bio 1.0.0 → 1.1.0

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Files changed (340) hide show
  1. data/bin/bioruby +14 -122
  2. data/bin/br_biofetch.rb +2 -2
  3. data/bin/br_bioflat.rb +2 -2
  4. data/bin/br_biogetseq.rb +2 -2
  5. data/bin/br_pmfetch.rb +3 -3
  6. data/doc/Changes-0.7.rd +77 -0
  7. data/doc/KEGG_API.rd +523 -232
  8. data/doc/KEGG_API.rd.ja +529 -207
  9. data/doc/Tutorial.rd +48 -11
  10. data/lib/bio.rb +59 -6
  11. data/lib/bio/alignment.rb +713 -103
  12. data/lib/bio/appl/bl2seq/report.rb +2 -18
  13. data/lib/bio/appl/blast.rb +108 -91
  14. data/lib/bio/appl/blast/format0.rb +33 -18
  15. data/lib/bio/appl/blast/format8.rb +6 -20
  16. data/lib/bio/appl/blast/report.rb +293 -429
  17. data/lib/bio/appl/blast/rexml.rb +8 -22
  18. data/lib/bio/appl/blast/wublast.rb +21 -12
  19. data/lib/bio/appl/blast/xmlparser.rb +180 -183
  20. data/lib/bio/appl/blat/report.rb +127 -30
  21. data/lib/bio/appl/clustalw.rb +87 -59
  22. data/lib/bio/appl/clustalw/report.rb +20 -22
  23. data/lib/bio/appl/emboss.rb +113 -20
  24. data/lib/bio/appl/fasta.rb +173 -198
  25. data/lib/bio/appl/fasta/format10.rb +244 -347
  26. data/lib/bio/appl/gcg/msf.rb +212 -0
  27. data/lib/bio/appl/gcg/seq.rb +195 -0
  28. data/lib/bio/appl/genscan/report.rb +5 -23
  29. data/lib/bio/appl/hmmer.rb +8 -45
  30. data/lib/bio/appl/hmmer/report.rb +2 -20
  31. data/lib/bio/appl/iprscan/report.rb +374 -0
  32. data/lib/bio/appl/mafft.rb +87 -50
  33. data/lib/bio/appl/mafft/report.rb +151 -44
  34. data/lib/bio/appl/muscle.rb +52 -0
  35. data/lib/bio/appl/phylip/alignment.rb +129 -0
  36. data/lib/bio/appl/phylip/distance_matrix.rb +96 -0
  37. data/lib/bio/appl/probcons.rb +41 -0
  38. data/lib/bio/appl/psort.rb +89 -96
  39. data/lib/bio/appl/psort/report.rb +6 -22
  40. data/lib/bio/appl/pts1.rb +263 -0
  41. data/lib/bio/appl/sim4.rb +26 -36
  42. data/lib/bio/appl/sim4/report.rb +2 -18
  43. data/lib/bio/appl/sosui/report.rb +5 -20
  44. data/lib/bio/appl/spidey/report.rb +2 -2
  45. data/lib/bio/appl/targetp/report.rb +4 -20
  46. data/lib/bio/appl/tcoffee.rb +55 -0
  47. data/lib/bio/appl/tmhmm/report.rb +4 -20
  48. data/lib/bio/command.rb +235 -64
  49. data/lib/bio/data/aa.rb +21 -26
  50. data/lib/bio/data/codontable.rb +2 -20
  51. data/lib/bio/data/na.rb +19 -4
  52. data/lib/bio/db.rb +27 -12
  53. data/lib/bio/db/aaindex.rb +2 -20
  54. data/lib/bio/db/embl/common.rb +4 -21
  55. data/lib/bio/db/embl/embl.rb +33 -85
  56. data/lib/bio/db/embl/sptr.rb +612 -302
  57. data/lib/bio/db/embl/swissprot.rb +10 -29
  58. data/lib/bio/db/embl/trembl.rb +10 -29
  59. data/lib/bio/db/embl/uniprot.rb +10 -29
  60. data/lib/bio/db/fantom.rb +15 -20
  61. data/lib/bio/db/fasta.rb +3 -3
  62. data/lib/bio/db/genbank/common.rb +37 -46
  63. data/lib/bio/db/genbank/ddbj.rb +6 -18
  64. data/lib/bio/db/genbank/genbank.rb +47 -186
  65. data/lib/bio/db/genbank/genpept.rb +4 -17
  66. data/lib/bio/db/genbank/refseq.rb +4 -17
  67. data/lib/bio/db/gff.rb +103 -35
  68. data/lib/bio/db/go.rb +4 -20
  69. data/lib/bio/db/kegg/brite.rb +26 -36
  70. data/lib/bio/db/kegg/compound.rb +81 -85
  71. data/lib/bio/db/kegg/drug.rb +98 -0
  72. data/lib/bio/db/kegg/enzyme.rb +133 -110
  73. data/lib/bio/db/kegg/expression.rb +2 -20
  74. data/lib/bio/db/kegg/genes.rb +208 -238
  75. data/lib/bio/db/kegg/genome.rb +164 -285
  76. data/lib/bio/db/kegg/glycan.rb +114 -157
  77. data/lib/bio/db/kegg/keggtab.rb +242 -303
  78. data/lib/bio/db/kegg/kgml.rb +117 -160
  79. data/lib/bio/db/kegg/orthology.rb +112 -0
  80. data/lib/bio/db/kegg/reaction.rb +54 -69
  81. data/lib/bio/db/kegg/taxonomy.rb +331 -0
  82. data/lib/bio/db/lasergene.rb +209 -0
  83. data/lib/bio/db/litdb.rb +3 -27
  84. data/lib/bio/db/medline.rb +228 -249
  85. data/lib/bio/db/nbrf.rb +3 -3
  86. data/lib/bio/db/newick.rb +510 -0
  87. data/lib/bio/db/nexus.rb +1854 -0
  88. data/lib/bio/db/pdb.rb +5 -17
  89. data/lib/bio/db/pdb/atom.rb +2 -18
  90. data/lib/bio/db/pdb/chain.rb +2 -18
  91. data/lib/bio/db/pdb/chemicalcomponent.rb +2 -18
  92. data/lib/bio/db/pdb/model.rb +2 -18
  93. data/lib/bio/db/pdb/pdb.rb +73 -34
  94. data/lib/bio/db/pdb/residue.rb +4 -20
  95. data/lib/bio/db/pdb/utils.rb +2 -18
  96. data/lib/bio/db/prosite.rb +403 -422
  97. data/lib/bio/db/rebase.rb +84 -40
  98. data/lib/bio/db/soft.rb +404 -0
  99. data/lib/bio/db/transfac.rb +5 -17
  100. data/lib/bio/feature.rb +106 -52
  101. data/lib/bio/io/das.rb +32 -42
  102. data/lib/bio/io/dbget.rb +2 -20
  103. data/lib/bio/io/ddbjxml.rb +77 -138
  104. data/lib/bio/io/ebisoap.rb +158 -0
  105. data/lib/bio/io/ensembl.rb +229 -0
  106. data/lib/bio/io/fastacmd.rb +89 -82
  107. data/lib/bio/io/fetch.rb +163 -96
  108. data/lib/bio/io/flatfile.rb +170 -73
  109. data/lib/bio/io/flatfile/bdb.rb +3 -16
  110. data/lib/bio/io/flatfile/index.rb +2 -2
  111. data/lib/bio/io/flatfile/indexer.rb +3 -2
  112. data/lib/bio/io/higet.rb +12 -31
  113. data/lib/bio/io/keggapi.rb +210 -269
  114. data/lib/bio/io/ncbisoap.rb +155 -0
  115. data/lib/bio/io/pubmed.rb +169 -147
  116. data/lib/bio/io/registry.rb +4 -20
  117. data/lib/bio/io/soapwsdl.rb +43 -38
  118. data/lib/bio/io/sql.rb +242 -305
  119. data/lib/bio/location.rb +407 -285
  120. data/lib/bio/map.rb +410 -0
  121. data/lib/bio/pathway.rb +558 -695
  122. data/lib/bio/reference.rb +272 -75
  123. data/lib/bio/sequence.rb +255 -13
  124. data/lib/bio/sequence/aa.rb +71 -10
  125. data/lib/bio/sequence/common.rb +187 -33
  126. data/lib/bio/sequence/compat.rb +59 -4
  127. data/lib/bio/sequence/format.rb +54 -7
  128. data/lib/bio/sequence/generic.rb +3 -3
  129. data/lib/bio/sequence/na.rb +328 -26
  130. data/lib/bio/shell.rb +11 -4
  131. data/lib/bio/shell/core.rb +221 -160
  132. data/lib/bio/shell/demo.rb +18 -15
  133. data/lib/bio/shell/interface.rb +14 -12
  134. data/lib/bio/shell/irb.rb +95 -0
  135. data/lib/bio/shell/object.rb +45 -26
  136. data/lib/bio/shell/plugin/blast.rb +42 -0
  137. data/lib/bio/shell/plugin/codon.rb +22 -14
  138. data/lib/bio/shell/plugin/das.rb +58 -0
  139. data/lib/bio/shell/plugin/emboss.rb +2 -2
  140. data/lib/bio/shell/plugin/entry.rb +22 -11
  141. data/lib/bio/shell/plugin/flatfile.rb +2 -2
  142. data/lib/bio/shell/plugin/keggapi.rb +13 -6
  143. data/lib/bio/shell/plugin/midi.rb +4 -4
  144. data/lib/bio/shell/plugin/obda.rb +2 -2
  145. data/lib/bio/shell/plugin/psort.rb +56 -0
  146. data/lib/bio/shell/plugin/seq.rb +35 -8
  147. data/lib/bio/shell/plugin/soap.rb +87 -0
  148. data/lib/bio/shell/rails/vendor/plugins/generators/bioruby/bioruby_generator.rb +29 -0
  149. data/lib/bio/shell/rails/vendor/plugins/generators/bioruby/templates/_classes.rhtml +4 -0
  150. data/lib/bio/shell/rails/vendor/plugins/generators/bioruby/templates/_log.rhtml +27 -0
  151. data/lib/bio/shell/rails/vendor/plugins/generators/bioruby/templates/_methods.rhtml +11 -0
  152. data/lib/bio/shell/rails/vendor/plugins/generators/bioruby/templates/_modules.rhtml +4 -0
  153. data/lib/bio/shell/rails/vendor/plugins/generators/bioruby/templates/_variables.rhtml +7 -0
  154. data/lib/bio/shell/rails/vendor/plugins/generators/bioruby/templates/bioruby-bg.gif +0 -0
  155. data/lib/bio/shell/rails/vendor/plugins/generators/bioruby/templates/bioruby-console.png +0 -0
  156. data/lib/bio/shell/rails/{public/images/icon.png → vendor/plugins/generators/bioruby/templates/bioruby-gem.png} +0 -0
  157. data/lib/bio/shell/rails/vendor/plugins/generators/bioruby/templates/bioruby-link.gif +0 -0
  158. data/lib/bio/shell/rails/vendor/plugins/generators/bioruby/templates/bioruby.css +369 -0
  159. data/lib/bio/shell/rails/vendor/plugins/generators/bioruby/templates/bioruby.rhtml +47 -0
  160. data/lib/bio/shell/rails/vendor/plugins/generators/bioruby/templates/bioruby_controller.rb +144 -0
  161. data/lib/bio/shell/rails/vendor/plugins/generators/bioruby/templates/bioruby_helper.rb +47 -0
  162. data/lib/bio/shell/rails/vendor/plugins/generators/bioruby/templates/commands.rhtml +8 -0
  163. data/lib/bio/shell/rails/vendor/plugins/generators/bioruby/templates/history.rhtml +10 -0
  164. data/lib/bio/shell/rails/vendor/plugins/generators/bioruby/templates/index.rhtml +22 -0
  165. data/lib/bio/shell/script.rb +25 -0
  166. data/lib/bio/shell/setup.rb +109 -0
  167. data/lib/bio/shell/web.rb +70 -58
  168. data/lib/bio/tree.rb +850 -0
  169. data/lib/bio/util/color_scheme.rb +84 -107
  170. data/lib/bio/util/color_scheme/buried.rb +5 -24
  171. data/lib/bio/util/color_scheme/helix.rb +5 -24
  172. data/lib/bio/util/color_scheme/hydropathy.rb +5 -24
  173. data/lib/bio/util/color_scheme/nucleotide.rb +5 -24
  174. data/lib/bio/util/color_scheme/strand.rb +5 -24
  175. data/lib/bio/util/color_scheme/taylor.rb +5 -24
  176. data/lib/bio/util/color_scheme/turn.rb +5 -24
  177. data/lib/bio/util/color_scheme/zappo.rb +5 -24
  178. data/lib/bio/util/contingency_table.rb +70 -43
  179. data/lib/bio/util/restriction_enzyme.rb +228 -0
  180. data/lib/bio/util/restriction_enzyme/analysis.rb +249 -0
  181. data/lib/bio/util/restriction_enzyme/analysis_basic.rb +217 -0
  182. data/lib/bio/util/restriction_enzyme/cut_symbol.rb +107 -0
  183. data/lib/bio/util/restriction_enzyme/double_stranded.rb +321 -0
  184. data/lib/bio/util/restriction_enzyme/double_stranded/aligned_strands.rb +130 -0
  185. data/lib/bio/util/restriction_enzyme/double_stranded/cut_location_pair.rb +103 -0
  186. data/lib/bio/util/restriction_enzyme/double_stranded/cut_location_pair_in_enzyme_notation.rb +38 -0
  187. data/lib/bio/util/restriction_enzyme/double_stranded/cut_locations.rb +76 -0
  188. data/lib/bio/util/restriction_enzyme/double_stranded/cut_locations_in_enzyme_notation.rb +107 -0
  189. data/lib/bio/util/restriction_enzyme/enzymes.yaml +7061 -0
  190. data/lib/bio/util/restriction_enzyme/range/cut_range.rb +24 -0
  191. data/lib/bio/util/restriction_enzyme/range/cut_ranges.rb +47 -0
  192. data/lib/bio/util/restriction_enzyme/range/horizontal_cut_range.rb +67 -0
  193. data/lib/bio/util/restriction_enzyme/range/sequence_range.rb +257 -0
  194. data/lib/bio/util/restriction_enzyme/range/sequence_range/calculated_cuts.rb +242 -0
  195. data/lib/bio/util/restriction_enzyme/range/sequence_range/fragment.rb +51 -0
  196. data/lib/bio/util/restriction_enzyme/range/sequence_range/fragments.rb +41 -0
  197. data/lib/bio/util/restriction_enzyme/range/vertical_cut_range.rb +77 -0
  198. data/lib/bio/util/restriction_enzyme/single_strand.rb +199 -0
  199. data/lib/bio/util/restriction_enzyme/single_strand/cut_locations_in_enzyme_notation.rb +135 -0
  200. data/lib/bio/util/restriction_enzyme/single_strand_complement.rb +23 -0
  201. data/lib/bio/util/restriction_enzyme/string_formatting.rb +111 -0
  202. data/lib/bio/util/sirna.rb +4 -22
  203. data/sample/color_scheme_na.rb +4 -12
  204. data/sample/enzymes.rb +78 -0
  205. data/sample/goslim.rb +5 -13
  206. data/sample/psortplot_html.rb +4 -12
  207. data/test/data/blast/2.2.15.blastp.m7 +876 -0
  208. data/test/data/embl/AB090716.embl.rel89 +63 -0
  209. data/test/data/fasta/example1.txt +75 -0
  210. data/test/data/fasta/example2.txt +21 -0
  211. data/test/data/iprscan/merged.raw +32 -0
  212. data/test/data/iprscan/merged.txt +74 -0
  213. data/test/data/soft/GDS100_partial.soft +92 -0
  214. data/test/data/soft/GSE3457_family_partial.soft +874 -0
  215. data/test/functional/bio/io/test_ensembl.rb +103 -0
  216. data/test/functional/bio/io/test_soapwsdl.rb +5 -17
  217. data/test/unit/bio/appl/bl2seq/test_report.rb +2 -2
  218. data/test/unit/bio/appl/blast/test_report.rb +3 -16
  219. data/test/unit/bio/appl/blast/test_xmlparser.rb +4 -16
  220. data/test/unit/bio/appl/genscan/test_report.rb +3 -16
  221. data/test/unit/bio/appl/hmmer/test_report.rb +3 -16
  222. data/test/unit/bio/appl/iprscan/test_report.rb +338 -0
  223. data/test/unit/bio/appl/mafft/test_report.rb +63 -0
  224. data/test/unit/bio/appl/sosui/test_report.rb +3 -16
  225. data/test/unit/bio/appl/targetp/test_report.rb +3 -16
  226. data/test/unit/bio/appl/test_blast.rb +3 -16
  227. data/test/unit/bio/appl/test_fasta.rb +4 -16
  228. data/test/unit/bio/appl/test_pts1.rb +140 -0
  229. data/test/unit/bio/appl/tmhmm/test_report.rb +3 -16
  230. data/test/unit/bio/data/test_aa.rb +4 -17
  231. data/test/unit/bio/data/test_codontable.rb +3 -16
  232. data/test/unit/bio/data/test_na.rb +3 -3
  233. data/test/unit/bio/db/embl/test_common.rb +3 -16
  234. data/test/unit/bio/db/embl/test_embl.rb +3 -16
  235. data/test/unit/bio/db/embl/test_embl_rel89.rb +219 -0
  236. data/test/unit/bio/db/embl/test_sptr.rb +1548 -41
  237. data/test/unit/bio/db/embl/test_uniprot.rb +3 -16
  238. data/test/unit/bio/db/kegg/test_genes.rb +3 -16
  239. data/test/unit/bio/db/pdb/test_pdb.rb +7 -24
  240. data/test/unit/bio/db/test_aaindex.rb +2 -2
  241. data/test/unit/bio/db/test_fasta.rb +3 -16
  242. data/test/unit/bio/db/test_gff.rb +3 -16
  243. data/test/unit/bio/db/test_lasergene.rb +95 -0
  244. data/test/unit/bio/db/test_newick.rb +56 -0
  245. data/test/unit/bio/db/test_nexus.rb +360 -0
  246. data/test/unit/bio/db/test_prosite.rb +5 -18
  247. data/test/unit/bio/db/test_rebase.rb +11 -25
  248. data/test/unit/bio/db/test_soft.rb +138 -0
  249. data/test/unit/bio/io/test_ddbjxml.rb +5 -17
  250. data/test/unit/bio/io/test_ensembl.rb +109 -0
  251. data/test/unit/bio/io/test_fastacmd.rb +3 -16
  252. data/test/unit/bio/io/test_flatfile.rb +237 -0
  253. data/test/unit/bio/io/test_soapwsdl.rb +4 -17
  254. data/test/unit/bio/sequence/test_aa.rb +3 -3
  255. data/test/unit/bio/sequence/test_common.rb +3 -16
  256. data/test/unit/bio/sequence/test_compat.rb +3 -16
  257. data/test/unit/bio/sequence/test_na.rb +29 -3
  258. data/test/unit/bio/shell/plugin/test_seq.rb +8 -8
  259. data/test/unit/bio/test_alignment.rb +16 -27
  260. data/test/unit/bio/test_command.rb +242 -25
  261. data/test/unit/bio/test_db.rb +3 -16
  262. data/test/unit/bio/test_feature.rb +4 -16
  263. data/test/unit/bio/test_location.rb +4 -16
  264. data/test/unit/bio/test_map.rb +230 -0
  265. data/test/unit/bio/test_pathway.rb +4 -16
  266. data/test/unit/bio/test_reference.rb +2 -2
  267. data/test/unit/bio/test_sequence.rb +7 -19
  268. data/test/unit/bio/test_shell.rb +3 -16
  269. data/test/unit/bio/test_tree.rb +593 -0
  270. data/test/unit/bio/util/restriction_enzyme/analysis/test_calculated_cuts.rb +299 -0
  271. data/test/unit/bio/util/restriction_enzyme/analysis/test_cut_ranges.rb +103 -0
  272. data/test/unit/bio/util/restriction_enzyme/analysis/test_sequence_range.rb +240 -0
  273. data/test/unit/bio/util/restriction_enzyme/double_stranded/test_aligned_strands.rb +100 -0
  274. data/test/unit/bio/util/restriction_enzyme/double_stranded/test_cut_location_pair.rb +75 -0
  275. data/test/unit/bio/util/restriction_enzyme/double_stranded/test_cut_location_pair_in_enzyme_notation.rb +73 -0
  276. data/test/unit/bio/util/restriction_enzyme/double_stranded/test_cut_locations.rb +53 -0
  277. data/test/unit/bio/util/restriction_enzyme/double_stranded/test_cut_locations_in_enzyme_notation.rb +104 -0
  278. data/test/unit/bio/util/restriction_enzyme/single_strand/test_cut_locations_in_enzyme_notation.rb +83 -0
  279. data/test/unit/bio/util/restriction_enzyme/test_analysis.rb +246 -0
  280. data/test/unit/bio/util/restriction_enzyme/test_cut_symbol.rb +44 -0
  281. data/test/unit/bio/util/restriction_enzyme/test_double_stranded.rb +115 -0
  282. data/test/unit/bio/util/restriction_enzyme/test_single_strand.rb +147 -0
  283. data/test/unit/bio/util/restriction_enzyme/test_single_strand_complement.rb +147 -0
  284. data/test/unit/bio/util/restriction_enzyme/test_string_formatting.rb +60 -0
  285. data/test/unit/bio/util/test_color_scheme.rb +6 -18
  286. data/test/unit/bio/util/test_contingency_table.rb +6 -18
  287. data/test/unit/bio/util/test_restriction_enzyme.rb +42 -0
  288. data/test/unit/bio/util/test_sirna.rb +3 -16
  289. metadata +228 -169
  290. data/doc/BioRuby.rd.ja +0 -225
  291. data/doc/Design.rd.ja +0 -341
  292. data/doc/TODO.rd.ja +0 -138
  293. data/lib/bio/appl/fasta/format6.rb +0 -37
  294. data/lib/bio/db/kegg/cell.rb +0 -88
  295. data/lib/bio/db/kegg/ko.rb +0 -178
  296. data/lib/bio/shell/rails/Rakefile +0 -10
  297. data/lib/bio/shell/rails/app/controllers/application.rb +0 -4
  298. data/lib/bio/shell/rails/app/controllers/shell_controller.rb +0 -94
  299. data/lib/bio/shell/rails/app/helpers/application_helper.rb +0 -3
  300. data/lib/bio/shell/rails/app/models/shell_connection.rb +0 -30
  301. data/lib/bio/shell/rails/app/views/layouts/shell.rhtml +0 -37
  302. data/lib/bio/shell/rails/app/views/shell/history.rhtml +0 -5
  303. data/lib/bio/shell/rails/app/views/shell/index.rhtml +0 -2
  304. data/lib/bio/shell/rails/app/views/shell/show.rhtml +0 -13
  305. data/lib/bio/shell/rails/config/boot.rb +0 -19
  306. data/lib/bio/shell/rails/config/database.yml +0 -85
  307. data/lib/bio/shell/rails/config/environment.rb +0 -53
  308. data/lib/bio/shell/rails/config/environments/development.rb +0 -19
  309. data/lib/bio/shell/rails/config/environments/production.rb +0 -19
  310. data/lib/bio/shell/rails/config/environments/test.rb +0 -19
  311. data/lib/bio/shell/rails/config/routes.rb +0 -19
  312. data/lib/bio/shell/rails/doc/README_FOR_APP +0 -2
  313. data/lib/bio/shell/rails/public/404.html +0 -8
  314. data/lib/bio/shell/rails/public/500.html +0 -8
  315. data/lib/bio/shell/rails/public/dispatch.cgi +0 -10
  316. data/lib/bio/shell/rails/public/dispatch.fcgi +0 -24
  317. data/lib/bio/shell/rails/public/dispatch.rb +0 -10
  318. data/lib/bio/shell/rails/public/favicon.ico +0 -0
  319. data/lib/bio/shell/rails/public/images/rails.png +0 -0
  320. data/lib/bio/shell/rails/public/index.html +0 -277
  321. data/lib/bio/shell/rails/public/javascripts/controls.js +0 -750
  322. data/lib/bio/shell/rails/public/javascripts/dragdrop.js +0 -584
  323. data/lib/bio/shell/rails/public/javascripts/effects.js +0 -854
  324. data/lib/bio/shell/rails/public/javascripts/prototype.js +0 -1785
  325. data/lib/bio/shell/rails/public/robots.txt +0 -1
  326. data/lib/bio/shell/rails/public/stylesheets/main.css +0 -187
  327. data/lib/bio/shell/rails/script/about +0 -3
  328. data/lib/bio/shell/rails/script/breakpointer +0 -3
  329. data/lib/bio/shell/rails/script/console +0 -3
  330. data/lib/bio/shell/rails/script/destroy +0 -3
  331. data/lib/bio/shell/rails/script/generate +0 -3
  332. data/lib/bio/shell/rails/script/performance/benchmarker +0 -3
  333. data/lib/bio/shell/rails/script/performance/profiler +0 -3
  334. data/lib/bio/shell/rails/script/plugin +0 -3
  335. data/lib/bio/shell/rails/script/process/reaper +0 -3
  336. data/lib/bio/shell/rails/script/process/spawner +0 -3
  337. data/lib/bio/shell/rails/script/process/spinner +0 -3
  338. data/lib/bio/shell/rails/script/runner +0 -3
  339. data/lib/bio/shell/rails/script/server +0 -42
  340. data/lib/bio/shell/rails/test/test_helper.rb +0 -28
@@ -1,584 +0,0 @@
1
- // Copyright (c) 2005 Thomas Fuchs (http://script.aculo.us, http://mir.aculo.us)
2
- //
3
- // See scriptaculous.js for full license.
4
-
5
- /*--------------------------------------------------------------------------*/
6
-
7
- var Droppables = {
8
- drops: [],
9
-
10
- remove: function(element) {
11
- this.drops = this.drops.reject(function(d) { return d.element==$(element) });
12
- },
13
-
14
- add: function(element) {
15
- element = $(element);
16
- var options = Object.extend({
17
- greedy: true,
18
- hoverclass: null
19
- }, arguments[1] || {});
20
-
21
- // cache containers
22
- if(options.containment) {
23
- options._containers = [];
24
- var containment = options.containment;
25
- if((typeof containment == 'object') &&
26
- (containment.constructor == Array)) {
27
- containment.each( function(c) { options._containers.push($(c)) });
28
- } else {
29
- options._containers.push($(containment));
30
- }
31
- }
32
-
33
- if(options.accept) options.accept = [options.accept].flatten();
34
-
35
- Element.makePositioned(element); // fix IE
36
- options.element = element;
37
-
38
- this.drops.push(options);
39
- },
40
-
41
- isContained: function(element, drop) {
42
- var parentNode = element.parentNode;
43
- return drop._containers.detect(function(c) { return parentNode == c });
44
- },
45
-
46
- isAffected: function(point, element, drop) {
47
- return (
48
- (drop.element!=element) &&
49
- ((!drop._containers) ||
50
- this.isContained(element, drop)) &&
51
- ((!drop.accept) ||
52
- (Element.classNames(element).detect(
53
- function(v) { return drop.accept.include(v) } ) )) &&
54
- Position.within(drop.element, point[0], point[1]) );
55
- },
56
-
57
- deactivate: function(drop) {
58
- if(drop.hoverclass)
59
- Element.removeClassName(drop.element, drop.hoverclass);
60
- this.last_active = null;
61
- },
62
-
63
- activate: function(drop) {
64
- if(drop.hoverclass)
65
- Element.addClassName(drop.element, drop.hoverclass);
66
- this.last_active = drop;
67
- },
68
-
69
- show: function(point, element) {
70
- if(!this.drops.length) return;
71
-
72
- if(this.last_active) this.deactivate(this.last_active);
73
- this.drops.each( function(drop) {
74
- if(Droppables.isAffected(point, element, drop)) {
75
- if(drop.onHover)
76
- drop.onHover(element, drop.element, Position.overlap(drop.overlap, drop.element));
77
- if(drop.greedy) {
78
- Droppables.activate(drop);
79
- throw $break;
80
- }
81
- }
82
- });
83
- },
84
-
85
- fire: function(event, element) {
86
- if(!this.last_active) return;
87
- Position.prepare();
88
-
89
- if (this.isAffected([Event.pointerX(event), Event.pointerY(event)], element, this.last_active))
90
- if (this.last_active.onDrop)
91
- this.last_active.onDrop(element, this.last_active.element, event);
92
- },
93
-
94
- reset: function() {
95
- if(this.last_active)
96
- this.deactivate(this.last_active);
97
- }
98
- }
99
-
100
- var Draggables = {
101
- drags: [],
102
- observers: [],
103
-
104
- register: function(draggable) {
105
- if(this.drags.length == 0) {
106
- this.eventMouseUp = this.endDrag.bindAsEventListener(this);
107
- this.eventMouseMove = this.updateDrag.bindAsEventListener(this);
108
- this.eventKeypress = this.keyPress.bindAsEventListener(this);
109
-
110
- Event.observe(document, "mouseup", this.eventMouseUp);
111
- Event.observe(document, "mousemove", this.eventMouseMove);
112
- Event.observe(document, "keypress", this.eventKeypress);
113
- }
114
- this.drags.push(draggable);
115
- },
116
-
117
- unregister: function(draggable) {
118
- this.drags = this.drags.reject(function(d) { return d==draggable });
119
- if(this.drags.length == 0) {
120
- Event.stopObserving(document, "mouseup", this.eventMouseUp);
121
- Event.stopObserving(document, "mousemove", this.eventMouseMove);
122
- Event.stopObserving(document, "keypress", this.eventKeypress);
123
- }
124
- },
125
-
126
- activate: function(draggable) {
127
- window.focus(); // allows keypress events if window isn't currently focused, fails for Safari
128
- this.activeDraggable = draggable;
129
- },
130
-
131
- deactivate: function(draggbale) {
132
- this.activeDraggable = null;
133
- },
134
-
135
- updateDrag: function(event) {
136
- if(!this.activeDraggable) return;
137
- var pointer = [Event.pointerX(event), Event.pointerY(event)];
138
- // Mozilla-based browsers fire successive mousemove events with
139
- // the same coordinates, prevent needless redrawing (moz bug?)
140
- if(this._lastPointer && (this._lastPointer.inspect() == pointer.inspect())) return;
141
- this._lastPointer = pointer;
142
- this.activeDraggable.updateDrag(event, pointer);
143
- },
144
-
145
- endDrag: function(event) {
146
- if(!this.activeDraggable) return;
147
- this._lastPointer = null;
148
- this.activeDraggable.endDrag(event);
149
- },
150
-
151
- keyPress: function(event) {
152
- if(this.activeDraggable)
153
- this.activeDraggable.keyPress(event);
154
- },
155
-
156
- addObserver: function(observer) {
157
- this.observers.push(observer);
158
- this._cacheObserverCallbacks();
159
- },
160
-
161
- removeObserver: function(element) { // element instead of observer fixes mem leaks
162
- this.observers = this.observers.reject( function(o) { return o.element==element });
163
- this._cacheObserverCallbacks();
164
- },
165
-
166
- notify: function(eventName, draggable, event) { // 'onStart', 'onEnd', 'onDrag'
167
- if(this[eventName+'Count'] > 0)
168
- this.observers.each( function(o) {
169
- if(o[eventName]) o[eventName](eventName, draggable, event);
170
- });
171
- },
172
-
173
- _cacheObserverCallbacks: function() {
174
- ['onStart','onEnd','onDrag'].each( function(eventName) {
175
- Draggables[eventName+'Count'] = Draggables.observers.select(
176
- function(o) { return o[eventName]; }
177
- ).length;
178
- });
179
- }
180
- }
181
-
182
- /*--------------------------------------------------------------------------*/
183
-
184
- var Draggable = Class.create();
185
- Draggable.prototype = {
186
- initialize: function(element) {
187
- var options = Object.extend({
188
- handle: false,
189
- starteffect: function(element) {
190
- new Effect.Opacity(element, {duration:0.2, from:1.0, to:0.7});
191
- },
192
- reverteffect: function(element, top_offset, left_offset) {
193
- var dur = Math.sqrt(Math.abs(top_offset^2)+Math.abs(left_offset^2))*0.02;
194
- element._revert = new Effect.MoveBy(element, -top_offset, -left_offset, {duration:dur});
195
- },
196
- endeffect: function(element) {
197
- new Effect.Opacity(element, {duration:0.2, from:0.7, to:1.0});
198
- },
199
- zindex: 1000,
200
- revert: false,
201
- snap: false // false, or xy or [x,y] or function(x,y){ return [x,y] }
202
- }, arguments[1] || {});
203
-
204
- this.element = $(element);
205
-
206
- if(options.handle && (typeof options.handle == 'string'))
207
- this.handle = Element.childrenWithClassName(this.element, options.handle)[0];
208
- if(!this.handle) this.handle = $(options.handle);
209
- if(!this.handle) this.handle = this.element;
210
-
211
- Element.makePositioned(this.element); // fix IE
212
-
213
- this.delta = this.currentDelta();
214
- this.options = options;
215
- this.dragging = false;
216
-
217
- this.eventMouseDown = this.initDrag.bindAsEventListener(this);
218
- Event.observe(this.handle, "mousedown", this.eventMouseDown);
219
-
220
- Draggables.register(this);
221
- },
222
-
223
- destroy: function() {
224
- Event.stopObserving(this.handle, "mousedown", this.eventMouseDown);
225
- Draggables.unregister(this);
226
- },
227
-
228
- currentDelta: function() {
229
- return([
230
- parseInt(this.element.style.left || '0'),
231
- parseInt(this.element.style.top || '0')]);
232
- },
233
-
234
- initDrag: function(event) {
235
- if(Event.isLeftClick(event)) {
236
- // abort on form elements, fixes a Firefox issue
237
- var src = Event.element(event);
238
- if(src.tagName && (
239
- src.tagName=='INPUT' ||
240
- src.tagName=='SELECT' ||
241
- src.tagName=='BUTTON' ||
242
- src.tagName=='TEXTAREA')) return;
243
-
244
- if(this.element._revert) {
245
- this.element._revert.cancel();
246
- this.element._revert = null;
247
- }
248
-
249
- var pointer = [Event.pointerX(event), Event.pointerY(event)];
250
- var pos = Position.cumulativeOffset(this.element);
251
- this.offset = [0,1].map( function(i) { return (pointer[i] - pos[i]) });
252
-
253
- Draggables.activate(this);
254
- Event.stop(event);
255
- }
256
- },
257
-
258
- startDrag: function(event) {
259
- this.dragging = true;
260
-
261
- if(this.options.zindex) {
262
- this.originalZ = parseInt(Element.getStyle(this.element,'z-index') || 0);
263
- this.element.style.zIndex = this.options.zindex;
264
- }
265
-
266
- if(this.options.ghosting) {
267
- this._clone = this.element.cloneNode(true);
268
- Position.absolutize(this.element);
269
- this.element.parentNode.insertBefore(this._clone, this.element);
270
- }
271
-
272
- Draggables.notify('onStart', this, event);
273
- if(this.options.starteffect) this.options.starteffect(this.element);
274
- },
275
-
276
- updateDrag: function(event, pointer) {
277
- if(!this.dragging) this.startDrag(event);
278
- Position.prepare();
279
- Droppables.show(pointer, this.element);
280
- Draggables.notify('onDrag', this, event);
281
- this.draw(pointer);
282
- if(this.options.change) this.options.change(this);
283
-
284
- // fix AppleWebKit rendering
285
- if(navigator.appVersion.indexOf('AppleWebKit')>0) window.scrollBy(0,0);
286
- Event.stop(event);
287
- },
288
-
289
- finishDrag: function(event, success) {
290
- this.dragging = false;
291
-
292
- if(this.options.ghosting) {
293
- Position.relativize(this.element);
294
- Element.remove(this._clone);
295
- this._clone = null;
296
- }
297
-
298
- if(success) Droppables.fire(event, this.element);
299
- Draggables.notify('onEnd', this, event);
300
-
301
- var revert = this.options.revert;
302
- if(revert && typeof revert == 'function') revert = revert(this.element);
303
-
304
- var d = this.currentDelta();
305
- if(revert && this.options.reverteffect) {
306
- this.options.reverteffect(this.element,
307
- d[1]-this.delta[1], d[0]-this.delta[0]);
308
- } else {
309
- this.delta = d;
310
- }
311
-
312
- if(this.options.zindex)
313
- this.element.style.zIndex = this.originalZ;
314
-
315
- if(this.options.endeffect)
316
- this.options.endeffect(this.element);
317
-
318
- Draggables.deactivate(this);
319
- Droppables.reset();
320
- },
321
-
322
- keyPress: function(event) {
323
- if(!event.keyCode==Event.KEY_ESC) return;
324
- this.finishDrag(event, false);
325
- Event.stop(event);
326
- },
327
-
328
- endDrag: function(event) {
329
- if(!this.dragging) return;
330
- this.finishDrag(event, true);
331
- Event.stop(event);
332
- },
333
-
334
- draw: function(point) {
335
- var pos = Position.cumulativeOffset(this.element);
336
- var d = this.currentDelta();
337
- pos[0] -= d[0]; pos[1] -= d[1];
338
-
339
- var p = [0,1].map(function(i){ return (point[i]-pos[i]-this.offset[i]) }.bind(this));
340
-
341
- if(this.options.snap) {
342
- if(typeof this.options.snap == 'function') {
343
- p = this.options.snap(p[0],p[1]);
344
- } else {
345
- if(this.options.snap instanceof Array) {
346
- p = p.map( function(v, i) {
347
- return Math.round(v/this.options.snap[i])*this.options.snap[i] }.bind(this))
348
- } else {
349
- p = p.map( function(v) {
350
- return Math.round(v/this.options.snap)*this.options.snap }.bind(this))
351
- }
352
- }}
353
-
354
- var style = this.element.style;
355
- if((!this.options.constraint) || (this.options.constraint=='horizontal'))
356
- style.left = p[0] + "px";
357
- if((!this.options.constraint) || (this.options.constraint=='vertical'))
358
- style.top = p[1] + "px";
359
- if(style.visibility=="hidden") style.visibility = ""; // fix gecko rendering
360
- }
361
- }
362
-
363
- /*--------------------------------------------------------------------------*/
364
-
365
- var SortableObserver = Class.create();
366
- SortableObserver.prototype = {
367
- initialize: function(element, observer) {
368
- this.element = $(element);
369
- this.observer = observer;
370
- this.lastValue = Sortable.serialize(this.element);
371
- },
372
-
373
- onStart: function() {
374
- this.lastValue = Sortable.serialize(this.element);
375
- },
376
-
377
- onEnd: function() {
378
- Sortable.unmark();
379
- if(this.lastValue != Sortable.serialize(this.element))
380
- this.observer(this.element)
381
- }
382
- }
383
-
384
- var Sortable = {
385
- sortables: new Array(),
386
-
387
- options: function(element){
388
- element = $(element);
389
- return this.sortables.detect(function(s) { return s.element == element });
390
- },
391
-
392
- destroy: function(element){
393
- element = $(element);
394
- this.sortables.findAll(function(s) { return s.element == element }).each(function(s){
395
- Draggables.removeObserver(s.element);
396
- s.droppables.each(function(d){ Droppables.remove(d) });
397
- s.draggables.invoke('destroy');
398
- });
399
- this.sortables = this.sortables.reject(function(s) { return s.element == element });
400
- },
401
-
402
- create: function(element) {
403
- element = $(element);
404
- var options = Object.extend({
405
- element: element,
406
- tag: 'li', // assumes li children, override with tag: 'tagname'
407
- dropOnEmpty: false,
408
- tree: false, // fixme: unimplemented
409
- overlap: 'vertical', // one of 'vertical', 'horizontal'
410
- constraint: 'vertical', // one of 'vertical', 'horizontal', false
411
- containment: element, // also takes array of elements (or id's); or false
412
- handle: false, // or a CSS class
413
- only: false,
414
- hoverclass: null,
415
- ghosting: false,
416
- format: null,
417
- onChange: Prototype.emptyFunction,
418
- onUpdate: Prototype.emptyFunction
419
- }, arguments[1] || {});
420
-
421
- // clear any old sortable with same element
422
- this.destroy(element);
423
-
424
- // build options for the draggables
425
- var options_for_draggable = {
426
- revert: true,
427
- ghosting: options.ghosting,
428
- constraint: options.constraint,
429
- handle: options.handle };
430
-
431
- if(options.starteffect)
432
- options_for_draggable.starteffect = options.starteffect;
433
-
434
- if(options.reverteffect)
435
- options_for_draggable.reverteffect = options.reverteffect;
436
- else
437
- if(options.ghosting) options_for_draggable.reverteffect = function(element) {
438
- element.style.top = 0;
439
- element.style.left = 0;
440
- };
441
-
442
- if(options.endeffect)
443
- options_for_draggable.endeffect = options.endeffect;
444
-
445
- if(options.zindex)
446
- options_for_draggable.zindex = options.zindex;
447
-
448
- // build options for the droppables
449
- var options_for_droppable = {
450
- overlap: options.overlap,
451
- containment: options.containment,
452
- hoverclass: options.hoverclass,
453
- onHover: Sortable.onHover,
454
- greedy: !options.dropOnEmpty
455
- }
456
-
457
- // fix for gecko engine
458
- Element.cleanWhitespace(element);
459
-
460
- options.draggables = [];
461
- options.droppables = [];
462
-
463
- // make it so
464
-
465
- // drop on empty handling
466
- if(options.dropOnEmpty) {
467
- Droppables.add(element,
468
- {containment: options.containment, onHover: Sortable.onEmptyHover, greedy: false});
469
- options.droppables.push(element);
470
- }
471
-
472
- (this.findElements(element, options) || []).each( function(e) {
473
- // handles are per-draggable
474
- var handle = options.handle ?
475
- Element.childrenWithClassName(e, options.handle)[0] : e;
476
- options.draggables.push(
477
- new Draggable(e, Object.extend(options_for_draggable, { handle: handle })));
478
- Droppables.add(e, options_for_droppable);
479
- options.droppables.push(e);
480
- });
481
-
482
- // keep reference
483
- this.sortables.push(options);
484
-
485
- // for onupdate
486
- Draggables.addObserver(new SortableObserver(element, options.onUpdate));
487
-
488
- },
489
-
490
- // return all suitable-for-sortable elements in a guaranteed order
491
- findElements: function(element, options) {
492
- if(!element.hasChildNodes()) return null;
493
- var elements = [];
494
- $A(element.childNodes).each( function(e) {
495
- if(e.tagName && e.tagName.toUpperCase()==options.tag.toUpperCase() &&
496
- (!options.only || (Element.hasClassName(e, options.only))))
497
- elements.push(e);
498
- if(options.tree) {
499
- var grandchildren = this.findElements(e, options);
500
- if(grandchildren) elements.push(grandchildren);
501
- }
502
- });
503
-
504
- return (elements.length>0 ? elements.flatten() : null);
505
- },
506
-
507
- onHover: function(element, dropon, overlap) {
508
- if(overlap>0.5) {
509
- Sortable.mark(dropon, 'before');
510
- if(dropon.previousSibling != element) {
511
- var oldParentNode = element.parentNode;
512
- element.style.visibility = "hidden"; // fix gecko rendering
513
- dropon.parentNode.insertBefore(element, dropon);
514
- if(dropon.parentNode!=oldParentNode)
515
- Sortable.options(oldParentNode).onChange(element);
516
- Sortable.options(dropon.parentNode).onChange(element);
517
- }
518
- } else {
519
- Sortable.mark(dropon, 'after');
520
- var nextElement = dropon.nextSibling || null;
521
- if(nextElement != element) {
522
- var oldParentNode = element.parentNode;
523
- element.style.visibility = "hidden"; // fix gecko rendering
524
- dropon.parentNode.insertBefore(element, nextElement);
525
- if(dropon.parentNode!=oldParentNode)
526
- Sortable.options(oldParentNode).onChange(element);
527
- Sortable.options(dropon.parentNode).onChange(element);
528
- }
529
- }
530
- },
531
-
532
- onEmptyHover: function(element, dropon) {
533
- if(element.parentNode!=dropon) {
534
- var oldParentNode = element.parentNode;
535
- dropon.appendChild(element);
536
- Sortable.options(oldParentNode).onChange(element);
537
- Sortable.options(dropon).onChange(element);
538
- }
539
- },
540
-
541
- unmark: function() {
542
- if(Sortable._marker) Element.hide(Sortable._marker);
543
- },
544
-
545
- mark: function(dropon, position) {
546
- // mark on ghosting only
547
- var sortable = Sortable.options(dropon.parentNode);
548
- if(sortable && !sortable.ghosting) return;
549
-
550
- if(!Sortable._marker) {
551
- Sortable._marker = $('dropmarker') || document.createElement('DIV');
552
- Element.hide(Sortable._marker);
553
- Element.addClassName(Sortable._marker, 'dropmarker');
554
- Sortable._marker.style.position = 'absolute';
555
- document.getElementsByTagName("body").item(0).appendChild(Sortable._marker);
556
- }
557
- var offsets = Position.cumulativeOffset(dropon);
558
- Sortable._marker.style.left = offsets[0] + 'px';
559
- Sortable._marker.style.top = offsets[1] + 'px';
560
-
561
- if(position=='after')
562
- if(sortable.overlap == 'horizontal')
563
- Sortable._marker.style.left = (offsets[0]+dropon.clientWidth) + 'px';
564
- else
565
- Sortable._marker.style.top = (offsets[1]+dropon.clientHeight) + 'px';
566
-
567
- Element.show(Sortable._marker);
568
- },
569
-
570
- serialize: function(element) {
571
- element = $(element);
572
- var sortableOptions = this.options(element);
573
- var options = Object.extend({
574
- tag: sortableOptions.tag,
575
- only: sortableOptions.only,
576
- name: element.id,
577
- format: sortableOptions.format || /^[^_]*_(.*)$/
578
- }, arguments[1] || {});
579
- return $(this.findElements(element, options) || []).map( function(item) {
580
- return (encodeURIComponent(options.name) + "[]=" +
581
- encodeURIComponent(item.id.match(options.format) ? item.id.match(options.format)[1] : ''));
582
- }).join("&");
583
- }
584
- }