bioroebe 0.10.80

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Files changed (802) hide show
  1. checksums.yaml +7 -0
  2. data/LICENSE.md +428 -0
  3. data/README.md +9280 -0
  4. data/bin/advanced_dotplot +7 -0
  5. data/bin/align_open_reading_frames +12 -0
  6. data/bin/all_positions_of_this_nucleotide +7 -0
  7. data/bin/aminoacid_composition +7 -0
  8. data/bin/aminoacid_frequencies +12 -0
  9. data/bin/aminoacid_substitution +7 -0
  10. data/bin/automatically_rename_this_fasta_file +7 -0
  11. data/bin/base_composition +7 -0
  12. data/bin/batch_create_windows_executables +7 -0
  13. data/bin/biomart_console +11 -0
  14. data/bin/bioroebe +27 -0
  15. data/bin/bioroebe_controller +10 -0
  16. data/bin/bioshell +26 -0
  17. data/bin/blosum_2D_table +12 -0
  18. data/bin/calculate_n50_value +12 -0
  19. data/bin/chunked_display +12 -0
  20. data/bin/codon_frequency +9 -0
  21. data/bin/codon_to_aminoacid +30 -0
  22. data/bin/colourize_this_fasta_sequence +14 -0
  23. data/bin/compact_fasta_file +7 -0
  24. data/bin/complement +7 -0
  25. data/bin/complementary_dna_strand +12 -0
  26. data/bin/complementary_rna_strand +12 -0
  27. data/bin/compseq +7 -0
  28. data/bin/consensus_sequence +17 -0
  29. data/bin/count_AT +12 -0
  30. data/bin/count_GC +12 -0
  31. data/bin/create_random_aminoacids +7 -0
  32. data/bin/decode_this_aminoacid_sequence +20 -0
  33. data/bin/deduce_aminoacid_sequence +13 -0
  34. data/bin/deduce_most_likely_aminoacid_sequence +7 -0
  35. data/bin/display_aminoacid_table +12 -0
  36. data/bin/display_open_reading_frames +7 -0
  37. data/bin/dna_to_aminoacid_sequence +7 -0
  38. data/bin/dna_to_rna +7 -0
  39. data/bin/downcase_chunked_display +12 -0
  40. data/bin/download_this_pdb +7 -0
  41. data/bin/fasta_index +7 -0
  42. data/bin/fetch_data_from_uniprot +12 -0
  43. data/bin/filter_away_invalid_nucleotides +12 -0
  44. data/bin/find_substring +19 -0
  45. data/bin/genbank_to_fasta +7 -0
  46. data/bin/hamming_distance +12 -0
  47. data/bin/input_as_dna +12 -0
  48. data/bin/is_palindrome +13 -0
  49. data/bin/leading_five_prime +7 -0
  50. data/bin/levensthein +7 -0
  51. data/bin/longest_ORF +14 -0
  52. data/bin/longest_substring +12 -0
  53. data/bin/n_stop_codons_in_this_sequence +15 -0
  54. data/bin/open_reading_frames +14 -0
  55. data/bin/overwrite_fasta_header +7 -0
  56. data/bin/palindrome_2D_structure +7 -0
  57. data/bin/palindrome_generator +7 -0
  58. data/bin/parse_fasta +7 -0
  59. data/bin/partner_nucleotide +9 -0
  60. data/bin/possible_codons_for_this_aminoacid +12 -0
  61. data/bin/random_dna_sequence +12 -0
  62. data/bin/random_sequence +12 -0
  63. data/bin/raw_hamming_distance +12 -0
  64. data/bin/return_longest_substring_via_LCS_algorithm +7 -0
  65. data/bin/reverse_complement +7 -0
  66. data/bin/reverse_sequence +7 -0
  67. data/bin/ruler +12 -0
  68. data/bin/scan_this_input_for_startcodons +12 -0
  69. data/bin/short_aminoacid_letter_from_long_aminoacid_name +7 -0
  70. data/bin/show_atomic_composition +7 -0
  71. data/bin/show_codon_usage +12 -0
  72. data/bin/show_fasta_header +7 -0
  73. data/bin/show_nucleotide_sequence +7 -0
  74. data/bin/show_this_codon_table +7 -0
  75. data/bin/show_this_dna_sequence +7 -0
  76. data/bin/showorf +14 -0
  77. data/bin/simplify_fasta +7 -0
  78. data/bin/sort_aminoacid_based_on_its_hydrophobicity +7 -0
  79. data/bin/split_this_fasta_file_into_chromosomes +7 -0
  80. data/bin/strict_filter_away_invalid_aminoacids +7 -0
  81. data/bin/taxonomy +63 -0
  82. data/bin/three_to_one +7 -0
  83. data/bin/to_rna +7 -0
  84. data/bin/trailing_three_prime +7 -0
  85. data/bin/trypsin_digest +7 -0
  86. data/bin/upcase_this_aminoacid_sequence_and_remove_numbers +7 -0
  87. data/bioroebe.gemspec +97 -0
  88. data/doc/IUPAC_aminoacids_code.md +36 -0
  89. data/doc/IUPAC_nucleotide_code.md +19 -0
  90. data/doc/README.gen +9237 -0
  91. data/doc/blosum.md +5 -0
  92. data/doc/compatibility/BIO_PHP.md +37 -0
  93. data/doc/compatibility/README.md +3 -0
  94. data/doc/compatibility/emboss.md +56 -0
  95. data/doc/extensive_usage_example.md +35 -0
  96. data/doc/german_names_for_the_aminoacids.md +27 -0
  97. data/doc/instructions_for_the_taxonomy_subproject.md +504 -0
  98. data/doc/legacy_paths.md +9 -0
  99. data/doc/pdb_ATOM_entry.md +33 -0
  100. data/doc/quality_control/README.md +2 -0
  101. data/doc/quality_control/commandline_applications.md +13 -0
  102. data/doc/resources.md +23 -0
  103. data/doc/setup.rb +1655 -0
  104. data/doc/statistics/statistics.md +41 -0
  105. data/doc/todo/README.md +5 -0
  106. data/doc/todo/bioroebe_GUI_todo.md +15 -0
  107. data/doc/todo/bioroebe_todo.md +2823 -0
  108. data/doc/using_biomart.md +258 -0
  109. data/html/test.html +144 -0
  110. data/lib/bioroebe/aminoacids/aminoacid_substitution.rb +118 -0
  111. data/lib/bioroebe/aminoacids/aminoacids_mass_table.rb +118 -0
  112. data/lib/bioroebe/aminoacids/codon_percentage.rb +189 -0
  113. data/lib/bioroebe/aminoacids/colourize_hydrophilic_and_hydrophobic_aminoacids.rb +110 -0
  114. data/lib/bioroebe/aminoacids/create_random_aminoacids.rb +221 -0
  115. data/lib/bioroebe/aminoacids/deduce_aminoacid_sequence.rb +460 -0
  116. data/lib/bioroebe/aminoacids/display_aminoacid_table.rb +231 -0
  117. data/lib/bioroebe/aminoacids/show_hydrophobicity.rb +184 -0
  118. data/lib/bioroebe/annotations/README.md +2 -0
  119. data/lib/bioroebe/annotations/create_annotation_format.rb +208 -0
  120. data/lib/bioroebe/autoinclude.rb +7 -0
  121. data/lib/bioroebe/base/base.rb +35 -0
  122. data/lib/bioroebe/base/colours.rb +14 -0
  123. data/lib/bioroebe/base/colours_for_base/colours_for_base.rb +275 -0
  124. data/lib/bioroebe/base/commandline_application/README.md +7 -0
  125. data/lib/bioroebe/base/commandline_application/aminoacids.rb +33 -0
  126. data/lib/bioroebe/base/commandline_application/commandline_application.rb +37 -0
  127. data/lib/bioroebe/base/commandline_application/commandline_arguments.rb +144 -0
  128. data/lib/bioroebe/base/commandline_application/directory.rb +33 -0
  129. data/lib/bioroebe/base/commandline_application/extract.rb +22 -0
  130. data/lib/bioroebe/base/commandline_application/misc.rb +485 -0
  131. data/lib/bioroebe/base/commandline_application/opn.rb +47 -0
  132. data/lib/bioroebe/base/commandline_application/reset.rb +40 -0
  133. data/lib/bioroebe/base/commandline_application/warnings.rb +36 -0
  134. data/lib/bioroebe/base/commandline_application/write_what_into.rb +29 -0
  135. data/lib/bioroebe/base/initialize.rb +18 -0
  136. data/lib/bioroebe/base/misc.rb +94 -0
  137. data/lib/bioroebe/base/namespace.rb +16 -0
  138. data/lib/bioroebe/base/prototype/README.md +12 -0
  139. data/lib/bioroebe/base/prototype/e_and_ee.rb +24 -0
  140. data/lib/bioroebe/base/prototype/misc.rb +108 -0
  141. data/lib/bioroebe/base/prototype/mkdir.rb +20 -0
  142. data/lib/bioroebe/base/prototype/prototype.rb +21 -0
  143. data/lib/bioroebe/base/prototype/reset.rb +26 -0
  144. data/lib/bioroebe/base/reset.rb +11 -0
  145. data/lib/bioroebe/biomart/LICENSE.md +27 -0
  146. data/lib/bioroebe/biomart/attribute.rb +77 -0
  147. data/lib/bioroebe/biomart/biomart.rb +227 -0
  148. data/lib/bioroebe/biomart/database.rb +128 -0
  149. data/lib/bioroebe/biomart/dataset.rb +572 -0
  150. data/lib/bioroebe/biomart/filter.rb +97 -0
  151. data/lib/bioroebe/biomart/server.rb +152 -0
  152. data/lib/bioroebe/blosum/blosum.rb +88 -0
  153. data/lib/bioroebe/calculate/calculate_blosum_score.rb +145 -0
  154. data/lib/bioroebe/calculate/calculate_gc_content.rb +301 -0
  155. data/lib/bioroebe/calculate/calculate_levensthein_distance.rb +100 -0
  156. data/lib/bioroebe/calculate/calculate_melting_temperature.rb +398 -0
  157. data/lib/bioroebe/calculate/calculate_melting_temperature_for_more_than_thirteen_nucleotides.rb +304 -0
  158. data/lib/bioroebe/calculate/calculate_the_position_specific_scoring_matrix.rb +166 -0
  159. data/lib/bioroebe/cell/README.md +1 -0
  160. data/lib/bioroebe/cell/cell.rb +63 -0
  161. data/lib/bioroebe/cleave_and_digest/README.md +2 -0
  162. data/lib/bioroebe/cleave_and_digest/cleave.rb +80 -0
  163. data/lib/bioroebe/cleave_and_digest/digestion.rb +75 -0
  164. data/lib/bioroebe/cleave_and_digest/trypsin.rb +192 -0
  165. data/lib/bioroebe/codon_tables/README.md +9 -0
  166. data/lib/bioroebe/codon_tables/frequencies/287_Pseudomonas_aeruginosa.yml +101 -0
  167. data/lib/bioroebe/codon_tables/frequencies/3702_Arabidopsis_thaliana.yml +77 -0
  168. data/lib/bioroebe/codon_tables/frequencies/4932_Saccharomyces_cerevisiae.yml +103 -0
  169. data/lib/bioroebe/codon_tables/frequencies/7227_Drosophila_melanogaster.yml +71 -0
  170. data/lib/bioroebe/codon_tables/frequencies/83333_Escherichia_coli_K12.yml +103 -0
  171. data/lib/bioroebe/codon_tables/frequencies/9606_Homo_sapiens.yml +123 -0
  172. data/lib/bioroebe/codon_tables/frequencies/9685_Felis_catus.yml +78 -0
  173. data/lib/bioroebe/codon_tables/frequencies/README.md +10 -0
  174. data/lib/bioroebe/codon_tables/frequencies/parse_frequency_table.rb +337 -0
  175. data/lib/bioroebe/codons/README.md +28 -0
  176. data/lib/bioroebe/codons/codon_table.rb +416 -0
  177. data/lib/bioroebe/codons/codon_tables.rb +123 -0
  178. data/lib/bioroebe/codons/codons.rb +517 -0
  179. data/lib/bioroebe/codons/convert_this_codon_to_that_aminoacid.rb +102 -0
  180. data/lib/bioroebe/codons/detect_minimal_codon.rb +180 -0
  181. data/lib/bioroebe/codons/determine_optimal_codons.rb +74 -0
  182. data/lib/bioroebe/codons/possible_codons_for_this_aminoacid.rb +380 -0
  183. data/lib/bioroebe/codons/sanitize_codon_frequency.rb +144 -0
  184. data/lib/bioroebe/codons/show_codon_tables.rb +130 -0
  185. data/lib/bioroebe/codons/show_codon_usage.rb +197 -0
  186. data/lib/bioroebe/codons/show_this_codon_table.rb +573 -0
  187. data/lib/bioroebe/codons/start_codons.rb +105 -0
  188. data/lib/bioroebe/colours/colour_schemes/README.md +10 -0
  189. data/lib/bioroebe/colours/colour_schemes/array_available_colour_schemes.rb +38 -0
  190. data/lib/bioroebe/colours/colour_schemes/buried.rb +70 -0
  191. data/lib/bioroebe/colours/colour_schemes/colour_scheme.rb +101 -0
  192. data/lib/bioroebe/colours/colour_schemes/colour_scheme_demo.rb +262 -0
  193. data/lib/bioroebe/colours/colour_schemes/helix.rb +65 -0
  194. data/lib/bioroebe/colours/colour_schemes/hydropathy.rb +70 -0
  195. data/lib/bioroebe/colours/colour_schemes/nucleotide.rb +47 -0
  196. data/lib/bioroebe/colours/colour_schemes/score.rb +112 -0
  197. data/lib/bioroebe/colours/colour_schemes/simple.rb +42 -0
  198. data/lib/bioroebe/colours/colour_schemes/strand.rb +65 -0
  199. data/lib/bioroebe/colours/colour_schemes/taylor.rb +58 -0
  200. data/lib/bioroebe/colours/colour_schemes/turn.rb +65 -0
  201. data/lib/bioroebe/colours/colour_schemes/zappo.rb +59 -0
  202. data/lib/bioroebe/colours/colourize_sequence.rb +262 -0
  203. data/lib/bioroebe/colours/colours.rb +119 -0
  204. data/lib/bioroebe/colours/misc_colours.rb +80 -0
  205. data/lib/bioroebe/colours/rev.rb +41 -0
  206. data/lib/bioroebe/colours/sdir.rb +21 -0
  207. data/lib/bioroebe/colours/sfancy.rb +21 -0
  208. data/lib/bioroebe/colours/sfile.rb +21 -0
  209. data/lib/bioroebe/colours/simp.rb +21 -0
  210. data/lib/bioroebe/colours/swarn.rb +29 -0
  211. data/lib/bioroebe/colours/use_colours.rb +27 -0
  212. data/lib/bioroebe/configuration/configuration.rb +114 -0
  213. data/lib/bioroebe/configuration/constants.rb +35 -0
  214. data/lib/bioroebe/constants/GUIs.rb +79 -0
  215. data/lib/bioroebe/constants/aminoacids_and_proteins.rb +146 -0
  216. data/lib/bioroebe/constants/base_directory.rb +120 -0
  217. data/lib/bioroebe/constants/carriage_return.rb +14 -0
  218. data/lib/bioroebe/constants/codon_tables.rb +77 -0
  219. data/lib/bioroebe/constants/database_constants.rb +107 -0
  220. data/lib/bioroebe/constants/files_and_directories.rb +579 -0
  221. data/lib/bioroebe/constants/misc.rb +189 -0
  222. data/lib/bioroebe/constants/newline.rb +14 -0
  223. data/lib/bioroebe/constants/nucleotides.rb +114 -0
  224. data/lib/bioroebe/constants/regex.rb +28 -0
  225. data/lib/bioroebe/constants/roebe.rb +38 -0
  226. data/lib/bioroebe/constants/row_terminator.rb +16 -0
  227. data/lib/bioroebe/constants/tabulator.rb +14 -0
  228. data/lib/bioroebe/constants/unicode.rb +12 -0
  229. data/lib/bioroebe/constants/urls.rb +50 -0
  230. data/lib/bioroebe/conversions/README.md +3 -0
  231. data/lib/bioroebe/conversions/convert_aminoacid_to_dna.rb +298 -0
  232. data/lib/bioroebe/conversions/dna_to_aminoacid_sequence.rb +569 -0
  233. data/lib/bioroebe/count/README.md +1 -0
  234. data/lib/bioroebe/count/count_amount_of_aminoacids.rb +352 -0
  235. data/lib/bioroebe/count/count_amount_of_nucleotides.rb +491 -0
  236. data/lib/bioroebe/count/count_at.rb +39 -0
  237. data/lib/bioroebe/count/count_gc.rb +43 -0
  238. data/lib/bioroebe/css/README.md +5 -0
  239. data/lib/bioroebe/css/project.css +121 -0
  240. data/lib/bioroebe/data/README.md +10 -0
  241. data/lib/bioroebe/data/bam/README.md +1 -0
  242. data/lib/bioroebe/data/data.txt +192 -0
  243. data/lib/bioroebe/data/fasta/GFP_mutant_3_coding_sequence.fasta +12 -0
  244. data/lib/bioroebe/data/fasta/alu_elements.fasta +42 -0
  245. data/lib/bioroebe/data/fasta/lady_slippers_orchid.fasta +1197 -0
  246. data/lib/bioroebe/data/fasta/loxP.fasta +2 -0
  247. data/lib/bioroebe/data/fasta/ls_orchid.fasta +1197 -0
  248. data/lib/bioroebe/data/fasta/pax6_in_mouse.fasta +1 -0
  249. data/lib/bioroebe/data/fasta/test.fasta +7 -0
  250. data/lib/bioroebe/data/fasta/test_DNA.fasta +1 -0
  251. data/lib/bioroebe/data/fastq/fastq_example_file.fastq +32 -0
  252. data/lib/bioroebe/data/fastq/fastq_example_file_SP1.fastq +1000 -0
  253. data/lib/bioroebe/data/fastq/one_random_fastq_entry.fastq +4 -0
  254. data/lib/bioroebe/data/genbank/sample_file.genbank +15 -0
  255. data/lib/bioroebe/data/genbank/standard.fasta +3 -0
  256. data/lib/bioroebe/data/gff/Escherichia_coli_K12_plasmid_F_DNA_NC_002483.1.gff3 +345 -0
  257. data/lib/bioroebe/data/gff/sample.gff +2 -0
  258. data/lib/bioroebe/data/gff/test_gene.gff +4 -0
  259. data/lib/bioroebe/data/gff/transcripts.gff +16 -0
  260. data/lib/bioroebe/data/gtf/README.md +1 -0
  261. data/lib/bioroebe/data/json/example_config.json +48 -0
  262. data/lib/bioroebe/data/pdb/1VII.pdb +754 -0
  263. data/lib/bioroebe/data/pdb/ala_phe_ala.pdb +228 -0
  264. data/lib/bioroebe/data/pdb/rcsb_pdb_1VII.fasta +2 -0
  265. data/lib/bioroebe/data/phylip/README.md +11 -0
  266. data/lib/bioroebe/data/phylip/example.phylip +7 -0
  267. data/lib/bioroebe/data/svg/example.svg +301 -0
  268. data/lib/bioroebe/databases/README.md +1 -0
  269. data/lib/bioroebe/databases/download_taxonomy_database.rb +102 -0
  270. data/lib/bioroebe/dotplots/README.md +5 -0
  271. data/lib/bioroebe/dotplots/advanced_dotplot.rb +256 -0
  272. data/lib/bioroebe/dotplots/dotplot.rb +184 -0
  273. data/lib/bioroebe/electron_microscopy/coordinate_analyzer.rb +191 -0
  274. data/lib/bioroebe/electron_microscopy/fix_pos_file.rb +102 -0
  275. data/lib/bioroebe/electron_microscopy/generate_em2em_file.rb +122 -0
  276. data/lib/bioroebe/electron_microscopy/parse_coordinates.rb +197 -0
  277. data/lib/bioroebe/electron_microscopy/read_file_xmd.rb +282 -0
  278. data/lib/bioroebe/electron_microscopy/simple_star_file_generator.rb +131 -0
  279. data/lib/bioroebe/encoding/README.md +2 -0
  280. data/lib/bioroebe/encoding/encoding.rb +45 -0
  281. data/lib/bioroebe/enzymes/README.md +2 -0
  282. data/lib/bioroebe/enzymes/has_this_restriction_enzyme.rb +46 -0
  283. data/lib/bioroebe/enzymes/restriction_enzyme.rb +200 -0
  284. data/lib/bioroebe/enzymes/restriction_enzymes_file.rb +72 -0
  285. data/lib/bioroebe/enzymes/return_restriction_enzyme_sequence_and_cut_position.rb +80 -0
  286. data/lib/bioroebe/enzymes/return_sequence_that_is_cut_via_restriction_enzyme.rb +65 -0
  287. data/lib/bioroebe/enzymes/show_restriction_enzymes.rb +119 -0
  288. data/lib/bioroebe/exceptions/README.md +2 -0
  289. data/lib/bioroebe/exceptions/exceptions.rb +17 -0
  290. data/lib/bioroebe/ext/LICENCE.md +5 -0
  291. data/lib/bioroebe/ext/README.md +7 -0
  292. data/lib/bioroebe/ext/main.cpp +45 -0
  293. data/lib/bioroebe/ext/nucleotide.cpp +24 -0
  294. data/lib/bioroebe/ext/nussinov_algorithm.cpp +348 -0
  295. data/lib/bioroebe/ext/sequence +0 -0
  296. data/lib/bioroebe/ext/sequence.cpp +162 -0
  297. data/lib/bioroebe/fasta_and_fastq/README.md +6 -0
  298. data/lib/bioroebe/fasta_and_fastq/autocorrect_the_name_of_this_fasta_file.rb +88 -0
  299. data/lib/bioroebe/fasta_and_fastq/compact_fasta_file/compact_fasta_file.rb +151 -0
  300. data/lib/bioroebe/fasta_and_fastq/display_how_many_fasta_entries_are_in_this_directory.rb +111 -0
  301. data/lib/bioroebe/fasta_and_fastq/download_fasta.rb +248 -0
  302. data/lib/bioroebe/fasta_and_fastq/fasta_defline/README.md +2 -0
  303. data/lib/bioroebe/fasta_and_fastq/fasta_defline/fasta_defline.rb +113 -0
  304. data/lib/bioroebe/fasta_and_fastq/fasta_parser.rb +167 -0
  305. data/lib/bioroebe/fasta_and_fastq/fastq_format_explainer.rb +131 -0
  306. data/lib/bioroebe/fasta_and_fastq/length_modifier/length_modifier.rb +87 -0
  307. data/lib/bioroebe/fasta_and_fastq/parse_fasta/constants.rb +50 -0
  308. data/lib/bioroebe/fasta_and_fastq/parse_fasta/initialize.rb +86 -0
  309. data/lib/bioroebe/fasta_and_fastq/parse_fasta/menu.rb +117 -0
  310. data/lib/bioroebe/fasta_and_fastq/parse_fasta/misc.rb +981 -0
  311. data/lib/bioroebe/fasta_and_fastq/parse_fasta/parse_fasta.rb +27 -0
  312. data/lib/bioroebe/fasta_and_fastq/parse_fasta/report.rb +156 -0
  313. data/lib/bioroebe/fasta_and_fastq/parse_fasta/reset.rb +128 -0
  314. data/lib/bioroebe/fasta_and_fastq/parse_fasta/run.rb +20 -0
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  577. data/lib/bioroebe/svg/track.rb +263 -0
  578. data/lib/bioroebe/taxonomy/README.md +1 -0
  579. data/lib/bioroebe/taxonomy/chart.rb +95 -0
  580. data/lib/bioroebe/taxonomy/class_methods.rb +181 -0
  581. data/lib/bioroebe/taxonomy/colours.rb +26 -0
  582. data/lib/bioroebe/taxonomy/constants.rb +218 -0
  583. data/lib/bioroebe/taxonomy/edit.rb +97 -0
  584. data/lib/bioroebe/taxonomy/help/help.rb +65 -0
  585. data/lib/bioroebe/taxonomy/help/helpline.rb +53 -0
  586. data/lib/bioroebe/taxonomy/info/check_available.rb +143 -0
  587. data/lib/bioroebe/taxonomy/info/info.rb +337 -0
  588. data/lib/bioroebe/taxonomy/info/is_dna.rb +150 -0
  589. data/lib/bioroebe/taxonomy/interactive.rb +1933 -0
  590. data/lib/bioroebe/taxonomy/menu.rb +905 -0
  591. data/lib/bioroebe/taxonomy/node.rb +118 -0
  592. data/lib/bioroebe/taxonomy/parse_fasta.rb +383 -0
  593. data/lib/bioroebe/taxonomy/shared.rb +287 -0
  594. data/lib/bioroebe/taxonomy/taxonomy.rb +521 -0
  595. data/lib/bioroebe/toplevel_methods/ad_hoc_task.rb +56 -0
  596. data/lib/bioroebe/toplevel_methods/aminoacids_and_proteins.rb +715 -0
  597. data/lib/bioroebe/toplevel_methods/atomic_composition.rb +198 -0
  598. data/lib/bioroebe/toplevel_methods/base_composition.rb +121 -0
  599. data/lib/bioroebe/toplevel_methods/blast.rb +153 -0
  600. data/lib/bioroebe/toplevel_methods/calculate_n50_value.rb +57 -0
  601. data/lib/bioroebe/toplevel_methods/cat.rb +71 -0
  602. data/lib/bioroebe/toplevel_methods/chunked_display.rb +92 -0
  603. data/lib/bioroebe/toplevel_methods/cliner.rb +81 -0
  604. data/lib/bioroebe/toplevel_methods/complement.rb +58 -0
  605. data/lib/bioroebe/toplevel_methods/convert_global_env.rb +39 -0
  606. data/lib/bioroebe/toplevel_methods/databases.rb +73 -0
  607. data/lib/bioroebe/toplevel_methods/delimiter.rb +19 -0
  608. data/lib/bioroebe/toplevel_methods/digest.rb +71 -0
  609. data/lib/bioroebe/toplevel_methods/download_and_fetch_data.rb +146 -0
  610. data/lib/bioroebe/toplevel_methods/e.rb +20 -0
  611. data/lib/bioroebe/toplevel_methods/editor.rb +21 -0
  612. data/lib/bioroebe/toplevel_methods/esystem.rb +22 -0
  613. data/lib/bioroebe/toplevel_methods/exponential_growth.rb +74 -0
  614. data/lib/bioroebe/toplevel_methods/extract.rb +56 -0
  615. data/lib/bioroebe/toplevel_methods/fasta_and_fastq.rb +353 -0
  616. data/lib/bioroebe/toplevel_methods/file_and_directory_related_actions.rb +257 -0
  617. data/lib/bioroebe/toplevel_methods/frequencies.rb +92 -0
  618. data/lib/bioroebe/toplevel_methods/hamming_distance.rb +60 -0
  619. data/lib/bioroebe/toplevel_methods/infer.rb +66 -0
  620. data/lib/bioroebe/toplevel_methods/is_on_roebe.rb +39 -0
  621. data/lib/bioroebe/toplevel_methods/leading_five_prime_and_trailing_three_prime.rb +101 -0
  622. data/lib/bioroebe/toplevel_methods/levensthein.rb +63 -0
  623. data/lib/bioroebe/toplevel_methods/log_directory.rb +109 -0
  624. data/lib/bioroebe/toplevel_methods/longest_common_substring.rb +55 -0
  625. data/lib/bioroebe/toplevel_methods/map_ncbi_entry_to_eutils_id.rb +88 -0
  626. data/lib/bioroebe/toplevel_methods/matches.rb +259 -0
  627. data/lib/bioroebe/toplevel_methods/misc.rb +432 -0
  628. data/lib/bioroebe/toplevel_methods/nucleotides.rb +715 -0
  629. data/lib/bioroebe/toplevel_methods/number_of_clones.rb +63 -0
  630. data/lib/bioroebe/toplevel_methods/open_in_browser.rb +77 -0
  631. data/lib/bioroebe/toplevel_methods/open_reading_frames.rb +236 -0
  632. data/lib/bioroebe/toplevel_methods/opn.rb +34 -0
  633. data/lib/bioroebe/toplevel_methods/palindromes.rb +127 -0
  634. data/lib/bioroebe/toplevel_methods/parse.rb +59 -0
  635. data/lib/bioroebe/toplevel_methods/phred_error_probability.rb +68 -0
  636. data/lib/bioroebe/toplevel_methods/rds.rb +24 -0
  637. data/lib/bioroebe/toplevel_methods/remove.rb +86 -0
  638. data/lib/bioroebe/toplevel_methods/return_source_code_of_this_method.rb +35 -0
  639. data/lib/bioroebe/toplevel_methods/return_subsequence_based_on_indices.rb +68 -0
  640. data/lib/bioroebe/toplevel_methods/rna_splicing.rb +73 -0
  641. data/lib/bioroebe/toplevel_methods/rnalfold.rb +69 -0
  642. data/lib/bioroebe/toplevel_methods/searching_and_finding.rb +116 -0
  643. data/lib/bioroebe/toplevel_methods/shuffleseq.rb +37 -0
  644. data/lib/bioroebe/toplevel_methods/statistics.rb +53 -0
  645. data/lib/bioroebe/toplevel_methods/sum_of_odd_integers.rb +62 -0
  646. data/lib/bioroebe/toplevel_methods/taxonomy.rb +187 -0
  647. data/lib/bioroebe/toplevel_methods/three_delimiter.rb +34 -0
  648. data/lib/bioroebe/toplevel_methods/time_and_date.rb +53 -0
  649. data/lib/bioroebe/toplevel_methods/to_camelcase.rb +26 -0
  650. data/lib/bioroebe/toplevel_methods/truncate.rb +48 -0
  651. data/lib/bioroebe/toplevel_methods/url.rb +36 -0
  652. data/lib/bioroebe/toplevel_methods/verbose.rb +59 -0
  653. data/lib/bioroebe/utility_scripts/align_open_reading_frames.rb +191 -0
  654. data/lib/bioroebe/utility_scripts/analyse_local_dataset.rb +119 -0
  655. data/lib/bioroebe/utility_scripts/check_for_mismatches/check_for_mismatches.rb +230 -0
  656. data/lib/bioroebe/utility_scripts/compacter.rb +131 -0
  657. data/lib/bioroebe/utility_scripts/compseq/compseq.rb +529 -0
  658. data/lib/bioroebe/utility_scripts/consensus_sequence.rb +374 -0
  659. data/lib/bioroebe/utility_scripts/create_batch_entrez_file.rb +130 -0
  660. data/lib/bioroebe/utility_scripts/determine_antigenic_areas.rb +115 -0
  661. data/lib/bioroebe/utility_scripts/determine_missing_nucleotides_percentage.rb +137 -0
  662. data/lib/bioroebe/utility_scripts/display_open_reading_frames/determine.rb +73 -0
  663. data/lib/bioroebe/utility_scripts/display_open_reading_frames/display_open_reading_frames.rb +31 -0
  664. data/lib/bioroebe/utility_scripts/display_open_reading_frames/initialize.rb +37 -0
  665. data/lib/bioroebe/utility_scripts/display_open_reading_frames/menu.rb +49 -0
  666. data/lib/bioroebe/utility_scripts/display_open_reading_frames/misc.rb +471 -0
  667. data/lib/bioroebe/utility_scripts/display_open_reading_frames/report.rb +113 -0
  668. data/lib/bioroebe/utility_scripts/display_open_reading_frames/reset.rb +56 -0
  669. data/lib/bioroebe/utility_scripts/dot_alignment.rb +177 -0
  670. data/lib/bioroebe/utility_scripts/download_files_from_rebase.rb +72 -0
  671. data/lib/bioroebe/utility_scripts/find_gene.rb +202 -0
  672. data/lib/bioroebe/utility_scripts/mirror_repeat.rb +235 -0
  673. data/lib/bioroebe/utility_scripts/move_file_to_its_correct_location.rb +151 -0
  674. data/lib/bioroebe/utility_scripts/parse_taxonomy.rb +168 -0
  675. data/lib/bioroebe/utility_scripts/pathways.rb +152 -0
  676. data/lib/bioroebe/utility_scripts/permutations.rb +145 -0
  677. data/lib/bioroebe/utility_scripts/punnet/punnet.rb +126 -0
  678. data/lib/bioroebe/utility_scripts/show_this_dna_sequence.rb +148 -0
  679. data/lib/bioroebe/utility_scripts/showorf/constants.rb +36 -0
  680. data/lib/bioroebe/utility_scripts/showorf/help.rb +33 -0
  681. data/lib/bioroebe/utility_scripts/showorf/initialize.rb +52 -0
  682. data/lib/bioroebe/utility_scripts/showorf/menu.rb +68 -0
  683. data/lib/bioroebe/utility_scripts/showorf/reset.rb +39 -0
  684. data/lib/bioroebe/utility_scripts/showorf/run.rb +152 -0
  685. data/lib/bioroebe/utility_scripts/showorf/show.rb +97 -0
  686. data/lib/bioroebe/utility_scripts/showorf/showorf.rb +488 -0
  687. data/lib/bioroebe/version/version.rb +44 -0
  688. data/lib/bioroebe/viennarna/README.md +3 -0
  689. data/lib/bioroebe/viennarna/rnafold_wrapper.rb +196 -0
  690. data/lib/bioroebe/with_gui.rb +18 -0
  691. data/lib/bioroebe/www/bioroebe.cgi +44 -0
  692. data/lib/bioroebe/www/embeddable_interface.rb +686 -0
  693. data/lib/bioroebe/www/sinatra/sinatra.rb +1013 -0
  694. data/lib/bioroebe/yaml/agarose/agarose_concentrations.yml +21 -0
  695. data/lib/bioroebe/yaml/aminoacids/amino_acids.yml +92 -0
  696. data/lib/bioroebe/yaml/aminoacids/amino_acids_abbreviations.yml +31 -0
  697. data/lib/bioroebe/yaml/aminoacids/amino_acids_average_mass_table.yml +33 -0
  698. data/lib/bioroebe/yaml/aminoacids/amino_acids_classification.yml +18 -0
  699. data/lib/bioroebe/yaml/aminoacids/amino_acids_english.yml +26 -0
  700. data/lib/bioroebe/yaml/aminoacids/amino_acids_frequency.yml +44 -0
  701. data/lib/bioroebe/yaml/aminoacids/amino_acids_long_name_to_one_letter.yml +61 -0
  702. data/lib/bioroebe/yaml/aminoacids/amino_acids_molecular_formula.yml +32 -0
  703. data/lib/bioroebe/yaml/aminoacids/amino_acids_monoisotopic_mass_table.yml +38 -0
  704. data/lib/bioroebe/yaml/aminoacids/amino_acids_reste.yml +35 -0
  705. data/lib/bioroebe/yaml/aminoacids/amino_acids_three_to_one.yml +34 -0
  706. data/lib/bioroebe/yaml/aminoacids/hydropathy_table.yml +44 -0
  707. data/lib/bioroebe/yaml/aminoacids/molecular_weight.yml +29 -0
  708. data/lib/bioroebe/yaml/aminoacids/simple_aminoacids.yml +66 -0
  709. data/lib/bioroebe/yaml/aminoacids/weight_of_common_proteins.yml +33 -0
  710. data/lib/bioroebe/yaml/antisense/antisense.yml +9 -0
  711. data/lib/bioroebe/yaml/base_composition_of_dna.yml +37 -0
  712. data/lib/bioroebe/yaml/blosum/blosum45.yml +36 -0
  713. data/lib/bioroebe/yaml/blosum/blosum50.yml +34 -0
  714. data/lib/bioroebe/yaml/blosum/blosum62.yml +35 -0
  715. data/lib/bioroebe/yaml/blosum/blosum80.yml +37 -0
  716. data/lib/bioroebe/yaml/blosum/blosum90.yml +36 -0
  717. data/lib/bioroebe/yaml/blosum/blosum_matrix.yml +200 -0
  718. data/lib/bioroebe/yaml/chromosomes/chromosome_numbers.yml +30 -0
  719. data/lib/bioroebe/yaml/codon_tables/1.yml +113 -0
  720. data/lib/bioroebe/yaml/codon_tables/10.yml +89 -0
  721. data/lib/bioroebe/yaml/codon_tables/11.yml +91 -0
  722. data/lib/bioroebe/yaml/codon_tables/12.yml +89 -0
  723. data/lib/bioroebe/yaml/codon_tables/13.yml +89 -0
  724. data/lib/bioroebe/yaml/codon_tables/14.yml +89 -0
  725. data/lib/bioroebe/yaml/codon_tables/15.yml +94 -0
  726. data/lib/bioroebe/yaml/codon_tables/16.yml +89 -0
  727. data/lib/bioroebe/yaml/codon_tables/2.yml +86 -0
  728. data/lib/bioroebe/yaml/codon_tables/21.yml +89 -0
  729. data/lib/bioroebe/yaml/codon_tables/22.yml +89 -0
  730. data/lib/bioroebe/yaml/codon_tables/23.yml +91 -0
  731. data/lib/bioroebe/yaml/codon_tables/24.yml +89 -0
  732. data/lib/bioroebe/yaml/codon_tables/25.yml +89 -0
  733. data/lib/bioroebe/yaml/codon_tables/26.yml +96 -0
  734. data/lib/bioroebe/yaml/codon_tables/27.yml +104 -0
  735. data/lib/bioroebe/yaml/codon_tables/28.yml +97 -0
  736. data/lib/bioroebe/yaml/codon_tables/29.yml +93 -0
  737. data/lib/bioroebe/yaml/codon_tables/3.yml +98 -0
  738. data/lib/bioroebe/yaml/codon_tables/30.yml +91 -0
  739. data/lib/bioroebe/yaml/codon_tables/31.yml +94 -0
  740. data/lib/bioroebe/yaml/codon_tables/33.yml +101 -0
  741. data/lib/bioroebe/yaml/codon_tables/4.yml +96 -0
  742. data/lib/bioroebe/yaml/codon_tables/5.yml +100 -0
  743. data/lib/bioroebe/yaml/codon_tables/6.yml +96 -0
  744. data/lib/bioroebe/yaml/codon_tables/9.yml +97 -0
  745. data/lib/bioroebe/yaml/codon_tables/overview.yml +42 -0
  746. data/lib/bioroebe/yaml/configuration/README.md +12 -0
  747. data/lib/bioroebe/yaml/configuration/browser.yml +1 -0
  748. data/lib/bioroebe/yaml/configuration/colourize_fasta_sequences.yml +14 -0
  749. data/lib/bioroebe/yaml/configuration/default_colours_for_the_aminoacids.yml +28 -0
  750. data/lib/bioroebe/yaml/configuration/temp_dir.yml +1 -0
  751. data/lib/bioroebe/yaml/configuration/try_to_use_matplotlib.yml +1 -0
  752. data/lib/bioroebe/yaml/configuration/use_opn.yml +1 -0
  753. data/lib/bioroebe/yaml/configuration/use_this_database.yml +1 -0
  754. data/lib/bioroebe/yaml/create_these_directories_on_startup/create_these_directories_on_startup.yml +9 -0
  755. data/lib/bioroebe/yaml/default_dna_input.yml +3 -0
  756. data/lib/bioroebe/yaml/enzymes/enzyme_classes.yml +15 -0
  757. data/lib/bioroebe/yaml/enzymes/pH-Optima.yml +11 -0
  758. data/lib/bioroebe/yaml/fasta_and_fastq/fastq_quality_schemes.yml +44 -0
  759. data/lib/bioroebe/yaml/genomes/README.md +16 -0
  760. data/lib/bioroebe/yaml/humans/README.md +2 -0
  761. data/lib/bioroebe/yaml/humans/human_chromosomes.yml +53 -0
  762. data/lib/bioroebe/yaml/laboratory/README.md +1 -0
  763. data/lib/bioroebe/yaml/laboratory/pipettes.yml +8 -0
  764. data/lib/bioroebe/yaml/mRNA/mRNA.yml +16 -0
  765. data/lib/bioroebe/yaml/nuclear_localization_sequences.yml +15 -0
  766. data/lib/bioroebe/yaml/nucleotides/abbreviations_for_nucleotides.yml +29 -0
  767. data/lib/bioroebe/yaml/nucleotides/nucleotide_density.yml +10 -0
  768. data/lib/bioroebe/yaml/nucleotides/nucleotides.yml +34 -0
  769. data/lib/bioroebe/yaml/nucleotides/nucleotides_weight.yml +12 -0
  770. data/lib/bioroebe/yaml/pathways/README.md +2 -0
  771. data/lib/bioroebe/yaml/pathways/citric_acid_cycle.yml +16 -0
  772. data/lib/bioroebe/yaml/pathways/glycolysis.yml +20 -0
  773. data/lib/bioroebe/yaml/pathways/shikimate_pathway.yml +23 -0
  774. data/lib/bioroebe/yaml/pathways/urea_cycle.yml +11 -0
  775. data/lib/bioroebe/yaml/primers/README.md +4 -0
  776. data/lib/bioroebe/yaml/primers/primers.yml +3 -0
  777. data/lib/bioroebe/yaml/promoters/35S.yml +15 -0
  778. data/lib/bioroebe/yaml/promoters/strong_promoters.yml +24 -0
  779. data/lib/bioroebe/yaml/proteases/proteases.yml +3 -0
  780. data/lib/bioroebe/yaml/proteins/ubiquitin.yml +4 -0
  781. data/lib/bioroebe/yaml/remote_urls/README.md +4 -0
  782. data/lib/bioroebe/yaml/remote_urls/remote_urls.yml +3 -0
  783. data/lib/bioroebe/yaml/restriction_enzymes/restriction_enzymes.yml +630 -0
  784. data/lib/bioroebe/yaml/sequences/JX472995_Green_fluorescent_protein_from_Aequorea_victoria.fasta +14 -0
  785. data/lib/bioroebe/yaml/sequences/README.md +2 -0
  786. data/lib/bioroebe/yaml/talens.yml +22 -0
  787. data/lib/bioroebe/yaml/viruses/ecoli_phages.yml +63 -0
  788. data/lib/bioroebe/yaml/viruses/viruses.yml +6 -0
  789. data/lib/bioroebe.rb +5 -0
  790. data/spec/testing_toplevel_method_editor.rb +20 -0
  791. data/spec/testing_toplevel_method_url.rb +15 -0
  792. data/spec/testing_toplevel_method_verbose.rb +13 -0
  793. data/test/advanced_svg_example.rb +307 -0
  794. data/test/testing_bioroebe.rb +25 -0
  795. data/test/testing_codons.rb +45 -0
  796. data/test/testing_dna_to_rna_conversion.rb +15 -0
  797. data/test/testing_parse_pdb_file.rb +23 -0
  798. data/test/testing_reverse_complement.rb +32 -0
  799. data/test/testing_svg_component_of_bioroebe.rb +311 -0
  800. data/test/testing_svg_component_of_bioroebe_from_json_dataset.rb +34 -0
  801. data/test/testing_taxonomy.rb +22 -0
  802. metadata +1059 -0
data/doc/setup.rb ADDED
@@ -0,0 +1,1655 @@
1
+ #!/usr/bin/ruby -w
2
+ # Encoding: UTF-8
3
+ # frozen_string_literal: true
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+ # =========================================================================== #
5
+ # === setup.rb
6
+ #
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+ # Copyright (c) 2000-2005 Minero Aoki
8
+ #
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+ # This program is free software.
10
+ #
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+ # You can distribute/modify this program under the terms of
12
+ # the GNU LGPL, Lesser General Public License version 2.1.
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+ #
14
+ # Note that this was modified in 2021 - a few begin/rescue clauses
15
+ # were added.
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+ # =========================================================================== #
17
+ unless Errno.const_defined?(:ENOTEMPTY) # Windows?
18
+ module Errno
19
+ class ENOTEMPTY
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+ # We do not raise this exception, implementation is not needed.
21
+ end
22
+ end
23
+ end
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+
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+ def File.binread(fname)
26
+ open(fname, 'rb') {|f|
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+ return f.read
28
+ }
29
+ end
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+
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+ # for corrupted Windows' stat(2)
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+ def File.dir?(path)
33
+ File.directory?((path[-1,1] == '/') ? path : path + '/')
34
+ end
35
+
36
+ class ConfigTable
37
+
38
+ include Enumerable
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+
40
+ # ========================================================================= #
41
+ # === initialize
42
+ # ========================================================================= #
43
+ def initialize(rbconfig)
44
+ @rbconfig = rbconfig
45
+ @items = []
46
+ @table = {}
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+ # options
48
+ @install_prefix = nil
49
+ @config_opt = nil
50
+ @verbose = true
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+ @no_harm = false
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+ end
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+
54
+ attr_accessor :install_prefix
55
+ attr_accessor :config_opt
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+
57
+ attr_writer :no_harm
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+ attr_writer :verbose
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+
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+ # ========================================================================= #
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+ # === verbose?
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+ # ========================================================================= #
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+ def verbose?
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+ @verbose
65
+ end
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+
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+ # ========================================================================= #
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+ # === no_harm?
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+ # ========================================================================= #
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+ def no_harm?
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+ @no_harm
72
+ end
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+
74
+ # ========================================================================= #
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+ # === []
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+ # ========================================================================= #
77
+ def [](key)
78
+ lookup(key).resolve(self)
79
+ end
80
+
81
+ def []=(key, val)
82
+ lookup(key).set val
83
+ end
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+
85
+ # ========================================================================= #
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+ # === names
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+ # ========================================================================= #
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+ def names
89
+ @items.map {|i| i.name }
90
+ end
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+
92
+ def each(&block)
93
+ @items.each(&block)
94
+ end
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+
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+ # === key?
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+ def key?(i)
98
+ @table.key?(i)
99
+ end
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+
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+ # ========================================================================= #
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+ # === lookup
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+ # ========================================================================= #
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+ def lookup(name)
105
+ @table[name] or setup_rb_error "no such config item: #{name}"
106
+ end
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+
108
+ # ========================================================================= #
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+ # === add
110
+ # ========================================================================= #
111
+ def add(item)
112
+ @items.push item
113
+ @table[item.name] = item
114
+ end
115
+
116
+ # ========================================================================= #
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+ # === remove
118
+ # ========================================================================= #
119
+ def remove(name)
120
+ item = lookup(name)
121
+ @items.delete_if {|i| i.name == name }
122
+ @table.delete_if {|inner_name, i| i.name == inner_name }
123
+ item
124
+ end
125
+
126
+ # ========================================================================= #
127
+ # === load_script
128
+ # ========================================================================= #
129
+ def load_script(path, inst = nil)
130
+ if File.file?(path)
131
+ MetaConfigEnvironment.new(self, inst).instance_eval File.read(path), path
132
+ end
133
+ end
134
+
135
+ # ========================================================================= #
136
+ # === savefile
137
+ # ========================================================================= #
138
+ def savefile
139
+ '.config'
140
+ end
141
+
142
+ # ========================================================================= #
143
+ # === load_savefile
144
+ # ========================================================================= #
145
+ def load_savefile
146
+ begin
147
+ File.foreach(savefile()) { |line|
148
+ k, v = *line.split(/=/, 2)
149
+ self[k] = v.strip
150
+ }
151
+ rescue Errno::ENOENT
152
+ setup_rb_error $!.message + "\n#{File.basename($0)} config first"
153
+ end
154
+ end
155
+
156
+ # ========================================================================= #
157
+ # === save
158
+ # ========================================================================= #
159
+ def save
160
+ @items.each {|i| i.value }
161
+ File.open(savefile(), 'w') {|f|
162
+ @items.each do |i|
163
+ f.printf "%s=%s\n", i.name, i.value if i.value? and i.value
164
+ end
165
+ }
166
+ end
167
+
168
+ # ========================================================================= #
169
+ # === load_standard_entries
170
+ # ========================================================================= #
171
+ def load_standard_entries
172
+ standard_entries(@rbconfig).each {|entry|
173
+ add entry
174
+ }
175
+ end
176
+
177
+ # ========================================================================= #
178
+ # === standard_entries
179
+ # ========================================================================= #
180
+ def standard_entries(rbconfig)
181
+ c = rbconfig
182
+
183
+ rubypath = File.join(c['bindir'], c['ruby_install_name'] + c['EXEEXT'])
184
+
185
+ major = c['MAJOR'].to_i
186
+ minor = c['MINOR'].to_i
187
+ teeny = c['TEENY'].to_i
188
+ version = "#{major}.#{minor}"
189
+
190
+ # ======================================================================= #
191
+ # ruby ver. >= 1.4.4?
192
+ # ======================================================================== #
193
+ newpath_p = ((major >= 2) or
194
+ ((major == 1) and
195
+ ((minor >= 5) or
196
+ ((minor == 4) and (teeny >= 4)))))
197
+
198
+ if c['rubylibdir']
199
+ # V > 1.6.3
200
+ libruby = "#{c['prefix']}/lib/ruby"
201
+ librubyver = c['rubylibdir']
202
+ librubyverarch = c['archdir']
203
+ siteruby = c['sitedir']
204
+ siterubyver = c['sitelibdir']
205
+ siterubyverarch = c['sitearchdir']
206
+ elsif newpath_p
207
+ # 1.4.4 <= V <= 1.6.3
208
+ libruby = "#{c['prefix']}/lib/ruby"
209
+ librubyver = "#{c['prefix']}/lib/ruby/#{version}"
210
+ librubyverarch = "#{c['prefix']}/lib/ruby/#{version}/#{c['arch']}"
211
+ siteruby = c['sitedir']
212
+ siterubyver = "$siteruby/#{version}"
213
+ siterubyverarch = "$siterubyver/#{c['arch']}"
214
+ else
215
+ # V < 1.4.4
216
+ libruby = "#{c['prefix']}/lib/ruby"
217
+ librubyver = "#{c['prefix']}/lib/ruby/#{version}"
218
+ librubyverarch = "#{c['prefix']}/lib/ruby/#{version}/#{c['arch']}"
219
+ siteruby = "#{c['prefix']}/lib/ruby/#{version}/site_ruby"
220
+ siterubyver = siteruby
221
+ siterubyverarch = "$siterubyver/#{c['arch']}"
222
+ end
223
+ parameterize = lambda {|path|
224
+ path.sub(/\A#{Regexp.quote(c['prefix'])}/, '$prefix')
225
+ }
226
+
227
+ if arg = c['configure_args'].split.detect {|inner_arg| /--with-make-prog=/ =~ inner_arg }
228
+ makeprog = arg.sub(/'/, '').split(/=/, 2)[1]
229
+ else
230
+ makeprog = 'make'
231
+ end
232
+
233
+ [
234
+ ExecItem.new('installdirs', 'std/site/home',
235
+ 'std: install under libruby; site: install under site_ruby; home: install under $HOME')\
236
+ {|val, table|
237
+ case val
238
+ when 'std'
239
+ table['rbdir'] = '$librubyver'
240
+ table['sodir'] = '$librubyverarch'
241
+ when 'site'
242
+ table['rbdir'] = '$siterubyver'
243
+ table['sodir'] = '$siterubyverarch'
244
+ when 'home'
245
+ setup_rb_error '$HOME was not set' unless ENV['HOME']
246
+ table['prefix'] = ENV['HOME']
247
+ table['rbdir'] = '$libdir/ruby'
248
+ table['sodir'] = '$libdir/ruby'
249
+ end
250
+ },
251
+ PathItem.new('prefix', 'path', c['prefix'],
252
+ 'path prefix of target environment'),
253
+ PathItem.new('bindir', 'path', parameterize.call(c['bindir']),
254
+ 'the directory for commands'),
255
+ PathItem.new('libdir', 'path', parameterize.call(c['libdir']),
256
+ 'the directory for libraries'),
257
+ PathItem.new('datadir', 'path', parameterize.call(c['datadir']),
258
+ 'the directory for shared data'),
259
+ PathItem.new('mandir', 'path', parameterize.call(c['mandir']),
260
+ 'the directory for man pages'),
261
+ PathItem.new('sysconfdir', 'path', parameterize.call(c['sysconfdir']),
262
+ 'the directory for system configuration files'),
263
+ PathItem.new('localstatedir', 'path', parameterize.call(c['localstatedir']),
264
+ 'the directory for local state data'),
265
+ PathItem.new('libruby', 'path', libruby,
266
+ 'the directory for ruby libraries'),
267
+ PathItem.new('librubyver', 'path', librubyver,
268
+ 'the directory for standard ruby libraries'),
269
+ PathItem.new('librubyverarch', 'path', librubyverarch,
270
+ 'the directory for standard ruby extensions'),
271
+ PathItem.new('siteruby', 'path', siteruby,
272
+ 'the directory for version-independent aux ruby libraries'),
273
+ PathItem.new('siterubyver', 'path', siterubyver,
274
+ 'the directory for aux ruby libraries'),
275
+ PathItem.new('siterubyverarch', 'path', siterubyverarch,
276
+ 'the directory for aux ruby binaries'),
277
+ PathItem.new('rbdir', 'path', '$siterubyver',
278
+ 'the directory for ruby scripts'),
279
+ PathItem.new('sodir', 'path', '$siterubyverarch',
280
+ 'the directory for ruby extentions'),
281
+ PathItem.new('rubypath', 'path', rubypath,
282
+ 'the path to set to #! line'),
283
+ ProgramItem.new('rubyprog', 'name', rubypath,
284
+ 'the ruby program using for installation'),
285
+ ProgramItem.new('makeprog', 'name', makeprog,
286
+ 'the make program to compile ruby extentions'),
287
+ SelectItem.new('shebang', 'all/ruby/never', 'ruby',
288
+ 'shebang line (#!) editing mode'),
289
+ BoolItem.new('without-ext', 'yes/no', 'no',
290
+ 'does not compile/install ruby extentions')
291
+ ]
292
+ end
293
+ private :standard_entries
294
+
295
+ # ========================================================================= #
296
+ # === load_multipackage_entries
297
+ # ========================================================================= #
298
+ def load_multipackage_entries
299
+ multipackage_entries().each do |ent|
300
+ add ent
301
+ end
302
+ end
303
+
304
+ # ========================================================================= #
305
+ # === multipackage_entries
306
+ # ========================================================================= #
307
+ def multipackage_entries
308
+ [
309
+ PackageSelectionItem.new('with', 'name,name...', '', 'ALL',
310
+ 'package names that you want to install'),
311
+ PackageSelectionItem.new('without', 'name,name...', '', 'NONE',
312
+ 'package names that you do not want to install')
313
+ ]
314
+ end
315
+ private :multipackage_entries
316
+
317
+ ALIASES = {
318
+ 'std-ruby' => 'librubyver',
319
+ 'stdruby' => 'librubyver',
320
+ 'rubylibdir' => 'librubyver',
321
+ 'archdir' => 'librubyverarch',
322
+ 'site-ruby-common' => 'siteruby', # For backward compatibility
323
+ 'site-ruby' => 'siterubyver', # For backward compatibility
324
+ 'bin-dir' => 'bindir',
325
+ 'rb-dir' => 'rbdir',
326
+ 'so-dir' => 'sodir',
327
+ 'data-dir' => 'datadir',
328
+ 'ruby-path' => 'rubypath',
329
+ 'ruby-prog' => 'rubyprog',
330
+ 'ruby' => 'rubyprog',
331
+ 'make-prog' => 'makeprog',
332
+ 'make' => 'makeprog'
333
+ }
334
+
335
+ # ========================================================================= #
336
+ # === fixup
337
+ # ========================================================================= #
338
+ def fixup
339
+ ALIASES.each { |ali, name|
340
+ @table[ali] = @table[name]
341
+ }
342
+ @items.freeze
343
+ @table.freeze
344
+ @options_re = /\A--(#{@table.keys.join('|')})(?:=(.*))?\z/
345
+ end
346
+
347
+ # ========================================================================= #
348
+ # === parse_opt
349
+ # ========================================================================= #
350
+ def parse_opt(opt)
351
+ m = @options_re.match(opt) or setup_rb_error "config: unknown option #{opt}"
352
+ m.to_a[1,2]
353
+ end
354
+
355
+ def dllext
356
+ @rbconfig['DLEXT']
357
+ end
358
+
359
+ def value_config?(name)
360
+ lookup(name).value?
361
+ end
362
+
363
+ class Item
364
+ def initialize(name, template, default, desc)
365
+ @name = name.freeze
366
+ @template = template
367
+ @value = default
368
+ @default = default
369
+ @description = desc
370
+ end
371
+
372
+ attr_reader :name
373
+ attr_reader :description
374
+
375
+ attr_accessor :default
376
+ alias help_default default
377
+
378
+ def help_opt
379
+ "--#{@name}=#{@template}"
380
+ end
381
+
382
+ def value?
383
+ true
384
+ end
385
+
386
+ def value
387
+ @value
388
+ end
389
+
390
+ def resolve(table)
391
+ @value.gsub(%r<\$([^/]+)>) { table[$1] }
392
+ end
393
+
394
+ def set(val)
395
+ @value = check(val)
396
+ end
397
+
398
+ private
399
+
400
+ def check(val)
401
+ setup_rb_error "config: --#{name} requires argument" unless val
402
+ val
403
+ end
404
+ end
405
+
406
+ class BoolItem < Item
407
+ def config_type
408
+ 'bool'
409
+ end
410
+
411
+ def help_opt
412
+ "--#{@name}"
413
+ end
414
+
415
+ private
416
+
417
+ def check(val)
418
+ return 'yes' unless val
419
+ case val
420
+ when /\Ay(es)?\z/i, /\At(rue)?\z/i then 'yes'
421
+ when /\An(o)?\z/i, /\Af(alse)\z/i then 'no'
422
+ else
423
+ setup_rb_error "config: --#{@name} accepts only yes/no for argument"
424
+ end
425
+ end
426
+ end
427
+
428
+ class PathItem < Item
429
+ def config_type
430
+ 'path'
431
+ end
432
+
433
+ private
434
+
435
+ def check(path)
436
+ setup_rb_error "config: --#{@name} requires argument" unless path
437
+ path[0,1] == '$' ? path : File.expand_path(path)
438
+ end
439
+ end
440
+
441
+ class ProgramItem < Item
442
+ def config_type
443
+ 'program'
444
+ end
445
+ end
446
+
447
+ class SelectItem < Item
448
+ def initialize(name, selection, default, desc)
449
+ super
450
+ @ok = selection.split('/')
451
+ end
452
+
453
+ def config_type
454
+ 'select'
455
+ end
456
+
457
+ private
458
+
459
+ def check(val)
460
+ unless @ok.include?(val.strip)
461
+ setup_rb_error "config: use --#{@name}=#{@template} (#{val})"
462
+ end
463
+ val.strip
464
+ end
465
+ end
466
+
467
+ class ExecItem < Item
468
+ def initialize(name, selection, desc, &block)
469
+ super name, selection, nil, desc
470
+ @ok = selection.split('/')
471
+ @action = block
472
+ end
473
+
474
+ def config_type
475
+ 'exec'
476
+ end
477
+
478
+ def value?
479
+ false
480
+ end
481
+
482
+ def resolve(table)
483
+ setup_rb_error "$#{name()} wrongly used as option value"
484
+ end
485
+
486
+ undef set
487
+
488
+ def evaluate(val, table)
489
+ v = val.strip.downcase
490
+ unless @ok.include?(v)
491
+ setup_rb_error "invalid option --#{@name}=#{val} (use #{@template})"
492
+ end
493
+ @action.call v, table
494
+ end
495
+ end
496
+
497
+ class PackageSelectionItem < Item
498
+ def initialize(name, template, default, help_default, desc)
499
+ super name, template, default, desc
500
+ @help_default = help_default
501
+ end
502
+
503
+ attr_reader :help_default
504
+
505
+ def config_type
506
+ 'package'
507
+ end
508
+
509
+ private
510
+
511
+ def check(val)
512
+ unless File.dir?("packages/#{val}")
513
+ setup_rb_error "config: no such package: #{val}"
514
+ end
515
+ val
516
+ end
517
+ end
518
+
519
+ class MetaConfigEnvironment
520
+ def initialize(config, installer)
521
+ @config = config
522
+ @installer = installer
523
+ end
524
+
525
+ def config_names
526
+ @config.names
527
+ end
528
+
529
+ def config?(name)
530
+ @config.key?(name)
531
+ end
532
+
533
+ def bool_config?(name)
534
+ @config.lookup(name).config_type == 'bool'
535
+ end
536
+
537
+ def path_config?(name)
538
+ @config.lookup(name).config_type == 'path'
539
+ end
540
+
541
+ def value_config?(name)
542
+ @config.lookup(name).config_type != 'exec'
543
+ end
544
+
545
+ def add_config(item)
546
+ @config.add item
547
+ end
548
+
549
+ def add_bool_config(name, default, desc)
550
+ @config.add BoolItem.new(name, 'yes/no', default ? 'yes' : 'no', desc)
551
+ end
552
+
553
+ def add_path_config(name, default, desc)
554
+ @config.add PathItem.new(name, 'path', default, desc)
555
+ end
556
+
557
+ def set_config_default(name, default)
558
+ @config.lookup(name).default = default
559
+ end
560
+
561
+ def remove_config(name)
562
+ @config.remove(name)
563
+ end
564
+
565
+ # For only multipackage
566
+ def packages
567
+ raise '[setup.rb fatal] multi-package metaconfig API packages() called for single-package; contact application package vendor' unless @installer
568
+ @installer.packages
569
+ end
570
+
571
+ # For only multipackage
572
+ def declare_packages(list)
573
+ raise '[setup.rb fatal] multi-package metaconfig API declare_packages() called for single-package; contact application package vendor' unless @installer
574
+ @installer.packages = list
575
+ end
576
+ end
577
+
578
+ end # class ConfigTable
579
+
580
+ # This module requires: #verbose?, #no_harm?
581
+ module FileOperations
582
+
583
+ def mkdir_p(dirname, prefix = nil)
584
+ dirname = prefix + File.expand_path(dirname) if prefix
585
+ $stderr.puts "mkdir -p #{dirname}" if verbose?
586
+ return if no_harm?
587
+
588
+ # Does not check '/', it's too abnormal.
589
+ dirs = File.expand_path(dirname).split(%r<(?=/)>)
590
+ if /\A[a-z]:\z/i =~ dirs[0]
591
+ disk = dirs.shift
592
+ dirs[0] = disk + dirs[0]
593
+ end
594
+ dirs.each_index do |idx|
595
+ path = dirs[0..idx].join('')
596
+ Dir.mkdir path unless File.dir?(path)
597
+ end
598
+ end
599
+
600
+ def rm_f(path)
601
+ $stderr.puts "rm -f #{path}" if verbose?
602
+ return if no_harm?
603
+ force_remove_file path
604
+ end
605
+
606
+ def rm_rf(path)
607
+ $stderr.puts "rm -rf #{path}" if verbose?
608
+ return if no_harm?
609
+ remove_tree path
610
+ end
611
+
612
+ def remove_tree(path)
613
+ if File.symlink?(path)
614
+ remove_file path
615
+ elsif File.dir?(path)
616
+ remove_tree0 path
617
+ else
618
+ force_remove_file path
619
+ end
620
+ end
621
+
622
+ def remove_tree0(path)
623
+ Dir.foreach(path) do |ent|
624
+ next if ent == '.'
625
+ next if ent == '..'
626
+ entpath = "#{path}/#{ent}"
627
+ if File.symlink?(entpath)
628
+ remove_file entpath
629
+ elsif File.dir?(entpath)
630
+ remove_tree0 entpath
631
+ else
632
+ force_remove_file entpath
633
+ end
634
+ end
635
+ begin
636
+ Dir.rmdir path
637
+ rescue Errno::ENOTEMPTY
638
+ # directory may not be empty
639
+ end
640
+ end
641
+
642
+ def move_file(src, dest)
643
+ force_remove_file dest
644
+ begin
645
+ File.rename src, dest
646
+ rescue
647
+ File.open(dest, 'wb') {|f|
648
+ f.write File.binread(src)
649
+ }
650
+ File.chmod File.stat(src).mode, dest
651
+ File.unlink src
652
+ end
653
+ end
654
+
655
+ def force_remove_file(path)
656
+ begin
657
+ remove_file path
658
+ rescue
659
+ end
660
+ end
661
+
662
+ def remove_file(path)
663
+ File.chmod 0777, path
664
+ File.unlink path
665
+ end
666
+
667
+ # === install
668
+ def install(from, dest, mode, prefix = nil)
669
+ $stderr.puts "install #{from} #{dest}" if verbose?
670
+ return if no_harm?
671
+
672
+ realdest = prefix ? prefix + File.expand_path(dest) : dest
673
+ realdest = File.join(realdest, File.basename(from)) if File.dir?(realdest)
674
+ str = File.binread(from)
675
+ if diff?(str, realdest)
676
+ verbose_off {
677
+ rm_f realdest if File.exist?(realdest)
678
+ }
679
+ begin
680
+ File.open(realdest, 'wb') {|f|
681
+ f.write(str)
682
+ }
683
+ rescue Errno::ENOENT => error
684
+ pp error
685
+ end
686
+ File.chmod(mode, realdest) if File.exist? realdest
687
+
688
+ File.open("#{objdir_root()}/InstalledFiles", 'a') {|f|
689
+ if prefix
690
+ f.puts realdest.sub(prefix, '')
691
+ else
692
+ f.puts realdest
693
+ end
694
+ }
695
+ end
696
+ end
697
+
698
+ # === diff?
699
+ def diff?(new_content, path)
700
+ return true unless File.exist?(path)
701
+ new_content != File.binread(path)
702
+ end
703
+
704
+ def command(*args)
705
+ $stderr.puts args.join(' ') if verbose?
706
+ system(*args) or raise RuntimeError,
707
+ "system(#{args.map{|a| a.inspect }.join(' ')}) failed"
708
+ end
709
+
710
+ def ruby(*args)
711
+ command config('rubyprog'), *args
712
+ end
713
+
714
+ def make(task = nil)
715
+ command(*[config('makeprog'), task].compact)
716
+ end
717
+
718
+ def extdir?(dir)
719
+ File.exist?("#{dir}/MANIFEST") or File.exist?("#{dir}/extconf.rb")
720
+ end
721
+
722
+ def files_of(dir)
723
+ Dir.open(dir) {|d|
724
+ return d.select {|ent| File.file?("#{dir}/#{ent}") }
725
+ }
726
+ end
727
+
728
+ DIR_REJECT = %w( . .. CVS SCCS RCS CVS.adm .svn )
729
+
730
+ def directories_of(dir)
731
+ Dir.open(dir) {|d|
732
+ return d.select {|ent| File.dir?("#{dir}/#{ent}") } - DIR_REJECT
733
+ }
734
+ end
735
+
736
+ end
737
+
738
+
739
+ # This module requires: #srcdir_root, #objdir_root, #relpath
740
+ module HookScriptAPI
741
+
742
+ def get_config(key)
743
+ @config[key]
744
+ end
745
+
746
+ alias config get_config
747
+
748
+ # obsolete: use metaconfig to change configuration
749
+ def set_config(key, val)
750
+ @config[key] = val
751
+ end
752
+
753
+ #
754
+ # srcdir/objdir (works only in the package directory)
755
+ #
756
+
757
+ def curr_srcdir
758
+ "#{srcdir_root()}/#{relpath()}"
759
+ end
760
+
761
+ def curr_objdir
762
+ "#{objdir_root()}/#{relpath()}"
763
+ end
764
+
765
+ def srcfile(path)
766
+ "#{curr_srcdir()}/#{path}"
767
+ end
768
+
769
+ def srcexist?(path)
770
+ File.exist?(srcfile(path))
771
+ end
772
+
773
+ def srcdirectory?(path)
774
+ File.dir?(srcfile(path))
775
+ end
776
+
777
+ def srcfile?(path)
778
+ File.file?(srcfile(path))
779
+ end
780
+
781
+ def srcentries(path = '.')
782
+ Dir.open("#{curr_srcdir()}/#{path}") {|d|
783
+ return d.to_a - %w(. ..)
784
+ }
785
+ end
786
+
787
+ def srcfiles(path = '.')
788
+ srcentries(path).select {|fname|
789
+ File.file?(File.join(curr_srcdir(), path, fname))
790
+ }
791
+ end
792
+
793
+ def srcdirectories(path = '.')
794
+ srcentries(path).select {|fname|
795
+ File.dir?(File.join(curr_srcdir(), path, fname))
796
+ }
797
+ end
798
+
799
+ end
800
+
801
+
802
+ class ToplevelInstaller
803
+
804
+ Version = '3.4.1'
805
+ Copyright = 'Copyright (c) 2000-2005 Minero Aoki'
806
+
807
+ TASKS = [
808
+ [ 'all', 'do config, setup, then install' ],
809
+ [ 'config', 'saves your configurations' ],
810
+ [ 'show', 'shows current configuration' ],
811
+ [ 'setup', 'compiles ruby extentions and others' ],
812
+ [ 'install', 'installs files' ],
813
+ [ 'test', 'run all tests in test/' ],
814
+ [ 'clean', "does `make clean' for each extention" ],
815
+ [ 'distclean',"does `make distclean' for each extention" ]
816
+ ]
817
+
818
+ def ToplevelInstaller.invoke
819
+ config = ConfigTable.new(load_rbconfig())
820
+ config.load_standard_entries
821
+ config.load_multipackage_entries if multipackage?
822
+ config.fixup
823
+ klass = (multipackage?() ? ToplevelInstallerMulti : ToplevelInstaller)
824
+ klass.new(File.dirname($0), config).invoke
825
+ end
826
+
827
+ def ToplevelInstaller.multipackage?
828
+ File.dir?(File.dirname($0) + '/packages')
829
+ end
830
+
831
+ def ToplevelInstaller.load_rbconfig
832
+ if arg = ARGV.detect {|inner_arg| /\A--rbconfig=/ =~ inner_arg }
833
+ ARGV.delete(arg)
834
+ load File.expand_path(arg.split(/=/, 2)[1])
835
+ $".push 'rbconfig.rb'
836
+ else
837
+ require 'rbconfig'
838
+ end
839
+ ::RbConfig::CONFIG
840
+ end
841
+
842
+ def initialize(ardir_root, config)
843
+ @ardir = File.expand_path(ardir_root)
844
+ @config = config
845
+ # cache
846
+ @valid_task_re = nil
847
+ end
848
+
849
+ # ========================================================================= #
850
+ # === config
851
+ # ========================================================================= #
852
+ def config(key)
853
+ @config[key]
854
+ end
855
+
856
+ def inspect
857
+ "#<#{self.class} #{__id__()}>"
858
+ end
859
+
860
+ def invoke
861
+ run_metaconfigs
862
+ case task = parsearg_global()
863
+ when nil, 'all'
864
+ parsearg_config
865
+ init_installers
866
+ exec_config
867
+ exec_setup
868
+ exec_install
869
+ else
870
+ case task
871
+ # === config
872
+ when 'config', 'test'
873
+ ;
874
+ when 'clean', 'distclean'
875
+ @config.load_savefile if File.exist?(@config.savefile)
876
+ else
877
+ @config.load_savefile
878
+ end
879
+ __send__ "parsearg_#{task}"
880
+ init_installers
881
+ __send__ "exec_#{task}"
882
+ end
883
+ end
884
+
885
+ def run_metaconfigs
886
+ @config.load_script "#{@ardir}/metaconfig"
887
+ end
888
+
889
+ def init_installers
890
+ @installer = Installer.new(@config, @ardir, File.expand_path('.'))
891
+ end
892
+
893
+ #
894
+ # Hook Script API bases
895
+ #
896
+
897
+ def srcdir_root
898
+ @ardir
899
+ end
900
+
901
+ def objdir_root
902
+ '.'
903
+ end
904
+
905
+ def relpath
906
+ '.'
907
+ end
908
+
909
+ #
910
+ # Option Parsing
911
+ #
912
+
913
+ def parsearg_global
914
+ while arg = ARGV.shift
915
+ case arg
916
+ when /\A\w+\z/
917
+ setup_rb_error "invalid task: #{arg}" unless valid_task?(arg)
918
+ return arg
919
+ when '-q', '--quiet'
920
+ @config.verbose = false
921
+ when '--verbose'
922
+ @config.verbose = true
923
+ when '--help'
924
+ print_usage $stdout
925
+ exit 0
926
+ when '--version'
927
+ puts "#{File.basename($0)} version #{Version}"
928
+ exit 0
929
+ when '--copyright'
930
+ puts Copyright
931
+ exit 0
932
+ else
933
+ setup_rb_error "unknown global option '#{arg}'"
934
+ end
935
+ end
936
+ nil
937
+ end
938
+
939
+ def valid_task?(t)
940
+ valid_task_re() =~ t
941
+ end
942
+
943
+ def valid_task_re
944
+ @valid_task_re ||= /\A(?:#{TASKS.map {|task,desc| task }.join('|')})\z/
945
+ end
946
+
947
+ def parsearg_no_options
948
+ unless ARGV.empty?
949
+ task = caller(0).first.slice(%r<`parsearg_(\w+)'>, 1)
950
+ setup_rb_error "#{task}: unknown options: #{ARGV.join(' ')}"
951
+ end
952
+ end
953
+
954
+ alias parsearg_show parsearg_no_options
955
+ alias parsearg_setup parsearg_no_options
956
+ alias parsearg_test parsearg_no_options
957
+ alias parsearg_clean parsearg_no_options
958
+ alias parsearg_distclean parsearg_no_options
959
+
960
+ def parsearg_config
961
+ evalopt = []
962
+ set = []
963
+ @config.config_opt = []
964
+ while i = ARGV.shift
965
+ if /\A--?\z/ =~ i
966
+ @config.config_opt = ARGV.dup
967
+ break
968
+ end
969
+ name, value = *@config.parse_opt(i)
970
+ if @config.value_config?(name)
971
+ @config[name] = value
972
+ else
973
+ evalopt.push [name, value]
974
+ end
975
+ set.push name
976
+ end
977
+ evalopt.each do |inner_name, inner_value|
978
+ @config.lookup(inner_name).evaluate inner_value, @config
979
+ end
980
+ # Check if configuration is valid
981
+ set.each do |n|
982
+ @config[n] if @config.value_config?(n)
983
+ end
984
+ end
985
+
986
+ def parsearg_install
987
+ @config.no_harm = false
988
+ @config.install_prefix = ''
989
+ while a = ARGV.shift
990
+ case a
991
+ when '--no-harm'
992
+ @config.no_harm = true
993
+ when /\A--prefix=/
994
+ path = a.split(/=/, 2)[1]
995
+ path = File.expand_path(path) unless path[0,1] == '/'
996
+ @config.install_prefix = path
997
+ else
998
+ setup_rb_error "install: unknown option #{a}"
999
+ end
1000
+ end
1001
+ end
1002
+
1003
+ def print_usage(out)
1004
+ out.puts 'Typical Installation Procedure:'
1005
+ out.puts " $ ruby #{File.basename $0} config"
1006
+ out.puts " $ ruby #{File.basename $0} setup"
1007
+ out.puts " # ruby #{File.basename $0} install (may require root privilege)"
1008
+ out.puts
1009
+ out.puts 'Detailed Usage:'
1010
+ out.puts " ruby #{File.basename $0} <global option>"
1011
+ out.puts " ruby #{File.basename $0} [<global options>] <task> [<task options>]"
1012
+
1013
+ fmt = " %-24s %s\n"
1014
+ out.puts
1015
+ out.puts 'Global options:'
1016
+ out.printf fmt, '-q,--quiet', 'suppress message outputs'
1017
+ out.printf fmt, ' --verbose', 'output messages verbosely'
1018
+ out.printf fmt, ' --help', 'print this message'
1019
+ out.printf fmt, ' --version', 'print version and quit'
1020
+ out.printf fmt, ' --copyright', 'print copyright and quit'
1021
+ out.puts
1022
+ out.puts 'Tasks:'
1023
+ TASKS.each do |name, desc|
1024
+ out.printf fmt, name, desc
1025
+ end
1026
+
1027
+ fmt = " %-24s %s [%s]\n"
1028
+ out.puts
1029
+ out.puts 'Options for CONFIG or ALL:'
1030
+ @config.each do |item|
1031
+ out.printf fmt, item.help_opt, item.description, item.help_default
1032
+ end
1033
+ out.printf fmt, '--rbconfig=path', 'rbconfig.rb to load',"running ruby's"
1034
+ out.puts
1035
+ out.puts 'Options for INSTALL:'
1036
+ out.printf fmt, '--no-harm', 'only display what to do if given', 'off'
1037
+ out.printf fmt, '--prefix=path', 'install path prefix', ''
1038
+ out.puts
1039
+ end
1040
+
1041
+ #
1042
+ # Task Handlers
1043
+ #
1044
+
1045
+ def exec_config
1046
+ @installer.exec_config
1047
+ @config.save # must be final
1048
+ end
1049
+
1050
+ def exec_setup
1051
+ @installer.exec_setup
1052
+ end
1053
+
1054
+ def exec_install
1055
+ @installer.exec_install
1056
+ end
1057
+
1058
+ def exec_test
1059
+ @installer.exec_test
1060
+ end
1061
+
1062
+ def exec_show
1063
+ @config.each do |i|
1064
+ printf "%-20s %s\n", i.name, i.value if i.value?
1065
+ end
1066
+ end
1067
+
1068
+ def exec_clean
1069
+ @installer.exec_clean
1070
+ end
1071
+
1072
+ def exec_distclean
1073
+ @installer.exec_distclean
1074
+ end
1075
+
1076
+ end # class ToplevelInstaller
1077
+
1078
+
1079
+ class ToplevelInstallerMulti < ToplevelInstaller
1080
+
1081
+ include FileOperations
1082
+
1083
+ def initialize(ardir_root, config)
1084
+ super
1085
+ @packages = directories_of("#{@ardir}/packages")
1086
+ raise 'no package exists' if @packages.empty?
1087
+ @root_installer = Installer.new(@config, @ardir, File.expand_path('.'))
1088
+ end
1089
+
1090
+ def run_metaconfigs
1091
+ @config.load_script "#{@ardir}/metaconfig", self
1092
+ @packages.each do |name|
1093
+ @config.load_script "#{@ardir}/packages/#{name}/metaconfig"
1094
+ end
1095
+ end
1096
+
1097
+ attr_reader :packages
1098
+
1099
+ def packages=(list)
1100
+ raise 'package list is empty' if list.empty?
1101
+ list.each do |name|
1102
+ raise "directory packages/#{name} does not exist"\
1103
+ unless File.dir?("#{@ardir}/packages/#{name}")
1104
+ end
1105
+ @packages = list
1106
+ end
1107
+
1108
+ def init_installers
1109
+ @installers = {}
1110
+ @packages.each do |pack|
1111
+ @installers[pack] = Installer.new(@config,
1112
+ "#{@ardir}/packages/#{pack}",
1113
+ "packages/#{pack}")
1114
+ end
1115
+ with = extract_selection(config('with'))
1116
+ without = extract_selection(config('without'))
1117
+ @selected = @installers.keys.select {|name|
1118
+ (with.empty? or with.include?(name)) \
1119
+ and not without.include?(name)
1120
+ }
1121
+ end
1122
+
1123
+ def extract_selection(list)
1124
+ a = list.split(/,/)
1125
+ a.each do |name|
1126
+ setup_rb_error "no such package: #{name}" unless @installers.key?(name)
1127
+ end
1128
+ a
1129
+ end
1130
+
1131
+ def print_usage(f)
1132
+ super
1133
+ f.puts 'Inluded packages:'
1134
+ f.puts ' ' + @packages.sort.join(' ')
1135
+ f.puts
1136
+ end
1137
+
1138
+ #
1139
+ # Task Handlers
1140
+ #
1141
+
1142
+ def exec_config
1143
+ run_hook 'pre-config'
1144
+ each_selected_installers {|inst| inst.exec_config }
1145
+ run_hook 'post-config'
1146
+ @config.save # must be final
1147
+ end
1148
+
1149
+ def exec_setup
1150
+ run_hook 'pre-setup'
1151
+ each_selected_installers {|inst| inst.exec_setup }
1152
+ run_hook 'post-setup'
1153
+ end
1154
+
1155
+ def exec_install
1156
+ run_hook 'pre-install'
1157
+ each_selected_installers {|inst| inst.exec_install }
1158
+ run_hook 'post-install'
1159
+ end
1160
+
1161
+ def exec_test
1162
+ run_hook 'pre-test'
1163
+ each_selected_installers {|inst| inst.exec_test }
1164
+ run_hook 'post-test'
1165
+ end
1166
+
1167
+ def exec_clean
1168
+ rm_f @config.savefile
1169
+ run_hook 'pre-clean'
1170
+ each_selected_installers {|inst| inst.exec_clean }
1171
+ run_hook 'post-clean'
1172
+ end
1173
+
1174
+ def exec_distclean
1175
+ rm_f @config.savefile
1176
+ run_hook 'pre-distclean'
1177
+ each_selected_installers {|inst| inst.exec_distclean }
1178
+ run_hook 'post-distclean'
1179
+ end
1180
+
1181
+ #
1182
+ # lib
1183
+ #
1184
+
1185
+ def each_selected_installers
1186
+ Dir.mkdir 'packages' unless File.dir?('packages')
1187
+ @selected.each do |pack|
1188
+ $stderr.puts "Processing the package `#{pack}' ..." if verbose?
1189
+ Dir.mkdir "packages/#{pack}" unless File.dir?("packages/#{pack}")
1190
+ Dir.chdir "packages/#{pack}"
1191
+ yield @installers[pack]
1192
+ Dir.chdir '../..'
1193
+ end
1194
+ end
1195
+
1196
+ def run_hook(id)
1197
+ @root_installer.run_hook id
1198
+ end
1199
+
1200
+ # module FileOperations requires this
1201
+ def verbose?
1202
+ @config.verbose?
1203
+ end
1204
+
1205
+ # module FileOperations requires this
1206
+ def no_harm?
1207
+ @config.no_harm?
1208
+ end
1209
+
1210
+ end # class ToplevelInstallerMulti
1211
+
1212
+
1213
+ class Installer
1214
+
1215
+ FILETYPES = %w( bin lib ext data conf man )
1216
+
1217
+ include FileOperations
1218
+ include HookScriptAPI
1219
+
1220
+ def initialize(config, srcroot, objroot)
1221
+ @config = config
1222
+ @srcdir = File.expand_path(srcroot)
1223
+ @objdir = File.expand_path(objroot)
1224
+ @currdir = '.'
1225
+ end
1226
+
1227
+ def inspect
1228
+ "#<#{self.class} #{File.basename(@srcdir)}>"
1229
+ end
1230
+
1231
+ def noop(rel)
1232
+ end
1233
+
1234
+ #
1235
+ # Hook Script API base methods
1236
+ #
1237
+
1238
+ def srcdir_root
1239
+ @srcdir
1240
+ end
1241
+
1242
+ def objdir_root
1243
+ @objdir
1244
+ end
1245
+
1246
+ def relpath
1247
+ @currdir
1248
+ end
1249
+
1250
+ #
1251
+ # Config Access
1252
+ #
1253
+
1254
+ # module FileOperations requires this
1255
+ def verbose?
1256
+ @config.verbose?
1257
+ end
1258
+
1259
+ # module FileOperations requires this
1260
+ def no_harm?
1261
+ @config.no_harm?
1262
+ end
1263
+
1264
+ def verbose_off
1265
+ begin
1266
+ save, @config.verbose = @config.verbose?, false
1267
+ yield
1268
+ ensure
1269
+ @config.verbose = save
1270
+ end
1271
+ end
1272
+
1273
+ #
1274
+ # TASK config
1275
+ #
1276
+
1277
+ def exec_config
1278
+ exec_task_traverse 'config'
1279
+ end
1280
+
1281
+ alias config_dir_bin noop
1282
+ alias config_dir_lib noop
1283
+
1284
+ def config_dir_ext(rel)
1285
+ extconf if extdir?(curr_srcdir())
1286
+ end
1287
+
1288
+ alias config_dir_data noop
1289
+ alias config_dir_conf noop
1290
+ alias config_dir_man noop
1291
+
1292
+ def extconf
1293
+ ruby "#{curr_srcdir()}/extconf.rb", *@config.config_opt
1294
+ end
1295
+
1296
+ #
1297
+ # TASK setup
1298
+ #
1299
+
1300
+ def exec_setup
1301
+ exec_task_traverse 'setup'
1302
+ end
1303
+
1304
+ def setup_dir_bin(rel)
1305
+ # files_of(curr_srcdir()).each do |fname|
1306
+ # update_shebang_line "#{curr_srcdir()}/#{fname}"
1307
+ # end # The above line was modifed by shevy Sep 2014.
1308
+ end
1309
+
1310
+ alias setup_dir_lib noop
1311
+
1312
+ def setup_dir_ext(rel)
1313
+ make if extdir?(curr_srcdir())
1314
+ end
1315
+
1316
+ alias setup_dir_data noop
1317
+ alias setup_dir_conf noop
1318
+ alias setup_dir_man noop
1319
+
1320
+ def update_shebang_line(path)
1321
+ return if no_harm?
1322
+ return if config('shebang') == 'never'
1323
+ old = Shebang.load(path)
1324
+ if old
1325
+ $stderr.puts "warning: #{path}: Shebang line includes too many args. It is not portable and your program may not work." if old.args.size > 1
1326
+ new = new_shebang(old)
1327
+ return if new.to_s == old.to_s
1328
+ else
1329
+ return unless config('shebang') == 'all'
1330
+ new = Shebang.new(config('rubypath'))
1331
+ end
1332
+ $stderr.puts "updating shebang: #{File.basename(path)}" if verbose?
1333
+ open_atomic_writer(path) {|output|
1334
+ File.open(path, 'rb') {|f|
1335
+ f.gets if old # discard
1336
+ output.puts new.to_s
1337
+ output.print f.read
1338
+ }
1339
+ }
1340
+ end
1341
+
1342
+ def new_shebang(old)
1343
+ if /\Aruby/ =~ File.basename(old.cmd)
1344
+ Shebang.new(config('rubypath'), old.args)
1345
+ elsif File.basename(old.cmd) == 'env' and old.args.first == 'ruby'
1346
+ Shebang.new(config('rubypath'), old.args[1..-1])
1347
+ else
1348
+ return old unless config('shebang') == 'all'
1349
+ Shebang.new(config('rubypath'))
1350
+ end
1351
+ end
1352
+
1353
+ def open_atomic_writer(path, &block)
1354
+ tmpfile = File.basename(path) + '.tmp'
1355
+ begin
1356
+ File.open(tmpfile, 'wb', &block)
1357
+ File.rename tmpfile, File.basename(path)
1358
+ ensure
1359
+ File.unlink tmpfile if File.exist?(tmpfile)
1360
+ end
1361
+ end
1362
+
1363
+ class Shebang
1364
+ def Shebang.load(path)
1365
+ line = nil
1366
+ File.open(path) {|f|
1367
+ line = f.gets
1368
+ }
1369
+ return nil unless /\A#!/ =~ line
1370
+ parse(line)
1371
+ end
1372
+
1373
+ def Shebang.parse(line)
1374
+ cmd, *args = *line.strip.sub(/\A\#!/, '').split(' ')
1375
+ new(cmd, args)
1376
+ end
1377
+
1378
+ def initialize(cmd, args = [])
1379
+ @cmd = cmd
1380
+ @args = args
1381
+ end
1382
+
1383
+ attr_reader :cmd
1384
+ attr_reader :args
1385
+
1386
+ def to_s
1387
+ "#! #{@cmd}" + (@args.empty? ? '' : " #{@args.join(' ')}")
1388
+ end
1389
+ end
1390
+
1391
+ #
1392
+ # TASK install
1393
+ #
1394
+
1395
+ GLOB2REGEX = {
1396
+ '.' => '\.',
1397
+ '$' => '\$',
1398
+ '#' => '\#',
1399
+ '*' => '.*'
1400
+ }
1401
+
1402
+ def exec_install
1403
+ rm_f 'InstalledFiles'
1404
+ exec_task_traverse 'install'
1405
+ end
1406
+
1407
+ # ========================================================================= #
1408
+ # === install_dir_bin
1409
+ # ========================================================================= #
1410
+ def install_dir_bin(rel)
1411
+ install_files targetfiles(), "#{config('bindir')}/#{rel}", 0755
1412
+ end
1413
+
1414
+ def install_dir_lib(rel)
1415
+ install_files libfiles(), "#{config('rbdir')}/#{rel}", 0644
1416
+ end
1417
+
1418
+ def install_dir_ext(rel)
1419
+ return unless extdir?(curr_srcdir())
1420
+ install_files rubyextentions('.'),
1421
+ "#{config('sodir')}/#{File.dirname(rel)}",
1422
+ 0555
1423
+ end
1424
+
1425
+ def install_dir_data(rel)
1426
+ install_files targetfiles(), "#{config('datadir')}/#{rel}", 0644
1427
+ end
1428
+
1429
+ def install_dir_conf(rel)
1430
+ # FIXME: should not remove current config files
1431
+ # (rename previous file to .old/.org)
1432
+ install_files targetfiles(), "#{config('sysconfdir')}/#{rel}", 0644
1433
+ end
1434
+
1435
+ def install_dir_man(rel)
1436
+ install_files targetfiles(), "#{config('mandir')}/#{rel}", 0644
1437
+ end
1438
+
1439
+ def install_files(list, dest, mode)
1440
+ mkdir_p dest, @config.install_prefix
1441
+ list.each { |fname|
1442
+ install fname, dest, mode, @config.install_prefix
1443
+ }
1444
+ end
1445
+
1446
+ def libfiles
1447
+ glob_reject(%w(*.y *.output), targetfiles())
1448
+ end
1449
+
1450
+ def rubyextentions(dir)
1451
+ ents = glob_select("*.#{@config.dllext}", targetfiles())
1452
+ if ents.empty?
1453
+ setup_rb_error "no ruby extention exists: 'ruby #{$0} setup' first"
1454
+ end
1455
+ ents
1456
+ end
1457
+
1458
+ def targetfiles
1459
+ mapdir(existfiles() - hookfiles())
1460
+ end
1461
+
1462
+ def mapdir(ents)
1463
+ ents.map {|ent|
1464
+ if File.exist?(ent)
1465
+ then ent # objdir
1466
+ else "#{curr_srcdir()}/#{ent}" # srcdir
1467
+ end
1468
+ }
1469
+ end
1470
+
1471
+ # picked up many entries from cvs-1.11.1/src/ignore.c
1472
+ JUNK_FILES = %w(
1473
+ core RCSLOG tags TAGS .make.state
1474
+ .nse_depinfo #* .#* cvslog.* ,* .del-* *.olb
1475
+ *~ *.old *.bak *.BAK *.orig *.rej _$* *$
1476
+
1477
+ *.org *.in .*
1478
+ )
1479
+
1480
+ def existfiles
1481
+ glob_reject(JUNK_FILES, (files_of(curr_srcdir()) | files_of('.')))
1482
+ end
1483
+
1484
+ def hookfiles
1485
+ %w( pre-%s post-%s pre-%s.rb post-%s.rb ).map {|fmt|
1486
+ %w( config setup install clean ).map {|t| sprintf(fmt, t) }
1487
+ }.flatten
1488
+ end
1489
+
1490
+ def glob_select(pat, ents)
1491
+ re = globs2re([pat])
1492
+ ents.select {|ent| re =~ ent }
1493
+ end
1494
+
1495
+ # ========================================================================= #
1496
+ # === glob_reject
1497
+ # ========================================================================= #
1498
+ def glob_reject(pats, ents)
1499
+ re = globs2re(pats)
1500
+ begin
1501
+ ents.reject {|ent| re =~ ent }
1502
+ rescue ArgumentError => error
1503
+ pp error
1504
+ end
1505
+ end
1506
+
1507
+ def globs2re(pats)
1508
+ /\A(?:#{
1509
+ pats.map {|pat| pat.gsub(/[\.\$\#\*]/) {|ch| GLOB2REGEX[ch] } }.join('|')
1510
+ })\z/
1511
+ end
1512
+
1513
+ #
1514
+ # TASK test
1515
+ #
1516
+
1517
+ TESTDIR = 'test'
1518
+
1519
+ def exec_test
1520
+ unless File.directory?('test')
1521
+ $stderr.puts 'no test in this package' if verbose?
1522
+ return
1523
+ end
1524
+ $stderr.puts 'Running tests...' if verbose?
1525
+ begin
1526
+ require 'test/unit'
1527
+ rescue LoadError
1528
+ setup_rb_error 'test/unit cannot loaded. You need Ruby 1.8 or later to invoke this task.'
1529
+ end
1530
+ runner = Test::Unit::AutoRunner.new(true)
1531
+ runner.to_run << TESTDIR
1532
+ runner.run
1533
+ end
1534
+
1535
+ #
1536
+ # TASK clean
1537
+ #
1538
+
1539
+ def exec_clean
1540
+ exec_task_traverse 'clean'
1541
+ rm_f @config.savefile
1542
+ rm_f 'InstalledFiles'
1543
+ end
1544
+
1545
+ alias clean_dir_bin noop
1546
+ alias clean_dir_lib noop
1547
+ alias clean_dir_data noop
1548
+ alias clean_dir_conf noop
1549
+ alias clean_dir_man noop
1550
+
1551
+ def clean_dir_ext(rel)
1552
+ return unless extdir?(curr_srcdir())
1553
+ make 'clean' if File.file?('Makefile')
1554
+ end
1555
+
1556
+ #
1557
+ # TASK distclean
1558
+ #
1559
+
1560
+ def exec_distclean
1561
+ exec_task_traverse 'distclean'
1562
+ rm_f @config.savefile
1563
+ rm_f 'InstalledFiles'
1564
+ end
1565
+
1566
+ alias distclean_dir_bin noop
1567
+ alias distclean_dir_lib noop
1568
+
1569
+ def distclean_dir_ext(rel)
1570
+ return unless extdir?(curr_srcdir())
1571
+ make 'distclean' if File.file?('Makefile')
1572
+ end
1573
+
1574
+ alias distclean_dir_data noop
1575
+ alias distclean_dir_conf noop
1576
+ alias distclean_dir_man noop
1577
+
1578
+ #
1579
+ # Traversing
1580
+ #
1581
+
1582
+ def exec_task_traverse(task)
1583
+ run_hook "pre-#{task}"
1584
+ FILETYPES.each do |type|
1585
+ if type == 'ext' and config('without-ext') == 'yes'
1586
+ $stderr.puts 'skipping ext/* by user option' if verbose?
1587
+ next
1588
+ end
1589
+ traverse task, type, "#{task}_dir_#{type}"
1590
+ end
1591
+ run_hook "post-#{task}"
1592
+ end
1593
+
1594
+ # ========================================================================= #
1595
+ # === traverse
1596
+ #
1597
+ # This method can fail when it comes to Encoding-related issues.
1598
+ # ========================================================================= #
1599
+ def traverse(task, rel, mid)
1600
+ dive_into(rel) {
1601
+ run_hook "pre-#{task}"
1602
+ __send__(mid, rel.sub(%r[\A.*?(?:/|\z)], ''))
1603
+ directories_of(curr_srcdir()).each { |d|
1604
+ traverse task, "#{rel}/#{d}", mid
1605
+ }
1606
+ run_hook "post-#{task}"
1607
+ }
1608
+ end
1609
+
1610
+ def dive_into(rel)
1611
+ return unless File.dir?("#{@srcdir}/#{rel}")
1612
+
1613
+ dir = File.basename(rel)
1614
+ Dir.mkdir dir unless File.dir?(dir)
1615
+ prevdir = Dir.pwd
1616
+ Dir.chdir dir
1617
+ $stderr.puts '---> ' + rel if verbose?
1618
+ @currdir = rel
1619
+ yield
1620
+ Dir.chdir prevdir
1621
+ $stderr.puts '<--- ' + rel if verbose?
1622
+ @currdir = File.dirname(rel)
1623
+ end
1624
+
1625
+ def run_hook(id)
1626
+ path = [ "#{curr_srcdir()}/#{id}",
1627
+ "#{curr_srcdir()}/#{id}.rb" ].detect {|cand| File.file?(cand) }
1628
+ return unless path
1629
+ begin
1630
+ instance_eval File.read(path), path, 1
1631
+ rescue
1632
+ raise if $DEBUG
1633
+ setup_rb_error "hook #{path} failed:\n" + $!.message
1634
+ end
1635
+ end
1636
+
1637
+ end # class Installer
1638
+
1639
+
1640
+ class SetupError < StandardError; end
1641
+
1642
+ def setup_rb_error(msg)
1643
+ raise SetupError, msg
1644
+ end
1645
+
1646
+ if $0 == __FILE__
1647
+ begin
1648
+ ToplevelInstaller.invoke
1649
+ rescue SetupError
1650
+ raise if $DEBUG
1651
+ $stderr.puts $!.message
1652
+ $stderr.puts "Try 'ruby #{$0} --help' for detailed usage."
1653
+ exit 1
1654
+ end
1655
+ end