Mercurial > repos > jankanis > blast2html

annotate blast2html.html.jinja @ 36:0f015cb32b93

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add argparse dependency for python <2.7
author Jan Kanis <jan.code@jankanis.nl>
date Thu, 15 May 2014 18:22:49 +0200
parents 3bb5da68305e
children 4217bb9cf1d3
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="blast2html; see https://github.com/thehyve/blast2html/">
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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 /* Galaxy with html sanitization enabled strips the header of this html page. If so, show the user a warning.*/
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24 #strip_html_warning {
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25 display: none;
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26 }
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27
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28 #content {
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29 margin: 0 2em;
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30 padding: 0.5em;
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31 border: 1px solid #888888;
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32 background-color: #d3dff5;
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33 }
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35 h1, h2, h3, h4, h5, h6 {
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36 color: #2A6979;
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37 font-family: arial,verdana,sans-serif;
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38 letter-spacing: -1px;
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39 margin: 1.2em 0 0.3em;
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40 }
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42 h1 {
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43 border-bottom: 1px solid #CCCCCC;
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44 font-size: 150%;
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45 padding-bottom: 0.1em;
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46 }
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48 h2 {
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49 font-size: 120%;
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50 font-weight: bold;
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51 }
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53 h4.darkHeader {
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54 color: #4D4D4D;
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55 letter-spacing: 0;
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56 font-weight: bold;
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57 }
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59 #nodata {
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60 font-weight: bold;
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61 }
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62
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63 .index {
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64 margin-bottom: 3em;
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65 }
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66 .index div.indexentry {
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67 margin: 1.2em 1.6em;
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68 font-weight: bold;
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69 font-size: 100%;
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70 }
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72 .headerdata {
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73 font-size: 90%;
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74 }
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75 .headerdata .param {
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76 font-weight: bold;
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77 text-align: right;
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78 padding: 0 1em;
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79 }
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80
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81 .grey {
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82 background-color: #eeeeee;
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83 border: 1px solid #cccccc;
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84 padding: 1em;
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85 }
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87 .white {
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88 background-color: white;
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89 border: 1px solid #cccccc;
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90 padding: 1.5em 2%;
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91 }
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92
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93 .graphicrow {
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94 clear: left;
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95 width: 100%;
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96 }
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97
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98 .graphicitem {
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99 float: left;
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100 }
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104 .graphics .grey {
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105 text-align: center;
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106 }
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107
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108 .graphic {
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109 background-color: white;
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110 border: 2px solid black;
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111 padding: 1.5em;
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112 margin: auto;
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113 }
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114
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115 .centered, .defline, div.legend, div.tablewrapper {
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116 margin-left: auto;
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117 margin-right: auto;
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118 }
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119
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120 .defline {
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121 background-color: white;
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122 border: 1px solid black;
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123 margin: .5em auto;
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124 padding-left: .2em;
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125 padding-right: .2em;
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126 max-width: 50em;
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127 text-align: left;
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128 height: 2.8em;
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129 overflow-y: hidden;
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130 }
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131
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132 div.legend {
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133 max-width: 40em;
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134 }
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135 div.legend div {
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136 width: 100%;
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137 color: white;
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138 font-weight: bold;
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139 border-spacing: 0;
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140 }
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141 div.legend div .graphicitem {
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142 width: 20%;
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143 padding: 0;
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144 margin: 0;
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145 border: none;
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146 }
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147
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148 div.tablewrapper {
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149 width: 50%;
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150 min-width: 60em;
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151 }
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152
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153 /* For small widths we give the graphic 100% */
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154 @media (max-width: 72.5em) {
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155 div.tablewrapper {
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156 width: 100%;
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157 min-width: 0px;
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158 }
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159 }
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160
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161 .scale {
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162 width: 100%;
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163 margin: .5em 0;
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164 font-weight: bold;
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165 }
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166 .scale div {
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167 color: red;
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168 text-align: left;
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169 }
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170 .scale .graphicrow {
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171 margin: .5em 0 .5em 0;
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172 color: white;
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173 }
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174 .scale .graphicitem {
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175 position: relative;
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176 }
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177 .scale .graphicitem div {
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178 margin: 0 1px;
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179 padding: 0 2px;
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180 text-align: right;
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181 background-color: red;
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182 color: white;
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183 }
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184 .scale .graphicitem:first-child div {
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185 margin-left: 0px;
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186 }
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187 .scale .graphicitem:last-child div {
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188 margin-right: 0px;
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189 }
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190 .scale .graphicitem .lastlabel {
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191 position: absolute;
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192 top: 0px;
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193 left: 100%;
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194 background-color: transparent;
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195 color: red;
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196 }
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197
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198 a.matchresult {
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199 display: block;
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200 margin: 0;
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201 padding: 0;
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202 }
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203 div.matchrow {
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204 margin-top: 4px;
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205 }
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206 div.matchrow, div.matchitem {
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207 height: 4px;
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208 }
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209
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210
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211 table.descriptiontable {
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212 font-size: 85%;
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213 border: 1px solid #97b0c8;
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214 border-spacing: 0;
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215 color: #222222;
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216 line-height: 1.3em;
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217 background-color: white;
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218 }
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219 table.descriptiontable col:first-child {
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220 width: 100%;
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221 }
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222 table.descriptiontable tr:hover {
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223 background-color: #D5DEE3;
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224 }
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225 table.descriptiontable th {
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226 color: #14376C;
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227 font-weight: normal;
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228 background-color: #F0F0F0;
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229 background: linear-gradient(#FFFFFF, #F0F0F0);
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230 border-bottom: 1px solid #D4DFE9;
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231 border-right: 1px solid #CFCFCF;
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232 border-left: 0px solid black;
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233 border-top: 0px solid black;
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234 }
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235 table.descriptiontable td {
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236 overflow: hidden;
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237 text-align: center;
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238 padding: .4em .8em;
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239 }
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240 table.descriptiontable td div {
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241 width: 1em;
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242 overflow: visible;
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243 white-space: nowrap;
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244 text-align: left;
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245 }
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246
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247
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248
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249 .alignments .white {
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250 padding: 1.5em 1em;
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251 }
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252
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253 .alignment {
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254 border-top: 1px solid black;
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255 padding-left: 1em;
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256 padding-right: 1em;
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257 }
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258
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259 div.linkheader {
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260 padding-top: .2em;
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261 font-size: 85%;
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262 color: #14376C;
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263 }
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264 div.linkheader a.linkheader {
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265 margin-right: 1em;
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266 }
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267 div.linkheader .right a {
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268 text-decoration: none;
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269 }
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270
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271 .title .hittitle {
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272 color: #222222;
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273 margin-bottom: .3em;
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274 }
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275 .title .titleinfo {
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276 font-size: 80%;
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277 margin-top: 0;
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278 margin-bottom: .3em;
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279 }
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280 .title .titleinfo .b {
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281 color: #606060;
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282 font-weight: bold;
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283 font-size: 90%;
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284 }
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285
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286 .moretitles {
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287 margin: 1.2em;
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288 }
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289 .moretitles .titleinfo {
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290 margin: 0;
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291 padding: 0;
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292 }
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293 .moretitles .hittitle {
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294 margin: .4em 0 .2em 0;
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295 padding: 0;
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296 }
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297
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298 a.showmoretitles {
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299 font-size: 75%;
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300 color: #336699;
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301 font-weight: bold;
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302 margin-top: 0;
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303 }
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diff changeset
304 a.showmoretitles:hover {
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diff changeset
305 }
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diff changeset
306
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diff changeset
307 .hotspot {
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diff changeset
308 color: #606060;
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309 font-family: verdana, arial, sans-serif;
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310 margin-bottom: 2.5em;
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diff changeset
311 }
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diff changeset
312
12
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diff changeset
313 .hotspot p.range {
11
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314 font-size: 70%;
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diff changeset
315 margin-top: 0;
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316 margin-top: 1em;
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317 margin-bottom: .2em;
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318 }
12
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319 .hotspot p.range span.range {
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320 font-weight: bold;
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321 }
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322 .hotspot p.range a.range {
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323 margin-left: .5em;
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324 }
11
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325
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326 table.hotspotstable {
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327 border-top: 1px solid;
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328 border-bottom: 1px solid;
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329 text-align: left;
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330 border-collapse: collapse;
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331 }
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332 table.hotspotstable th, table.hotspotstable td {
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333 padding: .1em 1em;
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334 }
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335 table.hotspotstable th {
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336 font-size: 70%;
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337 }
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338 table.hotspotstable td {
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339 min-width: 7em;
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340 color: #222222;
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341 font-size: 80%;
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342 }
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343
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344 pre.alignmentgraphic {
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345 color: #222222;
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346 }
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347
23
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348 footer {
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349 text-align: center;
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350 color: #cccccc;
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351 font-size: 70%;
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352 margin-top: 1em;
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353 }
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354 footer :link {
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355 color: #5588cc;
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356 }
11
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357
5
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358 </style>
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359
10
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360 <script type="text/javascript">
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361 function toggle_visibility(id) {
16
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362 var e = document.getElementById(id);
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363 if(e.style.display != 'block')
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364 e.style.display = 'block';
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365 else
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366 e.style.display = 'none';
10
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367 }
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368 </script>
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369
5
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370 </head>
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371
11
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diff changeset
372
5
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373 <body>
27
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diff changeset
374
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375 <div id="strip_html_warning">
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diff changeset
376 <!-- This div should be hidden by the header css block. Galaxy
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diff changeset
377 strips all css, breaking this page but making this warning
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diff changeset
378 visible. This warning contains some ugly old skool tabular html
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diff changeset
379 layout that is not stripped. -->
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diff changeset
380 <table bgcolor="#FFE5C9"><tr><td><font color="red"><b>
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diff changeset
381 <font size=5><center>This html page seems to have been stripped by Galaxy.</center></font>
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parents: 26
diff changeset
382 Disable Galaxy's html sanitization feature to view the full page (see <font face=monospace>sanitize_all_html</font> in your galaxy's universe_wsgi.ini), or download this page instead of viewing it in Galaxy.
4e6ac737ba17 improve the galaxy html stripping warning; make sure the tool can find the template from within galaxy
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parents: 26
diff changeset
383 </b></font></td></tr></table>
26
eee23a36c582 add a warning if galaxy strips the html header/stylesheet
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parents: 24
diff changeset
384 </div>
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parents: 24
diff changeset
385
5
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386 <div id=content>
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parents:
diff changeset
387
19
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diff changeset
388 {% if not blast.BlastOutput_iterations.findall('Iteration') %}
17
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diff changeset
389 <section class=nodata>
19
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390 <h1>No data</h1>
7
9e7927673089 intermediate commit before converting some tables to divs
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parents: 6
diff changeset
391 <div class=grey>
19
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diff changeset
392 No matches
7
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parents: 6
diff changeset
393 </div>
17
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parents: 16
diff changeset
394 </section>
5
1df2bfce5c24 first features are working, partial match table
Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
395
19
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diff changeset
396 {% else %}
20
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parents: 19
diff changeset
397
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parents: 19
diff changeset
398 {% if blast.BlastOutput_iterations.findall('Iteration') | length > 1 %}
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parents: 19
diff changeset
399 <section class=index>
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parents: 19
diff changeset
400 <h1>Queries</h1>
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parents: 19
diff changeset
401
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Jan Kanis <jan.code@jankanis.nl>
parents: 19
diff changeset
402 {% for result in blast.BlastOutput_iterations.Iteration %}
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parents: 19
diff changeset
403 <div class=indexentry><a href="#match{{result['Iteration_iter-num']}}">
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Jan Kanis <jan.code@jankanis.nl>
parents: 19
diff changeset
404 {% set hits = result|hits %}
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Jan Kanis <jan.code@jankanis.nl>
parents: 19
diff changeset
405 {{result['Iteration_query-ID']}}: {{result['Iteration_query-def']}}
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Jan Kanis <jan.code@jankanis.nl>
parents: 19
diff changeset
406 ({{result|len}} letters, {{hits|length}} hits)
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Jan Kanis <jan.code@jankanis.nl>
parents: 19
diff changeset
407 </a></div>
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Jan Kanis <jan.code@jankanis.nl>
parents: 19
diff changeset
408 {% endfor %}
21
9596fea636bb style changes
Jan Kanis <jan.code@jankanis.nl>
parents: 20
diff changeset
409
20
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Jan Kanis <jan.code@jankanis.nl>
parents: 19
diff changeset
410 </section>
53cd304c5f26 Add index for multiple results; fix layout of query ruler for edge case
Jan Kanis <jan.code@jankanis.nl>
parents: 19
diff changeset
411 {% endif %}
53cd304c5f26 Add index for multiple results; fix layout of query ruler for edge case
Jan Kanis <jan.code@jankanis.nl>
parents: 19
diff changeset
412
19
67ddcb807b7d make it work with multiple queries
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parents: 17
diff changeset
413 {% for result in blast.BlastOutput_iterations.Iteration %}
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parents: 17
diff changeset
414
20
53cd304c5f26 Add index for multiple results; fix layout of query ruler for edge case
Jan Kanis <jan.code@jankanis.nl>
parents: 19
diff changeset
415 <section class=match id=match{{result['Iteration_iter-num']}}>
10
2fbdf2eb27b4 All data is displayed now, still some formatting to do
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parents: 9
diff changeset
416
19
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Jan Kanis <jan.code@jankanis.nl>
parents: 17
diff changeset
417 <h1>Nucleotide Sequence ({{result|len}} letters)</h1>
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parents: 17
diff changeset
418
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Jan Kanis <jan.code@jankanis.nl>
parents: 17
diff changeset
419 <section class=header>
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Jan Kanis <jan.code@jankanis.nl>
parents: 17
diff changeset
420
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Jan Kanis <jan.code@jankanis.nl>
parents: 17
diff changeset
421 <table class=headerdata>
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Jan Kanis <jan.code@jankanis.nl>
parents: 17
diff changeset
422 {% for param, value in params %}
23
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parents: 22
diff changeset
423 <tr><td class=param>{{param}}:</td><td>{{value}}</td></tr>
19
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parents: 17
diff changeset
424 {% endfor %}
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parents: 17
diff changeset
425 </table>
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Jan Kanis <jan.code@jankanis.nl>
parents: 17
diff changeset
426
67ddcb807b7d make it work with multiple queries
Jan Kanis <jan.code@jankanis.nl>
parents: 17
diff changeset
427 </section>
67ddcb807b7d make it work with multiple queries
Jan Kanis <jan.code@jankanis.nl>
parents: 17
diff changeset
428
67ddcb807b7d make it work with multiple queries
Jan Kanis <jan.code@jankanis.nl>
parents: 17
diff changeset
429 {% set hits = result|hits %}
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parents: 17
diff changeset
430 {% if not hits %}
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Jan Kanis <jan.code@jankanis.nl>
parents: 17
diff changeset
431 <section>
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Jan Kanis <jan.code@jankanis.nl>
parents: 17
diff changeset
432 <h2>No Hits</h2>
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parents: 17
diff changeset
433 <div class=grey>
24
c8347745bbad use Iteration_message tag; also work with unexpected Hit_id values
Jan Kanis <jan.code@jankanis.nl>
parents: 23
diff changeset
434 <table class=headerdata>
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Jan Kanis <jan.code@jankanis.nl>
parents: 23
diff changeset
435 <tr><td class=param>Message:</td><td>{{result.Iteration_message}}</td></tr>
c8347745bbad use Iteration_message tag; also work with unexpected Hit_id values
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parents: 23
diff changeset
436 </table>
19
67ddcb807b7d make it work with multiple queries
Jan Kanis <jan.code@jankanis.nl>
parents: 17
diff changeset
437 </div>
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Jan Kanis <jan.code@jankanis.nl>
parents: 17
diff changeset
438 </section>
67ddcb807b7d make it work with multiple queries
Jan Kanis <jan.code@jankanis.nl>
parents: 17
diff changeset
439 {% else %}
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Jan Kanis <jan.code@jankanis.nl>
parents: 17
diff changeset
440
67ddcb807b7d make it work with multiple queries
Jan Kanis <jan.code@jankanis.nl>
parents: 17
diff changeset
441 <section class=graphics>
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Jan Kanis <jan.code@jankanis.nl>
parents: 17
diff changeset
442 <h2>Graphic Summary</h2>
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Jan Kanis <jan.code@jankanis.nl>
parents: 17
diff changeset
443
67ddcb807b7d make it work with multiple queries
Jan Kanis <jan.code@jankanis.nl>
parents: 17
diff changeset
444 <div class=grey>
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Jan Kanis <jan.code@jankanis.nl>
parents: 17
diff changeset
445 <h3 class=centered>Distribution of {{result|length}} Blast Hits on the Query Sequence</h3>
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parents: 17
diff changeset
446
67ddcb807b7d make it work with multiple queries
Jan Kanis <jan.code@jankanis.nl>
parents: 17
diff changeset
447 <div class=defline id=defline{{result['Iteration_iter-num']}}>
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parents: 17
diff changeset
448 Mouse-over to show defline and scores, click to show alignments
67ddcb807b7d make it work with multiple queries
Jan Kanis <jan.code@jankanis.nl>
parents: 17
diff changeset
449 </div>
5
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450
19
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451 <div class=graphic>
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452 <h4 class=darkHeader>Color key for alignment scores</h4>
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453 <div class=legend><div class=graphicrow>
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454 <div class=graphicitem style="background-color: {{colors[0]}}">&lt;40</div>
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455 <div class=graphicitem style="background-color: {{colors[1]}}">40–50</div>
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456 <div class=graphicitem style="background-color: {{colors[2]}}">50–80</div>
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457 <div class=graphicitem style="background-color: {{colors[3]}}">80–200</div>
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458 <div class=graphicitem style="background-color: {{colors[4]}}">200≤</div>
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diff changeset
459 </div></div>
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diff changeset
460 <div style="clear: left"></div>
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461
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diff changeset
462 <div class=tablewrapper>
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463
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464 <div class=scale>
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465 <div>query:</div>
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466 <div class=graphicrow>
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467 <div>
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468 {% for s in result|queryscale %}
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469 <div class=graphicitem style="width: {{s.width}}%">
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470 {% if s.width > 3.0 %}
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471 <div>{{s.label}}</div>
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472 {% else %}
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473 <div>&nbsp;</div>
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474 <div class=lastlabel>{{s.label}}</div>
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475 {% endif %}
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476 </div>
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477 {% endfor %}
19
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478 </div>
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479 </div>
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480 <div style="clear: left"></div>
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481 </div>
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482
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483 {% for line in result|match_colors %}
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484 <a class=matchresult
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485 href="{{line.link}}"
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486 onmouseover='document.getElementById("defline{{result['Iteration_iter-num']}}").innerHTML="{{line.defline|js_string_escape}}"'
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487 onmouseout='document.getElementById("defline{{result['Iteration_iter-num']}}").innerHTML="Mouse-over to show defline and scores, click to show alignments"'
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488 title="{{line.defline}}">
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489 <div class="matchrow graphicrow">
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490 {% for hit in line.colors %}
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491 <div class="matchitem graphicitem"
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492 style="background-color: {{hit[1]}}; width: {{hit[0]}}%"></div>
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493 {% endfor %}
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494 </div>
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495 </a>
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496
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497 {% endfor %}
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498 </div>
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499 </div>
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500 </div>
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501 </section>
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502
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503
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504
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505 <section class=descriptions>
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506 <h2>Descriptions</h2>
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507
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508 <div class=grey><div class=white>
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509 <h4 class=darkHeader>Sequences producing significant alignments:</h4>
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diff changeset
510
19
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511 <table class=descriptiontable>
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512 <col/><col/><col/><col/><col/><col/><col/>
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513 <tr>
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514 <th>Description</th>
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515 <th>Max score</th>
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516 <th>Total score</th>
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517 <th>Query cover</th>
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518 <th>E value</th>
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519 <th>Ident</th>
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520 <th>Accession</th>
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521 </tr>
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diff changeset
522 {% for hit in result|hit_info %}
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523 <tr>
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524 <td><div><a href="#hit{{hit.link_id}}"
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525 title="{{hit.title}}"
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526 id="description{{hit.link_id}}">
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527 {{hit.title}}
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528 </a></div></td>
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529 <td>{{hit.maxscore}}</td>
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530 <td>{{hit.totalscore}}</td>
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531 <td>{{hit.cover}}</td>
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diff changeset
532 <td>{{hit.e_value}}</td>
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533 <td>{{hit.ident}}</td>
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534 <td><a href="{{genelink(hit.hit|hitid)}}">{{hit.accession}}</a></td>
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535 </tr>
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536 {% endfor %}
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537 </table>
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538
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diff changeset
539 </div></div>
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diff changeset
540 </section>
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diff changeset
541
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parents: 17
diff changeset
542
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diff changeset
543
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diff changeset
544 <section class=alignments>
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diff changeset
545 <h2>Alignments</h2>
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diff changeset
546
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diff changeset
547 <div class=grey><div class=white>
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diff changeset
548 {% for hit in hits %}
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diff changeset
549 <div class=alignment id=hit{{hit.Hit_num}}>
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diff changeset
550
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diff changeset
551 <div class=linkheader>
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diff changeset
552 <div class=right><a href="#description{{hit.Hit_num}}">Descriptions</a></div>
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diff changeset
553 <a class=linkheader href="{{genelink(hit|hitid)}}">GenBank</a>
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diff changeset
554 <a class=linkheader href="{{genelink(hit|hitid, 'graph')}}">Graphics</a>
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diff changeset
555 </div>
5
1df2bfce5c24 first features are working, partial match table
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parents:
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556
19
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diff changeset
557 <div class=title>
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diff changeset
558 <p class=hittitle>{{hit|firsttitle}}</p>
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diff changeset
559 <p class=titleinfo>
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diff changeset
560 <span class=b>Sequence ID:</span> <a href="{{genelink(hit|hitid)}}">{{hit|seqid}}</a>
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561 <span class=b>Length:</span> {{hit.Hit_len}}
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diff changeset
562 <span class=b>Number of Matches:</span> {{hit.Hit_hsps.Hsp|length}}
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parents: 17
diff changeset
563 </p>
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parents: 17
diff changeset
564 </div>
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parents: 17
diff changeset
565
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parents: 17
diff changeset
566 {% if hit|othertitles|length %}
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diff changeset
567 <a class=showmoretitles onclick="toggle_visibility('moretitles{{hit.Hit_num|js_string_escape}}'); return false;" href=''>
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diff changeset
568 See {{hit|othertitles|length}} more title(s)
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diff changeset
569 </a>
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parents: 17
diff changeset
570
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diff changeset
571 <div class=moretitles id=moretitles{{hit.Hit_num}} style="display: none">
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diff changeset
572 {% for title in hit|othertitles %}
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diff changeset
573 <div class=title>
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diff changeset
574 <p class=hittitle>{{title.title}}</p>
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diff changeset
575 <p class=titleinfo>
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diff changeset
576 <span class=b>Sequence ID:</span> <a href="{{genelink(title.hitid)}}">{{title.id}}</a>
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diff changeset
577 </p>
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parents: 17
diff changeset
578 </div>
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diff changeset
579 {% endfor %}
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diff changeset
580 </div>
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diff changeset
581 {% endif %}
10
2fbdf2eb27b4 All data is displayed now, still some formatting to do
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parents: 9
diff changeset
582
19
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diff changeset
583 {% for hsp in hit.Hit_hsps.Hsp %}
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diff changeset
584 <div class=hotspot>
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diff changeset
585 <p class=range>
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diff changeset
586 <span class=range>Range {{hsp.Hsp_num}}: {{hsp['Hsp_hit-from']}} to {{hsp['Hsp_hit-to']}}</span>
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diff changeset
587 <a class=range href="{{genelink(hit|hitid, 'genbank', hsp)}}">GenBank</a>
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parents: 17
diff changeset
588 <a class=range href="{{genelink(hit|hitid, 'graph', hsp)}}">Graphics</a>
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parents: 17
diff changeset
589 </p>
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parents: 17
diff changeset
590
67ddcb807b7d make it work with multiple queries
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parents: 17
diff changeset
591 <table class=hotspotstable>
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diff changeset
592 <tr>
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diff changeset
593 <th>Score</th><th>Expect</th><th>Identities</th><th>Gaps</th><th>Strand</th>
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diff changeset
594 </tr>
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parents: 17
diff changeset
595 <tr>
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596 <td>{{hsp['Hsp_bit-score']|fmt('.1f')}} bits({{hsp.Hsp_score}})</td>
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597 <td>{{hsp.Hsp_evalue|fmt('.1f')}}</td>
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598 <td>{{ hsp.Hsp_identity }}/{{ hsp|len }}({{
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599 (hsp.Hsp_identity/hsp|len) |fmt('.0%') }})</td>
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600 <td>{{ hsp.Hsp_gaps }}/{{ hsp|len
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601 }}({{ (hsp.Hsp_gaps / hsp|len) | fmt('.0%') }})</td>
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602 <td>{{ hsp['Hsp_query-frame']|asframe }}/{{ hsp['Hsp_hit-frame']|asframe }}</td>
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603 </tr>
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604 </table>
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605
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606 <pre class=alignmentgraphic>{{hsp|alignment_pre}}</pre>
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607 </div>
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608 {% endfor %}
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609
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610 </div>
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611
19
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612 {% endfor %}
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613 </div></div>
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614 </section>
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615 {% endif %}
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616 </section>
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617 {% endfor %}
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618 {% endif %}
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619
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620 </div>
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621
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622 <footer>
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623 This page was generated by <a href="https://github.com/thehyve/blast2html/">blast2html</a>.
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624 </footer>
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625 </body>
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626 </html>
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627
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628 {#
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629 Local Variables:
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630 tab-width: 2
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631 indent-tabs-mode: nil
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632 End:
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633 #}