Math.PI){\n sign = -1;\n }\n else {\n sign = 1;\n }\n nmidx = xc + sign * radius * nrx;\n nmidy = yc + sign * radius * nry;\n if (rooted) {\n xc -= nmidx - midx;\n yc -= nmidy - midy;\n }\n else {\n for (ic = icstart;;) {\n cp = lp.getConnection(ic);\n i = cp.getStart();\n this.bases[i].setX(\n this.bases[i].getX() + nmidx - midx);\n this.bases[i].setY(\n this.bases[i].getY() + nmidy - midy);\n i = cp.getEnd();\n this.bases[i].setX(\n this.bases[i].getX() + nmidx - midx);\n this.bases[i].setY(\n this.bases[i].getY() + nmidy - midy);\n if (ic == icend){\n break;\n }\n if (++ic >= lp.getNconnection()){\n ic = 0;\n }\n }\n }\n }\n icstart = icnext;\n done_all_connections = icstart == icstart1;\n }\n for (ic = 0; ic < lp.getNconnection(); ic++) {\n cp = lp.getConnection(ic);\n j = ic + 1;\n if (j >= lp.getNconnection()){\n j = 0;\n }\n cpnext = lp.getConnection(j);\n dx = this.bases[cp.getEnd()].getX() - xc;\n dy = this.bases[cp.getEnd()].getY() - yc;\n rc = Math.sqrt(dx * dx + dy * dy);\n ac = Math.atan2(dy, dx);\n if (ac < 0.0){\n ac += 2 * Math.PI;\n }\n dx = this.bases[cpnext.getStart()].getX() - xc;\n dy = this.bases[cpnext.getStart()].getY() - yc;\n rcn = Math.sqrt(dx * dx + dy * dy);\n acn = Math.atan2(dy, dx);\n if (acn < 0.0){\n acn += 2 * Math.PI;\n }\n if (acn < ac){\n acn += 2 * Math.PI;\n }\n dan = acn - ac;\n dcp = cpnext.getAngle() - cp.getAngle();\n if (dcp <= 0.0){\n dcp += 2 * Math.PI;\n }\n if (Math.abs(dan - dcp) > Math.PI) {\n if (cp.isExtruded()) {\n console.log(\"Warning from traverse_loop. Loop \"\n + lp.getNumber() + \" has crossed regions\\n\");\n }\n else if ((cpnext.getStart() - cp.getEnd()) != 1) {\n cp.setExtruded(true);\n continue set_radius; // remplacement du goto\n }\n }\n if (cp.isExtruded()) {\n this.construct_extruded_segment(cp, cpnext);\n }\n else {\n n = cpnext.getStart() - cp.getEnd();\n if (n < 0){\n n += this.nbase + 1;\n }\n angleinc = dan / n;\n for (j = 1; j < n; j++) {\n i = cp.getEnd() + j;\n if (i > this.nbase){\n i -= this.nbase + 1;\n }\n a = ac + j * angleinc;\n rr = rc + (rcn - rc) * (a - ac) / dan;\n this.bases[i].setX(xc + rr * Math.cos(a));\n this.bases[i].setY(yc + rr * Math.sin(a));\n }\n }\n }\n break;\n }\n for (ic = 0; ic < lp.getNconnection(); ic++) {\n if (icroot != ic) {\n cp = lp.getConnection(ic);\n //IM HERE\n this.generate_region(cp);\n this.traverse_loop(cp.getLoop(), cp);\n }\n }\n n = 0;\n sx = 0.0;\n sy = 0.0;\n for (ic = 0; ic < lp.getNconnection(); ic++) {\n j = ic + 1;\n if (j >= lp.getNconnection()){\n j = 0;\n }\n cp = lp.getConnection(ic);\n cpnext = lp.getConnection(j);\n n += 2;\n sx += this.bases[cp.getStart()].getX()\n + this.bases[cp.getEnd()].getX();\n sy += this.bases[cp.getStart()].getY()\n + this.bases[cp.getEnd()].getY();\n if (!cp.isExtruded()) {\n for (j = cp.getEnd() + 1; j != cpnext.getStart(); j++) {\n if (j > this.nbase){\n j -= this.nbase + 1;\n }\n n++;\n sx += this.bases[j].getX();\n sy += this.bases[j].getY();\n }\n }\n }\n lp.setX(sx / n);\n lp.setY(sy / n);\n}\n\nNAView.prototype.determine_radius = function determine_radius(lp, lencut){\n var mindit, ci, dt, sumn, sumd, radius, dit;\n var i, j, end, start, imindit = 0;\n var cp = new Connection(), cpnext = new Connection();\n var rt2_2 = 0.7071068;\n\n do {\n mindit = 1.0e10;\n for (sumd = 0.0, sumn = 0.0, i = 0; i < lp.getNconnection(); i++) {\n cp = lp.getConnection(i);\n j = i + 1;\n if (j >= lp.getNconnection()){\n j = 0;\n }\n cpnext = lp.getConnection(j);\n end = cp.getEnd();\n start = cpnext.getStart();\n if (start < end){\n start += this.nbase + 1;\n }\n dt = cpnext.getAngle() - cp.getAngle();\n if (dt <= 0.0){\n dt += 2 * Math.PI;\n }\n if (!cp.isExtruded()){\n ci = start - end;\n }\n else {\n if (dt <= Math.PI / 2){\n ci = 2.0;\n }\n else {\n ci = 1.5;\n }\n }\n sumn += dt * (1.0 / ci + 1.0);\n sumd += dt * dt / ci;\n dit = dt / ci;\n if (dit < mindit && !cp.isExtruded() && ci > 1.0) {\n mindit = dit;\n imindit = i;\n }\n }\n radius = sumn / sumd;\n if (radius < rt2_2){\n radius = rt2_2;\n }\n if (mindit * radius < lencut) {\n lp.getConnection(imindit).setExtruded(true);\n }\n } while (mindit * radius < lencut);\n if (lp.getRadius() > 0.0){\n radius = lp.getRadius();\n }\n else {\n lp.setRadius(radius);\n }\n}\n\nNAView.prototype.find_ic_middle = function find_ic_middle(icstart, icend, anchor_connection, acp, lp){\n var count, ret, ic, i;\n var done;\n\n count = 0;\n ret = -1;\n ic = icstart;\n done = false;\n while (!done) {\n if (count++ > lp.getNconnection() * 2) {\n console.log(\"Infinite loop in 'find_ic_middle'\");\n }\n if (anchor_connection != null && lp.getConnection(ic) == acp) {\n ret = ic;\n }\n done = ic == icend;\n if (++ic >= lp.getNconnection()) {\n ic = 0;\n }\n }\n if (ret == -1) {\n for (i = 1, ic = icstart; i < (count + 1) / 2; i++) {\n if (++ic >= lp.getNconnection())\n ic = 0;\n }\n ret = ic;\n }\n return ret;\n}\n\nNAView.prototype.construct_extruded_segment = function construct_extruded_segment(cp, cpnext){\n var astart, aend1, aend2, aave, dx, dy, a1, a2, ac, rr, da, dac;\n var start, end, n, nstart, nend;\n var collision;\n\n astart = cp.getAngle();\n aend2 = aend1 = cpnext.getAngle();\n if (aend2 < astart){\n aend2 += 2 * Math.PI;\n }\n aave = (astart + aend2) / 2.0;\n start = cp.getEnd();\n end = cpnext.getStart();\n n = end - start;\n if (n < 0){\n n += this.nbase + 1;\n }\n da = cpnext.getAngle() - cp.getAngle();\n if (da < 0.0) {\n da += 2 * Math.PI;\n }\n if (n == 2) {\n this.construct_circle_segment(start, end);\n }\n else {\n dx = this.bases[end].getX() - this.bases[start].getX();\n dy = this.bases[end].getY() - this.bases[start].getY();\n rr = Math.sqrt(dx * dx + dy * dy);\n dx /= rr;\n dy /= rr;\n if (rr >= 1.5 && da <= Math.PI / 2) {\n nstart = start + 1;\n if (nstart > this.nbase){\n nstart -= this.nbase + 1;\n }\n nend = end - 1;\n if (nend < 0){\n nend += this.nbase + 1;\n }\n this.bases[nstart].setX(this.bases[start].getX() + 0.5 * dx);\n this.bases[nstart].setY(this.bases[start].getY() + 0.5 * dy);\n this.bases[nend].setX(this.bases[end].getX() - 0.5 * dx);\n this.bases[nend].setY(this.bases[end].getY() - 0.5 * dy);\n start = nstart;\n end = nend;\n }\n do {\n collision = false;\n this.construct_circle_segment(start, end);\n nstart = start + 1;\n if (nstart > this.nbase) {\n nstart -= this.nbase + 1;\n }\n dx = this.bases[nstart].getX() - this.bases[start].getX();\n dy = this.bases[nstart].getY() - this.bases[start].getY();\n a1 = Math.atan2(dy, dx);\n if (a1 < 0.0){\n a1 += 2 * Math.PI;\n }\n dac = a1 - astart;\n if (dac < 0.0){\n dac += 2 * Math.PI;\n }\n if (dac > Math.PI){\n collision = true;\n }\n nend = end - 1;\n if (nend < 0){\n nend += this.nbase + 1;\n }\n dx = this.bases[nend].getX() - this.bases[end].getX();\n dy = this.bases[nend].getY() - this.bases[end].getY();\n a2 = Math.atan2(dy, dx);\n if (a2 < 0.0){\n a2 += 2 * Math.PI;\n }\n dac = aend1 - a2;\n if (dac < 0.0){\n dac += 2 * Math.PI;\n }\n if (dac > Math.PI){\n collision = true;\n }\n if (collision) {\n ac = this.minf2(aave, astart + 0.5);\n this.bases[nstart].setX(\n this.bases[start].getX() + Math.cos(ac));\n this.bases[nstart].setY(\n this.bases[start].getY() + Math.sin(ac));\n start = nstart;\n ac = this.maxf2(aave, aend2 - 0.5);\n this.bases[nend].setX(this.bases[end].getX() + Math.cos(ac));\n this.bases[nend].setY(this.bases[end].getY() + Math.sin(ac));\n end = nend;\n n -= 2;\n }\n } while (collision && n > 1);\n }\n}\n\nNAView.prototype.construct_circle_segment = function construct_circle_segment(start, end){\n var dx, dy, rr, midx, midy, xn, yn, nrx, nry, mx, my, a;\n var l, j, i;\n\n dx = this.bases[end].getX() - this.bases[start].getX();\n dy = this.bases[end].getY() - this.bases[start].getY();\n rr = Math.sqrt(dx * dx + dy * dy);\n l = end - start;\n if (l < 0){\n l += this.nbase + 1;\n }\n if (rr >= l) {\n dx /= rr;\n dy /= rr;\n for (j = 1; j < l; j++) {\n i = start + j;\n if (i > this.nbase){\n i -= this.nbase + 1;\n }\n this.bases[i].setX(\n this.bases[start].getX() + dx * j / l);\n this.bases[i].setY(\n this.bases[start].getY() + dy * j / l);\n }\n }\n else {\n this.find_center_for_arc((l - 1), rr);\n dx /= rr;\n dy /= rr;\n midx = this.bases[start].getX() + dx * rr / 2.0;\n midy = this.bases[start].getY() + dy * rr / 2.0;\n xn = dy;\n yn = -dx;\n nrx = midx + this._h * xn;\n nry = midy + this._h * yn;\n mx = this.bases[start].getX() - nrx;\n my = this.bases[start].getY() - nry;\n rr = Math.sqrt(mx * mx + my * my);\n a = Math.atan2(my, mx);\n for (j = 1; j < l; j++) {\n i = start + j;\n if (i > this.nbase){\n i -= this.nbase + 1;\n }\n this.bases[i].setX(nrx + rr * Math.cos(a + j * this.angleinc));\n this.bases[i].setY(nry + rr * Math.sin(a + j * this.angleinc));\n }\n }\n}\n\nNAView.prototype.find_center_for_arc = function find_center_for_arc(n, b){\n var h, hhi, hlow, r, disc, theta, e, phi;\n var iter;\n\n hhi = (n + 1.0) / Math.PI;\n // changed to prevent div by zero if (ih)\n hlow = -hhi - b / (n + 1.000001 - b);\n if (b < 1){\n // otherwise we might fail below (ih)\n hlow = 0;\n }\n iter = 0;\n do {\n h = (hhi + hlow) / 2.0;\n r = Math.sqrt(h * h + b * b / 4.0);\n disc = 1.0 - 0.5 / (r * r);\n if (Math.abs(disc) > 1.0) {\n console.log(\"Unexpected large magnitude discriminant = \" + disc\n + \" \" + r);\n }\n theta = Math.acos(disc);\n phi = Math.acos(h / r);\n e = theta * (n + 1) + 2 * phi - 2 * Math.PI;\n if (e > 0.0) {\n hlow = h;\n }\n else {\n hhi = h;\n }\n } while (Math.abs(e) > 0.0001 && ++iter < this.MAXITER);\n if (iter >= this.MAXITER) {\n if (noIterationFailureYet) {\n console.log(\"Iteration failed in find_center_for_arc\");\n noIterationFailureYet = false;\n }\n h = 0.0;\n theta = 0.0;\n }\n this._h = h;\n this.angleinc = theta;\n}\n\nNAView.prototype.generate_region = function generate_region(cp){\n var l, start, end, i, mate;\n var rp;\n\n rp = cp.getRegion();\n l = 0;\n if (cp.getStart() == rp.getStart1()) {\n start = rp.getStart1();\n end = rp.getEnd1();\n }\n else {\n start = rp.getStart2();\n end = rp.getEnd2();\n }\n if (this.bases[cp.getStart()].getX() > this.ANUM - 100.0\n || this.bases[cp.getEnd()].getX() > this.ANUM - 100.0) {\n console.log(\n \"Bad region passed to generate_region. Coordinates not defined.\");\n }\n for (i = start + 1; i <= end; i++) {\n l++;\n this.bases[i].setX(\n this.bases[cp.getStart()].getX() + this.HELIX_FACTOR * l\n * cp.getXrad());\n this.bases[i].setY(\n this.bases[cp.getStart()].getY() + this.HELIX_FACTOR * l\n * cp.getYrad());\n mate = this.bases[i].getMate();\n this.bases[mate].setX(\n this.bases[cp.getEnd()].getX() + this.HELIX_FACTOR * l\n * cp.getXrad());\n this.bases[mate].setY(\n this.bases[cp.getEnd()].getY() + this.HELIX_FACTOR * l\n * cp.getYrad());\n\n }\n}\n\nNAView.prototype.minf2 = function minf2(x1, x2) {\n return ((x1) < (x2)) ? (x1) : (x2);\n}\n\nNAView.prototype.maxf2 = function maxf2(x1, x2) {\n return ((x1) > (x2)) ? (x1) : (x2);\n}\n\nNAView.prototype.connected_connection = function connected_connection(cp, cpnext) {\n if (cp.isExtruded()) {\n return true;\n }\n else if (cp.getEnd() + 1 == cpnext.getStart()) {\n return true;\n }\n else {\n return false;\n }\n}\n","/* Version: 0.2\n* Date: 2015-03-15\n*/\n\nimport fstyle from './fornac.css';\n\nimport d3 from 'd3';\nimport slugid from 'slugid';\nimport {contextMenu} from './d3-context-menu.js';\n\nimport {RNAGraph} from './rnagraph.js';\nimport {ColorScheme, rnaUtilities} from './rnautils.js';\n\nimport {simpleXyCoordinates} from './simplernaplot.js';\nimport {NAView} from './naview/naview.js';\n\nexport function FornaContainer(element, passedOptions = {}) {\n var self = this;\n\n let options = {\n 'editable': false,\n 'zoomable': true,\n 'animation': true,\n 'displayAllLinks': false,\n 'labelInterval': 10,\n 'chargeDistance': 110,\n 'friction': 0.35,\n 'middleCharge': -30,\n 'otherCharge': -30,\n 'linkDistanceMultiplier': 15,\n 'initialSize': null,\n 'layout': 'standard-polygonal',\n 'transitionDuration': 500,\n 'maxNodeRadius': 80 // the maximum radius of a node when the view is centered\n };\n\n self.options = Object.assign(options, passedOptions);\n\n if (self.options.initialSize !== null) {\n self.options.svgW = self.options.initialSize[0];\n self.options.svgH = self.options.initialSize[1];\n } else {\n self.options.svgW = 300;\n self.options.svgH = 300;\n }\n\n self.linkStrengths = {\n 'pseudoknot': 0.00,\n 'proteinChain': 0.00,\n 'chainChain': 0.00,\n 'intermolecule': 10.00,\n 'external': 0.00,\n 'other': 10.00\n };\n\n self.displayParameters = {\n 'displayNumbering': true,\n 'displayNodeOutline': true,\n 'displayNodeLabel': true,\n 'displayLinks': true,\n 'displayPseudoknotLinks': true,\n 'displayProteinLinks': true,\n 'displayDirectionArrows': true\n };\n\n self.colorScheme = 'structure';\n self.customColors = {};\n self.rnas = {};\n self.extraLinks = []; //store links between different RNAs\n\n // global mouse event vars\n var mousedownLink = null,\n mousedownNode = null,\n mouseupNode = null;\n let linkContextMenuShown = false;\n\n let resetMouseVars = () => {\n mousedownNode = null;\n mouseupNode = null;\n mousedownLink = null;\n }\n\n var graph = self.graph = {\n 'nodes':[],\n 'links':[]\n };\n\n Array.prototype.equals = function (array) {\n // if the other array is a falsy value, return\n if (!array)\n return false;\n\n // compare lengths - can save a lot of time\n if (this.length != array.length)\n return false;\n\n for (var i = 0, l=this.length; i < l; i++) {\n // Check if we have nested arrays\n if (this[i] instanceof Array && array[i] instanceof Array) {\n // recurse into the nested arrays\n if (!this[i].equals(array[i]))\n return false;\n }\n else if (this[i] != array[i]) {\n // Warning - two different object instances will never be equal: {x:20} != {x:20}\n return false;\n }\n }\n return true;\n };\n\n /* Register global mouse and key events */\n if (self.options.editable || self.options.animation) {\n var shiftKeydown = false;\n var ctrlKeydown = false;\n\n let keydown = () => {\n switch (d3.event.keyCode) {\n case 68: //'d' key\n console.log('dotbracket:', self.getStructuresDotBracket());\n break;\n case 16:\n shiftKeydown = true;\n break;\n case 17:\n ctrlKeydown = true;\n break;\n case 67: //c\n self.centerView();\n break;\n }\n\n if (ctrlKeydown) {\n // Ctrl key must disable panning and zooming\n if (self.options.zoomable)\n disableZooming()\n // Ctrl Button must enable crosshair and start brusher\n if (self.options.editable || self.options.animation) {\n enableBrushing()\n }\n }\n }\n\n let keyup = () => {\n shiftKeydown = false;\n ctrlKeydown = false;\n\n // enable zoomer\n if (self.options.zoomable)\n enableZooming()\n // disable brushing events\n disableBrushing()\n }\n\n d3.select('body')\n .on('keydown', keydown)\n .on('keyup', keyup)\n .on('contextmenu', function() {\n d3.event.preventDefault();\n });\n }\n\n /* Register global context menu */\n if (self.options.editable) {\n let backgroundMenu = [\n {\n title: 'Add Node',\n action: function(elm, d, i, mousePos) {\n\n },\n children: [{\n 'title': 'A',\n action: function(elm, d, i, mousePos) {\n console.log('mousePos:', mousePos, self.options.svgW, self.options.svgH);\n let canvasMousePos = [xScale.invert(mousePos[0]),\n yScale.invert(mousePos[1])];\n console.log('canvasMousePos', canvasMousePos);\n\n self.addRNA('.', {'sequence': 'A', 'centerPos': canvasMousePos});\n }\n },\n {\n 'title': 'C',\n action: function(elm, d, i, mousePos) {\n console.log('mousePos:', mousePos, self.options.svgW, self.options.svgH);\n let canvasMousePos = [xScale.invert(mousePos[0]),\n yScale.invert(mousePos[1])];\n console.log('canvasMousePos', canvasMousePos);\n\n self.addRNA('.', {'sequence': 'C', 'centerPos': canvasMousePos});\n }\n\n },\n {\n 'title': 'G',\n action: function(elm, d, i, mousePos) {\n console.log('mousePos:', mousePos, self.options.svgW, self.options.svgH);\n let canvasMousePos = [xScale.invert(mousePos[0]),\n yScale.invert(mousePos[1])];\n console.log('canvasMousePos', canvasMousePos);\n\n self.addRNA('.', {'sequence': 'G', 'centerPos': canvasMousePos});\n }\n\n },\n {\n 'title': 'U',\n action: function(elm, d, i, mousePos) {\n console.log('mousePos:', mousePos, self.options.svgW, self.options.svgH);\n let canvasMousePos = [xScale.invert(mousePos[0]),\n yScale.invert(mousePos[1])];\n console.log('canvasMousePos', canvasMousePos);\n\n self.addRNA('.', {'sequence': 'U', 'centerPos': canvasMousePos});\n\n }\n }\n ],\n disabled: false // optional, defaults to false\n }\n ]\n\n let nodeMenu = [\n {\n title: 'Delete Node',\n action: function(elm, d, i) {\n deleteNode(d);\n },\n disabled: false // optional, defaults to false\n },\n {\n title: 'Change Node',\n action: function(elm, d, i) {\n console.log('You have clicked the second item!');\n console.log('The data for this circle is: ' + d);\n },\n children: [\n {\n title: 'A',\n action: function(elm, d, i) {\n changeNode('A', d);\n }\n },\n {\n title: 'C',\n action: function(elm, d, i) {\n changeNode('C', d);\n\n }\n },\n {\n title: 'G',\n action: function(elm, d, i) {\n changeNode('G', d);\n\n }\n },\n {\n title: 'U',\n action: function(elm, d, i) {\n changeNode('U', d);\n }\n },\n ]\n },\n {\n title: 'Insert Before',\n action: function(elm, d, i) {\n\n },\n children: [\n {\n title: 'A',\n action: function(elm, d, i) {\n insertNodeBeforeOrAfter('A', d, -1);\n }\n },\n {\n title: 'C',\n action: function(elm, d, i) {\n insertNodeBeforeOrAfter('C', d, -1);\n\n }\n },\n {\n title: 'G',\n action: function(elm, d, i) {\n insertNodeBeforeOrAfter('G', d, -1);\n\n }\n },\n {\n title: 'U',\n action: function(elm, d, i) {\n insertNodeBeforeOrAfter('U', d, -1);\n }\n },\n ]\n },\n {\n title: 'Insert After',\n action: function(elm, d, i) {\n console.log('d:', d);\n\n },\n children: [\n {\n title: 'A',\n action: function(elm, d, i) {\n insertNodeBeforeOrAfter('A', d, 0);\n\n }\n },\n {\n title: 'C',\n action: function(elm, d, i) {\n insertNodeBeforeOrAfter('C', d, 0);\n }\n },\n {\n title: 'G',\n action: function(elm, d, i) {\n insertNodeBeforeOrAfter('G', d, 0);\n }\n },\n {\n title: 'U',\n action: function(elm, d, i) {\n insertNodeBeforeOrAfter('U', d, 0);\n }\n },\n ]\n }\n ]\n\n self.nodeContextMenu = contextMenu(nodeMenu);\n self.backgroundContextMenu = contextMenu(backgroundMenu);\n\n } else {\n //console.log('empty context menu');\n self.nodeContextMenu = function() {};\n }\n\n /* Draw the plot here */\n d3.select(element).select('svg').remove();\n\n var svg = d3.select(element)\n .attr('tabindex', 1)\n .each(function() { this.focus(); })\n .append('svg:svg')\n .attr('preserveAspectRatio', 'xMidYMid meet')\n .attr('viewBox', '0 0 ' + self.options.svgW + ' ' + self.options.svgH)\n\n self.options.svg = svg;\n\n if (self.options.editable || self.options.animation) {\n var mouseEventHelper = svg.append('svg:g')\n .on('mousemove', () => {\n // only if we are dragging\n if (!mousedownNode) return;\n\n // update drag line\n let mpos = d3.mouse(vis.node());\n dragLine\n .attr('x1', mousedownNode.x)\n .attr('y1', mousedownNode.y)\n .attr('x2', mpos[0])\n .attr('y2', mpos[1]);\n })\n .on('mousedown', () => {\n })\n .on('mouseup', () => {\n if (mousedownNode && !linkContextMenuShown) {\n dragLine.classed(fstyle.transparent, true);\n }\n // clear mouse event vars\n resetMouseVars();\n //update()\n })\n .classed(fstyle.mouseEventHelper, true)\n .style('pointer-events', 'all')\n\n // draw a background layer for mouse events\n mouseEventHelper.append('svg:rect')\n .classed('background', true)\n .style('visibility', 'hidden')\n .attr('width', self.options.svgW)\n .attr('height', self.options.svgH)\n .on('mousedown', function() {\n //console.log('background click');\n deselectAllNodes()\n })\n } else {\n var mouseEventHelper = svg;\n }\n\n var vis = mouseEventHelper.append('svg:g')\n .classed(fstyle.plot, true)\n var visLinks = vis.append('svg:g')\n .classed('fornac-links', true);\n var visNodes = vis.append('svg:g')\n .classed('fornac-nodes', true);\n\n // line displayed when dragging new nodes\n if (self.options.editable) {\n var dragLine = vis.append('line')\n .attr('class', fstyle.dragLine)\n .attr('x1', 0)\n .attr('y1', 0)\n .attr('x2', 0)\n .attr('y2', 0);\n\n svg.on('contextmenu', self.backgroundContextMenu);\n }\n\n /* Zooming related objects and functions */\n var xScale = d3.scale.linear()\n .domain([0,self.options.svgW]).range([0,self.options.svgW]);\n var yScale = d3.scale.linear()\n .domain([0,self.options.svgH]).range([0, self.options.svgH]);\n\n self.zoomer = d3.behavior.zoom()\n .scaleExtent([0.1,10])\n .x(xScale)\n .y(yScale)\n .on('zoom', () => {\n vis.attr('transform',\n 'translate(' + d3.event.translate + ')' + ' scale(' + d3.event.scale + ')');\n });\n\n let enableZooming = () => {\n svg.call(self.zoomer)\n .on(\"dblclick.zoom\", null);\n }\n\n let disableZooming = () => {\n svg.call(self.zoomer)\n .on(\"dblclick.zoom\", null)\n .on('mousedown.zoom', null)\n .on('touchstart.zoom', null)\n .on('touchmove.zoom', null)\n .on('touchend.zoom', null);\n }\n\n if (self.options.zoomable)\n enableZooming()\n\n /* Node selection related objects and functions */\n let toggleSelectNode = (node) => {\n node.selected = !node.selected;\n visNodes.selectAll('g.gnode').filter((d) => { return node.uid == d.uid; })\n .classed(fstyle.selectedNode, function(p) { return p.selected; });\n }\n\n let selectNode = (node) => {\n node.selected = true;\n visNodes.selectAll('g.gnode').filter((d) => { return node.uid == d.uid; })\n .classed(fstyle.selectedNode, function(p) { return p.selected; });\n }\n\n let deselectAllNodes = () => {\n visNodes.selectAll('g.gnode')\n .classed(fstyle.selectedNode, function(p) { return p.selected = false; });\n }\n\n let selectedNodes = () => {\n // return all selected nodes\n return visNodes.selectAll('g.gnode').filter(function(d) { return d.selected; });\n }\n\n self.brusher = d3.svg.brush()\n .x(xScale)\n .y(yScale)\n .on('brushstart', function(d) {})\n .on('brush', function() {\n // during brushing invert styling of selection as preview\n let extent = d3.event.target.extent();\n\n visNodes.selectAll('g.gnode')\n .classed(fstyle.selectedNode, function (d) {\n return d.selected ^ (extent[0][0] <= d.x && d.x < extent[1][0]\n && extent[0][1] <= d.y && d.y < extent[1][1])\n })\n })\n .on('brushend', function() {\n // after brushing finally toggle the selection\n let extent = d3.event.target.extent();\n\n visNodes.selectAll('g.gnode')\n .filter(function (d) {\n return extent[0][0] <= d.x && d.x < extent[1][0]\n && extent[0][1] <= d.y && d.y < extent[1][1]\n })\n .each(toggleSelectNode)\n\n d3.event.target.clear();\n d3.select(this).call(d3.event.target);\n });\n\n let enableBrushing = () => {\n // crosshair curson\n mouseEventHelper.select('.background').style('cursor', 'crosshair');\n // bind brusher\n mouseEventHelper.call(self.brusher);\n }\n\n let disableBrushing = () => {\n // normal cursor\n mouseEventHelper.select('.background').style('cursor', 'auto');\n // disable brushing events\n mouseEventHelper.call(self.brusher)\n .on('mousedown.brush', null)\n .on('touchstart.brush', null)\n .on('touchmove.brush', null)\n .on('touchend.brush', null);\n }\n\n /* Force related objects and functions */\n self.force = d3.layout.force()\n .charge(function(d) {\n if (d.nodeType == 'middle')\n return self.options.middleCharge;\n else\n return self.options.otherCharge;\n })\n .friction(self.options.friction)\n .linkDistance(function(d) { return self.options.linkDistanceMultiplier * d.value; })\n .linkStrength(function(d) { if (d.linkType in self.linkStrengths) {\n return self.linkStrengths[d.linkType];\n } else {\n return self.linkStrengths.other; }\n })\n .gravity(0.000)\n .nodes(self.graph.nodes)\n .links(self.graph.links)\n .chargeDistance(self.options.chargeDistance)\n .size([self.options.svgW, self.options.svgH]);\n\n var drag = d3.behavior.drag()\n .on('dragstart', function(d) {\n console.log('dragstart')\n d3.event.sourceEvent.stopPropagation();\n\n selectedNodes().each(function(d1) {\n d1.fixed |= 2;\n });\n })\n .on('drag', (d) => {\n if (shiftKeydown) return\n selectedNodes().each(function(d1) {\n d1.x += d3.event.dx;\n d1.y += d3.event.dy;\n\n d1.px += d3.event.dx;\n d1.py += d3.event.dy;\n });\n\n self.resumeForce();\n d3.event.sourceEvent.preventDefault();\n })\n .on('dragend', (d) => {\n console.log('dragend')\n selectedNodes().each(function(d1) {\n d1.fixed &= ~6;\n });\n });\n\n /* Main plot drawing functions */\n let createInitialLayout = function(structure, passedOptions = {}) {\n // the default options\n let options = {\n 'sequence': '',\n 'name': 'empty',\n 'positions': [],\n 'labelInterval': self.options.labelInterval,\n 'avoidOthers': true,\n 'uids': [],\n 'circularizeExternal': true\n };\n\n options = Object.assign(options, passedOptions);\n\n //console.log('options.uids:', options.uids);\n let rg = new RNAGraph(options.sequence, structure, options.name);\n rg.circularizeExternal = options.circularizeExternal;\n\n let rnaJson = rg.recalculateElements();\n\n if (options.positions.length === 0) {\n // no provided positions means we need to calculate an initial layout\n\n if (self.options.layout == 'naview') {\n let naview = new NAView();\n\n let naViewPositions = naview.naview_xy_coordinates(rg.pairtable);\n options.positions = []\n for (let i = 0; i < naViewPositions.nbase; i++)\n options.positions.push([naViewPositions.x[i], naViewPositions.y[i]]);\n } else {\n options.positions = simpleXyCoordinates(rnaJson.pairtable);\n }\n }\n\n rnaJson = rnaJson.elementsToJson()\n .addUids(options.uids)\n .addPositions('nucleotide', options.positions)\n .addLabels(1, options.labelInterval)\n .reinforceStems()\n .reinforceLoops()\n .connectFakeNodes()\n .reassignLinkUids()\n .breakNodesToFakeNodes();\n\n return rnaJson;\n };\n\n let createNewNodes = function(gnodesEnter) {\n gnodesEnter = gnodesEnter.append('g')\n .classed('gnode', true)\n .attr('struct_name', function(d) { return d.structName; })\n .attr('transform', function(d) {\n if (typeof d.x != 'undefined' && typeof d.y != 'undefined')\n return 'translate(' + [d.x, d.y] + ')';\n else\n return '';\n })\n .each( function(d) { d.selected = d.previouslySelected = false; });\n\n gnodesEnter\n .attr('num', function(d) { return 'n' + d.num; })\n .attr('rnum', function(d) {\n return 'n' + (d.rna.rnaLength - d.num + 1); })\n .transition()\n .duration(750)\n .ease('elastic');\n\n if (self.options.editable || self.options.animation) {\n gnodesEnter.on('mousedown', nodeMousedown)\n //.on('mousedrag', function(d) {})\n .on('mouseup', nodeMouseup)\n .on('contextmenu', self.nodeContextMenu)\n .call(drag)\n }\n\n let labelAndProteinNodes = gnodesEnter.filter(function(d) {\n return d.nodeType == 'label' || d.nodeType == 'protein';\n });\n\n let nucleotideNodes = gnodesEnter.filter(function(d) {\n return d.nodeType == 'nucleotide';\n });\n\n labelAndProteinNodes.append('svg:circle')\n .classed(fstyle.node, true)\n .attr('r', function(d) {\n if (d.nodeType == 'middle') return 0;\n else {\n return d.radius;\n }\n })\n .attr('node_type', function(d) { return d.nodeType; })\n .attr('node_num', function(d) { return d.num; });\n\n // direction arrows\n nucleotideNodes.append('svg:path')\n .attr('class', fstyle.directionArrow)\n .attr('node_num', function(d) { return d.num; })\n\n // nucleotide outlines\n nucleotideNodes.append('svg:circle')\n .attr('class', fstyle.node)\n .attr('node_type', function(d) { return d.nodeType; })\n .attr('node_num', function(d) { return d.num; })\n .attr('r', function(d) { return d.radius; })\n .append('svg:title')\n .text(function(d) {\n if (d.nodeType == 'nucleotide') {\n return d.structName + ':' + d.num;\n } else {\n return '';\n }\n });\n\n // nucleotide labels\n var labelsEnter = gnodesEnter.append('text')\n .text(function(d) { return d.name; })\n .attr('class', fstyle.nodeLabel)\n .attr('label_type', function(d) { return d.nodeType; })\n\n // nucleotide label title\n labelsEnter.append('svg:title')\n .text(function(d) {\n if (d.nodeType == 'nucleotide') {\n return d.structName + ':' + d.num;\n } else {\n return '';\n }\n });\n\n return gnodesEnter;\n };\n\n let createNewLinks = function(linksEnter) {\n var linkLines = linksEnter.append('svg:line');\n\n linkLines.append('svg:title')\n .text((d) => { return d.linkType + ':' + d.source.num + '-' + d.target.num });\n\n linkLines\n .classed('link', true)\n .classed(fstyle.link, true)\n .attr('x1', function(d) { return d.source.x; })\n .attr('y1', function(d) { return d.source.y; })\n .attr('x2', function(d) { return d.target.x; })\n .attr('y2', function(d) { return d.target.y; })\n .attr('link_type', function(d) { return d.linkType; } )\n .attr('pointer-events', function(d) { if (d.linkType == 'fake') return 'none'; else return 'all';});\n\n if (self.options.editable)\n linkLines.on('click', linkClick);\n\n /* We don't need to update the positions of the stabilizing links */\n /*\n basepairLinks = visLinks.selectAll('[link_type=basepair]');\n basepairLinks.classed('basepair', true);\n\n fakeLinks = visLinks.selectAll('[link_type=fake]')\n fakeLinks.classed('fake', true);\n\n intermolecule_links = vis_links.selectAll('[link_type=intermolecule]');\n intermolecule_links.classed('intermolecule', true);\n\n plink = vis_links.selectAll('[link_type=protein_chain],[link_type=chain_chain]');\n plink.classed('chain_chain', true);\n */\n\n return linkLines;\n };\n\n function drawDirectionArrow(d) {\n let magnitude = (x) => {\n return Math.sqrt(x[0] * x[0] + x[1] * x[1]);\n }\n\n let endPoint = d;\n let startPoint = d.prevNode;\n // get stroke width and arrow size values from css\n let nodeStroke = parseFloat(fstyle.nodeStrokeWidth) / 2;\n let lengthMult = parseFloat(fstyle.directionArrowSize);\n let arrowWidth = parseFloat(fstyle.directionArrowWidth);\n\n if (startPoint === null)\n return;\n\n // does this node have a link pointing to it?\n if (!d.linked)\n return;\n\n // point back toward the previous node\n let u = [-(endPoint.x - startPoint.x), -(endPoint.y - startPoint.y)];\n\n if (u[0] == 0 && u[1] == 0)\n return; // will lead to a NaN error\n\n // scale u to unit length\n u = [u[0] / magnitude(u), u[1] / magnitude(u)];\n // normal vector of u\n let v = [-u[1], u[0]];\n\n // calculate the tip position\n let arrowTip = [(d.radius + nodeStroke) * u[0], (d.radius + nodeStroke) * u[1]];\n\n let path = 'M' + (arrowTip[0] + lengthMult * (u[0]/2 + v[0]*arrowWidth/2)) + ',' + (arrowTip[1] + lengthMult * (u[1]/2 + v[1]*arrowWidth/2)) +\n 'L' + (arrowTip[0]) + ',' + (arrowTip[1]) +\n 'L' + (arrowTip[0] + lengthMult * (u[0]/2 - v[0]*arrowWidth/2)) + ',' + (arrowTip[1] + lengthMult * (u[1]/2 - v[1]*arrowWidth/2));\n\n d3.select(this).attr('d', path);\n }\n\n let realLinkFilter = (d) => {\n return d.linkType == 'basepair' ||\n d.linkType == 'backbone' ||\n d.linkType == 'intermolecule' ||\n d.linkType == 'pseudoknot' ||\n d.linkType == 'label_link' ||\n d.linkType == 'external' ||\n d.linkType == 'chain_chain';\n }\n\n let recalculateGraph = () => {\n // Condense all of the individual RNAs into one\n // collection of nodes and links\n self.graph.nodes = [];\n self.graph.links = [];\n for (let uid in self.rnas) {\n self.graph.nodes = self.graph.nodes.concat(self.rnas[uid].nodes);\n self.graph.links = self.graph.links.concat(self.rnas[uid].links);\n }\n\n // Create a lookup table so that we can access each node\n // based on its uid. This will be used to create the links\n // between different RNAs\n var uidsToNodes = {};\n\n for (let i = 0; i < self.graph.nodes.length; i++)\n uidsToNodes[self.graph.nodes[i].uid] = self.graph.nodes[i];\n\n self.graph.links.forEach(function(link) {\n link.source = uidsToNodes[link.source.uid];\n link.target = uidsToNodes[link.target.uid];\n });\n\n for (let i = 0; i < self.extraLinks.length; i++) {\n // the actual node objects may have changed, so we hae to recreate\n // the extra links based on the uids\n if (!(self.extraLinks[i].target.uid in uidsToNodes)) {\n console.log('not there:', self.extraLinks[i]);\n continue;\n }\n\n self.extraLinks[i].source = uidsToNodes[self.extraLinks[i].source.uid];\n self.extraLinks[i].target = uidsToNodes[self.extraLinks[i].target.uid];\n\n if (self.extraLinks[i].linkType == 'intermolecule') {\n //remove links to middle nodes\n let fakeLinks = self.graph.links.filter(function(d) {\n return ((d.source == self.extraLinks[i].source || d.source == self.extraLinks[i].target ||\n d.target == self.extraLinks[i].source || d.target == self.extraLinks[i].source) &&\n d.linkType == 'fake');\n });\n\n for (let j = 0; j < fakeLinks.length; j++) {\n let linkIndex = self.graph.links.indexOf(fakeLinks[j]);\n self.graph.links.splice(linkIndex, 1);\n }\n }\n\n graph.links.push(self.extraLinks[i]);\n }\n };\n\n self.update = function () {\n self.force.nodes(self.graph.nodes)\n .links(self.graph.links);\n\n if (self.options.animation) {\n self.force.start();\n }\n\n let allLinks = visLinks.selectAll('line.link')\n .data(self.graph.links.filter(realLinkFilter), elementKey);\n\n allLinks.attr('class', '')\n .classed('link', true)\n .classed(fstyle.link, true)\n .attr('link_type', function(d) { return d.linkType; } )\n\n let linksEnter = allLinks.enter();\n createNewLinks(linksEnter);\n\n allLinks.exit().remove();\n\n let gnodes = visNodes.selectAll('g.gnode')\n .data(self.graph.nodes, elementKey);\n //.attr('pointer-events', 'all');\n\n let gnodesEnter = gnodes.enter();\n createNewNodes(gnodesEnter);\n gnodes.exit().remove();\n\n\n //fake_nodes = self.graph.nodes.filter(function(d) { return d.nodeType == 'middle'; });\n //fakeNodes = self.graph.nodes.filter(function(d) { return true; });\n let realNodes = self.graph.nodes.filter(function(d) { return d.nodeType == 'nucleotide' || d.nodeType == 'label';});\n\n gnodes.select('.' + fstyle.directionArrow).each(drawDirectionArrow);\n\n self.force.on('tick', function() {\n let q = d3.geom.quadtree(realNodes);\n let i = 0;\n let n = realNodes.length;\n\n let collide = (node) => {\n let r = node.radius + 16,\n nx1 = node.x - r,\n nx2 = node.x + r,\n ny1 = node.y - r,\n ny2 = node.y + r;\n return function(quad, x1, y1, x2, y2) {\n if (quad.point && (quad.point !== node)) {\n let x = node.x - quad.point.x,\n y = node.y - quad.point.y,\n l = Math.sqrt(x * x + y * y),\n r = node.radius + quad.point.radius;\n if (l < r) {\n l = (l - r) / l * 0.1;\n node.x -= x *= l;\n node.y -= y *= l;\n quad.point.x += x;\n quad.point.y += y;\n }\n }\n return x1 > nx2 || x2 < nx1 || y1 > ny2 || y2 < ny1;\n };\n }\n\n while (++i < n) q.visit(collide(realNodes[i]));\n\n allLinks.attr('x1', function(d) { return d.source.x; })\n .attr('y1', function(d) { return d.source.y; })\n .attr('x2', function(d) { return d.target.x; })\n .attr('y2', function(d) { return d.target.y; });\n\n // Translate the groups\n gnodes.attr('transform', function(d) {\n return 'translate(' + [d.x, d.y] + ')';\n });\n\n gnodes.select('.' + fstyle.directionArrow).each(drawDirectionArrow);\n\n });\n\n self.force.on('end', () => {\n gnodes.selectAll('[node_type=nucleotide]')\n .filter((d,i) => { if (i == 0) return true; else return false; })\n .each((d,i) => {\n //console.log(\"pos\", d.num, d.x, d.y);\n });\n\n //for (let uid in self.rnas) {\n // for (let i = 1; i < self.rnas[uid].pairtable[0]; i++) {\n // console.log('pt', i, self.rnas[uid].pairtable[i]);\n // }\n //}\n\n });\n\n self.changeColorScheme(self.colorScheme);\n\n if (self.options.animation) {\n self.force.start();\n }\n\n updateStyle();\n };\n\n self.transitionRNA = function(newStructure, nextFunction) {\n if (self.dotbracket == newStructure) {\n return;\n } else {\n self.dotbracket = newStructure;\n }\n //transition from an RNA which is already displayed to a new structure\n var duration = self.options.transitionDuration;\n\n var uids = self.graph.nodes\n .filter(function(d) { return d.nodeType == 'nucleotide'; })\n .map(function(d) { return d.uid; });\n\n let options = {'uids': uids};\n var newRNAJson = createInitialLayout(newStructure, options);\n\n let gnodes = visNodes.selectAll('g.gnode').data(newRNAJson.nodes, elementKey);\n var links = visLinks.selectAll('line.link').data(newRNAJson.links.filter(realLinkFilter), elementKey);\n\n if (duration === 0)\n gnodes.attr('transform', function(d) {\n return 'translate(' + [d.x, d.y] + ')';\n });\n else {\n gnodes.transition()\n .attr('transform', function(d) {\n return 'translate(' + [d.x, d.y] + ')'; }).duration(duration);\n }\n\n\n var newNodes = createNewNodes(gnodes.enter())\n .attr('transform', function(d) {\n if (typeof d.x != 'undefined' && typeof d.y != 'undefined')\n return 'translate(' + [0, 0] + ')';\n else\n return '';\n });\n\n if (duration === 0)\n gnodes.exit().remove();\n else\n gnodes.exit().transition()\n .attr('transform', function(d) {\n if (typeof d.x != 'undefined' && typeof d.y != 'undefined')\n return 'translate(' + [0, 0] + ')';\n else\n return '';\n });\n\n self.graph.nodes = gnodes.data();\n gnodes.select('.' + fstyle.directionArrow).each(drawDirectionArrow);\n self.changeColorScheme(self.colorScheme);\n updateStyle();\n self.centerView(duration);\n\n function endall(transition, callback) {\n if (transition.size() === 0) { setTimeout(callback, duration); }\n var n = 0;\n transition\n .each(function() { ++n; })\n .each('end', function() { if (!--n) callback.apply(this, arguments); });\n }\n\n function afterAnimation() {\n var newLinks = createNewLinks(links.enter());\n self.graph.links = links.data();\n self.changeColorScheme(self.colorScheme);\n updateStyle();\n\n if (typeof nextFunction != 'undefined')\n nextFunction();\n\n }\n\n links.exit().remove();\n\n if (duration === 0) {\n links\n .attr('x1', function(d) { return d.source.x; })\n .attr('y1', function(d) { return d.source.y; })\n .attr('x2', function(d) { return d.target.x; })\n .attr('y2', function(d) { return d.target.y; });\n\n var newLinks = createNewLinks(links.enter());\n self.graph.links = links.data();\n\n updateStyle();\n } else {\n links.transition()\n .attr('x1', function(d) { return d.source.x; })\n .attr('y1', function(d) { return d.source.y; })\n .attr('x2', function(d) { return d.target.x; })\n .attr('y2', function(d) { return d.target.y; })\n .duration(duration)\n .call(endall, afterAnimation);\n }\n\n if (duration === 0) {\n newNodes\n .attr('transform', function(d) {\n if (typeof d.x != 'undefined' && typeof d.y != 'undefined')\n return 'translate(' + [d.x, d.y] + ')';\n else\n return '';\n });\n } else {\n newNodes.transition()\n .attr('transform', function(d) {\n if (typeof d.x != 'undefined' && typeof d.y != 'undefined')\n return 'translate(' + [d.x, d.y] + ')';\n else\n return '';\n });\n }\n\n };\n\n /* Plot presentation related functions */\n let getBoundingBoxTransform = () => {\n // Center the view on the molecule(s) and scale it so that everything\n // fits in the window\n\n //no molecules, nothing to do\n if (self.graph.nodes.length === 0)\n return {'translate': [0,0], 'scale': 1};\n\n // Get the bounding box\n var minX = d3.min(self.graph.nodes.map(function(d) {return d.x;}));\n var minY = d3.min(self.graph.nodes.map(function(d) {return d.y;}));\n\n var maxX = d3.max(self.graph.nodes.map(function(d) {return d.x;}));\n var maxY = d3.max(self.graph.nodes.map(function(d) {return d.y;}));\n\n var maxRadius = d3.max(self.graph.nodes.map(function(d) { return d.radius; }));\n\n // The width and the height of the molecule\n var molWidth = maxX - minX;\n var molHeight = maxY - minY;\n\n // how much larger the drawing area is than the width and the height\n var widthRatio = self.options.svgW / (molWidth + 1);\n var heightRatio = self.options.svgH / (molHeight + 1);\n\n // we need to fit it in both directions, so we scale according to\n // the direction in which we need to shrink the most\n var minRatio = Math.min(widthRatio, heightRatio,\n self.options.maxNodeRadius / maxRadius) * 0.8;\n\n // the new dimensions of the molecule\n var newMolWidth = molWidth * minRatio;\n var newMolHeight = molHeight * minRatio;\n\n // translate so that it's in the center of the window\n var xTrans = -(minX) * minRatio + (self.options.svgW - newMolWidth) / 2;\n var yTrans = -(minY) * minRatio + (self.options.svgH - newMolHeight) / 2;\n\n return {'translate': [xTrans, yTrans], 'scale': minRatio};\n };\n\n self.centerView = function(duration = 0) {\n var bbTransform = getBoundingBoxTransform();\n\n if (bbTransform === null)\n return;\n\n // do the actual moving\n vis.transition().attr('transform',\n 'translate(' + bbTransform.translate + ')' + ' scale(' + bbTransform.scale + ')').duration(duration);\n\n // tell the zoomer what we did so that next we zoom, it uses the\n // transformation we entered here\n self.zoomer.translate(bbTransform.translate);\n self.zoomer.scale(bbTransform.scale);\n };\n\n self.setSize = (\n svgW = d3.select(element).node().offsetWidth,\n svgH = d3.select(element).node().offsetHeight\n ) => {\n // save width and height\n self.options.svgW = svgW;\n self.options.svgH = svgH;\n\n // set the viewBox\n svg.attr('viewBox', \"0 0 \" + svgW + \" \" + svgH)\n\n //Set the output range of the scales\n xScale.range([0, svgW]).domain([0, svgW]);\n yScale.range([0, svgH]).domain([0, svgH]);\n\n //re-attach the scales to the zoom behaviour\n self.zoomer.x(xScale)\n .y(yScale);\n self.brusher.x(xScale)\n .y(yScale);\n\n //resize the background\n svg.select('.background')\n .attr('width', svgW)\n .attr('height', svgH);\n\n // center the view\n self.centerView();\n }\n\n /* Style and color related functions */\n self.setOutlineColor = function(color) {\n var nodes = visNodes.selectAll('g.gnode').select('[node_type=nucleotide]');\n nodes.style('fill', color);\n }\n\n self.addCustomColors = function addCustomColors(json) {\n // Add a json file containing the custom colors\n self.customColors = json;\n self.changeColorScheme('custom');\n };\n\n self.addCustomColorsText = function(customColorsText) {\n let cs = new ColorScheme(customColorsText);\n self.customColors = cs.colorsJson;\n self.changeColorScheme('custom');\n };\n\n self.changeColorScheme = function(newColorScheme) {\n var proteinNodes = visNodes.selectAll('[node_type=protein]');\n\n proteinNodes.classed(fstyle.node, true)\n .attr('r', function(d) { return d.radius; });\n\n var gnodes = visNodes.selectAll('g.gnode');\n var circles = visNodes.selectAll('g.gnode').selectAll('circle');\n var nodes = visNodes.selectAll('g.gnode').select('[node_type=nucleotide]');\n self.colorScheme = newColorScheme;\n\n\n if (newColorScheme == 'sequence') {\n var scale = d3.scale.ordinal()\n .range(['#dbdb8d', '#98df8a', '#ff9896', '#aec7e8', '#aec7e8'])\n .domain(['A','C','G','U','T']);\n nodes.style('fill', function(d) {\n return scale(d.name);\n });\n\n } else if (newColorScheme == 'structure') {\n var scale = d3.scale.category10()\n .domain(['s','m','i','e','t','h','x'])\n .range(['lightgreen', '#ff9896', '#dbdb8d', 'lightsalmon',\n 'lightcyan', 'lightblue', 'transparent']);\n\n nodes.style('fill', function(d) {\n return scale(d.elemType);\n });\n\n } else if (newColorScheme == 'positions') {\n nodes.style('fill', function(d) {\n var scale = d3.scale.linear()\n .range(['#98df8a', '#dbdb8d', '#ff9896'])\n .interpolate(d3.interpolateLab)\n .domain([1, 1 + (d.rna.rnaLength - 1) / 2, d.rna.rnaLength]);\n\n return scale(d.num);\n });\n } else if (newColorScheme == 'custom') {\n // scale to be used in case the user passes scalar\n // values rather than color names\n if (typeof self.customColors != 'undefined' &&\n 'domain' in self.customColors &&\n 'range' in self.customColors) {\n var scale = d3.scale.linear()\n .interpolate(d3.interpolateLab)\n .domain(self.customColors.domain)\n .range(self.customColors.range);\n }\n\n let changeColors = (moleculeColors, d, scale) => {\n if (moleculeColors.hasOwnProperty(d.num)) {\n let val = parseFloat(moleculeColors[d.num]);\n\n if (isNaN(val)) {\n // passed in color is not a scalar, so\n // treat it as a color\n return moleculeColors[d.num];\n } else {\n // the user passed in a float, let's use a colormap\n // to convert it to a color\n return scale(val);\n }\n } else {\n return 'white';\n }\n }\n\n nodes.style('fill', function(d) {\n if (typeof self.customColors == 'undefined' ||\n !self.customColors.hasOwnProperty('colorValues')) {\n return 'white';\n }\n\n if (self.customColors.colorValues.hasOwnProperty(d.structName) &&\n self.customColors.colorValues[d.structName].hasOwnProperty(d.num)) {\n // if a molecule name is specified, it supercedes the default colors\n // (for which no molecule name has been specified)\n let moleculeColors = self.customColors.colorValues[d.structName];\n return changeColors(moleculeColors, d, scale);\n } else if (self.customColors.colorValues.hasOwnProperty('')) {\n let moleculeColors = self.customColors.colorValues[''];\n return changeColors(moleculeColors, d, scale);\n }\n\n return 'white';\n });\n }\n };\n\n let updateStyle = () => {\n // Numbering\n visNodes.selectAll('[node_type=label]').classed(fstyle.transparent, !self.displayParameters.displayNumbering);\n visNodes.selectAll('[label_type=label]').classed(fstyle.transparent, !self.displayParameters.displayNumbering);\n visLinks.selectAll('[link_type=label_link]').classed(fstyle.transparent, !self.displayParameters.displayNumbering);\n // Node Outline\n svg.selectAll('[node_type=nucleotide]').classed(fstyle.transparent, !self.displayParameters.displayNodeOutline);\n // Node Labels\n visNodes.selectAll('[label_type=nucleotide]').classed(fstyle.transparent, !self.displayParameters.displayNodeLabel);\n // Links\n svg.selectAll('[link_type=real],[link_type=basepair],[link_type=backbone],[link_type=pseudoknot],[link_type=protein_chain],[link_type=chain_chain],[link_type=external]').classed(fstyle.transparent, !self.displayParameters.displayLinks);\n // Pseudoknot Links\n svg.selectAll('[link_type=pseudoknot]').classed(fstyle.transparent, !self.displayParameters.displayPseudoknotLinks);\n // Protein Links\n svg.selectAll('[link_type=protein_chain]').classed(fstyle.transparent, !self.displayParameters.displayProteinLinks);\n // Fake Links\n visLinks.selectAll('[link_type=fake]').classed(fstyle.transparent, !self.options.displayAllLinks);\n visLinks.selectAll('[link_type=fake_fake]').classed(fstyle.transparent, !self.options.displayAllLinks);\n // direction Arrows\n svg.selectAll('.' + fstyle.directionArrow).classed(fstyle.transparent, !self.displayParameters.displayDirectionArrows);\n };\n\n /* RNA edditing related functions */\n let changeNode = function(nodeName, referenceNode) {\n // change the label of a node\n let rna = referenceNode.rna;\n\n let dotbracket = rnaUtilities.pairtableToDotbracket(rna.pairtable);\n let positions = rna.getPositions('nucleotide');\n let sequence = rna.seq\n let uids = rna.getUids();\n\n let newNodeNum = referenceNode.num;\n\n let newDotbracket = dotbracket;\n let newSequence = sequence.slice(0,newNodeNum-1) + nodeName + sequence.slice(newNodeNum);\n\n console.log('newSequence:', newSequence);\n\n console.log('uids:', uids);\n uids.splice(newNodeNum-1, 1, slugid.nice());\n let newPositions = positions;\n\n delete self.rnas[rna.uid];\n let newRNA = self.addRNA(newDotbracket, {'sequence': newSequence,\n 'positions': newPositions,\n 'uids': uids,\n 'centerView': false});\n }\n\n let insertNodeBeforeOrAfter = function(nodeName, referenceNode, positionOffset) {\n //insert a new node before or after another one\n //positionOffset specifies who far from the original to insert the new node\n let rna = referenceNode.rna;\n\n let dotbracket = rnaUtilities.pairtableToDotbracket(rna.pairtable);\n let positions = rna.getPositions('nucleotide');\n let sequence = rna.seq\n let uids = rna.getUids();\n\n let newNodeNum = referenceNode.num + positionOffset;\n\n let newDotbracket = dotbracket.slice(0,newNodeNum) + '.' + dotbracket.slice(newNodeNum);\n let newSequence = sequence.slice(0,newNodeNum) + nodeName + sequence.slice(newNodeNum);\n\n console.log('newSequence:', newSequence);\n\n uids.splice(newNodeNum, 0, slugid.nice());\n positions.splice(newNodeNum, 0, positions[newNodeNum - positionOffset-1]);\n\n let newUids = uids;\n let newPositions = positions;\n\n console.log('positions:', positions);\n console.log('new node positions:', newPositions);\n\n delete self.rnas[rna.uid];\n let newRNA = self.addRNA(newDotbracket, {'sequence': newSequence,\n 'positions': newPositions,\n 'uids': newUids,\n 'centerView': false});\n }\n\n let deleteNode = function(node) {\n console.log('deleting...', node);\n // get the dotbracket string for this rna\n let rna = node.rna;\n let pair = rna.pairtable[node.num];\n\n // remove basepairs for this node\n if (pair != 0) {\n rna.pairtable[node.num] = 0;\n rna.pairtable[pair] = 0;\n }\n\n let dotbracket = rnaUtilities.pairtableToDotbracket(rna.pairtable);\n let positions = rna.getPositions('nucleotide');\n let sequence = rna.seq\n let uids = rna.getUids();\n\n let newDotbracket = dotbracket.slice(0, node.num-1) + dotbracket.slice(node.num)\n let newPositions = positions.slice(0, node.num-1)\n .concat(positions.slice(node.num));\n let newSequence = sequence.slice(0, node.num-1) + sequence.slice(node.num)\n let newUids = uids.slice(0, node.num-1)\n .concat(uids.slice(node.num));\n\n delete self.rnas[rna.uid];\n let newRNA = self.addRNA(newDotbracket, {'sequence': newSequence,\n 'positions': newPositions,\n 'uids': newUids,\n 'centerView': false});\n\n console.log('new dotbracket:', newDotbracket);\n //recalculateGraph();\n\n //remove backbone links associated with this node\n\n //remove this node\n\n }\n\n let elementKey = (d) => {\n return d.uid;\n };\n\n let updateRnaGraph = function(r) {\n let nucleotidePositions = r.getPositions('nucleotide');\n let labelPositions = r.getPositions('label');\n\n let uids = r.getUids();\n\n r.recalculateElements()\n .elementsToJson()\n .addPseudoknots()\n .addPositions('nucleotide', nucleotidePositions)\n .addUids(uids)\n .addLabels(1, self.options.labelInterval)\n .addPositions('label', labelPositions)\n .reinforceStems()\n .reinforceLoops()\n .updateLinkUids();\n };\n\n let removeBackBoneLink = function(d) {\n if (d.target.num - d.source.num != 1) {\n console.log('ERROR: non adjacent nodes. Target:', d.target,\n 'Source:', d.source, 'Link:', d);\n return;\n }\n\n let rna = d.target.rna;\n let toRemove = [];\n\n for (let i = 0; i < rna.links.length; i++) {\n let link = rna.links[i];\n\n if (link.linkType != 'basepair')\n continue;\n\n if (link.source.num <= d.source.num && link.target.num >= d.target.num) {\n console.log('crossing basepair', link);\n toRemove.push(link);\n }\n }\n\n\n // Remove all base pairs that are between these two nodes and add them as extra\n // links\n console.log('toRemove:', toRemove);\n\n for (let i = 0; i < toRemove.length; i++) {\n rna.pairtable[toRemove[i].source.num] = 0;\n rna.pairtable[toRemove[i].target.num] = 0;\n\n toRemove[i].from = toRemove[i].source.num;\n toRemove[i].to = toRemove[i].target.num - d.source.num;\n }\n\n // extract the dotbracket string of the rna\n // cut it at the position of this backbone bond\n let sequence = rna.seq;\n let sequence1 = rna.seq.slice(0, d.source.num);\n let sequence2 = rna.seq.slice(d.source.num);\n\n let rnaDotBracket = rnaUtilities.pairtableToDotbracket(rna.pairtable);\n let dotBracket1 = rnaDotBracket.slice(0, d.source.num);\n let dotBracket2 = rnaDotBracket.slice(d.source.num)\n\n // get the nucleotide positions\n // cut them at the positions of the backbone bond\n let positions = rna.getPositions('nucleotide')\n let uids = rna.getUids();\n\n let positions1 = positions.slice(0, d.source.num);\n let positions2 = positions.slice(d.source.num);\n\n let uids1 = uids.slice(0, d.source.num);\n let uids2 = uids.slice(d.source.num);\n\n console.log('positions1:', positions1);\n console.log('positions2:', positions2);\n\n delete self.rnas[rna.uid];\n let rna1 = self.addRNA(dotBracket1, { 'sequence': sequence1,\n 'positions': positions1,\n 'uids': uids1 });\n let rna2 = self.addRNA(dotBracket2, { 'sequence': sequence2,\n 'positions': positions2,\n 'uids': uids2 });\n for (let i = 0; i < toRemove.length; i++) {\n console.log('rna1:', rna1);\n console.log('rna2:', rna2);\n console.log('toRemove[i]', toRemove[i]);\n self.extraLinks.push(\n {'source': rna1.nodes[toRemove[i].from-1],\n 'target': rna2.nodes[toRemove[i].to-1],\n 'value': 1,\n 'uid': slugid.nice(),\n 'linkType': 'intermolecule'});\n recalculateGraph();\n self.update();\n\n }\n console.log('self.extraLinks:', self.extraLinks);\n //self.extraLinks.push({'source': rna1.nodes[\n\n // create two new rnas\n // add their positions\n // add them back to the plot\n }\n\n var removeLink = function(d) {\n // remove a link between two nodes\n let index = self.graph.links.indexOf(d);\n console.log('removing link:', index);\n\n if (index > -1) {\n //remove a link\n //graph.links.splice(index, 1);\n\n // there should be two cases\n // 1. The link is within a single molecule\n\n if (d.source.rna == d.target.rna) {\n if (d.linkType == 'backbone') {\n console.log('trying to remove a backbone link', d.source.num, d.target.num);\n removeBackBoneLink(d);\n return;\n } else {\n let r = d.source.rna;\n r.addPseudoknots();\n r.pairtable[d.source.num] = 0;\n r.pairtable[d.target.num] = 0;\n\n updateRnaGraph(r);\n }\n } else {\n // 2. The link is between two different molecules\n let extraLinkIndex = self.extraLinks.indexOf(d);\n\n self.extraLinks.splice(extraLinkIndex, 1);\n }\n recalculateGraph();\n }\n self.update();\n };\n\n let addBackBoneLink = function(newLink) {\n // opposite of deleting a link\n // get the two dotbracket strings\n let rna1 = newLink.target.rna;\n let rna2 = newLink.source.rna;\n if (newLink.target.num == 1) {\n rna1 = newLink.source.rna;\n rna2 = newLink.target.rna;\n }\n\n let dotbracket1 = rnaUtilities.pairtableToDotbracket(rna1.pairtable);\n let dotbracket2 = rnaUtilities.pairtableToDotbracket(rna2.pairtable);\n\n let seq1 = rna1.seq;\n let seq2 = rna2.seq;\n\n let positions1 = rna1.getPositions('nucleotide');\n let positions2 = rna2.getPositions('nucleotide');\n\n // concatenate them\n let newDotbracket = dotbracket1 + dotbracket2;\n let newSeq = seq1 + seq2;\n let newPositions = positions1.concat(positions2);\n\n let toAddInternal = [];\n let toAddExternal = [];\n let toDelete = {};\n\n for (let i = 0; i < self.extraLinks.length; i++) {\n console.log('self.extraLinks[i]', self.extraLinks[i]);\n console.log('rna1:', rna1);\n console.log('rna2:', rna2);\n if (self.extraLinks[i].source.rna == rna1) {\n if ( self.extraLinks[i].target.rna == rna2) {\n // both ends of the extra link are within what will become the new molecule\n // need to be added as base pairs afterwards\n //self.extraLinks[i].from = self.extraLinks[i].source.num;\n //self.extraLinks[i].to = dotbracket1.length + self.extraLinks[i].target.num;\n //toAddInternal.push(self.extraLinks[i]);\n } else {\n // only one end of the extra link is within what will become the newly\n // created molecule, needs to remain an extra link\n // source will always be the unchanged molecule, whereas target will be\n // the newly created one\n toAddExternal.push({\n 'source': self.extraLinks[i].target,\n 'target': self.extraLinks[i].source.num\n });\n\n toDelete[self.extraLinks[i].uid] = true;\n }\n } else if (self.extraLinks[i].source.rna == rna2) {\n if ( self.extraLinks[i].target.rna == rna1) {\n // add internal link\n // both ends of the extra link are within what will become the new molecule\n // need to be added as base pairs afterwards\n //self.extraLinks[i].from = self.extraLinks[i].target.num;\n //self.extraLinks[i].to = dotbracket1.length + self.extraLinks[i].source.num;\n\n //toAddInternal.push(self.extraLinks[i]);\n } else {\n toAddExternal.push({\n 'source': self.extraLinks[i].target,\n 'target': self.extraLinks[i].source.num + dotbracket1.length\n });\n toDelete[self.extraLinks[i].uid] = true;\n }\n }\n\n if (self.extraLinks[i].target.rna == rna1) {\n if (self.extraLinks[i].source.rna == rna2) {\n // covered in previous if statement\n } else {\n // only one end of the extra link is within what will become the newly\n // created molecule, needs to remain an extra link\n toAddExternal.push({\n 'source': self.extraLinks[i].source,\n 'target': self.extraLinks[i].target.num\n });\n\n toDelete[self.extraLinks[i].uid] = true;\n }\n } else if (self.extraLinks[i].target.rna == rna2) {\n if (self.extraLinks[i].source.rna == rna1) {\n toAddExternal.push({\n 'source': self.extraLinks[i].source,\n 'target': self.extraLinks[i].target.num + dotbracket1.length\n });\n\n toDelete[self.extraLinks[i].uid] = true;\n }\n }\n }\n\n\n self.extraLinks = self.extraLinks.filter((e) => { return !(e.uid in toDelete) });\n\n delete self.rnas[rna1.uid];\n delete self.rnas[rna2.uid];\n\n let newRna = null;\n // create a new RNA\n if (self.options.animation)\n newRna = self.addRNA(newDotbracket, { 'sequence': newSeq,\n 'positions': newPositions,\n 'centerView': false});\n else\n newRna = self.addRNA(newDotbracket, { 'sequence': newSeq,\n 'centerView': false });\n\n\n\n // add new external links\n for (let i = 0; i < toAddExternal.length; i++) {\n self.extraLinks.push({\n 'source': toAddExternal[i].source,\n 'target': newRna.nodes[toAddExternal[i].target-1],\n 'value': 1,\n 'uid': slugid.nice(),\n 'linkType': 'intermolecule'\n });\n }\n\n recalculateGraph();\n self.update();\n console.log('self.extraLinks:', self.extraLinks);\n };\n\n function nudge(dx, dy) {\n // TODO currently unused\n node.filter(function(d) { return d.selected; })\n .attr('cx', function(d) { return d.x += dx; })\n .attr('cy', function(d) { return d.y += dy; });\n\n link.filter(function(d) { return d.source.selected; })\n .attr('x1', function(d) { return d.source.x; })\n .attr('y1', function(d) { return d.source.y; });\n\n link.filter(function(d) { return d.target.selected; })\n .attr('x2', function(d) { return d.target.x; })\n .attr('y2', function(d) { return d.target.y; });\n\n d3.event.preventDefault();\n }\n\n let nodeMouseup = function(d,i) {\n console.log(\"nodeMouseup\")\n let backbonePossible = true, basepairPossible = true;\n\n if (mousedownNode) {\n mouseupNode = d;\n\n // if the node isn't a nucleotide, we can't create a link\n if (mouseupNode.nodeType == 'middle' || mousedownNode.nodeType == 'middle' || mouseupNode.nodeType == 'label' || mousedownNode.nodeType == 'label')\n return;\n\n if (mouseupNode == mousedownNode) { resetMouseVars(); return; }\n let newLink = {source: mousedownNode, target: mouseupNode, linkType: 'basepair', value: 1, uid: slugid.nice()};\n\n for (let i = 0; i < self.graph.links.length; i++) {\n if ((self.graph.links[i].source == mousedownNode) ||\n (self.graph.links[i].target == mousedownNode) ||\n (self.graph.links[i].source == mouseupNode) ||\n (self.graph.links[i].target == mouseupNode)) {\n // either one of the nodes is already in a link\n\n // if any of the nodes are already involved in a basepair or a pseudoknot\n // then we can't make a basepair link\n if (self.graph.links[i].linkType == 'basepair' ||\n self.graph.links[i].linkType == 'pseudoknot' ||\n self.graph.links[i].linkType == 'intermolecule') {\n // although should be able to make a backbone link\n console.log('no basepair possible');\n basepairPossible = false;\n }\n }\n\n if (((self.graph.links[i].source == mouseupNode) &&\n (self.graph.links[i].target == mousedownNode)) ||\n ((self.graph.links[i].source == mousedownNode) &&\n (self.graph.links[i].target == mouseupNode))) {\n\n // if we're trying to make a link between two nodes which already have\n // a backbone between them, then we can't make a link\n if (self.graph.links[i].linkType == 'backbone') {\n return;\n }\n }\n }\n\n\n if (newLink.source.rna != newLink.target.rna) {\n // could be either a backbone link or an intermolecule link\n\n if ((newLink.source.num == 1 &&\n newLink.target.num == newLink.target.rna.rnaLength) ||\n (newLink.target.num == 1 &&\n newLink.source.num == newLink.source.rna.rnaLength)) {\n //\n let linkMenu = [\n {\n title: 'Backbone Link',\n action: function(elm, d, i) {\n linkContextMenuShown = false;\n console.log('Item #1 clicked!');\n console.log('The data for this circle is: ' + d);\n dragLine.attr('class', fstyle.transparent);\n addBackBoneLink(newLink);\n },\n disabled: false // optional, defaults to false\n },\n {\n title: 'Basepair Link',\n action: function(elm, d, i) {\n linkContextMenuShown = false;\n console.log('You have clicked the second item!');\n console.log('The data for this circle is: ' + d);\n dragLine.attr('class', fstyle.transparent);\n self.addLink(newLink);\n }\n }\n ]\n linkContextMenuShown = true;\n let linkContextMenu = contextMenu(linkMenu);\n console.log('newLinkMenu');\n linkContextMenu.apply(this, [d,i,true,\n function() { dragLine.attr('class', fstyle.transparent) }]);\n } else {\n // between end points but can't make a backbone\n if (basepairPossible)\n self.addLink(newLink);\n }\n } else {\n if (basepairPossible)\n self.addLink(newLink);\n }\n\n }\n };\n\n let nodeMousedown = function(d) {\n console.log(\"nodeMousedown\")\n if (!d.selected && !ctrlKeydown) {\n // if this node isn't selected, then we have to unselect every other node\n deselectAllNodes()\n }\n\n if (!shiftKeydown) {\n // only without shift, toggle select or select\n if (ctrlKeydown) {\n toggleSelectNode(d)\n } else {\n selectNode(d)\n }\n }\n\n if (shiftKeydown && self.options.editable) {\n // with shift key and editable continue to draw dragline\n mousedownNode = d;\n\n dragLine\n .attr('class', fstyle.dragLine)\n .attr('x1', mousedownNode.x)\n .attr('y1', mousedownNode.y)\n .attr('x2', mousedownNode.x)\n .attr('y2', mousedownNode.y);\n\n d3.event.stopPropagation();\n }\n };\n\n let linkClick = (d) => {\n if (!shiftKeydown) {\n return;\n }\n\n var invalidLinks = { //'backbone': true,\n 'fake': true,\n 'fake_fake': true,\n 'label_link': true};\n\n console.log('d.linkType:', d.linkType);\n if (d.linkType in invalidLinks )\n return;\n\n removeLink(d);\n };\n\n /* I/O functions */\n self.toJSON = function toJSON() {\n var data = {'rnas': self.rnas, 'extraLinks': self.extraLinks};\n var dataString = JSON.stringify(data, function(key, value) {\n //remove circular references\n if (key == 'rna') {\n return;\n } else {\n return value;\n }\n }, '\\t');\n return dataString;\n };\n\n self.fromJSON = function(jsonString) {\n var rnas, extraLinks;\n\n try{\n var data = JSON.parse(jsonString);\n rnas = data.rnas;\n extraLinks = data.extraLinks;\n } catch(err) {\n throw err;\n }\n\n for (var uid in rnas) {\n if (rnas[uid].type == 'rna') {\n r = new RNAGraph();\n\n r.seq = rnas[uid].seq;\n r.dotbracket = rnas[uid].dotbracket;\n r.circular = rnas[uid].circular;\n r.pairtable = rnas[uid].pairtable;\n r.uid = rnas[uid].uid;\n r.structName = rnas[uid].structName;\n r.nodes = rnas[uid].nodes;\n r.links = rnas[uid].links;\n r.rnaLength = rnas[uid].rnaLength;\n r.elements = rnas[uid].elements;\n r.nucsToNodes = rnas[uid].nucsToNodes;\n r.pseudoknotPairs = rnas[uid].pseudoknotPairs;\n } else {\n r = new ProteinGraph();\n r.size = rnas[uid].size;\n r.nodes = rnas[uid].nodes;\n r.uid = rnas[uid].uid;\n }\n\n self.addRNAJSON(r, false);\n }\n\n extraLinks.forEach(function(link) {\n self.extraLinks.push(link);\n });\n\n recalculateGraph();\n self.update();\n };\n\n self.addRNA = function(structure, passedOptions = {}) {\n let rnaJson = createInitialLayout(structure, passedOptions);\n let centerView = false;\n\n /*\n * Code to display the JSONs representing the structure\n *\n rnaJson.nodes[0].rna = null;\n rnaJson.nodes[0].nextNode = null;\n\n rnaJson.links[0].source = null;\n rnaJson.links[0].target = null;\n\n console.log(rnaJson.nodes[0]);\n console.log(rnaJson.links[0]);\n console.log(JSON.stringify(rnaJson.nodes[0],null,2));\n console.log(JSON.stringify(rnaJson.links[0],null,2));\n */\n\n if ('extraLinks' in passedOptions) {\n // presumably the passed in links are within the passed molecule\n let newLinks = self.addExternalLinks(rnaJson, passedOptions.extraLinks);\n\n self.extraLinks = self.extraLinks.concat(newLinks);\n }\n\n if ('centerPos' in passedOptions)\n self.addRNAJSON(rnaJson, {centerPos: passedOptions.centerPos,\n centerView: false})\n else if ('avoidOthers' in passedOptions)\n self.addRNAJSON(rnaJson, {avoidOthers: passedOptions.avoidOthers});\n else\n self.addRNAJSON(rnaJson, {centerView: passedOptions.centerView});\n\n return rnaJson;\n };\n\n self.addRNAJSON = function(rnaGraph,\n { avoidOthers = false,\n centerPos = null,\n centerView = true}\n ) {\n // Add an RNAGraph, which contains nodes and links as part of the\n // structure\n // Each RNA will have uid to identify it\n // when it is modified, it is replaced in the global list of RNAs\n //\n var maxX, minX;\n //console.log('centerView:', centerView);\n\n if (centerPos != null) {\n // center the newly created RNA at a given position\n let totalX = 0;\n let totalY = 0;\n let nodeCount = 0;\n\n rnaGraph.nodes.forEach(function(node) {\n totalX += node.x;\n totalY += node.y;\n nodeCount += 1;\n });\n\n if (nodeCount > 0) {\n // center the nodes at centerPos\n\n rnaGraph.nodes.forEach(function(node) {\n node.x = node.x + centerPos[0] - totalX / nodeCount;\n node.y = node.y + centerPos[1] - totalY / nodeCount;\n\n node.px = node.x;\n node.py = node.y;\n });\n }\n }\n\n if (avoidOthers) {\n if (self.graph.nodes.length > 0)\n maxX = d3.max(self.graph.nodes.map(function(d) { return d.x; }));\n else\n maxX = 0;\n\n minX = d3.min(rnaGraph.nodes.map(function(d) { return d.x; }));\n\n rnaGraph.nodes.forEach(function(node) {\n node.x += (maxX - minX) + 20;\n node.px += (maxX - minX);\n });\n }\n\n rnaGraph.nodes.forEach(function(node) {\n node.rna = rnaGraph;\n });\n\n self.rnas[rnaGraph.uid] = rnaGraph;\n recalculateGraph();\n\n self.update();\n\n if (centerView)\n self.centerView();\n\n return rnaGraph;\n };\n\n self.addNodes = function addNodes(json) {\n // add a new set of nodes from a json file\n\n // Resolve the sources and targets of the links so that they\n // are not just indeces into an array\n json.links.forEach(function(entry) {\n if (typeof entry.source == 'number') entry.source = json.nodes[entry.source];\n if (typeof entry.target == 'number') entry.target = json.nodes[entry.target];\n });\n\n // Get the maximum x and y values of the current graph\n // so that we don't place a new structure on top of the\n // old one\n if (self.graph.nodes.length > 0) {\n maxX = d3.max(self.graph.nodes.map(function(d) {return d.x;}));\n maxY = d3.max(self.graph.nodes.map(function(d) {return d.y;}));\n } else {\n maxX = 0;\n maxY = 0;\n }\n\n json.nodes.forEach(function(entry) {\n if (!(entry.rna.uid in self.rnas)) {\n self.rnas[entry.rna.uid] = entry.rna;\n }\n\n entry.x += maxX;\n //entry.y += maxY;\n\n entry.px += maxX;\n //entry.py += maxY;\n });\n\n r = new RNAGraph('','');\n r.nodes = json.nodes;\n r.links = json.links;\n\n //self.addRNA(r);\n recalculateGraph();\n\n self.update();\n self.centerView();\n };\n\n self.clearNodes = () => {\n self.graph.nodes = [];\n self.graph.links = [];\n\n self.rnas = {};\n self.extraLinks = [];\n\n self.update();\n };\n\n self.addLink = function(newLink) {\n // this means we have a new json, which means we have\n // to recalculate the structure and change the colors\n // appropriately\n //\n console.log('adding new link');\n if (newLink.source.rna == newLink.target.rna) {\n // must be a basepair\n let r = newLink.source.rna;\n\n r.pairtable[newLink.source.num] = newLink.target.num;\n r.pairtable[newLink.target.num] = newLink.source.num;\n\n updateRnaGraph(r);\n\n } else {\n //Add an extra link\n console.log('intermolecule');\n newLink.linkType = 'intermolecule';\n self.extraLinks.push(newLink);\n }\n recalculateGraph();\n self.update();\n };\n\n self.addExternalLinks = function(rnaJson, externalLinks) {\n let newLinks = [];\n\n for (let i = 0; i < externalLinks.length; i++) {\n let newLink = {linkType: 'external', value: 1, uid: slugid.nice(),\n source: null, target: null};\n // check if the source node is an array\n if (Object.prototype.toString.call(externalLinks[i][0]) === '[object Array]') {\n for (let j = 0; j < rnaJson.nodes.length; j++) {\n if ('nucs' in rnaJson.nodes[j]) {\n if (rnaJson.nodes[j].nucs.equals(externalLinks[i][0])) {\n newLink.source = rnaJson.nodes[j];\n break;\n }\n }\n }\n } else {\n for (let j = 0; j < rnaJson.nodes.length; j++) {\n if (rnaJson.nodes[j].num == externalLinks[i][0]) {\n newLink.source = rnaJson.nodes[j];\n }\n }\n }\n\n // check if the target node is an array\n if (Object.prototype.toString.call(externalLinks[i][1]) === '[object Array]') {\n for (let j = 0; j < rnaJson.nodes.length; j++) {\n if ('nucs' in rnaJson.nodes[j]) {\n if (rnaJson.nodes[j].nucs.equals(externalLinks[i][1])) {\n newLink.target = rnaJson.nodes[j];\n }\n }\n }\n } else {\n for (let j = 0; j < rnaJson.nodes.length; j++) {\n if (rnaJson.nodes[j].num == externalLinks[i][1]) {\n newLink.target = rnaJson.nodes[j];\n }\n }\n }\n\n if (newLink.source == null || newLink.target == null) {\n console.log('ERROR: source or target of new link not found:', newLink, externalLinks[i]);\n continue;\n }\n\n newLinks.push(newLink);\n }\n\n return newLinks;\n };\n\n self.getStructuresDotBracket = function() {\n console.log('self.rnas:', self.rnas);\n let sequence = [];\n let currIdx = 1;\n let nodeIdxs = {};\n let breaks = [];\n let pairtable = [];\n\n // add the nodes\n for (let uid in self.rnas) {\n let rna = self.rnas[uid];\n\n for (let j = 0; j < rna.nodes.length; j++) {\n let node = rna.nodes[j];\n\n if (node.nodeType != 'nucleotide')\n continue;\n\n console.log('node:', node);\n nodeIdxs[node.uid] = currIdx;\n currIdx += 1;\n\n sequence.push(node.name);\n }\n\n breaks.push(currIdx);\n }\n\n pairtable = [currIdx-1]\n for (let i = 0; i < currIdx; i++)\n pairtable.push(0)\n\n // add the links\n for (let uid in self.rnas) {\n let rna = self.rnas[uid];\n\n for (let j = 0; j < rna.links.length; j++) {\n let link = rna.links[j];\n\n if (link.linkType != 'basepair')\n continue;\n\n let idx1 = nodeIdxs[link.source.uid];\n let idx2 = nodeIdxs[link.target.uid];\n pairtable[idx1] = idx2;\n pairtable[idx2] = idx1;\n }\n }\n\n for (let i = 0; i < self.extraLinks.length; i++) {\n let link = self.extraLinks[i];\n\n let idx1 = nodeIdxs[link.source.uid];\n let idx2 = nodeIdxs[link.target.uid];\n\n pairtable[idx1] = idx2;\n pairtable[idx2] = idx1;\n }\n\n let structure = rnaUtilities.pairtableToDotbracket(pairtable).split('');\n\n for (let i = 0; i < breaks.length - 1; i++) {\n console.log('breaks[i]:', breaks[i]);\n sequence.splice(breaks[i] + i - 1, 0, '&');\n structure.splice(breaks[i] + i - 1, 0, '&');\n }\n\n console.log('sequence:', sequence, sequence.join(''));\n console.log('structure:', structure, structure.join(''));\n return [sequence.join(''), structure.join('')];\n };\n\n /* APIs */\n self.startAnimation = function() {\n self.options.animation = true;\n vis.selectAll('g.gnode')\n .call(drag);\n self.force.start();\n };\n\n self.stopAnimation = function() {\n self.options.animation = false;\n vis.selectAll('g.gnode')\n .on('mousedown.drag', null);\n self.force.stop();\n };\n\n self.resumeForce = function() {\n if (self.options.animation)\n self.force.resume();\n };\n\n self.setFriction = function(value) {\n self.force.friction(value);\n self.resumeForce();\n };\n\n self.setCharge = function(value) {\n self.force.charge(value);\n self.resumeForce();\n };\n\n self.setGravity = function(value) {\n self.force.gravity(value);\n self.resumeForce();\n };\n\n self.setPseudoknotStrength = function(value) {\n self.linkStrengths.pseudoknot = value;\n self.update();\n };\n\n self.displayNumbering = function(value) {\n self.displayParameters.displayNumbering = value;\n updateStyle();\n };\n\n self.displayNodeOutline = function(value) {\n self.displayParameters.displayNodeOutline = value;\n updateStyle();\n };\n\n self.displayNodeLabel = function(value) {\n self.displayParameters.displayNodeLabel = value;\n updateStyle();\n };\n\n self.displayLinks = function(value) {\n self.displayParameters.displayLinks = value;\n updateStyle();\n };\n\n self.displayPseudoknotLinks = function(value) {\n self.displayParameters.displayPseudoknotLinks = value;\n updateStyle();\n };\n\n self.displayProteinLinks = function(value) {\n self.displayParameters.displayProteinLinks = value;\n updateStyle();\n };\n\n self.displayDirectionArrows = function(value) {\n self.displayParameters.displayDirectionArrows = value;\n updateStyle();\n };\n}\n","import {RNAGraph} from './rnagraph.js';\n\nimport {simpleXyCoordinates} from './simplernaplot.js';\nimport {NAView} from './naview/naview.js'\n\nimport fstyle from './fornac.css';\n\nexport function rnaPlot(passedOptions = {}) {\n var options = {\n 'width': 300,\n 'height': 300,\n 'nucleotideRadius': 5,\n 'rnaEdgePadding': 1, // how far the leftmost, rightmost, topmost and bottomost\n // nucleotides are from the edge of the plot\n 'labelInterval': 10,\n 'showNucleotideLabels': true,\n 'startNucleotideNumber': 1,\n 'bundleExternalLinks': false,\n\n 'rnaLayout': 'simple', // simple or naview\n 'namePosition': '0 0' // for x and y either 0, 0.5 or 1\n };\n var options = Object.assign(options, passedOptions);\n\n var xScale, yScale;\n\n function createTransformToFillViewport(xValues, yValues) {\n // create transform that will scale the x and y values so that\n // they fill the available viewport\n let xExtent = d3.extent(xValues);\n let yExtent = d3.extent(yValues);\n\n // add the radius of the nucleotides\n xExtent[0] -= options.nucleotideRadius + options.rnaEdgePadding;\n yExtent[0] -= options.nucleotideRadius + options.rnaEdgePadding;\n\n xExtent[1] += options.nucleotideRadius + options.rnaEdgePadding;\n yExtent[1] += options.nucleotideRadius + options.rnaEdgePadding;\n\n // find out how wide and height the molecule\n var xRange = xExtent[1] - xExtent[0];\n var yRange = yExtent[1] - yExtent[0];\n\n // how much wider / taller is it than the available viewport\n var xExtra = xRange - options.width;\n var yExtra = yRange - options.height;\n\n // once we have a scale for one dimension, we can create the scale for the other\n // keeping the same expansion / shrinking ratio\n function createOtherScale(firstScale, newDomain, newRange) {\n var scaleFactor = (firstScale.range()[1] - firstScale.range()[0]) /\n (firstScale.domain()[1] - firstScale.domain()[0]);\n var newWidth = (newDomain[1] - newDomain[0]) * scaleFactor\n var newMargin = ((newRange[1] - newRange[0]) - newWidth) / 2;\n\n return {'scaleFactor': scaleFactor,\n 'scale': d3.scale.linear()\n .domain(newDomain)\n .range([newRange[0] + newMargin, newRange[1] - newMargin])};\n }\n\n var ret;\n\n if (xExtra > yExtra) {\n // we have to shrink more in the x-dimension than the y\n xScale = d3.scale.linear()\n .domain(xExtent)\n .range([0, options.width])\n\n ret = createOtherScale(xScale, yExtent, [0, options.height]);\n yScale = ret.scale;\n } else {\n // we have to shrink more in the x-dimension than the y\n yScale = d3.scale.linear()\n .domain(yExtent)\n .range([0, options.height])\n\n ret = createOtherScale(yScale, xExtent, [0, options.width]);\n xScale = ret.scale;\n }\n\n var xOffset = xScale.range()[0] - xScale.domain()[0];\n var yOffset = yScale.range()[0] - yScale.domain()[0];\n\n return 'translate(' + -(xScale.domain()[0] * ret.scaleFactor - xScale.range()[0]) +\n ',' + -(yScale.domain()[0] * ret.scaleFactor - yScale.range()[0]) + ')' +\n 'scale(' + ret.scaleFactor + ')';\n }\n\n function createNucleotides(selection, nucleotideNodes) {\n // create groupings for each nucleotide and label\n var gs = selection\n .selectAll('.gnode')\n .data(nucleotideNodes)\n .enter()\n .append('svg:g')\n .classed('gnode', true)\n .attr('transform', function(d) {\n return 'translate(' + d.x + ',' + d.y + ')';\n });\n\n var circles = gs.append('svg:circle')\n .classed(fstyle.node, true)\n .attr('node_type', 'nucleotide')\n .attr('base_type', (d) => { if (d.name) { return d.name.toLowerCase(); }})\n .attr('r', options.nucleotideRadius)\n\n\n if (options.showNucleotideLabels) {\n var nucleotideLabels = gs.append('svg:text')\n .text(function(d) { return d.name; })\n .classed(fstyle.nodeLabel, true)\n .append('svg:title')\n .text(function(d) { return d.struct_name + ':' + d.num; });\n }\n }\n\n function createLabels(selection, labelNodes) {\n // create groupings for each nucleotide and label\n\n var gs = selection\n .selectAll()\n .data(labelNodes)\n .enter()\n .append('svg:g')\n .classed('gnode', true)\n .attr('transform', function(d) {\n return 'translate(' + d.x + ',' + d.y + ')';\n });\n\n var circles = gs.append('svg:circle')\n .classed(fstyle.node, true)\n .attr('node_type', 'label')\n .attr('r', options.nucleotideRadius)\n\n var numberLabels = gs.append('svg:text')\n .classed(fstyle.nodeLabel, true)\n .text(function(d) { return d.name; })\n }\n\n function createName(selection, name) {\n let nameLabel = selection.append('svg:text')\n //.attr('dy', -10)\n .classed(fstyle.plotLabel, true)\n .text(name);\n\n let xyPos = options.namePosition.split(\" \", 2) // 0 0.5 1\n let xy = []\n let textBBox = nameLabel.node().getBBox()\n let textSize = [textBBox.width, textBBox.height]\n let plotSize = [options.width, options.height]\n\n for (let p in [0, 1]) {\n switch (xyPos[p]) {\n case '0':\n xy[p] = textSize[p] / 2\n break;\n case '1':\n xy[p] = plotSize[p] - textSize[p] / 2\n break;\n case '0.5':\n xy[p] = plotSize[p] / 2\n break;\n }\n }\n nameLabel.attr('x', xy[0]).attr('y', xy[1])\n }\n\n function makeExternalLinksBundle(selection, links) {\n var nodesDict = {};\n var linksList = [];\n links = links.filter(function(d) { return d.linkType == 'correct' || d.linkType == 'incorrect' || d.linkType == 'extra'; });\n\n selection.selectAll('[link-type=extra]')\n .remove();\n\n\n for (var i = 0; i < links.length; i++) {\n if (links[i].source === null || links[i].target === null)\n continue;\n\n nodesDict[links[i].source.uid] = links[i].source;\n nodesDict[links[i].target.uid] = links[i].target;\n\n linksList.push({'source': links[i].source.uid, 'target': links[i].target.uid, 'linkType': links[i].linkType, 'extraLinkType': links[i].extraLinkType}) ;\n }\n\n var fbundling = d3.ForceEdgeBundling().nodes(nodesDict).edges(linksList)\n .compatibility_threshold(0.8).step_size(0.2);\n var results = fbundling();\n\n var d3line = d3.svg.line()\n .x(function(d){return d.x;})\n .y(function(d){return d.y;})\n .interpolate('linear');\n\n for (var i = 0; i < results.length; i++) {\n var edge_subpoint_data = results[i];\n // for each of the arrays in the results\n // draw a line between the subdivions points for that edge\n\n selection.append('path').attr('d', d3line(edge_subpoint_data))\n .style('fill', 'none')\n .attr('link-type', function(d) { return linksList[i].linkType; })\n .attr('extra-link-type', function(d) { return linksList[i].extraLinkType; })\n .style('stroke-opacity',0.4); //use opacity as blending\n }\n\n }\n\n function createLinks(selection, links) {\n links = links.filter(function(d) { return d.source !== null && d.target !== null; });\n var gs = selection.selectAll('.link')\n .data(links)\n .enter()\n .append('svg:line')\n .attr('x1', function(d) { return d.source.x; })\n .attr('x2', function(d) { return d.target.x; })\n .attr('y1', function(d) { return d.source.y; })\n .attr('y2', function(d) { return d.target.y; })\n .attr('link-type', function(d) { return d.linkType; })\n .attr('extra-link-type', function(d) { return d.extraLinkType; })\n .classed('link', true)\n .classed(fstyle.link, true)\n }\n\n function chart(selection) {\n selection.each(function(data) {\n let plot = d3.select(this).append('g')\n .classed(fstyle.plot, true)\n\n // data should be a dictionary containing at least a structure\n // and possibly a sequence\n let rg = new RNAGraph(data.sequence, data.structure, data.name, options.startNucleotideNumber)\n .recalculateElements()\n .elementsToJson()\n .addName(data.name);\n\n data.rnaGraph = rg;\n // calculate the position of each nucleotide\n // the positions of the labels will be calculated in\n // the addLabels function\n let positions = [];\n\n if (options.rnaLayout === 'naview') {\n var naview = new NAView();\n var naViewPositions = naview.naview_xy_coordinates(rg.pairtable);\n\n for (var i = 0; i < naViewPositions.nbase; i++) {\n positions.push([naViewPositions.x[i], naViewPositions.y[i]]);\n }\n } else {\n positions = simpleXyCoordinates(rg.pairtable);\n }\n\n rg.addPositions('nucleotide', positions)\n //.reinforceStems()\n //.reinforceLoops()\n //.addExtraLinks(data.extraLinks)\n .addLabels(options.startNucleotideNumber, options.labelInterval);\n\n // create a transform that will fit the molecule to the\n // size of the viewport (canvas, svg, whatever)\n let fillViewportTransform = createTransformToFillViewport(\n rg.nodes.map(function(d) { return d.x; }),\n rg.nodes.map(function(d) { return d.y; })\n );\n plot.attr('transform', fillViewportTransform);\n\n let nucleotideNodes = rg.nodes.filter(function(d) {\n return d.nodeType == 'nucleotide';\n });\n\n let labelNodes = rg.nodes.filter(function(d) {\n return d.nodeType == 'label';\n });\n\n let links = rg.links;\n\n createLinks(plot, links);\n createNucleotides(plot, nucleotideNodes);\n createLabels(plot, labelNodes);\n createName(d3.select(this), data.name);\n\n if (options.bundleExternalLinks) {\n makeExternalLinksBundle(plot, links);\n }\n\n });\n }\n\n chart.width = function(_) {\n if (!arguments.length) return options.width;\n options.width = _;\n return chart;\n };\n\n chart.height = function(_) {\n if (!arguments.length) return options.height;\n options.height = _;\n return chart;\n };\n\n chart.showNucleotideLabels = function(_) {\n if (!arguments.length) return options.showNucleotideLabels;\n options.showNucleotideLabels = _;\n return chart;\n };\n\n chart.rnaEdgePadding = function(_) {\n if (!arguments.length) return options.rnaEdgePadding;\n options.rnaEdgePadding = _;\n return chart;\n };\n\n chart.nucleotideRadius = function(_) {\n if (!arguments.length) return options.nucleotideRadius;\n options.nucleotideRadius = _;\n return chart;\n };\n\n chart.labelInterval = function(_) {\n if (!arguments.length) return options.labelInterval;\n options.labelInterval = _;\n return chart;\n };\n\n chart.showNucleotideLabels = function(_) {\n if (!arguments.length) return options.showNucleotideLabels;\n options.showNucleotideLabels = _;\n return chart;\n };\n\n chart.startNucleotideNumber = function(_) {\n if (!arguments.length) return options.startNucleotideNumber;\n options.startNucleotideNumber = _;\n return chart;\n };\n\n chart.bundleExternalLinks = function(_) {\n if (!arguments.length) return options.bundleExternalLinks;\n options.bundleExternalLinks = _;\n return chart;\n };\n\n chart.rnaLayout = function(_) {\n if (!arguments.length) return options.rnaLayout;\n options.rnaLayout = _;\n return chart;\n };\n\n chart.namePosition = function(_) {\n if (!arguments.length) return options.namePosition;\n options.namePosition = _;\n return chart;\n };\n\n return chart;\n}\n","import {rnaPlot} from './rnaplot.js';\n\nexport function rnaTreemap(passedOptions = {}) {\n var options = {\n 'width': 300,\n 'height': 300,\n 'nucleotideRadius': 5,\n 'rnaEdgePadding': 1, // how far the leftmost, rightmost, topmost and bottomost\n // nucleotides are from the edge of the plot\n 'labelInterval': 10,\n 'showNucleotideLabels': true,\n 'startNucleotideNumber': 1,\n 'bundleExternalLinks': false,\n\n 'rnaLayout': 'simple', // simple or naview\n 'namePosition': '0 0', // for x and y either 0, 0.5 or 1\n };\n\n var options = Object.assign(options, passedOptions);\n\n function rnaTreemapNode(selection) {\n // create a background rectangle for each RNA structure\n selection.each(function(d) {\n d3.select(this)\n .attr('transform', function(d) { return 'translate(' + d.x + ',' + d.y + ')' })\n .append('rect')\n .attr('fill', 'transparent')\n .attr('width', function(d) { return Math.max(0, d.dx); })\n .attr('height', function(d) { return Math.max(0, d.dy); })\n\n // draw the actual RNA structure\n var chart = rnaPlot(options)\n .width( Math.max(0, d.dx))\n .height( Math.max(0, d.dy))\n\n if ('structure' in d) d3.select(this).call(chart)\n });\n }\n\n var chart = function(selection) {\n selection.each(function(data) {\n console.log('data:', data)\n // initialize the treemap structure\n // sample input\n // { 'name': 'blah',\n // 'children: [{'structure': '..((..))',\n // 'sequence': 'ACCGGCC',\n // 'size': 50}]\n // }\n var treemap = d3.layout.treemap()\n .size([options.width, options.height])\n .sticky(false)\n .value(function(d) { return d.size; });\n\n // create a new for each node in the treemap\n // this may be a little redundant, since we expect the calling\n // selection to contain their own g elements\n var gEnter = d3.select(this)\n .append('g')\n .classed('rnatreemap', true)\n var treemapGnodes = gEnter.datum(data).selectAll('.treemapnode')\n .data(treemap.nodes)\n .enter()\n .append('g')\n .classed('treemapnode', true)\n .call(rnaTreemapNode);\n });\n };\n\n chart.width = function(_) {\n if (!arguments.length) return options.width;\n options.width = _;\n return chart;\n };\n\n chart.height = function(_) {\n if (!arguments.length) return options.height;\n options.height = _;\n return chart;\n };\n\n chart.showNucleotideLabels = function(_) {\n if (!arguments.length) return options.showNucleotideLabels;\n options.showNucleotideLabels = _;\n return chart;\n };\n\n chart.rnaEdgePadding = function(_) {\n if (!arguments.length) return options.rnaEdgePadding;\n options.rnaEdgePadding = _;\n return chart;\n };\n\n chart.nucleotideRadius = function(_) {\n if (!arguments.length) return options.nucleotideRadius;\n options.nucleotideRadius = _;\n return chart;\n };\n\n chart.labelInterval = function(_) {\n if (!arguments.length) return options.labelInterval;\n options.labelInterval = _;\n return chart;\n };\n\n chart.showNucleotideLabels = function(_) {\n if (!arguments.length) return options.showNucleotideLabels;\n options.showNucleotideLabels = _;\n return chart;\n };\n\n 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factory(require(\"d3\"));\n\telse if(typeof define === 'function' && define.amd)\n\t\tdefine([\"d3\"], factory);\n\telse if(typeof exports === 'object')\n\t\texports[\"fornac\"] = factory(require(\"d3\"));\n\telse\n\t\troot[\"fornac\"] = factory(root[\"d3\"]);\n})(self, (__WEBPACK_EXTERNAL_MODULE__893__) => {\nreturn ","import {Loop} from './loop.js';\nimport {Region} from './region.js';\n\nexport function Connection() {\n\tthis.loop = new Loop();\n\tthis.region = new Region();\n\t// Start and end form the 1st base pair of the region.\n\tthis.start = null;\n this.end = null;\n\tthis.xrad = null;\n this.yrad = null;\n this.angle = null;\n\t// True if segment between this connection and the\n\t// next must be extruded out of the circle\n\tthis.extruded = null;\n\t// True if the extruded segment must be drawn long.\n\tthis.broken = null;\n\n\tthis._isNull = false;\n}\n\nConnection.prototype.isNull = function(){\n\treturn this._isNull;\n}\n\nConnection.prototype.setNull = function(isNull){\n\tthis._isNull = isNull;\n}\n\nConnection.prototype.getLoop = function(){\n\treturn this.loop;\n}\n\nConnection.prototype.setLoop = function(loop) {\n\tthis.loop = loop;\n}\n\nConnection.prototype.getRegion = function(){\n\treturn this.region;\n}\n\nConnection.prototype.setRegion = function(region){\n\tthis.region = region;\n}\n\nConnection.prototype.getStart = function(){\n\treturn this.start;\n}\n\nConnection.prototype.setStart = function(start) {\n\tthis.start = start;\n}\n\nConnection.prototype.getEnd = function(){\n\treturn this.end;\n}\n\nConnection.prototype.setEnd = function(end){\n\tthis.end = end;\n}\n\nConnection.prototype.getXrad = function(){\n\treturn this.xrad;\n}\n\nConnection.prototype.setXrad = function(xrad){\n\tthis.xrad = xrad;\n}\n\nConnection.prototype.getYrad = function(){\n\treturn this.yrad;\n}\n\nConnection.prototype.setYrad = function(yrad) {\n\tthis.yrad = yrad;\n}\n\nConnection.prototype.getAngle = function(){\n\treturn this.angle;\n}\n\nConnection.prototype.setAngle = function(angle){\n\tthis.angle = angle;\n}\n\nConnection.prototype.isExtruded = function(){\n\treturn this.extruded;\n}\n\nConnection.prototype.setExtruded = function(extruded){\n\tthis.extruded = extruded;\n}\n\nConnection.prototype.isBroken = function(){\n\treturn this.broken;\n}\n\nConnection.prototype.setBroken = function(broken){\n\tthis.broken = broken;\n}\n","import {Connection} from './connection.js';\n\nexport function Loop() {\n\tthis.nconnection = null;\n\tthis.connections = [];\n\tthis._connections = [];\n\tthis.number = null;\n\tthis.depth = null;\n\tthis.mark = null;\n\tthis.x = null;\n this.y = null;\n this.radius = null;\n}\n\nLoop.prototype.getNconnection = function() {\n\treturn this.nconnection;\n}\n\nLoop.prototype.setNconnection = function(nconnection) {\n\tthis.nconnection = nconnection;\n}\n\nLoop.prototype.setConnection = function(i, c){\n\tif (c != null){\n\t\tthis._connections[i] = c;\n }\n\telse {\n\t\tif (!this._connections[i]){\n\t\t\tthis._connections[i] = new Connection();\n\t\t}\n\t\tthis._connections[i].setNull(true);\n\t}\n}\n\nLoop.prototype.getConnection = function(i){\n\tvar Connection = require(\"./connection\");\n\tif (!this._connections[i]){\n this._connections[i] = new Connection();\n }\n\tvar c = this._connections[i];\n\tif (c.isNull()){\n\t\treturn null;\n }\n\telse {\n\t\treturn c;\n }\n}\n\nLoop.prototype.addConnection = function(i, c){\n\tthis._connections.push(c);\n}\n\nLoop.prototype.getNumber = function(){\n\treturn this.number;\n}\n\nLoop.prototype.setNumber = function(number){\n\tthis.number = number;\n}\n\nLoop.prototype.getDepth = function(){\n\treturn this.depth;\n}\n\nLoop.prototype.setDepth = function(depth){\n\tthis.depth = depth;\n}\n\nLoop.prototype.isMark = function(){\n\treturn this.mark;\n}\n\nLoop.prototype.setMark = function(mark){\n\tthis.mark = mark;\n}\n\nLoop.prototype.getX = function(){\n\treturn this.x;\n}\n\nLoop.prototype.setX = function(x){\n\tthis.x = x;\n}\n\nLoop.prototype.getY = function(){\n\treturn this.y;\n}\n\nLoop.prototype.setY = function(y){\n\tthis.y = y;\n}\n\nLoop.prototype.getRadius = function(){\n\treturn this.radius;\n}\n\nLoop.prototype.setRadius = function(radius){\n\tthis.radius = radius;\n}\n","export function Region() {\n\tthis._start1 = null;\n this._end1 = null;\n this._start2 = null;\n this._end2 = null;\n}\n\nRegion.prototype.getStart1 = function(){\n\treturn this._start1;\n}\n\nRegion.prototype.setStart1 = function(start1){\n\tthis._start1 = start1;\n}\n\nRegion.prototype.getEnd1 = function(){\n\treturn this._end1;\n}\n\nRegion.prototype.setEnd1 = function(end1){\n\tthis._end1 = end1;\n}\n\nRegion.prototype.getStart2 = function(){\n\treturn this._start2;\n}\n\nRegion.prototype.setStart2 = function(start2){\n\tthis._start2 = start2;\n}\n\nRegion.prototype.getEnd2 = function(){\n\treturn this._end2;\n}\n\nRegion.prototype.setEnd2 = function(end2){\n\tthis._end2 = end2;\n}\n","'use strict'\n\nexports.byteLength = byteLength\nexports.toByteArray = toByteArray\nexports.fromByteArray = fromByteArray\n\nvar lookup = []\nvar revLookup = []\nvar Arr = typeof Uint8Array !== 'undefined' ? Uint8Array : Array\n\nvar code = 'ABCDEFGHIJKLMNOPQRSTUVWXYZabcdefghijklmnopqrstuvwxyz0123456789+/'\nfor (var i = 0, len = code.length; i < len; ++i) {\n lookup[i] = code[i]\n revLookup[code.charCodeAt(i)] = i\n}\n\n// Support decoding URL-safe base64 strings, as Node.js does.\n// See: https://en.wikipedia.org/wiki/Base64#URL_applications\nrevLookup['-'.charCodeAt(0)] = 62\nrevLookup['_'.charCodeAt(0)] = 63\n\nfunction getLens (b64) {\n var len = b64.length\n\n if (len % 4 > 0) {\n throw new Error('Invalid string. Length must be a multiple of 4')\n }\n\n // Trim off extra bytes after placeholder bytes are found\n // See: https://github.com/beatgammit/base64-js/issues/42\n var validLen = b64.indexOf('=')\n if (validLen === -1) validLen = len\n\n var placeHoldersLen = validLen === len\n ? 0\n : 4 - (validLen % 4)\n\n return [validLen, placeHoldersLen]\n}\n\n// base64 is 4/3 + up to two characters of the original data\nfunction byteLength (b64) {\n var lens = getLens(b64)\n var validLen = lens[0]\n var placeHoldersLen = lens[1]\n return ((validLen + placeHoldersLen) * 3 / 4) - placeHoldersLen\n}\n\nfunction _byteLength (b64, validLen, placeHoldersLen) {\n return ((validLen + placeHoldersLen) * 3 / 4) - placeHoldersLen\n}\n\nfunction toByteArray (b64) {\n var tmp\n var lens = getLens(b64)\n var validLen = lens[0]\n var placeHoldersLen = lens[1]\n\n var arr = new Arr(_byteLength(b64, validLen, placeHoldersLen))\n\n var curByte = 0\n\n // if there are placeholders, only get up to the last complete 4 chars\n var len = placeHoldersLen > 0\n ? validLen - 4\n : validLen\n\n var i\n for (i = 0; i < len; i += 4) {\n tmp =\n (revLookup[b64.charCodeAt(i)] << 18) |\n (revLookup[b64.charCodeAt(i + 1)] << 12) |\n (revLookup[b64.charCodeAt(i + 2)] << 6) |\n revLookup[b64.charCodeAt(i + 3)]\n arr[curByte++] = (tmp >> 16) & 0xFF\n arr[curByte++] = (tmp >> 8) & 0xFF\n arr[curByte++] = tmp & 0xFF\n }\n\n if (placeHoldersLen === 2) {\n tmp =\n (revLookup[b64.charCodeAt(i)] << 2) |\n (revLookup[b64.charCodeAt(i + 1)] >> 4)\n arr[curByte++] = tmp & 0xFF\n }\n\n if (placeHoldersLen === 1) {\n tmp =\n (revLookup[b64.charCodeAt(i)] << 10) |\n (revLookup[b64.charCodeAt(i + 1)] << 4) |\n (revLookup[b64.charCodeAt(i + 2)] >> 2)\n arr[curByte++] = (tmp >> 8) & 0xFF\n arr[curByte++] = tmp & 0xFF\n }\n\n return arr\n}\n\nfunction tripletToBase64 (num) {\n return lookup[num >> 18 & 0x3F] +\n lookup[num >> 12 & 0x3F] +\n lookup[num >> 6 & 0x3F] +\n lookup[num & 0x3F]\n}\n\nfunction encodeChunk (uint8, start, end) {\n var tmp\n var output = []\n for (var i = start; i < end; i += 3) {\n tmp =\n ((uint8[i] << 16) & 0xFF0000) +\n ((uint8[i + 1] << 8) & 0xFF00) +\n (uint8[i + 2] & 0xFF)\n output.push(tripletToBase64(tmp))\n }\n return output.join('')\n}\n\nfunction fromByteArray (uint8) {\n var tmp\n var len = uint8.length\n var extraBytes = len % 3 // if we have 1 byte left, pad 2 bytes\n var parts = []\n var maxChunkLength = 16383 // must be multiple of 3\n\n // go through the array every three bytes, we'll deal with trailing stuff later\n for (var i = 0, len2 = len - extraBytes; i < len2; i += maxChunkLength) {\n parts.push(encodeChunk(uint8, i, (i + maxChunkLength) > len2 ? len2 : (i + maxChunkLength)))\n }\n\n // pad the end with zeros, but make sure to not forget the extra bytes\n if (extraBytes === 1) {\n tmp = uint8[len - 1]\n parts.push(\n lookup[tmp >> 2] +\n lookup[(tmp << 4) & 0x3F] +\n '=='\n )\n } else if (extraBytes === 2) {\n tmp = (uint8[len - 2] << 8) + uint8[len - 1]\n parts.push(\n lookup[tmp >> 10] +\n lookup[(tmp >> 4) & 0x3F] +\n lookup[(tmp << 2) & 0x3F] +\n '='\n )\n }\n\n return parts.join('')\n}\n","/*!\n * The buffer module from node.js, for the browser.\n *\n * @author Feross Aboukhadijeh \n * @license MIT\n */\n/* eslint-disable no-proto */\n\n'use strict'\n\nconst base64 = require('base64-js')\nconst ieee754 = require('ieee754')\nconst customInspectSymbol =\n (typeof Symbol === 'function' && typeof Symbol['for'] === 'function') // eslint-disable-line dot-notation\n ? Symbol['for']('nodejs.util.inspect.custom') // eslint-disable-line dot-notation\n : null\n\nexports.Buffer = Buffer\nexports.SlowBuffer = SlowBuffer\nexports.INSPECT_MAX_BYTES = 50\n\nconst K_MAX_LENGTH = 0x7fffffff\nexports.kMaxLength = K_MAX_LENGTH\n\n/**\n * If `Buffer.TYPED_ARRAY_SUPPORT`:\n * === true Use Uint8Array implementation (fastest)\n * === false Print warning and recommend using `buffer` v4.x which has an Object\n * implementation (most compatible, even IE6)\n *\n * Browsers that support typed arrays are IE 10+, Firefox 4+, Chrome 7+, Safari 5.1+,\n * Opera 11.6+, iOS 4.2+.\n *\n * We report that the browser does not support typed arrays if the are not subclassable\n * using __proto__. Firefox 4-29 lacks support for adding new properties to `Uint8Array`\n * (See: https://bugzilla.mozilla.org/show_bug.cgi?id=695438). IE 10 lacks support\n * for __proto__ and has a buggy typed array implementation.\n */\nBuffer.TYPED_ARRAY_SUPPORT = typedArraySupport()\n\nif (!Buffer.TYPED_ARRAY_SUPPORT && typeof console !== 'undefined' &&\n typeof console.error === 'function') {\n console.error(\n 'This browser lacks typed array (Uint8Array) support which is required by ' +\n '`buffer` v5.x. Use `buffer` v4.x if you require old browser support.'\n )\n}\n\nfunction typedArraySupport () {\n // Can typed array instances can be augmented?\n try {\n const arr = new Uint8Array(1)\n const proto = { foo: function () { return 42 } }\n Object.setPrototypeOf(proto, Uint8Array.prototype)\n Object.setPrototypeOf(arr, proto)\n return arr.foo() === 42\n } catch (e) {\n return false\n }\n}\n\nObject.defineProperty(Buffer.prototype, 'parent', {\n enumerable: true,\n get: function () {\n if (!Buffer.isBuffer(this)) return undefined\n return this.buffer\n }\n})\n\nObject.defineProperty(Buffer.prototype, 'offset', {\n enumerable: true,\n get: function () {\n if (!Buffer.isBuffer(this)) return undefined\n return this.byteOffset\n }\n})\n\nfunction createBuffer (length) {\n if (length > K_MAX_LENGTH) {\n throw new RangeError('The value \"' + length + '\" is invalid for option \"size\"')\n }\n // Return an augmented `Uint8Array` instance\n const buf = new Uint8Array(length)\n Object.setPrototypeOf(buf, Buffer.prototype)\n return buf\n}\n\n/**\n * The Buffer constructor returns instances of `Uint8Array` that have their\n * prototype changed to `Buffer.prototype`. Furthermore, `Buffer` is a subclass of\n * `Uint8Array`, so the returned instances will have all the node `Buffer` methods\n * and the `Uint8Array` methods. Square bracket notation works as expected -- it\n * returns a single octet.\n *\n * The `Uint8Array` prototype remains unmodified.\n */\n\nfunction Buffer (arg, encodingOrOffset, length) {\n // Common case.\n if (typeof arg === 'number') {\n if (typeof encodingOrOffset === 'string') {\n throw new TypeError(\n 'The \"string\" argument must be of type string. Received type number'\n )\n }\n return allocUnsafe(arg)\n }\n return from(arg, encodingOrOffset, length)\n}\n\nBuffer.poolSize = 8192 // not used by this implementation\n\nfunction from (value, encodingOrOffset, length) {\n if (typeof value === 'string') {\n return fromString(value, encodingOrOffset)\n }\n\n if (ArrayBuffer.isView(value)) {\n return fromArrayView(value)\n }\n\n if (value == null) {\n throw new TypeError(\n 'The first argument must be one of type string, Buffer, ArrayBuffer, Array, ' +\n 'or Array-like Object. Received type ' + (typeof value)\n )\n }\n\n if (isInstance(value, ArrayBuffer) ||\n (value && isInstance(value.buffer, ArrayBuffer))) {\n return fromArrayBuffer(value, encodingOrOffset, length)\n }\n\n if (typeof SharedArrayBuffer !== 'undefined' &&\n (isInstance(value, SharedArrayBuffer) ||\n (value && isInstance(value.buffer, SharedArrayBuffer)))) {\n return fromArrayBuffer(value, encodingOrOffset, length)\n }\n\n if (typeof value === 'number') {\n throw new TypeError(\n 'The \"value\" argument must not be of type number. Received type number'\n )\n }\n\n const valueOf = value.valueOf && value.valueOf()\n if (valueOf != null && valueOf !== value) {\n return Buffer.from(valueOf, encodingOrOffset, length)\n }\n\n const b = fromObject(value)\n if (b) return b\n\n if (typeof Symbol !== 'undefined' && Symbol.toPrimitive != null &&\n typeof value[Symbol.toPrimitive] === 'function') {\n return Buffer.from(value[Symbol.toPrimitive]('string'), encodingOrOffset, length)\n }\n\n throw new TypeError(\n 'The first argument must be one of type string, Buffer, ArrayBuffer, Array, ' +\n 'or Array-like Object. Received type ' + (typeof value)\n )\n}\n\n/**\n * Functionally equivalent to Buffer(arg, encoding) but throws a TypeError\n * if value is a number.\n * Buffer.from(str[, encoding])\n * Buffer.from(array)\n * Buffer.from(buffer)\n * Buffer.from(arrayBuffer[, byteOffset[, length]])\n **/\nBuffer.from = function (value, encodingOrOffset, length) {\n return from(value, encodingOrOffset, length)\n}\n\n// Note: Change prototype *after* Buffer.from is defined to workaround Chrome bug:\n// https://github.com/feross/buffer/pull/148\nObject.setPrototypeOf(Buffer.prototype, Uint8Array.prototype)\nObject.setPrototypeOf(Buffer, Uint8Array)\n\nfunction assertSize (size) {\n if (typeof size !== 'number') {\n throw new TypeError('\"size\" argument must be of type number')\n } else if (size < 0) {\n throw new RangeError('The value \"' + size + '\" is invalid for option \"size\"')\n }\n}\n\nfunction alloc (size, fill, encoding) {\n assertSize(size)\n if (size <= 0) {\n return createBuffer(size)\n }\n if (fill !== undefined) {\n // Only pay attention to encoding if it's a string. This\n // prevents accidentally sending in a number that would\n // be interpreted as a start offset.\n return typeof encoding === 'string'\n ? createBuffer(size).fill(fill, encoding)\n : createBuffer(size).fill(fill)\n }\n return createBuffer(size)\n}\n\n/**\n * Creates a new filled Buffer instance.\n * alloc(size[, fill[, encoding]])\n **/\nBuffer.alloc = function (size, fill, encoding) {\n return alloc(size, fill, encoding)\n}\n\nfunction allocUnsafe (size) {\n assertSize(size)\n return createBuffer(size < 0 ? 0 : checked(size) | 0)\n}\n\n/**\n * Equivalent to Buffer(num), by default creates a non-zero-filled Buffer instance.\n * */\nBuffer.allocUnsafe = function (size) {\n return allocUnsafe(size)\n}\n/**\n * Equivalent to SlowBuffer(num), by default creates a non-zero-filled Buffer instance.\n */\nBuffer.allocUnsafeSlow = function (size) {\n return allocUnsafe(size)\n}\n\nfunction fromString (string, encoding) {\n if (typeof encoding !== 'string' || encoding === '') {\n encoding = 'utf8'\n }\n\n if (!Buffer.isEncoding(encoding)) {\n throw new TypeError('Unknown encoding: ' + encoding)\n }\n\n const length = byteLength(string, encoding) | 0\n let buf = createBuffer(length)\n\n const actual = buf.write(string, encoding)\n\n if (actual !== length) {\n // Writing a hex string, for example, that contains invalid characters will\n // cause everything after the first invalid character to be ignored. (e.g.\n // 'abxxcd' will be treated as 'ab')\n buf = buf.slice(0, actual)\n }\n\n return buf\n}\n\nfunction fromArrayLike (array) {\n const length = array.length < 0 ? 0 : checked(array.length) | 0\n const buf = createBuffer(length)\n for (let i = 0; i < length; i += 1) {\n buf[i] = array[i] & 255\n }\n return buf\n}\n\nfunction fromArrayView (arrayView) {\n if (isInstance(arrayView, Uint8Array)) {\n const copy = new Uint8Array(arrayView)\n return fromArrayBuffer(copy.buffer, copy.byteOffset, copy.byteLength)\n }\n return fromArrayLike(arrayView)\n}\n\nfunction fromArrayBuffer (array, byteOffset, length) {\n if (byteOffset < 0 || array.byteLength < byteOffset) {\n throw new RangeError('\"offset\" is outside of buffer bounds')\n }\n\n if (array.byteLength < byteOffset + (length || 0)) {\n throw new RangeError('\"length\" is outside of buffer bounds')\n }\n\n let buf\n if (byteOffset === undefined && length === undefined) {\n buf = new Uint8Array(array)\n } else if (length === undefined) {\n buf = new Uint8Array(array, byteOffset)\n } else {\n buf = new Uint8Array(array, byteOffset, length)\n }\n\n // Return an augmented `Uint8Array` instance\n Object.setPrototypeOf(buf, Buffer.prototype)\n\n return buf\n}\n\nfunction fromObject (obj) {\n if (Buffer.isBuffer(obj)) {\n const len = checked(obj.length) | 0\n const buf = createBuffer(len)\n\n if (buf.length === 0) {\n return buf\n }\n\n obj.copy(buf, 0, 0, len)\n return buf\n }\n\n if (obj.length !== undefined) {\n if (typeof obj.length !== 'number' || numberIsNaN(obj.length)) {\n return createBuffer(0)\n }\n return fromArrayLike(obj)\n }\n\n if (obj.type === 'Buffer' && Array.isArray(obj.data)) {\n return fromArrayLike(obj.data)\n }\n}\n\nfunction checked (length) {\n // Note: cannot use `length < K_MAX_LENGTH` here because that fails when\n // length is NaN (which is otherwise coerced to zero.)\n if (length >= K_MAX_LENGTH) {\n throw new RangeError('Attempt to allocate Buffer larger than maximum ' +\n 'size: 0x' + K_MAX_LENGTH.toString(16) + ' bytes')\n }\n return length | 0\n}\n\nfunction SlowBuffer (length) {\n if (+length != length) { // eslint-disable-line eqeqeq\n length = 0\n }\n return Buffer.alloc(+length)\n}\n\nBuffer.isBuffer = function isBuffer (b) {\n return b != null && b._isBuffer === true &&\n b !== Buffer.prototype // so Buffer.isBuffer(Buffer.prototype) will be false\n}\n\nBuffer.compare = function compare (a, b) {\n if (isInstance(a, Uint8Array)) a = Buffer.from(a, a.offset, a.byteLength)\n if (isInstance(b, Uint8Array)) b = Buffer.from(b, b.offset, b.byteLength)\n if (!Buffer.isBuffer(a) || !Buffer.isBuffer(b)) {\n throw new TypeError(\n 'The \"buf1\", \"buf2\" arguments must be one of type Buffer or Uint8Array'\n )\n }\n\n if (a === b) return 0\n\n let x = a.length\n let y = b.length\n\n for (let i = 0, len = Math.min(x, y); i < len; ++i) {\n if (a[i] !== b[i]) {\n x = a[i]\n y = b[i]\n break\n }\n }\n\n if (x < y) return -1\n if (y < x) return 1\n return 0\n}\n\nBuffer.isEncoding = function isEncoding (encoding) {\n switch (String(encoding).toLowerCase()) {\n case 'hex':\n case 'utf8':\n case 'utf-8':\n case 'ascii':\n case 'latin1':\n case 'binary':\n case 'base64':\n case 'ucs2':\n case 'ucs-2':\n case 'utf16le':\n case 'utf-16le':\n return true\n default:\n return false\n }\n}\n\nBuffer.concat = function concat (list, length) {\n if (!Array.isArray(list)) {\n throw new TypeError('\"list\" argument must be an Array of Buffers')\n }\n\n if (list.length === 0) {\n return Buffer.alloc(0)\n }\n\n let i\n if (length === undefined) {\n length = 0\n for (i = 0; i < list.length; ++i) {\n length += list[i].length\n }\n }\n\n const buffer = Buffer.allocUnsafe(length)\n let pos = 0\n for (i = 0; i < list.length; ++i) {\n let buf = list[i]\n if (isInstance(buf, Uint8Array)) {\n if (pos + buf.length > buffer.length) {\n if (!Buffer.isBuffer(buf)) buf = Buffer.from(buf)\n buf.copy(buffer, pos)\n } else {\n Uint8Array.prototype.set.call(\n buffer,\n buf,\n pos\n )\n }\n } else if (!Buffer.isBuffer(buf)) {\n throw new TypeError('\"list\" argument must be an Array of Buffers')\n } else {\n buf.copy(buffer, pos)\n }\n pos += buf.length\n }\n return buffer\n}\n\nfunction byteLength (string, encoding) {\n if (Buffer.isBuffer(string)) {\n return string.length\n }\n if (ArrayBuffer.isView(string) || isInstance(string, ArrayBuffer)) {\n return string.byteLength\n }\n if (typeof string !== 'string') {\n throw new TypeError(\n 'The \"string\" argument must be one of type string, Buffer, or ArrayBuffer. ' +\n 'Received type ' + typeof string\n )\n }\n\n const len = string.length\n const mustMatch = (arguments.length > 2 && arguments[2] === true)\n if (!mustMatch && len === 0) return 0\n\n // Use a for loop to avoid recursion\n let loweredCase = false\n for (;;) {\n switch (encoding) {\n case 'ascii':\n case 'latin1':\n case 'binary':\n return len\n case 'utf8':\n case 'utf-8':\n return utf8ToBytes(string).length\n case 'ucs2':\n case 'ucs-2':\n case 'utf16le':\n case 'utf-16le':\n return len * 2\n case 'hex':\n return len >>> 1\n case 'base64':\n return base64ToBytes(string).length\n default:\n if (loweredCase) {\n return mustMatch ? -1 : utf8ToBytes(string).length // assume utf8\n }\n encoding = ('' + encoding).toLowerCase()\n loweredCase = true\n }\n }\n}\nBuffer.byteLength = byteLength\n\nfunction slowToString (encoding, start, end) {\n let loweredCase = false\n\n // No need to verify that \"this.length <= MAX_UINT32\" since it's a read-only\n // property of a typed array.\n\n // This behaves neither like String nor Uint8Array in that we set start/end\n // to their upper/lower bounds if the value passed is out of range.\n // undefined is handled specially as per ECMA-262 6th Edition,\n // Section 13.3.3.7 Runtime Semantics: KeyedBindingInitialization.\n if (start === undefined || start < 0) {\n start = 0\n }\n // Return early if start > this.length. Done here to prevent potential uint32\n // coercion fail below.\n if (start > this.length) {\n return ''\n }\n\n if (end === undefined || end > this.length) {\n end = this.length\n }\n\n if (end <= 0) {\n return ''\n }\n\n // Force coercion to uint32. This will also coerce falsey/NaN values to 0.\n end >>>= 0\n start >>>= 0\n\n if (end <= start) {\n return ''\n }\n\n if (!encoding) encoding = 'utf8'\n\n while (true) {\n switch (encoding) {\n case 'hex':\n return hexSlice(this, start, end)\n\n case 'utf8':\n case 'utf-8':\n return utf8Slice(this, start, end)\n\n case 'ascii':\n return asciiSlice(this, start, end)\n\n case 'latin1':\n case 'binary':\n return latin1Slice(this, start, end)\n\n case 'base64':\n return base64Slice(this, start, end)\n\n case 'ucs2':\n case 'ucs-2':\n case 'utf16le':\n case 'utf-16le':\n return utf16leSlice(this, start, end)\n\n default:\n if (loweredCase) throw new TypeError('Unknown encoding: ' + encoding)\n encoding = (encoding + '').toLowerCase()\n loweredCase = true\n }\n }\n}\n\n// This property is used by `Buffer.isBuffer` (and the `is-buffer` npm package)\n// to detect a Buffer instance. It's not possible to use `instanceof Buffer`\n// reliably in a browserify context because there could be multiple different\n// copies of the 'buffer' package in use. This method works even for Buffer\n// instances that were created from another copy of the `buffer` package.\n// See: https://github.com/feross/buffer/issues/154\nBuffer.prototype._isBuffer = true\n\nfunction swap (b, n, m) {\n const i = b[n]\n b[n] = b[m]\n b[m] = i\n}\n\nBuffer.prototype.swap16 = function swap16 () {\n const len = this.length\n if (len % 2 !== 0) {\n throw new RangeError('Buffer size must be a multiple of 16-bits')\n }\n for (let i = 0; i < len; i += 2) {\n swap(this, i, i + 1)\n }\n return this\n}\n\nBuffer.prototype.swap32 = function swap32 () {\n const len = this.length\n if (len % 4 !== 0) {\n throw new RangeError('Buffer size must be a multiple of 32-bits')\n }\n for (let i = 0; i < len; i += 4) {\n swap(this, i, i + 3)\n swap(this, i + 1, i + 2)\n }\n return this\n}\n\nBuffer.prototype.swap64 = function swap64 () {\n const len = this.length\n if (len % 8 !== 0) {\n throw new RangeError('Buffer size must be a multiple of 64-bits')\n }\n for (let i = 0; i < len; i += 8) {\n swap(this, i, i + 7)\n swap(this, i + 1, i + 6)\n swap(this, i + 2, i + 5)\n swap(this, i + 3, i + 4)\n }\n return this\n}\n\nBuffer.prototype.toString = function toString () {\n const length = this.length\n if (length === 0) return ''\n if (arguments.length === 0) return utf8Slice(this, 0, length)\n return slowToString.apply(this, arguments)\n}\n\nBuffer.prototype.toLocaleString = Buffer.prototype.toString\n\nBuffer.prototype.equals = function equals (b) {\n if (!Buffer.isBuffer(b)) throw new TypeError('Argument must be a Buffer')\n if (this === b) return true\n return Buffer.compare(this, b) === 0\n}\n\nBuffer.prototype.inspect = function inspect () {\n let str = ''\n const max = exports.INSPECT_MAX_BYTES\n str = this.toString('hex', 0, max).replace(/(.{2})/g, '$1 ').trim()\n if (this.length > max) str += ' ... '\n return ''\n}\nif (customInspectSymbol) {\n Buffer.prototype[customInspectSymbol] = Buffer.prototype.inspect\n}\n\nBuffer.prototype.compare = function compare (target, start, end, thisStart, thisEnd) {\n if (isInstance(target, Uint8Array)) {\n target = Buffer.from(target, target.offset, target.byteLength)\n }\n if (!Buffer.isBuffer(target)) {\n throw new TypeError(\n 'The \"target\" argument must be one of type Buffer or Uint8Array. ' +\n 'Received type ' + (typeof target)\n )\n }\n\n if (start === undefined) {\n start = 0\n }\n if (end === undefined) {\n end = target ? target.length : 0\n }\n if (thisStart === undefined) {\n thisStart = 0\n }\n if (thisEnd === undefined) {\n thisEnd = this.length\n }\n\n if (start < 0 || end > target.length || thisStart < 0 || thisEnd > this.length) {\n throw new RangeError('out of range index')\n }\n\n if (thisStart >= thisEnd && start >= end) {\n return 0\n }\n if (thisStart >= thisEnd) {\n return -1\n }\n if (start >= end) {\n return 1\n }\n\n start >>>= 0\n end >>>= 0\n thisStart >>>= 0\n thisEnd >>>= 0\n\n if (this === target) return 0\n\n let x = thisEnd - thisStart\n let y = end - start\n const len = Math.min(x, y)\n\n const thisCopy = this.slice(thisStart, thisEnd)\n const targetCopy = target.slice(start, end)\n\n for (let i = 0; i < len; ++i) {\n if (thisCopy[i] !== targetCopy[i]) {\n x = thisCopy[i]\n y = targetCopy[i]\n break\n }\n }\n\n if (x < y) return -1\n if (y < x) return 1\n return 0\n}\n\n// Finds either the first index of `val` in `buffer` at offset >= `byteOffset`,\n// OR the last index of `val` in `buffer` at offset <= `byteOffset`.\n//\n// Arguments:\n// - buffer - a Buffer to search\n// - val - a string, Buffer, or number\n// - byteOffset - an index into `buffer`; will be clamped to an int32\n// - encoding - an optional encoding, relevant is val is a string\n// - dir - true for indexOf, false for lastIndexOf\nfunction bidirectionalIndexOf (buffer, val, byteOffset, encoding, dir) {\n // Empty buffer means no match\n if (buffer.length === 0) return -1\n\n // Normalize byteOffset\n if (typeof byteOffset === 'string') {\n encoding = byteOffset\n byteOffset = 0\n } else if (byteOffset > 0x7fffffff) {\n byteOffset = 0x7fffffff\n } else if (byteOffset < -0x80000000) {\n byteOffset = -0x80000000\n }\n byteOffset = +byteOffset // Coerce to Number.\n if (numberIsNaN(byteOffset)) {\n // byteOffset: it it's undefined, null, NaN, \"foo\", etc, search whole buffer\n byteOffset = dir ? 0 : (buffer.length - 1)\n }\n\n // Normalize byteOffset: negative offsets start from the end of the buffer\n if (byteOffset < 0) byteOffset = buffer.length + byteOffset\n if (byteOffset >= buffer.length) {\n if (dir) return -1\n else byteOffset = buffer.length - 1\n } else if (byteOffset < 0) {\n if (dir) byteOffset = 0\n else return -1\n }\n\n // Normalize val\n if (typeof val === 'string') {\n val = Buffer.from(val, encoding)\n }\n\n // Finally, search either indexOf (if dir is true) or lastIndexOf\n if (Buffer.isBuffer(val)) {\n // Special case: looking for empty string/buffer always fails\n if (val.length === 0) {\n return -1\n }\n return arrayIndexOf(buffer, val, byteOffset, encoding, dir)\n } else if (typeof val === 'number') {\n val = val & 0xFF // Search for a byte value [0-255]\n if (typeof Uint8Array.prototype.indexOf === 'function') {\n if (dir) {\n return Uint8Array.prototype.indexOf.call(buffer, val, byteOffset)\n } else {\n return Uint8Array.prototype.lastIndexOf.call(buffer, val, byteOffset)\n }\n }\n return arrayIndexOf(buffer, [val], byteOffset, encoding, dir)\n }\n\n throw new TypeError('val must be string, number or Buffer')\n}\n\nfunction arrayIndexOf (arr, val, byteOffset, encoding, dir) {\n let indexSize = 1\n let arrLength = arr.length\n let valLength = val.length\n\n if (encoding !== undefined) {\n encoding = String(encoding).toLowerCase()\n if (encoding === 'ucs2' || encoding === 'ucs-2' ||\n encoding === 'utf16le' || encoding === 'utf-16le') {\n if (arr.length < 2 || val.length < 2) {\n return -1\n }\n indexSize = 2\n arrLength /= 2\n valLength /= 2\n byteOffset /= 2\n }\n }\n\n function read (buf, i) {\n if (indexSize === 1) {\n return buf[i]\n } else {\n return buf.readUInt16BE(i * indexSize)\n }\n }\n\n let i\n if (dir) {\n let foundIndex = -1\n for (i = byteOffset; i < arrLength; i++) {\n if (read(arr, i) === read(val, foundIndex === -1 ? 0 : i - foundIndex)) {\n if (foundIndex === -1) foundIndex = i\n if (i - foundIndex + 1 === valLength) return foundIndex * indexSize\n } else {\n if (foundIndex !== -1) i -= i - foundIndex\n foundIndex = -1\n }\n }\n } else {\n if (byteOffset + valLength > arrLength) byteOffset = arrLength - valLength\n for (i = byteOffset; i >= 0; i--) {\n let found = true\n for (let j = 0; j < valLength; j++) {\n if (read(arr, i + j) !== read(val, j)) {\n found = false\n break\n }\n }\n if (found) return i\n }\n }\n\n return -1\n}\n\nBuffer.prototype.includes = function includes (val, byteOffset, encoding) {\n return this.indexOf(val, byteOffset, encoding) !== -1\n}\n\nBuffer.prototype.indexOf = function indexOf (val, byteOffset, encoding) {\n return bidirectionalIndexOf(this, val, byteOffset, encoding, true)\n}\n\nBuffer.prototype.lastIndexOf = function lastIndexOf (val, byteOffset, encoding) {\n return bidirectionalIndexOf(this, val, byteOffset, encoding, false)\n}\n\nfunction hexWrite (buf, string, offset, length) {\n offset = Number(offset) || 0\n const remaining = buf.length - offset\n if (!length) {\n length = remaining\n } else {\n length = Number(length)\n if (length > remaining) {\n length = remaining\n }\n }\n\n const strLen = string.length\n\n if (length > strLen / 2) {\n length = strLen / 2\n }\n let i\n for (i = 0; i < length; ++i) {\n const parsed = parseInt(string.substr(i * 2, 2), 16)\n if (numberIsNaN(parsed)) return i\n buf[offset + i] = parsed\n }\n return i\n}\n\nfunction utf8Write (buf, string, offset, length) {\n return blitBuffer(utf8ToBytes(string, buf.length - offset), buf, offset, length)\n}\n\nfunction asciiWrite (buf, string, offset, length) {\n return blitBuffer(asciiToBytes(string), buf, offset, length)\n}\n\nfunction base64Write (buf, string, offset, length) {\n return blitBuffer(base64ToBytes(string), buf, offset, length)\n}\n\nfunction ucs2Write (buf, string, offset, length) {\n return blitBuffer(utf16leToBytes(string, buf.length - offset), buf, offset, length)\n}\n\nBuffer.prototype.write = function write (string, offset, length, encoding) {\n // Buffer#write(string)\n if (offset === undefined) {\n encoding = 'utf8'\n length = this.length\n offset = 0\n // Buffer#write(string, encoding)\n } else if (length === undefined && typeof offset === 'string') {\n encoding = offset\n length = this.length\n offset = 0\n // Buffer#write(string, offset[, length][, encoding])\n } else if (isFinite(offset)) {\n offset = offset >>> 0\n if (isFinite(length)) {\n length = length >>> 0\n if (encoding === undefined) encoding = 'utf8'\n } else {\n encoding = length\n length = undefined\n }\n } else {\n throw new Error(\n 'Buffer.write(string, encoding, offset[, length]) is no longer supported'\n )\n }\n\n const remaining = this.length - offset\n if (length === undefined || length > remaining) length = remaining\n\n if ((string.length > 0 && (length < 0 || offset < 0)) || offset > this.length) {\n throw new RangeError('Attempt to write outside buffer bounds')\n }\n\n if (!encoding) encoding = 'utf8'\n\n let loweredCase = false\n for (;;) {\n switch (encoding) {\n case 'hex':\n return hexWrite(this, string, offset, length)\n\n case 'utf8':\n case 'utf-8':\n return utf8Write(this, string, offset, length)\n\n case 'ascii':\n case 'latin1':\n case 'binary':\n return asciiWrite(this, string, offset, length)\n\n case 'base64':\n // Warning: maxLength not taken into account in base64Write\n return base64Write(this, string, offset, length)\n\n case 'ucs2':\n case 'ucs-2':\n case 'utf16le':\n case 'utf-16le':\n return ucs2Write(this, string, offset, length)\n\n default:\n if (loweredCase) throw new TypeError('Unknown encoding: ' + encoding)\n encoding = ('' + encoding).toLowerCase()\n loweredCase = true\n }\n }\n}\n\nBuffer.prototype.toJSON = function toJSON () {\n return {\n type: 'Buffer',\n data: Array.prototype.slice.call(this._arr || this, 0)\n }\n}\n\nfunction base64Slice (buf, start, end) {\n if (start === 0 && end === buf.length) {\n return base64.fromByteArray(buf)\n } else {\n return base64.fromByteArray(buf.slice(start, end))\n }\n}\n\nfunction utf8Slice (buf, start, end) {\n end = Math.min(buf.length, end)\n const res = []\n\n let i = start\n while (i < end) {\n const firstByte = buf[i]\n let codePoint = null\n let bytesPerSequence = (firstByte > 0xEF)\n ? 4\n : (firstByte > 0xDF)\n ? 3\n : (firstByte > 0xBF)\n ? 2\n : 1\n\n if (i + bytesPerSequence <= end) {\n let secondByte, thirdByte, fourthByte, tempCodePoint\n\n switch (bytesPerSequence) {\n case 1:\n if (firstByte < 0x80) {\n codePoint = firstByte\n }\n break\n case 2:\n secondByte = buf[i + 1]\n if ((secondByte & 0xC0) === 0x80) {\n tempCodePoint = (firstByte & 0x1F) << 0x6 | (secondByte & 0x3F)\n if (tempCodePoint > 0x7F) {\n codePoint = tempCodePoint\n }\n }\n break\n case 3:\n secondByte = buf[i + 1]\n thirdByte = buf[i + 2]\n if ((secondByte & 0xC0) === 0x80 && (thirdByte & 0xC0) === 0x80) {\n tempCodePoint = (firstByte & 0xF) << 0xC | (secondByte & 0x3F) << 0x6 | (thirdByte & 0x3F)\n if (tempCodePoint > 0x7FF && (tempCodePoint < 0xD800 || tempCodePoint > 0xDFFF)) {\n codePoint = tempCodePoint\n }\n }\n break\n case 4:\n secondByte = buf[i + 1]\n thirdByte = buf[i + 2]\n fourthByte = buf[i + 3]\n if ((secondByte & 0xC0) === 0x80 && (thirdByte & 0xC0) === 0x80 && (fourthByte & 0xC0) === 0x80) {\n tempCodePoint = (firstByte & 0xF) << 0x12 | (secondByte & 0x3F) << 0xC | (thirdByte & 0x3F) << 0x6 | (fourthByte & 0x3F)\n if (tempCodePoint > 0xFFFF && tempCodePoint < 0x110000) {\n codePoint = tempCodePoint\n }\n }\n }\n }\n\n if (codePoint === null) {\n // we did not generate a valid codePoint so insert a\n // replacement char (U+FFFD) and advance only 1 byte\n codePoint = 0xFFFD\n bytesPerSequence = 1\n } else if (codePoint > 0xFFFF) {\n // encode to utf16 (surrogate pair dance)\n codePoint -= 0x10000\n res.push(codePoint >>> 10 & 0x3FF | 0xD800)\n codePoint = 0xDC00 | codePoint & 0x3FF\n }\n\n res.push(codePoint)\n i += bytesPerSequence\n }\n\n return decodeCodePointsArray(res)\n}\n\n// Based on http://stackoverflow.com/a/22747272/680742, the browser with\n// the lowest limit is Chrome, with 0x10000 args.\n// We go 1 magnitude less, for safety\nconst MAX_ARGUMENTS_LENGTH = 0x1000\n\nfunction decodeCodePointsArray (codePoints) {\n const len = codePoints.length\n if (len <= MAX_ARGUMENTS_LENGTH) {\n return String.fromCharCode.apply(String, codePoints) // avoid extra slice()\n }\n\n // Decode in chunks to avoid \"call stack size exceeded\".\n let res = ''\n let i = 0\n while (i < len) {\n res += String.fromCharCode.apply(\n String,\n codePoints.slice(i, i += MAX_ARGUMENTS_LENGTH)\n )\n }\n return res\n}\n\nfunction asciiSlice (buf, start, end) {\n let ret = ''\n end = Math.min(buf.length, end)\n\n for (let i = start; i < end; ++i) {\n ret += String.fromCharCode(buf[i] & 0x7F)\n }\n return ret\n}\n\nfunction latin1Slice (buf, start, end) {\n let ret = ''\n end = Math.min(buf.length, end)\n\n for (let i = start; i < end; ++i) {\n ret += String.fromCharCode(buf[i])\n }\n return ret\n}\n\nfunction hexSlice (buf, start, end) {\n const len = buf.length\n\n if (!start || start < 0) start = 0\n if (!end || end < 0 || end > len) end = len\n\n let out = ''\n for (let i = start; i < end; ++i) {\n out += hexSliceLookupTable[buf[i]]\n }\n return out\n}\n\nfunction utf16leSlice (buf, start, end) {\n const bytes = buf.slice(start, end)\n let res = ''\n // If bytes.length is odd, the last 8 bits must be ignored (same as node.js)\n for (let i = 0; i < bytes.length - 1; i += 2) {\n res += String.fromCharCode(bytes[i] + (bytes[i + 1] * 256))\n }\n return res\n}\n\nBuffer.prototype.slice = function slice (start, end) {\n const len = this.length\n start = ~~start\n end = end === undefined ? len : ~~end\n\n if (start < 0) {\n start += len\n if (start < 0) start = 0\n } else if (start > len) {\n start = len\n }\n\n if (end < 0) {\n end += len\n if (end < 0) end = 0\n } else if (end > len) {\n end = len\n }\n\n if (end < start) end = start\n\n const newBuf = this.subarray(start, end)\n // Return an augmented `Uint8Array` instance\n Object.setPrototypeOf(newBuf, Buffer.prototype)\n\n return newBuf\n}\n\n/*\n * Need to make sure that buffer isn't trying to write out of bounds.\n */\nfunction checkOffset (offset, ext, length) {\n if ((offset % 1) !== 0 || offset < 0) throw new RangeError('offset is not uint')\n if (offset + ext > length) throw new RangeError('Trying to access beyond buffer length')\n}\n\nBuffer.prototype.readUintLE =\nBuffer.prototype.readUIntLE = function readUIntLE (offset, byteLength, noAssert) {\n offset = offset >>> 0\n byteLength = byteLength >>> 0\n if (!noAssert) checkOffset(offset, byteLength, this.length)\n\n let val = this[offset]\n let mul = 1\n let i = 0\n while (++i < byteLength && (mul *= 0x100)) {\n val += this[offset + i] * mul\n }\n\n return val\n}\n\nBuffer.prototype.readUintBE =\nBuffer.prototype.readUIntBE = function readUIntBE (offset, byteLength, noAssert) {\n offset = offset >>> 0\n byteLength = byteLength >>> 0\n if (!noAssert) {\n checkOffset(offset, byteLength, this.length)\n }\n\n let val = this[offset + --byteLength]\n let mul = 1\n while (byteLength > 0 && (mul *= 0x100)) {\n val += this[offset + --byteLength] * mul\n }\n\n return val\n}\n\nBuffer.prototype.readUint8 =\nBuffer.prototype.readUInt8 = function readUInt8 (offset, noAssert) {\n offset = offset >>> 0\n if (!noAssert) checkOffset(offset, 1, this.length)\n return this[offset]\n}\n\nBuffer.prototype.readUint16LE =\nBuffer.prototype.readUInt16LE = function readUInt16LE (offset, noAssert) {\n offset = offset >>> 0\n if (!noAssert) checkOffset(offset, 2, this.length)\n return this[offset] | (this[offset + 1] << 8)\n}\n\nBuffer.prototype.readUint16BE =\nBuffer.prototype.readUInt16BE = function readUInt16BE (offset, noAssert) {\n offset = offset >>> 0\n if (!noAssert) checkOffset(offset, 2, this.length)\n return (this[offset] << 8) | this[offset + 1]\n}\n\nBuffer.prototype.readUint32LE =\nBuffer.prototype.readUInt32LE = function readUInt32LE (offset, noAssert) {\n offset = offset >>> 0\n if (!noAssert) checkOffset(offset, 4, this.length)\n\n return ((this[offset]) |\n (this[offset + 1] << 8) |\n (this[offset + 2] << 16)) +\n (this[offset + 3] * 0x1000000)\n}\n\nBuffer.prototype.readUint32BE =\nBuffer.prototype.readUInt32BE = function readUInt32BE (offset, noAssert) {\n offset = offset >>> 0\n if (!noAssert) checkOffset(offset, 4, this.length)\n\n return (this[offset] * 0x1000000) +\n ((this[offset + 1] << 16) |\n (this[offset + 2] << 8) |\n this[offset + 3])\n}\n\nBuffer.prototype.readBigUInt64LE = defineBigIntMethod(function readBigUInt64LE (offset) {\n offset = offset >>> 0\n validateNumber(offset, 'offset')\n const first = this[offset]\n const last = this[offset + 7]\n if (first === undefined || last === undefined) {\n boundsError(offset, this.length - 8)\n }\n\n const lo = first +\n this[++offset] * 2 ** 8 +\n this[++offset] * 2 ** 16 +\n this[++offset] * 2 ** 24\n\n const hi = this[++offset] +\n this[++offset] * 2 ** 8 +\n this[++offset] * 2 ** 16 +\n last * 2 ** 24\n\n return BigInt(lo) + (BigInt(hi) << BigInt(32))\n})\n\nBuffer.prototype.readBigUInt64BE = defineBigIntMethod(function readBigUInt64BE (offset) {\n offset = offset >>> 0\n validateNumber(offset, 'offset')\n const first = this[offset]\n const last = this[offset + 7]\n if (first === undefined || last === undefined) {\n boundsError(offset, this.length - 8)\n }\n\n const hi = first * 2 ** 24 +\n this[++offset] * 2 ** 16 +\n this[++offset] * 2 ** 8 +\n this[++offset]\n\n const lo = this[++offset] * 2 ** 24 +\n this[++offset] * 2 ** 16 +\n this[++offset] * 2 ** 8 +\n last\n\n return (BigInt(hi) << BigInt(32)) + BigInt(lo)\n})\n\nBuffer.prototype.readIntLE = function readIntLE (offset, byteLength, noAssert) {\n offset = offset >>> 0\n byteLength = byteLength >>> 0\n if (!noAssert) checkOffset(offset, byteLength, this.length)\n\n let val = this[offset]\n let mul = 1\n let i = 0\n while (++i < byteLength && (mul *= 0x100)) {\n val += this[offset + i] * mul\n }\n mul *= 0x80\n\n if (val >= mul) val -= Math.pow(2, 8 * byteLength)\n\n return val\n}\n\nBuffer.prototype.readIntBE = function readIntBE (offset, byteLength, noAssert) {\n offset = offset >>> 0\n byteLength = byteLength >>> 0\n if (!noAssert) checkOffset(offset, byteLength, this.length)\n\n let i = byteLength\n let mul = 1\n let val = this[offset + --i]\n while (i > 0 && (mul *= 0x100)) {\n val += this[offset + --i] * mul\n }\n mul *= 0x80\n\n if (val >= mul) val -= Math.pow(2, 8 * byteLength)\n\n return val\n}\n\nBuffer.prototype.readInt8 = function readInt8 (offset, noAssert) {\n offset = offset >>> 0\n if (!noAssert) checkOffset(offset, 1, this.length)\n if (!(this[offset] & 0x80)) return (this[offset])\n return ((0xff - this[offset] + 1) * -1)\n}\n\nBuffer.prototype.readInt16LE = function readInt16LE (offset, noAssert) {\n offset = offset >>> 0\n if (!noAssert) checkOffset(offset, 2, this.length)\n const val = this[offset] | (this[offset + 1] << 8)\n return (val & 0x8000) ? val | 0xFFFF0000 : val\n}\n\nBuffer.prototype.readInt16BE = function readInt16BE (offset, noAssert) {\n offset = offset >>> 0\n if (!noAssert) checkOffset(offset, 2, this.length)\n const val = this[offset + 1] | (this[offset] << 8)\n return (val & 0x8000) ? val | 0xFFFF0000 : val\n}\n\nBuffer.prototype.readInt32LE = function readInt32LE (offset, noAssert) {\n offset = offset >>> 0\n if (!noAssert) checkOffset(offset, 4, this.length)\n\n return (this[offset]) |\n (this[offset + 1] << 8) |\n (this[offset + 2] << 16) |\n (this[offset + 3] << 24)\n}\n\nBuffer.prototype.readInt32BE = function readInt32BE (offset, noAssert) {\n offset = offset >>> 0\n if (!noAssert) checkOffset(offset, 4, this.length)\n\n return (this[offset] << 24) |\n (this[offset + 1] << 16) |\n (this[offset + 2] << 8) |\n (this[offset + 3])\n}\n\nBuffer.prototype.readBigInt64LE = defineBigIntMethod(function readBigInt64LE (offset) {\n offset = offset >>> 0\n validateNumber(offset, 'offset')\n const first = this[offset]\n const last = this[offset + 7]\n if (first === undefined || last === undefined) {\n boundsError(offset, this.length - 8)\n }\n\n const val = this[offset + 4] +\n this[offset + 5] * 2 ** 8 +\n this[offset + 6] * 2 ** 16 +\n (last << 24) // Overflow\n\n return (BigInt(val) << BigInt(32)) +\n BigInt(first +\n this[++offset] * 2 ** 8 +\n this[++offset] * 2 ** 16 +\n this[++offset] * 2 ** 24)\n})\n\nBuffer.prototype.readBigInt64BE = defineBigIntMethod(function readBigInt64BE (offset) {\n offset = offset >>> 0\n validateNumber(offset, 'offset')\n const first = this[offset]\n const last = this[offset + 7]\n if (first === undefined || last === undefined) {\n boundsError(offset, this.length - 8)\n }\n\n const val = (first << 24) + // Overflow\n this[++offset] * 2 ** 16 +\n this[++offset] * 2 ** 8 +\n this[++offset]\n\n return (BigInt(val) << BigInt(32)) +\n BigInt(this[++offset] * 2 ** 24 +\n this[++offset] * 2 ** 16 +\n this[++offset] * 2 ** 8 +\n last)\n})\n\nBuffer.prototype.readFloatLE = function readFloatLE (offset, noAssert) {\n offset = offset >>> 0\n if (!noAssert) checkOffset(offset, 4, this.length)\n return ieee754.read(this, offset, true, 23, 4)\n}\n\nBuffer.prototype.readFloatBE = function readFloatBE (offset, noAssert) {\n offset = offset >>> 0\n if (!noAssert) checkOffset(offset, 4, this.length)\n return ieee754.read(this, offset, false, 23, 4)\n}\n\nBuffer.prototype.readDoubleLE = function readDoubleLE (offset, noAssert) {\n offset = offset >>> 0\n if (!noAssert) checkOffset(offset, 8, this.length)\n return ieee754.read(this, offset, true, 52, 8)\n}\n\nBuffer.prototype.readDoubleBE = function readDoubleBE (offset, noAssert) {\n offset = offset >>> 0\n if (!noAssert) checkOffset(offset, 8, this.length)\n return ieee754.read(this, offset, false, 52, 8)\n}\n\nfunction checkInt (buf, value, offset, ext, max, min) {\n if (!Buffer.isBuffer(buf)) throw new TypeError('\"buffer\" argument must be a Buffer instance')\n if (value > max || value < min) throw new RangeError('\"value\" argument is out of bounds')\n if (offset + ext > buf.length) throw new RangeError('Index out of range')\n}\n\nBuffer.prototype.writeUintLE =\nBuffer.prototype.writeUIntLE = function writeUIntLE (value, offset, byteLength, noAssert) {\n value = +value\n offset = offset >>> 0\n byteLength = byteLength >>> 0\n if (!noAssert) {\n const maxBytes = Math.pow(2, 8 * byteLength) - 1\n checkInt(this, value, offset, byteLength, maxBytes, 0)\n }\n\n let mul = 1\n let i = 0\n this[offset] = value & 0xFF\n while (++i < byteLength && (mul *= 0x100)) {\n this[offset + i] = (value / mul) & 0xFF\n }\n\n return offset + byteLength\n}\n\nBuffer.prototype.writeUintBE =\nBuffer.prototype.writeUIntBE = function writeUIntBE (value, offset, byteLength, noAssert) {\n value = +value\n offset = offset >>> 0\n byteLength = byteLength >>> 0\n if (!noAssert) {\n const maxBytes = Math.pow(2, 8 * byteLength) - 1\n checkInt(this, value, offset, byteLength, maxBytes, 0)\n }\n\n let i = byteLength - 1\n let mul = 1\n this[offset + i] = value & 0xFF\n while (--i >= 0 && (mul *= 0x100)) {\n this[offset + i] = (value / mul) & 0xFF\n }\n\n return offset + byteLength\n}\n\nBuffer.prototype.writeUint8 =\nBuffer.prototype.writeUInt8 = function writeUInt8 (value, offset, noAssert) {\n value = +value\n offset = offset >>> 0\n if (!noAssert) checkInt(this, value, offset, 1, 0xff, 0)\n this[offset] = (value & 0xff)\n return offset + 1\n}\n\nBuffer.prototype.writeUint16LE =\nBuffer.prototype.writeUInt16LE = function writeUInt16LE (value, offset, noAssert) {\n value = +value\n offset = offset >>> 0\n if (!noAssert) checkInt(this, value, offset, 2, 0xffff, 0)\n this[offset] = (value & 0xff)\n this[offset + 1] = (value >>> 8)\n return offset + 2\n}\n\nBuffer.prototype.writeUint16BE =\nBuffer.prototype.writeUInt16BE = function writeUInt16BE (value, offset, noAssert) {\n value = +value\n offset = offset >>> 0\n if (!noAssert) checkInt(this, value, offset, 2, 0xffff, 0)\n this[offset] = (value >>> 8)\n this[offset + 1] = (value & 0xff)\n return offset + 2\n}\n\nBuffer.prototype.writeUint32LE =\nBuffer.prototype.writeUInt32LE = function writeUInt32LE (value, offset, noAssert) {\n value = +value\n offset = offset >>> 0\n if (!noAssert) checkInt(this, value, offset, 4, 0xffffffff, 0)\n this[offset + 3] = (value >>> 24)\n this[offset + 2] = (value >>> 16)\n this[offset + 1] = (value >>> 8)\n this[offset] = (value & 0xff)\n return offset + 4\n}\n\nBuffer.prototype.writeUint32BE =\nBuffer.prototype.writeUInt32BE = function writeUInt32BE (value, offset, noAssert) {\n value = +value\n offset = offset >>> 0\n if (!noAssert) checkInt(this, value, offset, 4, 0xffffffff, 0)\n this[offset] = (value >>> 24)\n this[offset + 1] = (value >>> 16)\n this[offset + 2] = (value >>> 8)\n this[offset + 3] = (value & 0xff)\n return offset + 4\n}\n\nfunction wrtBigUInt64LE (buf, value, offset, min, max) {\n checkIntBI(value, min, max, buf, offset, 7)\n\n let lo = Number(value & BigInt(0xffffffff))\n buf[offset++] = lo\n lo = lo >> 8\n buf[offset++] = lo\n lo = lo >> 8\n buf[offset++] = lo\n lo = lo >> 8\n buf[offset++] = lo\n let hi = Number(value >> BigInt(32) & BigInt(0xffffffff))\n buf[offset++] = hi\n hi = hi >> 8\n buf[offset++] = hi\n hi = hi >> 8\n buf[offset++] = hi\n hi = hi >> 8\n buf[offset++] = hi\n return offset\n}\n\nfunction wrtBigUInt64BE (buf, value, offset, min, max) {\n checkIntBI(value, min, max, buf, offset, 7)\n\n let lo = Number(value & BigInt(0xffffffff))\n buf[offset + 7] = lo\n lo = lo >> 8\n buf[offset + 6] = lo\n lo = lo >> 8\n buf[offset + 5] = lo\n lo = lo >> 8\n buf[offset + 4] = lo\n let hi = Number(value >> BigInt(32) & BigInt(0xffffffff))\n buf[offset + 3] = hi\n hi = hi >> 8\n buf[offset + 2] = hi\n hi = hi >> 8\n buf[offset + 1] = hi\n hi = hi >> 8\n buf[offset] = hi\n return offset + 8\n}\n\nBuffer.prototype.writeBigUInt64LE = defineBigIntMethod(function writeBigUInt64LE (value, offset = 0) {\n return wrtBigUInt64LE(this, value, offset, BigInt(0), BigInt('0xffffffffffffffff'))\n})\n\nBuffer.prototype.writeBigUInt64BE = defineBigIntMethod(function writeBigUInt64BE (value, offset = 0) {\n return wrtBigUInt64BE(this, value, offset, BigInt(0), BigInt('0xffffffffffffffff'))\n})\n\nBuffer.prototype.writeIntLE = function writeIntLE (value, offset, byteLength, noAssert) {\n value = +value\n offset = offset >>> 0\n if (!noAssert) {\n const limit = Math.pow(2, (8 * byteLength) - 1)\n\n checkInt(this, value, offset, byteLength, limit - 1, -limit)\n }\n\n let i = 0\n let mul = 1\n let sub = 0\n this[offset] = value & 0xFF\n while (++i < byteLength && (mul *= 0x100)) {\n if (value < 0 && sub === 0 && this[offset + i - 1] !== 0) {\n sub = 1\n }\n this[offset + i] = ((value / mul) >> 0) - sub & 0xFF\n }\n\n return offset + byteLength\n}\n\nBuffer.prototype.writeIntBE = function writeIntBE (value, offset, byteLength, noAssert) {\n value = +value\n offset = offset >>> 0\n if (!noAssert) {\n const limit = Math.pow(2, (8 * byteLength) - 1)\n\n checkInt(this, value, offset, byteLength, limit - 1, -limit)\n }\n\n let i = byteLength - 1\n let mul = 1\n let sub = 0\n this[offset + i] = value & 0xFF\n while (--i >= 0 && (mul *= 0x100)) {\n if (value < 0 && sub === 0 && this[offset + i + 1] !== 0) {\n sub = 1\n }\n this[offset + i] = ((value / mul) >> 0) - sub & 0xFF\n }\n\n return offset + byteLength\n}\n\nBuffer.prototype.writeInt8 = function writeInt8 (value, offset, noAssert) {\n value = +value\n offset = offset >>> 0\n if (!noAssert) checkInt(this, value, offset, 1, 0x7f, -0x80)\n if (value < 0) value = 0xff + value + 1\n this[offset] = (value & 0xff)\n return offset + 1\n}\n\nBuffer.prototype.writeInt16LE = function writeInt16LE (value, offset, noAssert) {\n value = +value\n offset = offset >>> 0\n if (!noAssert) checkInt(this, value, offset, 2, 0x7fff, -0x8000)\n this[offset] = (value & 0xff)\n this[offset + 1] = (value >>> 8)\n return offset + 2\n}\n\nBuffer.prototype.writeInt16BE = function writeInt16BE (value, offset, noAssert) {\n value = +value\n offset = offset >>> 0\n if (!noAssert) checkInt(this, value, offset, 2, 0x7fff, -0x8000)\n this[offset] = (value >>> 8)\n this[offset + 1] = (value & 0xff)\n return offset + 2\n}\n\nBuffer.prototype.writeInt32LE = function writeInt32LE (value, offset, noAssert) {\n value = +value\n offset = offset >>> 0\n if (!noAssert) checkInt(this, value, offset, 4, 0x7fffffff, -0x80000000)\n this[offset] = (value & 0xff)\n this[offset + 1] = (value >>> 8)\n this[offset + 2] = (value >>> 16)\n this[offset + 3] = (value >>> 24)\n return offset + 4\n}\n\nBuffer.prototype.writeInt32BE = function writeInt32BE (value, offset, noAssert) {\n value = +value\n offset = offset >>> 0\n if (!noAssert) checkInt(this, value, offset, 4, 0x7fffffff, -0x80000000)\n if (value < 0) value = 0xffffffff + value + 1\n this[offset] = (value >>> 24)\n this[offset + 1] = (value >>> 16)\n this[offset + 2] = (value >>> 8)\n this[offset + 3] = (value & 0xff)\n return offset + 4\n}\n\nBuffer.prototype.writeBigInt64LE = defineBigIntMethod(function writeBigInt64LE (value, offset = 0) {\n return wrtBigUInt64LE(this, value, offset, -BigInt('0x8000000000000000'), BigInt('0x7fffffffffffffff'))\n})\n\nBuffer.prototype.writeBigInt64BE = defineBigIntMethod(function writeBigInt64BE (value, offset = 0) {\n return wrtBigUInt64BE(this, value, offset, -BigInt('0x8000000000000000'), BigInt('0x7fffffffffffffff'))\n})\n\nfunction checkIEEE754 (buf, value, offset, ext, max, min) {\n if (offset + ext > buf.length) throw new RangeError('Index out of range')\n if (offset < 0) throw new RangeError('Index out of range')\n}\n\nfunction writeFloat (buf, value, offset, littleEndian, noAssert) {\n value = +value\n offset = offset >>> 0\n if (!noAssert) {\n checkIEEE754(buf, value, offset, 4, 3.4028234663852886e+38, -3.4028234663852886e+38)\n }\n ieee754.write(buf, value, offset, littleEndian, 23, 4)\n return offset + 4\n}\n\nBuffer.prototype.writeFloatLE = function writeFloatLE (value, offset, noAssert) {\n return writeFloat(this, value, offset, true, noAssert)\n}\n\nBuffer.prototype.writeFloatBE = function writeFloatBE (value, offset, noAssert) {\n return writeFloat(this, value, offset, false, noAssert)\n}\n\nfunction writeDouble (buf, value, offset, littleEndian, noAssert) {\n value = +value\n offset = offset >>> 0\n if (!noAssert) {\n checkIEEE754(buf, value, offset, 8, 1.7976931348623157E+308, -1.7976931348623157E+308)\n }\n ieee754.write(buf, value, offset, littleEndian, 52, 8)\n return offset + 8\n}\n\nBuffer.prototype.writeDoubleLE = function writeDoubleLE (value, offset, noAssert) {\n return writeDouble(this, value, offset, true, noAssert)\n}\n\nBuffer.prototype.writeDoubleBE = function writeDoubleBE (value, offset, noAssert) {\n return writeDouble(this, value, offset, false, noAssert)\n}\n\n// copy(targetBuffer, targetStart=0, sourceStart=0, sourceEnd=buffer.length)\nBuffer.prototype.copy = function copy (target, targetStart, start, end) {\n if (!Buffer.isBuffer(target)) throw new TypeError('argument should be a Buffer')\n if (!start) start = 0\n if (!end && end !== 0) end = this.length\n if (targetStart >= target.length) targetStart = target.length\n if (!targetStart) targetStart = 0\n if (end > 0 && end < start) end = start\n\n // Copy 0 bytes; we're done\n if (end === start) return 0\n if (target.length === 0 || this.length === 0) return 0\n\n // Fatal error conditions\n if (targetStart < 0) {\n throw new RangeError('targetStart out of bounds')\n }\n if (start < 0 || start >= this.length) throw new RangeError('Index out of range')\n if (end < 0) throw new RangeError('sourceEnd out of bounds')\n\n // Are we oob?\n if (end > this.length) end = this.length\n if (target.length - targetStart < end - start) {\n end = target.length - targetStart + start\n }\n\n const len = end - start\n\n if (this === target && typeof Uint8Array.prototype.copyWithin === 'function') {\n // Use built-in when available, missing from IE11\n this.copyWithin(targetStart, start, end)\n } else {\n Uint8Array.prototype.set.call(\n target,\n this.subarray(start, end),\n targetStart\n )\n }\n\n return len\n}\n\n// Usage:\n// buffer.fill(number[, offset[, end]])\n// buffer.fill(buffer[, offset[, end]])\n// buffer.fill(string[, offset[, end]][, encoding])\nBuffer.prototype.fill = function fill (val, start, end, encoding) {\n // Handle string cases:\n if (typeof val === 'string') {\n if (typeof start === 'string') {\n encoding = start\n start = 0\n end = this.length\n } else if (typeof end === 'string') {\n encoding = end\n end = this.length\n }\n if (encoding !== undefined && typeof encoding !== 'string') {\n throw new TypeError('encoding must be a string')\n }\n if (typeof encoding === 'string' && !Buffer.isEncoding(encoding)) {\n throw new TypeError('Unknown encoding: ' + encoding)\n }\n if (val.length === 1) {\n const code = val.charCodeAt(0)\n if ((encoding === 'utf8' && code < 128) ||\n encoding === 'latin1') {\n // Fast path: If `val` fits into a single byte, use that numeric value.\n val = code\n }\n }\n } else if (typeof val === 'number') {\n val = val & 255\n } else if (typeof val === 'boolean') {\n val = Number(val)\n }\n\n // Invalid ranges are not set to a default, so can range check early.\n if (start < 0 || this.length < start || this.length < end) {\n throw new RangeError('Out of range index')\n }\n\n if (end <= start) {\n return this\n }\n\n start = start >>> 0\n end = end === undefined ? this.length : end >>> 0\n\n if (!val) val = 0\n\n let i\n if (typeof val === 'number') {\n for (i = start; i < end; ++i) {\n this[i] = val\n }\n } else {\n const bytes = Buffer.isBuffer(val)\n ? val\n : Buffer.from(val, encoding)\n const len = bytes.length\n if (len === 0) {\n throw new TypeError('The value \"' + val +\n '\" is invalid for argument \"value\"')\n }\n for (i = 0; i < end - start; ++i) {\n this[i + start] = bytes[i % len]\n }\n }\n\n return this\n}\n\n// CUSTOM ERRORS\n// =============\n\n// Simplified versions from Node, changed for Buffer-only usage\nconst errors = {}\nfunction E (sym, getMessage, Base) {\n errors[sym] = class NodeError extends Base {\n constructor () {\n super()\n\n Object.defineProperty(this, 'message', {\n value: getMessage.apply(this, arguments),\n writable: true,\n configurable: true\n })\n\n // Add the error code to the name to include it in the stack trace.\n this.name = `${this.name} [${sym}]`\n // Access the stack to generate the error message including the error code\n // from the name.\n this.stack // eslint-disable-line no-unused-expressions\n // Reset the name to the actual name.\n delete this.name\n }\n\n get code () {\n return sym\n }\n\n set code (value) {\n Object.defineProperty(this, 'code', {\n configurable: true,\n enumerable: true,\n value,\n writable: true\n })\n }\n\n toString () {\n return `${this.name} [${sym}]: ${this.message}`\n }\n }\n}\n\nE('ERR_BUFFER_OUT_OF_BOUNDS',\n function (name) {\n if (name) {\n return `${name} is outside of buffer bounds`\n }\n\n return 'Attempt to access memory outside buffer bounds'\n }, RangeError)\nE('ERR_INVALID_ARG_TYPE',\n function (name, actual) {\n return `The \"${name}\" argument must be of type number. Received type ${typeof actual}`\n }, TypeError)\nE('ERR_OUT_OF_RANGE',\n function (str, range, input) {\n let msg = `The value of \"${str}\" is out of range.`\n let received = input\n if (Number.isInteger(input) && Math.abs(input) > 2 ** 32) {\n received = addNumericalSeparator(String(input))\n } else if (typeof input === 'bigint') {\n received = String(input)\n if (input > BigInt(2) ** BigInt(32) || input < -(BigInt(2) ** BigInt(32))) {\n received = addNumericalSeparator(received)\n }\n received += 'n'\n }\n msg += ` It must be ${range}. Received ${received}`\n return msg\n }, RangeError)\n\nfunction addNumericalSeparator (val) {\n let res = ''\n let i = val.length\n const start = val[0] === '-' ? 1 : 0\n for (; i >= start + 4; i -= 3) {\n res = `_${val.slice(i - 3, i)}${res}`\n }\n return `${val.slice(0, i)}${res}`\n}\n\n// CHECK FUNCTIONS\n// ===============\n\nfunction checkBounds (buf, offset, byteLength) {\n validateNumber(offset, 'offset')\n if (buf[offset] === undefined || buf[offset + byteLength] === undefined) {\n boundsError(offset, buf.length - (byteLength + 1))\n }\n}\n\nfunction checkIntBI (value, min, max, buf, offset, byteLength) {\n if (value > max || value < min) {\n const n = typeof min === 'bigint' ? 'n' : ''\n let range\n if (byteLength > 3) {\n if (min === 0 || min === BigInt(0)) {\n range = `>= 0${n} and < 2${n} ** ${(byteLength + 1) * 8}${n}`\n } else {\n range = `>= -(2${n} ** ${(byteLength + 1) * 8 - 1}${n}) and < 2 ** ` +\n `${(byteLength + 1) * 8 - 1}${n}`\n }\n } else {\n range = `>= ${min}${n} and <= ${max}${n}`\n }\n throw new errors.ERR_OUT_OF_RANGE('value', range, value)\n }\n checkBounds(buf, offset, byteLength)\n}\n\nfunction validateNumber (value, name) {\n if (typeof value !== 'number') {\n throw new errors.ERR_INVALID_ARG_TYPE(name, 'number', value)\n }\n}\n\nfunction boundsError (value, length, type) {\n if (Math.floor(value) !== value) {\n validateNumber(value, type)\n throw new errors.ERR_OUT_OF_RANGE(type || 'offset', 'an integer', value)\n }\n\n if (length < 0) {\n throw new errors.ERR_BUFFER_OUT_OF_BOUNDS()\n }\n\n throw new errors.ERR_OUT_OF_RANGE(type || 'offset',\n `>= ${type ? 1 : 0} and <= ${length}`,\n value)\n}\n\n// HELPER FUNCTIONS\n// ================\n\nconst INVALID_BASE64_RE = /[^+/0-9A-Za-z-_]/g\n\nfunction base64clean (str) {\n // Node takes equal signs as end of the Base64 encoding\n str = str.split('=')[0]\n // Node strips out invalid characters like \\n and \\t from the string, base64-js does not\n str = str.trim().replace(INVALID_BASE64_RE, '')\n // Node converts strings with length < 2 to ''\n if (str.length < 2) return ''\n // Node allows for non-padded base64 strings (missing trailing ===), base64-js does not\n while (str.length % 4 !== 0) {\n str = str + '='\n }\n return str\n}\n\nfunction utf8ToBytes (string, units) {\n units = units || Infinity\n let codePoint\n const length = string.length\n let leadSurrogate = null\n const bytes = []\n\n for (let i = 0; i < length; ++i) {\n codePoint = string.charCodeAt(i)\n\n // is surrogate component\n if (codePoint > 0xD7FF && codePoint < 0xE000) {\n // last char was a lead\n if (!leadSurrogate) {\n // no lead yet\n if (codePoint > 0xDBFF) {\n // unexpected trail\n if ((units -= 3) > -1) bytes.push(0xEF, 0xBF, 0xBD)\n continue\n } else if (i + 1 === length) {\n // unpaired lead\n if ((units -= 3) > -1) bytes.push(0xEF, 0xBF, 0xBD)\n continue\n }\n\n // valid lead\n leadSurrogate = codePoint\n\n continue\n }\n\n // 2 leads in a row\n if (codePoint < 0xDC00) {\n if ((units -= 3) > -1) bytes.push(0xEF, 0xBF, 0xBD)\n leadSurrogate = codePoint\n continue\n }\n\n // valid surrogate pair\n codePoint = (leadSurrogate - 0xD800 << 10 | codePoint - 0xDC00) + 0x10000\n } else if (leadSurrogate) {\n // valid bmp char, but last char was a lead\n if ((units -= 3) > -1) bytes.push(0xEF, 0xBF, 0xBD)\n }\n\n leadSurrogate = null\n\n // encode utf8\n if (codePoint < 0x80) {\n if ((units -= 1) < 0) break\n bytes.push(codePoint)\n } else if (codePoint < 0x800) {\n if ((units -= 2) < 0) break\n bytes.push(\n codePoint >> 0x6 | 0xC0,\n codePoint & 0x3F | 0x80\n )\n } else if (codePoint < 0x10000) {\n if ((units -= 3) < 0) break\n bytes.push(\n codePoint >> 0xC | 0xE0,\n codePoint >> 0x6 & 0x3F | 0x80,\n codePoint & 0x3F | 0x80\n )\n } else if (codePoint < 0x110000) {\n if ((units -= 4) < 0) break\n bytes.push(\n codePoint >> 0x12 | 0xF0,\n codePoint >> 0xC & 0x3F | 0x80,\n codePoint >> 0x6 & 0x3F | 0x80,\n codePoint & 0x3F | 0x80\n )\n } else {\n throw new Error('Invalid code point')\n }\n }\n\n return bytes\n}\n\nfunction asciiToBytes (str) {\n const byteArray = []\n for (let i = 0; i < str.length; ++i) {\n // Node's code seems to be doing this and not & 0x7F..\n byteArray.push(str.charCodeAt(i) & 0xFF)\n }\n return byteArray\n}\n\nfunction utf16leToBytes (str, units) {\n let c, hi, lo\n const byteArray = []\n for (let i = 0; i < str.length; ++i) {\n if ((units -= 2) < 0) break\n\n c = str.charCodeAt(i)\n hi = c >> 8\n lo = c % 256\n byteArray.push(lo)\n byteArray.push(hi)\n }\n\n return byteArray\n}\n\nfunction base64ToBytes (str) {\n return base64.toByteArray(base64clean(str))\n}\n\nfunction blitBuffer (src, dst, offset, length) {\n let i\n for (i = 0; i < length; ++i) {\n if ((i + offset >= dst.length) || (i >= src.length)) break\n dst[i + offset] = src[i]\n }\n return i\n}\n\n// ArrayBuffer or Uint8Array objects from other contexts (i.e. iframes) do not pass\n// the `instanceof` check but they should be treated as of that type.\n// See: https://github.com/feross/buffer/issues/166\nfunction isInstance (obj, type) {\n return obj instanceof type ||\n (obj != null && obj.constructor != null && obj.constructor.name != null &&\n obj.constructor.name === type.name)\n}\nfunction numberIsNaN (obj) {\n // For IE11 support\n return obj !== obj // eslint-disable-line no-self-compare\n}\n\n// Create lookup table for `toString('hex')`\n// See: https://github.com/feross/buffer/issues/219\nconst hexSliceLookupTable = (function () {\n const alphabet = '0123456789abcdef'\n const table = new Array(256)\n for (let i = 0; i < 16; ++i) {\n const i16 = i * 16\n for (let j = 0; j < 16; ++j) {\n table[i16 + j] = alphabet[i] + alphabet[j]\n }\n }\n return table\n})()\n\n// Return not function with Error if BigInt not supported\nfunction defineBigIntMethod (fn) {\n return typeof BigInt === 'undefined' ? BufferBigIntNotDefined : fn\n}\n\nfunction BufferBigIntNotDefined () {\n throw new Error('BigInt not supported')\n}\n","// extracted by extract-css-chunks-webpack-plugin\nmodule.exports = {};","// extracted by extract-css-chunks-webpack-plugin\nmodule.exports = {\"nodeStrokeWidth\":\"0.8\",\"directionArrowSize\":\"6\",\"directionArrowWidth\":\"0.7\",\"node\":\"fornac-node\",\"directionArrow\":\"fornac-directionArrow\",\"plot\":\"fornac-plot\",\"selectedNode\":\"fornac-selectedNode\",\"nodeLabel\":\"fornac-nodeLabel\",\"link\":\"fornac-link\",\"plotLabel\":\"fornac-plotLabel\",\"transparent\":\"fornac-transparent\",\"dragLine\":\"fornac-dragLine\",\"mouseEventHelper\":\"fornac-mouseEventHelper\"};","/*! ieee754. BSD-3-Clause License. Feross Aboukhadijeh */\nexports.read = function (buffer, offset, isLE, mLen, nBytes) {\n var e, m\n var eLen = (nBytes * 8) - mLen - 1\n var eMax = (1 << eLen) - 1\n var eBias = eMax >> 1\n var nBits = -7\n var i = isLE ? (nBytes - 1) : 0\n var d = isLE ? -1 : 1\n var s = buffer[offset + i]\n\n i += d\n\n e = s & ((1 << (-nBits)) - 1)\n s >>= (-nBits)\n nBits += eLen\n for (; nBits > 0; e = (e * 256) + buffer[offset + i], i += d, nBits -= 8) {}\n\n m = e & ((1 << (-nBits)) - 1)\n e >>= (-nBits)\n nBits += mLen\n for (; nBits > 0; m = (m * 256) + buffer[offset + i], i += d, nBits -= 8) {}\n\n if (e === 0) {\n e = 1 - eBias\n } else if (e === eMax) {\n return m ? NaN : ((s ? -1 : 1) * Infinity)\n } else {\n m = m + Math.pow(2, mLen)\n e = e - eBias\n }\n return (s ? -1 : 1) * m * Math.pow(2, e - mLen)\n}\n\nexports.write = function (buffer, value, offset, isLE, mLen, nBytes) {\n var e, m, c\n var eLen = (nBytes * 8) - mLen - 1\n var eMax = (1 << eLen) - 1\n var eBias = eMax >> 1\n var rt = (mLen === 23 ? Math.pow(2, -24) - Math.pow(2, -77) : 0)\n var i = isLE ? 0 : (nBytes - 1)\n var d = isLE ? 1 : -1\n var s = value < 0 || (value === 0 && 1 / value < 0) ? 1 : 0\n\n value = Math.abs(value)\n\n if (isNaN(value) || value === Infinity) {\n m = isNaN(value) ? 1 : 0\n e = eMax\n } else {\n e = Math.floor(Math.log(value) / Math.LN2)\n if (value * (c = Math.pow(2, -e)) < 1) {\n e--\n c *= 2\n }\n if (e + eBias >= 1) {\n value += rt / c\n } else {\n value += rt * Math.pow(2, 1 - eBias)\n }\n if (value * c >= 2) {\n e++\n c /= 2\n }\n\n if (e + eBias >= eMax) {\n m = 0\n e = eMax\n } else if (e + eBias >= 1) {\n m = ((value * c) - 1) * Math.pow(2, mLen)\n e = e + eBias\n } else {\n m = value * Math.pow(2, eBias - 1) * Math.pow(2, mLen)\n e = 0\n }\n }\n\n for (; mLen >= 8; buffer[offset + i] = m & 0xff, i += d, m /= 256, mLen -= 8) {}\n\n e = (e << mLen) | m\n eLen += mLen\n for (; eLen > 0; buffer[offset + i] = e & 0xff, i += d, e /= 256, eLen -= 8) {}\n\n buffer[offset + i - d] |= s * 128\n}\n","// The MIT License (MIT)\n//\n// Copyright (c) 2014 Jonas Finnemann Jensen\n//\n// Permission is hereby granted, free of charge, to any person obtaining a copy\n// of this software and associated documentation files (the \"Software\"), to deal\n// in the Software without restriction, including without limitation the rights\n// to use, copy, modify, merge, publish, distribute, sublicense, and/or sell\n// copies of the Software, and to permit persons to whom the Software is\n// furnished to do so, subject to the following conditions:\n//\n// The above copyright notice and this permission notice shall be included in\n// all copies or substantial portions of the Software.\n//\n// THE SOFTWARE IS PROVIDED \"AS IS\", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR\n// IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,\n// FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE\n// AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER\n// LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,\n// OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN\n// THE SOFTWARE.\n\nmodule.exports = require('./slugid');\n","// The MIT License (MIT)\n//\n// Copyright (c) 2014 Jonas Finnemann Jensen\n//\n// Permission is hereby granted, free of charge, to any person obtaining a copy\n// of this software and associated documentation files (the \"Software\"), to deal\n// in the Software without restriction, including without limitation the rights\n// to use, copy, modify, merge, publish, distribute, sublicense, and/or sell\n// copies of the Software, and to permit persons to whom the Software is\n// furnished to do so, subject to the following conditions:\n//\n// The above copyright notice and this permission notice shall be included in\n// all copies or substantial portions of the Software.\n//\n// THE SOFTWARE IS PROVIDED \"AS IS\", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR\n// IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,\n// FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE\n// AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER\n// LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,\n// OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN\n// THE SOFTWARE.\n\nvar uuid = require('uuid');\n\n/** @type {(bytes: Uint8Array) => string} */\nvar toBase64 = (() => {\n if (typeof Buffer !== 'undefined') {\n return (bytes) => Buffer.from(bytes).toString('base64');\n }\n return (bytes) => btoa(String.fromCharCode(...bytes));\n})();\n\n/** @type {(base64: string) => Uint8Array | Buffer} */\nvar fromBase64 = (() => {\n if (typeof Buffer !== 'undefined') {\n return (base64) => Buffer.from(base64, 'base64');\n }\n return (base64) => Uint8Array.from(atob(base64), c => c.charCodeAt(0));\n})();\n\n/**\n * Returns the given uuid as a 22 character slug. This can be a regular v4\n * slug or a \"nice\" slug.\n */\nexports.encode = function(uuid_) {\n var bytes = uuid.parse(uuid_);\n var base64 = toBase64(bytes);\n var slug = base64\n .replace(/\\+/g, '-') // Replace + with - (see RFC 4648, sec. 5)\n .replace(/\\//g, '_') // Replace / with _ (see RFC 4648, sec. 5)\n .substring(0, 22); // Drop '==' padding\n return slug;\n};\n\n/**\n * Returns the uuid represented by the given v4 or \"nice\" slug\n */\nexports.decode = function(slug) {\n var base64 = slug\n .replace(/-/g, '+')\n .replace(/_/g, '/')\n + '==';\n return uuid.stringify(fromBase64(base64));\n};\n\n/**\n * Returns a randomly generated uuid v4 compliant slug\n */\nexports.v4 = function() {\n var bytes = uuid.v4(null, new Uint8Array(16));\n var base64 = toBase64(bytes);\n var slug = base64\n .replace(/\\+/g, '-') // Replace + with - (see RFC 4648, sec. 5)\n .replace(/\\//g, '_') // Replace / with _ (see RFC 4648, sec. 5)\n .substring(0, 22); // Drop '==' padding\n return slug;\n};\n\n/**\n * Returns a randomly generated uuid v4 compliant slug which conforms to a set\n * of \"nice\" properties, at the cost of some entropy. Currently this means one\n * extra fixed bit (the first bit of the uuid is set to 0) which guarantees the\n * slug will begin with [A-Za-f]. For example such slugs don't require special\n * handling when used as command line parameters (whereas non-nice slugs may\n * start with `-` which can confuse command line tools).\n *\n * Potentially other \"nice\" properties may be added in future to further\n * restrict the range of potential uuids that may be generated.\n */\nexports.nice = function() {\n var bytes = uuid.v4(null, new Uint8Array(16));\n bytes[0] = bytes[0] & 0x7f; // unset first bit to ensure [A-Za-f] first char\n var base64 = toBase64(bytes);\n var slug = base64\n .replace(/\\+/g, '-') // Replace + with - (see RFC 4648, sec. 5)\n .replace(/\\//g, '_') // Replace / with _ (see RFC 4648, sec. 5)\n .substring(0, 22); // Drop '==' padding\n return slug;\n};\n","// Unique ID creation requires a high quality random # generator. In the browser we therefore\n// require the crypto API and do not support built-in fallback to lower quality random number\n// generators (like Math.random()).\nvar getRandomValues;\nvar rnds8 = new Uint8Array(16);\nexport default function rng() {\n // lazy load so that environments that need to polyfill have a chance to do so\n if (!getRandomValues) {\n // getRandomValues needs to be invoked in a context where \"this\" is a Crypto implementation. Also,\n // find the complete implementation of crypto (msCrypto) on IE11.\n getRandomValues = typeof crypto !== 'undefined' && crypto.getRandomValues && crypto.getRandomValues.bind(crypto) || typeof msCrypto !== 'undefined' && typeof msCrypto.getRandomValues === 'function' && msCrypto.getRandomValues.bind(msCrypto);\n\n if (!getRandomValues) {\n throw new Error('crypto.getRandomValues() not supported. See https://github.com/uuidjs/uuid#getrandomvalues-not-supported');\n }\n }\n\n return getRandomValues(rnds8);\n}","export default /^(?:[0-9a-f]{8}-[0-9a-f]{4}-[1-5][0-9a-f]{3}-[89ab][0-9a-f]{3}-[0-9a-f]{12}|00000000-0000-0000-0000-000000000000)$/i;","import REGEX from './regex.js';\n\nfunction validate(uuid) {\n return typeof uuid === 'string' && REGEX.test(uuid);\n}\n\nexport default validate;","import validate from './validate.js';\n/**\n * Convert array of 16 byte values to UUID string format of the form:\n * XXXXXXXX-XXXX-XXXX-XXXX-XXXXXXXXXXXX\n */\n\nvar byteToHex = [];\n\nfor (var i = 0; i < 256; ++i) {\n byteToHex.push((i + 0x100).toString(16).substr(1));\n}\n\nfunction stringify(arr) {\n var offset = arguments.length > 1 && arguments[1] !== undefined ? arguments[1] : 0;\n // Note: Be careful editing this code! It's been tuned for performance\n // and works in ways you may not expect. See https://github.com/uuidjs/uuid/pull/434\n var uuid = (byteToHex[arr[offset + 0]] + byteToHex[arr[offset + 1]] + byteToHex[arr[offset + 2]] + byteToHex[arr[offset + 3]] + '-' + byteToHex[arr[offset + 4]] + byteToHex[arr[offset + 5]] + '-' + byteToHex[arr[offset + 6]] + byteToHex[arr[offset + 7]] + '-' + byteToHex[arr[offset + 8]] + byteToHex[arr[offset + 9]] + '-' + byteToHex[arr[offset + 10]] + byteToHex[arr[offset + 11]] + byteToHex[arr[offset + 12]] + byteToHex[arr[offset + 13]] + byteToHex[arr[offset + 14]] + byteToHex[arr[offset + 15]]).toLowerCase(); // Consistency check for valid UUID. If this throws, it's likely due to one\n // of the following:\n // - One or more input array values don't map to a hex octet (leading to\n // \"undefined\" in the uuid)\n // - Invalid input values for the RFC `version` or `variant` fields\n\n if (!validate(uuid)) {\n throw TypeError('Stringified UUID is invalid');\n }\n\n return uuid;\n}\n\nexport default stringify;","import rng from './rng.js';\nimport stringify from './stringify.js'; // **`v1()` - Generate time-based UUID**\n//\n// Inspired by https://github.com/LiosK/UUID.js\n// and http://docs.python.org/library/uuid.html\n\nvar _nodeId;\n\nvar _clockseq; // Previous uuid creation time\n\n\nvar _lastMSecs = 0;\nvar _lastNSecs = 0; // See https://github.com/uuidjs/uuid for API details\n\nfunction v1(options, buf, offset) {\n var i = buf && offset || 0;\n var b = buf || new Array(16);\n options = options || {};\n var node = options.node || _nodeId;\n var clockseq = options.clockseq !== undefined ? options.clockseq : _clockseq; // node and clockseq need to be initialized to random values if they're not\n // specified. We do this lazily to minimize issues related to insufficient\n // system entropy. See #189\n\n if (node == null || clockseq == null) {\n var seedBytes = options.random || (options.rng || rng)();\n\n if (node == null) {\n // Per 4.5, create and 48-bit node id, (47 random bits + multicast bit = 1)\n node = _nodeId = [seedBytes[0] | 0x01, seedBytes[1], seedBytes[2], seedBytes[3], seedBytes[4], seedBytes[5]];\n }\n\n if (clockseq == null) {\n // Per 4.2.2, randomize (14 bit) clockseq\n clockseq = _clockseq = (seedBytes[6] << 8 | seedBytes[7]) & 0x3fff;\n }\n } // UUID timestamps are 100 nano-second units since the Gregorian epoch,\n // (1582-10-15 00:00). JSNumbers aren't precise enough for this, so\n // time is handled internally as 'msecs' (integer milliseconds) and 'nsecs'\n // (100-nanoseconds offset from msecs) since unix epoch, 1970-01-01 00:00.\n\n\n var msecs = options.msecs !== undefined ? options.msecs : Date.now(); // Per 4.2.1.2, use count of uuid's generated during the current clock\n // cycle to simulate higher resolution clock\n\n var nsecs = options.nsecs !== undefined ? options.nsecs : _lastNSecs + 1; // Time since last uuid creation (in msecs)\n\n var dt = msecs - _lastMSecs + (nsecs - _lastNSecs) / 10000; // Per 4.2.1.2, Bump clockseq on clock regression\n\n if (dt < 0 && options.clockseq === undefined) {\n clockseq = clockseq + 1 & 0x3fff;\n } // Reset nsecs if clock regresses (new clockseq) or we've moved onto a new\n // time interval\n\n\n if ((dt < 0 || msecs > _lastMSecs) && options.nsecs === undefined) {\n nsecs = 0;\n } // Per 4.2.1.2 Throw error if too many uuids are requested\n\n\n if (nsecs >= 10000) {\n throw new Error(\"uuid.v1(): Can't create more than 10M uuids/sec\");\n }\n\n _lastMSecs = msecs;\n _lastNSecs = nsecs;\n _clockseq = clockseq; // Per 4.1.4 - Convert from unix epoch to Gregorian epoch\n\n msecs += 12219292800000; // `time_low`\n\n var tl = ((msecs & 0xfffffff) * 10000 + nsecs) % 0x100000000;\n b[i++] = tl >>> 24 & 0xff;\n b[i++] = tl >>> 16 & 0xff;\n b[i++] = tl >>> 8 & 0xff;\n b[i++] = tl & 0xff; // `time_mid`\n\n var tmh = msecs / 0x100000000 * 10000 & 0xfffffff;\n b[i++] = tmh >>> 8 & 0xff;\n b[i++] = tmh & 0xff; // `time_high_and_version`\n\n b[i++] = tmh >>> 24 & 0xf | 0x10; // include version\n\n b[i++] = tmh >>> 16 & 0xff; // `clock_seq_hi_and_reserved` (Per 4.2.2 - include variant)\n\n b[i++] = clockseq >>> 8 | 0x80; // `clock_seq_low`\n\n b[i++] = clockseq & 0xff; // `node`\n\n for (var n = 0; n < 6; ++n) {\n b[i + n] = node[n];\n }\n\n return buf || stringify(b);\n}\n\nexport default v1;","import validate from './validate.js';\n\nfunction parse(uuid) {\n if (!validate(uuid)) {\n throw TypeError('Invalid UUID');\n }\n\n var v;\n var arr = new Uint8Array(16); // Parse ########-....-....-....-............\n\n arr[0] = (v = parseInt(uuid.slice(0, 8), 16)) >>> 24;\n arr[1] = v >>> 16 & 0xff;\n arr[2] = v >>> 8 & 0xff;\n arr[3] = v & 0xff; // Parse ........-####-....-....-............\n\n arr[4] = (v = parseInt(uuid.slice(9, 13), 16)) >>> 8;\n arr[5] = v & 0xff; // Parse ........-....-####-....-............\n\n arr[6] = (v = parseInt(uuid.slice(14, 18), 16)) >>> 8;\n arr[7] = v & 0xff; // Parse ........-....-....-####-............\n\n arr[8] = (v = parseInt(uuid.slice(19, 23), 16)) >>> 8;\n arr[9] = v & 0xff; // Parse ........-....-....-....-############\n // (Use \"/\" to avoid 32-bit truncation when bit-shifting high-order bytes)\n\n arr[10] = (v = parseInt(uuid.slice(24, 36), 16)) / 0x10000000000 & 0xff;\n arr[11] = v / 0x100000000 & 0xff;\n arr[12] = v >>> 24 & 0xff;\n arr[13] = v >>> 16 & 0xff;\n arr[14] = v >>> 8 & 0xff;\n arr[15] = v & 0xff;\n return arr;\n}\n\nexport default parse;","import stringify from './stringify.js';\nimport parse from './parse.js';\n\nfunction stringToBytes(str) {\n str = unescape(encodeURIComponent(str)); // UTF8 escape\n\n var bytes = [];\n\n for (var i = 0; i < str.length; ++i) {\n bytes.push(str.charCodeAt(i));\n }\n\n return bytes;\n}\n\nexport var DNS = '6ba7b810-9dad-11d1-80b4-00c04fd430c8';\nexport var URL = '6ba7b811-9dad-11d1-80b4-00c04fd430c8';\nexport default function (name, version, hashfunc) {\n function generateUUID(value, namespace, buf, offset) {\n if (typeof value === 'string') {\n value = stringToBytes(value);\n }\n\n if (typeof namespace === 'string') {\n namespace = parse(namespace);\n }\n\n if (namespace.length !== 16) {\n throw TypeError('Namespace must be array-like (16 iterable integer values, 0-255)');\n } // Compute hash of namespace and value, Per 4.3\n // Future: Use spread syntax when supported on all platforms, e.g. `bytes =\n // hashfunc([...namespace, ... value])`\n\n\n var bytes = new Uint8Array(16 + value.length);\n bytes.set(namespace);\n bytes.set(value, namespace.length);\n bytes = hashfunc(bytes);\n bytes[6] = bytes[6] & 0x0f | version;\n bytes[8] = bytes[8] & 0x3f | 0x80;\n\n if (buf) {\n offset = offset || 0;\n\n for (var i = 0; i < 16; ++i) {\n buf[offset + i] = bytes[i];\n }\n\n return buf;\n }\n\n return stringify(bytes);\n } // Function#name is not settable on some platforms (#270)\n\n\n try {\n generateUUID.name = name; // eslint-disable-next-line no-empty\n } catch (err) {} // For CommonJS default export support\n\n\n generateUUID.DNS = DNS;\n generateUUID.URL = URL;\n return generateUUID;\n}","/*\n * Browser-compatible JavaScript MD5\n *\n * Modification of JavaScript MD5\n * https://github.com/blueimp/JavaScript-MD5\n *\n * Copyright 2011, Sebastian Tschan\n * https://blueimp.net\n *\n * Licensed under the MIT license:\n * https://opensource.org/licenses/MIT\n *\n * Based on\n * A JavaScript implementation of the RSA Data Security, Inc. MD5 Message\n * Digest Algorithm, as defined in RFC 1321.\n * Version 2.2 Copyright (C) Paul Johnston 1999 - 2009\n * Other contributors: Greg Holt, Andrew Kepert, Ydnar, Lostinet\n * Distributed under the BSD License\n * See http://pajhome.org.uk/crypt/md5 for more info.\n */\nfunction md5(bytes) {\n if (typeof bytes === 'string') {\n var msg = unescape(encodeURIComponent(bytes)); // UTF8 escape\n\n bytes = new Uint8Array(msg.length);\n\n for (var i = 0; i < msg.length; ++i) {\n bytes[i] = msg.charCodeAt(i);\n }\n }\n\n return md5ToHexEncodedArray(wordsToMd5(bytesToWords(bytes), bytes.length * 8));\n}\n/*\n * Convert an array of little-endian words to an array of bytes\n */\n\n\nfunction md5ToHexEncodedArray(input) {\n var output = [];\n var length32 = input.length * 32;\n var hexTab = '0123456789abcdef';\n\n for (var i = 0; i < length32; i += 8) {\n var x = input[i >> 5] >>> i % 32 & 0xff;\n var hex = parseInt(hexTab.charAt(x >>> 4 & 0x0f) + hexTab.charAt(x & 0x0f), 16);\n output.push(hex);\n }\n\n return output;\n}\n/**\n * Calculate output length with padding and bit length\n */\n\n\nfunction getOutputLength(inputLength8) {\n return (inputLength8 + 64 >>> 9 << 4) + 14 + 1;\n}\n/*\n * Calculate the MD5 of an array of little-endian words, and a bit length.\n */\n\n\nfunction wordsToMd5(x, len) {\n /* append padding */\n x[len >> 5] |= 0x80 << len % 32;\n x[getOutputLength(len) - 1] = len;\n var a = 1732584193;\n var b = -271733879;\n var c = -1732584194;\n var d = 271733878;\n\n for (var i = 0; i < x.length; i += 16) {\n var olda = a;\n var oldb = b;\n var oldc = c;\n var oldd = d;\n a = md5ff(a, b, c, d, x[i], 7, -680876936);\n d = md5ff(d, a, b, c, x[i + 1], 12, -389564586);\n c = md5ff(c, d, a, b, x[i + 2], 17, 606105819);\n b = md5ff(b, c, d, a, x[i + 3], 22, -1044525330);\n a = md5ff(a, b, c, d, x[i + 4], 7, -176418897);\n d = md5ff(d, a, b, c, x[i + 5], 12, 1200080426);\n c = md5ff(c, d, a, b, x[i + 6], 17, -1473231341);\n b = md5ff(b, c, d, a, x[i + 7], 22, -45705983);\n a = md5ff(a, b, c, d, x[i + 8], 7, 1770035416);\n d = md5ff(d, a, b, c, x[i + 9], 12, -1958414417);\n c = md5ff(c, d, a, b, x[i + 10], 17, -42063);\n b = md5ff(b, c, d, a, x[i + 11], 22, -1990404162);\n a = md5ff(a, b, c, d, x[i + 12], 7, 1804603682);\n d = md5ff(d, a, b, c, x[i + 13], 12, -40341101);\n c = md5ff(c, d, a, b, x[i + 14], 17, -1502002290);\n b = md5ff(b, c, d, a, x[i + 15], 22, 1236535329);\n a = md5gg(a, b, c, d, x[i + 1], 5, -165796510);\n d = md5gg(d, a, b, c, x[i + 6], 9, -1069501632);\n c = md5gg(c, d, a, b, x[i + 11], 14, 643717713);\n b = md5gg(b, c, d, a, x[i], 20, -373897302);\n a = md5gg(a, b, c, d, x[i + 5], 5, -701558691);\n d = md5gg(d, a, b, c, x[i + 10], 9, 38016083);\n c = md5gg(c, d, a, b, x[i + 15], 14, -660478335);\n b = md5gg(b, c, d, a, x[i + 4], 20, -405537848);\n a = md5gg(a, b, c, d, x[i + 9], 5, 568446438);\n d = md5gg(d, a, b, c, x[i + 14], 9, -1019803690);\n c = md5gg(c, d, a, b, x[i + 3], 14, -187363961);\n b = md5gg(b, c, d, a, x[i + 8], 20, 1163531501);\n a = md5gg(a, b, c, d, x[i + 13], 5, -1444681467);\n d = md5gg(d, a, b, c, x[i + 2], 9, -51403784);\n c = md5gg(c, d, a, b, x[i + 7], 14, 1735328473);\n b = md5gg(b, c, d, a, x[i + 12], 20, -1926607734);\n a = md5hh(a, b, c, d, x[i + 5], 4, -378558);\n d = md5hh(d, a, b, c, x[i + 8], 11, -2022574463);\n c = md5hh(c, d, a, b, x[i + 11], 16, 1839030562);\n b = md5hh(b, c, d, a, x[i + 14], 23, -35309556);\n a = md5hh(a, b, c, d, x[i + 1], 4, -1530992060);\n d = md5hh(d, a, b, c, x[i + 4], 11, 1272893353);\n c = md5hh(c, d, a, b, x[i + 7], 16, -155497632);\n b = md5hh(b, c, d, a, x[i + 10], 23, -1094730640);\n a = md5hh(a, b, c, d, x[i + 13], 4, 681279174);\n d = md5hh(d, a, b, c, x[i], 11, -358537222);\n c = md5hh(c, d, a, b, x[i + 3], 16, -722521979);\n b = md5hh(b, c, d, a, x[i + 6], 23, 76029189);\n a = md5hh(a, b, c, d, x[i + 9], 4, -640364487);\n d = md5hh(d, a, b, c, x[i + 12], 11, -421815835);\n c = md5hh(c, d, a, b, x[i + 15], 16, 530742520);\n b = md5hh(b, c, d, a, x[i + 2], 23, -995338651);\n a = md5ii(a, b, c, d, x[i], 6, -198630844);\n d = md5ii(d, a, b, c, x[i + 7], 10, 1126891415);\n c = md5ii(c, d, a, b, x[i + 14], 15, -1416354905);\n b = md5ii(b, c, d, a, x[i + 5], 21, -57434055);\n a = md5ii(a, b, c, d, x[i + 12], 6, 1700485571);\n d = md5ii(d, a, b, c, x[i + 3], 10, -1894986606);\n c = md5ii(c, d, a, b, x[i + 10], 15, -1051523);\n b = md5ii(b, c, d, a, x[i + 1], 21, -2054922799);\n a = md5ii(a, b, c, d, x[i + 8], 6, 1873313359);\n d = md5ii(d, a, b, c, x[i + 15], 10, -30611744);\n c = md5ii(c, d, a, b, x[i + 6], 15, -1560198380);\n b = md5ii(b, c, d, a, x[i + 13], 21, 1309151649);\n a = md5ii(a, b, c, d, x[i + 4], 6, -145523070);\n d = md5ii(d, a, b, c, x[i + 11], 10, -1120210379);\n c = md5ii(c, d, a, b, x[i + 2], 15, 718787259);\n b = md5ii(b, c, d, a, x[i + 9], 21, -343485551);\n a = safeAdd(a, olda);\n b = safeAdd(b, oldb);\n c = safeAdd(c, oldc);\n d = safeAdd(d, oldd);\n }\n\n return [a, b, c, d];\n}\n/*\n * Convert an array bytes to an array of little-endian words\n * Characters >255 have their high-byte silently ignored.\n */\n\n\nfunction bytesToWords(input) {\n if (input.length === 0) {\n return [];\n }\n\n var length8 = input.length * 8;\n var output = new Uint32Array(getOutputLength(length8));\n\n for (var i = 0; i < length8; i += 8) {\n output[i >> 5] |= (input[i / 8] & 0xff) << i % 32;\n }\n\n return output;\n}\n/*\n * Add integers, wrapping at 2^32. This uses 16-bit operations internally\n * to work around bugs in some JS interpreters.\n */\n\n\nfunction safeAdd(x, y) {\n var lsw = (x & 0xffff) + (y & 0xffff);\n var msw = (x >> 16) + (y >> 16) + (lsw >> 16);\n return msw << 16 | lsw & 0xffff;\n}\n/*\n * Bitwise rotate a 32-bit number to the left.\n */\n\n\nfunction bitRotateLeft(num, cnt) {\n return num << cnt | num >>> 32 - cnt;\n}\n/*\n * These functions implement the four basic operations the algorithm uses.\n */\n\n\nfunction md5cmn(q, a, b, x, s, t) {\n return safeAdd(bitRotateLeft(safeAdd(safeAdd(a, q), safeAdd(x, t)), s), b);\n}\n\nfunction md5ff(a, b, c, d, x, s, t) {\n return md5cmn(b & c | ~b & d, a, b, x, s, t);\n}\n\nfunction md5gg(a, b, c, d, x, s, t) {\n return md5cmn(b & d | c & ~d, a, b, x, s, t);\n}\n\nfunction md5hh(a, b, c, d, x, s, t) {\n return md5cmn(b ^ c ^ d, a, b, x, s, t);\n}\n\nfunction md5ii(a, b, c, d, x, s, t) {\n return md5cmn(c ^ (b | ~d), a, b, x, s, t);\n}\n\nexport default md5;","import v35 from './v35.js';\nimport md5 from './md5.js';\nvar v3 = v35('v3', 0x30, md5);\nexport default v3;","import rng from './rng.js';\nimport stringify from './stringify.js';\n\nfunction v4(options, buf, offset) {\n options = options || {};\n var rnds = options.random || (options.rng || rng)(); // Per 4.4, set bits for version and `clock_seq_hi_and_reserved`\n\n rnds[6] = rnds[6] & 0x0f | 0x40;\n rnds[8] = rnds[8] & 0x3f | 0x80; // Copy bytes to buffer, if provided\n\n if (buf) {\n offset = offset || 0;\n\n for (var i = 0; i < 16; ++i) {\n buf[offset + i] = rnds[i];\n }\n\n return buf;\n }\n\n return stringify(rnds);\n}\n\nexport default v4;","// Adapted from Chris Veness' SHA1 code at\n// http://www.movable-type.co.uk/scripts/sha1.html\nfunction f(s, x, y, z) {\n switch (s) {\n case 0:\n return x & y ^ ~x & z;\n\n case 1:\n return x ^ y ^ z;\n\n case 2:\n return x & y ^ x & z ^ y & z;\n\n case 3:\n return x ^ y ^ z;\n }\n}\n\nfunction ROTL(x, n) {\n return x << n | x >>> 32 - n;\n}\n\nfunction sha1(bytes) {\n var K = [0x5a827999, 0x6ed9eba1, 0x8f1bbcdc, 0xca62c1d6];\n var H = [0x67452301, 0xefcdab89, 0x98badcfe, 0x10325476, 0xc3d2e1f0];\n\n if (typeof bytes === 'string') {\n var msg = unescape(encodeURIComponent(bytes)); // UTF8 escape\n\n bytes = [];\n\n for (var i = 0; i < msg.length; ++i) {\n bytes.push(msg.charCodeAt(i));\n }\n } else if (!Array.isArray(bytes)) {\n // Convert Array-like to Array\n bytes = Array.prototype.slice.call(bytes);\n }\n\n bytes.push(0x80);\n var l = bytes.length / 4 + 2;\n var N = Math.ceil(l / 16);\n var M = new Array(N);\n\n for (var _i = 0; _i < N; ++_i) {\n var arr = new Uint32Array(16);\n\n for (var j = 0; j < 16; ++j) {\n arr[j] = bytes[_i * 64 + j * 4] << 24 | bytes[_i * 64 + j * 4 + 1] << 16 | bytes[_i * 64 + j * 4 + 2] << 8 | bytes[_i * 64 + j * 4 + 3];\n }\n\n M[_i] = arr;\n }\n\n M[N - 1][14] = (bytes.length - 1) * 8 / Math.pow(2, 32);\n M[N - 1][14] = Math.floor(M[N - 1][14]);\n M[N - 1][15] = (bytes.length - 1) * 8 & 0xffffffff;\n\n for (var _i2 = 0; _i2 < N; ++_i2) {\n var W = new Uint32Array(80);\n\n for (var t = 0; t < 16; ++t) {\n W[t] = M[_i2][t];\n }\n\n for (var _t = 16; _t < 80; ++_t) {\n W[_t] = ROTL(W[_t - 3] ^ W[_t - 8] ^ W[_t - 14] ^ W[_t - 16], 1);\n }\n\n var a = H[0];\n var b = H[1];\n var c = H[2];\n var d = H[3];\n var e = H[4];\n\n for (var _t2 = 0; _t2 < 80; ++_t2) {\n var s = Math.floor(_t2 / 20);\n var T = ROTL(a, 5) + f(s, b, c, d) + e + K[s] + W[_t2] >>> 0;\n e = d;\n d = c;\n c = ROTL(b, 30) >>> 0;\n b = a;\n a = T;\n }\n\n H[0] = H[0] + a >>> 0;\n H[1] = H[1] + b >>> 0;\n H[2] = H[2] + c >>> 0;\n H[3] = H[3] + d >>> 0;\n H[4] = H[4] + e >>> 0;\n }\n\n return [H[0] >> 24 & 0xff, H[0] >> 16 & 0xff, H[0] >> 8 & 0xff, H[0] & 0xff, H[1] >> 24 & 0xff, H[1] >> 16 & 0xff, H[1] >> 8 & 0xff, H[1] & 0xff, H[2] >> 24 & 0xff, H[2] >> 16 & 0xff, H[2] >> 8 & 0xff, H[2] & 0xff, H[3] >> 24 & 0xff, H[3] >> 16 & 0xff, H[3] >> 8 & 0xff, H[3] & 0xff, H[4] >> 24 & 0xff, H[4] >> 16 & 0xff, H[4] >> 8 & 0xff, H[4] & 0xff];\n}\n\nexport default sha1;","import v35 from './v35.js';\nimport sha1 from './sha1.js';\nvar v5 = v35('v5', 0x50, sha1);\nexport default v5;","export default '00000000-0000-0000-0000-000000000000';","import validate from './validate.js';\n\nfunction version(uuid) {\n if (!validate(uuid)) {\n throw TypeError('Invalid UUID');\n }\n\n return parseInt(uuid.substr(14, 1), 16);\n}\n\nexport default version;","module.exports = __WEBPACK_EXTERNAL_MODULE__893__;","// The module cache\nvar __webpack_module_cache__ = {};\n\n// The require function\nfunction __webpack_require__(moduleId) {\n\t// Check if module is in cache\n\tvar cachedModule = __webpack_module_cache__[moduleId];\n\tif (cachedModule !== undefined) {\n\t\treturn cachedModule.exports;\n\t}\n\t// Create a new module (and put it into the cache)\n\tvar module = __webpack_module_cache__[moduleId] = {\n\t\t// no module.id needed\n\t\t// no module.loaded needed\n\t\texports: {}\n\t};\n\n\t// Execute the module function\n\t__webpack_modules__[moduleId](module, module.exports, __webpack_require__);\n\n\t// Return the exports of the module\n\treturn module.exports;\n}\n\n","// getDefaultExport function for compatibility with non-harmony modules\n__webpack_require__.n = (module) => {\n\tvar getter = module && module.__esModule ?\n\t\t() => (module['default']) :\n\t\t() => (module);\n\t__webpack_require__.d(getter, { a: getter });\n\treturn getter;\n};","// define getter functions for harmony exports\n__webpack_require__.d = (exports, definition) => {\n\tfor(var key in definition) {\n\t\tif(__webpack_require__.o(definition, key) && !__webpack_require__.o(exports, key)) {\n\t\t\tObject.defineProperty(exports, key, { enumerable: true, get: definition[key] });\n\t\t}\n\t}\n};","__webpack_require__.g = (function() {\n\tif (typeof globalThis === 'object') return globalThis;\n\ttry {\n\t\treturn this || new Function('return this')();\n\t} catch (e) {\n\t\tif (typeof window === 'object') return window;\n\t}\n})();","__webpack_require__.o = (obj, prop) => (Object.prototype.hasOwnProperty.call(obj, prop))","// define __esModule on exports\n__webpack_require__.r = (exports) => {\n\tif(typeof Symbol !== 'undefined' && Symbol.toStringTag) {\n\t\tObject.defineProperty(exports, Symbol.toStringTag, { value: 'Module' });\n\t}\n\tObject.defineProperty(exports, '__esModule', { value: true });\n};","var scriptUrl;\nif (__webpack_require__.g.importScripts) scriptUrl = __webpack_require__.g.location + \"\";\nvar document = __webpack_require__.g.document;\nif (!scriptUrl && document) {\n\tif (document.currentScript)\n\t\tscriptUrl = document.currentScript.src;\n\tif (!scriptUrl) {\n\t\tvar scripts = document.getElementsByTagName(\"script\");\n\t\tif(scripts.length) {\n\t\t\tvar i = scripts.length - 1;\n\t\t\twhile (i > -1 && (!scriptUrl || !/^http(s?):/.test(scriptUrl))) scriptUrl = scripts[i--].src;\n\t\t}\n\t}\n}\n// When supporting browsers where an automatic publicPath is not supported you must specify an output.publicPath manually via configuration\n// or pass an empty string (\"\") and set the __webpack_public_path__ variable from your code to use your own logic.\nif (!scriptUrl) throw new Error(\"Automatic publicPath is not supported in this browser\");\nscriptUrl = scriptUrl.replace(/#.*$/, \"\").replace(/\\?.*$/, \"\").replace(/\\/[^\\/]+$/, \"/\");\n__webpack_require__.p = scriptUrl;","export default __webpack_public_path__ + \"02188894d5236b1517df3210b79c2a7f.svg\";","import './d3-context-menu.css';\nimport ArrowIcon from './img/play.svg';\n\nimport d3 from 'd3';\nimport slugid from 'slugid';\n\nexport function contextMenu(menu, opts) {\n let previouslyMouseUp = false;\n let clickAway = () => {};\n let uid = slugid.nice();\n let rootElement = null;\n let orientation = 'right'; // display the menu to the right of the mouse click\n // or parent elemement\n let initialPos = null;\n let parentStart = null;\n\n var openCallback,\n closeCallback;\n\n if (typeof opts === 'function') {\n openCallback = opts;\n } else {\n opts = opts || {};\n openCallback = opts.onOpen;\n closeCallback = opts.onClose;\n }\n\n if ('rootElement' in opts)\n rootElement = opts['rootElement']\n\n if ('pos' in opts) {\n // do we want to place this menu somewhere specific?\n initialPos = opts.pos;\n }\n\n if ('orientation' in opts) {\n orientation = opts.orientation;\n }\n\n if ('parentStart' in opts) {\n parentStart = opts.parentStart;\n }\n\n // create the div element that will hold the context menu\n d3.selectAll('.d3-context-menu-' + uid).data([1])\n .enter()\n .append('div')\n .classed('d3-context-menu', true)\n .classed('d3-context-menu-' + uid, true)\n\n // close menu\n d3.select('body').on('click.d3-context-menu-' + uid, function() {\n if (previouslyMouseUp) {\n previouslyMouseUp = false;\n return;\n }\n console.log('body click close');\n\n d3.select('.d3-context-menu-' + uid).style('display', 'none');\n orientation = 'right';\n\n if (closeCallback) {\n closeCallback();\n }\n });\n\n // this gets executed when a contextmenu event occurs\n return function(data, index, pMouseUp=false,\n clickAwayFunc = function() { } ) {\n var elm = this;\n var contextMenuPos = null;\n let mousePos = null;\n let currentThis = this;\n\n if (rootElement == null)\n mousePos = d3.mouse(this);\n else\n mousePos = d3.mouse(rootElement); // for recursive menus, we need the mouse\n // position relative to another element\n\n clickAway = clickAwayFunc;\n let openChildMenuUid = null;\n\n previouslyMouseUp = pMouseUp;\n\n d3.selectAll('.d3-context-menu-' + uid).html('');\n var list = d3.selectAll('.d3-context-menu-' + uid)\n .on('contextmenu', function(d) {\n console.log('context-menu close');\n d3.select('.d3-context-menu-' + uid).style('display', 'none'); \n orientation = 'right';\n\n d3.event.preventDefault();\n d3.event.stopPropagation();\n })\n .append('ul');\n\n list.selectAll('li').data(typeof menu === 'function' ? menu(data) : menu).enter()\n .append('li')\n .attr('class', function(d) {\n console.log('d:', d);\n var ret = '';\n if (d.divider) {\n ret += ' is-divider';\n }\n if (d.disabled) {\n ret += ' is-disabled';\n }\n if (!d.action) {\n ret += ' is-header';\n }\n if ('children' in d) {\n ret += ' d3-context-menu-recursive';\n }\n return ret;\n })\n .html(function(d) {\n if (d.divider) {\n return '
';\n }\n if (!d.title) {\n console.error('No title attribute set. Check the spelling of your options.');\n }\n return (typeof d.title === 'string') ? d.title : d.title(data);\n })\n .on('click', function(d, i) {\n if (d.disabled) return; // do nothing if disabled\n if (!d.action) return; // headers have no \"action\"\n d.action(elm, data, index, mousePos);\n console.log('click close');\n\n // close all context menus\n d3.selectAll('.d3-context-menu').style('display', 'none');\n orientation = 'right';\n\n if (closeCallback) {\n closeCallback();\n }\n })\n .on('mouseenter', function(d, i) {\n d3.select(this)\n .classed('d3-context-menu-selected', true)\n\n if (openChildMenuUid != null) {\n // there's a child menu open\n\n // unselect all items\n d3.select('.d3-context-menu-' + uid)\n .selectAll('li')\n .classed('d3-context-menu-selected', false);\n\n if (typeof d.children == 'undefined') {\n console.log(\"no children close\");\n // no children, so hide any open child menus\n d3.select('.d3-context-menu-' + openChildMenuUid)\n .style('display', 'none');\n\n openChildMenuUid = null;\n return;\n }\n\n if (d.childUid == openChildMenuUid) {\n // the correct child menu is already open\n return;\n\n } else {\n // need to open a different child menu\n console.log('open different child menu close');\n \n // close the already open one\n d3.select('.d3-context-menu-' + openChildMenuUid)\n .style('display', 'none');\n\n openChildMenuUid = null;\n\n }\n } \n\n // there should be no menu open right now\n if (typeof d.children != 'undefined') {\n let boundingRect = this.getBoundingClientRect();\n\n let childrenContextMenu = null\n if (orientation == 'left') {\n childrenContextMenu = contextMenu(d.children, {'rootElement': currentThis,\n 'pos': [ boundingRect.left + window.pageXOffset,\n boundingRect.top - 2 + window.pageYOffset],\n 'orientation': 'left'});\n } else {\n childrenContextMenu = contextMenu(d.children, \n {\n 'pos': [ boundingRect.left + boundingRect.width + window.pageXOffset,\n boundingRect.top - 2 + window.pageYOffset],\n 'rootElement': currentThis,\n 'parentStart': [boundingRect.left + window.pageXOffset,\n boundingRect.top - 2 + window.pageYOffset]});\n }\n\n d.childUid = childrenContextMenu.apply(this, [data,i,true,\n function() { }]);\n openChildMenuUid = d.childUid;\n }\n\n\n d3.select(this)\n .classed('d3-context-menu-selected', true)\n \n })\n .on('mouseleave', function(d, i) {\n\n if (openChildMenuUid == null) {\n d3.select(this)\n .classed('d3-context-menu-selected', false);\n }\n });\n\n list.selectAll('.d3-context-menu-recursive')\n .append('img')\n .attr('src', ArrowIcon)\n .attr('width', '14px')\n .attr('height', '14px')\n .style('position', 'absolute')\n .style('right', '5px')\n ;\n\n // the openCallback allows an action to fire before the menu is displayed\n // an example usage would be closing a tooltip\n if (openCallback) {\n if (openCallback(data, index) === false) {\n return uid;\n }\n }\n\n let contextMenuSelection = d3.select('.d3-context-menu-' + uid)\n .style('display', 'block');\n\n if (initialPos == null) {\n d3.select('.d3-context-menu-' + uid)\n .style('left', (d3.event.pageX - 2) + 'px')\n .style('top', (d3.event.pageY - 2) + 'px')\n } else {\n d3.select('.d3-context-menu-' + uid)\n .style('left', initialPos[0] + 'px')\n .style('top', initialPos[1] + 'px')\n }\n\n // check if the menu disappears off the side of the window\n let boundingRect = contextMenuSelection.node().getBoundingClientRect();\n\n if (boundingRect.left + boundingRect.width > window.innerWidth || orientation == 'left') {\n orientation = 'left';\n\n // menu goes of the end of the window, position it the other way\n if (initialPos == null) {\n // place the menu where the user clicked\n d3.select('.d3-context-menu-' + uid)\n .style('left', (d3.event.pageX - 2 - boundingRect.width) + 'px')\n .style('top', (d3.event.pageY - 2) + 'px')\n } else {\n if (parentStart != null) {\n d3.select('.d3-context-menu-' + uid)\n .style('left', (parentStart[0] - boundingRect.width) + 'px')\n .style('top', parentStart[1] + 'px')\n } else {\n d3.select('.d3-context-menu-' + uid)\n .style('left', (initialPos[0] - boundingRect.width) + 'px')\n .style('top', initialPos[1] + 'px')\n }\n }\n \n }\n\n // display context menu\n\n if (previouslyMouseUp)\n return uid;\n\n d3.event.preventDefault();\n d3.event.stopPropagation();\n //d3.event.stopImmediatePropagation();\n //\n return uid;\n };\n};\n","var numberSort = function(a,b) { return a - b; };\n\nexport function arraysEqual(a, b) {\n // courtesy of \n // http://stackoverflow.com/questions/3115982/how-to-check-if-two-arrays-are-equal-with-javascript\n if (a === b) return true;\n if (a === null || b === null) return false;\n if (a.length != b.length) return false;\n\n // If you don't care about the order of the elements inside\n // the array, you should sort both arrays here.\n\n for (var i = 0; i < a.length; ++i) {\n if (a[i] !== b[i]) return false;\n }\n return true;\n}\n\nexport function RNAUtilities() {\n var self = this;\n\n // the brackets to use when constructing dotbracket strings\n // with pseudoknots\n self.bracketLeft = \"([{abcdefghijklmnopqrstuvwxyz\".split(\"\");\n\n self.inverseBrackets = function(bracket) {\n var res = {};\n for (var i = 0; i < bracket.length; i++) {\n res[bracket[i]] = i;\n }\n return res;\n };\n\n self.maximumMatching = function maximumMatching(pt){\n // Courtesy of the great Ronny Lorenz\n\n var n = pt[0];\n var TURN = 0; //minimal number of nucleotides in the hairpin\n\n /* array init */\n var mm = new Array(n + 1);\n for(var i = 0; i <= n; i++){\n mm[i] = new Array(n + 1);\n for(var j = i; j <= n; j++)\n mm[i][j] = 0;\n }\n var maximum = 0;\n\n /* actual computation */\n for(var i = n - TURN - 1; i > 0; i--)\n\n for(var j = i + TURN + 1; j <= n; j++){\n maximum = mm[i][j-1];\n\n for(var l = j - TURN - 1; l >= i; l--) {\n if(pt[l] === j) {\n\n // we have a base pair here\n maximum = Math.max(maximum, ((l > i) ? mm[i][l-1] : 0) + 1 + ((j - l - 1 > 0) ? mm[l+1][j-1] : 0));\n }\n }\n\n mm[i][j] = maximum;\n }\n\n maximum = mm[1][n];\n\n return mm;\n };\n\n self.backtrackMaximumMatching = function(mm, oldPt) {\n var pt = Array.apply(null, \n Array(mm.length)).map(function() { return 0 }); \n //create an array containing zeros\n\n self.mmBt(mm, pt, oldPt, 1, mm.length-1);\n return pt;\n }\n\n self.mmBt = function(mm, pt, oldPt, i, j){\n // Create a pairtable from the backtracking\n var maximum = mm[i][j];\n var TURN = 0;\n\n if(j - i - 1 < TURN) return; /* no more pairs */\n\n if(mm[i][j-1] == maximum){ /* j is unpaired */\n self.mmBt(mm, pt, oldPt, i, j-1);\n return;\n }\n\n for(var q = j - TURN - 1; q >= i; q--){ /* j is paired with some q */\n if (oldPt[j] !== q)\n continue;\n\n var leftPart = (q > i) ? mm[i][q-1] : 0;\n var enclosedPart = (j - q - 1 > 0) ? mm[q+1][j-1] : 0;\n\n if(leftPart + enclosedPart + 1 == maximum) {\n // there's a base pair between j and q\n pt[q] = j;\n pt[j] = q;\n\n if(i < q) \n self.mmBt(mm, pt, oldPt, i, q - 1);\n\n self.mmBt(mm, pt, oldPt, q + 1, j - 1);\n return;\n }\n }\n\n //alert(i + \",\" + j + \": backtracking failed!\");\n console.log('FAILED!!!' + i + ',' + j + ': backtracking failed!');\n\n };\n\n self.dotbracketToPairtable = function(dotbracket) {\n // create an array and initialize it to 0\n var pt = Array.apply(null, new Array(dotbracket.length + 1)).map(Number.prototype.valueOf,0);\n \n // the first element is always the length of the RNA molecule\n pt[0] = dotbracket.length;\n\n // store the pairing partners for each symbol\n var stack = {};\n for (var i = 0; i < self.bracketLeft.length; i++) {\n stack[i] = [];\n }\n\n // lookup the index of each symbol in the bracket array\n var inverseBracketLeft = self.inverseBrackets(self.bracketLeft);\n var inverseBracketRight = self.inverseBrackets(self.bracketRight);\n\n for (var i = 0; i < dotbracket.length; i++) {\n var a = dotbracket[i];\n var ni = i + 1;\n\n if (a == '.' || a == 'o') {\n // unpaired\n pt[ni] = 0;\n } else {\n if (a in inverseBracketLeft) {\n // open pair?\n stack[inverseBracketLeft[a]].push(ni);\n } else if (a in inverseBracketRight){\n // close pair?\n var j = stack[inverseBracketRight[a]].pop();\n\n pt[ni] = j;\n pt[j] = ni;\n } else if (a == '&'){\n // there is a sequence break here, ignore it\n } else {\n throw \"Unknown symbol in dotbracket string\";\n }\n }\n }\n\n for (var key in stack) {\n if (stack[key].length > 0) {\n throw \"Unmatched base at position \" + stack[key][0];\n }\n }\n\n return pt;\n };\n\n self.insertIntoStack = function(stack, i, j) {\n var k = 0;\n while (stack[k].length > 0 && stack[k][stack[k].length - 1] < j) {\n k += 1;\n }\n\n stack[k].push(j);\n return k;\n };\n\n self.deleteFromStack = function(stack, j) {\n var k = 0;\n while (stack[k].length === 0 || stack[k][stack[k].length-1] != j) {\n k += 1;\n }\n stack[k].pop();\n return k;\n };\n\n self.pairtableToDotbracket = function(pt) {\n // store the pairing partners for each symbol\n var stack = {};\n for (var i = 0; i < pt[0]; i++) {\n stack[i] = [];\n }\n\n var seen = {};\n var res = \"\";\n var i;\n for (var i = 1; i < pt[0] + 1; i++) {\n if (pt[i] !== 0 && pt[i] in seen) {\n throw \"Invalid pairtable contains duplicate entries\";\n }\n seen[pt[i]] = true;\n\n if (pt[i] === 0) {\n res += '.';\n } else {\n if (pt[i] > i) {\n res += self.bracketLeft[self.insertIntoStack(stack, i, pt[i])];\n } else {\n res += self.bracketRight[self.deleteFromStack(stack, i)];\n }\n }\n }\n\n return res;\n };\n\n self.findUnmatched = function(pt, from, to) {\n /*\n * Find unmatched nucleotides in this molecule.\n */\n var toRemove = [];\n var unmatched = [];\n\n var origFrom = from;\n var origTo = to;\n var i;\n\n for (var i = from; i <= to; i++)\n if (pt[i] !== 0 && (pt[i] < from || pt[i] > to))\n unmatched.push([i,pt[i]]);\n\n for (var i = origFrom; i <= origTo; i++) {\n while (pt[i] === 0 && i <= origTo) i++;\n\n to = pt[i];\n\n while (pt[i] === to) {\n i++;\n to--;\n }\n \n toRemove = toRemove.concat(self.findUnmatched(pt, i, to));\n }\n\n if (unmatched.length > 0)\n toRemove.push(unmatched);\n\n return toRemove;\n };\n\n self.removePseudoknotsFromPairtable = function(pt) {\n /* Remove the pseudoknots from this structure in such a fashion\n * that the least amount of base-pairs need to be broken\n *\n * The pairtable is manipulated in place and a list of tuples\n * indicating the broken base pairs is returned.\n */\n\n var mm = self.maximumMatching(pt);\n var newPt = self.backtrackMaximumMatching(mm, pt);\n var removed = [];\n\n for (var i = 1; i < pt.length; i++) {\n if (pt[i] < i)\n continue;\n\n if (newPt[i] != pt[i]) {\n removed.push([i, pt[i]]);\n pt[pt[i]] = 0;\n pt[i] = 0;\n }\n }\n\n return removed;\n };\n\n self.ptToElements = function(pt, level, i, j, dotBracketBreaks) {\n /* Convert a pair table to a list of secondary structure \n * elements:\n *\n * [['s',1,[2,3]]\n *\n * The 's' indicates that an element can be a stem. It can also be\n * an interior loop ('i'), a hairpin loop ('h') or a multiloop ('m')\n *\n * The second number (1 in this case) indicates the depth or\n * how many base pairs have to be broken to get to this element.\n *\n * Finally, there is the list of nucleotides which are part of\n * of this element.\n */\n var elements = [];\n var u5 = [i-1];\n var u3 = [j+1];\n\n if (arguments.length < 5)\n dotBracketBreaks = [];\n\n if (i > j)\n return [];\n \n //iterate over the unpaired regions on either side\n //this is either 5' and 3' unpaired if level == 0\n //or an interior loop or a multiloop\n for (; pt[i] === 0; i++) { u5.push(i); }\n for (; pt[j] === 0; j--) { u3.push(j); }\n\n if (i > j) {\n //hairpin loop or one large unpaired molecule\n u5.push(i);\n if (level === 0)\n return [['e',level, u5.sort(numberSort)]];\n else {\n // check to see if we have chain breaks due\n // to multiple strands in the input\n var external = false;\n var left = [];\n var right = [];\n for (var k = 0; k < u5.length; k++) {\n if (external)\n right.push(u5[k]);\n else\n left.push(u5[k]);\n\n if (dotBracketBreaks.indexOf(u5[k]) >= 0)\n external = true;\n }\n\n if (external) {\n return [['h',level, u5.sort(numberSort)]];\n }\n else\n // if not, this is a simple hairpin loop\n return [['h',level, u5.sort(numberSort)]];\n }\n }\n\n if (pt[i] != j) {\n //multiloop\n var m = u5;\n var k = i;\n\n // the nucleotide before and the starting nucleotide\n m.push(k);\n while (k <= j) {\n // recurse into a stem\n elements = elements.concat(self.ptToElements(pt, level, k, pt[k], dotBracketBreaks));\n\n // add the nucleotides between stems\n m.push(pt[k]);\n k = pt[k] + 1;\n for (; pt[k] === 0 && k <= j; k++) { m.push(k);}\n m.push(k);\n }\n m.pop();\n m = m.concat(u3);\n \n if (m.length > 0) {\n if (level === 0)\n elements.push(['e', level, m.sort(numberSort)]);\n else\n elements.push(['m', level, m.sort(numberSort)]);\n }\n \n return elements;\n }\n\n if (pt[i] === j) {\n //interior loop\n u5.push(i);\n u3.push(j);\n\n var combined = u5.concat(u3);\n if (combined.length > 4) {\n if (level === 0)\n elements.push(['e',level, u5.concat(u3).sort(numberSort)]);\n else\n elements.push(['i',level, u5.concat(u3).sort(numberSort)]);\n }\n } \n\n var s = [];\n //go through the stem\n while (pt[i] === j && i < j) {\n //one stem\n s.push(i);\n s.push(j);\n\n i += 1;\n j -= 1;\n\n level += 1;\n }\n\n u5 = [i-1];\n u3 = [j+1];\n elements.push(['s', level, s.sort(numberSort)]);\n\n return elements.concat(self.ptToElements(pt, level, i, j, dotBracketBreaks));\n };\n\n}\n\nexport var rnaUtilities = new RNAUtilities();\n\nexport function ColorScheme(colorsText) {\n var self = this;\n self.colorsText = colorsText;\n\n self.parseRange = function(rangeText) {\n //parse a number range such as 1-10 or 3,7,9 or just 7\n var parts = rangeText.split(',')\n var nums = [];\n\n for (var i = 0; i < parts.length; i++) {\n //could be 1 or 10-11 or something like that\n var parts1 = parts[i].split('-');\n\n if (parts1.length == 1)\n nums.push(parseInt(parts1[0]));\n else if (parts1.length == 2) {\n var from = parseInt(parts1[0]);\n var to = parseInt(parts1[1]);\n\n // add each number in this range\n for (var j = from; j <= to; j++) \n nums.push(j)\n } else {\n console.log('Malformed range (too many dashes):', rangeText);\n }\n }\n\n return nums;\n }\n\n self.parseColorText = function(colorText) {\n /* Parse the text of an RNA color string. Instructions and description\n * of the format are given below.\n *\n * The return is a json double dictionary indexed first by the \n * molecule name, then by the nucleotide. This is then applied\n * by force.js to the RNAs it is displaying. When no molecule\n * name is specified, the color is applied to all molecules*/\n var lines = colorText.split('\\n');\n var currMolecule = '';\n var counter = 1;\n var colorsJson = {colorValues: {'':{}}, range:['white', 'steelblue']};\n var domainValues = [];\n\n\n for (var i = 0; i < lines.length; i++) {\n\n if (lines[i][0] == '>') {\n // new molecule\n currMolecule = lines[i].trim().slice(1);\n counter = 1;\n\n colorsJson.colorValues[currMolecule] = {};\n continue;\n }\n\n let words = lines[i].trim().split(/[\\s]+/);\n\n for (var j = 0; j < words.length; j++) {\n if (isNaN(words[j])) {\n if (words[j].search('range') === 0) {\n //there's a color scale in this entry\n let parts = words[j].split('=');\n let partsRight = parts[1].split(':')\n colorsJson.range = [partsRight[0], partsRight[1]];\n continue;\n }\n\n if (words[j].search('domain') == 0) {\n //there's a color scale in this entry\n let parts = words[j].split('=');\n let partsRight = parts[1].split(':')\n colorsJson.domain = [partsRight[0], partsRight[1]];\n continue;\n }\n\n // it's not a number, should be a combination \n // of a number (nucleotide #) and a color\n let parts = words[j].split(':');\n let nums = self.parseRange(parts[0]);\n let color = parts[1]\n\n for (var k = 0; k < nums.length; k++) {\n if (isNaN(color)) {\n colorsJson.colorValues[currMolecule][nums[k]] = color;\n } else {\n colorsJson.colorValues[currMolecule][nums[k]] = +color;\n domainValues.push(Number(color));\n }\n }\n } else {\n //it's a number, so we add it to the list of values\n //seen for this molecule\n colorsJson.colorValues[currMolecule][counter] = Number(words[j]);\n counter += 1;\n\n domainValues.push(Number(words[j]));\n }\n }\n }\n\n if (!('domain' in colorsJson))\n colorsJson.domain = [Math.min.apply(null, domainValues), Math.max.apply(null, domainValues)];\n\n self.colorsJson = colorsJson;\n\n return self;\n };\n\n self.normalizeColors = function() {\n /* \n * Normalize the passed in values so that they range from\n * 0 to 1\n */\n var value;\n\n for (var moleculeName in self.colorsJson) {\n var minNum = Number.MAX_VALUE;\n var maxNum = Number.MIN_VALUE;\n\n // iterate once to find the min and max values;\n for (var resnum in self.colorsJson.colorValues[moleculeName]) {\n value = self.colorsJson.colorValues[moleculeName][resnum];\n if (typeof value == 'number') {\n if (value < minNum)\n minNum = value;\n if (value > maxNum)\n maxNum = value;\n }\n }\n\n // iterate again to normalize\n for (resnum in self.colorsJson.colorValues[moleculeName]) {\n value = self.colorsJson.colorValues[moleculeName][resnum];\n if (typeof value == 'number') {\n self.colorsJson.colorValues[moleculeName][resnum] = (value - minNum ) / (maxNum - minNum);\n }\n }\n }\n\n return self;\n };\n\n self.parseColorText(self.colorsText);\n return self;\n}\n","import {arraysEqual,RNAUtilities,rnaUtilities} from './rnautils.js';\nimport slugid from 'slugid';\n\nvar numberSort = function(a,b) { return a - b; };\n\nif (typeof(String.prototype.trim) === 'undefined') {\n String.prototype.trim = function() {\n return String(this).replace(/^\\s+|\\s+$/g, '');\n };\n}\n\nexport function ProteinGraph(structName, size, uid) {\n var self = this;\n\n self.type = 'protein';\n self.size = size;\n self.nodes = [{'name': 'P',\n 'num': 1,\n 'radius': 3 * Math.sqrt(size),\n 'rna': self,\n 'nodeType': 'protein',\n 'structName': structName,\n 'elemType': 'p',\n 'size': size,\n 'uid': slugid.nice()}];\n\n self.links = [];\n self.uid = slugid.nice();\n\n self.addUids = function(uids) {\n for (let i = 0; i < uids.length; i++)\n self.nodes[i].uid = uids[i];\n\n return self;\n };\n\n self.getUids = function() {\n /* Get the positions of each node so that they\n * can be passed to elementsToJson later\n */\n uids = [];\n for (let i = 0; i < self.dotbracket.length; i++)\n uids.push(self.nodes[i].uid);\n\n return uids;\n };\n\n}\n\nexport function RNAGraph(seq = '', dotbracket = '', structName = '', startNumber = 1) {\n var self = this;\n\n self.type = 'rna';\n self.circularizeExternal = false;\n self.seq = seq;\n self.dotbracket = dotbracket; //i.e. ..((..))..\n self.structName = structName;\n self.circular = false;\n\n if (self.dotbracket.slice(-1) == '*') {\n //circular RNA\n self.dotbracket = self.dotbracket.slice(0, -1);\n self.circular = true;\n }\n\n self.uid = slugid.nice();\n\n self.elements = []; //store the elements and the\n //nucleotides they contain\n self.pseudoknotPairs = [];\n self.nucsToNodes = {};\n\n self.addUids = function(uids) {\n let nucleotideNodes = self.nodes.filter(function(d) { return d.nodeType == 'nucleotide'; });\n\n for (let i = 0; i < uids.length && i < nucleotideNodes.length; i++) {\n nucleotideNodes[i].uid = uids[i];\n }\n\n return self;\n };\n\n self.computePairtable = function() {\n self.pairtable = rnaUtilities.dotbracketToPairtable(self.dotbracket);\n };\n\n // self.removeBreaks = function(targetString) {\n // // Collect the indexes of the chain breaks in the targetString\n // // chain breaks are indicated by '&'\n // var breaks = [];\n // for (var i = 0; i < targetString.length; i++) {\n // if (targetString[i] === '&') {\n // breaks.push(i);\n // }\n // }\n\n // return {targetString: targetString, breaks: breaks};\n // };\n\n // var ret = self.removeBreaks(self.dotbracket);\n // commented out to avoid removing the break node, let's keep it in the dotbracket\n // self.dotbracket = ret.targetString;\n // self.dotBracketBreaks = ret.breaks;\n\n // ret = self.removeBreaks(self.seq);\n // commented out to avoid removing the break node, let's keep it in the sequence\n // self.seq = ret.targetString;\n // self.seqBreaks = ret.breaks;\n\n self.rnaLength = self.dotbracket.length;\n\n // if (!arraysEqual(self.dotBracketBreaks, self.seqBreaks)) {\n // console.log('WARNING: Sequence and structure breaks not equal');\n // console.log('WARNING: Using the breaks in the structure');\n // }\n\n self.computePairtable();\n\n self.addPositions = function(nodeType, positions) {\n let labelNodes = self.nodes.filter(function(d) { return d.nodeType == nodeType; });\n\n for (let i = 0; i < labelNodes.length; i++) {\n labelNodes[i].x = positions[i][0];\n labelNodes[i].y = positions[i][1];\n }\n\n return self;\n };\n\n self.breakNodesToFakeNodes = function() {\n // convert all the nodes following breaks to fake nodes\n let labelNodes = self.nodes.filter(function(d) { return d.nodeType == 'nucleotide'; });\n\n // // if a node was an artifical break node, convert it to a middle\n // for (let i = 0; i < labelNodes.length; i++) {\n // if (self.dotBracketBreaks.indexOf(i) >= 0) {\n // labelNodes[i].nodeType = 'middle';\n // // commented out to avoid removing the node after the break\n // // labelNodes[i+1].nodeType = 'middle';\n // }\n // }\n\n for (let i = 0; i < self.elements.length; i++) {\n var broken = false;\n\n // // change the elemType of the other nodes in the element containing\n // // the break\n // for (let j = 0; j < self.elements[i][2].length; j++) {\n // if (self.dotBracketBreaks.indexOf(self.elements[i][2][j]) >= 0)\n // broken = true;\n // }\n\n if (broken) {\n self.elements[i][2].map(function(x) {\n if (x == 0)\n return;\n self.nodes[x-1].elemType = 'e';\n });\n } else {\n self.elements[i][2].map(function(x) {\n if (x == 0)\n return;\n self.nodes[x-1].elemType = self.elements[i][0];\n });\n }\n }\n return self;\n };\n\n self.getPositions = function(nodeType) {\n var positions = [];\n let nucleotideNodes = self.nodes.filter(function(d) { return d.nodeType == nodeType; });\n\n for (let i = 0; i < nucleotideNodes.length; i++)\n positions.push([nucleotideNodes[i].x, nucleotideNodes[i].y]);\n\n return positions;\n };\n\n self.getUids = function() {\n /* Get the positions of each node so that they\n * can be passed to elementsToJson later\n */\n var uids = [];\n for (let i = 0; i < self.dotbracket.length; i++)\n uids.push(self.nodes[i].uid);\n\n return uids;\n };\n\n self.reinforceStems = function() {\n var pt = self.pairtable;\n let relevantElements = self.elements.filter( function(d) {\n return d[0] == 's' && d[2].length >= 4;\n });\n\n for (let i = 0; i < relevantElements.length; i++) {\n let allNucs = relevantElements[i][2];\n let nucs = allNucs.slice(0, allNucs.length / 2);\n\n for (let j = 0; j < nucs.length-1; j++) {\n self.addFakeNode([nucs[j], nucs[j+1], pt[nucs[j+1]], pt[nucs[j]]]);\n }\n }\n\n return self;\n };\n\n self.reinforceLoops = function() {\n /*\n * Add a set of fake nodes to enforce the structure\n */\n var filterNucs = function(d) {\n return d !== 0 && d <= self.dotbracket.length;\n };\n\n for (let i = 0; i < self.elements.length; i++) {\n if (self.elements[i][0] == 's' || (!self.circularizeExternal && self.elements[i][0] == 'e'))\n continue;\n\n var nucs = self.elements[i][2].filter(filterNucs);\n\n if (self.elements[i][0] == 'e') {\n var newNode1 = {'name': '',\n 'num': -3,\n //'radius': 18 * radius -6,\n 'radius': 0,\n 'rna': self,\n 'nodeType': 'middle',\n 'elemType': 'f',\n 'nucs': [],\n 'x': self.nodes[self.rnaLength-1].x,\n 'y': self.nodes[self.rnaLength-1].y,\n 'px': self.nodes[self.rnaLength-1].px,\n 'py': self.nodes[self.rnaLength-1].py,\n 'uid': slugid.nice() };\n var newNode2 = {'name': '',\n 'num': -2,\n //'radius': 18 * radius -6,\n 'radius': 0,\n 'rna': self,\n 'nodeType': 'middle',\n 'elemType': 'f',\n 'nucs': [],\n 'x': self.nodes[0].x,\n 'y': self.nodes[0].y,\n 'px': self.nodes[0].px,\n 'py': self.nodes[0].py,\n 'uid': slugid.nice() };\n\n nucs.push(self.nodes.length+1);\n nucs.push(self.nodes.length+2);\n self.nodes.push(newNode1);\n self.nodes.push(newNode2);\n }\n\n\n self.addFakeNode(nucs);\n }\n\n return self;\n };\n\n self.updateLinkUids = function() {\n for (let i = 0; i < self.links.length; i++) {\n self.links[i].uid = self.links[i].source.uid + self.links[i].target.uid;\n }\n\n return self;\n };\n\n self.addFakeNode = function(nucs) {\n var linkLength = 18; //make sure this is consistent with the value in force.js\n var nodeWidth = 6;\n var angle = (3.1415 * 2) / (2 * nucs.length);\n var radius = linkLength / (2 * Math.tan(angle));\n\n var fakeNodeUid = '';\n\n for (let i = 0; i < nucs.length; i++)\n fakeNodeUid += self.nodes[nucs[i]-1].uid;\n\n var newNode = {'name': '',\n 'num': -1,\n //'radius': 18 * radius -6,\n 'radius': radius,\n 'rna': self,\n 'nodeType': 'middle',\n 'elemType': 'f',\n 'nucs': nucs,\n 'uid': fakeNodeUid };\n self.nodes.push(newNode);\n\n var newX = 0;\n var newY = 0;\n var coordsCounted = 0;\n\n angle = (nucs.length - 2) * 3.14159 / (2 * nucs.length);\n radius = 0.5 / Math.cos(angle);\n\n for (let j = 0; j < nucs.length; j++) {\n if (nucs[j] === 0 || nucs[j] > self.dotbracket.length)\n continue;\n\n //link to the center node\n self.links.push({'source': self.nodes[nucs[j] - 1],\n 'target': self.nodes[self.nodes.length-1],\n 'linkType': 'fake',\n 'value': radius,\n 'uid': slugid.nice() });\n\n if (nucs.length > 4) {\n //link across the loop\n self.links.push({'source': self.nodes[nucs[j] - 1],\n 'target': self.nodes[nucs[(j + Math.floor(nucs.length / 2)) % nucs.length] - 1],\n 'linkType': 'fake',\n 'value': radius * 2,\n 'uid': slugid.nice() });\n }\n\n var ia = ((nucs.length - 2) * 3.14159) / nucs.length;\n var c = 2 * Math.cos(3.14159 / 2 - ia / 2);\n //link to over-neighbor\n self.links.push({'source': self.nodes[nucs[j] - 1],\n 'target': self.nodes[nucs[(j + 2) % nucs.length] - 1],\n 'linkType': 'fake',\n 'value': c});\n\n // calculate the mean of the coordinats in this loop\n // and place the fake node there\n var fromNode = self.nodes[nucs[j]-1];\n if ('x' in fromNode) {\n newX += fromNode.x;\n newY += fromNode.y;\n\n coordsCounted += 1;\n }\n }\n\n if (coordsCounted > 0) {\n // the nucleotides had set positions so we can calculate the position\n // of the fake node\n newNode.x = newX / coordsCounted;\n newNode.y = newY / coordsCounted;\n newNode.px = newNode.x;\n newNode.py = newNode.y;\n }\n\n return self;\n };\n\n self.connectFakeNodes = function() {\n var linkLength = 18;\n\n // We want to be able to connect all of the fake nodes\n // and create a structure consisting of just them\n var filterOutNonFakeNodes = function(d) {\n return d.nodeType == 'middle';\n }\n\n var nucsToNodes = {};\n var fakeNodes = self.nodes.filter(filterOutNonFakeNodes);\n var linked = {};\n\n // initialize the nucleotides to nodes\n for (var i = 1; i <= self.nodes.length; i++)\n nucsToNodes[i] = [];\n\n for (var i = 0; i < fakeNodes.length; i++) {\n var thisNode = fakeNodes[i];\n\n // each fake node represents a certain set of nucleotides (thisNode.nucs)\n for (var j = 0; j < thisNode.nucs.length; j++) {\n var thisNuc = thisNode.nucs[j];\n\n // check to see if this nucleotide has been seen in another fake node\n // if it has, then we add a link between the two nodes\n for (var k = 0; k < nucsToNodes[thisNuc].length; k++) {\n if (JSON.stringify([nucsToNodes[thisNuc][k].uid, thisNode.uid].sort()) in linked)\n continue; //already linked\n\n var distance = nucsToNodes[thisNuc][k].radius + thisNode.radius;\n\n self.links.push({'source': nucsToNodes[thisNuc][k],\n 'target': thisNode,\n 'value': distance / linkLength,\n 'linkType': 'fake_fake'});\n\n // note that we've already seen this link\n linked[JSON.stringify([nucsToNodes[thisNuc][k].uid, thisNode.uid].sort())] = true;\n }\n\n nucsToNodes[thisNuc].push(thisNode);\n }\n }\n\n return self;\n\n };\n\n self.addExtraLinks = function(extraLinks) {\n if (typeof extraLinks == 'undefined')\n return self;\n\n for (var i = 0; i < extraLinks.length; i++) {\n var source = self.getNodeFromNucleotides(extraLinks[i].from);\n var target = self.getNodeFromNucleotides(extraLinks[i].to);\n\n var newLink = {'source': source, 'target': target, 'linkType': 'extra',\n 'extraLinkType': extraLinks[i].linkType, 'uid': slugid.nice() };\n\n self.links.push(newLink);\n }\n\n return self;\n }\n\n\n self.elementsToJson = function() {\n /* Convert a set of secondary structure elements to a json\n * representation of the graph that can be used with d3's\n * force-directed layout to generate a visualization of\n * the structure.\n */\n var pt = self.pairtable;\n var elements = self.elements;\n\n self.nodes = [];\n self.links = [];\n\n //create a reverse lookup so we can find out the type\n //of element that a node is part of\n var elemTypes = {};\n\n //sort so that we count stems last\n self.elements.sort();\n\n for (let i = 0; i < self.elements.length; i++) {\n var nucs = self.elements[i][2];\n for (let j = 0; j < nucs.length; j++) {\n elemTypes[nucs[j]] = self.elements[i][0];\n }\n }\n\n for (let i = 1; i <= pt[0]; i++) {\n var nodeName = self.seq[i-1];\n\n // // remove only the breaks that are in the sequence\n // if (self.dotBracketBreaks.indexOf(i-1) >= 0) {\n // nodeName = '';\n // }\n\n //create a node for each nucleotide\n self.nodes.push({'name': nodeName,\n 'num': startNumber + i - 1,\n 'radius': 5,\n 'rna': self,\n 'nodeType': 'nucleotide',\n 'structName': self.structName,\n 'elemType': elemTypes[i],\n 'uid': slugid.nice(),\n 'linked': false});\n }\n\n for (let i = 0; i < self.nodes.length; i++) {\n if (i === 0)\n self.nodes[i].prevNode = null;\n else {\n self.nodes[i].prevNode = self.nodes[i-1];\n }\n\n if (i == self.nodes.length-1)\n self.nodes[i].nextNode = null;\n else {\n self.nodes[i].nextNode = self.nodes[i+1];\n }\n }\n\n for (let i = 1; i <= pt[0]; i++) {\n\n if (pt[i] !== 0) {\n // base-pair links\n self.links.push({'source': self.nodes[i-1],\n 'target': self.nodes[pt[i]-1],\n 'linkType': 'basepair',\n 'value': 1,\n 'uid': slugid.nice() });\n }\n\n if (i > 1) {\n // backbone links\n // unlink only the break and the nucleotide before it\n // if (self.dotBracketBreaks.indexOf(i-1) === -1 &&\n // self.dotBracketBreaks.indexOf(i-2) == -1) {\n // there is no break in the strands here\n // we can add a backbone link\n self.links.push({'source': self.nodes[i-2],\n 'target': self.nodes[i-1],\n 'linkType': 'backbone',\n 'value': 1,\n 'uid': slugid.nice() });\n self.nodes[i-1].linked = true;\n // }\n }\n }\n\n //add the pseudoknot links\n for (let i = 0; i < self.pseudoknotPairs.length; i++) {\n self.links.push({'source': self.nodes[self.pseudoknotPairs[i][0]-1],\n 'target': self.nodes[self.pseudoknotPairs[i][1]-1],\n 'linkType': 'pseudoknot',\n 'value': 1,\n 'uid': slugid.nice()});\n }\n\n if (self.circular) {\n self.links.push({'source': self.nodes[0],\n 'target': self.nodes[self.rnaLength-1],\n 'linkType': 'backbone',\n 'value': 1,\n 'uid': slugid.nice() });\n\n }\n\n return self;\n };\n\n self.ptToElements = function(pt, level, i, j) {\n /* Convert a pair table to a list of secondary structure\n * elements:\n *\n * [['s',1,[2,3]]\n *\n * The 's' indicates that an element can be a stem. It can also be\n * an interior loop ('i'), a hairpin loop ('h') or a multiloop ('m')\n *\n * The second number (1 in this case) indicates the depth or\n * how many base pairs have to be broken to get to this element.\n *\n * Finally, there is the list of nucleotides which are part of\n * of this element.\n */\n var elements = [];\n var u5 = [i-1];\n var u3 = [j+1];\n\n if (i > j)\n return [];\n\n //iterate over the unpaired regions on either side\n //this is either 5' and 3' unpaired if level == 0\n //or an interior loop or a multiloop\n for (; pt[i] === 0; i++) { u5.push(i); }\n for (; pt[j] === 0; j--) { u3.push(j); }\n\n if (i > j) {\n //hairpin loop or one large unpaired molecule\n u5.push(i);\n // if (level === 0)\n return [['e',level, u5.sort(numberSort)]];\n // else {\n // // check to see if we have chain breaks due\n // // to multiple strands in the input\n // var external = false;\n // var left = [];\n // var right = [];\n // for (var k = 0; k < u5.length; k++) {\n // if (external)\n // right.push(u5[k]);\n // else\n // left.push(u5[k]);\n\n // if (self.dotBracketBreaks.indexOf(u5[k]) >= 0)\n // external = true;\n // }\n\n // if (external) {\n // return [['h',level, u5.sort(numberSort)]];\n // }\n // else\n // // if not, this is a simple hairpin loop\n // return [['h',level, u5.sort(numberSort)]];\n // }\n }\n\n if (pt[i] != j) {\n //multiloop\n var m = u5;\n var k = i;\n\n // the nucleotide before and the starting nucleotide\n m.push(k);\n while (k <= j) {\n // recurse into a stem\n elements = elements.concat(self.ptToElements(pt, level, k, pt[k]));\n\n // add the nucleotides between stems\n m.push(pt[k]);\n k = pt[k] + 1;\n for (; pt[k] === 0 && k <= j; k++) { m.push(k);}\n m.push(k);\n }\n m.pop();\n m = m.concat(u3);\n\n if (m.length > 0) {\n if (level === 0)\n elements.push(['e', level, m.sort(numberSort)]);\n else\n elements.push(['m', level, m.sort(numberSort)]);\n }\n\n return elements;\n }\n\n if (pt[i] === j) {\n //interior loop\n u5.push(i);\n u3.push(j);\n\n var combined = u5.concat(u3);\n if (combined.length > 4) {\n if (level === 0)\n elements.push(['e',level, u5.concat(u3).sort(numberSort)]);\n else\n elements.push(['i',level, u5.concat(u3).sort(numberSort)]);\n }\n }\n\n var s = [];\n //go through the stem\n while (pt[i] === j && i < j) {\n //one stem\n s.push(i);\n s.push(j);\n\n i += 1;\n j -= 1;\n\n level += 1;\n }\n\n u5 = [i-1];\n u3 = [j+1];\n elements.push(['s', level, s.sort(numberSort)]);\n\n return elements.concat(self.ptToElements(pt, level, i, j));\n };\n\n self.addLabels = function(startNumber = 1, labelInterval = 10) {\n if (labelInterval === 0)\n return self;\n\n for (let i = 1; i <= self.rnaLength; i++) {\n // add labels\n if (i % labelInterval === 0) {\n //create a node for each label\n let newX, newY;\n\n let thisNode = self.nodes[i-1];\n let prevNode, nextNode;\n let prevVec, nextVec;\n\n if (self.rnaLength == 1) {\n nextVec = [thisNode.x - 15, thisNode.y];\n prevVec = [thisNode.x - 15, thisNode.y];\n } else {\n // if we're labelling the first node, then label it in relation to the last\n if (i == 1)\n prevNode = self.nodes[self.rnaLength - 1];\n else\n prevNode = self.nodes[i - 2];\n\n // if we're labelling the last node, then label it in relation to the first\n if (i == self.rnaLength)\n nextNode = self.nodes[0];\n else\n nextNode = self.nodes[i];\n\n // this nucleotide and its neighbors are paired\n if (self.pairtable[nextNode.num - startNumber+1] !== 0 &&\n self.pairtable[prevNode.num - startNumber+1] !== 0 &&\n self.pairtable[thisNode.num - startNumber+1] !== 0) {\n\n prevNode = nextNode = self.nodes[self.pairtable[thisNode.num - startNumber+1]-1];\n }\n\n // this node is paired but at least one of its neighbors is unpaired\n // place the label in the direction of the two neighbors\n if (self.pairtable[thisNode.num - startNumber+1] !== 0 && (\n self.pairtable[nextNode.num - startNumber+1] === 0 ||\n self.pairtable[prevNode.num - startNumber+1] === 0)) {\n nextVec = [thisNode.x - nextNode.x, thisNode.y - nextNode.y];\n prevVec = [thisNode.x - prevNode.x, thisNode.y - prevNode.y];\n\n } else {\n nextVec = [nextNode.x - thisNode.x, nextNode.y - thisNode.y];\n prevVec = [prevNode.x - thisNode.x, prevNode.y - thisNode.y];\n }\n }\n\n var combinedVec = [nextVec[0] + prevVec[0], nextVec[1] + prevVec[1]];\n var vecLength = Math.sqrt(combinedVec[0] * combinedVec[0] + combinedVec[1] * combinedVec[1]);\n var normedVec = [combinedVec[0] / vecLength, combinedVec[1] / vecLength];\n var offsetVec = [-15 * normedVec[0], -15 * normedVec[1]];\n\n newX = self.nodes[i-1].x + offsetVec[0];\n newY = self.nodes[i-1].y + offsetVec[1];\n\n var newNode = {'name': i + startNumber -1,\n 'num': -1,\n 'radius': 6,\n 'rna': self,\n 'nodeType': 'label',\n 'structName': self.structName,\n 'elemType': 'l',\n 'x': newX,\n 'y': newY,\n 'px': newX,\n 'py': newY,\n 'uid': slugid.nice() };\n var newLink = {'source': self.nodes[i-1],\n 'target': newNode,\n 'value': 1,\n 'linkType': 'label_link',\n 'uid': slugid.nice() };\n\n self.nodes.push(newNode);\n self.links.push(newLink);\n }\n }\n\n return self;\n };\n\n self.recalculateElements = function() {\n self.removePseudoknots();\n self.elements = self.ptToElements(self.pairtable, 0, 1, self.dotbracket.length);\n\n if (self.circular) {\n //check to see if the external loop is a hairpin or a multiloop\n let externalLoop = self.elements.filter(function(d) { if (d[0] == 'e') return true; });\n\n if (externalLoop.length > 0) {\n eloop = externalLoop[0];\n nucs = eloop[2].sort(numberSort);\n\n prev = nucs[0];\n hloop = true;\n numGreater = 0;\n for (let i = 1; i < nucs.length; i++) {\n if (nucs[i] - prev > 1) {\n numGreater += 1;\n }\n prev = nucs[i];\n }\n\n if (numGreater == 1) {\n eloop[0] = 'h';\n } else if (numGreater == 2) {\n eloop[0] = 'i';\n } else {\n eloop[0] = 'm';\n }\n }\n }\n\n return self;\n };\n\n self.reassignLinkUids = function() {\n // reassign uids to the links, corresponding to the uids of the two nodes\n // they connect\n var i;\n\n for (var i = 0; i < self.links.length; i++) {\n self.links[i].uid = self.links[i].source.uid + self.links[i].target.uid;\n }\n\n return self;\n }\n\n self.removePseudoknots = function() {\n if (self.pairtable.length > 1)\n self.pseudoknotPairs = self.pseudoknotPairs.concat(rnaUtilities.removePseudoknotsFromPairtable(self.pairtable));\n\n return self;\n };\n\n self.addPseudoknots = function() {\n /* Add all of the pseudoknot pairs which are stored outside\n * of the pairtable back to the pairtable\n */\n var pt = self.pairtable;\n var pseudoknotPairs = self.pseudoknotPairs;\n\n for (var i = 0; i < pseudoknotPairs.length; i++) {\n pt[pseudoknotPairs[i][0]] = pseudoknotPairs[i][1];\n pt[pseudoknotPairs[i][1]] = pseudoknotPairs[i][0];\n }\n\n self.pseudoknotPairs = [];\n return self;\n };\n\n self.addName = function(name) {\n if (typeof name == 'undefined') {\n self.name = '';\n return self;\n } else {\n self.name = name;\n return self;\n }\n };\n\n\n if (self.rnaLength > 0)\n self.recalculateElements();\n\n self.getNodeFromNucleotides = function(nucs) {\n /* Get a node given a nucleotide number or an array of nucleotide\n * numbers indicating an element node */\n if (Object.prototype.toString.call(nucs) === '[object Array]') {\n for (let j = 0; j < self.nodes.length; j++) {\n if ('nucs' in self.nodes[j]) {\n if (self.nodes[j].nucs.equals(nucs)) {\n return self.nodes[j];\n }\n }\n }\n } else {\n for (let j = 0; j < self.nodes.length; j++) {\n if (self.nodes[j].num == nucs) {\n return self.nodes[j];\n }\n }\n }\n\n console.log('ERROR: No node found for nucs:', nucs);\n return null;\n }\n}\n\nexport function moleculesToJson(moleculesJson) {\n /* Convert a list of RNA and protein molecules to a list of RNAGraph\n * ProteinGraph and extraLinks structure */\n\n var nodes = {}; //index the nodes by uid\n var graphs = [];\n var extraLinks = [];\n\n\n // Create the graphs for each molecule\n for (var i = 0; i < moleculesJson.molecules.length; i++) {\n var molecule = moleculesJson.molecules[i];\n var rg;\n\n if (molecule.type == 'rna') {\n rg = new RNAGraph(molecule.seq, molecule.ss, molecule.header);\n rg.circularizeExternal = true;\n rg.elementsToJson()\n .addPositions('nucleotide', molecule.positions)\n .addLabels()\n .reinforceStems()\n .reinforceLoops();\n\n\n } else if (molecule.type == 'protein') {\n rg = new ProteinGraph(molecule.header, molecule.size);\n\n }\n\n rg.addUids(molecule.uids);\n\n for (var j = 0; j < rg.nodes.length; j++) {\n nodes[rg.nodes[j].uid] = rg.nodes[j];\n }\n\n graphs.push(rg);\n }\n\n //Add the extra links\n for (var i = 0; i < moleculesJson.extraLinks.length; i++) {\n link = moleculesJson.extraLinks[i];\n\n link.source = nodes[link.source];\n link.target = nodes[link.target];\n link.uid = slugid.nice();\n\n extraLinks.push(link);\n }\n\n return {'graphs': graphs, 'extraLinks': extraLinks};\n};\n","export function simpleXyCoordinates (pair_table) {\n var INIT_ANGLE=0.; /* initial bending angle */\n var INIT_X = 100.; /* coordinate of first digit */\n var INIT_Y = 100.; /* see above */\n var RADIUS = 15.;\n\n var x = [], y = [];\n\n var i, len;\n var alpha;\n\n len = pair_table[0];\n var angle = Array.apply(null, new Array(len+5)).map(Number.prototype.valueOf,0); \n var loop_size = Array.apply(null, new Array(16+Math.floor(len/5)))\n .map(Number.prototype.valueOf, 0); \n var stack_size = Array.apply(null, new Array(16+Math.floor(len/5)))\n .map(Number.prototype.valueOf, 0); \n\n var lp = 0;\n var stk = 0;\n var PIHALF = Math.PI / 2;\n\n\n var loop = function(i, j, pair_table)\n /* i, j are the positions AFTER the last pair of a stack; i.e\n i-1 and j+1 are paired. */\n {\n var count = 2; /* counts the VERTICES of a loop polygon; that's\n NOT necessarily the number of unpaired bases!\n Upon entry the loop has already 2 vertices, namely\n the pair i-1/j+1. */\n\n var r = 0, bubble = 0; /* bubble counts the unpaired digits in loops */\n\n var i_old, partner, k, l, start_k, start_l, fill, ladder;\n var begin, v, diff;\n var polygon;\n\n var remember = Array.apply(null, new Array((3+Math.floor((j-i)/5)*2))).map(Number.prototype.valueOf, 0);\n\n i_old = i-1, j++; /* j has now been set to the partner of the\n previous pair for correct while-loop\n termination. */\n while (i != j) {\n partner = pair_table[i];\n if ((!partner) || (i==0))\n i++, count++, bubble++;\n else {\n count += 2;\n k = i, l = partner; /* beginning of stack */\n remember[++r] = k;\n remember[++r] = l;\n i = partner+1; /* next i for the current loop */\n\n start_k = k, start_l = l;\n ladder = 0;\n do {\n k++, l--, ladder++; /* go along the stack region */\n }\n while ((pair_table[k] == l) && (pair_table[k] > k));\n\n fill = ladder-2;\n if (ladder >= 2) {\n angle[start_k+1+fill] += PIHALF; /* Loop entries and */\n angle[start_l-1-fill] += PIHALF; /* exits get an */\n angle[start_k] += PIHALF; /* additional PI/2. */\n angle[start_l] += PIHALF; /* Why ? (exercise) */\n if (ladder > 2) {\n for (; fill >= 1; fill--) {\n angle[start_k+fill] = Math.PI; /* fill in the angles */\n angle[start_l-fill] = Math.PI; /* for the backbone */\n }\n }\n }\n stack_size[++stk] = ladder;\n if (k <= l)\n loop(k, l, pair_table);\n }\n }\n\n polygon = Math.PI*(count-2)/count; /* bending angle in loop polygon */\n remember[++r] = j;\n begin = i_old < 0 ? 0 : i_old;\n for (v = 1; v <= r; v++) {\n diff = remember[v]-begin;\n for (fill = 0; fill <= diff; fill++)\n angle[begin+fill] += polygon;\n if (v > r)\n break;\n begin = remember[++v];\n }\n loop_size[++lp] = bubble;\n }\n\n loop(0, len+1, pair_table);\n loop_size[lp] -= 2; /* correct for cheating with function loop */\n\n alpha = INIT_ANGLE;\n x[0] = INIT_X;\n y[0] = INIT_Y;\n\n var poss = [];\n\n poss.push([x[0], y[0]]);\n for (i = 1; i < len; i++) {\n x[i] = x[i-1]+RADIUS*Math.cos(alpha);\n y[i] = y[i-1]+RADIUS*Math.sin(alpha);\n\n poss.push([x[i], y[i]]);\n alpha += Math.PI-angle[i+1];\n }\n\n return poss;\n}\n","export function Radloop() {\n\tthis.radius = null;\n\tthis.loopnumber = null;\n\tthis.next = null;\n this.prev = null;\n}\n\nRadloop.prototype.getRadius = function(){\n\treturn this.radius;\n}\n\nRadloop.prototype.setRadius = function(radius){\n\tthis.radius = radius;\n}\n\nRadloop.prototype.getLoopnumber = function(){\n\treturn this.loopnumber;\n}\n\nRadloop.prototype.setLoopnumber = function(loopnumber){\n\tthis.loopnumber = loopnumber;\n}\n\nRadloop.prototype.getNext = function(){\n\treturn this.next;\n}\n\nRadloop.prototype.setNext = function(next){\n\tthis.next = next;\n}\n\nRadloop.prototype.getPrev = function(){\n\treturn this.prev;\n}\n\nRadloop.prototype.setPrev = function(prev){\n\tthis.prev = prev;\n}\n","import {Region} from './region.js';\n\nexport function Base() {\n\tthis.mate = null;\n\tthis.x = null;\n this.y = null;\n\tthis.extracted = null;\n\tthis.region = new Region();\n}\n\nBase.prototype.getMate = function(){\n\treturn this.mate;\n}\n\nBase.prototype.setMate = function(mate){\n\tthis.mate = mate;\n}\n\nBase.prototype.getX = function(){\n\treturn this.x;\n}\n\nBase.prototype.setX = function(x){\n\tthis.x = x;\n}\n\nBase.prototype.getY = function(){\n\treturn this.y;\n}\n\nBase.prototype.setY = function(y){\n\tthis.y = y;\n}\n\nBase.prototype.isExtracted = function(){\n\treturn this.extracted;\n}\n\nBase.prototype.setExtracted = function(extracted){\n\tthis.extracted = extracted;\n}\n\nBase.prototype.getRegion = function(){\n\treturn this.region;\n}\n\nBase.prototype.setRegion = function(region){\n\tthis.region = region;\n}\n","import {Radloop} from './radloop.js';\nimport {Connection} from './connection.js';\nimport {Region} from './region.js';\nimport {Base} from './base.js';\nimport {Loop} from './loop.js';\n\nexport function NAView(){\n this.ANUM = 9999.0;\n\tthis.MAXITER = 500;\n\n\tthis.bases = [];\n\tthis.nbase = null;\n this.nregion = null;\n this.loop_count = null;\n\n\tthis.root = new Loop();\n\tthis.loops = [];\n\n\tthis.regions = [];\n\n\tthis.rlphead = new Radloop();\n\n\tthis.lencut = 0.8;\n\tthis.RADIUS_REDUCTION_FACTOR = 1.4;\n\n\t// show algorithm step by step\n\tthis.angleinc = null;\n\n\tthis._h = null;\n\n\t// private boolean noIterationFailureYet = true;\n\n\tthis.HELIX_FACTOR = 0.6;\n\tthis.BACKBONE_DISTANCE = 27;\n}\n\nNAView.prototype.naview_xy_coordinates = function(pair_table){\n var x = [];\n\tvar y = [];\n if (pair_table.length === 0 || pair_table[0] === 0){\n return 0;\n }\n var i;\n this.nbase = pair_table[0];\n this.bases = [];\n for (var index = 0; index < this.nbase + 1; index++){\n this.bases.push(new Base());\n }\n this.regions = [];\n for (var index = 0; index < this.nbase + 1; index++){\n this.regions.push(new Region());\n }\n this.read_in_bases(pair_table);\n this.rlphead = null;\n this.find_regions();\n this.loop_count = 0;\n this.loops = [];\n for (var index = 0; index < this.nbase + 1; index++){\n this.loops.push(new Loop());\n }\n this.construct_loop(0);\n this.find_central_loop();\n this.traverse_loop(this.root, null);\n\n for (i = 0; i < this.nbase; i++){\n x.push(100 + this.BACKBONE_DISTANCE * this.bases[i + 1].getX());\n y.push(100 + this.BACKBONE_DISTANCE * this.bases[i + 1].getY());\n }\n\n return {\n nbase: this.nbase,\n x: x,\n y: y\n }\n}\n\nNAView.prototype.read_in_bases = function read_in_bases(pair_table){\n var i = null;\n var npairs = null;\n\n // Set up an origin.\n this.bases.push(new Base());\n this.bases[0].setMate(0);\n this.bases[0].setExtracted(false);\n this.bases[0].setX(this.ANUM);\n this.bases[0].setY(this.ANUM);\n\n for (npairs = 0, i = 1; i <= this.nbase; i++){\n this.bases.push(new Base());\n this.bases[i].setExtracted(false);\n this.bases[i].setX(this.ANUM);\n this.bases[i].setY(this.ANUM);\n this.bases[i].setMate(pair_table[i]);\n if (pair_table[i] > i)\n npairs++;\n }\n // must have at least 1 pair to avoid segfault\n if (npairs == 0){\n this.bases[1].setMate(this.nbase);\n this.bases[this.nbase].setMate(1);\n }\n}\n\nNAView.prototype.find_regions = function find_regions(){\n var i = null;\n var mate = null;\n var nb1 = null;\n\n nb1 = this.nbase + 1;\n var mark = [];\n for (i = 0; i < nb1; i++){\n mark.push(false);\n }\n this.nregion = 0;\n for (i = 0; i <= this.nbase; i++) {\n if ((mate = this.bases[i].getMate()) != 0 && !mark[i]) {\n this.regions[this.nregion].setStart1(i);\n this.regions[this.nregion].setEnd2(mate);\n mark[i] = true;\n mark[mate] = true;\n this.bases[i].setRegion(this.regions[this.nregion]);\n this.bases[mate].setRegion(this.regions[this.nregion]);\n for (i++, mate--; i < mate && this.bases[i].getMate() == mate; i++, mate--) {\n mark[mate] = true;\n mark[i]= true;\n this.bases[i].setRegion(this.regions[this.nregion]);\n this.bases[mate].setRegion(this.regions[this.nregion]);\n }\n this.regions[this.nregion].setEnd1(--i);\n this.regions[this.nregion].setStart2(mate + 1);\n\n this.nregion++;\n }\n }\n}\n\nNAView.prototype.construct_loop = function construct_loop(ibase){\n var i = null;\n var mate = null;\n var retloop = new Loop();\n var lp = new Loop();\n var cp = new Connection();\n var rp = new Region();\n var rlp = new Radloop();\n retloop = this.loops[this.loop_count++];\n retloop.setNconnection(0);\n retloop.setDepth(0);\n retloop.setNumber(this.loop_count);\n retloop.setRadius(0.0);\n\n for (rlp = this.rlphead; rlp != null; rlp = rlp.getNext())\n if (rlp.getLoopnumber() == this.loop_count)\n retloop.setRadius(rlp.getRadius());\n i = ibase;\n do {\n if ((mate = this.bases[i].getMate()) != 0) {\n rp = this.bases[i].getRegion();\n if (!this.bases[rp.getStart1()].isExtracted()) {\n if (i == rp.getStart1()) {\n this.bases[rp.getStart1()].setExtracted(true);\n this.bases[rp.getEnd1()].setExtracted(true);\n this.bases[rp.getStart2()].setExtracted(true);\n this.bases[rp.getEnd2()].setExtracted(true);\n lp = this.construct_loop(rp.getEnd1() < this.nbase ? rp.getEnd1() + 1\n : 0);\n } else if (i == rp.getStart2()) {\n this.bases[rp.getStart2()].setExtracted(true);\n this.bases[rp.getEnd2()].setExtracted(true);\n this.bases[rp.getStart1()].setExtracted(true);\n this.bases[rp.getEnd1()].setExtracted(true);\n lp = this.construct_loop(rp.getEnd2() < this.nbase ? rp.getEnd2() + 1\n : 0);\n } else {\n console.log(\"Something went terribly wrong ....\");\n }\n retloop.setNconnection(retloop.getNconnection() + 1);\n cp = new Connection();\n retloop.setConnection(retloop.getNconnection() - 1,\tcp);\n retloop.setConnection(retloop.getNconnection(), null);\n cp.setLoop(lp);\n cp.setRegion(rp);\n if(i == rp.getStart1()) {\n cp.setStart(rp.getStart1());\n cp.setEnd(rp.getEnd2());\n } else {\n cp.setStart(rp.getStart2());\n cp.setEnd(rp.getEnd1());\n }\n cp.setExtruded(false);\n cp.setBroken(false);\n lp.setNconnection(lp.getNconnection() + 1);\n cp = new Connection();\n lp.setConnection(lp.getNconnection() - 1, cp);\n lp.setConnection(lp.getNconnection(), null);\n cp.setLoop(retloop);\n cp.setRegion(rp);\n if (i == rp.getStart1()) {\n cp.setStart(rp.getStart2());\n cp.setEnd(rp.getEnd1());\n } else {\n cp.setStart(rp.getStart1());\n cp.setEnd(rp.getEnd2());\n }\n cp.setExtruded(false);\n cp.setBroken(false);\n }\n i = mate;\n }\n if (++i > this.nbase)\n i = 0;\n } while (i != ibase);\n return retloop;\n}\n\nNAView.prototype.find_central_loop = function find_central_loop(){\n var lp = new Loop();\n var maxconn = null;\n var maxdepth = null;\n var i = null;\n\n determine_depths.bind(this)();\n maxconn = 0;\n maxdepth = -1;\n for (i = 0; i < this.loop_count; i++) {\n lp = this.loops[i];\n if (lp.getNconnection() > maxconn) {\n maxdepth = lp.getDepth();\n maxconn = lp.getNconnection();\n this.root = lp;\n } else if (lp.getDepth() > maxdepth\n && lp.getNconnection() == maxconn) {\n maxdepth = lp.getDepth();\n this.root = lp;\n }\n }\n}\n\nfunction determine_depths() {\n var lp = new Loop();\n var i = null;\n var j = null;\n\n for (i = 0; i < this.loop_count; i++) {\n lp = this.loops[i];\n for (j = 0; j < this.loop_count; j++){\n this.loops[j].setMark(false);\n }\n lp.setDepth(depth(lp));\n }\n}\n\nfunction depth(lp){\n var count = null;\n var ret = null;\n var d = null;\n\n if (lp.getNconnection() <= 1){\n return 0;\n }\n if (lp.isMark()){\n return -1;\n }\n lp.setMark(true);\n count = 0;\n ret = 0;\n for (var i = 0; lp.getConnection(i) != null; i++) {\n d = depth(lp.getConnection(i).getLoop());\n if (d >= 0) {\n if (++count == 1){\n ret = d;\n }\n else if (ret > d){\n ret = d;\n }\n }\n }\n lp.setMark(false);\n return ret + 1;\n}\n\nNAView.prototype.traverse_loop = function traverse_loop(lp, anchor_connection){\n var xs, ys, xe, ye, xn, yn, angleinc, r;\n var radius, xc, yc, xo, yo, astart, aend, a;\n var cp, cpnext, acp, cpprev;\n var i, j, n, ic;\n var da, maxang;\n var count, icstart, icend, icmiddle, icroot;\n var done, done_all_connections, rooted;\n var sign;\n var midx, midy, nrx, nry, mx, my, vx, vy, dotmv, nmidx, nmidy;\n var icstart1, icup, icdown, icnext, direction;\n var dan, dx, dy, rr;\n var cpx, cpy, cpnextx, cpnexty, cnx, cny, rcn, rc, lnx, lny, rl, ac, acn, sx, sy, dcp;\n var imaxloop = 0;\n\n angleinc = 2 * Math.PI / (this.nbase + 1);\n acp = null;\n icroot = -1;\n var indice = 0;\n\n for (ic = 0; (cp = lp.getConnection(indice)) != null; indice++, ic++) {\n xs = -Math.sin(angleinc * cp.getStart());\n ys = Math.cos(angleinc * cp.getStart());\n xe = -Math.sin(angleinc * cp.getEnd());\n ye = Math.cos(angleinc * cp.getEnd());\n xn = ye - ys;\n yn = xs - xe;\n r = Math.sqrt(xn * xn + yn * yn);\n cp.setXrad(xn / r);\n cp.setYrad(yn / r);\n cp.setAngle(Math.atan2(yn, xn));\n if (cp.getAngle() < 0.0){\n cp.setAngle(cp.getAngle() + 2 * Math.PI);\n }\n if (anchor_connection != null\n && anchor_connection.getRegion() == cp.getRegion()) {\n acp = cp;\n icroot = ic;\n }\n }\n set_radius: while (true) {\n this.determine_radius(lp, this.lencut);\n radius = lp.getRadius()/this.RADIUS_REDUCTION_FACTOR;\n if (anchor_connection == null){\n xc = yc = 0.0;\n }\n else {\n xo = (this.bases[acp.getStart()].getX() + this.bases\n [acp.getEnd()].getX()) / 2.0;\n yo = (this.bases[acp.getStart()].getY() + this.bases\n [acp.getEnd()].getY()) / 2.0;\n xc = xo - radius * acp.getXrad();\n yc = yo - radius * acp.getYrad();\n }\n\n // The construction of the connectors will proceed in blocks of\n // connected connectors, where a connected connector pairs means two\n // connectors that are forced out of the drawn circle because they\n // are too close together in angle.\n\n // First, find the start of a block of connected connectors\n\n if (icroot == -1){\n icstart = 0;\n }\n else {\n icstart = icroot;\n }\n cp = lp.getConnection(icstart);\n count = 0;\n done = false;\n do {\n j = icstart - 1;\n if (j < 0){\n j = lp.getNconnection() - 1;\n }\n cpprev = lp.getConnection(j);\n if (!this.connected_connection(cpprev, cp)) {\n done = true;\n }\n else {\n icstart = j;\n cp = cpprev;\n }\n if (++count > lp.getNconnection()) {\n // Here everything is connected. Break on maximum angular\n // separation between connections.\n maxang = -1.0;\n for (ic = 0; ic < lp.getNconnection(); ic++) {\n j = ic + 1;\n if (j >= lp.getNconnection()){\n j = 0;\n }\n cp = lp.getConnection(ic);\n cpnext = lp.getConnection(j);\n ac = cpnext.getAngle() - cp.getAngle();\n if (ac < 0.0){\n ac += 2 * Math.PI;\n }\n if (ac > maxang) {\n maxang = ac;\n imaxloop = ic;\n }\n }\n icend = imaxloop;\n icstart = imaxloop + 1;\n if (icstart >= lp.getNconnection()){\n icstart = 0;\n }\n cp = lp.getConnection(icend);\n cp.setBroken(true);\n done = true;\n }\n } while (!done);\n done_all_connections = false;\n icstart1 = icstart;\n while (!done_all_connections) {\n count = 0;\n done = false;\n icend = icstart;\n rooted = false;\n while (!done) {\n cp = lp.getConnection(icend);\n if (icend == icroot){\n rooted = true;\n }\n j = icend + 1;\n if (j >= lp.getNconnection()) {\n j = 0;\n }\n cpnext = lp.getConnection(j);\n if (this.connected_connection(cp, cpnext)) {\n if (++count >= lp.getNconnection()){\n break;\n }\n icend = j;\n }\n else {\n done = true;\n }\n }\n icmiddle = this.find_ic_middle(icstart, icend, anchor_connection,\n acp, lp);\n ic = icup = icdown = icmiddle;\n done = false;\n direction = 0;\n while (!done) {\n if (direction < 0) {\n ic = icup;\n }\n else if (direction == 0) {\n ic = icmiddle;\n }\n else {\n ic = icdown;\n }\n if (ic >= 0) {\n cp = lp.getConnection(ic);\n if (anchor_connection == null || acp != cp) {\n if (direction == 0) {\n astart = cp.getAngle()\n - Math.asin(1.0 / 2.0 / radius);\n aend = cp.getAngle()\n + Math.asin(1.0 / 2.0 / radius);\n this.bases[cp.getStart()].setX(\n xc + radius * Math.cos(astart));\n this.bases[cp.getStart()].setY(\n yc + radius * Math.sin(astart));\n this.bases[cp.getEnd()].setX(\n xc + radius * Math.cos(aend));\n this.bases[cp.getEnd()].setY(\n yc + radius * Math.sin(aend));\n }\n else if (direction < 0) {\n j = ic + 1;\n if (j >= lp.getNconnection()){\n j = 0;\n }\n cp = lp.getConnection(ic);\n cpnext = lp.getConnection(j);\n cpx = cp.getXrad();\n cpy = cp.getYrad();\n ac = (cp.getAngle() + cpnext.getAngle()) / 2.0;\n if (cp.getAngle() > cpnext.getAngle()){\n ac -= Math.PI;\n }\n cnx = Math.cos(ac);\n cny = Math.sin(ac);\n lnx = cny;\n lny = -cnx;\n da = cpnext.getAngle() - cp.getAngle();\n if (da < 0.0){\n da += 2 * Math.PI;\n }\n if (cp.isExtruded()) {\n if (da <= Math.PI / 2){\n rl = 2.0;\n }\n else {\n rl = 1.5;\n }\n }\n else {\n rl = 1.0;\n }\n this.bases[cp.getEnd()].setX(\n this.bases[cpnext.getStart()].getX()\n + rl * lnx);\n this.bases[cp.getEnd()].setY(\n this.bases[cpnext.getStart()].getY()\n + rl * lny);\n this.bases[cp.getStart()].setX(\n this.bases[cp.getEnd()].getX() + cpy);\n this.bases[cp.getStart()].setY(\n this.bases[cp.getEnd()].getY() - cpx);\n } else {\n j = ic - 1;\n if (j < 0){\n j = lp.getNconnection() - 1;\n }\n cp = lp.getConnection(j);\n cpnext = lp.getConnection(ic);\n cpnextx = cpnext.getXrad();\n cpnexty = cpnext.getYrad();\n ac = (cp.getAngle() + cpnext.getAngle()) / 2.0;\n if (cp.getAngle() > cpnext.getAngle()){\n ac -= Math.PI;\n }\n cnx = Math.cos(ac);\n cny = Math.sin(ac);\n lnx = -cny;\n lny = cnx;\n da = cpnext.getAngle() - cp.getAngle();\n if (da < 0.0){\n da += 2 * Math.PI;\n }\n if (cp.isExtruded()) {\n if (da <= Math.PI / 2){\n rl = 2.0;\n }\n else {\n rl = 1.5;\n }\n }\n else {\n rl = 1.0;\n }\n this.bases[cpnext.getStart()].setX(\n this.bases[cp.getEnd()].getX() + rl\n * lnx);\n this.bases[cpnext.getStart()].setY(\n this.bases[cp.getEnd()].getY() + rl\n * lny);\n this.bases[cpnext.getEnd()].setX(\n this.bases[cpnext.getStart()].getX()\n - cpnexty);\n this.bases[cpnext.getEnd()].setY(\n this.bases[cpnext.getStart()].getY()\n + cpnextx);\n }\n }\n }\n if (direction < 0) {\n if (icdown == icend) {\n icdown = -1;\n }\n else if (icdown >= 0) {\n if (++icdown >= lp.getNconnection()) {\n icdown = 0;\n }\n }\n direction = 1;\n }\n else {\n if (icup == icstart){\n icup = -1;\n }\n else if (icup >= 0) {\n if (--icup < 0) {\n icup = lp.getNconnection() - 1;\n }\n }\n direction = -1;\n }\n done = icup == -1 && icdown == -1;\n }\n icnext = icend + 1;\n if (icnext >= lp.getNconnection()){\n icnext = 0;\n }\n if (icend != icstart\n && (!(icstart == icstart1 && icnext == icstart1))) {\n\n // Move the bases just constructed (or the radius) so that\n // the bisector of the end points is radius distance away\n // from the loop center.\n\n cp = lp.getConnection(icstart);\n cpnext = lp.getConnection(icend);\n dx = this.bases[cpnext.getEnd()].getX()\n - this.bases[cp.getStart()].getX();\n dy = this.bases[cpnext.getEnd()].getY()\n - this.bases[cp.getStart()].getY();\n midx = this.bases[cp.getStart()].getX() + dx / 2.0;\n midy = this.bases[cp.getStart()].getY() + dy / 2.0;\n rr = Math.sqrt(dx * dx + dy * dy);\n mx = dx / rr;\n my = dy / rr;\n vx = xc - midx;\n vy = yc - midy;\n rr = Math.sqrt(dx * dx + dy * dy);\n vx /= rr;\n vy /= rr;\n dotmv = vx * mx + vy * my;\n nrx = dotmv * mx - vx;\n nry = dotmv * my - vy;\n rr = Math.sqrt(nrx * nrx + nry * nry);\n nrx /= rr;\n nry /= rr;\n\n // Determine which side of the bisector the center should\n // be.\n\n dx = this.bases[cp.getStart()].getX() - xc;\n dy = this.bases[cp.getStart()].getY() - yc;\n ac = Math.atan2(dy, dx);\n if (ac < 0.0){\n ac += 2 * Math.PI;\n }\n dx = this.bases[cpnext.getEnd()].getX() - xc;\n dy = this.bases[cpnext.getEnd()].getY() - yc;\n acn = Math.atan2(dy, dx);\n if (acn < 0.0){\n acn += 2 * Math.PI;\n }\n if (acn < ac){\n acn += 2 * Math.PI;\n }\n if (acn - ac > Math.PI){\n sign = -1;\n }\n else {\n sign = 1;\n }\n nmidx = xc + sign * radius * nrx;\n nmidy = yc + sign * radius * nry;\n if (rooted) {\n xc -= nmidx - midx;\n yc -= nmidy - midy;\n }\n else {\n for (ic = icstart;;) {\n cp = lp.getConnection(ic);\n i = cp.getStart();\n this.bases[i].setX(\n this.bases[i].getX() + nmidx - midx);\n this.bases[i].setY(\n this.bases[i].getY() + nmidy - midy);\n i = cp.getEnd();\n this.bases[i].setX(\n this.bases[i].getX() + nmidx - midx);\n this.bases[i].setY(\n this.bases[i].getY() + nmidy - midy);\n if (ic == icend){\n break;\n }\n if (++ic >= lp.getNconnection()){\n ic = 0;\n }\n }\n }\n }\n icstart = icnext;\n done_all_connections = icstart == icstart1;\n }\n for (ic = 0; ic < lp.getNconnection(); ic++) {\n cp = lp.getConnection(ic);\n j = ic + 1;\n if (j >= lp.getNconnection()){\n j = 0;\n }\n cpnext = lp.getConnection(j);\n dx = this.bases[cp.getEnd()].getX() - xc;\n dy = this.bases[cp.getEnd()].getY() - yc;\n rc = Math.sqrt(dx * dx + dy * dy);\n ac = Math.atan2(dy, dx);\n if (ac < 0.0){\n ac += 2 * Math.PI;\n }\n dx = this.bases[cpnext.getStart()].getX() - xc;\n dy = this.bases[cpnext.getStart()].getY() - yc;\n rcn = Math.sqrt(dx * dx + dy * dy);\n acn = Math.atan2(dy, dx);\n if (acn < 0.0){\n acn += 2 * Math.PI;\n }\n if (acn < ac){\n acn += 2 * Math.PI;\n }\n dan = acn - ac;\n dcp = cpnext.getAngle() - cp.getAngle();\n if (dcp <= 0.0){\n dcp += 2 * Math.PI;\n }\n if (Math.abs(dan - dcp) > Math.PI) {\n if (cp.isExtruded()) {\n console.log(\"Warning from traverse_loop. Loop \"\n + lp.getNumber() + \" has crossed regions\\n\");\n }\n else if ((cpnext.getStart() - cp.getEnd()) != 1) {\n cp.setExtruded(true);\n continue set_radius; // remplacement du goto\n }\n }\n if (cp.isExtruded()) {\n this.construct_extruded_segment(cp, cpnext);\n }\n else {\n n = cpnext.getStart() - cp.getEnd();\n if (n < 0){\n n += this.nbase + 1;\n }\n angleinc = dan / n;\n for (j = 1; j < n; j++) {\n i = cp.getEnd() + j;\n if (i > this.nbase){\n i -= this.nbase + 1;\n }\n a = ac + j * angleinc;\n rr = rc + (rcn - rc) * (a - ac) / dan;\n this.bases[i].setX(xc + rr * Math.cos(a));\n this.bases[i].setY(yc + rr * Math.sin(a));\n }\n }\n }\n break;\n }\n for (ic = 0; ic < lp.getNconnection(); ic++) {\n if (icroot != ic) {\n cp = lp.getConnection(ic);\n //IM HERE\n this.generate_region(cp);\n this.traverse_loop(cp.getLoop(), cp);\n }\n }\n n = 0;\n sx = 0.0;\n sy = 0.0;\n for (ic = 0; ic < lp.getNconnection(); ic++) {\n j = ic + 1;\n if (j >= lp.getNconnection()){\n j = 0;\n }\n cp = lp.getConnection(ic);\n cpnext = lp.getConnection(j);\n n += 2;\n sx += this.bases[cp.getStart()].getX()\n + this.bases[cp.getEnd()].getX();\n sy += this.bases[cp.getStart()].getY()\n + this.bases[cp.getEnd()].getY();\n if (!cp.isExtruded()) {\n for (j = cp.getEnd() + 1; j != cpnext.getStart(); j++) {\n if (j > this.nbase){\n j -= this.nbase + 1;\n }\n n++;\n sx += this.bases[j].getX();\n sy += this.bases[j].getY();\n }\n }\n }\n lp.setX(sx / n);\n lp.setY(sy / n);\n}\n\nNAView.prototype.determine_radius = function determine_radius(lp, lencut){\n var mindit, ci, dt, sumn, sumd, radius, dit;\n var i, j, end, start, imindit = 0;\n var cp = new Connection(), cpnext = new Connection();\n var rt2_2 = 0.7071068;\n\n do {\n mindit = 1.0e10;\n for (sumd = 0.0, sumn = 0.0, i = 0; i < lp.getNconnection(); i++) {\n cp = lp.getConnection(i);\n j = i + 1;\n if (j >= lp.getNconnection()){\n j = 0;\n }\n cpnext = lp.getConnection(j);\n end = cp.getEnd();\n start = cpnext.getStart();\n if (start < end){\n start += this.nbase + 1;\n }\n dt = cpnext.getAngle() - cp.getAngle();\n if (dt <= 0.0){\n dt += 2 * Math.PI;\n }\n if (!cp.isExtruded()){\n ci = start - end;\n }\n else {\n if (dt <= Math.PI / 2){\n ci = 2.0;\n }\n else {\n ci = 1.5;\n }\n }\n sumn += dt * (1.0 / ci + 1.0);\n sumd += dt * dt / ci;\n dit = dt / ci;\n if (dit < mindit && !cp.isExtruded() && ci > 1.0) {\n mindit = dit;\n imindit = i;\n }\n }\n radius = sumn / sumd;\n if (radius < rt2_2){\n radius = rt2_2;\n }\n if (mindit * radius < lencut) {\n lp.getConnection(imindit).setExtruded(true);\n }\n } while (mindit * radius < lencut);\n if (lp.getRadius() > 0.0){\n radius = lp.getRadius();\n }\n else {\n lp.setRadius(radius);\n }\n}\n\nNAView.prototype.find_ic_middle = function find_ic_middle(icstart, icend, anchor_connection, acp, lp){\n var count, ret, ic, i;\n var done;\n\n count = 0;\n ret = -1;\n ic = icstart;\n done = false;\n while (!done) {\n if (count++ > lp.getNconnection() * 2) {\n console.log(\"Infinite loop in 'find_ic_middle'\");\n }\n if (anchor_connection != null && lp.getConnection(ic) == acp) {\n ret = ic;\n }\n done = ic == icend;\n if (++ic >= lp.getNconnection()) {\n ic = 0;\n }\n }\n if (ret == -1) {\n for (i = 1, ic = icstart; i < (count + 1) / 2; i++) {\n if (++ic >= lp.getNconnection())\n ic = 0;\n }\n ret = ic;\n }\n return ret;\n}\n\nNAView.prototype.construct_extruded_segment = function construct_extruded_segment(cp, cpnext){\n var astart, aend1, aend2, aave, dx, dy, a1, a2, ac, rr, da, dac;\n var start, end, n, nstart, nend;\n var collision;\n\n astart = cp.getAngle();\n aend2 = aend1 = cpnext.getAngle();\n if (aend2 < astart){\n aend2 += 2 * Math.PI;\n }\n aave = (astart + aend2) / 2.0;\n start = cp.getEnd();\n end = cpnext.getStart();\n n = end - start;\n if (n < 0){\n n += this.nbase + 1;\n }\n da = cpnext.getAngle() - cp.getAngle();\n if (da < 0.0) {\n da += 2 * Math.PI;\n }\n if (n == 2) {\n this.construct_circle_segment(start, end);\n }\n else {\n dx = this.bases[end].getX() - this.bases[start].getX();\n dy = this.bases[end].getY() - this.bases[start].getY();\n rr = Math.sqrt(dx * dx + dy * dy);\n dx /= rr;\n dy /= rr;\n if (rr >= 1.5 && da <= Math.PI / 2) {\n nstart = start + 1;\n if (nstart > this.nbase){\n nstart -= this.nbase + 1;\n }\n nend = end - 1;\n if (nend < 0){\n nend += this.nbase + 1;\n }\n this.bases[nstart].setX(this.bases[start].getX() + 0.5 * dx);\n this.bases[nstart].setY(this.bases[start].getY() + 0.5 * dy);\n this.bases[nend].setX(this.bases[end].getX() - 0.5 * dx);\n this.bases[nend].setY(this.bases[end].getY() - 0.5 * dy);\n start = nstart;\n end = nend;\n }\n do {\n collision = false;\n this.construct_circle_segment(start, end);\n nstart = start + 1;\n if (nstart > this.nbase) {\n nstart -= this.nbase + 1;\n }\n dx = this.bases[nstart].getX() - this.bases[start].getX();\n dy = this.bases[nstart].getY() - this.bases[start].getY();\n a1 = Math.atan2(dy, dx);\n if (a1 < 0.0){\n a1 += 2 * Math.PI;\n }\n dac = a1 - astart;\n if (dac < 0.0){\n dac += 2 * Math.PI;\n }\n if (dac > Math.PI){\n collision = true;\n }\n nend = end - 1;\n if (nend < 0){\n nend += this.nbase + 1;\n }\n dx = this.bases[nend].getX() - this.bases[end].getX();\n dy = this.bases[nend].getY() - this.bases[end].getY();\n a2 = Math.atan2(dy, dx);\n if (a2 < 0.0){\n a2 += 2 * Math.PI;\n }\n dac = aend1 - a2;\n if (dac < 0.0){\n dac += 2 * Math.PI;\n }\n if (dac > Math.PI){\n collision = true;\n }\n if (collision) {\n ac = this.minf2(aave, astart + 0.5);\n this.bases[nstart].setX(\n this.bases[start].getX() + Math.cos(ac));\n this.bases[nstart].setY(\n this.bases[start].getY() + Math.sin(ac));\n start = nstart;\n ac = this.maxf2(aave, aend2 - 0.5);\n this.bases[nend].setX(this.bases[end].getX() + Math.cos(ac));\n this.bases[nend].setY(this.bases[end].getY() + Math.sin(ac));\n end = nend;\n n -= 2;\n }\n } while (collision && n > 1);\n }\n}\n\nNAView.prototype.construct_circle_segment = function construct_circle_segment(start, end){\n var dx, dy, rr, midx, midy, xn, yn, nrx, nry, mx, my, a;\n var l, j, i;\n\n dx = this.bases[end].getX() - this.bases[start].getX();\n dy = this.bases[end].getY() - this.bases[start].getY();\n rr = Math.sqrt(dx * dx + dy * dy);\n l = end - start;\n if (l < 0){\n l += this.nbase + 1;\n }\n if (rr >= l) {\n dx /= rr;\n dy /= rr;\n for (j = 1; j < l; j++) {\n i = start + j;\n if (i > this.nbase){\n i -= this.nbase + 1;\n }\n this.bases[i].setX(\n this.bases[start].getX() + dx * j / l);\n this.bases[i].setY(\n this.bases[start].getY() + dy * j / l);\n }\n }\n else {\n this.find_center_for_arc((l - 1), rr);\n dx /= rr;\n dy /= rr;\n midx = this.bases[start].getX() + dx * rr / 2.0;\n midy = this.bases[start].getY() + dy * rr / 2.0;\n xn = dy;\n yn = -dx;\n nrx = midx + this._h * xn;\n nry = midy + this._h * yn;\n mx = this.bases[start].getX() - nrx;\n my = this.bases[start].getY() - nry;\n rr = Math.sqrt(mx * mx + my * my);\n a = Math.atan2(my, mx);\n for (j = 1; j < l; j++) {\n i = start + j;\n if (i > this.nbase){\n i -= this.nbase + 1;\n }\n this.bases[i].setX(nrx + rr * Math.cos(a + j * this.angleinc));\n this.bases[i].setY(nry + rr * Math.sin(a + j * this.angleinc));\n }\n }\n}\n\nNAView.prototype.find_center_for_arc = function find_center_for_arc(n, b){\n var h, hhi, hlow, r, disc, theta, e, phi;\n var iter;\n\n hhi = (n + 1.0) / Math.PI;\n // changed to prevent div by zero if (ih)\n hlow = -hhi - b / (n + 1.000001 - b);\n if (b < 1){\n // otherwise we might fail below (ih)\n hlow = 0;\n }\n iter = 0;\n do {\n h = (hhi + hlow) / 2.0;\n r = Math.sqrt(h * h + b * b / 4.0);\n disc = 1.0 - 0.5 / (r * r);\n if (Math.abs(disc) > 1.0) {\n console.log(\"Unexpected large magnitude discriminant = \" + disc\n + \" \" + r);\n }\n theta = Math.acos(disc);\n phi = Math.acos(h / r);\n e = theta * (n + 1) + 2 * phi - 2 * Math.PI;\n if (e > 0.0) {\n hlow = h;\n }\n else {\n hhi = h;\n }\n } while (Math.abs(e) > 0.0001 && ++iter < this.MAXITER);\n if (iter >= this.MAXITER) {\n if (noIterationFailureYet) {\n console.log(\"Iteration failed in find_center_for_arc\");\n noIterationFailureYet = false;\n }\n h = 0.0;\n theta = 0.0;\n }\n this._h = h;\n this.angleinc = theta;\n}\n\nNAView.prototype.generate_region = function generate_region(cp){\n var l, start, end, i, mate;\n var rp;\n\n rp = cp.getRegion();\n l = 0;\n if (cp.getStart() == rp.getStart1()) {\n start = rp.getStart1();\n end = rp.getEnd1();\n }\n else {\n start = rp.getStart2();\n end = rp.getEnd2();\n }\n if (this.bases[cp.getStart()].getX() > this.ANUM - 100.0\n || this.bases[cp.getEnd()].getX() > this.ANUM - 100.0) {\n console.log(\n \"Bad region passed to generate_region. Coordinates not defined.\");\n }\n for (i = start + 1; i <= end; i++) {\n l++;\n this.bases[i].setX(\n this.bases[cp.getStart()].getX() + this.HELIX_FACTOR * l\n * cp.getXrad());\n this.bases[i].setY(\n this.bases[cp.getStart()].getY() + this.HELIX_FACTOR * l\n * cp.getYrad());\n mate = this.bases[i].getMate();\n this.bases[mate].setX(\n this.bases[cp.getEnd()].getX() + this.HELIX_FACTOR * l\n * cp.getXrad());\n this.bases[mate].setY(\n this.bases[cp.getEnd()].getY() + this.HELIX_FACTOR * l\n * cp.getYrad());\n\n }\n}\n\nNAView.prototype.minf2 = function minf2(x1, x2) {\n return ((x1) < (x2)) ? (x1) : (x2);\n}\n\nNAView.prototype.maxf2 = function maxf2(x1, x2) {\n return ((x1) > (x2)) ? (x1) : (x2);\n}\n\nNAView.prototype.connected_connection = function connected_connection(cp, cpnext) {\n if (cp.isExtruded()) {\n return true;\n }\n else if (cp.getEnd() + 1 == cpnext.getStart()) {\n return true;\n }\n else {\n return false;\n }\n}\n","/* Version: 0.2\n* Date: 2015-03-15\n*/\n\nimport fstyle from './fornac.css';\n\nimport d3 from 'd3';\nimport slugid from 'slugid';\nimport {contextMenu} from './d3-context-menu.js';\n\nimport {RNAGraph} from './rnagraph.js';\nimport {ColorScheme, rnaUtilities} from './rnautils.js';\n\nimport {simpleXyCoordinates} from './simplernaplot.js';\nimport {NAView} from './naview/naview.js';\n\nexport function FornaContainer(element, passedOptions = {}) {\n var self = this;\n\n let options = {\n 'editable': false,\n 'zoomable': true,\n 'animation': true,\n 'displayAllLinks': false,\n 'labelInterval': 10,\n 'chargeDistance': 110,\n 'friction': 0.35,\n 'middleCharge': -30,\n 'otherCharge': -30,\n 'linkDistanceMultiplier': 15,\n 'initialSize': null,\n 'layout': 'standard-polygonal',\n 'transitionDuration': 500,\n 'maxNodeRadius': 80 // the maximum radius of a node when the view is centered\n };\n\n self.options = Object.assign(options, passedOptions);\n\n if (self.options.initialSize !== null) {\n self.options.svgW = self.options.initialSize[0];\n self.options.svgH = self.options.initialSize[1];\n } else {\n self.options.svgW = 300;\n self.options.svgH = 300;\n }\n\n self.linkStrengths = {\n 'pseudoknot': 0.00,\n 'proteinChain': 0.00,\n 'chainChain': 0.00,\n 'intermolecule': 10.00,\n 'external': 0.00,\n 'other': 10.00\n };\n\n self.displayParameters = {\n 'displayNumbering': true,\n 'displayNodeOutline': true,\n 'displayNodeLabel': true,\n 'displayLinks': true,\n 'displayPseudoknotLinks': true,\n 'displayProteinLinks': true,\n 'displayDirectionArrows': true\n };\n\n self.colorScheme = 'structure';\n self.customColors = {};\n self.rnas = {};\n self.extraLinks = []; //store links between different RNAs\n\n // global mouse event vars\n var mousedownLink = null,\n mousedownNode = null,\n mouseupNode = null;\n let linkContextMenuShown = false;\n\n let resetMouseVars = () => {\n mousedownNode = null;\n mouseupNode = null;\n mousedownLink = null;\n }\n\n var graph = self.graph = {\n 'nodes':[],\n 'links':[]\n };\n\n Array.prototype.equals = function (array) {\n // if the other array is a falsy value, return\n if (!array)\n return false;\n\n // compare lengths - can save a lot of time\n if (this.length != array.length)\n return false;\n\n for (var i = 0, l=this.length; i < l; i++) {\n // Check if we have nested arrays\n if (this[i] instanceof Array && array[i] instanceof Array) {\n // recurse into the nested arrays\n if (!this[i].equals(array[i]))\n return false;\n }\n else if (this[i] != array[i]) {\n // Warning - two different object instances will never be equal: {x:20} != {x:20}\n return false;\n }\n }\n return true;\n };\n\n /* Register global mouse and key events */\n if (self.options.editable || self.options.animation) {\n var shiftKeydown = false;\n var ctrlKeydown = false;\n\n let keydown = () => {\n switch (d3.event.keyCode) {\n case 68: //'d' key\n console.log('dotbracket:', self.getStructuresDotBracket());\n break;\n case 16:\n shiftKeydown = true;\n break;\n case 17:\n ctrlKeydown = true;\n break;\n case 67: //c\n self.centerView();\n break;\n }\n\n if (ctrlKeydown) {\n // Ctrl key must disable panning and zooming\n if (self.options.zoomable)\n disableZooming()\n // Ctrl Button must enable crosshair and start brusher\n if (self.options.editable || self.options.animation) {\n enableBrushing()\n }\n }\n }\n\n let keyup = () => {\n shiftKeydown = false;\n ctrlKeydown = false;\n\n // enable zoomer\n if (self.options.zoomable)\n enableZooming()\n // disable brushing events\n disableBrushing()\n }\n\n d3.select('body')\n .on('keydown', keydown)\n .on('keyup', keyup)\n .on('contextmenu', function() {\n d3.event.preventDefault();\n });\n }\n\n /* Register global context menu */\n if (self.options.editable) {\n let backgroundMenu = [\n {\n title: 'Add Node',\n action: function(elm, d, i, mousePos) {\n\n },\n children: [{\n 'title': 'A',\n action: function(elm, d, i, mousePos) {\n console.log('mousePos:', mousePos, self.options.svgW, self.options.svgH);\n let canvasMousePos = [xScale.invert(mousePos[0]),\n yScale.invert(mousePos[1])];\n console.log('canvasMousePos', canvasMousePos);\n\n self.addRNA('.', {'sequence': 'A', 'centerPos': canvasMousePos});\n }\n },\n {\n 'title': 'C',\n action: function(elm, d, i, mousePos) {\n console.log('mousePos:', mousePos, self.options.svgW, self.options.svgH);\n let canvasMousePos = [xScale.invert(mousePos[0]),\n yScale.invert(mousePos[1])];\n console.log('canvasMousePos', canvasMousePos);\n\n self.addRNA('.', {'sequence': 'C', 'centerPos': canvasMousePos});\n }\n\n },\n {\n 'title': 'G',\n action: function(elm, d, i, mousePos) {\n console.log('mousePos:', mousePos, self.options.svgW, self.options.svgH);\n let canvasMousePos = [xScale.invert(mousePos[0]),\n yScale.invert(mousePos[1])];\n console.log('canvasMousePos', canvasMousePos);\n\n self.addRNA('.', {'sequence': 'G', 'centerPos': canvasMousePos});\n }\n\n },\n {\n 'title': 'U',\n action: function(elm, d, i, mousePos) {\n console.log('mousePos:', mousePos, self.options.svgW, self.options.svgH);\n let canvasMousePos = [xScale.invert(mousePos[0]),\n yScale.invert(mousePos[1])];\n console.log('canvasMousePos', canvasMousePos);\n\n self.addRNA('.', {'sequence': 'U', 'centerPos': canvasMousePos});\n\n }\n }\n ],\n disabled: false // optional, defaults to false\n }\n ]\n\n let nodeMenu = [\n {\n title: 'Delete Node',\n action: function(elm, d, i) {\n deleteNode(d);\n },\n disabled: false // optional, defaults to false\n },\n {\n title: 'Change Node',\n action: function(elm, d, i) {\n console.log('You have clicked the second item!');\n console.log('The data for this circle is: ' + d);\n },\n children: [\n {\n title: 'A',\n action: function(elm, d, i) {\n changeNode('A', d);\n }\n },\n {\n title: 'C',\n action: function(elm, d, i) {\n changeNode('C', d);\n\n }\n },\n {\n title: 'G',\n action: function(elm, d, i) {\n changeNode('G', d);\n\n }\n },\n {\n title: 'U',\n action: function(elm, d, i) {\n changeNode('U', d);\n }\n },\n ]\n },\n {\n title: 'Insert Before',\n action: function(elm, d, i) {\n\n },\n children: [\n {\n title: 'A',\n action: function(elm, d, i) {\n insertNodeBeforeOrAfter('A', d, -1);\n }\n },\n {\n title: 'C',\n action: function(elm, d, i) {\n insertNodeBeforeOrAfter('C', d, -1);\n\n }\n },\n {\n title: 'G',\n action: function(elm, d, i) {\n insertNodeBeforeOrAfter('G', d, -1);\n\n }\n },\n {\n title: 'U',\n action: function(elm, d, i) {\n insertNodeBeforeOrAfter('U', d, -1);\n }\n },\n ]\n },\n {\n title: 'Insert After',\n action: function(elm, d, i) {\n console.log('d:', d);\n\n },\n children: [\n {\n title: 'A',\n action: function(elm, d, i) {\n insertNodeBeforeOrAfter('A', d, 0);\n\n }\n },\n {\n title: 'C',\n action: function(elm, d, i) {\n insertNodeBeforeOrAfter('C', d, 0);\n }\n },\n {\n title: 'G',\n action: function(elm, d, i) {\n insertNodeBeforeOrAfter('G', d, 0);\n }\n },\n {\n title: 'U',\n action: function(elm, d, i) {\n insertNodeBeforeOrAfter('U', d, 0);\n }\n },\n ]\n }\n ]\n\n self.nodeContextMenu = contextMenu(nodeMenu);\n self.backgroundContextMenu = contextMenu(backgroundMenu);\n\n } else {\n //console.log('empty context menu');\n self.nodeContextMenu = function() {};\n }\n\n /* Draw the plot here */\n d3.select(element).select('svg').remove();\n\n var svg = d3.select(element)\n .attr('tabindex', 1)\n .each(function() { this.focus(); })\n .append('svg:svg')\n .attr('preserveAspectRatio', 'xMidYMid meet')\n .attr('viewBox', '0 0 ' + self.options.svgW + ' ' + self.options.svgH)\n\n self.options.svg = svg;\n\n if (self.options.editable || self.options.animation) {\n var mouseEventHelper = svg.append('svg:g')\n .on('mousemove', () => {\n // only if we are dragging\n if (!mousedownNode) return;\n\n // update drag line\n let mpos = d3.mouse(vis.node());\n dragLine\n .attr('x1', mousedownNode.x)\n .attr('y1', mousedownNode.y)\n .attr('x2', mpos[0])\n .attr('y2', mpos[1]);\n })\n .on('mousedown', () => {\n })\n .on('mouseup', () => {\n if (mousedownNode && !linkContextMenuShown) {\n dragLine.classed(fstyle.transparent, true);\n }\n // clear mouse event vars\n resetMouseVars();\n //update()\n })\n .classed(fstyle.mouseEventHelper, true)\n .style('pointer-events', 'all')\n\n // draw a background layer for mouse events\n mouseEventHelper.append('svg:rect')\n .classed('background', true)\n .style('visibility', 'hidden')\n .attr('width', self.options.svgW)\n .attr('height', self.options.svgH)\n .on('mousedown', function() {\n //console.log('background click');\n deselectAllNodes()\n })\n } else {\n var mouseEventHelper = svg;\n }\n\n var vis = mouseEventHelper.append('svg:g')\n .classed(fstyle.plot, true)\n var visLinks = vis.append('svg:g')\n .classed('fornac-links', true);\n var visNodes = vis.append('svg:g')\n .classed('fornac-nodes', true);\n\n // line displayed when dragging new nodes\n if (self.options.editable) {\n var dragLine = vis.append('line')\n .attr('class', fstyle.dragLine)\n .attr('x1', 0)\n .attr('y1', 0)\n .attr('x2', 0)\n .attr('y2', 0);\n\n svg.on('contextmenu', self.backgroundContextMenu);\n }\n\n /* Zooming related objects and functions */\n var xScale = d3.scale.linear()\n .domain([0,self.options.svgW]).range([0,self.options.svgW]);\n var yScale = d3.scale.linear()\n .domain([0,self.options.svgH]).range([0, self.options.svgH]);\n\n self.zoomer = d3.behavior.zoom()\n .scaleExtent([0.1,10])\n .x(xScale)\n .y(yScale)\n .on('zoom', () => {\n vis.attr('transform',\n 'translate(' + d3.event.translate + ')' + ' scale(' + d3.event.scale + ')');\n });\n\n let enableZooming = () => {\n svg.call(self.zoomer)\n .on(\"dblclick.zoom\", null);\n }\n\n let disableZooming = () => {\n svg.call(self.zoomer)\n .on(\"dblclick.zoom\", null)\n .on('mousedown.zoom', null)\n .on('touchstart.zoom', null)\n .on('touchmove.zoom', null)\n .on('touchend.zoom', null);\n }\n\n if (self.options.zoomable)\n enableZooming()\n\n /* Node selection related objects and functions */\n let toggleSelectNode = (node) => {\n node.selected = !node.selected;\n visNodes.selectAll('g.gnode').filter((d) => { return node.uid == d.uid; })\n .classed(fstyle.selectedNode, function(p) { return p.selected; });\n }\n\n let selectNode = (node) => {\n node.selected = true;\n visNodes.selectAll('g.gnode').filter((d) => { return node.uid == d.uid; })\n .classed(fstyle.selectedNode, function(p) { return p.selected; });\n }\n\n let deselectAllNodes = () => {\n visNodes.selectAll('g.gnode')\n .classed(fstyle.selectedNode, function(p) { return p.selected = false; });\n }\n\n let selectedNodes = () => {\n // return all selected nodes\n return visNodes.selectAll('g.gnode').filter(function(d) { return d.selected; });\n }\n\n self.brusher = d3.svg.brush()\n .x(xScale)\n .y(yScale)\n .on('brushstart', function(d) {})\n .on('brush', function() {\n // during brushing invert styling of selection as preview\n let extent = d3.event.target.extent();\n\n visNodes.selectAll('g.gnode')\n .classed(fstyle.selectedNode, function (d) {\n return d.selected ^ (extent[0][0] <= d.x && d.x < extent[1][0]\n && extent[0][1] <= d.y && d.y < extent[1][1])\n })\n })\n .on('brushend', function() {\n // after brushing finally toggle the selection\n let extent = d3.event.target.extent();\n\n visNodes.selectAll('g.gnode')\n .filter(function (d) {\n return extent[0][0] <= d.x && d.x < extent[1][0]\n && extent[0][1] <= d.y && d.y < extent[1][1]\n })\n .each(toggleSelectNode)\n\n d3.event.target.clear();\n d3.select(this).call(d3.event.target);\n });\n\n let enableBrushing = () => {\n // crosshair curson\n mouseEventHelper.select('.background').style('cursor', 'crosshair');\n // bind brusher\n mouseEventHelper.call(self.brusher);\n }\n\n let disableBrushing = () => {\n // normal cursor\n mouseEventHelper.select('.background').style('cursor', 'auto');\n // disable brushing events\n mouseEventHelper.call(self.brusher)\n .on('mousedown.brush', null)\n .on('touchstart.brush', null)\n .on('touchmove.brush', null)\n .on('touchend.brush', null);\n }\n\n /* Force related objects and functions */\n self.force = d3.layout.force()\n .charge(function(d) {\n if (d.nodeType == 'middle')\n return self.options.middleCharge;\n else\n return self.options.otherCharge;\n })\n .friction(self.options.friction)\n .linkDistance(function(d) { return self.options.linkDistanceMultiplier * d.value; })\n .linkStrength(function(d) { if (d.linkType in self.linkStrengths) {\n return self.linkStrengths[d.linkType];\n } else {\n return self.linkStrengths.other; }\n })\n .gravity(0.000)\n .nodes(self.graph.nodes)\n .links(self.graph.links)\n .chargeDistance(self.options.chargeDistance)\n .size([self.options.svgW, self.options.svgH]);\n\n var drag = d3.behavior.drag()\n .on('dragstart', function(d) {\n console.log('dragstart')\n d3.event.sourceEvent.stopPropagation();\n\n selectedNodes().each(function(d1) {\n d1.fixed |= 2;\n });\n })\n .on('drag', (d) => {\n if (shiftKeydown) return\n selectedNodes().each(function(d1) {\n d1.x += d3.event.dx;\n d1.y += d3.event.dy;\n\n d1.px += d3.event.dx;\n d1.py += d3.event.dy;\n });\n\n self.resumeForce();\n d3.event.sourceEvent.preventDefault();\n })\n .on('dragend', (d) => {\n console.log('dragend')\n selectedNodes().each(function(d1) {\n d1.fixed &= ~6;\n });\n });\n\n /* Main plot drawing functions */\n let createInitialLayout = function(structure, passedOptions = {}) {\n // the default options\n let options = {\n 'sequence': '',\n 'name': 'empty',\n 'positions': [],\n 'labelInterval': self.options.labelInterval,\n 'avoidOthers': true,\n 'uids': [],\n 'circularizeExternal': true\n };\n\n options = Object.assign(options, passedOptions);\n\n //console.log('options.uids:', options.uids);\n let rg = new RNAGraph(options.sequence, structure, options.name);\n rg.circularizeExternal = options.circularizeExternal;\n\n let rnaJson = rg.recalculateElements();\n\n if (options.positions.length === 0) {\n // no provided positions means we need to calculate an initial layout\n\n if (self.options.layout == 'naview') {\n let naview = new NAView();\n\n let naViewPositions = naview.naview_xy_coordinates(rg.pairtable);\n options.positions = []\n for (let i = 0; i < naViewPositions.nbase; i++)\n options.positions.push([naViewPositions.x[i], naViewPositions.y[i]]);\n } else {\n options.positions = simpleXyCoordinates(rnaJson.pairtable);\n }\n }\n\n rnaJson = rnaJson.elementsToJson()\n .addUids(options.uids)\n .addPositions('nucleotide', options.positions)\n .addLabels(1, options.labelInterval)\n .reinforceStems()\n .reinforceLoops()\n .connectFakeNodes()\n .reassignLinkUids()\n .breakNodesToFakeNodes();\n\n return rnaJson;\n };\n\n let createNewNodes = function(gnodesEnter) {\n gnodesEnter = gnodesEnter.append('g')\n .classed('gnode', true)\n .attr('struct_name', function(d) { return d.structName; })\n .attr('transform', function(d) {\n if (typeof d.x != 'undefined' && typeof d.y != 'undefined')\n return 'translate(' + [d.x, d.y] + ')';\n else\n return '';\n })\n .each( function(d) { d.selected = d.previouslySelected = false; });\n\n gnodesEnter\n .attr('num', function(d) { return 'n' + d.num; })\n .attr('rnum', function(d) {\n return 'n' + (d.rna.rnaLength - d.num + 1); })\n .transition()\n .duration(750)\n .ease('elastic');\n\n if (self.options.editable || self.options.animation) {\n gnodesEnter.on('mousedown', nodeMousedown)\n //.on('mousedrag', function(d) {})\n .on('mouseup', nodeMouseup)\n .on('contextmenu', self.nodeContextMenu)\n .call(drag)\n }\n\n let labelAndProteinNodes = gnodesEnter.filter(function(d) {\n return d.nodeType == 'label' || d.nodeType == 'protein';\n });\n\n let nucleotideNodes = gnodesEnter.filter(function(d) {\n return d.nodeType == 'nucleotide';\n });\n\n labelAndProteinNodes.append('svg:circle')\n .classed(fstyle.node, true)\n .attr('r', function(d) {\n if (d.nodeType == 'middle') return 0;\n else {\n return d.radius;\n }\n })\n .attr('node_type', function(d) { return d.nodeType; })\n .attr('node_num', function(d) { return d.num; });\n\n // direction arrows\n nucleotideNodes.append('svg:path')\n .attr('class', fstyle.directionArrow)\n .attr('node_num', function(d) { return d.num; })\n\n // nucleotide outlines\n nucleotideNodes.append('svg:circle')\n .attr('class', fstyle.node)\n .attr('node_type', function(d) { return d.nodeType; })\n .attr('node_num', function(d) { return d.num; })\n .attr('r', function(d) { return d.radius; })\n .append('svg:title')\n .text(function(d) {\n if (d.nodeType == 'nucleotide') {\n return d.structName + ':' + d.num;\n } else {\n return '';\n }\n });\n\n // nucleotide labels\n var labelsEnter = gnodesEnter.append('text')\n .text(function(d) { return d.name; })\n .attr('class', fstyle.nodeLabel)\n .attr('label_type', function(d) { return d.nodeType; })\n\n // nucleotide label title\n labelsEnter.append('svg:title')\n .text(function(d) {\n if (d.nodeType == 'nucleotide') {\n return d.structName + ':' + d.num;\n } else {\n return '';\n }\n });\n\n return gnodesEnter;\n };\n\n let createNewLinks = function(linksEnter) {\n var linkLines = linksEnter.append('svg:line');\n\n linkLines.append('svg:title')\n .text((d) => { return d.linkType + ':' + d.source.num + '-' + d.target.num });\n\n linkLines\n .classed('link', true)\n .classed(fstyle.link, true)\n .attr('x1', function(d) { return d.source.x; })\n .attr('y1', function(d) { return d.source.y; })\n .attr('x2', function(d) { return d.target.x; })\n .attr('y2', function(d) { return d.target.y; })\n .attr('link_type', function(d) { return d.linkType; } )\n .attr('pointer-events', function(d) { if (d.linkType == 'fake') return 'none'; else return 'all';});\n\n if (self.options.editable)\n linkLines.on('click', linkClick);\n\n /* We don't need to update the positions of the stabilizing links */\n /*\n basepairLinks = visLinks.selectAll('[link_type=basepair]');\n basepairLinks.classed('basepair', true);\n\n fakeLinks = visLinks.selectAll('[link_type=fake]')\n fakeLinks.classed('fake', true);\n\n intermolecule_links = vis_links.selectAll('[link_type=intermolecule]');\n intermolecule_links.classed('intermolecule', true);\n\n plink = vis_links.selectAll('[link_type=protein_chain],[link_type=chain_chain]');\n plink.classed('chain_chain', true);\n */\n\n return linkLines;\n };\n\n function drawDirectionArrow(d) {\n let magnitude = (x) => {\n return Math.sqrt(x[0] * x[0] + x[1] * x[1]);\n }\n\n let endPoint = d;\n let startPoint = d.prevNode;\n // get stroke width and arrow size values from css\n let nodeStroke = parseFloat(fstyle.nodeStrokeWidth) / 2;\n let lengthMult = parseFloat(fstyle.directionArrowSize);\n let arrowWidth = parseFloat(fstyle.directionArrowWidth);\n\n if (startPoint === null)\n return;\n\n // does this node have a link pointing to it?\n if (!d.linked)\n return;\n\n // point back toward the previous node\n let u = [-(endPoint.x - startPoint.x), -(endPoint.y - startPoint.y)];\n\n if (u[0] == 0 && u[1] == 0)\n return; // will lead to a NaN error\n\n // scale u to unit length\n u = [u[0] / magnitude(u), u[1] / magnitude(u)];\n // normal vector of u\n let v = [-u[1], u[0]];\n\n // calculate the tip position\n let arrowTip = [(d.radius + nodeStroke) * u[0], (d.radius + nodeStroke) * u[1]];\n\n let path = 'M' + (arrowTip[0] + lengthMult * (u[0]/2 + v[0]*arrowWidth/2)) + ',' + (arrowTip[1] + lengthMult * (u[1]/2 + v[1]*arrowWidth/2)) +\n 'L' + (arrowTip[0]) + ',' + (arrowTip[1]) +\n 'L' + (arrowTip[0] + lengthMult * (u[0]/2 - v[0]*arrowWidth/2)) + ',' + (arrowTip[1] + lengthMult * (u[1]/2 - v[1]*arrowWidth/2));\n\n d3.select(this).attr('d', path);\n }\n\n let realLinkFilter = (d) => {\n return d.linkType == 'basepair' ||\n d.linkType == 'backbone' ||\n d.linkType == 'intermolecule' ||\n d.linkType == 'pseudoknot' ||\n d.linkType == 'label_link' ||\n d.linkType == 'external' ||\n d.linkType == 'chain_chain';\n }\n\n let recalculateGraph = () => {\n // Condense all of the individual RNAs into one\n // collection of nodes and links\n self.graph.nodes = [];\n self.graph.links = [];\n for (let uid in self.rnas) {\n self.graph.nodes = self.graph.nodes.concat(self.rnas[uid].nodes);\n self.graph.links = self.graph.links.concat(self.rnas[uid].links);\n }\n\n // Create a lookup table so that we can access each node\n // based on its uid. This will be used to create the links\n // between different RNAs\n var uidsToNodes = {};\n\n for (let i = 0; i < self.graph.nodes.length; i++)\n uidsToNodes[self.graph.nodes[i].uid] = self.graph.nodes[i];\n\n self.graph.links.forEach(function(link) {\n link.source = uidsToNodes[link.source.uid];\n link.target = uidsToNodes[link.target.uid];\n });\n\n for (let i = 0; i < self.extraLinks.length; i++) {\n // the actual node objects may have changed, so we hae to recreate\n // the extra links based on the uids\n if (!(self.extraLinks[i].target.uid in uidsToNodes)) {\n console.log('not there:', self.extraLinks[i]);\n continue;\n }\n\n self.extraLinks[i].source = uidsToNodes[self.extraLinks[i].source.uid];\n self.extraLinks[i].target = uidsToNodes[self.extraLinks[i].target.uid];\n\n if (self.extraLinks[i].linkType == 'intermolecule') {\n //remove links to middle nodes\n let fakeLinks = self.graph.links.filter(function(d) {\n return ((d.source == self.extraLinks[i].source || d.source == self.extraLinks[i].target ||\n d.target == self.extraLinks[i].source || d.target == self.extraLinks[i].source) &&\n d.linkType == 'fake');\n });\n\n for (let j = 0; j < fakeLinks.length; j++) {\n let linkIndex = self.graph.links.indexOf(fakeLinks[j]);\n self.graph.links.splice(linkIndex, 1);\n }\n }\n\n graph.links.push(self.extraLinks[i]);\n }\n };\n\n self.update = function () {\n self.force.nodes(self.graph.nodes)\n .links(self.graph.links);\n\n if (self.options.animation) {\n self.force.start();\n }\n\n let allLinks = visLinks.selectAll('line.link')\n .data(self.graph.links.filter(realLinkFilter), elementKey);\n\n allLinks.attr('class', '')\n .classed('link', true)\n .classed(fstyle.link, true)\n .attr('link_type', function(d) { return d.linkType; } )\n\n let linksEnter = allLinks.enter();\n createNewLinks(linksEnter);\n\n allLinks.exit().remove();\n\n let gnodes = visNodes.selectAll('g.gnode')\n .data(self.graph.nodes, elementKey);\n //.attr('pointer-events', 'all');\n\n let gnodesEnter = gnodes.enter();\n createNewNodes(gnodesEnter);\n gnodes.exit().remove();\n\n\n //fake_nodes = self.graph.nodes.filter(function(d) { return d.nodeType == 'middle'; });\n //fakeNodes = self.graph.nodes.filter(function(d) { return true; });\n let realNodes = self.graph.nodes.filter(function(d) { return d.nodeType == 'nucleotide' || d.nodeType == 'label';});\n\n gnodes.select('.' + fstyle.directionArrow).each(drawDirectionArrow);\n\n self.force.on('tick', function() {\n let q = d3.geom.quadtree(realNodes);\n let i = 0;\n let n = realNodes.length;\n\n let collide = (node) => {\n let r = node.radius + 16,\n nx1 = node.x - r,\n nx2 = node.x + r,\n ny1 = node.y - r,\n ny2 = node.y + r;\n return function(quad, x1, y1, x2, y2) {\n if (quad.point && (quad.point !== node)) {\n let x = node.x - quad.point.x,\n y = node.y - quad.point.y,\n l = Math.sqrt(x * x + y * y),\n r = node.radius + quad.point.radius;\n if (l < r) {\n l = (l - r) / l * 0.1;\n node.x -= x *= l;\n node.y -= y *= l;\n quad.point.x += x;\n quad.point.y += y;\n }\n }\n return x1 > nx2 || x2 < nx1 || y1 > ny2 || y2 < ny1;\n };\n }\n\n while (++i < n) q.visit(collide(realNodes[i]));\n\n allLinks.attr('x1', function(d) { return d.source.x; })\n .attr('y1', function(d) { return d.source.y; })\n .attr('x2', function(d) { return d.target.x; })\n .attr('y2', function(d) { return d.target.y; });\n\n // Translate the groups\n gnodes.attr('transform', function(d) {\n return 'translate(' + [d.x, d.y] + ')';\n });\n\n gnodes.select('.' + fstyle.directionArrow).each(drawDirectionArrow);\n\n });\n\n self.force.on('end', () => {\n gnodes.selectAll('[node_type=nucleotide]')\n .filter((d,i) => { if (i == 0) return true; else return false; })\n .each((d,i) => {\n //console.log(\"pos\", d.num, d.x, d.y);\n });\n\n //for (let uid in self.rnas) {\n // for (let i = 1; i < self.rnas[uid].pairtable[0]; i++) {\n // console.log('pt', i, self.rnas[uid].pairtable[i]);\n // }\n //}\n\n });\n\n self.changeColorScheme(self.colorScheme);\n\n if (self.options.animation) {\n self.force.start();\n }\n\n updateStyle();\n };\n\n self.transitionRNA = function(newStructure, nextFunction) {\n if (self.dotbracket == newStructure) {\n return;\n } else {\n self.dotbracket = newStructure;\n }\n //transition from an RNA which is already displayed to a new structure\n var duration = self.options.transitionDuration;\n\n var uids = self.graph.nodes\n .filter(function(d) { return d.nodeType == 'nucleotide'; })\n .map(function(d) { return d.uid; });\n\n let options = {'uids': uids};\n var newRNAJson = createInitialLayout(newStructure, options);\n\n let gnodes = visNodes.selectAll('g.gnode').data(newRNAJson.nodes, elementKey);\n var links = visLinks.selectAll('line.link').data(newRNAJson.links.filter(realLinkFilter), elementKey);\n\n if (duration === 0)\n gnodes.attr('transform', function(d) {\n return 'translate(' + [d.x, d.y] + ')';\n });\n else {\n gnodes.transition()\n .attr('transform', function(d) {\n return 'translate(' + [d.x, d.y] + ')'; }).duration(duration);\n }\n\n\n var newNodes = createNewNodes(gnodes.enter())\n .attr('transform', function(d) {\n if (typeof d.x != 'undefined' && typeof d.y != 'undefined')\n return 'translate(' + [0, 0] + ')';\n else\n return '';\n });\n\n if (duration === 0)\n gnodes.exit().remove();\n else\n gnodes.exit().transition()\n .attr('transform', function(d) {\n if (typeof d.x != 'undefined' && typeof d.y != 'undefined')\n return 'translate(' + [0, 0] + ')';\n else\n return '';\n });\n\n self.graph.nodes = gnodes.data();\n gnodes.select('.' + fstyle.directionArrow).each(drawDirectionArrow);\n self.changeColorScheme(self.colorScheme);\n updateStyle();\n self.centerView(duration);\n\n function endall(transition, callback) {\n if (transition.size() === 0) { setTimeout(callback, duration); }\n var n = 0;\n transition\n .each(function() { ++n; })\n .each('end', function() { if (!--n) callback.apply(this, arguments); });\n }\n\n function afterAnimation() {\n var newLinks = createNewLinks(links.enter());\n self.graph.links = links.data();\n self.changeColorScheme(self.colorScheme);\n updateStyle();\n\n if (typeof nextFunction != 'undefined')\n nextFunction();\n\n }\n\n links.exit().remove();\n\n if (duration === 0) {\n links\n .attr('x1', function(d) { return d.source.x; })\n .attr('y1', function(d) { return d.source.y; })\n .attr('x2', function(d) { return d.target.x; })\n .attr('y2', function(d) { return d.target.y; });\n\n var newLinks = createNewLinks(links.enter());\n self.graph.links = links.data();\n\n updateStyle();\n } else {\n links.transition()\n .attr('x1', function(d) { return d.source.x; })\n .attr('y1', function(d) { return d.source.y; })\n .attr('x2', function(d) { return d.target.x; })\n .attr('y2', function(d) { return d.target.y; })\n .duration(duration)\n .call(endall, afterAnimation);\n }\n\n if (duration === 0) {\n newNodes\n .attr('transform', function(d) {\n if (typeof d.x != 'undefined' && typeof d.y != 'undefined')\n return 'translate(' + [d.x, d.y] + ')';\n else\n return '';\n });\n } else {\n newNodes.transition()\n .attr('transform', function(d) {\n if (typeof d.x != 'undefined' && typeof d.y != 'undefined')\n return 'translate(' + [d.x, d.y] + ')';\n else\n return '';\n });\n }\n\n };\n\n /* Plot presentation related functions */\n let getBoundingBoxTransform = () => {\n // Center the view on the molecule(s) and scale it so that everything\n // fits in the window\n\n //no molecules, nothing to do\n if (self.graph.nodes.length === 0)\n return {'translate': [0,0], 'scale': 1};\n\n // Get the bounding box\n var minX = d3.min(self.graph.nodes.map(function(d) {return d.x;}));\n var minY = d3.min(self.graph.nodes.map(function(d) {return d.y;}));\n\n var maxX = d3.max(self.graph.nodes.map(function(d) {return d.x;}));\n var maxY = d3.max(self.graph.nodes.map(function(d) {return d.y;}));\n\n var maxRadius = d3.max(self.graph.nodes.map(function(d) { return d.radius; }));\n\n // The width and the height of the molecule\n var molWidth = maxX - minX;\n var molHeight = maxY - minY;\n\n // how much larger the drawing area is than the width and the height\n var widthRatio = self.options.svgW / (molWidth + 1);\n var heightRatio = self.options.svgH / (molHeight + 1);\n\n // we need to fit it in both directions, so we scale according to\n // the direction in which we need to shrink the most\n var minRatio = Math.min(widthRatio, heightRatio,\n self.options.maxNodeRadius / maxRadius) * 0.8;\n\n // the new dimensions of the molecule\n var newMolWidth = molWidth * minRatio;\n var newMolHeight = molHeight * minRatio;\n\n // translate so that it's in the center of the window\n var xTrans = -(minX) * minRatio + (self.options.svgW - newMolWidth) / 2;\n var yTrans = -(minY) * minRatio + (self.options.svgH - newMolHeight) / 2;\n\n return {'translate': [xTrans, yTrans], 'scale': minRatio};\n };\n\n self.centerView = function(duration = 0) {\n var bbTransform = getBoundingBoxTransform();\n\n if (bbTransform === null)\n return;\n\n // do the actual moving\n vis.transition().attr('transform',\n 'translate(' + bbTransform.translate + ')' + ' scale(' + bbTransform.scale + ')').duration(duration);\n\n // tell the zoomer what we did so that next we zoom, it uses the\n // transformation we entered here\n self.zoomer.translate(bbTransform.translate);\n self.zoomer.scale(bbTransform.scale);\n };\n\n self.setSize = (\n svgW = d3.select(element).node().offsetWidth,\n svgH = d3.select(element).node().offsetHeight\n ) => {\n // save width and height\n self.options.svgW = svgW;\n self.options.svgH = svgH;\n\n // set the viewBox\n svg.attr('viewBox', \"0 0 \" + svgW + \" \" + svgH)\n\n //Set the output range of the scales\n xScale.range([0, svgW]).domain([0, svgW]);\n yScale.range([0, svgH]).domain([0, svgH]);\n\n //re-attach the scales to the zoom behaviour\n self.zoomer.x(xScale)\n .y(yScale);\n self.brusher.x(xScale)\n .y(yScale);\n\n //resize the background\n svg.select('.background')\n .attr('width', svgW)\n .attr('height', svgH);\n\n // center the view\n self.centerView();\n }\n\n /* Style and color related functions */\n self.setOutlineColor = function(color) {\n var nodes = visNodes.selectAll('g.gnode').select('[node_type=nucleotide]');\n nodes.style('fill', color);\n }\n\n self.addCustomColors = function addCustomColors(json) {\n // Add a json file containing the custom colors\n self.customColors = json;\n self.changeColorScheme('custom');\n };\n\n self.addCustomColorsText = function(customColorsText) {\n let cs = new ColorScheme(customColorsText);\n self.customColors = cs.colorsJson;\n self.changeColorScheme('custom');\n };\n\n self.changeColorScheme = function(newColorScheme) {\n var proteinNodes = visNodes.selectAll('[node_type=protein]');\n\n proteinNodes.classed(fstyle.node, true)\n .attr('r', function(d) { return d.radius; });\n\n var gnodes = visNodes.selectAll('g.gnode');\n var circles = visNodes.selectAll('g.gnode').selectAll('circle');\n var nodes = visNodes.selectAll('g.gnode').select('[node_type=nucleotide]');\n self.colorScheme = newColorScheme;\n\n\n if (newColorScheme == 'sequence') {\n var scale = d3.scale.ordinal()\n .range(['#dbdb8d', '#98df8a', '#ff9896', '#aec7e8', '#aec7e8'])\n .domain(['A','C','G','U','T']);\n nodes.style('fill', function(d) {\n return scale(d.name);\n });\n\n } else if (newColorScheme == 'structure') {\n var scale = d3.scale.category10()\n .domain(['s','m','i','e','t','h','x'])\n .range(['lightgreen', '#ff9896', '#dbdb8d', 'lightsalmon',\n 'lightcyan', 'lightblue', 'transparent']);\n\n nodes.style('fill', function(d) {\n return scale(d.elemType);\n });\n\n } else if (newColorScheme == 'positions') {\n nodes.style('fill', function(d) {\n var scale = d3.scale.linear()\n .range(['#98df8a', '#dbdb8d', '#ff9896'])\n .interpolate(d3.interpolateLab)\n .domain([1, 1 + (d.rna.rnaLength - 1) / 2, d.rna.rnaLength]);\n\n return scale(d.num);\n });\n } else if (newColorScheme == 'custom') {\n // scale to be used in case the user passes scalar\n // values rather than color names\n if (typeof self.customColors != 'undefined' &&\n 'domain' in self.customColors &&\n 'range' in self.customColors) {\n var scale = d3.scale.linear()\n .interpolate(d3.interpolateLab)\n .domain(self.customColors.domain)\n .range(self.customColors.range);\n }\n\n let changeColors = (moleculeColors, d, scale) => {\n if (moleculeColors.hasOwnProperty(d.num)) {\n let val = parseFloat(moleculeColors[d.num]);\n\n if (isNaN(val)) {\n // passed in color is not a scalar, so\n // treat it as a color\n return moleculeColors[d.num];\n } else {\n // the user passed in a float, let's use a colormap\n // to convert it to a color\n return scale(val);\n }\n } else {\n return 'white';\n }\n }\n\n nodes.style('fill', function(d) {\n if (typeof self.customColors == 'undefined' ||\n !self.customColors.hasOwnProperty('colorValues')) {\n return 'white';\n }\n\n if (self.customColors.colorValues.hasOwnProperty(d.structName) &&\n self.customColors.colorValues[d.structName].hasOwnProperty(d.num)) {\n // if a molecule name is specified, it supercedes the default colors\n // (for which no molecule name has been specified)\n let moleculeColors = self.customColors.colorValues[d.structName];\n return changeColors(moleculeColors, d, scale);\n } else if (self.customColors.colorValues.hasOwnProperty('')) {\n let moleculeColors = self.customColors.colorValues[''];\n return changeColors(moleculeColors, d, scale);\n }\n\n return 'white';\n });\n }\n };\n\n let updateStyle = () => {\n // Numbering\n visNodes.selectAll('[node_type=label]').classed(fstyle.transparent, !self.displayParameters.displayNumbering);\n visNodes.selectAll('[label_type=label]').classed(fstyle.transparent, !self.displayParameters.displayNumbering);\n visLinks.selectAll('[link_type=label_link]').classed(fstyle.transparent, !self.displayParameters.displayNumbering);\n // Node Outline\n svg.selectAll('[node_type=nucleotide]').classed(fstyle.transparent, !self.displayParameters.displayNodeOutline);\n // Node Labels\n visNodes.selectAll('[label_type=nucleotide]').classed(fstyle.transparent, !self.displayParameters.displayNodeLabel);\n // Links\n svg.selectAll('[link_type=real],[link_type=basepair],[link_type=backbone],[link_type=pseudoknot],[link_type=protein_chain],[link_type=chain_chain],[link_type=external]').classed(fstyle.transparent, !self.displayParameters.displayLinks);\n // Pseudoknot Links\n svg.selectAll('[link_type=pseudoknot]').classed(fstyle.transparent, !self.displayParameters.displayPseudoknotLinks);\n // Protein Links\n svg.selectAll('[link_type=protein_chain]').classed(fstyle.transparent, !self.displayParameters.displayProteinLinks);\n // Fake Links\n visLinks.selectAll('[link_type=fake]').classed(fstyle.transparent, !self.options.displayAllLinks);\n visLinks.selectAll('[link_type=fake_fake]').classed(fstyle.transparent, !self.options.displayAllLinks);\n // direction Arrows\n svg.selectAll('.' + fstyle.directionArrow).classed(fstyle.transparent, !self.displayParameters.displayDirectionArrows);\n };\n\n /* RNA edditing related functions */\n let changeNode = function(nodeName, referenceNode) {\n // change the label of a node\n let rna = referenceNode.rna;\n\n let dotbracket = rnaUtilities.pairtableToDotbracket(rna.pairtable);\n let positions = rna.getPositions('nucleotide');\n let sequence = rna.seq\n let uids = rna.getUids();\n\n let newNodeNum = referenceNode.num;\n\n let newDotbracket = dotbracket;\n let newSequence = sequence.slice(0,newNodeNum-1) + nodeName + sequence.slice(newNodeNum);\n\n console.log('newSequence:', newSequence);\n\n console.log('uids:', uids);\n uids.splice(newNodeNum-1, 1, slugid.nice());\n let newPositions = positions;\n\n delete self.rnas[rna.uid];\n let newRNA = self.addRNA(newDotbracket, {'sequence': newSequence,\n 'positions': newPositions,\n 'uids': uids,\n 'centerView': false});\n }\n\n let insertNodeBeforeOrAfter = function(nodeName, referenceNode, positionOffset) {\n //insert a new node before or after another one\n //positionOffset specifies who far from the original to insert the new node\n let rna = referenceNode.rna;\n\n let dotbracket = rnaUtilities.pairtableToDotbracket(rna.pairtable);\n let positions = rna.getPositions('nucleotide');\n let sequence = rna.seq\n let uids = rna.getUids();\n\n let newNodeNum = referenceNode.num + positionOffset;\n\n let newDotbracket = dotbracket.slice(0,newNodeNum) + '.' + dotbracket.slice(newNodeNum);\n let newSequence = sequence.slice(0,newNodeNum) + nodeName + sequence.slice(newNodeNum);\n\n console.log('newSequence:', newSequence);\n\n uids.splice(newNodeNum, 0, slugid.nice());\n positions.splice(newNodeNum, 0, positions[newNodeNum - positionOffset-1]);\n\n let newUids = uids;\n let newPositions = positions;\n\n console.log('positions:', positions);\n console.log('new node positions:', newPositions);\n\n delete self.rnas[rna.uid];\n let newRNA = self.addRNA(newDotbracket, {'sequence': newSequence,\n 'positions': newPositions,\n 'uids': newUids,\n 'centerView': false});\n }\n\n let deleteNode = function(node) {\n console.log('deleting...', node);\n // get the dotbracket string for this rna\n let rna = node.rna;\n let pair = rna.pairtable[node.num];\n\n // remove basepairs for this node\n if (pair != 0) {\n rna.pairtable[node.num] = 0;\n rna.pairtable[pair] = 0;\n }\n\n let dotbracket = rnaUtilities.pairtableToDotbracket(rna.pairtable);\n let positions = rna.getPositions('nucleotide');\n let sequence = rna.seq\n let uids = rna.getUids();\n\n let newDotbracket = dotbracket.slice(0, node.num-1) + dotbracket.slice(node.num)\n let newPositions = positions.slice(0, node.num-1)\n .concat(positions.slice(node.num));\n let newSequence = sequence.slice(0, node.num-1) + sequence.slice(node.num)\n let newUids = uids.slice(0, node.num-1)\n .concat(uids.slice(node.num));\n\n delete self.rnas[rna.uid];\n let newRNA = self.addRNA(newDotbracket, {'sequence': newSequence,\n 'positions': newPositions,\n 'uids': newUids,\n 'centerView': false});\n\n console.log('new dotbracket:', newDotbracket);\n //recalculateGraph();\n\n //remove backbone links associated with this node\n\n //remove this node\n\n }\n\n let elementKey = (d) => {\n return d.uid;\n };\n\n let updateRnaGraph = function(r) {\n let nucleotidePositions = r.getPositions('nucleotide');\n let labelPositions = r.getPositions('label');\n\n let uids = r.getUids();\n\n r.recalculateElements()\n .elementsToJson()\n .addPseudoknots()\n .addPositions('nucleotide', nucleotidePositions)\n .addUids(uids)\n .addLabels(1, self.options.labelInterval)\n .addPositions('label', labelPositions)\n .reinforceStems()\n .reinforceLoops()\n .updateLinkUids();\n };\n\n let removeBackBoneLink = function(d) {\n if (d.target.num - d.source.num != 1) {\n console.log('ERROR: non adjacent nodes. Target:', d.target,\n 'Source:', d.source, 'Link:', d);\n return;\n }\n\n let rna = d.target.rna;\n let toRemove = [];\n\n for (let i = 0; i < rna.links.length; i++) {\n let link = rna.links[i];\n\n if (link.linkType != 'basepair')\n continue;\n\n if (link.source.num <= d.source.num && link.target.num >= d.target.num) {\n console.log('crossing basepair', link);\n toRemove.push(link);\n }\n }\n\n\n // Remove all base pairs that are between these two nodes and add them as extra\n // links\n console.log('toRemove:', toRemove);\n\n for (let i = 0; i < toRemove.length; i++) {\n rna.pairtable[toRemove[i].source.num] = 0;\n rna.pairtable[toRemove[i].target.num] = 0;\n\n toRemove[i].from = toRemove[i].source.num;\n toRemove[i].to = toRemove[i].target.num - d.source.num;\n }\n\n // extract the dotbracket string of the rna\n // cut it at the position of this backbone bond\n let sequence = rna.seq;\n let sequence1 = rna.seq.slice(0, d.source.num);\n let sequence2 = rna.seq.slice(d.source.num);\n\n let rnaDotBracket = rnaUtilities.pairtableToDotbracket(rna.pairtable);\n let dotBracket1 = rnaDotBracket.slice(0, d.source.num);\n let dotBracket2 = rnaDotBracket.slice(d.source.num)\n\n // get the nucleotide positions\n // cut them at the positions of the backbone bond\n let positions = rna.getPositions('nucleotide')\n let uids = rna.getUids();\n\n let positions1 = positions.slice(0, d.source.num);\n let positions2 = positions.slice(d.source.num);\n\n let uids1 = uids.slice(0, d.source.num);\n let uids2 = uids.slice(d.source.num);\n\n console.log('positions1:', positions1);\n console.log('positions2:', positions2);\n\n delete self.rnas[rna.uid];\n let rna1 = self.addRNA(dotBracket1, { 'sequence': sequence1,\n 'positions': positions1,\n 'uids': uids1 });\n let rna2 = self.addRNA(dotBracket2, { 'sequence': sequence2,\n 'positions': positions2,\n 'uids': uids2 });\n for (let i = 0; i < toRemove.length; i++) {\n console.log('rna1:', rna1);\n console.log('rna2:', rna2);\n console.log('toRemove[i]', toRemove[i]);\n self.extraLinks.push(\n {'source': rna1.nodes[toRemove[i].from-1],\n 'target': rna2.nodes[toRemove[i].to-1],\n 'value': 1,\n 'uid': slugid.nice(),\n 'linkType': 'intermolecule'});\n recalculateGraph();\n self.update();\n\n }\n console.log('self.extraLinks:', self.extraLinks);\n //self.extraLinks.push({'source': rna1.nodes[\n\n // create two new rnas\n // add their positions\n // add them back to the plot\n }\n\n let splitMultiStrand = function(rna) {\n // split a multi strand RNA into its individual strands\n // get the position of the '&' character in the dotbracket string\n let breakPositions = [];\n for (let i = 0; i < rna.dotbracket.length; i++) {\n if (rna.dotbracket[i] == '&') {\n breakPositions.push(i);\n }\n }\n\n let toRemove = [];\n // collect all the base pairs that are between split strands\n for (let i = 0; i < rna.links.length; i++) {\n let link = rna.links[i];\n\n if (link.linkType != 'basepair')\n continue; // only consider base pairs\n \n for (let j = 0; j < breakPositions.length; j++) {\n let node = rna.nodes[breakPositions[j]]; // take the split node\n // take the two links that connect the split node \n let linkSource = rna.links.filter(link => link.source === node)[0];\n let linkTarget = rna.links.filter(link => link.target === node)[0];\n if (link.source.num <= linkSource.source.num && link.target.num >= linkTarget.target.num) {\n console.log('crossing basepair', link);\n link.breakFrom = 0;\n // find the strand that the source is in\n for (let k = 0; k < breakPositions.length - 1; k++) {\n if (link.source.num > breakPositions[k] && link.source.num < breakPositions[k+1])\n link.breakFrom = k+1;\n }\n // find the strand that the target is in\n link.breakTo = j+1; \n link.from = link.source.num;\n // find the position of the source in the strand\n if (link.breakFrom > 0) link.from -= breakPositions[link.breakFrom-1] + link.breakFrom;\n // find the position of the target in the strand\n link.to = link.target.num - linkTarget.target.num;\n toRemove.push(link);\n }\n }\n }\n\n\n // Remove all base pairs that are between these two nodes and add them as extra\n // links\n console.log('toRemove:', toRemove);\n let sequences = rna.seq.split('&');\n\n // remove the base pairs\n for (let i = 0; i < toRemove.length; i++) {\n rna.pairtable[toRemove[i].source.num] = 0;\n rna.pairtable[toRemove[i].target.num] = 0;\n }\n\n // extract the dotbracket string of the rna\n // cut it at the position of this backbone bond\n console.log('sequences:', sequences);\n\n let rnaDotBracket = rnaUtilities.pairtableToDotbracket(rna.pairtable);\n let dotbrackets = []; // array to hold the dotbracket strings of the individual strands\n let rnaPositions = rna.getPositions('nucleotide') // get the nucleotide positions, cut them at the positions of the backbone bond\n let positions = [];\n let rnaUids = rna.getUids();\n let uids = [];\n let lastBreak = 0; // the position of the last break\n for (let i = 0; i <= breakPositions.length; i++) {\n // cut the dotbracket\n dotbrackets.push(rnaDotBracket.slice(lastBreak, breakPositions[i]));\n // add the positions\n positions.push(rnaPositions.slice(lastBreak, breakPositions[i]));\n // add the uids\n uids.push(rnaUids.slice(lastBreak, breakPositions[i]));\n lastBreak = breakPositions[i] + 1;\n }\n\n console.log('positions:', positions);\n\n delete self.rnas[rna.uid];\n let newRnas = [];\n for (let i = 0; i < sequences.length; i++) {\n let newRna = self.addRNA(dotbrackets[i], { 'sequence': sequences[i],\n 'positions': positions[i], \n 'uids': uids[i] });\n newRnas.push(newRna);\n }\n // add the extra links\n for (let i = 0; i < toRemove.length; i++) {\n console.log('toRemove[i]', toRemove[i]);\n self.extraLinks.push(\n {'source': newRnas[toRemove[i].breakFrom].nodes[toRemove[i].from-1],\n 'target': newRnas[toRemove[i].breakTo].nodes[toRemove[i].to-1],\n 'value': 1,\n 'uid': slugid.nice(),\n 'linkType': 'intermolecule'});\n recalculateGraph();\n self.update();\n }\n console.log('self.extraLinks:', self.extraLinks);\n }\n\n var removeLink = function(d) {\n // remove a link between two nodes\n let index = self.graph.links.indexOf(d);\n console.log('removing link:', index);\n\n if (index > -1) {\n //remove a link\n //graph.links.splice(index, 1);\n\n // there should be two cases\n // 1. The link is within a single molecule\n\n if (d.source.rna == d.target.rna) {\n if (d.linkType == 'backbone') {\n console.log('trying to remove a backbone link', d.source.num, d.target.num);\n removeBackBoneLink(d);\n return;\n } else {\n let r = d.source.rna;\n r.addPseudoknots();\n r.pairtable[d.source.num] = 0;\n r.pairtable[d.target.num] = 0;\n\n updateRnaGraph(r);\n }\n } else {\n // 2. The link is between two different molecules\n let extraLinkIndex = self.extraLinks.indexOf(d);\n\n self.extraLinks.splice(extraLinkIndex, 1);\n }\n recalculateGraph();\n }\n self.update();\n };\n\n let addBackBoneLink = function(newLink) {\n // opposite of deleting a link\n // get the two dotbracket strings\n let rna1 = newLink.target.rna;\n let rna2 = newLink.source.rna;\n if (newLink.target.num == 1) {\n rna1 = newLink.source.rna;\n rna2 = newLink.target.rna;\n }\n\n let dotbracket1 = rnaUtilities.pairtableToDotbracket(rna1.pairtable);\n let dotbracket2 = rnaUtilities.pairtableToDotbracket(rna2.pairtable);\n\n let seq1 = rna1.seq;\n let seq2 = rna2.seq;\n\n let positions1 = rna1.getPositions('nucleotide');\n let positions2 = rna2.getPositions('nucleotide');\n\n // concatenate them\n let newDotbracket = dotbracket1 + dotbracket2;\n let newSeq = seq1 + seq2;\n let newPositions = positions1.concat(positions2);\n\n let toAddInternal = [];\n let toAddExternal = [];\n let toDelete = {};\n\n for (let i = 0; i < self.extraLinks.length; i++) {\n console.log('self.extraLinks[i]', self.extraLinks[i]);\n console.log('rna1:', rna1);\n console.log('rna2:', rna2);\n if (self.extraLinks[i].source.rna == rna1) {\n if ( self.extraLinks[i].target.rna == rna2) {\n // both ends of the extra link are within what will become the new molecule\n // need to be added as base pairs afterwards\n //self.extraLinks[i].from = self.extraLinks[i].source.num;\n //self.extraLinks[i].to = dotbracket1.length + self.extraLinks[i].target.num;\n //toAddInternal.push(self.extraLinks[i]);\n } else {\n // only one end of the extra link is within what will become the newly\n // created molecule, needs to remain an extra link\n // source will always be the unchanged molecule, whereas target will be\n // the newly created one\n toAddExternal.push({\n 'source': self.extraLinks[i].target,\n 'target': self.extraLinks[i].source.num\n });\n\n toDelete[self.extraLinks[i].uid] = true;\n }\n } else if (self.extraLinks[i].source.rna == rna2) {\n if ( self.extraLinks[i].target.rna == rna1) {\n // add internal link\n // both ends of the extra link are within what will become the new molecule\n // need to be added as base pairs afterwards\n //self.extraLinks[i].from = self.extraLinks[i].target.num;\n //self.extraLinks[i].to = dotbracket1.length + self.extraLinks[i].source.num;\n\n //toAddInternal.push(self.extraLinks[i]);\n } else {\n toAddExternal.push({\n 'source': self.extraLinks[i].target,\n 'target': self.extraLinks[i].source.num + dotbracket1.length\n });\n toDelete[self.extraLinks[i].uid] = true;\n }\n }\n\n if (self.extraLinks[i].target.rna == rna1) {\n if (self.extraLinks[i].source.rna == rna2) {\n // covered in previous if statement\n } else {\n // only one end of the extra link is within what will become the newly\n // created molecule, needs to remain an extra link\n toAddExternal.push({\n 'source': self.extraLinks[i].source,\n 'target': self.extraLinks[i].target.num\n });\n\n toDelete[self.extraLinks[i].uid] = true;\n }\n } else if (self.extraLinks[i].target.rna == rna2) {\n if (self.extraLinks[i].source.rna == rna1) {\n toAddExternal.push({\n 'source': self.extraLinks[i].source,\n 'target': self.extraLinks[i].target.num + dotbracket1.length\n });\n\n toDelete[self.extraLinks[i].uid] = true;\n }\n }\n }\n\n\n self.extraLinks = self.extraLinks.filter((e) => { return !(e.uid in toDelete) });\n\n delete self.rnas[rna1.uid];\n delete self.rnas[rna2.uid];\n\n let newRna = null;\n // create a new RNA\n if (self.options.animation)\n newRna = self.addRNA(newDotbracket, { 'sequence': newSeq,\n 'positions': newPositions,\n 'centerView': false});\n else\n newRna = self.addRNA(newDotbracket, { 'sequence': newSeq,\n 'centerView': false });\n\n\n\n // add new external links\n for (let i = 0; i < toAddExternal.length; i++) {\n self.extraLinks.push({\n 'source': toAddExternal[i].source,\n 'target': newRna.nodes[toAddExternal[i].target-1],\n 'value': 1,\n 'uid': slugid.nice(),\n 'linkType': 'intermolecule'\n });\n }\n\n recalculateGraph();\n self.update();\n console.log('self.extraLinks:', self.extraLinks);\n };\n\n function nudge(dx, dy) {\n // TODO currently unused\n node.filter(function(d) { return d.selected; })\n .attr('cx', function(d) { return d.x += dx; })\n .attr('cy', function(d) { return d.y += dy; });\n\n link.filter(function(d) { return d.source.selected; })\n .attr('x1', function(d) { return d.source.x; })\n .attr('y1', function(d) { return d.source.y; });\n\n link.filter(function(d) { return d.target.selected; })\n .attr('x2', function(d) { return d.target.x; })\n .attr('y2', function(d) { return d.target.y; });\n\n d3.event.preventDefault();\n }\n\n let nodeMouseup = function(d,i) {\n console.log(\"nodeMouseup\")\n let backbonePossible = true, basepairPossible = true;\n\n if (mousedownNode) {\n mouseupNode = d;\n\n // if the node isn't a nucleotide, we can't create a link\n if (mouseupNode.nodeType == 'middle' || mousedownNode.nodeType == 'middle' || mouseupNode.nodeType == 'label' || mousedownNode.nodeType == 'label')\n return;\n\n if (mouseupNode == mousedownNode) { resetMouseVars(); return; }\n let newLink = {source: mousedownNode, target: mouseupNode, linkType: 'basepair', value: 1, uid: slugid.nice()};\n\n for (let i = 0; i < self.graph.links.length; i++) {\n if ((self.graph.links[i].source == mousedownNode) ||\n (self.graph.links[i].target == mousedownNode) ||\n (self.graph.links[i].source == mouseupNode) ||\n (self.graph.links[i].target == mouseupNode)) {\n // either one of the nodes is already in a link\n\n // if any of the nodes are already involved in a basepair or a pseudoknot\n // then we can't make a basepair link\n if (self.graph.links[i].linkType == 'basepair' ||\n self.graph.links[i].linkType == 'pseudoknot' ||\n self.graph.links[i].linkType == 'intermolecule') {\n // although should be able to make a backbone link\n console.log('no basepair possible');\n basepairPossible = false;\n }\n }\n\n if (((self.graph.links[i].source == mouseupNode) &&\n (self.graph.links[i].target == mousedownNode)) ||\n ((self.graph.links[i].source == mousedownNode) &&\n (self.graph.links[i].target == mouseupNode))) {\n\n // if we're trying to make a link between two nodes which already have\n // a backbone between them, then we can't make a link\n if (self.graph.links[i].linkType == 'backbone') {\n return;\n }\n }\n }\n\n\n if (newLink.source.rna != newLink.target.rna) {\n // could be either a backbone link or an intermolecule link\n\n if ((newLink.source.num == 1 &&\n newLink.target.num == newLink.target.rna.rnaLength) ||\n (newLink.target.num == 1 &&\n newLink.source.num == newLink.source.rna.rnaLength)) {\n //\n let linkMenu = [\n {\n title: 'Backbone Link',\n action: function(elm, d, i) {\n linkContextMenuShown = false;\n console.log('Item #1 clicked!');\n console.log('The data for this circle is: ' + d);\n dragLine.attr('class', fstyle.transparent);\n addBackBoneLink(newLink);\n },\n disabled: false // optional, defaults to false\n },\n {\n title: 'Basepair Link',\n action: function(elm, d, i) {\n linkContextMenuShown = false;\n console.log('You have clicked the second item!');\n console.log('The data for this circle is: ' + d);\n dragLine.attr('class', fstyle.transparent);\n self.addLink(newLink);\n }\n }\n ]\n linkContextMenuShown = true;\n let linkContextMenu = contextMenu(linkMenu);\n console.log('newLinkMenu');\n linkContextMenu.apply(this, [d,i,true,\n function() { dragLine.attr('class', fstyle.transparent) }]);\n } else {\n // between end points but can't make a backbone\n if (basepairPossible)\n self.addLink(newLink);\n }\n } else {\n if (basepairPossible)\n self.addLink(newLink);\n }\n\n }\n };\n\n let nodeMousedown = function(d) {\n console.log(\"nodeMousedown\")\n if (!d.selected && !ctrlKeydown) {\n // if this node isn't selected, then we have to unselect every other node\n deselectAllNodes()\n }\n\n if (!shiftKeydown) {\n // only without shift, toggle select or select\n if (ctrlKeydown) {\n toggleSelectNode(d)\n } else {\n selectNode(d)\n }\n }\n\n if (shiftKeydown && self.options.editable) {\n // with shift key and editable continue to draw dragline\n mousedownNode = d;\n\n dragLine\n .attr('class', fstyle.dragLine)\n .attr('x1', mousedownNode.x)\n .attr('y1', mousedownNode.y)\n .attr('x2', mousedownNode.x)\n .attr('y2', mousedownNode.y);\n\n d3.event.stopPropagation();\n }\n };\n\n let linkClick = (d) => {\n if (!shiftKeydown) {\n return;\n }\n\n var invalidLinks = { //'backbone': true,\n 'fake': true,\n 'fake_fake': true,\n 'label_link': true};\n\n console.log('d.linkType:', d.linkType);\n if (d.linkType in invalidLinks )\n return;\n\n removeLink(d);\n };\n\n /* I/O functions */\n self.toJSON = function toJSON() {\n var data = {'rnas': self.rnas, 'extraLinks': self.extraLinks};\n var dataString = JSON.stringify(data, function(key, value) {\n //remove circular references\n if (key == 'rna') {\n return;\n } else {\n return value;\n }\n }, '\\t');\n return dataString;\n };\n\n self.fromJSON = function(jsonString) {\n var rnas, extraLinks;\n\n try{\n var data = JSON.parse(jsonString);\n rnas = data.rnas;\n extraLinks = data.extraLinks;\n } catch(err) {\n throw err;\n }\n\n for (var uid in rnas) {\n if (rnas[uid].type == 'rna') {\n r = new RNAGraph();\n\n r.seq = rnas[uid].seq;\n r.dotbracket = rnas[uid].dotbracket;\n r.circular = rnas[uid].circular;\n r.pairtable = rnas[uid].pairtable;\n r.uid = rnas[uid].uid;\n r.structName = rnas[uid].structName;\n r.nodes = rnas[uid].nodes;\n r.links = rnas[uid].links;\n r.rnaLength = rnas[uid].rnaLength;\n r.elements = rnas[uid].elements;\n r.nucsToNodes = rnas[uid].nucsToNodes;\n r.pseudoknotPairs = rnas[uid].pseudoknotPairs;\n } else {\n r = new ProteinGraph();\n r.size = rnas[uid].size;\n r.nodes = rnas[uid].nodes;\n r.uid = rnas[uid].uid;\n }\n\n self.addRNAJSON(r, false);\n }\n\n extraLinks.forEach(function(link) {\n self.extraLinks.push(link);\n });\n\n recalculateGraph();\n self.update();\n };\n\n self.addRNA = function(structure, passedOptions = {}) {\n let rnaJson = createInitialLayout(structure, passedOptions);\n let centerView = false;\n\n /*\n * Code to display the JSONs representing the structure\n *\n rnaJson.nodes[0].rna = null;\n rnaJson.nodes[0].nextNode = null;\n\n rnaJson.links[0].source = null;\n rnaJson.links[0].target = null;\n\n console.log(rnaJson.nodes[0]);\n console.log(rnaJson.links[0]);\n console.log(JSON.stringify(rnaJson.nodes[0],null,2));\n console.log(JSON.stringify(rnaJson.links[0],null,2));\n */\n\n if ('extraLinks' in passedOptions) {\n // presumably the passed in links are within the passed molecule\n let newLinks = self.addExternalLinks(rnaJson, passedOptions.extraLinks);\n\n self.extraLinks = self.extraLinks.concat(newLinks);\n }\n\n if ('centerPos' in passedOptions)\n self.addRNAJSON(rnaJson, {centerPos: passedOptions.centerPos,\n centerView: false})\n else if ('avoidOthers' in passedOptions)\n self.addRNAJSON(rnaJson, {avoidOthers: passedOptions.avoidOthers});\n else\n self.addRNAJSON(rnaJson, {centerView: passedOptions.centerView});\n\n // if the structure containes multistrands, let's split before the '&'\n console.log('structure:', structure);\n if (structure.indexOf('&') !== -1 && structure != '&' && structure.indexOf('&') !== 0) {\n console.log('splitting multistrand');\n splitMultiStrand(rnaJson);\n return;\n };\n return rnaJson;\n };\n\n self.addRNAJSON = function(rnaGraph,\n { avoidOthers = false,\n centerPos = null,\n centerView = true}\n ) {\n // Add an RNAGraph, which contains nodes and links as part of the\n // structure\n // Each RNA will have uid to identify it\n // when it is modified, it is replaced in the global list of RNAs\n //\n var maxX, minX;\n //console.log('centerView:', centerView);\n\n if (centerPos != null) {\n // center the newly created RNA at a given position\n let totalX = 0;\n let totalY = 0;\n let nodeCount = 0;\n\n rnaGraph.nodes.forEach(function(node) {\n totalX += node.x;\n totalY += node.y;\n nodeCount += 1;\n });\n\n if (nodeCount > 0) {\n // center the nodes at centerPos\n\n rnaGraph.nodes.forEach(function(node) {\n node.x = node.x + centerPos[0] - totalX / nodeCount;\n node.y = node.y + centerPos[1] - totalY / nodeCount;\n\n node.px = node.x;\n node.py = node.y;\n });\n }\n }\n\n if (avoidOthers) {\n if (self.graph.nodes.length > 0)\n maxX = d3.max(self.graph.nodes.map(function(d) { return d.x; }));\n else\n maxX = 0;\n\n minX = d3.min(rnaGraph.nodes.map(function(d) { return d.x; }));\n\n rnaGraph.nodes.forEach(function(node) {\n node.x += (maxX - minX) + 20;\n node.px += (maxX - minX);\n });\n }\n\n rnaGraph.nodes.forEach(function(node) {\n node.rna = rnaGraph;\n });\n\n self.rnas[rnaGraph.uid] = rnaGraph;\n recalculateGraph();\n\n self.update();\n\n if (centerView)\n self.centerView();\n\n return rnaGraph;\n };\n\n self.addNodes = function addNodes(json) {\n // add a new set of nodes from a json file\n\n // Resolve the sources and targets of the links so that they\n // are not just indeces into an array\n json.links.forEach(function(entry) {\n if (typeof entry.source == 'number') entry.source = json.nodes[entry.source];\n if (typeof entry.target == 'number') entry.target = json.nodes[entry.target];\n });\n\n // Get the maximum x and y values of the current graph\n // so that we don't place a new structure on top of the\n // old one\n if (self.graph.nodes.length > 0) {\n maxX = d3.max(self.graph.nodes.map(function(d) {return d.x;}));\n maxY = d3.max(self.graph.nodes.map(function(d) {return d.y;}));\n } else {\n maxX = 0;\n maxY = 0;\n }\n\n json.nodes.forEach(function(entry) {\n if (!(entry.rna.uid in self.rnas)) {\n self.rnas[entry.rna.uid] = entry.rna;\n }\n\n entry.x += maxX;\n //entry.y += maxY;\n\n entry.px += maxX;\n //entry.py += maxY;\n });\n\n r = new RNAGraph('','');\n r.nodes = json.nodes;\n r.links = json.links;\n\n //self.addRNA(r);\n recalculateGraph();\n\n self.update();\n self.centerView();\n };\n\n self.clearNodes = () => {\n self.graph.nodes = [];\n self.graph.links = [];\n\n self.rnas = {};\n self.extraLinks = [];\n\n self.update();\n };\n\n self.addLink = function(newLink) {\n // this means we have a new json, which means we have\n // to recalculate the structure and change the colors\n // appropriately\n //\n console.log('adding new link');\n if (newLink.source.rna == newLink.target.rna) {\n // must be a basepair\n let r = newLink.source.rna;\n\n r.pairtable[newLink.source.num] = newLink.target.num;\n r.pairtable[newLink.target.num] = newLink.source.num;\n\n updateRnaGraph(r);\n\n } else {\n //Add an extra link\n console.log('intermolecule');\n newLink.linkType = 'intermolecule';\n self.extraLinks.push(newLink);\n }\n recalculateGraph();\n self.update();\n };\n\n self.addExternalLinks = function(rnaJson, externalLinks) {\n let newLinks = [];\n\n for (let i = 0; i < externalLinks.length; i++) {\n let newLink = {linkType: 'external', value: 1, uid: slugid.nice(),\n source: null, target: null};\n // check if the source node is an array\n if (Object.prototype.toString.call(externalLinks[i][0]) === '[object Array]') {\n for (let j = 0; j < rnaJson.nodes.length; j++) {\n if ('nucs' in rnaJson.nodes[j]) {\n if (rnaJson.nodes[j].nucs.equals(externalLinks[i][0])) {\n newLink.source = rnaJson.nodes[j];\n break;\n }\n }\n }\n } else {\n for (let j = 0; j < rnaJson.nodes.length; j++) {\n if (rnaJson.nodes[j].num == externalLinks[i][0]) {\n newLink.source = rnaJson.nodes[j];\n }\n }\n }\n\n // check if the target node is an array\n if (Object.prototype.toString.call(externalLinks[i][1]) === '[object Array]') {\n for (let j = 0; j < rnaJson.nodes.length; j++) {\n if ('nucs' in rnaJson.nodes[j]) {\n if (rnaJson.nodes[j].nucs.equals(externalLinks[i][1])) {\n newLink.target = rnaJson.nodes[j];\n }\n }\n }\n } else {\n for (let j = 0; j < rnaJson.nodes.length; j++) {\n if (rnaJson.nodes[j].num == externalLinks[i][1]) {\n newLink.target = rnaJson.nodes[j];\n }\n }\n }\n\n if (newLink.source == null || newLink.target == null) {\n console.log('ERROR: source or target of new link not found:', newLink, externalLinks[i]);\n continue;\n }\n\n newLinks.push(newLink);\n }\n\n return newLinks;\n };\n\n self.getStructuresDotBracket = function() {\n console.log('self.rnas:', self.rnas);\n let sequence = [];\n let currIdx = 1;\n let nodeIdxs = {};\n let breaks = [];\n let pairtable = [];\n\n // add the nodes\n for (let uid in self.rnas) {\n let rna = self.rnas[uid];\n\n for (let j = 0; j < rna.nodes.length; j++) {\n let node = rna.nodes[j];\n\n if (node.nodeType != 'nucleotide')\n continue;\n\n // console.log('node:', node);\n nodeIdxs[node.uid] = currIdx;\n currIdx += 1;\n\n sequence.push(node.name);\n }\n\n breaks.push(currIdx);\n }\n\n pairtable = [currIdx-1]\n for (let i = 0; i < currIdx; i++)\n pairtable.push(0)\n\n // add the links\n for (let uid in self.rnas) {\n let rna = self.rnas[uid];\n\n for (let j = 0; j < rna.links.length; j++) {\n let link = rna.links[j];\n\n if (link.linkType != 'basepair')\n continue;\n\n let idx1 = nodeIdxs[link.source.uid];\n let idx2 = nodeIdxs[link.target.uid];\n pairtable[idx1] = idx2;\n pairtable[idx2] = idx1;\n }\n }\n\n for (let i = 0; i < self.extraLinks.length; i++) {\n let link = self.extraLinks[i];\n\n let idx1 = nodeIdxs[link.source.uid];\n let idx2 = nodeIdxs[link.target.uid];\n\n pairtable[idx1] = idx2;\n pairtable[idx2] = idx1;\n }\n\n let structure = rnaUtilities.pairtableToDotbracket(pairtable).split('');\n\n for (let i = 0; i < breaks.length - 1; i++) {\n console.log('breaks[i]:', breaks[i]);\n sequence.splice(breaks[i] + i - 1, 0, '&');\n structure.splice(breaks[i] + i - 1, 0, '&');\n }\n\n console.log('sequence:', sequence, sequence.join(''));\n console.log('structure:', structure, structure.join(''));\n return [sequence.join(''), structure.join('')];\n };\n\n /* APIs */\n self.startAnimation = function() {\n self.options.animation = true;\n vis.selectAll('g.gnode')\n .call(drag);\n self.force.start();\n };\n\n self.stopAnimation = function() {\n self.options.animation = false;\n vis.selectAll('g.gnode')\n .on('mousedown.drag', null);\n self.force.stop();\n };\n\n self.resumeForce = function() {\n if (self.options.animation)\n self.force.resume();\n };\n\n self.setFriction = function(value) {\n self.force.friction(value);\n self.resumeForce();\n };\n\n self.setCharge = function(value) {\n self.force.charge(value);\n self.resumeForce();\n };\n\n self.setGravity = function(value) {\n self.force.gravity(value);\n self.resumeForce();\n };\n\n self.setPseudoknotStrength = function(value) {\n self.linkStrengths.pseudoknot = value;\n self.update();\n };\n\n self.displayNumbering = function(value) {\n self.displayParameters.displayNumbering = value;\n updateStyle();\n };\n\n self.displayNodeOutline = function(value) {\n self.displayParameters.displayNodeOutline = value;\n updateStyle();\n };\n\n self.displayNodeLabel = function(value) {\n self.displayParameters.displayNodeLabel = value;\n updateStyle();\n };\n\n self.displayLinks = function(value) {\n self.displayParameters.displayLinks = value;\n updateStyle();\n };\n\n self.displayPseudoknotLinks = function(value) {\n self.displayParameters.displayPseudoknotLinks = value;\n updateStyle();\n };\n\n self.displayProteinLinks = function(value) {\n self.displayParameters.displayProteinLinks = value;\n updateStyle();\n };\n\n self.displayDirectionArrows = function(value) {\n self.displayParameters.displayDirectionArrows = value;\n updateStyle();\n };\n}\n","import {RNAGraph} from './rnagraph.js';\n\nimport {simpleXyCoordinates} from './simplernaplot.js';\nimport {NAView} from './naview/naview.js'\n\nimport fstyle from './fornac.css';\n\nexport function rnaPlot(passedOptions = {}) {\n var options = {\n 'width': 300,\n 'height': 300,\n 'nucleotideRadius': 5,\n 'rnaEdgePadding': 1, // how far the leftmost, rightmost, topmost and bottomost\n // nucleotides are from the edge of the plot\n 'labelInterval': 10,\n 'showNucleotideLabels': true,\n 'startNucleotideNumber': 1,\n 'bundleExternalLinks': false,\n\n 'rnaLayout': 'simple', // simple or naview\n 'namePosition': '0 0' // for x and y either 0, 0.5 or 1\n };\n var options = Object.assign(options, passedOptions);\n\n var xScale, yScale;\n\n function createTransformToFillViewport(xValues, yValues) {\n // create transform that will scale the x and y values so that\n // they fill the available viewport\n let xExtent = d3.extent(xValues);\n let yExtent = d3.extent(yValues);\n\n // add the radius of the nucleotides\n xExtent[0] -= options.nucleotideRadius + options.rnaEdgePadding;\n yExtent[0] -= options.nucleotideRadius + options.rnaEdgePadding;\n\n xExtent[1] += options.nucleotideRadius + options.rnaEdgePadding;\n yExtent[1] += options.nucleotideRadius + options.rnaEdgePadding;\n\n // find out how wide and height the molecule\n var xRange = xExtent[1] - xExtent[0];\n var yRange = yExtent[1] - yExtent[0];\n\n // how much wider / taller is it than the available viewport\n var xExtra = xRange - options.width;\n var yExtra = yRange - options.height;\n\n // once we have a scale for one dimension, we can create the scale for the other\n // keeping the same expansion / shrinking ratio\n function createOtherScale(firstScale, newDomain, newRange) {\n var scaleFactor = (firstScale.range()[1] - firstScale.range()[0]) /\n (firstScale.domain()[1] - firstScale.domain()[0]);\n var newWidth = (newDomain[1] - newDomain[0]) * scaleFactor\n var newMargin = ((newRange[1] - newRange[0]) - newWidth) / 2;\n\n return {'scaleFactor': scaleFactor,\n 'scale': d3.scale.linear()\n .domain(newDomain)\n .range([newRange[0] + newMargin, newRange[1] - newMargin])};\n }\n\n var ret;\n\n if (xExtra > yExtra) {\n // we have to shrink more in the x-dimension than the y\n xScale = d3.scale.linear()\n .domain(xExtent)\n .range([0, options.width])\n\n ret = createOtherScale(xScale, yExtent, [0, options.height]);\n yScale = ret.scale;\n } else {\n // we have to shrink more in the x-dimension than the y\n yScale = d3.scale.linear()\n .domain(yExtent)\n .range([0, options.height])\n\n ret = createOtherScale(yScale, xExtent, [0, options.width]);\n xScale = ret.scale;\n }\n\n var xOffset = xScale.range()[0] - xScale.domain()[0];\n var yOffset = yScale.range()[0] - yScale.domain()[0];\n\n return 'translate(' + -(xScale.domain()[0] * ret.scaleFactor - xScale.range()[0]) +\n ',' + -(yScale.domain()[0] * ret.scaleFactor - yScale.range()[0]) + ')' +\n 'scale(' + ret.scaleFactor + ')';\n }\n\n function createNucleotides(selection, nucleotideNodes) {\n // create groupings for each nucleotide and label\n var gs = selection\n .selectAll('.gnode')\n .data(nucleotideNodes)\n .enter()\n .append('svg:g')\n .classed('gnode', true)\n .attr('transform', function(d) {\n return 'translate(' + d.x + ',' + d.y + ')';\n });\n\n var circles = gs.append('svg:circle')\n .classed(fstyle.node, true)\n .attr('node_type', 'nucleotide')\n .attr('base_type', (d) => { if (d.name) { return d.name.toLowerCase(); }})\n .attr('r', options.nucleotideRadius)\n\n\n if (options.showNucleotideLabels) {\n var nucleotideLabels = gs.append('svg:text')\n .text(function(d) { return d.name; })\n .classed(fstyle.nodeLabel, true)\n .append('svg:title')\n .text(function(d) { return d.struct_name + ':' + d.num; });\n }\n }\n\n function createLabels(selection, labelNodes) {\n // create groupings for each nucleotide and label\n\n var gs = selection\n .selectAll()\n .data(labelNodes)\n .enter()\n .append('svg:g')\n .classed('gnode', true)\n .attr('transform', function(d) {\n return 'translate(' + d.x + ',' + d.y + ')';\n });\n\n var circles = gs.append('svg:circle')\n .classed(fstyle.node, true)\n .attr('node_type', 'label')\n .attr('r', options.nucleotideRadius)\n\n var numberLabels = gs.append('svg:text')\n .classed(fstyle.nodeLabel, true)\n .text(function(d) { return d.name; })\n }\n\n function createName(selection, name) {\n let nameLabel = selection.append('svg:text')\n //.attr('dy', -10)\n .classed(fstyle.plotLabel, true)\n .text(name);\n\n let xyPos = options.namePosition.split(\" \", 2) // 0 0.5 1\n let xy = []\n let textBBox = nameLabel.node().getBBox()\n let textSize = [textBBox.width, textBBox.height]\n let plotSize = [options.width, options.height]\n\n for (let p in [0, 1]) {\n switch (xyPos[p]) {\n case '0':\n xy[p] = textSize[p] / 2\n break;\n case '1':\n xy[p] = plotSize[p] - textSize[p] / 2\n break;\n case '0.5':\n xy[p] = plotSize[p] / 2\n break;\n }\n }\n nameLabel.attr('x', xy[0]).attr('y', xy[1])\n }\n\n function makeExternalLinksBundle(selection, links) {\n var nodesDict = {};\n var linksList = [];\n links = links.filter(function(d) { return d.linkType == 'correct' || d.linkType == 'incorrect' || d.linkType == 'extra'; });\n\n selection.selectAll('[link-type=extra]')\n .remove();\n\n\n for (var i = 0; i < links.length; i++) {\n if (links[i].source === null || links[i].target === null)\n continue;\n\n nodesDict[links[i].source.uid] = links[i].source;\n nodesDict[links[i].target.uid] = links[i].target;\n\n linksList.push({'source': links[i].source.uid, 'target': links[i].target.uid, 'linkType': links[i].linkType, 'extraLinkType': links[i].extraLinkType}) ;\n }\n\n var fbundling = d3.ForceEdgeBundling().nodes(nodesDict).edges(linksList)\n .compatibility_threshold(0.8).step_size(0.2);\n var results = fbundling();\n\n var d3line = d3.svg.line()\n .x(function(d){return d.x;})\n .y(function(d){return d.y;})\n .interpolate('linear');\n\n for (var i = 0; i < results.length; i++) {\n var edge_subpoint_data = results[i];\n // for each of the arrays in the results\n // draw a line between the subdivions points for that edge\n\n selection.append('path').attr('d', d3line(edge_subpoint_data))\n .style('fill', 'none')\n .attr('link-type', function(d) { return linksList[i].linkType; })\n .attr('extra-link-type', function(d) { return linksList[i].extraLinkType; })\n .style('stroke-opacity',0.4); //use opacity as blending\n }\n\n }\n\n function createLinks(selection, links) {\n links = links.filter(function(d) { return d.source !== null && d.target !== null; });\n var gs = selection.selectAll('.link')\n .data(links)\n .enter()\n .append('svg:line')\n .attr('x1', function(d) { return d.source.x; })\n .attr('x2', function(d) { return d.target.x; })\n .attr('y1', function(d) { return d.source.y; })\n .attr('y2', function(d) { return d.target.y; })\n .attr('link-type', function(d) { return d.linkType; })\n .attr('extra-link-type', function(d) { return d.extraLinkType; })\n .classed('link', true)\n .classed(fstyle.link, true)\n }\n\n function chart(selection) {\n selection.each(function(data) {\n let plot = d3.select(this).append('g')\n .classed(fstyle.plot, true)\n\n // data should be a dictionary containing at least a structure\n // and possibly a sequence\n let rg = new RNAGraph(data.sequence, data.structure, data.name, options.startNucleotideNumber)\n .recalculateElements()\n .elementsToJson()\n .addName(data.name);\n\n data.rnaGraph = rg;\n // calculate the position of each nucleotide\n // the positions of the labels will be calculated in\n // the addLabels function\n let positions = [];\n\n if (options.rnaLayout === 'naview') {\n var naview = new NAView();\n var naViewPositions = naview.naview_xy_coordinates(rg.pairtable);\n\n for (var i = 0; i < naViewPositions.nbase; i++) {\n positions.push([naViewPositions.x[i], naViewPositions.y[i]]);\n }\n } else {\n positions = simpleXyCoordinates(rg.pairtable);\n }\n\n rg.addPositions('nucleotide', positions)\n //.reinforceStems()\n //.reinforceLoops()\n //.addExtraLinks(data.extraLinks)\n .addLabels(options.startNucleotideNumber, options.labelInterval);\n\n // create a transform that will fit the molecule to the\n // size of the viewport (canvas, svg, whatever)\n let fillViewportTransform = createTransformToFillViewport(\n rg.nodes.map(function(d) { return d.x; }),\n rg.nodes.map(function(d) { return d.y; })\n );\n plot.attr('transform', fillViewportTransform);\n\n let nucleotideNodes = rg.nodes.filter(function(d) {\n return d.nodeType == 'nucleotide';\n });\n\n let labelNodes = rg.nodes.filter(function(d) {\n return d.nodeType == 'label';\n });\n\n let links = rg.links;\n\n createLinks(plot, links);\n createNucleotides(plot, nucleotideNodes);\n createLabels(plot, labelNodes);\n createName(d3.select(this), data.name);\n\n if (options.bundleExternalLinks) {\n makeExternalLinksBundle(plot, links);\n }\n\n });\n }\n\n chart.width = function(_) {\n if (!arguments.length) return options.width;\n options.width = _;\n return chart;\n };\n\n chart.height = function(_) {\n if (!arguments.length) return options.height;\n options.height = _;\n return chart;\n };\n\n chart.showNucleotideLabels = function(_) {\n if (!arguments.length) return options.showNucleotideLabels;\n options.showNucleotideLabels = _;\n return chart;\n };\n\n chart.rnaEdgePadding = function(_) {\n if (!arguments.length) return options.rnaEdgePadding;\n options.rnaEdgePadding = _;\n return chart;\n };\n\n chart.nucleotideRadius = function(_) {\n if (!arguments.length) return options.nucleotideRadius;\n options.nucleotideRadius = _;\n return chart;\n };\n\n chart.labelInterval = function(_) {\n if (!arguments.length) return options.labelInterval;\n options.labelInterval = _;\n return chart;\n };\n\n chart.showNucleotideLabels = function(_) {\n if (!arguments.length) return options.showNucleotideLabels;\n options.showNucleotideLabels = _;\n return chart;\n };\n\n chart.startNucleotideNumber = function(_) {\n if (!arguments.length) return options.startNucleotideNumber;\n options.startNucleotideNumber = _;\n return chart;\n };\n\n chart.bundleExternalLinks = function(_) {\n if (!arguments.length) return options.bundleExternalLinks;\n options.bundleExternalLinks = _;\n return chart;\n };\n\n chart.rnaLayout = function(_) {\n if (!arguments.length) return options.rnaLayout;\n options.rnaLayout = _;\n return chart;\n };\n\n chart.namePosition = function(_) {\n if (!arguments.length) return options.namePosition;\n options.namePosition = _;\n return chart;\n };\n\n return chart;\n}\n","import {rnaPlot} from './rnaplot.js';\n\nexport function rnaTreemap(passedOptions = {}) {\n var options = {\n 'width': 300,\n 'height': 300,\n 'nucleotideRadius': 5,\n 'rnaEdgePadding': 1, // how far the leftmost, rightmost, topmost and bottomost\n // nucleotides are from the edge of the plot\n 'labelInterval': 10,\n 'showNucleotideLabels': true,\n 'startNucleotideNumber': 1,\n 'bundleExternalLinks': false,\n\n 'rnaLayout': 'simple', // simple or naview\n 'namePosition': '0 0', // for x and y either 0, 0.5 or 1\n };\n\n var options = Object.assign(options, passedOptions);\n\n function rnaTreemapNode(selection) {\n // create a background rectangle for each RNA structure\n selection.each(function(d) {\n d3.select(this)\n .attr('transform', function(d) { return 'translate(' + d.x + ',' + d.y + ')' })\n .append('rect')\n .attr('fill', 'transparent')\n .attr('width', function(d) { return Math.max(0, d.dx); })\n .attr('height', function(d) { return Math.max(0, d.dy); })\n\n // draw the actual RNA structure\n var chart = rnaPlot(options)\n .width( Math.max(0, d.dx))\n .height( Math.max(0, d.dy))\n\n if ('structure' in d) d3.select(this).call(chart)\n });\n }\n\n var chart = function(selection) {\n selection.each(function(data) {\n console.log('data:', data)\n // initialize the treemap structure\n // sample input\n // { 'name': 'blah',\n // 'children: [{'structure': '..((..))',\n // 'sequence': 'ACCGGCC',\n // 'size': 50}]\n // }\n var treemap = d3.layout.treemap()\n .size([options.width, options.height])\n .sticky(false)\n .value(function(d) { return d.size; });\n\n // create a new for each node in the treemap\n // this may be a little redundant, since we expect the calling\n // selection to contain their own g elements\n var gEnter = d3.select(this)\n .append('g')\n .classed('rnatreemap', true)\n var treemapGnodes = gEnter.datum(data).selectAll('.treemapnode')\n .data(treemap.nodes)\n .enter()\n .append('g')\n .classed('treemapnode', true)\n .call(rnaTreemapNode);\n });\n };\n\n chart.width = function(_) {\n if (!arguments.length) return options.width;\n options.width = _;\n return chart;\n };\n\n chart.height = function(_) {\n if (!arguments.length) return options.height;\n options.height = _;\n return chart;\n };\n\n chart.showNucleotideLabels = function(_) {\n if (!arguments.length) return options.showNucleotideLabels;\n options.showNucleotideLabels = _;\n return chart;\n };\n\n chart.rnaEdgePadding = function(_) {\n if (!arguments.length) return options.rnaEdgePadding;\n options.rnaEdgePadding = _;\n return chart;\n };\n\n chart.nucleotideRadius = function(_) {\n if (!arguments.length) return options.nucleotideRadius;\n 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\ No newline at end of file diff --git a/doc/img/cofold_example.png b/doc/img/cofold_example.png index 05bb1bb..5ca1687 100644 Binary files a/doc/img/cofold_example.png and b/doc/img/cofold_example.png differ diff --git a/doc/img/uncircularized_exterior.png b/doc/img/uncircularized_exterior.png index 70ea687..af784a4 100644 Binary files a/doc/img/uncircularized_exterior.png and b/doc/img/uncircularized_exterior.png differ diff --git a/examples/demo.html b/examples/demo.html index 7b7bf38..2c29519 100644 --- a/examples/demo.html +++ b/examples/demo.html @@ -95,7 +95,7 @@

This is a custom-colored RNA

function cofoldContainer() { var container = new fornac.FornaContainer("#cofold_ss", - {'animation': true, 'zoomable': false, 'initialSize':[500,300]}); + {'animation': false, 'zoomable': false, 'initialSize':[500,300]}); var options = {'structure': '..((((...))))...((...((...((..&............))...))...))..', 'sequence': 'ACGAUCAGAGAUCAGAGCAUACGACAGCAG&ACGAAAAAAAGAGCAUACGACAGCAG' diff --git a/src/fornac.js b/src/fornac.js index f117407..bcafff5 100644 --- a/src/fornac.js +++ b/src/fornac.js @@ -1490,6 +1490,107 @@ export function FornaContainer(element, passedOptions = {}) { // add them back to the plot } + let splitMultiStrand = function(rna) { + // split a multi strand RNA into its individual strands + // get the position of the '&' character in the dotbracket string + let breakPositions = []; + for (let i = 0; i < rna.dotbracket.length; i++) { + if (rna.dotbracket[i] == '&') { + breakPositions.push(i); + } + } + + let toRemove = []; + // collect all the base pairs that are between split strands + for (let i = 0; i < rna.links.length; i++) { + let link = rna.links[i]; + + if (link.linkType != 'basepair') + continue; // only consider base pairs + + for (let j = 0; j < breakPositions.length; j++) { + let node = rna.nodes[breakPositions[j]]; // take the split node + // take the two links that connect the split node + let linkSource = rna.links.filter(link => link.source === node)[0]; + let linkTarget = rna.links.filter(link => link.target === node)[0]; + if (link.source.num <= linkSource.source.num && link.target.num >= linkTarget.target.num) { + console.log('crossing basepair', link); + link.breakFrom = 0; + // find the strand that the source is in + for (let k = 0; k < breakPositions.length - 1; k++) { + if (link.source.num > breakPositions[k] && link.source.num < breakPositions[k+1]) + link.breakFrom = k+1; + } + // find the strand that the target is in + link.breakTo = j+1; + link.from = link.source.num; + // find the position of the source in the strand + if (link.breakFrom > 0) link.from -= breakPositions[link.breakFrom-1] + link.breakFrom; + // find the position of the target in the strand + link.to = link.target.num - linkTarget.target.num; + toRemove.push(link); + } + } + } + + + // Remove all base pairs that are between these two nodes and add them as extra + // links + console.log('toRemove:', toRemove); + let sequences = rna.seq.split('&'); + + // remove the base pairs + for (let i = 0; i < toRemove.length; i++) { + rna.pairtable[toRemove[i].source.num] = 0; + rna.pairtable[toRemove[i].target.num] = 0; + } + + // extract the dotbracket string of the rna + // cut it at the position of this backbone bond + console.log('sequences:', sequences); + + let rnaDotBracket = rnaUtilities.pairtableToDotbracket(rna.pairtable); + let dotbrackets = []; // array to hold the dotbracket strings of the individual strands + let rnaPositions = rna.getPositions('nucleotide') // get the nucleotide positions, cut them at the positions of the backbone bond + let positions = []; + let rnaUids = rna.getUids(); + let uids = []; + let lastBreak = 0; // the position of the last break + for (let i = 0; i <= breakPositions.length; i++) { + // cut the dotbracket + dotbrackets.push(rnaDotBracket.slice(lastBreak, breakPositions[i])); + // add the positions + positions.push(rnaPositions.slice(lastBreak, breakPositions[i])); + // add the uids + uids.push(rnaUids.slice(lastBreak, breakPositions[i])); + lastBreak = breakPositions[i] + 1; + } + + console.log('positions:', positions); + + delete self.rnas[rna.uid]; + let newRnas = []; + for (let i = 0; i < sequences.length; i++) { + let newRna = self.addRNA(dotbrackets[i], { 'sequence': sequences[i], + 'positions': positions[i], + 'uids': uids[i] }); + newRnas.push(newRna); + } + // add the extra links + for (let i = 0; i < toRemove.length; i++) { + console.log('toRemove[i]', toRemove[i]); + self.extraLinks.push( + {'source': newRnas[toRemove[i].breakFrom].nodes[toRemove[i].from-1], + 'target': newRnas[toRemove[i].breakTo].nodes[toRemove[i].to-1], + 'value': 1, + 'uid': slugid.nice(), + 'linkType': 'intermolecule'}); + recalculateGraph(); + self.update(); + } + console.log('self.extraLinks:', self.extraLinks); + } + var removeLink = function(d) { // remove a link between two nodes let index = self.graph.links.indexOf(d); @@ -1907,6 +2008,13 @@ export function FornaContainer(element, passedOptions = {}) { else self.addRNAJSON(rnaJson, {centerView: passedOptions.centerView}); + // if the structure containes multistrands, let's split before the '&' + console.log('structure:', structure); + if (structure.indexOf('&') !== -1 && structure != '&' && structure.indexOf('&') !== 0) { + console.log('splitting multistrand'); + splitMultiStrand(rnaJson); + return; + }; return rnaJson; }; @@ -2126,7 +2234,7 @@ export function FornaContainer(element, passedOptions = {}) { if (node.nodeType != 'nucleotide') continue; - console.log('node:', node); + // console.log('node:', node); nodeIdxs[node.uid] = currIdx; currIdx += 1; diff --git a/src/rnagraph.js b/src/rnagraph.js index ab3a4d7..790e353 100644 --- a/src/rnagraph.js +++ b/src/rnagraph.js @@ -84,35 +84,35 @@ export function RNAGraph(seq = '', dotbracket = '', structName = '', startNumber self.pairtable = rnaUtilities.dotbracketToPairtable(self.dotbracket); }; - self.removeBreaks = function(targetString) { - // Remove all chain breaks (denoted with a '&', which indicate - // that the input represents more than one strand) - var breaks = []; - var breakIndex = -1; - - while ((breakIndex = targetString.indexOf('&')) >= 0) { - breaks.push(breakIndex); - targetString = targetString.substring(0, breakIndex) + targetString.substring(breakIndex+1, targetString.length); - - } - - return {targetString: targetString, breaks: breaks}; - }; - - var ret = self.removeBreaks(self.dotbracket); - self.dotbracket = ret.targetString; - self.dotBracketBreaks = ret.breaks; - - ret = self.removeBreaks(self.seq); - self.seq = ret.targetString; - self.seqBreaks = ret.breaks; + // self.removeBreaks = function(targetString) { + // // Collect the indexes of the chain breaks in the targetString + // // chain breaks are indicated by '&' + // var breaks = []; + // for (var i = 0; i < targetString.length; i++) { + // if (targetString[i] === '&') { + // breaks.push(i); + // } + // } + + // return {targetString: targetString, breaks: breaks}; + // }; + + // var ret = self.removeBreaks(self.dotbracket); + // commented out to avoid removing the break node, let's keep it in the dotbracket + // self.dotbracket = ret.targetString; + // self.dotBracketBreaks = ret.breaks; + + // ret = self.removeBreaks(self.seq); + // commented out to avoid removing the break node, let's keep it in the sequence + // self.seq = ret.targetString; + // self.seqBreaks = ret.breaks; self.rnaLength = self.dotbracket.length; - if (!arraysEqual(self.dotBracketBreaks, self.seqBreaks)) { - console.log('WARNING: Sequence and structure breaks not equal'); - console.log('WARNING: Using the breaks in the structure'); - } + // if (!arraysEqual(self.dotBracketBreaks, self.seqBreaks)) { + // console.log('WARNING: Sequence and structure breaks not equal'); + // console.log('WARNING: Using the breaks in the structure'); + // } self.computePairtable(); @@ -131,23 +131,24 @@ export function RNAGraph(seq = '', dotbracket = '', structName = '', startNumber // convert all the nodes following breaks to fake nodes let labelNodes = self.nodes.filter(function(d) { return d.nodeType == 'nucleotide'; }); - // if a node was an artifical break node, convert it to a middle - for (let i = 0; i < labelNodes.length; i++) { - if (self.dotBracketBreaks.indexOf(i) >= 0) { - labelNodes[i].nodeType = 'middle'; - labelNodes[i+1].nodeType = 'middle'; - } - } + // // if a node was an artifical break node, convert it to a middle + // for (let i = 0; i < labelNodes.length; i++) { + // if (self.dotBracketBreaks.indexOf(i) >= 0) { + // labelNodes[i].nodeType = 'middle'; + // // commented out to avoid removing the node after the break + // // labelNodes[i+1].nodeType = 'middle'; + // } + // } for (let i = 0; i < self.elements.length; i++) { var broken = false; - // change the elemType of the other nodes in the element containing - // the break - for (let j = 0; j < self.elements[i][2].length; j++) { - if (self.dotBracketBreaks.indexOf(self.elements[i][2][j]) >= 0) - broken = true; - } + // // change the elemType of the other nodes in the element containing + // // the break + // for (let j = 0; j < self.elements[i][2].length; j++) { + // if (self.dotBracketBreaks.indexOf(self.elements[i][2][j]) >= 0) + // broken = true; + // } if (broken) { self.elements[i][2].map(function(x) { @@ -444,10 +445,10 @@ export function RNAGraph(seq = '', dotbracket = '', structName = '', startNumber for (let i = 1; i <= pt[0]; i++) { var nodeName = self.seq[i-1]; - if (self.dotBracketBreaks.indexOf(i-1) >= 0 || - self.dotBracketBreaks.indexOf(i-2) >= 0) { - nodeName = ''; - } + // // remove only the breaks that are in the sequence + // if (self.dotBracketBreaks.indexOf(i-1) >= 0) { + // nodeName = ''; + // } //create a node for each nucleotide self.nodes.push({'name': nodeName, @@ -488,9 +489,9 @@ export function RNAGraph(seq = '', dotbracket = '', structName = '', startNumber if (i > 1) { // backbone links - if (self.dotBracketBreaks.indexOf(i-1) === -1 && - self.dotBracketBreaks.indexOf(i-2) == -1 && - self.dotBracketBreaks.indexOf(i-3) == -1) { + // unlink only the break and the nucleotide before it + // if (self.dotBracketBreaks.indexOf(i-1) === -1 && + // self.dotBracketBreaks.indexOf(i-2) == -1) { // there is no break in the strands here // we can add a backbone link self.links.push({'source': self.nodes[i-2], @@ -499,7 +500,7 @@ export function RNAGraph(seq = '', dotbracket = '', structName = '', startNumber 'value': 1, 'uid': slugid.nice() }); self.nodes[i-1].linked = true; - } + // } } } @@ -555,31 +556,31 @@ export function RNAGraph(seq = '', dotbracket = '', structName = '', startNumber if (i > j) { //hairpin loop or one large unpaired molecule u5.push(i); - if (level === 0) + // if (level === 0) return [['e',level, u5.sort(numberSort)]]; - else { - // check to see if we have chain breaks due - // to multiple strands in the input - var external = false; - var left = []; - var right = []; - for (var k = 0; k < u5.length; k++) { - if (external) - right.push(u5[k]); - else - left.push(u5[k]); - - if (self.dotBracketBreaks.indexOf(u5[k]) >= 0) - external = true; - } - - if (external) { - return [['h',level, u5.sort(numberSort)]]; - } - else - // if not, this is a simple hairpin loop - return [['h',level, u5.sort(numberSort)]]; - } + // else { + // // check to see if we have chain breaks due + // // to multiple strands in the input + // var external = false; + // var left = []; + // var right = []; + // for (var k = 0; k < u5.length; k++) { + // if (external) + // right.push(u5[k]); + // else + // left.push(u5[k]); + + // if (self.dotBracketBreaks.indexOf(u5[k]) >= 0) + // external = true; + // } + + // if (external) { + // return [['h',level, u5.sort(numberSort)]]; + // } + // else + // // if not, this is a simple hairpin loop + // return [['h',level, u5.sort(numberSort)]]; + // } } if (pt[i] != j) { diff --git a/src/rnautils.js b/src/rnautils.js index 0c6c54c..444d8b2 100644 --- a/src/rnautils.js +++ b/src/rnautils.js @@ -149,6 +149,8 @@ export function RNAUtilities() { pt[ni] = j; pt[j] = ni; + } else if (a == '&'){ + // there is a sequence break here, ignore it } else { throw "Unknown symbol in dotbracket string"; }