Mercurial > repos > frogs > frogs_2_0_0

annotate test-data/references/05-clustersStat.html @ 0:76c750c5f0d1 draft default tip

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planemo upload for repository https://github.com/oinizan/FROGS-wrappers commit 0b900a51e220ce6f17c1e76292c06a5f4d934055-dirty
author frogs
date Thu, 25 Oct 2018 05:01:13 -0400
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0
76c750c5f0d1 planemo upload for repository https://github.com/oinizan/FROGS-wrappers commit 0b900a51e220ce6f17c1e76292c06a5f4d934055-dirty
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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
76c750c5f0d1 planemo upload for repository https://github.com/oinizan/FROGS-wrappers commit 0b900a51e220ce6f17c1e76292c06a5f4d934055-dirty
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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
76c750c5f0d1 planemo upload for repository https://github.com/oinizan/FROGS-wrappers commit 0b900a51e220ce6f17c1e76292c06a5f4d934055-dirty
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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
76c750c5f0d1 planemo upload for repository https://github.com/oinizan/FROGS-wrappers commit 0b900a51e220ce6f17c1e76292c06a5f4d934055-dirty
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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>FROGS Cluster stat</title>
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21 <meta charset="UTF-8">
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22 <meta name="version" content="1.4.1">
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23 <!-- CSS -->
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24 <link rel="stylesheet" href="https://cdn.datatables.net/1.10.6/css/jquery.dataTables.css"></link>
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25 <link rel="stylesheet" href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.4/css/bootstrap.min.css"></link>
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26 <style type="text/css">
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27 #js-alert {
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28 width: 90%;
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29 margin-right: auto;
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30 margin-left: auto;
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31 }
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32 #content {
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33 width: 90%;
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34 margin-right: auto;
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35 margin-left: auto;
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36 }
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37 .clear {
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38 clear: both;
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39 height: 0px;
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40 width: 100%;
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41 float: none !important;
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42 }
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43 ul.nav-tabs {
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44 margin-bottom: 30px;
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45 }
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46 #hc-graph {
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47 height: 500px;
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48 overflow: auto;
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49 }
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50 #hc-warning {
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51 margin-top: 8px;
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52 }
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53 #hc-newick {
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54 width: 90%;
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55 position: absolute;
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56 background-color: white;
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57 border: 1px solid lightgrey;
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58 border-radius:5px;
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59 padding: 5px 5px 5px 5px;
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60 margin-top: 10px;
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61 }
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62 #dispersion {
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63 height: 500px;
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64 }
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65 .label-badge {
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66 position: absolute;
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67 top: -10px;
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68 left: -10px;
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69 }
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70 .graph-nb {
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71 color: #95959C;
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72 font-style: italic;
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73 text-align: center;
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74 }
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75
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76 .circle {
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77 border-style: solid;
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78 border-width: 3px;
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79 border-radius: 50px;
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80 box-shadow: 2px 2px 2px #555;
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81 border-color: #3871A8;
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82 background: radial-gradient( #649DD4, #3871A8);
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83 color: white;
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84 padding: 10px;
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85 width: 180px;
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86 height: 98px;
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87 line-height: 30px;
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88 text-align: center;
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89 margin-left: auto;
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90 margin-right: auto;
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91 margin-bottom: 10px;
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92 vertical-align: middle;
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93 }
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94 .circle-value {
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95 font-weight: bold;
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96 }
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97
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98 .d3-node {
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99 cursor: pointer;
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100 }
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101 .d3-node-dot {
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102 fill: #fff;
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103 stroke: steelblue;
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104 stroke-width: 3px;
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105 }
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106 .d3-collapsed-node {
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107 fill: #B0C4DE;
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108 stroke: #663399;
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109 stroke-width: 3px;
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110 }
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111 .d3-node text {
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112 font: 13px sans-serif;
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113 }
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114 .d3-link {
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115 fill: none;
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116 stroke: #ccc;
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117 stroke-width: 2px;
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118 }
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119 </style>
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120 <!-- JS -->
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121 <script type="text/javascript" src="http://code.jquery.com/jquery-2.1.3.min.js"></script>
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122 <script type="text/javascript" src="http://code.highcharts.com/4.1.4/highcharts.js"></script>
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123 <script type="text/javascript" src="http://code.highcharts.com/4.1.4/highcharts-more.js"></script>
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124 <script type="text/javascript" src="http://code.highcharts.com/4.1.4/modules/exporting.js"></script>
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125 <script type="text/javascript" src="https://cdn.datatables.net/1.10.6/js/jquery.dataTables.min.js"></script>
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126 <script type="text/javascript" src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.4/js/bootstrap.min.js"></script>
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127 <script type="text/javascript">
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128 /*
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129 * d3 v3 - JavaScript d3 Library
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130 * (http://d3js.org/)
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131 */
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132 !function(){function n(n){return n&&(n.ownerDocument||n.document||n).documentElement}function t(n){return n&&(n.ownerDocument&&n.ownerDocument.defaultView||n.document&&n||n.defaultView)}function e(n,t){return t>n?-1:n>t?1:n>=t?0:0/0}function r(n){return null===n?0/0:+n}function u(n){return!isNaN(n)}function i(n){return{left:function(t,e,r,u){for(arguments.length<3&&(r=0),arguments.length<4&&(u=t.length);u>r;){var i=r+u>>>1;n(t[i],e)<0?r=i+1:u=i}return r},right:function(t,e,r,u){for(arguments.length<3&&(r=0),arguments.length<4&&(u=t.length);u>r;){var i=r+u>>>1;n(t[i],e)>0?u=i:r=i+1}return r}}}function o(n){return n.length}function a(n){for(var t=1;n*t%1;)t*=10;return t}function c(n,t){for(var e in t)Object.defineProperty(n.prototype,e,{value:t[e],enumerable:!1})}function l(){this._=Object.create(null)}function s(n){return(n+="")===pa||n[0]===va?va+n:n}function f(n){return(n+="")[0]===va?n.slice(1):n}function h(n){return s(n)in this._}function g(n){return(n=s(n))in this._&&delete 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76c750c5f0d1 planemo upload for repository https://github.com/oinizan/FROGS-wrappers commit 0b900a51e220ce6f17c1e76292c06a5f4d934055-dirty
frogs
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76c750c5f0d1 planemo upload for repository https://github.com/oinizan/FROGS-wrappers commit 0b900a51e220ce6f17c1e76292c06a5f4d934055-dirty
frogs
parents:
diff changeset
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76c750c5f0d1 planemo upload for repository https://github.com/oinizan/FROGS-wrappers commit 0b900a51e220ce6f17c1e76292c06a5f4d934055-dirty
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137 </script>
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138 <script type="text/javascript">
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139 /*
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140 * Node 0.1.0 - JavaScript Node Library
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141 *
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142 * Copyright (c) 2015 Escudie Frederic
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143 * Licensed under the MIT (http://www.opensource.org/licenses/mit-license.php) license.
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144 */
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145 var Node=function(e,t,n,r){if(this.name=e,this.parent=t,this.children=new Array,null!=n)for(var i=0;i<n.length;i++)this.addChild(n[i]);this.metadata=new Array,null!=r&&(this.metadata=r)};Node.fromNewick=function(e){for(var t=new Array,n=0;n<e.length;n++){var r=e[n];if("("==r)t.push("(");else if(")"==r){for(var i=new Node(null,null,null,null);"("!=t[t.length-1];)i.addChild(t.pop());t.pop(),t.push(i)}else if(","==r);else if(";"==r);else if(":"==r){for(var h="";","!=e[n+1]&&")"!=e[n+1]&&";"!=e[n+1];)n++,h+=e[n];t[t.length-1].metadata.dist=h}else{'"'==r?(stop_markers=['"'],n++):stop_markers=[",",")",":",";"];for(var o=e[n];-1==stop_markers.indexOf(e[n+1]);)n++,o+=e[n];-1!=stop_markers.indexOf('"')&&n++;var l=new Node(o,null,null,null);t.push(l)}}return t[0]},Node.prototype.toNewick=function(){},Node.prototype.toJson=function(){var e={name:null!=this.name?this.name:""};if(this.hasChild()){for(var t=new Array,n=0;n<this.children.length;n++)t.push(this.children[n].toJson());e.children=t}return e},Node.prototype.getLeavesNames=function(){var e=new Array;if(this.hasChild())for(var t=0;t<this.children.length;t++)for(var n=this.children[t].getLeavesNames(),r=0;r<n.length;r++)e.push(n[r]);else e.push(this.name);return e},Node.prototype.nbLeaves=function(){var e=0;if(this.hasChild())for(var t=0;t<this.children.length;t++)e+=this.children[t].nbLeaves();else e=1;return e},Node.prototype.maxDepth=function(){var e=0;if(this.hasChild())for(var t=0;t<this.children.length;t++)e=Math.max(e,this.children[t].maxDepth());return 1+e},Node.prototype.toAsciiTree=function(e){null==e&&(e=0);var t="--- "+(null!=this.name?this.name:"ancestor")+" ";e+=t.length;for(var n=0;n<this.children.length;n++)t+="\n"+Array(e).join(" ")+"\\"+this.children[n].toAsciiTree(e);return t},Node.prototype.toString=function(){var e="Node: "+this.name;return e+="\n Parent="+(null!=this.parent?this.parent.name:"-"),e+=this.hasChild()?"\n Children="+Object.keys(this.children).join(", "):"\n Children=-"},Node.prototype.hasChild=function(e){if(null==e)return this.children.length>0;for(var t=!1,n=0;n<this.children.length&&!t;n++)e==this.children[n]&&(t=!0);return t},Node.prototype.getChild=function(e){if(!this.hasChild(e))throw this.name+" doesn't have child named '"+e+"'.";return this.children[e]},Node.prototype.getParent=function(){return this.parent},Node.prototype.addChild=function(e){null==e.parent&&(e.parent=this),this.children.push(e)};
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146 </script>
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147 <script type="text/javascript">
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148 /*
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149 * HTMLTable.js 0.1.0 - HTMLTable Library
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150 *
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151 * Copyright (c) 2015 Escudie Frederic
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152 * Licensed under the MIT (http://www.opensource.org/licenses/mit-license.php) license.
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153 */
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154 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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155
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156 /*
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157 * dataTableExtractor.plugin.js 0.1.0 - datatableExport Library
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158 *
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159 * Copyright (c) 2015 Escudie Frederic
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160 * Licensed under the MIT (http://www.opensource.org/licenses/mit-license.php) license.
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161 */
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162 !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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163 </script>
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164 <script type="text/javascript">
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165 //HC global var
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166 var linkage_data = null ;
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167 var d3_tree = null ;
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168 var diagonal = null ;
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169 var svg_layout = null ;
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170 var node_id = 0 ;
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171
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172 /**
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173 * Draw/update linkage tree.
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174 */
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175 function update_linkage_nodes(source) {
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176 var duration = d3.event && d3.event.altKey ? 5000 : 500;
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177
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178 // Compute the new tree layout.
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179 var nodes = d3_tree.nodes(linkage_data).reverse();
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180
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181 // Normalize for fixed-depth.
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182 nodes.forEach(function(d) { d.y = d.depth * 100; });
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183
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184 // Update the nodes.
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185 var node = svg_layout.selectAll("g.d3-node")
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186 .data(nodes, function(d) { return d.id || (d.id = ++node_id); });
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187
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188 // Enter any new nodes at the parent's previous position.
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189 var nodeEnter = node.enter().append("svg:g")
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190 .attr("class", "d3-node")
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191 .attr("transform", function(d) { return "translate(" + source.y0 + "," + source.x0 + ")"; })
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192 .on("click", function(d) { toggle(d); });
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193
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194 nodeEnter.append("svg:circle")
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195 .attr("r", 1e-6)
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196 .attr("class", function(d) { return d._children ? "d3-collapsed-node" : "d3-node-dot"; });
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197
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198 nodeEnter.append("svg:text")
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199 .attr("x", function(d) { return d.children || d._children ? -10 : 10; })
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200 .attr("dy", ".35em")
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201 .attr("text-anchor", function(d) { return d.children || d._children ? "end" : "start"; })
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202 .text(function(d) { return d.name; })
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203 .style("fill-opacity", 1e-6);
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204
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205 // Transition nodes to their new position.
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206 var nodeUpdate = node.transition()
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207 .duration(duration)
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208 .attr("transform", function(d) { return "translate(" + d.y + "," + d.x + ")"; });
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209
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210 nodeUpdate.select("circle")
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211 .attr("r", 6)
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212 .attr("class", function(d) { return d._children ? "d3-collapsed-node" : "d3-node-dot"; });
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213
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214 nodeUpdate.select("text")
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215 .style("fill-opacity", 1);
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216
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217 // Transition exiting nodes to the parent's new position.
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218 var nodeExit = node.exit().transition()
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219 .duration(duration)
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220 .attr("transform", function(d) { return "translate(" + source.y + "," + source.x + ")"; })
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221 .remove();
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222
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223 nodeExit.select("circle")
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224 .attr("r", 1e-6);
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225
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226 nodeExit.select("text")
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227 .style("fill-opacity", 1e-6);
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228
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229 // Update the links
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230 var link = svg_layout.selectAll("path.d3-link")
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231 .data( d3_tree.links(nodes), function(d) { return d.target.id; } );
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232
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233 // Enter any new links at the parent's previous position.
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234 link.enter().insert("svg:path", "g")
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235 .attr("class", "d3-link")
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236 .attr("d", function(d) {
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237 var o = {x: source.x0, y: source.y0};
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238 return diagonal({source: o, target: o});
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239 })
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240 .transition()
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241 .duration(duration)
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242 .attr("d", diagonal);
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243
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244 // Transition links to their new position.
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245 link.transition()
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246 .duration(duration)
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247 .attr("d", diagonal);
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248
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249 // Transition exiting nodes to the parent's new position.
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250 link.exit().transition()
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251 .duration(duration)
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252 .attr("d", function(d) {
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253 var o = {x: source.x, y: source.y};
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254 return diagonal({source: o, target: o});
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255 })
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256 .remove();
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257
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258 // Stash the old positions for transition.
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259 nodes.forEach(function(d) {
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260 d.x0 = d.x;
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261 d.y0 = d.y;
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262 });
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263 }
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264
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265 /**
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266 * Hide/Unhide children's node when toggle on node in linkage view.
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267 */
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268 function toggle( d ) {
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269 //Hide/Unhide attributes
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270 if (d.children) {
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271 d._children = d.children;
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272 d.children = null;
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273 } else {
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274 d.children = d._children;
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275 d._children = null;
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276 }
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277 //Update node and her children in SVG
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278 update_linkage_nodes(d);
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279 }
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280 </script>
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281
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282 <script type="text/javascript">
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283 /**
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284 * Returns the string representation of the number.
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285 * @param pValue {Float} The number to process.
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286 * @return {String} The string representation (example: 12856892.11111 => 12,856,892.11).
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287 */
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288 var numberDisplay = function( pValue ){
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289 var new_val = "" ;
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290 if( ("" + pValue + "").indexOf(".") != -1 ){
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291 new_val = pValue.toFixed(2).replace(/(\d)(?=(\d{3})+\b)/g, '$1,');
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292 } else {
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293 new_val = pValue.toFixed().replace(/(\d)(?=(\d{3})+\b)/g, '$1,');
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294 }
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295 return new_val ;
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296 }
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297
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298 /**
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299 * Returns the HTML table representation of the data.
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300 * @param pTitle {String} The title of the table.
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301 * @param pCategories {Array} The title of each column.
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302 * @param pData {Array} 2D matrix with row and column data.
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303 * @return {String} The HTML table representation.
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304 */
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305 var table = function( pTitle, pCategories, pData ) {
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306 // Header
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307 var table_header = ' <tr>\n<th colspan="' + pCategories.length + '">' + pTitle + '</th> </tr>\n' ;
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308 var table_header_line = "" ;
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309 for(var idx = 0 ; idx < pCategories.length ; idx++){
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310 table_header_line += " <th>" + pCategories[idx] + "</th>\n" ;
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311 }
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312 table_header += " <tr>\n" + table_header_line + " </tr>\n" ;
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313 table_header = " <thead>\n" + table_header + " </thead>\n" ;
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314
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315 // Body
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316 var table_body = '' ;
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317 for(var data_idx = 0 ; data_idx < pData.length ; data_idx++){
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318 var table_body_row = "" ;
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319 for(var category_idx = 0 ; category_idx < pCategories.length ; category_idx++){
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320 if( typeof pData[data_idx][category_idx] === "number" ) {
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321 table_body_row += " <td>" + numberDisplay(pData[data_idx][category_idx]) + "</td>\n" ;
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322 } else {
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323 table_body_row += " <td>" + pData[data_idx][category_idx] + "</td>\n" ;
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324 }
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325 }
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326 table_body += " <tr>\n" + table_body_row + " </tr>\n" ;
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327 }
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328 table_body = " <tbody>\n" + table_body + " </tbody>\n" ;
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329
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330 return '<table class="table table-striped">\n' + table_header + table_body + "</table>\n" ;
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331 }
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332
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333 /**
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334 * Returns hash use to init HightChart object (without 'type').
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335 * @param pTitle {String} The title of the chart.
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336 * @param pXTitle {String} The xAxis title.
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337 * @param pYTitle {String} The yAxis title.
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338 * @param pXCategories {Array} The title of each category (x scale labels).
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339 * @param pData {Array} The HightChart series.
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340 * @return {Hash} The hash.
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341 * @warning This method use HightChart xAxis.categories.
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342 */
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343 var chartplot = function( pTitle, pXTitle, pYTitle, pXCategories, pData ) {
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344 var chart = {
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345 title: {
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346 text: pTitle
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347 },
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348 xAxis: {},
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349 yAxis: {
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350 title: {
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351 text: pYTitle
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352 }
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353 },
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354 series: pData,
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355 credits: {
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356 enabled: false
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357 }
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358 }
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359 if( pXCategories != null ){
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360 chart['xAxis']['categories'] = pXCategories ;
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361 }
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362 if( pXTitle != null ){
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363 chart['xAxis']['title'] = { text: pXTitle } ;
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364 }
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365 if( pData.length <= 1 ) {
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366 chart['legend'] = {'enabled': false};
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367 } else {
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368 chart['legend'] = {'enabled': true};
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369 }
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370 return chart ;
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371 }
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372 /**
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373 * Returns hash use to init HightChart boxplot.
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374 * @param pTitle {String} The title of the chart.
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375 * @param pXTitle {String} The xAxis title.
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376 * @param pYTitle {String} The yAxis title.
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377 * @param pXCategories {Array} x scale labels.
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378 * @param pData {Array} The HightChart series.
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379 * @return {Hash} Parameters to use in Highchart's constructor.
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380 */
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381 var boxplot_param = function(pTitle, pXTitle, pYTitle, pXCategories, pData) {
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382 var chart = chartplot( pTitle, null, pYTitle, pXCategories, pData );
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383 chart['chart'] = { type: 'boxplot', zoomType: 'y' };
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384 chart['yAxis']['min'] = 0 ;
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385 return chart ;
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386 };
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387
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388 /**
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389 * Returns hash use to init HightChart area.
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390 * @param pTitle {String} The title of the chart.
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391 * @param pXTitle {String} The xAxis title.
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392 * @param pYTitle {String} The yAxis title.
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393 * @param pXCategories {Array} x scale labels.
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394 * @param pData {Array} The HightChart series.
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395 * @return {Hash} Parameters to use in Highchart's constructor.
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396 */
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397 var areaplot_param = function(pTitle, pXTitle, pYTitle, pXCategories, pData) {
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398 var x_max = 0 ;
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399 for( var series_idx = 0 ; series_idx < pData.length ; series_idx++ ){
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400 for( var val_idx = 0 ; val_idx < pData[series_idx].length ; val_idx++ ){
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401 x_max = Math.max(parseInt(pData[series_idx][val_idx][0]), parseInt(x_max));
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402 }
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403 }
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404 var chart = chartplot( pTitle, pXTitle, pYTitle, pXCategories, pData );
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405 chart['chart'] = {
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406 type: 'area',
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407 zoomType:"x"
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408 };
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409 chart['xAxis']['tickInterval'] = Math.max(1, parseInt(x_max/10));
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410 chart['plotOptions'] = {
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411 area: {
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412 marker: {
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413 enabled: true,
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414 symbol: 'circle',radius:4,
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415 }
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416 }
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417 };
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418 return chart ;
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419 }
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420
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421 /**
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422 * Returns hash use to init HightChart line.
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423 * @param pTitle {String} The title of the chart.
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424 * @param pXTitle {String} The xAxis title.
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425 * @param pYTitle {String} The yAxis title.
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426 * @param pXCategories {Array} x scale labels.
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427 * @param pData {Array} The HightChart series.
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428 * @return {Hash} Parameters to use in Highchart's constructor.
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429 */
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430 var lineplot_param = function(pTitle, pXTitle, pYTitle, pXCategories, pData) {
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431 var chart = chartplot( pTitle, pXTitle, pYTitle, pXCategories, pData );
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432 chart['chart'] = {
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433 type: 'line'
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434 };
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435 chart['yAxis']['min'] = 0 ;
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436 chart['legend'] = {'enabled': true};
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437 chart['plotOptions'] = {
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438 area: {
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439 marker: {
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440 enabled: true,
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441 symbol: 'circle',radius:4,
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442 }
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443 }
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444 };
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445 return chart ;
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446 }
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447
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448 var get_dispersion = function( values, counts ) {
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449 var dispersion = new Array();
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450
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451 // Unstack list
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452 unstacked_list = new Array();
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453 for( var idx = 0 ; idx < values.length ; idx++ ){
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454 for( var nb_add = 0 ; nb_add < counts[idx] ; nb_add++ ){
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455 unstacked_list.push( values[idx] );
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456 }
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457 }
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458
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459 // Process metrics
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460 var nb_elt = unstacked_list.length ;
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461 dispersion['min'] = unstacked_list[0] ;
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462 dispersion['max'] = unstacked_list[nb_elt - 1];
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463 if( nb_elt % 2 == 0 ) {
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464 dispersion['median'] = unstacked_list[(nb_elt/2) -1] ;
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465 } else {
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466 dispersion['median'] = (unstacked_list[parseInt((nb_elt/2) -1)] + unstacked_list[parseInt(nb_elt/2)])/2 ;
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467 }
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468 // Deciles
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469 for( var idx = 1 ; idx <= 9 ; idx++ ){
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470 if( idx != 5 ) {
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471 dispersion[idx + '_decile'] = unstacked_list[Math.floor(idx*(nb_elt/10) + 0.5) -1] ;
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472 } else {
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473 dispersion['5_decile'] = dispersion['median'] ;
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474 }
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475 }
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476 // Quartiles
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477 dispersion['lower_quartile'] = unstacked_list[Math.floor((nb_elt/4) + 0.5) -1] ;
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478 dispersion['upper_quartile'] = unstacked_list[Math.floor((3*(nb_elt/4)) + 0.5) -1] ;
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479
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480 return dispersion ;
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481 };
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482
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483 ///////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////
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484 //
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485 // Nav templates
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486 //
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diff changeset
487 ///////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////
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diff changeset
488 var cluster_distrib_load = function( container_id ) {
76c750c5f0d1 planemo upload for repository https://github.com/oinizan/FROGS-wrappers commit 0b900a51e220ce6f17c1e76292c06a5f4d934055-dirty
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489 var dispersion = get_dispersion( clusters_sizes, series[0]['data'] );
76c750c5f0d1 planemo upload for repository https://github.com/oinizan/FROGS-wrappers commit 0b900a51e220ce6f17c1e76292c06a5f4d934055-dirty
frogs
parents:
diff changeset
490
76c750c5f0d1 planemo upload for repository https://github.com/oinizan/FROGS-wrappers commit 0b900a51e220ce6f17c1e76292c06a5f4d934055-dirty
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parents:
diff changeset
491 // Nb clusters and nb sequences
76c750c5f0d1 planemo upload for repository https://github.com/oinizan/FROGS-wrappers commit 0b900a51e220ce6f17c1e76292c06a5f4d934055-dirty
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diff changeset
492 var nb_clusters = 0 ;
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frogs
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diff changeset
493 var nb_sequences = 0 ;
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diff changeset
494 for( var clusters_sizes_idx = 0 ; clusters_sizes_idx < clusters_sizes.length ; clusters_sizes_idx++ ){
76c750c5f0d1 planemo upload for repository https://github.com/oinizan/FROGS-wrappers commit 0b900a51e220ce6f17c1e76292c06a5f4d934055-dirty
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diff changeset
495 nb_clusters += series[0]['data'][clusters_sizes_idx] ;
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diff changeset
496 nb_sequences += ( series[0]['data'][clusters_sizes_idx] * clusters_sizes[clusters_sizes_idx] );
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diff changeset
497 }
76c750c5f0d1 planemo upload for repository https://github.com/oinizan/FROGS-wrappers commit 0b900a51e220ce6f17c1e76292c06a5f4d934055-dirty
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diff changeset
498 $('#nb-clusters').append( '' +
76c750c5f0d1 planemo upload for repository https://github.com/oinizan/FROGS-wrappers commit 0b900a51e220ce6f17c1e76292c06a5f4d934055-dirty
frogs
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diff changeset
499 '<div class="circle">' +
76c750c5f0d1 planemo upload for repository https://github.com/oinizan/FROGS-wrappers commit 0b900a51e220ce6f17c1e76292c06a5f4d934055-dirty
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diff changeset
500 ' <span class="circle-title">Clusters</span>' +
76c750c5f0d1 planemo upload for repository https://github.com/oinizan/FROGS-wrappers commit 0b900a51e220ce6f17c1e76292c06a5f4d934055-dirty
frogs
parents:
diff changeset
501 ' <br />' +
76c750c5f0d1 planemo upload for repository https://github.com/oinizan/FROGS-wrappers commit 0b900a51e220ce6f17c1e76292c06a5f4d934055-dirty
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502 ' <span class="circle-value">' + numberDisplay(nb_clusters) + '</span>' +
76c750c5f0d1 planemo upload for repository https://github.com/oinizan/FROGS-wrappers commit 0b900a51e220ce6f17c1e76292c06a5f4d934055-dirty
frogs
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diff changeset
503 '</div>'
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504 );
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505 $('#nb-sequences').append( '' +
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506 '<div class="circle">' +
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507 ' <span class="circle-title">Sequences</span>' +
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diff changeset
508 ' <br />' +
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509 ' <span class="circle-value">' + numberDisplay(nb_sequences) + '</span>' +
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diff changeset
510 '</div>'
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511 );
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frogs
parents:
diff changeset
512
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diff changeset
513 // Boxplot
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514 var boxplot_series = [{
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515 'name': "Cluster size",
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516 'data': [[dispersion['min'],
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frogs
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diff changeset
517 dispersion['lower_quartile'],
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diff changeset
518 dispersion['median'],
76c750c5f0d1 planemo upload for repository https://github.com/oinizan/FROGS-wrappers commit 0b900a51e220ce6f17c1e76292c06a5f4d934055-dirty
frogs
parents:
diff changeset
519 dispersion['upper_quartile'],
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diff changeset
520 dispersion['max']]]
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521 }];
76c750c5f0d1 planemo upload for repository https://github.com/oinizan/FROGS-wrappers commit 0b900a51e220ce6f17c1e76292c06a5f4d934055-dirty
frogs
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diff changeset
522 $('#' + container_id).append( '<div id="dispersion"></div>' );
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diff changeset
523 $('#dispersion').append( '<h1 class="page-header">Clusters size summary<h1/>' );
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frogs
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diff changeset
524 $('#dispersion').append( '<div class="col-md-8" style="height:100%;">' );
76c750c5f0d1 planemo upload for repository https://github.com/oinizan/FROGS-wrappers commit 0b900a51e220ce6f17c1e76292c06a5f4d934055-dirty
frogs
parents:
diff changeset
525 $('#dispersion div').last().highcharts( boxplot_param("Clusters size distribution", null, "Cluster size", ["All"], boxplot_series) );
76c750c5f0d1 planemo upload for repository https://github.com/oinizan/FROGS-wrappers commit 0b900a51e220ce6f17c1e76292c06a5f4d934055-dirty
frogs
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diff changeset
526
76c750c5f0d1 planemo upload for repository https://github.com/oinizan/FROGS-wrappers commit 0b900a51e220ce6f17c1e76292c06a5f4d934055-dirty
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diff changeset
527 // Deciles
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parents:
diff changeset
528 var decile_data = [
76c750c5f0d1 planemo upload for repository https://github.com/oinizan/FROGS-wrappers commit 0b900a51e220ce6f17c1e76292c06a5f4d934055-dirty
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diff changeset
529 ["Min", dispersion['min']],
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frogs
parents:
diff changeset
530 [1, dispersion['1_decile']],
76c750c5f0d1 planemo upload for repository https://github.com/oinizan/FROGS-wrappers commit 0b900a51e220ce6f17c1e76292c06a5f4d934055-dirty
frogs
parents:
diff changeset
531 [2, dispersion['2_decile']],
76c750c5f0d1 planemo upload for repository https://github.com/oinizan/FROGS-wrappers commit 0b900a51e220ce6f17c1e76292c06a5f4d934055-dirty
frogs
parents:
diff changeset
532 [3, dispersion['3_decile']],
76c750c5f0d1 planemo upload for repository https://github.com/oinizan/FROGS-wrappers commit 0b900a51e220ce6f17c1e76292c06a5f4d934055-dirty
frogs
parents:
diff changeset
533 [4, dispersion['4_decile']],
76c750c5f0d1 planemo upload for repository https://github.com/oinizan/FROGS-wrappers commit 0b900a51e220ce6f17c1e76292c06a5f4d934055-dirty
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diff changeset
534 ["Median", dispersion['5_decile']],
76c750c5f0d1 planemo upload for repository https://github.com/oinizan/FROGS-wrappers commit 0b900a51e220ce6f17c1e76292c06a5f4d934055-dirty
frogs
parents:
diff changeset
535 [6, dispersion['6_decile']],
76c750c5f0d1 planemo upload for repository https://github.com/oinizan/FROGS-wrappers commit 0b900a51e220ce6f17c1e76292c06a5f4d934055-dirty
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diff changeset
536 [7, dispersion['7_decile']],
76c750c5f0d1 planemo upload for repository https://github.com/oinizan/FROGS-wrappers commit 0b900a51e220ce6f17c1e76292c06a5f4d934055-dirty
frogs
parents:
diff changeset
537 [8, dispersion['8_decile']],
76c750c5f0d1 planemo upload for repository https://github.com/oinizan/FROGS-wrappers commit 0b900a51e220ce6f17c1e76292c06a5f4d934055-dirty
frogs
parents:
diff changeset
538 [9, dispersion['9_decile']],
76c750c5f0d1 planemo upload for repository https://github.com/oinizan/FROGS-wrappers commit 0b900a51e220ce6f17c1e76292c06a5f4d934055-dirty
frogs
parents:
diff changeset
539 ["Max", dispersion['max']]
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frogs
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diff changeset
540 ];
76c750c5f0d1 planemo upload for repository https://github.com/oinizan/FROGS-wrappers commit 0b900a51e220ce6f17c1e76292c06a5f4d934055-dirty
frogs
parents:
diff changeset
541 $('#dispersion').append( '<div class="col-md-4">' );
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diff changeset
542 $('#dispersion div').last().append( table("Clusters size distribution (decile)", ["Decile", "Value"], decile_data) );
76c750c5f0d1 planemo upload for repository https://github.com/oinizan/FROGS-wrappers commit 0b900a51e220ce6f17c1e76292c06a5f4d934055-dirty
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parents:
diff changeset
543
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frogs
parents:
diff changeset
544 // Details
76c750c5f0d1 planemo upload for repository https://github.com/oinizan/FROGS-wrappers commit 0b900a51e220ce6f17c1e76292c06a5f4d934055-dirty
frogs
parents:
diff changeset
545 var cluster_sum = 0 ;
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diff changeset
546 for( var idx=0 ; idx < clusters_sizes.length ; idx++ ){
76c750c5f0d1 planemo upload for repository https://github.com/oinizan/FROGS-wrappers commit 0b900a51e220ce6f17c1e76292c06a5f4d934055-dirty
frogs
parents:
diff changeset
547 cluster_sum += series[0]['data'][idx] ;
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frogs
parents:
diff changeset
548 }
76c750c5f0d1 planemo upload for repository https://github.com/oinizan/FROGS-wrappers commit 0b900a51e220ce6f17c1e76292c06a5f4d934055-dirty
frogs
parents:
diff changeset
549 var distrib_data = new Array();
76c750c5f0d1 planemo upload for repository https://github.com/oinizan/FROGS-wrappers commit 0b900a51e220ce6f17c1e76292c06a5f4d934055-dirty
frogs
parents:
diff changeset
550 for( var idx=0 ; idx < clusters_sizes.length ; idx++ ){
76c750c5f0d1 planemo upload for repository https://github.com/oinizan/FROGS-wrappers commit 0b900a51e220ce6f17c1e76292c06a5f4d934055-dirty
frogs
parents:
diff changeset
551 var cluster_prct = Math.round((series[0]['data'][idx]/cluster_sum)*10000)/100 ;
76c750c5f0d1 planemo upload for repository https://github.com/oinizan/FROGS-wrappers commit 0b900a51e220ce6f17c1e76292c06a5f4d934055-dirty
frogs
parents:
diff changeset
552 distrib_data.push([ clusters_sizes[idx], series[0]['data'][idx], cluster_prct ]);
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frogs
parents:
diff changeset
553 }
76c750c5f0d1 planemo upload for repository https://github.com/oinizan/FROGS-wrappers commit 0b900a51e220ce6f17c1e76292c06a5f4d934055-dirty
frogs
parents:
diff changeset
554 $('#dispersion').append( '<div class="col-md-12"></div>' );
76c750c5f0d1 planemo upload for repository https://github.com/oinizan/FROGS-wrappers commit 0b900a51e220ce6f17c1e76292c06a5f4d934055-dirty
frogs
parents:
diff changeset
555 $('#dispersion div').last().append( '<h1 class="page-header">Clusters size details<h1/>' );
76c750c5f0d1 planemo upload for repository https://github.com/oinizan/FROGS-wrappers commit 0b900a51e220ce6f17c1e76292c06a5f4d934055-dirty
frogs
parents:
diff changeset
556 $('#dispersion div').last().append( table("Clusters size", ["Cluster size", "Number of cluster", "% of all clusters"], distrib_data) );
76c750c5f0d1 planemo upload for repository https://github.com/oinizan/FROGS-wrappers commit 0b900a51e220ce6f17c1e76292c06a5f4d934055-dirty
frogs
parents:
diff changeset
557 $('#dispersion table').last().prop( 'id', 'dispersion-table' );
76c750c5f0d1 planemo upload for repository https://github.com/oinizan/FROGS-wrappers commit 0b900a51e220ce6f17c1e76292c06a5f4d934055-dirty
frogs
parents:
diff changeset
558 $('#' + container_id + ' table').last().DataTable({
76c750c5f0d1 planemo upload for repository https://github.com/oinizan/FROGS-wrappers commit 0b900a51e220ce6f17c1e76292c06a5f4d934055-dirty
frogs
parents:
diff changeset
559 "sDom": '<"top"<"#dispersion-csv-export"><"clear">lf>rt<"bottom"ip><"clear">'
76c750c5f0d1 planemo upload for repository https://github.com/oinizan/FROGS-wrappers commit 0b900a51e220ce6f17c1e76292c06a5f4d934055-dirty
frogs
parents:
diff changeset
560 });
76c750c5f0d1 planemo upload for repository https://github.com/oinizan/FROGS-wrappers commit 0b900a51e220ce6f17c1e76292c06a5f4d934055-dirty
frogs
parents:
diff changeset
561 $('#dispersion-csv-export').addClass( 'dataTables_filter' );
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frogs
parents:
diff changeset
562 $('#dispersion-csv-export').html( '<button class="btn btn-primary"><span class="glyphicon glyphicon-open-file" aria-hidden="true">CSV</span></button>' );
76c750c5f0d1 planemo upload for repository https://github.com/oinizan/FROGS-wrappers commit 0b900a51e220ce6f17c1e76292c06a5f4d934055-dirty
frogs
parents:
diff changeset
563 $('#dispersion-csv-export').datatableExport({
76c750c5f0d1 planemo upload for repository https://github.com/oinizan/FROGS-wrappers commit 0b900a51e220ce6f17c1e76292c06a5f4d934055-dirty
frogs
parents:
diff changeset
564 'table_id': "dispersion-table"
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frogs
parents:
diff changeset
565 });
76c750c5f0d1 planemo upload for repository https://github.com/oinizan/FROGS-wrappers commit 0b900a51e220ce6f17c1e76292c06a5f4d934055-dirty
frogs
parents:
diff changeset
566 }
76c750c5f0d1 planemo upload for repository https://github.com/oinizan/FROGS-wrappers commit 0b900a51e220ce6f17c1e76292c06a5f4d934055-dirty
frogs
parents:
diff changeset
567
76c750c5f0d1 planemo upload for repository https://github.com/oinizan/FROGS-wrappers commit 0b900a51e220ce6f17c1e76292c06a5f4d934055-dirty
frogs
parents:
diff changeset
568 var sample_table_load = function( container_id ){
76c750c5f0d1 planemo upload for repository https://github.com/oinizan/FROGS-wrappers commit 0b900a51e220ce6f17c1e76292c06a5f4d934055-dirty
frogs
parents:
diff changeset
569 var table_data = new Array();
76c750c5f0d1 planemo upload for repository https://github.com/oinizan/FROGS-wrappers commit 0b900a51e220ce6f17c1e76292c06a5f4d934055-dirty
frogs
parents:
diff changeset
570 for( sample in samples_distrib ){
76c750c5f0d1 planemo upload for repository https://github.com/oinizan/FROGS-wrappers commit 0b900a51e220ce6f17c1e76292c06a5f4d934055-dirty
frogs
parents:
diff changeset
571 table_data.push([
76c750c5f0d1 planemo upload for repository https://github.com/oinizan/FROGS-wrappers commit 0b900a51e220ce6f17c1e76292c06a5f4d934055-dirty
frogs
parents:
diff changeset
572 sample,
76c750c5f0d1 planemo upload for repository https://github.com/oinizan/FROGS-wrappers commit 0b900a51e220ce6f17c1e76292c06a5f4d934055-dirty
frogs
parents:
diff changeset
573 samples_distrib[sample]['shared_observations'] + samples_distrib[sample]['own_observations'],
76c750c5f0d1 planemo upload for repository https://github.com/oinizan/FROGS-wrappers commit 0b900a51e220ce6f17c1e76292c06a5f4d934055-dirty
frogs
parents:
diff changeset
574 samples_distrib[sample]['shared_observations'],
76c750c5f0d1 planemo upload for repository https://github.com/oinizan/FROGS-wrappers commit 0b900a51e220ce6f17c1e76292c06a5f4d934055-dirty
frogs
parents:
diff changeset
575 samples_distrib[sample]['own_observations'],
76c750c5f0d1 planemo upload for repository https://github.com/oinizan/FROGS-wrappers commit 0b900a51e220ce6f17c1e76292c06a5f4d934055-dirty
frogs
parents:
diff changeset
576 samples_distrib[sample]['shared_seq'] + samples_distrib[sample]['own_seq'],
76c750c5f0d1 planemo upload for repository https://github.com/oinizan/FROGS-wrappers commit 0b900a51e220ce6f17c1e76292c06a5f4d934055-dirty
frogs
parents:
diff changeset
577 samples_distrib[sample]['shared_seq'],
76c750c5f0d1 planemo upload for repository https://github.com/oinizan/FROGS-wrappers commit 0b900a51e220ce6f17c1e76292c06a5f4d934055-dirty
frogs
parents:
diff changeset
578 samples_distrib[sample]['own_seq'],
76c750c5f0d1 planemo upload for repository https://github.com/oinizan/FROGS-wrappers commit 0b900a51e220ce6f17c1e76292c06a5f4d934055-dirty
frogs
parents:
diff changeset
579 ])
76c750c5f0d1 planemo upload for repository https://github.com/oinizan/FROGS-wrappers commit 0b900a51e220ce6f17c1e76292c06a5f4d934055-dirty
frogs
parents:
diff changeset
580 }
76c750c5f0d1 planemo upload for repository https://github.com/oinizan/FROGS-wrappers commit 0b900a51e220ce6f17c1e76292c06a5f4d934055-dirty
frogs
parents:
diff changeset
581 $('#' + container_id).html( table("Samples information", ["Sample", "Total clusters", "Shared clusters", "Own clusters", "Total sequences", "Shared sequences", "Own sequences"], table_data) );
76c750c5f0d1 planemo upload for repository https://github.com/oinizan/FROGS-wrappers commit 0b900a51e220ce6f17c1e76292c06a5f4d934055-dirty
frogs
parents:
diff changeset
582 $('#' + container_id + ' table').prop( 'id', 'samples-table' );
76c750c5f0d1 planemo upload for repository https://github.com/oinizan/FROGS-wrappers commit 0b900a51e220ce6f17c1e76292c06a5f4d934055-dirty
frogs
parents:
diff changeset
583 $('#' + container_id + ' table').DataTable({
76c750c5f0d1 planemo upload for repository https://github.com/oinizan/FROGS-wrappers commit 0b900a51e220ce6f17c1e76292c06a5f4d934055-dirty
frogs
parents:
diff changeset
584 "sDom": '<"top"<"#samples-csv-export"><"clear">lf>rt<"bottom"ip><"clear">'
76c750c5f0d1 planemo upload for repository https://github.com/oinizan/FROGS-wrappers commit 0b900a51e220ce6f17c1e76292c06a5f4d934055-dirty
frogs
parents:
diff changeset
585 });
76c750c5f0d1 planemo upload for repository https://github.com/oinizan/FROGS-wrappers commit 0b900a51e220ce6f17c1e76292c06a5f4d934055-dirty
frogs
parents:
diff changeset
586 $('#samples-csv-export').addClass( 'dataTables_filter' );
76c750c5f0d1 planemo upload for repository https://github.com/oinizan/FROGS-wrappers commit 0b900a51e220ce6f17c1e76292c06a5f4d934055-dirty
frogs
parents:
diff changeset
587 $('#samples-csv-export').html( '<button class="btn btn-primary"><span class="glyphicon glyphicon-open-file" aria-hidden="true">CSV</span></button>' );
76c750c5f0d1 planemo upload for repository https://github.com/oinizan/FROGS-wrappers commit 0b900a51e220ce6f17c1e76292c06a5f4d934055-dirty
frogs
parents:
diff changeset
588 $('#samples-csv-export').datatableExport({
76c750c5f0d1 planemo upload for repository https://github.com/oinizan/FROGS-wrappers commit 0b900a51e220ce6f17c1e76292c06a5f4d934055-dirty
frogs
parents:
diff changeset
589 'table_id': "samples-table"
76c750c5f0d1 planemo upload for repository https://github.com/oinizan/FROGS-wrappers commit 0b900a51e220ce6f17c1e76292c06a5f4d934055-dirty
frogs
parents:
diff changeset
590 });
76c750c5f0d1 planemo upload for repository https://github.com/oinizan/FROGS-wrappers commit 0b900a51e220ce6f17c1e76292c06a5f4d934055-dirty
frogs
parents:
diff changeset
591 }
76c750c5f0d1 planemo upload for repository https://github.com/oinizan/FROGS-wrappers commit 0b900a51e220ce6f17c1e76292c06a5f4d934055-dirty
frogs
parents:
diff changeset
592
76c750c5f0d1 planemo upload for repository https://github.com/oinizan/FROGS-wrappers commit 0b900a51e220ce6f17c1e76292c06a5f4d934055-dirty
frogs
parents:
diff changeset
593 var hierarchical_clustering_load = function( container_id ) {
76c750c5f0d1 planemo upload for repository https://github.com/oinizan/FROGS-wrappers commit 0b900a51e220ce6f17c1e76292c06a5f4d934055-dirty
frogs
parents:
diff changeset
594 var tree = Node.fromNewick( newick );
76c750c5f0d1 planemo upload for repository https://github.com/oinizan/FROGS-wrappers commit 0b900a51e220ce6f17c1e76292c06a5f4d934055-dirty
frogs
parents:
diff changeset
595 var leaves_names = tree.getLeavesNames();
76c750c5f0d1 planemo upload for repository https://github.com/oinizan/FROGS-wrappers commit 0b900a51e220ce6f17c1e76292c06a5f4d934055-dirty
frogs
parents:
diff changeset
596 var leaf_name_length = 0 ;
76c750c5f0d1 planemo upload for repository https://github.com/oinizan/FROGS-wrappers commit 0b900a51e220ce6f17c1e76292c06a5f4d934055-dirty
frogs
parents:
diff changeset
597 for( var idx = 0 ; idx < leaves_names.length ; idx++ ) {
76c750c5f0d1 planemo upload for repository https://github.com/oinizan/FROGS-wrappers commit 0b900a51e220ce6f17c1e76292c06a5f4d934055-dirty
frogs
parents:
diff changeset
598 leaf_name_length = Math.max( leaf_name_length, leaves_names[idx].length );
76c750c5f0d1 planemo upload for repository https://github.com/oinizan/FROGS-wrappers commit 0b900a51e220ce6f17c1e76292c06a5f4d934055-dirty
frogs
parents:
diff changeset
599 }
76c750c5f0d1 planemo upload for repository https://github.com/oinizan/FROGS-wrappers commit 0b900a51e220ce6f17c1e76292c06a5f4d934055-dirty
frogs
parents:
diff changeset
600 var width = tree.maxDepth() * 95 + (leaf_name_length * 8) ; // nb_link * width_link + text_length
76c750c5f0d1 planemo upload for repository https://github.com/oinizan/FROGS-wrappers commit 0b900a51e220ce6f17c1e76292c06a5f4d934055-dirty
frogs
parents:
diff changeset
601 var height = 50 + tree.nbLeaves() * 40 ; //margin_top + nb_terminal_nodes + height_nodes
76c750c5f0d1 planemo upload for repository https://github.com/oinizan/FROGS-wrappers commit 0b900a51e220ce6f17c1e76292c06a5f4d934055-dirty
frogs
parents:
diff changeset
602
76c750c5f0d1 planemo upload for repository https://github.com/oinizan/FROGS-wrappers commit 0b900a51e220ce6f17c1e76292c06a5f4d934055-dirty
frogs
parents:
diff changeset
603 // Display tree
76c750c5f0d1 planemo upload for repository https://github.com/oinizan/FROGS-wrappers commit 0b900a51e220ce6f17c1e76292c06a5f4d934055-dirty
frogs
parents:
diff changeset
604 linkage_data = tree.toJson();
76c750c5f0d1 planemo upload for repository https://github.com/oinizan/FROGS-wrappers commit 0b900a51e220ce6f17c1e76292c06a5f4d934055-dirty
frogs
parents:
diff changeset
605 d3_tree = null ;
76c750c5f0d1 planemo upload for repository https://github.com/oinizan/FROGS-wrappers commit 0b900a51e220ce6f17c1e76292c06a5f4d934055-dirty
frogs
parents:
diff changeset
606 diagonal = null ;
76c750c5f0d1 planemo upload for repository https://github.com/oinizan/FROGS-wrappers commit 0b900a51e220ce6f17c1e76292c06a5f4d934055-dirty
frogs
parents:
diff changeset
607 svg_layout = null ;
76c750c5f0d1 planemo upload for repository https://github.com/oinizan/FROGS-wrappers commit 0b900a51e220ce6f17c1e76292c06a5f4d934055-dirty
frogs
parents:
diff changeset
608 node_id = 0 ;
76c750c5f0d1 planemo upload for repository https://github.com/oinizan/FROGS-wrappers commit 0b900a51e220ce6f17c1e76292c06a5f4d934055-dirty
frogs
parents:
diff changeset
609
76c750c5f0d1 planemo upload for repository https://github.com/oinizan/FROGS-wrappers commit 0b900a51e220ce6f17c1e76292c06a5f4d934055-dirty
frogs
parents:
diff changeset
610 d3_tree = d3.layout.cluster()
76c750c5f0d1 planemo upload for repository https://github.com/oinizan/FROGS-wrappers commit 0b900a51e220ce6f17c1e76292c06a5f4d934055-dirty
frogs
parents:
diff changeset
611 .size([height, width]);
76c750c5f0d1 planemo upload for repository https://github.com/oinizan/FROGS-wrappers commit 0b900a51e220ce6f17c1e76292c06a5f4d934055-dirty
frogs
parents:
diff changeset
612
76c750c5f0d1 planemo upload for repository https://github.com/oinizan/FROGS-wrappers commit 0b900a51e220ce6f17c1e76292c06a5f4d934055-dirty
frogs
parents:
diff changeset
613 diagonal = d3.svg.diagonal()
76c750c5f0d1 planemo upload for repository https://github.com/oinizan/FROGS-wrappers commit 0b900a51e220ce6f17c1e76292c06a5f4d934055-dirty
frogs
parents:
diff changeset
614 .projection(function(d) { return [d.y, d.x]; });
76c750c5f0d1 planemo upload for repository https://github.com/oinizan/FROGS-wrappers commit 0b900a51e220ce6f17c1e76292c06a5f4d934055-dirty
frogs
parents:
diff changeset
615 $('#' + container_id).append('<div style="margin-left:auto;margin-right:auto;"></div>');
76c750c5f0d1 planemo upload for repository https://github.com/oinizan/FROGS-wrappers commit 0b900a51e220ce6f17c1e76292c06a5f4d934055-dirty
frogs
parents:
diff changeset
616 svg_layout = d3.select('#' + container_id + ' div').append("svg:svg")
76c750c5f0d1 planemo upload for repository https://github.com/oinizan/FROGS-wrappers commit 0b900a51e220ce6f17c1e76292c06a5f4d934055-dirty
frogs
parents:
diff changeset
617 .attr("width", width)
76c750c5f0d1 planemo upload for repository https://github.com/oinizan/FROGS-wrappers commit 0b900a51e220ce6f17c1e76292c06a5f4d934055-dirty
frogs
parents:
diff changeset
618 .attr("height", height)
76c750c5f0d1 planemo upload for repository https://github.com/oinizan/FROGS-wrappers commit 0b900a51e220ce6f17c1e76292c06a5f4d934055-dirty
frogs
parents:
diff changeset
619 .append("svg:g")
76c750c5f0d1 planemo upload for repository https://github.com/oinizan/FROGS-wrappers commit 0b900a51e220ce6f17c1e76292c06a5f4d934055-dirty
frogs
parents:
diff changeset
620 .attr("transform", "translate(20,20)");
76c750c5f0d1 planemo upload for repository https://github.com/oinizan/FROGS-wrappers commit 0b900a51e220ce6f17c1e76292c06a5f4d934055-dirty
frogs
parents:
diff changeset
621
76c750c5f0d1 planemo upload for repository https://github.com/oinizan/FROGS-wrappers commit 0b900a51e220ce6f17c1e76292c06a5f4d934055-dirty
frogs
parents:
diff changeset
622 linkage_data.x0 = height / 2;
76c750c5f0d1 planemo upload for repository https://github.com/oinizan/FROGS-wrappers commit 0b900a51e220ce6f17c1e76292c06a5f4d934055-dirty
frogs
parents:
diff changeset
623 linkage_data.y0 = 0;
76c750c5f0d1 planemo upload for repository https://github.com/oinizan/FROGS-wrappers commit 0b900a51e220ce6f17c1e76292c06a5f4d934055-dirty
frogs
parents:
diff changeset
624
76c750c5f0d1 planemo upload for repository https://github.com/oinizan/FROGS-wrappers commit 0b900a51e220ce6f17c1e76292c06a5f4d934055-dirty
frogs
parents:
diff changeset
625 update_linkage_nodes(linkage_data);
76c750c5f0d1 planemo upload for repository https://github.com/oinizan/FROGS-wrappers commit 0b900a51e220ce6f17c1e76292c06a5f4d934055-dirty
frogs
parents:
diff changeset
626
76c750c5f0d1 planemo upload for repository https://github.com/oinizan/FROGS-wrappers commit 0b900a51e220ce6f17c1e76292c06a5f4d934055-dirty
frogs
parents:
diff changeset
627 // Display warnings
76c750c5f0d1 planemo upload for repository https://github.com/oinizan/FROGS-wrappers commit 0b900a51e220ce6f17c1e76292c06a5f4d934055-dirty
frogs
parents:
diff changeset
628 var excluded_samples = $.grep(
76c750c5f0d1 planemo upload for repository https://github.com/oinizan/FROGS-wrappers commit 0b900a51e220ce6f17c1e76292c06a5f4d934055-dirty
frogs
parents:
diff changeset
629 Object.keys(samples_distrib),
76c750c5f0d1 planemo upload for repository https://github.com/oinizan/FROGS-wrappers commit 0b900a51e220ce6f17c1e76292c06a5f4d934055-dirty
frogs
parents:
diff changeset
630 function(el){ return $.inArray(el, leaves_names) == -1 }
76c750c5f0d1 planemo upload for repository https://github.com/oinizan/FROGS-wrappers commit 0b900a51e220ce6f17c1e76292c06a5f4d934055-dirty
frogs
parents:
diff changeset
631 );
76c750c5f0d1 planemo upload for repository https://github.com/oinizan/FROGS-wrappers commit 0b900a51e220ce6f17c1e76292c06a5f4d934055-dirty
frogs
parents:
diff changeset
632 if( excluded_samples.length > 0 ){
76c750c5f0d1 planemo upload for repository https://github.com/oinizan/FROGS-wrappers commit 0b900a51e220ce6f17c1e76292c06a5f4d934055-dirty
frogs
parents:
diff changeset
633 $('#' + container_id).append( '' +
76c750c5f0d1 planemo upload for repository https://github.com/oinizan/FROGS-wrappers commit 0b900a51e220ce6f17c1e76292c06a5f4d934055-dirty
frogs
parents:
diff changeset
634 '<div id="hc-warning" class="alert alert-warning alert-dismissible">' +
76c750c5f0d1 planemo upload for repository https://github.com/oinizan/FROGS-wrappers commit 0b900a51e220ce6f17c1e76292c06a5f4d934055-dirty
frogs
parents:
diff changeset
635 ' <span>' +
76c750c5f0d1 planemo upload for repository https://github.com/oinizan/FROGS-wrappers commit 0b900a51e220ce6f17c1e76292c06a5f4d934055-dirty
frogs
parents:
diff changeset
636 ' <span class="glyphicon glyphicon-exclamation-sign"></span>' +
76c750c5f0d1 planemo upload for repository https://github.com/oinizan/FROGS-wrappers commit 0b900a51e220ce6f17c1e76292c06a5f4d934055-dirty
frogs
parents:
diff changeset
637 ' Excluded because they have no sequence: ' +
76c750c5f0d1 planemo upload for repository https://github.com/oinizan/FROGS-wrappers commit 0b900a51e220ce6f17c1e76292c06a5f4d934055-dirty
frogs
parents:
diff changeset
638 ' </span>' +
76c750c5f0d1 planemo upload for repository https://github.com/oinizan/FROGS-wrappers commit 0b900a51e220ce6f17c1e76292c06a5f4d934055-dirty
frogs
parents:
diff changeset
639 ' <span>' + excluded_samples.sort().join(", ") + '</span>' +
76c750c5f0d1 planemo upload for repository https://github.com/oinizan/FROGS-wrappers commit 0b900a51e220ce6f17c1e76292c06a5f4d934055-dirty
frogs
parents:
diff changeset
640 '</div>'
76c750c5f0d1 planemo upload for repository https://github.com/oinizan/FROGS-wrappers commit 0b900a51e220ce6f17c1e76292c06a5f4d934055-dirty
frogs
parents:
diff changeset
641 );
76c750c5f0d1 planemo upload for repository https://github.com/oinizan/FROGS-wrappers commit 0b900a51e220ce6f17c1e76292c06a5f4d934055-dirty
frogs
parents:
diff changeset
642 }
76c750c5f0d1 planemo upload for repository https://github.com/oinizan/FROGS-wrappers commit 0b900a51e220ce6f17c1e76292c06a5f4d934055-dirty
frogs
parents:
diff changeset
643
76c750c5f0d1 planemo upload for repository https://github.com/oinizan/FROGS-wrappers commit 0b900a51e220ce6f17c1e76292c06a5f4d934055-dirty
frogs
parents:
diff changeset
644 // Display newick
76c750c5f0d1 planemo upload for repository https://github.com/oinizan/FROGS-wrappers commit 0b900a51e220ce6f17c1e76292c06a5f4d934055-dirty
frogs
parents:
diff changeset
645 $('#' + container_id).append( '' +
76c750c5f0d1 planemo upload for repository https://github.com/oinizan/FROGS-wrappers commit 0b900a51e220ce6f17c1e76292c06a5f4d934055-dirty
frogs
parents:
diff changeset
646 '<div id="hc-newick">' +
76c750c5f0d1 planemo upload for repository https://github.com/oinizan/FROGS-wrappers commit 0b900a51e220ce6f17c1e76292c06a5f4d934055-dirty
frogs
parents:
diff changeset
647 ' <span class="label label-primary label-badge">Newick</span>' +
76c750c5f0d1 planemo upload for repository https://github.com/oinizan/FROGS-wrappers commit 0b900a51e220ce6f17c1e76292c06a5f4d934055-dirty
frogs
parents:
diff changeset
648 ' <span>' + newick + '</span>' +
76c750c5f0d1 planemo upload for repository https://github.com/oinizan/FROGS-wrappers commit 0b900a51e220ce6f17c1e76292c06a5f4d934055-dirty
frogs
parents:
diff changeset
649 '</div>'
76c750c5f0d1 planemo upload for repository https://github.com/oinizan/FROGS-wrappers commit 0b900a51e220ce6f17c1e76292c06a5f4d934055-dirty
frogs
parents:
diff changeset
650 );
76c750c5f0d1 planemo upload for repository https://github.com/oinizan/FROGS-wrappers commit 0b900a51e220ce6f17c1e76292c06a5f4d934055-dirty
frogs
parents:
diff changeset
651 }
76c750c5f0d1 planemo upload for repository https://github.com/oinizan/FROGS-wrappers commit 0b900a51e220ce6f17c1e76292c06a5f4d934055-dirty
frogs
parents:
diff changeset
652
76c750c5f0d1 planemo upload for repository https://github.com/oinizan/FROGS-wrappers commit 0b900a51e220ce6f17c1e76292c06a5f4d934055-dirty
frogs
parents:
diff changeset
653 var sequence_distrib_load = function( container_id ) {
76c750c5f0d1 planemo upload for repository https://github.com/oinizan/FROGS-wrappers commit 0b900a51e220ce6f17c1e76292c06a5f4d934055-dirty
frogs
parents:
diff changeset
654 var series_cumulative = new Array() ;
76c750c5f0d1 planemo upload for repository https://github.com/oinizan/FROGS-wrappers commit 0b900a51e220ce6f17c1e76292c06a5f4d934055-dirty
frogs
parents:
diff changeset
655 for( var series_idx = 0 ; series_idx < series.length ; series_idx++ ){
76c750c5f0d1 planemo upload for repository https://github.com/oinizan/FROGS-wrappers commit 0b900a51e220ce6f17c1e76292c06a5f4d934055-dirty
frogs
parents:
diff changeset
656 series_cumulative.push({
76c750c5f0d1 planemo upload for repository https://github.com/oinizan/FROGS-wrappers commit 0b900a51e220ce6f17c1e76292c06a5f4d934055-dirty
frogs
parents:
diff changeset
657 'name': series[series_idx]['name'],
76c750c5f0d1 planemo upload for repository https://github.com/oinizan/FROGS-wrappers commit 0b900a51e220ce6f17c1e76292c06a5f4d934055-dirty
frogs
parents:
diff changeset
658 'data': new Array(),
76c750c5f0d1 planemo upload for repository https://github.com/oinizan/FROGS-wrappers commit 0b900a51e220ce6f17c1e76292c06a5f4d934055-dirty
frogs
parents:
diff changeset
659 'pointStart': 1
76c750c5f0d1 planemo upload for repository https://github.com/oinizan/FROGS-wrappers commit 0b900a51e220ce6f17c1e76292c06a5f4d934055-dirty
frogs
parents:
diff changeset
660 });
76c750c5f0d1 planemo upload for repository https://github.com/oinizan/FROGS-wrappers commit 0b900a51e220ce6f17c1e76292c06a5f4d934055-dirty
frogs
parents:
diff changeset
661 var sum = 0 ;
76c750c5f0d1 planemo upload for repository https://github.com/oinizan/FROGS-wrappers commit 0b900a51e220ce6f17c1e76292c06a5f4d934055-dirty
frogs
parents:
diff changeset
662 var previous_cumulative_count = 0 ;
76c750c5f0d1 planemo upload for repository https://github.com/oinizan/FROGS-wrappers commit 0b900a51e220ce6f17c1e76292c06a5f4d934055-dirty
frogs
parents:
diff changeset
663 for( var val_idx = 0 ; val_idx < series[series_idx]['data'].length ; val_idx++ ){
76c750c5f0d1 planemo upload for repository https://github.com/oinizan/FROGS-wrappers commit 0b900a51e220ce6f17c1e76292c06a5f4d934055-dirty
frogs
parents:
diff changeset
664 var current_count = series[series_idx]['data'][val_idx] * clusters_sizes[val_idx] ;
76c750c5f0d1 planemo upload for repository https://github.com/oinizan/FROGS-wrappers commit 0b900a51e220ce6f17c1e76292c06a5f4d934055-dirty
frogs
parents:
diff changeset
665 var cumulative_count = previous_cumulative_count + current_count ;
76c750c5f0d1 planemo upload for repository https://github.com/oinizan/FROGS-wrappers commit 0b900a51e220ce6f17c1e76292c06a5f4d934055-dirty
frogs
parents:
diff changeset
666 series_cumulative[series_idx]['data'].push( [clusters_sizes[val_idx], cumulative_count] );
76c750c5f0d1 planemo upload for repository https://github.com/oinizan/FROGS-wrappers commit 0b900a51e220ce6f17c1e76292c06a5f4d934055-dirty
frogs
parents:
diff changeset
667 previous_cumulative_count = cumulative_count ;
76c750c5f0d1 planemo upload for repository https://github.com/oinizan/FROGS-wrappers commit 0b900a51e220ce6f17c1e76292c06a5f4d934055-dirty
frogs
parents:
diff changeset
668 }
76c750c5f0d1 planemo upload for repository https://github.com/oinizan/FROGS-wrappers commit 0b900a51e220ce6f17c1e76292c06a5f4d934055-dirty
frogs
parents:
diff changeset
669 sum_series[series[series_idx]['name']] = previous_cumulative_count ;
76c750c5f0d1 planemo upload for repository https://github.com/oinizan/FROGS-wrappers commit 0b900a51e220ce6f17c1e76292c06a5f4d934055-dirty
frogs
parents:
diff changeset
670 }
76c750c5f0d1 planemo upload for repository https://github.com/oinizan/FROGS-wrappers commit 0b900a51e220ce6f17c1e76292c06a5f4d934055-dirty
frogs
parents:
diff changeset
671 for( var series_idx = 0 ; series_idx < series.length ; series_idx++ ){
76c750c5f0d1 planemo upload for repository https://github.com/oinizan/FROGS-wrappers commit 0b900a51e220ce6f17c1e76292c06a5f4d934055-dirty
frogs
parents:
diff changeset
672 for( var val_idx = 0 ; val_idx < series[series_idx]['data'].length ; val_idx++ ){
76c750c5f0d1 planemo upload for repository https://github.com/oinizan/FROGS-wrappers commit 0b900a51e220ce6f17c1e76292c06a5f4d934055-dirty
frogs
parents:
diff changeset
673 var current_prct = (series_cumulative[series_idx]['data'][val_idx][1] / sum_series[series[series_idx]['name']])*100 ;
76c750c5f0d1 planemo upload for repository https://github.com/oinizan/FROGS-wrappers commit 0b900a51e220ce6f17c1e76292c06a5f4d934055-dirty
frogs
parents:
diff changeset
674 series_cumulative[series_idx]['data'][val_idx][1] = Math.round(current_prct*100)/100 ;
76c750c5f0d1 planemo upload for repository https://github.com/oinizan/FROGS-wrappers commit 0b900a51e220ce6f17c1e76292c06a5f4d934055-dirty
frogs
parents:
diff changeset
675 }
76c750c5f0d1 planemo upload for repository https://github.com/oinizan/FROGS-wrappers commit 0b900a51e220ce6f17c1e76292c06a5f4d934055-dirty
frogs
parents:
diff changeset
676 }
76c750c5f0d1 planemo upload for repository https://github.com/oinizan/FROGS-wrappers commit 0b900a51e220ce6f17c1e76292c06a5f4d934055-dirty
frogs
parents:
diff changeset
677 var seq_by_depth = areaplot_param("Cumulative sequences proportion by cluster size", "Cluster size", "% sequences", null, series_cumulative);
76c750c5f0d1 planemo upload for repository https://github.com/oinizan/FROGS-wrappers commit 0b900a51e220ce6f17c1e76292c06a5f4d934055-dirty
frogs
parents:
diff changeset
678 seq_by_depth['tooltip'] = {
76c750c5f0d1 planemo upload for repository https://github.com/oinizan/FROGS-wrappers commit 0b900a51e220ce6f17c1e76292c06a5f4d934055-dirty
frogs
parents:
diff changeset
679 formatter:function() {
76c750c5f0d1 planemo upload for repository https://github.com/oinizan/FROGS-wrappers commit 0b900a51e220ce6f17c1e76292c06a5f4d934055-dirty
frogs
parents:
diff changeset
680 tooltip_head = '<b>Clusters with size <= ' + this.x + '</b>' ;
76c750c5f0d1 planemo upload for repository https://github.com/oinizan/FROGS-wrappers commit 0b900a51e220ce6f17c1e76292c06a5f4d934055-dirty
frogs
parents:
diff changeset
681 tooltip_body = '' ;
76c750c5f0d1 planemo upload for repository https://github.com/oinizan/FROGS-wrappers commit 0b900a51e220ce6f17c1e76292c06a5f4d934055-dirty
frogs
parents:
diff changeset
682 for( var i=0 ; i<this.points.length ; i++) {
76c750c5f0d1 planemo upload for repository https://github.com/oinizan/FROGS-wrappers commit 0b900a51e220ce6f17c1e76292c06a5f4d934055-dirty
frogs
parents:
diff changeset
683 var pcnt = (this.points[i].point.y / sum_series[this.points[i].series.name]) * 100;
76c750c5f0d1 planemo upload for repository https://github.com/oinizan/FROGS-wrappers commit 0b900a51e220ce6f17c1e76292c06a5f4d934055-dirty
frogs
parents:
diff changeset
684 tooltip_body += '<tr>' +
76c750c5f0d1 planemo upload for repository https://github.com/oinizan/FROGS-wrappers commit 0b900a51e220ce6f17c1e76292c06a5f4d934055-dirty
frogs
parents:
diff changeset
685 '<td style="color:' + this.points[i].series.color +'">' + this.points[i].series.name + ' : </td>' +
76c750c5f0d1 planemo upload for repository https://github.com/oinizan/FROGS-wrappers commit 0b900a51e220ce6f17c1e76292c06a5f4d934055-dirty
frogs
parents:
diff changeset
686 '<td> ' + this.points[i].point.y + '% </td>' +
76c750c5f0d1 planemo upload for repository https://github.com/oinizan/FROGS-wrappers commit 0b900a51e220ce6f17c1e76292c06a5f4d934055-dirty
frogs
parents:
diff changeset
687 '<td> sequences</td>' +
76c750c5f0d1 planemo upload for repository https://github.com/oinizan/FROGS-wrappers commit 0b900a51e220ce6f17c1e76292c06a5f4d934055-dirty
frogs
parents:
diff changeset
688 '</tr>' ;
76c750c5f0d1 planemo upload for repository https://github.com/oinizan/FROGS-wrappers commit 0b900a51e220ce6f17c1e76292c06a5f4d934055-dirty
frogs
parents:
diff changeset
689 }
76c750c5f0d1 planemo upload for repository https://github.com/oinizan/FROGS-wrappers commit 0b900a51e220ce6f17c1e76292c06a5f4d934055-dirty
frogs
parents:
diff changeset
690 return tooltip_head + '<table>' + tooltip_body + '</table>' ;
76c750c5f0d1 planemo upload for repository https://github.com/oinizan/FROGS-wrappers commit 0b900a51e220ce6f17c1e76292c06a5f4d934055-dirty
frogs
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diff changeset
691 },
76c750c5f0d1 planemo upload for repository https://github.com/oinizan/FROGS-wrappers commit 0b900a51e220ce6f17c1e76292c06a5f4d934055-dirty
frogs
parents:
diff changeset
692 shared: true,
76c750c5f0d1 planemo upload for repository https://github.com/oinizan/FROGS-wrappers commit 0b900a51e220ce6f17c1e76292c06a5f4d934055-dirty
frogs
parents:
diff changeset
693 useHTML: true
76c750c5f0d1 planemo upload for repository https://github.com/oinizan/FROGS-wrappers commit 0b900a51e220ce6f17c1e76292c06a5f4d934055-dirty
frogs
parents:
diff changeset
694 };
76c750c5f0d1 planemo upload for repository https://github.com/oinizan/FROGS-wrappers commit 0b900a51e220ce6f17c1e76292c06a5f4d934055-dirty
frogs
parents:
diff changeset
695 $('#' + container_id).append('<div></div>');
76c750c5f0d1 planemo upload for repository https://github.com/oinizan/FROGS-wrappers commit 0b900a51e220ce6f17c1e76292c06a5f4d934055-dirty
frogs
parents:
diff changeset
696 $('#' + container_id).highcharts( seq_by_depth );
76c750c5f0d1 planemo upload for repository https://github.com/oinizan/FROGS-wrappers commit 0b900a51e220ce6f17c1e76292c06a5f4d934055-dirty
frogs
parents:
diff changeset
697 $('#' + container_id).append('<p class="graph-nb">N.B.: Select area to zoom in.</p>');
76c750c5f0d1 planemo upload for repository https://github.com/oinizan/FROGS-wrappers commit 0b900a51e220ce6f17c1e76292c06a5f4d934055-dirty
frogs
parents:
diff changeset
698 }
76c750c5f0d1 planemo upload for repository https://github.com/oinizan/FROGS-wrappers commit 0b900a51e220ce6f17c1e76292c06a5f4d934055-dirty
frogs
parents:
diff changeset
699
76c750c5f0d1 planemo upload for repository https://github.com/oinizan/FROGS-wrappers commit 0b900a51e220ce6f17c1e76292c06a5f4d934055-dirty
frogs
parents:
diff changeset
700
76c750c5f0d1 planemo upload for repository https://github.com/oinizan/FROGS-wrappers commit 0b900a51e220ce6f17c1e76292c06a5f4d934055-dirty
frogs
parents:
diff changeset
701 ///////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////
76c750c5f0d1 planemo upload for repository https://github.com/oinizan/FROGS-wrappers commit 0b900a51e220ce6f17c1e76292c06a5f4d934055-dirty
frogs
parents:
diff changeset
702 //
76c750c5f0d1 planemo upload for repository https://github.com/oinizan/FROGS-wrappers commit 0b900a51e220ce6f17c1e76292c06a5f4d934055-dirty
frogs
parents:
diff changeset
703 // Data
76c750c5f0d1 planemo upload for repository https://github.com/oinizan/FROGS-wrappers commit 0b900a51e220ce6f17c1e76292c06a5f4d934055-dirty
frogs
parents:
diff changeset
704 //
76c750c5f0d1 planemo upload for repository https://github.com/oinizan/FROGS-wrappers commit 0b900a51e220ce6f17c1e76292c06a5f4d934055-dirty
frogs
parents:
diff changeset
705 ///////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////
76c750c5f0d1 planemo upload for repository https://github.com/oinizan/FROGS-wrappers commit 0b900a51e220ce6f17c1e76292c06a5f4d934055-dirty
frogs
parents:
diff changeset
706 var clusters_sizes = [6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 92, 93, 94, 95, 96, 97, 98, 99, 100, 101, 102, 103, 104, 106, 107, 108, 109, 110, 112, 113, 114, 115, 116, 117, 118, 119, 120, 121, 123, 124, 126, 127, 128, 129, 132, 135, 136, 137, 138, 140, 141, 142, 149, 153, 155, 157, 158, 159, 162, 165, 166, 168, 169, 171, 173, 175, 178, 184, 185, 187, 190, 193, 196, 201, 204, 205, 206, 211, 212, 213, 215, 216, 217, 219, 228, 236, 241, 255, 260, 267, 283, 288, 289, 298, 304, 317, 320, 322, 325, 326, 330, 336, 341, 343, 352, 366, 372, 386, 388, 414, 417, 422, 427, 479, 487, 504, 525, 559, 572, 606, 618, 665, 688, 740, 744, 779, 831, 832, 860, 1133, 1139, 1140, 1269, 1293, 1390, 1572, 2356, 2370, 3113, 3433, 4282] ;
76c750c5f0d1 planemo upload for repository https://github.com/oinizan/FROGS-wrappers commit 0b900a51e220ce6f17c1e76292c06a5f4d934055-dirty
frogs
parents:
diff changeset
707 var series = [{
76c750c5f0d1 planemo upload for repository https://github.com/oinizan/FROGS-wrappers commit 0b900a51e220ce6f17c1e76292c06a5f4d934055-dirty
frogs
parents:
diff changeset
708 'name': "All",
76c750c5f0d1 planemo upload for repository https://github.com/oinizan/FROGS-wrappers commit 0b900a51e220ce6f17c1e76292c06a5f4d934055-dirty
frogs
parents:
diff changeset
709 'data': [141, 140, 80, 94, 71, 64, 62, 53, 51, 41, 43, 36, 34, 25, 35, 15, 24, 17, 22, 27, 11, 11, 20, 13, 12, 10, 11, 10, 7, 5, 12, 10, 9, 10, 6, 8, 2, 6, 6, 8, 7, 11, 5, 6, 5, 5, 5, 10, 1, 5, 4, 7, 4, 2, 2, 2, 7, 4, 2, 2, 6, 3, 5, 8, 2, 4, 1, 1, 4, 3, 3, 3, 2, 3, 7, 3, 2, 4, 2, 1, 2, 2, 2, 3, 1, 2, 1, 2, 4, 3, 3, 2, 1, 3, 2, 3, 1, 4, 3, 1, 2, 1, 1, 1, 2, 2, 2, 1, 2, 1, 2, 1, 1, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 3, 2, 1, 1, 2, 1, 1, 1, 2, 1, 1, 1, 1, 1, 2, 1, 1, 1, 1, 1, 1, 1, 1, 2, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 2, 1, 1, 1, 1, 1, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1]
76c750c5f0d1 planemo upload for repository https://github.com/oinizan/FROGS-wrappers commit 0b900a51e220ce6f17c1e76292c06a5f4d934055-dirty
frogs
parents:
diff changeset
710 }];
76c750c5f0d1 planemo upload for repository https://github.com/oinizan/FROGS-wrappers commit 0b900a51e220ce6f17c1e76292c06a5f4d934055-dirty
frogs
parents:
diff changeset
711 var sum_series = new Array() ;
76c750c5f0d1 planemo upload for repository https://github.com/oinizan/FROGS-wrappers commit 0b900a51e220ce6f17c1e76292c06a5f4d934055-dirty
frogs
parents:
diff changeset
712 var samples_distrib = {"splA_01": {"shared_observations": 1609, "own_seq": 0, "shared_seq": 47633, "own_observations": 0}, "splA_02": {"shared_observations": 1609, "own_seq": 0, "shared_seq": 27088, "own_observations": 0}, "splA_03": {"shared_observations": 1609, "own_seq": 0, "shared_seq": 17297, "own_observations": 0}} ;
76c750c5f0d1 planemo upload for repository https://github.com/oinizan/FROGS-wrappers commit 0b900a51e220ce6f17c1e76292c06a5f4d934055-dirty
frogs
parents:
diff changeset
713 var newick = "((splA_02,(splA_01,splA_03):0.098):0.114);" ;
76c750c5f0d1 planemo upload for repository https://github.com/oinizan/FROGS-wrappers commit 0b900a51e220ce6f17c1e76292c06a5f4d934055-dirty
frogs
parents:
diff changeset
714
76c750c5f0d1 planemo upload for repository https://github.com/oinizan/FROGS-wrappers commit 0b900a51e220ce6f17c1e76292c06a5f4d934055-dirty
frogs
parents:
diff changeset
715
76c750c5f0d1 planemo upload for repository https://github.com/oinizan/FROGS-wrappers commit 0b900a51e220ce6f17c1e76292c06a5f4d934055-dirty
frogs
parents:
diff changeset
716 ///////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////
76c750c5f0d1 planemo upload for repository https://github.com/oinizan/FROGS-wrappers commit 0b900a51e220ce6f17c1e76292c06a5f4d934055-dirty
frogs
parents:
diff changeset
717 //
76c750c5f0d1 planemo upload for repository https://github.com/oinizan/FROGS-wrappers commit 0b900a51e220ce6f17c1e76292c06a5f4d934055-dirty
frogs
parents:
diff changeset
718 // Main
76c750c5f0d1 planemo upload for repository https://github.com/oinizan/FROGS-wrappers commit 0b900a51e220ce6f17c1e76292c06a5f4d934055-dirty
frogs
parents:
diff changeset
719 //
76c750c5f0d1 planemo upload for repository https://github.com/oinizan/FROGS-wrappers commit 0b900a51e220ce6f17c1e76292c06a5f4d934055-dirty
frogs
parents:
diff changeset
720 ///////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////
76c750c5f0d1 planemo upload for repository https://github.com/oinizan/FROGS-wrappers commit 0b900a51e220ce6f17c1e76292c06a5f4d934055-dirty
frogs
parents:
diff changeset
721 $(function() {
76c750c5f0d1 planemo upload for repository https://github.com/oinizan/FROGS-wrappers commit 0b900a51e220ce6f17c1e76292c06a5f4d934055-dirty
frogs
parents:
diff changeset
722 // Remove alert
76c750c5f0d1 planemo upload for repository https://github.com/oinizan/FROGS-wrappers commit 0b900a51e220ce6f17c1e76292c06a5f4d934055-dirty
frogs
parents:
diff changeset
723 $('#js-alert').remove();
76c750c5f0d1 planemo upload for repository https://github.com/oinizan/FROGS-wrappers commit 0b900a51e220ce6f17c1e76292c06a5f4d934055-dirty
frogs
parents:
diff changeset
724 $('#content').removeClass("hidden");
76c750c5f0d1 planemo upload for repository https://github.com/oinizan/FROGS-wrappers commit 0b900a51e220ce6f17c1e76292c06a5f4d934055-dirty
frogs
parents:
diff changeset
725
76c750c5f0d1 planemo upload for repository https://github.com/oinizan/FROGS-wrappers commit 0b900a51e220ce6f17c1e76292c06a5f4d934055-dirty
frogs
parents:
diff changeset
726 // Load active tab
76c750c5f0d1 planemo upload for repository https://github.com/oinizan/FROGS-wrappers commit 0b900a51e220ce6f17c1e76292c06a5f4d934055-dirty
frogs
parents:
diff changeset
727 cluster_distrib_load( "cluster-distrib" );
76c750c5f0d1 planemo upload for repository https://github.com/oinizan/FROGS-wrappers commit 0b900a51e220ce6f17c1e76292c06a5f4d934055-dirty
frogs
parents:
diff changeset
728
76c750c5f0d1 planemo upload for repository https://github.com/oinizan/FROGS-wrappers commit 0b900a51e220ce6f17c1e76292c06a5f4d934055-dirty
frogs
parents:
diff changeset
729 // Add tab listener
76c750c5f0d1 planemo upload for repository https://github.com/oinizan/FROGS-wrappers commit 0b900a51e220ce6f17c1e76292c06a5f4d934055-dirty
frogs
parents:
diff changeset
730 $('.nav-tabs a').click(function (e) {
76c750c5f0d1 planemo upload for repository https://github.com/oinizan/FROGS-wrappers commit 0b900a51e220ce6f17c1e76292c06a5f4d934055-dirty
frogs
parents:
diff changeset
731 e.preventDefault();
76c750c5f0d1 planemo upload for repository https://github.com/oinizan/FROGS-wrappers commit 0b900a51e220ce6f17c1e76292c06a5f4d934055-dirty
frogs
parents:
diff changeset
732 $(this).tab('show');
76c750c5f0d1 planemo upload for repository https://github.com/oinizan/FROGS-wrappers commit 0b900a51e220ce6f17c1e76292c06a5f4d934055-dirty
frogs
parents:
diff changeset
733 if( $(this).attr('href') == "#sequence-distrib" && $('#sequence-distrib').hasClass('disabled') ){
76c750c5f0d1 planemo upload for repository https://github.com/oinizan/FROGS-wrappers commit 0b900a51e220ce6f17c1e76292c06a5f4d934055-dirty
frogs
parents:
diff changeset
734 $('#sequence-distrib').removeClass("disabled");
76c750c5f0d1 planemo upload for repository https://github.com/oinizan/FROGS-wrappers commit 0b900a51e220ce6f17c1e76292c06a5f4d934055-dirty
frogs
parents:
diff changeset
735 sequence_distrib_load( "sequence-distrib" );
76c750c5f0d1 planemo upload for repository https://github.com/oinizan/FROGS-wrappers commit 0b900a51e220ce6f17c1e76292c06a5f4d934055-dirty
frogs
parents:
diff changeset
736 } else if( $(this).attr('href') == "#samples-distrib" && $('#samples-distrib').hasClass('disabled') ){
76c750c5f0d1 planemo upload for repository https://github.com/oinizan/FROGS-wrappers commit 0b900a51e220ce6f17c1e76292c06a5f4d934055-dirty
frogs
parents:
diff changeset
737 $('#samples-distrib').removeClass("disabled");
76c750c5f0d1 planemo upload for repository https://github.com/oinizan/FROGS-wrappers commit 0b900a51e220ce6f17c1e76292c06a5f4d934055-dirty
frogs
parents:
diff changeset
738 sample_table_load( "samples-distrib-table" );
76c750c5f0d1 planemo upload for repository https://github.com/oinizan/FROGS-wrappers commit 0b900a51e220ce6f17c1e76292c06a5f4d934055-dirty
frogs
parents:
diff changeset
739 hierarchical_clustering_load( "samples-distrib-hc" );
76c750c5f0d1 planemo upload for repository https://github.com/oinizan/FROGS-wrappers commit 0b900a51e220ce6f17c1e76292c06a5f4d934055-dirty
frogs
parents:
diff changeset
740 }
76c750c5f0d1 planemo upload for repository https://github.com/oinizan/FROGS-wrappers commit 0b900a51e220ce6f17c1e76292c06a5f4d934055-dirty
frogs
parents:
diff changeset
741 })
76c750c5f0d1 planemo upload for repository https://github.com/oinizan/FROGS-wrappers commit 0b900a51e220ce6f17c1e76292c06a5f4d934055-dirty
frogs
parents:
diff changeset
742 });
76c750c5f0d1 planemo upload for repository https://github.com/oinizan/FROGS-wrappers commit 0b900a51e220ce6f17c1e76292c06a5f4d934055-dirty
frogs
parents:
diff changeset
743 </script>
76c750c5f0d1 planemo upload for repository https://github.com/oinizan/FROGS-wrappers commit 0b900a51e220ce6f17c1e76292c06a5f4d934055-dirty
frogs
parents:
diff changeset
744 </head>
76c750c5f0d1 planemo upload for repository https://github.com/oinizan/FROGS-wrappers commit 0b900a51e220ce6f17c1e76292c06a5f4d934055-dirty
frogs
parents:
diff changeset
745 <body>
76c750c5f0d1 planemo upload for repository https://github.com/oinizan/FROGS-wrappers commit 0b900a51e220ce6f17c1e76292c06a5f4d934055-dirty
frogs
parents:
diff changeset
746 <p id="js-alert" class="alert alert-warning">
76c750c5f0d1 planemo upload for repository https://github.com/oinizan/FROGS-wrappers commit 0b900a51e220ce6f17c1e76292c06a5f4d934055-dirty
frogs
parents:
diff changeset
747 javascript is needed to display data.<br />
76c750c5f0d1 planemo upload for repository https://github.com/oinizan/FROGS-wrappers commit 0b900a51e220ce6f17c1e76292c06a5f4d934055-dirty
frogs
parents:
diff changeset
748 If you try to view this data on galaxy please contact your administrator to authorise javascript or download the file to view.
76c750c5f0d1 planemo upload for repository https://github.com/oinizan/FROGS-wrappers commit 0b900a51e220ce6f17c1e76292c06a5f4d934055-dirty
frogs
parents:
diff changeset
749 </p>
76c750c5f0d1 planemo upload for repository https://github.com/oinizan/FROGS-wrappers commit 0b900a51e220ce6f17c1e76292c06a5f4d934055-dirty
frogs
parents:
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750
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751 <div id="content" class="hidden">
76c750c5f0d1 planemo upload for repository https://github.com/oinizan/FROGS-wrappers commit 0b900a51e220ce6f17c1e76292c06a5f4d934055-dirty
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752 <ul class="nav nav-tabs">
76c750c5f0d1 planemo upload for repository https://github.com/oinizan/FROGS-wrappers commit 0b900a51e220ce6f17c1e76292c06a5f4d934055-dirty
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753 <li role="presentation" class="active"><a href="#cluster-distrib">Clusters distribution</a></li>
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754 <li role="presentation"><a href="#sequence-distrib">Sequences distribution</a></li>
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755 <li role="presentation"><a href="#samples-distrib">Samples distribution</a></li>
76c750c5f0d1 planemo upload for repository https://github.com/oinizan/FROGS-wrappers commit 0b900a51e220ce6f17c1e76292c06a5f4d934055-dirty
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756 </ul>
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757 <div class="tab-content">
76c750c5f0d1 planemo upload for repository https://github.com/oinizan/FROGS-wrappers commit 0b900a51e220ce6f17c1e76292c06a5f4d934055-dirty
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758 <div id="cluster-distrib" role="tabpanel" class="tab-pane active">
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759 <div class="row">
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760 <div class="col-md-2"></div>
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761 <div id="nb-clusters" class="col-sm-6 col-md-4"></div>
76c750c5f0d1 planemo upload for repository https://github.com/oinizan/FROGS-wrappers commit 0b900a51e220ce6f17c1e76292c06a5f4d934055-dirty
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762 <div id="nb-sequences" class="col-sm-6 col-md-4"></div>
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763 <div class="col-md-2"></div>
76c750c5f0d1 planemo upload for repository https://github.com/oinizan/FROGS-wrappers commit 0b900a51e220ce6f17c1e76292c06a5f4d934055-dirty
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764 </div>
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765 </div>
76c750c5f0d1 planemo upload for repository https://github.com/oinizan/FROGS-wrappers commit 0b900a51e220ce6f17c1e76292c06a5f4d934055-dirty
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766 <div id="sequence-distrib" role="tabpanel" class="tab-pane disabled"></div>
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767 <div id="samples-distrib" role="tabpanel" class="tab-pane disabled">
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768 <div>
76c750c5f0d1 planemo upload for repository https://github.com/oinizan/FROGS-wrappers commit 0b900a51e220ce6f17c1e76292c06a5f4d934055-dirty
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769 <h1 class="page-header">Sequences count</h1>
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770 <div id="samples-distrib-table"></div>
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771 </div>
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772 <div>
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773 <h1 class="page-header">Hierarchical clustering</h1>
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774 <div id="samples-distrib-hc"></div>
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775 </div>
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776 </div>
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777 </div>
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778 </div>
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779 </body>
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780 </html>