sequenceserver 2.0.0.rc5 → 2.0.0.rc6

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Files changed (8) hide show
  1. checksums.yaml +4 -4
  2. data/lib/sequenceserver/routes.rb +5 -0
  3. data/lib/sequenceserver/version.rb +1 -1
  4. data/public/css/sequenceserver.css +2 -1
  5. data/public/css/sequenceserver.min.css +1 -1
  6. data/public/js/query.js +31 -15
  7. data/public/sequenceserver-report.min.js +15 -15
  8. metadata +2 -2
checksums.yaml CHANGED
@@ -1,7 +1,7 @@
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  ---
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  SHA256:
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- metadata.gz: b04c2f43509bf7d4a15d555e3bd9cea86d3c7770c7a3e35016f963f877055ecf
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- data.tar.gz: 25678397eacb2c3f445902624baff80a90d2a47ca98d2b703e13de3eca84cf1e
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+ metadata.gz: f1097c442726e14676ae77941ea50f89d5d652e2a24d7f5b37bc6a287da1345e
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+ data.tar.gz: bb7159b49248e91bb23a17e51f5a07aed05d42c7417bf647306061dbf476dc2a
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  SHA512:
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- metadata.gz: a8e6a4c1b4917d9bd35d07ef8e580e1b75105bfd1709fb892d9ed523da91f8c3a08d50c1c9da304530cd0bb5d77da00a4944c65cd5ce90fc979c9d6099149058
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- data.tar.gz: ef493ec4cf1aef63b2f535251143b34154d0d332a47a1d15668c7a74b139d5e6c2a2f9c33b5c7072ae9c2fbbcf33048fad4e828273c85a199a6ab79874d6e766
6
+ metadata.gz: 890c530fe2c1ec713ed16f22a4ae975d2894c6f6085e8aefc6b540b1e7779852227e46177ad63f8e2ecd4370ce857485773a547ee98bab11121ae4f2a3bcc07a
7
+ data.tar.gz: fc6f4715b77936d831f429ef0f9a00a236165e12f2faba7705c083027cc2f3a748d476d721f395e0f0e22c32f48f34af8b2057caa3f55094fca46cedaf381e99
data/lib/sequenceserver/routes.rb CHANGED
@@ -60,6 +60,11 @@ module SequenceServer
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  logger.debug params
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  end
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+ # Set JSON content type for JSON endpoints.
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+ before '*.json' do
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+ content_type 'application/json'
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+ end
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+
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  # Returns base HTML. Rest happens client-side: rendering the search form.
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  get '/' do
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  erb :search, layout: true
data/lib/sequenceserver/version.rb CHANGED
@@ -1,4 +1,4 @@
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  # Define version number.
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  module SequenceServer
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- VERSION = '2.0.0.rc5'.freeze
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+ VERSION = '2.0.0.rc6'.freeze
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  end
data/public/css/sequenceserver.css CHANGED
@@ -251,7 +251,8 @@ a.disabled:hover,
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  * Do not wrap text or show horizontal scrollbar if text overflows the width of
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  * the element. Show ellipsis instead.
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  */
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- .nowrap-ellipsis {
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+ td.nowrap-ellipsis {
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+ max-width: 0; /* https://stackoverflow.com/a/11877033 */
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  overflow-x: hidden;
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  white-space: nowrap;
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  text-overflow: ellipsis;
data/public/css/sequenceserver.min.css CHANGED
@@ -5,4 +5,4 @@ a,pre code,table{background-color:transparent}.label,audio,canvas,progress,sub,s
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  *//*! normalize.css v3.0.3 | MIT License | github.com/necolas/normalize.css */html{font-family:sans-serif;-webkit-text-size-adjust:100%;-ms-text-size-adjust:100%}article,aside,details,figcaption,figure,footer,header,hgroup,main,menu,nav,section,summary{display:block}audio,canvas,progress,video{display:inline-block}audio:not([controls]){display:none;height:0}[hidden],template{display:none}a:active,a:hover{outline:0}b,optgroup,strong{font-weight:700}dfn{font-style:italic}h1{margin:.67em 0}mark{color:#000;background:#ff0}sub,sup{position:relative;font-size:75%;line-height:0}sup{top:-.5em}sub{bottom:-.25em}img{border:0;vertical-align:middle}hr{height:0;-webkit-box-sizing:content-box;-moz-box-sizing:content-box;box-sizing:content-box}*,:after,:before,input[type=search]{-webkit-box-sizing:border-box;-moz-box-sizing:border-box}pre,textarea{overflow:auto}code,kbd,pre,samp{font-size:1em}button,input,optgroup,select,textarea{margin:0;font:inherit;color:inherit}button{overflow:visible}button,select{text-transform:none}button,html input[type=button],input[type=reset],input[type=submit]{-webkit-appearance:button;cursor:pointer}button[disabled],html input[disabled]{cursor:default}button::-moz-focus-inner,input::-moz-focus-inner{padding:0;border:0}input[type=checkbox],input[type=radio]{-webkit-box-sizing:border-box;-moz-box-sizing:border-box;box-sizing:border-box;padding:0}input[type=number]::-webkit-inner-spin-button,input[type=number]::-webkit-outer-spin-button{height:auto}input[type=search]::-webkit-search-cancel-button,input[type=search]::-webkit-search-decoration{-webkit-appearance:none}table{border-spacing:0;border-collapse:collapse}td,th{padding:0}/*! 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data/public/js/query.js CHANGED
@@ -92,10 +92,20 @@ export default React.createClass({
92
92
  var HitsTable = React.createClass({
93
93
  mixins: [Utils],
94
94
  render: function () {
95
- var count = 0,
96
- hasName = _.every(this.props.query.hits, function(hit) {
97
- return hit.sciname !== '';
98
- });
95
+ var hasName = _.every(this.props.query.hits, function(hit) {
96
+ return hit.sciname !== '';
97
+ });
98
+
99
+ // Width of sequence column is 55% when species name is not shown and
100
+ // query coverage is.
101
+ var seqwidth = 55;
102
+ // If we are going to show species name, then reduce the width of
103
+ // sequence column by the width of species column.
104
+ if (hasName) seqwidth -= 15;
105
+ // If we are not going to show query coverage (i.e. for imported XML),
106
+ // then increase the width of sequence column by the width of coverage
107
+ // column.
108
+ if (this.props.imported_xml) seqwidth += 15;
99
109
 
100
110
  return (
101
111
  <div className="table-hit-overview">
@@ -108,12 +118,12 @@ var HitsTable = React.createClass({
108
118
  className="table table-hover table-condensed tabular-view ">
109
119
  <thead>
110
120
  <th className="text-left">#</th>
111
- <th>Similar sequences</th>
112
- {hasName && <th className="text-left">Species</th>}
113
- {!this.props.imported_xml && <th className="text-right">Query coverage (%)</th>}
114
- <th className="text-right">Total score</th>
115
- <th className="text-right">E value</th>
116
- <th className="text-right" data-toggle="tooltip"
121
+ <th width={`${seqwidth}%`}>Similar sequences</th>
122
+ {hasName && <th width="15%" className="text-left">Species</th>}
123
+ {!this.props.imported_xml && <th width="15%" className="text-right">Query coverage (%)</th>}
124
+ <th width="10%" className="text-right">Total score</th>
125
+ <th width="10%" className="text-right">E value</th>
126
+ <th width="10%" className="text-right" data-toggle="tooltip"
117
127
  data-placement="left" title="Total identity of all hsps / total length of all hsps">
118
128
  Identity (%)
119
129
  </th>
@@ -124,12 +134,18 @@ var HitsTable = React.createClass({
124
134
  return (
125
135
  <tr key={hit.number}>
126
136
  <td className="text-left">{hit.number + '.'}</td>
127
- <td>
128
- <a href={'#Query_' + this.props.query.number + '_hit_' + hit.number} className="btn-link">
129
- {hit.id}
130
- </a>
137
+ <td className="nowrap-ellipsis"
138
+ title={`${hit.id} ${hit.title}`}
139
+ data-toggle="tooltip" data-placement="left">
140
+ <a href={'#Query_' + this.props.query.number + '_hit_' + hit.number}
141
+ className="btn-link">{hit.id} {hit.title}</a>
131
142
  </td>
132
- {hasName && <td className="text-left">{hit.sciname}</td>}
143
+ {hasName &&
144
+ <td className="nowrap-ellipsis" title={hit.sciname}
145
+ data-toggle="tooltip" data-placement="top">
146
+ {hit.sciname}
147
+ </td>
148
+ }
133
149
  {!this.props.imported_xml && <td className="text-right">{hit.qcovs}</td>}
134
150
  <td className="text-right">{hit.score}</td>
135
151
  <td className="text-right">{this.inExponential(hit.hsps[0].evalue)}</td>
data/public/sequenceserver-report.min.js CHANGED
@@ -2,18 +2,18 @@
2
2
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a.value}),max:d3.max(a,function(a){return a.value})}}},e.parsePositionTextData=function(a,b){var c,d;return d=a[0],"parent_id"in d&&"position"in d&&(a=a.map(function(a){return[a.parent_id,a.position,a.value]})),a=a.filter(function(a,c){return e.checkParent(a[0],c,b,"parent")}).filter(function(a,b){return e.checkNumber({position:a[1]},b)}).map(function(a){return{block_id:a[0],position:Math.min(b[a[0]],parseFloat(a[1])),value:a[2]}}),c=d3.nest().key(function(a){return a.block_id}).entries(a),{data:c,meta:{min:d3.min(a,function(a){return a.value}),max:d3.max(a,function(a){return a.value})}}},e.parseChordData=function(a,b){var c;return c=a[0],"source_id"in c&&"source_start"in c&&"target_id"in c&&"target_start"in c&&"target_end"in c&&(a=a.map(function(a){var b;return b=[a.source_id,a.source_start,a.source_end,a.target_id,a.target_start,a.target_end],null!=a.value&&b.push(a.value),b})),a=a.filter(function(a,c){return e.checkParent(a[0],c,b,"source_id")}).filter(function(a,c){return e.checkParent(a[3],c,b,"target_id")}).filter(function(a,b){return e.checkNumber({source_start:a[1],source_end:a[2],target_start:a[4],target_end:a[5],value:a[6]||1},b)}).map(function(a){return{source:{id:a[0],start:Math.max(0,parseFloat(a[1])),end:Math.min(b[a[0]],parseFloat(a[2]))},target:{id:a[3],start:Math.max(0,parseFloat(a[4])),end:Math.min(b[a[3]],parseFloat(a[5]))},value:parseFloat(a[6]),hsp:a[7]}}),{data:a,meta:{min:d3.min(a,function(a){return a.value}),max:d3.max(a,function(a){return a.value})}}},e.Layout=function(a,b){var c,d,f,g,h,i,j,k;null==b&&e.log(2,"no layout data",""),this.conf=e.mixConf(a,JSON.parse(JSON.stringify(this.defaultConf))),this.data=b,this.blocks={},this.size=0,g=0,h=this.data;for(f in h)k=h[f],this.blocks[k.id]={label:k.label,len:k.len,color:k.color,offset:g},k.offset=g,g+=k.len;this.size=g,d=this.conf.gap,j=this.size,c=this.data.length,i=this.data;for(f in i)k=i[f],this.blocks[k.id].start=k.offset/j*(2*Math.PI-c*d)+f*d,this.blocks[k.id].end=(k.offset+k.len)/j*(2*Math.PI-c*d)+f*d,k.start=k.offset/j*(2*Math.PI-c*d)+f*d,k.end=(k.offset+k.len)/j*(2*Math.PI-c*d)+f*d;return this.getAngle=function(a,b){var c;return c=this.blocks[a].start/this._size,"deg"===b?360*c:"rad"===b?2*c*Math.PI:null},this.summary=function(){var a,b,c,d,e;for(c={},e=this._data,b=0,d=e.length;b<d;b++)a=e[b],c[a.id]=a.len;return c},this},e.Core.prototype.heatmap=function(a,b,c){var d;return d=new e.Heatmap,d.build(this,b,c),this.tracks.heatmaps[a]=d,this},e.Core.prototype.histogram=function(a,b,c){var d;return d=new e.Histogram,d.build(this,b,c),this.tracks.histograms[a]=d,this},e.Core.prototype.chord=function(a,b,c){var d;return d=new e.Chord,d.build(this,b,c),this.tracks.chords[a]=d,this},e.Core.prototype.scatter=function(a,b,c){var d;return d=new e.Scatter,d.build(this,b,c),this.tracks.scatters[a]=d,this},e.Core.prototype.line=function(a,b,c){var d;return d=new 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("id",function(a){return a.source.id+"_"+a.target.id}).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),
4
4
  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("1c",["1b"],!0,function(a,b,c){this||self;c.exports=a("1b")}),c.register("1d",["17","20","21","22","23","1e","1c","1f"],function(a){var b,c,d,e,f,g,h,i,j,k;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},function(a){i=a.default}],execute:function(){j=function(){function a(b,d){var e=this;f(this,a),this.queries=[],d.queries.forEach(function(a){a.hits.length>0&&e.queries.push(a)}),this.svgContainer=b,this.seq_type=c.get_seq_type(d.program),this.algorithm=d.program,this.initiate()}return e(a,null,[{key:"name",value:function(){return"Queries and their top hits: chord diagram"}},{key:"className",value:function(){return"circos"}},{key:"collapseId",value:function(a){return"circos-collapse"}},{key:"dataName",value:function(a){return"Circos-visualisation"}}]),e(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=1,this.spacing=20,this.labelSpacing=10;var a={amino_acid:"aa",nucleic_acid:"bp"};this.construct_layout(),this.iterator_for_edits(),this.hit_arr=b.uniq(this.hit_arr),this.handle_spacing();var c=g.formatPrefix(this.max_length);this.suffix=" "+c.symbol+a[this.seq_type.subject_seq_type],"k"==c.symbol?this.denominator=1e3:"M"==c.symbol?(this.denominator=1e6,this.spacing=1e6,this.labelSpacing=2e5):"g"==c.symbol&&(this.denominator=1e9),g.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,c=32,d=this.queries.length,e=Math.min(c/2,d),f=(c-e)/e;this.new_layout=[],this.data=b.map(this.queries,b.bind(function(c){if(a<e){var d=c.id,g=c.length,h={len:g,color:"#8dd3c7",label:d,id:"Query_"+this.clean_id(c.id),ori_id:d};this.layout_arr.push(h);b.map(c.hits,b.bind(function(a){if(a.number<f){b.map(a.hsps,b.bind(function(d){if(b.indexOf(this.hit_arr,a.id)==-1){var e=a.id,f=a.length;this.hit_arr.push(a.id);var g={len:f,color:"#80b1d3",label:e,id:"Hit_"+this.clean_id(a.id),ori_id:e};this.layout_arr.push(g)}var h=["Query_"+this.clean_id(c.id),d.qstart,d.qend,"Hit_"+this.clean_id(a.id),d.sstart,d.send,a.number,d];return this.chords_arr.push(h),d},this));return a}},this))}return this.query_arr.push(c.id),c},this))}},{key:"rearrange_new_layout",value:function(){b.each(this.new_layout,b.bind(function(a){var b=a.id.slice(0,3);"Que"==b&&this.layout_arr.push(a)},this)),b.each(this.new_layout,b.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=[],b.each(this.layout_arr,b.bind(function(a,c){var d=(a.len/this.max_length).toFixed(3);a.label;d<.1&&"Que"!=a.id.slice(0,3)&&(this.delete_from_layout.push(a),this.hit_arr.slice(b.indexOf(this.hit_arr,a.label),1))},this))}},{key:"check_in_chords_arr",value:function(a,c,d){var e=0;b.each(this.chords_arr,b.bind(function(b){"Que"==c&&b[0]!=a&&e++},this)),e==this.chords_arr.length&&(console.log("no record found "+a),this.delete_arr.push(d))}},{key:"find_index_of_hit",value:function(a){var c;return b.each(this.queries,b.bind(function(d){b.each(d.hits,b.bind(function(b){var d="Hit_"+this.clean_id(b.id);a==d&&(c=b.id)},this))},this)),b.indexOf(this.layout_arr,c)}},{key:"edit_labels",value:function(){console.log("label edits"),b.each(this.layout_arr,b.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,c=0;b.each(this.query_arr,b.bind(function(c){b.each(this.data,b.bind(function(b){c==b.id&&(a+=b.length)},this))},this)),b.each(this.data,b.bind(function(a){b.each(a.hits,b.bind(function(a){var d=b.indexOf(this.hit_arr,a.id);d>=0&&(c+=a.length)},this))},this));var d=(a+c)/2;console.log("mid sum "+d+" hit_sum "+c+" query_sum "+a),this.query_multiplier=(d/a).toFixed(3),this.hit_multiplier=(d/c).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 b.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=g.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=[],b.each(this.layout_arr,function(a){$("."+a.id).css("opacity",1)})}},{key:"chordsReset",value:function(){this.chordsHide=[],b.each(this.chords_arr,function(a){var b=a[1]+a[2],c=a[4]+a[5];$("#"+a[0]+"_"+b+"_"+a[3]+"_"+c).show()})}},{key:"chordsCheck",value:function(a,c){b.each(this.chords_arr,b.bind(function(b,d){"Que"==c&&b[0]==a&&(this.chordsHide.push(d),this.layoutHide.push(b[3])),"Hit"==c&&b[3]==a&&(this.chordsHide.push(d),this.layoutHide.push(b[0]))},this))}},{key:"chordsClean",value:function(){b.each(this.chords_arr,b.bind(function(a,c){if(b.indexOf(this.chordsHide,c)==-1){var d=a[1]+a[2],e=a[4]+a[5];$("#"+a[0]+"_"+d+"_"+a[3]+"_"+e).hide()}},this))}},{key:"layoutClean",value:function(){b.each(this.layout_arr,b.bind(function(a,c){b.indexOf(this.layoutHide,a.id)==-1&&$("."+a.id).css("opacity",.1)},this))}},{key:"setupTooltip",value:function(){var a={};$(".circos-distribution").on("click",b.bind(function(b){b.stopPropagation(),this.layoutReset(),this.chordsReset(),a={}},this)),b.each(this.query_arr,b.bind(function(c,d){this.chordsHide=[],this.layoutHide=[],c&&$(".circos .Query_"+this.clean_id(c)).attr("data-toggle","tooltip").attr("title",c).on("click",b.bind(function(b){if(b.stopPropagation(),a[d]!=c){a[d]=c;var e="Query_"+this.clean_id(c);this.layoutHide.push(e),this.chordsCheck(e,"Que"),this.chordsClean(),this.layoutClean()}else a[d]=0,this.layoutReset(),this.chordsReset()},this))},this)),b.each(this.hit_arr,b.bind(function(c,d){this.chordsHide=[],this.layoutHide=[],c&&$(".circos .Hit_"+this.clean_id(c)).attr("data-toggle","tooltip").attr("title",c).on("click",b.bind(function(b){if(b.stopPropagation(),a[d]!=c){a[d]=c;var e="Hit_"+this.clean_id(c);this.layoutHide.push(e),this.chordsCheck(e,"Hit"),this.chordsClean(),this.layoutClean()}else a[d]=0,this.layoutReset(),this.chordsReset()},this))},this));var e=this.algorithm;b.each(this.chords_arr,function(a){$("#"+a[0]+"_"+a[3]).attr("data-toggle","tooltip").attr("title",function(){var b="E value: "+c.prettify_evalue(a[7].evalue)+(", Identities: "+d.inPercentage(a[7].identity,a[7].length));return"blastn"!=e&&(b+="<br>Positives: "+d.inPercentage(a[7].positives,a[7].length)),b+=", Gaps: "+d.inPercentage(a[7].gaps,a[7].length)})}),$('[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=[],b.each(this.chords_arr,b.bind(function(a){var b={number:a[6],evalue:a[7].evalue};this.ratioHSP.push(b)},this));var a=g.min(this.ratioHSP,function(a){return a.number}),c=g.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 "+c),this.legend=g.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",b.bind(function(b,d){var e=this.ratioCalculate(b.number,a,c,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),g.scale.linear().domain([0,250]).range([0,100])}}]),a}(),k=i(j),a("default",k)}}}),c.register("24",["17","20","21","22","23","1e","1f"],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,c){f(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 e(a,null,[{key:"name",value:function(){return"Graphical overview of hits"}},{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}}]),e(a,[{key:"extractData",value:function(a,c){var d=[];return a.map(function(a){var e=[],f=a.hsps;b.each(f,function(b){var d={};d.hspEvalue=b.evalue,d.hspStart=b.qstart,d.hspEnd=b.qend,d.hspFrame=b.sframe,d.hspId="Query_"+c+"_hit_"+a.number+"_hsp_"+b.number,d.hspIdentity=b.identity,d.hspGaps=b.gaps,d.hspPositives=b.positives,d.hspLength=b.length,e.push(d)}),e.hitId=a.id,e.hitDef="Query_"+c+"_hit_"+a.number,e.hitEvalue=a.evalue,d.push(e)}),d}},{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,c,d,e,f){var g,h,i,j,k=20,l=function(){g=f.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(),g===k||h<k?(i.hide(),j.hide()):h===g?(j.hide(),i.show()):h===k?(i.hide(),j.show()):(i.show(),j.show())};d===!0&&(m(a,c),n()),j.on("click",b.bind(function(b){l(),this.graphIt(a,c,h,k,e,f),n(),this.setupTooltip(),b.stopPropagation()},this)),i.on("click",b.bind(function(b){l();var d=h-k;d>=k?(this.graphIt(a,c,h,-k,e,f),n()):0!==d&&(this.graphIt(a,c,h,k-h,e,f),n()),this.setupTooltip(),b.stopPropagation()},this))}},{key:"drawLegend",value:function(a,b,c,d,e){var f=a.append("g").attr("transform","translate(0,"+(d-1.75*b.margin)+")");f.append("rect").attr("x",7.5*(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",9.5*(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",6.7*(c-2*b.margin)/10-b.margin/2).text("Stronger hits"),a.append("linearGradient").attr("id","legend-grad").selectAll("stop").data([{offset:"0%",color:"#000"},{offset:"45%",color:"#c74f14"},{offset:"100%",color:"#f6bea2"}]).enter().append("stop").attr("offset",function(a){return a.offset}).attr("stop-color",function(a){return a.color})}},{key:"graphIt",value:function(a,b,e,f,h,i){var j={barHeight:4,legend:i.length>1?3:0,margin:20},k=$.extend(j,h),l=i.slice(0,e+f);if(l.length<1)return!1;0!==e&&b.find("svg").remove();var m=a.data().queryLen,n=a.attr("id"),o=b.width(),p=l.length*k.barHeight+2*k.legend+4*k.margin,q={blastn:"nucleic_acid",blastp:"amino_acid",blastx:"nucleic_acid",tblastx:"nucleic_acid",tblastn:"amino_acid"},r=g.select(b[0]).selectAll("svg").data([l]).enter().insert("svg",":first-child").attr("width",o).attr("height",p).append("g").attr("transform","translate("+k.margin/2+", "+1.5*k.margin+")"),s=g.scale.linear().range([0,o-k.margin]);s.domain([1,m]);var t=a.data().algorithm,u=c.tick_formatter(s,q[t]),v=s.ticks(11);v.pop();var w=g.svg.axis().scale(s).orient("top").tickValues(v.concat([1,m])).tickFormat(u),x=r.append("g").attr("transform","translate(0, "+k.margin+")").append("g").attr("class","x axis").call(w);x.selectAll("text").attr("x","25px").attr("y","2px").attr("transform","rotate(-90)");var y=g.scale.ordinal().rangeBands([0,p-3*k.margin-2*k.legend],.3);y.domain(l.map(function(a){return a.hitId}));var z=g.scale.log().domain([g.min([1e-5,g.min(l.map(function(a){if(0!==parseFloat(a.hitEvalue))return a.hitEvalue}))]),g.max(l.map(function(a){return a.hitEvalue}))]).range([0,.8]);r.append("g").attr("class","ghit").attr("transform","translate(0, "+1.65*(k.margin-k.legend)+")").selectAll(".hits").data(l).enter().append("g").each(function(a,b){g.select(this).selectAll(".hsp").data(a).enter().append("a").each(function(e,f){var h=y(a.hitId)+k.barHeight/2,i=g.hsl(20,.82,z(e.hspEvalue));f+1<a.length&&(a[f].hspEnd<=a[f+1].hspStart?g.select(this.parentNode).append("line").attr("x1",s(a[f].hspEnd)).attr("y1",h).attr("x2",s(a[f+1].hspStart)).attr("y2",h).attr("stroke",i):a[f].hspStart>a[f+1].hspEnd&&g.select(this.parentNode).append("line").attr("x1",s(a[f+1].hspEnd)).attr("y1",h).attr("x2",s(a[f].hspStart)).attr("y2",h).attr("stroke",i));var j=a.hitId+"<br>E value: "+c.prettify_evalue(e.hspEvalue)+("<br>Identities: "+d.inPercentage(e.hspIdentity,e.hspLength));"blastn"!=t&&(j+="<br>Positives: "+d.inPercentage(e.hspPositives,e.hspLength)),j+=", Gaps: "+d.inPercentage(e.hspGaps,e.hspLength),g.select(this).attr("xlink:href","#"+n+"_hit_"+(b+1)).append("rect").attr("data-toggle","tooltip").attr("title",j).attr("class","bar").attr("x",function(a){return s(a.hspStart)}).attr("y",y(a.hitId)).attr("width",function(a){return s(a.hspEnd-a.hspStart+1)}).attr("height",k.barHeight).attr("fill",g.rgb(i))})}),l.length>1&&this.drawLegend(r,k,o,p,i),0===e&&this.graphControls(a,b,!0,h,i),this.setupTooltip(),this.setupClick(b)}}]),a}(),j=h(i),a("default",j)}}}),c.register("25",["17","20","22","23","1e","1f"],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,"blastx"==d.algorithm?this.query_length=this.query.length/3:"tblastn"==d.algorithm?this.query_length=3*this.query.length:this.query_length=this.query.length,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([0,1.01*f.max([this.query_length,f.max(this._data)])]).nice().range([0,this._width]),this._bins=f.layout.histogram().range(this._scale_x.domain()).bins(this._scale_x.ticks(50))(this._data),
5
- this._scale_y=f.scale.linear().domain([0,f.max(this._bins,function(a){return a.length})]).range([this._height,0]).nice()}},{key:"hit_lengths",value:function(){this._data=b.map(this.query.hits,b.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 c=b.debounce(b.bind(function(){a!=$(window).width()&&(console.log("redraw initiated "+this._height),this.draw(),a=$(window).width())},this),125);$(window).resize(c)}},{key:"tick_formatter",value:function(a){var c=this._scale_x.ticks(),d=f.format(".1f"),e=f.formatPrefix(c[c.length-1]),g={amino_acid:"aa",nucleic_acid:"bp"};return function(f){if(0!==f)return b.indexOf(c,f)>=0?"aa"==g[a]?f+" "+g[a]:d(e.scale(f))+" "+e.symbol+g[a]:void 0}}},{key:"update_data",value:function(){var a=this,d=[];this._bins.map(function(e){var f=[];e.reverse();var g=e.length;e.map(function(d,h){var i=e.length-(h+1),j=b.findIndex(a.query.hits,{length:d}),k={value:d,id:a.query.hits[j].id,evalue:a.query.hits[j].evalue,url:"#Query_"+a.query.number+"_hit_"+a.query.hits[j].number,y0:g,y1:g+=i-g,color:c.get_colors_for_evalue(a.query.hits[j].evalue,a.query.hits)};f.push(k)});var h={data:f,x:e.x,dx:e.dx,length:e.length};d.push(h)}),this._update_data=d}},{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","#c74f14"),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,c;c=this._scale_y.ticks().length,a=c>=5?5:c;var d=this.tick_formatter(this._seq_type.subject_seq_type),e=f.svg.axis().scale(this._scale_x).orient("bottom").ticks(50).tickFormat(d),g=f.svg.axis().scale(this._scale_y).orient("left").tickValues(this._scale_y.ticks(a)).outerTickSize(0).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){g.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(e);k.selectAll("line").attr("y2",function(a){var c=j._scale_x.ticks();return b.indexOf(c,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(g)}}]),a}(),i=g(h),a("default",i)}}}),c.register("26",["17","21","24","25","1a"],function(a){var b,c,d,e,f,g;return{setters:[function(a){b=a.default},function(a){c=a.default},function(a){d=a.default},function(a){e=a.default},function(a){f=a.default}],execute:function(){a("default",f.createClass({displayName:"query",domID:function(){return"Query_"+this.props.query.number},queryLength:function(){return this.props.query.length},numhits:function(){return this.props.query.hits.length},render:function(){return f.createElement("div",{className:"resultn",id:this.domID(),"data-query-len":this.props.query.length,"data-algorithm":this.props.program},this.headerJSX(),this.numhits()&&this.hitsListJSX()||this.noHitsJSX())},headerJSX:function(){var a="length: "+this.queryLength().toLocaleString();return this.props.showQueryCrumbs&&(a="query "+this.props.query.number+", "+a),f.createElement("div",{className:"section-header"},f.createElement("h3",null,f.createElement("strong",null,"Query= ",this.props.query.id)," ",this.props.query.title),f.createElement("span",{className:"label label-reset 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value"),f.createElement("th",{className:"text-right","data-toggle":"tooltip","data-placement":"left",title:"Total identity of all hsps / total length of all hsps"},"Identity (%)")),f.createElement("tbody",null,b.map(this.props.query.hits,b.bind(function(b){return f.createElement("tr",{key:b.number},f.createElement("td",{className:"text-left"},b.number+"."),f.createElement("td",null,f.createElement("a",{href:"#Query_"+this.props.query.number+"_hit_"+b.number,className:"btn-link"},b.id)),a&&f.createElement("td",{className:"text-left"},b.sciname),!this.props.imported_xml&&f.createElement("td",{className:"text-right"},b.qcovs),f.createElement("td",{className:"text-right"},b.score),f.createElement("td",{className:"text-right"},this.inExponential(b.hsps[0].evalue)),f.createElement("td",{className:"text-right"},b.identity))},this))))))}})}}}),c.registerDynamic("27",[],!1,function(a,b,d){var e=c.get("@@global-helpers").prepareGlobal(d.id,"d3",null);return function(a){"format global";"exports 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and database(s). The page will update automatically when BLAST is done.",f.createElement("br",null),f.createElement("br",null),"You can bookmark the page and come back to it later or share the link with someone.")))},resultsJSX:function(){return f.createElement("div",{className:"row"},this.shouldShowSidebar()&&f.createElement("div",{className:"col-md-3 hidden-sm hidden-xs"},f.createElement(b,{data:this.state,shouldShowIndex:this.shouldShowIndex()})),f.createElement("div",{className:this.shouldShowSidebar()?"col-md-9":"col-md-12"},this.overviewJSX(),this.circosJSX(),this.state.results))},overviewJSX:function(){return f.createElement("div",{className:"overview"},f.createElement("p",null,f.createElement("strong",null,"SequenceServer ",this.state.seqserv_version)," using ",f.createElement("strong",null,this.state.program_version),this.state.submitted_at&&", query submitted on "+this.state.submitted_at),f.createElement("p",null,f.createElement("strong",null," Databases: "),this.state.querydb.map(function(a){return a.title}).join(", ")," (",this.state.stats.nsequences," sequences, ",this.state.stats.ncharacters," characters)"),f.createElement("p",null,f.createElement("strong",null,"Parameters: ")," ",c.map(this.state.params,function(a,b){return b+" "+a}).join(", ")),f.createElement("p",null,"Please cite: ",f.createElement("a",{href:"https://doi.org/10.1093/molbev/msz185"},"https://doi.org/10.1093/molbev/msz185")))},circosJSX:function(){return this.atLeastTwoHits()?f.createElement(g,{queries:this.state.queries,program:this.state.program,collapsed:"true"}):f.createElement("span",null)},isResultAvailable:function(){return this.state.queries.length>=1},atLeastOneHit:function(){return this.state.queries.some(function(a){return a.hits.length>0})},atLeastTwoHits:function(){var a=0;return this.state.queries.some(function(b){return a+=b.hits.length,a>1})},shouldShowSidebar:function(){return!(1==this.state.queries.length&&0==this.state.queries[0].hits.length)},shouldShowIndex:function(){var a=this.state.queries.length;return a>=2&&a<=12},preventCollapseOnSelection:function(){$("body").on("mousedown",".hit > .section-header > h4",function(a){var b=$(this);b.on("mouseup mousemove",function a(c){if("mouseup"===c.type){var d=b.parents(".hit").attr("id");$("div[data-parent-hit="+d+"]").toggle(),b.find("i").toggleClass("fa-minus-square-o fa-plus-square-o")}else b.attr("data-toggle","");b.off("mouseup mousemove",a)})})},toggleTable:function(){$("body").on("mousedown",".resultn > .section-content > .table-hit-overview > .caption",function(a){var b=$(this);b.on("mouseup mousemove",function a(c){b.find("i").toggleClass("fa-minus-square-o fa-plus-square-o"),b.off("mouseup mousemove",a)})})},affixSidebar:function(){var a=$(".sidebar"),b=a.offset();b&&a.affix({offset:{top:b.top}})},setupScrollSpy:function(){$("body").scrollspy({target:".sidebar"})},selectHit:function(a){var b=$("#"+a),c=$(".hit-links :checkbox:checked").length;if(b&&b.val()){var d=$(b.data("target"));if(b.is(":checked")?(d.addClass("glow"),d.next(".hsp").addClass("glow"),$(".download-fasta-of-selected").enable(),$(".download-alignment-of-selected").enable()):(d.removeClass("glow"),d.next(".hsp").removeClass("glow")),c>=1){var e=$(".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("")}}}}),f.render(f.createElement(l,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: 2.0.0.rc5
4
+ version: 2.0.0.rc6
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: 2020-06-23 00:00:00.000000000 Z
14
+ date: 2020-08-10 00:00:00.000000000 Z
15
15
  dependencies:
16
16
  - !ruby/object:Gem::Dependency
17
17
  name: json_pure