sequenceserver 1.1.0.beta7 → 1.1.0.beta8
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Potentially problematic release.
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- checksums.yaml +4 -4
- data/lib/sequenceserver/version.rb +1 -1
- data/public/js/hits_overview.js +1 -1
- data/public/js/report.js +7 -4
- data/public/sequenceserver-report.min.js +2 -2
- metadata +2 -2
checksums.yaml
CHANGED
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@@ -1,7 +1,7 @@
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1
1
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---
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2
2
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SHA1:
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3
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-
metadata.gz:
|
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4
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-
data.tar.gz:
|
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3
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+
metadata.gz: a84db1a31e7b1e1a9b89ce2a6dacaf9721c2983d
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4
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+
data.tar.gz: 16414f4af1a58ebf682213d955f18145206dc167
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5
5
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SHA512:
|
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6
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-
metadata.gz:
|
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7
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-
data.tar.gz:
|
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6
|
+
metadata.gz: 7c2b63cbec445107926636009ea439c6bcbac7f4acfca3246ad91a0f166d8290d9fb2af9254045fc989374ac882d419b13c49273a39f61f2186107775448cfa0
|
|
7
|
+
data.tar.gz: 7669b574fb3e19490857d22acdbbc1d05558b6bcae86b87a9cf1d0ad64deaf4e8c882becbb25d6e8e0eac2d7e0cd510d751daed2c0fea6ed2944de91ae6993c6
|
data/public/js/hits_overview.js
CHANGED
data/public/js/report.js
CHANGED
|
@@ -941,8 +941,9 @@ var Report = React.createClass({
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941
941
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*/
|
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942
942
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fetchResults: function () {
|
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943
943
|
var intervals = [200, 400, 800, 1200, 2000, 3000, 5000];
|
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944
|
+
var component = this;
|
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944
945
|
|
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945
|
-
|
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946
|
+
function poll () {
|
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946
947
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$.getJSON(location.pathname + '.json')
|
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947
948
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.complete(function (jqXHR) {
|
|
948
949
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switch (jqXHR.status) {
|
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@@ -952,12 +953,12 @@ var Report = React.createClass({
|
|
|
952
953
|
interval = intervals[0];
|
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953
954
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}
|
|
954
955
|
else {
|
|
955
|
-
interval = intervals.shift;
|
|
956
|
+
interval = intervals.shift();
|
|
956
957
|
}
|
|
957
958
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setTimeout(poll, interval);
|
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958
959
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break;
|
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959
960
|
case 200:
|
|
960
|
-
|
|
961
|
+
component.updateState(jqXHR.responseJSON);
|
|
961
962
|
break;
|
|
962
963
|
case 404:
|
|
963
964
|
case 400:
|
|
@@ -966,7 +967,9 @@ var Report = React.createClass({
|
|
|
966
967
|
break;
|
|
967
968
|
}
|
|
968
969
|
});
|
|
969
|
-
}
|
|
970
|
+
}
|
|
971
|
+
|
|
972
|
+
poll();
|
|
970
973
|
},
|
|
971
974
|
|
|
972
975
|
/**
|
|
@@ -1,7 +1,7 @@
|
|
|
1
1
|
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2
2
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this.transitioning=1;var h=function(){this.$element.removeClass("collapsing").addClass("collapse in")[g](""),this.transitioning=0,this.$element.trigger("shown.bs.collapse")};if(!a.support.transition)return h.call(this);var i=a.camelCase(["scroll",g].join("-"));this.$element.one("bsTransitionEnd",a.proxy(h,this)).emulateTransitionEnd(d.TRANSITION_DURATION)[g](this.$element[0][i])}}}},d.prototype.hide=function(){if(!this.transitioning&&this.$element.hasClass("in")){var b=a.Event("hide.bs.collapse");if(this.$element.trigger(b),!b.isDefaultPrevented()){var c=this.dimension();this.$element[c](this.$element[c]())[0].offsetHeight,this.$element.addClass("collapsing").removeClass("collapse in").attr("aria-expanded",!1),this.$trigger.addClass("collapsed").attr("aria-expanded",!1),this.transitioning=1;var e=function(){this.transitioning=0,this.$element.removeClass("collapsing").addClass("collapse").trigger("hidden.bs.collapse")};return a.support.transition?void 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e.Line,d.build(this,b,c),this.tracks.lines[a]=d,this},e.Core.prototype.stack=function(a,b,c){var d;return d=new e.Stack,d.build(this,b,c),this.tracks.stacks[a]=d,this},e.Core.prototype.highlight=function(a,b,c){var d;return d=new e.Highlight,d.build(this,b,c),this.tracks.highlights[a]=d,this},e.Core.prototype.text=function(a,b,c){var d;return d=new e.Text,d.build(this,b,c),this.tracks.texts[a]=d,this},e.Chord=function(){return e.Track.call(this),this.parseData=e.parseChordData,this.applyRules=function(a,b){var c,d,e,f,g;for(a=a||[],f=[],d=0,e=b.length;d<e;d++)c=b[d],f.push(function(){var b,d,e;for(e=[],d=0,b=a.length;d<b;d++)g=a[d],g.condition(c)?e.push(c[g.parameter]=g.value):e.push(void 0);return e}());return f},this.getSource=function(a){return function(a,b){var c,d,e,f;return a=a.source,c=b.blocks[a.id],f=c.start+a.start/c.len*(c.end-c.start),d=c.start+a.end/c.len*(c.end-c.start),e={radius:b.conf.innerRadius,startAngle:f,endAngle:d}}}(this),this.getTarget=function(a){return function(a,b){var c,d,e,f;return a=a.target,c=b.blocks[a.id],f=c.start+a.start/c.len*(c.end-c.start),d=c.start+a.end/c.len*(c.end-c.start),e={radius:b.conf.innerRadius,startAngle:f,endAngle:d}}}(this),this.dimChords=function(a,b,c,d){a.selectAll("path").style("opacity",function(a,b){return d==b?1:0})},this.resetChords=function(a,b){a.selectAll("path").style("opacity",b.opacity)},this.renderChords=function(a,b,c,d,e,f,g,h){var i,j;return j=a.append("g").attr("class",c.colorPalette),i=j.selectAll(".chord").data(d).enter().append("path").attr("class","chord").attr("d",d3.svg.chord().source(function(a){return g(a,e)}).target(function(a){return h(a,e)})).attr("opacity",function(a){return c.opacity}).attr("data-toggle","tooltip").attr("title",function(a){return"Identity "+a.hsp.identity+"<br> Evalue "+a.hsp.evalue}).attr("id",function(a){var b=a.source.start+a.source.end,c=a.target.start+a.target.end;return a.source.id+"_"+b+"_"+a.target.id+"_"+c}).on("mouseover",function(a){return 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){
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4
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-
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($("<button/>").addClass("btn btn-link more").attr("type","button").attr("data-parent-query",a.attr("id")).html("View More ").append($("<i/>").html(" ").addClass("fa fa-angle-double-down")),$("<button/>").addClass("btn btn-link less").attr("type","button").attr("data-parent-query",a.attr("id")).html("View Less ").append($("<i/>").html(" ").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 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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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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 ").append($("<i/>").html(" ").addClass("fa fa-angle-double-down")),$("<button/>").addClass("btn btn-link less").attr("type","button").attr("data-parent-query",a.attr("id")).html("View Less ").append($("<i/>").html(" ").addClass("fa fa-angle-double-up"))),i=$(".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 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@@ -16,4 +16,4 @@ u.uniqueId=function(a){var b=++M+"";return a?a+b:b},u.templateSettings={evaluate
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16
16
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e.createElement("tr",{key:b.number},e.createElement("td",{className:"text-left"},b.number+"."),e.createElement("td",null,e.createElement("a",{href:"#Query_"+this.props.query.number+"_hit_"+b.number},b.id)),a&&e.createElement("td",{className:"text-left"},b.sciname),e.createElement("td",{className:"text-right"},b.qcovs),e.createElement("td",{className:"text-right"},b.score),e.createElement("td",{className:"text-right"},this.inExponential(b.hsps[0].evalue)),e.createElement("td",{className:"text-right"},b.identity))},this))))}}),p=e.createClass({displayName:"Query",domID:function(){return"Query_"+this.props.query.number},numhits:function(){return this.props.query.hits.length},render:function(){return e.createElement("div",{className:"resultn",id:this.domID(),"data-query-len":this.props.query.length,"data-algorithm":this.props.data.program},e.createElement("div",{className:"section-header"},e.createElement("h3",null,"Query= ",this.props.query.id," ",e.createElement("small",null,this.props.query.title)),e.createElement("span",{className:"label label-reset pos-label",title:"Query"+this.props.query.number+".","data-toggle":"tooltip"},this.props.query.number+"/"+this.props.data.queries.length)),this.numhits()&&e.createElement("div",{className:"section-content"},e.createElement(c,{key:"GO_"+this.props.query.number,query:this.props.query,program:this.props.data.program,collapsed:this.props.data.veryBig}),e.createElement(d,{key:"LD_"+this.props.query.id,query:this.props.query,algorithm:this.props.data.program,collapsed:"true"}),e.createElement(o,{key:"HT_"+this.props.query.number,query:this.props.query}),e.createElement("div",{id:"hits"},f.map(this.props.query.hits,f.bind(function(a){return e.createElement(n,{hit:a,key:"HIT_"+a.number,algorithm:this.props.data.program,querydb:this.props.data.querydb,query:this.props.query,selectHit:this.props.selectHit})},this))))||e.createElement("div",{className:"section-content"},e.createElement("p",null,"Query length: ",this.props.query.length),e.createElement("br",null),e.createElement("br",null),e.createElement("p",null,e.createElement("strong",null," ****** No hits found ****** "))))}}),q=e.createClass({displayName:"SideBar",downloadFastaOfAll:function(){var a=$(".hit-links :checkbox").map(function(){return this.value}).get(),b=f.map(this.props.data.querydb,f.iteratee("id"));k(a,b)},downloadFastaOfSelected:function(){var a=$(".hit-links :checkbox:checked").map(function(){return this.value}).get(),b=f.map(this.props.data.querydb,f.iteratee("id"));k(a,b)},downloadAlignmentOfAll:function(){var a=$(".hit-links :checkbox").map(function(){return this.value}).get(),b=[],c=new i;f.each(this.props.data.queries,f.bind(function(a){f.each(a.hits,function(c){f.each(c.hsps,function(d){d.hit_id=c.id,d.query_id=a.id,b.push(d)})})},this)),console.log("len "+b.length),c.export_alignments(b,"alignment-"+a.length+"_hits")},downloadAlignmentOfSelected:function(){var a=$(".hit-links :checkbox:checked").map(function(){return this.value}).get(),b=[],c=new i;console.log("check "+a.toString()),f.each(this.props.data.queries,f.bind(function(c){f.each(c.hits,function(d){f.indexOf(a,d.id)!=-1&&f.each(d.hsps,function(a){a.hit_id=d.id,a.query_id=c.id,b.push(a)})})},this)),c.export_alignments(b,"alignment-"+a.length+"_hits")},render:function(){return e.createElement("div",{className:"sidebar"},this.props.shouldShowIndex&&this.index(),this.downloads())},index:function(){return e.createElement("div",{className:"index"},e.createElement("div",{className:"section-header"},e.createElement("h4",null,this.summary())),e.createElement("ul",{className:"nav hover-reset active-bold"},f.map(this.props.data.queries,f.bind(function(a){return e.createElement("li",{key:"Side_bar_"+a.id},e.createElement("a",{className:"nowrap-ellipsis hover-bold",href:"#Query_"+a.number,title:"Query= "+a.id+" "+a.title},"Query= "+a.id))},this))))},summary:function(){var a=this.props.data.program,b=this.props.data.queries.length,c=this.props.data.querydb.length;return a.toUpperCase()+": "+b+" "+(b>1?"queries":"query")+", "+c+" "+(c>1?"databases":"database")},downloads:function(){return e.createElement("div",{className:"downloads"},e.createElement("div",{className:"section-header"},e.createElement("h4",null,"Download FASTA, XML, TSV")),e.createElement("ul",{className:"nav"},e.createElement("li",null,e.createElement("a",{className:"download-fasta-of-all",onClick:this.downloadFastaOfAll},"FASTA of all hits")),e.createElement("li",null,e.createElement("a",{className:"download-fasta-of-selected disabled",onClick:this.downloadFastaOfSelected},"FASTA of ",e.createElement("span",{className:"text-bold"})," selected hit(s)")),e.createElement("li",null,e.createElement("a",{className:"download-alignment-of-all",onClick:this.downloadAlignmentOfAll},"Alignment of all hits")),e.createElement("li",null,e.createElement("a",{className:"download-alignment-of-selected disabled",onClick:this.downloadAlignmentOfSelected},"Alignment of ",e.createElement("span",{className:"text-bold"})," selected hit(s)")),e.createElement("li",null,e.createElement("a",{className:"download","data-toggle":"tooltip",title:"15 columns: query and subject ID; scientific name, alignment length, mismatches, gaps, identity, start and end coordinates, e value, bitscore, query coverage per subject and per HSP.",
|
|
19
|
-
href:"download/"+this.props.data.search_id+".std_tsv"},"Standard tabular report")),e.createElement("li",null,e.createElement("a",{className:"download","data-toggle":"tooltip",title:"44 columns: query and subject ID, GI, accessions, and length; alignment details; taxonomy details of subject sequence(s) and query coverage per subject and per HSP.",href:"download/"+this.props.data.search_id+".full_tsv"},"Full tabular report")),e.createElement("li",null,e.createElement("a",{className:"download","data-toggle":"tooltip",title:"Results in XML format.",href:"download/"+this.props.data.search_id+".xml"},"Full XML report"))))}}),r=e.createClass({displayName:"Report",getInitialState:function(){return this.fetchResults(),this.updateCycle=0,{search_id:"",program:"",program_version:"",queries:[],querydb:[],params:[],stats:[]}},fetchResults:function(){
|
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19
|
+
href:"download/"+this.props.data.search_id+".std_tsv"},"Standard tabular report")),e.createElement("li",null,e.createElement("a",{className:"download","data-toggle":"tooltip",title:"44 columns: query and subject ID, GI, accessions, and length; alignment details; taxonomy details of subject sequence(s) and query coverage per subject and per HSP.",href:"download/"+this.props.data.search_id+".full_tsv"},"Full tabular report")),e.createElement("li",null,e.createElement("a",{className:"download","data-toggle":"tooltip",title:"Results in XML format.",href:"download/"+this.props.data.search_id+".xml"},"Full XML report"))))}}),r=e.createClass({displayName:"Report",getInitialState:function(){return this.fetchResults(),this.updateCycle=0,{search_id:"",program:"",program_version:"",queries:[],querydb:[],params:[],stats:[]}},fetchResults:function(){function a(){$.getJSON(location.pathname+".json").complete(function(d){switch(d.status){case 202:var e;e=1===b.length?b[0]:b.shift(),setTimeout(a,e);break;case 200:c.updateState(d.responseJSON);break;case 404:case 400:case 500:j(d.responseJSON)}})}var b=[200,400,800,1200,2e3,3e3,5e3],c=this;a()},updateState:function(a){var b=a.queries;a.veryBig=b.length>250,a.queries=b.splice(0,50),this.setState(a);var c=function a(){b.length>0?(this.setState({queries:this.state.queries.concat(b.splice(0,50))}),setTimeout(a.bind(this),500)):this.componentFinishedUpdating()};setTimeout(c.bind(this),500)},render:function(){return this.isResultAvailable()?this.resultsJSX():this.loadingJSX()},loadingJSX:function(){return e.createElement("div",{className:"row"},e.createElement("div",{className:"col-md-6 col-md-offset-3 text-center"},e.createElement("h1",null,e.createElement("i",{className:"fa fa-cog fa-spin"})," BLAST-ing"),e.createElement("p",null,e.createElement("br",null),"This can take some time depending on the size of your query and database(s). The page will update automatically when BLAST is done.",e.createElement("br",null),e.createElement("br",null),"You can bookmark the page and come back to it later or share the link with someone.")))},resultsJSX:function(){return e.createElement("div",{className:"row"},this.shouldShowSidebar()&&e.createElement("div",{className:"col-md-3 hidden-sm hidden-xs"},e.createElement(q,{data:this.state,shouldShowIndex:this.shouldShowIndex()})),e.createElement("div",{className:this.shouldShowSidebar()?"col-md-9":"col-md-12"},this.overviewJSX(),this.isHitsAvailable()?e.createElement(g,{queries:this.state.queries,program:this.state.program,collapsed:"true"}):e.createElement("span",null),f.map(this.state.queries,f.bind(function(a){return e.createElement(p,{key:"Query_"+a.id,query:a,data:this.state,selectHit:this.selectHit})},this))))},overviewJSX:function(){return e.createElement("div",{className:"overview"},e.createElement("pre",{className:"pre-reset"},this.state.program_version,e.createElement("br",null),e.createElement("br",null),f.map(this.state.querydb,function(a){return a.title}).join(", "),e.createElement("br",null),"Total: ",this.state.stats.nsequences," sequences,",this.state.stats.ncharacters," characters",e.createElement("br",null),e.createElement("br",null),f.map(this.state.params,function(a,b){return b+" "+a}).join(", ")))},isResultAvailable:function(){return this.state.queries.length>=1},isHitsAvailable:function(){var a=0;return f.each(this.state.queries,function(b){0==b.hits.length&&a++}),!(a==this.state.queries.length)},shouldShowSidebar:function(){return!(1==this.state.queries.length&&0==this.state.queries[0].hits.length)},shouldShowIndex:function(){return this.state.queries.length<=8},componentDidMount:function(){this.preventCollapseOnSelection()},componentDidUpdate:function(){this.updateCycle+=1,1===this.updateCycle&&this.affixSidebar()},componentFinishedUpdating:function(){this.shouldShowIndex()&&this.setupScrollSpy()},preventCollapseOnSelection:function(){$("body").on("mousedown",".hit > .section-header > h4",function(a){var b=$(this);b.on("mouseup mousemove",function a(c){"mouseup"===c.type?(b.attr("data-toggle","collapse"),b.find(".fa-chevron-down").toggleClass("fa-rotate-270")):b.attr("data-toggle",""),b.off("mouseup mousemove",a)})})},affixSidebar:function(){var a=$(".sidebar");a.affix({offset:{top:a.offset().top}})},setupScrollSpy:function(){$("body").scrollspy({target:".sidebar"})},selectHit:function(a){var b=$("#"+a),c=$(".hit-links :checkbox:checked").length;if(b&&b.val()){var d=$(b.data("target"));if(b.is(":checked")){d.addClass("glow").find(":checkbox").not(b).check();var e=$(".download-fasta-of-selected"),f=$(".download-alignment-of-selected");f.enable();e.find("span");e.enable()}else d.removeClass("glow").find(":checkbox").not(b).uncheck();if(c>=1){var e=$(".download-fasta-of-selected"),f=$(".download-alignment-of-selected");e.find(".text-bold").html(c),f.find(".text-bold").html(c)}if(0==c){var e=$(".download-fasta-of-selected"),f=$(".download-alignment-of-selected");e.addClass("disabled").find(".text-bold").html(""),f.addClass("disabled").find(".text-bold").html("")}}}}),s=e.createClass({displayName:"Page",render:function(){return e.createElement("div",null,e.createElement("div",{className:"container"},e.createElement(r,{ref:"report"})),e.createElement("div",{id:"circos-demo",className:"modal"}),e.createElement("canvas",{id:"png-exporter",hidden:!0}))}}),e.render(e.createElement(s,null),document.getElementById("view"))}}})})(function(a){a()});
|
metadata
CHANGED
|
@@ -1,7 +1,7 @@
|
|
|
1
1
|
--- !ruby/object:Gem::Specification
|
|
2
2
|
name: sequenceserver
|
|
3
3
|
version: !ruby/object:Gem::Version
|
|
4
|
-
version: 1.1.0.
|
|
4
|
+
version: 1.1.0.beta8
|
|
5
5
|
platform: ruby
|
|
6
6
|
authors:
|
|
7
7
|
- Anurag Priyam
|
|
@@ -11,7 +11,7 @@ authors:
|
|
|
11
11
|
autorequire:
|
|
12
12
|
bindir: bin
|
|
13
13
|
cert_chain: []
|
|
14
|
-
date: 2018-05-
|
|
14
|
+
date: 2018-05-30 00:00:00.000000000 Z
|
|
15
15
|
dependencies:
|
|
16
16
|
- !ruby/object:Gem::Dependency
|
|
17
17
|
name: sinatra
|