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n.previouslySelected=n.selected,n.selected=u.options.applyForce&&!0}),L&&(d=n,N.attr("class","drag_line").attr("x1",d.x).attr("y1",d.y).attr("x2",d.x).attr("y2",d.y))},u.startAnimation=function(){u.animation=!0,x.selectAll("g.gnode").call(P),u.force.start()},u.stopAnimation=function(){u.animation=!1,x.selectAll("g.gnode").on("mousedown.drag",null),u.force.stop()},u.setFriction=function(e){u.force.friction(e),u.resumeForce()},u.setCharge=function(e){u.force.charge(e),u.resumeForce()},u.setGravity=function(e){u.force.gravity(e),u.resumeForce()},u.setPseudoknotStrength=function(e){u.linkStrengths.pseudoknot=e,u.update()},u.displayBackground=function(e){u.displayParameters.displayBackground=e,u.updateStyle()},u.displayNumbering=function(e){u.displayParameters.displayNumbering=e,u.updateStyle()},u.displayNodeOutline=function(e){u.displayParameters.displayNodeOutline=e,u.updateStyle()},u.displayNodeLabel=function(e){u.displayParameters.displayNodeLabel=e,u.updateStyle()},u.displayLinks=function(e){u.displayParameters.displayLinks=e,u.updateStyle()},u.displayPseudoknotLinks=function(e){u.displayParameters.displayPseudoknotLinks=e,u.updateStyle()},u.displayProteinLinks=function(e){u.displayParameters.displayProteinLinks=e,u.updateStyle()},u.updateStyle=function(){k.classed("transparent",!u.displayParameters.displayBackground),w.selectAll("[node_type=label]").classed("transparent",!u.displayParameters.displayNumbering),w.selectAll("[label_type=label]").classed("transparent",!u.displayParameters.displayNumbering),b.selectAll("[link_type=label_link]").classed("transparent",!u.displayParameters.displayNumbering),f.selectAll("circle").classed("hidden_outline",!u.displayParameters.displayNodeOutline),w.selectAll("[label_type=nucleotide]").classed("transparent",!u.displayParameters.displayNodeLabel),f.selectAll("[link_type=real],[link_type=basepair],[link_type=backbone],[link_type=pseudoknot],[link_type=protein_chain],[link_type=chain_chain]").classed("transparent",!u.displayParameters.displayLinks),f.selectAll("[link_type=pseudoknot]").classed("transparent",!u.displayParameters.displayPseudoknotLinks),f.selectAll("[link_type=protein_chain]").classed("transparent",!u.displayParameters.displayProteinLinks),b.selectAll("[link_type=fake]").classed("transparent",!u.options.displayAllLinks)},u.update=function(){u.force.nodes(u.graph.nodes).links(u.graph.links),u.animation&&u.force.start();var e=b.selectAll("line.link").data(u.graph.links,link_key);link_lines=e.enter().append("svg:line"),link_lines.append("svg:title").text(link_key),link_lines.classed("link",!0).attr("x1",function(e){return e.source.x}).attr("y1",function(e){return e.source.y}).attr("x2",function(e){return e.target.x}).attr("y2",function(e){return e.target.y}).attr("link_type",function(e){return e.link_type}).attr("class",function(e){return d3.select(this).attr("class")+" "+e.link_type}).attr("pointer-events",function(e){return"fake"==e.link_type?"none":"all"}),e.attr("class","").classed("link",!0).attr("link_type",function(e){return e.link_type}).attr("class",function(e){return d3.select(this).attr("class")+" "+e.link_type}),e.exit().remove(),xlink=u.displayFakeLinks?e:b.selectAll("[link_type=real],[link_type=pseudoknot],[link_type=protein_chain],[link_type=chain_chain],[link_type=label_link],[link_type=backbone],[link_type=basepair],[link_type=fake],[link_type=intermolecule]"),domain=[0,1,2,3,4,5,6,7,8,9],d3.scale.category10().domain(domain);var r=w.selectAll("g.gnode").data(u.graph.nodes,node_key);gnodes_enter=r.enter().append("g").classed("noselect",!0).classed("gnode",!0).attr("struct_name",function(e){return e.struct_name}).attr("transform",function(e){return void 0!==e.x&&void 0!==e.y?"translate("+[e.x,e.y]+")":""}).each(function(e){e.selected=e.previouslySelected=!1}),gnodes_enter.call(P).on("mousedown",node_mousedown).on("mousedrag",function(e){}).on("mouseup",node_mouseup).on("click",node_mouseclick).transition().duration(750).ease("elastic").attr("r",6.5),node_tooltip=function(e){return node_tooltips={},node_tooltips.nucleotide=e.num,node_tooltips.label="",node_tooltips.pseudo="",node_tooltips.middle="",node_tooltips.protein=e.struct_name,node_tooltips[e.node_type]},xlink.on("click",link_click),r.select("circle"),gnodes_enter.filter(function(e){return"nucleotide"==e.node_type||"label"==e.node_type||"protein"==e.node_type}).append("svg:circle").attr("class","outline_node").attr("r",function(e){return e.radius+1}),e=gnodes_enter.append("svg:circle").attr("class","node").classed("label",function(e){return"label"==e.node_type}).attr("r",function(e){return"middle"==e.node_type?0:e.radius}).attr("node_type",function(e){return e.node_type}),gnodes_enter.append("text").text(function(e){return e.name}).attr("text-anchor","middle").attr("font-size",8).attr("font-weight","bold").attr("y",2.5).attr("class","node-label").attr("label_type",function(e){return e.node_type}).append("svg:title").text(function(e){return"nucleotide"==e.node_type?e.struct_name+":"+e.num:""}),e.append("svg:title").text(function(e){return"nucleotide"==e.node_type?e.struct_name+":"+e.num:""}),r.exit().remove(),real_nodes=u.graph.nodes.filter(function(e){return"nucleotide"==e.node_type||"label"==e.node_type}),u.force.on("tick",function(){for(var e=d3.geom.quadtree(real_nodes),n=0,t=real_nodes.length;++n<t;)e.visit(function(u){var e=u.radius+16,c=u.x-e,d=u.x+e,p=u.y-e,h=u.y+e;return function(e,n,t,r,o){var a,s,i,l;return e.point&&e.point!==u&&(a=u.x-e.point.x,s=u.y-e.point.y,(i=Math.sqrt(a*a+s*s))<(l=u.radius+e.point.radius)&&(i=(i-l)/i*.1,u.x-=a*=i,u.y-=s*=i,e.point.x+=a,e.point.y+=s)),d<n||r<c||h<t||o<p}}(real_nodes[n]));xlink.attr("x1",function(e){return e.source.x}).attr("y1",function(e){return e.source.y}).attr("x2",function(e){return e.target.x}).attr("y2",function(e){return e.target.y}),r.attr("transform",function(e){return"translate("+[e.x,e.y]+")"})}),u.changeColorScheme(u.colorScheme),u.animation&&u.force.start(),u.updateStyle()},n()}var number_sort=function(e,n){return e-n};function generateUUID(){var t=(new Date).getTime();return"xxxxxxxx-xxxx-4xxx-yxxx-xxxxxxxxxxxx".replace(/[xy]/g,function(e){var n=(t+16*Math.random())%16|0;return t=Math.floor(t/16),("x"==e?n:3&n|8).toString(16)})}function isNormalInteger(e){return/^\+?(0|[1-9]\d*)$/.test(e)}function ColorScheme(e){var l=this;l.colorsText=e,l.parseRange=function(e){for(var n=e.split(","),t=[],r=0;r<n.length;r++)if(1==(a=n[r].split("-")).length)t.push(parseInt(a[0]));else if(2==a.length)for(var o=parseInt(a[0]),a=parseInt(a[1]);o<=a;o++)t.push(o);else console.log("Malformed range (too many dashes):",e);return t},l.parseColorText=function(e){e=e.split("\n");for(var n="",t=1,r={color_values:{"":{}},range:["white","steelblue"]},o=[],a=0;a<e.length;a++)if(">"==e[a][0])n=e[a].trim().slice(1),t=1,r.color_values[n]={};else{words=e[a].trim().split(/[\s]+/);for(var s=0;s<words.length;s++)if(isNaN(words[s]))if(0===words[s].search("range"))parts=words[s].split("="),parts_right=parts[1].split(":"),r.range=[parts_right[0],parts_right[1]];else if(0==words[s].search("domain"))parts=words[s].split("="),parts_right=parts[1].split(":"),r.domain=[parts_right[0],parts_right[1]];else{parts=words[s].split(":"),nums=l.parseRange(parts[0]),color=parts[1];for(var i=0;i<nums.length;i++)isNaN(color)?r.color_values[n][nums[i]]=color:(r.color_values[n][nums[i]]=+color,o.push(Number(color)))}else r.color_values[n][t]=Number(words[s]),t+=1,o.push(Number(words[s]))}return"domain"in r||(r.domain=[Math.min.apply(null,o),Math.max.apply(null,o)]),l.colors_json=r,l},l.normalizeColors=function(){var e,n;for(n in l.colors_json){var t,r=Number.MAX_VALUE,o=Number.MIN_VALUE;for(t in l.colors_json.color_values[n])e=l.colors_json.color_values[n][t],"number"==typeof e&&(e<r&&(r=e),o<e&&(o=e));for(t in l.colors_json.color_values[n])e=l.colors_json.color_values[n][t],"number"==typeof e&&(l.colors_json.color_values[n][t]=(e-r)/(o-r))}return l},l.parseColorText(l.colorsText)}function ProteinGraph(e,n,t){var r=this;r.type="protein",r.size=n,r.nodes=[{name:"P",num:1,radius:3*Math.sqrt(n),rna:r,node_type:"protein",struct_name:e,elem_type:"p",size:n,uid:generateUUID()}],r.links=[],r.uid=generateUUID(),r.addUids=function(e){for(var n=0;n<e.length;n++)r.nodes[n].uid=e[n];return r},r.get_uids=function(){uids=[];for(var e=0;e<r.dotbracket.length;e++)uids.push(r.nodes[e].uid);return uids}}function RNAGraph(e,n,t){var l=this;l.type="rna",l.circularizeExternal=!1,0==arguments.length?(l.seq="",l.dotbracket="",l.struct_name=""):(l.seq=e,l.dotbracket=n,l.struct_name=t),l.circular=!1,0<l.dotbracket.length&&"*"==l.dotbracket[l.dotbracket.length-1]&&(l.dotbracket=l.dotbracket.slice(0,l.dotbracket.length-1),l.circular=!0),l.uid=generateUUID(),l.rnaLength=l.dotbracket.length,l.elements=[],l.pseudoknotPairs=[],l.nucs_to_nodes={},l.addUids=function(e){for(var n=0;n<e.length;n++)l.nodes[n].uid=e[n];return l},l.computePairtable=function(){l.pairtable=rnaUtilities.dotbracketToPairtable(l.dotbracket)},l.computePairtable(),l.addPositions=function(n,e){label_nodes=l.nodes.filter(function(e){return e.node_type==n});for(var t=0;t<label_nodes.length;t++)label_nodes[t].x=e[t][0],label_nodes[t].px=e[t][0],label_nodes[t].y=e[t][1],label_nodes[t].py=e[t][1];return l},l.get_positions=function(n){positions=[],nucleotide_nodes=l.nodes.filter(function(e){return e.node_type==n});for(var e=0;e<nucleotide_nodes.length;e++)positions.push([nucleotide_nodes[e].x,nucleotide_nodes[e].y]);return positions},l.get_uids=function(){uids=[];for(var e=0;e<l.dotbracket.length;e++)uids.push(l.nodes[e].uid);return uids},l.reinforceStems=function(){pt=l.pairtable,relevant_elements=elements.filter(function(e){return"s"==e[0]&&4<=e[2].length});for(var e=0;e<relevant_elements.length;e++){all_nucs=relevant_elements[e][2],nucs=all_nucs.slice(0,all_nucs.length/2);for(var n=0;n<nucs.length-1;n++)l.addFakeNode([nucs[n],nucs[n+1],pt[nucs[n+1]],pt[nucs[n]]])}return l},l.reinforceLoops=function(){function e(e){return 0!==e&&e<=l.dotbracket.length}var n,t,r;for(i=0;i<l.elements.length;i++)"s"==l.elements[i][0]||!l.circularizeExternal&&"e"==l.elements[i][0]||(n=l.elements[i][2].filter(e),"e"==l.elements[i][0]&&(t={name:"",num:-1,radius:0,rna:l,node_type:"middle",elem_type:"f",nucs:[],x:l.nodes[l.rnaLength-1].x,y:l.nodes[l.rnaLength-1].y,px:l.nodes[l.rnaLength-1].px,py:l.nodes[l.rnaLength-1].py,uid:generateUUID()},r={name:"",num:-1,radius:0,rna:l,node_type:"middle",elem_type:"f",nucs:[],x:l.nodes[0].x,y:l.nodes[0].y,px:l.nodes[0].px,py:l.nodes[0].py,uid:generateUUID()},n.push(l.nodes.length+1),n.push(l.nodes.length+2),l.nodes.push(t),l.nodes.push(r)),l.addFakeNode(n));return l},l.updateLinkUids=function(){for(var e=0;e<l.links.length;e++)l.links[e].uid=l.links[e].source.uid+l.links[e].target.uid;return l},l.addFakeNode=function(e){for(var n=6.283/(2*e.length),n=18/(2*Math.tan(n)),t="",r=0;r<e.length;r++)t+=l.nodes[e[r]-1].uid;for(new_node={name:"",num:-1,radius:n,rna:l,node_type:"middle",elem_type:"f",nucs:e,uid:t},l.nodes.push(new_node),coords_counted=new_y=new_x=0,n=3.14159*(e.length-2)/(2*e.length),n=.5/Math.cos(n),j=0;j<e.length;j++)0===e[j]||e[j]>l.dotbracket.length||(l.links.push({source:l.nodes[e[j]-1],target:l.nodes[l.nodes.length-1],link_type:"fake",value:n,uid:generateUUID()}),4<e.length&&l.links.push({source:l.nodes[e[j]-1],target:l.nodes[e[(j+Math.floor(e.length/2))%e.length]-1],link_type:"fake",value:2*n,uid:generateUUID()}),ia=3.14159*(e.length-2)/e.length,c=2*Math.cos(1.570795-ia/2),l.links.push({source:l.nodes[e[j]-1],target:l.nodes[e[(j+2)%e.length]-1],link_type:"fake",value:c}),from_node=l.nodes[e[j]-1],"x"in from_node&&(new_x+=from_node.x,new_y+=from_node.y,coords_counted+=1));return 0<coords_counted&&(new_node.x=new_x/coords_counted,new_node.y=new_y/coords_counted,new_node.px=new_node.x,new_node.py=new_node.y),l},l.connectFakeNodes=function(){for(var e={},n=l.nodes.filter(function(e){return"middle"==e.node_type}),t=new Set,r=1;r<=l.nodes.length;r++)e[r]=[];for(r=0;r<n.length;r++)for(var o=n[r],a=0;a<o.nucs.length;a++){for(var s=o.nucs[a],i=0;i<e[s].length;i++)t.has(JSON.stringify([e[s][i].uid,o.uid].sort()))||(l.links.push({source:e[s][i],target:o,value:(e[s][i].radius+o.radius)/18,link_type:"fake_fake"}),t.add(JSON.stringify([e[s][i].uid,o.uid].sort())));e[s].push(o)}return l},l.elementsToJson=function(){pt=l.pairtable,elements=l.elements,l.nodes=[],l.links=[],elem_types={},l.elements.sort();for(var e=0;e<l.elements.length;e++)for(nucs=l.elements[e][2],j=0;j<nucs.length;j++)elem_types[nucs[j]]=l.elements[e][0];for(e=1;e<=pt[0];e++)l.nodes.push({name:l.seq[e-1],num:e,radius:6,rna:l,node_type:"nucleotide",struct_name:l.struct_name,elem_type:elem_types[e],uid:generateUUID()});for(e=1;e<=pt[0];e++)0!==pt[e]&&l.links.push({source:l.nodes[e-1],target:l.nodes[pt[e]-1],link_type:"basepair",value:1,uid:generateUUID()}),1<e&&l.links.push({source:l.nodes[e-2],target:l.nodes[e-1],link_type:"backbone",value:1,uid:generateUUID()});for(e=0;e<l.pseudoknotPairs.length;e++)l.links.push({source:l.nodes[l.pseudoknotPairs[e][0]-1],target:l.nodes[l.pseudoknotPairs[e][1]-1],link_type:"pseudoknot",value:1,uid:generateUUID()});return l.circular&&l.links.push({source:l.nodes[0],target:l.nodes[l.rnaLength-1],link_type:"backbone",value:1,uid:generateUUID()}),l},l.pt_to_elements=function(e,n,t,r){var o=[],a=[t-1],s=[r+1];if(r<t)return[];for(;0===e[t];t++)a.push(t);for(;0===e[r];r--)s.push(r);if(r<t)return a.push(t),0===n?[["e",n,a.sort(number_sort)]]:[["h",n,a.sort(number_sort)]];if(e[t]!=r){for(a.push(t);t<=r;){for(o=o.concat(l.pt_to_elements(e,n,t,e[t])),a.push(e[t]),t=e[t]+1;0===e[t]&&t<=r;t++)a.push(t);a.push(t)}return a.pop(),0<(a=a.concat(s)).length&&(0===n?o.push(["e",n,a.sort(number_sort)]):o.push(["m",n,a.sort(number_sort)])),o}for(e[t]===r&&(a.push(t),s.push(r),combined=a.concat(s),4<combined.length&&(0===n?o.push(["e",n,a.concat(s).sort(number_sort)]):o.push(["i",n,a.concat(s).sort(number_sort)]))),s=[];e[t]===r&&t<r;)s.push(t),s.push(r),t+=1,--r,n+=1;return o.push(["s",n,s.sort(number_sort)]),o.concat(l.pt_to_elements(e,n,t,r))},l.addLabels=function(e,n){if(0===arguments.length&&(e=1,n=10),1===arguments.length&&(n=10),0===n)return l;for(n<=0&&console.log("The label interval entered in invalid:",n),i=1;i<=pt[0];i++){var t,r;0==i%n&&(thisNode=l.nodes[i-1],prevVec=1==l.rnaLength?(nextVec=[thisNode.x-15,thisNode.y],[thisNode.x-15,thisNode.y]):(prevNode=1==i?l.nodes[l.rnaLength-1]:l.nodes[i-2],nextNode=i==l.rnaLength?l.nodes[0]:l.nodes[i],0!==l.pairtable[nextNode.num]&&0!==l.pairtable[prevNode.num]&&0!==l.pairtable[thisNode.num]&&(prevNode=nextNode=l.nodes[l.pairtable[thisNode.num]-1]),0===l.pairtable[thisNode.num]||0!==l.pairtable[nextNode.num]&&0!==l.pairtable[prevNode.num]?(nextVec=[nextNode.x-thisNode.x,nextNode.y-thisNode.y],[prevNode.x-thisNode.x,prevNode.y-thisNode.y]):(nextVec=[thisNode.x-nextNode.x,thisNode.y-nextNode.y],[thisNode.x-prevNode.x,thisNode.y-prevNode.y])),combinedVec=[nextVec[0]+prevVec[0],nextVec[1]+prevVec[1]],vecLength=Math.sqrt(combinedVec[0]*combinedVec[0]+combinedVec[1]*combinedVec[1]),normedVec=[combinedVec[0]/vecLength,combinedVec[1]/vecLength],offsetVec=[-15*normedVec[0],-15*normedVec[1]],t=l.nodes[i-1].x+offsetVec[0],r=l.nodes[i-1].y+offsetVec[1],new_node={name:i+e-1,num:-1,radius:6,rna:l,node_type:"label",struct_name:l.struct_name,elem_type:"l",x:t,y:r,px:t,py:r,uid:generateUUID()},new_link={source:l.nodes[i-1],target:new_node,value:1,link_type:"label_link",uid:generateUUID()},l.nodes.push(new_node),l.links.push(new_link))}return l},l.recalculateElements=function(){if(l.removePseudoknots(),l.elements=l.pt_to_elements(l.pairtable,0,1,l.dotbracket.length),l.circular&&(external_loop=l.elements.filter(function(e){if("e"==e[0])return!0}),0<external_loop.length)){eloop=external_loop[0],nucs=eloop[2].sort(number_sort),prev=nucs[0],hloop=!0,num_greater=0;for(var e=1;e<nucs.length;e++)1<nucs[e]-prev&&(num_greater+=1),prev=nucs[e];eloop[0]=1==num_greater?"h":2==num_greater?"i":"m"}return l},l.removePseudoknots=function(){return l.pseudoknotPairs=1<l.pairtable.length?rnaUtilities.removePseudoknotsFromPairtable(l.pairtable):[],l},l.addPseudoknots=function(){var e=l.pairtable,n=l.pseudoknotPairs;for(i=0;i<n.length;i++)e[n[i][0]]=n[i][1],e[n[i][1]]=n[i][0];return l.pseudoknotPairs=[],l},0<l.rnaLength&&l.recalculateElements()}function RNAUtilities(){var l=this;l.bracket_left="([{<ABCDEFGHIJKLMNOPQRSTUVWXYZ".split(""),l.bracket_right=")]}>abcdefghijklmnopqrstuvwxyz".split(""),l.inverse_brackets=function(e){for(res={},i=0;i<e.length;i++)res[e[i]]=i;return res},l.maximumMatching=function(e){var n=e[0];mm=Array(n+1);for(var t=0;t<=n;t++){mm[t]=Array(n+1);for(var r=t;r<=n;r++)mm[t][r]=0}for(var o=0,t=+n-1;0<t;t--)for(r=t+0+1;r<=n;r++){for(var o=mm[t][r-1],a=+r-1;t<=a;a--)e[a]===r&&(o=Math.max(o,(t<a?mm[t][a-1]:0)+1+(0<r-a-1?mm[a+1][r-1]:0)));mm[t][r]=o}return mm},l.backtrackMaximumMatching=function(e,n){var t=Array.apply(null,Array(e.length)).map(function(){return 0});return l.mm_bt(e,t,n,1,e.length-1),t},l.mm_bt=function(e,n,t,r,o){var a=e[r][o];if(!(o-r-1<0))if(e[r][o-1]==a)l.mm_bt(e,n,t,r,o-1);else{for(var s=+o-1;r<=s;s--)if(t[o]===s&&(r<s?e[r][s-1]:0)+(0<o-s-1?e[s+1][o-1]:0)+1==a)return n[s]=o,r<(n[o]=s)&&l.mm_bt(e,n,t,r,s-1),void l.mm_bt(e,n,t,s+1,o-1);console.log("FAILED!!!"+r+","+o+": backtracking failed!")}},l.dotbracketToPairtable=function(e){for(pt=Array.apply(null,Array(e.length+1)).map(Number.prototype.valueOf,0),pt[0]=e.length,stack={},i=0;i<l.bracket_left.length;i++)stack[i]=[];for(inverse_bracket_left=l.inverse_brackets(l.bracket_left),inverse_bracket_right=l.inverse_brackets(l.bracket_right),i=0;i<e.length;i++)if(a=e[i],ni=i+1,"."==a)pt[ni]=0;else if(a in inverse_bracket_left)stack[inverse_bracket_left[a]].push(ni);else{if(!(a in inverse_bracket_right))throw"Unknown symbol in dotbracket string";j=stack[inverse_bracket_right[a]].pop(),pt[ni]=j,pt[j]=ni}for(key in stack)if(0<stack[key].length)throw"Unmatched base at position "+stack[key][0];return pt},l.insert_into_stack=function(e,n,t){for(n=0;0<e[n].length&&e[n][e[n].length-1]<t;)n+=1;return e[n].push(t),n},l.delete_from_stack=function(e,n){for(var t=0;0===e[t].length||e[t][e[t].length-1]!=n;)t+=1;return e[t].pop(),t},l.pairtableToDotbracket=function(e){for(stack={},i=0;i<e[0];i++)stack[i]=[];for(seen={},res="",i=1;i<e[0]+1;i++){if(0!==e[i]&&e[i]in seen)throw"Invalid pairtable contains duplicate entries";seen[e[i]]=!0,res=0===e[i]?res+".":e[i]>i?res+l.bracket_left[l.insert_into_stack(stack,i,e[i])]:res+l.bracket_right[l.delete_from_stack(stack,i)]}return res},l.find_unmatched=function(e,n,t){for(var r=[],o=[],a=t,s=n;s<=t;s++)0!==e[s]&&(e[s]<n||e[s]>t)&&o.push([s,e[s]]);for(s=n;s<=a;s++){for(;0===e[s]&&s<=a;)s++;for(t=e[s];e[s]===t;)s++,t--;r=r.concat(l.find_unmatched(e,s,t))}return 0<o.length&&r.push(o),r},l.removePseudoknotsFromPairtable=function(e){for(var n=l.maximumMatching(e),n=l.backtrackMaximumMatching(n,e),t=[],r=1;r<e.length;r++)e[r]<r||n[r]==e[r]||(t.push([r,e[r]]),e[e[r]]=0,e[r]=0);return t}}void 0===String.prototype.trim&&(String.prototype.trim=function(){return String(this).replace(/^\s+|\s+$/g,"")}),molecules_to_json=function(e){for(var n={},t=[],r=[],o=0;o<e.molecules.length;o++){var a=e.molecules[o];for("rna"==a.type?(rg=new RNAGraph(a.seq,a.ss,a.header),rg.circularizeExternal=!0,rg.elementsToJson().addPositions("nucleotide",a.positions).addLabels().reinforceStems().reinforceLoops()):"protein"==a.type&&(rg=new ProteinGraph(a.header,a.size)),rg.addUids(a.uids),a=0;a<rg.nodes.length;a++)n[rg.nodes[a].uid]=rg.nodes[a];t.push(rg)}for(o=0;o<e.extra_links.length;o++)link=e.extra_links[o],link.source=n[link.source],link.target=n[link.target],link.uid=generateUUID(),r.push(link);return{graphs:t,extraLinks:r}},number_sort=function(e,n){return e-n},rnaUtilities=new RNAUtilities,simple_xy_coordinates=function(e){var n,t,r=[],o=[];console.log("pair_table",e),n=e[0];var g=Array.apply(null,Array(n+5)).map(Number.prototype.valueOf,0),m=Array.apply(null,Array(16+Math.floor(n/5))).map(Number.prototype.valueOf,0),f=Array.apply(null,Array(16+Math.floor(n/5))).map(Number.prototype.valueOf,0);lp=stk=0;var _=Math.PI/2;for(loop=function(e,n,t){var r,o,a,s,i,l,u=2,c=0,d=0;console.log("i:",e,"j:",n);var p=Array.apply(null,Array(1+2*Math.floor((n-e)/5))).map(Number.prototype.valueOf,0),h=e-1;for(n++;e!=n;)if((r=t[e])&&0!=e){for(u+=2,o=e,a=r,p[++c]=o,p[++c]=a,e=r+1,s=o,i=a,l=0;o++,a--,l++,t[o]==a;);if(r=l-2,2<=l&&(g[s+1+r]+=_,g[i-1-r]+=_,g[s]+=_,g[i]+=_,2<l))for(;1<=r;r--)g[s+r]=Math.PI,g[i-r]=Math.PI;f[++stk]=l,loop(o,a,t)}else e++,u++,d++;for(e=Math.PI*(u-2)/u,p[++c]=n,n=h<0?0:h,h=1;h<=c;h++){for(t=p[h]-n,r=0;r<=t;r++)g[n+r]+=e;if(c<h)break;n=p[++h]}m[++lp]=d},loop(0,n+1,e),m[lp]-=2,r[t=0]=100,o[0]=100,poss=[],poss.push([r[0],o[0]]),e=1;e<n;e++)r[e]=r[e-1]+15*Math.cos(t),o[e]=o[e-1]+15*Math.sin(t),poss.push([r[e],o[e]]),t+=Math.PI-g[e+1];return poss};
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<script type='text/javascript'>
var container = new FornaContainer("#rna_ss", {'applyForce': true});
var options = {'structure': '<FOLDING>',
'sequence': '<SEQUENCE>'};
container.addRNA(options.structure, options);
</script>
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