sequenceserver 1.1.0.beta7 → 1.1.0.beta8

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA1:
-  metadata.gz: 596bc25ee4cb80b8fad1de7a63b7677f291a0743
-  data.tar.gz: bb5bda8278682fb5a79526542023d3addfce8933
+  metadata.gz: a84db1a31e7b1e1a9b89ce2a6dacaf9721c2983d
+  data.tar.gz: 16414f4af1a58ebf682213d955f18145206dc167
 SHA512:
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+  data.tar.gz: 7669b574fb3e19490857d22acdbbc1d05558b6bcae86b87a9cf1d0ad64deaf4e8c882becbb25d6e8e0eac2d7e0cd510d751daed2c0fea6ed2944de91ae6993c6

data/lib/sequenceserver/version.rb

@@ -1,4 +1,4 @@
 # Define version number.
 module SequenceServer
-  VERSION = '1.1.0.beta7'
+  VERSION = '1.1.0.beta8'
 end

data/public/js/hits_overview.js

@@ -6,7 +6,7 @@ import * as Helpers from './visualisation_helpers';
 class Graph {
 
   static name() {
-    return 'Alignments Overview';
+    return 'Matching sequences';
   }
 
   static className() {

data/public/js/report.js

@@ -941,8 +941,9 @@ var Report = React.createClass({
      */
     fetchResults: function () {
         var intervals = [200, 400, 800, 1200, 2000, 3000, 5000];
+        var component = this;
 
-        (function poll (comp) {
+        function poll () {
             $.getJSON(location.pathname + '.json')
                 .complete(function (jqXHR) {
                     switch (jqXHR.status) {
@@ -952,12 +953,12 @@ var Report = React.createClass({
                                 interval = intervals[0];
                             }
                             else {
-                                interval = intervals.shift;
+                                interval = intervals.shift();
                             }
                             setTimeout(poll, interval);
                             break;
                         case 200:
-                            comp.updateState(jqXHR.responseJSON);
+                            component.updateState(jqXHR.responseJSON);
                             break;
                         case 404:
                         case 400:
@@ -966,7 +967,9 @@ var Report = React.createClass({
                             break;
                     }
                 });
-        }(this));
+        }
+
+        poll();
     },
 
     /**

data/public/sequenceserver-report.min.js

@@ -1,7 +1,7 @@
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function(b,d,e){return a.dimChords(j,b,c,d),a.dispatch.mouseover(b,d,e)}}(this)).on("mouseout",function(a){return function(b,d,e){return a.resetChords(j,c),a.dispatch.mouseout(b,d,e)}}(this)),c.usePalette?i.attr("class",function(a){return"q"+f(a.value,c.cmin,c.cmax,c.colorPaletteSize,c.colorPaletteReverse,c.logScale)+"-"+c.colorPaletteSize}):i.attr("fill",function(a){return a.color||c.color}),i},this.render=function(a){return function(b,c,d){var f,g;if(c.select("."+d).remove(),g=c.append("g").attr("class",d).attr("z-index",a.conf.zIndex),f=a.renderChords(g,d,a.conf,a.data,b._layout,a.ratio,a.getSource,a.getTarget),null!=a.conf.tooltipContent)return e.registerTooltip(b,a,f,a.conf)}}(this),this},e.Heatmap=function(){return e.Track.call(this),this.parseData=e.parseSpanValueData,this.renderDatumContainer=function(a){return function(b,c,d,e,f){var g,h;return h=c.append("g").attr("class",f.colorPalette),g=a.renderBlock(h,e,b._layout,f)}}(this),this.renderDatum=function(a,b,c,d){return a.selectAll("tile").data(function(a){return a.values}).enter().append("path").attr("class","tile").attr("opacity",function(a){return a.opacity||b.opacity}).attr("d",d3.svg.arc().innerRadius(b.innerRadius).outerRadius(b.outerRadius).startAngle(function(a,b){return d.theta(a.start,c.blocks[a.block_id])}).endAngle(function(a,b){return d.theta(a.end,c.blocks[a.block_id])})).attr("class",function(a){return"q"+d.ratio(a.value,b.cmin,b.cmax,b.colorPaletteSize,b.colorPaletteReverse,b.logScale)+"-"+b.colorPaletteSize})},this},e.Highlight=function(){return e.Track.call(this),this.parseData=e.parseSpanStringData,this.renderDatumContainer=function(a){return function(b,c,d,e,f){var g;return g=a.renderBlock(c,e,b._layout,f)}}(this),this.renderDatum=function(a,b,c,d){return a.selectAll("tile").data(function(a){return a.values}).enter().append("path").attr("class","tile").attr("d",d3.svg.arc().innerRadius(b.innerRadius).outerRadius(b.outerRadius).startAngle(function(a,b){return d.theta(a.start,c.blocks[a.block_id])}).endAngle(function(a,b){return d.theta(a.end,c.blocks[a.block_id])})).attr("fill",function(a){return a.value||b.color}).attr("opacity",function(a){return a.opacity||b.opacity}).attr("stroke-width",function(a){return a.strokeWidth||b.strokeWidth}).attr("stroke",function(a){return a.strokeColor||b.strokeColor})},this},e.Histogram=function(){return e.Track.call(this),this.parseData=e.parseSpanValueData,this.renderDatumContainer=function(a){return function(b,c,d,e,f){var g,h;return h=c.append("g").attr("class",a.conf.colorPalette),g=a.renderBlock(h,e,b._layout,f)}}(this),this.renderDatum=function(a,b,c,e){var f;return f=a.selectAll(".bin").data(function(a){return a.values}).enter().append("path").attr("class","bin").attr("opacity",function(a){return a.opacity||b.opacity}).attr("d",d3.svg.arc().innerRadius(function(a){var c;return"in"===b.direction?(c=e.ratio(a.value,b.cmin,b.cmax,b.outerRadius-b.innerRadius,!1,b.logscale),b.outerRadius-c):b.innerRadius}).outerRadius(function(a){var c;return"out"===b.direction?(c=e.ratio(a.value,b.cmin,b.cmax,b.outerRadius-b.innerRadius,!1,b.logscale),b.innerRadius+c):b.outerRadius}).startAngle(function(a){return e.theta(a.start,c.blocks[a.block_id])}).endAngle(function(a){return e.theta(a.end,c.blocks[a.block_id])})),b.usePalette?f.attr("class",function(a){return"q"+e.ratio(a.value,b.cmin,b.cmax,b.colorPaletteSize,b.colorPaletteReverse,b.logScale)+"-"+b.colorPaletteSize}):f.attr("fill",d.color||b.color),f},this},e.Line=function(){return e.Track.call(this),this.parseData=e.parsePositionValueData,this.renderDatumContainer=function(a){return function(b,c,d,e,f){var g,h;return h=c.append("g").attr("class",d),g=a.renderBlock(h,e,b._layout,f)}}(this),this.renderDatum=function(a,b,c,d){var e;return e=d3.svg.line().x(function(a){return d.x(a,c,b)}).y(function(a){return d.y(a,c,b)}).interpolate(b.interpolation),a.append("path").datum(function(a){return a.values}).attr("class","line").attr("d",e).attr("opacity",function(a){return a.opacity||b.opacity}).attr("stroke-width",function(a){return a.thickness||b.thickness}).attr("stroke",function(a){return a.color||b.color}).attr("fill",function(a){var c,d;return d=a.fill||b.fill,c=a.fill_color||b.fill_color,d?c:"none"})},this},e.Scatter=function(){return e.Track.call(this),this.parseData=e.parsePositionValueData,this.renderDatumContainer=function(a){return function(b,c,d,e,f){var g,h;return h=c.append("g").attr("class",d),g=a.renderBlock(h,e,b._layout,f)}}(this),this.renderDatum=function(a,b,c,d){var e;return e=a.selectAll(".point").data(function(a){return a.values}).enter().append("path").attr("class","point").attr("opacity",function(a){return a.opacity||b.opacity}).attr("d",d3.svg.symbol().type(b.glyph.shape).size(b.glyph.size)).attr("transform",function(a){return function(a){return"translate("+d.x(a,c,b)+","+d.y(a,c,b)+") rotate("+360*d.theta(a.position,c.blocks[a.block_id])/(2*Math.PI)+")"}}(this)).attr("stroke",function(a){return a.glyph_strokeColor||b.glyph.strokeColor}).attr("stroke-width",function(a){return a.glyph_strokeWidth||b.glyph.strokeWidth}).attr("fill",function(a){var c,d;return d=a.glyph_fill||b.glyph.fill,c=a.glyph_color||b.glyph.color,d?c:"none"})},this},e.Stack=function(){return e.Track.call(this),this.parseData=e.parseSpanValueData,this.build=function(a,b,c,d,e){return this.loadData(c,a),this.conf=this.processConf(b,this.defaultConf,this.meta,a,this),this.buildLayers(this.data,this.conf.margin),this.applyRules(b.rules,this.data)},this.buildLayers=function(a,b){var c,d,e,f,g,h,i,j,k,l,m,n,o;for(f in a)for(c=a[f],c.values=c.values.sort(function(a,b){return a.start<b.start?-1:a.start===b.start&&a.end>b.end?-1:a.start===b.start&&a.end===b.end?0:1}),j=[],o=c.values,g=0,k=o.length;g<k;g++){for(d=o[g],n=!1,e=m=0,l=j.length;m<l;e=++m)if(i=j[e],h=i.slice(0).pop(),h.end+b<d.start){i.push(d),d.layer=e,n=!0;break}n||(d.layer=j.length),n||j.push([d])}},this.applyRules=function(a,b){var c,d,e,f,g,h,i;a=a||[],g=[];for(e in b)i=b[e],g.push(function(){var b,e;b=i.layers,e=[];for(d in b)f=b[d],e.push(function(){var b,e,g;for(g=[],b=0,e=f.length;b<e;b++)c=f[b],g.push(function(){var b,e,f;for(f=[],e=0,b=a.length;e<b;e++)h=a[e],h.condition(i.parent,c,d)?f.push(c[h.parameter]=h.value):f.push(void 0);return f}());return g}());return e}());return g},this.datumRadialPosition=function(a){return function(b){var c,d,e;return e=(a.conf.thickness+a.conf.radialMargin)*b.layer,d=e+a.conf.thickness,"out"===a.conf.direction?[a.conf.innerRadius+e,Math.min(a.conf.innerRadius+d,a.conf.outerRadius)]:"in"===a.conf.direction?[Math.max(a.conf.outerRadius-d,a.conf.innerRadius),a.conf.outerRadius-e]:"center"===a.conf.direction?(c=Math.floor((a.conf.outerRadius+a.conf.innerRadius)/2),e=(a.conf.thickness+a.conf.radialMargin)*Math.floor(b.layer/2),d=e+a.conf.thickness,b.layer%2===0?[c+e,c+d]:[c-e-a.conf.radialMargin,c-d-a.conf.radialMargin]):void 0}}(this),this.datumInnerRadius=function(a){return function(b,c,d){return a.datumRadialPosition(b,c,d)[0]}}(this),this.datumOuterRadius=function(a){return function(b,c,d){return a.datumRadialPosition(b,c,d)[1]}}(this),this.renderDatumContainer=function(a){return function(b,c,d,e,f){var g,h;return h=c.append("g").attr("class",f.colorPalette),g=a.renderBlock(h,e,b._layout,f)}}(this),this.renderDatum=function(a,b,c,d){var e;return e=a.selectAll(".tile").data(function(a){return a.values}).enter().append("path").attr("class","tile").attr("d",d3.svg.arc().innerRadius(d.datumInnerRadius).outerRadius(d.datumOuterRadius).startAngle(function(a){return d.theta(a.start,c.blocks[a.block_id])}).endAngle(function(a){return d.theta(a.end,c.blocks[a.block_id])})),e.attr("opacity",function(a){return a.opacity||b.opacity}),e.attr("stroke-width",function(a){return a.strokeWidth||b.strokeWidth}),e.attr("stroke",function(a){return a.strokeColor||b.strokeColor}),e.attr("fill",function(a){return a.color||b.color}),e.attr("class",function(a){var c;if(c=a.usePalette||b.usePalette)return"q"+d.ratio(a.value,b.cmin,b.cmax,b.colorPaletteSize,b.colorPaletteReverse,b.logScale)+"-"+b.colorPaletteSize}),e},this},e.Text=function(){return e.Track.call(this),this.parseData=e.parsePositionTextData,this.renderDatumContainer=function(a){return function(b,c,d,e,f){var g,h;return h=c.append("g").attr("class",d),g=a.renderBlock(h,e,b._layout,f)}}(this),this.renderDatum=function(a,b,c,d){var e,f,g,h;g=a.selectAll("g").data(function(a){return a.values}).enter().append("g").append("text").text(function(a){return a.value}).attr("transform",function(a){var e;return e=360*d.theta(a.position,c.blocks[a.block_id])/(2*Math.PI)-90,"rotate("+e+")translate("+b.innerRadius+",0)"}),f=b.style;for(e in f)h=f[e],g.style(e,h);return g},this},e.Track=function(){return this.build=function(a,b,c){return this.dispatch=d3.dispatch("mouseover","mouseout"),this.loadData(c,a),this.conf=this.processConf(b,this.defaultConf,this.meta,a,this),this.applyRules(b.rules,this.data)},this.loadData=function(a,b){var c,d,e,f,g,h;for(e={},g=b._layout.data,d=0,f=g.length;d<f;d++)c=g[d],e[c.id]=c.len;return h=this.parseData(a,e),this.data=h.data,this.meta=h.meta},this.processConf=function(a,b,c,d,f){var g;return a=e.mixConf(a,Object.assign({},b)),a=f.computeMinMax(a,c),0===a.innerRadius&&0===a.outerRadius&&(g=d.smartBorders(),a.innerRadius=g.in,a.outerRadius=g.out),a},this.applyRules=function(a,b){var c,d,e,f,g,h;a=a||[],f=[];for(e in b)h=b[e],f.push(function(){var b,e;b=h.values,e=[];for(d in b)c=b[d],e.push(function(){var b,e,f;for(f=[],b=0,e=a.length;b<e;b++)g=a[b],g.condition(h.key,c,d)?f.push(c[g.parameter]=g.value):f.push(void 0);return f}());return e}());return f},this.computeMinMax=function(a,b){return a.cmin="smart"===a.min?b.min:a.min,a.cmax="smart"===a.max?b.max:a.max,a},this.ratio=function(a,b,c,d,e,f){var g,h,i;return h=f?2.3:1,b===c||a===b&&!e||a===c&&e?0:a===c||a===b&&e?d-1:(g=(a-b)/(c-b),i=Math.exp(1/h*Math.log(g)),e&&(i=1-i),Math.floor(d*i))},this.render=function(a){return function(b,c,d){var f,g,h,i;return c.select("."+d).remove(),i=c.append("g").attr("class",d).attr("z-index",a.conf.zIndex),f=a.renderDatumContainer(b,i,d,a.data,a.conf),(null!=(g=a.conf.axes)?g.display:void 0)&&a.renderAxes(f,a.conf,b._layout,a.data),h=a.renderDatum(f,a.conf,b._layout,a),null!=a.conf.tooltipContent&&e.registerTooltip(b,a,h,a.conf),h.on("mouseover",function(b,c,d){return a.dispatch.mouseover(b,c,d)}),h.on("mouseout",function(b,c,d){
-return a.dispatch.mouseout(b,c,d)})}}(this),this.renderBlock=function(a,b,c,d){var e,f;return f=d.outerRadius-d.innerRadius,e=a.selectAll(".block").data(b).enter().append("g").attr("class","block").attr("transform",function(a){return"rotate("+360*c.blocks[a.key].start/(2*Math.PI)+")"}),d.backgrounds&&e.selectAll(".background").data(d.backgrounds).enter().append("path").attr("class","background").attr("fill",function(a){return a.color}).attr("opacity",function(a){return a.opacity||1}).attr("d",d3.svg.arc().innerRadius(function(a){return"in"===d.direction?d.outerRadius-f*a.start:d.innerRadius+f*a.start}).outerRadius(function(a){return"in"===d.direction?d.outerRadius-f*a.end:d.innerRadius+f*a.end}).startAngle(function(a,b,c){return 0}).endAngle(function(a,d,e){return c.blocks[b[e].key].end-c.blocks[b[e].key].start})),e},this.renderAxes=function(a,b,c,d){var e,f,g;return"pixel"===b.axes.minor.spacingType&&(e=function(){var a,c,d,e,f;for(f=[],g=a=c=b.innerRadius,d=b.outerRadius,e=b.axes.minor.spacing;e>0?a<=d:a>=d;g=a+=e)f.push(g);return f}()),f=d3.svg.arc().innerRadius(function(a){return a}).outerRadius(function(a){return a}).startAngle(0).endAngle(function(a,b,e){var f;return f=c.blocks[d[e].key],f.end-f.start}),a.selectAll(".axis").data(e).enter().append("path").attr("opacity",b.opacity).attr("class","axis").attr("d",f).attr("stroke-width",function(a,c){return c%b.axes.major.spacing===0?b.axes.major.thickness:b.axes.minor.thickness}).attr("stroke",function(a,c){return c%b.axes.major.spacing===0?b.axes.major.color:b.axes.minor.color})},this.theta=function(a,b){return a/b.len*(b.end-b.start)},this.x=function(a){return function(b,c,d){var e,f,g;return f=a.ratio(b.value,d.cmin,d.cmax,d.outerRadius-d.innerRadius,!1,d.logscale),g="in"===d.direction?d.outerRadius-f:d.innerRadius+f,e=a.theta(b.position,c.blocks[b.block_id])-Math.PI/2,g*Math.cos(e)}}(this),this.y=function(a){return function(b,c,d){var e,f,g;return f=a.ratio(b.value,d.cmin,d.cmax,d.outerRadius-d.innerRadius,!1,d.logscale),g="in"===d.direction?d.outerRadius-f:d.innerRadius+f,e=a.theta(b.position,c.blocks[b.block_id])-Math.PI/2,g*Math.sin(e)}}(this),this.ratio=function(a,b,c,d,e,f){var g,h,i;return h=f?2.3:1,b===c||a===b&&!e||a===c&&e?0:a===c||a===b&&e?d-1:(g=(a-b)/(c-b),i=Math.exp(1/h*Math.log(g)),e&&(i=1-i),Math.floor(d*i))},this},e.renderLayout=function(a,b,c){var d,f,g,h;if(f=c._layout.conf,b.select(".cs-layout").remove(),h=b.append("g").attr("class","cs-layout").attr("z-index",f.zIndex).on("click",f.onClick),d=h.selectAll("g").data(c._layout.data).enter().append("g").attr("class",function(a){return a.id}).attr("opacity",f.opacity),g=a.svg.arc().innerRadius(f.innerRadius).outerRadius(f.outerRadius).cornerRadius(f.cornerRadius).startAngle(function(a){return a.start}).endAngle(function(a){return a.end}),d.append("path").attr("d",g).attr("fill",function(a){return a.color}).attr("id",function(a){return a.id}),f.labels.display&&e.renderLayoutLabels(f,a,d),f.ticks.display)return e.renderLayoutTicks(f,h,a,c)},e.renderLayoutLabels=function(a,b,c){var d,e,f;return f=a.innerRadius+a.labels.radialOffset,e=b.svg.arc().innerRadius(f).outerRadius(f).startAngle(function(a,b){return a.start}).endAngle(function(a,b){return a.end}),c.append("path").attr("fill","none").attr("stroke","none").attr("d",e).attr("id",function(a){return"arc-label"+a.id}),d=c.append("text").attr("font-size",a.labels.size).attr("text-anchor","middle"),d.append("textPath").attr("startOffset","25%").attr("xlink:href",function(a){return"#arc-label"+a.id}).style("fill",a.labels.color).text(function(a){var b=a.end-a.start;return a.label.slice(0,Math.floor(21*b))+".."})},e.renderLayoutTicks=function(a,b,c,d){var e,f,g;return e=function(b){var d,e;d=(b.end-b.start)/b.len,b.end-b.start>1.57?e=8:b.end-b.start>.785?e=4:b.end-b.start>.3925?e=2:b.end-b.start>0&&(e=0);var f=[],g={angle:0*d+b.start,label:0};f.push(g);var h=c.scale.linear().domain([1,b.len]).range([b.start,b.end]),i=h.ticks(e).length;h.ticks(e).map(function(c,e){var g=(c*d+b.start,b.len*d+b.start,{angle:c*d+b.start,label:c/a.ticks.labelDenominator+a.ticks.labelSuffix});f.push(g)}),f.splice(i,1);var g={angle:b.len*d+b.start-.006,label:b.len/a.ticks.labelDenominator+a.ticks.labelSuffix};return f.push(g),f},f=function(b,c){return a.ticks.labels===!1?null:a.ticks.labelDisplay0===!1&&0===c?null:c%a.ticks.labelSpacing?null:0===c?b/a.ticks.labelDenominator:b/a.ticks.labelDenominator+a.ticks.labelSuffix},g=b.append("g").selectAll("g").data(d._layout.data).enter().append("g").selectAll("g").data(e).enter().append("g").attr("transform",function(b){return"rotate("+(180*b.angle/Math.PI-90)+")translate("+a.outerRadius+",0)"}),g.append("line").attr("x1",0).attr("y1",1).attr("x2",function(b,c){return a.ticks.size.major}).attr("y2",1).style("stroke",a.ticks.color),g.append("text").attr("x",8).attr("dy",".35em").attr("transform",function(a){return a.angle>Math.PI?"rotate(180)translate(-16)":null}).attr("text-anchor",function(a){return a.angle>Math.PI?"end":null}).attr("font-size",a.ticks.labelSize).style("fill",a.ticks.labelColor).text(function(a){return a.label})},e.Core.prototype.render=function(a,b){var c,d,g,h,i,j,k,l,m,n;if("undefined"==typeof a&&(h=!0,a=[]),b){d=this.tracks;for(l in d){k=d[l];for(c in k)j=k[c],i.select("."+c).remove()}}i=d3.select(this.conf.container).attr("width",this.conf.width).attr("height",this.conf.height),n=i.select(".all"),n.empty()&&(n=i.append("g").attr("class","all").attr("transform","translate("+parseInt(this.conf.width/2)+","+parseInt(this.conf.height/2)+")")),g=this.tracks;for(l in g){k=g[l];for(c in k)j=k[c],(h||f.call(a,c)>=0)&&j.render(this,n,c)}return(h||f.call(a,"layout")>=0)&&e.renderLayout(d3,n,this),m=i.selectAll(".all > g").remove(),m[0].sort(function(a,b){return parseInt(a.getAttribute("z-index"))<parseInt(b.getAttribute("z-index"))?-1:parseInt(a.getAttribute("z-index"))>parseInt(b.getAttribute("z-index"))?1:0}),i.select(".all").selectAll("g").data(m[0]).enter().append(function(a){return a}),this},e.Core.prototype.defaultConf={width:700,height:700,container:"circos",defaultTrackWidth:10},e.Layout.prototype.defaultConf={innerRadius:250,outerRadius:300,cornerRadius:5,gap:.04,opacity:1,labels:{position:"center",display:!0,size:14,color:"#000",radialOffset:20},ticks:{display:!0,color:"grey",spacing:1e7,labels:!0,labelSpacing:10,labelSuffix:"Mb",labelDenominator:1e6,labelDisplay0:!0,labelSize:10,labelColor:"#000",labelFont:"default",majorSpacing:5,size:{minor:2,major:5}},onClick:null,onMouseOver:null,zIndex:100},e.axes={display:!1,minor:{spacing:5,spacingType:"pixel",color:"#d3d3d3",thickness:2},major:{spacing:5,color:"#000000",thickness:2}},e.Heatmap.prototype.defaultConf={innerRadius:0,outerRadius:0,min:"smart",max:"smart",colorPalette:"YlGnBu",colorPaletteSize:9,colorPaletteReverse:!1,logScale:!1,rules:[],backgrounds:[],zIndex:1,opacity:1,tooltipContent:null},e.Histogram.prototype.defaultConf={innerRadius:0,outerRadius:0,min:"smart",max:"smart",direction:"out",colorPaletteSize:9,colorPalette:"YlGnBu",usePalette:!0,colorPaletteReverse:!1,color:"#fd6a62",logScale:!1,axes:e.axes,rules:[],backgrounds:[],zIndex:1,opacity:1,tooltipContent:null},e.Chord.prototype.defaultConf={colorPaletteSize:9,colorPalette:"PuBuGn",usePalette:!0,colorPaletteReverse:!1,color:"#fd6a62",opacity:.7,min:"smart",max:"smart",logScale:!1,rules:[],backgrounds:[],zIndex:1,tooltipContent:null},e.Scatter.prototype.defaultConf={innerRadius:0,outerRadius:0,min:"smart",max:"smart",direction:"out",logScale:!1,glyph:{color:"#fd6a62",fill:!0,size:15,shape:"circle",strokeColor:"#d3d3d3",strokeWidth:2},axes:e.axes,rules:[],backgrounds:[],zIndex:1,opacity:1,tooltipContent:null},e.Line.prototype.defaultConf={innerRadius:0,outerRadius:0,min:"smart",max:"smart",direction:"out",logScale:!1,color:"#fd6a62",fill:!0,fill_color:"#d3d3d3",thickness:2,max_gap:1e7,interpolation:"linear",axes:e.axes,rules:[],backgrounds:[],zIndex:1,opacity:1,tooltipContent:null},e.Stack.prototype.defaultConf={innerRadius:0,outerRadius:0,colorPaletteSize:9,colorPalette:"PuBuGn",usePalette:!0,colorPaletteReverse:!1,color:"#fd6a62",min:"smart",max:"smart",direction:"out",logScale:!1,color:"#fd6a62",thickness:10,radialMargin:2,margin:2,strokeWidth:1,strokeColor:"#000000",axes:e.axes,rules:[],backgrounds:[],zIndex:1,opacity:1,tooltipContent:null},e.Highlight.prototype.defaultConf={innerRadius:0,outerRadius:0,defaultColor:"#fd6a62",opacity:.5,rules:[],zIndex:101,strokeColor:"#d3d3d3",strokeWidth:0,tooltipContent:null},e.Text.prototype.defaultConf={innerRadius:0,outerRadius:0,rules:[],backgrounds:[],zIndex:1,style:{},tooltipContent:null},e.registerTooltip=function(a,b,c,d){return b.tip=d3.tip().direction("s").offset([20,0]).html(d.tooltipContent),c.call(b.tip),b.dispatch.on("mouseover",function(a,c,d){return b.tip.attr("class","d3-tip appear").show(a)}),b.dispatch.on("mouseout",function(a,c,d){return b.tip.attr("class","d3-tip").show(a),b.tip.hide()})}}),c.registerDynamic("c",["b"],!0,function(a,b,c){this||self;c.exports=a("b")}),c.register("d",["10","11","12","13","e","f","c"],function(a){var b,c,d,e,f,g,h,i,j;return{setters:[function(a){b=a.default},function(a){c=a},function(a){d=a.default},function(a){e=a.default},function(a){f=a.default},function(a){g=a.default},function(a){h=a.default}],execute:function(){i=function(){function a(b,d){e(this,a),this.queries=d.queries,this.svgContainer=b,this.seq_type=c.get_seq_type(d.program),this.initiate()}return d(a,null,[{key:"name",value:function(){return"Circos"}},{key:"className",value:function(){return"circos-distribution collapse"}},{key:"collapseId",value:function(a){return"circos-collapse"}},{key:"dataName",value:function(a){return"Circos-visualisation"}}]),d(a,[{key:"initiate",value:function(){this.width=this.svgContainer.width(),this.height=600,this.innerRadius=200,this.outerRadius=230,this.query_arr=[],this.hit_arr=[],this.layout_arr=[],this.chords_arr=[],this.hsp_count=50,this.denominator=100,this.spacing=20,this.labelSpacing=10;var a={amino_acid:"aa",nucleic_acid:"bp"};this.construct_layout(),this.iterator_for_edits(),this.hit_arr=g.uniq(this.hit_arr),this.handle_spacing();var b=f.formatPrefix(this.max_length);this.suffix=" "+b.symbol+a[this.seq_type.subject_seq_type],"k"==b.symbol?this.denominator=1e3:"M"==b.symbol?(this.denominator=1e6,this.spacing=1e6,this.labelSpacing=2e5):"g"==b.symbol&&(this.denominator=1e9),f.select(this.svgContainer[0]).insert("svg",":first-child").attr("class","circosContainer"),this.create_instance(this.svgContainer,this.width,this.height),this.chords_arr.length&&this.layout_arr.length?this.instance_render():this.render_error(),this.setupTooltip()}},{key:"iterator_for_edits",value:function(){this.max_length=this.calculate_max_length(),this.hit_arr.length>10&&this.complex_layout_edits()}},{key:"construct_layout",value:function(){var a=0,b=32,c=this.queries.length,d=Math.min(b/2,c),e=(b-d)/d;this.new_layout=[],this.data=g.map(this.queries,g.bind(function(b){if(a<d){var c=b.id,f=b.length,h={len:f,color:"#8dd3c7",label:c,id:"Query_"+this.clean_id(b.id),ori_id:c};this.layout_arr.push(h);g.map(b.hits,g.bind(function(a){if(a.number<e){g.map(a.hsps,g.bind(function(c){if(g.indexOf(this.hit_arr,a.id)==-1){var d=a.id,e=a.length;this.hit_arr.push(a.id);var f={len:e,color:"#80b1d3",label:d,id:"Hit_"+this.clean_id(a.id),ori_id:d};this.layout_arr.push(f)}var h=["Query_"+this.clean_id(b.id),c.qstart,c.qend,"Hit_"+this.clean_id(a.id),c.sstart,c.send,a.number,c];return this.chords_arr.push(h),c},this));return a}},this))}return this.query_arr.push(b.id),b},this))}},{key:"rearrange_new_layout",value:function(){g.each(this.new_layout,g.bind(function(a){var b=a.id.slice(0,3);"Que"==b&&this.layout_arr.push(a)},this)),g.each(this.new_layout,g.bind(function(a){var b=a.id.slice(0,3);"Hit"==b&&this.layout_arr.push(a)},this))}},{key:"complex_layout_edits",value:function(){this.delete_from_layout=[],this.delete_from_chords=[],g.each(this.layout_arr,g.bind(function(a,b){var c=(a.len/this.max_length).toFixed(3);a.label;c<.1&&"Que"!=a.id.slice(0,3)&&(this.delete_from_layout.push(a),this.hit_arr.slice(g.indexOf(this.hit_arr,a.label),1))},this))}},{key:"check_in_chords_arr",value:function(a,b,c){var d=0;g.each(this.chords_arr,g.bind(function(c){"Que"==b&&c[0]!=a&&d++},this)),d==this.chords_arr.length&&(console.log("no record found "+a),this.delete_arr.push(c))}},{key:"find_index_of_hit",value:function(a){var b;return g.each(this.queries,g.bind(function(c){g.each(c.hits,g.bind(function(c){var d="Hit_"+this.clean_id(c.id);a==d&&(b=c.id)},this))},this)),g.indexOf(this.layout_arr,b)}},{key:"edit_labels",value:function(){console.log("label edits"),g.each(this.layout_arr,g.bind(function(a){var b=(a.len/this.max_length).toFixed(3),c=a.label;b<.41?a.label="..":c.length>10?a.label=c.slice(0,2)+"...":a.label=a.ori_id},this))}},{key:"calculate_multipliers",value:function(){var a=0,b=0;g.each(this.query_arr,g.bind(function(b){g.each(this.data,g.bind(function(c){b==c.id&&(a+=c.length)},this))},this)),g.each(this.data,g.bind(function(a){g.each(a.hits,g.bind(function(a){var c=g.indexOf(this.hit_arr,a.id);c>=0&&(b+=a.length)},this))},this));var c=(a+b)/2;console.log("mid sum "+c+" hit_sum "+b+" query_sum "+a),this.query_multiplier=(c/a).toFixed(3),this.hit_multiplier=(c/b).toFixed(3),console.log("query "+this.query_multiplier+" hit "+this.hit_multiplier)}},{key:"handle_spacing",value:function(){this.max_length>16e3?this.spacing=200:this.max_length>12e3?this.spacing=150:this.max_length>8e3?this.spacing=100:this.max_length>4e3?this.spacing=75:this.max_length>1800&&(this.spacing=50)}},{key:"calculate_max_length",value:function(){var a=0;return g.each(this.layout_arr,function(b){a<b.len&&(a=b.len)}),a}},{key:"clean_id",value:function(a){return a.replace(/[^a-zA-Z0-9]/g,"")}},{key:"create_instance",value:function(a,b,c){this.instance=new h({container:".circosContainer",width:b,height:c}),this.chord_layout(),this.instance_layout()}},{key:"chord_layout",value:function(){return this.chords_arr.length>32?this.paletteSize=32:this.paletteSize=this.chords_arr.length,{usePalette:!0,colorPaletteSize:this.paletteSize,colorPalette:"RdYlBu",opacity:.85}}},{key:"instance_layout",value:function(){return{innerRadius:this.innerRadius,outerRadius:this.outerRadius,cornerRadius:1,labels:{display:!0,size:"10px",radialOffset:10},ticks:{display:!0,spacing:this.spacing,labelSpacing:this.labelSpacing,labelDenominator:this.denominator,labelSuffix:this.suffix,labelSize:"10px",majorSpacing:this.labelSpacing,size:{minor:0,major:4}}}}},{key:"instance_render",value:function(){this.instance.layout(this.instance_layout(),this.layout_arr),this.instance.chord("chord1",this.chord_layout(),this.chords_arr),this.instance.render()}},{key:"render_error",value:function(){this.svgContainer.find("svg").remove(),this.svg=f.select(this.svgContainer[0]).insert("svg",":first-child").attr("width",this.svgContainer.width()).attr("height",this.svgContainer.height()).append("g").attr("class","circos-error").attr("transform","translate("+this.svgContainer.width()/2+","+this.svgContainer.height()/2+")").append("text").attr("text-anchor","start").attr("dy","-0.25em").attr("x",-175).style("font-size","14px").text("Circos looks great with less than 16 queries")}},{key:"layoutReset",value:function(){this.layoutHide=[],g.each(this.layout_arr,function(a){$("."+a.id).css("opacity",1)})}},{key:"chordsReset",value:function(){this.chordsHide=[],g.each(this.chords_arr,function(a){var b=a[1]+a[2],c=a[4]+a[5];$("#"+a[0]+"_"+b+"_"+a[3]+"_"+c).show()})}},{key:"chordsCheck",value:function(a,b){g.each(this.chords_arr,g.bind(function(c,d){"Que"==b&&c[0]==a&&(this.chordsHide.push(d),this.layoutHide.push(c[3])),"Hit"==b&&c[3]==a&&(this.chordsHide.push(d),this.layoutHide.push(c[0]))},this))}},{key:"chordsClean",value:function(){g.each(this.chords_arr,g.bind(function(a,b){if(g.indexOf(this.chordsHide,b)==-1){var c=a[1]+a[2],d=a[4]+a[5];$("#"+a[0]+"_"+c+"_"+a[3]+"_"+d).hide()}},this))}},{key:"layoutClean",value:function(){g.each(this.layout_arr,g.bind(function(a,b){g.indexOf(this.layoutHide,a.id)==-1&&$("."+a.id).css("opacity",.1)},this))}},{key:"setupTooltip",value:function(){var a={};$(".circos-distribution").on("click",g.bind(function(b){b.stopPropagation(),this.layoutReset(),this.chordsReset(),a={}},this)),g.each(this.query_arr,g.bind(function(b,c){this.chordsHide=[],this.layoutHide=[],b&&$(".circos-distribution .Query_"+this.clean_id(b)).attr("data-toggle","tooltip").attr("title",b).on("click",g.bind(function(d){if(d.stopPropagation(),a[c]!=b){a[c]=b;var e="Query_"+this.clean_id(b);this.layoutHide.push(e),this.chordsCheck(e,"Que"),this.chordsClean(),this.layoutClean()}else a[c]=0,this.layoutReset(),this.chordsReset()},this))},this)),g.each(this.hit_arr,g.bind(function(b,c){this.chordsHide=[],this.layoutHide=[],b&&$(".circos-distribution .Hit_"+this.clean_id(b)).attr("data-toggle","tooltip").attr("title",b).on("click",g.bind(function(d){if(d.stopPropagation(),a[c]!=b){a[c]=b;var e="Hit_"+this.clean_id(b);this.layoutHide.push(e),this.chordsCheck(e,"Hit"),this.chordsClean(),this.layoutClean()}else a[c]=0,this.layoutReset(),this.chordsReset()},this))},this)),$('[data-toggle="tooltip"]').tooltip({placement:"top",container:"body",html:"true",delay:0,"white-space":"nowrap"})}},{key:"ratioCalculate",value:function(a,b,c,d,e,f){var g,h,i;return h=f?2.3:1,b===c||a===b&&!e||a===c&&e?0:a===c||a===b&&e?d-1:(g=(a-b)/(c-b),i=Math.exp(1/h*Math.log(g)),e&&(i=1-i),Math.floor(d*i))}},{key:"drawLegend",value:function(){this.ratioHSP=[],g.each(this.chords_arr,g.bind(function(a){var b={number:a[6],evalue:a[7].evalue};this.ratioHSP.push(b)},this));var a=f.min(this.ratioHSP,function(a){return a.number}),b=f.max(this.ratioHSP,function(a){return a.number});console.log("chords_arr "+this.chords_arr.length),console.log("ratioHSP test "+this.ratioHSP.length),console.log("paletteSize "+this.paletteSize),console.log("min "+a+" max "+b),this.legend=f.select(this.svgContainer[0]).insert("svg",":first-child").attr("height",20).attr("width",30*this.ratioHSP.length).attr("transform","translate(10, 10)").append("g").attr("class","RdYlBu").attr("transform","translate(10, 0)");this.legend.selectAll(".bar").data(this.ratioHSP).enter().append("g").attr("class","g").attr("transform",function(a,b){return"translate("+30*b+",0)"}).append("rect").attr("class",g.bind(function(c,d){var e=this.ratioCalculate(c.number,a,b,this.paletteSize,!1,!1);return console.log("calc ratio "+e),"q"+e+"-"+this.paletteSize},this)).attr("data-toggle","tooltip").attr("title",function(a){return a.evalue}).attr("x",1).attr("width",30).attr("height",20),f.scale.linear().domain([0,250]).range([0,100])}}]),a}(),j=b(i),a("default",j)}}}),c.register("14",["10","11","12","13","e","f"],function(a){var b,c,d,e,f,g,h,i;return{setters:[function(a){b=a.default},function(a){c=a},function(a){d=a.default},function(a){e=a.default},function(a){f=a.default},function(a){g=a.default}],execute:function(){h=function(){function a(b,c){e(this,a),this.svg_container=b,$queryDiv=b.parents(".resultn"),hits=this.extractData(c.query.hits,c.query.number),this.graphIt($queryDiv,b,0,20,null,hits)}return d(a,null,[{key:"name",value:function(){return"Alignments Overview"}},{key:"className",value:function(){return"alignment-overview"}},{key:"collapseId",value:function(a){return"alignment_"+a.query.number}},{key:"dataName",value:function(a){return"Alignment-Overview-"+a.query.id}}]),d(a,[{key:"extractData",value:function(a,b){var c=[];return a.map(function(a){var d=[],e=a.hsps;g.each(e,function(c){var e={};e.hspEvalue=c.evalue,e.hspStart=c.qstart,e.hspEnd=c.qend,e.hspFrame=c.sframe,e.hspId="Query_"+b+"_hit_"+a.number+"_hsp_"+c.number,d.push(e)}),d.hitId=a.id,d.hitDef="Query_"+b+"_hit_"+a.number,d.hitEvalue=a.evalue,c.push(d)}),c}},{key:"setupTooltip",value:function(){this.svg_container.find('[data-toggle="tooltip"]').tooltip({placement:"top",container:"body",html:"true",delay:0,"white-space":"nowrap"})}},{key:"setupClick",value:function(a){$("a",a).click(function(a){a.preventDefault(),a.stopPropagation(),window.location.hash=$(this).attr("href")})}},{key:"graphControls",value:function(a,b,c,d,e){var f,h,i,j,k=20,l=function(){f=e.length,h=a.find(".ghit > g").length},m=function(a,b){b.append($("<button/>").addClass("btn btn-link more").attr("type","button").attr("data-parent-query",a.attr("id")).html("View More&nbsp;").append($("<i/>").html("&nbsp;&nbsp;").addClass("fa fa-angle-double-down")),$("<button/>").addClass("btn btn-link less").attr("type","button").attr("data-parent-query",a.attr("id")).html("View Less&nbsp;").append($("<i/>").html("&nbsp;&nbsp;").addClass("fa fa-angle-double-up"))),i=$(".less",b),j=$(".more",b)},n=function(){l(),f===k||h<k?(i.hide(),j.hide()):h===f?(j.hide(),i.show()):h===k?(i.hide(),j.show()):(i.show(),j.show())};c===!0&&(m(a,b),n()),j.on("click",g.bind(function(c){l(),this.graphIt(a,b,h,k,d,e),n(),this.setupTooltip(),c.stopPropagation()},this)),i.on("click",g.bind(function(c){l();var f=h-k;f>=k?(this.graphIt(a,b,h,-k,d,e),n()):0!==f&&(this.graphIt(a,b,h,k-h,d,e),n()),this.setupTooltip(),c.stopPropagation()},this))}},{key:"drawLegend",value:function(a,b,c,d,e){var f=a.append("g").attr("transform","translate(0,"+(d-1.88*b.margin)+")");f.append("rect").attr("x",7*(c-2*b.margin)/10).attr("width",2*(c-4*b.margin)/10).attr("height",b.legend).attr("fill","url(#legend-grad)"),f.append("text").attr("class"," legend-text").attr("transform","translate(0, "+b.legend+")").attr("x",6*(c-2*b.margin)/10-b.margin/2).text("Weaker hits"),f.append("text").attr("class"," legend-text").attr("transform","translate(0, "+b.legend+")").attr("x",9*(c-2*b.margin)/10+b.margin/2).text("Stronger hits"),a.append("linearGradient").attr("id","legend-grad").selectAll("stop").data([{offset:"0%",color:"#ccc"},{offset:"50%",color:"#888"},{offset:"100%",color:"#000"}]).enter().append("stop").attr("offset",function(a){return a.offset}).attr("stop-color",function(a){return a.color})}},{key:"graphIt",value:function(a,b,d,e,g,h){var i={barHeight:2,barPadding:1,legend:5,margin:20},j=$.extend(i,g),k=h.slice(0,d+e);if(k.length<1)return!1;0!==d&&b.find("svg").remove();var l=a.data().queryLen,m=a.attr("id"),n=b.width(),o=k.length*(j.barHeight+j.barPadding)+2*j.legend+5*j.margin,p={blastn:"nucleic_acid",blastp:"amino_acid",blastx:"nucleic_acid",tblastx:"nucleic_acid",tblastn:"amino_acid"},q=f.select(b[0]).selectAll("svg").data([k]).enter().insert("svg",":first-child").attr("width",n).attr("height",o).append("g").attr("transform","translate("+j.margin/2+", "+1.5*j.margin+")"),r=f.scale.linear().range([0,n-j.margin]);r.domain([1,l]);var s=a.data().algorithm,t=c.tick_formatter(r,p[s]),u=r.ticks(11);u.pop();var v=f.svg.axis().scale(r).orient("top").tickValues(u.concat([1,l])).tickFormat(t),w=q.append("g").attr("transform","translate(0, "+j.margin+")").append("g").attr("class","x axis").call(v);w.selectAll("text").attr("x","25px").attr("y","2px").attr("transform","rotate(-90)");var x=f.scale.ordinal().rangeBands([0,o-3*j.margin-2*j.legend],.3);x.domain(k.map(function(a){return a.hitId}));var y=f.scale.log().domain([f.min([1e-5,f.min(k.map(function(a){if(0!==parseFloat(a.hitEvalue))return a.hitEvalue}))]),f.max(k.map(function(a){return a.hitEvalue}))]).range([40,150]);q.append("g").attr("class","ghit").attr("transform","translate(0, "+1.65*(j.margin-j.legend)+")").selectAll(".hits").data(k).enter().append("g").each(function(a,b){f.select(this).selectAll(".hsp").data(a).enter().append("a").each(function(d,e){var g=x(a.hitId)+j.barHeight/2,h=f.rgb(y(d.hspEvalue),y(d.hspEvalue),y(d.hspEvalue));e+1<a.length&&(a[e].hspEnd<=a[e+1].hspStart?f.select(this.parentNode).append("line").attr("x1",r(a[e].hspEnd)).attr("y1",g).attr("x2",r(a[e+1].hspStart)).attr("y2",g).attr("stroke",h):a[e].hspStart>a[e+1].hspEnd&&f.select(this.parentNode).append("line").attr("x1",r(a[e+1].hspEnd)).attr("y1",g).attr("x2",r(a[e].hspStart)).attr("y2",g).attr("stroke",h)),f.select(this).attr("xlink:href","#"+m+"_hit_"+(b+1)).append("rect").attr("data-toggle","tooltip").attr("title",a.hitId+"<br><strong>E value:</strong> "+c.prettify_evalue(d.hspEvalue)).attr("class","bar").attr("x",function(a){return r(a.hspStart)}).attr("y",x(a.hitId)).attr("width",function(a){return r(a.hspEnd-a.hspStart+1)}).attr("height",j.barHeight).attr("fill",f.rgb(h))})}),k.length>1&&this.drawLegend(q,j,n,o,h),0===d&&this.graphControls(a,b,!0,g,h),this.setupTooltip(),this.setupClick(b)}}]),a}(),i=b(h),a("default",i)}}}),c.register("15",["10","11","12","13","e","f"],function(a){var b,c,d,e,f,g,h,i;return{setters:[function(a){b=a.default},function(a){c=a},function(a){d=a.default},function(a){e=a.default},function(a){f=a.default},function(a){g=a.default}],execute:function(){h=function(){function a(b,d){e(this,a),this.query=d.query,this._seq_type=c.get_seq_type(d.algorithm),this.svg_container=b,this._margin={top:30,right:25,bottom:55,left:12.5},this.initiate(b.width(),b.height())}return d(a,null,[{key:"name",value:function(){return"Length distribution of hits"}},{key:"className",value:function(){return"length-distribution"}},{key:"collapseId",value:function(a){return"length_"+a.query.number}},{key:"dataName",value:function(a){return"length-distribution-"+a.query.id}}]),d(a,[{key:"initiate",value:function(a,b){this._width=a-this._margin.left-this._margin.right,this._height=b-this._margin.top-this._margin.bottom,this.svg=f.select(this.svg_container[0]).insert("svg",":first-child").attr("width",this._width+this._margin.right+this._margin.left).attr("height",this._height+this._margin.top+this._margin.bottom).append("g").attr("transform","translate("+this._margin.left+","+this._margin.top+")"),this.hit_lengths(),this.define_scale_and_bins(),this.update_data(),this.draw()}},{key:"draw",value:function(){this.draw_rectangles(),this.draw_query_line(),this.draw_axes(),this.setupTooltip()}},{key:"define_scale_and_bins",value:function(){this._scale_x=f.scale.linear().domain([0,1.05*f.max([this.query.length,f.max(this._data)])]).range([0,this._width]),this._bins=f.layout.histogram().range(this._scale_x.domain()).bins(this._scale_x.ticks(50))(this._data),this._scale_y=f.scale.linear().domain([0,f.max(this._bins,function(a){return a.length})]).range([this._height,0])}},{key:"hit_lengths",value:function(){this._data=g.map(this.query.hits,g.iteratee("length"))}},{key:"setupTooltip",value:function(){this.svg_container.find('[data-toggle="tooltip"]').tooltip({placement:"top",container:"body",html:"true",delay:0,"white-space":"nowrap"})}},{key:"setupResponsiveness",value:function(){var a=$(window).width();console.log("cureent "+a);var b=g.debounce(g.bind(function(){a!=$(window).width()&&(console.log("redraw initiated "+this._height),this.draw(),a=$(window).width())},this),125);$(window).resize(b)}},{key:"tick_formatter",value:function(a){var b=this._scale_x.ticks(),c=f.format(".1f"),d=f.formatPrefix(b[b.length-1]),e={amino_acid:"aa",nucleic_acid:"bp"};return function(f){if(0!==f)return g.indexOf(b,f)>=0?"aa"==e[a]?f+" "+e[a]:c(d.scale(f))+" "+d.symbol+e[a]:void 0}}},{key:"update_data",value:function(){var a=this,b=[];this._bins.map(function(d){var e=[];d.reverse();var f=d.length;d.map(function(b,h){var i=d.length-(h+1),j=g.findIndex(a.query.hits,{length:b}),k={value:b,id:a.query.hits[j].id,evalue:a.query.hits[j].evalue,url:"#Query_"+a.query.number+"_hit_"+a.query.hits[j].number,y0:f,y1:f+=i-f,color:c.get_colors_for_evalue(a.query.hits[j].evalue,a.query.hits)};e.push(k)});var h={data:e,x:d.x,dx:d.dx,length:d.length};b.push(h)}),this._update_data=b}},{key:"draw_rectangles",value:function(){var a=this,b=this.svg.selectAll(".bar").data(this._update_data).enter().append("g").attr("class","g").attr("transform",function(b){return"translate("+(a._scale_x(b.x)+a._margin.left)+",0)"});b.selectAll("rect").data(function(a){return a.data}).enter().append("a").attr("xlink:href",function(a){return a.url}).append("rect").attr("class","bar").attr("data-toggle","tooltip").attr("title",function(a){return a.id+" <br>E Value: "+c.prettify_evalue(a.evalue)+"<br>Length: "+a.value}).attr("x",1).attr("y",function(b){return a._scale_y(b.y0)}).attr("width",a._scale_x(this._bins[1].x)-a._scale_x(this._bins[0].x)-1).attr("height",function(b){return a._scale_y(b.y1)-a._scale_y(b.y0)}).attr("fill",function(a){return a.color})}},{key:"draw_query_line",value:function(){var a=this.svg.append("g").attr("class","query_line").attr("transform","translate("+(this._margin.left+this._scale_x(this.query.length))+",0)");a.append("rect").attr("x",1).attr("class","bar").attr("width",4).attr("height",this._height).style("fill","rgb(95,122,183)"),a.append("text").attr("dy","0.75em").attr("y",-10).attr("x",2).attr("text-anchor","start").text("Query").style("fill","#000").attr("transform","rotate(-45)")}},{key:"draw_axes",value:function(){var a,b;b=this._scale_y.ticks().length,a=b>=8?8:b;var c=this.tick_formatter(this._seq_type.subject_seq_type),d=f.svg.axis().scale(this._scale_x).orient("bottom").ticks(50).tickFormat(c),e=f.svg.axis().scale(this._scale_y).orient("left").tickValues(this._scale_y.ticks(a)).tickFormat(function(a){if(Math.floor(a)==a)return a}),h=this._scale_y.ticks();for(var i in h)if(h[i]%1!=0){e.tickValues(f.range(0,f.max(this._bins,function(a){return a.length})+1));break}var j=this,k=this.svg.append("g").attr("class","axis axis--x").attr("transform","translate("+this._margin.left+","+this._height+")").call(d);k.selectAll("line").attr("y2",function(a){var b=j._scale_x.ticks();return g.indexOf(b,a)>=0?7:4}),k.selectAll("text").style("text-anchor","end").attr("x","-8px").attr("y","3px").attr("dy","0").attr("transform","rotate(-90)");this.svg.append("g").attr("class","axis axis--y").attr("transform","translate("+this._margin.left+",0)").call(e)}}]),a}(),i=b(h),a("default",i)}}}),c.registerDynamic("16",[],!1,function(a,b,d){var e=c.get("@@global-helpers").prepareGlobal(d.id,"d3",null);return function(a){"format global";"exports d3";!function(){function a(a){return a&&(a.ownerDocument||a.document||a).documentElement}function b(a){return a&&(a.ownerDocument&&a.ownerDocument.defaultView||a.document&&a||a.defaultView)}function c(a,b){return a<b?-1:a>b?1:a>=b?0:NaN}function d(a){return null===a?NaN:+a}function e(a){return!isNaN(a)}function g(a){return{left:function(b,c,d,e){for(arguments.length<3&&(d=0),arguments.length<4&&(e=b.length);d<e;){var f=d+e>>>1;a(b[f],c)<0?d=f+1:e=f}return d},right:function(b,c,d,e){for(arguments.length<3&&(d=0),arguments.length<4&&(e=b.length);d<e;){var f=d+e>>>1;a(b[f],c)>0?e=f:d=f+1}return d}}}function h(a){return a.length}function i(a){for(var b=1;a*b%1;)b*=10;return b}function j(a,b){for(var c in b)Object.defineProperty(a.prototype,c,{value:b[c],enumerable:!1})}function k(){this._=Object.create(null)}function l(a){return(a+="")===ng||a[0]===og?og+a:a}function 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a,b=cg.event;a=b.sourceEvent;)b=a;return b}function B(a){for(var b=new x,c=0,d=arguments.length;++c<d;)b[arguments[c]]=y(b);return b.of=function(c,d){return function(e){try{var f=e.sourceEvent=cg.event;e.target=a,
+return a.dispatch.mouseout(b,c,d)})}}(this),this.renderBlock=function(a,b,c,d){var e,f;return f=d.outerRadius-d.innerRadius,e=a.selectAll(".block").data(b).enter().append("g").attr("class","block").attr("transform",function(a){return"rotate("+360*c.blocks[a.key].start/(2*Math.PI)+")"}),d.backgrounds&&e.selectAll(".background").data(d.backgrounds).enter().append("path").attr("class","background").attr("fill",function(a){return a.color}).attr("opacity",function(a){return a.opacity||1}).attr("d",d3.svg.arc().innerRadius(function(a){return"in"===d.direction?d.outerRadius-f*a.start:d.innerRadius+f*a.start}).outerRadius(function(a){return"in"===d.direction?d.outerRadius-f*a.end:d.innerRadius+f*a.end}).startAngle(function(a,b,c){return 0}).endAngle(function(a,d,e){return c.blocks[b[e].key].end-c.blocks[b[e].key].start})),e},this.renderAxes=function(a,b,c,d){var e,f,g;return"pixel"===b.axes.minor.spacingType&&(e=function(){var a,c,d,e,f;for(f=[],g=a=c=b.innerRadius,d=b.outerRadius,e=b.axes.minor.spacing;e>0?a<=d:a>=d;g=a+=e)f.push(g);return f}()),f=d3.svg.arc().innerRadius(function(a){return a}).outerRadius(function(a){return a}).startAngle(0).endAngle(function(a,b,e){var f;return f=c.blocks[d[e].key],f.end-f.start}),a.selectAll(".axis").data(e).enter().append("path").attr("opacity",b.opacity).attr("class","axis").attr("d",f).attr("stroke-width",function(a,c){return c%b.axes.major.spacing===0?b.axes.major.thickness:b.axes.minor.thickness}).attr("stroke",function(a,c){return c%b.axes.major.spacing===0?b.axes.major.color:b.axes.minor.color})},this.theta=function(a,b){return a/b.len*(b.end-b.start)},this.x=function(a){return function(b,c,d){var e,f,g;return f=a.ratio(b.value,d.cmin,d.cmax,d.outerRadius-d.innerRadius,!1,d.logscale),g="in"===d.direction?d.outerRadius-f:d.innerRadius+f,e=a.theta(b.position,c.blocks[b.block_id])-Math.PI/2,g*Math.cos(e)}}(this),this.y=function(a){return function(b,c,d){var e,f,g;return f=a.ratio(b.value,d.cmin,d.cmax,d.outerRadius-d.innerRadius,!1,d.logscale),g="in"===d.direction?d.outerRadius-f:d.innerRadius+f,e=a.theta(b.position,c.blocks[b.block_id])-Math.PI/2,g*Math.sin(e)}}(this),this.ratio=function(a,b,c,d,e,f){var g,h,i;return h=f?2.3:1,b===c||a===b&&!e||a===c&&e?0:a===c||a===b&&e?d-1:(g=(a-b)/(c-b),i=Math.exp(1/h*Math.log(g)),e&&(i=1-i),Math.floor(d*i))},this},e.renderLayout=function(a,b,c){var d,f,g,h;if(f=c._layout.conf,b.select(".cs-layout").remove(),h=b.append("g").attr("class","cs-layout").attr("z-index",f.zIndex).on("click",f.onClick),d=h.selectAll("g").data(c._layout.data).enter().append("g").attr("class",function(a){return a.id}).attr("opacity",f.opacity),g=a.svg.arc().innerRadius(f.innerRadius).outerRadius(f.outerRadius).cornerRadius(f.cornerRadius).startAngle(function(a){return a.start}).endAngle(function(a){return a.end}),d.append("path").attr("d",g).attr("fill",function(a){return a.color}).attr("id",function(a){return a.id}),f.labels.display&&e.renderLayoutLabels(f,a,d),f.ticks.display)return e.renderLayoutTicks(f,h,a,c)},e.renderLayoutLabels=function(a,b,c){var d,e,f;return f=a.innerRadius+a.labels.radialOffset,e=b.svg.arc().innerRadius(f).outerRadius(f).startAngle(function(a,b){return a.start}).endAngle(function(a,b){return a.end}),c.append("path").attr("fill","none").attr("stroke","none").attr("d",e).attr("id",function(a){return"arc-label"+a.id}),d=c.append("text").attr("font-size",a.labels.size).attr("text-anchor","middle"),d.append("textPath").attr("startOffset","25%").attr("xlink:href",function(a){return"#arc-label"+a.id}).style("fill",a.labels.color).text(function(a){var b=a.end-a.start;return a.label.slice(0,Math.floor(21*b))+".."})},e.renderLayoutTicks=function(a,b,c,d){var e,f,g;return e=function(b){var d,e;d=(b.end-b.start)/b.len,b.end-b.start>1.57?e=8:b.end-b.start>.785?e=4:b.end-b.start>.3925?e=2:b.end-b.start>0&&(e=0);var f=[],g={angle:0*d+b.start,label:0};f.push(g);var h=c.scale.linear().domain([1,b.len]).range([b.start,b.end]),i=h.ticks(e).length;h.ticks(e).map(function(c,e){var g=(c*d+b.start,b.len*d+b.start,{angle:c*d+b.start,label:c/a.ticks.labelDenominator+a.ticks.labelSuffix});f.push(g)}),f.splice(i,1);var g={angle:b.len*d+b.start-.006,label:b.len/a.ticks.labelDenominator+a.ticks.labelSuffix};return f.push(g),f},f=function(b,c){return a.ticks.labels===!1?null:a.ticks.labelDisplay0===!1&&0===c?null:c%a.ticks.labelSpacing?null:0===c?b/a.ticks.labelDenominator:b/a.ticks.labelDenominator+a.ticks.labelSuffix},g=b.append("g").selectAll("g").data(d._layout.data).enter().append("g").selectAll("g").data(e).enter().append("g").attr("transform",function(b){return"rotate("+(180*b.angle/Math.PI-90)+")translate("+a.outerRadius+",0)"}),g.append("line").attr("x1",0).attr("y1",1).attr("x2",function(b,c){return a.ticks.size.major}).attr("y2",1).style("stroke",a.ticks.color),g.append("text").attr("x",8).attr("dy",".35em").attr("transform",function(a){return a.angle>Math.PI?"rotate(180)translate(-16)":null}).attr("text-anchor",function(a){return a.angle>Math.PI?"end":null}).attr("font-size",a.ticks.labelSize).style("fill",a.ticks.labelColor).text(function(a){return a.label})},e.Core.prototype.render=function(a,b){var c,d,g,h,i,j,k,l,m,n;if("undefined"==typeof a&&(h=!0,a=[]),b){d=this.tracks;for(l in d){k=d[l];for(c in k)j=k[c],i.select("."+c).remove()}}i=d3.select(this.conf.container).attr("width",this.conf.width).attr("height",this.conf.height),n=i.select(".all"),n.empty()&&(n=i.append("g").attr("class","all").attr("transform","translate("+parseInt(this.conf.width/2)+","+parseInt(this.conf.height/2)+")")),g=this.tracks;for(l in g){k=g[l];for(c in k)j=k[c],(h||f.call(a,c)>=0)&&j.render(this,n,c)}return(h||f.call(a,"layout")>=0)&&e.renderLayout(d3,n,this),m=i.selectAll(".all > g").remove(),m[0].sort(function(a,b){return parseInt(a.getAttribute("z-index"))<parseInt(b.getAttribute("z-index"))?-1:parseInt(a.getAttribute("z-index"))>parseInt(b.getAttribute("z-index"))?1:0}),i.select(".all").selectAll("g").data(m[0]).enter().append(function(a){return a}),this},e.Core.prototype.defaultConf={width:700,height:700,container:"circos",defaultTrackWidth:10},e.Layout.prototype.defaultConf={innerRadius:250,outerRadius:300,cornerRadius:5,gap:.04,opacity:1,labels:{position:"center",display:!0,size:14,color:"#000",radialOffset:20},ticks:{display:!0,color:"grey",spacing:1e7,labels:!0,labelSpacing:10,labelSuffix:"Mb",labelDenominator:1e6,labelDisplay0:!0,labelSize:10,labelColor:"#000",labelFont:"default",majorSpacing:5,size:{minor:2,major:5}},onClick:null,onMouseOver:null,zIndex:100},e.axes={display:!1,minor:{spacing:5,spacingType:"pixel",color:"#d3d3d3",thickness:2},major:{spacing:5,color:"#000000",thickness:2}},e.Heatmap.prototype.defaultConf={innerRadius:0,outerRadius:0,min:"smart",max:"smart",colorPalette:"YlGnBu",colorPaletteSize:9,colorPaletteReverse:!1,logScale:!1,rules:[],backgrounds:[],zIndex:1,opacity:1,tooltipContent:null},e.Histogram.prototype.defaultConf={innerRadius:0,outerRadius:0,min:"smart",max:"smart",direction:"out",colorPaletteSize:9,colorPalette:"YlGnBu",usePalette:!0,colorPaletteReverse:!1,color:"#fd6a62",logScale:!1,axes:e.axes,rules:[],backgrounds:[],zIndex:1,opacity:1,tooltipContent:null},e.Chord.prototype.defaultConf={colorPaletteSize:9,colorPalette:"PuBuGn",usePalette:!0,colorPaletteReverse:!1,color:"#fd6a62",opacity:.7,min:"smart",max:"smart",logScale:!1,rules:[],backgrounds:[],zIndex:1,tooltipContent:null},e.Scatter.prototype.defaultConf={innerRadius:0,outerRadius:0,min:"smart",max:"smart",direction:"out",logScale:!1,glyph:{color:"#fd6a62",fill:!0,size:15,shape:"circle",strokeColor:"#d3d3d3",strokeWidth:2},axes:e.axes,rules:[],backgrounds:[],zIndex:1,opacity:1,tooltipContent:null},e.Line.prototype.defaultConf={innerRadius:0,outerRadius:0,min:"smart",max:"smart",direction:"out",logScale:!1,color:"#fd6a62",fill:!0,fill_color:"#d3d3d3",thickness:2,max_gap:1e7,interpolation:"linear",axes:e.axes,rules:[],backgrounds:[],zIndex:1,opacity:1,tooltipContent:null},e.Stack.prototype.defaultConf={innerRadius:0,outerRadius:0,colorPaletteSize:9,colorPalette:"PuBuGn",usePalette:!0,colorPaletteReverse:!1,color:"#fd6a62",min:"smart",max:"smart",direction:"out",logScale:!1,color:"#fd6a62",thickness:10,radialMargin:2,margin:2,strokeWidth:1,strokeColor:"#000000",axes:e.axes,rules:[],backgrounds:[],zIndex:1,opacity:1,tooltipContent:null},e.Highlight.prototype.defaultConf={innerRadius:0,outerRadius:0,defaultColor:"#fd6a62",opacity:.5,rules:[],zIndex:101,strokeColor:"#d3d3d3",strokeWidth:0,tooltipContent:null},e.Text.prototype.defaultConf={innerRadius:0,outerRadius:0,rules:[],backgrounds:[],zIndex:1,style:{},tooltipContent:null},e.registerTooltip=function(a,b,c,d){return b.tip=d3.tip().direction("s").offset([20,0]).html(d.tooltipContent),c.call(b.tip),b.dispatch.on("mouseover",function(a,c,d){return b.tip.attr("class","d3-tip appear").show(a)}),b.dispatch.on("mouseout",function(a,c,d){return b.tip.attr("class","d3-tip").show(a),b.tip.hide()})}}),c.registerDynamic("c",["b"],!0,function(a,b,c){this||self;c.exports=a("b")}),c.register("d",["10","11","12","13","e","f","c"],function(a){var b,c,d,e,f,g,h,i,j;return{setters:[function(a){b=a.default},function(a){c=a},function(a){d=a.default},function(a){e=a.default},function(a){f=a.default},function(a){g=a.default},function(a){h=a.default}],execute:function(){i=function(){function a(b,d){e(this,a),this.queries=d.queries,this.svgContainer=b,this.seq_type=c.get_seq_type(d.program),this.initiate()}return d(a,null,[{key:"name",value:function(){return"Circos"}},{key:"className",value:function(){return"circos-distribution collapse"}},{key:"collapseId",value:function(a){return"circos-collapse"}},{key:"dataName",value:function(a){return"Circos-visualisation"}}]),d(a,[{key:"initiate",value:function(){this.width=this.svgContainer.width(),this.height=600,this.innerRadius=200,this.outerRadius=230,this.query_arr=[],this.hit_arr=[],this.layout_arr=[],this.chords_arr=[],this.hsp_count=50,this.denominator=100,this.spacing=20,this.labelSpacing=10;var a={amino_acid:"aa",nucleic_acid:"bp"};this.construct_layout(),this.iterator_for_edits(),this.hit_arr=g.uniq(this.hit_arr),this.handle_spacing();var b=f.formatPrefix(this.max_length);this.suffix=" "+b.symbol+a[this.seq_type.subject_seq_type],"k"==b.symbol?this.denominator=1e3:"M"==b.symbol?(this.denominator=1e6,this.spacing=1e6,this.labelSpacing=2e5):"g"==b.symbol&&(this.denominator=1e9),f.select(this.svgContainer[0]).insert("svg",":first-child").attr("class","circosContainer"),this.create_instance(this.svgContainer,this.width,this.height),this.chords_arr.length&&this.layout_arr.length?this.instance_render():this.render_error(),this.setupTooltip()}},{key:"iterator_for_edits",value:function(){this.max_length=this.calculate_max_length(),this.hit_arr.length>10&&this.complex_layout_edits()}},{key:"construct_layout",value:function(){var a=0,b=32,c=this.queries.length,d=Math.min(b/2,c),e=(b-d)/d;this.new_layout=[],this.data=g.map(this.queries,g.bind(function(b){if(a<d){var c=b.id,f=b.length,h={len:f,color:"#8dd3c7",label:c,id:"Query_"+this.clean_id(b.id),ori_id:c};this.layout_arr.push(h);g.map(b.hits,g.bind(function(a){if(a.number<e){g.map(a.hsps,g.bind(function(c){if(g.indexOf(this.hit_arr,a.id)==-1){var d=a.id,e=a.length;this.hit_arr.push(a.id);var f={len:e,color:"#80b1d3",label:d,id:"Hit_"+this.clean_id(a.id),ori_id:d};this.layout_arr.push(f)}var h=["Query_"+this.clean_id(b.id),c.qstart,c.qend,"Hit_"+this.clean_id(a.id),c.sstart,c.send,a.number,c];return this.chords_arr.push(h),c},this));return a}},this))}return this.query_arr.push(b.id),b},this))}},{key:"rearrange_new_layout",value:function(){g.each(this.new_layout,g.bind(function(a){var b=a.id.slice(0,3);"Que"==b&&this.layout_arr.push(a)},this)),g.each(this.new_layout,g.bind(function(a){var b=a.id.slice(0,3);"Hit"==b&&this.layout_arr.push(a)},this))}},{key:"complex_layout_edits",value:function(){this.delete_from_layout=[],this.delete_from_chords=[],g.each(this.layout_arr,g.bind(function(a,b){var c=(a.len/this.max_length).toFixed(3);a.label;c<.1&&"Que"!=a.id.slice(0,3)&&(this.delete_from_layout.push(a),this.hit_arr.slice(g.indexOf(this.hit_arr,a.label),1))},this))}},{key:"check_in_chords_arr",value:function(a,b,c){var d=0;g.each(this.chords_arr,g.bind(function(c){"Que"==b&&c[0]!=a&&d++},this)),d==this.chords_arr.length&&(console.log("no record found "+a),this.delete_arr.push(c))}},{key:"find_index_of_hit",value:function(a){var b;return g.each(this.queries,g.bind(function(c){g.each(c.hits,g.bind(function(c){var d="Hit_"+this.clean_id(c.id);a==d&&(b=c.id)},this))},this)),g.indexOf(this.layout_arr,b)}},{key:"edit_labels",value:function(){console.log("label edits"),g.each(this.layout_arr,g.bind(function(a){var b=(a.len/this.max_length).toFixed(3),c=a.label;b<.41?a.label="..":c.length>10?a.label=c.slice(0,2)+"...":a.label=a.ori_id},this))}},{key:"calculate_multipliers",value:function(){var a=0,b=0;g.each(this.query_arr,g.bind(function(b){g.each(this.data,g.bind(function(c){b==c.id&&(a+=c.length)},this))},this)),g.each(this.data,g.bind(function(a){g.each(a.hits,g.bind(function(a){var c=g.indexOf(this.hit_arr,a.id);c>=0&&(b+=a.length)},this))},this));var c=(a+b)/2;console.log("mid sum "+c+" hit_sum "+b+" query_sum "+a),this.query_multiplier=(c/a).toFixed(3),this.hit_multiplier=(c/b).toFixed(3),console.log("query "+this.query_multiplier+" hit "+this.hit_multiplier)}},{key:"handle_spacing",value:function(){this.max_length>16e3?this.spacing=200:this.max_length>12e3?this.spacing=150:this.max_length>8e3?this.spacing=100:this.max_length>4e3?this.spacing=75:this.max_length>1800&&(this.spacing=50)}},{key:"calculate_max_length",value:function(){var a=0;return g.each(this.layout_arr,function(b){a<b.len&&(a=b.len)}),a}},{key:"clean_id",value:function(a){return a.replace(/[^a-zA-Z0-9]/g,"")}},{key:"create_instance",value:function(a,b,c){this.instance=new h({container:".circosContainer",width:b,height:c}),this.chord_layout(),this.instance_layout()}},{key:"chord_layout",value:function(){return this.chords_arr.length>32?this.paletteSize=32:this.paletteSize=this.chords_arr.length,{usePalette:!0,colorPaletteSize:this.paletteSize,colorPalette:"RdYlBu",opacity:.85}}},{key:"instance_layout",value:function(){return{innerRadius:this.innerRadius,outerRadius:this.outerRadius,cornerRadius:1,labels:{display:!0,size:"10px",radialOffset:10},ticks:{display:!0,spacing:this.spacing,labelSpacing:this.labelSpacing,labelDenominator:this.denominator,labelSuffix:this.suffix,labelSize:"10px",majorSpacing:this.labelSpacing,size:{minor:0,major:4}}}}},{key:"instance_render",value:function(){this.instance.layout(this.instance_layout(),this.layout_arr),this.instance.chord("chord1",this.chord_layout(),this.chords_arr),this.instance.render()}},{key:"render_error",value:function(){this.svgContainer.find("svg").remove(),this.svg=f.select(this.svgContainer[0]).insert("svg",":first-child").attr("width",this.svgContainer.width()).attr("height",this.svgContainer.height()).append("g").attr("class","circos-error").attr("transform","translate("+this.svgContainer.width()/2+","+this.svgContainer.height()/2+")").append("text").attr("text-anchor","start").attr("dy","-0.25em").attr("x",-175).style("font-size","14px").text("Circos looks great with less than 16 queries")}},{key:"layoutReset",value:function(){this.layoutHide=[],g.each(this.layout_arr,function(a){$("."+a.id).css("opacity",1)})}},{key:"chordsReset",value:function(){this.chordsHide=[],g.each(this.chords_arr,function(a){var b=a[1]+a[2],c=a[4]+a[5];$("#"+a[0]+"_"+b+"_"+a[3]+"_"+c).show()})}},{key:"chordsCheck",value:function(a,b){g.each(this.chords_arr,g.bind(function(c,d){"Que"==b&&c[0]==a&&(this.chordsHide.push(d),this.layoutHide.push(c[3])),"Hit"==b&&c[3]==a&&(this.chordsHide.push(d),this.layoutHide.push(c[0]))},this))}},{key:"chordsClean",value:function(){g.each(this.chords_arr,g.bind(function(a,b){if(g.indexOf(this.chordsHide,b)==-1){var c=a[1]+a[2],d=a[4]+a[5];$("#"+a[0]+"_"+c+"_"+a[3]+"_"+d).hide()}},this))}},{key:"layoutClean",value:function(){g.each(this.layout_arr,g.bind(function(a,b){g.indexOf(this.layoutHide,a.id)==-1&&$("."+a.id).css("opacity",.1)},this))}},{key:"setupTooltip",value:function(){var a={};$(".circos-distribution").on("click",g.bind(function(b){b.stopPropagation(),this.layoutReset(),this.chordsReset(),a={}},this)),g.each(this.query_arr,g.bind(function(b,c){this.chordsHide=[],this.layoutHide=[],b&&$(".circos-distribution .Query_"+this.clean_id(b)).attr("data-toggle","tooltip").attr("title",b).on("click",g.bind(function(d){if(d.stopPropagation(),a[c]!=b){a[c]=b;var e="Query_"+this.clean_id(b);this.layoutHide.push(e),this.chordsCheck(e,"Que"),this.chordsClean(),this.layoutClean()}else a[c]=0,this.layoutReset(),this.chordsReset()},this))},this)),g.each(this.hit_arr,g.bind(function(b,c){this.chordsHide=[],this.layoutHide=[],b&&$(".circos-distribution .Hit_"+this.clean_id(b)).attr("data-toggle","tooltip").attr("title",b).on("click",g.bind(function(d){if(d.stopPropagation(),a[c]!=b){a[c]=b;var e="Hit_"+this.clean_id(b);this.layoutHide.push(e),this.chordsCheck(e,"Hit"),this.chordsClean(),this.layoutClean()}else a[c]=0,this.layoutReset(),this.chordsReset()},this))},this)),$('[data-toggle="tooltip"]').tooltip({placement:"top",container:"body",html:"true",delay:0,"white-space":"nowrap"})}},{key:"ratioCalculate",value:function(a,b,c,d,e,f){var g,h,i;return h=f?2.3:1,b===c||a===b&&!e||a===c&&e?0:a===c||a===b&&e?d-1:(g=(a-b)/(c-b),i=Math.exp(1/h*Math.log(g)),e&&(i=1-i),Math.floor(d*i))}},{key:"drawLegend",value:function(){this.ratioHSP=[],g.each(this.chords_arr,g.bind(function(a){var b={number:a[6],evalue:a[7].evalue};this.ratioHSP.push(b)},this));var a=f.min(this.ratioHSP,function(a){return a.number}),b=f.max(this.ratioHSP,function(a){return a.number});console.log("chords_arr "+this.chords_arr.length),console.log("ratioHSP test "+this.ratioHSP.length),console.log("paletteSize "+this.paletteSize),console.log("min "+a+" max "+b),this.legend=f.select(this.svgContainer[0]).insert("svg",":first-child").attr("height",20).attr("width",30*this.ratioHSP.length).attr("transform","translate(10, 10)").append("g").attr("class","RdYlBu").attr("transform","translate(10, 0)");this.legend.selectAll(".bar").data(this.ratioHSP).enter().append("g").attr("class","g").attr("transform",function(a,b){return"translate("+30*b+",0)"}).append("rect").attr("class",g.bind(function(c,d){var e=this.ratioCalculate(c.number,a,b,this.paletteSize,!1,!1);return console.log("calc ratio "+e),"q"+e+"-"+this.paletteSize},this)).attr("data-toggle","tooltip").attr("title",function(a){return a.evalue}).attr("x",1).attr("width",30).attr("height",20),f.scale.linear().domain([0,250]).range([0,100])}}]),a}(),j=b(i),a("default",j)}}}),c.register("14",["10","11","12","13","e","f"],function(a){var b,c,d,e,f,g,h,i;return{setters:[function(a){b=a.default},function(a){c=a},function(a){d=a.default},function(a){e=a.default},function(a){f=a.default},function(a){g=a.default}],execute:function(){h=function(){function a(b,c){e(this,a),this.svg_container=b,$queryDiv=b.parents(".resultn"),hits=this.extractData(c.query.hits,c.query.number),this.graphIt($queryDiv,b,0,20,null,hits)}return d(a,null,[{key:"name",value:function(){return"Matching sequences"}},{key:"className",value:function(){return"alignment-overview"}},{key:"collapseId",value:function(a){return"alignment_"+a.query.number}},{key:"dataName",value:function(a){return"Alignment-Overview-"+a.query.id}}]),d(a,[{key:"extractData",value:function(a,b){var c=[];return a.map(function(a){var d=[],e=a.hsps;g.each(e,function(c){var e={};e.hspEvalue=c.evalue,e.hspStart=c.qstart,e.hspEnd=c.qend,e.hspFrame=c.sframe,e.hspId="Query_"+b+"_hit_"+a.number+"_hsp_"+c.number,d.push(e)}),d.hitId=a.id,d.hitDef="Query_"+b+"_hit_"+a.number,d.hitEvalue=a.evalue,c.push(d)}),c}},{key:"setupTooltip",value:function(){this.svg_container.find('[data-toggle="tooltip"]').tooltip({placement:"top",container:"body",html:"true",delay:0,"white-space":"nowrap"})}},{key:"setupClick",value:function(a){$("a",a).click(function(a){a.preventDefault(),a.stopPropagation(),window.location.hash=$(this).attr("href")})}},{key:"graphControls",value:function(a,b,c,d,e){var f,h,i,j,k=20,l=function(){f=e.length,h=a.find(".ghit > g").length},m=function(a,b){b.append($("<button/>").addClass("btn btn-link more").attr("type","button").attr("data-parent-query",a.attr("id")).html("View More&nbsp;").append($("<i/>").html("&nbsp;&nbsp;").addClass("fa fa-angle-double-down")),$("<button/>").addClass("btn btn-link less").attr("type","button").attr("data-parent-query",a.attr("id")).html("View Less&nbsp;").append($("<i/>").html("&nbsp;&nbsp;").addClass("fa fa-angle-double-up"))),i=$(".less",b),j=$(".more",b)},n=function(){l(),f===k||h<k?(i.hide(),j.hide()):h===f?(j.hide(),i.show()):h===k?(i.hide(),j.show()):(i.show(),j.show())};c===!0&&(m(a,b),n()),j.on("click",g.bind(function(c){l(),this.graphIt(a,b,h,k,d,e),n(),this.setupTooltip(),c.stopPropagation()},this)),i.on("click",g.bind(function(c){l();var f=h-k;f>=k?(this.graphIt(a,b,h,-k,d,e),n()):0!==f&&(this.graphIt(a,b,h,k-h,d,e),n()),this.setupTooltip(),c.stopPropagation()},this))}},{key:"drawLegend",value:function(a,b,c,d,e){var f=a.append("g").attr("transform","translate(0,"+(d-1.88*b.margin)+")");f.append("rect").attr("x",7*(c-2*b.margin)/10).attr("width",2*(c-4*b.margin)/10).attr("height",b.legend).attr("fill","url(#legend-grad)"),f.append("text").attr("class"," legend-text").attr("transform","translate(0, "+b.legend+")").attr("x",6*(c-2*b.margin)/10-b.margin/2).text("Weaker hits"),f.append("text").attr("class"," legend-text").attr("transform","translate(0, "+b.legend+")").attr("x",9*(c-2*b.margin)/10+b.margin/2).text("Stronger hits"),a.append("linearGradient").attr("id","legend-grad").selectAll("stop").data([{offset:"0%",color:"#ccc"},{offset:"50%",color:"#888"},{offset:"100%",color:"#000"}]).enter().append("stop").attr("offset",function(a){return a.offset}).attr("stop-color",function(a){return a.color})}},{key:"graphIt",value:function(a,b,d,e,g,h){var i={barHeight:2,barPadding:1,legend:5,margin:20},j=$.extend(i,g),k=h.slice(0,d+e);if(k.length<1)return!1;0!==d&&b.find("svg").remove();var l=a.data().queryLen,m=a.attr("id"),n=b.width(),o=k.length*(j.barHeight+j.barPadding)+2*j.legend+5*j.margin,p={blastn:"nucleic_acid",blastp:"amino_acid",blastx:"nucleic_acid",tblastx:"nucleic_acid",tblastn:"amino_acid"},q=f.select(b[0]).selectAll("svg").data([k]).enter().insert("svg",":first-child").attr("width",n).attr("height",o).append("g").attr("transform","translate("+j.margin/2+", "+1.5*j.margin+")"),r=f.scale.linear().range([0,n-j.margin]);r.domain([1,l]);var s=a.data().algorithm,t=c.tick_formatter(r,p[s]),u=r.ticks(11);u.pop();var v=f.svg.axis().scale(r).orient("top").tickValues(u.concat([1,l])).tickFormat(t),w=q.append("g").attr("transform","translate(0, "+j.margin+")").append("g").attr("class","x axis").call(v);w.selectAll("text").attr("x","25px").attr("y","2px").attr("transform","rotate(-90)");var x=f.scale.ordinal().rangeBands([0,o-3*j.margin-2*j.legend],.3);x.domain(k.map(function(a){return a.hitId}));var y=f.scale.log().domain([f.min([1e-5,f.min(k.map(function(a){if(0!==parseFloat(a.hitEvalue))return a.hitEvalue}))]),f.max(k.map(function(a){return a.hitEvalue}))]).range([40,150]);q.append("g").attr("class","ghit").attr("transform","translate(0, "+1.65*(j.margin-j.legend)+")").selectAll(".hits").data(k).enter().append("g").each(function(a,b){f.select(this).selectAll(".hsp").data(a).enter().append("a").each(function(d,e){var g=x(a.hitId)+j.barHeight/2,h=f.rgb(y(d.hspEvalue),y(d.hspEvalue),y(d.hspEvalue));e+1<a.length&&(a[e].hspEnd<=a[e+1].hspStart?f.select(this.parentNode).append("line").attr("x1",r(a[e].hspEnd)).attr("y1",g).attr("x2",r(a[e+1].hspStart)).attr("y2",g).attr("stroke",h):a[e].hspStart>a[e+1].hspEnd&&f.select(this.parentNode).append("line").attr("x1",r(a[e+1].hspEnd)).attr("y1",g).attr("x2",r(a[e].hspStart)).attr("y2",g).attr("stroke",h)),f.select(this).attr("xlink:href","#"+m+"_hit_"+(b+1)).append("rect").attr("data-toggle","tooltip").attr("title",a.hitId+"<br><strong>E value:</strong> "+c.prettify_evalue(d.hspEvalue)).attr("class","bar").attr("x",function(a){return r(a.hspStart)}).attr("y",x(a.hitId)).attr("width",function(a){return r(a.hspEnd-a.hspStart+1)}).attr("height",j.barHeight).attr("fill",f.rgb(h))})}),k.length>1&&this.drawLegend(q,j,n,o,h),0===d&&this.graphControls(a,b,!0,g,h),this.setupTooltip(),this.setupClick(b)}}]),a}(),i=b(h),a("default",i)}}}),c.register("15",["10","11","12","13","e","f"],function(a){var b,c,d,e,f,g,h,i;return{setters:[function(a){b=a.default},function(a){c=a},function(a){d=a.default},function(a){e=a.default},function(a){f=a.default},function(a){g=a.default}],execute:function(){h=function(){function a(b,d){e(this,a),this.query=d.query,this._seq_type=c.get_seq_type(d.algorithm),this.svg_container=b,this._margin={top:30,right:25,bottom:55,left:12.5},this.initiate(b.width(),b.height())}return d(a,null,[{key:"name",value:function(){return"Length distribution of hits"}},{key:"className",value:function(){return"length-distribution"}},{key:"collapseId",value:function(a){return"length_"+a.query.number}},{key:"dataName",value:function(a){return"length-distribution-"+a.query.id}}]),d(a,[{key:"initiate",value:function(a,b){this._width=a-this._margin.left-this._margin.right,this._height=b-this._margin.top-this._margin.bottom,this.svg=f.select(this.svg_container[0]).insert("svg",":first-child").attr("width",this._width+this._margin.right+this._margin.left).attr("height",this._height+this._margin.top+this._margin.bottom).append("g").attr("transform","translate("+this._margin.left+","+this._margin.top+")"),this.hit_lengths(),this.define_scale_and_bins(),this.update_data(),this.draw()}},{key:"draw",value:function(){this.draw_rectangles(),this.draw_query_line(),this.draw_axes(),this.setupTooltip()}},{key:"define_scale_and_bins",value:function(){this._scale_x=f.scale.linear().domain([0,1.05*f.max([this.query.length,f.max(this._data)])]).range([0,this._width]),this._bins=f.layout.histogram().range(this._scale_x.domain()).bins(this._scale_x.ticks(50))(this._data),this._scale_y=f.scale.linear().domain([0,f.max(this._bins,function(a){return a.length})]).range([this._height,0])}},{key:"hit_lengths",value:function(){this._data=g.map(this.query.hits,g.iteratee("length"))}},{key:"setupTooltip",value:function(){this.svg_container.find('[data-toggle="tooltip"]').tooltip({placement:"top",container:"body",html:"true",delay:0,"white-space":"nowrap"})}},{key:"setupResponsiveness",value:function(){var a=$(window).width();console.log("cureent "+a);var b=g.debounce(g.bind(function(){a!=$(window).width()&&(console.log("redraw initiated "+this._height),this.draw(),a=$(window).width())},this),125);$(window).resize(b)}},{key:"tick_formatter",value:function(a){var b=this._scale_x.ticks(),c=f.format(".1f"),d=f.formatPrefix(b[b.length-1]),e={amino_acid:"aa",nucleic_acid:"bp"};return function(f){if(0!==f)return g.indexOf(b,f)>=0?"aa"==e[a]?f+" "+e[a]:c(d.scale(f))+" "+d.symbol+e[a]:void 0}}},{key:"update_data",value:function(){var a=this,b=[];this._bins.map(function(d){var e=[];d.reverse();var f=d.length;d.map(function(b,h){var i=d.length-(h+1),j=g.findIndex(a.query.hits,{length:b}),k={value:b,id:a.query.hits[j].id,evalue:a.query.hits[j].evalue,url:"#Query_"+a.query.number+"_hit_"+a.query.hits[j].number,y0:f,y1:f+=i-f,color:c.get_colors_for_evalue(a.query.hits[j].evalue,a.query.hits)};e.push(k)});var h={data:e,x:d.x,dx:d.dx,length:d.length};b.push(h)}),this._update_data=b}},{key:"draw_rectangles",value:function(){var a=this,b=this.svg.selectAll(".bar").data(this._update_data).enter().append("g").attr("class","g").attr("transform",function(b){return"translate("+(a._scale_x(b.x)+a._margin.left)+",0)"});b.selectAll("rect").data(function(a){return a.data}).enter().append("a").attr("xlink:href",function(a){return a.url}).append("rect").attr("class","bar").attr("data-toggle","tooltip").attr("title",function(a){return a.id+" <br>E Value: "+c.prettify_evalue(a.evalue)+"<br>Length: "+a.value}).attr("x",1).attr("y",function(b){return 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metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: sequenceserver
 version: !ruby/object:Gem::Version
-  version: 1.1.0.beta7
+  version: 1.1.0.beta8
 platform: ruby
 authors:
 - Anurag Priyam
@@ -11,7 +11,7 @@ authors:
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2018-05-26 00:00:00.000000000 Z
+date: 2018-05-30 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: sinatra