sequenceserver 2.0.0.beta4 → 2.0.0.rc5

data/public/js/sequence_modal.js

@@ -0,0 +1,167 @@
+import './sequence';
+import React from 'react';
+import _ from 'underscore';
+import showErrorModal from './error_modal';
+
+/**
+ * Takes sequence accession as props, fetches the sequence from the server, and
+ * displays it in a modal.
+ */
+export default class SequenceModal extends React.Component {
+
+    constructor(props) {
+        super(props);
+        this.state = {
+            error_msgs: [],
+            sequences:  [],
+            requestCompleted: false
+        };
+    }
+
+    // Lifecycle methods. //
+
+    render () {
+        return (
+            <div className="modal sequence-viewer" ref="modal" tabIndex="-1">
+                <div className="modal-dialog">
+                    <div className="modal-content">
+                        <div className="modal-header">
+                            <h3>View sequence</h3>
+                        </div>
+
+                        { this.state.requestCompleted &&
+                            this.resultsJSX() || this.loadingJSX() }
+                    </div>
+                </div>
+            </div>
+        );
+    }
+
+    /*
+    * Returns jQuery reference to the main modal container.
+    */
+    modal () {
+        return $(React.findDOMNode(this.refs.modal));
+    }
+
+    /**
+     * Shows sequence viewer.
+     */
+    show (url) {
+        this.setState({requestCompleted: false}, () => {
+            this.modal().modal('show');
+            this.loadJSON(url);
+        });
+    }
+
+    /**
+     * Loads sequence using AJAX and updates modal state.
+     */
+    loadJSON (url) {
+        // Fetch sequence and update state.
+        $.getJSON(url)
+            .done(_.bind(function (response) {
+                this.setState({
+                    sequences: response.sequences,
+                    error_msgs: response.error_msgs,
+                    requestCompleted: true
+                });
+            }, this))
+            .fail(function (jqXHR, status, error) {
+                showErrorModal(jqXHR, function () {
+                    this.hide();
+                });
+            });
+
+    }
+
+    resultsJSX () {
+        return (
+            <div className="modal-body">
+                {
+                    _.map(this.state.error_msgs, _.bind(function (error_msg) {
+                        return (
+                            <div className="fastan">
+                                <div className="section-header">
+                                    <h4>
+                                        {error_msg[0]}
+                                    </h4>
+                                </div>
+                                <div className="section-content">
+                                    <pre className="pre-reset">
+                                        {error_msg[1]}
+                                    </pre>
+                                </div>
+                            </div>
+                        );
+                    }, this))
+                }
+                {
+                    _.map(this.state.sequences, _.bind(function (sequence) {
+                        return (<SequenceViewer sequence={sequence}/>);
+                    }, this))
+                }
+            </div>
+        );
+    }
+
+    loadingJSX () {
+        return (
+            <div className="modal-body text-center">
+                <i className="fa fa-spinner fa-3x fa-spin"></i>
+            </div>
+        );
+    }
+}
+
+class SequenceViewer extends React.Component {
+
+    /**
+     * The CSS class name that will be assigned to the widget container. ID
+     * assigned to the widget container is derived from the same.
+     */
+    static widgetClass () {
+        return 'biojs-vis-sequence';
+    }
+
+    render () {
+        this.widgetID =
+            this.widgetClass + '-' + (new Date().getUTCMilliseconds());
+
+        return (
+            <div className="fastan">
+                <div className="section-header">
+                    <h4>
+                        {this.props.sequence.id}
+                        <small>
+                            &nbsp; {this.props.sequence.title}
+                        </small>
+                    </h4>
+                </div>
+                <div className="section-content">
+                    <div
+                        className={this.widgetClass} id={this.widgetID}>
+                    </div>
+                </div>
+            </div>
+        );
+    }
+
+    componentDidMount () {
+        // attach BioJS sequence viewer
+        var widget = new Sequence({
+            sequence: this.props.sequence.value,
+            target: this.widgetID,
+            format: 'PRIDE',
+            columns: {
+                size: 40,
+                spacedEach: 0
+            },
+            formatOptions: {
+                title: false,
+                footer: false
+            }
+        });
+        widget.hideFormatSelector();
+    }
+}

data/public/js/sidebar.js

@@ -0,0 +1,210 @@
+import React from 'react';
+import _ from 'underscore';
+
+import downloadFASTA from './download_fasta';
+import AlignmentExporter from './alignment_exporter'; // to download textual alignment
+
+/**
+ * Renders links for downloading hit information in different formats.
+ * Renders links for navigating to each query.
+ */
+export default React.createClass({
+    /**
+     * Event-handler for downloading fasta of all hits.
+     */
+    downloadFastaOfAll: function () {
+        var sequence_ids = [];
+        this.props.data.queries.forEach(
+            (query) => query.hits.forEach(
+                (hit) => sequence_ids.push(hit.accession)));
+        var database_ids = this.props.data.querydb.map((querydb) => querydb.id);
+        downloadFASTA(sequence_ids, database_ids);
+        return false;
+    },
+
+    /**
+     * Handles downloading fasta of selected hits.
+     */
+    downloadFastaOfSelected: function () {
+        var sequence_ids = $('.hit-links :checkbox:checked').map(function () {
+            return this.value;
+        }).get();
+        var database_ids = _.map(this.props.data.querydb, _.iteratee('id'));
+        downloadFASTA(sequence_ids, database_ids);
+        return false;
+    },
+
+    downloadAlignmentOfAll: function() {
+        // Get number of hits and array of all hsps.
+        var num_hits = 0;
+        var hsps_arr = [];
+        this.props.data.queries.forEach(
+            (query) => query.hits.forEach(
+                (hit) => {
+                    num_hits++;
+                    hit.hsps.forEach((hsp) => {
+                        hsp.query_id = query.id;
+                        hsp.hit_id = hit.id;
+                        hsps_arr.push(hsp);
+                    });
+                }
+            )
+        );
+
+        var aln_exporter = new AlignmentExporter();
+        var file_name = `alignment-${num_hits}_hits`;
+        aln_exporter.export_alignments(hsps_arr, file_name);
+        return false;
+    },
+
+    downloadAlignmentOfSelected: function () {
+        var sequence_ids = $('.hit-links :checkbox:checked').map(function () {
+            return this.value;
+        }).get();
+        var hsps_arr = [];
+        var aln_exporter = new AlignmentExporter();
+        console.log('check '+sequence_ids.toString());
+        _.each(this.props.data.queries, _.bind(function (query) {
+            _.each(query.hits, function (hit) {
+                if (_.indexOf(sequence_ids, hit.accession) != -1) {
+                    _.each(hit.hsps, function (hsp) {
+                        hsp.hit_id = hit.id;
+                        hsp.query_id = query.id;
+                        hsps_arr.push(hsp);
+                    });
+                }
+            });
+        }, this));
+        aln_exporter.export_alignments(hsps_arr, 'alignment-'+sequence_ids.length+'_hits');
+        return false;
+    },
+
+
+    // JSX //
+    render: function () {
+        return (
+            <div className="sidebar">
+                { this.props.shouldShowIndex && this.index() }
+                { this.downloads() }
+            </div>
+        );
+    },
+
+    index: function () {
+        return (
+            <div className="index">
+                <div
+                    className="section-header-sidebar">
+                    <h4>
+                        { this.summary() }
+                    </h4>
+                </div>
+                <ul
+                    className="nav hover-reset active-bold">
+                    {
+                        _.map(this.props.data.queries, _.bind(function (query) {
+                            return (
+                                <li key={'Side_bar_'+query.id}>
+                                    <a
+                                        className="btn-link nowrap-ellipsis hover-bold"
+                                        href={'#Query_' + query.number}
+                                        title={'Query= ' + query.id + ' ' + query.title}>
+                                        {'Query= ' + query.id}
+                                    </a>
+                                </li>
+                            );
+                        }, this))
+                    }
+                </ul>
+            </div>
+        );
+    },
+
+    summary: function () {
+        var program = this.props.data.program;
+        var numqueries = this.props.data.queries.length;
+        var numquerydb = this.props.data.querydb.length;
+
+        return (
+            program.toUpperCase() + ': ' +
+            numqueries + ' ' + (numqueries > 1 ? 'queries' : 'query') + ', ' +
+            numquerydb + ' ' + (numquerydb > 1 ? 'databases' : 'database')
+        );
+    },
+
+    downloads: function () {
+        return (
+            <div className="downloads">
+                <div className="section-header-sidebar">
+                    <h4>
+                        Download FASTA, XML, TSV
+                    </h4>
+                </div>
+                <ul className="nav">
+                    {
+                        !this.props.data.imported_xml && <li>
+                            <a href="#" className="btn-link download-fasta-of-all"
+                                onClick={this.downloadFastaOfAll}>
+                                FASTA of all hits
+                            </a>
+                        </li>
+                    }
+                    {
+                        !this.props.data.imported_xml && <li>
+                            <a href="#" className="btn-link download-fasta-of-selected disabled"
+                                onClick={this.downloadFastaOfSelected}>
+                                FASTA of <span className="text-bold"></span> selected hit(s)
+                            </a>
+                        </li>
+                    }
+                    <li>
+                        <a href="#" className="btn-link download-alignment-of-all"
+                            onClick={this.downloadAlignmentOfAll}>
+                            Alignment of all hits
+                        </a>
+                    </li>
+                    <li>
+                        <a href="#" className="btn-link download-alignment-of-selected disabled"
+                            onClick={this.downloadAlignmentOfSelected}>
+                            Alignment of <span className="text-bold"></span> selected hit(s)
+                        </a>
+                    </li>
+                    {
+                        !this.props.data.imported_xml && <li>
+                            <a className="btn-link 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."
+                                href={'download/' + this.props.data.search_id + '.std_tsv'}>
+                                Standard tabular report
+                            </a>
+                        </li>
+                    }
+                    {
+                        !this.props.data.imported_xml && <li>
+                            <a className="btn-link 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
+                            </a>
+                        </li>
+                    }
+                    {
+                        !this.props.data.imported_xml && <li>
+                            <a className="btn-link download" data-toggle="tooltip"
+                                title="Results in XML format."
+                                href={'download/' + this.props.data.search_id + '.xml'}>
+                                Full XML report
+                            </a>
+                        </li>
+                    }
+                </ul>
+            </div>
+        );
+    },
+});
+

data/public/js/utils.js

@@ -1,23 +1,6 @@
 import React from 'react';
 
 var Utils = {
-
-    /**
-     * Render URL for sequence-viewer.
-     */
-    a: function (link) {
-        if (link.title && link.url)
-        {
-            return (
-                <a href={link.url} className={link.class} target='_blank'>
-                    {link.icon && <i className={'fa ' + link.icon}></i>}
-                    {' ' + link.title + ' '}
-                </a>
-            );
-        }
-    },
-
-
     /***********************************
      * Formatters for hits & hsp table *
      ***********************************/
@@ -31,7 +14,7 @@ var Utils = {
      * Returns fraction as percentage
      */
     inPercentage: function (num, den) {
-        var x = (num * 100.0 / den).toFixed(2);
+        var x = (num * 100.0 / den).toFixed(1);
         if (x % 1 == 0) {
             x = parseInt(x, 10);
             return `${x}%`;
@@ -77,7 +60,7 @@ var Utils = {
         var parts = exp.split('e');
         var base  = parts[0];
         var power = parts[1];
-        return <span>{base} &times; 10<sup>{power}</sup></span>;
+        return <span>{base}&times;10<sup>{power}</sup></span>;
     }
 };
 

data/public/js/visualisation_helpers.js

@@ -12,9 +12,9 @@ export function get_colors_for_evalue(evalue, hits) {
                 return d.evalue;
             }))
         ])
-        .range([40,150]);
+        .range([0,0.8]);
     var rgb = colors(evalue);
-    return d3.rgb(rgb, rgb , rgb);
+    return d3.hsl(20, 0.82 , rgb);
 }
 
 export function toLetters(num) {

data/public/sequenceserver-report.min.js

@@ -1,19 +1,19 @@
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a.opacity||b.opacity}).attr("d",d3.svg.arc().innerRadius(b.innerRadius).outerRadius(b.outerRadius).startAngle(function(a,b){return d.theta(a.start,c.blocks[a.block_id])}).endAngle(function(a,b){return d.theta(a.end,c.blocks[a.block_id])})).attr("class",function(a){return"q"+d.ratio(a.value,b.cmin,b.cmax,b.colorPaletteSize,b.colorPaletteReverse,b.logScale)+"-"+b.colorPaletteSize})},this},e.Highlight=function(){return e.Track.call(this),this.parseData=e.parseSpanStringData,this.renderDatumContainer=function(a){return function(b,c,d,e,f){var g;return g=a.renderBlock(c,e,b._layout,f)}}(this),this.renderDatum=function(a,b,c,d){return a.selectAll("tile").data(function(a){return a.values}).enter().append("path").attr("class","tile").attr("d",d3.svg.arc().innerRadius(b.innerRadius).outerRadius(b.outerRadius).startAngle(function(a,b){return d.theta(a.start,c.blocks[a.block_id])}).endAngle(function(a,b){return d.theta(a.end,c.blocks[a.block_id])})).attr("fill",function(a){return a.value||b.color}).attr("opacity",function(a){return a.opacity||b.opacity}).attr("stroke-width",function(a){return a.strokeWidth||b.strokeWidth}).attr("stroke",function(a){return a.strokeColor||b.strokeColor})},this},e.Histogram=function(){return e.Track.call(this),this.parseData=e.parseSpanValueData,this.renderDatumContainer=function(a){return function(b,c,d,e,f){var g,h;return h=c.append("g").attr("class",a.conf.colorPalette),g=a.renderBlock(h,e,b._layout,f)}}(this),this.renderDatum=function(a,b,c,e){var f;return f=a.selectAll(".bin").data(function(a){return a.values}).enter().append("path").attr("class","bin").attr("opacity",function(a){return a.opacity||b.opacity}).attr("d",d3.svg.arc().innerRadius(function(a){var c;return"in"===b.direction?(c=e.ratio(a.value,b.cmin,b.cmax,b.outerRadius-b.innerRadius,!1,b.logscale),b.outerRadius-c):b.innerRadius}).outerRadius(function(a){var c;return"out"===b.direction?(c=e.ratio(a.value,b.cmin,b.cmax,b.outerRadius-b.innerRadius,!1,b.logscale),b.innerRadius+c):b.outerRadius}).startAngle(function(a){return e.theta(a.start,c.blocks[a.block_id])}).endAngle(function(a){return e.theta(a.end,c.blocks[a.block_id])})),b.usePalette?f.attr("class",function(a){return"q"+e.ratio(a.value,b.cmin,b.cmax,b.colorPaletteSize,b.colorPaletteReverse,b.logScale)+"-"+b.colorPaletteSize}):f.attr("fill",d.color||b.color),f},this},e.Line=function(){return e.Track.call(this),this.parseData=e.parsePositionValueData,this.renderDatumContainer=function(a){return function(b,c,d,e,f){var g,h;return h=c.append("g").attr("class",d),g=a.renderBlock(h,e,b._layout,f)}}(this),this.renderDatum=function(a,b,c,d){var e;return e=d3.svg.line().x(function(a){return d.x(a,c,b)}).y(function(a){return d.y(a,c,b)}).interpolate(b.interpolation),a.append("path").datum(function(a){return a.values}).attr("class","line").attr("d",e).attr("opacity",function(a){return a.opacity||b.opacity}).attr("stroke-width",function(a){return a.thickness||b.thickness}).attr("stroke",function(a){return a.color||b.color}).attr("fill",function(a){var c,d;return d=a.fill||b.fill,c=a.fill_color||b.fill_color,d?c:"none"})},this},e.Scatter=function(){return e.Track.call(this),this.parseData=e.parsePositionValueData,this.renderDatumContainer=function(a){return function(b,c,d,e,f){var g,h;return h=c.append("g").attr("class",d),g=a.renderBlock(h,e,b._layout,f)}}(this),this.renderDatum=function(a,b,c,d){var e;return e=a.selectAll(".point").data(function(a){return a.values}).enter().append("path").attr("class","point").attr("opacity",function(a){return a.opacity||b.opacity}).attr("d",d3.svg.symbol().type(b.glyph.shape).size(b.glyph.size)).attr("transform",function(a){return function(a){return"translate("+d.x(a,c,b)+","+d.y(a,c,b)+") rotate("+360*d.theta(a.position,c.blocks[a.block_id])/(2*Math.PI)+")"}}(this)).attr("stroke",function(a){return a.glyph_strokeColor||b.glyph.strokeColor}).attr("stroke-width",function(a){return a.glyph_strokeWidth||b.glyph.strokeWidth}).attr("fill",function(a){var c,d;return d=a.glyph_fill||b.glyph.fill,c=a.glyph_color||b.glyph.color,d?c:"none"})},this},e.Stack=function(){return e.Track.call(this),this.parseData=e.parseSpanValueData,this.build=function(a,b,c,d,e){return this.loadData(c,a),this.conf=this.processConf(b,this.defaultConf,this.meta,a,this),this.buildLayers(this.data,this.conf.margin),this.applyRules(b.rules,this.data)},this.buildLayers=function(a,b){var c,d,e,f,g,h,i,j,k,l,m,n,o;for(f in a)for(c=a[f],c.values=c.values.sort(function(a,b){return a.start<b.start?-1:a.start===b.start&&a.end>b.end?-1:a.start===b.start&&a.end===b.end?0:1}),j=[],o=c.values,g=0,k=o.length;g<k;g++){for(d=o[g],n=!1,e=m=0,l=j.length;m<l;e=++m)if(i=j[e],h=i.slice(0).pop(),h.end+b<d.start){i.push(d),d.layer=e,n=!0;break}n||(d.layer=j.length),n||j.push([d])}},this.applyRules=function(a,b){var c,d,e,f,g,h,i;a=a||[],g=[];for(e in b)i=b[e],g.push(function(){var b,e;b=i.layers,e=[];for(d in b)f=b[d],e.push(function(){var b,e,g;for(g=[],b=0,e=f.length;b<e;b++)c=f[b],g.push(function(){var b,e,f;for(f=[],e=0,b=a.length;e<b;e++)h=a[e],h.condition(i.parent,c,d)?f.push(c[h.parameter]=h.value):f.push(void 0);return f}());return g}());return e}());return g},this.datumRadialPosition=function(a){return function(b){var c,d,e;return e=(a.conf.thickness+a.conf.radialMargin)*b.layer,d=e+a.conf.thickness,"out"===a.conf.direction?[a.conf.innerRadius+e,Math.min(a.conf.innerRadius+d,a.conf.outerRadius)]:"in"===a.conf.direction?[Math.max(a.conf.outerRadius-d,a.conf.innerRadius),a.conf.outerRadius-e]:"center"===a.conf.direction?(c=Math.floor((a.conf.outerRadius+a.conf.innerRadius)/2),e=(a.conf.thickness+a.conf.radialMargin)*Math.floor(b.layer/2),d=e+a.conf.thickness,b.layer%2===0?[c+e,c+d]:[c-e-a.conf.radialMargin,c-d-a.conf.radialMargin]):void 0}}(this),this.datumInnerRadius=function(a){return function(b,c,d){return a.datumRadialPosition(b,c,d)[0]}}(this),this.datumOuterRadius=function(a){return function(b,c,d){return a.datumRadialPosition(b,c,d)[1]}}(this),this.renderDatumContainer=function(a){return function(b,c,d,e,f){var g,h;return h=c.append("g").attr("class",f.colorPalette),g=a.renderBlock(h,e,b._layout,f)}}(this),this.renderDatum=function(a,b,c,d){var e;return e=a.selectAll(".tile").data(function(a){return a.values}).enter().append("path").attr("class","tile").attr("d",d3.svg.arc().innerRadius(d.datumInnerRadius).outerRadius(d.datumOuterRadius).startAngle(function(a){return d.theta(a.start,c.blocks[a.block_id])}).endAngle(function(a){return d.theta(a.end,c.blocks[a.block_id])})),e.attr("opacity",function(a){return a.opacity||b.opacity}),e.attr("stroke-width",function(a){return a.strokeWidth||b.strokeWidth}),e.attr("stroke",function(a){return a.strokeColor||b.strokeColor}),e.attr("fill",function(a){return a.color||b.color}),e.attr("class",function(a){var c;if(c=a.usePalette||b.usePalette)return"q"+d.ratio(a.value,b.cmin,b.cmax,b.colorPaletteSize,b.colorPaletteReverse,b.logScale)+"-"+b.colorPaletteSize}),e},this},e.Text=function(){return e.Track.call(this),this.parseData=e.parsePositionTextData,this.renderDatumContainer=function(a){return function(b,c,d,e,f){var g,h;return h=c.append("g").attr("class",d),g=a.renderBlock(h,e,b._layout,f)}}(this),this.renderDatum=function(a,b,c,d){var e,f,g,h;g=a.selectAll("g").data(function(a){return a.values}).enter().append("g").append("text").text(function(a){return a.value}).attr("transform",function(a){var e;return e=360*d.theta(a.position,c.blocks[a.block_id])/(2*Math.PI)-90,"rotate("+e+")translate("+b.innerRadius+",0)"}),f=b.style;for(e in f)h=f[e],g.style(e,h);return g},this},e.Track=function(){return this.build=function(a,b,c){return this.dispatch=d3.dispatch("mouseover","mouseout"),this.loadData(c,a),this.conf=this.processConf(b,this.defaultConf,this.meta,a,this),this.applyRules(b.rules,this.data)},this.loadData=function(a,b){var c,d,e,f,g,h;for(e={},g=b._layout.data,d=0,f=g.length;d<f;d++)c=g[d],e[c.id]=c.len;return h=this.parseData(a,e),this.data=h.data,this.meta=h.meta},this.processConf=function(a,b,c,d,f){var g;return a=e.mixConf(a,Object.assign({},b)),a=f.computeMinMax(a,c),0===a.innerRadius&&0===a.outerRadius&&(g=d.smartBorders(),a.innerRadius=g.in,a.outerRadius=g.out),a},this.applyRules=function(a,b){var c,d,e,f,g,h;a=a||[],f=[];for(e in b)h=b[e],f.push(function(){var b,e;b=h.values,e=[];for(d in b)c=b[d],e.push(function(){var b,e,f;for(f=[],b=0,e=a.length;b<e;b++)g=a[b],g.condition(h.key,c,d)?f.push(c[g.parameter]=g.value):f.push(void 0);return f}());return e}());return f},this.computeMinMax=function(a,b){return a.cmin="smart"===a.min?b.min:a.min,a.cmax="smart"===a.max?b.max:a.max,a},this.ratio=function(a,b,c,d,e,f){var g,h,i;return h=f?2.3:1,b===c||a===b&&!e||a===c&&e?0:a===c||a===b&&e?d-1:(g=(a-b)/(c-b),i=Math.exp(1/h*Math.log(g)),e&&(i=1-i),Math.floor(d*i))},this.render=function(a){return function(b,c,d){var f,g,h,i;return c.select("."+d).remove(),i=c.append("g").attr("class",d).attr("z-index",a.conf.zIndex),f=a.renderDatumContainer(b,i,d,a.data,a.conf),(null!=(g=a.conf.axes)?g.display:void 0)&&a.renderAxes(f,a.conf,b._layout,a.data),h=a.renderDatum(f,a.conf,b._layout,a),null!=a.conf.tooltipContent&&e.registerTooltip(b,a,h,a.conf),h.on("mouseover",function(b,c,d){return a.dispatch.mouseover(b,c,d)}),h.on("mouseout",function(b,c,d){return a.dispatch.mouseout(b,c,d)})}}(this),this.renderBlock=function(a,b,c,d){var e,f;return f=d.outerRadius-d.innerRadius,e=a.selectAll(".block").data(b).enter().append("g").attr("class","block").attr("transform",function(a){</span>
        </div>
    </td>
</tr><tr>
    <td class="d2h-code-linenumber d2h-del d2h-change">
      <div class="line-num1">4</div>
<div class="line-num2"></div>
    </a></td>
    <td class="d2h-del d2h-change">
        <div class="d2h-code-line d2h-del d2h-change">
            <span class="d2h-code-line-prefix">-</span>
            <span class="d2h-code-line-ctn">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","14","e","f","c"],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"Chord diagram: queries and their top hits"}},{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=h.uniq(this.hit_arr),this.handle_spacing();var b=g.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),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,b=32,c=this.queries.length,d=Math.min(b/2,c),e=(b-d)/d;this.new_layout=[],this.data=h.map(this.queries,h.bind(function(b){if(a<d){var c=b.id,f=b.length,g={len:f,color:"#8dd3c7",label:c,id:"Query_"+this.clean_id(b.id),ori_id:c};this.layout_arr.push(g);h.map(b.hits,h.bind(function(a){if(a.number<e){h.map(a.hsps,h.bind(function(c){if(h.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 g=["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(g),c},this));return a}},this))}return this.query_arr.push(b.id),b},this))}},{key:"rearrange_new_layout",value:function(){h.each(this.new_layout,h.bind(function(a){var b=a.id.slice(0,3);"Que"==b&&this.layout_arr.push(a)},this)),h.each(this.new_layout,h.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=[],h.each(this.layout_arr,h.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(h.indexOf(this.hit_arr,a.label),1))},this))}},{key:"check_in_chords_arr",value:function(a,b,c){var d=0;h.each(this.chords_arr,h.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 h.each(this.queries,h.bind(function(c){h.each(c.hits,h.bind(function(c){var d="Hit_"+this.clean_id(c.id);a==d&&(b=c.id)},this))},this)),h.indexOf(this.layout_arr,b)}},{key:"edit_labels",value:function(){console.log("label edits"),h.each(this.layout_arr,h.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;h.each(this.query_arr,h.bind(function(b){h.each(this.data,h.bind(function(c){b==c.id&&(a+=c.length)},this))},this)),h.each(this.data,h.bind(function(a){h.each(a.hits,h.bind(function(a){var c=h.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 h.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 i({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=[],h.each(this.layout_arr,function(a){$("."+a.id).css("opacity",1)})}},{key:"chordsReset",value:function(){this.chordsHide=[],h.each(this.chords_arr,function(a){var b=a[1]+a[2],c=a[4]+a[5];$("#"+a[0]+"_"+b+"_"+a[3]+"_"+c).show()})}},{key:"chordsCheck",value:function(a,b){h.each(this.chords_arr,h.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(){h.each(this.chords_arr,h.bind(function(a,b){if(h.indexOf(this.chordsHide,b)==-1){var c=a[1]+a[2],d=a[4]+a[5];$("#"+a[0]+"_"+c+"_"+a[3]+"_"+d).hide()}},this))}},{key:"layoutClean",value:function(){h.each(this.layout_arr,h.bind(function(a,b){h.indexOf(this.layoutHide,a.id)==-1&&$("."+a.id).css("opacity",.1)},this))}},{key:"setupTooltip",value:function(){var a={};$(".circos-distribution").on("click",h.bind(function(b){b.stopPropagation(),this.layoutReset(),this.chordsReset(),a={}},this)),h.each(this.query_arr,h.bind(function(b,c){this.chordsHide=[],this.layoutHide=[],b&&$(".circos .Query_"+this.clean_id(b)).attr("data-toggle","tooltip").attr("title",b).on("click",h.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)),h.each(this.hit_arr,h.bind(function(b,c){this.chordsHide=[],this.layoutHide=[],b&&$(".circos .Hit_"+this.clean_id(b)).attr("data-toggle","tooltip").attr("title",b).on("click",h.bind(function(d){if(d.stopPropagation(),a[c]!=b){a[c]=b;var e="Hit_"+this.clean_id(b);this.layoutHide.push(e),this.chordsCheck(e,"Hit"),this.chordsClean(),this.layoutClean()}else a[c]=0,this.layoutReset(),this.chordsReset()},this))},this));var b=this.algorithm;h.each(this.chords_arr,function(a){$("#"+a[0]+"_"+a[3]).attr("data-toggle","tooltip").attr("title",function(){var e="E value: "+c.prettify_evalue(a[7].evalue)+(", Identities: "+d.inPercentage(a[7].identity,a[7].length));return"blastn"!=b&&(e+="<br>Positives: "+d.inPercentage(a[7].positives,a[7].length)),e+=", Gaps: "+d.inPercentage(a[7].gaps,a[7].length)})}),$('[data-toggle="tooltip"]').tooltip({placement:"top",container:"body",html:"true",delay:0,"white-space":"nowrap"})}},{key:"ratioCalculate",value:function(a,b,c,d,e,f){var g,h,i;return h=f?2.3:1,b===c||a===b&&!e||a===c&&e?0:a===c||a===b&&e?d-1:(g=(a-b)/(c-b),i=Math.exp(1/h*Math.log(g)),e&&(i=1-i),Math.floor(d*i))}},{key:"drawLegend",value:function(){this.ratioHSP=[],h.each(this.chords_arr,h.bind(function(a){var b={number:a[6],evalue:a[7].evalue};this.ratioHSP.push(b)},this));var a=g.min(this.ratioHSP,function(a){return a.number}),b=g.max(this.ratioHSP,function(a){return a.number});console.log("chords_arr "+this.chords_arr.length),console.log("ratioHSP test "+this.ratioHSP.length),console.log("paletteSize "+this.paletteSize),console.log("min "+a+" max "+b),this.legend=g.select(this.svgContainer[0]).insert("svg",":first-child").attr("height",20).attr("width",30*this.ratioHSP.length).attr("transform","translate(10, 10)").append("g").attr("class","RdYlBu").attr("transform","translate(10, 0)");this.legend.selectAll(".bar").data(this.ratioHSP).enter().append("g").attr("class","g").attr("transform",function(a,b){return"translate("+30*b+",0)"}).append("rect").attr("class",h.bind(function(c,d){var e=this.ratioCalculate(c.number,a,b,this.paletteSize,!1,!1);return console.log("calc ratio "+e),"q"+e+"-"+this.paletteSize},this)).attr("data-toggle","tooltip").attr("title",function(a){return a.evalue}).attr("x",1).attr("width",30).attr("height",20),g.scale.linear().domain([0,250]).range([0,100])}}]),a}(),k=b(j),a("default",k)}}}),c.register("15",["10","11","12","13","14","e","f"],function(a){var b,c,d,e,f,g,h,i,j;return{setters:[function(a){b=a.default},function(a){c=a},function(a){d=a.default},function(a){e=a.default},function(a){f=a.default},function(a){g=a.default},function(a){h=a.default}],execute:function(){i=function(){function a(b,c){f(this,a),this.svg_container=b,$queryDiv=b.parents(".resultn"),hits=this.extractData(c.query.hits,c.query.number),this.graphIt($queryDiv,b,0,20,null,hits)}return e(a,null,[{key:"name",value:function(){return"Graphical overview of hits"}},{key:"className",value:function(){return"alignment-overview"}},{key:"collapseId",value:function(a){return"alignment_"+a.query.number}},{key:"dataName",value:function(a){return"Alignment-Overview-"+a.query.id}}]),e(a,[{key:"extractData",value:function(a,b){var c=[];return a.map(function(a){var d=[],e=a.hsps;h.each(e,function(c){var e={};e.hspEvalue=c.evalue,e.hspStart=c.qstart,e.hspEnd=c.qend,e.hspFrame=c.sframe,e.hspId="Query_"+b+"_hit_"+a.number+"_hsp_"+c.number,e.hspIdentity=c.identity,e.hspGaps=c.gaps,e.hspPositives=c.positives,e.hspLength=c.length,d.push(e)}),d.hitId=a.id,d.hitDef="Query_"+b+"_hit_"+a.number,d.hitEvalue=a.evalue,c.push(d)}),c}},{key:"setupTooltip",value:function(){this.svg_container.find('[data-toggle="tooltip"]').tooltip({placement:"top",container:"body",html:"true",delay:0,"white-space":"nowrap"})}},{key:"setupClick",value:function(a){$("a",a).click(function(a){a.preventDefault(),a.stopPropagation(),window.location.hash=$(this).attr("href")})}},{key:"graphControls",value:function(a,b,c,d,e){var f,g,i,j,k=20,l=function(){f=e.length,g=a.find(".ghit > g").length},m=function(a,b){b.append($("<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=$(".more",b)},n=function(){l(),f===k||g<k?(i.hide(),j.hide()):g===f?(j.hide(),i.show()):g===k?(i.hide(),j.show()):(i.show(),j.show())};c===!0&&(m(a,b),n()),j.on("click",h.bind(function(c){l(),this.graphIt(a,b,g,k,d,e),n(),this.setupTooltip(),c.stopPropagation()},this)),i.on("click",h.bind(function(c){l();var f=g-k;f>=k?(this.graphIt(a,b,g,-k,d,e),n()):0!==f&&(this.graphIt(a,b,g,k-g,d,e),n()),this.setupTooltip(),c.stopPropagation()},this))}},{key:"drawLegend",value:function(a,b,c,d,e){var f=a.append("g").attr("transform","translate(0,"+(d-1.88*b.margin)+")");f.append("rect").attr("x",7*(c-2*b.margin)/10).attr("width",2*(c-4*b.margin)/10).attr("height",b.legend).attr("fill","url(#legend-grad)"),f.append("text").attr("class"," legend-text").attr("transform","translate(0, "+b.legend+")").attr("x",6*(c-2*b.margin)/10-b.margin/2).text("Weaker hits"),f.append("text").attr("class"," legend-text").attr("transform","translate(0, "+b.legend+")").attr("x",9*(c-2*b.margin)/10+b.margin/2).text("Stronger hits"),a.append("linearGradient").attr("id","legend-grad").selectAll("stop").data([{offset:"0%",color:"#ccc"},{offset:"50%",color:"#888"},{offset:"100%",color:"#000"}]).enter().append("stop").attr("offset",function(a){return a.offset}).attr("stop-color",function(a){return a.color})}},{key:"graphIt",value:function(a,b,e,f,h,i){var j={barHeight:3,legend:i.length>1?3:0,margin:20},k=$.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+5*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([40,150]);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.rgb(z(e.hspEvalue),z(e.hspEvalue),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=b(i),a("default",j)}}}),c.register("16",["10","11","13","14","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,"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 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<div class="line-num2"></div>
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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=$(b.data("target"));if(b.is(":checked")?(d.find(".section-content").addClass("glow"),$(".download-alignment-of-selected").enable(),$(".download-fasta-of-selected").enable()):d.find(".section-content").removeClass("glow"),c>=1){var e=$(".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("")}}}}),p=g.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 g.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),g.createElement("div",{className:"section-header"},g.createElement("h3",null,"Query= ",this.props.query.id," ",g.createElement("small",null,this.props.query.title)),g.createElement("span",{className:"label label-reset pos-label"},a))},hitsListJSX:function(){return g.createElement("div",{className:"section-content"},g.createElement(d,{key:"GO_"+this.props.query.number,query:this.props.query,program:this.props.program,collapsed:this.props.veryBig}),g.createElement(e,{key:"LD_"+this.props.query.id,query:this.props.query,algorithm:this.props.program,collapsed:"true"}),g.createElement(q,{key:"HT_"+this.props.query.number,query:this.props.query,imported_xml:this.props.imported_xml}),g.createElement("div",{id:"hits"},h.map(this.props.query.hits,h.bind(function(a){return g.createElement(r,{key:"HIT_"+a.number,hit:a,algorithm:this.props.program,querydb:this.props.querydb,query:this.props.query,imported_xml:this.props.imported_xml,selectHit:this.props.selectHit,showHitCrumbs:this.numhits()>1,showQueryCrumbs:this.props.showQueryCrumbs})},this))))},noHitsJSX:function(){return g.createElement("div",{className:"section-content"},g.createElement("br",null),g.createElement("p",null,g.createElement("strong",null," ****** No hits found ****** ")))},shouldComponentUpdate:function(a,b){if(!this.props.query)return!0}}),q=g.createClass({displayName:"HitsTable",mixins:[c],render:function(){var a=h.every(this.props.query.hits,function(a){return""!==a.sciname});return g.createElement("table",{className:"table table-hover table-condensed tabular-view"},g.createElement("thead",null,g.createElement("th",{className:"text-left"},"#"),g.createElement("th",null,"Similar sequences"),a&&g.createElement("th",{className:"text-left"},"Species"),!this.props.imported_xml&&g.createElement("th",{className:"text-right"},"Query coverage (%)"),g.createElement("th",{className:"text-right"},"Total score"),g.createElement("th",{className:"text-right"},"E value"),g.createElement("th",{className:"text-right","data-toggle":"tooltip","data-placement":"left",title:"Total identity of all hsps / total length of all hsps"},"Identity (%)")),g.createElement("tbody",null,h.map(this.props.query.hits,h.bind(function(b){return g.createElement("tr",{key:b.number},g.createElement("td",{className:"text-left"},b.number+"."),g.createElement("td",null,g.createElement("a",{</span>
        </div>
    </td>
</tr><tr>
    <td class="d2h-code-linenumber d2h-del d2h-change">
      <div class="line-num1">19</div>
<div class="line-num2"></div>
    </a></td>
    <td class="d2h-del d2h-change">
        <div class="d2h-code-line d2h-del d2h-change">
            <span class="d2h-code-line-prefix">-</span>
            <span class="d2h-code-line-ctn">href:"#Query_"+this.props.query.number+"_hit_"+b.number},b.id)),a&&g.createElement("td",{className:"text-left"},b.sciname),!this.props.imported_xml&&g.createElement("td",{className:"text-right"},b.qcovs),g.createElement("td",{className:"text-right"},b.score),g.createElement("td",{className:"text-right"},this.inExponential(b.hsps[0].evalue)),g.createElement("td",{className:"text-right"},b.identity))},this))))}}),r=g.createClass({displayName:"Hit",mixins:[c],accession:function(){return this.props.hit.accession},hitLength:function(){return this.props.hit.length},domID:function(){return"Query_"+this.props.query.number+"_hit_"+this.props.hit.number},databaseIDs:function(){return h.map(this.props.querydb,h.iteratee("id"))},showSequenceViewer:function(a){this.setState({showSequenceViewer:!0}),a&&a.preventDefault()},hideSequenceViewer:function(){this.setState({showSequenceViewer:!1})},viewSequenceLink:function(){return encodeURI("get_sequence/?sequence_ids="+this.accession()+"&database_ids="+this.databaseIDs())},downloadFASTA:function(a){var b=[this.accession()];m(b,this.databaseIDs())},downloadAlignment:function(a){var b=h.map(this.props.hit.hsps,h.bind(function(a){return a.query_id=this.props.query.id,a.hit_id=this.props.hit.id,a},this)),c=new k;c.export_alignments(b,this.props.query.id+"_"+this.props.hit.id)},getInitialState:function(){return{showSequenceViewer:!1}},viewSequenceButton:function(){return this.hitLength()>1e4?g.createElement("button",{className:"btn btn-link view-sequence disabled",title:"Sequence too long",disabled:"true"},g.createElement("i",{className:"fa fa-eye"})," Sequence"):g.createElement("button",{className:"btn btn-link view-sequence",onClick:this.showSequenceViewer},g.createElement("i",{className:"fa fa-eye"})," Sequence")},render:function(){return g.createElement("div",{className:"hit",id:this.domID(),"data-hit-def":this.props.hit.id,"data-hit-len":this.props.hit.length,"data-hit-evalue":this.props.hit.evalue},this.headerJSX()," ",this.contentJSX())},headerJSX:function(){var a="length: "+this.hitLength().toLocaleString();return this.props.showQueryCrumbs&&this.props.showHitCrumbs?a="hit "+this.props.hit.number+" of query "+this.props.query.number+", "+a:this.props.showQueryCrumbs&&!this.props.showHitCrumbs?a="the only hit of query "+this.props.query.number+", "+a:!this.props.showQueryCrumbs&&this.props.showHitCrumbs&&(a="hit "+this.props.hit.number+", "+a),g.createElement("div",{className:"section-header"},g.createElement("h4",{"data-toggle":"collapse","data-target":this.domID()+"_content"},g.createElement("i",{className:"fa fa-chevron-down"})," ",g.createElement("span",null,this.props.hit.id," ",g.createElement("small",null,this.props.hit.title))),g.createElement("span",{className:"label label-reset pos-label"},a))},contentJSX:function(){return g.createElement("div",{id:this.domID()+"_content",className:"section-content collapse in"},this.hitLinks(),g.createElement(j,{key:"kablammo"+this.props.query.id,query:this.props.query,hit:this.props.hit,algorithm:this.props.algorithm}),this.hspListJSX())},hitLinks:function(){return g.createElement("div",{className:"hit-links"},g.createElement("label",null,g.createElement("input",{type:"checkbox",id:this.domID()+"_checkbox",value:this.accession(),onChange:function(){this.props.selectHit(this.domID()+"_checkbox")}.bind(this),"data-target":"#"+this.domID()})," Select"),!this.props.imported_xml&&[g.createElement("span",null," | "),this.viewSequenceButton(),this.state.showSequenceViewer&&g.createElement(s,{url:this.viewSequenceLink(),onHide:this.hideSequenceViewer})],!this.props.imported_xml&&[g.createElement("span",null," | "),g.createElement("button",{className:"btn btn-link download-fa",onClick:this.downloadFASTA},g.createElement("i",{className:"fa fa-download"})," FASTA")],g.createElement("span",null," | "),g.createElement("button",{className:"btn btn-link download-aln",onClick:this.downloadAlignment},g.createElement("i",{className:"fa fa-download"})," Alignment"),h.map(this.props.hit.links,h.bind(function(a){return[g.createElement("span",null," | "),this.a(a)]},this)))},hspListJSX:function(){var a=this;return g.createElement("div",{className:"hsps"},this.props.hit.hsps.map(function(b){return g.createElement(f,{key:b.number,algorithm:a.props.algorithm,queryNumber:a.props.query.number,hitNumber:a.props.hit.number,hsp:b})},this))}}),s=function(){var a=g.createClass({displayName:"Viewer",widgetClass:"biojs-vis-sequence",render:function(){return this.widgetID=this.widgetClass+"-"+(new Date).getUTCMilliseconds(),g.createElement("div",{className:"fastan"},g.createElement("div",{className:"section-header"},g.createElement("h4",null,this.props.sequence.id,g.createElement("small",null,"  ",this.props.sequence.title))),g.createElement("div",{className:"section-content"},g.createElement("div",{className:this.widgetClass,id:this.widgetID})))},componentDidMount:function(){var a=new Sequence({sequence:this.props.sequence.value,target:this.widgetID,format:"PRIDE",columns:{size:40,spacedEach:0},formatOptions:{title:!1,footer:!1}});a.hideFormatSelector()}});return g.createClass({show:function(){this.modal().modal("show")},modal:function(){return $(g.findDOMNode(this.refs.modal))},resultsJSX:function(){return g.createElement("div",{className:"modal-body"},h.map(this.state.error_msgs,h.bind(function(a){return g.createElement("div",{className:"fastan"},g.createElement("div",{className:"section-header"},g.createElement("h4",null,a[0])),g.createElement("div",{className:"section-content"},g.createElement("pre",{className:"pre-reset"},a[1])))},this)),h.map(this.state.sequences,h.bind(function(b){return g.createElement(a,{sequence:b})},this)))},loadingJSX:function(){return g.createElement("div",{className:"modal-body text-center"},g.createElement("i",{className:"fa fa-spinner fa-3x fa-spin"}))},getInitialState:function(){return{error_msgs:[],sequences:[],requestCompleted:!1}},render:function(){return g.createElement("div",{className:"modal sequence-viewer",ref:"modal",tabIndex:"-1"},g.createElement("div",{className:"modal-dialog"},g.createElement("div",{className:"modal-content"},g.createElement("div",{className:"modal-header"},g.createElement("h3",null,"View sequence")),this.state.requestCompleted&&this.resultsJSX()||this.loadingJSX())))},componentDidMount:function(){this.show(),$.getJSON(this.props.url).done(h.bind(function(a){this.setState({sequences:a.sequences,error_msgs:a.error_msgs,requestCompleted:!0})},this)).fail(function(a,b,c){l(a,function(){this.hide()})}),this.modal().on("hidden.bs.modal",this.props.onHide)}})}(),t=g.createClass({displayName:"SideBar",downloadFastaOfAll:function(){var a=$(".hit-links :checkbox").map(function(){return this.value}).get(),b=h.map(this.props.data.querydb,h.iteratee("id"));return m(a,b),!1},downloadFastaOfSelected:function(){var a=$(".hit-links :checkbox:checked").map(function(){return this.value}).get(),b=h.map(this.props.data.querydb,h.iteratee("id"));return m(a,b),!1},downloadAlignmentOfAll:function(){var a=$(".hit-links :checkbox").map(function(){return this.value}).get(),b=[],c=new k;return h.each(this.props.data.queries,h.bind(function(a){h.each(a.hits,function(c){h.each(c.hsps,function(d){d.hit_id=c.id,d.query_id=a.id,b.push(d)})})},this)),console.log("len "+b.length),c.export_alignments(b,"alignment-"+a.length+"_hits"),!1},downloadAlignmentOfSelected:function(){var a=$(".hit-links :checkbox:checked").map(function(){return this.value}).get(),b=[],c=new k;return console.log("check "+a.toString()),h.each(this.props.data.queries,h.bind(function(c){h.each(c.hits,function(d){h.indexOf(a,d.accession)!=-1&&h.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"),!1},render:function(){return g.createElement("div",{className:"sidebar"},this.props.shouldShowIndex&&this.index(),this.downloads())},index:function(){return g.createElement("div",{className:"index"},g.createElement("div",{className:"section-header"},g.createElement("h4",null,this.summary())),g.createElement("ul",{className:"nav hover-reset active-bold"},h.map(this.props.data.queries,h.bind(function(a){return g.createElement("li",{key:"Side_bar_"+a.id},g.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 g.createElement("div",{className:"downloads"},g.createElement("div",{className:"section-header"},g.createElement("h4",null,"Download FASTA, XML, TSV")),g.createElement("ul",{className:"nav"},!this.props.data.imported_xml&&g.createElement("li",null,g.createElement("a",{href:"#",className:"btn-link download-fasta-of-all",onClick:this.downloadFastaOfAll},"FASTA of all hits")),!this.props.data.imported_xml&&g.createElement("li",null,g.createElement("a",{href:"#",className:"btn-link download-fasta-of-selected disabled",onClick:this.downloadFastaOfSelected},"FASTA of ",g.createElement("span",{className:"text-bold"})," selected hit(s)")),g.createElement("li",null,g.createElement("a",{href:"#",className:"btn-link download-alignment-of-all",onClick:this.downloadAlignmentOfAll},"Alignment of all hits")),g.createElement("li",null,g.createElement("a",{href:"#",className:"btn-link download-alignment-of-selected disabled",onClick:this.downloadAlignmentOfSelected},"Alignment of ",g.createElement("span",{className:"text-bold"})," selected hit(s)")),!this.props.data.imported_xml&&g.createElement("li",null,g.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.",href:"download/"+this.props.data.search_id+".std_tsv"},"Standard tabular report")),!this.props.data.imported_xml&&g.createElement("li",null,g.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")),!this.props.data.imported_xml&&g.createElement("li",null,g.createElement("a",{className:"download","data-toggle":"tooltip",title:"Results in XML format.",href:"download/"+this.props.data.search_id+".xml"},"Full XML report"))))}}),g.render(g.createElement(n,null),document.getElementById("view"))}}})})(function(a){a()});</span>
        </div>
    </td>
</tr><tr>
    <td class="d2h-code-linenumber d2h-ins d2h-change">
      <div class="line-num1"></div>
<div class="line-num2">1</div>
    </a></td>
    <td class="d2h-ins d2h-change">
        <div class="d2h-code-line d2h-ins d2h-change">
            <span class="d2h-code-line-prefix">+</span>
            <span class="d2h-code-line-ctn">!function(a){function b(a,b,e){return 4===arguments.length?c.apply(this,arguments):void d(a,{declarative:!0,deps:b,declare:e})}function c(a,b,c,e){d(a,{declarative:!1,deps:b,executingRequire:c,execute:e})}function d(a,b){b.name=a,a in o||(o[a]=b),b.normalizedDeps=b.deps}function e(a,b){if(b[a.groupIndex]=b[a.groupIndex]||[],-1==p.call(b[a.groupIndex],a)){b[a.groupIndex].push(a);for(var c=0,d=a.normalizedDeps.length;d>c;c++){var f=a.normalizedDeps[c],g=o[f];if(g&&!g.evaluated){var h=a.groupIndex+(g.declarative!=a.declarative);if(void 0===g.groupIndex||g.groupIndex<h){if(void 0!==g.groupIndex&&(b[g.groupIndex].splice(p.call(b[g.groupIndex],g),1),0==b[g.groupIndex].length))throw new TypeError("Mixed dependency cycle detected");g.groupIndex=h}e(g,b)}}}}function f(a){var b=o[a];b.groupIndex=0;var c=[];e(b,c);for(var d=!!b.declarative==c.length%2,f=c.length-1;f>=0;f--){for(var g=c[f],i=0;i<g.length;i++){var k=g[i];d?h(k):j(k)}d=!d}}function g(a){return s[a]||(s[a]={name:a,dependencies:[],exports:{},importers:[]})}function h(b){if(!b.module){var c=b.module=g(b.name),d=b.module.exports,e=b.declare.call(a,function(a,b){if(c.locked=!0,"object"==typeof a)for(var e in a)d[e]=a[e];else d[a]=b;for(var f=0,g=c.importers.length;g>f;f++){var h=c.importers[f];if(!h.locked)for(var i=0;i<h.dependencies.length;++i)h.dependencies[i]===c&&h.setters[i](d)}return c.locked=!1,b},{id:b.name});c.setters=e.setters,c.execute=e.execute;for(var f=0,i=b.normalizedDeps.length;i>f;f++){var j,k=b.normalizedDeps[f],l=o[k],m=s[k];m?j=m.exports:l&&!l.declarative?j=l.esModule:l?(h(l),m=l.module,j=m.exports):j=n(k),m&&m.importers?(m.importers.push(c),c.dependencies.push(m)):c.dependencies.push(null),c.setters[f]&&c.setters[f](j)}}}function i(a){var b,c=o[a];if(c)c.declarative?m(a,[]):c.evaluated||j(c),b=c.module.exports;else if(b=n(a),!b)throw new Error("Unable to load dependency "+a+".");return(!c||c.declarative)&&b&&b.__useDefault?b.default:b}function 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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),</span>
        </div>
    </td>
</tr><tr>
    <td class="d2h-code-linenumber d2h-ins d2h-change">
      <div class="line-num1"></div>
<div class="line-num2">4</div>
    </a></td>
    <td class="d2h-ins d2h-change">
        <div class="d2h-code-line d2h-ins d2h-change">
            <span class="d2h-code-line-prefix">+</span>
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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 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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 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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: 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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 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    </td>
</tr><tr>
    <td class="d2h-code-linenumber d2h-ins d2h-change">
      <div class="line-num1"></div>
<div class="line-num2">6</div>
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<div class="line-num2">8</div>
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        </div>
    </td>
</tr><tr>
    <td class="d2h-code-linenumber d2h-ins d2h-change">
      <div class="line-num1"></div>
<div class="line-num2">9</div>
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    <td class="d2h-ins d2h-change">
        <div class="d2h-code-line d2h-ins d2h-change">
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<div class="line-num2">12</div>
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value="RAW">RAW</option></select>').appendTo(a._headerDiv),this._formatSelector.change(function(b){a.opt.format=jQuery(this).val(),a._redraw()}),this._formatSelector.val(a.opt.format),this.formatSelectorVisible(this.opt.formatSelectorVisible)},addHighlight:function(a){var b="-1",c="",d="",e={};return a instanceof Object&&a.start<=a.end&&(c="string"==typeof a.color?a.color:this.opt.highlightFontColor,d="string"==typeof a.background?a.background:this.opt.highlightBackgroundColor,b="string"==typeof a.id?a.id:new Number(this._highlightsCount++).toString(),e={start:a.start,end:a.end,color:c,background:d,id:b},this._highlights.push(e),this._applyHighlight(e),this._restoreSelection(a.start,a.end)),b},_applyHighlight:function(a){for(var 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e={numCols:d,numColsForSpace:0};c+=this._drawSequence(a,e),b.html(c),this._drawAnnotations(e)},_drawCodata:function(){var a=this.opt.sequence.toUpperCase().split("");if(void 0!==this.opt.formatOptions&&void 0!==this.opt.formatOptions.title&&0!=this.opt.formatOptions.title){var b=j("<pre/>").addClass("header").appendTo(this._contentDiv);b.html("ENTRY           "+this.opt.id+"<br/>SEQUENCE<br/>")}var c=this.opt.columns.size;this.opt.sequence.length<this.opt.columns.size&&(c=this.opt.sequence.length);var d={numLeft:!0,numLeftSize:7,numLeftPad:" ",numTop:!0,numTopEach:5,numCols:c,numColsForSpace:0,spaceBetweenChars:!0};if(this._drawSequence(a,d),void 0!==this.opt.formatOptions&&void 0!==this.opt.formatOptions.footer&&0!=this.opt.formatOptions.footer){var e=j("<pre/>").addClass("footer").appendTo(this._contentDiv);e.html("<br/>///")}this._drawAnnotations(d)},_drawAnnotations:function(a){var b=this,c=this.opt.sequence.toLowerCase().split(""),d=this._annotations,e="",f="",g="";a.numLeft&&(e+=this._formatIndex(" ",a.numLeftSize+2," "));for(var h=0;h<c.length;h+=a.numCols){f="";for(var i in d)d[i].id=this.getId()+"_"+i,g=this._getHTMLRowAnnot(h+1,d[i],a),g.length>0&&(f+="<br/>",f+=e,f+=g,f+="<br/>");var j=a.numCols,l=c.length-h;l<j&&(j=l),a.numRight?jQuery(f).insertAfter("div#"+b.opt.target+" div pre span#numRight_"+this.getId()+"_"+(h+j)):jQuery(f).insertAfter("div#"+b.opt.target+" div pre span#"+this.getId()+"_"+(h+j))}jQuery(this._contentDiv).find(".annotation").each(function(){b._addToolTip(this,function(){return b._getAnnotationString(jQuery(this).attr("id"))}),jQuery(this).mouseover(function(a){jQuery(".annotation."+jQuery(a.target).attr("id")).each(function(){jQuery(this).css("background-color",jQuery(this).attr("color"))})}).mouseout(function(){jQuery(".annotation").css("background-color","transparent")}).click(function(a){for(var c=void 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a=this.opt.sequence.toUpperCase().split(""),b=this.opt.columns.size;this.opt.sequence.length<this.opt.columns.size&&(b=this.opt.sequence.length),opt={numLeft:!0,numLeftSize:5,numLeftPad:" ",numRight:!1,numRightSize:5,numRightPad:"",numCols:b,numColsForSpace:this.opt.columns.spacedEach},this._drawSequence(a,opt),this._drawAnnotations(opt)},_drawSequence:function(a,b){var c="",d="",e="\n",f="";if(b.numTop){d+='<span class="numTop pos-marker">';var g=b.spaceBetweenChars?2*b.numTopEach:b.numTopEach;b.numLeft&&(d+=this._formatIndex(" ",b.numLeftSize," ")),d+=this._formatIndex(" ",g," ");for(var h=b.numTopEach;h<b.numCols;h+=b.numTopEach)d+=this._formatIndex(h,g," ",!0);d+="</span>"}b.numLeft&&(c+='<span id="numLeft_'+this.getId()+'_0"',c+='class="pos-marker">',c+=this._formatIndex(1,b.numLeftSize,b.numLeftPad),c+="  ",c+="</span>",c+="\n");for(var i=1,k=1;k<=a.length;k++)if(k%b.numCols==0){f+='<span class="sequence" id="'+this.getId()+"_"+k+'">'+a[k-1]+"</span>",b.numRight&&(e+='<span 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b.numTop&&j("<pre/>").html(d).addClass("indT").css({color:"#aaa"}).appendTo(this._contentDiv),b.numLeft&&j("<pre/>").html(c).addClass("indL").css({color:"#aaa",display:"inline-block"}).appendTo(this._contentDiv),j("<pre/>").html(f).addClass("seqF").css({display:"inline-block"}).appendTo(this._contentDiv),b.numRight&&j("<pre/>").html(e).addClass("indR").css({color:"#aaa",display:"inline-block"}).appendTo(this._contentDiv),f},_formatIndex:function(a,b,c,d){var e=a.toString(),f="",g=b-e.length;if(g>0){for(;g-- >0;)f+="<span>"+c+"</span>";e=d?a+f:f+a}return e},_addSpanEvents:function(){var a,b,c=this,d=!1;c._contentDiv.find(".sequence").each(function(){jQuery(this).mousedown(function(){var e=jQuery(this).attr("id");b=parseInt(e.substr(e.indexOf("_")+1)),a=b,c._setSelection(a,b),d=!0,c.trigger(g,{start:c.opt.selection.start,end:c.opt.selection.end})}).mouseover(function(){var e=jQuery(this).attr("id");b=parseInt(e.substr(e.indexOf("_")+1)),d&&(b>a?c._setSelection(a,b):c._setSelection(b,a),c.trigger(g,{start:c.opt.selection.start,end:c.opt.selection.end}))}).mouseup(function(){d=!1,c.trigger(h,{start:c.opt.selection.start,end:c.opt.selection.end})}),c._addToolTip.call(c,this,function(){return d?"["+c.opt.selection.start+", "+c.opt.selection.end+"]":b})}).css("cursor","pointer")},_addToolTip:function(a,b){var c=this.opt._tooltip;jQuery(a).mouseover(function(d){var e=jQuery(d.target).offset();jQuery(c).is(":visible")||jQuery(c).css({"background-color":"#000",padding:"3px 10px 3px 10px",top:e.top+jQuery(d.target).height()+"px",left:e.left+jQuery(d.target).width()+"px"}).animate({opacity:"0.85"},10).html(b.call(a)).show()}).mouseout(function(){jQuery(c).hide()})},addAnnotation:function(a){this._annotations.push(a),this._redraw()},removeAnnotation:function(a){for(var 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        </div>
    </td>
</tr><tr>
    <td class="d2h-code-linenumber d2h-ins d2h-change">
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<div class="line-num2">17</div>
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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()});</span>
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