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1 <!DOCTYPE html>
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2 <!--
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3 # Copyright (C) 2015 INRA
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4 #
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5 # This program is free software: you can redistribute it and/or modify
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6 # it under the terms of the GNU General Public License as published by
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7 # the Free Software Foundation, either version 3 of the License, or
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8 # (at your option) any later version.
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9 #
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10 # This program is distributed in the hope that it will be useful,
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11 # but WITHOUT ANY WARRANTY; without even the implied warranty of
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12 # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
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13 # GNU General Public License for more details.
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14 #
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15 # You should have received a copy of the GNU General Public License
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16 # along with this program. If not, see <http://www.gnu.org/licenses/>.
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17 -->
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18 <html>
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19 <head>
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20 <title>Jvenn+</title>
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21 <meta charset="UTF-8">
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22 <meta name="version" content="2.0.1">
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23 <link rel="stylesheet" href="https://cdn.datatables.net/1.10.6/css/jquery.dataTables.css"></link>
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24 <link rel="stylesheet" href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.4/css/bootstrap.min.css"></link>
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25 <style type="text/css">
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26 #js-alert {
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27 width: 90%;
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28 margin-right: auto;
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29 margin-left: auto;
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30 }
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31 #content {
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32 width: 90%;
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33 margin-right: auto;
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34 margin-left: auto;
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35 }
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36 .clear {
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37 clear: both;
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38 height: 0px;
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39 width: 100%;
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40 float: none !important;
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41 }
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42 ul.nav-tabs {
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43 margin-bottom: 30px;
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44 }
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45 #venn-filters {
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46 padding: 10px;
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47 background-color: #FFF;
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48 background-clip: padding-box;
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49 border: 1px solid rgba(0, 0, 0, 0.15);
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50 border-radius: 4px;
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51 box-shadow: 0px 6px 12px rgba(0, 0, 0, 0.176);
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52 margin-right: auto;
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53 margin-left: auto;
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54 margin-bottom: 30px;
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55 }
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56 #byFilters-jvenn {
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57 margin-right: auto;
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58 margin-left: auto;
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59 }
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60 #venn-filters ul {
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61 list-style-type: none;
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62 }
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63 </style>
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64
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65 <script type="text/javascript" src="http://code.jquery.com/jquery-2.1.3.min.js"></script>
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66 <script type="text/javascript" src="http://code.highcharts.com/4.1.4/highcharts.js"></script>
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67 <script type="text/javascript" src="http://code.highcharts.com/4.1.4/modules/exporting.js"></script>
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68 <script type="text/javascript" src="https://cdn.datatables.net/1.10.6/js/jquery.dataTables.min.js"></script>
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69 <script type="text/javascript" src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.4/js/bootstrap.min.js"></script>
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70 <script type="text/javascript">
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71 /***************************************************************
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72 * Copyright notice
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73 *
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74 * (c) 2014 PF bioinformatique de Toulouse
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75 * All rights reserved
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76 *
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77 *
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78 * This script is an adaptation of the venny script developed by
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79 * Juan Carlos Oliveros, BioinfoGP, CNB-CSIC:
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80 * Oliveros, J.C. (2007) VENNY. An interactive tool for comparing
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81 * lists with Venn Diagrams.
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82 * http://bioinfogp.cnb.csic.es/tools/venny/index.html.
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83 * It is distributed under the terms of the GNU General Public
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84 * License as published by the Free Software Foundation; either
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85 * version 2 of the License, or (at your option) any later version.
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86 *
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87 * The GNU General Public License can be found at
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88 * http://www.gnu.org/copyleft/gpl.html.
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89 *
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90 * This script is distributed in the hope that it will be useful,
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91 * but WITHOUT ANY WARRANTY; without even the implied warranty of
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92 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
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93 * GNU General Public License for more details.
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94 *
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95 * This copyright notice MUST APPEAR in all copies of the script!
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96 ***************************************************************/
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97 !function(){"use strict";function s(s,t){var e,l=Object.keys(t);for(e=0;e<l.length;e++)s=s.replace(new RegExp("\\{"+l[e]+"\\}","gi"),t[l[e]]);return s}function t(s){var t,e,l;if(!s)throw new Error("cannot create a random attribute name for an undefined object");t="ABCDEFGHIJKLMNOPQRSTUVWXTZabcdefghiklmnopqrstuvwxyz",e="";do for(e="",l=0;12>l;l++)e+=t[Math.floor(Math.random()*t.length)];while(s[e]);return e}function e(s,t){var e,l,r,o={};for(s=s.split(","),t=t||10,e=0;e<s.length;e+=2)l="&"+s[e+1]+";",r=parseInt(s[e],t),o[l]="&#"+r+";";return o["\\xa0"]=" ",o}function l(s){var t={left:"start",right:"end",center:"middle",start:"start",end:"end"};return t[s]||t.start}function r(s){var t={alphabetic:"alphabetic",hanging:"hanging",top:"text-before-edge",bottom:"text-after-edge",middle:"central"};return t[s]||t.alphabetic}var 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class="number-black" style="position: absolute; left: -1000px; top: -2200px;" id="resultC000010"></div>',o+='<div class="number-black" style="position: absolute; left: -1000px; top: -2200px;" id="resultC110000"></div>',o+='<div class="number-black" style="position: absolute; left: -1000px; top: -2200px;" id="resultC101000"></div>',o+='<div class="number-black" style="position: absolute; left: -1000px; top: -2200px;" id="resultC100100"></div>',o+='<div class="number-black" style="position: absolute; left: -1000px; top: -2200px;" id="resultC100010"></div>',o+='<div class="number-black" style="position: absolute; left: -1000px; top: -2200px;" id="resultC011000"></div>',o+='<div class="number-black" style="position: absolute; left: -1000px; top: -2200px;" id="resultC010100"></div>',o+='<div class="number-black" style="position: absolute; left: -1000px; top: -2200px;" id="resultC010010"></div>',o+='<div class="number-black" style="position: absolute; left: -1000px; top: -2200px;" id="resultC001100"></div>',o+='<div class="number-black" style="position: absolute; left: -1000px; top: -2200px;" id="resultC001010"></div>',o+='<div class="number-black" style="position: absolute; left: -1000px; top: -2200px;" id="resultC000110"></div>',o+='<div class="number-black" style="position: absolute; left: -1000px; top: -2200px;" id="resultC111000"></div>',o+='<div class="number-black" style="position: absolute; left: -1000px; top: -2200px;" id="resultC110100"></div>',o+='<div class="number-black" style="position: absolute; left: -1000px; top: -2200px;" id="resultC110010"></div>',o+='<div class="number-black" style="position: absolute; left: -1000px; top: -2200px;" id="resultC101100"></div>',o+='<div class="number-black" style="position: absolute; left: -1000px; top: -2200px;" id="resultC101010"></div>',o+='<div class="number-black" style="position: absolute; left: -1000px; top: -2200px;" id="resultC100110"></div>',o+='<div class="number-black" style="position: absolute; left: -1000px; top: -2200px;" id="resultC011100"></div>',o+='<div class="number-black" style="position: absolute; left: -1000px; top: -2200px;" id="resultC011010"></div>',o+='<div class="number-black" style="position: absolute; left: -1000px; top: -2200px;" id="resultC010110"></div>',o+='<div class="number-black" style="position: absolute; left: -1000px; top: -2200px;" id="resultC001110"></div>',o+='<div class="number-black" style="position: absolute; left: -1000px; top: -2200px;" id="resultC111100"></div>',o+='<div class="number-black" style="position: absolute; left: -1000px; top: -2200px;" id="resultC111010"></div>',o+='<div class="number-black" style="position: absolute; left: -1000px; top: -2200px;" id="resultC110110"></div>',o+='<div class="number-black" style="position: absolute; left: -1000px; top: -2200px;" id="resultC101110"></div>',o+='<div class="number-black" style="position: absolute; left: -1000px; top: -2200px;" id="resultC011110"></div>',o+='<div class="number-black" style="position: absolute; left: -1000px; top: -2200px;" id="resultC111110"></div>',o+='<div class="number-black" style="position: absolute; left: -1000px; top: -2200px;" id="resultC000001"></div>',o+='<div class="number-black" style="position: absolute; left: -1000px; top: -2200px;" id="resultC000011"></div>',o+='<div class="number-black" style="position: absolute; left: -1000px; top: -2200px;" id="resultC000101"></div>',o+='<div class="number-black" style="position: absolute; left: -1000px; top: -2200px;" id="resultC000111"></div>',o+='<div class="number-black" style="position: absolute; left: -1000px; top: -2200px;" id="resultC001001"></div>',o+='<div class="number-black" style="position: absolute; left: -1000px; top: -2200px;" id="resultC001011"></div>',o+='<div class="number-black" style="position: absolute; left: -1000px; top: -2200px;" id="resultC001101"></div>',o+='<div class="number-black" style="position: absolute; left: -1000px; top: -2200px;" id="resultC001111"></div>',o+='<div class="number-black" style="position: absolute; left: -1000px; top: -2200px;" id="resultC010001"></div>',o+='<div class="number-black" style="position: absolute; left: -1000px; top: -2200px;" id="resultC010011"></div>',o+='<div class="number-black" style="position: absolute; left: -1000px; top: -2200px;" id="resultC010101"></div>',o+='<div class="number-black" style="position: absolute; left: -1000px; top: -2200px;" id="resultC010111"></div>',o+='<div class="number-black" style="position: absolute; left: -1000px; top: -2200px;" id="resultC011001"></div>',o+='<div class="number-black" style="position: absolute; left: -1000px; top: -2200px;" id="resultC011011"></div>',o+='<div class="number-black" style="position: absolute; left: -1000px; top: -2200px;" id="resultC011101"></div>',o+='<div class="number-black" style="position: absolute; left: -1000px; top: -2200px;" id="resultC011111"></div>',o+='<div class="number-black" style="position: absolute; left: -1000px; top: -2200px;" id="resultC100001"></div>',o+='<div class="number-black" style="position: absolute; left: -1000px; top: -2200px;" id="resultC100011"></div>',o+='<div class="number-black" style="position: absolute; left: -1000px; top: -2200px;" id="resultC100101"></div>',o+='<div class="number-black" style="position: absolute; left: -1000px; top: -2200px;" id="resultC100111"></div>',o+='<div class="number-black" style="position: absolute; left: -1000px; top: -2200px;" id="resultC101001"></div>',o+='<div class="number-black" style="position: absolute; left: -1000px; top: -2200px;" id="resultC101011"></div>',o+='<div class="number-black" style="position: absolute; left: -1000px; top: -2200px;" id="resultC101101"></div>',o+='<div class="number-black" style="position: absolute; left: -1000px; top: -2200px;" id="resultC101111"></div>',o+='<div class="number-black" style="position: absolute; left: -1000px; top: -2200px;" id="resultC110001"></div>',o+='<div class="number-black" style="position: absolute; left: -1000px; top: -2200px;" id="resultC110011"></div>',o+='<div class="number-black" style="position: absolute; left: -1000px; top: -2200px;" id="resultC110101"></div>',o+='<div class="number-black" style="position: absolute; left: -1000px; top: -2200px;" id="resultC110111"></div>',o+='<div class="number-black" style="position: absolute; left: -1000px; top: -2200px;" id="resultC111001"></div>',o+='<div class="number-black" style="position: absolute; left: -1000px; top: -2200px;" id="resultC111011"></div>',o+='<div class="number-black" style="position: absolute; left: -1000px; top: -2200px;" id="resultC111101"></div>',o+='<div class="number-black" style="position: absolute; left: -1000px; top: -2200px;" id="resultC111111"></div>',o+='<div style="position: absolute; left: -1000px; top: -1000px; opacity:0.5;" id="label1"></div>',o+='<div style="position: absolute; left: -1000px; top: -1000px; opacity:0.5;" id="label2"></div>',o+='<div style="position: absolute; left: -1000px; top: -1000px; opacity:0.5;" id="label3"></div>',o+='<div style="position: absolute; left: -1000px; top: -1000px; opacity:0.5;" id="label4"></div>',o+='<div style="position: absolute; left: -1000px; top: -1000px; opacity:0.5;" id="label5"></div>',o+='<div style="position: absolute; left: -1000px; top: -1000px; opacity:0.5;" id="label6"></div>',o+="</div>",t.html(o),j=new C2S(O,N),s("*[id^=resultC]").each(function(){s(this).html(0),s(this).addClass("number-empty"),s(this).css("font-size",B.fontSize),s(this).css("font-family",B.fontFamily)}),s("*[id^=label]").each(function(){s(this).css("font-family",B.fontFamily)});var c=z();"list"==c[0]?w():"count"==c[0]&&E(),null!=B.searchInput&&B.searchInput.keyup(function(){F(B.searchInput.val(),B.searchMinSize)}),"edwards"==B.displayMode?y(c[1]):x(c[1]),B.displayStat&&v(c[1]),B.exporting===!0&&S(t,e,c[0]),c[1]>=4&&_(t,c[1]),s(".number-black").hover(function(){var t=!1;s("*[id^=item]").each(function(){"on"===s(this).children("span").text()&&(t=!0)});var e=!1;if(null!=B.searchInput&&""!=B.searchInput.val()&&(e=!0),!t&&!e&&""!==s(this).text()){var l=this.listnames,r=this;s("*[id^=label]").each(function(){l.indexOf(s(this).text())<0?s(this).css("opacity",.1):s(this).css("opacity",.6)}),s(".number-black").each(function(){this!=r&&s(this).css("opacity",.1)}),b(),"edwards"==B.displayMode?y(c[1]):x(c[1]),B.displayStat&&v(c[1])}},function(){var t=!1;s("*[id^=item]").each(function(){"on"===s(this).children("span").text()&&(t=!0)});var e=!1;if(null!=B.searchInput&&""!=B.searchInput.val()&&(e=!0),!t&&!e&&""!==s(this).text()){{this.listnames}s("*[id^=label]").each(function(){s(this).css("opacity",.5)}),s(".number-black").each(function(){s(this).css("opacity",1)}),b(),"edwards"==B.displayMode?y(c[1]):x(c[1]),B.displayStat&&v(c[1])}}),s("#canvasEllipse").html(j.getSvg())}),this}}(jQuery);
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100 </script>
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101 <script type="text/javascript">
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102 /*
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103 * HTMLTable.js 0.1.0 - HTMLTable Library
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|
104 *
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105 * Copyright (c) 2015 Escudie Frederic
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106 * Licensed under the MIT (http://www.opensource.org/licenses/mit-license.php) license.
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107 */
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|
108 function HTMLtable(e){var t,r,n=e,a=";";this.deleteColumns=function(e){for(var a=n.getElementsByTagName("tr"),o=0;o<a.length;o++){s=0;var i=a[o].getElementsByTagName("td");0==i.length&&(i=a[o].getElementsByTagName("th"));for(var v=0,s=0;s<t[1];s++)if(!r[o][s]){var f=i[v].getAttribute("colspan");if(null!=f)for(var m=0;f>m;m++){if(in_array(s+m,e)){var u=i[v].getAttribute("colspan");u-1==0?i[v].removeAttribute("colspan"):i[v].setAttribute("colspan",u-1)}if(null==i[v].getAttribute("colspan")){var h=i[v];a[o].removeChild(h),v--}}else if(in_array(s,e)){var h=i[v];a[o].removeChild(h),v--}v++}}l(),g()},this.filter=function(e,a){var l=new RegExp(e),g=new Array;null!=a&&a||(g.c0=!0);for(var o=n.getElementsByTagName("tr"),i=0;i<o.length;i++){f=0;var v=o[i].getElementsByTagName("td");if(0!=v.length)for(var s=0,f=0;f<t[1];f++)r[i][f]||(l.test(v[s].innerHTML)&&(g["c"+f]=!0),s++)}for(var m=new Array,u=0;u<t[1];u++)void 0===g["c"+u]&&m.push(u);this.deleteColumns(m)},this.getModel=function(){return n};var l=function(){for(var e=0,r=0,a=n.getElementsByTagName("tr"),l=0;l<a.length;l++){var g=0;e++;var o=a[l].getElementsByTagName("td");0==o.length&&(o=a[l].getElementsByTagName("th"));for(var i=0;i<o.length;i++){var v=o[i].getAttribute("colspan");g+=null==v?1:parseInt(v)}g>r&&(r=g)}t=new Array(2),t[0]=e,t[1]=r},g=function(){r=new Array(t[0]);for(var e=0;e<t[0];e++){r[e]=new Array(t[1]);for(var a=0;a<t[1];a++)r[e][a]=!1}for(var l=n.getElementsByTagName("tr"),g=0;g<l.length;g++){v=0;var o=l[g].getElementsByTagName("td");0==o.length&&(o=l[g].getElementsByTagName("th"));for(var i=0,v=0;v<t[1];v++)if(!r[g][v]){var s=0,f=0,m=o[i].getAttribute("rowspan");null!=m&&(s=parseInt(m)-1);var u=o[i].getAttribute("colspan");null!=u&&(f=parseInt(u)-1);for(var h=s;h>=0;h--)for(var y=f;y>=0;y--)(0!=h||0!=y)&&(r[g+h][v+y]=!0);i++}}};this.replace=function(e,a,l){var g=new RegExp(e);null==a&&(a=""),null==l&&(l="");for(var o=n.getElementsByTagName("tr"),i=0;i<o.length;i++){f=0;var v=o[i].getElementsByTagName("td");if(0!=v.length)for(var s=0,f=0;f<t[1];f++)if(!r[i][f]){var m=g.exec(v[s].innerHTML);null!=m&&(void 0===m[1]&&(m[1]=""),v[s].innerHTML=a+m[1]+l),s++}}},this.toCSV=function(){for(var e="",l=n.getElementsByTagName("tr"),g=0;g<l.length;g++){var o=l[g].getElementsByTagName("td");0==o.length&&(o=l[g].getElementsByTagName("th"));for(var i=0,v=0;v<t[1];v++)r[g][v]||(e+=o[i].innerHTML,i++),e+=a;e=e.substr(0,e.length-1)+"\n"}return e},l(),g()}var in_array=function(e,t){for(var r in t)if(t[r]==e)return!0;return!1};
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109
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110 /*
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111 * dataTableExtractor.plugin.js 0.1.0 - datatableExport Library
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112 *
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113 * Copyright (c) 2015 Escudie Frederic
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114 * Licensed under the MIT (http://www.opensource.org/licenses/mit-license.php) license.
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115 */
|
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|
116 !function(t){t.fn.datatableExport=function(a){var e={anchor_id:t(this).attr("id"),table_id:null,csv_separator:";",omitted_columns:[]},n=t.extend(e,a);if(!t(this).length)throw"The element where the datatableExport is called does not exist.";if(void 0==n.anchor_id)throw"The datatableExport plugin must be called on an element with id.";if(null==n.table_id)throw"You must set the table_id parameter in datatableExport plugin.";if(!t("#"+n.table_id))throw"The datatable '#"+n.table_id+"' cannot be retieve in DOM.";return this.each(function(){var a=t(this);a.on("click",function(){t.fn.datatableExport.csv(n.anchor_id,n.table_id,n.csv_separator,n.omitted_columns)})})},t.fn.datatableExport.cleanCellMarkup=function(a,e){t.parseHTML(e);t("#"+a).append('<div class="hidden data-tmp">'+e+"</div>"),t("#"+a+" .data-tmp").find("input").each(function(){var a="";a=t(this).is(":checkbox")?t(this).is(":checked")?"true":"false":t(this).val(),t(this).replaceWith(a)});var n=t("#"+a+" .data-tmp").text();return t("#"+a+" .data-tmp").remove(),n},t.fn.datatableExport.csv=function(a,e,n,i){var l="",r=t("#"+e).DataTable(),d=t("#"+e+" thead")[0],o=new HTMLtable(d.cloneNode(!0));o.deleteColumns(i),l+=o.toCSV();var c=r.rows().data();t.each(c,function(e,n){for(var r="",d=0;d<n.length;d++)-1==t.inArray(d,i)&&(r+='"'+t.fn.datatableExport.cleanCellMarkup(a,n[d])+'";');""!=r&&(r=r.slice(0,-1)),l+=r+"\n"}),t("#"+a+"-extract-csv").length||t("#"+a).append('<a id="'+a+'-extract-csv" href="data:text/csv;charset=UTF-8,'+encodeURI(l)+'" download="data.csv" style="display:none;"></a>'),t("#"+a+"-extract-csv")[0].click()}}(jQuery);
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117 </script>
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118
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119 <script type="text/javascript">
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120 /*
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121 $(document).ready(function(){
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122 $('#example').jvenn({
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123 series: [{
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124 name: {A: 'Actors',
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125 B: 'Singers'},
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126 data: {A: ["Arnold Schwarzenegger", "Jack Nicholson", "Robert de Niro", "Harrison Ford"], B: ["Freddy Mercury", "Ricky Martin", "Celine Dion"], AB: ["Marilyn Monroe", "Barbra Streisand", "Dean Martin"]},
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127 values: {A: 4, B: 3, AB: 3}
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128 }],
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129 });
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130 });
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131 */
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132 var jvenn_data = ###JVENN_DATA### ;
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133 $(document).ready(function(){
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134 $('#example').jvenn(jvenn_data);
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135 });
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136
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137 ///////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////
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138 //
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139 // Data
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140 //
|
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141 ///////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////
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142 //var processed_filters = ###PORCESSED_FILTERS### ;
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143 /* Example:
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144 ['filterA', 'filterB', 'filterC']
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145 */
|
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146 //var global_results = ###GLOBAL_RESULTS### ;
|
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147 /* Example:
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148 {
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149 'nb_clstr_kept': 100,
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150 'nb_clstr_ini': 300,
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151 'nb_seq_kept': 100,
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152 'nb_seq_ini': 100000
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153 }
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154 */
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155 //var by_samples_results = ###SAMPLES_RESULTS### ;
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156 /* Example:
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157 {
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158 'sampleA':{
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159 'filtered':{
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160 'filterA': 10,
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161 'filterB': 20
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162 },
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163 'initial': 75,
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164 'kept': 50
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165 },
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166 'sampleB':{
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167 'filtered':{
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168 'filterB': 20,
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169 },
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170 'initial': 110,
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171 'kept': 90
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172 }
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173 }
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174 */
|
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175 //var by_filters_results = ###FILTERS_RESULTS### ;
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176 /* Example:
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177 [
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178 {'filters':['filterA'], 'count': 10},
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179 {'filters':['filterB'], 'count': 20},
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180 {'filters':['filterC'], 'count': 30},
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181 {'filters':['filterA', 'filterB'], 'count': 1},
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182 {'filters':['filterA', 'filterC'], 'count': 2},
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183 {'filters':['filterB', 'filterC'], 'count': 3},
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184 {'filters':['filterA', 'filterB', 'filterC'], 'count': 4}
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185 ];
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186 */
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187
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188 ///////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////
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189 //
|
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190 // Main
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191 //
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192 ///////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////
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193 $(function() {
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194 // Remove alert
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195 $('#js-alert').remove();
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196 $('#content').removeClass("hidden");
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197
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198 // Load active tab
|
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199 global_filters_load();
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200 intersections_filters_load();
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201
|
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202 // Add tab listener
|
|
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203 $('.nav-tabs a').click(function (e) {
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204 e.preventDefault();
|
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205 $(this).tab('show');
|
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206 if( $(this).attr('href') == "#view-by-samples" && $('#view-by-samples').hasClass('disabled') ){
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207 $('#view-by-samples').removeClass('disabled')
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208 samples_filters_load( "filter-log" );
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209 }
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210 })
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211 });
|
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212 </script>
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213
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214 </head>
|
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215 <body>
|
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216 <!-- Alert -->
|
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217 <p id="js-alert" class="alert alert-warning">
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218 javascript is needed to display data.<br />
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219 If you try to view this data on galaxy please contact your administrator to authorise javascript or download the file to view.
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220 </p>
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221
|
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222 <!-- Content -->
|
|
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223 <div id="example"></div>
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224 </div>
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225
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226
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227 </body>
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228 </html>
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