sequenceserver 1.0.0.pre.2 → 1.0.0.pre.3

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Files changed (337) hide show
  1. checksums.yaml +4 -4
  2. data/Gemfile +1 -1
  3. data/README.md +18 -4
  4. data/bin/sequenceserver +219 -124
  5. data/lib/sequenceserver.rb +156 -153
  6. data/lib/sequenceserver/blast.rb +163 -432
  7. data/lib/sequenceserver/blast/exceptions.rb +27 -0
  8. data/lib/sequenceserver/blast/hit.rb +32 -0
  9. data/lib/sequenceserver/blast/hsp.rb +260 -0
  10. data/lib/sequenceserver/blast/query.rb +28 -0
  11. data/lib/sequenceserver/blast/report.rb +123 -0
  12. data/lib/sequenceserver/config.rb +94 -0
  13. data/lib/sequenceserver/database.rb +89 -49
  14. data/lib/sequenceserver/exceptions.rb +154 -0
  15. data/lib/sequenceserver/links.rb +1 -1
  16. data/lib/sequenceserver/logger.rb +5 -7
  17. data/lib/sequenceserver/sequence.rb +40 -39
  18. data/public/css/bootstrap.min.css +5 -7
  19. data/public/css/custom.css +28 -27
  20. data/public/dist/css/sequenceserver.min.css +1 -0
  21. data/public/dist/css/sequenceserver.min.css.gz +0 -0
  22. data/public/dist/fonts/FontAwesome.otf +0 -0
  23. data/public/dist/fonts/fontawesome-webfont.eot +0 -0
  24. data/public/dist/fonts/fontawesome-webfont.svg +565 -0
  25. data/public/dist/fonts/fontawesome-webfont.ttf +0 -0
  26. data/public/dist/fonts/fontawesome-webfont.woff +0 -0
  27. data/public/dist/fonts/fontawesome-webfont.woff2 +0 -0
  28. data/public/dist/js/sequenceserver.min.js +12 -0
  29. data/public/dist/js/sequenceserver.min.js.gz +0 -0
  30. data/public/dist/js/shims/FlashCanvas/canvas2png.js +1 -0
  31. data/public/dist/js/shims/FlashCanvas/flashcanvas.js +1 -0
  32. data/public/dist/js/shims/FlashCanvas/flashcanvas.swf +0 -0
  33. data/public/dist/js/shims/FlashCanvasPro/canvas2png.js +1 -0
  34. data/public/dist/js/shims/FlashCanvasPro/flash10canvas.swf +0 -0
  35. data/public/dist/js/shims/FlashCanvasPro/flash9canvas.swf +0 -0
  36. data/public/dist/js/shims/FlashCanvasPro/flashcanvas.js +1 -0
  37. data/public/dist/js/shims/canvas-blob.js +1 -0
  38. data/public/dist/js/shims/color-picker.js +2 -0
  39. data/public/dist/js/shims/combos/1.js +6 -0
  40. data/public/dist/js/shims/combos/10.js +2 -0
  41. data/public/dist/js/shims/combos/11.js +2 -0
  42. data/public/dist/js/shims/combos/12.js +6 -0
  43. data/public/dist/js/shims/combos/13.js +1 -0
  44. data/public/dist/js/shims/combos/14.js +1 -0
  45. data/public/dist/js/shims/combos/15.js +2 -0
  46. data/public/dist/js/shims/combos/16.js +7 -0
  47. data/public/dist/js/shims/combos/17.js +2 -0
  48. data/public/dist/js/shims/combos/18.js +3 -0
  49. data/public/dist/js/shims/combos/2.js +7 -0
  50. data/public/dist/js/shims/combos/21.js +2 -0
  51. data/public/dist/js/shims/combos/22.js +1 -0
  52. data/public/dist/js/shims/combos/23.js +6 -0
  53. data/public/dist/js/shims/combos/25.js +2 -0
  54. data/public/dist/js/shims/combos/27.js +1 -0
  55. data/public/dist/js/shims/combos/28.js +1 -0
  56. data/public/dist/js/shims/combos/29.js +1 -0
  57. data/public/dist/js/shims/combos/3.js +1 -0
  58. data/public/dist/js/shims/combos/30.js +2 -0
  59. data/public/dist/js/shims/combos/31.js +1 -0
  60. data/public/dist/js/shims/combos/33.js +1 -0
  61. data/public/dist/js/shims/combos/34.js +1 -0
  62. data/public/dist/js/shims/combos/4.js +1 -0
  63. data/public/dist/js/shims/combos/5.js +2 -0
  64. data/public/dist/js/shims/combos/6.js +2 -0
  65. data/public/dist/js/shims/combos/7.js +7 -0
  66. data/public/dist/js/shims/combos/8.js +7 -0
  67. data/public/dist/js/shims/combos/9.js +2 -0
  68. data/public/dist/js/shims/combos/97.js +1 -0
  69. data/public/dist/js/shims/combos/98.js +1 -0
  70. data/public/dist/js/shims/combos/99.js +1 -0
  71. data/public/dist/js/shims/details.js +1 -0
  72. data/public/dist/js/shims/dom-extend.js +1 -0
  73. data/public/dist/js/shims/es5.js +1 -0
  74. data/public/dist/js/shims/es6.js +1 -0
  75. data/public/dist/js/shims/excanvas.js +1 -0
  76. data/public/dist/js/shims/filereader-xhr.js +1 -0
  77. data/public/dist/js/shims/form-combat.js +1 -0
  78. data/public/dist/js/shims/form-core.js +1 -0
  79. data/public/dist/js/shims/form-datalist-lazy.js +1 -0
  80. data/public/dist/js/shims/form-datalist.js +1 -0
  81. data/public/dist/js/shims/form-fixrangechange.js +1 -0
  82. data/public/dist/js/shims/form-inputmode.js +1 -0
  83. data/public/dist/js/shims/form-message.js +1 -0
  84. data/public/dist/js/shims/form-native-extend.js +1 -0
  85. data/public/dist/js/shims/form-number-date-api.js +1 -0
  86. data/public/dist/js/shims/form-number-date-ui.js +1 -0
  87. data/public/dist/js/shims/form-shim-extend.js +1 -0
  88. data/public/dist/js/shims/form-shim-extend2.js +1 -0
  89. data/public/dist/js/shims/form-validation.js +1 -0
  90. data/public/dist/js/shims/form-validators.js +1 -0
  91. data/public/dist/js/shims/forms-picker.js +1 -0
  92. data/public/dist/js/shims/geolocation.js +1 -0
  93. data/public/dist/js/shims/i18n/formcfg-ar.js +1 -0
  94. data/public/dist/js/shims/i18n/formcfg-ch-CN.js +1 -0
  95. data/public/dist/js/shims/i18n/formcfg-cs.js +1 -0
  96. data/public/dist/js/shims/i18n/formcfg-de.js +1 -0
  97. data/public/dist/js/shims/i18n/formcfg-el.js +1 -0
  98. data/public/dist/js/shims/i18n/formcfg-en.js +1 -0
  99. data/public/dist/js/shims/i18n/formcfg-es.js +1 -0
  100. data/public/dist/js/shims/i18n/formcfg-fa.js +1 -0
  101. data/public/dist/js/shims/i18n/formcfg-fr.js +1 -0
  102. data/public/dist/js/shims/i18n/formcfg-he.js +1 -0
  103. data/public/dist/js/shims/i18n/formcfg-hi.js +1 -0
  104. data/public/dist/js/shims/i18n/formcfg-hu.js +1 -0
  105. data/public/dist/js/shims/i18n/formcfg-it.js +1 -0
  106. data/public/dist/js/shims/i18n/formcfg-ja.js +1 -0
  107. data/public/dist/js/shims/i18n/formcfg-lt.js +1 -0
  108. data/public/dist/js/shims/i18n/formcfg-nl.js +1 -0
  109. data/public/dist/js/shims/i18n/formcfg-pl.js +1 -0
  110. data/public/dist/js/shims/i18n/formcfg-pt-BR.js +1 -0
  111. data/public/dist/js/shims/i18n/formcfg-pt-PT.js +1 -0
  112. data/public/dist/js/shims/i18n/formcfg-pt.js +1 -0
  113. data/public/dist/js/shims/i18n/formcfg-ru.js +1 -0
  114. data/public/dist/js/shims/i18n/formcfg-sv.js +1 -0
  115. data/public/dist/js/shims/i18n/formcfg-zh-CN.js +1 -0
  116. data/public/dist/js/shims/i18n/formcfg-zh-TW.js +1 -0
  117. data/public/dist/js/shims/jme/alternate-media.js +1 -0
  118. data/public/dist/js/shims/jme/base.js +1 -0
  119. data/public/dist/js/shims/jme/controls.css +1 -0
  120. data/public/dist/js/shims/jme/jme.eot +0 -0
  121. data/public/dist/js/shims/jme/jme.svg +36 -0
  122. data/public/dist/js/shims/jme/jme.ttf +0 -0
  123. data/public/dist/js/shims/jme/jme.woff +0 -0
  124. data/public/dist/js/shims/jme/mediacontrols-lazy.js +1 -0
  125. data/public/dist/js/shims/jme/mediacontrols.js +1 -0
  126. data/public/dist/js/shims/jme/playlist.js +1 -0
  127. data/public/dist/js/shims/jpicker/images/AlphaBar.png +0 -0
  128. data/public/dist/js/shims/jpicker/images/Bars.png +0 -0
  129. data/public/dist/js/shims/jpicker/images/Maps.png +0 -0
  130. data/public/dist/js/shims/jpicker/images/NoColor.png +0 -0
  131. data/public/dist/js/shims/jpicker/images/bar-opacity.png +0 -0
  132. data/public/dist/js/shims/jpicker/images/map-opacity.png +0 -0
  133. data/public/dist/js/shims/jpicker/images/mappoint.gif +0 -0
  134. data/public/dist/js/shims/jpicker/images/picker.gif +0 -0
  135. data/public/dist/js/shims/jpicker/images/preview-opacity.png +0 -0
  136. data/public/dist/js/shims/jpicker/images/rangearrows.gif +0 -0
  137. data/public/dist/js/shims/jpicker/jpicker.css +1 -0
  138. data/public/dist/js/shims/matchMedia.js +3 -0
  139. data/public/dist/js/shims/mediacapture-picker.js +1 -0
  140. data/public/dist/js/shims/mediacapture.js +1 -0
  141. data/public/dist/js/shims/mediaelement-core.js +1 -0
  142. data/public/dist/js/shims/mediaelement-debug.js +1 -0
  143. data/public/dist/js/shims/mediaelement-jaris.js +1 -0
  144. data/public/dist/js/shims/mediaelement-native-fix.js +1 -0
  145. data/public/dist/js/shims/mediaelement-yt.js +1 -0
  146. data/public/dist/js/shims/moxie/flash/Moxie.cdn.swf +0 -0
  147. data/public/dist/js/shims/moxie/flash/Moxie.min.swf +0 -0
  148. data/public/dist/js/shims/moxie/js/moxie-html4.js +3 -0
  149. data/public/dist/js/shims/moxie/js/moxie-swf.js +2 -0
  150. data/public/dist/js/shims/picture.js +1 -0
  151. data/public/dist/js/shims/plugins/jquery.ui.position.js +11 -0
  152. data/public/dist/js/shims/range-ui.js +1 -0
  153. data/public/dist/js/shims/sizzle.js +11 -0
  154. data/public/dist/js/shims/sticky.js +1 -0
  155. data/public/dist/js/shims/styles/color-picker.png +0 -0
  156. data/public/dist/js/shims/styles/forms-ext.css +1 -0
  157. data/public/dist/js/shims/styles/forms-picker.css +1 -0
  158. data/public/dist/js/shims/styles/progress.gif +0 -0
  159. data/public/dist/js/shims/styles/progress.png +0 -0
  160. data/public/dist/js/shims/styles/shim-ext.css +1 -0
  161. data/public/dist/js/shims/styles/shim.css +1 -0
  162. data/public/dist/js/shims/styles/transparent.png +0 -0
  163. data/public/dist/js/shims/styles/widget.eot +0 -0
  164. data/public/dist/js/shims/styles/widget.svg +12 -0
  165. data/public/dist/js/shims/styles/widget.ttf +0 -0
  166. data/public/dist/js/shims/styles/widget.woff +0 -0
  167. data/public/dist/js/shims/swf/JarisFLVPlayer.swf +0 -0
  168. data/public/dist/js/shims/swfmini-embed.js +1 -0
  169. data/public/dist/js/shims/swfmini.js +6 -0
  170. data/public/dist/js/shims/track-ui.js +1 -0
  171. data/public/dist/js/shims/track.js +1 -0
  172. data/public/dist/js/shims/url.js +1 -0
  173. data/public/dist/js/shims/usermedia-core.js +1 -0
  174. data/public/dist/js/shims/usermedia-shim.js +1 -0
  175. data/public/dist/js/webshims/shims/FlashCanvas/canvas2png.js +1 -0
  176. data/public/dist/js/webshims/shims/FlashCanvas/flashcanvas.js +1 -0
  177. data/public/dist/js/webshims/shims/FlashCanvas/flashcanvas.swf +0 -0
  178. data/public/dist/js/webshims/shims/FlashCanvasPro/canvas2png.js +1 -0
  179. data/public/dist/js/webshims/shims/FlashCanvasPro/flash10canvas.swf +0 -0
  180. data/public/dist/js/webshims/shims/FlashCanvasPro/flash9canvas.swf +0 -0
  181. data/public/dist/js/webshims/shims/FlashCanvasPro/flashcanvas.js +1 -0
  182. data/public/dist/js/webshims/shims/canvas-blob.js +1 -0
  183. data/public/dist/js/webshims/shims/color-picker.js +2 -0
  184. data/public/dist/js/webshims/shims/combos/1.js +6 -0
  185. data/public/dist/js/webshims/shims/combos/10.js +2 -0
  186. data/public/dist/js/webshims/shims/combos/11.js +2 -0
  187. data/public/dist/js/webshims/shims/combos/12.js +6 -0
  188. data/public/dist/js/webshims/shims/combos/13.js +1 -0
  189. data/public/dist/js/webshims/shims/combos/14.js +1 -0
  190. data/public/dist/js/webshims/shims/combos/15.js +2 -0
  191. data/public/dist/js/webshims/shims/combos/16.js +7 -0
  192. data/public/dist/js/webshims/shims/combos/17.js +2 -0
  193. data/public/dist/js/webshims/shims/combos/18.js +3 -0
  194. data/public/dist/js/webshims/shims/combos/2.js +7 -0
  195. data/public/dist/js/webshims/shims/combos/21.js +2 -0
  196. data/public/dist/js/webshims/shims/combos/22.js +1 -0
  197. data/public/dist/js/webshims/shims/combos/23.js +6 -0
  198. data/public/dist/js/webshims/shims/combos/25.js +2 -0
  199. data/public/dist/js/webshims/shims/combos/27.js +1 -0
  200. data/public/dist/js/webshims/shims/combos/28.js +1 -0
  201. data/public/dist/js/webshims/shims/combos/29.js +1 -0
  202. data/public/dist/js/webshims/shims/combos/3.js +1 -0
  203. data/public/dist/js/webshims/shims/combos/30.js +2 -0
  204. data/public/dist/js/webshims/shims/combos/31.js +1 -0
  205. data/public/dist/js/webshims/shims/combos/33.js +1 -0
  206. data/public/dist/js/webshims/shims/combos/34.js +1 -0
  207. data/public/dist/js/webshims/shims/combos/4.js +1 -0
  208. data/public/dist/js/webshims/shims/combos/5.js +2 -0
  209. data/public/dist/js/webshims/shims/combos/6.js +2 -0
  210. data/public/dist/js/webshims/shims/combos/7.js +7 -0
  211. data/public/dist/js/webshims/shims/combos/8.js +7 -0
  212. data/public/dist/js/webshims/shims/combos/9.js +2 -0
  213. data/public/dist/js/webshims/shims/combos/97.js +1 -0
  214. data/public/dist/js/webshims/shims/combos/98.js +1 -0
  215. data/public/dist/js/webshims/shims/combos/99.js +1 -0
  216. data/public/dist/js/webshims/shims/details.js +1 -0
  217. data/public/dist/js/webshims/shims/dom-extend.js +1 -0
  218. data/public/dist/js/webshims/shims/es5.js +1 -0
  219. data/public/dist/js/webshims/shims/es6.js +1 -0
  220. data/public/dist/js/webshims/shims/excanvas.js +1 -0
  221. data/public/dist/js/webshims/shims/filereader-xhr.js +1 -0
  222. data/public/dist/js/webshims/shims/form-combat.js +1 -0
  223. data/public/dist/js/webshims/shims/form-core.js +1 -0
  224. data/public/dist/js/webshims/shims/form-datalist-lazy.js +1 -0
  225. data/public/dist/js/webshims/shims/form-datalist.js +1 -0
  226. data/public/dist/js/webshims/shims/form-fixrangechange.js +1 -0
  227. data/public/dist/js/webshims/shims/form-inputmode.js +1 -0
  228. data/public/dist/js/webshims/shims/form-message.js +1 -0
  229. data/public/dist/js/webshims/shims/form-native-extend.js +1 -0
  230. data/public/dist/js/webshims/shims/form-number-date-api.js +1 -0
  231. data/public/dist/js/webshims/shims/form-number-date-ui.js +1 -0
  232. data/public/dist/js/webshims/shims/form-shim-extend.js +1 -0
  233. data/public/dist/js/webshims/shims/form-shim-extend2.js +1 -0
  234. data/public/dist/js/webshims/shims/form-validation.js +1 -0
  235. data/public/dist/js/webshims/shims/form-validators.js +1 -0
  236. data/public/dist/js/webshims/shims/forms-picker.js +1 -0
  237. data/public/dist/js/webshims/shims/geolocation.js +1 -0
  238. data/public/dist/js/webshims/shims/i18n/formcfg-ar.js +1 -0
  239. data/public/dist/js/webshims/shims/i18n/formcfg-ch-CN.js +1 -0
  240. data/public/dist/js/webshims/shims/i18n/formcfg-cs.js +1 -0
  241. data/public/dist/js/webshims/shims/i18n/formcfg-de.js +1 -0
  242. data/public/dist/js/webshims/shims/i18n/formcfg-el.js +1 -0
  243. data/public/dist/js/webshims/shims/i18n/formcfg-en.js +1 -0
  244. data/public/dist/js/webshims/shims/i18n/formcfg-es.js +1 -0
  245. data/public/dist/js/webshims/shims/i18n/formcfg-fa.js +1 -0
  246. data/public/dist/js/webshims/shims/i18n/formcfg-fr.js +1 -0
  247. data/public/dist/js/webshims/shims/i18n/formcfg-he.js +1 -0
  248. data/public/dist/js/webshims/shims/i18n/formcfg-hi.js +1 -0
  249. data/public/dist/js/webshims/shims/i18n/formcfg-hu.js +1 -0
  250. data/public/dist/js/webshims/shims/i18n/formcfg-it.js +1 -0
  251. data/public/dist/js/webshims/shims/i18n/formcfg-ja.js +1 -0
  252. data/public/dist/js/webshims/shims/i18n/formcfg-lt.js +1 -0
  253. data/public/dist/js/webshims/shims/i18n/formcfg-nl.js +1 -0
  254. data/public/dist/js/webshims/shims/i18n/formcfg-pl.js +1 -0
  255. data/public/dist/js/webshims/shims/i18n/formcfg-pt-BR.js +1 -0
  256. data/public/dist/js/webshims/shims/i18n/formcfg-pt-PT.js +1 -0
  257. data/public/dist/js/webshims/shims/i18n/formcfg-pt.js +1 -0
  258. data/public/dist/js/webshims/shims/i18n/formcfg-ru.js +1 -0
  259. data/public/dist/js/webshims/shims/i18n/formcfg-sv.js +1 -0
  260. data/public/dist/js/webshims/shims/i18n/formcfg-zh-CN.js +1 -0
  261. data/public/dist/js/webshims/shims/i18n/formcfg-zh-TW.js +1 -0
  262. data/public/dist/js/webshims/shims/jme/alternate-media.js +1 -0
  263. data/public/dist/js/webshims/shims/jme/base.js +1 -0
  264. data/public/dist/js/webshims/shims/jme/controls.css +1 -0
  265. data/public/dist/js/webshims/shims/jme/jme.eot +0 -0
  266. data/public/dist/js/webshims/shims/jme/jme.svg +36 -0
  267. data/public/dist/js/webshims/shims/jme/jme.ttf +0 -0
  268. data/public/dist/js/webshims/shims/jme/jme.woff +0 -0
  269. data/public/dist/js/webshims/shims/jme/mediacontrols-lazy.js +1 -0
  270. data/public/dist/js/webshims/shims/jme/mediacontrols.js +1 -0
  271. data/public/dist/js/webshims/shims/jme/playlist.js +1 -0
  272. data/public/dist/js/webshims/shims/jpicker/images/AlphaBar.png +0 -0
  273. data/public/dist/js/webshims/shims/jpicker/images/Bars.png +0 -0
  274. data/public/dist/js/webshims/shims/jpicker/images/Maps.png +0 -0
  275. data/public/dist/js/webshims/shims/jpicker/images/NoColor.png +0 -0
  276. data/public/dist/js/webshims/shims/jpicker/images/bar-opacity.png +0 -0
  277. data/public/dist/js/webshims/shims/jpicker/images/map-opacity.png +0 -0
  278. data/public/dist/js/webshims/shims/jpicker/images/mappoint.gif +0 -0
  279. data/public/dist/js/webshims/shims/jpicker/images/picker.gif +0 -0
  280. data/public/dist/js/webshims/shims/jpicker/images/preview-opacity.png +0 -0
  281. data/public/dist/js/webshims/shims/jpicker/images/rangearrows.gif +0 -0
  282. data/public/dist/js/webshims/shims/jpicker/jpicker.css +1 -0
  283. data/public/dist/js/webshims/shims/matchMedia.js +3 -0
  284. data/public/dist/js/webshims/shims/mediacapture-picker.js +1 -0
  285. data/public/dist/js/webshims/shims/mediacapture.js +1 -0
  286. data/public/dist/js/webshims/shims/mediaelement-core.js +1 -0
  287. data/public/dist/js/webshims/shims/mediaelement-debug.js +1 -0
  288. data/public/dist/js/webshims/shims/mediaelement-jaris.js +1 -0
  289. data/public/dist/js/webshims/shims/mediaelement-native-fix.js +1 -0
  290. data/public/dist/js/webshims/shims/mediaelement-yt.js +1 -0
  291. data/public/dist/js/webshims/shims/moxie/flash/Moxie.cdn.swf +0 -0
  292. data/public/dist/js/webshims/shims/moxie/flash/Moxie.min.swf +0 -0
  293. data/public/dist/js/webshims/shims/moxie/js/moxie-html4.js +3 -0
  294. data/public/dist/js/webshims/shims/moxie/js/moxie-swf.js +2 -0
  295. data/public/dist/js/webshims/shims/picture.js +1 -0
  296. data/public/dist/js/webshims/shims/plugins/jquery.ui.position.js +11 -0
  297. data/public/dist/js/webshims/shims/range-ui.js +1 -0
  298. data/public/dist/js/webshims/shims/sizzle.js +11 -0
  299. data/public/dist/js/webshims/shims/sticky.js +1 -0
  300. data/public/dist/js/webshims/shims/styles/color-picker.png +0 -0
  301. data/public/dist/js/webshims/shims/styles/forms-ext.css +1 -0
  302. data/public/dist/js/webshims/shims/styles/forms-picker.css +1 -0
  303. data/public/dist/js/webshims/shims/styles/progress.gif +0 -0
  304. data/public/dist/js/webshims/shims/styles/progress.png +0 -0
  305. data/public/dist/js/webshims/shims/styles/shim-ext.css +1 -0
  306. data/public/dist/js/webshims/shims/styles/shim.css +1 -0
  307. data/public/dist/js/webshims/shims/styles/transparent.png +0 -0
  308. data/public/dist/js/webshims/shims/styles/widget.eot +0 -0
  309. data/public/dist/js/webshims/shims/styles/widget.svg +12 -0
  310. data/public/dist/js/webshims/shims/styles/widget.ttf +0 -0
  311. data/public/dist/js/webshims/shims/styles/widget.woff +0 -0
  312. data/public/dist/js/webshims/shims/swf/JarisFLVPlayer.swf +0 -0
  313. data/public/dist/js/webshims/shims/swfmini-embed.js +1 -0
  314. data/public/dist/js/webshims/shims/swfmini.js +6 -0
  315. data/public/dist/js/webshims/shims/track-ui.js +1 -0
  316. data/public/dist/js/webshims/shims/track.js +1 -0
  317. data/public/dist/js/webshims/shims/url.js +1 -0
  318. data/public/dist/js/webshims/shims/usermedia-core.js +1 -0
  319. data/public/dist/js/webshims/shims/usermedia-shim.js +1 -0
  320. data/public/js/bootstrap.min.js +3 -8
  321. data/public/js/jquery-ui.min.js +6 -0
  322. data/public/js/jquery.min.js +4 -0
  323. data/public/js/jquery.t.js +4 -4
  324. data/public/js/sequenceserver.blast.js +20 -18
  325. data/public/js/sequenceserver.js +116 -74
  326. data/sequenceserver.gemspec +20 -16
  327. data/views/400.erb +2 -1
  328. data/views/500.erb +6 -1
  329. data/views/result.erb +38 -18
  330. data/views/search.erb +49 -32
  331. metadata +389 -11
  332. data/public/img/glyphicons-halflings-white.png +0 -0
  333. data/public/img/glyphicons-halflings.png +0 -0
  334. data/public/js/jquery-ui.js +0 -14987
  335. data/public/js/jquery.js +0 -5
  336. data/public/js/jquery.scrollspy.js +0 -74
  337. data/public/sequence.min.js +0 -1
data/views/search.erb CHANGED
@@ -1,14 +1,17 @@
1
1
  <!DOCTYPE html>
2
2
  <html lang="en">
3
3
  <head>
4
+ <meta charset="utf-8">
5
+ <meta http-equiv="X-UA-Compatible" content="IE=edge">
6
+ <meta name="viewport" content="width=device-width, initial-scale=1">
7
+
4
8
  <title>SequenceServer: Custom BLAST Server</title>
5
- <meta name="author" content="Anurag Priyam" />
6
- <meta name="author" content="Ben J. Woodcroft" />
7
- <meta name="author" content="Vivek Rai" />
8
- <meta name="author" content="Yannick Wurm" />
9
- <meta name="author" content="Cedric Wurm" />
9
+ <meta name="author" content="Anurag Priyam">
10
+ <meta name="author" content="Ben J. Woodcroft">
11
+ <meta name="author" content="Vivek Rai">
12
+ <meta name="author" content="Cedric Wurm">
13
+ <meta name="author" content="Yannick Wurm">
10
14
  <meta name="description" content="Custom BLAST server provided by SequenceServer (http://www.sequenceserver.com)"/>
11
- <meta content="text/html; charset=UTF-8" http-equiv="Content-Type"/>
12
15
 
13
16
  <!--[if lt IE 9]>
14
17
  <script src="js/html5shiv.js"></script>
@@ -16,9 +19,13 @@
16
19
 
17
20
  <link href='http://fonts.googleapis.com/css?family=Roboto:400' rel='stylesheet' type='text/css'>
18
21
  <link href='http://fonts.googleapis.com/css?family=Open+Sans:400,700' rel='stylesheet' type='text/css'>
19
- <link rel="stylesheet" media="screen,print" type="text/css" href="css/bootstrap.min.css"/>
20
- <link rel="stylesheet" media="screen,print" type="text/css" href="css/font-awesome.min.css"/>
21
- <link rel="stylesheet" media="screen,print" type="text/css" href="css/custom.css"/>
22
+ <% if settings.production? %>
23
+ <link rel="stylesheet" media="screen,print" type="text/css" href="css/sequenceserver.min.css"/>
24
+ <% else %>
25
+ <link rel="stylesheet" media="screen,print" type="text/css" href="css/bootstrap.min.css"/>
26
+ <link rel="stylesheet" media="screen,print" type="text/css" href="css/font-awesome.min.css"/>
27
+ <link rel="stylesheet" media="screen,print" type="text/css" href="css/custom.css"/>
28
+ <% end %>
22
29
  </head>
23
30
 
24
31
  <body>
@@ -215,15 +222,18 @@
215
222
  Advanced Parameters:
216
223
  </label>
217
224
  <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>
225
+ class="col-md-9">
226
+ <div
227
+ class="input-group">
228
+ <input
229
+ type="text"
230
+ class="form-control" name="advanced" id="advanced"
231
+ title="View, and enter advanced parameters."
232
+ placeholder="eg: -evalue 1.0e-5 -num_alignments 100"/>
233
+ <div class="input-group-addon cursor-pointer" data-toggle="modal" data-toggle="modal" data-target="#help">
234
+ <i class="fa fa-question"></i>
235
+ </div>
236
+ </div>
227
237
  </div>
228
238
  </div>
229
239
  </div>
@@ -316,7 +326,12 @@
316
326
 
317
327
  <div
318
328
  class="modal-footer">
319
- <button class="btn btn-danger" data-dismiss="modal">Okay</button>
329
+ <button
330
+ type="button"
331
+ class="btn btn-danger"
332
+ data-dismiss="modal">
333
+ Okay
334
+ </button>
320
335
  </div>
321
336
  </div>
322
337
  </div>
@@ -340,6 +355,7 @@
340
355
  <div
341
356
  class="modal-footer">
342
357
  <button
358
+ type="button"
343
359
  class="btn btn-default btn-primary"
344
360
  data-dismiss="modal">
345
361
  Got it!
@@ -402,19 +418,20 @@
402
418
  </div> <!-- sequence viewing -->
403
419
 
404
420
  <!-- JS -->
405
- <script type="text/javascript" src="js/underscore.min.js"></script>
406
- <script type="text/javascript" src="js/jquery.js"></script>
407
- <script type="text/javascript" src="js/webshims/polyfiller.js"></script>
408
- <script type="text/javascript">
409
- $.webshims.polyfill('forms');
410
- </script>
411
- <script type="text/javascript" src="js/jquery-ui.js"></script>
412
- <script type="text/javascript" src="js/bootstrap.min.js"></script>
413
- <script type="text/javascript" src="js/d3.v3.min.js"></script>
414
- <script type="text/javascript" src="js/sequenceserver.js"></script>
415
- <script type="text/javascript" src="js/sequenceserver.blast.js"></script>
416
- <script type="text/javascript" src="js/jquery.t.js"></script>
417
- <script type="text/javascript" src="js/sequence.js"></script>
421
+ <% if settings.production? %>
422
+ <script src="js/sequenceserver.min.js"></script>
423
+ <% else %>
424
+ <script type="text/javascript" src="js/underscore.min.js"></script>
425
+ <script type="text/javascript" src="js/jquery.min.js"></script>
426
+ <script type="text/javascript" src="js/jquery-ui.min.js"></script>
427
+ <script type="text/javascript" src="js/bootstrap.min.js"></script>
428
+ <script type="text/javascript" src="js/webshims/polyfiller.js"></script>
429
+ <script type="text/javascript" src="js/d3.v3.min.js"></script>
430
+ <script type="text/javascript" src="js/sequenceserver.js"></script>
431
+ <script type="text/javascript" src="js/sequenceserver.blast.js"></script>
432
+ <script type="text/javascript" src="js/jquery.t.js"></script>
433
+ <script type="text/javascript" src="js/sequence.js"></script>
434
+ <% end %>
418
435
 
419
436
  <!-- twitter -->
420
437
  <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>
metadata CHANGED
@@ -1,7 +1,7 @@
1
1
  --- !ruby/object:Gem::Specification
2
2
  name: sequenceserver
3
3
  version: !ruby/object:Gem::Version
4
- version: 1.0.0.pre.2
4
+ version: 1.0.0.pre.3
5
5
  platform: ruby
6
6
  authors:
7
7
  - Anurag Priyam
@@ -11,13 +11,16 @@ authors:
11
11
  autorequire:
12
12
  bindir: bin
13
13
  cert_chain: []
14
- date: 2015-01-29 00:00:00.000000000 Z
14
+ date: 2015-02-16 00:00:00.000000000 Z
15
15
  dependencies:
16
16
  - !ruby/object:Gem::Dependency
17
17
  name: thin
18
18
  requirement: !ruby/object:Gem::Requirement
19
19
  requirements:
20
20
  - - "~>"
21
+ - !ruby/object:Gem::Version
22
+ version: '1.6'
23
+ - - ">="
21
24
  - !ruby/object:Gem::Version
22
25
  version: 1.6.2
23
26
  type: :runtime
@@ -25,6 +28,9 @@ dependencies:
25
28
  version_requirements: !ruby/object:Gem::Requirement
26
29
  requirements:
27
30
  - - "~>"
31
+ - !ruby/object:Gem::Version
32
+ version: '1.6'
33
+ - - ">="
28
34
  - !ruby/object:Gem::Version
29
35
  version: 1.6.2
30
36
  - !ruby/object:Gem::Dependency
@@ -32,6 +38,9 @@ dependencies:
32
38
  requirement: !ruby/object:Gem::Requirement
33
39
  requirements:
34
40
  - - "~>"
41
+ - !ruby/object:Gem::Version
42
+ version: '1.4'
43
+ - - ">="
35
44
  - !ruby/object:Gem::Version
36
45
  version: 1.4.5
37
46
  type: :runtime
@@ -39,6 +48,9 @@ dependencies:
39
48
  version_requirements: !ruby/object:Gem::Requirement
40
49
  requirements:
41
50
  - - "~>"
51
+ - !ruby/object:Gem::Version
52
+ version: '1.4'
53
+ - - ">="
42
54
  - !ruby/object:Gem::Version
43
55
  version: 1.4.5
44
56
  - !ruby/object:Gem::Dependency
@@ -46,6 +58,9 @@ dependencies:
46
58
  requirement: !ruby/object:Gem::Requirement
47
59
  requirements:
48
60
  - - "~>"
61
+ - !ruby/object:Gem::Version
62
+ version: '2.1'
63
+ - - ">="
49
64
  - !ruby/object:Gem::Version
50
65
  version: 2.1.1
51
66
  type: :runtime
@@ -53,6 +68,9 @@ dependencies:
53
68
  version_requirements: !ruby/object:Gem::Requirement
54
69
  requirements:
55
70
  - - "~>"
71
+ - !ruby/object:Gem::Version
72
+ version: '2.1'
73
+ - - ">="
56
74
  - !ruby/object:Gem::Version
57
75
  version: 2.1.1
58
76
  - !ruby/object:Gem::Dependency
@@ -60,6 +78,9 @@ dependencies:
60
78
  requirement: !ruby/object:Gem::Requirement
61
79
  requirements:
62
80
  - - "~>"
81
+ - !ruby/object:Gem::Version
82
+ version: '3.6'
83
+ - - ">="
63
84
  - !ruby/object:Gem::Version
64
85
  version: 3.6.0
65
86
  type: :runtime
@@ -67,6 +88,9 @@ dependencies:
67
88
  version_requirements: !ruby/object:Gem::Requirement
68
89
  requirements:
69
90
  - - "~>"
91
+ - !ruby/object:Gem::Version
92
+ version: '3.6'
93
+ - - ">="
70
94
  - !ruby/object:Gem::Version
71
95
  version: 3.6.0
72
96
  - !ruby/object:Gem::Dependency
@@ -74,6 +98,9 @@ dependencies:
74
98
  requirement: !ruby/object:Gem::Requirement
75
99
  requirements:
76
100
  - - "~>"
101
+ - !ruby/object:Gem::Version
102
+ version: '0.6'
103
+ - - ">="
77
104
  - !ruby/object:Gem::Version
78
105
  version: 0.6.2
79
106
  type: :development
@@ -81,6 +108,9 @@ dependencies:
81
108
  version_requirements: !ruby/object:Gem::Requirement
82
109
  requirements:
83
110
  - - "~>"
111
+ - !ruby/object:Gem::Version
112
+ version: '0.6'
113
+ - - ">="
84
114
  - !ruby/object:Gem::Version
85
115
  version: 0.6.2
86
116
  - !ruby/object:Gem::Dependency
@@ -88,6 +118,9 @@ dependencies:
88
118
  requirement: !ruby/object:Gem::Requirement
89
119
  requirements:
90
120
  - - "~>"
121
+ - !ruby/object:Gem::Version
122
+ version: '2.8'
123
+ - - ">="
91
124
  - !ruby/object:Gem::Version
92
125
  version: 2.8.0
93
126
  type: :development
@@ -95,6 +128,9 @@ dependencies:
95
128
  version_requirements: !ruby/object:Gem::Requirement
96
129
  requirements:
97
130
  - - "~>"
131
+ - !ruby/object:Gem::Version
132
+ version: '2.8'
133
+ - - ">="
98
134
  - !ruby/object:Gem::Version
99
135
  version: 2.8.0
100
136
  - !ruby/object:Gem::Dependency
@@ -102,6 +138,9 @@ dependencies:
102
138
  requirement: !ruby/object:Gem::Requirement
103
139
  requirements:
104
140
  - - "~>"
141
+ - !ruby/object:Gem::Version
142
+ version: '10.3'
143
+ - - ">="
105
144
  - !ruby/object:Gem::Version
106
145
  version: 10.3.2
107
146
  type: :development
@@ -109,6 +148,9 @@ dependencies:
109
148
  version_requirements: !ruby/object:Gem::Requirement
110
149
  requirements:
111
150
  - - "~>"
151
+ - !ruby/object:Gem::Version
152
+ version: '10.3'
153
+ - - ">="
112
154
  - !ruby/object:Gem::Version
113
155
  version: 10.3.2
114
156
  - !ruby/object:Gem::Dependency
@@ -117,19 +159,28 @@ dependencies:
117
159
  requirements:
118
160
  - - "~>"
119
161
  - !ruby/object:Gem::Version
120
- version: 0.26.1
162
+ version: '0.28'
163
+ - - ">="
164
+ - !ruby/object:Gem::Version
165
+ version: 0.28.0
121
166
  type: :development
122
167
  prerelease: false
123
168
  version_requirements: !ruby/object:Gem::Requirement
124
169
  requirements:
125
170
  - - "~>"
126
171
  - !ruby/object:Gem::Version
127
- version: 0.26.1
172
+ version: '0.28'
173
+ - - ">="
174
+ - !ruby/object:Gem::Version
175
+ version: 0.28.0
128
176
  - !ruby/object:Gem::Dependency
129
177
  name: capybara
130
178
  requirement: !ruby/object:Gem::Requirement
131
179
  requirements:
132
180
  - - "~>"
181
+ - !ruby/object:Gem::Version
182
+ version: '2.4'
183
+ - - ">="
133
184
  - !ruby/object:Gem::Version
134
185
  version: 2.4.4
135
186
  type: :development
@@ -137,6 +188,9 @@ dependencies:
137
188
  version_requirements: !ruby/object:Gem::Requirement
138
189
  requirements:
139
190
  - - "~>"
191
+ - !ruby/object:Gem::Version
192
+ version: '2.4'
193
+ - - ">="
140
194
  - !ruby/object:Gem::Version
141
195
  version: 2.4.4
142
196
  - !ruby/object:Gem::Dependency
@@ -144,6 +198,9 @@ dependencies:
144
198
  requirement: !ruby/object:Gem::Requirement
145
199
  requirements:
146
200
  - - "~>"
201
+ - !ruby/object:Gem::Version
202
+ version: '1.3'
203
+ - - ">="
147
204
  - !ruby/object:Gem::Version
148
205
  version: 1.3.0
149
206
  type: :development
@@ -151,10 +208,28 @@ dependencies:
151
208
  version_requirements: !ruby/object:Gem::Requirement
152
209
  requirements:
153
210
  - - "~>"
211
+ - !ruby/object:Gem::Version
212
+ version: '1.3'
213
+ - - ">="
154
214
  - !ruby/object:Gem::Version
155
215
  version: 1.3.0
216
+ - !ruby/object:Gem::Dependency
217
+ name: codeclimate-test-reporter
218
+ requirement: !ruby/object:Gem::Requirement
219
+ requirements:
220
+ - - ">="
221
+ - !ruby/object:Gem::Version
222
+ version: '0'
223
+ type: :development
224
+ prerelease: false
225
+ version_requirements: !ruby/object:Gem::Requirement
226
+ requirements:
227
+ - - ">="
228
+ - !ruby/object:Gem::Version
229
+ version: '0'
156
230
  description: |
157
- SequenceServer lets you rapidly set up a BLAST+ server with an intuitive user interface for use locally or over the web.
231
+ SequenceServer lets you rapidly set up a BLAST+ server with an intuitive user
232
+ interface for use locally or over the web.
158
233
  email:
159
234
  - anurag08priyam@gmail.com
160
235
  - b.woodcroft@uq.edu.au
@@ -171,27 +246,331 @@ files:
171
246
  - config.ru
172
247
  - lib/sequenceserver.rb
173
248
  - lib/sequenceserver/blast.rb
249
+ - lib/sequenceserver/blast/exceptions.rb
250
+ - lib/sequenceserver/blast/hit.rb
251
+ - lib/sequenceserver/blast/hsp.rb
252
+ - lib/sequenceserver/blast/query.rb
253
+ - lib/sequenceserver/blast/report.rb
254
+ - lib/sequenceserver/config.rb
174
255
  - lib/sequenceserver/database.rb
256
+ - lib/sequenceserver/exceptions.rb
175
257
  - lib/sequenceserver/links.rb
176
258
  - lib/sequenceserver/logger.rb
177
259
  - lib/sequenceserver/sequence.rb
178
260
  - public/css/bootstrap.min.css
179
261
  - public/css/custom.css
180
262
  - public/css/font-awesome.min.css
263
+ - public/dist/css/sequenceserver.min.css
264
+ - public/dist/css/sequenceserver.min.css.gz
265
+ - public/dist/fonts/FontAwesome.otf
266
+ - public/dist/fonts/fontawesome-webfont.eot
267
+ - public/dist/fonts/fontawesome-webfont.svg
268
+ - public/dist/fonts/fontawesome-webfont.ttf
269
+ - public/dist/fonts/fontawesome-webfont.woff
270
+ - public/dist/fonts/fontawesome-webfont.woff2
271
+ - public/dist/js/sequenceserver.min.js
272
+ - public/dist/js/sequenceserver.min.js.gz
273
+ - public/dist/js/shims/FlashCanvas/canvas2png.js
274
+ - public/dist/js/shims/FlashCanvas/flashcanvas.js
275
+ - public/dist/js/shims/FlashCanvas/flashcanvas.swf
276
+ - public/dist/js/shims/FlashCanvasPro/canvas2png.js
277
+ - public/dist/js/shims/FlashCanvasPro/flash10canvas.swf
278
+ - public/dist/js/shims/FlashCanvasPro/flash9canvas.swf
279
+ - public/dist/js/shims/FlashCanvasPro/flashcanvas.js
280
+ - public/dist/js/shims/canvas-blob.js
281
+ - public/dist/js/shims/color-picker.js
282
+ - public/dist/js/shims/combos/1.js
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