sequenceserver 0.8.9 → 1.0.0.pre.1

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Files changed (213) hide show
  1. checksums.yaml +4 -4
  2. data/{README.txt → README.md} +2 -0
  3. data/bin/sequenceserver +255 -55
  4. data/config.ru +2 -4
  5. data/lib/sequenceserver.rb +293 -447
  6. data/lib/sequenceserver/blast.rb +464 -64
  7. data/lib/sequenceserver/database.rb +185 -19
  8. data/lib/sequenceserver/links.rb +114 -0
  9. data/lib/sequenceserver/logger.rb +27 -0
  10. data/lib/sequenceserver/sequence.rb +141 -0
  11. data/public/css/bootstrap.min.css +8 -413
  12. data/public/css/custom.css +363 -122
  13. data/public/css/font-awesome.min.css +4 -0
  14. data/public/fonts/FontAwesome.otf +0 -0
  15. data/public/fonts/fontawesome-webfont.eot +0 -0
  16. data/public/fonts/fontawesome-webfont.svg +565 -0
  17. data/public/fonts/fontawesome-webfont.ttf +0 -0
  18. data/public/fonts/fontawesome-webfont.woff +0 -0
  19. data/public/fonts/fontawesome-webfont.woff2 +0 -0
  20. data/public/js/bootstrap.min.js +11 -0
  21. data/public/js/d3.v3.min.js +5 -0
  22. data/public/js/html5shiv.min.js +4 -0
  23. data/public/js/jquery.scrollspy.js +74 -0
  24. data/public/js/jquery.t.js +353 -0
  25. data/public/js/sequence.js +2419 -0
  26. data/public/js/sequenceserver.blast.js +29 -30
  27. data/public/js/sequenceserver.js +544 -120
  28. data/public/js/underscore.min.js +6 -0
  29. data/public/js/webshims/polyfiller.js +1 -0
  30. data/public/js/webshims/shims/FlashCanvas/canvas2png.js +1 -0
  31. data/public/js/webshims/shims/FlashCanvas/flashcanvas.js +1 -0
  32. data/public/js/webshims/shims/FlashCanvas/flashcanvas.swf +0 -0
  33. data/public/js/webshims/shims/FlashCanvasPro/canvas2png.js +1 -0
  34. data/public/js/webshims/shims/FlashCanvasPro/flash10canvas.swf +0 -0
  35. data/public/js/webshims/shims/FlashCanvasPro/flash9canvas.swf +0 -0
  36. data/public/js/webshims/shims/FlashCanvasPro/flashcanvas.js +1 -0
  37. data/public/js/webshims/shims/canvas-blob.js +1 -0
  38. data/public/js/webshims/shims/color-picker.js +2 -0
  39. data/public/js/webshims/shims/combos/1.js +6 -0
  40. data/public/js/webshims/shims/combos/10.js +2 -0
  41. data/public/js/webshims/shims/combos/11.js +2 -0
  42. data/public/js/webshims/shims/combos/12.js +6 -0
  43. data/public/js/webshims/shims/combos/13.js +1 -0
  44. data/public/js/webshims/shims/combos/14.js +1 -0
  45. data/public/js/webshims/shims/combos/15.js +2 -0
  46. data/public/js/webshims/shims/combos/16.js +7 -0
  47. data/public/js/webshims/shims/combos/17.js +2 -0
  48. data/public/js/webshims/shims/combos/18.js +3 -0
  49. data/public/js/webshims/shims/combos/2.js +7 -0
  50. data/public/js/webshims/shims/combos/21.js +2 -0
  51. data/public/js/webshims/shims/combos/22.js +1 -0
  52. data/public/js/webshims/shims/combos/23.js +6 -0
  53. data/public/js/webshims/shims/combos/25.js +2 -0
  54. data/public/js/webshims/shims/combos/27.js +1 -0
  55. data/public/js/webshims/shims/combos/28.js +1 -0
  56. data/public/js/webshims/shims/combos/29.js +1 -0
  57. data/public/js/webshims/shims/combos/3.js +1 -0
  58. data/public/js/webshims/shims/combos/30.js +2 -0
  59. data/public/js/webshims/shims/combos/31.js +1 -0
  60. data/public/js/webshims/shims/combos/33.js +1 -0
  61. data/public/js/webshims/shims/combos/34.js +1 -0
  62. data/public/js/webshims/shims/combos/4.js +1 -0
  63. data/public/js/webshims/shims/combos/5.js +2 -0
  64. data/public/js/webshims/shims/combos/6.js +2 -0
  65. data/public/js/webshims/shims/combos/7.js +7 -0
  66. data/public/js/webshims/shims/combos/8.js +7 -0
  67. data/public/js/webshims/shims/combos/9.js +2 -0
  68. data/public/js/webshims/shims/combos/97.js +1 -0
  69. data/public/js/webshims/shims/combos/98.js +1 -0
  70. data/public/js/webshims/shims/combos/99.js +1 -0
  71. data/public/js/webshims/shims/details.js +1 -0
  72. data/public/js/webshims/shims/dom-extend.js +1 -0
  73. data/public/js/webshims/shims/es5.js +1 -0
  74. data/public/js/webshims/shims/es6.js +1 -0
  75. data/public/js/webshims/shims/excanvas.js +1 -0
  76. data/public/js/webshims/shims/filereader-xhr.js +1 -0
  77. data/public/js/webshims/shims/form-combat.js +1 -0
  78. data/public/js/webshims/shims/form-core.js +1 -0
  79. data/public/js/webshims/shims/form-datalist-lazy.js +1 -0
  80. data/public/js/webshims/shims/form-datalist.js +1 -0
  81. data/public/js/webshims/shims/form-fixrangechange.js +1 -0
  82. data/public/js/webshims/shims/form-inputmode.js +1 -0
  83. data/public/js/webshims/shims/form-message.js +1 -0
  84. data/public/js/webshims/shims/form-native-extend.js +1 -0
  85. data/public/js/webshims/shims/form-number-date-api.js +1 -0
  86. data/public/js/webshims/shims/form-number-date-ui.js +1 -0
  87. data/public/js/webshims/shims/form-shim-extend.js +1 -0
  88. data/public/js/webshims/shims/form-shim-extend2.js +1 -0
  89. data/public/js/webshims/shims/form-validation.js +1 -0
  90. data/public/js/webshims/shims/form-validators.js +1 -0
  91. data/public/js/webshims/shims/forms-picker.js +1 -0
  92. data/public/js/webshims/shims/geolocation.js +1 -0
  93. data/public/js/webshims/shims/i18n/formcfg-ar.js +1 -0
  94. data/public/js/webshims/shims/i18n/formcfg-ch-CN.js +1 -0
  95. data/public/js/webshims/shims/i18n/formcfg-cs.js +1 -0
  96. data/public/js/webshims/shims/i18n/formcfg-de.js +1 -0
  97. data/public/js/webshims/shims/i18n/formcfg-el.js +1 -0
  98. data/public/js/webshims/shims/i18n/formcfg-en.js +1 -0
  99. data/public/js/webshims/shims/i18n/formcfg-es.js +1 -0
  100. data/public/js/webshims/shims/i18n/formcfg-fa.js +1 -0
  101. data/public/js/webshims/shims/i18n/formcfg-fr.js +1 -0
  102. data/public/js/webshims/shims/i18n/formcfg-he.js +1 -0
  103. data/public/js/webshims/shims/i18n/formcfg-hi.js +1 -0
  104. data/public/js/webshims/shims/i18n/formcfg-hu.js +1 -0
  105. data/public/js/webshims/shims/i18n/formcfg-it.js +1 -0
  106. data/public/js/webshims/shims/i18n/formcfg-ja.js +1 -0
  107. data/public/js/webshims/shims/i18n/formcfg-lt.js +1 -0
  108. data/public/js/webshims/shims/i18n/formcfg-nl.js +1 -0
  109. data/public/js/webshims/shims/i18n/formcfg-pl.js +1 -0
  110. data/public/js/webshims/shims/i18n/formcfg-pt-BR.js +1 -0
  111. data/public/js/webshims/shims/i18n/formcfg-pt-PT.js +1 -0
  112. data/public/js/webshims/shims/i18n/formcfg-pt.js +1 -0
  113. data/public/js/webshims/shims/i18n/formcfg-ru.js +1 -0
  114. data/public/js/webshims/shims/i18n/formcfg-sv.js +1 -0
  115. data/public/js/webshims/shims/i18n/formcfg-zh-CN.js +1 -0
  116. data/public/js/webshims/shims/i18n/formcfg-zh-TW.js +1 -0
  117. data/public/js/webshims/shims/jme/alternate-media.js +1 -0
  118. data/public/js/webshims/shims/jme/base.js +1 -0
  119. data/public/js/webshims/shims/jme/controls.css +1 -0
  120. data/public/js/webshims/shims/jme/jme.eot +0 -0
  121. data/public/js/webshims/shims/jme/jme.svg +36 -0
  122. data/public/js/webshims/shims/jme/jme.ttf +0 -0
  123. data/public/js/webshims/shims/jme/jme.woff +0 -0
  124. data/public/js/webshims/shims/jme/mediacontrols-lazy.js +1 -0
  125. data/public/js/webshims/shims/jme/mediacontrols.js +1 -0
  126. data/public/js/webshims/shims/jme/playlist.js +1 -0
  127. data/public/js/webshims/shims/jpicker/images/AlphaBar.png +0 -0
  128. data/public/js/webshims/shims/jpicker/images/Bars.png +0 -0
  129. data/public/js/webshims/shims/jpicker/images/Maps.png +0 -0
  130. data/public/js/webshims/shims/jpicker/images/NoColor.png +0 -0
  131. data/public/js/webshims/shims/jpicker/images/bar-opacity.png +0 -0
  132. data/public/js/webshims/shims/jpicker/images/map-opacity.png +0 -0
  133. data/public/js/webshims/shims/jpicker/images/mappoint.gif +0 -0
  134. data/public/js/webshims/shims/jpicker/images/picker.gif +0 -0
  135. data/public/js/webshims/shims/jpicker/images/preview-opacity.png +0 -0
  136. data/public/js/webshims/shims/jpicker/images/rangearrows.gif +0 -0
  137. data/public/js/webshims/shims/jpicker/jpicker.css +1 -0
  138. data/public/js/webshims/shims/matchMedia.js +3 -0
  139. data/public/js/webshims/shims/mediacapture-picker.js +1 -0
  140. data/public/js/webshims/shims/mediacapture.js +1 -0
  141. data/public/js/webshims/shims/mediaelement-core.js +1 -0
  142. data/public/js/webshims/shims/mediaelement-debug.js +1 -0
  143. data/public/js/webshims/shims/mediaelement-jaris.js +1 -0
  144. data/public/js/webshims/shims/mediaelement-native-fix.js +1 -0
  145. data/public/js/webshims/shims/mediaelement-yt.js +1 -0
  146. data/public/js/webshims/shims/moxie/flash/Moxie.cdn.swf +0 -0
  147. data/public/js/webshims/shims/moxie/flash/Moxie.min.swf +0 -0
  148. data/public/js/webshims/shims/moxie/js/moxie-html4.js +3 -0
  149. data/public/js/webshims/shims/moxie/js/moxie-swf.js +2 -0
  150. data/public/js/webshims/shims/picture.js +1 -0
  151. data/public/js/webshims/shims/plugins/jquery.ui.position.js +11 -0
  152. data/public/js/webshims/shims/range-ui.js +1 -0
  153. data/public/js/webshims/shims/sizzle.js +11 -0
  154. data/public/js/webshims/shims/sticky.js +1 -0
  155. data/public/js/webshims/shims/styles/color-picker.png +0 -0
  156. data/public/js/webshims/shims/styles/forms-ext.css +1 -0
  157. data/public/js/webshims/shims/styles/forms-picker.css +1 -0
  158. data/public/js/webshims/shims/styles/progress.gif +0 -0
  159. data/public/js/webshims/shims/styles/progress.png +0 -0
  160. data/public/js/webshims/shims/styles/shim-ext.css +1 -0
  161. data/public/js/webshims/shims/styles/shim.css +1 -0
  162. data/public/js/webshims/shims/styles/transparent.png +0 -0
  163. data/public/js/webshims/shims/styles/widget.eot +0 -0
  164. data/public/js/webshims/shims/styles/widget.svg +12 -0
  165. data/public/js/webshims/shims/styles/widget.ttf +0 -0
  166. data/public/js/webshims/shims/styles/widget.woff +0 -0
  167. data/public/js/webshims/shims/swf/JarisFLVPlayer.swf +0 -0
  168. data/public/js/webshims/shims/swfmini-embed.js +1 -0
  169. data/public/js/webshims/shims/swfmini.js +6 -0
  170. data/public/js/webshims/shims/track-ui.js +1 -0
  171. data/public/js/webshims/shims/track.js +1 -0
  172. data/public/js/webshims/shims/url.js +1 -0
  173. data/public/js/webshims/shims/usermedia-core.js +1 -0
  174. data/public/js/webshims/shims/usermedia-shim.js +1 -0
  175. data/sequenceserver.gemspec +16 -13
  176. data/views/400.erb +28 -0
  177. data/views/500.erb +35 -19
  178. data/views/_options.erb +6 -15
  179. data/views/result.erb +218 -0
  180. data/views/search.erb +354 -151
  181. metadata +254 -62
  182. data/example.config.yml +0 -39
  183. data/lib/sequenceserver/customisation.rb +0 -60
  184. data/lib/sequenceserver/database_formatter.rb +0 -190
  185. data/lib/sequenceserver/helpers.rb +0 -136
  186. data/lib/sequenceserver/sequencehelpers.rb +0 -93
  187. data/lib/sequenceserver/sinatralikeloggerformatter.rb +0 -12
  188. data/lib/sequenceserver/version.rb +0 -9
  189. data/public/css/beige.css.css +0 -254
  190. data/public/css/bootstrap.dropdown.css +0 -29
  191. data/public/css/bootstrap.icons.css +0 -155
  192. data/public/css/bootstrap.modal.css +0 -28
  193. data/public/js/bootstrap.dropdown.js +0 -92
  194. data/public/js/bootstrap.modal.js +0 -7
  195. data/public/js/bootstrap.transition.js +0 -7
  196. data/public/js/jquery-scrollspy.js +0 -98
  197. data/public/js/jquery.activity.js +0 -10
  198. data/public/js/jquery.enablePlaceholder.min.js +0 -10
  199. data/public/js/store.min.js +0 -2
  200. data/public/sequence.html +0 -28
  201. data/tests/database/nucleotide/Sinvicta2-2-3.cdna.subset.fasta +0 -5486
  202. data/tests/database/nucleotide/Sinvicta2-2-3.cdna.subset.fasta.nhr +0 -0
  203. data/tests/database/nucleotide/Sinvicta2-2-3.cdna.subset.fasta.nin +0 -0
  204. data/tests/database/nucleotide/Sinvicta2-2-3.cdna.subset.fasta.nsq +0 -0
  205. data/tests/database/protein/Sinvicta2-2-3.prot.subset.fasta +0 -6449
  206. data/tests/database/protein/Sinvicta2-2-3.prot.subset.fasta.phr +0 -0
  207. data/tests/database/protein/Sinvicta2-2-3.prot.subset.fasta.pin +0 -0
  208. data/tests/database/protein/Sinvicta2-2-3.prot.subset.fasta.psq +0 -0
  209. data/tests/run +0 -26
  210. data/tests/test_sequencehelpers.rb +0 -77
  211. data/tests/test_sequenceserver_blast.rb +0 -60
  212. data/tests/test_ui.rb +0 -104
  213. data/tests/ui.specs.todo +0 -10
data/views/search.erb CHANGED
@@ -4,215 +4,418 @@
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  <title>SequenceServer: Custom BLAST Server</title>
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  <meta name="author" content="Anurag Priyam" />
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  <meta name="author" content="Ben J. Woodcroft" />
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+ <meta name="author" content="Vivek Rai" />
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  <meta name="author" content="Yannick Wurm" />
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  <meta name="author" content="Cedric Wurm" />
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  <meta name="description" content="Custom BLAST server provided by SequenceServer (http://www.sequenceserver.com)"/>
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  <meta content="text/html; charset=UTF-8" http-equiv="Content-Type"/>
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- <script type="text/javascript" src="<%= uri('/js/store.min.js') %>"></script>
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- <script type="text/javascript" src="<%= uri('/js/jquery.js') %>"></script>
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- <script type="text/javascript" src="<%= uri('/js/jquery-ui.js') %>"></script>
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- <script type="text/javascript" src="<%= uri('/js/jquery.enablePlaceholder.min.js') %>"></script>
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- <script type="text/javascript" src="<%= uri('/js/jquery.activity.js') %>"></script>
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- <script type="text/javascript" src="<%= uri('/js/jquery-scrollspy.js') %>"></script>
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- <script type="text/javascript" src="<%= uri('/js/bootstrap.transition.js') %>"></script>
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- <script type="text/javascript" src="<%= uri('/js/bootstrap.dropdown.js') %>"></script>
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- <script type="text/javascript" src="<%= uri('/js/bootstrap.modal.js') %>"></script>
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- <script type="text/javascript" src="<%= uri('/js/sequenceserver.js') %>"></script>
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- <script type="text/javascript" src="<%= uri('/js/sequenceserver.blast.js') %>"></script>
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-
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- <%# without a space after erb's closing tag, a / gets appended to css' path %>
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- <link rel="stylesheet" media="screen" type="text/css" href="<%= uri('/css/bootstrap.min.css') %>" />
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- <link rel="stylesheet" media="screen" type="text/css" href="<%= uri('/css/bootstrap.dropdown.css') %>" />
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- <link rel="stylesheet" media="screen" type="text/css" href="<%= uri('/css/bootstrap.modal.css') %>" />
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- <link rel="stylesheet" media="screen" type="text/css" href="<%= uri('/css/bootstrap.icons.css') %>" />
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- <link rel="stylesheet" media="screen" type="text/css" href="<%= uri('/css/custom.css') %>" />
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+
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+ <!--[if lt IE 9]>
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+ <script src="js/html5shiv.js"></script>
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+ <![endif]-->
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+
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+ <link href='http://fonts.googleapis.com/css?family=Roboto:400' rel='stylesheet' type='text/css'>
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+ <link href='http://fonts.googleapis.com/css?family=Open+Sans:400,700' rel='stylesheet' type='text/css'>
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+ <link rel="stylesheet" media="screen" type="text/css" href="css/bootstrap.min.css"/>
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+ <link rel="stylesheet" media="screen" type="text/css" href="css/font-awesome.min.css"/>
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+ <link rel="stylesheet" media="screen" type="text/css" href="css/custom.css"/>
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  </head>
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  <body>
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- <div class="container">
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+ <div
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+ class="navbar">
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+ <div
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+ class="container">
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+ <a
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+ class="navbar-brand"
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+ href="http://sequenceserver.com" target="_blank">
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+ SequenceServer
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+ <small>
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+ BLAST searching made easy!
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+ </small>
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+ </a>
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+ </div>
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+ </div>
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+
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+ <div
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+ class="dnd-overlay"
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+ style="display: none;">
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+ <div
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+ class="container dnd-overlay-container">
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+ <div
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+ class="row">
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+ <div
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+ class="col-md-offset-2 col-md-10">
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+ <p
50
+ class="dnd-overlay-drop"
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+ style="display: none;">
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+ <i class="fa fa-2x fa-file-o"></i>
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+ Drop query sequence file here
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+ </p>
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+ <p
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+ class="dnd-overlay-overwrite"
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+ style="display: none;">
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+ <i class="fa fa-2x fa-file-o"></i>
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+ <span style="color: red;">Overwrite</span> query sequence file
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+ </p>
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+
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+ <div
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+ class="dnd-errors">
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+ <div
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+ class="dnd-error"
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+ id="dnd-multi-notification"
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+ style="display: none;">
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+ <div
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+ class="col-md-6 col-md-offset-3">
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+ One file at a time please.
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+ </div>
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+ </div>
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+
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+ <div
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+ class="dnd-error"
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+ id="dnd-large-file-notification"
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+ style="display: none;">
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+ <div
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+ class="col-md-6 col-md-offset-3">
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+ Too big a file. Can only do less than 10 MB. &gt;_&lt;
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+ </div>
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+ </div>
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+
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+ <div
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+ class="dnd-error"
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+ id="dnd-format-notification"
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+ style="display: none;">
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+ <div
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+ class="col-md-6 col-md-offset-3">
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+ Only FASTA files please.
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+ </div>
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+ </div>
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+ </div>
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+ </div>
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+ </div>
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+ </div>
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+ </div>
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+
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+ <div
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+ class="container">
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  <noscript>
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- <div class="nojs-error">
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+ <div
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+ class="nojs-error">
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  <h3>SequenceServer can't work without JavaScript.</h3>
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- <ul>
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- <li>Please see if you can enable JavaScript in your browser's preferences.</li>
38
- <li>If your browser doesn't support JavaScript, please consider upgrading to the latest version or using Firefox or Chrome.</li>
39
- </ul>
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+ <ul>
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+ <li>Please see if you can enable JavaScript in your browser's preferences.</li>
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+ <li>If your browser doesn't support JavaScript, please consider upgrading to the latest version or using Firefox or Chrome.</li>
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+ </ul>
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  </div>
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  </noscript>
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43
- <div class="page">
44
- <div id="banner">
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- <h1>BLAST Sequence(s)</h1>
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- </div>
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-
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- <form method="post" id="blast" action="<%= uri('/#result') %>">
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- <div class="row">
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- <div class="span16">
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- <div class="control-group">
52
- <textarea name="sequence" id="sequence" spellcheck="false" autofocus="true" placeholder="Paste your sequence(s) here..." ></textarea>
53
- </div>
112
+ <form
113
+ class="form-horizontal" id="blast"
114
+ method="post" action="#result">
115
+ <div
116
+ class="form-group">
117
+ <div
118
+ class="col-md-12">
119
+ <div
120
+ class="sequence-controls hidden">
121
+ <button
122
+ type="button"
123
+ class="btn btn-sm btn-default" id="btn-sequence-clear"
124
+ title="Clear query sequence(s).">
125
+ <span id="sequence-file"></span>
126
+ <i class="fa fa-times"></i>
127
+ </button>
128
+ </div>
129
+ <div
130
+ class="sequence">
131
+ <textarea
132
+ class="form-control text-monospace" name="sequence" id="sequence"
133
+ rows="10"
134
+ autofocus="true"
135
+ spellcheck="false"
136
+ placeholder="Paste query sequence(s) or drag file containing query sequence(s) here ..." ></textarea>
54
137
  </div>
55
138
  </div>
139
+ </div>
56
140
 
57
- <div class="notifications">
58
- <div class="notification alert-info hide" id="nucleotide-sequence-notification">
141
+ <div
142
+ class="notifications">
143
+ <div
144
+ class="notification"
145
+ id="nucleotide-sequence-notification"
146
+ style="display: none;">
147
+ <div
148
+ class="alert-info col-md-6 col-md-offset-3">
59
149
  Detected: nucleotide sequence(s).
60
150
  </div>
151
+ </div>
61
152
 
62
- <div class="notification alert-info hide" id="protein-sequence-notification">
153
+ <div
154
+ class="notification"
155
+ id="protein-sequence-notification"
156
+ style="display: none;">
157
+ <div
158
+ class="alert-info col-md-6 col-md-offset-3">
63
159
  Detected: protein sequence(s).
64
160
  </div>
161
+ </div>
65
162
 
66
- <div class="notification alert-error hide" id="mixed-sequence-notification">
163
+ <div
164
+ class="notification"
165
+ id="mixed-sequence-notification"
166
+ style="display: none;">
167
+ <div
168
+ class="alert-danger col-md-10 col-md-offset-1">
67
169
  Detected: mixed nucleotide and protein sequences. We can't handle that. Please try one sequence at a time.
68
170
  </div>
69
171
  </div>
70
172
 
71
- <br class="large"/>
173
+ </div>
72
174
 
73
- <div class="row">
74
- <div class="span8">
75
- <div class="offset-left box databases nucleotide">
76
- <div class="clearfix">
77
- <fieldset>
78
- <legend>Nucleotide databases</legend>
79
- <div class="controls offset-left">
80
- <% settings.databases.values.select{|database| database.type == :nucleotide}.sort.each do |database| %>
81
- <label class="checkbox">
82
- <input type="checkbox" name="databases[]" value="<%=database.hash%>" data-type="<%=database.type%>" />
83
- <span> <%= database.title or database.name %></span>
84
- </label>
85
- <% end %>
86
- </div>
87
- </fieldset>
175
+ <div
176
+ class="form-group databases-container">
177
+ <%# sort => same ordering of nucleotide and protein datbases %>
178
+ <% databases.keys.sort.each do |type| %>
179
+ <div
180
+ class="<%= databases[(databases.keys - [type]).first] ? 'col-md-6' : 'col-md-12' %>">
181
+ <div
182
+ class="panel panel-default">
183
+ <div
184
+ class="panel-heading">
185
+ <h4><%= type.capitalize %> databases</h4>
88
186
  </div>
187
+ <ul
188
+ class="list-group databases <%= type %>">
189
+ <% databases[type].sort_by(&:title).each do |database| %>
190
+ <li class="list-group-item">
191
+ <div
192
+ class="checkbox">
193
+ <label>
194
+ <input type="checkbox" name="databases[]" value="<%=database.id%>" data-type="<%=database.type%>" />
195
+ <%= database.title or database.name %>
196
+ </label>
197
+ </div>
198
+ </li>
199
+ <% end %>
200
+ </ul>
89
201
  </div>
90
202
  </div>
203
+ <% end %>
204
+ </div>
91
205
 
92
- <div class="span8">
93
- <div class="offset-right box databases protein">
94
- <div class="clearfix">
95
- <fieldset>
96
- <legend>Protein databases</legend>
97
- <div class="controls offset-left">
98
- <% settings.databases.values.select{|database| database.type == :protein}.sort.each do |database| %>
99
- <label class="checkbox">
100
- <input type="checkbox" name="databases[]" value="<%=database.hash%>" data-type="<%=database.type%>" />
101
- <span> <%= database.title or database.name %></span>
102
- </label>
103
- <% end %>
104
- </div>
105
- </fieldset>
106
- </div>
206
+ <div
207
+ class="form-group">
208
+ <div
209
+ class="col-md-8">
210
+ <div
211
+ class="form-group advanced">
212
+ <label
213
+ class="col-md-3 control-label"
214
+ for="advanced">
215
+ Advanced Parameters:
216
+ </label>
217
+ <div
218
+ class="col-md-9 input-group">
219
+ <input
220
+ type="text"
221
+ class="form-control" name="advanced" id="advanced"
222
+ title="View, and enter advanced parameters."
223
+ placeholder="eg: -evalue 1.0e-5 -num_alignments 100"/>
224
+ <div class="input-group-addon cursor-pointer" data-toggle="modal" data-toggle="modal" data-target="#help">
225
+ <i class="fa fa-question"></i>
226
+ </div>
107
227
  </div>
108
228
  </div>
109
229
  </div>
110
230
 
111
- <br class="large"/>
231
+ <div
232
+ class="col-md-4">
233
+ <div
234
+ class="btn-group btn-block" id="methods">
235
+ <button
236
+ type="submit"
237
+ id="method" class="btn btn-primary col-md-12"
238
+ title="Use Ctrl+Enter as shortcut."
239
+ disabled="disabled">
240
+ blast
241
+ </button>
242
+ </div>
243
+ </div>
244
+ </div>
245
+ </form>
112
246
 
113
- <div class="row">
114
- <div class="span12">
115
- <div class="offset-left box advanced">
116
- <div class="clearfix">
117
- <label for="advanced">Advanced Parameters:</label>
118
- <input class="span8" type="text" name="advanced" id="advanced" title="View, and enter advanced parameters." placeholder="eg: -evalue 1.0e-5 -num_alignments 100"/>
119
- <span class="icon-question-sign" data-toggle="modal" href="#help"></span>
120
- </div>
247
+ <div
248
+ class="result" id="result"
249
+ style="display: none;">
250
+ </div>
251
+ </div> <!-- /container -->
121
252
 
122
- <div class="modal hide fade" id="help">
123
- <div class="modal-header">
124
- <h3>Advanced Options</h3>
125
- </div>
126
- <div class="modal-body">
127
- <%= erb :_options %>
128
- </div>
129
- <div class="modal-footer">
130
- <button class="btn btn-primary" data-dismiss="modal">Got it!</button>
131
- </div>
132
- </div>
133
- </div>
134
- </div>
253
+ <div
254
+ class="footer" id="footer">
255
+ <hr>
256
+ <p
257
+ class="text-center">
258
+ <a
259
+ href='http://www.sequenceserver.com'>
260
+ <%=
261
+ quote = [
262
+ "Custom BLAST web interface by SequenceServer.",
263
+ "SequenceServer: Local BLAST with bespoke html interface.",
264
+ "Set up custom BLAST interface with SequenceServer.",
265
+ "Easy BLASTing with SequenceServer."
266
+ ][rand(4)]
267
+ %>
268
+ </a>
269
+ <a
270
+ class="twitter-share-button"
271
+ href="https://twitter.com/share"
272
+ data-url="http://www.sequenceserver.com" data-text="<%= quote %>" data-via="yeban" data-hashtags="bioinformatics">
273
+ Tweet
274
+ </a>
275
+ <%#<div class="g-plusone" data-annotation="none" data-href="http://www.sequenceserver.com"></div>%>
135
276
 
136
- <div class="span4">
137
- <div id="methods">
138
- <button type="submit" class="span3 btn btn-large btn-primary" id="method" disabled="disabled">blast</button>
139
- <button class="btn btn-primary btn-large dropdown-toggle hide" data-toggle="dropdown">
140
- <span class="caret"></span>
141
- </button>
142
- <ul class="dropdown-menu"></ul>
143
- </div>
144
- </div>
277
+ <br>
278
+ Please Cite:
279
+ <a href='http://www.sequenceserver.com'>
280
+ Priyam, Woodcroft, Rai & Wurm, <strong>SequenceServer</strong> (<em>in prep</em>)</a>
281
+ </a>
282
+ &amp; relevant data sources.
283
+ </p>
284
+ </div>
285
+
286
+ <div
287
+ id="error"
288
+ class="modal fade"
289
+ tabindex="-1">
290
+ </div> <!-- error -->
291
+
292
+ <div
293
+ class="modal fade" id="error-no-response">
294
+ <div
295
+ class="modal-dialog">
296
+ <div
297
+ class="modal-content">
298
+ <div
299
+ class="modal-header">
300
+ <h3>Server didn't respond</h3>
145
301
  </div>
146
- </form>
147
302
 
148
- <div class="modal hide" id="spinner" data-keyboard="false" data-backdrop="static">
149
- <div class="modal-body">
303
+ <div
304
+ class="modal-body">
305
+ <p>
306
+ Could be a temporary network issue, or the service might be
307
+ configured to "time out" long requests.
308
+ </p>
309
+
310
+ <p>
311
+ Please try again
312
+ later, or report to the admin or <a
313
+ href="https://groups.google.com/forum/?fromgroups#!forum/sequenceserver">SequenceServer
314
+ Google Group</a> (if you are the admin) if problem persists.
315
+ </p>
150
316
  </div>
151
- </div>
152
317
 
153
- <div class="results hide">
154
- <div id="result">Waiting for BLAST to be run <!-- need bit before for UI testing so it knows when BLAST is finished -->
318
+ <div
319
+ class="modal-footer">
320
+ <button class="btn btn-danger" data-dismiss="modal">Okay</button>
155
321
  </div>
156
322
  </div>
323
+ </div>
324
+ </div> <!-- error-no-response -->
157
325
 
158
- <div class="modal hide fade" id="error">
159
- <div class="modal-header">
160
- <h3 id="error-short">Oops! BLAST Failed</h3>
326
+ <div
327
+ class="modal fade" id="help"
328
+ tabindex="-1">
329
+ <div
330
+ class="modal-dialog modal-lg">
331
+ <div
332
+ class="modal-content">
333
+ <div
334
+ class="modal-header">
335
+ <h3>Advanced Options</h3>
161
336
  </div>
162
- <div class="modal-body">
163
- <h4 id="error-type"></h4>
164
- <br/>
165
- <p id="error-message"></p>
337
+ <div
338
+ class="modal-body">
339
+ <%= erb :_options %>
166
340
  </div>
167
- <div class="modal-footer">
168
- <button class="btn btn-danger" data-dismiss="modal">Close</button>
341
+ <div
342
+ class="modal-footer">
343
+ <button
344
+ class="btn btn-default btn-primary"
345
+ data-dismiss="modal">
346
+ Got it!
347
+ </button>
169
348
  </div>
170
349
  </div>
350
+ </div>
351
+ </div> <!-- advanced options -->
171
352
 
172
- <div id="underbar">
173
- <p><strong><a href='http://www.sequenceserver.com'>
174
- <%= [ "&copy; SequenceServer: BLAST search made easy!",
175
- "Custom BLAST web interface by SequenceServer.",
176
- "SequenceServer: Local BLAST with bespoke html interface.",
177
- "Set up custom BLAST interface with SequenceServer.",
178
- "Please cite: Priyam A, Woodcroft BJ, Wurm Y (<em>in prep</em>). " +
179
- "Sequenceserver: BLAST searching made easy."
180
- ][rand(5)]
181
- %>
182
- </a></strong></p>
353
+ <div
354
+ class="modal" id="spinner"
355
+ tabindex="-1"
356
+ data-backdrop="static" data-keyboard="false">
357
+ <div
358
+ class="modal-dialog">
359
+ <div
360
+ class="modal-content">
361
+ <div
362
+ class="modal-body text-center">
363
+ <h2>
364
+ BLAST-ing ...
365
+ </h2>
366
+ <i class="fa fa-spinner fa-5x fa-spin"></i>
367
+ <p>
368
+ <br>
369
+ This could take some time depending on the size of your query and
370
+ database(s).
371
+ </p>
372
+ </div>
183
373
  </div>
184
- </div> <!-- /page -->
185
- </div> <!-- /container -->
186
-
187
- <div id="social" class="modal hide fade">
188
- <div class="modal-header">
189
- <h3 id="error-short">Looks like you are fond of SequenceServer :).</h3>
190
374
  </div>
191
- <div class="modal-body">
192
- <p>Please consider giving us a plus-one and/or tweeting about us. Thanks!</p>
193
- <br/>
194
- <div class="buttons">
195
- <div class="button-container well">
196
- <div class="g-plusone" data-annotation="none" data-href="http://www.sequenceserver.com"></div>
375
+ </div> <!-- spinner -->
376
+
377
+ <div
378
+ id="sequence-viewer" class="modal"
379
+ tabindex=-1>
380
+ <div
381
+ class="modal-dialog">
382
+ <div
383
+ class="modal-content">
384
+ <div
385
+ class="modal-header">
386
+ <h3>View and download sequence</h3>
387
+ </div>
388
+
389
+ <div
390
+ class="modal-body">
197
391
  </div>
198
- <div class="button-container well">
199
- <a href="https://twitter.com/share" class="twitter-share-button" data-url="http://www.sequenceserver.com" data-text="SequenceServer: BLAST search made easy." data-via="yeban" data-size="large" data-count="none" data-hashtags="bioinformatics">Tweet</a>
392
+
393
+ <div
394
+ class="spinner">
395
+ <i class="fa fa-spinner fa-3x fa-spin"></i>
396
+ </div>
397
+
398
+ <div
399
+ class="modal-footer">
200
400
  </div>
201
401
  </div>
202
402
  </div>
203
- <div class="modal-footer">
204
- <button class="btn btn-primary" data-dismiss="modal">Done</button>
205
- </div>
206
- </div> <!-- /social -->
403
+ </div> <!-- sequence viewing -->
207
404
 
208
- <!-- google plus -->
405
+ <!-- JS -->
406
+ <script type="text/javascript" src="js/underscore.min.js"></script>
407
+ <script type="text/javascript" src="js/jquery.js"></script>
408
+ <script type="text/javascript" src="js/webshims/polyfiller.js"></script>
209
409
  <script type="text/javascript">
210
- (function() {
211
- var po = document.createElement('script'); po.type = 'text/javascript'; po.async = true;
212
- po.src = 'https://apis.google.com/js/plusone.js';
213
- var s = document.getElementsByTagName('script')[0]; s.parentNode.insertBefore(po, s);
214
- })();
410
+ $.webshims.polyfill('forms');
215
411
  </script>
412
+ <script type="text/javascript" src="js/jquery-ui.js"></script>
413
+ <script type="text/javascript" src="js/bootstrap.min.js"></script>
414
+ <script type="text/javascript" src="js/d3.v3.min.js"></script>
415
+ <script type="text/javascript" src="js/sequenceserver.js"></script>
416
+ <script type="text/javascript" src="js/sequenceserver.blast.js"></script>
417
+ <script type="text/javascript" src="js/jquery.t.js"></script>
418
+ <script type="text/javascript" src="js/sequence.js"></script>
216
419
 
217
420
  <!-- twitter -->
218
421
  <script>!function(d,s,id){var js,fjs=d.getElementsByTagName(s)[0];if(!d.getElementById(id)){js=d.createElement(s);js.id=id;js.src="//platform.twitter.com/widgets.js";fjs.parentNode.insertBefore(js,fjs);}}(document,"script","twitter-wjs");</script>