rna2d.min.js

(function(){var a=window.Rna2D||function(b){var c=function(g,f){var e=g["class"](),h=g.classOf();a.utils.attachHandlers(f,g);return f.attr("id",g.elementID).attr("class",function(k,j){return h(k,j).concat(e).join(" ")}).attr("visibility",g.visibility)};var d=function(){d.nucleotides.computeOrder();d.view.setup();var f=d.margin(),e=d3.select(d.selection()),h=function(j,i){return d3.scale.linear().domain(j()).range([0,i])};e.select("svg").remove();var g=e.append("svg").attr("width",d.width()+f.left+f.right).attr("height",d.height()+f.above+f.below);d.vis=g.append("g").attr("transform","translate("+f.left+","+f.above+")");d.xScale(h(d.xDomain,d.width()-f.right));d.yScale(h(d.yDomain,d.height()-f.above));d.components();d.coordinates(function(j){var i=d.views[d.view()].xCoord(),k=d.views[d.view()].yCoord();c(d.nucleotides,j).datum(function(m,l){m.__x=i(m,l);m.__y=k(m,l);return m}).attr("data-sequence",d.nucleotides.getSequence());return j});d.connections(function(i){var 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d=arguments;$.each(c,function(e,f){d=[f.apply(this,d)]});return d}};return b}());a.views=function(b){b.view.setup=function(){var c=a.views[b.view()];if(c===undefined){console.log("Unknown view "+b.view());return false}b.coordinates=c.coordinates;b.connections=c.connections;b.groups=c.groups;b.xDomain=c.xDomain;b.yDomain=c.yDomain;c.sideffects()};b.views={};$.each(a.views,function(e,c){c=c(b);var d=c.config;if(typeof(d)==="function"){d=d(b)}b.views[e]={};a.utils.generateAccessors(b.views[e],d);a.views[e]=c})};a.components.brush=(function(){return{config:function(b){return{enabled:true,"class":"brush",update:Object,clear:Object}},sideffects:function(b){b.brush.jmol=function(e){var c=b.nucleotides.getID(),d=$.map(e,c);return b.jmol.showNTs(d)}},actions:function(b){b.brush.enable=function(){b.vis.append("g").classed(b.brush["class"](),true).call(b.brush());b.brush.enabled(true);return 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c=b.interactions.getFamily()(f),e=b.interactions.getNTs()(f);if(b.interactions.isSymmetric()(f)){e.sort()}e.push(c);return e.join("-")},encodeID:function(c){return c},color:"black"}},sideffects:function(b){b.interactions.valid=function(){var i=b.interactions(),f=b.interactions.getID(),e=b.interactions.getNTs(),h=b.interactions.isForward(),g=[],c={},d=b.nucleotides.indexOf;$.each(i,function(j,l){var m=f(l),k=e(l);if(h(l)&&!c[m]&&k.length&&d(k[0])!==null&&d(k[1])!==null){c[m]=true;g.push(l)}});return g};b.interactions.jmol=function(f,c){var e=b.interactions.getNTs();return b.jmol.showNTs(e(f,c))}},actions:function(b){b.interactions.visible("cWW","ncWW");b.interactions.nucleotides=function(f){f=f||this;var e=d3.select(f).datum(),d=b.interactions.ntElements(e),c="#"+d.join(", #");return b.vis.selectAll(c)}}}}());a.components.jmol={config:function(b){return{divID:"jmol",appID:"jmolApplet0",tmpID:"tempJmolToolsObj",neighborhoodID:"neighborhood",numbersID:"showNtNums",stereoID:"stero",maxSize:200,overflow:Object,windowSize:400,windowBuild:function(c){c.append('<label><input type="checkbox" id="showNtNums">Numbers</label>').append('<input type="button" id="neighborhood" value="Show neighborhood">').append('<input type="button" id="stereo" value="Stereo">')}}},sideffects:function(b){b.jmol.setup=function(){var c=$("#"+b.jmol.appID()),d=$("#"+b.jmol.divID());if(c.length===0){d.html(jmolApplet(b.jmol.windowSize(),"",0));b.jmol.windowBuild()(d);d.show()}jmolScript("zap;");$.jmolTools.numModels=0;$.jmolTools.stereo=false;$.jmolTools.neighborhood=false;$("#"+b.jmol.neighborhoodID()).val("Show neighborhood");$.jmolTools.models={};$("#"+b.jmol.stereoID()).unbind();$("#"+b.jmol.neighborhoodID()).unbind();$("#"+b.jmol.numbersID()).unbind();return b.jmol};b.jmol.showNTs=function(c){b.jmol.setup();if(c.length>b.jmol.maxSize()){return b.jmol.overflow()}$("#"+b.jmol.tmpID()).remove();$("body").append("<input type='radio' id='"+b.jmol.tmpID()+"' data-coord='"+c.join(",")+"'>");$("#"+b.jmol.tmpID()).hide();$("#"+b.jmol.tmpID()).jmolTools({showNeighborhoodId:b.jmol.neighborhoodID(),showNumbersId:b.jmol.numbersID(),showStereoId:b.jmol.stereoID()}).jmolToggle();return b.jmol}}};a.components.labels={config:function(b){return{majorTickClass:"major-tick",minorTickClass:"minor-tick",labelClass:"label",width:5,fontSize:12,majorTickCount:30,minorTickCount:150,}}};a.components.motifs=(function(){return{togglable:true,config:function(b){return{classOf:function(c){return[c.id.split("_")[0]]},"class":"motif",highlightColor:function(){return"red"},click:Object,mouseover:null,mouseout:null,getID:function(c){return c.id},encodeID:function(c){return c},getNTs:function(c){return c.nts},highlight:Object,normalize:Object}},sideffects:function(b){b.motifs.jmol=function(f,c){var e=b.motifs.getNTs();return b.jmol.showNTs(e(f,c))}},actions:function(b){b.motifs.visible("IL","HL","J3");b.motifs.nucleotides=function(e){var f=d3.select(e).datum(),d=b.motifs.ntElements(f),c="#"+d.join(", #");return b.vis.selectAll(c)}}}}());a.components.nucleotides=(function(){var b={};return{togglable:true,config:function(c){return{highlightColor:function(){return"red"},"class":"nucleotide",classOf:function(f,e){return[f.sequence]},color:"black",click:Object,mouseover:null,mouseout:null,getID:function(e){return e.id},getX:function(e){return e.x},getY:function(e){return e.y},encodeID:function(d){return d},getSequence:function(e){return e.sequence},highlight:Object,normalize:Object,toggleLetters:Object}},sideffects:function(c){c.nucleotides.computeOrder=function(){var e=c.nucleotides(),d=c.nucleotides.getID();$.each(e,function(g,f){b[d(f)]=g});return 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p=i.nucleotides().length,v=i.nucleotides.indexOf,s=i.interactions.getNTs()(u).sort(function(B,z){var A=v(B),y=v(z);if(Math.abs(A-y)>p/2){return y-A}return A-y});var w=h(s[0]),x=h(s[1]),t=j(null,v(s[0]))-j(null,v(s[1])),r=Math.abs(f.innerRadius()()*Math.tan(t/2));return"M "+w.x+" "+w.y+" A "+r+","+r+" 0 0,0 "+x.x+","+x.y};var l=function(p){m=i.views.circular.radius()();o=m-i.views.circular.width();c=i.views.circular.center()();k=(2*Math.PI-i.views.circular.arcGap())/i.nucleotides().length;b=i.views.circular.arcGap()/2;j=function(r,q){return q*k+b};e=function(r,q){return(q+1)*k+b};g=d3.svg.arc().outerRadius(m).innerRadius(o).startAngle(j).endAngle(e);i.xScale(d3.scale.identity().domain([0,i.width()])).yScale(d3.scale.identity().domain([0,i.height()]));i.vis.selectAll(i.nucleotides["class"]()).append("g").data(i.nucleotides()).enter().append("svg:path").call(p).attr("d",g).attr("transform","translate("+c.x+","+c.y+")").attr("fill",i.nucleotides.color());return i};var n=function(p){f=d3.svg.arc().outerRadius(o).innerRadius(o-i.views.circular.interactionGap()).startAngle(j).endAngle(e);return i.vis.selectAll(i.interactions["class"]()).data(i.interactions.valid()).enter().append("path").call(p).attr("d",d).attr("fill","none").attr("stroke",i.interactions.color())};return{xDomain:function(){return[0,1000]},yDomain:function(){return[0,1000]},coordinates:l,connections:n,groups:function(p){return i},config:{radius:function(){return i.width()/4},width:4,arcGap:0.2,interactionGap:3,letterClass:"nucleotide-letter",xCoord:function(q,p){return g.centroid(null,p).x},yCoord:function(q,p){return g.centroid(null,p).y},center:function(){return{x:i.width()/2,y:i.height()/2}},letterID:function(p){return p.getAttribute("id")+"-letter"},letterSize:20,letterPosition:function(t){var s=d3.select(t).datum(),r=i.nucleotides.indexOf(i.nucleotides.getID()(s)),q=g.centroid(null,r),p=i.views.circular.center()();return{x:p.x+q[0],y:p.y+q[1]}},addLetters:function(q){var p=i.views.circular.letterPosition(),r=i.nucleotides.highlightColor();i.vis.selectAll(i.views.circular.letterClass()).data(q).enter().append("svg:text").attr("id",i.views.circular.letterID()).attr("class",i.views.circular.letterClass()).attr("x",function(s){return p(s).x}).attr("y",function(s){return p(s).y}).attr("font-size",i.views.circular.letterSize()).attr("pointer-events","none").text(function(s){return s.getAttribute("data-sequence")}).attr("fill",function(s){return r(s)});return i},clearLetters:function(){return i.vis.selectAll("."+i.views.circular.letterClass()).remove()}},sideffects:function(){i.nucleotides.highlight(function(r,p){var q=this,s=i.nucleotides.highlightColor();d3.select(q).style("stroke",s(q));i.views.circular.addLetters()([q]);return i.nucleotides.interactions(r,p).style("stroke",s(q))});i.nucleotides.normalize(function(r,p){var q=this;d3.select(q).style("stroke",null);i.views.circular.clearLetters()();return i.nucleotides.interactions(r,p).style("stroke",null)});i.interactions.highlight(function(s,p){var r=this,t=i.interactions.highlightColor(),q=i.interactions.nucleotides(r);d3.select(r).style("stroke",t(r));i.views.circular.addLetters()(q[0]);return q.style("stroke",t(r))});i.interactions.normalize(function(r,p){var q=this;d3.select(q).style("stroke",null);i.views.circular.clearLetters()();i.interactions.nucleotides(q).style("stroke",null);return i.interactions})}}}}());