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

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