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annotate blast_html.html.jinja @ 20:53cd304c5f26

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Add index for multiple results; fix layout of query ruler for edge case The query ruler did not layout nicely if the last segment was too short to contain the text. For very short last segments the text is now displayed after the ruler.
author Jan Kanis <jan.code@jankanis.nl>
date Wed, 14 May 2014 16:20:29 +0200
parents 67ddcb807b7d
children 9596fea636bb
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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1 <!DOCTYPE html>
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2 <html>
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3 <head>
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4 <meta charset="UTF-8">
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5 <meta name=generator content="blast_html; see ...">
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6
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7 <title>Blast output</title>
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8
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9 <style>
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10 body {
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11 color: #333333;
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12 font-family: Arial,Sans-Serif;
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13 }
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15 :link {
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16 color: #336699;
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17 }
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18
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19 .right {
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20 float: right;
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21 }
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23 #content {
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24 margin: 0 2em;
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25 padding: 0.5em;
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26 border: 1px solid #888888;
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27 background-color: #d3dff5;
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28 }
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30 h1, h2, h3, h4, h5, h6 {
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31 color: #2A6979;
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32 font-family: arial,verdana,sans-serif;
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33 letter-spacing: -1px;
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34 margin: 1.2em 0 0.3em;
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35 }
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37 h1 {
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38 border-bottom: 1px solid #CCCCCC;
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39 font-size: 150%;
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40 padding-bottom: 0.1em;
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41 }
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43 h2 {
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44 font-size: 120%;
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45 font-weight: bold;
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46 }
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48 h4.darkHeader {
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49 color: #4D4D4D;
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50 letter-spacing: 0;
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51 font-weight: bold;
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52 }
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54 #nodata {
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55 font-weight: bold;
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56 }
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57
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58 .index div.indexentry {
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59 margin: .6em;
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60 font-weight: bold;
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61 font-size: 100%;
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62 }
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63
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64 .headerdata {
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65 font-size: 90%;
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66 }
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67 .headerdata .param {
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68 font-weight: bold;
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69 text-align: right;
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70 padding: 0 1em;
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71 }
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73 .grey {
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74 background-color: #eeeeee;
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75 border: 1px solid #cccccc;
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76 padding: 1em;
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77 }
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79 .white {
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80 background-color: white;
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81 border: 1px solid #cccccc;
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82 padding: 1.5em 2%;
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83 }
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84
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85 .graphicrow {
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86 clear: left;
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87 width: 100%;
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88 }
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89
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90 .graphicitem {
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91 float: left;
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92 }
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96 .graphics .grey {
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97 text-align: center;
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98 }
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99
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100 .graphic {
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101 background-color: white;
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102 border: 2px solid black;
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103 padding: 1.5em;
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104 margin: auto;
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105 }
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106
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107 .centered, .defline, div.legend, div.tablewrapper {
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108 margin-left: auto;
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109 margin-right: auto;
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110 }
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111
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112 .defline {
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113 background-color: white;
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114 border: 1px solid black;
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115 margin: .5em auto;
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116 padding-left: .2em;
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117 padding-right: .2em;
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118 max-width: 50em;
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119 text-align: left;
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120 height: 2.8em;
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121 overflow-y: hidden;
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122 }
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123
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124 div.legend {
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125 max-width: 40em;
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126 }
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127 div.legend div {
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128 width: 100%;
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129 color: white;
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130 font-weight: bold;
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131 border-spacing: 0;
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132 }
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133 div.legend div .graphicitem {
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134 width: 20%;
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135 padding: 0;
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136 margin: 0;
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137 border: none;
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138 }
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139
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140 div.tablewrapper {
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141 width: 50%;
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142 min-width: 60em;
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143 }
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144
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145 /* For small widths we give the graphic 100% */
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146 @media (max-width: 72.5em) {
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147 div.tablewrapper {
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148 width: 100%;
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149 min-width: 0px;
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150 }
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151 }
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152
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153 .scale {
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154 width: 100%;
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155 margin: .5em 0;
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156 font-weight: bold;
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157 }
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158 .scale div {
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159 color: red;
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160 text-align: left;
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161 }
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162 .scale .graphicrow {
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163 margin: .5em 0 .5em 0;
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164 color: white;
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165 }
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166 .scale .graphicitem {
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167 position: relative;
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168 }
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169 .scale .graphicitem div {
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170 margin: 0 1px;
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171 padding: 0 2px;
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172 text-align: right;
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173 background-color: red;
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174 color: white;
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175 }
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176 .scale .graphicitem:first-child div {
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177 margin-left: 0px;
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178 }
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179 .scale .graphicitem:last-child div {
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180 margin-right: 0px;
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181 }
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182 .scale .graphicitem .lastlabel {
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183 position: absolute;
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184 top: 0px;
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185 left: 100%;
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186 background-color: transparent;
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187 color: red;
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188 }
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189
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190 a.matchresult {
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191 display: block;
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192 margin: 0;
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193 padding: 0;
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194 }
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195 div.matchrow {
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196 margin-top: 4px;
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197 }
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198 div.matchrow, div.matchitem {
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199 height: 4px;
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200 }
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201
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202
7
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203 table.descriptiontable {
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204 font-size: 85%;
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205 border: 1px solid #97b0c8;
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diff changeset
206 border-spacing: 0;
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207 color: #222222;
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208 line-height: 1.3em;
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diff changeset
209 background-color: white;
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210 }
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211 table.descriptiontable col:first-child {
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212 width: 100%;
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parents:
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213 }
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214 table.descriptiontable tr:hover {
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215 background-color: #D5DEE3;
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216 }
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217 table.descriptiontable th {
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218 color: #14376C;
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219 font-weight: normal;
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220 background-color: #F0F0F0;
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221 background: linear-gradient(#FFFFFF, #F0F0F0);
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222 border-bottom: 1px solid #D4DFE9;
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223 border-right: 1px solid #CFCFCF;
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224 border-left: 0px solid black;
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225 border-top: 0px solid black;
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226 }
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227 table.descriptiontable td {
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228 overflow: hidden;
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229 text-align: center;
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230 padding: .4em .8em;
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231 }
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232 table.descriptiontable td div {
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233 width: 1em;
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234 overflow: visible;
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235 white-space: nowrap;
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236 text-align: left;
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237 }
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238
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239
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240
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241 .alignments .white {
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242 padding: 1.5em 1em;
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243 }
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244
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245 .alignment {
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246 border-top: 1px solid black;
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247 padding-left: 1em;
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248 padding-right: 1em;
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249 }
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250
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251 div.linkheader {
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252 padding-top: .2em;
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253 font-size: 85%;
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254 color: #14376C;
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255 }
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256 div.linkheader a.linkheader {
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257 margin-right: 1em;
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258 }
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259 div.linkheader .right a {
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260 text-decoration: none;
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261 }
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262
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263 .title .hittitle {
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264 color: #222222;
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265 margin-bottom: .3em;
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266 }
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267 .title .titleinfo {
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268 font-size: 80%;
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269 margin-top: 0;
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270 margin-bottom: .3em;
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271 }
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272 .title .titleinfo .b {
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273 color: #606060;
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274 font-weight: bold;
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275 font-size: 90%;
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276 }
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277
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278 .moretitles {
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279 margin: 1.2em;
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280 }
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281 .moretitles .titleinfo {
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282 margin: 0;
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283 padding: 0;
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284 }
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285 .moretitles .hittitle {
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286 margin: .4em 0 .2em 0;
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diff changeset
287 padding: 0;
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288 }
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289
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diff changeset
290 a.showmoretitles {
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291 font-size: 75%;
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diff changeset
292 color: #336699;
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293 font-weight: bold;
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diff changeset
294 margin-top: 0;
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diff changeset
295 }
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diff changeset
296 a.showmoretitles:hover {
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297 }
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298
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299 .hotspot {
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300 color: #606060;
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diff changeset
301 font-family: verdana, arial, sans-serif;
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diff changeset
302 margin-bottom: 2.5em;
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303 }
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304
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305 .hotspot p.range {
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306 font-size: 70%;
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307 margin-top: 0;
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308 margin-top: 1em;
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309 margin-bottom: .2em;
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310 }
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311 .hotspot p.range span.range {
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312 font-weight: bold;
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313 }
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314 .hotspot p.range a.range {
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315 margin-left: .5em;
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316 }
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317
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318 table.hotspotstable {
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319 border-top: 1px solid;
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320 border-bottom: 1px solid;
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321 text-align: left;
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322 border-collapse: collapse;
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323 }
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324 table.hotspotstable th, table.hotspotstable td {
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325 padding: .1em 1em;
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326 }
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327 table.hotspotstable th {
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328 font-size: 70%;
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329 }
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330 table.hotspotstable td {
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331 min-width: 7em;
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332 color: #222222;
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333 font-size: 80%;
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334 }
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335
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336 pre.alignmentgraphic {
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337 color: #222222;
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338 }
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339
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340
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341 </style>
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342
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343 <script type="text/javascript">
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344 function toggle_visibility(id) {
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345 var e = document.getElementById(id);
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346 if(e.style.display != 'block')
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347 e.style.display = 'block';
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348 else
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349 e.style.display = 'none';
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350 }
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351 </script>
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352
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353 </head>
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354
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355
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356 <body>
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357 <div id=content>
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358
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359 {% if not blast.BlastOutput_iterations.findall('Iteration') %}
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360 <section class=nodata>
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361 <h1>No data</h1>
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362 <div class=grey>
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363 No matches
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364 </div>
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365 </section>
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366
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367 {% else %}
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368
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369 {% if blast.BlastOutput_iterations.findall('Iteration') | length > 1 %}
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370 <section class=index>
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371 <h1>Queries</h1>
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372
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373 {% for result in blast.BlastOutput_iterations.Iteration %}
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374 <div class=indexentry><a href="#match{{result['Iteration_iter-num']}}">
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375 {% set hits = result|hits %}
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376 {{result['Iteration_query-ID']}}: {{result['Iteration_query-def']}}
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377 ({{result|len}} letters, {{hits|length}} hits)
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378 </a></div>
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379 {% endfor %}
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380
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381 </section>
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382 {% endif %}
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383
19
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384 {% for result in blast.BlastOutput_iterations.Iteration %}
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385
20
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386 <section class=match id=match{{result['Iteration_iter-num']}}>
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387
19
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388 <h1>Nucleotide Sequence ({{result|len}} letters)</h1>
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389
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390 <section class=header>
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391
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392 <table class=headerdata>
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393 {% for param, value in params %}
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394 <tr><td class=param>{{param}}:</td><td>{{value}}</td></tr>
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395 {% endfor %}
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396 </table>
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397
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398 </section>
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399
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400 {% set hits = result|hits %}
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401 {% if not hits %}
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402 <section>
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403 <h2>No Hits</h2>
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diff changeset
404 <div class=grey>
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diff changeset
405 This query did not match anywhere
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diff changeset
406 </div>
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407 </section>
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408 {% else %}
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409
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410 <section class=graphics>
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411 <h2>Graphic Summary</h2>
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diff changeset
412
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diff changeset
413 <div class=grey>
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414 <h3 class=centered>Distribution of {{result|length}} Blast Hits on the Query Sequence</h3>
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415
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diff changeset
416 <div class=defline id=defline{{result['Iteration_iter-num']}}>
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417 Mouse-over to show defline and scores, click to show alignments
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diff changeset
418 </div>
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419
19
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420 <div class=graphic>
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421 <h4 class=darkHeader>Color key for alignment scores</h4>
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422 <div class=legend><div class=graphicrow>
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423 <div class=graphicitem style="background-color: {{colors[0]}}">&lt;40</div>
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424 <div class=graphicitem style="background-color: {{colors[1]}}">40–50</div>
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diff changeset
425 <div class=graphicitem style="background-color: {{colors[2]}}">50–80</div>
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diff changeset
426 <div class=graphicitem style="background-color: {{colors[3]}}">80–200</div>
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diff changeset
427 <div class=graphicitem style="background-color: {{colors[4]}}">200≤</div>
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diff changeset
428 </div></div>
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diff changeset
429 <div style="clear: left"></div>
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diff changeset
430
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diff changeset
431 <div class=tablewrapper>
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diff changeset
432
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diff changeset
433 <div class=scale>
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diff changeset
434 <div>query:</div>
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diff changeset
435 <div class=graphicrow>
20
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diff changeset
436 <div>
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diff changeset
437 {% for s in result|queryscale %}
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diff changeset
438 <div class=graphicitem style="width: {{s.width}}%">
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diff changeset
439 {% if s.width > 3.0 %}
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440 <div>{{s.label}}</div>
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diff changeset
441 {% else %}
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diff changeset
442 <div>&nbsp;</div>
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diff changeset
443 <div class=lastlabel>{{s.label}}</div>
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diff changeset
444 {% endif %}
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diff changeset
445 </div>
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diff changeset
446 {% endfor %}
19
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diff changeset
447 </div>
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diff changeset
448 </div>
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diff changeset
449 <div style="clear: left"></div>
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diff changeset
450 </div>
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parents: 17
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451
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452 {% for line in result|match_colors %}
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453 <a class=matchresult
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454 href="{{line.link}}"
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455 onmouseover='document.getElementById("defline{{result['Iteration_iter-num']}}").innerHTML="{{line.defline|js_string_escape}}"'
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456 onmouseout='document.getElementById("defline{{result['Iteration_iter-num']}}").innerHTML="Mouse-over to show defline and scores, click to show alignments"'
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457 title="{{line.defline}}">
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458 <div class="matchrow graphicrow">
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459 {% for hit in line.colors %}
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460 <div class="matchitem graphicitem"
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461 style="background-color: {{hit[1]}}; width: {{hit[0]}}%"></div>
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462 {% endfor %}
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463 </div>
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diff changeset
464 </a>
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465
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466 {% endfor %}
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467 </div>
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468 </div>
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469 </div>
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470 </section>
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471
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472
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473
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474 <section class=descriptions>
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475 <h2>Descriptions</h2>
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476
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477 <div class=grey><div class=white>
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478 <h4 class=darkHeader>Sequences producing significant alignments:</h4>
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479
19
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480 <table class=descriptiontable>
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481 <col/><col/><col/><col/><col/><col/><col/>
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482 <tr>
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483 <th>Description</th>
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484 <th>Max score</th>
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485 <th>Total score</th>
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486 <th>Query cover</th>
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487 <th>E value</th>
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488 <th>Ident</th>
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489 <th>Accession</th>
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490 </tr>
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491 {% for hit in result|hit_info %}
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492 <tr>
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493 <td><div><a href="#hit{{hit.link_id}}"
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494 title="{{hit.title}}"
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495 id="description{{hit.link_id}}">
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496 {{hit.title}}
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diff changeset
497 </a></div></td>
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498 <td>{{hit.maxscore}}</td>
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499 <td>{{hit.totalscore}}</td>
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500 <td>{{hit.cover}}</td>
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501 <td>{{hit.e_value}}</td>
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502 <td>{{hit.ident}}</td>
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diff changeset
503 <td><a href="{{genelink(hit.hit|hitid)}}">{{hit.accession}}</a></td>
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504 </tr>
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505 {% endfor %}
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506 </table>
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507
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508 </div></div>
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diff changeset
509 </section>
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diff changeset
510
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diff changeset
511
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diff changeset
512
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diff changeset
513 <section class=alignments>
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diff changeset
514 <h2>Alignments</h2>
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515
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diff changeset
516 <div class=grey><div class=white>
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diff changeset
517 {% for hit in hits %}
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diff changeset
518 <div class=alignment id=hit{{hit.Hit_num}}>
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519
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diff changeset
520 <div class=linkheader>
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diff changeset
521 <div class=right><a href="#description{{hit.Hit_num}}">Descriptions</a></div>
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522 <a class=linkheader href="{{genelink(hit|hitid)}}">GenBank</a>
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diff changeset
523 <a class=linkheader href="{{genelink(hit|hitid, 'graph')}}">Graphics</a>
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diff changeset
524 </div>
5
1df2bfce5c24 first features are working, partial match table
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diff changeset
525
19
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diff changeset
526 <div class=title>
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parents: 17
diff changeset
527 <p class=hittitle>{{hit|firsttitle}}</p>
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diff changeset
528 <p class=titleinfo>
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529 <span class=b>Sequence ID:</span> <a href="{{genelink(hit|hitid)}}">{{hit|seqid}}</a>
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530 <span class=b>Length:</span> {{hit.Hit_len}}
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Jan Kanis <jan.code@jankanis.nl>
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diff changeset
531 <span class=b>Number of Matches:</span> {{hit.Hit_hsps.Hsp|length}}
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diff changeset
532 </p>
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Jan Kanis <jan.code@jankanis.nl>
parents: 17
diff changeset
533 </div>
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Jan Kanis <jan.code@jankanis.nl>
parents: 17
diff changeset
534
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Jan Kanis <jan.code@jankanis.nl>
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diff changeset
535 {% if hit|othertitles|length %}
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Jan Kanis <jan.code@jankanis.nl>
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diff changeset
536 <a class=showmoretitles onclick="toggle_visibility('moretitles{{hit.Hit_num|js_string_escape}}'); return false;" href=''>
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Jan Kanis <jan.code@jankanis.nl>
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diff changeset
537 See {{hit|othertitles|length}} more title(s)
67ddcb807b7d make it work with multiple queries
Jan Kanis <jan.code@jankanis.nl>
parents: 17
diff changeset
538 </a>
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Jan Kanis <jan.code@jankanis.nl>
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diff changeset
539
67ddcb807b7d make it work with multiple queries
Jan Kanis <jan.code@jankanis.nl>
parents: 17
diff changeset
540 <div class=moretitles id=moretitles{{hit.Hit_num}} style="display: none">
67ddcb807b7d make it work with multiple queries
Jan Kanis <jan.code@jankanis.nl>
parents: 17
diff changeset
541 {% for title in hit|othertitles %}
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Jan Kanis <jan.code@jankanis.nl>
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diff changeset
542 <div class=title>
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Jan Kanis <jan.code@jankanis.nl>
parents: 17
diff changeset
543 <p class=hittitle>{{title.title}}</p>
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diff changeset
544 <p class=titleinfo>
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Jan Kanis <jan.code@jankanis.nl>
parents: 17
diff changeset
545 <span class=b>Sequence ID:</span> <a href="{{genelink(title.hitid)}}">{{title.id}}</a>
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parents: 17
diff changeset
546 </p>
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Jan Kanis <jan.code@jankanis.nl>
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diff changeset
547 </div>
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diff changeset
548 {% endfor %}
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diff changeset
549 </div>
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diff changeset
550 {% endif %}
10
2fbdf2eb27b4 All data is displayed now, still some formatting to do
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diff changeset
551
19
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diff changeset
552 {% for hsp in hit.Hit_hsps.Hsp %}
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diff changeset
553 <div class=hotspot>
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Jan Kanis <jan.code@jankanis.nl>
parents: 17
diff changeset
554 <p class=range>
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Jan Kanis <jan.code@jankanis.nl>
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diff changeset
555 <span class=range>Range {{hsp.Hsp_num}}: {{hsp['Hsp_hit-from']}} to {{hsp['Hsp_hit-to']}}</span>
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parents: 17
diff changeset
556 <a class=range href="{{genelink(hit|hitid, 'genbank', hsp)}}">GenBank</a>
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Jan Kanis <jan.code@jankanis.nl>
parents: 17
diff changeset
557 <a class=range href="{{genelink(hit|hitid, 'graph', hsp)}}">Graphics</a>
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parents: 17
diff changeset
558 </p>
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parents: 17
diff changeset
559
67ddcb807b7d make it work with multiple queries
Jan Kanis <jan.code@jankanis.nl>
parents: 17
diff changeset
560 <table class=hotspotstable>
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diff changeset
561 <tr>
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diff changeset
562 <th>Score</th><th>Expect</th><th>Identities</th><th>Gaps</th><th>Strand</th>
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diff changeset
563 </tr>
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Jan Kanis <jan.code@jankanis.nl>
parents: 17
diff changeset
564 <tr>
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Jan Kanis <jan.code@jankanis.nl>
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diff changeset
565 <td>{{hsp['Hsp_bit-score']|fmt('.1f')}} bits({{hsp.Hsp_score}})</td>
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Jan Kanis <jan.code@jankanis.nl>
parents: 17
diff changeset
566 <td>{{hsp.Hsp_evalue|fmt('.1f')}}</td>
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Jan Kanis <jan.code@jankanis.nl>
parents: 17
diff changeset
567 <td>{{ hsp.Hsp_identity }}/{{ hsp|len }}({{
67ddcb807b7d make it work with multiple queries
Jan Kanis <jan.code@jankanis.nl>
parents: 17
diff changeset
568 (hsp.Hsp_identity/hsp|len) |fmt('.0%') }})</td>
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Jan Kanis <jan.code@jankanis.nl>
parents: 17
diff changeset
569 <td>{{ hsp.Hsp_gaps }}/{{ hsp|len
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Jan Kanis <jan.code@jankanis.nl>
parents: 17
diff changeset
570 }}({{ (hsp.Hsp_gaps / hsp|len) | fmt('.0%') }})</td>
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Jan Kanis <jan.code@jankanis.nl>
parents: 17
diff changeset
571 <td>{{ hsp['Hsp_query-frame']|asframe }}/{{ hsp['Hsp_hit-frame']|asframe }}</td>
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Jan Kanis <jan.code@jankanis.nl>
parents: 17
diff changeset
572 </tr>
67ddcb807b7d make it work with multiple queries
Jan Kanis <jan.code@jankanis.nl>
parents: 17
diff changeset
573 </table>
67ddcb807b7d make it work with multiple queries
Jan Kanis <jan.code@jankanis.nl>
parents: 17
diff changeset
574
67ddcb807b7d make it work with multiple queries
Jan Kanis <jan.code@jankanis.nl>
parents: 17
diff changeset
575 <pre class=alignmentgraphic>{{hsp|alignment_pre}}</pre>
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Jan Kanis <jan.code@jankanis.nl>
parents: 17
diff changeset
576 </div>
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parents: 17
diff changeset
577 {% endfor %}
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parents: 17
diff changeset
578
16
db7e4ee3be03 fix validation, reindent
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parents: 13
diff changeset
579 </div>
10
2fbdf2eb27b4 All data is displayed now, still some formatting to do
Jan Kanis <jan.code@jankanis.nl>
parents: 9
diff changeset
580
19
67ddcb807b7d make it work with multiple queries
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diff changeset
581 {% endfor %}
67ddcb807b7d make it work with multiple queries
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parents: 17
diff changeset
582 </div></div>
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parents: 17
diff changeset
583 </section>
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Jan Kanis <jan.code@jankanis.nl>
parents: 17
diff changeset
584 {% endif %}
10
2fbdf2eb27b4 All data is displayed now, still some formatting to do
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parents: 9
diff changeset
585
19
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diff changeset
586 {% endfor %}
67ddcb807b7d make it work with multiple queries
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diff changeset
587 {% endif %}
5
1df2bfce5c24 first features are working, partial match table
Jan Kanis <jan.code@jankanis.nl>
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diff changeset
588 </div>
1df2bfce5c24 first features are working, partial match table
Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
589 </body>
1df2bfce5c24 first features are working, partial match table
Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
590 </html>
1df2bfce5c24 first features are working, partial match table
Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
591
16
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diff changeset
592 {#
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diff changeset
593 Local Variables:
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diff changeset
594 tab-width: 2
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diff changeset
595 indent-tabs-mode: nil
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diff changeset
596 End:
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Jan Kanis <jan.code@jankanis.nl>
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diff changeset
597 #}