varri-js 1.0.0

package/fornac/fornac.js

@@ -0,0 +1,3 @@
+/*! For license information please see fornac.js.LICENSE.txt */
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e=t.radius+16,n=t.x-e,r=t.x+e,o=t.y-e,i=t.y+e;return function(e,s,a,u,l){if(e.point&&e.point!==t){var c=t.x-e.point.x,f=t.y-e.point.y,d=Math.sqrt(c*c+f*f),h=t.radius+e.point.radius;d<h&&(d=(d-h)/d*.1,t.x-=c*=d,t.y-=f*=d,e.point.x+=c,e.point.y+=f)}return s>r||u<n||a>i||l<o}};++o<i;)n.visit(u(a[o]));t.attr("x1",(function(t){return t.source.x})).attr("y1",(function(t){return t.source.y})).attr("x2",(function(t){return t.target.x})).attr("y2",(function(t){return t.target.y})),r.attr("transform",(function(t){return"translate("+[t.x,t.y]+")"})),r.select("."+e().directionArrow).each(j)})),o.force.on("end",(function(){r.selectAll("[node_type=nucleotide]").filter((function(t,e){return 0==e})).each((function(t,e){}))})),o.changeColorScheme(o.colorScheme),o.options.animation&&o.force.start(),J()},o.transitionRNA=function(t,n){if(o.dotbracket!=t){o.dotbracket=t;var r=o.options.transitionDuration,i=o.graph.nodes.filter((function(t){return"nucleotide"==t.nodeType})).map((function(t){return t.uid})),s=F(t,{uids:i}),a=M.selectAll("g.gnode").data(s.nodes,Q),u=_.selectAll("line.link").data(s.links.filter($),Q);0===r?a.attr("transform",(function(t){return"translate("+[t.x,t.y]+")"})):a.transition().attr("transform",(function(t){return"translate("+[t.x,t.y]+")"})).duration(r);var l=z(a.enter()).attr("transform",(function(t){return void 0!==t.x&&void 0!==t.y?"translate("+[0,0]+")":""}));0===r?a.exit().remove():a.exit().transition().attr("transform",(function(t){return void 0!==t.x&&void 0!==t.y?"translate("+[0,0]+")":""})),o.graph.nodes=a.data(),a.select("."+e().directionArrow).each(j),o.changeColorScheme(o.colorScheme),J(),o.centerView(r),u.exit().remove(),0===r?(u.attr("x1",(function(t){return t.source.x})).attr("y1",(function(t){return t.source.y})).attr("x2",(function(t){return t.target.x})).attr("y2",(function(t){return t.target.y})),V(u.enter()),o.graph.links=u.data(),J()):u.transition().attr("x1",(function(t){return t.source.x})).attr("y1",(function(t){return t.source.y})).attr("x2",(function(t){return t.target.x})).attr("y2",(function(t){return t.target.y})).duration(r).call((function(t,e){0===t.size()&&setTimeout(e,r);var n=0;t.each((function(){++n})).each("end",(function(){--n||e.apply(this,arguments)}))}),(function(){V(u.enter()),o.graph.links=u.data(),o.changeColorScheme(o.colorScheme),J(),void 0!==n&&n()})),0===r?l.attr("transform",(function(t){return void 0!==t.x&&void 0!==t.y?"translate("+[t.x,t.y]+")":""})):l.transition().attr("transform",(function(t){return void 0!==t.x&&void 0!==t.y?"translate("+[t.x,t.y]+")":""}))}};var G=function(){if(0===o.graph.nodes.length)return{translate:[0,0],scale:1};var t=s().min(o.graph.nodes.map((function(t){return t.x}))),e=s().min(o.graph.nodes.map((function(t){return t.y}))),n=s().max(o.graph.nodes.map((function(t){return t.x}))),r=s().max(o.graph.nodes.map((function(t){return t.y}))),i=s().max(o.graph.nodes.map((function(t){return 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"+n),B.range([0,e]).domain([0,e]),I.range([0,n]).domain([0,n]),o.zoomer.x(B).y(I),o.brusher.x(B).y(I),N.select(".background").attr("width",e).attr("height",n),o.centerView()},o.setOutlineColor=function(t){M.selectAll("g.gnode").select("[node_type=nucleotide]").style("fill",t)},o.addCustomColors=function(t){o.customColors=t,o.changeColorScheme("custom")},o.addCustomColorsText=function(t){var e=new p(t);o.customColors=e.colorsJson,o.changeColorScheme("custom")},o.changeColorScheme=function(t){M.selectAll("[node_type=protein]").classed(e().node,!0).attr("r",(function(t){return t.radius})),M.selectAll("g.gnode"),M.selectAll("g.gnode").selectAll("circle");var n=M.selectAll("g.gnode").select("[node_type=nucleotide]");if(o.colorScheme=t,"sequence"==t){var r=s().scale.ordinal().range(["#dbdb8d","#98df8a","#ff9896","#aec7e8","#aec7e8"]).domain(["A","C","G","U","T"]);n.style("fill",(function(t){return r(t.name)}))}else if("structure"==t)r=s().scale.category10().domain(["s","m","i","e","t","h","x"]).range(["lightgreen","#ff9896","#dbdb8d","lightsalmon","lightcyan","lightblue","transparent"]),n.style("fill",(function(t){return r(t.elemType)}));else if("positions"==t)n.style("fill",(function(t){return s().scale.linear().range(["#98df8a","#dbdb8d","#ff9896"]).interpolate(s().interpolateLab).domain([1,1+(t.rna.rnaLength-1)/2,t.rna.rnaLength])(t.num)}));else if("custom"==t){void 0!==o.customColors&&"domain"in o.customColors&&"range"in o.customColors&&(r=s().scale.linear().interpolate(s().interpolateLab).domain(o.customColors.domain).range(o.customColors.range));var i=function(t,e,n){if(t.hasOwnProperty(e.num)){var r=parseFloat(t[e.num]);return isNaN(r)?t[e.num]:n(r)}return"white"};n.style("fill",(function(t){if(void 0===o.customColors||!o.customColors.hasOwnProperty("colorValues"))return"white";if(o.customColors.colorValues.hasOwnProperty(t.structName)&&o.customColors.colorValues[t.structName].hasOwnProperty(t.num)){var e=o.customColors.colorValues[t.structName];return i(e,t,r)}if(o.customColors.colorValues.hasOwnProperty("")){var n=o.customColors.colorValues[""];return i(n,t,r)}return"white"}))}};var J=function(){M.selectAll("[node_type=label]").classed(e().transparent,!o.displayParameters.displayNumbering),M.selectAll("[label_type=label]").classed(e().transparent,!o.displayParameters.displayNumbering),_.selectAll("[link_type=label_link]").classed(e().transparent,!o.displayParameters.displayNumbering),N.selectAll("[node_type=nucleotide]").classed(e().transparent,!o.displayParameters.displayNodeOutline),M.selectAll("[label_type=nucleotide]").classed(e().transparent,!o.displayParameters.displayNodeLabel),N.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(e().transparent,!o.displayParameters.displayLinks),N.selectAll("[link_type=pseudoknot]").classed(e().transparent,!o.displayParameters.displayPseudoknotLinks),N.selectAll("[link_type=protein_chain]").classed(e().transparent,!o.displayParameters.displayProteinLinks),_.selectAll("[link_type=fake]").classed(e().transparent,!o.options.displayAllLinks),_.selectAll("[link_type=fake_fake]").classed(e().transparent,!o.options.displayAllLinks),N.selectAll("."+e().directionArrow).classed(e().transparent,!o.displayParameters.displayDirectionArrows)},H=function(t,e){var 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<e.links.length;r++){var i=e.links[r];"basepair"==i.linkType&&i.source.num<=t.source.num&&i.target.num>=t.target.num&&(console.log("crossing basepair",i),n.push(i))}console.log("toRemove:",n);for(var s=0;s<n.length;s++)e.pairtable[n[s].source.num]=0,e.pairtable[n[s].target.num]=0,n[s].from=n[s].source.num,n[s].to=n[s].target.num-t.source.num;e.seq;var u=e.seq.slice(0,t.source.num),l=e.seq.slice(t.source.num),c=h.pairtableToDotbracket(e.pairtable),f=c.slice(0,t.source.num),d=c.slice(t.source.num),p=e.getPositions("nucleotide"),g=e.getUids(),y=p.slice(0,t.source.num),m=p.slice(t.source.num),b=g.slice(0,t.source.num),v=g.slice(t.source.num);console.log("positions1:",y),console.log("positions2:",m),delete o.rnas[e.uid];for(var k=o.addRNA(f,{sequence:u,positions:y,uids:b}),x=o.addRNA(d,{sequence:l,positions:m,uids:v}),w=0;w<n.length;w++)console.log("rna1:",k),console.log("rna2:",x),console.log("toRemove[i]",n[w]),o.extraLinks.push({source:k.nodes[n[w].from-1],target:x.nodes[n[w].to-1],value:1,uid:a.nice(),linkType:"intermolecule"}),W(),o.update();console.log("self.extraLinks:",o.extraLinks)}else console.log("ERROR: non adjacent nodes. Target:",t.target,"Source:",t.source,"Link:",t)},nt=function(t){var e=o.graph.links.indexOf(t);if(console.log("removing link:",e),e>-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;m<o.extraLinks.length;m++)console.log("self.extraLinks[i]",o.extraLinks[m]),console.log("rna1:",e),console.log("rna2:",n),o.extraLinks[m].source.rna==e?o.extraLinks[m].target.rna==n||(g.push({source:o.extraLinks[m].target,target:o.extraLinks[m].source.num}),y[o.extraLinks[m].uid]=!0):o.extraLinks[m].source.rna==n&&(o.extraLinks[m].target.rna==e||(g.push({source:o.extraLinks[m].target,target:o.extraLinks[m].source.num+r.length}),y[o.extraLinks[m].uid]=!0)),o.extraLinks[m].target.rna==e?o.extraLinks[m].source.rna==n||(g.push({source:o.extraLinks[m].source,target:o.extraLinks[m].target.num}),y[o.extraLinks[m].uid]=!0):o.extraLinks[m].target.rna==n&&o.extraLinks[m].source.rna==e&&(g.push({source:o.extraLinks[m].source,target:o.extraLinks[m].target.num+r.length}),y[o.extraLinks[m].uid]=!0);o.extraLinks=o.extraLinks.filter((function(t){return!(t.uid in y)})),delete o.rnas[e.uid],delete o.rnas[n.uid];var b;b=o.options.animation?o.addRNA(f,{sequence:d,positions:p,centerView:!1}):o.addRNA(f,{sequence:d,centerView:!1});for(var v=0;v<g.length;v++)o.extraLinks.push({source:g[v].source,target:b.nodes[g[v].target-1],value:1,uid:a.nice(),linkType:"intermolecule"});W(),o.update(),console.log("self.extraLinks:",o.extraLinks)},ot=function(t,n){var r=!0;if(u){if("middle"==(c=t).nodeType||"middle"==u.nodeType||"label"==c.nodeType||"label"==u.nodeType)return;if(c==u)return void d();for(var i={source:u,target:c,linkType:"basepair",value:1,uid:a.nice()},s=0;s<o.graph.links.length;s++)if(o.graph.links[s].source!=u&&o.graph.links[s].target!=u&&o.graph.links[s].source!=c&&o.graph.links[s].target!=c||"basepair"!=o.graph.links[s].linkType&&"pseudoknot"!=o.graph.links[s].linkType&&"intermolecule"!=o.graph.links[s].linkType||(console.log("no basepair possible"),r=!1),(o.graph.links[s].source==c&&o.graph.links[s].target==u||o.graph.links[s].source==u&&o.graph.links[s].target==c)&&"backbone"==o.graph.links[s].linkType)return;if(i.source.rna!=i.target.rna)if(1==i.source.num&&i.target.num==i.target.rna.rnaLength||1==i.target.num&&i.source.num==i.source.rna.rnaLength){var h=[{title:"Backbone Link",action:function(t,n,r){f=!1,console.log("Item #1 clicked!"),console.log("The data for this circle is: "+n),S.attr("class",e().transparent),rt(i)},disabled:!1},{title:"Basepair Link",action:function(t,n,r){f=!1,console.log("You have clicked the second item!"),console.log("The data for this circle is: "+n),S.attr("class",e().transparent),o.addLink(i)}}];f=!0;var p=l(h);console.log("newLinkMenu"),p.apply(this,[t,n,!0,function(){S.attr("class",e().transparent)}])}else r&&o.addLink(i);else r&&o.addLink(i)}},it=function(t){console.log("nodeMousedown"),t.selected||v||O(),b||(v?C(t):U(t)),b&&o.options.editable&&(u=t,S.attr("class",e().dragLine).attr("x1",u.x).attr("y1",u.y).attr("x2",u.x).attr("y2",u.y),s().event.stopPropagation())},st=function(t){b&&(console.log("d.linkType:",t.linkType),t.linkType in{fake:!0,fake_fake:!0,label_link:!0}||nt(t))};o.toJSON=function(){var t={rnas:o.rnas,extraLinks:o.extraLinks};return JSON.stringify(t,(function(t,e){return"rna"==t?void 0:e}),"\t")},o.fromJSON=function(t){var e,n;try{var i=JSON.parse(t);e=i.rnas,n=i.extraLinks}catch(t){throw t}for(var s in e)"rna"==e[s].type?(r=new y,r.seq=e[s].seq,r.dotbracket=e[s].dotbracket,r.circular=e[s].circular,r.pairtable=e[s].pairtable,r.uid=e[s].uid,r.structName=e[s].structName,r.nodes=e[s].nodes,r.links=e[s].links,r.rnaLength=e[s].rnaLength,r.elements=e[s].elements,r.nucsToNodes=e[s].nucsToNodes,r.pseudoknotPairs=e[s].pseudoknotPairs):(r=new ProteinGraph,r.size=e[s].size,r.nodes=e[s].nodes,r.uid=e[s].uid),o.addRNAJSON(r,!1);n.forEach((function(t){o.extraLinks.push(t)})),W(),o.update()},o.addRNA=function(t){var e=arguments.length>1&&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;r<e.length;r++){var o={linkType:"external",value:1,uid:a.nice(),source:null,target:null};if("[object Array]"===Object.prototype.toString.call(e[r][0])){for(var i=0;i<t.nodes.length;i++)if("nucs"in t.nodes[i]&&t.nodes[i].nucs.equals(e[r][0])){o.source=t.nodes[i];break}}else for(var s=0;s<t.nodes.length;s++)t.nodes[s].num==e[r][0]&&(o.source=t.nodes[s]);if("[object Array]"===Object.prototype.toString.call(e[r][1]))for(var u=0;u<t.nodes.length;u++)"nucs"in t.nodes[u]&&t.nodes[u].nucs.equals(e[r][1])&&(o.target=t.nodes[u]);else for(var l=0;l<t.nodes.length;l++)t.nodes[l].num==e[r][1]&&(o.target=t.nodes[l]);null!=o.source&&null!=o.target?n.push(o):console.log("ERROR: source or target of new link not found:",o,e[r])}return n},o.getStructuresDotBracket=function(){console.log("self.rnas:",o.rnas);var t=[],e=1,n={},r=[],i=[];for(var s in o.rnas){for(var a=o.rnas[s],u=0;u<a.nodes.length;u++){var l=a.nodes[u];"nucleotide"==l.nodeType&&(n[l.uid]=e,e+=1,t.push(l.name))}r.push(e)}i=[e-1];for(var c=0;c<e;c++)i.push(0);for(var f in o.rnas)for(var d=o.rnas[f],p=0;p<d.links.length;p++){var g=d.links[p];if("basepair"==g.linkType){var y=n[g.source.uid],m=n[g.target.uid];i[y]=m,i[m]=y}}for(var b=0;b<o.extraLinks.length;b++){var v=o.extraLinks[b],k=n[v.source.uid],x=n[v.target.uid];i[k]=x,i[x]=k}for(var w=h.pairtableToDotbracket(i).split(""),E=0;E<r.length-1;E++)console.log("breaks[i]:",r[E]),t.splice(r[E]+E-1,0,"&"),w.splice(r[E]+E-1,0,"&");return [t.join(""),w.join("")]},o.startAnimation=function(){o.options.animation=!0,T.selectAll("g.gnode").call(D),o.force.start()},o.stopAnimation=function(){o.options.animation=!1,T.selectAll("g.gnode").on("mousedown.drag",null),o.force.stop()},o.resumeForce=function(){o.options.animation&&o.force.resume()},o.setFriction=function(t){o.force.friction(t),o.resumeForce()},o.setCharge=function(t){o.force.charge(t),o.resumeForce()},o.setGravity=function(t){o.force.gravity(t),o.resumeForce()},o.setPseudoknotStrength=function(t){o.linkStrengths.pseudoknot=t,o.update()},o.displayNumbering=function(t){o.displayParameters.displayNumbering=t,J()},o.displayNodeOutline=function(t){o.displayParameters.displayNodeOutline=t,J()},o.displayNodeLabel=function(t){o.displayParameters.displayNodeLabel=t,J()},o.displayLinks=function(t){o.displayParameters.displayLinks=t,J()},o.displayPseudoknotLinks=function(t){o.displayParameters.displayPseudoknotLinks=t,J()},o.displayProteinLinks=function(t){o.displayParameters.displayProteinLinks=t,J()},o.displayDirectionArrows=function(t){o.displayParameters.displayDirectionArrows=t,J()}}function T(){var t,n,r=arguments.length>0&&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;o<e.length;o++)null!==e[o].source&&null!==e[o].target&&(n[e[o].source.uid]=e[o].source,n[e[o].target.uid]=e[o].target,r.push({source:e[o].source.uid,target:e[o].target.uid,linkType:e[o].linkType,extraLinkType:e[o].extraLinkType}));var i=d3.ForceEdgeBundling().nodes(n).edges(r).compatibility_threshold(.8).step_size(.2)(),s=d3.svg.line().x((function(t){return t.x})).y((function(t){return t.y})).interpolate("linear");for(o=0;o<i.length;o++){var a=i[o];t.append("path").attr("d",s(a)).style("fill","none").attr("link-type",(function(t){return r[o].linkType})).attr("extra-link-type",(function(t){return r[o].extraLinkType})).style("stroke-opacity",.4)}}function c(t,n){n=n.filter((function(t){return null!==t.source&&null!==t.target})),t.selectAll(".link").data(n).enter().append("svg:line").attr("x1",(function(t){return t.source.x})).attr("x2",(function(t){return t.target.x})).attr("y1",(function(t){return t.source.y})).attr("y2",(function(t){return t.target.y})).attr("link-type",(function(t){return t.linkType})).attr("extra-link-type",(function(t){return t.extraLinkType})).classed("link",!0).classed(e().link,!0)}function f(t){t.each((function(t){var n=d3.select(this).append("g").classed(e().plot,!0),r=new y(t.sequence,t.structure,t.name,o.startNucleotideNumber).recalculateElements().elementsToJson().addName(t.name);t.rnaGraph=r;var f=[];if("naview"===o.rnaLayout)for(var d=(new E).naview_xy_coordinates(r.pairtable),h=0;h<d.nbase;h++)f.push([d.x[h],d.y[h]]);else f=m(r.pairtable);r.addPositions("nucleotide",f).addLabels(o.startNucleotideNumber,o.labelInterval);var p=i(r.nodes.map((function(t){return t.x})),r.nodes.map((function(t){return t.y})));n.attr("transform",p);var g=r.nodes.filter((function(t){return"nucleotide"==t.nodeType})),b=r.nodes.filter((function(t){return"label"==t.nodeType})),v=r.links;c(n,v),s(n,g),a(n,b),u(d3.select(this),t.name),o.bundleExternalLinks&&l(n,v)}))}return o=Object.assign(o,r),f.width=function(t){return arguments.length?(o.width=t,f):o.width},f.height=function(t){return arguments.length?(o.height=t,f):o.height},f.showNucleotideLabels=function(t){return arguments.length?(o.showNucleotideLabels=t,f):o.showNucleotideLabels},f.rnaEdgePadding=function(t){return arguments.length?(o.rnaEdgePadding=t,f):o.rnaEdgePadding},f.nucleotideRadius=function(t){return arguments.length?(o.nucleotideRadius=t,f):o.nucleotideRadius},f.labelInterval=function(t){return arguments.length?(o.labelInterval=t,f):o.labelInterval},f.showNucleotideLabels=function(t){return arguments.length?(o.showNucleotideLabels=t,f):o.showNucleotideLabels},f.startNucleotideNumber=function(t){return arguments.length?(o.startNucleotideNumber=t,f):o.startNucleotideNumber},f.bundleExternalLinks=function(t){return arguments.length?(o.bundleExternalLinks=t,f):o.bundleExternalLinks},f.rnaLayout=function(t){return arguments.length?(o.rnaLayout=t,f):o.rnaLayout},f.namePosition=function(t){return arguments.length?(o.namePosition=t,f):o.namePosition},f}function _(){var t=arguments.length>0&&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;o<this.nbase+1;o++)this.bases.push(new x);for(this.regions=[],o=0;o<this.nbase+1;o++)this.regions.push(new k.y);for(this.read_in_bases(t),this.rlphead=null,this.find_regions(),this.loop_count=0,this.loops=[],o=0;o<this.nbase+1;o++)this.loops.push(new w.r);for(this.construct_loop(0),this.find_central_loop(),this.traverse_loop(this.root,null),e=0;e<this.nbase;e++)n.push(100+this.BACKBONE_DISTANCE*this.bases[e+1].getX()),r.push(100+this.BACKBONE_DISTANCE*this.bases[e+1].getY());return{nbase:this.nbase,x:n,y:r}},E.prototype.read_in_bases=function(t){var e=null,n=null;for(this.bases.push(new x),this.bases[0].setMate(0),this.bases[0].setExtracted(!1),this.bases[0].setX(this.ANUM),this.bases[0].setY(this.ANUM),n=0,e=1;e<=this.nbase;e++)this.bases.push(new x),this.bases[e].setExtracted(!1),this.bases[e].setX(this.ANUM),this.bases[e].setY(this.ANUM),this.bases[e].setMate(t[e]),t[e]>e&&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;e<t;e++)r.push(!1);for(this.nregion=0,e=0;e<=this.nbase;e++)if(0!=(n=this.bases[e].getMate())&&!r[e]){for(this.regions[this.nregion].setStart1(e),this.regions[this.nregion].setEnd2(n),r[e]=!0,r[n]=!0,this.bases[e].setRegion(this.regions[this.nregion]),this.bases[n].setRegion(this.regions[this.nregion]),e++,n--;e<n&&this.bases[e].getMate()==n;e++,n--)r[n]=!0,r[e]=!0,this.bases[e].setRegion(this.regions[this.nregion]),this.bases[n].setRegion(this.regions[this.nregion]);this.regions[this.nregion].setEnd1(--e),this.regions[this.nregion].setStart2(n+1),this.nregion++}},E.prototype.construct_loop=function(t){var e=null,n=null,r=new w.r,o=new w.r,i=new v.Connection,s=new k.y,a=new b;for((r=this.loops[this.loop_count++]).setNconnection(0),r.setDepth(0),r.setNumber(this.loop_count),r.setRadius(0),a=this.rlphead;null!=a;a=a.getNext())a.getLoopnumber()==this.loop_count&&r.setRadius(a.getRadius());e=t;do{0!=(n=this.bases[e].getMate())&&(s=this.bases[e].getRegion(),this.bases[s.getStart1()].isExtracted()||(e==s.getStart1()?(this.bases[s.getStart1()].setExtracted(!0),this.bases[s.getEnd1()].setExtracted(!0),this.bases[s.getStart2()].setExtracted(!0),this.bases[s.getEnd2()].setExtracted(!0),o=this.construct_loop(s.getEnd1()<this.nbase?s.getEnd1()+1:0)):e==s.getStart2()?(this.bases[s.getStart2()].setExtracted(!0),this.bases[s.getEnd2()].setExtracted(!0),this.bases[s.getStart1()].setExtracted(!0),this.bases[s.getEnd1()].setExtracted(!0),o=this.construct_loop(s.getEnd2()<this.nbase?s.getEnd2()+1:0)):console.log("Something went terribly wrong ...."),r.setNconnection(r.getNconnection()+1),i=new v.Connection,r.setConnection(r.getNconnection()-1,i),r.setConnection(r.getNconnection(),null),i.setLoop(o),i.setRegion(s),e==s.getStart1()?(i.setStart(s.getStart1()),i.setEnd(s.getEnd2())):(i.setStart(s.getStart2()),i.setEnd(s.getEnd1())),i.setExtruded(!1),i.setBroken(!1),o.setNconnection(o.getNconnection()+1),i=new v.Connection,o.setConnection(o.getNconnection()-1,i),o.setConnection(o.getNconnection(),null),i.setLoop(r),i.setRegion(s),e==s.getStart1()?(i.setStart(s.getStart2()),i.setEnd(s.getEnd1())):(i.setStart(s.getStart1()),i.setEnd(s.getEnd2())),i.setExtruded(!1),i.setBroken(!1)),e=n),++e>this.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;r<this.loop_count;r++)(t=this.loops[r]).getNconnection()>e?(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();A++)(w=A+1)>=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),ht<dt&&(ht+=2*Math.PI),j=c+(C=ht-dt>Math.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();A++){if(m=t.getConnection(A),(w=A+1)>=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),ht<dt&&(ht+=2*Math.PI),Z=ht-dt,(yt=b.getAngle()-m.getAngle())<=0&&(yt+=2*Math.PI),Math.abs(Z-yt)>Math.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;w<E;w++)(x=m.getEnd()+w)>this.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();A++)B!=A&&(m=t.getConnection(A),this.generate_region(m),this.traverse_loop(m.getLoop(),m));for(E=0,pt=0,gt=0,A=0;A<t.getNconnection();A++)if((w=A+1)>=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();l++)p=t.getConnection(l),(c=l+1)>=t.getNconnection()&&(c=0),g=t.getConnection(c),f=p.getEnd(),(d=g.getStart())<f&&(d+=this.nbase+1),(o=g.getAngle()-p.getAngle())<=0&&(o+=2*Math.PI),i+=o*(1/(r=p.isExtruded()?o<=Math.PI/2?2:1.5:d-f)+1),s+=o*o/r,(u=o/r)<n&&!p.isExtruded()&&r>1&&(n=u,h=l);(a=i/s)<y&&(a=y),n*a<e&&t.getConnection(h).setExtruded(!0)}while(n*a<e);t.getRadius()>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())<n&&(o+=2*Math.PI),i=(n+o)/2,p=t.getEnd(),(y=(g=e.getStart())-p)<0&&(y+=this.nbase+1),(d=e.getAngle()-t.getAngle())<0&&(d+=2*Math.PI),2==y)this.construct_circle_segment(p,g);else{s=this.bases[g].getX()-this.bases[p].getX(),a=this.bases[g].getY()-this.bases[p].getY(),s/=f=Math.sqrt(s*s+a*a),a/=f,f>=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;g<p;g++)(y=t+g)>this.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;g<p;g++)(y=t+g)>this.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);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 t<e?t:e},E.prototype.maxf2=function(t,e){return t>e?t:e},E.prototype.connected_connection=function(t,e){return!!t.isExtruded()||t.getEnd()+1==e.getStart()}})(),i})()}));
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